identifier
stringlengths 11
32
| pdf_url
stringlengths 17
4.62k
⌀ | lang
stringclasses 120
values | error
stringclasses 1
value | title
stringlengths 2
500
⌀ | source_name
stringlengths 1
435
⌀ | publication_year
float64 1.9k
2.02k
| license
stringclasses 3
values | word_count
int64 0
1.64M
| text
stringlengths 1
9.75M
|
|---|---|---|---|---|---|---|---|---|---|
https://openalex.org/W2066752448
|
https://www.biodiversitylibrary.org/partpdf/91880
|
English
| null |
The Australian land shell, Thersites bipartita, and its allies
|
Proceedings of the United States National Museum
| 1,927
|
public-domain
| 6,999
|
2711.—PRocEEDINGS U. S. NATIONAL MUSEUM, VoL. 72, ArT. I5. 1 Manual of Conchology, vol. 6, p. 276, 1892.
2Man. Conch., vol. 2, p. 132, 1894. No. 2711.—PRocEEDINGS U. S. NATIONAL MUSEUM, VoL. 72, ArT. I5.
55223—27
1 By
Witu1aM
B.
MarsHann Assistant
Curator,
Division
of
Mollusks,
United
States
National
Musewn Recently
Mr. C. Walton
of
Peterhead,
Port
Adelaide,
South
Aus-
tralia,
presented
the
United
States
National
Museum
with
a
number
of
land
shells
of
northeastern
Australia
and
islands
in
Torres
Strait. All
of
the
specimens
received
belong
in
the
group
Thersites
(Hadra)
bipartita
Ferussac. They
present
a
great
variation
in
size
and
form,
and
the
color
varies
from
bipartite
(whitish
spire,
chocolate
base)
to
specimens
which
are
entirely
pale
straw
color,
and
to
others
which
are
entirely
dark
chestnut,
and
to
others
which
are
chestnut
above,
darker,
sometimes
nearly
black
below. Most
of
them
have
a
white
or
pale
spiral
band
at
or
near
the
periphery,
and
a
dark
band
just
below
the
suture. When
the
mass
of
material
now
in
the
Museum
collection
is
arranged
in
geographic
sequence,
many
characteristics
which
hitherto
have
escaped
attention
become
evident,,. and
show
plainly
that
specialization
has
taken
place
along
certain
definite
lines,
and
requires
the
recognition
of
additional
species
and
subspecies
to
properly
understand
the
problem
presented. Pilsbry
in
his
first
study
of
Thersttes
bipartita*
placed
it
in
the
genus
Camaena,
subgenus
Hadra,
section
Hadra
s. s.,
and
gavé
the
following
note: The main feature distinguishing Hadra from Chloritis is that the apex in the
former is neither concave, notably flattened, nor sculptured. This group seems
more justly regarded as a subgenus of Chloritis than as a separate genus. Hedley suggests to me that the microscopic sculpturing of Hadra is a reminis-
eence of the hair granules of Chloritis. Later
in
his
analysis
of
the
bipartita
group? he
places
it
in
the
genus
Thersiies,
subgenus
T'hersites,
section
Hadra
and
uses
the
fol-
lowing
names: bipartita
Ferussac+semibadia
Albers
form unicolor Cox
form minor Pilsbry
var. semicastanea
Pfeiffer
funiculata
Pfeiffer
forsteriana
Pfeiffer--hetaera
Pfeiffer
form major Dohrn
darwint
Brazier. form major Dohrn darwint
Brazier. 1 2 DINGS
OF
THE
NATIONAL
MUSEUM 72 Dr. James
C. Cox
*
treated
Thersites
bipartita
and
semicastanea
as
distinct
species,
but
under
the
latter
he
says: This species, unquestionably a modified H. bipartita, is so variable that a
dozen well-marked varieties might easily be selected from among the hundreds
of specimens now before me. I haye taken the preceding description from a
Lizard Island specimen. He
also
treats
funiculata
as
a
distinct
species,
but
under
sem/-
castanea
he
says:
“
H. 3 Monograph of Australian Land Shells, p. 56, 1868. By
Witu1aM
B.
MarsHann funiculata,
described
elsewhere,
I
would
refer
to
this
head
without
hesitation. *
*
*.” The
land
shells
from
the
Northeastern
coast
of
Australia
and
ad-
jacent
islands,
the
largest
of
which
heretofore
have
been
called
Ther-
sites
bipartita
Ferussac
and
the
smaller
ones
either
positively
or
doubtfully
subspecies
of
that
species,
have
been
analyzed
in
this
paper. It
should
be
remembered
that
the
region
includes
not
only
the
mainland
of
northeastern
Australia
but
some
of
the
islands
off
the
east
coast
of
Queensland
and
the
islands
of
Torres
Strait. Tor-
res
Strait
is
about
80
miles
across
and
crowded
with
reefs,
shoals,
and
islands. Isolation
and
environment
undoubtedly
have
been
ef-
fective
causes
producing
the
characteristics
of
the
various
subspecies
of
mollusks
living
on
these
islands. Restricting
ourselves
now
to
specimens
known
or
believed
to
come
from
islands
in
Torres
Strait,
we
find
that
so
far
as
known
they
may
be
divided
inte
two
great
groups,
one
of
which
is
characterized
by
being
large,
pale,
angular
at
the
periphery
and
with
the
spire
but
little
lighter
than
the
base. This
group
includes
two
species,
both
new,
described
in
this
paper
under
the
names
Thersites
waltoni
and. Thersites
dalli. The
second
group,
characterized
by
being
smaller,
the
spire
dark
reddish
in
color,
the
base
much
darker,
sometimes
nearly
black,
and
with
the
periphery
rounded,
or
at
least
less
angu-
lar. This
group
includes
three
species,
namely:
7’. semicastanea
Pfeiffer,
7. bartschi
Marshall,
and
7. funiculata
Pfeiffer. The
first
two
are
divided
into
two
or
more
subspecies. Shells
from
Lizard
Island
on
the
east
coast
of
Queensland
resemble
these
dark
shells
from
the
islands
in
Torres
Strait,
which,
however,
are
easily
dis-
tinguishable
by
their
very
dark
colors
and
unctuous
appearance. In
the
group
of
Thersites
bipartita
we
now
recognize
the
follow-
ing
species
and
subspecies: NEW
AUSTRALIAN
LAND
SHELLS—-MAR ART. lizardensis swma, new. lizardensis rada, new. bartschi
barischi,
new. bartschi mobiagensis, new. bartschi yamensis, new. bartschi oma, new. baritschi mura, new. barischi nesia, new
barischi paulensis, new. barischi murrayensis, new. barischi fama, new. bartschi elfa, new. barischi diva, new. barischit cepa, new. waliom, new. dalli, new. forsteriana
forsteriana
Pfeiffer. forsteriana major Pfeiffer. forsteriana ada, new. darwin
Brazier. lizardensis swma, new. lizardensis rada, new. bartschi
barischi,
new. bartschi mobiagensis, new. bartschi yamensis, new. bartschi oma, new. baritschi mura, new. barischi nesia, new
barischi paulensis, new. barischi murrayensis, new. barischi fama, new. bartschi elfa, new. barischi diva, new. barischit cepa, new. waliom, new. dalli, new. forsteriana
forsteriana
Pfeiffer. forsteriana major Pfeiffer. forsteriana ada, new. darwin
Brazier. lizardensis swma, new. lizardensis rada, new. bartschi
barischi,
new. bartschi mobiagensis, new. bartschi yamensis, new. bartschi oma, new. baritschi mura, new. barischi nesia, new
barischi paulensis, new. barischi murrayensis, new. barischi fama, new. bartschi elfa, new. barischi diva, new. barischit cepa, new. waliom, new. dalli, new. forsteriana
forsteriana
Pfeiffer. forsteriana major Pfeiffer. forsteriana ada, new. darwin
Brazier. lizardensis swma, new. bartschi oma, new. baritschi mura, new. baritschi mura, new. barischi nesia, new barischi paulensis, new. barischi murrayensis, new. barischi murrayensis, new. barischi fama, new. bartschi elfa, new. barischi diva, new. barischit cepa, new. waliom, new. forsteriana
forsteriana
Pfeiffer. At
the
present
time
this
arrangement
makes
possible
a
satisfac-
tory
classification
of
all
the
material
of
this
group
in
the
collection
of
the
United
States
National
Museum. We
believe,
however,
that
when
specimens
from
others
of
the
multitude
of
islands
in
Torres
Strait
are
collected,
that
the
list
of
subspecies
will
have
to
be
ma-
terially
enlarged. THERSITES
(HADRA)
BIPARTITA
BIPARTITA
Ferussac Plate 1, fig. 3 Plate 1, fig. 3 THDRSITHS
(HADRA) bipartita bipartita Kerussae. bipartita minor Pilsbry. bipartiia unicolor Cox. semicastanea semicastanea Pfeiffer. semicastenea alma, new. funiculata
Pfeiffer. lizardensis lizardensis, new. 3 NEW
AUSTRALIAN
LAND
SHELLS—-MAR Heliz bipartita Frrussac, Histoire Naturelle des Mollusques, vol. 1, p. 176,
pl. 75a, fig. 1. Heliz bipartita Frrussac, Histoire Naturelle des Mollusques, vol. 1, p. 176,
pl. 75a, fig. 1. Shell
large,
globosely
turbinate,
thick. Whorls
slightly
more
than
seven,
slightly
rounded
and
convex,
each
appearing
to
be
a
little
sunken
into
the
succeeding
one,
giving
a
somewhat
beehive
appear-
ance
to
the
spire. Sculpture
of
many
retractive
growth
riblets
which
are
strongest
on
the
body
whorl. Upper
whorls
with
microscopic
reticulations,
which
on
the
body
whorl
become
minute
pittings. Base
very
convex,
widely
umbilicated,
the
face
of
the
umbilicus
somewhat
flattened. Aperture
oblique,
whitish
but
indistinctly
showing
the
bipartite
coloring
of
the
exterior. Peristome
white,
reflected,
par-
tially
concealing
the
umbilicus. Parietal
wall
with
a
rather
thick
callus
which
extends
as
a
glaze
some
distance
within
the
shell. Periphery
rounded,
showing
no
sign
of
an
angle. Suture
well
im-
pressed,
irregularly
crenulated
by
the
upper
ends
of
the
growth
riblets. Body
whorl
slowly
descending
about
7
mm. as
it
approaches
the
aperture. Color
very
conspicuously
bipartite,
the
spire
pale
straw
color,
the
base
chocolate,
a
white
spiral
line
dividing
the
colors
of the spire and base. DINGS
OF
THE
NATIONAL
MUSEUM 4 72 The
suture
marked
by
a
faint
band
of
chestnut
below
it. The
figured
specimen,
United
States
National
Museum,
Cat. No. 100058
measures:
Greater
diameter,
64
mm.;
lesser
diameter,
56
mm.;
height,
59
mm. It
comes
from
northeast
Australia
and
was
received
from
R. E. C. Stearns,
who
obtained
it
from
Dr. J. C. Cox. The
collection
contains
also
15
other
specimens,
5
of
which
are
labeled
Cape
York;
6
Australia;
1
northeast
Australia;
1
north
Australia;
1
Queensland;
and
1
Gulf
of
Carpentaria. Probably
all
these
speci-
mens
came
from
Queensland. Pilsbry
cites
the
following
localities:
Cape
York,
Cape
Direction,
Cape
Grenville,
Daintree
River,
and
Albany
Island,
northeast
Australia. Albany
Island
is
so
close
to
the
mainland
that
it
may
be
regarded
as
a
part
of
it. All
the
localities
mentioned
are
in
Queensland. Specimens
at
hand
vary
considerably
in
size
and
other
features. The
specimen
figured
is
the
largest;
the
smallest
of
all
is
a
specimen
labeled
Australia
(Cat. No. 321077)
which
measures:
Greater
diam-
eter,
50
mm.;
lesser
diameter,
40
mm.;
height,
36.5
mm. Tour
other
specimens,
part
of
this
same
lot,
are
much
smaller
than
the
specimen
figured. One
labeled
Gulf
of
Carpentaria,
North
Australia
(Cat. No. 333790,
U.S.N.M.),
received
from
Mr. Heliz bipartita Frrussac, Histoire Naturelle des Mollusques, vol. 1, p. 176,
pl. 75a, fig. 1. Walton,
measures:
Greater
diameter,
51
m.;
lesser
diameter,
43
mm.;
height,
41
mm. With
more
material
available
and
with
definite
locality
data,
this
subspecies
as
now
considered
may
have
further
subdivisions. THERSITES (HADRA) BIPARTITA MINOR Pilsbry 1890. Huhadra
(Hadra)
bipartita
minor
PitsBry,
Man. Conch.,
vol. 6,
p. 126, pl. 21, f. 44. Like
typical
bipartita
in
all
respects
but
size,
which
Pilsbry
gives
as
diameter,
31
mm.;
altitude,
26
mm. No. mention
is
made
of
its
distribution. THERSITES (HADRA) LIZARDENSIS LIZARDENSIS, new subspecies
Plate 2, fig. 7 THERSITES (HADRA) LIZARDENSIS LIZARDENSIS, new subspecies
Plate 2, fig. 7 1892. Chloritis (Hadra) bipartita unicolor Cox, in Pilsbry’s Man. Conch.,
vol. 8, p. 276. 1892. Chloritis (Hadra) bipartita unicolor Cox, in Pilsbry’s Man. Conch.,
vol. 8, p. 276. Similar
to
the
typical
bipartita
in
size,
form,
sculpture
and
thick-
ness,
but
of
a
nearly
uniform
yellowish
color. All
four
of
the
speci-
mens
in
the
Museum
collection
have
the
white
or
whitish
band
which,
in
typical
dbéipartéta,
marks
the
division
between
the
yellowish
color
of
the
spire
and
the
chocolate
color
of
the
base. The
distribution
of
unicolor
is
apparently
the
same
as
that
of
typical
b¢partita,
and
it
may
be
only
a
partially
albinistic
manifestation
instead
of
a
zoogeo-
graphic
race. THERSITES (HADRA) LIZARDENSIS LIZARDENSIS, new subspecies Plate 2, fig. 7 Shell
globosely
conical,
rather
elevated,
moderately
thick. Whorls
614,
slowly
increasing
in
size,
a
little
convex. Base
convex; 5 NEW
AUSTRALIAN
LAND
SHELLS—MARS ART. ART. body
whorl
round,
its
upper
edge
descending
near
the
aperture. Sculpture
of
many
retractive
fine
growth
striae
and
a
microscopic
reticulation. Sutures
moderately
impressed,
emphasized
by
a
crenu-
lated
edging
to
each
whorl,
and
by
a
narrow
white
margin
below
which
is
a
reddish
narrow
band. Umbilicus
wide,
partly
concealed
by
the
reflected
columellar
lip. Parietal
wall
glazed. Aperture
broad-
ly
rounded;
peristome
white,
reflected. Color
bipartite,
the
spire
light
chestnut
and
the
base
much
darker,
rich,
glossy
chestnut. A
distinct
white
band
at
the
periphery
between
the
two
shades
of
color. Interior
showing
the
exterior
colors
softened
by
a
glaze. The
type
(Cat. No. 317035,
U.S.N.M.)
measures:
Greater
diam-
eter, 41 mm.; lesser diameter, 36 mm.; height, 32 mm. It and a para-
type
(Cat. No. 333791,
U.S.N.M.)
are
in
the
Henderson
collection,
and
came
from
Lizard
Island
off
east
coast
of
Queensland. This
is
the
species
figured
by
Cox
as
Helix
semicastanea
on
Plate
5,
Figure
10.4
His
specimen
came
from
Lizard
Island. It
seems
to
stand
mid-
way
between
Vhersites
bipartita
and
T. semécastanea,
partaking
of
the
characters
of
each
and
yet
distinct
from
both. Cat. No. 317032,
U.S.N.M. includes
two
specimens
from
Lizard
Island
of
much
lighter
colors. Cat. No. 317034,
U.S.N.M. includes
two
specimens
labeled
Islands
of
northeast
coast
of
Australia. These
probably
come
from
Lizard
Island. Cat. No. 321080,
U.S.N.M. includes
one
specimen
labeled
“Australia.”
This,
too,
probably
came
from
Lizard
Island. Cat. No. 100032,
U.S.N.M. labeled
“
Northeast
Australia,”
from
Dr. J. C. Cox,
in
the
Stearns
collection,
also
are
so
like
specimens
from
Lizard
Island
that
it
seems
likely
they
came
from
that
island. THERSITES (HADRA) LIZARDENSIS SUMA, new subspecies Plate 1, fig. 2 Similar
to
7. lizardensis
lizardensis
but
larger,
more
elevated,
and
differently
colored,
the
spire
being
fawn
color,
the
base
light
choco-
late
with
a
chestnut
tinge,
the
white
line
dividing
the
colors
of
base
and
spire
very
prominent. The
type
(Cat. No. 99944,
U.S.N.M.)
measures:
Greater
diameter,
48
mm.;
lesser
diameter,
41.5
mm.;
height,
35
mm. It
and
a
para-
type
(Cat. No. 333792,
U.S.N.M.)
form
part
of
the
Stearns
collec-
tion. They
are
labeled
?Borneo. No
similar
shells
have
been
found
in
Borneo,
and
it
seems
from
their
resemblance
to
Lizard
Island
specimens
that
they
probably
came
from
some
island
in
its
imme-
diate
vicinity,
and
probably
belong
to
a
subspecies
of
7’. lizardensis. 4 Monograph of Australian Land Shells, 1868. Plate 2, fig. 4 Shell
similar
to
Vhersttes
lizardensis
lizardensis
but
much
smaller,
more
elevated,
with
the
umbilicus
largely
concealed
by
the
reflected 6 DINGS
OF
THE
NATIONAL
MUSEUM 72 columellar
lip,
the
peristome
thicker
and
less
expanded,
a
heavy
callus
across
the
parietal
wall
joining
the
two
ends
of
the
peristome. Colors
much
lighter
but
distinctly
bipartite,
the
spire
pale
yellowish
white,
the
base
faded
chestnut. The
type
(Cat. No. 317033,
U.S.N.M.)
measures:
Greater
diameter,
33
mm.;
lesser
diameter,
28.5
mm.;
height,
22.5
mm. Jt
and
a
para-
type
(Cat. No. 333798,
U.S.N.M.)
are
part
of
the
Henderson
collec-
tion
and
come
from
Lizard
Island
on
the
east
coast
of
Queens-
land,
Australia. While
the
condition
of
the
interior
of
these
two
specimens
show
that
they
were
“living”
shells
when
collected,
the
pale
colors
of
the
spire and base seem to be due mostly to loss of nearly all the perio-
stracum,
though
a
few
remaining
vestiges
of
periostracum
show
that
the
shell
was
naturally
of
very
light
colors. At
first
glance
this
subspecies
bears
a
resemblance
to
7’. bipartita,
but
careful
compari-
son
with
that
species
and
with
7’. lizardensis
shows
that
it
is
more
closely
related
to
the
latter. THERSITES
(HADRA)
SEMICASTANEA
SEMICASTANEA
Pfeiffer
Plate 2, fig. 5 Plate 2, fig. 5 1849. Helix semicastanea Pruirrrrn Zeitsch. fur Malak., vol. 6, p. 77; in
Chemnitz Conch. Cab. ed. 2, Helix, no. 319, plate 56, figs. 3-5 (title page
dated 1846, but the species is quoted from the Zeitschrift for 1849, thus
showing that it was described in that year). 1849. Helix semicastanea Pruirrrrn Zeitsch. fur Malak., vol. 6, p. 77; in
Chemnitz Conch. Cab. ed. 2, Helix, no. 319, plate 56, figs. 3-5 (title page
dated 1846, but the species is quoted from the Zeitschrift for 1849, thus
showing that it was described in that year). Shell
small,
rather
thin,
depressed
conic,
whorls
from
514
to
6
in
number,
slowly
increasing,
slightly
convex,
body
whorl
rounded,
but
just
in
front
of
the
aperture
it
-is
somewhat
angular
showing
that
the
concealed
periphery
of
the
earlier
whorls
was
angular. Surface
with
numerous
retractive
growth
striae
and
surface
mi-
nutely
reticulate,
with
faint
indications
here
and
there
of
spiral
striae. Base
convex,
umbilicus
rather
narrow. Aperture
rounded,
scarcely
oblique. Peristome
thin,
reflected,
its
columellar
portion
partially
concealing
the
umbilicus. Parietal
wall
glazed. Color
reddish,
the
base
darker
than
the
spire
and
glossy,
a
spiral
white
or
whitish
band
at
the
periphery. Interior
showing
the
two
shades
of
the
exterior
and
the
white
line
dividing
them. Sutures
well
im-
pressed,
irregularly
crenulated,
marked
by
a
dark
lne
below
and
a
whitish
line
above. A
very
slight
descent
of
the
body
whorl
at
the
aperture. The
figured
specimen
(Cat. No. 169124,
U.S.N.M.)
measures:
Greater
diameter,
34.5
mm.;
lesser
diameter,
30
mm.;
height,
23
mm. Another
specimen
with
the
same
catalogue
number,
exactly
like
the
type
but
smaller,
measures:
Major
diameter,
28
mm.;
minor
diam-
eter,
24
mm.;
height,
19.5
mm. They
are
labeled
“
Queensland,
Australia,”
and
were
presented
by
Mr. S. W. Jackson. Cat. No. 100033,
U.S.N.M.,
includes
two
specimens
received
from
R,
E. C. re NEW
AUSTRALIAN
LAND
SHELLS—MARSH ART.15 Stearns,
who
obtained
them
from
Dr. J. C. Cox. These
are
labeled
“Northeast
Australia.”
They
are
dark
reddish
chestnut,
much
darker
than
the
type. In
one
the
light
peripheral
band
is
quite
marked
;
in
the
other
it
is
faint. Apparently
the
localities
“‘
Queens-
land”
and
“Northeast
Australia”
supplied
by
Jackson
and
Cox
would
lie
on
the
mainiand,
but
it
seems
probable
that
these
localities
being
general
would
include
islands
in
Torres
Strait. Plate 3, fig. 8 Similar
to
Thersites
(Hadra)
semicastanea
semicastanea,
but
much
smaller,
more
fragile,
slightly
less
depressed
and
with
the
peristome
thin
and
but
slightly
reflected. The
body
whorl
does
not
descend
near
the
aperture. It
has
514
whorls. The
type
(Cat. No. 100034,
U.S.N.M.)
measures:
Greater
diameter,
25.5
mm.;
lesser
diameter,
22
mm.;
height,
15
mm. It
comes
from
Cape
York,
Queensland,
Australia,
and
was
received
from
R. E. C. Stearns,
who
obtained
it
from
Legrand. THERSITES
(HADRA)
SEMICASTANEA
SEMICASTANEA
Pfeiffer
Plate 2, fig. 5 Pfeiffer’s
type
locality
“Nova
Hollandia?”
would
include
both
mainland
and
-
islands. Cox
and
also
Pilsbry
say
“Islands
of
Torres
Strait,
Australia,
from
Lizard
Island
to
Stephens
Island.”
Doctor
Cox
in
describing
and
figuring
specimens
from
Lizard
Island
apparently
did
not
deal
with
Thersites
semicastanea,
but
with
larger
and
differently
colored
shells. The
specimen
figured
by
Cox
on
Plate
5,
Figure
10,°
is
not
T. semicastanea
but
rather
bipartita
minor
Pilsbry. The
specimen
figured
on
Plate
20,
Figure
3,°
is
7’. semicastanea
semicastenea. 5 Monograph of Australian Land Shells, 1868. THERSITES (HADRA) FUNICULATA Pfeiffer 1854. Helix funiculata Pretrrer, Proc. Zool. Soc., p. 147. Shell
umbilicated,
depressed,
thin,
often
rudely
granulated,
some-
what
shining,
reddish;
spire
obtusely
conic;
suture
subcanaliculate;
whorls
6,
somewhat
convex,
slowly
increasing;
body
whorl
rounded,
a
white
band
above
the
periphery
and
with
a
cord-like
carina,
de-
scending
anteriorly;
base
convex,
umbilicus
moderate,
deep,
aperture
oblique,
subangularly
lunate;
peristome
simple,
margins
scarcely
converging;
above
straight,
a
little
reflected
at
the
base,
upper
end
of
columelia
dilated. Greater
diameter,
29
mm.;
lesser
diameter,
24
mm.;
height,
14
mm. Plate 1, fig. 1 Similar
to
Thersttes
bartschi
bartscht,
but
thinner,
slightly
more
depressed
and
less
highly
colored. The
type
(Cat. No. 333797,
U.S.N.M.)
measures:
Greater
diameter,
44
mm.;
lesser
diameter,
37.5
mm.;
height,
28.5
mm. It
comes
from
Mobiag
Island
in
Torres
Strait,
and
was
presented
by
Mr. C. Walton. (Cat. No. 883798,
U.S.N.M.)
contains
three
specimens
from
the
same
island
sent
by
Mr. Walton. One
of
these
is
young,
but
when
grown
apparently
will
be
quite
like
the
adult. The
other
two
specimens
are
very
thin,
more
elevated,
and
have
a
tendency
to
globoseness. One
is
nearly
adult. Its
sutures
do
not
lie
accurately
along
the
periphery
of
the
preceding
whorls. The
other
specimen
is
adult. The
suture
of
its
whole
body
whorl
and
part
of
the
penultimate
whorl
fall
below
the
periphery
of
the
preceding
whorl. This
irregu-
larity
of
growth
probably
accounts
for
the
departure
from
usual
form. Plate 2, fig. 1 Shell
rather
thin,
depressed,
whorls
614,
somewhat
round,
slowly
descending,
each
appearing
to
be
a
little
immersed
in
the
succeeding
whorl. Base
convex,
about
as
deep
as
the
spire
is
high,
umbilicus
moderate,
partly
concealed
by
the
reflected
columellar
lip. Body
whorl
large,
with
rounded
periphery,
its
anterior
upper
edge
slightly
descending
at
the
aperture. Sculpture
of
numerous
retractive
growth
lines
and
microscopic
reticulations;
sutures
deeply
impressed,
crenu-
lated
by
the
ends
of
the
growth
striae. Color
rich,
dark
chestnut
fumed
with
darker
color,
especially
along
the
suture. Base
very
dark,
nearly
black,
the
colors
of
the
spire
and
base
separated
by
a
very
distinct
white
line. Aperture
nearly
horizontal,
widely
rounded
with
the
lip
moderately
reflected. Interior
livid
purplish. Parietal
wall
thinly
glazed. The
type
(Cat. No. 333794,
U.S.N.M.)
measures:
Greater
diameter,
44
mm.;
lesser
diameter,
36
mm.;
height,
28.5
mm. It
and
two
para-
types
come
from
Darnley
Island,
and
were
presented
by
Mr. C. Walton. | OCEEDINGS
OF
THE
NATIONAL
MUSEUM
V
THERSITES (HADRA) BARTSCHI BARTSCHI, new subspecies 8 DINGS
OF
THE
NATIONAL
MUSEUM THERSITES (HADRA) BARTSCHI MOBIAGENSIS, new subspecies Plate 1, fig. 1 mm. Habitat.—Torres
Strait,
Australia. This
may
be
a
subspecies
of
Thersites
semicastanea
Pfeiffer,
but
the
presence
of
a
cordlike
keel
at
the
periphery
makes
it
somewhat
doubtful. Unfortunately
a
definite
locality
was
not
cited. Torres
Strait
includes
a
multitude
of
islands. 72 THERSITES (HADRA) BARTSCHI YAMENSIS, new subspecies Plate 1, fig. 4 Shell
similar
to
Thersites
bartschd
bartscha
but
larger,
more
de-
pressed,
whorls
less
rounded,
growth
riblets
more
marked,
body
whorl
angulated
at
the
periphery
(the
angle
more
appreciable
to
touch
than
to
sight),
base
slightly
less
convex;
aperture
smaller,
less 9 NEW
AUSTRALIAN
LAND
SHELLS—-MAR ART. ART. flaring,
with
the
outer
lip
indistinctly
angulated
by
the
angle
of
the
periphery;
the
whitish
line
above
the
nearly
black
color
of
the
base
less
distinct
but
wider. The
type
(Cat. No. 333799,
U.S.N.M.)
measures:
Greater
diameter,
48
mm.;
lesser
diameter,
44
mm.;
height,
32
mm. It
and
three
para-
types
(one
of
them
juvenile)
come
from
Yam
Island
in
Torres
Strait
and
were
presented
by
Mr. C. Walton. The
angulated
periphery,
the
less
convex
base
and
the
smaller,
less
flaring
aperture
distinctly
differentiate
this
subspecies
from
7’
hersites
bartsche
bartschi. One
of
the
paratypes
is
juvenile,
another
varies
from
the
type
in
form,
being
depressed
and
each
whorl
slightly
sunken
into
the
suc-
ceeding whorl, due to the fact that the suture does not fall along the
periphery but is attached a trifle above it. Plate 3, fig. 2 Shell
thin,
inflated,
whorls
614,
well-exserted,
rounded;
body
whorl
rounded,
inflated,
its
upper
edge
descending
near
the
aperture. Base
very
convex,
umbilicus
rather
wide,
but
little
concealed
by
the
expanded
columellar
tip. Sculpture
of
rather
indistinct
lines
of
growth
and
microscopic
reticulations. Sutures
well
impressed,
irregularly
crenulated
by
the
upper
ends
of
the
growth
lines. Color
nearly
uniformly
rich
dark
chestnut,
the
color
of
the
base
very
little
darker
than
the
spire
except
near
the
aperture
where
it
is
several
shades
darker. In
place
of
the
whitish
line
dividing
the
colors
of
the
spire
and
base
this
shell
has
a
narrow
band
of
chestnut
darker
than
that
of
either
base
or
spire. Suture
obscurely
margined
below
by
dark
chestnut. Aperture
horizontal,
widely
rounded,
peristome
thin,
reflected,
parietal
wall
glazed. Interior
violaceous;
by
trans-
mitted
light
distinctly
divided
by
a
dark
line,
into
two
parts,
the
upper of which is much lighter in color than the lower. The
type
(Cat. No. 333801,
U.S.N.M.)
measures:
Greater
diameter,
38.5
mm.;
lesser
diameter,
30
mm.;
height,
26
mm. It
comes
from
Yam
Island,
Torres
Strait,
and
was
presented
by
Mr. C. Walton. THERSITES (HADRA) BARTSCHI NURA, new subspecies Plate 3, fig. 7 Plate 3, fig. 7 Shell
small,
about
one-half
the
size
of
Thersites
bartschi
bartschi
similar
to
it
in
other
respects
but
with
characters
less
pronounced. The
band
at
the
periphery
is
yellowish-white,
the
peristome
very
little
reflected,
interior
violaceous,
the
upper
part
lighter
than
the
lower,
a
clear-white
band
between
them. _
The
type
(Cat. No. 333802,
U.S.N.M.)
measures:
Major
diameter,
31
mm.;
minor
diameter,
¥8
mm.;
height,
21
mm. It
comes
from
Yam
Island,
Torres
Strait,
and
was
presented
by
Mr. C. Walton. DINGS
OF
THE
NATIONAL
MUSEUM 72 10 Another
specimen
(Cat. No. 333808,
U.S.N.M.)
of
this
subspecies
is
larger
but
somewhat
abnormal
in
that
the
whorls
at
places
do
not
attach
themselves
accurately
to
the
periphery
of
the
preceding
whorl,
thus
making
the
shell
a
little
more
elevated
than
it
should
be
for
its
diameter. It
measures:
Major
diameter,
34
mm.;
minor
diameter,
33.5
mm.;
height,
25.5
mm. This
subspecies
resembles
a
typical
T'hersttes
bartschi
bartscha
very
much
reduced
in
size. It
resembles
also
Thersites
bartschi
oma
but
is
smaller,
the
whorls
less
rounded,
the
aperture
very
much
less
flaring
and
with
a
light
peripheral
band
instead
of
a
dark
chestnut-
colored one. Plate 8, fig. 5 Shell
very
small,
thin;
whorls
514,
rather
flattened. Base
very
convex,
its
depth
exceeding
the
height
of
the
spire;
umbilicus
moder-
ate,
but
little
concealed
by
the
reflected
columellar
tip. Sculpture
of
many
fine
retractive
growth
lines
and
microscopic
reticulations. Body
whorl
sloping,
periphery
rounded
except
in
front
of
the
aper-
ture
where
it
is
sharply
angulated. Sutures
not
deeply
impressed,
crenulated
by
the
upper
ends
of
growth
lines. Aperture
very
oblique,
peristome
white,
slightly
refiected. Color
dark
chestnut
brown,
the
base
somewhat
darker
than
the
spire,
the
sutures
margined
by
an
irregular
darker
band
at
the
top
of
each
whorl,
the
colors
of
the
base
and
spire
divided
by
a
narrow
yellowish
band
at
the
perphery. Interior
dark
brown
below,
whitish
mottled
with
chestnut
above
and
a
clear
white
band
marking
the
periphery. The
type
(Cat. No. 333804,
U.S.N.M.)
measures:
Major
diameter,
25.5
mm.;
minor
diameter,
22.5
mm.;
height,
20
mm. It
comes
from
Yam
Island,
Torres
Strait,
and
was
presented
by
Mr. C. Walton. The
small
size,
the
deep
base,
and
the
oblique
aperture
distinguish
this
shell
from
all
others
of
the
group. Its
nearest
relative
is
Thersites
bartschi
nura. Plate 3, fig. 9 This
is
somewhat
smaller
than
Thersites
bartschi
murrayensis
with
the
whorls
more
rounded
and
more
exserted,
the
sutures
more
deeply
impressed,
the
colors
less
pronounced
and
lighter,
the
peristome
more
expanded
and
the
periphery
less
angulated. The
type
(Cat. No. 333809,
U.S.N.M.)
measures:
Greater
diameter,
43
mm.;
lesser
diameter,
35.5
mm.;
height,
31
mm. It
and
a
para-
type
(Cat. No. 333810,
U.S.N.M.)
come
from
Murray
Islands,
‘Torres
Strait,
and
were
presented
by
Mr. C. Walton. THERSITES (HADRA) BARTSCHI PAULENSIS, new subspecies Plate 3. fig. 10 Sunilar
to
Thersites
bartscht
bartscht,
but
smaller,
whorls
a
trifle
more
rounded,
base
slightly
more
convex,
aperture
less
flaring. Color
nearly
uniform
dark
rich
chestnut,
a
little
darker
on
the
base,
darkest
just
behind
the
aperture. The
peripheral
band
is
not
whitish
but
light
chestnut. Interior
sharply
divided
into
upper
lighter
and
lower
darker
portions
by
a
very
distinct
white
band. | The
type
(Cat. No. 333805,
U.S.N.M.)
measures:
Greater
di-
ameter,
41
mm.;
lesser
diameter,
35
mm.;
height,
28.5
mm. It
and 11 NEW
AUSTRALIAN
LAND
SHELLS—MABS ART. three
paratypes
(Cat. No. 333806,
U.S.N.M.)
come
from
St. Paul’s
Island,
Torres
Strait,
and
were
presented
by
Mr. C. Walton. Material
at
hand
from
Murray
Islands
is
divisible
into
two
species,
namely,
the
large
whitish
form
described
herein
as
Thersites
waltont;
and
the
smaller,
dark
forms. The
latter
are
divided
in
this
paper
into
the
five
subspecies
of
Thersites
bartschi
which
are
described
below. As
Murray
Islands
are
a
group
of
islands,
it
is
probable
that
these
five
subspecies
come
from
separate
islands,
or
perhaps
in
some
cases
from
the
same
island
but
from
different
locations. three
paratypes
(Cat. No. 333806,
U.S.N.M.)
come
from
St. Paul’s
Island,
Torres
Strait,
and
were
presented
by
Mr. C. Walton. Material
at
hand
from
Murray
Islands
is
divisible
into
two
species,
namely,
the
large
whitish
form
described
herein
as
Thersites
waltont;
and
the
smaller,
dark
forms. The
latter
are
divided
in
this
paper
into
the
five
subspecies
of
Thersites
bartschi
which
are
described
below. As
Murray
Islands
are
a
group
of
islands,
it
is
probable
that
these
five
subspecies
come
from
separate
islands,
or
perhaps
in
some
cases
from
the
same
island
but
from
different
locations. Plate 1, fig. 5 Shell
large,
rather
thick,
conic. Whorls
614
but
little
rounded. Base
moderately
convex,
umbilicus
large,
partly
concealed
by
the
refiected
columellar
lip. Body
whorl
angled
at
the
periphery,
the
angle
more
appreciable
to
touch
than
to
sight,
abruptly
descending
at
the
aperture. Sculpture
rather
crude,
of
many
prominent,
retrac-
tive
growth
riblets,
and
with
microscopic
reticulations,
which
have
a
tendency
to
spiral
arrangement,
especially
on
the
body-whorl. Aper-
ture
moderate,
slightly
oblique,
peristome
white
simple
at
its
upper
part,
reflected
from
the
periphery
around
to
the
umbilicus. Parietal
wall
with
a
transparent
glaze. Sutures
crenulated
by
the
upper
ends
of
the
growth
riblets,
not
deeply
impressed,
but
emphasized
by
a
faint
dark
line
below. Color
of
spire
light
chestnut,
deepening
to
dark
chestnut
on
the
last
two
whorls. Base
very
dark,
nearly
black,
an
irregular
whitish
line
suffusing
the
periphery
and
dividing
the
colors
of
the
spire
and
base. Interior
bipartite
in
color,
the
upper
part
nearly
white,
the
lower
part
light
violaceous. The
type
(Cat. No. 333807,
U.S.N.M.)
measures:
Greater
diameter,
46
mm.;
lesser
diameter,
41
mm.;
height,
28.5
mm. It
comes
from
Murray
Islands,
Torres
Strait,
and
was
presented
by
Mr. C. Walton. Plate 3, fig. 3 This
is
a
dwarfed
form
very
like
Thersites
bartschi
fama,
which
it
approaches
in
all
features
but
size. 12 EDINGS
OF
THE
NATIONAL
MUSEUM 72 The
type
(Cat. No. 333811,
U.S.N.M.)
measures:
Greater
diameter,
30
mm.;
lesser
diameter,
25
mm.;
height,
21
mm. It
and
a
paratype
(Cat. No. 833812,
U.S.N.M.)
come
from
Murray
Islands,
Torres
Strait,
and
were
presented
by
Mr. C. Walton. Plate 3, fig. 1 Plate 3, fig. 1 Resembles
Vhersites
bartschi
diva,
but
smaller,
whorls
not
quite
so
rounded,
colors
still
less
pronounced,
the
body
whorl
very
faintly
angulated
at
the
periphery,
the
angle
more
appreciable
by
touch
than
by sight. The
type
(Cat. No. 333814,
U.S.N.M.)
measures:
Greater
diam-
eter,
388
mm.;
lesser
diameter,
32
mm.;
height,
29
mm. It
and
a
paratype
(Cat. No. 333815,
U.S.N.M.)
come
from
Murray
Islands,
Torres
Strait,
and
were
presented
by
Mr. C. Walton. Plate 2, fig. 2 More
elevated
than
Vhersites
bartschi
fama,
the
whorls
still
more
rounded
and
more
exserted,
the
base
more
convex,
and
the
colors
lighter
and
less
pronounced,
the
body
whorl
rounded,
with
no
angle
at
the
periphery
except
just
in
front
of
the
aperture. | The
type
(Cat. No. 333813,
U.S.N.M.)
measures:
Major
diameter,
41.5
mm.;
minor
diameter,
35.5
mm.;
height,
31.5
mm. It
comes
from
Murray
Islands,
Torres
Strait,
and
was
presented
by
Mr. C. Walton. THERSITES (HADRA) WALTONI, new species THERSITES (HADRA) WALTONI, new species Plate 2, fig. 3 Plate 2, fig. 3 Shell
rather
large,
thin,
much
depressed,
whorls
614,
flattened,
slowly
increasing. Body
whorl
abruptly
descending
near
the
aper-
ture,
periphery
rather
sharply
angulated. Sculpture
of
many
slightly
retractive,
nearly
obsolete
lines
of
growth,
and
a
microscopic
reticulation
which
has
a
tendency
to
spiral
arrangement. Sutures
not
deeply
impressed,
crudely
crenulated
by
the
upper
ends
of
the
growth
lines. Base
convex,
its
depth
nearly
equal
to
the
height
of
the
spire. Umbilicus
wide,
but
largely
concealed
by
the
reflected
columella. Peristome
simple
at
its
upper
portion
and
not
reflected
there. At
the
peripheral
angle
the
peristome
begins
to
expand
and
is
broadly
reflected,
especially
at
its
junction
with
the
parietal
wall
which
is
covered
with
a
thin
glaze. Color
of
spire
pale
tawny,
base
slightly
darker,
the
darker
shade
more
pronounced
just
behind
the
aperture;
periphery
marked
by
a
fairly
broad
white
spiral
band. The
type
(Cat. No. 333816,
U.S.N.M.)
measures:
Major
diameter,
62
mm.;
minor
diameter,
46
mm.;
height,
35
mm. It
comes
from 15
NEW
AUSTRAL 13 NEW
AUSTRALIAN
LAND
SHELLS—MARS ART. Murray
Islands,
Torres
Strait,
and
was
presented
by
Mr. C. Walton,
in whose honor the species is named. Mr. Walton
presented
seven
other
specimens
of
this
species
from
the
same
locality
(Cat. No. 333817
and
333820,
U.S.N.M.). Three
of
these
are
immature;
one
is
abnormal
in
that
it
has
the
whorls
rounded,
and
each
slightly
sunken
into
the
succeeding
whorl,
has
the
periphery
rounded
instead
of
angular,
and
is
distinctly
spirally
striate
on
the
body
whorl
near
the
suture;
the
other
two
specimens
are similar to the type but smaller. The
pale
colors,
flattened
whorls,
angular
periphery
and
peculiar
peristome,
sharp
at
its
upper
portion
and
widely
reflected
from
the
peripheral
angle
to
the
umbilicus,
make
this
one
of
most
distinct
species
of
the
fauna
of
Torres
Strait. °Monographia Heliceorum Viventium, vol. 5, p. 377, 1868. Plate 2, fig. 8 Shell
turbinate-conical,
thin,
rather
elevated;
whorls
614,
slightly
convex,
each
appearing
to
be
a
little
sunken
into
the
succeeding
whorl. Body
whorl
suddenly
bent
down
near
the
aperture;
pe-
riphery
moderately
angulated
on
the
back
of
the
body
whorl,
strongly
angulated
in
front
of
the
aperture,
the
outer
lip
showing
scarcely
any
sign
of
being
affected
by
the
angle
of
the
periphery. Sculpture
of
many
slightly
retractive
growth
riblets
and
a
micro-
scopic
reticulation
of
fine
lines. Sutures
well
impressed,
somewhat
crenulated
by
the
upper
ends
of
the
growth
riblets. Base
convex,
its
depth
slightly
less
than
the
height
of
the
spire. Umbilicus
wide,
largely
concealed
by
the
reflected
columellar
ip. Aperture
rounded,
upper
portion
of
the
peristome
simple,
scarcely
reflected;
beginning
to
expand
at
the
periphery
until
at
the
columella
it
is
very
broadly
reflected
and
conceals
a
large
part
of
the
umbilicus. Parietal
wall
with
a
moderately
thick
glaze. Color
of
entire
shell
tawny,
the
base
very
slightly
darker
than
the
spire;
an
indistinct
whitish
band
mark-
ing
the
periphery. The
type
(Cat. No. 100176,
U.S.N.M.)
measures:
Greater
diameter,
44
mm.;
lesser
diameter,
88
mm.;
height,
30.5
mm. It
and
a
para-
type
(Cat. No. 333818,
U.S.N.M.)
were
received
from
R. E. C. Stearns
to
whom
they
were
sent
by
Dr. J. C. Cox,
with
the
label
“Helix
(Camaena)
semicastanea
Pfeiffer;
northeast
Australia.”
‘These
specimens
show
the
wide
range
of
variation
allowed
by
Doctor
Cox
in
his
identifications
of
Thersites
semicastanea. They
bear
but
little
resemblance
to
that
species. They
are
closely
related
to
Thersites
waltont
Marshall
in
color,
texture,
and
general
form,
but
differ
from
it
in
being
smaller,
less
angular
at
the
periphery,
more
elevated,
with
the
whorls
slightly
more
rounded,
and
in
having
the 14 EDINGS
OF
THE
NATIONAL
MUSEUM 72 aperture
rounded
with
no
sign
of
an
angle
in
the
outer
lip
to
mark
the
angle
of
the
periphery. Doctor
Cox’s
locality
“
northeast
Australia
”
seems
to
indicate
that
these
specimens
came
from
the
mainland. More
likely
it
is
simply
a
general
locality
and
as
such
would
include
the
islands
in
Torres
Strait. Because
of
their
close
relationship
to
Thersites
waltona
of
Murray
Islands
which
are
quite
distant
from
the
coast
it
seems
almost
certain
that
they
came
from
an
island
and
not
from
the
mainland. Plate 3, fig. 6 Plate 3, fig. 6 1859. Helix
forsteriana
major
Prrirrer,
Monographia
Heliceorum
Viven-
tium, vol. 4, p. 174. (Not Helix forsteriana major Pfeiffer, Monographia
Heliceorum Viventium, vol. 5, p. 377, 1866.) 1859. Helix
forsteriana
major
Prrirrer,
Monographia
Heliceorum
Viven-
tium, vol. 4, p. 174. (Not Helix forsteriana major Pfeiffer, Monographia
Heliceorum Viventium, vol. 5, p. 377, 1866.) Similar
to
Thersites
forsteriana
forsteriana
but
somewhat
larger,
with
lines
of
growth
more
prominent
and
with
the
periphery
ob-
scurely
angulate,
and
with
colors
less
delicate. The
figured
specimen
is
one
belonging
with
four
others
under
Cat. No. 100188,
U.S.N.M. It
measures:
Major
diameter,
24.5
mm.;
minor
diameter,
21
mm.;
height,
17
mm. They
belong
to
the
Stearns
collection
and
came
from
Dr. J. C. Cox,
who
labeled
them
“
Helix
(Camaena)
forsteriana
Pfeiffer
”
and
quoted
the
locality
as
northeast
Australia. Tt
seems
almost
certain
that
Pfeiffer
described
specimens
like
these
as
var. major. Later
he
gave
another
description
of
major’
which
was
for
a
much
larger
shell
and
which
Dohrn
figured.*
These
are
not
subspecies
major,
but
belong
to
the
new
subspecies
described
below. THERSITE (HADRA) FORSTERIANA FORSTERIANA Pfeiffer Plate 2, fig. 6 Plate 2, fig. 6 Plate 2, fig. 6
1854. Helix forsteriana Preirrer, Proc. Zool. Soc., p. 254. 1846-53. Helix forsieriana PreirreR, Conch. Cab., p. 373, pl. 140, figs. 9-10. 1860. Helix hetaera PrEirrER Proc. Zool. Soc., p. 134. 1854. Helix forsteriana Preirrer, Proc. Zool. Soc., p. 254. 1846-53. Helix forsieriana PreirreR, Conch. Cab., p. 373, pl. 140, figs. 9-10. 1860. Helix hetaera PrEirrER Proc. Zool. Soc., p. 134. Shell
small,
depressed-conic,
moderately
thick;
whorls
6,
slightly
convex,
body
whorl
narrowly
rounded,
scarcely
descending
in
front;
base
moderately
convex,
umbilicus
rather
small,
partly
concealed
by
the
reflected
columella. Sutures
well
impressed,
crenulated. Sculp-
ture
of
fine,
slightly
retractive
growth
lines
and
microsopic
reticula-
tions
or
granulations
finer
and
more
plentiful
than
in
other
species
of
the
group. Aperture
sublunate,
peristome
thin,
reflected
at
its
lower
part
and
broadly
reflected
at
the
columella. Color
of
spire
pale
yellowish
with
three
spiral
bands
of
light
chestnut,
one
below
and one above the periphery and one at the suture. A whitish periph-
eral
band. Base
very
pale
straw
color
much
lighter
than
the
spire. Columella
with
a
tint
of
chestnut
at
its
upper
end. Interior
whitish
with
the
three
exterior
bands
showing
as
tints
of
lavendar,
the
periph-
eral
white
band
very
distinct,
peristome
margined
inside
with
pale
lavendar. The
specimen
figured
(Cat. No. 317037
U.S.N.M.)
measures:
Greater
diameter,
21.5
mm.;
lesser
diameter,
18.5
mm.;
height,
15
mm. It
forms
part
of
the
Henderson
collection
and
is
labeled
“Lizard
Island,
Northeast
Australia.” The
same
lot
contains
two
other
specimens
in
the
same
collection
and
from
the
same
place. They
are
almost
exactly
like
the
figured
specimen. This
species,
although
belonging
in
the
group
of
Thersites
bi-
panrtita, has a different color pattern and has a spire lighter than the
base. The
granulation
or
reticulations
of
the
spire
while
finer
and
more
plentiful
than
in
other
species
is
essentially
of
the
same
kind. Pfeiffer
himself
®
says
that
his
Helix
hetaera
is
the
same
as
his
Helix
forsteriana. 15 NEW
AUSTRALIAN
LAND
SHELLS—MARS ART. ART. ®§ Conch, Cab., pl. 171, figs. 8, 9, 10, 1879. 7Monographia Heliceorum Viventium, vol. 5, p. 377, 1868. ,
, p
,
g
, ,
,
9 Mon. Hel. Viv., vol. 5, p. 377, 1868. 1871. Helix (Hadra) darwint Brazizr, Proce. Zool. Soc., p. 639. Having
no
specimens
and
no
illustrations
to
which
to
refer,
the
best
that
can
be
done
for
this
species
is
to
reproduce
Brazier’s
origi-
nal
description
and
remarks. Shell
umbilicated,
depressedly
globose,
very
thin,
finely
granulated
and
radiately striated; spire moderately elevated, obtuse; whorls 5, slowly inereas-
ing, convex, last roundly convex, slightly descending in front, dirty yellow;
base convex, sculptured the same as the upper surface; umbilicus rather
small, deep; aperture diagonal, ovately lunate; peristome very little reflected,
white; margins approximating and joined by a thin callus, columellar mar-
gin reflected and half covering the umbilicus. Diam. maj. 7, min. 5%, alt. 4 lines. Habitat: North coast of Australia (coll. Brazier). I received two specimens
of this species from a friend who collected them in the far north of Australia,
but the precise locality was not sent with them. It is allied to Helix forsteri-
ana Pfr., from Northeast Australia. PLATE 1 Fie. 1. Thersites (Hadra) barischi mebiagensis, new subspecies. 2. Thersites (Hadra) lizgardensis suma, new subspecies. . Thersites
(Hadra)
bipartita
bivartita
Ferussac. . Thersites (Hadra) bartschi yamensis, new subspecies. . Thersites (Hadra) bartschi murrayensis, new subspecies. OU
we
CO THERSITES (HADRA) FORSTERIANA ADA, new subspecies Plate 3, fig. 4 1866. Helix
forsteriana
major
Prrrrrer,
Monographia
Heliceorum
Viven-
tium,
vol. 5,
p. 377. (Not
Helix
forsteriana
major
Pfeiffer,
Mono-
graphia Heliceorum Viventium, vol. 4, p. 174, 1859.)
1879. Helix forsteriana major DoHREN, Conch, Cab., pl. 171, figs. 8-10. Shell
similar
to
Thersites
forsteriana
forstertana,
but
very
much
larger,
more
depressed
and
the
body
whori
more
descending
in
front. The
type
(Cat. No. 317036,
U.S.N.M.)
comes
from
Lizard
Island,
off
»
the
east
coast
of
Queensland,
and
belongs
in
the
Henderson
collection. it
measures:
Greater
diameter,
31
mm.;
lesser
diameter,
27
mm.;
height,
18
mm. A
paratype
(Cat. No. 333819,
U.S.N.M.)
agrees
in
all
respects
with
the
type. Probably
the
specimens
used
by
Pfeiffer
in
his
second
description
of
“var
major”®
were
from
the
same
locality
as
the
specimens
used
here. He
cites
Cape
Flattery,
Aus-
tralia. Lizard
Island
les
just
off
Cape
Flattery
on
the
east
coast
of
Queensland. The
specimens
figured
by
Dohrn
as
Helix
forsteriana
mujor were from the same lot as those used by Pfeiffer in his second
description
of
major,
though
he
gives
no
definite
locality. Dohrn’s
figures
agree
exactly
with
our
specimens
of
Thersites
forsteriana
ada. 16 EDINGS
OF
THE
NATIONAL
MUSEUM 72 PLATE 2 Fie. 1. Thersites (Hadra) barischi bartschi, new subspecies. . Thersites (Hadra) bartschi diva, new subspecies. . Thersites (Hadra)
wationi,
new species. Thersites (Hadra) lizardensis rada, new subspecies. Thersites
(Hadra)
semicastanea
semicastanea
Pfeiffer. . Thersites
(Hadra)
forsteriana
forsteriana
Pfeiffer. . Thersites (Hadra) lizardensis ligardensis, new subspecies. . Thersites (Hadra) dalli, new species. MAD
NR
wD
pe Fie. 1. Thersites (Hadra) barischi bartschi, new subspecies. . Thersites (Hadra) bartschi diva, new subspecies. . Thersites (Hadra)
wationi,
new species. Thersites (Hadra) lizardensis rada, new subspecies. Thersites
(Hadra)
semicastanea
semicastanea
Pfeiffer. . Thersites
(Hadra)
forsteriana
forsteriana
Pfeiffer. . Thersites (Hadra) lizardensis ligardensis, new subspecies. . Thersites (Hadra) dalli, new species. MAD
NR
wD
pe THERSITES (HADRA) DARWINI Brazier 1871. Helix (Hadra) darwint Brazizr, Proce. Zool. Soc., p. 639. Marshall, William B. 1927. "The Australian land shell Thersites bipartita and its
allies." Proceedings of the United States National Museum 72, 1–16. View This Item Online: https://www.biodiversitylibrary.org/item/100797
Permalink: https://www.biodiversitylibrary.org/partpdf/91880 Sponsored by Sponsored by
Biodiversity Heritage Library Biodiversity Heritage Library Smithsonian Libraries and Archives Smithsonian Libraries and Archives PLATE 3 Fic. Thersites (Hadra) bartschi cepa, new subspecies. . Thersites (Hadra) bartschi oma, new subspecies. . Thersites (Hadra) bartschi elfa, new subspecies. . Thersites (Hadra) forsteriana ada, new subspecies. . Thersites (Hadra) bartschi nesia, new subspecies. Thersites
(Hadra)
forsteriana
major
Pfeiffer. . Thersites (Hadra) bartschi nura, new subspecies. . Thersites (Hadra) semicasianea alma, new subspecies. . Thersites (Hadra) bartschi fama, new subspecies. . Thersites (Hadra) baritschi poulensis, new subspecies. SOMARDMA
WDE
= . Thersites (Hadra) bartschi fama, new subspecies. . Thersites (Hadra) baritschi poulensis, new subspecies. = O O This file was generated 1 April 2024 at 13:25 UTC Copyright & Reuse Copyright Status: Public domain. The BHL considers that this work is no longer under
copyright protection. This document was created from content at the Biodiversity Heritage Library, the world's
largest open access digital library for biodiversity literature and archives. Visit BHL at
https://www.biodiversitylibrary.org. This file was generated 1 April 2024 at 13:25 UTC
|
https://openalex.org/W4230785317
|
https://e-archivo.uc3m.es/bitstream/10016/30688/1/metodologia_agullo_RIS_2013.pdf
|
Spanish; Castilian
| null | null |
Revista internacional de sociología
| 2,013
|
cc-by
| 3,366
|
Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ
Metodología de la investigación social
Técnicas innovadoras y sus aplicaciones
Madrid, Ediciones Síntesis, 2012 No leer esta obra sería perder la opor
tunidad de explorar y (re)conocer un
“manual de última generación o de
nuevo cuño” en el área de Metodología
e Investigación Social. Varios son los
criterios o puntos fuertes que otorgan
a esta compilación, desde mi punto de
vista, los adjetivos o título de “manual
o handbook” en mayúsculas y en la
mejor de las acepciones. Cumple todos
los requisitos para ser etiquetado como
manual pero incluso camina unos pasos
más allá. Estamos ante un trabajo per
tinente, minucioso, excelente y nece
sario. Por tanto, varios son los avales
que permiten calificarlo como altamente
“recomendable” y darle toda legitimidad
y credibilidad. Véanse: antigüedad con profesionalidad y contri
buciones clave. Dinámico y didáctico. Las 350 pági
nas parecen acortarse debido al estilo
pedagógico y ameno que desprende. El
libro puede leerse tanto capítulo a capí
tulo, de manera independiente, como de
una vez; ofrece una linealidad y coheren
cia argumental en la que el lector/a no
se pierde. Además, los capítulos están
vinculados y articulados. Por ejemplo, el
capítulo 5 (página 111) hace referencia
al capítulo 9, el capítulo 10 (pág. 227) se
refiere al capítulo 11. El capítulo 9 alude
al capítulo 4 y al 10, y así en diversas
ocasiones. La adecuada coordinación de
Arroyo y Sádaba, ese hombro a hombro
de los autores y textos, es indicador del
nexo que les une y que ayuda a sumer
girse en todos sus contenidos. Se reco
mienda hacer una lectura entre líneas
de cada uno de los capítulos, de manera
pormenorizada y que aquí no ha lugar. Sin
embargo, se invita a realizar esta grata
inmersión en Metodología. Autoría. Es una garantía indudable. El equipo de 23 autores/as constituye
un punto de partida que explica el buen
resultado final.Se observa que todos son
especialistas en su campo y parecen
aportar lo mejor de sus investigaciones
y enseñanzas. Nueve de ellos son profe
sores e investigadores del Departamento
de Sociología IV de la UCM. Los otros
catorce, vinculados al mismo departa
mento y colaboradores (de centros públi
cos o privados, españoles o de otros
países), ratifican que la obrapuede servir
para consolidar los más recientes apor
tes metodológicos. El texto reúne tanto a
veteranos y prestigiosos autores, como a
“jóvenes” académicos que suplen su corta g
Todo ello permite la consulta en un
tiempo prudencial. 482 • LIBROS / BOOK REVIEWS 482 • LIBROS / BOOK REVIEWS RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ
Metodología de la investigación social
Técnicas innovadoras y sus aplicaciones
Madrid, Ediciones Síntesis, 2012 Se denota que este
grupo de docentes e investigadores cuen
tan con una sólida formación en metodolo
gía adquirida, a juzgar por las referencias,
del buen hacer de profesionales que les
precedieron y de otros manuales tanto
españoles como extranjeros. Se suma el
hecho de que nos desvelan la tramoya
o trastienda de investigaciones propias RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 LIBROS / BOOK REVIEWS • 483 actuales para ejemplificar sus técnicas
expuestas. actuales para ejemplificar sus técnicas
expuestas. estudiantes de Ciencias Sociales y profe
sionales de la investigación social). Sin
embargo, también sacia la necesidad de
lectores/as ávidos de otras perspectivas
o de actualizarse en las herramientas
clásicas de abordaje de la sociedad de la
información o sociedad web 2.0. El carác
ter “avezado” del mismo podría ser una
rémora; por contra, desmenuzan cada
técnica o tendencia, ofrecen una inmer
sión práctica a dichos instrumentos. Tal
como mencionan Arroyo y Sádaba en la
introducción, “se ha procurado evitar (…)
un enfoque excesivamente teórico, por lo
que se pretende una enseñanza aplicada”
(pág. 13). Y, desde mi punto de mira, lo
consiguen. Pretenden colmar las necesi
dades que plantean el EEES, la exigencia
de complementar y ampliar la bibliografía,
de mayor especialización metodológica. Y
también lo consiguen. Presentacióny formato. Al hilo del
punto anterior, la obra incluye cuadros,
esquemas, imágenes-fotos, que ilustran
la consulta. La distribución de los 14 capí
tulos en 4 partes o bloques es adecuada
y congruente: la primera focaliza el análi
sis discursivo desde perspectivas plura
les (caps. 1 al 3). La segunda abarca el
análisis cuantitativo de datos obtenidos
mediante encuesta virtual (cap. 4), análisis
de imágenes (cap.5) y de textos (cap. 6). La tercera se centra en metodologías parti
cipativas (cap. 7) y evaluativas (cap. 8). En
la cuarta y última, no en importancia sino
porque trata metodologías emergentes,
abordan la investigación online (cap. 9), de
materiales visuales y espaciales (caps. 10
al 12), redes sociales (cap. 13) y simulación
social (cap. 14).Nos encontramos ante una
brillante visión y (re)visión de estos temas. Además, los autores huyen de un estilo
recargado y distante y se expresan en un
lenguaje cercano a la par queriguroso. Cubre carencias y es equilibrado. Completa el hueco existente en la biblio
grafía metodológica en castellano y en las
lenguas co-oficiales españolas. Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ
Metodología de la investigación social
Técnicas innovadoras y sus aplicaciones
Madrid, Ediciones Síntesis, 2012 Se dispo
nede diversos manuales básicos y centra
dos en algunas técnicas pero no abundan
los dedicados a otras perspectivas. Los
textos previos, imprescindibles, están más
orientados a herramientas clásicas de
investigación. Metodología, sin embargo,
se ubica en esta sociedad global y cam
biante y nace en un momento idóneo de
revitalización. Estas características de la
Investigación Social son bien explicadas
porque se abordan temáticas fundamen
tales para el análisis sociológico del siglo
XXI y con las vías que abre la tecnología:
tratamiento de materiales audiovisuales y
geoespaciales; crecientes análisis de con
tenido de tipo diverso; adaptación de la Planteamiento general y destina
tarios. Se trata de un manual avanzado
sobre metodología y aplicaciones selec
cionadas por su carácter original o por la
frecuencia de utilización (v. gr. encuesta)
en la investigación. La obra tiene espe
cialmente en cuenta las nuevas estrate
gias de recogida y análisis de información
sociológica, las mediciones desde la apa
ratologíadigital, la gestión integral y rápida
de información (como los datos geo-
espaciales), y los medios de registro e
interpretación de materialesvirtuales (que
incluyen imagen, audio y vídeo). Metodología se destina a un público
iniciado en los fundamentos básicos (para RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 484 • LIBROS / BOOK REVIEWS siempreurge la reflexión y actualización,
que es lo que viene a cubrir Metodología. Arroyo y Sádaba coordinan un manual
actual sin olvidar los orígenes, lo cual
sería inexcusable. El enfoque histórico
se desarrolla de manera transversal y se
observa en muchos capítulos. Los autores
se curan en salud y cuando van a obviar
algo lo advierten y nos (re-)conducen a los
clásicos para justificar las ausencias y no
exceden el espacio recomendable en un
texto de este perfil. investigación demoscópica clásica a apli
caciones recientes (sistemas CATI/CAWI,
etc.); nuevas tendencias de estudios on
line y otras opciones cualitativas (etnogra
fía virtual, entrevistas en línea, p.e.); resur
gimiento del interés por el análisis de redes
sociales, aproximaciones de simulación
social como resultado de la inteligencia
artificial, etc. No da preminencia a unas perspecti
vas sobre otras, las trata en condiciones
de igualdad. Eso sí, dedica 6 capítulos
de 14 a los “Paradigmas y metodologías
emergentes en Investigación Social”
(parte IV), cuando el resto de las partes
transitan por las más clásicas pero con aire
renovado, tanto cualitativas (parte I, caps. 1 al 3) como cuantitativas (parte II, caps. Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ
Metodología de la investigación social
Técnicas innovadoras y sus aplicaciones
Madrid, Ediciones Síntesis, 2012 Todo ello deviene más
importante que lo aplicado: p.e., el SPSS,
el OpenGeoDA o Atlas.ti nos ofrecen
cruces pero no seleccionanlos códigos,
nodos o variables a analizar. Estamos de
acuerdo en que este prisma “nos acerca
a una nueva forma de “artesanía digital”
[entrecomillado de los autores] que ve en
el software libre su máxima expresión”
(pág. 279). Las técnicas ayudan pero, de
momento, no suplen al cerebro y la crea
tividad. Ello me sugiere las palabras de
Wright Mills: “Sed buenos artesanos. Huid
de todo procedimiento rígido. Sobre todo,
desarrollad y usad la imaginación socioló
gica”, o “Evitad el fetichismo del método y
de la técnica”. siempre… Es de “nueva generación” en
cuanto que contempla tecnologías y ten
dencias novedosas. En la última década,
se están fraguando importantes cambios
que se han reflejado poco y de forma frag
mentada en la bibliografía metodológica
española. Arroyo y Sádaba mencionan
que nuestro contexto hipertecnológico
“nos alejará del protagonismo casi hege
mónico de la investigación demoscópica
cuantitativa y cualitativa del siglo XX”; y
también suscribo cuando matizan: “dicha
evolución, sin renunciar a la aproximación
clásica, nos aproximará paulatinamente a
una mayor diversificación, pluralidad y a
los enfoques multimétodo” (pág. 14). (
g
)
Alguna muestra de ello. Por ejemplo,
los autores presentan la “minería de textos
y de opiniones” (págs. 146-150) como
herramientas aún infrautilizadas y que,
junto a un componente teórico necesa
rio para respaldarlas, podría pasar de un
niveldescriptivo a otro escalafón más expli
cativo y profundo. También se propone un
“modelo interpretativo estructural” que da
lugar a cuatro posibles tipos de IAP (pág. 173). Entre varias convergencias, coincido
con los autores en que “nuestras técnicas
de investigación poseen grosso modo la
misma filosofía que usaban los incipientes
sociólogos de antaño. Por decirlo un poco
provocativamente, los métodos de investi
gación social han ido sumando recursos y
herramientas (…), pero han mantenido el
núcleo epistemológico relativamente inal
terado” (pág. 199). Además, parece que
“Está servido el debate sobre si estamos
ante antiguas técnicas de investigación
bajo el disfraz de la mediación digital o
si realmente asistimos al nacimiento de
nuevas técnicas stricto sensu” (pág. 202). Metodología no se queda anclada en
el pasado, ni en el presente. Tampoco se
deja llevar por la euforia de las TIC. Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ
Metodología de la investigación social
Técnicas innovadoras y sus aplicaciones
Madrid, Ediciones Síntesis, 2012 4
al 6). La parte III, más breve, y eso podría
ser un punto “crítico”, sólocuenta con dos
capítulos (el 7 y 8) dedicados a metodolo
gías participativas y evaluativas respecti
vamente. En cualquier caso, el texto invita
a recuperar, aunque no lo mencionen, la
estela de Lewin al abogar por esa unión
teoría-praxis que puede lograrse “si el teó
rico no mira los problemas aplicados con
aversión erudita o con temor a los proble
mas sociales, y si el aplicado comprende
que no hay nada tan práctico como una
buena teoría” (1951/1984:161). Los artefactos tecnológicos no suelen
ser sólo eso, meros adelantos técnicos,
sino que han permitido reorientar algunas
estrategias metodológicas e incluso desa
rrollar formas originales de investigar. Nos
situamos, pues, ante una obra de incues
tionable pertinencia en este contexto
supratecnológico e idónea para observarla
crisis como reto y oportunidad. Por añadi
dura, siguiendo a los autores, para ofrecer
una perspectiva integral y reformada, han
decidido acertadamente al abordar aspec
tos no tan innovadores pero que siguen y
seguirán, comparto con ellos, presentes
en la praxis investigadora: metodologías
participativas; encuesta; planificación y
evaluación de programas sociales; y dis
tintos enfoques de análisis discursivo. Tienen razón los coordinadores cuando
afirman que los manuales de metodología
apenas cubren otras alternativas o, si es
así, se perfila sólo de manera monográ
fica los aspectos señalados. Esta obra sí
integra todo ello y lo realiza de manera
convincente. Tradicional y “artesano” y… Como
si de un producto de alta gama o de cali
dad certificada se tratara, que conserva el
mejor sabor y aroma que indica la marca,
han amasado un manual siguiendo las
recetas de sus progenitores y prede
cesores, pero ahora aportando nuevos
ingredientes y especias. Las bibliotecas
(bibliografía y webgrafía) sobre metodolo
gía sonvastas y exhaustivas. Sin embargo, Mucho más relevante que el procedi
miento de técnicas o software sofisticados,
procede diseñar y analizar correctamente,
organizar adecuadamente la informa RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 LIBROS / BOOK REVIEWS • 485 ción, seleccionar lo esencial. Entre varias
sinergias, coincido con los autores en
que “Cabe reservar un papel estelar a
los métodos demoscópicos conversacio
nales tradicionales, a la investigación por
encuesta y a la investigación cualitativa,
herramientas que han sido, son y seguirán
siendo fundamentales para la aprehen
sión de las representaciones mentales”
(págs. 110-111). Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ
Metodología de la investigación social
Técnicas innovadoras y sus aplicaciones
Madrid, Ediciones Síntesis, 2012 Esta
obra ofrece una visión de conjunto del
panorama emergente y crecientemente
diversificado de opciones metodológicas,
más allá de la profesión clásica de inves
tigador social y siguiendo la huella que
dejaron Bourdie, Chamboredon y Passe
ron en su El oficio de sociólogo. …Y al mismo tiempo de vanguar
dia. Renovar o morir. Este libro “renueva”
o, mejor dicho, complementa los ante
riores. No es manual al uso de los que
se encuentra en la literatura, de los de RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 486 • LIBROS / BOOK REVIEWS Mejorando lo presente, como se suele
decir, supera anteriores manuales de
los que tanto hemos aprendido y/o refe
renciado, pero olvida partes que estos
tienen (ver argumento posterior). Este
libro debería catalogarse en esa biblioteca
metodológica que hay que (re)generar en
nuestras estanterías para seguir nutriendo
un área ya consolidada, que no debe/
puede quedar atrapada ni estancada. Estamos ante un texto intergeneracional,
tanto para las cohortes jóvenes, para las
intermedias o las más decanas. Nadie
puede negar que es un texto de prêt-à-
porter, de avance de temporada, dado
que está preparado para iniciar una etapa
convulsa que vivimos y en la que no nos
sobran herramientas. Aunque unos capí
tulos más que otros, en conjunto fascina
la sensación de “modernidad” que rezuma
su contenido. camino a la refundación y fusión de méto
dos, recupera reflexiones fundamentales,
pone al día o es un buen “estado del arte”. Sin embargo, por eso mismo, es “algo
extensa”, muy completa, y podría dar de sí
para dos textos o para lo que se denomina
una “segunda edición ampliada”.i Muchos manuales, al final de cada
capítulo, presentan enunciados de ejer
cicios con sus respuestas, ejemplos,
resumen, conceptos clave o glosario,
referencias bibliográficas (o webgrafía)
básicas y/o complementarias del tema,
links, principalmente. Este texto no des
cribe estos “trucos” para investigarque sí
nos muestran tanto manuales consagra
dos como los más recientes, por ejemplo
el de H. Becker, Trucos del oficio. Cómo
conducir su Investigación en Ciencias
Sociales (2012, Siglo XXI) o en nuestro
contexto español el de D. Guinea-Martín
(coord., 2012, Gedisa) Trucos del oficio de
investigador. El lector/a de Metodología se
puede quedar ávido, tómese como crítica
constructiva, de leer más sobre algunos
aspectos solo esbozados. Sin embargo,
estamos ante un “manual avanzado”, todo
esto se presupone, y lo compensan con
los puntos excelentes arriba mencionados. RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ
Metodología de la investigación social
Técnicas innovadoras y sus aplicaciones
Madrid, Ediciones Síntesis, 2012 Recomendable sin reservas. Por
todo ello, nos encontramos ante una
obra recomendable tanto para el alum
nado como para colegas y/o compañeros
(académicos o profesionales). El público
destinatario trasciende el ámbito acadé
mico. Puede incluso convertirse en un
libro de cabecera o “manual” de los de
tener “a mano”; a mano para consultarlo
como compilación de lo importante o para
bajar al detalle de capítulos por separado. Cuando se recomienda una obra es señal
de que convence, aporta algo más y no va
a defraudar. Diferencias en la extensión y organiza
ción. Cada capítulo sigue una estructura
(véase el índice) y longitud. Ello podría
justificarse con la mayor/menor utilización
de determinadas técnicas pero quizás no
estaría de más unificar el formato y que
algunos tuvieran una estructura similar y
clásica: introducción, fases, partes, con
clusiones, referencias, ejercicios, glosario,
por ejemplo. Aun así, pensamos que la
diversidad o hibridación es más recomen
dable, al igual que enunciaba el novelista Aun con todo lo positivo, y con objeto
de realizar una evaluación más ponde
rada, también se percibe alguna debili
dad o, mejor dicho, aspecto mejorable
para una próxima edición que podría
demandarse. Metodología se sitúa en el RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 LIBROS / BOOK REVIEWS • 487 Maurois “En literatura, como en genética
(o sociología, añadiríamos), los cruces
son saludables”. Presentarlo, además,
en formato virtual, adjuntar un CD en sus
solapas (o una versión en epub, flash,
accesible) con el contenido del mismo
también facilitaría la difusión e impacto de
sus bondades entre las redes sociales de
alumnos y profesionales. portamiento individual puede explicarse
en función de nuestra posición en la red
de relaciones sociales” (pág. 304). Se
toma la “red como dato” pero el objeto de
estudio son los actores o fenómenos rela
cionados con los agentes sociales. Ofre
cen una guía práctica y protocolo para
orientar el trabajo de modelado y simu
lación. Nos facilitan las principales plata
formas y recursos disponibles en la web
(pág. 339-342) para seguir profundizando
en estos “laboratorios sociales virtuales”
que permiten contrastar explicaciones
sin tener que recrear en la vida real situa
ciones de experimentación, etc. La obra
coordinada por Arroyo y Sádaba puede
dar respuesta a las demandas recurren
tes del alumnado y colegas sobre últimas
tendencias metodológicas. RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ
Metodología de la investigación social
Técnicas innovadoras y sus aplicaciones
Madrid, Ediciones Síntesis, 2012 Algunos de los
capítulos resultan más cortos pero ello se
suple con los textos que conocemos y que
siguen siendo imprescindibles. Junto a la introducción escrita por los
coordinadores, se echa en falta, por pedir
para la próxima edición (de lo que poco
que adolece, insisto), un prólogo que
podría resumir y atraer más, si cabe, al
alumnado y/o a los lectores/as en gene
ral. Un análisis diseccionado, a modo de
prefacio, del cual carece el texto presen
tado, podría mostrar de otra manera las
fortalezas de cada capítulo que en esta
recensión han podido quedar diluidas
entre comentarios generales. La que
aquí escribe ha realizado este análisis
pormenorizado pero que, obviamente por
motivos de espacio, no se puede facilitar
ahora; sin embargo, podría enviarse al
lector/a más motivado. Abrir la edición a
otros países sería otra idea a considerar. Aunque los autores no lo mencionan,
en el libro sobrevuela el mejor espíritu de
los clásicos combinado de manera solven
tecon las aportaciones de metodólogos y
metodologías recientes. Ese espíritu, por
ejemplo el de Peter Berger, cuando nos
advertía del error (“insensibilidad” por lo
social) en el que no incurre, desde luego,
esta obra: “Algunos sociólogos… se
preocupan tanto de las cuestiones metodo
lógicas que han dejado de interesarse por
la sociedad. Como resultado, nada apa
rece como significativo en la vida social,
ya que en la ciencia, como en el amor, una
excesiva concentración en las técnicas lo
más probable es que conduzca a la impo
tencia”. Para cerrar, en pocas palabras,
felicitar a los coordinadores y autores, y
retomar los argumentos de mayor calado En suma, la parte I, compuesta por
3 capítulos, ofrece un “Análisis del dis
curso y de datos cualitativos. Perspecti
vas plurales”. El bloque II también incluye
3 capítulos sobre últimas tendencias en
torno al “Desarrollo en la investigación
cuantitativa”. La parte IIIsobre “Metodolo
gías participativas y evaluativas”, resulta
breve pero igualmente de gran interés. La IV, “Paradigmas y metodologías emer
gentes”, quizás es la más extensa no sólo
por “moda” sino también por necesidad de
mayores y mejores aportaciones actuales. Por ejemplo, subrayan que nuestro “com RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 488 • LIBROS / BOOK REVIEWS que abren esta reseña: garantía desde la
autoría, formato, pertinencia, dinamismo,
minuciosidad, vanguardia, rigurosidad,
aplicabilidad, reflexión, equilibrio,… obra
recomendable sin reservas. María Silveria Agulló Tomás. Universidad Carlos III de Madrid. Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ
Metodología de la investigación social
Técnicas innovadoras y sus aplicaciones
Madrid, Ediciones Síntesis, 2012 msat@polsoc.uc3m.es María Silveria Agulló Tomás. Universidad Carlos III de Madrid. msat@polsoc.uc3m.es
|
W3128777554.txt
|
https://aricjournal.biomedcentral.com/counter/pdf/10.1186/s13756-021-00930-x
|
en
|
Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments
|
Antimicrobial resistance and infection control
| 2,021
|
cc-by
| 8,912
|
Aworh et al. Antimicrob Resist Infect Control
https://doi.org/10.1186/s13756-021-00930-x
(2021) 10:58
Open Access
RESEARCH
Genetic relatedness of multidrug resistant
Escherichia coli isolated from humans, chickens
and poultry environments
Mabel Kamweli Aworh1,2,3,4* , Jacob K. P. Kwaga3, Rene S. Hendriksen5, Emmanuel C. Okolocha3 and
Siddhartha Thakur4
Abstract
Background: Inappropriate use of antimicrobial agents in animal production has led to the development of antimicrobial resistance (AMR) in foodborne pathogens. Transmission of AMR foodborne pathogens from reservoirs, particularly chickens to the human population does occur. Recently, we reported that occupational exposure was a risk
factor for multidrug-resistant (MDR) Escherichia coli (E. coli) among poultry-workers. Here we determined the prevalence and genetic relatedness among MDR E. coli isolated from poultry-workers, chickens, and poultry environments
in Abuja, Nigeria. This study was conducted to address the gaps identified by the Nigerian AMR situation analysis.
Methods: We conducted a cross-sectional study among poultry-workers, chickens, and poultry farm/live bird market
(LBM) environments. The isolates were tested phenotypically for their antimicrobial susceptibility profiles, genotypically characterized using whole-genome sequencing (WGS) and in silico multilocus sequence types (MLST). We
conducted a phylogenetic single nucleotide polymorphism (SNPs) analysis to determine relatedness and clonality
among the isolates.
Results: A total of 115 (26.8%) out of 429 samples were positive for E. coli. Of these, 110 isolates were viable for phenotypic and genotypic characterization. The selection comprised 47 (42.7%) isolates from poultry-workers, 36 (32.7%)
from chickens, and 27 (24.5%) from poultry-farm or LBM environments. Overall, 101 (91.8%) of the isolates were
MDR conferring resistance to at least three drug classes. High frequency of resistance was observed for tetracycline
(n = 102; 92.7%), trimethoprim/sulfamethoxazole (n = 93; 84.5%), streptomycin (n = 87; 79.1%) and ampicillin (n = 88;
80%). Two plasmid-mediated colistin genes—mcr-1.1 harboured on IncX4 plasmids were detected in environmental
isolates. The most prevalent sequence types (ST) were ST-155 (n = 8), ST-48 (n = 8) and ST-10 (n = 6). Two isolates of
human and environmental sources with a SNPs difference of 6161 originating from the same farm shared a novel ST.
The isolates had similar AMR genes and plasmid replicons.
Conclusion: MDR E.coli isolates were prevalent amongst poultry-workers, poultry, and the poultry farm/LBM environment. The emergence of MDR E. coli with novel ST in two isolates may be plasmid-mediated. Competent authorities
should enforce AMR regulations to ensure prudent use of antimicrobials to limit the risk of transmission along the
food chain.
*Correspondence: mabelaworh@yahoo.com
1
Department of Veterinary and Pest Control Services, Federal Ministry
of Agriculture and Rural Development, Abuja, Nigeria
Full list of author information is available at the end of the article
© The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
Page 2 of 13
Keywords: Escherichia coli, Antimicrobial resistance, Prevalence, Chicken, Multidrug resistance, Genetic relatedness,
One health, Nigeria
Background
Antimicrobial resistance (AMR), is one of the biggest
threats to food safety and considered a One-Health issue
with the potential of spreading to other countries since
resistant pathogens do not recognize boundaries [1, 2].
Recently, we have shown the transmission of AMR E. coli
among chickens, humans, and the poultry environment
[3, 4]. Globally, antimicrobial agents are used in food animal production to ensure good health and productivity
of the animals [5–7]. Multiple studies have shown that
inappropriate use of these antimicrobial agents in food
animal production particularly poultry has led to the
development of AMR [8–10].
Commensal E. coli are known to be part of the normal
flora of the gastrointestinal tracts of man and animals
without causing any harm to their host [11, 12]. Several
E. coli strains have been used as indicator organisms in
various studies on AMR [11, 13]. Although commensal
E. coli are harmless to the host, the bacteria can acquire
resistance genes and act as a reservoir for the spread of
multidrug resistance (MDR) to and from food to humans
[13]. The genetic structure of E. coli strains is usually
influenced by several factors including the host and environment enabling the bacteria to acquire various AMR
mechanisms [13, 14].
In September 2016, 193 member countries including
Nigeria signed the United Nations General Assembly resolution to develop national action plans (NAP) on AMR
[15]. In November 2016, Nigeria established its AMR
coordinating body at the Nigeria Center for Disease Control (NCDC), and in January 2017, a One-Health AMR
Technical working group was inaugurated to conduct
AMR situation analysis and develop Nigeria’s NAP [16].
One of the data gaps identified from the AMR situation
analysis was the paucity of AMR studies done in Nigeria
across humans, food-producing animals, and the environment [16].
It has been documented that the continuous use of
antimicrobial agents for therapeutic purposes against
infections has led to the emergence of drug-resistant bacteria such as MDR E. coli [17]. MDR bacteria have made
it difficult to treat certain infections effectively with modern or conventional antimicrobial agents [18]. AMR has
resulted in treatment failure in human and animal populations, because of the emergence of MDR foodborne
pathogens like E. coli arising from the abuse or misuse
of antimicrobial agents [19]. This scenario further deteriorates in Nigeria because of the increasing number of
farmers who practice self-prescription as well as selfadministration of antimicrobials to their animals [5, 20].
Poultry farmers have easy access to antimicrobials that
are available over-the-counter without prescription [3]
and evidence shows that farmers administer the antimicrobials repeatedly against non-responsive infections
[20, 21]. These actions by the farmers further promote
the emergence and spread of antimicrobial-resistant
foodborne pathogens with serious implications on public health [22]. Continuous administration of antimicrobial agents to chickens for prophylaxis, therapeutic,
or growth promotion purposes increases the antibiotic
selection pressure for resistance in the bacteria [23]. Our
recent publication demonstrates that occupational exposure over ten years to chickens on poultry farms or live
bird markets (LBMs) was a risk factor for MDR E. coli
among poultry workers in Abuja [3].
We hypothesized that chickens harbouring MDR E.
coli as well as contaminated poultry farm or LBM environment can become potential sources for transmission
of resistance genes to poultry workers exposed to chickens and the environment on poultry farms or markets.
To better understand the association between MDR E.
coli isolates recovered from humans, chickens and poultry environment, we investigated the genetic relatedness
of MDR E. coli isolates from poultry-workers, chickens,
and selected poultry farms/LBM environments in Abuja,
Nigeria.
Methods
Study overview
Our current study was part of a larger project conducted
from December 2018 to February 2020 exploring MDR
E. coli in humans, chickens, and the poultry farm/market environment. An aspect of this research exploring the
risk factors for MDR E. coli among poultry workers has
already been previously published [3].
Characterization of E. coli isolates
Of 429 samples collected in the course of the present
study, 110 E. coli strains isolated from the stool of apparently healthy poultry workers, faecal samples obtained
from chickens as well as from poultry litter and water
obtained from farm and LBM environments were characterized. The sample collection procedures, isolation of E.
coli from these samples, and antimicrobial susceptibility
profiling of E. coli using the disk diffusion method have
been described previously [3]. Briefly, suspected dark
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
pink E. coli colonies on MacConkey agar were streaked
on Eosin Methylene Blue agar and incubated at 37 °C for
24 h. Isolates were confirmed as E. coli using Microbact
GNB 24E (Oxoid, UK).
Genotypic Detection of E. coli isolates
Whole genome sequencing (WGS) of E. coli isolates
All isolates were subjected to WGS as previously
described [4]. Briefly, libraries for each E. coli isolates
were prepared for WGS using a Nextera XT kit. We processed 0.3 ng/µL of DNA from each isolate using a Nextera XT DNA Sample Prep Kit (Illumina Inc., San Diego,
CA), pooled together, and sequenced on an Illumina
Miseq platform using a 2 × 250 paired-end approach
(Illumina Inc., San Diego, CA). Raw sequencing reads
were de-multiplexed and converted to fastq files using
CLC Genomics workbench version 9.4 (Qiagen bioinformatics, Valencia, CA). The DNA sequences for each
isolate were transferred to the National Center for Biotechnology Information (NCBI) database after which
each isolate was assigned an accession number.
Bioinformatic analysis of WGS data
Antimicrobial susceptibility determinants of E. coli isolates
High-quality Illumina paired-end reads were assembled
de novo into the draft genome sequence for each isolate
using SPAdes assembler v.3.13.1 [24]. In silico detection
and typing of resistance genes was done using ResFinder
3.2, a Center for Genomics Epidemiology (CGE) bioinformatics tool (database version 2020–02-11), to determine
the acquired AMR genes as well as assess chromosomal
point mutations [25]. For each isolate, we used between
95–100% identity to match individual genes to an annotated resistance gene. [25]. In silico determination of the
existing plasmid replicon types of each E. coli isolate was
done by submitting the assembled genomes to PlasmidFinder 2.1, a CGE bioinformatics tool (database version
2020–04-02). The selected threshold for minimum percentage identity was 95% while the minimum coverage
of the contig was set at 60% [26]. The in silico plasmid
MLST typing of replicons (IncHI2 and IncF) were determined by submitting the assembled genome to pMLST
2.0 (database version: 2020–04-20) bioinformatics tool
on the CGE website [26].
Multilocus sequence typing (MLST) of MDR E. coli isolates
As previously described [4] in silico MLST-analyses of
the E. coli isolates were determined using schemes demonstrated by Achtman which made use of allelic variation
amongst seven housekeeping genes (adk, fumC, gyrB, icd,
mdh, purA, and recA) to assign sequence types (STs) [27].
We used whole-genome sequence data to generate the
E. coli MLST assignment for each isolate that perfectly
Page 3 of 13
matched the alleles in the MLST database. MLST Finder
2.0, a CGE bioinformatics tool was used to assign STs
to the isolates with 100% match against known MLST
alleles while those without perfect matches were identified as unknown [28]. Some isolates were assigned as a
new type after matching with MLST alleles of unknown
ST in the MLST database.
Determination of E. coli Phylogroups, SNPs calling
and Phylogeny
Phylogroups of E. coli genomes were determined using
an in silico Clermont typing method [29]. The Clermont
Typer web interface is hosted by CATIBioMed (IAME
UMR 1137) and accessible at http://clermontyping.iame-
research.center/.
Phylogenetic trees were constructed to determine the
phylogenetic relatedness of the E. coli isolates using the
technique known as SNP calling described by Kaas et al.
[30]. Briefly, the tool CSI Phylogeny, a CGE bioinformatics tool accessed online at https://cge.cbs.dtu.dk/servi
ces/CSIPhylogeny/ was used for SNP calling. The CSI
phylogeny uses BWA to map raw reads to a reference
sequence and uses Samtools for SNP calling. E. coli strain
NCTC11129 was used as the reference strain for SNPs
calling to identify variants present in the chromosome of
each isolate. The selected thresholds used were: cut-offs
for depth = 10x; SNP quality = 30; mapping quality = 25
and Z score = 1.96. The phylogenetic SNP-based maximum likelihood tree were annotated and visualized using
the programs Figtree (http://tree.bio.ed.ac.uk/software/
figtree/) and interactive Tree of Life tool—iTOL (http://
itol.embl.de/itol.cgi). Pairwise SNP differences between
genomes were computed to determine if isolates of different origins were related.
Data analyses
Antimicrobial susceptibility data were analyzed using Epi
Info 7 software by computing frequencies and proportions. The 108 assembled E. coli genomes of the present
study have been deposited by the Thakur Molecular Epidemiology Laboratory, NC State University (GenomeTrakr Project) in the NCBI database under the Bioproject
ID number PRJNA293225. The remaining two isolates
have accession obtained from the DNA Data Bank of
Japan (DDBJ) as previously reported [4].
Results
Antimicrobial susceptibility profile of E. coli isolates
A total of 110 E. coli strains were isolated from 122
human stool samples obtained from poultry workers on farms and LBMs; 111 faecal samples obtained
from chickens on farms and LBMs; and 196 poultry
litter and water samples obtained from farm and LBM
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
Page 4 of 13
environments. Of the 110 E. coli strains 42.7% (n = 47)
were recovered from humans; 37.7% (n = 36) from
chickens and 24.5% (n = 27) from poultry environment. High resistance rates were observed for tetracycline, trimethoprim/ sulfamethoxazole, streptomycin,
ampicillin, nalidixic acid and gentamicin. On the contrary resistance to colistin, imipenem, ceftazidime,
amoxicillin/clavulanic acid, cefuroxime, cefotaxime
and ceftriaxone were quite low although colistin resistance rate of 11.8% in commensal E. coli is quite worrisome (Table 1).
Analysis of resistance profiles of the 110 isolates
showed that a single isolate (0.9%) from a poultry
farmer was susceptible to all antimicrobial drugs
tested; 4 (3.6%) were resistant to only one antimicrobial drug, 4 (3.6%) were resistant to two antimicrobial
drugs and interestingly 101 (91.8%) were MDR (resistant to three or more classes of antimicrobial drugs).
The number of antimicrobials against which each isolate showed resistance was between one and thirteen.
Surprisingly, a single isolate from a poultry farm was
resistant to 13 out of 16 antimicrobials tested. The
AMR phenotypes with AMP, CEP, CHL, CT, GEN,
NAL, S, SXT, and TET profile had the highest frequency of 13.6% (n = 15). Figure 1 summarizes the
multiple AMR patterns exhibited by the isolates.
Prevalence of MDR E. coli in humans, chickens and poultry
farm/LBM environment
The overall prevalence of E. coli from all sources was
26.8% (n = 115), however, only 110 were further characterized due to viability as the remaining five isolates were
mistakenly discarded. Of the 110 E. coli isolates, 91.8%
(n = 101) were MDR E. coli. Of these MDR E. coli isolates 38.6% (n = 39), 34.7% (n = 35), and 26.7% (n = 27)
were recovered from humans, chickens and poultry environment respectively (Fig. 2). Surprisingly, all the poultry environment isolates were MDR. Of the 101 MDR
E. coli isolates 47.5% (n = 48) were MDR5 (resistant to
more than 5 classes) and 38.6% (n = 39) were classified
as XDR (resistant to 8 or more classes i.e. extensively
drug-resistant isolates). Overall, 36.6% (n = 37) of the
isolates originated from the LBMs while 63.4% (n = 64)
originated from farms. Of the 39 XDR E. coli isolates 41%
(n = 16), 33.3% (n = 13), and 25.6% (n = 10) were recovered from chickens, humans and the poultry environment respectively.
In silico AMR gene analysis of MDR E. coli isolates
in humans, chickens and poultry environment
This study identified 57 different resistance determinants from 101 MDR E. coli isolates. Genes encoding resistance to aminoglycosides accounted for the
majority with about 14 different determinants (aadA1,
Table 1 Antimicrobial resistance profiles of E. coli isolates from humans, chickens and farm/market environments in Abuja—Nigeria,
2019
Drug class
Drug
Tetracyclines
Tetracycline
Folate Pathway antagonists
Sulfamethoxazole/Trimethoprim
Penicillins
Ampicillin
Quinolones
Nalidixic acid
Aminoglycosides
Streptomycin
Gentamicin
Phenicols
Chloramphenicol
1st Generation
Cephalosporins
Cephalothin
Nitrofurans
Nitrofurantoin
Carbapenems
Imipenem
B-lactam inhibitors
Amoxicillin-clavulanate
3rd and 4th Generation
Cephalosporins
Ceftriaxone
Cefuroxime
Cefotaxime
Ceftazidime
Polymyxin
Colistin
Resistance to 3 or more classes MDR
of antibiotics
Resistance break
point µg/mL
≤ 11
≤ 10
≤ 13
≤ 13
≤ 11
≤ 12
≤ 12
≤ 14
≤ 14
≤ 19
≤ 13
≤ 19
≤ 14
≤ 22
≤ 17
≤ 11
n/a
Human
n = 47
(%)
Chicken
n = 36
(%)
Environment
n = 27
(%)
Total
n = 110
(%)
39 (83.0)
35 (97.2)
27 (100.0)
101 (91.8)
39 (83.0)
31 (86.1)
24 (88.9)
94 (85.5)
36 (76.6)
31 (86.1)
20 (74.1)
87 (79.1)
26 (55.3)
27 (75.0)
19 (70.4)
72 (65.5)
35 (74.5)
30 (83.3)
22 (81.5)
87 (79.1)
20 (42.5)
27 (75.0)
16 (59.3)
63 (57.3)
15 (31.9)
17 (47.2)
7 (25.9)
39 (35.5)
13 (27.7)
15 (41.7)
5 (18.5)
33 (30.0)
5 (10.6)
13 (36.1)
8 (29.6)
26 (23.6)
3 (6.4)
6 (16.7)
3 (11.1)
12 (10.9)
2 (4.3)
5 (13.9)
3 (11.1)
10 (9.1)
3 (6.4)
1 (2.8)
1 (3.7)
5 (4.6)
4 (8.5)
3 (8.3)
0 (0)
7 (6.4)
4 (8.5)
1 (2.8)
1 (3.7)
6 (5.5)
4 (8.5)
2 (5.6)
5 (18.5)
11 (10.0)
7 (14.9)
3 (8.3)
3 (11.1)
13 (11.8)
39 (82.9)
35 (97.2)
27 (100)
101(91.8)
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
Page 5 of 13
Fig. 1 Antimicrobial resistance pattern of E. coli strains from humans, chickens, and poultry farm or market environment in Abuja-Nigeria, 2019.
*DR means drug resistance; 1DR means the E. coli isolate was only resistant to one antimicrobial agent while > 10DR means the E. coli isolate was
resistant to more than ten different antimicrobial drugs tested. The minimum number of antimicrobial drugs the human and chicken E. coli isolates
were resistant to was one while the poultry environmental E. coli isolates were resistant to a minimum of three antimicrobial agents. Hence, all the
poultry environmental E. coli isolates were multidrug-resistant
30
Live bird Market
Poultry Farm
25
25
Frequency
21
20
15
18
14
14
10
9
5
0
Human
Chicken
Environment
Source of MDR E. coli isolates
Fig. 2 Distribution of MDR E. coli isolates based on isolation sources.
The bars represent the number of MDR E. coli isolates from humans
working on the poultry farm or selling chickens at the live bird market
(LBM); the number of MDR E. coli isolates from chickens at the poultry
farm or LBM and the number of MDR E. coli isolates from poultry farm
or LBM environment
aadA2, aadA2b, aadA5, aadA16, armA, aac(3)-IIa,
aac(3)-IId, aac(3)-Ib, aac(6)-Ib-cr, aph(3)-Ia, aph(3)Ib, aph(6)-Id, ant(2)-Ia) detected. A high prevalence
(70.3%) of aph(6)-Id, which is a plasmid-encoded
gene, was also observed. About two-thirds of the isolates (67.3%) exhibited aph(3)-Ib gene, a metabolic
enzyme that confers aminoglycoside resistance. The
aac(3)-IId gene responsible for conferring gentamicin
resistance was observed in 27.7% of the MDR E. coli
isolates. We also detected aac(6)-Ib-cr gene, responsible for the reduction in ciprofloxacin activity in two
MDR E. coli isolates. Six different variants of β-lactam
resistance genes were detected (blaTEM-1, blaOXA-1,
blaOXA-10, blaOXA-129, blaCTX-M-15, blaCTXM-65) out of which blaCTX-M type was classical of
the ESBL producing E. coli. Ten different fluoroquinolone resistance determinants were observed, an
important antimicrobial on the WHO list, (qnrB1,
qnrB19, qnrB52, qnrS1, qnrS2, qnrS3, qnrS7, qnrS11,
qnrS13, aac(6)-Ib-cr) and associated with mutations
in the gyrA, parC, and parE genes. We detected other
important resistance determinants such as trimethoprim resistance (dfrA1, dfrA8, dfrA12, dfrA14, dfrA15,
dfrA17, dfrA21, and dfrA27), macrolide resistance
(mdfA, mphA, mefB, ermB, ereA, mphE and msrE),
phenicol resistance (cmlA1, catA1, catA2, catB3, floR),
rifampicin resistance (ARR-2 and ARR-3), sulphonamide resistance (sul1, sul2, sul3), tetracycline resistance
(tetA, tetB, tetM) and plasmid-mediated colistin resistance gene (PMCR)—mcr-1.1.
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
Page 6 of 13
Multi‑locus sequence determination of MDR E. coli isolates
The 101 MDR E. coli isolates belonged to 66 different sequence types (ST), out of which one (1) was
non-conclusive and eight (8) were new types. In the in
silico MLST analysis of E. coli isolates, the following were
observed to appear more than once: ST155 (7.9%; n = 8),
ST48 (7.9%; n = 8), ST10 (5.9%; n = 6), ST1638 (4%;
n = 4), ST398 (3%; n = 3), ST216 (3%; n = 3), ST226 (3%;
n = 3), ST101 (2%; n = 2), ST117 (2%; n = 2), ST165 (2%;
n = 2), ST206 (2%; n = 2), ST4663 (2%; n = 2), ST1286
(2%; n = 2), and ST1196 (2%; n = 2). The most prevalent
STs are shown in Fig. 3.
Phylogroups of E. coli isolates from humans, chickens
and poultry environment
A majority of the isolates belonged to phylogroup A
(n = 61, 55.5%) followed by phylogroup B1 (n = 36, 32.7%)
while the rest belonged to phylogroup G (n = 3, 2.7%); D
(n = 2, 1.8%); E (n = 2, 1.8%); F (n = 2, 1.8%); B2 (n = 1,
0.9%); C (n = 1, 0.9%); clade I (n = 1, 0.9%) and clade IV
(n = 1, 0.9%). Isolates with phylogroup A originated from
workers (n = 36) and poultry environment (n = 13) while
6
Human
isolates recovered from chickens mostly belonged to phylogroup B1 (Fig. 4). Of the 36 E. coli isolates, belonging
to phylogroup B1, 22.2% (n = 8); 50% (n = 18) and 27.8%
(n = 10) were recovered from humans, chickens and the
poultry environment respectively.
All isolates assigned ST10 (n = 6), ST218 (n = 3),
ST398 (n = 3) and ST1638 (n = 4) belonged to phylogroup A. However, all but one isolate assigned ST48 (7/8)
and ST226 (2/3) also belonged to phylogroup A while a
majority with ST155 (7/8) and novel ST (5/8) belonged to
phylogroup B1.
Plasmid replicon profiles of MDR E. coli isolates
from humans, chickens and poultry environment
Forty (40) different plasmid replicon types were detected
among 97 MDR E. coli isolates however, 4% (n = 4) did
not harbour any plasmid replicons. The most prevalent
plasmid replicons detected in descending order were
p0111 (36.6%, n = 37); IncFIB(AP001918) (33.7%, n = 34);
IncFII (18.8%, n = 19); ColpHAD28 (14.9%, n = 15);
IncQ1 (13.9%, n = 14); IncFIB(K) (13.9%, n = 14); ColpVC
(12.9%, n = 13); IncFIC(FII) (12.9%, n = 13); IncR (9.9%,
Enviroment
Chicken
5
Frequency
4
3
2
1
0
ST-1638
ST- 398
ST- 218
ST- 226
ST-10
ST- 48
ST-155
Novel
Multilocus Sequence Types
Fig. 3 Multilocus Sequence Types for E. coli isolates from humans, chickens, and poultry farm/market environment, Abuja-Nigeria, 2019. Each bar
represents the various E. coli sequence types for isolates obtained from humans, chickens, and poultry farm/LBM environments
Aworh et al. Antimicrob Resist Infect Control
Human
Chicken
40
Clade IV
(2021) 10:58
Page 7 of 13
Environment
A
35
B1
30
25
20
15
Clade I
B2
10
5
0
G
C
F
D
E
Fig. 4 Phylogenetic classification of E. coli isolates from humans,
chickens and poultry farm/market environments, Abuja-Nigeria,
2019. The peak of the blue triangle denotes the highest frequency of
human E. coli isolates in phylogroup A. The orange triangle denotes
the highest frequency of chicken E. coli isolates in phylogroup B1.
The black triangle peaks in the same direction as the blue triangle
indicating that the phylogroup A has the highest frequency for the E.
coli isolates from the poultry farm/LBM environment
n = 10); IncFII(pCoo) (9.9%, n = 10); IncY (9.9%, n = 10);
IncX1 (8.9%, n = 9) and IncI1-I(gamma) (8.9%, n = 9).
The plasmid replicons recovered from human isolates
were more genetically diverse than those recovered from
chickens and the poultry environment. Eighteen replicon types were common to isolates from all sources:
p0111, IncFIB(AP001918), IncFII, ColpHAD28, IncQ1,
IncFIB(K), ColpVC, IncFIC(FII), IncX1, IncFII(pCoo),
IncI1-I (gamma), IncFII (29), IncFII(pHN7A8), IncFIA,
Col156, IncHI2, IncHI2A and IncX4.
IncFIB(AP001918) was the most common among
human isolates (n = 12) while p0111 was commonly
detected in both chicken (n = 15) and poultry environment isolates (n = 14). Interestingly, IncFIB (pLF82), a
phage plasmid was detected in one isolate recovered from
the LBM environment. Eight different plasmids were
observed to harbour AMR genes. The following AMR
genes were carried on plasmid replicons: mcr-1.1 + IncX4
(n = 2); tetA + IncX1 (n = 1); qnrB19 + Col440I (n = 7);
sul2 + IncQ1
(n = 5);
aph(3)-Ib + IncQ1
(n = 1);
blaTEM-1 + IncFIC(FII) (n = 1); mdf(A) + IncFIB (n = 1);
qnrS13 + IncFII (n = 1) and aac(3)-IIa + IncHI1B (n = 1).
The plasmid replicons harbouring the AMR genes was
commonly detected in commensal E. coli isolates recovered from poultry workers, chickens and the poultry
environment.
Determination of pMLST for IncHI2 and IncF plasmid
replicons
In silico pMLST identification and typing of IncHI2 and
IncF plasmid replicons, were based on the combination
of the alleles identified for the genes. For the IncHI2 the
assigned ST was ST4 for isolates (MA_251 and MA_252)
originating from a poultry farmworker and poultry litter
on the same farm. The pMLST analysis assigned the two
IncF plasmids for isolates MA_251 and MA_252 with
ST[F18:A-B1]. It is interesting to note that although the
plasmid structures of the two isolates were so similar,
there was no clonal relationship between them.
Phylogenetic analysis of E. coli isolates from humans,
chickens and poultry environments
All isolates assigned a phylogenetic group and ST were
used to construct phylogenetic trees to determine if
the isolates were genetically related or very diverse.
Three phylogenetic trees were constructed: one for all
the isolates (Fig. 5), one focusing on isolates with novel
STs (Fig. 6a) and one with isolates of different origins
assigned the same ST (Fig. 6b).
Overall, 110 isolates used to construct a maximum likelihood phylogenetic tree showed that the isolates were
genetically diverse. The isolates were grouped based on
similarities among them. Whole-genome (wg) SNPsbased phylogenetic analysis showed that some isolates
sharing the same ST and phylogroups were not clonally
related. The strains were in completely different clades
in the SNP tree, separated by strains belonging to other
STs. Three isolates with ST-1638 recovered from human,
chicken and poultry environment were clustered together
on the same clade. Pairwise SNP differences between the
(See figure on next page.)
Fig. 5 SNP-based phylogeny of MDR E. coli isolates from humans, chickens, and poultry environments in Abuja, 2019. SNP-based maximum
likelihood phylogeny of E. coli isolates visualized in iterative Tree of life tool (iTol). The tree was rooted in a reference isolate E. coli strain NCTC11129.
Clustering of isolates was found to be following the core genome and SNP-based phylogenies. The clustering of isolates belonging to the
same phylogenetic group and sequence type was consistent. Shown for each isolate is the source/origin: farm (F) or live bird market (LBM) and
phylogroup. AMR genes cluster for 110 E. coli strains are displayed on the phylogenetic tree. The presence (orange) and absence (white) of 12 AMR
genes that were most prevalent are represented in the image while the presence (gray) and absence (white) of 10 prevalent plasmid replicons are
also represented in the image
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
Page 8 of 13
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
Page 9 of 13
a
b
Fig. 6 a Phylogenetic SNP-based maximum likelihood tree for E. coli isolates with Novel ST from humans, chickens and poultry farm or market
environments. The phylogenetic SNP-based maximum likelihood tree was rooted in a reference isolate E. coli strain NCTC11129. For each isolate,
the source and origin: farm (F) or live bird market (LBM) as well as the phylogenetic group is displayed. The phylogenetic tree has several clades
with a common ancestor however the red clade has two isolates from the same farm belonging to the same phylogroup and sharing a novel ST.
These two isolates from human and poultry farm environments although quite diverse had similar plasmid replicons harbouring AMR genes. b
Phylogenetic maximum likelihood tree for E. coli isolates with ST 1638. The SNP-based maximum likelihood tree was rooted in a reference isolate E.
coli strain NCTC11129. Two isolates of human and avian origin although not clonally related acquired similar AMR genes
genomes of the isolates showed that they were not clonally related (Fig. 6b).
Two isolates of human and environmental origin
with SNPs difference of 6161 were not clonally related
although the isolates shared a novel ST and belonged to
phylogroup B1 (Fig. 6a). The two isolates originating from
the same farm had similar AMR gene profile (qnrB19,
qnrS1, mdfA, mefB, sul 2, sul 3, blaTEM1, tetA, tetM,
floR); as well as plasmid replicons (p0111, IncFIC(FII),
IncHI2A, IncHI2, Col(pHAD28).
Discussion
To the best of our knowledge, this is the first study to
investigate the prevalence of MDR E. coli in poultry
workers, chickens, and the poultry farm/market environments in Nigeria.
The first objective of this study was to characterize E.
coli from poultry workers, chickens, and poultry environments. The unhygienic LBM environment where these
chickens are sold acts as a reservoir of antimicrobialresistant bacteria and eventually poses a health risk to
people working in such an environment. A similar study
done in the Netherlands reported a lower prevalence of
MDR E. coli in chickens (23%) and chicken farmers (22%)
when compared with the present study where a prevalence of 34.7% and 38.6% was detected in chickens and
poultry workers respectively [31]. Access to antimicrobials is better regulated in the Netherlands as well as the
implementation of antimicrobial stewardship programs
when compared to Nigeria and could explain the differences observed in both studies. A related study conducted
in Bangladesh among poultry and poultry environment
reported a much higher prevalence of E. coli (82%) from
chicken faecal samples when compared with the findings
from this study, with a much lower prevalence of 32.2%
[32]. Two similar studies performed among chickens
from poultry farms in northern Nigeria also reported a
much higher E. coli prevalence of 67.7% [33] and 69.8%
[34] from cloacal swabs obtained from chickens on the
farm. A possible explanation for the difference between
studies carried out in northern Nigeria and our study
could be due to the sample types collected as our study
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
isolated E. coli from freshly dropped chicken faecal samples as opposed to cloacal swabs. A study conducted in
Pakistan, reported a slightly higher E. coli prevalence of
36% from the poultry farm environment when compared
to 26.1% obtained from the poultry environment in the
present study [35]. Our study findings are consistent with
the reports of a related study carried out in Egypt where
E. coli prevalence of 26.8% was obtained from the poultry
environment [36]. The similarity observed between our
study findings and that of the Egyptian study may be due
to similarities in poultry farming practices.
Our study examined AMR in E. coli isolates from poultry farm workers and chicken sellers and compared them
to resistance rates of E. coli isolates from chickens and
poultry farm/market environment. The patterns of resistance were similar for human and chicken isolates. High
resistance rates were observed in isolates recovered from
humans, chickens, and poultry farm/market environments for tetracycline, trimethoprim/ sulfamethoxazole,
ampicillin, and streptomycin. This is in agreement with
the findings of a study conducted in southwest Nigeria,
where high resistance rates of E. coli isolates to beta-lactams, tetracyclines, macrolides, and sulfonamides were
reported [37]. This finding is not surprising as these antimicrobials are easily accessible and commonly used in
poultry production in Nigeria for therapeutic purposes
especially in the absence of antimicrobial stewardship
programs [38].
Our study revealed a very high proportion (91.8%) of
MDR E. coli isolates from all the sources. Interestingly,
83% of human, 97% of chicken, and 100% of poultry environment isolates were MDR E. coli. A possible explanation for this very high level of resistance observed could
be because of the lack of prudent use of antimicrobials
and the required regulation to support it resulting in
over-the-counter availability often without prescription
as reported in many studies [16, 38–40]. The potential
transmission of the drug-resistant strains between different hosts could also be responsible for this observation
because E. coli is a known zoonotic bacteria [13].
The most common beta-lactamase gene observed in
this study was the blaTEM-1 gene, which confers ampicillin resistance in E. coli isolates and is in agreement
with a previous study that reported ampicillin-resistant E. coli isolates in food, humans, and healthy animals [41]. Our study however, did not detect any genes
encoding carbapenem-hydrolyzing enzymes in any
of the isolates although phenotypic characterization
showed that 10.9% of the isolates were carbapenemresistant. This may possibly be as a result of borderline
interpretation of breakpoint settings between resistance and susceptibility. The present study identified
one of the most important AMR genes [42], being the
Page 10 of 13
PMCR gene—mcr 1.1 harboured on IncX4 plasmids in
two isolates recovered from the poultry environment.
Evidence shows that the IncX4 plasmids harbouring
mcr-1 genes have been detected in human and animal
E. coli isolates however, our study recovered these plasmids from the poultry environment [43]. Another study
conducted in China also detected PMCR genes—mcr 1
in E. coli isolates sourced from the aquatic environment
[44] however, the mcr 3.1 gene was detected in a human
Salmonella case in the US [45]. This further buttresses
that mcr gene has spread across multiple pathogens.
Our study highlights that poultry workers, chickens,
and the poultry environments share identical plasmid
replicons and this is consistent with the literature [46,
47]. The IncF plasmids reported as one of the epidemic
plasmids were observed in humans, chickens, and the
poultry environments to harbour different AMR genes;
blaTEM-1, mdf(A) and qnrS13 in the present study and
these are consistent with the literature [43]. The IncQ1
plasmids were detected in isolates with ST48 recovered
from chickens and poultry farm environments harbouring the sul2 genes that confer sulphonamide resistance
and this is consistent with reports of other studies [43,
48]. The poor biosecurity measures, unhygienic practices in poultry farms and LBMs, and occupational
exposure of over ten years are factors that predispose
these humans to get infected with these drug-resistant
bacterial strains [3].
To determine the genetic relatedness of the isolates,
we analyzed by WGS, E. coli recovered from humans,
chickens, and poultry environments. Our results revealed
that these isolates showed very diverse genetic profiles.
Common STs were assigned based on MLST including
ST155, ST48, ST10, ST1638, and ST398 in isolates from
humans, chickens, and poultry environments, although
ST155 was mostly detected in isolates of poultry origin at
the LBM. The most common ST detected among isolates
recovered from the poultry farm environment was ST48.
Previous studies have reported that E. coli with ST48 in
phylogroup A has been detected in healthy volunteers,
seafood, and water [49–51]. Our study detected ST48 in
E. coli recovered from healthy people, chickens, and the
poultry environment. E. coli strains with ST10 have previously been reported as being emerging and pathogenic
as implicated in human infections although MDR strains
with ST10 have also been detected in poultry and other
animal sources [52]. Our study detected MDR E. coli
strains with ST10 in healthy individuals, poultry manure,
and water. A possible explanation could be that this is
becoming an emerging public health issue arising due to
possible mutations in the bacteria.
The majority of E. coli isolates in this present study
belonged to phylogroup A (55.5%) and phylogroup B1
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
(32.7%). Most human and poultry environment isolates
belonged to phylogroup A while majority of the chicken
isolates belonged to phylogroup B1. Our study findings
are in agreement with the results of a similar study conducted in Pakistan that reported that phylogroups B1 and
A were the most prevalent detected among human and
animal E. coli isolates [53]. Interestingly, a study carried
out in south-west Nigeria reported that chicken E. coli
isolates were evenly distributed into phylogroups A and
B1 while phylogroup B1 was the most prevalent among
human isolates [37]. Previous studies also showed that E.
coli isolates belonging to phylogroup B2 are usually the
most virulent, hence MDR [54–56]. However, our study
observed that majority of the isolates, which belonged
to either phylogroups A, and B1 were MDR. This is consistent with findings from a similar study conducted in
south-west Nigeria which reported that isolates belonging to phylogroups B1 and A were MDR [37]. Our study
findings are not surprising and consistent with the literature that most commensal E. coli belong to phylogenetic
groups A and B1 [57, 58]. However, it is worrisome that
these indicator bacteria have become MDR with a negative impact on public health since they could be transferred to more virulent strains or species thus causing
disease.
The phylogenetic SNP tree rooted using NCTC11129
reference strain revealed that the isolates were genetically diverse among the identified STs. Two unrelated
isolates of human and environmental origin belonging to
phylogroup B1 and sharing a novel ST, had Col440I replicons harbouring the qnrB19 genes that confer quinolone
resistance and consistent with the literature [43]. In silico
pMLST typing of the two isolates further confirmed that
the isolates shared the same plasmids: IncHI2[ST-4] and
IncF[ST-F18:A-:B1]. The two isolates although not clonally related, shared the same plasmids (Col440I) harbouring AMR genes (qnrB19) possibly due to horizontal gene
transfer. Studies have shown that the IncF and IncHI2
plasmids mainly found in E. coli strains, are frequently
detected in humans and animals serving as reservoirs for
the spread of AMR genes and have been associated with
MDR E. coli [43, 59]. This evidence supports our study
results and explanation of a possibility of horizontal gene
transfer of AMR genes harboured in the plasmids. Our
study did not find evidence of the clonal spread of MDR
E. coli at the human-animal-environment interface; however, our findings suggest that mobile genetic elements
may have facilitated the horizontal transfer of MDR
genes between the plasmids among commensal E. coli
which could potentially mutate into real pathogens with
serious public health implications [47].
Page 11 of 13
Conclusion
MDR E.coli isolates were found to be prevalent amongst
poultry-workers, chickens, and poultry farm/market
environments in Abuja, Nigeria. The highest resistance rates among MDR E. coli isolates were observed
to tetracycline, sulphonamides, penicillins, aminoglycosides, and quinolones which are classes of antimicrobials commonly used in poultry production for treating
avian diseases in Abuja. ST-155, ST-48, and ST-1638
were the only STs detected in humans, chickens, and
poultry farm/LBM environments in our study. Our
findings showed the emergence and spread of MDR E.
coli with novel-ST from a poultry farm environment
to a poultry farmer, which may have resulted from
horizontal transfer of AMR genes harboured in plasmids. Consequent upon these, healthcare and poultryworkers should be educated on the fact that people in
proximity with poultry are a high-risk group for faecal
carriage of MDR E. coli. Competent authorities should
enforce AMR regulation to ensure prudent use of antimicrobials to limit the risk of transmission along the
food chain and to poultry workers. Farmers should be
discouraged from indiscriminate use of antimicrobials
in poultry production and encouraged to adopt preventive measures by observing biosecurity as well as good
management practices on their farms.
Abbreviations
AMR: Antimicrobial resistance; CGE: Center for Genomics Epidemiology; DDBJ:
DNA Data Bank of Japan; DNA: Deoxyribonucleic acid; E. coli: Escherichia coli;
iTOL: Interactive Tree of Life; LBM: Live bird market; MDR: Multidrug resistance;
MLST: Multilocus sequence typing; NAP: National Action Plan; NCBI: National
Center for Biotechnology Information; NCDC: Nigeria Center for Disease
Control; pMLST: Plasmid multilocus sequence typing; PMCR: Plasmid-mediated colistin resistance; SNPs: Single nucleotide polymorphisms; SSR: Simple
sequence repeat; ST: Sequence type; WGS: Whole-genome sequencing; Wg:
Whole genome.
Supplementary Information
The online version contains supplementary material available at https://doi.
org/10.1186/s13756-021-00930-x.
Additional file1: Supplementary Data.
Acknowledgements
The authors would like to appreciate the support of Dr. Chikwe Ihekweazu,
Director General, Nigeria Center for Disease Control, Abuja for providing
laboratory space towards this research at the National Reference Laboratory,
NCDC. Special appreciation goes to Dr. Adebayo Adedeji, Mrs. Mba Nwando,
Dr. Abiodun Egwuenu, Miss Eme Ekeng, Mr. Akinpelu Afolabi, Mr. Micheal Popoola and Mr. Chris Chukwu of the NCDC, Abuja, towards the success of this
research. The authors appreciate the efforts of members of Thakur Molecular
laboratory, North Carolina State University; Lyndy Harden, Erin Harrell, Nigatu
Atlaw, Ayanna Glaize, Dawn Hall, Morgan Young, Luke Raymond, Bryson Staley
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
and Steven Branz towards the success of the research. Special appreciation
goes to Dr. Muhammad Shakir Balogun and Dr. Bola Biliaminu Lawal of Nigeria
FELTP for their contributions to the success of this research. We also acknowledge the contributions of Judit Szarvas and Pimlapas Leekitcharoenphon at
the National Food Institute, Denmark Technical University towards the success
of this research.
Authors’ contributions
MA was the principal investigator, designed data collection tools, collected
data, isolated the organism, performed antibiotic sensitivity testing on the
isolates, analyzed and interpreted the data and wrote the first draft of the
manuscript. JK made substantial contributions to conception and design.
JK, and ST supervised the laboratory aspect of the research. MA performed
bioinformatic analysis and RSH assisted with interpretation. JK, EO, RSH, and ST
revised the article critically for important intellectual content. All authors read
and approved the final manuscript.
Funding
The author(s) received funding from FDA GenomeTrakr program grant
1U18FD00678801 for whole-genome sequencing of the isolates.
Availability of data and materials
The datasets used and analyzed during the present study are available upon
reasonable request from the corresponding author. All data generated or
analyzed during this study are also included in this published article [and
Additional file 1]. Raw sequence data have been submitted to NCBI (https://
www.ncbi.nlm.nih.gov/) under accession no PRJNA293225.
Page 12 of 13
2.
3.
4.
5.
6.
7.
8.
9.
10.
Declarations
Ethics approval and consent to participate
Ethics approval for this study was obtained from the FCT Health Research
Ethics Committee in July 2018 (Approval Number: FHREC/2018/01/84/16–0718). Permission was obtained from farm and LBM managers before the
commencement of the study. We assured participants of confidentiality for
the information obtained. An informed consent form clearly stating the study
details and benefits was duly signed by participants who were willing to participate in addition to the farm and LBM managers before sample collection.
Ethics approval for this study was also obtained from the Scientific and Ethical
Committee of the Ahmadu Bello University Committee on Animal Use and
Care (Approval Number: ABUCAUC/2020/35).
11.
12.
13.
14.
Consent for publication
Not applicable.
15.
Competing interests
The authors declare that they have no competing interests.
16.
Author details
1
Department of Veterinary and Pest Control Services, Federal Ministry of Agriculture and Rural Development, Abuja, Nigeria. 2 Nigeria Field Epidemiology
and Laboratory Training Programme, Abuja, Nigeria. 3 Department of Veterinary Public Health and Preventive Medicine, Ahmadu Bello University, Zaria,
Nigeria. 4 Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA. 5 WHO,
FAO, EU, Reference Laboratory for Antimicrobial Resistance, National Food
Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
Received: 19 June 2020 Accepted: 19 March 2021
17.
18.
19.
20.
21.
References
1. Parmley J, Leung Z, Léger D, Finley R, Irwin R, Pintar K, et al. One Health
and Food Safety—The Canadian Experience: A Holistic approach toward
enteric bacteria pathogens and antimicrobial resistance surveillance.
Natl Acad Press. 2012. Available online at https://www.ncbi.nlm.nih.gov/
books/NBK114511/.
22.
Manyi-Loh C, Mamphweli S, Meyer E, Okoh A. Antibiotic use in agriculture
and its consequential resistance in environmental sources: potential public health implications. Molecules. 2018. https://doi.org/10.3390/molec
ules23040795.
Aworh MK, Kwaga J, Okolocha E, Mba N, Thakur S. Prevalence and risk
factors for multi-drug resistant Escherichia coli among poultry workers in
the Federal Capital Territory, Abuja, Nigeria. PLoS ONE. 2019;14:e0225379.
https://doi.org/10.1371/journal.pone.0225379.
Aworh MK, Kwaga J, Okolocha E, Harden L, Hull D, Hendriksen RS, et al.
Extended-spectrum ß-lactamase-producing Escherichia coli among
humans, chickens and poultry environments in Abuja, Nigeria. One
Health Outlook. 2020;2:8. https://doi.org/10.1186/s42522-020-00014-7.
Alhaji NB, Isola TO. Antimicrobial usage by pastoralists in food animals in
North-central Nigeria: the associated socio-cultural drivers for antimicrobials misuse and public health implications. One Health. 2018;6:41–7.
Van TTH, Yidana Z, Smooker PM, Coloe PJ. Antibiotic use in food animals
worldwide, with a focus on Africa: pluses and minuses. J Glob Antimicrob
Resist. 2020;20:170–7.
Hao H, Cheng G, Iqbal Z, Ai X, Hussain HI, Huang L, et al. Benefits and
risks of antimicrobial use in food-producing animals. Front Microbiol.
2014;5:288. https://doi.org/10.3389/fmicb.2014.00288.
Marshall BM, Levy SB. Food animals and antimicrobials: impacts on
human health. Clin Microbiol Rev. 2011;24:718–33.
Zhuge X, Ji Y, Tang F, Sun Y, Jiang M, Hu W. Population structure and
antimicrobial resistance traits of Avian-origin. Transbound Emerg Dis.
2017;66:1920–9.
Agyare C, Etsiapa Boamah V, Ngofi Zumbi C, Boateng Osei F. Antibiotic
use in poultry production and its effects on bacterial resistance. In: Antimicrobial resistance—a global threat. IntechOpen; 2019. https://doi.org/
10.5772/intechopen.79371.
Delmani F, Jaran AS, Tarazi YA, Masaadeh H, Zaki O, Irbid T. Characterization of ampicillin resistant gene (blaTEM-1) isolated from E. coli in Northern Jordan. Asian J Biomed Pharm Sci. 2017;7:11–5.
Sarowska J, Futoma-Koloch B, Jama-Kmiecik A, Frej-Madrzak M, Ksiazczyk
M, Bugla-Ploskonska G, et al. Virulence factors, prevalence and potential
transmission of extraintestinal pathogenic Escherichia coli isolated from
different sources: recent reports. Gut Pathogens. 2019;11:10. https://doi.
org/10.1186/s13099-019-0290-0.
Szmolka A, Nagy B. Multidrug resistant commensal Escherichia coli in animals and its impact for public health. Front Microbiol. 2013;4:258. https://
doi.org/10.3389/fmicb.2013.00258.
Tenaillon O, Skurnik D, Picard B, Denamur E. The population genetics of
commensal Escherichia coli. Nat Rev Microbiol. 2010;8:207–17. https://doi.
org/10.1038/nrmicro2298.
WHO. At UN, global leaders commit to act on antimicrobial resistance.
2016. https://www.who.int/news-room/detail/21-09-2016-at-un-global-
leaders-commit-to-act-on-antimicrobial-resistance. Accessed 8 May 2020.
Nigeria Centre for Disease Control. Antimicrobial use and resistance in
Nigeria. 2017;:1–158. http://www.ncdc.gov.ng/themes/common/docs/
protocols/56_1510840387.pdf.
Tanwar J, Das S, Fatima Z, Hameed S. Multidrug resistance: an emerging
crisis. Interdiscip Perspect Infect Dis. 2014. https://doi.org/10.1155/2014/
541340.
Frieri M, Kumar K, Boutin A. Antibiotic resistance. J Infect Public Health.
2017;10:369–78.
Manyi-Loh C, Mamphweli S, Meyer E, Okoh A. Antibiotic use in agriculture
and its consequential resistance in environmental sources: Potential
public health implications. Molecules. 2018;23:795.
Adesokan HK, Akanbi IO, Akanbi IM, Obaweda RA. Pattern of antimicrobial usage in livestock animals in south-western Nigeria: the need for
alternative plans. Onderstepoort J Vet Res. 2015;82(1):816. https://doi.org/
10.4102/ojvr.v82i1.816.
Moyer MW. The looming threat of factory superbugs. Sci Am.
2016;315:70–9.
Trung NV, Carrique-Mas JJ, Thi Hoa N, Mai HH, Tuyen HT, Campbell JI, et al.
Prevalence and risk factors for carriage of antimicrobial-resistant Escherichia coli on household and small-scale chicken farms in the Mekong
Delta of Vietnam. J Antimicrob Chemother. 2015;70:2144–52. https://doi.
org/10.1093/jac/dkv053.
Aworh et al. Antimicrob Resist Infect Control
(2021) 10:58
23. Miles TD, McLaughlin W, Brown PD. Antimicrobial resistance of Escherichia
coli isolates from broiler chickens and humans. BMC Vet Res. 2006;2:7.
https://doi.org/10.1186/1746-6148-2-7.
24. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,
et al. SPAdes: a new genome assembly algorithm and its applications to
single-cell sequencing. J Comput Biol. 2012;19:455–77.
25. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O,
et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67:2640–4. https://doi.org/10.1093/jac/dks261.
26. Carattoli A, Zankari E, Garciá-Fernández A, Larsen MV, Lund O, Villa L,
et al. In Silico detection and typing of plasmids using plasmidfinder and
plasmid multilocus sequence typing. Antimicrob Agents Chemother.
2014;58:3895–903.
27. Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, et al. Sex and
virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol.
2006;60:1136–51.
28. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, et al.
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin
Microbiol. 2012;50:1355–61.
29. Beghain J, Bridier-Nahmias A, Le NH, Denamur E, Clermont O. ClermonTyping: an easy-to-use and accurate in silico method for Escherichia
genus strain phylotyping. Microb Genom. 2018;4(7):e000192. https://doi.
org/10.1099/mgen.0.000192.
30. Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O. Solving the problem of comparing whole bacterial genomes across different sequencing
platforms. PLoS ONE. 2014;9:e104984. https://doi.org/10.1371/journal.
pone.0104984.
31. van den Bogaard AE. Antibiotic resistance of faecal Escherichia coli in
poultry, poultry farmers and poultry slaughterers. J Antimicrob Chemother. 2001;47:763–71.
32. Akond MA, Alam S, Hassan SMR, Shirin M. Antibiotic resistance of Escherichia coli Isolated from poultry and poultry environment of Bangladesh.
Am J Environ Sci. 2009;5(1):47–52. https://doi.org/10.3844/ajessp.2009.47.
52.
33. Kwoji ID, Musa JA, Daniel N, Mohzo DL, Bitrus AA, Ojo AA, et al. Extendedspectrum beta-lactamase-producing Escherichia coli in chickens from
small-scale (backyard) poultry farms in Maiduguri, Nigeria. Int J One
Health. 2019;5:26–30.
34. Geidam YA, Ambali AG, Onyeyili PA. Detection and antibiotic sensitivity
pattern of avian pathogenic Escherichia coli strains among rural chickens
in the arid region of north-eastern Nigeria. Vet World. 2012;5:325. https://
doi.org/10.5455/vetworld.2012.325-329.
35. Ur Rahman S, Ahmad S, Khan I. Incidence of ESBL-producing-Escherichia
coli in poultry farm environment and retail poultry meat. Pak Vet J.
2018;39:116–20. https://doi.org/10.29261/pakvetj/2018.091.
36. Enany ME, Algammal AM, Nasef SA, Abo-Eillil SAM, Bin-Jumah M, Taha AE,
et al. The occurrence of the multidrug resistance (MDR) and the prevalence of virulence genes and QACs resistance genes in E. coli isolated
from environmental and avian sources. AMB Express. 2019;9:192. https://
doi.org/10.1186/s13568-019-0920-4.
37. Olowe OA, Adefioye OJ, Ajayeoba TA, Schiebel J, Weinreich J, Ali A, et al.
Phylogenetic grouping and biofilm formation of multidrug resistant
Escherichia coli isolates from humans, animals and food products in
South-West Nigeria. Sci Afr. 2019;6:e00158. https://doi.org/10.1016/j.sciaf.
2019.e00158.
38. Oluwasile B, Agbaje M, Ojo O, Dipeolu M. Antibiotic usage pattern in
selected poultry farms in Ogun state. Sokoto J Vet Sci. 2014;12:45. https://
doi.org/10.4314/sokjvs.v12i1.7.
39. Akinyandenu O, Akinyandenu A. Irrational use and non-prescription
sale of antibiotics in Nigeria: a need for change. J Sci Innov Res.
2014;3(2):251–7.
40. Awosan KJ, Ibitoye PK, Abubakar AK. Knowledge, risk perception and
practices related to antibiotic resistance among patent medicine vendors
in Sokoto metropolis, Nigeria. Niger J Clin Pract. 2018;21(11):1476–83.
https://doi.org/10.4103/njcp.njcp_69_18.
41. Briñas L, Zarazaga M, Sáenz Y, Ruiz-Larrea F, Torres C. β-lactamases in
ampicillin-resistant Escherichia coli isolates from foods, humans, and
healthy animals. Antimicrob Agents Chemother. 2002;46:3156–63.
42. WHO. WHO | WHO list of Critically Important Antimicrobials (CIA). 2019.
http://www.who.int/foodborne_disease/resistance/cia/en/#.UiMEZ
7zmSDA.mendeley.
Page 13 of 13
43. Rozwandowicz M, Brouwer M, Fischer J, Wagenaar JA, Gonzalez-Zorn B,
Guerra B, et al. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother. 2018;73:1121–37. https://doi.org/
10.1093/jac/dkx488.
44. Zhu L, Zhou Z, Liu Y, Lin Z, Shuai X, Xu L, et al. Comprehensive understanding of the plasmid-mediated colistin resistance gene mcr-1 in
aquatic environments. Cite This Environ Sci Technol. 2020;54:1603–13.
https://doi.org/10.1021/acs.est.9b05919.
45. Monte DF, Nelson V, Cerdeira L, Keelara S, Greene S, Griffin D, et al.
Multidrug-and colistin-resistant Salmonella enterica 4,[5],12:i:-sequence
type 34 carrying the mcr-3.1 gene on the IncHI2 plasmid recovered from
a human. J Med Microbiol. 2019;68:986–90.
46. Nguyen VT, Jamrozy D, Matamoros S, Carrique-Mas JJ, Ho HM, Thai QH,
et al. Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis. J Antimicrob Chemother. 2019;74:561–70.
https://doi.org/10.1093/jac/dky506.
47. Salinas L, Cárdenas P, Johnson TJ, Vasco K, Graham J, Trueba G. Diverse
commensal escherichia coli clones and plasmids disseminate antimicrobial resistance genes in domestic animals and children in a semirural
community in ecuador. mSphere. 2019;4(3):1–8. https://doi.org/10.1128/
msphere.00316-19.
48. Clément M, Keller PM, Bernasconi OJ, Stirnimann G, Frey PM, Bloemberg
GV, et al. First clinical case of in vivo acquisition of DHA-1 plasmid-mediated AmpC in a Salmonella enterica subsp. Enterica Isolate. Antimicrob
Agents Chemother. 2019. https://doi.org/10.1128/AAC.00992-19.
49. Ben Sallem R, Ben Slama K, Estepa V, Jouini A, Gharsa H, Klibi N, et al.
Prevalence and characterisation of extended-spectrum beta-lactamase
(ESBL)-producing Escherichia coli isolates in healthy volunteers in Tunisia.
Eur J Clin Microbiol Infect Dis. 2012;31:1511–6.
50. Said LB, Hamdaoui M, Jouini A, Boudabous A, Slama KB, Torres C, et al.
First detection of CTX-M-1 in extended-spectrum b-lactamase-producing
Escherichia coli in seafood from Tunisia. J Food Prot. 2017;80:1877–81.
51. Madec JY, Haenni M, Ponsin C, Kieffer N, Rion E, Gassilloud B. Sequence
type 48 Escherichia coli carrying the blaCTX-M-1 IncI1/ST3 plasmid in
drinking water in France. Antimicrob Agents Chemother. 2016;60:6430–2.
52. Manges AR, Johnson JR. Food-borne origins of escherichia coli causing
extraintestinal infections. Clin Infect Dis. 2012;55:712–9.
53. Umair M, Mohsin M, Ali Q, Qamar MU, Raza S, Ali A, et al. Prevalence
and genetic relatedness of extended spectrum-β-lactamase-producing
Escherichia coli among humans, cattle, and poultry in Pakistan. Microb
Drug Resist. 2019;25:1374–81.
54. Iranpour D, Hassanpour M, Ansari H, Tajbakhsh S, Khamisipour G, Najafi A.
Phylogenetic groups of escherichia coli strains from patients with urinary
tract infection in Iran based on the new Clermont phylotyping method.
Biomed Res Int. 2015;2015:5–12.
55. Yang F, Zhang S, Shang X, Wang L, Li H, Wang X. Characteristics of
quinolone-resistant Escherichia coli isolated from bovine mastitis in
China. J Dairy Sci. 2018;101:6244–52.
56. Moreno E, Prats G, Sabaté M, Pérez T, Johnson JR, Andreu A. Quinolone,
fluoroquinolone and trimethoprim/sulfamethoxazole resistance in relation to virulence determinants and phylogenetic background among
uropathogenic Escherichia coli. J Antimicrob Chemother. 2006;57:204–11.
57. Clermont O, Bonacorsi S, Bingen E, Bonacorsi P. Rapid and Simple Determination of the Escherichia coli Phylogenetic Group Rapid and Simple
Determination of the Escherichia coli Phylogenetic Group Downloaded
from http://aem.asm.org/ on January 18 , 2013 by University of Pretoria :
Academic Information S. Appl Environ Microbiol. 2000;66:4555–8.
58. Ramadan HH, Jackson CR, Taha SA, Moawad AA, Barrett JB, Woodley TA.
Contribution of healthy chickens to antimicrobial-resistant Escherichia
coli associated with human extraintestinal infections in Egypt. VectorBorne Zoonotic Dis. 2018;18:408–16.
59. Yang Q-E, Sun J, Li L, Deng H, Liu B-T, Fang L-X, et al. IncF plasmid diversity
in multi-drug resistant Escherichia coli strains from animals in China. Front
Microbiol. 2015;6:964. https://doi.org/10.3389/fmicb.2015.00964.
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
|
|
https://openalex.org/W4232141541
|
https://journals.plos.org/plosone/article/file?type=printable&id=10.1371/journal.pone.0075303
|
English
| null |
Correction: Non-Secreted Clusterin Isoforms Are Translated in Rare Amounts from Distinct Human mRNA Variants and Do Not Affect Bax-Mediated Apoptosis or the NF-κB Signaling Pathway
|
PloS one
| 2,013
|
cc-by
| 14,598
|
Abstract (2013) Non-Secreted Clusterin Isoforms Are Translated in Rare Amounts
from Distinct Human mRNA Variants and Do Not Affect Bax-Mediated Apoptosis or the NF-κB Signaling Pathway. PLoS ONE 8(9): e75303. doi:10.1371/
journal.pone.0075303 Editor: Guillermo Velasco, Complutense University, Spain Editor: Guillermo Velasco, Complutense University, Spain Received April 22, 2013; Accepted August 14, 2013; Published September 20, 2013 Copyright: © 2013 Prochnow et al. This is an open-access article distributed under the terms of the Creative Commons Attribu
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Competing interests: The authors have declared that no competing interests exist. * E-mail: mbaiersdoerfer@gmx.de Non-Secreted Clusterin Isoforms Are Translated in Rare
Amounts from Distinct Human mRNA Variants and Do
Not Affect Bax-Mediated Apoptosis or the NF-κB
Signaling Pathway Hans Prochnow1, Rene Gollan2, Philipp Rohne1, Matthias Hassemer1, Claudia Koch-Brandt1, Markus
Baiersdörfer1* Hans Prochnow1, Rene Gollan2, Philipp Rohne1, Matthias Hassemer1, Claudia Koch
Baiersdörfer1* 1 Institute of Pharmacy and Biochemistry, Therapeutical Life Sciences, Johannes Gutenberg - University, Mainz, Mainz, Germany, 2 Department of Neurology
University Medical Center Mainz, Johannes Gutenberg-University, Mainz, Mainz, Germany Abstract Clusterin, also known as apolipoprotein J, is expressed from a variety of tissues and implicated in pathological
disorders such as neurodegenerative diseases, ischemia and cancer. In contrast to secretory clusterin (sCLU), which
acts as an extracellular chaperone, the synthesis, subcellular localization and function(s) of intracellular CLU
isoforms is currently a matter of intense discussion. By investigating human CLU mRNAs we here unravel
mechanisms leading to the synthesis of distinct CLU protein isoforms and analyze their subcellular localization and
their impact on apoptosis and on NF-κB-activity. Quantitative PCR-analyses revealed the expression of four different
stress-inducible CLU mRNA variants in non-cancer and cancer cell lines. In all cell lines variant 1 represents the
most abundant mRNA, whereas all other variants collectively account for no more than 0.34% of total CLU mRNA,
even under stressed conditions. Overexpression of CLU cDNAs combined with in vitro mutagenesis revealed distinct
translational start sites including a so far uncharacterized non-canonical CUG start codon. We show that all exon 2-
containing mRNAs encode sCLU and at least three non-glycosylated intracellular isoforms, CLU1‑449, CLU21‑449 and
CLU34‑449, which all reside in the cytosol of unstressed and stressed HEK‑293 cells. The latter is the only form
expressed from an alternatively spliced mRNA variant lacking exon 2. Functional analysis revealed that none of
these cytosolic CLU forms modulate caspase-mediated intrinsic apoptosis or significantly affects TNF-α-induced NF-
κB-activity. Therefore our data challenge some of the current ideas regarding the physiological functions of CLU
isoforms in pathologies. Citation: Prochnow H, Gollan R, Rohne P, Hassemer M, Koch-Brandt C, et al. (2013) Non-Secreted Clusterin Isoforms Are Translated in Rare Amounts
from Distinct Human mRNA Variants and Do Not Affect Bax-Mediated Apoptosis or the NF-κB Signaling Pathway. PLoS ONE 8(9): e75303. doi:10.1371/
journal.pone.0075303
Editor: Guillermo Velasco, Complutense University, Spain
Received April 22, 2013; Accepted August 14, 2013; Published September 20, 2013
Copyright: © 2013 Prochnow et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors have no funding or support to report. Competing interests: The authors have declared that no competing interests exist. * E-mail: mbaiersdoerfer@gmx.de Citation: Prochnow H, Gollan R, Rohne P, Hassemer M, Koch-Brandt C, et al. Citation: Prochnow H, Gollan R, Rohne P, Hassemer M, Koch-Brandt C, et al. (2013) Non-Secreted Clusterin Isoforms Are Translated in Rare Amounts
from Distinct Human mRNA Variants and Do Not Affect Bax-Mediated Apoptosis or the NF-κB Signaling Pathway. PLoS ONE 8(9): e75303. doi:10.1371/
journal.pone.0075303
Editor: Guillermo Velasco Complutense University Spain Introduction However, in some
studies sCLU has also been reported to exert anti-proliferative
activity leading to an arrest in the G0-phase of the cell cycle or
to even induce apoptosis [26,30,31]. expression of CLU isoforms with pro-apoptotic functions would
be inhibited in cancer cells, this could undermine the ultimate
goal of this strategy. To limit such therapeutic risks a stringent
analysis of CLU mRNA expression profiles and of the encoded
secreted and intracellular proteins is fundamental. Data
gathered from such investigations will not only support further
studies on CLU-based cancer therapy but will also help to
unravel the contradictory data on the protein’s role in
pathologies such as brain ischemia [4,47,48], Alzheimer’s
disease [49,50], atherosclerosis [7,8,22,51] and cancer
[41,42,52,53]. For the first time we here present a quantitative analysis of
distinct CLU mRNA variants and a characterization of the
encoded CLU isoforms. We use non-malignant HEK‑293 cells
as well as prostate cancer (PC‑3), mammary gland carcinoma
(MCF‑7) and colorectal adenocarcinoma cells (Caco‑2) since
expression of intracellular CLU isoforms and/or different CLU
mRNA variants has been reported in these cells and for these
types of cancer [14,39,54]. By using the proteasome inhibitor
MG‑132, we induced proteotoxic stress leading to the induction
of distinct CLU mRNA variants and the concomitant
appearance
of
non-secreted
CLU
isoforms. In
vitro
mutagenesis and overexpression of individual CLU forms from
engineered cDNAs allowed us to characterize the biogenesis,
the subcellular location and the impact of distinct isoforms on
Bcl-2-associated X protein (Bax)-mediated apoptosis and on
NF-κB signaling. Apart from sCLU non-secreted, intracellular forms of CLU
have been found within stressed cells. The functions,
properties, subcellular localization and the biogenesis of these
CLU proteins are not clear, yet. Several mechanisms as to their
biogenesis are being discussed: 1) Retrotranslocation of a
post-translationally modified sCLU precursor form from the
endoplasmic reticulum (ER) to the cytosol after stress induction
presumably by the ER-associated protein degradation pathway
[32,33]. 2) Internal translation initiation at AUG codons
downstream the ER signal sequence coding region (SSCR)
would generate non-secreted CLU isoforms [34,35]. 3)
Translational initiation at AUG codons upstream of the SSCR
on exon 1 of individual CLU mRNA variants could result in the
synthesis of N‑terminally elongated CLU proteins with
presumably impaired functionality of the ER signal sequence
[36]. 4) Alternative splicing of CLU mRNA could generate an
mRNA lacking exon 2 which includes the SSCR. Introduction cancer [9]. Common to these diverse pathological disorders is
the induction of a cellular stress response due to injury,
increased oxidative or proteotoxic stress or dysregulation of
particular signal transduction pathways [10]. This in turn poses
a severe threat for cells but can be antagonized by
upregulation of a “defense machinery” including proteolytic,
metabolic and DNA/RNA modifying enzymes, detoxifying
proteins and molecular chaperones altogether known as heat
shock proteins [11]. Clusterin (CLU), also known as Apolipoprotein J, is a
secreted glycoprotein constitutively expressed from a broad
spectrum of tissues, especially in brain, neuronal tissue, liver,
adrenal glands and testis. It is found in body fluids including
serum, cerebrospinal fluid, mother’s milk, semen and urine. CLU has been identified and characterized by virtue of its
upregulation in degenerative conditions. Thus its expression
has been shown to be induced in a broad range of pathologies
such
as
Alzheimer’s
disease
[1,2],
spongiform
encephalopathies [3], ischemic injury of the hippocampus and
the heart [4,5], myocarditis [6], atherosclerosis [7,8] as well as As part of this cellular stress program, CLU mRNA
expression is induced. This transcriptional response is
mediated by different elements in the CLU promoter region like
AP‑1 elements [12,13], TCF-binding sites [14], putative binding PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 1 1 Non-Secreted CLU Forms Translated in Rare Amounts sites for NF-κB and Stat1 [15] and a CLE (Clusterin element), a
sequence with high similarity to HSEs (heat shock elements)
[16,17,18] resulting in a concomitant increase in CLU protein
synthesis and secretion. Secreted CLU (sCLU) has been
shown to bind a whole set of target proteins via interaction with
hydrophobic domains and exhibits properties similar to small
heat shock proteins (sHsps) i.e. binding to unfolding client
proteins, preventing their aggregation as well as initiating their
disposal by uptake into non-professional phagocytic cells,
thereby exerting a cytoprotective function in the affected tissue
[19,20,21,22]. This is exemplified by various studies reporting
increased proliferation rates, cell-viability and invasiveness of
cells upon CLU overexpression under stress conditions
[23,24,25,26]. In
accordance,
siRNA-
or
antisense
oligodeoxynucleotide-mediated CLU knockdown results in
opposite effects i.e. in a decrease in cell proliferation and
viability as well as in an increase in the sensitivity of cells to
chemotherapeutic drugs [16,27,28,29]. For a detailed description, please refer to Protocol S1. For a detailed description, please refer to Protocol S1. Introduction Translation of
this mRNA would initiate at an AUG on exon 3 leading to
synthesis of an N-terminal truncated, non-secreted CLU
isoform. Such a splicing event has been observed in the
human mammary gland carcinoma cell line MCF‑7 subjected to
ionizing radiation. Owing to the presence of a putative nuclear
localization sequence this CLU isoform - termed nuclear
Clusterin (nCLU) - has been suggested to translocate into the
nucleus of cells where it might act as a pro-death factor
[37,38,39]. Functions for these intracellular CLU isoforms are
still debated; both, the activation and inhibition of the intrinsic
apoptotic pathway [40,41,42,43] as well as the NF-κB signaling
cascade have been reported [44,45]. Cell culture HEK-293, PC-3, MCF-7 and Caco-2 cell lines were grown in
the presence of 10% FBS at 37 °C in a humidified atmosphere
with 5% CO2. Proteasome activity was inhibited by incubation
of the cells in presence of 10 µM N-(benzyloxycarbonyl)
leucinylleucinylleucinal
(MG-132)
(Calbiochem)
for
the
indicated times. For heat-shock HEK-293 cells were kept at
37°C as control for 24 hours or subjected to 45°C for 1 hour
followed by regeneration for 23 hours at 37°C. Generation and transfection of expression plasmids The cDNAs of the different CLU mRNA variants as well as
Bax and Bcl-xL cDNAs were cloned into expression vector
pcDNA6-V5/6×His (Life Sciences). For recombinant cDNA
expression 4 × 106HEK-293 cells were grown in 6-well plates
and transfected for 6 hours with 2 µg of plasmid DNA using
OptiMem® (Life Technologies) and Turbofect™ in vitro
transfection reagent (Thermo Scientific) according to the
manufacturer’s protocol. Prior to Western blot analyses
transfected cells were incubated for 24 hours in serum-free
medium. Despite the controversial data on the function of different
CLU isoforms, modulating their expression is currently
considered an attractive strategy in cancer treatment. Thus,
therapies combining conventional chemotherapeutic drugs with
an antisense oligonucleotide strategy targeting CLU to block its
cytoprotective effect have been developed for the treatment of
non-small cell lung cancer and prostate cancer, of which the
latter is currently in phase III of clinical trials [9,46]. If, however, Reverse transcription, real-time PCR and 5’ RACE
analyses Clusterin induction upon cell stress such as heat-shock or
proteasome inhibition is a well-established phenomenon [41]. Here we focus on CLU expression in normal and in cancer
cells after treatment with MG‑132, a peptide-aldehyde blocking
proteasome function. First we monitored by Western blot
analysis CLU expression patterns in whole cell lysates and
culture supernatants of four different cell lines. Secretory CLU
is synthesized as a pre-pro-protein comprising 449 amino acids
(aa) with an N-terminal 22 aa signal sequence. In the ER the
protein is present as a high mannose single chain precursor
(psCLU) that is terminally glycosylated in the Golgi, where it is
further cleaved by a furin-like protease in an N-terminal α-chain
and a C-terminal β-chain. Mature sCLU is secreted as a
heterodimeric protein with an apparent molecular weight (MW)
of 75-80 kDa in non-reducing SDS-PAGE analyses. Under
reducing conditions the α- and β-chains appear as 34-36 kDa
and 37-39 kDa protein bands, respectively [55,56]. In lysates of
untreated cells the antibody sc‑6419 exclusively detects psCLU
(60 kDa) and the β-chain of mature sCLU (37-39 kDa). The
latter is also observed in the culture medium as expected for
sCLU (Figure 1). In all cell lines treatment with MG‑132 results
in increased CLU protein levels in the cell lysates, however
processing and secretion are modulated to various extents. Interestingly in all cell lines tested MG‑132 gives rise to
additional protein bands present in minor amounts in the cell
lysates: a 50 kDa band in all cell lines examined and a 45 kDa
band in HEK‑293 cells. The 50 and 45 kDa bands are also
observed in heat stressed HEK‑293 cells indicating that their
appearance is not restricted to MG‑132 treatment but appears
to be a general stress-induced phenomenon (Figure 1). The
absence of these protein bands from the culture media
suggests that they represent stress-induced intracellular CLU
isoforms. Total cellular RNA was isolated using the innuPrep RNA Mini
Kit (Analytic Jena). Quantitative real-time PCRs were
performed using 20 ng/µl of oligo dT-reverse transcribed RNA
and the SYBR green / ROX based RealQ PCR Master Mix
(Biomol). Quantification of mRNAs was performed in triplicates
using the 7500 Fast System and SDS Software (Applied
Biosystems). Plasmids carrying the respective CLU cDNAs at
concentrations ranging from 103-10-5 pg/µl served as standards
for the calculation of mRNA copy numbers per ng of total RNA. For primer sequences refer to Table S1. Modulation of CLU mRNAs and proteins in response to
proteasome inhibition Modulation of CLU mRNAs and proteins in response to
proteasome inhibition Preparation of cell lysates and Western blot analysis Cells were lysed in ice-cold lysis buffer (50 mM Tris/HCl [pH
8], 150 mM NaCl, 1% (v/v) Triton® X-100) containing protease
inhibitor (Complete mini, Roche). Deglycosylation of proteins PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 2 Non-Secreted CLU Forms Translated in Rare Amounts was carried out by incubation of 40 µg total protein with 1,000
units PNGase F (NEB) according to the manufacturer’s
protocol. For Western blot analyses 40-150 µg of total protein
or 30-40 µl of culture medium were subjected to reducing SDS-
PAGE and blotted onto nitrocellulose membranes. The
polyclonal antibody sc‑6419 (1:1,000 dilution, Santa Cruz) was
used for detection of human CLU and monoclonal anti‑V5
antibody (Life Technologies) for detection of recombinant
CLU‑V5. Human α-Tubulin was analysed via a monoclonal
antibody (Sigma). Reactive bands were visualized by
chemiluminescence. ng/ml TNF-α (Sigma, diluted in 1 mg/ml BSA-solution) or an
equivalent volume of 1 mg/ml BSA-solution. Cells were lysed in
100 µl Luciferase Assay Buffer (Promega). Luciferase activity
was determined using the Luciferase Assay System (Promega)
according to the manufacturer’s protocol and the FLUOstar
Omega luminometer. Measured values were expressed relative
to protein concentrations of respective wells as determined by
Bradford assay. Reverse transcription, real-time PCR and 5’ RACE
analyses 5’ RACE-PCR was
performed according to the protocol “5’ RACE System for
Rapid Amplification of cDNA Ends, Version 2.0” (Life
Technologies). Determination of caspase‑3/7 activity 1.5 × 104 HEK‑293 cells were cultivated in 96-wells and
transfected with 0.2 µg of plasmid DNA. After 18 hours cells
were treated under serum-free conditions for 10 hours with 10
µM MG‑132 or an equivalent volume of DMSO. Caspase
activity was determined using the Caspase-Glo®-3/7 Assay
(Promega) according to the manufacturer’s protocol and a
FLUOstar Omega luminometer with Omega-Data Analysis
Mars software (BMG Labtech). To investigate the biogenesis of these CLU forms we first
analyzed the properties and expression of CLU mRNAs. The
CLU gene (8p21-p12) encodes at least three different mRNA
variants as currently listed in the NCBI database: variant 1
(NM_001831.3), variant 2 (NR_038335.1) and variant 3
(NR_045494.1). Since we and others revealed by 5’ RACE that
the 5’-end of variant 1 differs from NM_001831.3 [14], which
contains a 5’-extended exon 1 sequence, but is highly similar to
the mRNA database entry BC010514.1 (Figure S1A), we
hereafter refer to this sequence as mRNA variant 1. All variants
are transcribed as pre-mRNAs each comprising 9 exons and 8
introns. Exon 1 sequences are unique to each of the mRNA Immunocytochemistry HEK‑293 cells were grown on coverslips (Ø 1 cm) and
transfected with recombinant CLU cDNAs. If indicated, the cells
were treated with 10 µM MG‑132 as described above. Paraformaldehyde-fixed cells were incubated with Alexa Fluor®
488 conjugated lectins ConA or WGA (Life Technologies). After
blocking cells were incubated consecutively with anti‑V5
antibody (Life Sciences) and Cy3-conjugated secondary
antibody (Dianova) followed by chromatin staining with DAPI. Cells were imaged by confocal laser scanning microscopy
(LSM) at a Z‑stack step size of 0.13 µm with a 63× oil
immersion objective (1.4 optical aperture) using the LSM SP5
microscope (Leica) and Imaris software (Bitplane). NF-κB-Luciferase reporter assay 4 × 105 HEK‑293 cells were cultivated in 24-wells and
cotransfected with 0.3 µg of pNF-κB-Luc (Clontech) together
with 0.7 µg of recombinant CLU cDNA. After 18 hours cells
were treated under serum-free conditions for 24 hours with 10 September 2013 | Volume 8 | Issue 9 | e75303 PLOS ONE | www.plosone.org 3 Non-Secreted CLU Forms Translated in Rare Amounts Figure 2. Overview of the human CLU gene and mRNA variants. The human CLU gene encodes at least 3 different pre-
mRNAs which contain unique exons 1 but share exons 2-9. Alternative splicing of variant 1 pre-mRNA generates an mRNA
(variant 1 [Δex2]) that lacks exon 2 and the SSCR (black box). The position of the sCLU start codon (framed) is defined as nt = 1. Notice the additional in-frame AUG codons on exon 3 of all mRNAs and on exon 1c of variant 3. doi: 10.1371/journal.pone.0075303.g002 Figure 2. Overview of the human CLU gene and mRNA variants. The human CLU gene encodes at least 3 different pre-
mRNAs which contain unique exons 1 but share exons 2-9. Alternative splicing of variant 1 pre-mRNA generates an mRNA
(variant 1 [Δex2]) that lacks exon 2 and the SSCR (black box). The position of the sCLU start codon (framed) is defined as nt = 1. Notice the additional in-frame AUG codons on exon 3 of all mRNAs and on exon 1c of variant 3. doi: 10.1371/journal.pone.0075303.g002 SSCR on exon 2 (hereafter referred to as the sCLU start
codon). A putative downstream in-frame start codon resides on
exon 3. This codon represents the first AUG present on the
previously reported alternatively spliced mRNA of variant 1 that
lacks exon 2 (variant 1 [Δex2]) [38]. Translation initiation at this
AUG will result in a CLU protein lacking the signal sequence,
hence yielding an intracellular isoform corresponding to aa 34–
449 (CLU34‑449) of the full-length pre-pro-protein. Variant 3
mRNA also carries a potential upstream in-frame start codon
on exon 1 (Figure 2). Figure 1. Proteasomal inhibition and heat stress modulate
sCLU and intracellular CLU protein expression in cancer
and non-cancer cells. HEK‑293, PC‑3, MCF‑7 and Caco-2
cells were treated with DMSO as control (C), 10 µM MG-132
(MG) or subjected to heat shock (45°C). Whole cell lysates
(upper panel) and cell culture media (lower panel) of cells were
analyzed for CLU expression by Western blot. NF-κB-Luciferase reporter assay 45-50 kDa CLU
protein bands were detected primarily in stressed cells (*). Data
shown are representative of three independent experiments. doi: 10.1371/journal.pone.0075303.g001 Using variant-specific primer sets for RT‑PCR we could
demonstrate the expression of all CLU mRNAs in all cell lines
tested (Figure 3A). However, the copy numbers of the
individual CLU mRNAs differ considerably as determined by
quantitative real-time PCR (qPCR). In untreated HEK‑293 cells,
variant 1 fundamentally accounts for the total amount of CLU
mRNA with about 3,500 copies/ng total RNA. However, the
copy numbers of variant 2 and variant 3 only add up to 0.009%
of the total CLU mRNA amount. Similar ratios of CLU mRNA
variants were observed in untreated MCF‑7 and PC‑3 (Figure
3B, C, D, light gray bars). Using specific primer sets for
variant 1 [Δex2] we show that all four cell lines express this
mRNA (Figure 3; Figure S1D, E), although in very low amounts
(0.008%-0.01% of total CLU mRNA). Further, we detected
minor expression of the 5’-extended variant 1 (NM_001831.3)
in HEK‑293, MCF‑7 and Caco‑2 cells (Figure S1B, C). Incubation of the cells in presence of MG‑132 leads to an
increase in CLU mRNAs variant 1 [Δex2], variant 2 and Figure 1. Proteasomal inhibition and heat stress modulate
sCLU and intracellular CLU protein expression in cancer
and non-cancer cells. HEK‑293, PC‑3, MCF‑7 and Caco-2
cells were treated with DMSO as control (C), 10 µM MG-132
(MG) or subjected to heat shock (45°C). Whole cell lysates
(upper panel) and cell culture media (lower panel) of cells were
analyzed for CLU expression by Western blot. 45-50 kDa CLU
protein bands were detected primarily in stressed cells (*). Data
shown are representative of three independent experiments. doi: 10.1371/journal.pone.0075303.g001 variants arguing for distinct transcription start sites (exons 1a,
1b, and 1c). Variant 1 is known to encode sCLU that is
translated from an AUG start codon located upstream of the September 2013 | Volume 8 | Issue 9 | e75303 4 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Figure 3. Expression of CLU mRNA variants in cancer and non-cancer cells upon proteotoxic stress. (A) Semi-quantitative
RT‑PCR analyses of the expression of different CLU mRNA variants in control and MG‑132-treated HEK‑293, MCF‑7, Caco-2 and
PC‑3 cells. The different numbers of amplification cycles performed reflect the varying amounts of individual CLU mRNA variants
expressed. NF-κB-Luciferase reporter assay Analysis of Hsp27 mRNA indicates the induction of a heat-shock response upon MG‑132 treatment. GAPDH RT‑PCR
served as control to ensure the use of equal amounts of reverse transcribed mRNA. Data shown are representative of at least 3
independent experiments. (B, C, D) Quantification of CLU mRNA expression in control and MG‑132-treated HEK‑293 (B), MCF‑7
(C) and PC‑3 cells (D) by qPCR. The amounts of individual transcripts are expressed as copy number per ng of total RNA (mean ±
SD, n = 3). Variant 1 is the pre-dominant CLU mRNA in all cell lines conforming to the amounts of total CLU mRNA. The other
variants represent low abundant CLU mRNAs. doi: 10.1371/journal.pone.0075303.g003 3. Expression of CLU mRNA variants in cancer and non-cancer cells upon proteotoxic stress. (A) Figure 3. Expression of CLU mRNA variants in cancer and non-cancer cells upon proteotoxic stress. (A) Semi-quantitative
RT‑PCR analyses of the expression of different CLU mRNA variants in control and MG‑132-treated HEK‑293, MCF‑7, Caco-2 and
PC‑3 cells. The different numbers of amplification cycles performed reflect the varying amounts of individual CLU mRNA variants
expressed. Analysis of Hsp27 mRNA indicates the induction of a heat-shock response upon MG‑132 treatment. GAPDH RT‑PCR
served as control to ensure the use of equal amounts of reverse transcribed mRNA. Data shown are representative of at least 3
independent experiments. (B, C, D) Quantification of CLU mRNA expression in control and MG‑132-treated HEK‑293 (B), MCF‑7
(C) and PC‑3 cells (D) by qPCR. The amounts of individual transcripts are expressed as copy number per ng of total RNA (mean ±
SD, n = 3). Variant 1 is the pre-dominant CLU mRNA in all cell lines conforming to the amounts of total CLU mRNA. The other
variants represent low abundant CLU mRNAs. doi: 10.1371/journal.pone.0075303.g003 Figure 3. Expression of CLU mRNA variants in cancer and non-cancer cells upon proteotoxic stress. (A) Semi-quantitative
RT‑PCR analyses of the expression of different CLU mRNA variants in control and MG‑132-treated HEK‑293, MCF‑7, Caco-2 and
PC‑3 cells. The different numbers of amplification cycles performed reflect the varying amounts of individual CLU mRNA variants
expressed. Analysis of Hsp27 mRNA indicates the induction of a heat-shock response upon MG‑132 treatment. GAPDH RT‑PCR
served as control to ensure the use of equal amounts of reverse transcribed mRNA. Data shown are representative of at least 3
independent experiments. NF-κB-Luciferase reporter assay (B, C, D) Quantification of CLU mRNA expression in control and MG‑132-treated HEK‑293 (B), MCF‑7
(C) and PC‑3 cells (D) by qPCR. The amounts of individual transcripts are expressed as copy number per ng of total RNA (mean ±
SD, n = 3). Variant 1 is the pre-dominant CLU mRNA in all cell lines conforming to the amounts of total CLU mRNA. The other
variants represent low abundant CLU mRNAs. doi: 10.1371/journal.pone.0075303.g003 secretion of sCLU (Figure 4A, lanes 3-5). Although these
variants are expressed from recombinant DNA under the
control of the CMV promotor sCLU expression from variant 1
cDNA vastly exceeds the amounts synthesized from variant 2
and variant 3 cDNAs. As shown by in vitro mutagenesis this is
attributed to out of frame upstream open reading frames
(uORFs) on variant 2 and 3 mRNAs interfering with translation
initiation at the sCLU start codon (Figure S2A). Variant 3
mRNA contains an additional upstream in-frame AUG codon
on exon 1. It has been speculated that expression from this
codon would lead to intracellular CLU by suppressing the
function of the signal sequence [36]. However, in vitro
mutagenesis of the exon 1 ATG and/or the sCLU start codon
on variant 3 cDNA revealed that usage of both start codons
results in the synthesis of sCLU (Figure 4B), thus
demonstrating that expression from the upstream ATG may
occur and does not suppress signal sequence function. Similar
results were obtained for the upstream in frame ATG on exon 1
of the 5’ extended variant 1 (NM 001831.3) (Figure S2B). variant 3 as well as in Hsp27 mRNA (Figure 3A), the latter
confirming the induction of a heat shock response. The
inductions of variant 1 [Δex2], variant 2 and variant 3 range
from 5- to 50-fold upon proteasome inhibition in all cells
examined, yet they account for no more than 0.34% of total
CLU mRNA. The copy number of the major variant 1 mRNA is
increased only in HEK‑293 and MCF‑7 cells. As expected, the
amount of total CLU mRNA reflects the expression level of
variant 1 mRNA (Figure 3B, C, D, dark gray bars). Expression of variant specific cDNAs reveals the
biogenesis of distinct CLU isoforms (A) Transfection of cDNA CLU‑V5 protein is also expressed, although to a lesser extent,
from variant 1, 2 and 3 cDNAs (Figure 4A, lanes 3-5). As
shown by in vitro mutagenesis, translation of this protein
initiates at the downstream in-frame ATG on exon 3 (Figure 5B,
lanes 2, 4, 6, 8). Therefore the 45 kDa CLU form observed in
stressed HEK‑293 cells could arise from variant 1 [Δex2] CLU
mRNA and/or internal translation initiation on exon 3 of
variant 1, 2 and 3 CLU mRNAs and represents the isoform
CLU34‑449. With regard to the endogenous 50 kDa CLU protein band
observed within stressed cells it is interesting that a 50 kDa
CLU‑V5 form cannot be detected upon expression of
variant 1 [Δex2] cDNA but is exclusively synthesized from
cDNA variants 1, 2 and 3 (Figure 4A, lanes 3-5). To elucidate
the nature of this CLU protein, we asked: 1) whether it could
originate from still unknown in-frame start codons on exon 2
downstream the sCLU start codon and/or 2) whether it
represents unglycosylated sCLU pre-pro-protein that has not
been translocated into the ER. In support of possibility 1,
inactivation of the sCLU start codon on variant 1 abrogates
sCLU synthesis, but does not impair expression of the 50 kDa
CLU‑V5 protein (Figure 5B, lane 5). Therefore we proposed a
CTG codon surrounded by an adequate Kozak sequence on
exon 2 (Figure 5A, underlined) as an unconventional
translation initiation site. Indeed, point-mutation of this CTG
codon on a cDNA carrying an inactivated sCLU start codon
strongly inhibits the expression of the 50 kDa CLU‑V5 form,
demonstrating translational initiation at this site (Figure 5B,
lane 7). However, after transfection of a cDNA containing
exclusively the sCLU start codon as active translational start
site, apart from sCLU also significant amounts of a 50 kDa
CLU‑V5 protein are expressed (Figure 5B, lane 4). This
indicates that the 50 kDa CLU band actually represents two
distinct CLU proteins with a similar apparent molecular weight
in SDS-PAGE analyses. One is translated from the proposed
CTG codon and corresponds to aa 21–449 (CLU21‑449) therefore
lacking the SSCR. Since the other 50 kDa CLU protein
depends on translational initiation at the sCLU start codon it
could well represent sCLU pre-pro-protein which is not
segregated into the ER as proposed above (CLU1‑449). Expression of variant specific cDNAs reveals the
biogenesis of distinct CLU isoforms We then aimed to characterize the biogenesis of the distinct
CLU forms by overexpressing cDNA constructs of all mRNA
variants. To
differentiate
between
endogenously
and
ectopically expressed CLU forms the recombinant proteins
were tagged with a 5 kDa C-terminal V5-epitope (hereafter
abbreviated “‑V5”). We chose HEK‑293 cells for these
experiments, as they endogenously express all mRNA variants
and should therefore be capable to correctly synthesize all
recombinant CLU forms. Transfection of CLU cDNAs variant 1,
2 and 3 which contain exon 2, leads to the synthesis and Cells transfected with variant 1 [Δex2] cDNA do not secrete
recombinant sCLU but express a 45 kDa CLU‑V5 protein in the
lysates (Figure 4A, lane 6). Notably, an intracellular 45 kDa PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 5 Non-Secreted CLU Forms Translated in Rare Amounts Figure
4. Expression
of
CLU-V5
proteins
from
recombinant cDNAs. Lysates (upper panels) and culture
media (lower panels) of HEK-293 cells transiently expressing
the indicated CLU cDNA variants were analyzed by Western
blotting. Lanes are labeled with circled numbers. Untransfected
cells (HEK‑293) or cells transfected with empty pcDNA6 (mock)
served as controls. Data shown are representative of at least
three independent experiments. (A) Transfection of cDNA
variants 1, 2 and 3 leads to expression and secretion of sCLU
(lanes 3-5). Variant 1 [Δex2] produces a non-secreted 45 kDa
CLU‑V5 protein corresponding to CLU34‑449 (lane 6). This form
is also present in low amounts in the lysates of cells
transfected with the cDNA variants 1, 2 and 3. Furthermore,
cells transfected with these variants express an additional non-
secreted 50 kDa CLU‑V5 protein. (B) A schematic outline of the
5’-end of cDNA variant 3 is shown. Neither point-mutations
(crossed out codons) of the sCLU start codon (framed, lane 5)
nor the in-frame ATG on exon 1c (lane 4) completely block
sCLU expression. Concurrent mutation of both codons
eliminates sCLU synthesis (lane 6). doi: 10.1371/journal.pone.0075303.g004 Figure
4. Expression
of
CLU-V5
proteins
from
recombinant cDNAs. Lysates (upper panels) and culture
media (lower panels) of HEK-293 cells transiently expressing
the indicated CLU cDNA variants were analyzed by Western
blotting. Lanes are labeled with circled numbers. Untransfected
cells (HEK‑293) or cells transfected with empty pcDNA6 (mock)
served as controls. Data shown are representative of at least
three independent experiments. Expression of variant specific cDNAs reveals the
biogenesis of distinct CLU isoforms Furthermore,
cells transfected with these variants express an additional non-
secreted 50 kDa CLU‑V5 protein. (B) A schematic outline of the
5’-end of cDNA variant 3 is shown. Neither point-mutations
(crossed out codons) of the sCLU start codon (framed, lane 5)
nor the in-frame ATG on exon 1c (lane 4) completely block
sCLU expression. Concurrent mutation of both codons
eliminates sCLU synthesis (lane 6). doi: 10.1371/journal.pone.0075303.g004 Expression of variant specific cDNAs reveals the
biogenesis of distinct CLU isoforms To
scrutinize this notion we treated lysates obtained from
HEK‑293
cells
overexpressing
sCLU–V5/CLU1‑449-V5,
CLU21‑449-V5 or CLU34‑449-V5 with PNGase F. The molecular
weights of CLU21‑449-V5 and CLU34‑449-V5 proteins remain
unaffected by deglycosylation demonstrating that these CLU
forms do not contain any polysaccharide moieties (Figure 5C,
lanes 5-8). As expected, deglycosylation leads to a drop in
molecular weight of psCLU-V5 and sCLU-V5 to 50 kDa and 35
kDa respectively. However, no additional bands, which would
correspond to deglycosylated CLU1‑449-V5 are observed after
PNGase F-treatment indicating an unglycosylated state of
CLU1‑449 (Figure 5C, lanes 3, 4). Figure
4. Expression
of
CLU-V5
proteins
from
recombinant cDNAs. Lysates (upper panels) and culture
media (lower panels) of HEK-293 cells transiently expressing
the indicated CLU cDNA variants were analyzed by Western
blotting. Lanes are labeled with circled numbers. Untransfected
cells (HEK‑293) or cells transfected with empty pcDNA6 (mock)
served as controls. Data shown are representative of at least
three independent experiments. (A) Transfection of cDNA
variants 1, 2 and 3 leads to expression and secretion of sCLU
(lanes 3-5). Variant 1 [Δex2] produces a non-secreted 45 kDa
CLU‑V5 protein corresponding to CLU34‑449 (lane 6). This form
is also present in low amounts in the lysates of cells
transfected with the cDNA variants 1, 2 and 3. Furthermore,
cells transfected with these variants express an additional non-
secreted 50 kDa CLU‑V5 protein. (B) A schematic outline of the
5’-end of cDNA variant 3 is shown. Neither point-mutations
(crossed out codons) of the sCLU start codon (framed, lane 5)
nor the in-frame ATG on exon 1c (lane 4) completely block
sCLU expression. Concurrent mutation of both codons
eliminates sCLU synthesis (lane 6). doi: 10.1371/journal.pone.0075303.g004 Figure
4. Expression
of
CLU-V5
proteins
from
recombinant cDNAs. Lysates (upper panels) and culture
media (lower panels) of HEK-293 cells transiently expressing
the indicated CLU cDNA variants were analyzed by Western
blotting. Lanes are labeled with circled numbers. Untransfected
cells (HEK‑293) or cells transfected with empty pcDNA6 (mock)
served as controls. Data shown are representative of at least
three independent experiments. (A) Transfection of cDNA
variants 1, 2 and 3 leads to expression and secretion of sCLU
(lanes 3-5). Variant 1 [Δex2] produces a non-secreted 45 kDa
CLU‑V5 protein corresponding to CLU34‑449 (lane 6). This form
is also present in low amounts in the lysates of cells
transfected with the cDNA variants 1, 2 and 3. Post-translational mechanisms contribute to the
accumulation of both 50 kDa CLU isoforms, but not the
45 kDa CLU isoform in MG-132-treated cells After having revealed the origin of the intracellular CLU
isoforms generated within unstressed and stressed cells, we PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 6 Non-Secreted CLU Forms Translated in Rare Amounts Figure 5. Characterization of CLU-isoform biogenesis. (A) Schematic outline of the 5’-sequence of variant 1 showing the sCLU
start codon (framed) and the downstream start codon on exon 3 (underlined). A non-canonical CTG start codon is present on
exon 2 (underlined). The SSCR (black shaded nucleotides) and the exon 2/exon 3 border (arrow) are indicated. (B) Western blots of
recombinant CLU-V5 proteins in lysates (upper panel) and culture media (lower panel) of HEK-293 cells transiently expressing
unmodified or point-mutated (crossed out codons) CLU cDNA variant 1. CLU34‑449 is translated from the ATG codon on exon 3 (lanes
2, 7). The 50 kDa CLU‑V5 band consists of the sCLU pre-pro-protein (CLU1‑449) translated from the sCLU start codon and CLU21‑449
translated from the CTG codon (lanes 4, 6). (C) Western blot of recombinant CLU-V5 proteins in lysates of HEK-293 cells transiently
expressing sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 from point-mutated variant 1 cDNAs or unmodified variant 1 cDNA (wildtype). Lysates were treated with PNGase F as indicated. The molecular weights of psCLU and sCLU decrease upon deglycosylation
(psCLU/sCLU n.g., lanes 3, 4). PNGase F treatment does not alter the molecular weights of CLU1‑449 (lanes 3, 4), CLU21‑449 (lanes 5,
6) and CLU34‑449 (lanes 7, 8). (D) Western blots of untagged CLU proteins in lysates (upper panel) and culture media (lower panel) of
control and MG-132-treated HEK-293 cells transiently expressing sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 from point-mutated variant 1
cDNAs or transfected with pcDNA (mock). In contrast to CLU1‑449 and CLU21‑449 which accumulate upon proteasome inhibition (lanes
3-6), the amount of CLU34‑449 is not affected (lanes 7, 8). (B, C, D) Data shown are representative of three independent experiments. Lanes are labeled with circled numbers. Recombinant CLU protein bands with a molecular weight of ~38 kDa presumably originate
from even further downstream translation initiation sites on CLU cDNAs. doi: 10 1371/journal pone 0075303 g005 Figure 5. Characterization of CLU-isoform biogenesis. (A) Schematic outline of the 5’-sequence of variant 1 showing the sCLU
start codon (framed) and the downstream start codon on exon 3 (underlined). A non-canonical CTG start codon is present on
exon 2 (underlined). Post-translational mechanisms contribute to the
accumulation of both 50 kDa CLU isoforms, but not the
45 kDa CLU isoform in MG-132-treated cells The SSCR (black shaded nucleotides) and the exon 2/exon 3 border (arrow) are indicated. (B) Western blots of
recombinant CLU-V5 proteins in lysates (upper panel) and culture media (lower panel) of HEK-293 cells transiently expressing
unmodified or point-mutated (crossed out codons) CLU cDNA variant 1. CLU34‑449 is translated from the ATG codon on exon 3 (lanes
2, 7). The 50 kDa CLU‑V5 band consists of the sCLU pre-pro-protein (CLU1‑449) translated from the sCLU start codon and CLU21‑449
translated from the CTG codon (lanes 4, 6). (C) Western blot of recombinant CLU-V5 proteins in lysates of HEK-293 cells transiently
expressing sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 from point-mutated variant 1 cDNAs or unmodified variant 1 cDNA (wildtype). Lysates were treated with PNGase F as indicated. The molecular weights of psCLU and sCLU decrease upon deglycosylation
(psCLU/sCLU n.g., lanes 3, 4). PNGase F treatment does not alter the molecular weights of CLU1‑449 (lanes 3, 4), CLU21‑449 (lanes 5,
6) and CLU34‑449 (lanes 7, 8). (D) Western blots of untagged CLU proteins in lysates (upper panel) and culture media (lower panel) of
control and MG-132-treated HEK-293 cells transiently expressing sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 from point-mutated variant 1
cDNAs or transfected with pcDNA (mock). In contrast to CLU1‑449 and CLU21‑449 which accumulate upon proteasome inhibition (lanes
3-6), the amount of CLU34‑449 is not affected (lanes 7, 8). (B, C, D) Data shown are representative of three independent experiments. Lanes are labeled with circled numbers. Recombinant CLU protein bands with a molecular weight of ~38 kDa presumably originate
from even further downstream translation initiation sites on CLU cDNAs. doi: 10.1371/journal.pone.0075303.g005 treatment does not affect the amounts of psCLU and mature
sCLU but selectively leads to an accumulation of CLU1‑449,
which comigrates with the endogenous 50 kDa protein band
detected in stressed mock-transfected cells (Figure 5D, lanes
3, 4). Likewise, we observed an MG‑132-induced accumulation
of recombinant CLU21‑449, but not of recombinant CLU34‑449,
which comigrates with the endogenous 45 kDa CLU form
observed in MG‑132-treated mock-transfected cells (Figure 5D,
lanes 5-8). These results strengthen the idea that the
endogenous 50 kDa CLU protein expressed in various cells
after proteasome inhibition corresponds to CLU1‑449 and/or investigated whether in addition to transcriptional upregulation
also post-translational mechanisms (i.e. reduced proteasomal
degradation) contribute to the MG‑132‑induced accumulation
of endogenous intracellular CLU forms. Post-translational mechanisms contribute to the
accumulation of both 50 kDa CLU isoforms, but not the
45 kDa CLU isoform in MG-132-treated cells We therefore
overexpressed sCLU/CLU1‑449, CLU21‑449 and CLU34‑449 as
untagged proteins under control of the constitutive CMV-
promotor followed by treatment of the cells with MG‑132. By
this experimental design we could exclude the involvement of
transcriptional regulation in the accumulation of CLU proteins
and exactly align recombinantly with endogenously expressed
CLU bands. When exclusively sCLU is expressed, MG‑132 7 September 2013 | Volume 8 | Issue 9 | e75303 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Figure 6. Subcellular localization of individual CLU isoforms. HEK‑293 cells were transfected with unmodified variant 1,
variant 1 [Δex2] or point-mutated versions of variant 1 cDNA encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 and subjected to
LSM. CLU-V5 was detected by the anti‑V5 primary antibody and the Cy3-conjugated secondary antibody (red). Alexa Fluor® 488-
conjugated ConA (green) and DAPI (blue) served as counterstains for the nuclear membrane-ER continuum and the nucleus,
respectively. Images shown represent the middle plane of the analyzed cells. When unmodified variant 1 cDNA or sCLU/CLU1‑449
are expressed the staining of CLU and ConA shows an overlay (yellow) caused by the presence of psCLU in the ER (variant 1,
sCLU/CLU1‑449, control). Expression of variant 1 [Δex2] leads to a mutual exclusive CLU and ConA staining (variant 1 [Δex2],
control). A similar staining is observed for CLU21‑449 and CLU34‑449 (CLU21‑449, CLU34‑449, control). The presence of 10 µM MG‑132
does not lead to alterations in the subcellular localization of the individual CLU isoforms when compared to untreated controls. The
disruption of intracellular membranes, condensed chromatin and nuclear fragmentation is indicative for apoptotic processes induced
by MG‑132 treatment. d i 10 1371/j
l
0075303
006 Figure 6. Subcellular localization of individual CLU isoforms. HEK‑293 cells were transfected with unmodified variant 1,
variant 1 [Δex2] or point-mutated versions of variant 1 cDNA encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 and subjected to
LSM. CLU-V5 was detected by the anti‑V5 primary antibody and the Cy3-conjugated secondary antibody (red). Alexa Fluor® 488-
conjugated ConA (green) and DAPI (blue) served as counterstains for the nuclear membrane-ER continuum and the nucleus,
respectively. Images shown represent the middle plane of the analyzed cells. When unmodified variant 1 cDNA or sCLU/CLU1‑449
are expressed the staining of CLU and ConA shows an overlay (yellow) caused by the presence of psCLU in the ER (variant 1,
sCLU/CLU1‑449, control). Post-translational mechanisms contribute to the
accumulation of both 50 kDa CLU isoforms, but not the
45 kDa CLU isoform in MG-132-treated cells Expression of variant 1 [Δex2] leads to a mutual exclusive CLU and ConA staining (variant 1 [Δex2],
control). A similar staining is observed for CLU21‑449 and CLU34‑449 (CLU21‑449, CLU34‑449, control). The presence of 10 µM MG‑132
does not lead to alterations in the subcellular localization of the individual CLU isoforms when compared to untreated controls. The
disruption of intracellular membranes, condensed chromatin and nuclear fragmentation is indicative for apoptotic processes induced
by MG‑132 treatment. d i 10 1371/j
l
0075303
006 doi: 10.1371/journal.pone.0075303.g006 results when the cells were transfected with point-mutated
variant 1 cDNA carrying only an active sCLU start codon
(Figure 6, Figure S3; sCLU / CLU1‑449 control). In contrast, after
transfection with variant 1 [Δex2] cDNA or modified variant 1
cDNA encoding only CLU34‑449 the resulting CLU fluorescence
shows no overlay with ConA, WGA or DAPI staining but an
almost even distribution throughout the rest of the cell that is
characteristic of a soluble cytoplasmic protein (Figure 6, Figure
S3; variant 1 [Δex2] control, CLU34‑449 control). The same
applies to the subcellular localization of CLU21‑449 in unstressed
cells (Figure 6, Figure S3; CLU21‑449 control). CLU21‑449 and, that an impaired proteasomal degradation
contributes to the accumulation of these CLU form(s) within
stressed cells. In contrast, upregulation of the endogenous 45
kDa CLU form in MG‑132-treated HEK‑293 cells seems to
occur exclusively on the transcriptional level probably by
induction of CLU mRNAs variant 1 and variant 1 [Δex2]. Distinct CLU isoforms do not affect caspase‑3/7-
mediated apoptosis or NF-κB-activity The ability to express distinct CLU isoforms independently
allowed us to analyze their impact on cellular processes in
which the function of CLU isoforms is intensively discussed. In
apoptosis, intracellular CLU isoforms have been reported to act
as pro-death factors [34,38]. Therefore we first of all
investigated
whether
overexpression
of
individual
CLU
isoforms is sufficient to promote caspase‑3/7 activation. Compared to overexpressed Bax, which served as a positive
control, neither expression of sCLU/ CLU1‑449, CLU21‑449 nor
CLU34‑449 increases caspase 3/7 activity within unstressed
HEK‑293 (Figure 7A) and PC‑3 cells (Figure S4). Since CLU is
further suggested to mediate MG-132-induced apoptosis [54]
we next investigated the effect of individual CLU isoforms on
the extent of caspase‑3/7 activity in MG-132-treated cells. As
expected, MG‑132 induces caspase 3/7 activity in mock
transfected HEK‑293 cells. Upon overexpression of individual
CLU isoforms, however, we observed no significant differences
in the extent of MG-132-induced caspase 3/7 activity (Figure
7B) arguing against a CLU-isoform specific modulation of
MG-132-induced apoptotic processes. In this context the role of
CLU in the regulation of Bax-function is debated since it has
been reported to promote as well as to inhibit Bax-mediated
intrinsic apoptosis [41,42,43]. In contrast to B-cell lymphoma 2-
like 1 (Bcl-xL), a Bax-antagonizing anti-apoptotic protein that
was used as positive control, neither sCLU/CLU1‑449, CLU21‑449
nor
CLU34‑449
affected
caspase
3/7
activation
when
coexpressed with Bax in HEK‑293 cells (Figure 7C). In
summary, we could not detect any pro- or anti-apoptotic
functions under normal and stress conditions of either the
secretory or the non-secreted intracellular CLU forms. In addition to modulating sCLU expression, cellular stress
induces the accumulation of non-glycosylated cytosolic 50 and
45 kDa CLU isoforms (Figure 8A). Here we show that the
former actually consists of two distinct proteins translated from
variant 1 mRNA: One protein represents unglycosylated sCLU
pre-pro-protein (CLU1‑449) that is not translocated into the ER
lumen under stress conditions. Very recently, the existence of
this CLU isoform has been demonstrated in the cytosol of HeLa
cells [58]. Remarkably, similar observations have been made
for major prion protein (PrP) that is normally cotranslationally
segregated across the ER membrane. However, ER stress
favors the ‘mistranslocation’ of a PrP isoform still carrying the
signal sequence to the cytosol, where it accumulates as a
potentially cytotoxic protein [59]. Discussion In this study we have addressed an issue that has engaged
the interest of researchers for a long time; namely the
regulation and function of distinct CLU mRNAs and protein
isoforms during proteotoxic stress. Here we could show for the
first time, that translation of all exon 2-containing CLU mRNAs
(BC010514.1, NR_038335.1, NR_045494.1, NM_001831.3)
leads to predominant sCLU synthesis. Contrary to previous
suggestions [36,57] our data demonstrate that in addition to the
sCLU start codon, the initiation of sCLU translation may also
occur at in-frame AUGs on exon 1 of variant 3 and the 5’-
extended version of variant 1 (NM_001831.3). However,
variant 1 (BC010514.1) is the dominant CLU mRNA
contributing to the vast majority of extracellular sCLU protein. Variant 2 and variant 3 mRNAs represent low-abundant CLU
mRNAs with suppressed sCLU synthesis due to interfering
uORFs on their exon 1 sequences. Hence, the translational
contribution of these variants to total CLU protein amount is
insignificant,
therefore
challenging
their
physiological
relevance. CLU21–449 and CLU34–449 are located in the cytosol of
unstressed and stressed cells To track the subcellular localization of the different CLU
forms under physiologic conditions and upon proteotoxic stress
we expressed these as V5-tagged proteins. After transfection
of corresponding CLU cDNAs in HEK‑293 cells we performed
immunocytochemistry followed by laser scanning microscopy
(LSM). Upon incubation with MG‑132, the number of cells rounding
up and detaching from the culture surface increased. In LSM
analyses
these
cells
appear
shrunken
with
nuclear
fragmentation and disruption of intracellular compartments like
ER and Golgi, which is indicative of advanced stages of
apoptosis. Concomitantly, sCLU perinuclear staining becomes
spotty throughout the cytoplasm (Figure 6, Figure S3; variant 1
MG‑132, sCLU / CLU1‑449 MG‑132). In contrast, CLU21‑449 and
CLU34‑449 keep their cytosolic localization after MG‑132
treatment. However, the slightly spottier distribution of their
fluorescence indicates the formation of CLU21‑449- and CLU34‑449-
containing protein aggregates upon proteotoxic stress (Figure
6, Figure S3; variant 1 [Δex2] MG‑132, CLU21‑449 MG‑132,
CLU34‑449 MG‑132). In none of these experiments, we were able In unstressed cells, expression of variant 1 cDNA results in a
vesicular and perinuclear CLU staining. As expected for sCLU,
which is the major form expressed from variant 1 cDNA (Figure
4A), CLU staining colocalizes with both, Concanavalin A
(ConA) and wheat germ agglutinin (WGA) staining, indicating
its localization in the ER and the Golgi compartments (Figure 6,
Figure S3; variant 1 control). CLU1‑449, CLU21‑449 and CLU34‑449
which are also synthesized in small amounts upon expression
of variant 1 are not detectable in these samples due to the
overwhelming sCLU and psCLU staining. We obtained identical PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 8 Non-Secreted CLU Forms Translated in Rare Amounts Non-Secreted CLU Forms Translated in Rare Amounts to detect an unambiguous nuclear localization of CLU. In rare
cases we observed individual cells displaying an apparent
nuclear spotty CLU staining (Figure S3). Detailed analysis of
these cells by animated Z‑stacks of the LSM data revealed that
these CLU spots are caused by cytoplasmic/cytosolic
invaginations into the nuclear compartment rather than
representing a localization of CLU in the nucleoplasm (Video
S1). Distinct CLU isoforms do not affect caspase‑3/7-
mediated apoptosis or NF-κB-activity HEK‑293 cells were transfected with
pcDNA6 (mock), unmodified variant 1 (wildtype), variant 1 [Δex2] (Δex2) or point-mutated versions of variant 1 cDNA encoding only
sCLU/CLU1‑449, CLU21‑449 or CLU34‑449. (A) 24 hours after transfection the activity of caspases 3 and 7 was determined. Data are
expressed relative to the values obtained from Bax cDNA transfected cells (mean ± SD, n = 3), which served as a positive control. In contrast to Bax, the expression of all CLU protein forms does not activate caspase‑3/7. (B) 24 hours after transfection 10 µM
MG‑132 or DMSO (control) was added for 10 hours followed by measurement of caspase 3/7 activity. Data are expressed relative to
the values obtained from corresponding control cells (mean ± SD, n = 3). MG‑132 treatment causes an increase in caspase 3/7
activity in all cells analyzed. Neither CLU protein form significantly affects the extent of MG‑132-induced caspase‑3/7 activation. (C)
HEK-293 were cotransfected with Bax cDNA together with pcDNA6 (mock +Bax), Bcl-xL or point-mutated versions of variant 1
cDNA. 24 hours after transfection the activity of caspases 3 and 7 was determined. Cells transfected with pcDNA6 alone (mock)
served as negative control. Data are expressed relative to the values obtained from mock +Bax transfected cells (mean ± SD, n =
3). While cotransfection with Bcl-xL cDNA, suppresses caspase 3/7 activation demonstrating the validity of the experimental setup,
neither of the CLU isoforms significantly modulates Bax-mediated apoptosis. (D) HEK-293 were cotransfected with pNF-κB-Luc and
the indicated versions of variant 1. 18 hours after transfection cells were incubated for 24 hours with either 10 ng/ml TNF-α (+TNF)
or with BSA solution (-TNF). Cells were lysed and luciferase activity was determined as a measure of NF-κB-activity. Data are
expressed as increase in Luciferase activity relative to mock transfected cells incubated with BSA solution (mean ± SD, n=4). A
representative Western Blot of cell lysates is embedded showing CLU expression in the samples analyzed. The order is: mock,
wildtype, Δex2, sCLU/CLU1‑449, CLU21‑449 and CLU34‑449. Only CLU34‑449 expressed from variant 1 [Δex2] reduces NF-κB activity
(Δex2). d i 10 1371/j
l
0075303
007 Figure 7. Impact of individual CLU isoforms on apoptosis and on NF-κB-activity. HEK‑293 cells were transfected with
pcDNA6 (mock), unmodified variant 1 (wildtype), variant 1 [Δex2] (Δex2) or point-mutated versions of variant 1 cDNA encoding only
sCLU/CLU1‑449, CLU21‑449 or CLU34‑449. Distinct CLU isoforms do not affect caspase‑3/7-
mediated apoptosis or NF-κB-activity The other 50 kDa CLU
protein, CLU21‑449, is generated, by unconventional translation
from a well-conserved CUG codon located on exon 2 resulting
in an unglycosylated isoform lacking the signal sequence. Interestingly, 10 nucleotides surrounding this CUG codon show
a high degree of homology to a CUG translation initiation site
found in the internal ribosome entry site of human fibroblast
growth factor 2 [60] suggesting that a similar functional
sequence on exon 2 of CLU mRNAs could lead to the
expression of cytosolic CLU21‑449. The 45 kDa CLU protein
represents yet another cytosolic and non-glycosylated CLU
isoform lacking the signal sequence (CLU34‑449). It is generated
from alternatively spliced variant 1 mRNA in which exon 2 has
been removed. Thus far, this mRNA variant 1 [Δex2] has only
been reported for gamma-irradiated MCF-7 mammary gland
carcinoma cells [39]. We here demonstrate for the first time
that this mRNA is present in other cell types, most intriguingly
even under normal conditions (HEK-293 cells). Stress-induced
alternative mRNA splicing is well-known. It involves canonical
splicosome
dependent
and
unconventional
cytosolic
mechanisms [61,62], thereby increasing the diversity or shifting
the
balance
between
stress-related
protein
isoforms. Interestingly, similar to CLU1‑449 and CLU21‑449 minor amounts of
CLU34‑449 are also synthesized from non-spliced variant 1 The regulation of NF-κB-activation is another proposed
function of CLU. However, both, NF-κB-stimulatory and -
inhibitory properties have been described [44,45], which might
be attributed to different CLU isoforms. By using an NF-κB-
controlled Luciferase reporter plasmid, we determined the
impact of individual CLU isoforms on the TNF-α-induced NF-κB
activity. Incubation with TNF-α leads to an 8-fold increase in
NF-κB activity in HEK-293 cells cotransfected with pNF-κB-Luc
and pcDNA6 (Figure 7D, mock). Neither expression of
unmodified variant 1, of sCLU/CLU1‑449 nor of CLU21‑449 does
affect TNF-α-induced NF-κB activity. The same is observed for
CLU34‑449 when being expressed from point-mutated variant 1
(Figure 7D, CLU34‑449). However, the latter isoform reduces NF-
κB activity when being expressed from variant 1 [Δex2] (Figure
7D, Δex2) which might reflect the higher amount of CLU34‑449
expressed from this cDNA. September 2013 | Volume 8 | Issue 9 | e75303 9 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Figure 7. Impact of individual CLU isoforms on apoptosis and on NF-κB-activity. doi: 10.1371/journal.pone.0075303.g007 Distinct CLU isoforms do not affect caspase‑3/7-
mediated apoptosis or NF-κB-activity (A) 24 hours after transfection the activity of caspases 3 and 7 was determined. Data are
expressed relative to the values obtained from Bax cDNA transfected cells (mean ± SD, n = 3), which served as a positive control. In contrast to Bax, the expression of all CLU protein forms does not activate caspase‑3/7. (B) 24 hours after transfection 10 µM
MG‑132 or DMSO (control) was added for 10 hours followed by measurement of caspase 3/7 activity. Data are expressed relative to
the values obtained from corresponding control cells (mean ± SD, n = 3). MG‑132 treatment causes an increase in caspase 3/7
activity in all cells analyzed. Neither CLU protein form significantly affects the extent of MG‑132-induced caspase‑3/7 activation. (C)
HEK-293 were cotransfected with Bax cDNA together with pcDNA6 (mock +Bax), Bcl-xL or point-mutated versions of variant 1
cDNA. 24 hours after transfection the activity of caspases 3 and 7 was determined. Cells transfected with pcDNA6 alone (mock)
served as negative control. Data are expressed relative to the values obtained from mock +Bax transfected cells (mean ± SD, n =
3). While cotransfection with Bcl-xL cDNA, suppresses caspase 3/7 activation demonstrating the validity of the experimental setup,
neither of the CLU isoforms significantly modulates Bax-mediated apoptosis. (D) HEK-293 were cotransfected with pNF-κB-Luc and
the indicated versions of variant 1. 18 hours after transfection cells were incubated for 24 hours with either 10 ng/ml TNF-α (+TNF)
or with BSA solution (-TNF). Cells were lysed and luciferase activity was determined as a measure of NF-κB-activity. Data are
expressed as increase in Luciferase activity relative to mock transfected cells incubated with BSA solution (mean ± SD, n=4). A
representative Western Blot of cell lysates is embedded showing CLU expression in the samples analyzed. The order is: mock,
wildtype, Δex2, sCLU/CLU1‑449, CLU21‑449 and CLU34‑449. Only CLU34‑449 expressed from variant 1 [Δex2] reduces NF-κB activity
(Δex2). doi: 10.1371/journal.pone.0075303.g007 September 2013 | Volume 8 | Issue 9 | e75303 10 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Figure 8. Properties of distinct CLU isoforms and their synthesis in unstressed and stressed cells. (A) A CLU-specific
Western blot of cell lysate of MG‑132-treated HEK‑293 cells is shown. All detectable protein bands can be assigned to distinct CLU
forms with different properties and subcellular localization (1 determined MWs of secretory CLU forms according to Kapron et al. [55]). Distinct CLU isoforms do not affect caspase‑3/7-
mediated apoptosis or NF-κB-activity (B) Model depicting the synthesis of CLU isoforms in unstressed and stressed HEK-293 cells. Under unstressed conditions,
the dominant isoform sCLU is translated from variant 1, which accounts virtually for the total CLU mRNA amount. Cytosolic CLU1‑449
(‘mistranlocated’ sCLU pre-pro-protein) and CLU21‑449 (translated from exon 2 CUG) are not detectable due to presumably low
expression and proteasomal degradation. CLU34‑449 is translated from exon 3 AUG on variant 1 and from variant 1 [Δex2]. Although
CLU34‑449 is not proteasomally degraded, it is not detectable in unstressed cells reflecting its low expression level. Induction of
cellular stress (MG-132, heat) induces transcriptional upregulation of variant 1 and its splicing to variant 1 [Δex2] leading to
enhanced synthesis of all CLU isoforms. Further, the ‘mistranslocation’ of CLU1‑449 to the cytosol is increased. In the case of
proteotoxic stress induced by MG-132, diminished proteasomal degradation of CLU1‑449 and CLU21‑449 further promotes their
accumulation. Altogether these events generate amounts of the rare cytosolic CLU isoforms that are detectable in Western Blot
analyses. They account for 3.6% ± 1.6% (mean ± SD, n=5) of total cell-associated CLU in stressed cells as determined by
densitometric quantification of corresponding bands. Note that different expression levels (from low to high) are indicated by the
different line width of arrows (from dashed to bold). Variants 2 and 3 are not illustrated because they are expressed in very low
amounts and virtually do not contribute to the synthesis of any CLU isoform. Figure 8. Properties of distinct CLU isoforms and their synthesis in unstressed and stressed cells. (A) A CLU-specific
Western blot of cell lysate of MG‑132-treated HEK‑293 cells is shown. All detectable protein bands can be assigned to distinct CLU
forms with different properties and subcellular localization (1 determined MWs of secretory CLU forms according to Kapron et al. [55]). (B) Model depicting the synthesis of CLU isoforms in unstressed and stressed HEK-293 cells. Under unstressed conditions,
the dominant isoform sCLU is translated from variant 1, which accounts virtually for the total CLU mRNA amount. Cytosolic CLU1‑449
(‘mistranlocated’ sCLU pre-pro-protein) and CLU21‑449 (translated from exon 2 CUG) are not detectable due to presumably low
expression and proteasomal degradation. CLU34‑449 is translated from exon 3 AUG on variant 1 and from variant 1 [Δex2]. Although
CLU34‑449 is not proteasomally degraded, it is not detectable in unstressed cells reflecting its low expression level. Distinct CLU isoforms do not affect caspase‑3/7-
mediated apoptosis or NF-κB-activity Induction of
cellular stress (MG-132, heat) induces transcriptional upregulation of variant 1 and its splicing to variant 1 [Δex2] leading to
enhanced synthesis of all CLU isoforms. Further, the ‘mistranslocation’ of CLU1‑449 to the cytosol is increased. In the case of
proteotoxic stress induced by MG-132, diminished proteasomal degradation of CLU1‑449 and CLU21‑449 further promotes their
accumulation. Altogether these events generate amounts of the rare cytosolic CLU isoforms that are detectable in Western Blot
analyses. They account for 3.6% ± 1.6% (mean ± SD, n=5) of total cell-associated CLU in stressed cells as determined by
densitometric quantification of corresponding bands. Note that different expression levels (from low to high) are indicated by the
different line width of arrows (from dashed to bold). Variants 2 and 3 are not illustrated because they are expressed in very low
amounts and virtually do not contribute to the synthesis of any CLU isoform. doi: 10.1371/journal.pone.0075303.g008 rties of distinct CLU isoforms and their synthesis in unstressed and stressed cells. (A) A CLU- Figure 8. Properties of distinct CLU isoforms and their synthesis in unstressed and stresse Figure 8. Properties of distinct CLU isoforms and their synthesis in unstressed and stressed cells. (A) A CLU-specific
Western blot of cell lysate of MG‑132-treated HEK‑293 cells is shown. All detectable protein bands can be assigned to distinct CLU
forms with different properties and subcellular localization (1 determined MWs of secretory CLU forms according to Kapron et al. [55]). (B) Model depicting the synthesis of CLU isoforms in unstressed and stressed HEK-293 cells. Under unstressed conditions,
the dominant isoform sCLU is translated from variant 1, which accounts virtually for the total CLU mRNA amount. Cytosolic CLU1‑449
(‘mistranlocated’ sCLU pre-pro-protein) and CLU21‑449 (translated from exon 2 CUG) are not detectable due to presumably low
expression and proteasomal degradation. CLU34‑449 is translated from exon 3 AUG on variant 1 and from variant 1 [Δex2]. Although
CLU34‑449 is not proteasomally degraded, it is not detectable in unstressed cells reflecting its low expression level. Induction of
cellular stress (MG-132, heat) induces transcriptional upregulation of variant 1 and its splicing to variant 1 [Δex2] leading to
enhanced synthesis of all CLU isoforms. Further, the ‘mistranslocation’ of CLU1‑449 to the cytosol is increased. In the case of
proteotoxic stress induced by MG-132, diminished proteasomal degradation of CLU1‑449 and CLU21‑449 further promotes their
accumulation. Distinct CLU isoforms do not affect caspase‑3/7-
mediated apoptosis or NF-κB-activity Altogether these events generate amounts of the rare cytosolic CLU isoforms that are detectable in Western Blot
analyses. They account for 3.6% ± 1.6% (mean ± SD, n=5) of total cell-associated CLU in stressed cells as determined by
densitometric quantification of corresponding bands. Note that different expression levels (from low to high) are indicated by the
different line width of arrows (from dashed to bold). Variants 2 and 3 are not illustrated because they are expressed in very low
amounts and virtually do not contribute to the synthesis of any CLU isoform. doi: 10.1371/journal.pone.0075303.g008 the CLU promotor [18,63]. Thus, the increased sCLU/CLU1‑449,
CLU21‑449 and in part CLU34‑449 expression are attributed to
upregulation of variant 1 within stressed cells. mRNA. This supports previous publications which proposed
internal initiation at the exon 3 AUG on CLU mRNA,
contributing to CLU34‑449 synthesis [34,35]. We here show that
in HEK-293, MCF-7 and Caco-2 cells variant 1 mRNA is
induced upon MG-132 treatment. This is in accordance to
previous studies demonstrating regulation of CLU mRNA by
heat-shock factors (HSFs) which bind to the CLE motif within Our data further reveal that in contrast to CLU1‑449 and
CLU21‑449, which accumulate upon proteasome inhibition,
CLU34‑449 is not subjected to proteosomal degradation. Thus,
we suggest that under conditions of impaired proteasomal September 2013 | Volume 8 | Issue 9 | e75303 11 PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Non-Secreted CLU Forms Translated in Rare Amounts activity, expression of CLU34‑449 is regulated exclusively on the
transcriptional level by increased synthesis of variant 1 and
variant
1
[Δex2]
mRNA,
while
reduced
proteasomal
degradation clearly contributes to the accumulation of the
endogenous 50 kDa isoforms CLU1‑449 and CLU21‑449 [54,63]. These cytosolic proteins represent rare CLU isoforms
altogether accounting for less than 5% of total cell-associated
CLU in stressed cells (Figure 8B). Recently, hypoglycosylated
psCLU (55-60 kDa) after retrotranslocation from the ER has
been reported to represent an additional cytosolic CLU isoform
[32,33]. In support of this, we observed a CLU protein band of
~55 kDa in MG-132-treated HEK-293 cells that presumably
corresponds to hypoglycosylated CLU (Figure 1, Figure 5D,
lane 4, Figure 8A). NF-κB-activity in a dose-dependent manner. However, a
physiological relevance of this effect seems unlikely, as
respective amounts of CLU34‑449 are not reached endogenously,
even under conditions of massive stress. Supporting Information Figure S1. BC010514.1 is the predominantly expressed
CLU mRNA variant 1 and can be spliced to produce variant
1 [Δex2]. (A) Different entries for CLU mRNA variant 1 exist in
the NCBI database having various lengths at their 5’ ends. 5’
RACE-PCR analyses of 6 different cell lines produces a DNA
fragment (upper panel) that is identical to the EST BP211675
and highly similar to the 5’ end of mRNA BC010514.1 but not
to that of NM_001831.3 or NM_001831.1 (lower panel). Hence,
the canonical transcription start site of CLU mRNA variant 1 is
located 23 nucleotides downstream of the TATA promotor
element, as expected. (B) Semi-quantitative RT‑PCR analyses
of CLU variant 1 mRNA expression in unstressed HEK‑293,
PC‑3, MCF‑7 and Caco-2 cells using primer sets specific for
BC010514.1 or NM_001831.3. Upon using 22 cycles of PCR-
amplification the expression of BC010514.1 is observed in all
cell lines. CLU mRNA NM_001831.3, however, is expressed in
minor amounts only in HEK‑293 cells. (C) Semi-quantitative
RT‑PCR analyses of CLU mRNA NM_001831.3 expression in
unstressed and MG‑132 treated HEK‑293, PC‑3, MCF‑7 and
Caco-2 cells using 35 cycles of PCR-amplification. CLU mRNA
NM_001831.3 shows low abundant expression in HEK‑293,
MCF‑7 and Caco-2 cells and a cell line specific pattern of
regulation upon MG‑132 treatment. (D) RT‑PCR analysis of
CLU variant 1 mRNA and variant 1 [Δex2] mRNA expression in
MG‑132 treated PC‑3 cells using variant 1-specific primers and
35 cycles of amplification. Specificity of both resulting PCR
products was verified by DNA sequencing. They represent
variant 1 mRNA containing exon 2 (+ exon 2) and variant 1
[Δex2] (Δ exon 2). (E) Plasmids carrying variant 1 or variant 1
[Δex2] cDNA served as templates for PCRs performed with a The function of distinct CLU isoforms in intrinsic apoptosis
and NF-κB-mediated signaling is unclear. Here, we neither
could
detect
spontaneous
induction
of
apoptosis
nor
modulation of MG‑132- and Bax-induced apoptosis upon
overexpression of sCLU/CLU1‑449, CLU21‑449 or CLU34‑449. Thus
we cannot confirm previous studies showing both, anti-
apoptotic [41,42] as well as pro-apoptotic [38,43] functions of
CLU. We suggest that the reported effects of sCLU and
cytosolic CLU isoforms on intrinsic apoptosis may either
depend on a specific cellular context or represent responses
that are restricted to certain cell types or cell lines. Interestingly, similar possibilities are being discussed regarding
the role of cytosolic PrP on cell viability [69]. Distinct CLU isoforms do not affect caspase‑3/7-
mediated apoptosis or NF-κB-activity Regardless of the complexity of CLU proteins and functions
and their still incompletely understood influence on cell viability
and apoptosis, a current strategy to optimize the treatment of
androgen-independent prostate cancer is to minimize sCLU
synthesis while leaving cytosolic CLU expression unaffected in
order
to
make
cancer
cells
more
susceptible
to
chemotherapeutic drugs. However, on the basis of our results,
it may be difficult to accomplish by common antisense
oligonucleotide or RNAi strategies. The approach of Essabani
and colleagues to force exon 2 skipping of CLU mRNAs by
suppressing
an
exon
splicing
enhancer
using
hairpin
oligonucleotides seems more promising. This leads to a
decrease in sCLU expression and a concomitant increase in
the synthesis of CLU34‑449 resulting in a higher mortality of
LNCaP prostate cancer cells [70]. On the basis of our results it
is reasonable that this strategy would suppress the expression
of sCLU, but also CLU1‑449 and CLU21‑449, while increasing
CLU34‑449. However, our data indicate that none of the rare
cytosolic CLU isoforms reduces cell viability. Therefore, in
contrast to sCLU, these isoforms appear likely to be irrelevant
in the context of cancer and other pathologies. In
summary,
alternative
splicing
(CLU34‑449),
internal
translation initiation (CLU21‑449, CLU34‑449), ‘mistranslocation’ of
sCLU
pre-pro-protein
(CLU1‑449)
as
well
as
impaired
proteasomal degradation (CLU1‑449, CLU21‑449) contribute to the
biogenesis of cytosolic CLU isoforms. The properties of all
individual CLU isoforms are summarized in Figure 8A. Previous
works describe a 50 kDa CLU protein band as a post-
translationally modified, “activated” form of CLU34‑449 [38,39]. Our results, however, demonstrate that the 50 kDa CLU forms
(CLU1‑449 and CLU21‑449) as well as CLU34‑449 are all
independently synthesized proteins. The subcellular localization of intracellular CLU has been
studied previously by immunofluorescence microscopy. We
could confirm the presence of psCLU/sCLU in the ER/Golgi
continuum [33,64] and the cytosolic distribution of CLU34‑449
[43,65,66]. However, no nuclear localization of CLU, even in
late-stage apoptotic cells was detectable. This does not
support previous reports suggesting translocation of CLU34‑449
into
nucleus
under
stress
conditions
[38,54,67,68]. Furthermore, considering the low endogenous amounts of
CLU1‑449, CLU21‑449 and CLU34‑449 (compared to psCLU/sCLU)
present within stressed cells, it has to be concluded that none
of these cytosolic isoforms can realistically account for the
often reported major stressed-induced changes in subcellular
distribution of CLU in cells. Supporting Information (A+B)
Western blot analysis of whole cell lysates (50 µg total protein)
and cell culture media (30 µl) of HEK‑293 cells transiently
expressing unmodified or point-mutated versions of the
indicated CLU cDNA variants. Recombinant CLU protein was
detected using the V5-tag specific antibody. Cells transfected
with blank pcDNA6 (mock) served as controls (lanes 1). Analysis of α-tubulin was performed as a loading control. Lanes
are
labeled
with
circled
numbers. Data
shown
are
representative
of
three
independent
experiments. (A)
Schematic outlines of the 5’-ends of cDNA variants 2 and 3 are
shown. Exon 1 sequences of both variants contain a set of
uORFs (indicated by brackets) which differ from the CLU
reading frame. On each variant the longest uORF (* or **)
overlaps with the CLU reading frame leading to lower
expression of sCLU compared to variant 1, which does not
contain any uORFs (lanes 2, 3, 5). Point-mutation of the start
codons of these uORFs leads to an increase in the amount of
sCLU expressed from variant 2 and 3 which is comparable to
that synthesized from variant 1 (lanes 4, 6), strongly indicating
that these uORFs inhibit translation initiation at the sCLU start
codon (framed) as well as the alternative sCLU start codon on
variant 3. (B) A schematic outline of the 5’-end of the 5’-
extended cDNA variant 1 (NM_001831.3) is shown. Neither
point-mutations of the sCLU start codon (framed) nor the in-
frame ATG on exon 1, which is part of the 5’-extended exon 1a
sequence (dark grey box), do inhibit sCLU expression,
indicating
that
both
codons
initiate
sCLU
translation. Concurrent mutation of both codons, however, almost
completely blocks sCLU synthesis. Note that ATG on exon 1a
also initiates the translation of a 60 kDa CLU protein that likely
represents an N-terminal elongated sCLU pre-proprotein
corresponding
to
CLU1‑449
expressed
from
variant
1
(BC010514.1). Respective mutated start sites of modified
cDNAs are indicated above each lane (crossed out). (PDF) Figure S4. Impact of individual CLU isoforms on
apoptosis of PC-3 cells. PC-3 cells were transfected with
pcDNA6 (mock), unmodified variant 1 (wildtype), variant 1
[Δex2] (Δex2) or point-mutated versions of variant 1 cDNA
encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449. 24 hours
after transfection the activity of caspases 3 and 7 was
determined. Data are expressed as fold changes in caspase
activity compared to mock-transfected cells (mean ± SD, n =
3). Supporting Information Luciferase reporter assays revealed a significant inhibitory
effect of CLU34‑449 on NF-κB -activity only when overexpressed
from variant 1 [Δex2] but not from point-mutated variant 1
cDNA. Since the amount of CLU34‑449 translated from
variant 1 [Δex2] vastly exceeds that translated from the point-
mutated variant 1 cDNA indicates that this isoform influences PLOS ONE | www.plosone.org 12 September 2013 | Volume 8 | Issue 9 | e75303 Non-Secreted CLU Forms Translated in Rare Amounts and subjected to LSM. CLU-V5 was detected by the anti‑V5
primary antibody and the Cy3-conjugated secondary antibody
(red). Alexa Fluor® 488-conjugated WGA (green) and DAPI
(blue) served as counterstains for Golgi/plasmamembrane and
the nucleus, respectively. Images shown represent the middle
plane of the analyzed cells. When unmodified variant 1 cDNA
or sCLU/CLU1‑449 are expressed the staining of CLU and WGA
shows an overlay (yellow) caused by the presence of psCLU in
the ER (variant 1, sCLU/CLU1‑449, control). Expression of
variant 1 [Δex2] leads to a mutual exclusive CLU and WGA
staining (variant 1 [Δex2], control). A similar staining is
observed for CLU21‑449 and CLU34‑449 (CLU21‑449, CLU34‑449,
control). The presence of 10 µM MG‑132 does not lead to
alterations in the subcellular localization of the individual CLU
isoforms when compared to untreated controls. The disruption
of intracellular membranes, condensed chromatin and nuclear
fragmentation is indicative for apoptotic processes induced by
MG‑132 treatment. (PDF) variant 1- (upper panel) or a variant 1 [Δex2]-specific primer set
(lower panel). While both cDNAs can be detected by variant 1-
specific primers resulting in the amplification of two PCRs with
different length, variant 1 [Δex2]-specific primers solely detect
variant 1 [Δex2] cDNA. When mixtures of both cDNAs with
ratios of variant 1: variant 1 [Δex2] = 100:1 or higher were used
as a template, variant 1 [Δex2] cDNA is only detectable by
variant 1 [Δex2] primers, but no longer by the variant 1 primer
set. Considering that in cells usually amounts of variant
1mRNA exceed those of variant 1 [Δex2] by four orders of
magnitude does result in difficulties when detecting the CLU
variant 1 [Δex2] mRNA by conventional variant 1 specific
primer sets. (PDF) p
(PDF) Figure S2. Upstream ORFs impair sCLU translation from
variants 2 and 3 whereas an upstream in-frame start codon
on NM_001831.3 initiates translation of sCLU. Supporting Information In contrast to Bax-overexpression, which served as positive
control, the expression of all CLU protein forms does not
activate caspase‑3/7. (PDF) References 17. Michel D, Chatelain G, North S, Brun G (1997) Stress-induced
transcription of the clusterin/apoJ gene. Biochem J 328(1): 45-50. PubMed: 9359832. 1. Calero M, Rostagno A, Frangione B, Ghiso J (2005) Clusterin and
Alzheimer’s
disease. Subcell
Biochem
38:
273-298. doi:
10.1007/0-387-23226-5_14. PubMed: 15709484. 2. Nuutinen T, Suuronen T, Kauppinen A, Salminen A (2009) Clusterin: a
forgotten player in Alzheimer’s disease. Brain. Res Rev 61: 89-104. doi:
10.1016/j.brainresrev.2009.05.007. 18. Loison F, Debure L, Nizard P, le Goff P, Michel D et al. (2006) Up-
regulation of the clusterin gene after proteotoxic stress: implication of
HSF1-HSF2 heterocomplexes. Biochem J 395: 223-231. doi:10.1042/
BJ20051190. PubMed: 16336210. 3. Kempster S, Collins ME, Aronow BJ, Simmons M, Green RB et al. (2004) Clusterin shortens the incubation and alters the histopathology
of bovine spongiform encephalopathy in mice. Neuroreport 15:
1735-1738. doi:10.1097/01.wnr.0000134990.97051.22. PubMed:
15257138. 19. Humphreys DT, Carver JA, Easterbrook-Smith SB, Wilson MR (1999)
Clusterin has chaperone-like activity similar to that of small heat shock
proteins. J Biol Chem 274: 6875-6881. doi:10.1074/jbc.274.11.6875. PubMed: 10066740. 4. Han BH, DeMattos RB, Dugan LL, Kim-Han JS, Brendza RP et al. (2001) Clusterin contributes to caspase-3-independent brain injury
following neonatal hypoxia-ischemia. Nat Med 7: 338-343. doi:
10.1038/85487. PubMed: 11231633. 20. Carver JA, Rekas A, Thorn DC, Wilson MR (2003) Small heat-shock
proteins and clusterin: intra- and extracellular molecular chaperones
with a common mechanism of action and function? IUBMB Life 55:
661-668. doi:10.1080/15216540310001640498. PubMed: 14769002. 5. Van Dijk A, Vermond RA, Krijnen PA, Juffermans LJ, Hahn NE et al. (2010) Intravenous clusterin administration reduces myocardial infarct
size in rats. Eur J Clin Invest 40: 893-902. doi:10.1111/j. 1365-2362.2010.02345.x. PubMed: 20854280. 21. Bartl MM, Luckenbach T, Bergner O, Ullrich O, Koch-Brandt C (2001)
Multiple receptors mediate apoJ-dependent clearance of cellular debris
into nonprofessional phagocytes. Exp Cell Res 271: 130-141. doi:
10.1006/excr.2001.5358. PubMed: 11697889. 6. McLaughlin L, Zhu G, Mistry M, Ley-Ebert C, Stuart WD et al. (2000)
Apolipoprotein J/clusterin limits the severity of murine autoimmune
myocarditis. J Clin Invest 106: 1105-1113. doi:10.1172/JCI9037. PubMed: 11067863. 22. Baiersdörfer M, Schwarz M, Seehafer K, Lehmann C, Heit A et al. (2010) Toll-like receptor 3 mediates expression of clusterin/
apolipoprotein J in vascular smooth muscle cells stimulated with RNA
released from necrotic cells. Exp Cell Res 316: 3489-3500. 7. Schwarz M, Spath L, Lux CA, Paprotka K, Torzewski M et al. References (2008)
Potential protective role of apoprotein J (clusterin) in atherogenesis:
binding to enzymatically modified low-density lipoprotein reduces fatty
acid-mediated cytotoxicity. Thromb Haemost 100: 110-118. 23. Ammar H, Closset JL (2008) Clusterin activates survival through the
phosphatidylinositol
3-kinase/Akt
pathway. J
Biol
Chem
283:
12851-12861. doi:10.1074/jbc.M800403200. PubMed: 18321852. 24. Dumont P, Chainiaux F, Eliaers F, Petropoulou C, Remacle J et al. (2002) Overexpression of apolipoprotein J in human fibroblasts protects
against cytotoxicity and premature senescence induced by ethanol and
tert-butylhydroperoxide. Cell Stress Chaperones 7: 23-35. 8. Kim HJ, Yoo EK, Kim JY, Choi YK, Lee HJ et al. (2009) Protective role
of clusterin/apolipoprotein J against neointimal hyperplasia via
antiproliferative effect on vascular smooth muscle cells and
cytoprotective effect on endothelial cells. Arterioscler Thromb Vasc Biol
29: 1558-1564. 25. Miyake H, Hara I, Gleave ME, Eto H (2004) Protection of androgen-
dependent human prostate cancer cells from oxidative stress-induced
DNA damage by overexpression of clusterin and its modulation by
androgen. Prostate 61: 318-323. doi:10.1002/pros.20087. PubMed:
15389725. 9. Zoubeidi A, Gleave M (2012) Small heat shock proteins in cancer
therapy and prognosis. Int J Biochem Cell Biol, 44: 1646–56. PubMed:
22571949. 10. Trougakos IP, Gonos ES (2009) Oxidative stress in malignant
progression: The role of Clusterin, a sensitive cellular biosensor of free
radicalschapter 9. Adv Cancer Res 104: 171-210. doi:10.1016/
S0065-230X(09)04009-3. PubMed: 19878777. 26. Trougakos IP, Lourda M, Agiostratidou G, Kletsas D, Gonos ES (2005)
Differential effects of clusterin/apolipoprotein J on cellular growth and
survival. Free Radic Biol Med 38: 436-449. 27. Redondo M, Téllez T, Roldan MJ, Serrano A, García-Aranda M et al. (2007) Anticlusterin treatment of breast cancer cells increases the
sensitivities of chemotherapy and tamoxifen and counteracts the
inhibitory
action
of
dexamethasone
on
chemotherapy-induced
cytotoxicity. Breast Cancer Res 9: R86. doi:10.1186/bcr1835. PubMed:
18078515. (
)
11. Richter K, Haslbeck M, Buchner J (2010) The heat shock response: life
on the verge of death. Mol Cell 40: 253-266. doi:10.1016/j.molcel. 2010.10.006. PubMed: 20965420. 12. Wong P, Taillefer D, Lakins J, Pineault J, Chader G et al. (1994)
Molecular characterization of human TRPM-2/clusterin, a gene
associated with sperm maturation, apoptosis and neurodegeneration. Eur J Biochem 221: 917-925. doi:10.1111/j.1432-1033.1994.tb18807.x. PubMed: 8181474. 28. So A, Sinnemann S, Huntsman D, Fazli L, Gleave M (2005)
Knockdown of the cytoprotective chaperone, clusterin, chemosensitizes
human breast cancer cells both in vitro and in vivo. Mol Cancer Ther 4:
1837-1849. doi:10.1158/1535-7163.MCT-05-0178. PubMed: 16373699. 13. Protocol S1. Trial protocol.
(DOCX) Table S1. Sequences of DNA oligomers which were used
as primers for semi-quantitative RT PCR, quantitative real-
time PCR and 5’ RACE. (DOCX) Video S1. (A) Animated LSM Z stack of MG 132-treated
HEK 293 cells expressing sCLU/CLU1-449. CLU-V5 was
detected by the anti V5 primary antibody and the Cy3-
conjugated secondary antibody (red). Alexa Fluor® 488-
conjugated ConA (green) and DAPI (blue) served as
counterstains for the nuclear membrane-ER continuum and the
nucleus, respectively. Staining of CLU and ConA shows an
overlay (yellow). (B) Animated LSM Z stack of MG 132-treated
HEK 293 cells expressing CLU21-449. CLU-V5 was detected by
the anti V5 primary antibody and the Cy3-conjugated
secondary antibody (red). Alexa Fluor® 488-conjugated ConA
(green) and DAPI (blue) served as counterstains for the
nuclear
membrane-ER
continuum
and
the
nucleus,
respectively. (C) Animated LSM Z stack of MG 132-treated
HEK 293 cells expressing CLU34-449 from variant 1 [Δex2]
cDNA. CLU-V5 was detected by the anti V5 primary antibody
and the Cy3-conjugated secondary antibody (red). Alexa Figure S3. Subcellular localization of individual CLU
isoforms. HEK‑293 cells were transfected with unmodified
variant 1, variant 1 [Δex2] or point-mutated versions of variant
1 cDNA encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 13 September 2013 | Volume 8 | Issue 9 | e75303 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts correcting the manuscript and Prof. Dr. Frauke Zipp for
providing the LSM microscope. Fluor® 488-conjugated WGA (green) and DAPI (blue) served
as counterstains for the Golgi/plasma membrane and the
nucleus, respectively. Fluor® 488-conjugated WGA (green) and DAPI (blue) served
as counterstains for the Golgi/plasma membrane and the
nucleus, respectively. Author Contributions (ZIP) Conceived and designed the experiments: HP MB. Performed
the experiments: HP RG PR MH MB. Analyzed the data: HP
RG CKB MB. Contributed reagents/materials/analysis tools: HP
RG MB. Wrote the manuscript: HP CKB MB. Acknowledgements We thank Markus Rövekamp for his help with protein
purification, Hildegard Pearson for carefully reading and References Bettuzzi S, Davalli P, Davoli S, Chayka O, Rizzi F et al. (2009) Genetic
inactivation of ApoJ/clusterin: effects on prostate tumourigenesis and
metastatic spread. Oncogene 28: 4344-4352. doi:10.1038/onc. 2009.286. PubMed: 19784068. 34. Moretti RM, Marelli MM, Mai S, Cariboni A, Scaltriti M et al. (2007)
Clusterin isoforms differentially affect growth and motility of prostate
cells: possible implications in prostate tumorigenesis. Cancer Res 67:
10325-10333. doi:10.1158/0008-5472.CAN-07-0516. PubMed:
17974975. 54. Rizzi F, Caccamo AE, Belloni L, Bettuzzi S (2009) Clusterin is a short
half-life, poly-ubiquitinated protein, which controls the fate of prostate
cancer cells. J Cell Physiol 219: 314-323. doi:10.1002/jcp.21671. PubMed: 19137541. 55. Kapron JT, Hilliard GM, Lakins JN, Tenniswood MP, West KA et al. (1997) Identification and characterization of glycosylation sites in
human serum clusterin. Protein Sci 6: 2120-2133. PubMed: 9336835. 35. Reddy KB, Jin G, Karode MC, Harmony JA, Howe PH (1996)
Transforming
growth
factor
beta
(TGF
beta)-induced
nuclear
localization of apolipoprotein J/clusterin in epithelial cells. Biochemistry
35: 6157-6163. doi:10.1021/bi952981b. PubMed: 8634259. 56. Urban J, Parczyk K, Leutz A, Kayne M, Kondor-Koch C (1987)
Constitutive apical secretion of an 80-kD sulfated glycoprotein complex
in the polarized epithelial Madin-Darby canine kidney cell line. J Cell
Biol 105: 2735-2743. doi:10.1083/jcb.105.6.2735. PubMed: 3693398. 36. Rizzi F, Coletta M, Bettuzzi S (2009) Clusterin (CLU): From one gene
and two transcripts to many proteinschapter 2. Adv Cancer Res 104:
9-23. doi:10.1016/S0065-230X(09)04002-0. PubMed: 19878770. j
57. Trougakos IP, Djeu JY, Gonos ES, Boothman DA (2009) Advances and
challenges in basic and translational research on clusterin. Cancer Res
69:
403-406. doi:10.1158/0008-5472.CAN-08-2912. PubMed:
19147550. (
)
37. Bettuzzi S, Rizzi F (2009) Nuclear CLU (nCLU) and the fate of the
cellchapter
5. Adv
Cancer
Res
104:
59-88. doi:10.1016/
S0065-230X(09)04005-6. PubMed: 19878773. (
)
38. Leskov KS, Araki S, Lavik JP, Gomez JA, Gama V et al. (2011) CRM1
protein-mediated regulation of nuclear clusterin (nCLU), an ionizing
radiation-stimulated, Bax-dependent pro-death factor. J Biol Chem 286:
40083-40090. doi:10.1074/jbc.M111.252957. PubMed: 21953454. 58. Choi I, Kim J, Park JY, Kang SW (2013) Cotransin induces
accumulation of a cytotoxic clusterin variant that cotranslationally
rerouted to the cytosol. Exp Cell Res. 59. Orsi A, Fioriti L, Chiesa R, Sitia R (2006) Conditions of endoplasmic
reticulum stress favor the accumulation of cytosolic prion protein. J Biol
Chem 281: 30431-30438. doi:10.1074/jbc.M605320200. PubMed:
16908519. j
39. References Leskov KS, Klokov DY, Li J, Kinsella TJ, Boothman DA (2003)
Synthesis and functional analysis of nuclear clusterin, a cell death
protein. J Biol Chem 278: 11590-11600. doi:10.1074/jbc.M209233200. PubMed: 12551933. 60. Vagner S, Gensac MC, Maret A, Bayard F, Amalric F et al. (1995)
Alternative translation of human fibroblast growth factor 2 mRNA
occurs by internal entry of ribosomes. Mol Cell Biol 15: 35-44. PubMed:
7799942. 40. Scaltriti M, Santamaria A, Paciucci R, Bettuzzi S (2004) Intracellular
clusterin induces G2-M phase arrest and cell death in PC-3 prostate
cancer
cells1. Cancer
Res
64:
6174-6182. doi:
10.1158/0008-5472.CAN-04-0920. PubMed: 15342402. 61. Biamonti G, Caceres JF (2009) Cellular stress and RNA splicing. Trends Biochem Sci 34: 146-153. doi:10.1016/j.tibs.2008.11.004. PubMed: 19208481. 41. Trougakos IP, Lourda M, Antonelou MH, Kletsas D, Gorgoulis VG et al. (2009) Intracellular clusterin inhibits mitochondrial apoptosis by
suppressing p53-activating stress signals and stabilizing the cytosolic
Ku70-Bax protein complex. Clin Cancer Res 15: 48-59. doi:
10.1158/1078-0432.CCR-08-1805. PubMed: 19118032. 62. Rüegsegger U, Leber JH, Walter P (2001) Block of HAC1 mRNA
translation by long-range base pairing is released by cytoplasmic
splicing upon induction of the unfolded protein response. Cell 107:
103-114. doi:10.1016/S0092-8674(01)00505-0. PubMed: 11595189. 42. Zhang H, Kim JK, Edwards CA, Xu Z, Taichman R et al. (2005)
Clusterin inhibits apoptosis by interacting with activated Bax. Nat Cell
Biol 7: 909-915. doi:10.1038/ncb1291. PubMed: 16113678. 63. Balantinou E, Trougakos IP, Chondrogianni N, Margaritis LH, Gonos
ES (2009) Transcriptional and posttranslational regulation of clusterin
by the two main cellular proteolytic pathways. Free Radic Biol Med 46:
1267-1274. doi:10.1016/j.freeradbiomed.2009.01.025. PubMed:
19353783. 43. Kim N, Yoo JC, Han JY, Hwang EM, Kim YS et al. (2011) Human
nuclear clusterin mediates apoptosis by interacting with Bcl-XL through
C-terminal coiled coil domain. J Cell Physiol 227: 1157-1167. PubMed:
21567405. 44. Santilli G, Aronow BJ, Sala A (2003) Essential requirement of
apolipoprotein J (clusterin) signaling for IkappaB expression and
regulation of NF-kappaB activity. J Biol Chem 278: 38214-38219 64. Ling IF, Bhongsatiern J, Simpson JF, Fardo DW, Estus S (2012)
Genetics of clusterin isoform expression and Alzheimer’s disease risk. PLOS ONE 7: e33923. doi:10.1371/journal.pone.0033923. PubMed:
22506010. g
y
45. Zoubeidi A, Ettinger S, Beraldi E, Hadaschik B, Zardan A et al. (2010)
Clusterin facilitates COMMD1 and I-kappaB degradation to enhance
NF-kappaB activity in prostate cancer cells. Mol Cancer Res 8:
119-130. doi:10.1158/1541-7786.MCR-09-0277. PubMed: 20068069. 65. Wei L, Xue T, Wang J, Chen B, Lei Y et al. References (2009) Roles of clusterin in
progression, chemoresistance and metastasis of human ovarian
cancer. Int J Cancer 125: 791-806. doi:10.1002/ijc.24316. PubMed:
19391138. 46. Laskin JJ, Nicholas G, Lee C, Gitlitz B, Vincent M et al. (2011) Phase
I/II trial of custirsen (OGX-011), an inhibitor of clusterin, in combination
with a gemcitabine and platinum regimen in patients with previously
untreated advanced non-small cell lung cancer. J Thorac Oncol 7:
579-586. PubMed: 22198426. 66. Xue J, Lv DD, Jiao S, Zhao W, Li X et al. (2012) pVHL mediates K63-
linked ubiquitination of nCLU. PLOS ONE 7: e35848. doi:10.1371/
journal.pone.0035848. PubMed: 22532874. 67. Bhutia SK, Das SK, Kegelman TP, Azab B, Dash R et al. (2012) mda-7/
IL-24 differentially regulates soluble and nuclear clusterin in prostate
cancer. J Cell Physiol 227: 1805-1813. doi:10.1002/jcp.22904. PubMed: 21732348. 47. Wehrli P, Charnay Y, Vallet P, Zhu G, Harmony J et al. (2001) Inhibition
of post-ischemic brain injury by clusterin overexpression. Nat Med 7:
977-979. doi:10.1038/nm0901-977. PubMed: 11533682. 48. Imhof A, Charnay Y, Vallet PG, Aronow B, Kovari E et al. (2006)
Sustained astrocytic clusterin expression improves remodeling after
brain ischemia. Neurobiol Dis 22: 274-283. doi:10.1016/j.nbd. 2005.11.009. PubMed: 16473512. 68. Caccamo AE, Desenzani S, Belloni L, Borghetti AF, Bettuzzi S (2006)
Nuclear
clusterin
accumulation
during
heat
shock
response:
implications for cell survival and thermo-tolerance induction in
immortalized and prostate cancer cells. J Cell Physiol 207: 208-219. doi:10.1002/jcp.20561. PubMed: 16331665. 49. Bell RD, Sagare AP, Friedman AE, Bedi GS, Holtzman DM et al. (2007)
Transport pathways for clearance of human Alzheimer’s amyloid beta-
peptide and apolipoproteins E and J in the mouse central nervous
system. J Cereb Blood Flow Metab 27: 909-918. PubMed: 17077814. 69. Roucou X, Guo Q, Zhang Y, Goodyer CG, LeBlanc AC (2003)
Cytosolic prion protein is not toxic and protects against Bax-mediated
cell death in human primary neurons. J Biol Chem 278: 40877-40881. doi:10.1074/jbc.M306177200. PubMed: 12917444. ystem. J Cereb Blood Flow Metab 27: 909-918. PubMed: 17077 50. DeMattos RB, O’Dell MA, Parsadanian M, Taylor JW, Harmony JA et
al. (2002) Clusterin promotes amyloid plaque formation and is critical
for neuritic toxicity in a mouse model of Alzheimer’s disease. Proc Natl
Acad Sci U S A 99: 10843-10848. doi:10.1073/pnas.162228299. PubMed: 12145324. doi:10.1074/jbc.M306177200. PubMed: 12917444. 70. Essabbani A, Garcia L, Zonetti MJ, Fisco T, Pucci S et al. References Gutacker C, Klock G, Diel P, Koch-Brandt C (1999) Nerve growth factor
and epidermal growth factor stimulate clusterin gene expression in
PC12
cells. Biochem
J
339(3):
759-766. doi:
10.1042/0264-6021:3390759. PubMed: 10215617. 29. Trougakos IP, So A, Jansen B, Gleave ME, Gonos ES (2004) Silencing
expression of the clusterin/apolipoprotein j gene in human cancer cells
using small interfering RNA induces spontaneous apoptosis, reduced
growth ability, and cell sensitization to genotoxic and oxidative stress. Cancer Res 64: 1834-1842. doi:10.1158/0008-5472.CAN-03-2664. PubMed: 14996747. 14. Schepeler T, Mansilla F, Christensen LL, Orntoft TF, Andersen CL
(2007) Clusterin expression can be modulated by changes in TCF1-
mediated Wnt signaling. J Mol Signal 2: 6. doi:10.1186/1750-2187-2-6. PubMed: 17634137. 30. Thomas-Tikhonenko A, Viard-Leveugle I, Dews M, Wehrli P, Sevignani
C et al. (2004) Myc-transformed epithelial cells down-regulate clusterin,
which inhibits their growth in vitro and carcinogenesis in vivo. Cancer
Res 64: 3126-3136. doi:10.1158/0008-5472.CAN-03-1953. PubMed:
15126350. 15. Sala A, Bettuzzi S, Pucci S, Chayka O, Dews M et al. (2009)
Regulation of CLU gene expression by oncogenes and epigenetic
factors implications for tumorigenesis. Adv Cancer Res 105: 115-132. doi:10.1016/S0065-230X(09)05007-6. PubMed: 19879426. 16. Viard I, Wehrli P, Jornot L, Bullani R, Vechietti JL et al. (1999) Clusterin
gene expression mediates resistance to apoptotic cell death induced by
heat shock and oxidative stress. J Invest Dermatol 112: 290-296. doi:
10.1046/j.1523-1747.1999.00531.x. PubMed: 10084304. 31. Bettuzzi S, Scorcioni F, Astancolle S, Davalli P, Scaltriti M et al. (2002)
Clusterin (SGP-2) transient overexpression decreases proliferation rate
of SV40-immortalized human prostate epithelial cells by slowing down 14 PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 Non-Secreted CLU Forms Translated in Rare Amounts cell cycle progression. Oncogene 21: 4328-4334. doi:10.1038/sj.onc. 1205594. PubMed: 12082621. reduced expression of Egr-1 and TNF-alpha. J Atheroscler Thromb 18:
209-216. doi:10.5551/jat.5819. PubMed: 21099169. reduced expression of Egr-1 and TNF-alpha. J Atheroscler Thromb 18:
209-216. doi:10.5551/jat.5819. PubMed: 21099169. j
52. Zoubeidi A, Chi K, Gleave M (2010) Targeting the cytoprotective
chaperone, clusterin, for treatment of advanced cancer. Clin Cancer
Res 16: 1088-1093. doi:10.1158/1078-0432.CCR-09-2917. PubMed:
20145158. 32. Nizard P, Tetley S, Le Drean Y, Watrin T, Le Goff P et al. (2007)
Stress-induced retrotranslocation of clusterin/ApoJ into the cytosol. Traffic 8: 554-565. doi:10.1111/j.1600-0854.2007.00549.x. PubMed:
17451556. 33. Li N, Zoubeidi A, Beraldi E, Gleave ME (2012) GRP78 regulates
clusterin stability, retrotranslocation and mitochondrial localization
under ER stress in prostate cancer. Oncogene, 32: 1933–42. PubMed:
22689054. 53. References (2013) Exon-
Skipping Strategy by Ratio Modulation between Cytoprotective versus
Pro-Apoptotic Clusterin Forms Increased Sensitivity of LNCaP to Cell
Death. PLOS ONE 8: e54920. doi:10.1371/journal.pone.0054920. PubMed: 23418433. 51. Hamada N, Miyata M, Eto H, Ikeda Y, Shirasawa T et al. (2011) Loss of
clusterin limits atherosclerosis in apolipoprotein E-deficient mice via September 2013 | Volume 8 | Issue 9 | e75303 15 PLOS ONE | www.plosone.org
|
https://openalex.org/W2101609101
|
https://link.springer.com/content/pdf/10.1007/s00418-012-1026-0.pdf
|
English
| null |
Localization of decorin gene expression in normal human breast tissue and in benign and malignant tumors of the human breast
|
Histochemistry and cell biology
| 2,012
|
cc-by
| 8,601
|
Histochem Cell Biol (2013) 139:161–171
DOI 10.1007/s00418-012-1026-0 Histochem Cell Biol (2013) 139:161–171
DOI 10.1007/s00418-012-1026-0 ORIGINAL PAPER ORIGINAL PAPER Localization of decorin gene expression in normal human breast
tissue and in benign and malignant tumors of the human breast Sainio T. Kakko H. Ja¨rvela¨inen
Department of Medical Biochemistry and Genetics,
University of Turku, Kiinamyllynkatu 10,
20520 Turku, Finland
e-mail: anorsa@utu.fi Localization of decorin gene expression in normal human breast
tissue and in benign and malignant tumors of the human breast Pia Bostro¨m • Annele Sainio • Tanja Kakko •
Mikko Savontaus • Mirva So¨derstro¨m •
Hannu Ja¨rvela¨inen Accepted: 28 August 2012 / Published online: 25 September 2012
The Author(s) 2012. This article is published with open access at Springerlink.com Abstract
The small extracellular matrix proteoglycan
decorin which possesses a potent antitumor activity has
been shown to be present in various amounts in the stroma
of several tumors including those of the breast. Regarding
decorin in breast malignancies the published data are
conflicting, i.e., whether breast cancer cells express it or
not. Here, we first compared decorin gene expression levels
between healthy human breast tissue and selected types of
human breast cancer using GeneSapiens databank. Next,
we localized decorin mRNA in tissue specimen of normal
human breast, intraductal breast papillomas and various
histologic types of human breast cancer using in situ
hybridization (ISH) with digoxigenin-labeled RNA probes for decorin. We also examined the effect of decorin
transduction on the behavior of cultured human breast
cancer MCF7 cells. Analysis of GeneSapiens databank
revealed that in various human breast cancers decorin
expression is significant. However, ISH results clearly
demonstrated that human breast cancer cells independently
of the type of the cancer do not express decorin mRNA. This was also true for papilloma-forming cells of the
human breast. Indeed, decorin gene expression in healthy
human breast tissue as well as in benign and malignant
tumors of human breast was shown to take place solely in
cells of the original stroma. Decorin transduction using
decorin adenoviral vector in decorin-negative MCF7 cells
resulted in a significant decrease in the proliferation of
these cells and changed cell cohesion. Decorin-transduced
MCF7 cells also exhibited increased apoptosis. In conclu-
sion, our study shows that in human breast tissue only cells
of the original stroma are capable of decorin gene
expression. Our study also shows that transduction of
decorin in decorin-negative human breast cancer cells
markedly modulates the growth pattern of these cells. P. Bostro¨m and A. Sainio contributed equally to this work. P. Bostro¨m and A. Sainio contributed equally to this work. P. Bostro¨m M. So¨derstro¨m
Department of Pathology, Turku University Hospital,
University of Turku, Kiinamyllynkatu 4-8,
20520 Turku, Finland
e-mail: pia.bostrom@tyks.fi
M S¨d
¨ Keywords
Breast cancer Extracellular matrix
Decorin In situ hybridization Cell behavior Keywords
Breast cancer Extracellular matrix
Decorin In situ hybridization Cell behavior A. P. Bostro¨m and A. Sainio contributed equally to this work. Introduction In recent years, growing interest has been focused on the
role and therapeutic potential of extracellular matrix
(ECM) macromolecules in various diseases including the
evolution and progression of cancer (Hielscher et al. 2012;
Ja¨rvela¨inen et al. 2009; Lu et al. 2012; Marastoni et al. 2008). This is because today we understand that ECM
macromolecules form not only an inert, space-filling 3 12 Histochem Cell Biol (2013) 139:161–171 162 et al. 1999; Lu et al. 2012). These alterations in turn are
likely to play an important role in the growth and invasion
of breast lesions (Brown et al. 1999; Lu et al. 2012). Regarding decorin, its expression has been shown to be
increased in the peritumoral stroma of the malignant
lesions but decreased within the breast tumor tissue (Brown
et al. 1999; Leygue et al. 2000). However, results on
decorin expression in human breast cancer have been
somewhat conflicting, i.e., whether breast cancer cells
express this small proteoglycan or not (Cawthorn et al. 2012; Gu et al. 2010; Leygue et al. 2000; Skandalis et al. 2011). Thus, in the present study, we aimed to localize
decorin mRNA in individual cells within normal and
malignant human breast tissues using in situ hybridization
(ISH) with digoxigenin (DIG)-labeled RNA probes for
decorin. In addition, by utilizing cultures of MCF7 human
breast adenocarcinoma cells and a decorin producing
adenoviral vector, we also examined whether targeted
decorin delivery can modulate the behavior of these cells. microenvironment around the cells but they also interact
with cells and generate signals that regulate the behavior of
the cells (Hynes 2009; Rozario and DeSimone 2010) and
control angiogenesis (Hielscher et al. 2012). Indeed, indi-
vidual ECM macromolecules display important functional
roles in the control of key cellular events of physiologic
and pathological processes, namely adhesion, migration,
proliferation, differentiation, and survival (Daley et al. 2008; Ja¨rvela¨inen et al. 2009; Marastoni et al. 2008;
Rozario and DeSimone 2010). An ECM molecule that has been shown to be involved
in the regulation of all the aforementioned cellular events,
and thereby markedly contributes to health and disease, is
decorin, a small leucine-rich extracellular matrix proteo-
glycan (Ferdous et al. 2010; Iozzo and Schaefer 2010;
Seidler and Dreier 2008). The evidence suggests that
decorin represents a potent antitumor molecule (Iozzo and
Sanderson 2011; Theocharis et al. 2010). Introduction For example,
early studies with decorin-deficient mice have indicated
that although the lack of decorin does not lead to the
development of spontaneous tumors (Danielson et al. 1997), it is permissive for tumorigenesis (Iozzo et al. 1999). In concordance with this, we have recently dem-
onstrated that there is a striking difference in the expression
of decorin between malignant and benign vascular tumors
in human, i.e., within Kaposi’s sarcoma, and angiosarcoma,
decorin expression is completely lacking; while within
hemangiomas, decorin is expressed in abundant amounts
(Saloma¨ki et al. 2008). Decorin has also been shown to
inhibit tumor growth by antagonizing tumor angiogenesis
(Neill et al. 2012). Furthermore, ectopic expression of
decorin has been shown to cause generalized growth sup-
pression in neoplastic cells of various histologic origin
(Santra et al. 1997). As can be expected, several other
studies supporting the antitumor and antimetastatic activity
for decorin have been published (Biaoxue et al. 2011;
Goldoni and Iozzo 2008; Hu et al. 2009; Reed et al. 2005;
Shintani et al. 2008; Troup et al. 2003), and low levels of
decorin have been found to be associated with a shorter
progression time and poorer survival in lymph node-
negative invasive human breast carcinomas (Araki et al. 2009; Troup et al. 2003). As such, a lot of interest has been
paid to the potential use of decorin as an anticancer agent
in the future (Neill et al. 2012; Pucci-Minafra et al. 2008;
Theocharis et al. 2010). GeneSapiens database receptors (ER) were determined positive in 56 cases and
progesterone receptors (PR) were positive in 53 cases. Ki-67 status was intermediate (16–30 %) or high ([30 %)
in 46 cases. Among the 69 cases of invasive breast cancer
specimen studied, Her2 chromogenic in situ hybridization
(CISH) positivity was found in 11 patients. The GeneSapiens database was used to analyze previous
published results of the gene expression levels of decorin in
healthy and malignant human breast tissues (Kilpinen et al. 2008). This database (http://www.genesapiens.org/) covers
the relative gene expression patterns for 17,330 genes
across all the 9,783 annotated healthy and pathological
human tissue samples from publicly available Affymetrix
microarray experiments. The database contains 15 healthy
breast tissue samples and 1,504 different human breast
carcinoma samples. Table 1 Patients and tumor characteristics
Variable
Number of patients (%)
Number of the patients
69 (aged 40–94, mean 65.4)
Grade
I
8 (11.6 %)
II
36 (52.2 %)
III
25 (36.2 %)
Axillary nodal status
N0
33 (47.8 %)
[N1
33 (47.8 %)
Unknown
3 (4.3 %)
Tumor size
B2 cm
23 (33.3 %)
[2 cm
46 (66.7 %)
Estrogen receptor status (ER)a
Positive
56 (81.2 %)
Negative
13 (18.8 %)
Progesterone receptor status (PR)a
Positive
53 (76.8 %)
Negative
16 (23.2 %)
Ki-67 statusb
Low B15 %
23 (33.3 %)
Intermediate 16–30 %
26 (37.7 %)
High [30 %
20 (29 %)
Histologic type
Ductal
49 (71.0 %)
Lobular
11 (15.9 %)
Subtypes
9 (13.0 %)
Her2c
IHC positive (2? and 3?)
27 (39.1 %)
IHC negative (0 and 1?)
42 (60.9 %)
CISH positive
11 (15.9 %)
a Cut off point used for ER and PR immunohistochemistry is 10 % of
positively stained tumor nuclei. b Proliferation index according to St Gallen Consesus (Goldhirsch
et al. 2009)
c Scoring of HER2 immunohistochemistry: Score 0 no staining is
observed or cell membrane staining is observed in less than 10 % of
tumor cells. Score 1? a faint perceptible membrane staining can be
detected in more than 10 % of the tumor cells or cells are only stained
in part of their membrane. Score 2? a weak-to-moderate complete
membrane staining is observed in more than 10 % of the tumor cells. Table 1 Patients and tumor characteristics Immunohistochemistry Five different ready-to-use mouse or rabbit monoclonal
antibodies were used from Ventana Medical Systems/
Roche Diagnostics: Estrogen Receptor (SP1, rabbit), Pro-
gesterone Receptor (1E2, rabbit), HER-2/neu (4B5, rab-
bit), Ki-67 (30-9, rabbit), and p63 (4A4, mouse) with
BenchMark XT immunostainer and ultraVIEW Universal
DAB Detection Kit (Ventana/Roche, Tucson, Arizona,
USA). The percentage of nuclei with immunoreactivity to
ER, PR, and Ki-67 was classified as continuous data from
0 to 100 %. ER-positive and PR-positive cases showed
staining in at least 10 % of the tumor cell nuclei. Carci-
nomas revealing 3? immunohistochemical membrane
staining for Her2 or positive gene amplification by CISH
were accepted as positive (Bostro¨m et al. 2009). Immu-
nostaining for p63 was done to identify myoepithelial cells
in some cases. Immunohistochemical analyses for decorin
were performed as previously described in detail (Salo-
ma¨ki et al. 2008). Patients and tumors Ethical approval for the use of the clinical material of this
study was given by Turku University Hospital Ethics
committee
(no
241/2005)
and
the
Finnish
National
Authority for Medicolegal Affairs (no 4424/32/300/02). Well-characterized human breast cancer material consisted
of tumor samples collected from 69 female breast cancer
patients
(mean
age
at
surgery
65.4 years,
range
40–94 years) who were operated and treated at Turku
University Hospital during the years 2004–2007 (Table 1). All patients had over 10 mm invasive breast tumor and
were treated with a radical mastectomy. Tissue samples
from the invasive border of the tumor were excised within
30 min after the surgical removal of the breast. Normal
human female breast tissue (three samples) and intraductal
papillomas (three samples) were obtained through reduc-
tion mammoplasty of the healthy side. The specimen were
fixed in 10 % phosphate buffered formaldehyde and
embedded in paraffin. Four lm serial sections were cut and
stained with hematoxylin and eosin. The slides were
reviewed to confirm the diagnosis of the breast cancer, and
the histologic typing and grading of the specimen were
performed according to the World Health Organization
(WHO) classification (Ellis et al. 2003). Of the 69 patients,
25 cases were grade III tumors, 36 cases were grade II
tumors, and 8 cases were grade I tumors. Histologically,
the majority were invasive ductal carcinomas (71 %). Lymph node metastases were found in 33 cases. Estrogen Breast cancer is the leading cancer malignancy among
women aged 20–59 years (WHO 2009). It comprises a
collection of diseases that have different histopathology,
genetic, and genomic variations, and prognostic outcomes
(Geyer et al. 2009). In both benign and malignant breast
tumors, alterations of stromal structure and composition are
well-recognized phenomena (Alowami et al. 2003; Brown 123 123 123 Histochem Cell Biol (2013) 139:161–171 163 GeneSapiens database a Cut off point used for ER and PR immunohistochemistry is 10 % of
positively stained tumor nuclei. Statistical analysis Statistical analysis Unpaired Student’s t test was employed in statistical
analyses. All p values \0.05 were considered statistically
significant. Decorin transduction Human breast adenocarcinoma cell line MCF7 was used
for transduction with a recombinant replication-deficient
adenoviral vector dcn-pxc1c-1. MCF7 cells were main-
tained in RPMI-1640 medium containing 10 % fetal
bovine serum (FBS), 25 lM insulin, 1 nM b-estradiol,
2 mM L-glutamine, penicillin (100 IU/mL), and strepto-
mycin (100 lg/mL) and grown at 37 C with 5 % CO2. The cells were plated on a 24-well plate (Greiner Bio-One,
Kremsmuenster, Austria), 30,000 per well. The next day,
cells were transduced with 0, 3, 30, 100, 300, and
1000 pfu/cell of dcn-pxc1c-1 or RAdlacZ in reduced
medium containing no FBS. Four parallels were made of
each vector concentration. After 24-h incubation, the cells
were washed twice with reduced medium and incubated in
this medium for another 24 h. The cells were trypsinized,
pooled, and the RNA was extracted using NucleoSpin
RNA II–kit (Macherey–Nagel, Du¨ren, Germany) according
to the manufacturer’s instructions. Results Relative decorin gene expression in human breast
cancer tissues based on the GeneSapiens in silico
transcriptomics data In order to analyze published data on decorin gene
expression in different types of human breast cancer, we
used an in silico database from the GeneSapiens website
(Kilpinen et al. 2008). The analysis indicated that the rel-
ative decorin gene expression is significant in both healthy
and various malignant conditions of human breast tissue
(Fig. 1). Fig. 1 Box plot analysis of decorin gene expression levels using the
GeneSapiens in silico database at www.genesapiens.org in healthy
human breast tissues and in different types of human breast cancer. Y axis indicates the level of relative decorin gene expression in the
tissues. The continuous lines in the box plot images represent the
median gene expression level of decorin in breast tissue samples
included in the database. Compared to decorin expression in healthy
breast tissue decorin expression is decreased in ductal, lobular, and
other breast cancers but increased in breast carcinomas not otherwise
specified (breast carcinoma NOS) pairs used in qPCR were: 50-GGACCGTTTCAACAGAG
AGG-30 (for) and 50-GAGTTGTGTCAGG GGGAAGA-30
(rev) for decorin and 50-GAGTGTGGCCTTCTCCTCTG-30
(for) and 50-GCTTG CAGTTAGCCAGGTTC-30 (rev) for
GNB2L1. Reactions were run on an Applied Biosystems
7900HT machine (Applied Biosystems, Carlsbad, CA,
USA). The qPCR protocol consisted of initial denaturation
at 95 C for 2 min followed by 40 cycles of denaturation at
95 C for 40 s and extension at 60 C for 45 s. The spec-
ificity of the reactions was confirmed by melt-curve and
agarose gel analysis. Triplicate CT values were analyzed
using the comparative CT (2-44CT) method. pairs used in qPCR were: 50-GGACCGTTTCAACAGAG
AGG-30 (for) and 50-GAGTTGTGTCAGG GGGAAGA-30
(rev) for decorin and 50-GAGTGTGGCCTTCTCCTCTG-30
(for) and 50-GCTTG CAGTTAGCCAGGTTC-30 (rev) for
GNB2L1. Reactions were run on an Applied Biosystems
7900HT machine (Applied Biosystems, Carlsbad, CA,
USA). The qPCR protocol consisted of initial denaturation
at 95 C for 2 min followed by 40 cycles of denaturation at
95 C for 40 s and extension at 60 C for 45 s. The spec-
ificity of the reactions was confirmed by melt-curve and
agarose gel analysis. Triplicate CT values were analyzed
using the comparative CT (2-44CT) method. pairs used in qPCR were: 50-GGACCGTTTCAACAGAG
AGG-30 (for) and 50-GAGTTGTGTCAGG GGGAAGA-30
(rev) for decorin and 50-GAGTGTGGCCTTCTCCTCTG-30
(for) and 50-GCTTG CAGTTAGCCAGGTTC-30 (rev) for
GNB2L1. Reactions were run on an Applied Biosystems
7900HT machine (Applied Biosystems, Carlsbad, CA,
USA). The qPCR protocol consisted of initial denaturation
at 95 C for 2 min followed by 40 cycles of denaturation at
95 C for 40 s and extension at 60 C for 45 s. The spec-
ificity of the reactions was confirmed by melt-curve and
agarose gel analysis. Triplicate CT values were analyzed
using the comparative CT (2-44CT) method. Adenoviral vectors Adenoviral vectors For transduction experiments, a recombinant replication-
deficient adenoviral vector dcn-pxc1c-1 was used. This
vector harbors the human decorin (DCN) cDNA under
the control of cytomegalovirus (CMV) promoter. For the
preparation of the vector, full length human decorin cDNA
(Fisher et al. 1989) in pGEM plasmids was cloned and
inserted into shuttle plasmid pxcJL-1. The viruses were
prepared by cotransfecting HEK293–cells with back bone
plasmid pBHG10. As a control vector RAdlacZ, which
harbors the E. coli b-galactosidase gene (lacZ) under the
control of CMV IE promoter was used (Wilkinson and
Akrigg 1992). This vector was purchased from the Virus
Vector Facility, Centre for Biotechnology, University of
Turku, Turku, Finland. Decorin in situ hybridization Decorin ISH was performed on 4 lm breast tissue sec-
tions by probing with human decorin antisense and sense
single-stranded RNA riboprobes. A 533 bp fragment
containing human decorin cDNA was cloned into the Eco
RI/Hind III site of pGEM-4Z transcription vector (kindly
provided by Dr. Liliana Schaefer, University of Frank-
furt, Frankfurt am Main, Germany). Linearized plasmid
DNA was purified with QIAquick PCR Purification Kit
(QIAGEN, Hilden, Germany) and DIG-labeled sense and
antisense RNA probes were synthesized by in vitro
transcription with SP6 and T7 polymerases, respectively,
using a DIG RNA Labeling Kit (Roche, Applied Science,
Mannheim, Germany). Probe quantification was carried
out with a DIG Nucleic Acid Detection Kit (Roche),
and ISH was performed as described (Saloma¨ki et al. 2008). a Cut off point used for ER and PR immunohistochemistry is 10 % of
positively stained tumor nuclei. c Scoring of HER2 immunohistochemistry: Score 0 no staining is
observed or cell membrane staining is observed in less than 10 % of
tumor cells. Score 1? a faint perceptible membrane staining can be
detected in more than 10 % of the tumor cells or cells are only stained
in part of their membrane. Score 2? a weak-to-moderate complete
membrane staining is observed in more than 10 % of the tumor cells. Score 3? a strong complete membrane staining is observed in more
than 10 % of the tumor cells 12 123 Histochem Cell Biol (2013) 139:161–171 164 RT-qPCR RNA concentration from the extractions was determined
using a Nano-Drop spectrophotometer (ThermoScientific,
Waltham, MA, USA), and the integrity of the RNA was
confirmed with agarose gel electrophoresis. One lg of
RNA was DNase treated with RQ1 RNase-Free DNase
(Promega, Madison, WI, USA) and reverse transcribed
into cDNA using M-MLV reverse transcriptase and Oli-
go(dT)15 primer (Promega, Madison, WI, USA) according
to manufacturer’s instructions. RT-qPCR was performed
using GoTaq qPCR Master Mix (Promega, Madison, WI,
USA) with 100 nM primer concentrations and final volume
of 10 lL according to manufacturer’s protocol. GNB2L1
was chosen as a reference gene (Zhang et al. 2005). Primer Fig. 1 Box plot analysis of decorin gene expression levels using the
GeneSapiens in silico database at www.genesapiens.org in healthy
human breast tissues and in different types of human breast cancer. Y axis indicates the level of relative decorin gene expression in the
tissues. The continuous lines in the box plot images represent the
median gene expression level of decorin in breast tissue samples
included in the database. Compared to decorin expression in healthy
breast tissue decorin expression is decreased in ductal, lobular, and
other breast cancers but increased in breast carcinomas not otherwise
specified (breast carcinoma NOS) Fig. 1 Box plot analysis of decorin gene expression levels using the
GeneSapiens in silico database at www.genesapiens.org in healthy
human breast tissues and in different types of human breast cancer. Y axis indicates the level of relative decorin gene expression in the
tissues. The continuous lines in the box plot images represent the
median gene expression level of decorin in breast tissue samples
included in the database. Compared to decorin expression in healthy
breast tissue decorin expression is decreased in ductal, lobular, and
other breast cancers but increased in breast carcinomas not otherwise
specified (breast carcinoma NOS) 123 165 Histochem Cell Biol (2013) 139:161–171 3–1,000 pfu/cell of a decorin expression vector and a viral
concentration of 100 pfu/cell was chosen for further
experiments. Transduction with a decorin adenoviral vector
changed markedly the growth pattern of MCF7 cells. Cell
cohesion clearly decreased and decorin-transduced MCF7
cells exhibited abnormal features (Fig. 6a), compared
either to the cells transduced with a control vector LacZ
(Fig. 6b) or to negative control cells (data not shown),
which both grew as large cohesive solid sheets. Discussion Previously, decreased level of decorin expression has been
reported in breast cancer (Eshchenko et al. 2007; Gu et al. 2010; Leygue et al. 2000). However, in a recent study, even
increased amounts of decorin in breast carcinoma has been
observed (Skandalis et al. 2011). In addition to these
conflicting results, it has also not been convincingly dem-
onstrated whether breast cancer cells themselves express
decorin or not (Cawthorn et al. 2012; Gu et al. 2010). In the present study, we have first analyzed previously
published data on decorin gene expression using GeneSa-
piens databank. Thereafter, we have localized decorin
mRNA in tissues samples of normal human breast and
selected human breast tumors using ISH with DIG-labeled
decorin probes. We have also examined the influence of
adenoviral mediated decorin transduction on the behavior
of human breast cancer cells in vitro. GeneSapiens data-
bank analysis demonstrated that the relative decorin gene
expression is significant in both healthy and various
malignant conditions of human breast tissue. ISH of heal-
thy human breast tissue and selected human breast tumor
samples revealed that decorin mRNA can merely be
localized to the normal stroma. Indeed, no decorin mRNA
could be detected in benign epithelial cells or in malignant
cancer cells of the human breast. In previous studies, it has
been demonstrated that decorin expression is high in nor-
mal human breast tissue stroma adjacent to lobules and
reduced in the breast tumor itself (Brown et al. 1999;
Leygue et al. 2000). However, these studies have used Localization of decorin mRNA in normal human breast
tissue, and in benign and malignant tumors
of the human breast Next, we localized decorin mRNA in healthy human breast
tissue, and in benign and selected types of malignant human
breast tumors. Using ISH with DIG-labeled RNA probes for
decorin, we were able to demonstrate that in healthy human
breast tissue decorin gene expression takes place only in
cells in the stromal area surrounding the lobules and in the
intralobular stroma, whereas in cells of the epithelium of
ducts or lobules no decorin gene expression was detected
(Fig. 2a, b). Identical analysis of intraductal papillomas of
the human breast (Fig. 2c) revealed that in these benign
ductal tumors no decorin gene expression takes place
(Fig. 2d, e). Similarly to the healthy human breast tissue,
decorin mRNA was solely localized to the original stroma
around the dilated duct of the papillomas and not at all
within the papillomas (Fig. 2d, e). There was also no
decorin mRNA detected in the area within breast tissue
specimen containing malignant proliferation of ductal or
lobular epithelial cells with myoepithelium, the so-called
ductal carcinoma in situ (DCIS) (Fig. 3a–f), and lobular
carcinoma in situ (LCIS) (data not shown). Indeed, in
DCIS- and LCIS-containing samples, expression of decorin
mRNA was localized merely to the peritumoral stroma. Decorin mRNA was also lacking from the infiltrating can-
cer cells of the invasive ductal carcinoma (IDC) (Fig. 4a, b)
and the invasive lobular carcinoma (ILC) (data not shown). All decorin mRNA in the above-mentioned invasive human
breast cancer samples was localized to the original stromal
cells. Furthermore, in invasive mucinous carcinomas cancer
cells in the mucin lakes or those within the original stroma
did not express decorin mRNA (Fig. 5a, b). In conformity
with IDC and ILC described above, the surrounding original
stromal cells were highly positive for decorin mRNA. Positive immunoreactivity for decorin was seen in the same
original non-malignant stromal area as decorin mRNA (data
not shown). RT-qPCR Several of
the decorin-transduced MCF7 cells were also found to
contain a large vacuole within another larger cell with a
crescent-shaped nucleus at its periphery (Fig. 6c). Micro-
scopic examination further revealed apoptotic features in
many of these internalized cells. These so-called cannibal
cells were also sporadically seen among the MCF7 cells
transduced with the control vector and among the MCF7
cells without any transduction (data not shown). The
mitosis rate was statistically significantly lower in the de-
corin-transduced MCF7 cell cultures compared to their
counterpart cell cultures treated with the control vector
LacZ (Fig. 6d). Localization of decorin mRNA in normal human breast
tissue, and in benign and malignant tumors
of the human breast Effect of adenoviral decorin transduction
on MCF7 cells Arrowheads indicate the borders between intraductal
papillomas and normal breast tissue. a, b and d, e scale bar 50 lm, c
scale bar 500 lm Fig. 2 Decorin mRNA is localized solely to the stromal cells
surrounding the lobulus and to the intralobular stromal cells of
normal human breast tissue. a HE staining of normal lobulus and its
stroma. b ISH for decorin of a serial section of the same normal
lobulus as in (a). Examples of individual stromal cells expressing
decorin mRNA are indicated by arrows. In the epithelium of ducts or
lobules, no decorin mRNA can be detected (examples indicated by
asterisks). c HE staining of human breast tissue containing intraductal Fig. 2 Decorin mRNA is localized solely to the stromal cells
surrounding the lobulus and to the intralobular stromal cells of
normal human breast tissue. a HE staining of normal lobulus and its
stroma. b ISH for decorin of a serial section of the same normal
lobulus as in (a). Examples of individual stromal cells expressing
decorin mRNA are indicated by arrows. In the epithelium of ducts or
lobules, no decorin mRNA can be detected (examples indicated by
asterisks). c HE staining of human breast tissue containing intraductal Fig. 2 Decorin mRNA is localized solely to the stromal cells
surrounding the lobulus and to the intralobular stromal cells of
normal human breast tissue. a HE staining of normal lobulus and its
stroma. b ISH for decorin of a serial section of the same normal
lobulus as in (a). Examples of individual stromal cells expressing
decorin mRNA are indicated by arrows. In the epithelium of ducts or
lobules, no decorin mRNA can be detected (examples indicated by
asterisks). c HE staining of human breast tissue containing intraductal papillomas. d, e ISH for decorin of a serial section of the same sample
as in (c), magnified illustrations of the boxed regions shown in (c). Positive DIG-reaction in ISH can be seen in purple. No decorin
mRNA is detected within the intraductal papilloma tissue (indicated
by asterisks). Arrowheads indicate the borders between intraductal
papillomas and normal breast tissue. a, b and d, e scale bar 50 lm, c
scale bar 500 lm clearly shown that human breast cancer cells do not express
decorin at all and that in human breast tissue specimen
decorin is derived from original stromal cells, not from
benign or malignant tumor-forming epithelial cells. Effect of adenoviral decorin transduction
on MCF7 cells The ISH results clearly demonstrated that decorin is not
expressed by benign or malignant ductal or lobular epi-
thelial cells of the human breast. Therefore, next we
wanted to examine the effects of targeted decorin trans-
duction on the behavior of human breast adenocarcinoma
cells. Human breast adenocarcinoma cell line MCF7 and
decorin producing adenoviral vector were applied for this
purpose. Using RT-qPCR, it was first shown that MCF7
cells do not express decorin mRNA (data not shown). These cells were then transduced with a titer range of 12 3 Histochem Cell Biol (2013) 139:161–171 166 Fig. 2 Decorin mRNA is localized solely to the stromal cells
surrounding the lobulus and to the intralobular stromal cells of
normal human breast tissue. a HE staining of normal lobulus and its
stroma. b ISH for decorin of a serial section of the same normal
lobulus as in (a). Examples of individual stromal cells expressing
decorin mRNA are indicated by arrows. In the epithelium of ducts or
lobules, no decorin mRNA can be detected (examples indicated by
asterisks). c HE staining of human breast tissue containing intraductal Fig. 2 Decorin mRNA is localized solely to the stromal cells
surrounding the lobulus and to the intralobular stromal cells of
normal human breast tissue. a HE staining of normal lobulus and its
stroma. b ISH for decorin of a serial section of the same normal
lobulus as in (a). Examples of individual stromal cells expressing
decorin mRNA are indicated by arrows. In the epithelium of ducts or
lobules, no decorin mRNA can be detected (examples indicated by
asterisks). c HE staining of human breast tissue containing intraductal
papillomas. d, e ISH for decorin of a serial section of the same sample
as in (c), magnified illustrations of the boxed regions shown in (c). Positive DIG-reaction in ISH can be seen in purple. No decorin
mRNA is detected within the intraductal papilloma tissue (indicated
by asterisks). Arrowheads indicate the borders between intraductal
papillomas and normal breast tissue. a, b and d, e scale bar 50 lm, c
scale bar 500 lm papillomas. d, e ISH for decorin of a serial section of the same sample
as in (c), magnified illustrations of the boxed regions shown in (c). Positive DIG-reaction in ISH can be seen in purple. No decorin
mRNA is detected within the intraductal papilloma tissue (indicated
by asterisks). Effect of adenoviral decorin transduction
on MCF7 cells How-
ever, the specific cell types responsible for decorin
expression in the original stroma compartment still remains
to be studied. To the best of our knowledge, this study is
the first to exactly localize decorin mRNA at the cellular
level in human breast tissue including different types of
human breast cancer. radioactive probes use of which is limited, if the purpose is
to exactly localize the mRNA at the cellular level. With
radioactive probes, all the cellular relationships are lost
because of tissue digest and mRNA levels are averaged
from all of the cells contained in the original sample
(Wilcox 1993). When methods like Northern (Tralha˜o et al. 2003) or western blot analyses (Leygue et al. 2000; Nash
et al. 2002; Troup et al. 2003) and more modern methods
such as RT-PCR (Eshchenko et al. 2007) are used to
evaluate the expression of molecules, e.g., decorin, they are
usually performed with pooled samples consisting of the
sectioned tumor which also contain its surrounding original
stroma. Therefore,
these
above-mentioned
methods
including GeneSapiens database used in the present study
are unable to tell the cellular origin of a specific molecule. Our results using ISH with DIG-labeled decorin probe have Next, we examined whether by introducing decorin, a
known antitumoral molecule, to widely used MCF7 (Bur-
dall et al. 2003) human breast adenocarcinoma cells, we
could modulate the behavior of these cells. We showed that
decorin transduction causes marked changes in the prolif-
eration and growth pattern of the MCF7 cells. In particular, 123 Histochem Cell Biol (2013) 139:161–171 167 Fig. 3 Decorin gene expression is lacking in human ductal carci-
noma in situ tumor (DCIS). IHC and ISH of serial sections of a
representative DCIS GII sample. Tumor tissue in the sections is
indicated by an asterisk. a, d HE staining. b, e Immunostaining for
p63. Brown color indicates p63 positive myoepithelial cells lining the
tumor mass. c, f ISH for decorin. Positive DIG-reaction in ISH
indicating the cells expressing decorin mRNA can be seen in purple. Arrows (d–e) indicate the border between DCIS and surrounding
tissue. Arrows (f) indicate examples of decorin positive cells. a–c
scale bar 100 lm, d–f scale bar 20 lm tumor mass. c, f ISH for decorin. Positive DIG-reaction in ISH
indicating the cells expressing decorin mRNA can be seen in purple. Arrows (d–e) indicate the border between DCIS and surrounding
tissue. Effect of adenoviral decorin transduction
on MCF7 cells Arrows (f) indicate examples of decorin positive cells. a–c
scale bar 100 lm, d–f scale bar 20 lm Fig. 3 Decorin gene expression is lacking in human ductal carci-
noma in situ tumor (DCIS). IHC and ISH of serial sections of a
representative DCIS GII sample. Tumor tissue in the sections is
indicated by an asterisk. a, d HE staining. b, e Immunostaining for
p63. Brown color indicates p63 positive myoepithelial cells lining the (Winnemo¨ller et al. 1992). It is also possible that altera-
tions in the expression of metalloproteinases (MMPs) and
their inhibitors (TIMPs) by MCF7 cells are responsible for
the observed decreased cell cohesion. Indeed, adenovirus-
mediated overexpression of decorin has been shown to
modulate the expression of certain MMPs and TIMPs by
human gingival fibroblasts (Al Haj Zen et al. 2003). Fur-
thermore, the possibility that the decreased cell cohesion of
MCF7 cells in response to decorin transduction is mediated
via direct interactions between decorin and certain inte-
grins remains to be explored (Guidetti et al. 2002). The
decreased proliferation of decorin-transduced MCF7 cells,
on the other hand, is most likely mediated via decorin’s
ability to antagonize receptor tyrosine kinases, particularly
the signaling through epidermal growth factor receptor
(Hu et al. 2009), the receptor for hepatocyte growth factor
called Met (Goldoni et al. 2009), insulin-like growth factor
receptor (Iozzo et al. 2011) and/or vascular endothelial
growth factor 2 receptor (Khan et al. 2011). In addition,
induction of apoptotic features of MCF7 cells due to
decorin transduction may also have a role in the finding of
this study that decorin-transduced MCF7 human breast
cancer cells exhibit decreased proliferation. Interestingly, (Winnemo¨ller et al. 1992). It is also possible that altera-
tions in the expression of metalloproteinases (MMPs) and
their inhibitors (TIMPs) by MCF7 cells are responsible for
the observed decreased cell cohesion. Indeed, adenovirus-
mediated overexpression of decorin has been shown to
modulate the expression of certain MMPs and TIMPs by
human gingival fibroblasts (Al Haj Zen et al. 2003). Fur-
thermore, the possibility that the decreased cell cohesion of
MCF7 cells in response to decorin transduction is mediated
via direct interactions between decorin and certain inte-
grins remains to be explored (Guidetti et al. 2002). Effect of adenoviral decorin transduction
on MCF7 cells In conclusion, by utilizing ISH with DIG-labeled probes
for decorin, we have shown that in human breast cancer,
the cancer cells do not express decorin mRNA, but the
expression of decorin takes place merely in cells of the
original stroma both in healthy human breast tissue and in
breast tissues containing benign or malignant breast
Fig. 4 Cells of invasive ductal cancer (IDC) of human breast are
negative for decorin mRNA. a ISH of an infiltrating ductal breast
carcinoma GIII tissue sample. b Magnified illustration of the boxed
region shown in (a). Positive DIG-reaction of stromal cells in ISH
indicating the localization of decorin mRNA can be seen in purple. Asterisks in (b) indicate areas of infiltrating cancer cells that are
negative for decorin gene expression. Note that all decorin mRNA
within invasive cancer tissue sample is detected in the original
stromal cells, not in the cancer cells. a scale bar 100 lm, b scale bar
50 lm
Fig. 5 Invasive mucinous carcinoma cells of human breast lack
decorin gene expression. a ISH for decorin of a representative
invasive mucinous breast cancer tissue sample. b Magnified illustra-
tion of the boxed region shown in (a). Positive DIG-reaction in ISH
indicating decorin expressing cells can be seen in purple. Asterisks in
(b) indicate areas of invasive cancer cells. Note that these areas do not
express decorin mRNA and all detected decorin mRNA is located in
the original stromal cells. a scale bar 100 lm, b scale bar 50 lm
168
Histochem Cell Biol (2013) 139:161–171 Fig. 5 Invasive mucinous carcinoma cells of human breast lack
decorin gene expression. a ISH for decorin of a representative Fig. 4 Cells of invasive ductal cancer (IDC) of human breast are
negative for decorin mRNA. a ISH of an infiltrating ductal breast
carcinoma GIII tissue sample. b Magnified illustration of the boxed
region shown in (a). Positive DIG-reaction of stromal cells in ISH
indicating the localization of decorin mRNA can be seen in purple. Asterisks in (b) indicate areas of infiltrating cancer cells that are
negative for decorin gene expression. Note that all decorin mRNA
within invasive cancer tissue sample is detected in the original
stromal cells, not in the cancer cells. a scale bar 100 lm, b scale bar
50 lm Fig. 5 Invasive mucinous carcinoma cells of human breast lack
decorin gene expression. Effect of adenoviral decorin transduction
on MCF7 cells The
decreased proliferation of decorin-transduced MCF7 cells,
on the other hand, is most likely mediated via decorin’s
ability to antagonize receptor tyrosine kinases, particularly
the signaling through epidermal growth factor receptor
(Hu et al. 2009), the receptor for hepatocyte growth factor
called Met (Goldoni et al. 2009), insulin-like growth factor
receptor (Iozzo et al. 2011) and/or vascular endothelial
growth factor 2 receptor (Khan et al. 2011). In addition,
induction of apoptotic features of MCF7 cells due to
decorin transduction may also have a role in the finding of
this study that decorin-transduced MCF7 human breast
cancer cells exhibit decreased proliferation. Interestingly, compared to control MCF7 cells, decorin-transduced
MCF7 cells exhibited statistically significantly lower
mitosis rate, and they also revealed increased apoptotic
features such as the formation of the so-called cannibal
cells. Earlier, it has been shown in mice that decorin gene
delivery decreases the proliferative index (Pucci-Minafra
et al. 2008) and alters the architecture and differentiation of
the tumor xenografts, thereby retarding the growth of colon
and squamous cell carcinomas (Reed et al. 2002). Using an
animal model of orthotopic breast carcinoma, decorin has
also been shown to slow mammary carcinoma cell motility,
induce significant apoptosis and impede cell invasion
through a three-dimensional extracellular matrix (Goldoni
et al. 2008). The mechanism(s) of action of decorin transduction on
the behavior of MCF7 human breast cancer cells was not in
our focus in this study and therefore remains to be
explored. However, the observed decreased cell cohesion
of MCF7 cells in response to decorin transduction could be
caused by modulated pericellular matrix around the cells,
because previously decorin has been shown to influence
cellular adhesion via its capability to interact e.g., with
fibronectin (Winnemo¨ller et al. 1991) and thrombospondin 12 3 3 Histochem Cell Biol (2013) 139:161–171 168 exogenous decorin core protein has been shown to inhibit
cancer growth by triggering apoptosis via activation of
caspase-3 (Seidler et al. 2006). Finally, decorin’s ability to
bind and block transforming growth factor-b should be
kept in mind (Yamaguchi et al. 1990), although trans-
forming growth factors have been shown not to act as
major growth regulators of MCF7 cells (Herman and
Katzenellenbogen 1994). Effect of adenoviral decorin transduction
on MCF7 cells a, b scale bar 50 lm, c scale bar
10 lm, **p \ 0.001, Student’s t test
Histochem Cell Biol (2013) 139:161–171
169 t
c Magnified illustration of cannibal cells from figure (a). Arrows
indicate the presence of cannibal cells after Ad-Dcn transduction of
MCF7 cells. d Number of observed mitoses per 100 cells, 2 days after
in vitro incubation with Ad vectors. a, b scale bar 50 lm, c scale bar
10 lm, **p \ 0.001, Student’s t test Fig. 6 Decorin
gene transduction
mediated
by a
recombinant
adenovirus has a significant effect on the growth pattern and
proliferation of MCF7 cells. HE staining of MCF7 cell cultures
transduced with human decorin cDNA-containing adenovirus (Ad-
Dcn) (a) and lacZ gene-contaning adenovirus (Ad-LacZ) (b). c Magnified illustration of cannibal cells from figure (a). Arrows
indicate the presence of cannibal cells after Ad-Dcn transduction of
MCF7 cells. d Number of observed mitoses per 100 cells, 2 days after
in vitro incubation with Ad vectors. a, b scale bar 50 lm, c scale bar
10 lm, **p \ 0.001, Student’s t test the early stages of this study. Financially, this study was supported by
Medical Research Fund (EVO) of Turku University Hospital, Cancer
Foundation of South-Western Finland, and by grant from the Finnish
Breast Cancer Group. epithelial tumors. By introducing a decorin producing
adenoviral vector to the MCF7 human breast adenocarci-
noma cells, we have also shown that decorin transduction
in these decorin-negative cells results in marked changes in
their behavior. Specifically, we have shown that decorin-
transduced MCF7 cells exhibit decreased cell cohesion and
statistically significantly lower mitosis rate and increased
apoptotic features. Thus, our study provides evidence that
targeted decorin transduction to breast cancer cells could
be used as a novel adjuvant therapy in the treatment of
human breast cancer in the future. Open Access
This article is distributed under the terms of the
Creative Commons Attribution License which permits any use, dis-
tribution, and reproduction in any medium, provided the original
author(s) and the source are credited. Al Haj Zen A, Lafont A, Durand E et al (2003) Effect of adenovirus-
mediated overexpression of decorin on metalloproteinases, tissue
inhibitors of metalloproteinases and cytokines secretion by
human gingival fibroblasts. Matrix Biol 22:251–258 Effect of adenoviral decorin transduction
on MCF7 cells a ISH for decorin of a representative
invasive mucinous breast cancer tissue sample. b Magnified illustra-
tion of the boxed region shown in (a). Positive DIG-reaction in ISH
indicating decorin expressing cells can be seen in purple. Asterisks in
(b) indicate areas of invasive cancer cells. Note that these areas do not
express decorin mRNA and all detected decorin mRNA is located in
the original stromal cells. a scale bar 100 lm, b scale bar 50 lm Fig. 5 Invasive mucinous carcinoma cells of human breast lack
decorin gene expression. a ISH for decorin of a representative
invasive mucinous breast cancer tissue sample. b Magnified illustra-
tion of the boxed region shown in (a). Positive DIG-reaction in ISH
indicating decorin expressing cells can be seen in purple. Asterisks in
(b) indicate areas of invasive cancer cells. Note that these areas do not
express decorin mRNA and all detected decorin mRNA is located in
the original stromal cells. a scale bar 100 lm, b scale bar 50 lm exogenous decorin core protein has been shown to inhibit
cancer growth by triggering apoptosis via activation of
caspase-3 (Seidler et al. 2006). Finally, decorin’s ability to
bind and block transforming growth factor-b should be
kept in mind (Yamaguchi et al. 1990), although trans-
forming growth factors have been shown not to act as
major growth regulators of MCF7 cells (Herman and
Katzenellenbogen 1994). In conclusion, by utilizing ISH with DIG-labeled probes
for decorin, we have shown that in human breast cancer,
the cancer cells do not express decorin mRNA, but the
expression of decorin takes place merely in cells of the
original stroma both in healthy human breast tissue and in
breast tissues containing benign or malignant breast 123 169 Histochem Cell Biol (2013) 139:161–171 Fig. 6 Decorin
gene transduction
mediated
by a
recombinant
adenovirus has a significant effect on the growth pattern and
proliferation of MCF7 cells. HE staining of MCF7 cell cultures
transduced with human decorin cDNA-containing adenovirus (Ad-
Dcn) (a) and lacZ gene-contaning adenovirus (Ad-LacZ) (b). c Magnified illustration of cannibal cells from figure (a). Arrows
indicate the presence of cannibal cells after Ad-Dcn transduction of
MCF7 cells. d Number of observed mitoses per 100 cells, 2 days after
in vitro incubation with Ad vectors. References Acknowledgments
The authors are grateful to Ms. Minnamaija
Lintunen, PhD, for the validation of the immunohistochemical sta-
inings. The expert technical assistance of Ms. Sinikka Kollanus is
gratefully acknowledged. Ms. Henriikka Saloma¨ki, MSc, is also
gratefully acknowledged for her excellent technical assistance during Al Haj Zen A, Lafont A, Durand E et al (2003) Effect of adenovirus-
mediated overexpression of decorin on metalloproteinases, tissue
inhibitors of metalloproteinases and cytokines secretion by
human gingival fibroblasts. Matrix Biol 22:251–258 123 12 123 170 Histochem Cell Biol (2013) 139:161–171 Alowami S, Troup S, Al-Haddad S et al (2003) Mammographic
density is related to stroma and stromal proteoglycan expression. Breast Cancer Res 5:R129–R135 Hu Y, Sun H, Owens RT et al (2009) Decorin suppresses prostate
tumor growth through inhibition of epidermal growth factor and
androgen receptor pathways. Neoplasia 11(10):1042–1053 Araki K, Wakabayashi H, Shintani K et al (2009) Decorin suppresses
bone metastasis in a breast cancer cell line. Oncology 77:92–99 Hynes RO (2009) The extracellular matrix: not just pretty fibrils. Science 326:1216–1219 Iozzo RV, Sanderson RD (2011) Proteoglycans in cancer biology,
tumour microenvironment and angiogenesis. J Cell Mol Med
15:1013–1031 Biaoxue R, Xiguang C, Hua L et al (2011) Decreased expression of
decorin and p57(KIP2) correlates with poor survival and lymphatic
metastasis in lung cancer patients. Int J Biol Markers 26:9–21 Iozzo RV, Schaefer L (2010) Proteoglycans in health and disease:
novel regulatory signalling mechanisms evoked by the small
leucine-rich proteoglycans. FEBS J 277:3864–3875 Bostro¨m P, So¨derstro¨m M, Palokangas T et al (2009) Analysis of
cyclins A, B1, D1 and E in breast cancer in relation to tumour
grade and other prognostic factors. BMC Res Notes 2:140 Brown LF, Guidi AJ, Schnitt SJ et al (1999) Vascular stroma
formation in carcinoma in situ, invasive carcinoma, and meta-
static carcinoma of the breast. Clin Cancer Res 5:1041–1056 Iozzo RV, Chakrani F, Perrotti D et al (1999) Cooperative action of
germline mutations in decorin and p53 accelerates lymphoma
tumorigenesis. Proc Natl Acad Sci USA 96:3092–3097 Burdall SE, Hanby AM, Lansdown MRJ, Speirs V (2003) Breast
cancer cell lines: friend of foe? Breast Cancer Res 5:89–95 Iozzo RV, Buraschi S, Genua M et al (2011) Decorin anatagonizes
IGF-IR function by interfering with IGF-IR activity and
attenuating downstream signaling. References J Biol Chem 286:34712–
34721 Cawthorn TR, Moreno JC, Dharsee M et al (2012) Proteomic
Analyses reveal high expression of decorin and endoplasmin
(HSP90B1) are associated with breast cancer metastasis and
decreased survival. PLoS One 7:e30992 Ja¨rvela¨inen H, Sainio A, Koulu M et al (2009) Extracellular matrix
molecules: potential targets in pharmacotherapy. Pharmacol Rev
61:198–223 Daley WP, Peters SB, Larsen M (2008) Extracellular matrix dynamics
in development and regenerative medicine. J Cell Sci 121:
255–264 Khan GA, Girish GV, Lala N et al (2011) Decorin is a novel VEGFR-
2-binding antagonist for the human extravillous trophoblast. Mol
Endocrinol 25:1431–1443 Danielson KG, Baribault H, Holmes DF et al (1997) Targeted
disruption of decorin leads to abnormal collagen fibril morphol-
ogy and skin fragility. J Cell Biol 136:729–743 Kilpinen S, Autio R, Ojala K et al (2008) Systematic bioinformatic
analysis of expression levels of 17,330 human genes across
9,783 samples from 175 types of healthy and pathological
tissues. Genome Biol 9:R139 Ellis P, Schnitt S, Sastre-Garau X et al (2003) WHO classification of
tumours pathology and genetics of tumours of the breast and
female genital organs. IARC Press, Lyon, pp 9–59 Leygue E, Snell L, Dotzlaw H et al (2000) Lumican and decorin are
differentially expressed in human breast carcinoma. J Pathol
2000:313–320 Eshchenko T, Rykova V, Chernakov A et al (2007) Expression of
different proteoglycans in human breast tumors. Biochemistry
(Moscow) 72:1016–1020 Lu P, Weaver VM, Werb Z (2012) The extracellular matrix: a
dynamic niche in cancer progression. J Cell Biol 196:395–406 Ferdous Z, Peterson SB, Tseng H et al (2010) A role for decorin in
controlling proliferation, adhesion, and migration of murine
embryonic fibroblasts. J Biomed Mater Res A 93:419–428 Marastoni S, Ligresti G, Lorenzon E et al (2008) Extracellular matrix:
a matter of life and death. Connect Tissue Res 3:203–206 Fisher LW, Termine JD, Young MF (1989) Deduced protein sequence
of bone small proteoglycan I (biglycan) shows homology with
proteoglycan II (decorin) and several nonconnective tissue
proteins in a variety of species. J Biol Chem 264:4571–4576 Nash MA, Deavers MT, Freedman RS (2002) The expression of
decorin in human ovarian tumors. Clin Cancer Res 8:1754–1760 Neill T, Painter H, Buraschi S et al (2012) Decorin antagonizes the
angiogenic network: concurrent inhibition of Met, hypoxia
inducible factor 1a, vascular endothelial growth factor A, and
induction of thrombospondin-1 and TIMP3. References J Biol Chem
287:5492–5506 Geyer F, Marchio C, Reis-Filho J (2009) The role of molecular
analysis in breast cancer. Pathology 41:77–88 Goldhirsch A, Ingle JN, Gelber RD et al (2009) Thresholds for
therapies: highlights of the St Gallen international expert
consensus on the primary therapy of early breast cancer 2009. Ann Oncol 20:1319–1329 Pucci-Minafra I, Cancemi P, Di Cara G et al (2008) Decorin
transfection induces proteomic and phenotypic modulation in
breast cancer cells 8701-BC. Connect Tissue Res 49:30–41 Reed CC, Gauldie J, Iozzo RV (2002) Suppression of tumorigenicity
by adenovirus-mediated gene transfer of decorin. Oncogene
21:3688–3695 Goldoni S, Iozzo RV (2008) Tumor microenvironment: modulation
by decorin and related molecules harboring leucine-rich tandem
motifs. Int J Cancer 123:2473–2479 Goldoni S, Seidler DG, Heath J et al (2008) An antimetastatic role for
decorin in breast cancer. Am J Pathol 173:844–855 Reed CC, Waterhouse A, Kirby S et al (2005) Decorin prevents
metastatic spreading of breast cancer. Oncogene 24:1104–1110 Rozario T, DeSimone DW (2010) The extracellular matrix in
development and morphogenesis: a dynamic review. Dev Biol
341:126–140 Goldoni S, Humphries A, Nystro¨m A et al (2009) Decorin is a novel
antagonistic ligand of the Met receptor. J Cell Biol 18:743–754 Gu Y, Zhang S, Wu Q et al (2010) Differential expression of decorin,
EGFR and cyclin D1 during mammary gland carcinogenesis in
TA2 mice with spontaneous breast cancer. J Exp Clin Cancer
Res 29:6 Saloma¨ki HH, Sainio AO, So¨derstro¨m M et al (2008) Differential
expression of decorin by human malignant and benign vascular
tumors. J Histochem Cytochem 56:639–646 Santra M, Mann DM, Mercer EW et al (1997) Ectopic expression of
decorin protein core causes a generilized growth suppression in
neoplastic cells of various histogenetic origin and requires
endogenous p21, an inhibitor of cyclin-dependent kinases. J Clin
Invest 100:149–157 Guidetti G, Bertoni A, Viola M et al (2002) The small proteoglycan
decorin supports adhesion and activation of human platelets. Blood 100:1707–1714 Herman ME, Katzenellenbogen BS (1994) Alterations in transform-
ing growth factor-alpha and –beta production and cell respon-
siveness during the progression of MCF-7 human breast cancer
cells to estrogen-autonomous growth. Cancer Res 54:5867–5874 Seidler DG, Dreier R (2008) Decorin and its galactosaminoglycan
chain: extracellular regulator of cellular function? IUBMB Life
60:729–733 Hielscher AC, Qiu C, Gerecht S (2012) Breast cancer cell-derived
matrix supports vascular morphogenesis. References Am J Physiol Cell
Physiol 302:C1243–C1256 Seidler DG, Goldoni S, Agnew C et al (2006) Decorin protein core
inhibits in vivo cancer growth and metabolism by hindering 12 3 Histochem Cell Biol (2013) 139:161–171 171 epidermal growth factor receptor function and triggering apop-
tosis via caspase-3 activation. J Biol Chem 281:26408–26418 associated with poor outcome in node-negative invasive breast
cancer. Clin Cancer Res 9:207–214 Shintani K, Matsumine A, Kusuzaki K et al (2008) Decorin
suppresses lung metastases of murine osteosarcoma. Oncol
Rep 19:1533–1539 Wilcox JN (1993) Fundamental principles of in situ hybridization. J Histochem Cytochem 41:1725–1733 J Histochem Cytochem 41:1725–1733 Wilkinson GW, Akrigg A (1992) Constitutive and enhanced expres-
sion from the CMV major IE promoter in a defective adenovirus
vector. Nucleic Acids Res 20:2233–2239 Skandalis SS, Labropoulou VT, Ravazoula P et al (2011) Versican but
not decorin accumulation is related to malignancy in mammo-
graphically detected high density and malignant-appearing
microcalcifications in non-palpable breast carcinomas. BMC
Cancer 11:314 Winnemo¨ller M, Schmidt G, Kresse H (1991) Influence of decorin on
fibroblast adhesion to fibronectin. Eur J Cell Biol 34:10–17 Winnemo¨ller M, Scho¨n P, Vischer P, Kresse H (1992) Interactions
between thrombospondin and small proteoglycan decorin: inter-
ference with cell attachment. Eur J Cell Biol 59:47–55 Theocharis AD, Skandalis SS, Tzanakakis GN, Karamanos NK
(2010) Proteoglycans in health and disease: novel roles for
proteoglycans in malignancy and their pharmacological target-
ing. FEBS J 277:3904–3923 World Health Organization Fact sheet N334, November 2009 Yamaguchi Y, Mann DM, Ruoslahti E (1990) Negative regulation of
transforming growth factor-beta by the proteoglycan decorin. Nature 346:281–284 g
Tralha˜o JG, Schaefer L, Micegova M et al (2003) In vivo selective
and distant killing of cancer cells, using adenovirus-mediated
decorin gene transfer. FASEB J 17:464–466 Zhang X, Ding L, Sandford AJ (2005) Selection of reference genes
for gene expression studies in human neutrophils by real-time
PCR. BMC Mol Biol 6:4 Troup S, Njue C, Kliewer EV et al (2003) Reduced expression of
small leucine-rich proteoglycans, lumican, and decorin is 12 123
|
https://openalex.org/W2954604515
|
https://europepmc.org/articles/pmc6687668?pdf=render
|
English
| null |
Partial trisomy 21 map: Ten cases further supporting the highly restricted Down syndrome critical region (HR‐DSCR) on human chromosome 21
|
Molecular genetics & genomic medicine
| 2,019
|
cc-by
| 9,929
|
O R I G I N A L A R T I C L E O R I G I N A L A R T I C L E © 2019 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc. Correspondence Correspondence
Allison Piovesan, Department of
Experimental, Diagnostic and Specialty
Medicine (DIMES), Unit of Histology,
Embryology and Applied Biology,
University of Bologna, via Belmeloro 8,
40126 Bologna (BO), Italy. Email: allison.piovesan2@unibo.it Abstract Background: Down syndrome (DS) is characterized by the presence of an extra
full or partial human chromosome 21 (Hsa21). An invaluable model to define geno-
type‐phenotype correlations in DS is the study of the extremely rare cases of partial
(segmental) trisomy 21 (PT21), the duplication of only a delimited region of Hsa21
associated or not to DS. A systematic retrospective reanalysis of 125 PT21 cases
described up to 2015 allowed the creation of the most comprehensive PT21 map and
the identification of a 34‐kb highly restricted DS critical region (HR‐DSCR) as the
minimal region whose duplication is shared by all PT21 subjects diagnosed with DS. We reanalyzed at higher resolution three cases previously published and we accu-
rately searched for any new PT21 reports in order to verify whether HR‐DSCR limits
could prospectively be confirmed and possibly refined. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original
work is properly cited.
© 2019 Th A h
M l
l
G
i
& G
i M di i
bli h d b Wil
P i di
l
I Received: 15 October 2018 |
Accepted: 22 May 2019
DOI: 10.1002/mgg3.797 Received: 15 October 2018 |
Accepted: 22 May 2019
DOI: 10.1002/mgg3.797 Received: 15 October 2018 |
Accepted: 22 May 2019 Maria Chiara Pelleri1 | Elena Cicchini1 | Michael B. Petersen2,3 | Lisbeth Tranebjærg4,5 |
Teresa Mattina6 | Pamela Magini7 | Francesca Antonaros1 | Maria Caracausi1 |
Lorenza Vitale1 | Chiara Locatelli8 | Marco Seri9 | Pierluigi Strippoli1 |
Allison Piovesan1
| Guido Cocchi10 Maria Chiara Pelleri1 | Elena Cicchini1 | Michael B. Petersen2,3 | Lisbeth Tranebjærg4,5 |
Teresa Mattina6 | Pamela Magini7 | Francesca Antonaros1 | Maria Caracausi1 |
Lorenza Vitale1 | Chiara Locatelli8 | Marco Seri9 | Pierluigi Strippoli1 |
Allison Piovesan1
| Guido Cocchi10 Maria Chiara Pelleri1 | Elena Cicchini1 | Michael B. Petersen2,3 | Lisbeth Tranebjærg4,5 |
Teresa Mattina6 | Pamela Magini7 | Francesca Antonaros1 | Maria Caracausi1 |
Lorenza Vitale1 | Chiara Locatelli8 | Marco Seri9 | Pierluigi Strippoli1 |
Allison Piovesan1
| Guido Cocchi10 1Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna,
Bologna (BO), Italy Bologna (BO), Italy
2Department of Genetics, Aalborg University Hospital, Aalborg, Denmark
3Department of Clinical Genetics, Aalborg University, Aalborg, Denmark
4Department of Clinical Genetics/Rigshospitalet, The Kennedy Centre, Glostrup, Denmark
5University of Copenhagen, Institute of Clinical Medicine, The Panum Institute, Copenhagen N, Denmark
6Department of Pediatrics, Medical Genetics University of Catania, Italy
7Medical Genetics Unit, St. Orsola‐Malpighi Polyclinic, Bologna (BO), Italy
8Neonatology Unit, St. Orsola‐Malpighi Polyclinic, Bologna (BO), Italy
9Medical Genetics Unit, Department of Medical and Surgical Sciences (DIMEC), St. Orsola‐Malpighi Polyclinic, University of Bologna, Bologna (BO), Italy
10Neonatology Unit, Department of Medical and Surgical Sciences (DIMEC), St. Orsola‐Malpighi Polyclinic, University of Bologna, Bologna (BO), Italy rms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original 1 |
INTRODUCTION Following multiple case reports of individuals with PT21
in the 70s–90s, the concept of "Down syndrome critical re-
gion" (DSCR) arose, with different grades of support from
different authors (reviewed in (Pelleri et al. (2016)). Systematic
attempts were then published in 2009 to identify "critical re-
gions" on Hsa21 for several distinct phenotypes observed in
DS, exploiting the availability of a larger number of cases
(Korbel et al., 2009; Lyle et al., 2009). We have recently pro-
posed a systematic reanalysis of all described PT21 cases
(from 1973 to 2015) by building an integrated, comparative
map of 125 cases with or without DS fulfilling stringent cyto-
genetic and clinical criteria (Pelleri et al., 2016). An innova-
tion was also the use of the diagnosis of DS as the phenotype
to be mapped, thus focusing on the Hsa21 minimal duplicated
region shared by all the subjects diagnosed with DS, whose
most constant features are ID and some facial phenotypes,
that is oblique eyes and flat nasal bridge. The thorough re-
analysis and comparison of the data available over several de-
cades required the correction and update of cytogenetic band
boundaries as well as of relative order and exact position of
many genomic markers, integration of analyses subsequently
performed in the course of years on the same identifiable
subjects even if reported by different authors, corrections
of incongruencies in clinical classification or cytogenetic
characterization, and removal of cases with any residual un-
certainty in the presentation of data. This approach finally
allowed the inclusion or exclusion of fine Hsa21 sequence
intervals as candidates for DS, also integrating duplication
copy number variants (CNVs) data. The main result was
the identification of a highly restricted DSCR (HR‐DSCR)
of only 34 kilobases (kb) on distal 21q22.13 as the minimal
region whose duplication is shared by all DS subjects and
is absent in all non‐DS subjects, containing no known gene
and with relevant homology only to the chimpanzee genome
(Pelleri et al., 2016). In 1959 Lejeune, Gautier, and Turpin showed that human
chromosome 21 (Hsa21) is present in an extra copy (tri-
somy 21) in the cells of subjects with Down syndrome (DS,
OMIM #190685) (Lejeune, Gauthier, & Turpin, 1959), the
most common constitutional form of intellectual disability
(ID) (Gardiner et al., 2010; Menghini, Costanzo, & Vicari,
2011; Tolksdorf & Wiedemann, 1981). K E Y W O R D S computational biology, Down syndrome, highly restricted Down syndrome critical region, human
chromosome 21, intellectual disability, partial trisomy 21 Radius S.r.l.—Technology for life (www. radiustech.it). Radius S.r.l.—Technology for life (www. radiustech.it). Results: The PT21 map now integrates fine structure of Hsa21 sequence intervals
of 132 subjects onto a common framework fully consistent with the presence of a
duplicated HR‐DSCR, on distal 21q22.13 sub‐band, only in DS subjects and not in
non‐DS individuals. No documented exception to the HR‐DSCR model was found. Conclusions: The findings presented here further support the association of the HR‐
DSCR with the diagnosis of DS, representing an unbiased validation of the original
model. Further studies are needed to identify and characterize genetic determinants
presumably located in the HR‐DSCR and functionally associated to the critical mani-
festations of DS. Funding information Funding information
MCP's fellowship has been co‐funded
by a donation from Fondazione Umano
Progresso, Milano, Italy and by donations
following the international fundraising
initiative by Vittoria Aiello and
Massimiliano Albanese. The fellowship for
EC has been funded by Centro Universitario
Cattolico, Italy. The fellowship for FA has
been funded by Illumia S.p.A. (Bologna,
Italy). The fellowships for MC and AP have
been funded by the Fondazione Umano
Progresso, Matteo and Elisa Mele and Methods: Hsa21 partial duplications of three PT21 subjects were refined by adding
array‐based comparative genomic hybridization data. Seven newly described PT21
cases fulfilling stringent cytogenetic and clinical criteria have been incorporated into
the PT21 integrated map. | 1 of 14
wileyonlinelibrary.com/journal/mgg3 Mol Genet Genomic Med. 2019;7:e797. https://doi.org/10.1002/mgg3.797 2 of 14 PELLERI et al. 1 |
INTRODUCTION Although Hsa21 has
the smallest number of genes among the human autosomal
chromosomes (Piovesan, Caracausi, Antonaros, Pelleri, &
Vitale, 2016), it has been difficult to link the function of spe-
cific Hsa21 genes to distinct phenotypic features of subjects
with DS, whose more constant manifestations are a typical
facies (oblique eyes, flat nasal bridge) and ID, together with
other variable signs and symptoms (Epstein, 1989; Gardiner
et al., 2010; Hickey, Hickey, & Summar, 2012; Letourneau
& Antonarakis, 2012; Megarbane et al., 2009; Roizen &
Patterson, 2003; Strippoli et al., 2013). An invaluable model for linking genotype and phenotype
in DS is the study of the extremely rare cases of partial (seg-
mental) trisomy 21 (PT21), the duplication of only a delim-
ited segment of Hsa21 associated or not to DS. PT21 was first
reported by Ilbery and coll. (Ilbery, Lee, & Winn, 1961) as
"incomplete trisomy" and has been widely studied by meth-
ods with an increasing power of resolution in order to estab-
lish correlations between the gene content of the duplicated
segment and the associated signs and symptoms (reviewed in
(Pelleri et al., 2016)). These studies have strongly supported
the concept that not all Hsa21 loci are required for the mani-
festation of DS, as anticipated by Lejeune who hypothesized
the presence of a few "culprits among so many innocents" on
Hsa21 because if most of the genes would produce harm when
in triplicate, "trisomic children would not survive at all. Few
of the accelerated reactions are dangerous" (Lejeune, 1990). 3 of 14 PELLERI et al. TABLE 1
Summarized data about partial trisomy 21 cases mapped here. Cases 1–3 were reanalyzed here, cases 4 and 7–10 were newly described and reviewed here, cases 5 and 6 were the two
additionally retrieved cases. Sex and age: as in the first report about the subject; M: male; F: female. Map ID here: identification numbers as reported in Tables S1 and S2
Case no. Subject
Diagnosis
Sex
Age
Karyotype
Method
Country
Reference
Map ID in
Pelleri et al. (2016)
Map ID here
1
MP01
DS
M
6.5 yrs
46,XY,dup(21)(q22.1‐‐>qter) de
novo
Banding
Southern Blot
Array‐CGH (here)
Denmark
McCormick et al. (1989),
Petersen et al. (1990)
#043
#044
2
MP03
Non‐DS
F
25 yrs
46,XX,dup(21)(q11.2‐‐>q21.2)
pat de novo
Banding
Southern Blot
Array‐CGH (here)
Denmark
McCormick et al. (1989),
Petersen et al. When a similar systematic approach has been applied to
congenital heart disease (CHD) in subjects with DS, a more
distal region has been shown to be associated to CHD in DS,
possibly with different limits according to the specific type of
CHD, in the context of a multifactorial model (Pelleri et al.,
2017). These findings further support the specificity of the
results previously obtained for the HR‐DSCR that appears to
be more proximal, well‐delimited, and monofactorial in its
association to the diagnosis of DS. in the previous map. These three reanalyzed cases are num-
bered here from 1 to 3 (Table 1); the correspondence with
previous map identifiers ("Map ID" in (Pelleri et al., 2016))
and with updated map identification numbers ("Map ID
here") is reported in Table 1. Array–based comparative genomic hybridization (array‐
CGH) analysis was performed on DNA from three patients
by using two different Agilent Technologies platforms
(Agilent Technologies, Santa Clara, CA), following the
manufacturer's protocol: SurePrint G3 Unrestricted CGH
ISCA v2, with an average resolution of 60 kb, for MP01
and MP03 (cases 1 and 2, Table 1), and Human Genome
CGH 60k Oligo Microarray Kit, with a median spatial res-
olution of 41.5 Kb, for proband case number 3 (Table 1). A
graphical visualization of the results was provided by the
Genomic Workbench software v.7.0 for the three patients
and aberrations were called by the ADM1 algorithm with
threshold at 6.0. Further studies are needed to confirm that HR‐DSCR is
really functionally associated to the critical manifestations
of DS, and in particular to ID. While research is in progress
to identify functioning loci still unknown but possibly pres-
ent in the HR‐DSCR, it is also fundamental to continue the
study of any new cases of PT21 and to refine the limits of
the trisomic Hsa21 portions in cases already studied at low
resolution. The confirmation that there is no documented
exception to the HR‐DSCR model would further encourage
molecular studies in this small segment of Hsa21 as well as
high resolution analysis to investigate some very interesting
cases reported in 90s: they are five phenocopies (people with
DS phenotype and no evidence of cytogenetic/molecular
alteration) (Ahlbom et al., 1996; Anneren & Edman, 1993;
McCormick et al., 1989) and the opposite condition of appar-
ent full trisomy 21 without DS phenotype (Avramopoulos et
al., 1997). No marker through high resolution techniques was
analyzed within the HR‐DSCR, therefore the possibility that
a very small Hsa21 region might be involved in the expres-
sion of basic DS features cannot be excluded. 2.2 | Bibliographic searches and
case selection We accurately searched for any reports of PT21 to integrate
the new data in the previous PT21 map. Bibliographic searches performed to build the starting map
(Pelleri et al., 2016) were repeated in order to identify newly
reported cases of PT21. "Mirror duplication chromosome
21" was used as additional PubMed query on the National
Center for Biotechnology Information (NCBI) site (https://
www.ncbi.nlm.nih.gov/pubmed/) and references cited in turn
in the retrieved reports were examined. In addition, a search
for "partial trisomy 21" through Google web search engine
(https://www.google.com/) was performed. Due to the rarity of these particular cases as well as of
PT21 cases, an international collaborative effort would be de-
sirable in order to perform cutting‐edge analysis and collect
new data. Only new PT21 subjects with sufficient and unambiguous
descriptions at the cytogenetic, molecular, and clinical levels
were included in the study, following inclusion and exclu-
sion criteria as previously described in detail (Pelleri et al.,
2016). Briefly, the main cytogenetic inclusion criterion was
the presence of a 21q partial duplication, excluding from the
analysis cases presenting translocations and ring Hsa21 with
a complete 21q, tetrasomies of Hsa21, mosaic trisomy 21,
chromosomal rearrangements involving the X chromosome,
and chromosomal alterations described in leukemic cell
clones. For the molecular analysis criteria, the condition was
a detailed and unambiguous description of the duplicated seg-
ment boundaries. At the clinical level, subjects were classi-
fied as "DS" or "non‐DS" according to the following criteria:
(a) explicit statements found in the study; (b) whether authors
judged recognizable DS as present or absent, irrespectively
of other symptoms or signs associated to possibly concur-
rent aneuploidies of non‐Hsa21 chromosomal segments; (c)
assessment of detailed phenotype description when present
in the article. In this light, the aim of this study was to reanalyze at
higher resolution three cases already included in the PT21
integrated map in order to verify whether this analysis could
help in confirming and refining the limits of the HR‐DSCR. In addition, we accurately searched for any new reports of
PT21 subsequent to the original study to integrate the new
data in the existing PT21 map searching again for confirma-
tion or rejection of the original model. This second approach
is of particular relevance because, being a prospective study
started after the first description of HR‐DSCR, it represents
an unbiased validation of the original model that could also
be performed in the future. 1 |
INTRODUCTION (1990)
#045
#046
3
Proband
Non‐DS
F
1 yr
47,XX,+der(21),t(9;21)
(34.1;q22.1)mat
Banding
FISH
Array‐CGH (here)
Italy
Mattina et al. (1997)
#076
#077
4
B.B. DS
M
6 yrs
t(15;21)
Banding
Array‐CHG
Alabama (US)
Finley et al. (1965),
Hamm et al. (2015)
—
#002
5
Proband
DS
M
5 yrs
46,XY, idic(21)(q22.3)
FISH
India
Sheth et al. (2007)
—
#105
6
Patient
DS
F
2 yrs
46,XX, psu idic(21) (q22.3)
Banding
FISH
Japan
Egashira et al. (2008)
—
#108
7
Proband
DS
M
2 mos
46,XY,der20t(20,21)
(21qter‐>21q22::20p13‐>21qter)
Banding
FISH
Array‐CGH
Poland
Biaduń‐Popławska et al. (2014)
—
#127
8
Patient
Non‐DS
F
5 yrs
46,XX,
dup21q22.11(chr21:32,583,901‐
35,355,969;hg19)
Array‐CGH
Colorado (US)
Weisfeld‐Adams et al. (2016)
—
#130
9
Case 1
Non‐DS
F
2 yrs
46,XX, dup(21) q22.2q22.3
Banding
Array‐CGH
Taiwan
Su et al. (2016)
—
#131
10
Case 2
Non‐DS
F
14 mos
46, XX, dup(21)q11.2q21
Banding
Array‐CGH
Taiwan
Su et al. (2016)
—
#132 4 of 14 PELLERI et al. 2.4 We revised and updated all the sequence features of Hsa21
reported to build the starting map (Pelleri et al., 2016) (here
Table S1): known Hsa21 genes, coordinates for single nu-
cleotide polymorphisms (SNPs), sequence‐tagged sites,
bacterial artificial chromosome clones, nucleotide posi-
tions determined by array‐CGH as limits of altered regions
in individual subjects and cytogenetic band limits. All the
genomic coordinates refer to the current Genome Reference
Consortium (GRC) human genome assembly GRCh38, or
hg38 (December 2013). (
)
The third reanalyzed case (case 3 in Table 1) was first
reported in 1997 (Mattina et al., 1997) and we present clini-
cal data from the follow‐up of the patient here. The proband
is the only child of nonconsanguineous parents, born at the
40th week of gestation with eutocic delivery after an un-
complicated pregnancy; low‐risk triple test; birth weight was
3,020 g. The child was admitted to hospital for the first time
at birth due to neonatal asphyxia and dysmorphic signs. The
traditional karyotype through fluorescence in situ hybridiza-
tion (FISH) was: 47, XX, +der21, t(9;21), but the patient was
recognized as affected by a chromosomal syndrome due to
a double partial trisomy 9q34.1‐>qter, 21pter‐>21q22.11. She was repeatedly admitted to the polyclinic due to frequent
bronchopneumonic episodes and apnea crises. She is cur-
rently followed by annual follow‐up at the Medical Genetics
Clinic. In agreement with the parents, clinical controls are
carried out only within the limits of the "availability" of the
girl. The girl shows a clinical picture with characteristics in
agreement with partial trisomy 9q. Apparently, there are no
clinical signs attributable to partial trisomy 21. Dysmorphic
signs include brachycephaly, small anteverted ears with sim-
ple pavillon, straight forehead, divergent strabismus, propto-
sis, beak nose deviated to the left with narrow bridge, short
philtrum, and "carp" mouth with thin lips. Prognathism, long
and thin arms, hands and feet with arachnodactyly, and bi-
lateral patella dislocation were also observed. Congenital
malformations involved the heart (ventricular sept defect),
brain (hypoplasia of the corpus callosum and subarachnoid
space dilation), eyes (proptosis, nystagmus, divergent stra-
bismus, pupil optic nerve pallor and hypoplasia, the patient
underwent surgery to correct ectopia of crystalline lens and
cataracts developed over years), skeleton (additional thoracic
metameres with corresponding costal segments) and kidneys
(hypoplasia‐dysplasia of the left kidney). 2.4 During neonatal
period and the first year of life, the patient did not thermo-
regulate and showed significant apnea crises, serious psychic In summary, each spreadsheet row corresponds to a spe-
cific and relevant sequence feature on Hsa21 for a total of
724 sequence intervals (rows), providing anchor points useful
to homogeneously map each cytogenetic feature described in
the reports of PT21. 2.3 Descriptions of seven cases (summary in Table 1, cases
4–10) retrieved by the new bibliographic search performed
and mapped here have been reported in detail in the respec-
tive reports (Biaduń‐Popławska et al., 2014; Egashira et al.,
2008; Finley, Finley, Rosecrans, & Phillips, 1965; Hamm,
Carroll, Mikhail, Korf, & Finley, 2015; Sheth et al., 2007; Su
et al., 2016; Weisfeld‐Adams, Tkachuk, Maclean, Meeks, &
Scott, 2016). Main clinical data of the reanalyzed or reviewed cases are
summarized in Table 1. Briefly, the first two reanalyzed cases were subjects
MP01 and MP03 (cases 1 and 2, Table 1). They were
firstly reported in 1989 (McCormick et al., 1989) and
1990 (Petersen et al., 1990). According to the checklist of
Jackson et al. (Jackson, North, & Thomas, 1976), a pheno-
typic score consistent with the clinical diagnosis of DS was
reported for patient MP01, while patient MP03's pheno-
typic score is below the threshold for the clinical diagnosis
of DS (Petersen et al., 1990). 2.1 | Molecular cytogenetic characterization 2.1 | Molecular cytogenetic characterization 2.1 | Molecular cytogenetic characterization
In order to update the PT21 map (125 PT21 cases with or
without DS) previously published (Pelleri et al., 2016), we
reanalyzed at higher resolution three cases already included In order to update the PT21 map (125 PT21 cases with or
without DS) previously published (Pelleri et al., 2016), we
reanalyzed at higher resolution three cases already included 5 of 14 PELLERI et al. The cases thus retrieved were numbered starting from 4
to 10 following chronological order of first description in
literature. and motor deficits, muscle hypotonia and hypotrophy, and
afinalistic and uncoordinated hand movements. She pro-
nounces "mom" and "dad", does not deambulate. Menarche
was reported in September, 2009; irregular menstrual cycle. She presents with hand tremor. 2.5 For each subject studied, a column on the map file built as
explained above was added, representing the structure of his/
her Hsa21. Each row represents a specific sequence inter-
val on Hsa21. Starting from the 125 PT21 cases previously
described (Pelleri et al., 2016), we added refined limits of
the duplicated portion for cases 1–3 to the map and mapped
the additionally retrieved cases found with additional biblio-
graphic searches performed here (Table 1, cases 4–10). Each row represents a specific sequence interval on Hsa21
and for each subject with DS the corresponding cell was col-
ored following this code: red = trisomic, therefore possible
candidate as causing DS; green = disomic, therefore excluded
as causing DS; blue = monosomic, considered as "not dupli-
cated", therefore excluded as candidate; white = information
not available with certainty. A complementary reasoning
was used to color the cells representing sequence intervals
when the subject presented cytogenetically with a segmental
trisomy 21 in absence of a typical DS picture. In particular:
red = disomic in non‐DS, therefore not excluded as causing 6 of 14 PELLERI et al. DS; green = trisomic in non‐DS, therefore excluded as caus-
ing DS; blue = monosomic, considered as "not duplicated",
therefore indirectly not excluded as candidate; white = in-
formation not available with certainty. Headings of non‐DS
cases are highlighted in yellow. 2.6 | Scoring system Using "mirror duplication chromosome 21" as additional
PubMed query (Pelleri et al., 2016) and examining references
cited in turn in the retrieved reports led to the retrieval of
two additional PT21 cases (Egashira et al., 2008; Sheth et
al., 2007) to be included here according to selection criteria
detailed above (Table 1, cases 5 and 6). A score was assigned to each interval sequence substantially
following the scoring system applied by Lyle and coll. (Lyle
et al., 2009), but attributing a lower score to not excluded
regions in non‐DS subjects due to the fact that these regions
would only be candidate regions indirectly. A score of +1 was assigned to each trisomic (candidate)
sequence interval in DS subjects, while +0.5 was assigned to
disomic (not excluded) intervals in non‐DS subjects. A score
of −1 was assigned to each sequence interval that was ex-
cluded as candidate for DS, being disomic in DS or trisomic
in non‐DS subjects. Monosomic regions are considered as
"not duplicated", therefore they should be excluded as candi-
dates in DS subjects (score = −1) and indirectly not excluded
in non‐DS (score = +0.5). For each sequence interval, the
algebraic sum of the scores is calculated, generating the final
score for the interval. The Excel macro and the Python scripts
implementing the described algorithms for the calculations
of the scores and for summarizing scores along Hsa21 regular
intervals, respectively, are available upon request. In addition, a search for "partial trisomy 21" through
Google web search engine revealed a new described PT21
report case (Biaduń‐Popławska et al., 2014) not included in
PubMed to be included according to matching selection cri-
teria (Table 1, case 7) detailed above. In total, seven cases were added to the map (Table S1)
following the new bibliographic search performed and inclu-
sion/exclusion criteria described in Materials and Methods
section. A complete list of all retrieved included and excluded
reports of PT21 cases is available in the Supplementary
References file. The complete description of all these PT21
cases is available in the Table S2, along with reasons for in-
clusion and exclusion. Higher scores indicate increased probability of associa-
tion to DS. Detailed partial and final scores for each interval
are reported in Table S1 at the right of the columns represent-
ing mapping for the 132 analyzed cases. 3 |
RESULTS Scores for association with DS for each sequence interval
are graphed in Figure 4. Complete data for each distinct se-
quence interval placed in the map are given in Table S1. 3.3 The updated integrated comparative map obtained as de-
scribed in the Materials and Methods section showing the
localization of segmental anomalies of Hsa21 includes a total
of 132 PT21 DS or non‐DS cases. 3.2 | Bibliographic searches Bibliographic searches performed to build the starting map
(Pelleri et al., 2016) were repeated in order to identify newly
reported cases of PT21, resulting in four newly described
PT21 cases to be included (Table 1, cases 4 and 8–10) (Finley
et al., 1965; Hamm et al., 2015; Su et al., 2016; Weisfeld‐
Adams et al., 2016). These new limits have been recorded in the Table S1. 3.1 | Molecular cytogenetic characterization The array‐CGH analysis of DNA from patient MP01 (case
1, Map ID here #044) revealed a duplication of Hsa21 from
36,760,100 to 46,329,175 bp (GRCh38) (Figure 1). Analysis of the PT21 comparative map confirmed the ex-
clusion of several regions of Hsa21 as associated to DS, in
particular 21p, 21q11, and 21q21. Highest scores were found
in the 21q22.13 and 21q22.2 sub‐bands (Figure 4). The 34‐kb
interval from 37,929,229 to 37,963,130 previously described
as the minimal region associated to DS and located on distal
21q22.13 (Pelleri et al., 2016), still has the highest scores,
even when considering pure positively candidate scores not
integrated with penalization/exclusion scores (Table S1). In
addition, the duplication of this region is shared by all 92 DS
subjects with available data about it and is absent in all 40
non‐DS subjects with available data about it, thus confirming
consistency with the HR‐DSCR. The array‐CGH analysis of DNA from patient MP03 (case 2,
Map ID here #046) revealed trisomy of Hsa21 from 14,112,687
to 28,015,203 bp (GRCh38) (Figure 2). The array did not allow
evaluation of the Hsa21 portion upstream the proximal limit. Regarding case 3 (Map ID here #077), duplications
of about 13.4 megabases (Mb) in the 9q33.3‐q34.3 chro-
mosome region, of about 0.45 Mb in the 9q34.3 chromo-
some region, and of about 19 Mb in the 21q11.2‐q22.11
chromosomal region have been highlighted. According to
ISCN 2016 nomenclature, the alterations may be described
as:
arr[GRCh38]
9q33.3‐q34.3(123265569_136502696)
x3,
9q34.3(137666340_138059636)x3,
21q11.2‐
q22.11(13268071_32197958)x3 (Figure 3). A concise, sample outlook of a portion of the map is de-
picted in Figure 5a, showing in particular the three reana-
lyzed cases (Table 1, cases 1–3; #044, #046, #077 Map ID These new limits have been recorded in the Table S1. 7 of 14 PELLERI et al. |
7 of 14
PELLERI et al. FIGURE 1
Array‐CGH analysis of DNA from patient MP01. Profile of chromosome 21 showing the duplication from 36,760,100 to
46,329,175 bases present in MP01 (reanalyzed case 1). Genomic coordinates refer to the current GRCh38 human assembly FIGURE 1
Array‐CGH analysis of DNA from patient MP01. Profile of chromosome 21 showing the duplication from 36,760,100 to
46,329,175 bases present in MP01 (reanalyzed case 1). 3.1 | Molecular cytogenetic characterization Genomic coordinates refer to the current GRCh38 human assembly here), two additionally retrieved cases (Table 1, cases 5 and
6; #105 and #108 Map ID here), and the five newly described
cases (Table 1, cases 4 and 7–10; #002, #127, #130, #131,
#132 Map ID here). PT21 cases has turned into the study of distinct phenotypic
features, in order to associate each of them to a specific re-
gion most constantly duplicated in subjects presenting with
the feature (Korbel et al., 2009; Korenberg et al., 1994; Lyle
et al., 2009). This approach has certainly been successful in
suggesting that specific Hsa21 subregions of various sizes are
mostly associated to hypotonia (Lyle et al., 2009), to acute
megakaryoblastic leukemia and transient myeloproliferative
disorder (Korbel et al., 2009; Pelleri et al., 2014), and to CHD
(Pelleri et al., 2017), among others. Due to high frequency of
an Alzheimer‐like disease in DS and the location of the APP
(amyloid beta precursor protein) gene on Hsa21, this pheno-
type represents a particularly suggestive example of the use-
fulness of PT21 study in defining genetic determinants for a
phenotypic feature. Recently, it has been possible to confirm 4 |
DISCUSSION Over time, the concept of a "Down syndrome critical region"
on Hsa21 has assumed different meanings. It was mainly
criticized observing that a certain single duplicated region is
not responsible for all or most DS features, that is, it is not
sufficient to cause the full DS phenotype (Korbel et al., 2009;
Lyle et al., 2009; Papoulidis et al., 2014). From this point of
view, modeling the genotype‐phenotype correlations using 8 of 14 PELLERI et al. 8 of 14 |
PELLERI et al. FIGURE 2
Array‐CGH analysis of DNA from patient MP03. Profile of chromosome 21 showing the duplication from 14,112,687 to
28,015,203 bases present in MP03 (reanalyzed case 2). Genomic coordinates refer to the current GRCh38 human assembly FIGURE 2
Array‐CGH analysis of DNA from patient MP03. Profile of chromosome 21 showing the duplication from 14,112,687 to
28,015,203 bases present in MP03 (reanalyzed case 2). Genomic coordinates refer to the current GRCh38 human assembly observed in DS may be absent in a proportion of the subjects,
even at a high extent, ID and the typical facies are virtually
universal, if cases with mosaicism are excluded. The genetic
marker associated to these features should be, in principle,
robust as the extra copy of the whole Hsa21. Dissection of
small regions allowed by the variety of breakpoints delimit-
ing duplicated regions in subjects with PT21 has repeatedly
pointed to 21q22 band as associated to DS. Our systematic
reanalysis of cytogenetic maps from 125 subjects with PT21,
integrating them under a common and updated framework,
has suggested that the duplication of a small 34‐kb region on
distal 21q22.13 (HR‐DSCR) is fully coherent with the diag-
nosis of DS, while the disomic state of this region is consis-
tent with a non‐DS phenotype (Pelleri et al., 2016). the obligatory role of APP in the clinical, biochemical, and
neuropathological findings of Alzheimer‐like disease study-
ing a case of PT21 with DS and without Alzheimer disease,
lacking the APP duplication (Doran et al., 2017). In addition to the search for genotype‐phenotype correla-
tions aimed at dissecting single phenotypes, a few features
regularly present at the highest frequency in subjects with
DS can be considered so that the DSCR is viewed as the re-
gion which "suffices to induce the main phenotypic symp-
toms of the classic syndrome of trisomy 21" (Rethore, 1981). |
9 o
PELLERI et al. FIGURE 3
Array‐CGH analysis of DNA from patient #077. Profile of chromosomes 9 and 21 showing the duplication of chromosome
9 from 123,265,569 to 136,502,696 and from 137,666,340 to 138,059,636 bases and the duplication of chromosome 21 from 13,268,071 to
32,197,958 present in case #077 (reanalyzed case 3). Genomic coordinates refer to the current GRCh38 human assembly FIGURE 3
Array‐CGH analysis of DNA from patient #077. Profile of chromosomes 9 and 21 showing the duplication of chromosome
9 from 123,265,569 to 136,502,696 and from 137,666,340 to 138,059,636 bases and the duplication of chromosome 21 from 13,268,071 to
32,197,958 present in case #077 (reanalyzed case 3). Genomic coordinates refer to the current GRCh38 human assembly In this work, we have tested if the HR‐DSCR limits could
be refined by reanalyzing PT21 cases already included in the
integrated map, and also if this model is prospectively consis-
tent with additional PT21 cases not described at the moment
of building the original map. Regarding the reanalysis, we were successful in delineating
duplicated regions from subjects MP01 (case 1, Map ID here
#044), MP03 (case 2, Map ID here #046), and proband case
number 3 (Map ID here #077), whose DNA was originally
investigated by McCormick and coll. (McCormick et al.,
1989), Petersen and coll. (Petersen et al., 1990), and Mattina
and coll. (Mattina et al., 1997), respectively, and in this work
has been subjected to array‐CGH. The array‐CGH analysis was
able to clarify the breakpoints of the trisomic portions. The
refinement of the limits in these reanalyzed cases was fully
consistent with the previous reports and was fully consistent
with the trisomic state of HR‐DSCR in the subject with DS
and its disomic state in the subjects without a diagnosis of DS. FIGURE 4
Genotype–phenotype
correlation in 132 cases of partial trisomy
21. The X‐axis displays the score for
association with DS for each sequence
interval of 50 kb, shown as median of the
values assigned to each map row (Table
S1) that is comprised in each interval. The
Y‐axis represents the position along Hsa21
(scale in megabases, Mb) FIGURE 4
Genotype–phenotype
correlation in 132 cases of partial trisomy
21. The X‐axis displays the score for
association with DS for each sequence
interval of 50 kb, shown as median of the
values assigned to each map row (Table
S1) that is comprised in each interval. 4 |
DISCUSSION Therefore, using the diagnosis of DS itself as the phenotype
to be mapped, the PT21 approach should point to the "mini-
mal" Hsa21 region associated to the DS core features, notably
ID. Actually, while any of the long list of symptoms and signs 9 of 14 PELLERI et al. | A zoom‐in (b) of the case (#116
here and #113 in the previous study (Pelleri et al., 2016)) and the CNV (nsv1060057) strictly defining HR‐DSCR limits are shown here. Rows:
Hsa21 sequence intervals (only those centered on HR‐DSCR are represented here). Red = candidate or not excluded regions; green = excluded
regions. Levels of overlapping among intervals are indicated by increasingly darker violet color of the coordinates; blue italics indicate coordinates
overlapping (Start or End) or nesting (Start and End) with the immediately previous interval (row). HR‐DSCR coordinates: 37,929,229–37,963,130. Complete map is available as Table S1 Interestingly, the girl with a duplication of 2.78 Mb of
chromosome 21q22.11 (Table 1, case 8) (Weisfeld‐Adams
et al., 2016) was considered borderline and without a clear
diagnosis of DS. Regarding the two most constant features,
the typical facies and the characteristic ID, the observation of
the girl's picture (Figure 1 in (Weisfeld‐Adams et al., 2016):
absence of oblique eyes and of gestalt recognition of the typi-
cal DS facies assessed through blind, independent evaluation
by the clinicians involved in this work) and the phenotypic
description lead to the non‐DS classification of the patient. In addition, the author reporting the case stated that, although
showing some grade of developmental delay, the patient
"lacked the happy, sociable affect observed in many children
with DS". These findings are consistent with the lack of HR‐
DSCR in this subject. Regarding the verification of new cases, we accurately
checked for any new reports published in the last two years
and thus not considered in the original PT21 map. We further
found five recent detailed descriptions (Table 1, cases 4 and
7–10) and two previously described cases not included in the
original PT21 map (Table 1, cases 5 and 6) fulfilling criteria
for the inclusion on the PT21 integrated map. Each of them
deserved a specific publication due to the extreme rarity of
each of these cases. The stringent criteria that we have defined
for the establishment of genotype‐phenotype correlations in
this type of study (Pelleri et al., 2016) have been very use-
ful to guide the analysis of these new cases. The
Y‐axis represents the position along Hsa21
(scale in megabases, Mb) In this work, we have tested if the HR‐DSCR limits could
be refined by reanalyzing PT21 cases already included in the
integrated map, and also if this model is prospectively consis-
tent with additional PT21 cases not described at the moment
of building the original map. investigated by McCormick and coll. (McCormick et al.,
1989), Petersen and coll. (Petersen et al., 1990), and Mattina
and coll. (Mattina et al., 1997), respectively, and in this work
has been subjected to array‐CGH. The array‐CGH analysis was
able to clarify the breakpoints of the trisomic portions. The
refinement of the limits in these reanalyzed cases was fully
consistent with the previous reports and was fully consistent
with the trisomic state of HR‐DSCR in the subject with DS
and its disomic state in the subjects without a diagnosis of DS. Regarding the reanalysis, we were successful in delineating
duplicated regions from subjects MP01 (case 1, Map ID here
#044), MP03 (case 2, Map ID here #046), and proband case
number 3 (Map ID here #077), whose DNA was originally 4 | 10 of 14 PELLERI et al. 10 of 14 |
PELLERI et al. 10 of 14 |
PELLERI et al. FIGURE 5
Concise outlook (a) of a portion of the partial trisomy 21 map. Each column represents the chromosome 21 structure (in
megabases, Mb) of partial trisomy 21 subjects with or without Down syndrome (DS or non‐DS). For each subject the case number (n.), the updated
map identifier (ID) and the corresponding previous map ID if present (Pelleri et al., 2016) are reported. The ten cases reanalyzed or reviewed
here are reported together with Map ID #116 and the duplication coded as structural variant nsv1060057 which delimited the proximal and distal
highly restricted DS critical region (HR‐DSCR, red continuous line) boundaries, respectively. Red boxes, candidate or not excluded regions; green
boxes, excluded regions; white boxes: information not available with certainty; blue boxes, monosomic regions. A zoom‐in (b) of the case (#116
here and #113 in the previous study (Pelleri et al., 2016)) and the CNV (nsv1060057) strictly defining HR‐DSCR limits are shown here. Rows:
Hsa21 sequence intervals (only those centered on HR‐DSCR are represented here). Red = candidate or not excluded regions; green = excluded
regions. Levels of overlapping among intervals are indicated by increasingly darker violet color of the coordinates; blue italics indicate coordinates
overlapping (Start or End) or nesting (Start and End) with the immediately previous interval (row). HR‐DSCR coordinates: 37,929,229–37,963,130. Complete map is available as Table S1 | FIGURE 5
Concise outlook (a) of a portion of the partial trisomy 21 map. Each column represents the chromosome 21 structure (in
megabases, Mb) of partial trisomy 21 subjects with or without Down syndrome (DS or non‐DS). For each subject the case number (n.), the updated
map identifier (ID) and the corresponding previous map ID if present (Pelleri et al., 2016) are reported. The ten cases reanalyzed or reviewed
here are reported together with Map ID #116 and the duplication coded as structural variant nsv1060057 which delimited the proximal and distal
highly restricted DS critical region (HR‐DSCR, red continuous line) boundaries, respectively. Red boxes, candidate or not excluded regions; green
boxes, excluded regions; white boxes: information not available with certainty; blue boxes, monosomic regions. A zoom‐in (b) of the case (#116
here and #113 in the previous study (Pelleri et al., 2016)) and the CNV (nsv1060057) strictly defining HR‐DSCR limits are shown here. Rows:
Hsa21 sequence intervals (only those centered on HR‐DSCR are represented here). Red = candidate or not excluded regions; green = excluded
regions. Levels of overlapping among intervals are indicated by increasingly darker violet color of the coordinates; blue italics indicate coordinates
overlapping (Start or End) or nesting (Start and End) with the immediately previous interval (row). HR‐DSCR coordinates: 37,929,229–37,963,130. Complete map is available as Table S1 FIGURE 5
Concise outlook (a) of a portion of the partial trisomy 21 map. Each column represents the chromosome 21 structure (in
megabases, Mb) of partial trisomy 21 subjects with or without Down syndrome (DS or non‐DS). For each subject the case number (n.), the updated
map identifier (ID) and the corresponding previous map ID if present (Pelleri et al., 2016) are reported. The ten cases reanalyzed or reviewed
here are reported together with Map ID #116 and the duplication coded as structural variant nsv1060057 which delimited the proximal and distal
highly restricted DS critical region (HR‐DSCR, red continuous line) boundaries, respectively. Red boxes, candidate or not excluded regions; green
boxes, excluded regions; white boxes: information not available with certainty; blue boxes, monosomic regions. that variability both in Hsa21 (Sailani et al., 2013) or in other
chromosomes (Priest et al., 2012) originating from CNVs or
SNPs also contributes to both normal and DS phenotypes
(Antonarakis, 2017). Moreover, the HR‐DSCR might function as a long‐range
interactor with other chromosomes, although preliminary
analysis of databases derived from high‐throughput chromo-
some conformation capture data (Hi‐C) (Durand et al., 2016)
was not able to retrieve useful results (data not shown). An
interesting possibility is to generate trisomy 21 cells with the
selective deletion of a single copy of the HR‐DSCR to com-
pare the features of fully trisomic, HR‐DSCR deleted and
normal cells to prove that the critical region is exerting some
function, for example, modifying the metabolic profile that
has recently been found to be specifically altered in DS by
metabolome analysis (Caracausi et al., 2018). The descrip-
tion of the CRISPR/Cas9 method (Bauer, Canver, & Orkin,
2015) may make the realization of such a sophisticated study
model realistic (Harrison, Sanz, & Hollywood, 2016). (
,
)
A relevant problem remains to be the identification and
characterization of the genetic determinants presumably lo-
cated in the HR‐DSCR. Gene databases, as well as accurate
transcriptome maps based on the use of known probes to ob-
tain gene expression profiling data for organs involved in DS
phenotypes such as hippocampus (Caracausi et al., 2016) or
heart (Caracausi, Piovesan, Vitale, & Pelleri, 2017) might be
of limited help in the hypothesis that the genetic determinants
are presently uncharacterized. It is still possible that, due to
the possible extremely low size of human introns (Piovesan
et al., 2015), one or more spliced transcripts originate from
this small region. RNA high‐throughput sequencing (Wang,
Gerstein, & Snyder, 2009) or ENCODE (Encyclopedia of
DNA Elements) project (ENCODE Project Consortium,
2012) data may offer the possibility to identify novel func-
tional elements; however, we have not had to date success in
using them to the aim of a better characterization of the HR‐
DSCR. Other possibilities include the presence of unknown
microRNA in the HR‐DSCR (Kozomara & Griffiths‐Jones,
2014), as the field of non‐coding RNA involved in DS patho-
genesis has been recently explored (Karaca et al., 2017; Xu
et al., 2013; Zhao, Jaber, Percy, & Lukiw, 2017) revealing
the functions of several microRNA located on other Hsa21
regions with the capability to potentially regulate over 3,600
protein‐encoding genes (Alexandrov, Percy, & Lukiw, 2017;
Li et al., 2012; Quinones‐Lombrana & Blanco, 2015). Therefore, while a relevant body of cytogenetic data ob-
tained from the analysis of PT21 cases strongly suggests that
there should be some critical elements for the pathogenesis
of DS present in the distal part of the 21q22.13 sub‐band,
further studies are needed for additional verification of the
limits of the region in any case of PT21 reported in the future
as well as for the characterization of functional loci within it. The success of these objectives might be critical to build a
rational foundation for a treatment of DS ID. In conclusion, the findings presented here represent the
most comprehensive study on PT21 and further support the
association of the HR‐DSCR with the diagnosis of DS, rep-
resenting an unbiased validation of the original model that
could be performed also in the future. Further studies are
needed to identify and characterize genetic determinants pre-
sumably located in the HR‐DSCR and functionally associ-
ated to the critical manifestations of DS. ,
; Q
,
)
While this work was in revision, an update in the Ensembl
and UCSC genome browsers actually mapped two small new
exons on the KCNJ6 locus (OMIM # 600877) encoding po-
tassium voltage‐gated channel subfamily J member 6, based
on automated parsing of high throughput RNA sequencing
(RNA‐Seq) data. Remarkably, this predicts a size extension
for the KCNJ6 locus from 292,216 bp as currently reported
in NCBI Gene database (coordinates 37,624,223–37,916,438
in human genome map GRCh38.p12) to 497,787 bp
(37,623,559–38,121,345). This transcript allows the predic-
tion of a new intron which totally encompasses HR‐DSCR
and preliminary experimental data confirm the existence of
this intron. Interestingly, according to RNA‐Seq Expression
Data from GTEx as reported in the UCSC browser, this tran-
script appears to be expressed at a high level in the brain and
in the pituitary gland, in particular in the cerebellum, hip-
pocampus, and cortex within the brain, regions well known
for their specific alteration in DS (Stagni, Giacomini, Emili,
Guidi, & Bartesaghi, 2018). While this update suggests the
presence of transcribed DNA in the HR‐DSCR for the first
time, further work will be necessary to characterize structure
and function of this complex locus. ACKNOWLEDGMENTS As DIMES and Neonatology Unit group, we are profoundly
grateful to the Fondazione Umano Progresso, Milano, Italy
for their fundamental support to the research on trisomy 21
and to this study. We also wish to sincerely thank Matteo and
Elisa Mele; Illumia S.p.A., Bologna, Italy; Radius S.r.l.—
Technology for life (www.radiustech.it); the community
of Dozza (Bologna, Italy): "Comitato Arzdore di Dozza",
"Parrocchia di Dozza", and "Pro‐Loco di Dozza" as well as
the Costa family for their support to our research. Very spe-
cial thanks to the newlyweds Leonardo Costa and Camilla
Casadio for the donation in occasion of their holy matrimony
in Dozza. We are grateful to Kirsten Welter for her kind and
expert revision of the manuscript. Correlation of
the clinical data to the cytogenetic map was consistent with
the notion that all the subjects lacking the duplication of the
HR‐DSCR were not diagnosed with DS, although these new
cases did not allow further refinement of the region because
the breakpoints of the duplicated portions were not within it. Remarkably, cases 1 and 9 (Figure 5a) alone would be suffi-
cient to exclude very large portions of Hsa21 as associated
to the diagnosis of DS delimiting a region of about 2.8 Mb
(36,760,100–39,605,955) in which the HR‐DSCR is located
in the center. Taken together, all the findings presented here further
support the concept that the distal part of the 21q22.13 sub‐
band is strongly associated to diagnosis of DS while other
regions are not, and they were all consistent with the HR‐
DSCR model, although the limits of the reported duplications
did not allow further refinement of the region or the con-
firmation of its narrowest extension. It should also be noted 11 of 14 PELLERI et al. REFERENCES org/10.1111/j.1442-200X.2008.02680.x Ahlbom, B. E., Goetz, P., Korenberg, J. R., Pettersson, U., Seemanova,
E., Wadelius, C., … Anneren, G. (1996). Molecular analysis of chro-
mosome 21 in a patient with a phenotype of Down syndrome and ap-
parently normal karyotype. American Journal of Medical Genetics,
63(4),
566–572. https://doi.org/10.1002/(sici)1096-8628(19960
628)63:4<566:aid-ajmg10>3.0.co;2-g ENCODE Project Consortium. (2012). An integrated encyclopedia of
DNA elements in the human genome. Nature, 489(7414), 57–74. https://doi.org/10.1038/nature11247 Epstein, C. J. (1989). Down syndrome, trisomy 21. Metabolic basis of
inherited disease (pp. 291–326). New York, NY: McGraw‐Hill. Finley, S. C., Finley, W. H., Rosecrans, C. J., & Phillips, C. (1965). Exceptional intelligence in a Mongoloid child of a family with a
13–15/partial 21 (D/partial G) translocation. New England Journal
of Medicine, 272, 1089–1092. https://doi.org/10.1056/nejm196505
272722102 Alexandrov, P. N., Percy, M. E., & Lukiw, W. J. (2017). Chromosome
21‐encoded microRNAs (mRNAs): Impact on Down's syndrome and
trisomy‐21 linked disease. Cellular and Molecular Neurobiology,
38(3), 769–774. https://doi.org/10.1007/s10571-017-0514-0 Anneren, G., & Edman, B. (1993). Down syndrome–a gene dosage dis-
ease caused by trisomy of genes within a small segment of the long
arm of chromosome 21, exemplified by the study of effects from the
superoxide‐dismutase type 1 (SOD‐1) gene. APMIS Supplementum,
40, 71–79. Gardiner, K., Herault, Y., Lott, I. T., Antonarakis, S. E., Reeves, R. H.,
& Dierssen, M. (2010). Down syndrome: From understanding the
neurobiology to therapy. Journal of Neuroscience, 30(45), 14943–
14945. https://doi.org/10.1523/jneurosci.3728-10.2010 14945. https://doi.org/10.1523/jneurosci.3728-10.2010 Hamm, J. A., Carroll, A. J., Mikhail, F. M., Korf, B. R., & Finley, W. H. (2015). Partial trisomy 21: A fifty‐year follow‐up visit. American
Journal of Medical Genetics. Part A, 167(7), 1610–1613. https://
doi.org/10.1002/ajmg.a.37031 Antonarakis, S. E. (2017). Down syndrome and the complexity of ge-
nome dosage imbalance. Nature Reviews Genetics, 18(3), 147–163. https://doi.org/10.1038/nrg.2016.154 Avramopoulos, D., Kennerknecht, I., Barbi, G., Eckert, D., Delabar, J. M.,
Maunoury, C., … Petersen, M. B. (1997). A case of apparent trisomy
21 without the Down's syndrome phenotype. Journal of Medical
Genetics, 34(7), 597–600. https://doi.org/10.1136/jmg.34.7.597 Harrison, P. T., Sanz, D. J., & Hollywood, J. A. (2016). Impact of gene
editing on the study of cystic fibrosis. Human Genetics, 135(9),
983–992. https://doi.org/10.1007/s00439-016-1693-3 Hickey, F., Hickey, E., & Summar, K. L. (2012). Medical update for
children with Down syndrome for the pediatrician and family
practitioner. Advances in Pediatrics, 59(1), 137–157. https://doi. org/10.1016/j.yapd.2012.04.006 Bauer, D. E., Canver, M. C., & Orkin, S. H. (2015). Generation of
genomic deletions in mammalian cell lines via CRISPR/Cas9. ETHICS APPROVAL The patients described here were studied in the context of di-
agnostic genetic testing at the relative Institution as described
in the original report for each subject. Durand, N. C., Robinson, J. T., Shamim, M. S., Machol, I., Mesirov,
J. P., Lander, E. S., & Aiden, E. L. (2016). Juicebox provides
a visualization system for Hi‐C contact maps with unlimited
zoom. Cell Systems, 3(1), 99–101. https://doi.org/10.1016/j. cels.2015.07.012 AUTHORS' CONTRIBUTIONS Biaduń‐Popławska, A., Jamsheer, A., Henkelman, M., Tuziak,
M., Pietrzyk, A., Piotrowski, K., … Zajączek, S. (2014). Down syndrome phenotype in a child with partial trisomy of
chromosome 21 and paternally derived translocation t (20p;
21q). General Medicine: Open Access, 02(04), https://doi. org/10.4172/2327-5146.1000149 MCP designed the study. MCP, EC, and FA collected the
data, built the integrated map, and performed the analy-
sis. MBP, LT, and TM obtained and interpreted clinical
and molecular data for the three cases reanalyzed here. PM
performed the array‐CGH analysis for two cases and inter-
preted the data. GC and CL performed case selection and
discussed the clinical data. MS analyzed and discussed the
cytogenetic data. LV and MC performed the bibliographic
data search and contributed to mapping data collection and
analysis. AP developed the scoring system, the pertinent
software and graphed the data. MCP, AP, and PS wrote
the manuscript draft. AP and GC supervised the project. All authors contributed to the discussion of the data and
to the Discussion section and read and approved the final
manuscript. Caracausi, M., Ghini, V., Locatelli, C., Mericio, M., Piovesan, A.,
Antonaros, F., … Cocchi, G. (2018). Plasma and urinary metabo-
lomic profiles of Down syndrome correlate with alteration of mi-
tochondrial metabolism. Scientific Reports, 8(1), 2977. https://doi. org/10.1038/s41598-018-20834-y Caracausi, M., Piovesan, A., Vitale, L., & Pelleri, M. C. (2017). Integrated transcriptome map highlights structural and functional
aspects of the normal human heart. Journal of Cellular Physiology,
232(4), 759–770. https://doi.org/10.1002/jcp.25471 Caracausi, M., Rigon, V., Piovesan, A., Strippoli, P., Vitale, L., &
Pelleri, M. C. (2016). A quantitative transcriptome reference map
of the normal human hippocampus. Hippocampus, 26(1), 13–26. https://doi.org/10.1002/hipo.22483 Doran, E., Keator, D., Head, E., Phelan, M. J., Kim, R., Totoiu, M.,
… Lott, I. T. (2017). Down syndrome, partial trisomy 21, and
absence of Alzheimer's disease: The role of APP. Journal of
Alzheimer's Disease, 56(2), 459–470. https://doi.org/10.3233/
jad-160836 Allison Piovesan
https://orcid.org/0000-0001-7038-5557 Egashira, M., Kondoh, T., Kawara, H., Motomura, H., Tagawa,
M., Harada, N., & Moriuchi, H. (2008). Mirror duplication
of chromosome 21 with complete phenotype of Down syn-
drome. Pediatrics International, 50(4), 597–599. https://doi. org/10.1111/j.1442-200X.2008.02680.x CONFLICT OF INTEREST The authors declare that they have no competing interests. 12 of 14 PELLERI et al. Ilbery, P. L., Lee, C. W., & Winn, S. M. (1961). Incomplete trisomy in
a mongoloid child exhibiting minimal stigmata. Medical Journal of
Australia, 48(2), 182–184. Menghini, D., Costanzo, F., & Vicari, S. (2011). Relationship between
brain and cognitive processes in Down syndrome. Behavior Genetics,
41(3), 381–393. https://doi.org/10.1007/s10519-011-9448-3 Jackson, J. F., North, E. R. 3rd, & Thomas, J. G. (1976). Clinical diag-
nosis of Down's syndrome. Clinical Genetics, 9(5), 483–487. https
://doi.org/10.1111/j.1399-0004.1976.tb01601.x Papoulidis, I., Papageorgiou, E., Siomou, E., Oikonomidou, E.,
Thomaidis, L., Vetro, A., … Vassilis, P. (2014). A patient with
partial trisomy 21 and 7q deletion expresses mild Down syndrome
phenotype. Gene, 536(2), 441–443. https://doi.org/10.1016/j. gene.2013.11.078 Karaca, E., Aykut, A., Ertürk, B., Durmaz, B., Güler, A., Büke, B., …
Çoğulu, Ö. (2017). Diagnostic role of microRNA expression pro-
file in the prenatal amniotic fluid samples of pregnant women with
Down syndrome. Balkan Medical Journal, 35(2), 163–166. https://
doi.org/10.4274/balkanmedj.2017.0511 Pelleri, M. C., Cicchini, E., Locatelli, C., Vitale, L., Caracausi, M.,
Piovesan, A., … Cocchi, G. (2016). Systematic reanalysis of partial
trisomy 21 cases with or without Down syndrome suggests a small
region on 21q22.13 as critical to the phenotype. Human Molecular
Genetics, 25, 2525–2538. https://doi.org/10.1093/hmg/ddw116 Korbel, J. O., Tirosh‐Wagner, T., Urban, A. E., Chen, X.‐N., Kasowski,
M., Dai, L., … Korenberg, J. R. (2009). The genetic architecture of
Down syndrome phenotypes revealed by high‐resolution analysis of
human segmental trisomies. Proceedings of the National Academy
of Sciences of the United States of America, 106(29), 12031–12036. https://doi.org/10.1073/pnas.0813248106 Pelleri, M. C., Gennari, E., Locatelli, C., Piovesan, A., Caracausi, M.,
Antonaros, F., … Cocchi, G. (2017). Genotype‐phenotype correla-
tion for congenital heart disease in Down syndrome through analysis
of partial trisomy 21 cases. Genomics, 109(5‐6), 391–400. https://
doi.org/10.1016/j.ygeno.2017.06.004 Korenberg, J. R., Chen, X. N., Schipper, R., Sun, Z., Gonsky, R.,
Gerwehr, S., … Disteche, C. (1994). Down syndrome phenotypes:
The consequences of chromosomal imbalance. Proceedings of the
National Academy of Sciences of the United States of America,
91(11), 4997–5001. https://doi.org/10.1073/pnas.91.11.4997 Pelleri, M. C., Piovesan, A., Caracausi, M., Berardi, A. C., Vitale, L.,
& Strippoli, P. (2014). Integrated differential transcriptome maps
of Acute Megakaryoblastic Leukemia (AMKL) in children with
or without Down Syndrome (DS). BMC Medical Genomics, 7, 63. https://doi.org/10.1186/s12920-014-0063-z Kozomara, A., & Griffiths‐Jones, S. (2014). miRBase: Annotating high
confidence microRNAs using deep sequencing data. Nucleic Acids
Research, 42(D1), D68–D73. https://doi.org/10.1093/nar/gkt1181 Petersen, M. B., Tranebjaerg, L., McCormick, M. K., Michelsen, N.,
Mikkelsen, M., & Antonarakis, S. E. (1990). Clinical, cytogenetic,
and molecular genetic characterization of two unrelated patients
with different duplications of 21q. American Journal of Medical
Genetics. Supplement, 7, 104–109. Lejeune, J. (1990). Pathogenesis of mental deficiency in trisomy 21. American Journal of Medical Genetics. Supplement, 7, 20–30. Lejeune, J., Gauthier, M., Turpin, R. (1959). Human chromosomes in
tissue cultures. Comptes Rendus Hebdomadaires Des Séances De
L'académie Des Sciences, 248(4), 602–603. Piovesan, A., Caracausi, M., Antonaros, F., Pelleri, M. C., & Vitale, L. (2016). GeneBase 1.1: a tool to summarize data from NCBI gene
datasets and its application to an update of human gene statistics. Database, 2016, baw153. https://doi.org/10.1093/database/baw153 Letourneau, A., & Antonarakis, S. E. (2012). Genomic deter-
minants in the phenotypic variability of Down syndrome. Progress in Brain Research, 197, 15–28. https://doi.org/10.1016/
b978-0-444-54299-100002-9 Piovesan, A., Caracausi, M., Ricci, M., Strippoli, P., Vitale, L., &
Pelleri, M. C. (2015). Identification of minimal eukaryotic introns
through GeneBase, a user‐friendly tool for parsing the NCBI Gene
databank. DNA Research, 22(6), 495–503. https://doi.org/10.1093/
dnares/dsv028 Li, Y. Y., Alexandrov, P. N., Pogue, A. I., Zhao, Y., Bhattacharjee, S., &
Lukiw, W. J. (2012). miRNA‐155 upregulation and complement fac-
tor H deficits in Down's syndrome. NeuroReport, 23(3), 168–173. https://doi.org/10.1097/WNR.0b013e32834f4eb4 Priest, J. R., Girirajan, S., Vu, T. H., Olson, A., Eichler, E. E., &
Portman, M. A. (2012). Rare copy number variants in isolated
sporadic and syndromic atrioventricular septal defects. American
Journal of Medical Genetics. Part A, 158A(6), 1279–1284. https://
doi.org/10.1002/ajmg.a.35315 Lyle, R., Béna, F., Gagos, S., Gehrig, C., Lopez, G., Schinzel, A., …
Antonarakis, S. E. (2009). Genotype‐phenotype correlations in
Down syndrome identified by array CGH in 30 cases of partial tri-
somy and partial monosomy chromosome 21. European Journal
of Human Genetics, 17(4), 454–466. https://doi.org/10.1038/
ejhg.2008.214 Quinones‐Lombrana, A., & Blanco, J. G. (2015). Chromosome 21‐de-
rived hsa‐miR‐155‐5p regulates mitochondrial biogenesis by tar-
geting mitochondrial transcription factor A (TFAM). Biochimica
Et Biophysica Acta (BBA)—Molecular Basis of Disease, 1852(7),
1420–1427. https://doi.org/10.1016/j.bbadis.2015.04.004 Mattina, T., Pierluigi, M., Mazzone, D., Scardilli, S., Perfumo, C.,
& Mollica, F. (1997). Double partial trisomy 9q34.1–>qter and
21pter–>q22.11: FISH and clinical findings. Journal of Medical
Genetics, 34(11), 945–948 http://jmg.bmj.com/content/34/11/945. full.pdf Rethore, M. O. (1981). Structural variation of chromosome 21 and
symptoms of Down's syndrome. In G. R. Burgio, M. Fraccaro,
L. Tiepolo, & U. Wolf (Eds.), Trisomy 21 (pp. 173–182). Berlin,
Germany: Springer‐Verlag. McCormick, M. K., Schinzel, A., Petersen, M. REFERENCES Journal of Visualized Experiments, (95), e52118. https://doi. org/10.3791/52118 13 of 14 PELLERI et al. | | 14 of 14 14 of 14 | PELLERI et al. phenotype. NPJ Genomic Medicine, 1, https://doi.org/10.1038/npjge
nmed.2016.3 Sheth, F. J., Radhakrishna, U., Morris, M. A., Blouin, J. L., Sheth,
J. J., Multani, A., & Antonarakis, E. S. (2007). Cytogenetic, mo-
lecular and FISH analysis of an isodicentric chromosome 21
idic(21)(q22.3) in a mildly‐affected patient with Down syndrome. International Journal of Human Genetics, 7(3), 215–218. https://
doi.org/10.1080/09723757.2007.11885998 Xu, Y., Li, W., Liu, X., Ma, H., Tu, Z., & Dai, Y. (2013). Analysis of
microRNA expression profile by small RNA sequencing in Down
syndrome fetuses. International Journal of Molecular Medicine,
32(5) 1115 1125 https://doi org/10 3892/ijmm 2013 1499 32(5), 1115–1125. https://doi.org/10.3892/ijmm.2013.1499 Stagni, F., Giacomini, A., Emili, M., Guidi, S., & Bartesaghi, R. (2018). Neurogenesis impairment: An early developmental defect in Down
syndrome. Free Radical Biology and Medicine, 114, 15–32. https://
doi.org/10.1016/j.freeradbiomed.2017.07.026 Zhao, Y., Jaber, V., Percy, M. E., & Lukiw, W. J. (2017). A microRNA
cluster (let‐7c, miRNA‐99a, miRNA‐125b, miRNA‐155 and
miRNA‐802) encoded at chr21q21.1‐chr21q21.3 and the phenotypic
diversity of Down's syndrome (DS; trisomy 21). Journal of Natural
Sciences, 3(9), e446. Strippoli, P., Pelleri, M. C., Caracausi, M., Vitale, L., Piovesan, A.,
Locatelli, C., … Cocchi, G. (2013). An integrated route to identify-
ing new pathogenesis‐based therapeutic approaches for trisomy 21
(Down Syndrome) following the thought of Jérôme Lejeune. Science
Postprint, 1(1), e00010. https://doi.org/10.14340/spp.2013.12R0005 B., Stetten, G., Driscoll,
D. J., Cantu, E. S., … Antonarakis, S. E. (1989). Molecular ge-
netic approach to the characterization of the "Down syndrome re-
gion" of chromosome 21. Genomics, 5(2), 325–331. https://doi. org/10.1016/0888-7543(89)90065-7 Roizen, N. J., & Patterson, D. (2003). Down's syndrome. Lancet,
361(9365),
1281–1289. https://doi.org/10.1016/
s0140-6736(03)12987-x Mégarbané, A., Ravel, A., Mircher, C., Sturtz, F., Grattau, Y., Rethoré,
M.‐O., … Mobley, W. C. (2009). The 50th anniversary of the dis-
covery of trisomy 21: The past, present, and future of research and
treatment of Down syndrome. Genetics in Medicine, 11(9), 611–
616. https://doi.org/10.1097/GIM.0b013e3181b2e34c Sailani, M. R., Makrythanasis, P., Valsesia, A., Santoni, F. A., Deutsch,
S., Popadin, K., … Antonarakis, S. E. (2013). The complex SNP and
CNV genetic architecture of the increased risk of congenital heart
defects in Down syndrome. Genome Research, 23(9), 1410–1421. https://doi.org/10.1101/gr.147991.112 SUPPORTING INFORMATION Additional supporting information may be found online
in the Supporting Information section at the end of the
article. Su, M. T., Kuan, L. C., Chou, Y. Y., Tan, S. Y., Kuo, T. C., & Kuo,
P. L. (2016). Partial trisomy of chromosome 21 without the Down
syndrome phenotype. Prenatal Diagnosis, 36(5), 492–495. https://
doi.org/10.1002/pd.4796 Tolksdorf, M., & Wiedemann, H. R. (1981). Clinical aspects of Down's
syndrome from infancy to adult life. In G. R. Burgio, M. Fraccaro, L. Tiepolo, & U. Wolf (Eds.), Trisomy 21 (pp. 3–32). Berlin, Germany:
Springer‐Verlag. How to cite this article: Pelleri MC, Cicchini E,
Petersen MB, et al. Partial trisomy 21 map: Ten cases
further supporting the highly restricted Down
syndrome critical region (HR‐DSCR) on human
chromosome 21. Mol Genet Genomic Med. 2019;7:e797. https://doi.org/10.1002/mgg3.797 How to cite this article: Pelleri MC, Cicchini E,
Petersen MB, et al. Partial trisomy 21 map: Ten cases
further supporting the highly restricted Down
syndrome critical region (HR‐DSCR) on human
chromosome 21. Mol Genet Genomic Med. 2019;7:e797. https://doi.org/10.1002/mgg3.797 Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA‐Seq: A revolution-
ary tool for transcriptomics. Nature Reviews Genetics, 10(1), 57–63. https://doi.org/10.1038/nrg2484 Weisfeld‐Adams, J. D., Tkachuk, A. K., Maclean, K. N., Meeks, N. L.,
& Scott, S. A. (2016). A de novo 2.78‐Mb duplication on chromo-
some 21q22.11 implicates candidate genes in the partial trisomy 21
|
https://openalex.org/W2989777713
|
http://www.scielo.br/pdf/reben/v72n6/0034-7167-reben-72-06-1519.pdf
|
Portuguese
| null |
Tecnologia educativa para manejo da fadiga relacionada à quimioterapia antineoplásica
| null | 2,019
|
cc-by
| 6,915
|
ORIGINAL ARTICLE RESUMO Objetivo: Construir e validar tecnologia educativa (TE) sobre fadiga e estratégias não
farmacológicas para manejo desse sintoma em pessoas com câncer em tratamento
quimioterápico antineoplásico ambulatorial. Método: Estudo metodológico composto por
três etapas: 1) elaboração da TE, utilizando o modelo teórico-metodológico de Doak, Doak
e Root; 2) validação de conteúdo e aparência por sete juízes enfermeiros, por meio do índice
de validade de conteúdo (IVC); e 3) realização de teste piloto com 10 pacientes. Resultados:
A TE “Conhecendo e lidando com a fadiga” contempla a definição de fadiga, suas causas e
as intervenções de prática de exercícios físicos, higiene do sono, conservação de energia e
intervenção comportamental. O IVC global obtido com os juízes foi de 0,95. Conclusão: A
TE apresentou validade de conteúdo e aparência para a educação em saúde com relação à
fadiga relacionada à quimioterapia antineoplásica em pacientes oncológicos ambulatoriais. Descritores: Pacotes de Assistência ao Paciente; Enfermagem Oncológica; Fadiga;
Estudos de Validação; Tecnologia Educacional. Patrícia Peres de OliveiraIII
ORCID: 0000-0002-0325-4917 I Universidade Federal do Ceará. Fortaleza, Ceará, Brazil. II Universidade Estadual do Ceará. Fortaleza, Ceará, Brazil. III Universidade Federal de São João Del Rei. Divinópolis,
Minas Gerais, Brazil. Fernanda Macedo Cartaxo FreitasI
ORCID: 0000-0002-2944-0291 Descriptors: Patient Care Bundles; Oncology Nursing; Fatigue; Validation Studies; Educational
Technology. Lia Guedes BravoII
ORCID: 0000-0002-0974-7931 How to cite this article: Perdigão MMM, Rodrigues AB, Magalhães TL,
Freitas FMC, Bravo LG, Oliveira PP. Educational technology
for fatigue management related to antineoplastic
chemotherapy. Rev Bras Enferm. 2019;72(6):1519-25. doi: http://dx.doi.org/10.1590/0034-7167-2018-0505 Marcela Maria de Melo PerdigãoI
ORCID: 0000-0001-9084-1249 Andrea Bezerra RodriguesI
ORCID: 0000-0002-2137-0663 Tayanne de Lima MagalhãesI
ORCID: 0000-0003-2511-3901 Fernanda Macedo Cartaxo FreitasI
ORCID: 0000-0002-2944-0291 ABSTRACT Objective: To construct and validate an educational technology (ET) on fatigue and non-
pharmacological strategies for the management of this symptom in people with cancer
undergoing outpatient antineoplastic chemotherapy. Method: This is a methodological
study composed of three stages: 1) elaboration of the ET using the theoretical-methodological
model of Doak, Doak and Root; 2) validation of content and appearance by seven nurses via the
content validity index (CVI); and 3) a pilot test with 10 patients. Results: The ET “Knowing and
coping with fatigue” contemplates the definition of fatigue, its causes and the interventions
of physical exercise practice, sleep hygiene, energy conservation and behavioral intervention. The overall CVI obtained with the judges was 0.95. Conclusion: The ET presented content
and appearance validity for health education regarding fatigue related to antineoplastic
chemotherapy in outpatient cancer patients. INTRODUCTION This is a three-stage methodological study. The first relates to
the construction of the instrument; the second, to the validation of
its content and appearance by judges; and the third, the pilot test. In oncology, an ever increasing number of pharmacological
and non-pharmacological strategies have been implemented
to care for patients with cancer. In spite of this, both the disease
and its therapy trigger many signs and symptoms – among
them, fatigue. The first stage took place from December 2016 to February
2017 and was guided by the theoretical and methodological
framework of Doak, Doak and Root(8), which presents some es-
sential guidelines for the construction planning of educational
materials. They are: a) defining the target audience – although
it seems to be an obvious step, it is often neglected; b) limiting
and defining the learning objectives, which must be compatible
with the desired actions and behaviors from the educational in-
tervention; c) during the construction itself, the active voice must
be used in writing, since it makes reading easier and the reader
more likely to practice the action; d) writing short sentences and
avoiding technical terms that make comprehension difficult; e)
including interactions that may make the guidelines simpler to
understand and remember; and f) testing to ensure quality(8). Cancer-related fatigue is defined as “a subjective and persis-
tent sensation of tiredness, physical, emotional and/or cognitive
exhaustion, disproportionate to any recent activity, and that does
not improve with rest and sleep, interfering in the activities of
daily living”(1). Fatigue is also described in the Nursing Diagnostic
Classification proposed by NANDA-I, described as “an overwhelm-
ing sustained sense of exhaustion and decreased capacity for
physical and mental work at the usual level”(2). This symptom is often experienced by cancer patients and
affects about 75 to 95% of them, leading to compromises of daily
living activities(3). In a study that compared adults with cancer to
another group of adults without the disease, 56% of the cancer
population experienced fatigue(4). g
q
y
After this stage, content and appearance were evaluated by
judges from March to May 2017. The next phase – the pilot study
–, occurred in the outpatient chemotherapy clinic of a university
hospital in the city of Fortaleza, Ceará, from July to August 2017. RESUMEN
Obj
i
C Objetivo: Construir y validar una tecnología educativa (TE) sobre fatiga y estrategias
no farmacológicas para el manejo del síntoma en personas con cáncer en tratamiento
quimioterápico antineoplásico ambulatorio. Método: Estudio metodológico que consta
de tres etapas: 1) elaboración de la TE utilizando el modelo teórico-metodológico de
Doak, Doak y Root; 2) validación de contenido y apariencia por siete jueces enfermeros,
por medio del índice de validez de contenido (IVC); y 3) realización de una prueba piloto
con 10 pacientes. Resultados: La TE “Conociendo y lidiando con la fatiga” contempla la
definición de fatiga, sus causas y las intervenciones con la práctica de ejercicios físicos,
la higiene del sueño, la conservación de energía y la intervención comportamental. El
IVC total obtenido con los jueces fue de 0,95. Conclusión: La TE presentó validez de
contenido y apariencia para la educación en salud con relación a la fatiga relacionada a
la quimioterapia antineoplásica en pacientes oncológicos ambulatorios. Descriptores:Paq etesdeAtenciónalPaciente EnfermeríaOncológica Fatiga Est diosde Corresponding Author:
Marcela Maria de Melo Perdigão
E-mail: marcelaperdigao@hotmail.com Submission: 06-14-2018 Approval: 04-10-2019 Descriptores: Paquetes de Atención al Paciente; Enfermería Oncológica; Fatiga; Estudios de
Validación; Tecnología Educacional. http://dx.doi.org/10.1590/0034-7167-2018-0505 1519
Rev Bras Enferm. 2019;72(6):1519-25. Educational technology for fatigue management related to antineoplastic chemotherapy
Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. INTRODUCTION Due to being a health problem, one of the obstacles related
to its detection is that patients associate fatigue with the ineffec-
tiveness of therapy – believing that it is necessary to stop it – or,
believing that fatigue indicates the evolution of the disease. Thus,
providing clarification about this symptom and its natural history
to patients is fundamental due to causing such effect, especially
patients who will undergo antineoplastic chemotherapy(5). Sample and inclusion and exclusion criteria In the selection of judges for validation of content and ap-
pearance of the educational material, the criteria proposed by
Jasper(9) were followed, which indicate that a judge must have
a body of specialized knowledge or skill, experience in the field
of practice, highly developed levels of recognition of standards
and recognition by others. Following, Pasquali’s(10) proposal was
also used, in which the number of judges must be at least six. To
avoid a tie of opinions, this study chose to adopt an odd number
of judges, establishing seven as the number of judges. Therefore, educational programs conducted by health pro-
fessionals, including the use of technologies, are fundamental
for the patient to adapt to and cope with fatigue. Counseling
should be started from the first meeting, involving orientation
on exercise practice, balancing activities and day-to-day rest,
establishing priorities and delegating tasks, relaxation techniques,
sleep hygiene measures, feeding and dietary supplementation(6). Given this context, the role of nurses stands out since non-
pharmacological interventions can reduce patient fatigue, some-
thing that has already been proven in a study about its benefit(7). Educational Technologies (ET) have contributed significantly to
support the guidance provided. Therefore, educational programs conducted by health pro-
fessionals, including the use of technologies, are fundamental
for the patient to adapt to and cope with fatigue. Counseling
should be started from the first meeting, involving orientation
on exercise practice, balancing activities and day-to-day rest,
establishing priorities and delegating tasks, relaxation techniques,
sleep hygiene measures, feeding and dietary supplementation(6). Given this context, the role of nurses stands out since non-
pharmacological interventions can reduce patient fatigue, some-
thing that has already been proven in a study about its benefit(7). Educational Technologies (ET) have contributed significantly to
support the guidance provided. Thus, the seven judges were selected according to their clinical
and scientific experience with cancer patients on chemotherapeutic
treatment through the Lattes platform of the CNPq Portal. The
search was conducted using the simple search option for subject/
keyword (oncology, health education, printed educational materials). Sampling was conducted using the snowball method: when one
participant was selected according to the established criteria, such
participant recommended another with the same characteristics. OBJECTIVE To construct and validate an educational technology on fatigue
and non-pharmacological strategies to cope with this symptom
in people with cancer undergoing outpatient antineoplastic
chemotherapy. During the pilot test stage, the sample of patients was de-
lineated based on the hospital records, being composed of 73
individuals. Considering that the suggested sample for a pilot
study to be effective is 10%(11), seven patients were calculated as
an effective number and researchers chose to work with 10 to
ensure greater efficacy. Sample selection occurred by convenience
at the outpatient chemotherapy clinic on the days of collection,
meeting the following inclusion criteria: being 18 years old or older,
15 score on the Glasgow scale and undergoing antineoplastic
chemotherapy for gastric or colorectal cancer. This last criterion
was based on a study that inferred that patients with gastric
cancer presented more fatigue(12). The Glasgow scale was applied
to ensure that the patient presented adequate level of temporal,
personal and spatial orientation, as stressed in the item “verbal RESULTS The elaboration of the first version of the instrument was made
based on 34 studies identified in the selected databases, which were
organized in the following categories: presence of fatigue in cancer
patients; health-related quality of life (HRQoL) in cancer patients
undergoing antineoplastic chemotherapy; fatigue management
by non-pharmacological methods in cancer patients undergoing
antineoplastic therapy; and interpretation of family members of
the factors that can cause fatigue. Of these, the categories “the
presence of fatigue in cancer patients” and “fatigue management
by non-pharmacological methods in cancer patients undergo-
ing antineoplastic chemotherapy” were considered relevant in
the preparation of the preliminary version of the instrument. The
educational technology named “Knowing and coping with fatigue”
(Conhecendo e lidando com a fadiga), was composed by three topics
in its final version – the last topic has four subtopics. The folder’s image design, typography, choice of colors and layout
mas made with the help of a visual arts professional. The researchers
received updates on the process to provide their feedback and ap-
proval. The art was done in the program Adobe Photoshop CC 2015. After finishing the preparation of the ET, an invitation letter was
sent to the judges with a brief presentation of the research project,
the objective to be evaluated, an explanation of the importance
of its validation for later use in practice and what would be his/her
function as a judge. After the accepting, the judges received an
informed consent form, the ET and the instrument for content and
appearance validation of the technology via e-mail. The content
and appearance validation instrument was made using the Google
Forms program. The validation questionnaire was adapted from
Oliveira, Fernandes and Sawada(15). This instrument is divided into
two parts: the first contains the characterization data on the judge,
and the second presents the instructions for completion and the
items to be evaluated (objectives, structure, presentation, relevance
and content). The judges were asked to evaluate the ET regarding
its content and appearance, with responses given by a Likert-type
scale – 1 = inadequate; 2 = partially adequate; 3 = adequate; and
4 = totally adequate(15) –, as well as a space for comments and
suggestions when options 1 and 2 were marked. On average, the
reviews were returned to researchers after 30 days. Initially, the technology explains the definition of fatigue, its
causes, and what can be done to improve the condition. Analysis of results and statistics Data were organized in a spreadsheet in the statistical soft-
ware Microsoft Excel 2007. After tabulation, data were analyzed
by descriptive statistics. To perform the agreement analysis of the experts, the Con-
tent Validity Index (CVI) method was adopted, which measures
the proportion or percentage of experts who agree on certain
aspects of an instrument and its items. This study adopted < 0.80
CVI values, i.e., equivalent to 80% agreement among the judges,
which is considered to be great for the items to be considered
validated(16). The CVI was calculated by summing the number of
responses marked as “3” or “4” by the judges and dividing the
result by the total number of responses. Moreover, the written
suggestions made by the judges were considered. Ethical aspects Following, they answered
a validation questionnaire adapted from Oliveira, Fernandes and
Sawada(15), containing instructions for completing the instru-
ment and the items to be evaluated regarding the objectives,
organization, writing style, appearance and motivation of the ET. Ethical aspects This study was approved by the Research Ethics Committee
of the Walter Cantídio University Hospital/Universidade Federal
do Ceará. Participants involved in the study signed an informed
consent form. The ethical precepts of research with human beings,
based on Resolution 466/2012 of the Brazilian National Health
Council, were respected. 1520
Rev Bras Enferm. 2019;72(6):1519-25. 1520 Educational technology for fatigue management related to antineoplastic chemotherapy
Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. Educational technology for fatigue management related to antineoplastic chemotherapy
Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. response” of the scale, as well as an adequate motor response –
another scale item – to comply some of the guidelines provided
for fatigue control, such as performing physical activities. These
items, coupled to eye opening, consistently indicate the highest
degree of integration of the central nervous system. Regarding
colorectal cancer, there are few studies that investigate the pres-
ence of fatigue in patients with this neoplasm(13). Finally, also as
an inclusion criterion, the patient should score at least 60% in
the Karnofsky index, which indicates one’s capacity to take care
of their personal needs, requiring only occasional help. Exclusion
criteria were: illiteracy; chronic pain; use of megestrol acetate or
antidepressants; and/or concomitant radiotherapy, which could
have influence on fatigue(14). Megestrol acetate use was considered
an exclusion criterion to ensure homogeneity in the sample, since
this drug may be indicated for the pharmacological treatment of
fatigue in cancer patients, improving the levels of this symptom
and increasing the sensation of well-being(6). with the judges, the instrument was applied by three trained inter-
viewers. They followed a standard operating procedure elaborated
by the authors, containing conceptual and operational definitions. Patients were guided about their participation, having their
anonymity and confidentiality of information ensured. All partici-
pants signed an informed consent form. Following, they answered
a validation questionnaire adapted from Oliveira, Fernandes and
Sawada(15), containing instructions for completing the instru-
ment and the items to be evaluated regarding the objectives,
organization, writing style, appearance and motivation of the ET. with the judges, the instrument was applied by three trained inter-
viewers. They followed a standard operating procedure elaborated
by the authors, containing conceptual and operational definitions. Patients were guided about their participation, having their
anonymity and confidentiality of information ensured. All partici-
pants signed an informed consent form. Study protocol In the first stage of construction of the instrument, a search
was made on the databases Medical Literature Analysis and
Retrieval System Online (Medline), Latin American Literature in
Health Sciences (Lilacs) and Nursing Database (Bdenf), using the
Health Sciences Descriptors (DeCS/MeSH) “fatigue”, “cancer” and
“chemotherapy”, with the Boolean term ‘and’. Studies published
from 2011 to 2016 and that were available in full were considered
for this study. In addition to searching the databases, materials
published by Brazilian Consensus on Fatigue (Consenso Brasileiro
de Fadiga)(6), Oncology Nurses Society (ONS), American Society of
Clinical Oncology (Asco) and Brazilian Cancer Institute (Instituto
Nacional de Câncer – Inca) were also used. RESULTS The last topic
covers non-pharmacological interventions for fatigue management:
“Practice physical exercises”, “Improve your sleep” and “Conserve
your energy” and a subtopic with no specific title with information
on behavioral intervention. Each of these subtopics presents an
explanation of the concept of each intervention and how to apply
each of them. Finally, part of the bibliography used is presented. After completing the elaboration of the text, the selection of
images began by performing an electronic search on Google Im-
ages; these images were sent to the visual arts professional so he
could understand the idea that the illustrations were supposed to
evoke, as they would be placed close to the texts to which they The third step refers to the pilot test performed with the patients
from an outpatient chemotherapy clinic. After the validation process Rev Bras Enferm. 2019;72(6):1519-25. 1521 Educational technology for fatigue management related to antineoplastic chemotherapy
Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. Educational technology for fatigue management related to antineoplastic chemotherapy
Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. referred, to represent some information from the ET. The text
was written in Garamond typeface, size 13 for the information,
size 14 for the subheadings and size 28 for the title of the cover,
and for subheadings and the title bold was also applied. Text
boxes were used for pieces of information that required greater
emphasis, using letter size 13 or 16 in bold or with a call for “at-
tention”. A4-size coated paper with a light-colored background
was used with black text and colored printing. rephrasing the sentence “Seek to know more about your fatigue”
to “Seek to know more about the cause(s) of your fatigue” and
to perform the necessary grammar corrections. Therefore, the
material was sent to be revised by a specialized professional. As general comments, the judges stressed the excellent pro-
posal of the ET to address a symptom that is so little known and
valued and that nurses have difficulty to approach, arousing the
need for greater knowledge of the professional. The CVI values of all items analyzed by the judges are de-
scribed in Table 1. After finishing the ET, the content and appearance validation
was performed by seven judges, all of whom were nurses and
female. RESULTS Most judges had a master’s degree (57.1%), followed
by Ph.D (28.5%); the training time of most was over 20 years
(85.7%); and the professional practice time greater than 15 years
(85.7%). Regarding professional practice, most were professors
(57.1%) and others worked in care (42.8%), considering that, of
these, 14.2% work in clinical oncology, 14.2% in palliative care
and pain, and 14.2% quality in oncology. Regarding scientific
publication, most were judges who published articles on cancer,
ET, and instrument validation (71.4%). Table 1 – Content validity index of all items (objectives, structure and
presentation, relevance and overall index), according to the analysis of the
judges, Fortaleza, Ceará, Brazil, 2017 Items
CVI
Objectives
0,93
1) Does the folder cover the needs of cancer patients
undergoing chemotherapy and facing fatigue? 1,00
2) Does the folder provide relevant information and
guidance that contributes to the health education process? 0,86
3) Is the folder effective for the maintenance of self-care
related to fatigue management? 1,00
4) Is the folder capable of promoting changes in behavior
and attitude? 0,71
5) Can the folder circulate in the scientific field in the field
of oncology? 1,00
6) Can this folder be implemented in the daily clinical practice
of a nurse who works in an outpatient chemotherapy clinic? 1,00
Structure and presentation
0,94
1) Is the information presented clearly and objectively? 1,00
2) Is the information presented scientifically correct? 0,86
3) Does the instrument have a logical sequence? 1,00
4) Is the information well structured in terms of agreement
and spelling? 1,00
5) Is the typeface adequate? 1,00
6) Is the font size adequate? 0,71
7) Is the spacing between the lines appropriate? 1,00
8) Is the instrument easy to read and to understand? 1,00
9) Are the images adequate? 0,86
10) Do the pictures depict what one actually wants to
convey as information? 1,00
Relevance
1,00
1) Is the folder effective in suggesting to the patient he/she
acquires knowledge on managing his/her fatigue at home? 1,00
2) Is the instrument relevant for guiding patients with
fatigue who are undergoing chemotherapy? 1,00
3) Is the instrument relevant to the care provided by nurses
to these patients? 1,00
4) Does this folder allow the transfer of relevant
information about fatigue between the nurse professional
and the patient undergoing chemotherapy? 1,00
Global CVI
0,95
Note: CVI = Content Validity Index Objectives The CVI result obtained for the item “objectives” was 0.93; 0.94
for structure and presentation; and 1.0 for relevance. The global
IVC score was 0.95, thus assuring the validity of the content and
appearance of the folder for use in the target population (Table 1). The CVI result obtained for the item “objectives” was 0.93; 0.94
for structure and presentation; and 1.0 for relevance. The global
IVC score was 0.95, thus assuring the validity of the content and
appearance of the folder for use in the target population (Table 1). One of the topics in “objectives”, represented by the question “Is
this folder capable of promoting changes in behavior and attitude?”,
obtained a 0.71 CVI. In the comments, the judges stated that behav-
ioral change is something more complex, requiring a more specific
indicator for evaluation, and also that the ET alone would not be able
to promote changes without proper individual follow-up. One of the topics in “objectives”, represented by the question “Is
this folder capable of promoting changes in behavior and attitude?”,
obtained a 0.71 CVI. In the comments, the judges stated that behav-
ioral change is something more complex, requiring a more specific
indicator for evaluation, and also that the ET alone would not be able
to promote changes without proper individual follow-up. Another item, represented by the question “Does the folder
provide relevant information and guidance that contributes to
the health education process?”, showed a 0.86 CVI. Two judges
classified it as “partially adequate”. One of the judges advised that
the suggestion for swimming should be removed as an interven-
tion, which was justified by these patients being immunosup-
pressed. Moreover, they stressed the importance having the
medic responsible for the patient allowing them practice physical
exercises. Another judge commented that the use of sunscreen
should be included in the guidelines for physical exercises that
are practiced outdoors. Both suggestions were followed. Regarding the “structure and presentation”, the item “Is the font
size adequate?” totaled 0.71 CVI score. The judges suggested an
increase in the font size. The judge’s suggestion was accepted. Given
the small space available, font size was increased from 12 to 13. In
the item: “Are the images adequate?”, 0.86 CVI, a judge considered
it “partially adequate”, explaining that the cover should contain the
image of an energetic person, conveying a positive message. Note: CVI = Content Validity Index Objectives This
suggestion was accepted and the image of the ET cover was modified. Still considering “structure and presentation”, in the item “Is
the typeface adequate?”, although it presented 1.0 CVI, a judge
stated that the typeface used was tiring and suggested that it
was changed to the Calibri typeface. However, the style used is
in accordance with the guidelines proposed by the theoretical
reference adopted: a serif typeface and size starting from 12. Therefore, the suggestion was not complied to. Regarding the “structure and presentation”, the item “Is the font
size adequate?” totaled 0.71 CVI score. The judges suggested an
increase in the font size. The judge’s suggestion was accepted. Given
the small space available, font size was increased from 12 to 13. In
the item: “Are the images adequate?”, 0.86 CVI, a judge considered
it “partially adequate”, explaining that the cover should contain the
image of an energetic person, conveying a positive message. This
suggestion was accepted and the image of the ET cover was modified. Global CVI Note: CVI = Content Validity Index After applying the changes proposed by the judges and the
folder was finished, the pilot test began. Of the 10 participants,
six (60%) were female, five (50%) were aged between 51 and 70
years, four (40%) had incomplete primary education, five (50%)
had colon cancer and four (40%) were undergoing the FLOX
regimen (leucovorin, oxaliplatin and 5-fluorouracil). Still considering “structure and presentation”, in the item “Is
the typeface adequate?”, although it presented 1.0 CVI, a judge
stated that the typeface used was tiring and suggested that it
was changed to the Calibri typeface. However, the style used is
in accordance with the guidelines proposed by the theoretical
reference adopted: a serif typeface and size starting from 12. Therefore, the suggestion was not complied to. Participants answered the evaluation instrument of ET, which
comprised questions about the objectives (CVI = 0.90), organization
(CVI = 1.00), writing style (CVI = 0.93), appearance (CVI = 1.00) and
motivation (CVI = 0.98). CVI was also used in this phase to ensure There were other specific questions on items with CVI great-
er than 0.80, such as changing the word “tumor” to “disease”, Rev Bras Enferm. 2019;72(6):1519-25. 1522 Educational technology for fatigue management related to antineoplastic chemotherapy
Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. Educational technology for fatigue management related to antineoplastic chemotherapy
Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. Energy conservation techniques refer to the deliberate and
planned management of activities that expend energy, thus
preventing its depletion. These strategies include planning, del-
egation, setting priorities, and scheduling activities that require
the use of high energy at peak energy times. These measures aim
to reduce energy expenditure in the activities of daily living and
are significantly effective in minimizing fatigue(6). the reliability of the results. The overall CVI was 0.95, and the validity
of content and appearance was evidenced by the target popula-
tion. A patient suggested the increase in the font size of the ET,
due to the patient’s low visual acuity. After finishing the content
and appearance validation process, the final version presents three
topics, and the last one is composed of four subtopics. In the structure and presentation aspect, the item “Is the typeface
adequate?” showed a 1.0 CVI. However, a judge suggested changing
the typeface. This was the only unaccepted suggestion, since the
theoretical reference adopted(14) points out that a serif typeface,
from size 12, is considered easy to read, allowing greater fluidity. This typeface is un-stylized, of Roman origin, with perfect circles
and balanced linear forms, making reading easier(22). Figure 1 – Final version of the educational technology for fatigue manage-
ment in cancer patients undergoing antineoplastic chemotherapy, validated
by judges and patients, Fortaleza, Ceará, Brazil, 2017 Note: CVI = Content Validity Index Figure 1 shows the final version of the ET – validated for con-
tent and appearance by the specialized judges and participants
of the pilot test – for fatigue management in cancer patients
undergoing antineoplastic chemotherapy in outpatient clinics. Likewise, behavioral intervention and sleep hygiene presented
favorable results in fatigue management, with evidence sup-
porting its use(1,6,19). A very positive aspect in this study is the long experience in
oncology of the judges, and in addition to their knowledge on
the oncology area, ET and instrument validation, the fact that
the judges are from different geographic regions of Brazil may
reflect on different ways of dealing with symptoms. Figure 1 – Final version of the educational technology for fatigue manage-
ment in cancer patients undergoing antineoplastic chemotherapy, validated
by judges and patients, Fortaleza, Ceará, Brazil, 2017 The judges considered the non-pharmacological interventions
proposed for fatigue to be relevant. One of them pointed out that,
among the physical exercises suggested as intervention, swimming
should be removed, considering that this patient population is often
immunosuppressed due to antineoplastic agents have the adverse
effect of myelosuppression, which carries the risk of a significant
increase in infections. Due to being a natural reservoir for many
pathogens, water could make the patient more susceptible to
infections. The risk of disease or infection associated with swim-
ming pools is mainly due to the fecal contamination of the water,
which may be caused by feces released by swimmers or sources
of contaminated water(20), which was confirmed in a study that
identified Cryptosporidium and Giardia in swimming pools, leading
to the occurrence of outbreaks among swimmers(21). Figure 1 – Final version of the educational technology for fatigue manage-
ment in cancer patients undergoing antineoplastic chemotherapy, validated
by judges and patients, Fortaleza, Ceará, Brazil, 2017 Still considering physical exercises, a judge stated that the guide-
lines should include instructions for the patient to ingest water, and
wear appropriate clothes and shoes when practicing exercises; the
use of sunscreen during outdoors practice was also mentioned. These suggestions were followed. It must be considered that this
study was based in the Northeast region of Brazil, with a predomi-
nantly tropical climate during the whole year, and that secondary
diseases, such as dehydration and skin cancer must be prevented. DISCUSSION The only items that did not reach CVI higher than 0.80 were “font
size” (CVI = 0.71) and “Is the folder capable of promoting changes in
behavior and attitude?” (CVI = 0.71). Regarding the font size, although
the recommendation of the adopted theorists was followed, the
judges’ suggestion was accepted, since in the pilot study with the
patients they also suggested an increase in size. Given the reduced
space available, font size was increased from 12 to 13. Although fatigue presents high prevalence and its crucial
consequences in the life of cancer patients, this condition is not
always valued by health professionals(5). The routine evaluation
of the presence of fatigue is recommended to these professionals,
from the initial diagnosis to the end of treatment(1). Regarding the item “to promote changes of behavior and at-
titude”, two judges pointed out that the ET alone would not be
capable of generating changes of behavior. We must emphasize
that the study protocol foresees a quasi-experimental study,
which corresponds to the second phase of this work. However,
the judges recognized that the ET can contribute to the health Among the non-pharmacological interventions included in the
ET as a strategy for the management of fatigue, we can highlight
physical exercises, energy conservation measures, behavioral inter-
vention and sleep hygiene. Performing physical exercises presents a
strong level of evidence about its effectiveness in the maintenance
of the symptom, with aerobics being the most suggested(6,17-18). Rev Bras Enferm. 2019;72(6):1519-25. 1523 Educational technology for fatigue management related to antineoplastic chemotherapy
Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. CONCLUSION The process of constructing the instrument was based on the
search for non-pharmacological interventions based on scientific
evidence on how to manage fatigue. The items of the instru-
ment were directed to physical exercises, energy conservation,
behavioral interventions and sleep hygiene. The purpose of written educational material is to reinforce
verbal information, act as a guideline for subsequent doubts, and
assist in decision making(25). However, these instruments must be
developed and validated to be used effectively(26). The validation process resulted in the adequacy of content and
appearance of the educational technology to guide patients on
chemotherapy-related fatigue, with a 0.95 global CVI, indicating
an excellent level of agreement among judges. Furthermore, the
target population considered the educational technology to
be useful considering its objectives, organization, writing style,
appearance and motivation, with a 95% global agreement rate. Therefore, clinical validation is foreseen in subsequent stud-
ies to evaluate the efficiency of the instrument constructed and
validated as a facilitator for obtaining data from patients seen
at outpatient chemotherapy clinics. Study limitations The validation process resulted in the adequacy of content and
appearance of the educational technology to guide patients on
chemotherapy-related fatigue, with a 0.95 global CVI, indicating
an excellent level of agreement among judges. Furthermore, the
target population considered the educational technology to
be useful considering its objectives, organization, writing style,
appearance and motivation, with a 95% global agreement rate. As limitations of this study we can point that the results to
be achieved via non-pharmacological interventions for fatigue
cannot always be guaranteed, since cancer-related fatigue is
multifactorial in most cases and may depend on some pharma-
cological approaches. On the other hand, the definition of judges
is not always easy to achieve. In this study, we chose to use the
criteria proposed by Jasper(9), which considers aspects based on
clinical experience, but it cannot be guaranteed, in fact, that all
items will ensure clinical expertise. Therefore, clinical validation is foreseen in subsequent stud-
ies to evaluate the efficiency of the instrument constructed and
validated as a facilitator for obtaining data from patients seen
at outpatient chemotherapy clinics. Contributions to the field of nursing education process (CVI = 0.86), which is effective for the main-
tenance of self-care related to fatigue management (CVI = 1.0)
and that can be implemented in the daily clinical practice of the
nurse who works in an outpatient chemotherapy clinic (CVI =
1.0); thus, being a relevant instrument for the care provided by
nursing professionals to these patients (CVI = 1.0). On the other
hand, the patients who participated in the pilot study considered
the folder to have a motivator effect (CVI = 0.98). We believe that the educational technology “Knowing and cop-
ing with fatigue” will enable health professionals, especially nursing
professionals, to provide care more in line with the needs of their
patients, as well as to complement guidelines and clarifications
provided to the patient, allowing him/her to better know and cope
with fatigue. Furthermore, studies in the context of outpatient care
are in line with international efforts to improve nurses’ activities in
this specialty. In the Brazilian context, the specialty of outpatient
oncology still lacks studies that seek to improve the practice of
nurses, seeking care based on scientific evidence. We thus believe
that the elaboration of an ET may better subsidize the practice of
this professional in outpatient environments. Motivation is the first step for behavior change. A study aimed
at the participation of middle-aged people in high-impact physical
activity showed that the perception of clear and tangible benefits
acts as a motivator for adherence to the practice of physical ac-
tivities(23). Another study, conducted with patients submitted to
stem cell transplantation, reported that being part of a physical
activity motivation program reduced the hospitalization period,
in addition to arousing a sense of commitment to physical activ-
ity, even when the participants were tired(24). REFERENCES 1. Bower JE, Bak K, Berger A, Breitbart W, Escalante CP, Ganz PA, et al. Screening, assessment, and management of fatigue in adult survivors
of cancer: an American Society of Clinical Oncology clinical practice guideline adaptation. J Clin Oncol. 2014;32(17):1840-50. doi: 10.1200/
JCO.2013.53.4495 1. Bower JE, Bak K, Berger A, Breitbart W, Escalante CP, Ganz PA, et al. Screening, assessment, and management of fatigue in adult survivors
of cancer: an American Society of Clinical Oncology clinical practice guideline adaptation. J Clin Oncol. 2014;32(17):1840-50. doi: 10.1200/
JCO.2013.53.4495 2. Herdman TH, Kamitsuru S. Diagnósticos de enfermagem da NANDA: definições e classificação 2015-2017. 10ª ed. Porto Alegre: Artmed;
2015. 2. Herdman TH, Kamitsuru S. Diagnósticos de enfermagem da NANDA: definições e classificação 2015-2017. 10ª ed. Porto Alegre: Artmed;
2015. 3. Mansano-Schlosser TC, Ceolim MF. Fadiga em idosos em tratamento quimioterápico. Rev Bras Enferm. 2014;67(4):623-9. doi:
10.1590/0034-7167.2014670419 3. Mansano-Schlosser TC, Ceolim MF. Fadiga em idosos em tratamento quimioterápico. Rev Bras Enferm. 2014;67(4):623-9. doi:
10.1590/0034-7167.2014670419 4. Deckx L, van den Akker M, Vergeer D, van Abbema D, van den Berkmortel F, Linsen L, et al. The value of fatigue severity to rule out
depression in older adult patients with cancer. Oncol Nurs Forum. 2015;42(4):E302-9. doi: 10.1188/15.ONF.E302-E309 4. Deckx L, van den Akker M, Vergeer D, van Abbema D, van den Berkmortel F, Linsen L, et al. The value of fatigue severity to rule out
depression in older adult patients with cancer. Oncol Nurs Forum. 2015;42(4):E302-9. doi: 10.1188/15.ONF.E302-E309 5. Berger AN, Mooney K, Banerjee C, Breitbart WS, Carpenter KM, Chang Y, et al. Cancer-related fatigue – version 1.2018. J Natl Compr Canc
Netw. 2018:1-62. 5. Berger AN, Mooney K, Banerjee C, Breitbart WS, Carpenter KM, Chang Y, et al. Cancer-related fatigue – version 1.2018. J Natl Compr Canc
Netw. 2018:1-62. 6. Caponero R. Consenso brasileiro de fadiga. Rev Bras Cuidados Paliativos. 2010;3(2; Supl 1):1-32. 6. Caponero R. Consenso brasileiro de fadiga. Rev Bras Cuidados Paliativos. 2010;3(2; Supl 1):1-32. 7. Costa AIS, Reis PED. Complementary techniques to control cancer symptoms. Rev Dor. 2014;15(1):61-4. doi: 10.5935 7. Costa AIS, Reis PED. Complementary techniques to control cancer symptoms. Rev Dor. 2014;15(1):61-4. doi: 10.5935/1806-0013.20140014
8. Doak CC, Doak LG, Root JH. Teaching patients with low literacy skills. 2nd ed. Philadelphia: JB Lippincott; 1996. 8. Doak CC, Doak LG, Root JH. Teaching patients with low literacy skills. 2nd ed. Philadelphia: JB Lippincott; 1996. 9. Jasper MA. REFERENCES Expert: a discussion of the implications of the concept as used in nursing. J Adv Nurs. 1994; 20:769-76. doi:
10.1046/j.1365-2648.1994.20040769.x 9. Jasper MA. Expert: a discussion of the implications of the concept as used in nursing. J Adv Nurs. 1994; 20:769-76. doi:
10.1046/j.1365-2648.1994.20040769.x 10. Pasquali L. Instrumentos psicológicos: manual prático de elaboração. Brasília: LabPAM/IBAPP; 1999. 1524 Rev Bras Enferm. 2019;72(6):1519-25. Educational technology for fatigue management related to antineoplastic chemotherapy
Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. 11. Canhota C. Qual a importância do estudo piloto. In: Silva EE, organizador. Investigação passo a passo: perguntas e respostas para
investigação clínica. Lisboa: APMCG; 2008. p. 69-72. 12. Nicolussi AC, Sawada NO, Cardozo FMC, Andrade V, Paula JM. Health-related quality of life of cancer patients undergoing chemotherapy. Rev Rene. 2014;15(1):132-40. doi: 10.15253/2175-6783.2014000100017 12. Nicolussi AC, Sawada NO, Cardozo FMC, Andrade V, Paula JM. Health-related quality of life of cancer patients undergoing chemotherapy. Rev Rene. 2014;15(1):132-40. doi: 10.15253/2175-6783.2014000100017 13. Mota DDCF, Pimenta CAM, Caponero R. Fatigue in colorectal cancer patients: prevalence and associated factors. Rev Latino-Am
Enfermagem. 2012;20(3):495-503. doi: 10.1590/S0104-11692012000300010 13. Mota DDCF, Pimenta CAM, Caponero R. Fatigue in colorectal cancer patients: prevalence and associated factors. Rev Latino-Am
Enfermagem. 2012;20(3):495-503. doi: 10.1590/S0104-11692012000300010 14. Barsevick AM, Dudley W, Beck S, Sweeney C, Whitmer K, Nail L. A randomized clinical trial of energy conservation for patients with cancer-
related fatigue. Cancer. 2004;100(6):1302-10. doi: 10.1002/cncr.20111 14. Barsevick AM, Dudley W, Beck S, Sweeney C, Whitmer K, Nail L. A randomized clinical trial of energy conservation for patients with cancer-
related fatigue. Cancer. 2004;100(6):1302-10. doi: 10.1002/cncr.20111 15. Oliveira MS, Fernandes AFC, Sawada NO. Manual educativo para o autocuidado da mulher mastectomizada: um estudo de validação. Texto
Contexto Enferm. 2008;17(1):115-23. doi: 10.1590/S0104-07072008000100013 15. Oliveira MS, Fernandes AFC, Sawada NO. Manual educativo para o autocuidado da mulher mastectomizada: um estudo de validação. Texto
Contexto Enferm. 2008;17(1):115-23. doi: 10.1590/S0104-07072008000100013 16. Souza Neto VL, Silva RAR, Silva CC, Negreiros RV, Rocha CCT, Nóbrega MML. Proposal of nursing care plan in people hospitalized with AIDS. Rev Esc Enferm USP. 2017;51:e03204. doi: 10.1590/s1980-220x2016027203204 16. Souza Neto VL, Silva RAR, Silva CC, Negreiros RV, Rocha CCT, Nóbrega MML. Proposal of nursing care plan in people hospitalized with AIDS. Rev Esc Enferm USP. 2017;51:e03204. doi: 10.1590/s1980-220x2016027203204 17. Al-Majid S, Wilson LD, Rakovski C, Coburn JW. Effects of exercise on biobehavioral outcomes of fatigue during cancer treatment: results of a
feasibility study. REFERENCES Biol Res Nurs. 2015;17(1):40-8. doi: 10.1177/1099800414523489 18. Jensen W, Baumamm FT, Stein A, Bloch W, Bokemeyer C, de Wit M, et al. Exercise training in patients with advanced gastrointestinal cancer
undergoing palliative chemotherapy: a pilot study. Support Care Cancer. 2014;22(7):1797-806. doi: 10.1007/s00520-014-2139-x 19. Casault L, Savard J, Ivers H, Savard MH. A randomized-controlled trial of an early minimal cognitive-behavioural therapy for insomnia
comorbid with cancer. Behav Res Ther. 2015;67:45-54. doi: 10.1016/j.brat.2015.02.003 20. World Health Organization (WHO). Guidelines for safe recreational water environments. Volume 2: swimming pools and similar
environments [Internet]. Geneva: WHO; 2006 [cited 2018 Jan 24]. Available from: https://www.who.int/water_sanitation_health/bathing/
srwe2full.pdf 21. Xiao S, Yin P, Zhang Y, Hu S. Occurrence of Cryptosporidium and Giard relationship between protozoa and wate indicators in swimming
pools. Korean J Parasitol. 2017;55(2):129-35. doi: 10.3347/kjp.2017.55.2.129 22. Passamai MPB, Sampaio HAC, Sabry MOD, Sá MLB, Cabral LA. Letramento funcional em saúde e nutrição. Fortaleza: EdUECE; 2011. 23. Simmonds BAJ, Hannam KJ, Fox KR, Tobias JH. An exploration of barriers and facilitators to older adults participation in higher impact
physical activity and bone health: a qualitative study. Osteoporos Int. 2016;27(3):979-87. doi: 10.1007/s00198-015-3376-7 24. Brassil KJ, Szewczyk N, Fellman B, Neumann J, Burgess J, Urbauer D, et al. Impact of an incentive-based mobility program, “Motivated and
Moving,” on physiologic and quality of life outcomes in a stem cell transplant population. Cancer Nurs. 2014;37(5):345-54. doi: 10.1097/
NCC.0b013e3182a40db2 25. Moreira MF, Nóbrega MML, Silva MIT. Comunicação escrita: contribuição para elaboração de material educativo em saúde. Rev Bras Enferm. 2003;56(2):184-8. doi: 10.1590/S0034-71672003000200015 25. Moreira MF, Nóbrega MML, Silva MIT. Comunicação escrita: contribuição para elaboração de material educativo em saúde. Rev Bras Enferm. 2003;56(2):184-8. doi: 10.1590/S0034-71672003000200015 26. Benevides JL, Coutinho JFV, Pascoal LC, Joventino ES, Martins MC, Gubert FA, et al. Development and validation of educational technology
for venous ulcer care. Rev Esc Enferm USP. 2016;50(2):306-12. doi: 10.1590/S0080-623420160000200018 26. Benevides JL, Coutinho JFV, Pascoal LC, Joventino ES, Martins MC, Gubert FA, et al. Development and validation of educational technology
for venous ulcer care. Rev Esc Enferm USP. 2016;50(2):306-12. doi: 10.1590/S0080-623420160000200018 1525
Rev Bras Enferm. 2019;72(6):1519-25.
|
https://openalex.org/W3091868035
|
https://pure.manchester.ac.uk/ws/files/188266416/nejmoa2022926.pdf
|
English
| null |
Effect of Hydroxychloroquine in Hospitalized Patients with Covid-19
|
New England journal of medicine/The New England journal of medicine
| 2,020
|
cc-by
| 9,450
|
The University of Manchester Research The University of Manchester Research The University of Manchester Research Link to publication record in Manchester Research Explorer Link to publication record in Manchester Research Explorer Citation for published version (APA):
RECOVERY Collaborative Group, & Evans, D. G. (2020). Effect of Hydroxychloroquine in Hospitalized Patients
with Covid-19. The New England Journal of Medicine, 383(21), 2030-2040. https://doi.org/10.1056/NEJMoa2022926, https://doi.org/10.1056/nejmoa2022926 Citing this paper Citing this paper
Please note that where the full-text provided on Manchester Research Explorer is the Author Accepted Manuscript
or Proof version this may differ from the final Published version. If citing, it is advised that you check and use the
publisher's definitive version. Published in: Published in: The New England Journal of Medicine Effect of Hydroxychloroquine in Hospitalized Patients with
Covid-19 DOI:
10.1056/NEJMoa2022926
10.1056/nejmoa2022926 Document Version
Final published version General rights General rights
Copyright and moral rights for the publications made accessible in the Research Explorer are retained by the
authors and/or other copyright owners and it is a condition of accessing publications that users recognise and
abide by the legal requirements associated with these rights. Takedown policy
If you believe that this document breaches copyright please refer to the University of Manchester’s Takedown
Procedures [http://man.ac.uk/04Y6Bo] or contact uml.scholarlycommunications@manchester.ac.uk providing
relevant details, so we can investigate your claim. Download date:24. Oct. 2024 Takedown policy
If you believe that this document breaches copyright please refer to the University of Manchester’s Takedown
Procedures [http://man.ac.uk/04Y6Bo] or contact uml.scholarlycommunications@manchester.ac.uk providing
relevant details, so we can investigate your claim. Citation for published version (APA): Citation for published version (APA):
RECOVERY Collaborative Group, & Evans, D. G. (2020). Effect of Hydroxychloroquine in Hospitalized Patients
with Covid-19. The New England Journal of Medicine, 383(21), 2030-2040. https://doi.org/10.1056/NEJMoa2022926, https://doi.org/10.1056/nejmoa2022926 BACKGROUND Hydroxychloroquine and chloroquine have been proposed as treatments for coro-
navirus disease 2019 (Covid-19) on the basis of in vitro activity and data from
uncontrolled studies and small, randomized trials. The members of the writing committee
(Peter Horby, F.R.C.P., Marion Mafham,
M.D., Louise Linsell, D.Phil., Jennifer L. Bell, M.Sc., Natalie Staplin, Ph.D., Jona-
than R. Emberson, Ph.D., Martin Wiselka,
Ph.D., Andrew Ustianowski, Ph.D., Einas
Elmahi, M.Phil., Benjamin Prudon, F.R.C.P.,
Tony Whitehouse, F.R.C.A., Timothy Fel-
ton, Ph.D., John Williams, M.R.C.P., Jakki
Faccenda, M.D., Jonathan Underwood,
Ph.D., J. Kenneth Baillie, M.D., Ph.D.,
Lucy C. Chappell, Ph.D., Saul N. Faust,
F.R.C.P.C.H., Thomas Jaki, Ph.D., Katie
Jeffery, Ph.D., Wei Shen Lim, F.R.C.P.,
Alan Montgomery, Ph.D., Kathryn Rowan,
Ph.D., Joel Tarning, Ph.D., James A. Wat-
son, D.Phil., Nicholas J. White, F.R.S., Ed-
mund Juszczak, M.Sc., Richard Haynes,
D.M., and Martin J. Landray, Ph.D.) as-
sume responsibility for the overall con-
tent and integrity of this article. Effect of Hydroxychloroquine
in Hospitalized Patients with Covid-19 The RECOVERY Collaborative Group* ABSTR ACT RESULTS The enrollment of patients in the hydroxychloroquine group was closed on June 5,
2020, after an interim analysis determined that there was a lack of efficacy. Death
within 28 days occurred in 421 patients (27.0%) in the hydroxychloroquine group
and in 790 (25.0%) in the usual-care group (rate ratio, 1.09; 95% confidence inter-
val [CI], 0.97 to 1.23; P = 0.15). Consistent results were seen in all prespecified
subgroups of patients. The results suggest that patients in the hydroxychloroquine
group were less likely to be discharged from the hospital alive within 28 days than
those in the usual-care group (59.6% vs. 62.9%; rate ratio, 0.90; 95% CI, 0.83 to
0.98). Among the patients who were not undergoing mechanical ventilation at
baseline, those in the hydroxychloroquine group had a higher frequency of invasive
mechanical ventilation or death (30.7% vs. 26.9%; risk ratio, 1.14; 95% CI, 1.03 to
1.27). There was a small numerical excess of cardiac deaths (0.4 percentage points)
but no difference in the incidence of new major cardiac arrhythmia among the
patients who received hydroxychloroquine. The affiliations of the members of the
writing committee are listed in the Ap-
pendix. Address reprint requests to Dr. Horby or Dr. Landray at the RECOVERY
Central Coordinating Office, Richard Doll
Bldg., Old Road Campus, Roosevelt Dr.,
Oxford OX3 7LF, United Kingdom, or at
recoverytrial@ndph.ox.ac.uk. *A complete list of collaborators in the
RECOVERY trial is provided in the Supple-
mentary Appendix, available at NEJM.org. Drs. Horby, Mafham, and Linsell and Prof. Juszczak, Dr. Haynes, and Dr. Landray
contributed equally to this article. METHODS In this randomized, controlled, open-label platform trial comparing a range of
possible treatments with usual care in patients hospitalized with Covid-19, we
randomly assigned 1561 patients to receive hydroxychloroquine and 3155 to receive
usual care. The primary outcome was 28-day mortality. Takedown policy Download date:24. Oct. 2024 The new engl and jour nal of medicine CONCLUSIONS Among patients hospitalized with Covid-19, those who received hydroxychloro-
quine did not have a lower incidence of death at 28 days than those who received
usual care. (Funded by UK Research and Innovation and National Institute for
Health Research and others; RECOVERY ISRCTN number, ISRCTN50189673;
ClinicalTrials.gov number, NCT04381936.) j
;
j
,
The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission.
Copyright © 2020 Massachusetts Medical Society. All rights reserved. N Engl J Med 2020;383:2030-40.
DOI: 10.1056/NEJMoa2022926
Copyright © 2020 Massachusetts Medical Society. This article was published on October 8,
2020, at NEJM.org. This article was published on October 8,
2020, at NEJM.org. This is the New England Journal of Medicine
version of record, which includes all Journal
editing and enhancements. The Author Fi-
nal Manuscript, which is the author’s ver-
sion after external peer review and before
publication in the Journal, is available un-
der a CC BY license at PMC7556338. N Engl J Med 2020;383:2030-40. DOI: 10.1056/NEJMoa2022926
Copyright © 2020 Massachusetts Medical Society. N Engl J Med 2020;383:2030-40. DOI: 10.1056/NEJMoa2022926
Copyright © 2020 Massachusetts Medical Society. 2030 n engl j med 383;21 nejm.org November 19, 2020 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. n engl j med 383;21 nejm.org November 19, 2020
The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission.
Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 S hospitalized with mild-to-moderate Covid-19
showed that hydroxychloroquine (at a dose of
400 mg twice daily, with or without azithromy-
cin) did not improve clinical status at day 15, as
compared with usual care.25-29 Here, as part of
the controlled, open-label Randomized Evalua-
tion of Covid-19 Therapy (RECOVERY) trial, we
report the results of a comparison between hy-
droxychloroquine and usual care involving pa-
tients hospitalized with Covid-19. S
evere acute respiratory syndrome
coronavirus 2 (SARS-CoV-2), the cause of
coronavirus disease 2019 (Covid-19), emerged
in China in late 2019 from a zoonotic source.1
The majority of Covid-19 infections are either
asymptomatic or result in only mild disease. However, in a substantial proportion of infected
persons, the infection leads to a respiratory ill-
ness requiring hospital care,2 which can progress
to critical illness with hypoxemic respiratory fail-
ure and lead to prolonged ventilatory support.3-6
Among the patients with Covid-19 who have been
admitted to hospitals in the United Kingdom,
the case fatality rate is approximately 30%.7 Trial Design and Oversight
The RECOVERY trial is an investigator-initiated
platform trial to evaluate the effects of potential
treatments in patients hospitalized with Covid-19. The trial is being conducted at 176 hospitals in
the United Kingdom. (Details are provided in the
Supplementary Appendix, available with the full
text of this article at NEJM.org.) The investigators
were assisted by the National Institute for Health
Research Clinical Research Network, and the
trial is coordinated by the Nuffield Department
of Population Health at the University of Oxford,
the trial sponsor. Although patients are no lon-
ger being enrolled in the hydroxychloroquine,
dexamethasone, and lopinavir–ritonavir groups,
the trial continues to study the effects of azithro-
mycin, tocilizumab, convalescent plasma, and
REGN-COV2 (a combination of two monoclonal
antibodies directed against the SARS-CoV-2 spike
protein). Other treatments may be studied in the
future. The hydroxychloroquine that was used in
this phase of the trial was supplied by the U.K. National Health Service (NHS). Trial Design and Oversight Hydroxychloroquine and chloroquine, two
4-aminoquinoline drugs that were developed
more than 70 years ago and have been used to
treat malaria and rheumatologic conditions, have
been proposed as treatments for Covid-19. Chloro-
quine has been shown to have in vitro activity
against a variety of viruses, including SARS-CoV-2
and the related SARS-CoV-1.8-13 The exact mecha-
nism of antiviral action is uncertain, but these
drugs increase the pH of endosomes that the
virus uses for cell entry and also interfere with
the glycosylation of angiotensin-converting–
enzyme 2 (ACE2), which is the cellular receptor
of SARS-CoV, and of associated gangliosides.10,14
The 4-aminoquinoline levels that are required to
inhibit SARS-CoV-2 replication in vitro are higher
than the free plasma levels that have been ob-
served in the prevention and treatment of ma-
laria.15 These drugs generally have an acceptable
side-effect profile and are inexpensive and wide-
ly available. After oral administration, they are
rapidly absorbed, even in severely ill patients. Therapeutic hydroxychloroquine levels could be
expected to be reached in human lung tissue
shortly after an initial loading dose. Hospitalized patients were eligible for the
trial if they had clinically-suspected or laboratory-
confirmed SARS-CoV-2 infection and no medical
history that might, in the opinion of the attend-
ing clinician, put patients at substantial risk if
they were to participate in the trial. Initially,
recruitment was limited to patients who were at
least 18 years of age, but the age limit was re-
moved as of May 9, 2020. In small preclinical studies of SARS-CoV-2
infection in animals, prophylaxis or treatment
with hydroxychloroquine had no beneficial ef-
fect on clinical disease or viral replication.16 A
clinical benefit and an antiviral effect from the
administration of these drugs alone or in com-
bination with azithromycin in patients with
Covid-19 have been reported in some observa-
tional studies17-21 but not in others.22-24 The re-
sults of a few small trials of hydroxychloroquine
or chloroquine for the treatment of Covid-19 have
been inconclusive, whereas one larger random-
ized, controlled trial involving patients who were Written informed consent was obtained from
all the patients or from a legal representative if
they were too unwell or unable to provide con-
sent. The trial was conducted in accordance with
Good Clinical Practice guidelines of the Interna-
tional Conference on Harmonisation and was
approved by the U.K. The new engl and jour nal of medicine Products Regulatory Agency (MHRA) and the
Cambridge East Research Ethics Committee. The protocol with its statistical analysis plan are
available at NEJM.org, with additional informa-
tion in the Supplementary Appendix and on the
trial website at www.recoverytrial.net. In the hydroxychloroquine group, patients re-
ceived hydroxychloroquine sulfate (in the form
of a 200-mg tablet containing a 155-mg base
equivalent) in a loading dose of four tablets (total
dose, 800 mg) at baseline and at 6 hours, which
was followed by two tablets (total dose, 400 mg)
starting at 12 hours after the initial dose and
then every 12 hours for the next 9 days or until
discharge, whichever occurred earlier (see the
Supplementary Appendix).15 The assigned treat-
ment was prescribed by the attending clinician. The patients and local trial staff members were
aware of the assigned trial groups. The initial version of the manuscript was
drafted by the first and last authors, developed
by the writing committee, and approved by all
members of the trial steering committee. The
funders had no role in the analysis of the data,
in the preparation or approval of the manuscript,
or in the decision to submit the manuscript for
publication. The first and last members of the
writing committee vouch for the completeness
and accuracy of the data and for the fidelity of the
trial to the protocol and statistical analysis plan. Procedures A single online follow-up form was to be com-
pleted by the local trial staff members when
each trial patient was discharged, at 28 days af-
ter randomization, or at the time of death, which-
ever occurred first. Information was recorded
regarding the adherence to the assigned treat-
ment, receipt of other treatments for Covid-19,
duration of admission, receipt of respiratory
support (with duration and type), receipt of renal
dialysis or hemofiltration, and vital status (in-
cluding cause of death). Starting on May 12, 2020,
extra information was recorded on the occur-
rence of new major cardiac arrhythmia. In addi-
tion, we obtained routine health care and regis-
try data that included information on vital status
(with date and cause of death) and discharge
from the hospital. Trial Design and Oversight Medicines and Healthcare 2031 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Randomization and Treatment We collected baseline data using a Web-based
case-report form that included demographic
data, level of respiratory support, major coexist-
ing illnesses, the suitability of the trial treat-
ment for a particular patient, and treatment
availability at the trial site. Using a Web-based
unstratified randomization method with the con-
cealment of trial group, we assigned patients to
receive either the usual standard of care or the
usual standard of care plus hydroxychloroquine
or one of the other available treatments that were
being evaluated. The number of patients who
were assigned to receive usual care was twice the
number who were assigned to any of the active
treatments for which the patient was eligible
(e.g., 2:1 ratio in favor of usual care if the patient
was eligible for only one active treatment group,
2:1:1 if the patient was eligible for two active
treatments, etc.). n engl j med 383;21 nejm.org November 19, 2020
The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission.
Copyright © 2020 Massachusetts Medical Society. All rights reserved. n engl j med 383;21 nejm.org November 19, 2020
The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission.
Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 data cutoff of September 21, 2020. Information
regarding the primary outcome is complete for
all the trial patients. a range of uncertainty around the results that was
narrow enough) to affect national and global
treatment strategies. In such a circumstance, the
committee would inform the members of the trial
steering committee, who would make the results
available to the public and amend the trial ac-
cordingly. Unless that happened, the steering
committee, investigators, and all others involved
in the trial would remain unaware of the interim
results until 28 days after the last patient had
been randomly assigned to a particular treatment
group. Outcome Measures The primary outcome was all-cause mortality
within 28 days after randomization; further
analyses were specified at 6 months. Secondary
outcomes were the time until discharge from the
hospital and a composite of the initiation of in-
vasive mechanical ventilation including extracor-
poreal membrane oxygenation or death among
patients who were not receiving invasive mechani-
cal ventilation at the time of randomization. Decisions to initiate invasive mechanical ventila-
tion were made by the attending clinicians, who
were informed by guidance from NHS England
and the National Institute for Health and Care
Excellence. Subsidiary clinical outcomes included
cause-specific mortality (which was recorded in
all patients) and major cardiac arrhythmia (which
was recorded in a subgroup of patients). All in-
formation presented in this report is based on a For some patients, hydroxychloroquine was
unavailable at the hospital at the time of enroll-
ment or was considered by the managing physi-
cian to be either definitely indicated or definitely
contraindicated. Patients with a known prolonged
corrected QT interval on electrocardiography
were ineligible to receive hydroxychloroquine. (Coadministration with medications that prolong
the QT interval was not an absolute contraindi-
cation, but attending clinicians were advised to
check the QT interval by performing electrocar-
diography.) These patients were excluded from
entry in the randomized comparison between
hydroxychloroquine and usual care. 2032 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Patients From March 25 to June 5, 2020, a total of 11,197
patients underwent randomization; of these pa-
tients, 7513 (67%) were eligible to receive hy-
droxychloroquine (i.e., the patient had no known
indication for or contraindication to hydroxy-
chloroquine, and the drug was available in the
hospital at the time) (Fig. 1). Of the eligible pa-
tients, 1561 were assigned to receive hydroxy-
chloroquine and 3155 were assigned to receive
usual care; the remainder of the patients were
randomly assigned to one of the other treatment
groups. v ded
t e Supp e e ta y
ppe d .)
Estimates of rate and risk ratios are shown
with 95% confidence intervals without adjust-
ment for multiple testing. The P value for the
assessment of the primary outcome is two-sided. The full database is held by the trial team, which
collected the data from the trial sites and per-
formed the analyses, at the Nuffield Department
of Population Health at the University of Oxford. The independent data monitoring committee
was asked to review unblinded analyses of the
trial data and any other information that was
considered to be relevant at intervals of approxi-
mately 2 weeks. The committee was then charged
with determining whether the randomized com-
parisons in the trial provided evidence with re-
spect to mortality that was strong enough (with Estimates of rate and risk ratios are shown
with 95% confidence intervals without adjust-
ment for multiple testing. The P value for the
assessment of the primary outcome is two-sided. The full database is held by the trial team, which
collected the data from the trial sites and per-
formed the analyses, at the Nuffield Department
of Population Health at the University of Oxford. The mean (±SD) age of the patients in this
trial was 65.4±15.3 years (Table 1 and Table S1
in the Supplementary Appendix). A total of 38%
of the patients were female; 18% were Black or
Asian or had a minority ethnic background. No
children were enrolled. A history of diabetes was
present in 27% of patients, heart disease in 26%,
and chronic lung disease in 22%, with 57% hav- The independent data monitoring committee
was asked to review unblinded analyses of the
trial data and any other information that was
considered to be relevant at intervals of approxi-
mately 2 weeks. Statistical Analysis For the primary outcome of 28-day mortality, we
used the log-rank observed-minus-expected sta-
tistic and its variance both to test the null hy-
pothesis of equal survival curves and to calculate
the one-step estimate of the average mortality
rate ratio in the comparison between the hydroxy-
chloroquine group and the usual-care group. Kaplan–Meier survival curves were constructed
to show cumulative mortality over the 28-day
period. The same methods were used to analyze
the time until hospital discharge, with censor-
ing of data on day 29 for patients who had died
in the hospital. We used the Kaplan–Meier esti-
mates to calculate the median time until hospi-
tal discharge. For the prespecified composite
secondary outcome of invasive mechanical venti-
lation or death within 28 days (among patients
who had not been receiving invasive mechanical
ventilation at randomization), the precise date of
the initiation of invasive mechanical ventilation
was not available, so the risk ratio was estimated
instead. Estimates of the between-group differ-
ence in absolute risk were also calculated. On June 4, 2020, in response to a request
from the MHRA, the independent data monitor-
ing committee conducted a review of the data
and recommended that the chief investigators
review the unblinded data for the hydroxychloro-
quine group. The chief investigators and steer-
ing committee members concluded that the data
showed no beneficial effect of hydroxychloro-
quine in patients hospitalized with Covid-19. Therefore, the enrollment of patients in the hy-
droxychloroquine group was closed on June 5,
2020, and the preliminary result for the primary
outcome was made public. Investigators were
advised that any patients who were receiving
hydroxychloroquine as part of the trial should
discontinue the treatment. All the analyses were performed according to
the intention-to-treat principle. Prespecified analy-
ses of the primary outcome were performed in
six subgroups, as defined by characteristics at
randomization: age, sex, race, level of respira-
tory support, days since symptom onset, and
predicted 28-day risk of death. (Details are pro-
vided in the Supplementary Appendix.) Primary Outcome Death at 28 days occurred in 421 of 1561 pa-
tients (27.0%) in the hydroxychloroquine group
and in 790 of 3155 patients (25.0%) in the usual-
care group (rate ratio, 1.09; 95% confidence in-
terval [CI], 0.97 to 1.23; P = 0.15) (Fig. 2). Similar
results were seen across all six prespecified sub-
groups (Fig. 3). In a post hoc exploratory analysis
that was restricted to the 4266 patients (90.5%)
with a positive SARS-CoV-2 test result, the result
was similar to the overall result (rate ratio, 1.09;
95% CI, 0.96 to 1.23). ing at least one major coexisting illness that was
recorded. In this analysis, 90% of the patients
had laboratory-confirmed SARS-CoV-2 infection,
with the result not known for less than 1%. At
randomization, 17% were receiving invasive me-
chanical ventilation including extracorporeal
membrane oxygenation, 60% were receiving oxy-
gen only (with or without noninvasive ventila-
tion), and 24% were receiving neither. Figure 1. Enrollment and Outcomes in the RECOVERY
Trial. The enrollment number that is shown is the total num-
ber of patients in the RECOVERY platform trial during
the period in which adult patients could be recruited
for the comparison between hydroxychloroquine and
usual care. Patients could have more than one reason
for not participating in the hydroxychloroquine trial. At
the time of this analysis, data from the trial follow-up
form were available for 1553 of 1561 patients (99.5%)
in the hydroxychloroquine group and for 3140 of 3155
patients (99.5%) in the usual-care group. The subgroup
of patients who later underwent a second randomiza-
tion to tocilizumab versus usual care in the RECOVERY
trial included 37 of 1561 patients (2.4%) in the hydroxy-
chloroquine group and 89 of 3155 patients (2.8%) in
the usual care group. In addition, 6 patients were ran-
domly assigned to receive either convalescent plasma
or usual care alone (1 patient [0.1%] in the hydroxy-
chloroquine group and 5 patients [0.2%] in the usual-
care group) in accordance with protocol version 6.0. Among the 167 sites at which at least 1 patient was
assigned to receive hydroxychloroquine, the median
number of patients who underwent randomization
was 20 (interquartile range, 11 to 41). 7513 (67%) Underwent randomization to receive
hydroxychloroquine or other treatments 2797 Were assigned to another
active treatment
1010 Were assigned to lopinavir–
ritonavir
1170 Were assigned to dexameth-
asone
617 Were assigned to azithro-
mycin 4716 (42%) Underwent randomization to receive
hydroxychloroquine or usual care alone group received hydroxychloroquine. The frequen-
cy of use of azithromycin or other macrolide
drug during the follow-up period was similar in
the hydroxychloroquine group and the usual-
care group (18.6% vs. 20.3%), as was the use of
dexamethasone (9.1% vs. 9.2%). Remdesivir was
administered to less than 0.1% of the patients in
each group. Patients The committee was then charged
with determining whether the randomized com-
parisons in the trial provided evidence with re-
spect to mortality that was strong enough (with 2033 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. The new engl and jour nal of medicine 7513 (67%) Underwent randomization to receive
hydroxychloroquine or other treatments
11,197 Patients were recruited
639 (6%) Did not have access
to hydroxychloroquine at their
hospital
3199 (29%) Were considered
unsuitable for receiving
hydroxychloroquine
4716 (42%) Underwent randomization to receive
hydroxychloroquine or usual care alone
2797 Were assigned to another
active treatment
1010 Were assigned to lopinavir–
ritonavir
1170 Were assigned to dexameth-
asone
617 Were assigned to azithro-
mycin
1561 (100%) Were assigned to receive
hydroxychloroquine
1430 of 1553 (92%) Received
hydroxychloroquine
3155 (100%) Were assigned to receive
usual care
12 of 3140 (0.4%) Received
hydroxychloroquine
3 (0.2%) Withdrew consent
5 (0.2%) Withdrew consent
75 (4.8%) Proceeded to second
randomization
178 (5.6%) Proceeded to second
randomization
1561 (100%) Were included in the
28-day intention-to-treat analysis
3155 (100%) Were included in the
28-day intention-to-treat analysis Figure 1. Enrollment and Outcomes in the RECOVERY
Trial. n engl j med 383;21 nejm.org November 19, 2020
The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission.
Copyright © 2020 Massachusetts Medical Society. All rights reserved. Secondary Outcomes Patients in the hydroxychloroquine group had a
longer duration of hospitalization than those in
the usual-care group (median, 16 days vs. 13 days)
and a lower probability of discharge alive within
28 days (59.6% vs. 62.9%; rate ratio, 0.90; 95%
CI, 0.83 to 0.98) (Table 2). Among the patients A total of 1430 patients in the hydroxychloro-
quine group (92%) received at least one dose
(Table S2). The median duration of treatment
was 6 days (interquartile range, 3 to 10 days). In
addition, 12 patients (0.4%) in the usual-care 2034 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 Table 1. Characteristics of the Patients at Baseline.*
Characteristic
Hydroxychloroquine
(N = 1561)
Usual Care
(N = 3155)
Age
Mean ±SD
65.2±15.2
65.4±15.4
Distribution — no. (%)
<70 yr
925 (59.3)
1873 (59.4)
≥70 to <80 yr
342 (21.9)
630 (20.0)
≥80 yr
294 (18.8)
652 (20.7)
Sex — no. (%)
Male
960 (61.5)
1974 (62.6)
Female†
601 (38.5)
1181 (37.4)
Race or ethnic group — no. (%)‡
White
1181 (75.7)
2298 (72.8)
Black, Asian, or minority ethnic group
264 (16.9)
593 (18.8)
Unknown
116 (7.4)
264 (8.4)
Median no. of days since symptom onset (IQR)§
9 (5–14)
9 (5–13)
Median no. of days since hospitalization (IQR)
3 (1–6)
3 (1–5)
Respiratory support — no. (%)
No oxygen received
362 (23.2)
750 (23.8)
Oxygen only
938 (60.1)
1873 (59.4)
Invasive mechanical ventilation
261 (16.7)
532 (16.9)
Previous disease — no. (%)
Any of the listed conditions
882 (56.5)
1807 (57.3)
Diabetes
427 (27.4)
856 (27.1)
Heart disease
422 (27.0)
789 (25.0)
Chronic lung disease
334 (21.4)
712 (22.6)
Tuberculosis
4 (0.3)
9 (0.3)
HIV infection
8 (0.5)
13 (0.4)
Severe liver disease¶
18 (1.2)
46 (1.5)
Severe kidney impairment‖
111 (7.1)
261 (8.3)
SARS-CoV-2 test result — no. (%)
Positive
1399 (89.6)
2867 (90.9)
Negative
156 (10.0)
275 (8.7)
Unknown
6 (0.4)
13 (0.4)
* Percentages may not total 100 because of rounding. HIV denotes human immunodeficiency virus, IQR interquartile
range, and SD standard deviation. * Percentages may not total 100 because of rounding. HIV denotes human immunodeficiency virus, IQR interquartile
range, and SD standard deviation. * Percentages may not total 100 because of rounding. * Percentages may not total 100 because of rounding. HIV denotes human immunodeficiency virus, IQR interquartile
range, and SD standard deviation.
† Among the women, 2 in the hydroxychloroquine group and 4 in the usual-care group were pregnant.
‡ Race or ethnic group is reported as it was recorded in the patient’s electronic health record.
§ Data regarding the number of days since symptom onset were missing for 9 patients in the hydroxychloroquine group
and 9 patients in the usual-care group.
¶ Severe liver disease was defined as a diagnosis that resulted in ongoing specialist care.
‖ Severe kidney impairment was defined as an estimated glomerular filtration rate of less than 30 ml per minute per 1.73
m2 of body-surface area. Secondary Outcomes HIV denotes human immunodeficiency virus, IQR interquartile
range, and SD standard deviation. † Among the women, 2 in the hydroxychloroquine group and 4 in the usual-care group were pregnant. ‡ Race or ethnic group is reported as it was recorded in the patient’s electronic health record. § Data regarding the number of days since symptom onset were missing for 9 patients in the hydroxychloroquine group
and 9 patients in the usual-care group. ¶ Severe liver disease was defined as a diagnosis that resulted in ongoing specialist care. ‖ Severe kidney impairment was defined as an estimated glomerular filtration rate of less than 30 ml per minute per 1.73
m2 of body-surface area. who were not undergoing invasive mechanical
ventilation at baseline, the number of patients
who had progression to the prespecified com-
posite secondary outcome of invasive mechani-
cal ventilation or death was higher among those
in the hydroxychloroquine group than among posite secondary outcome of invasive mechani-
cal ventilation or death was higher among those
in the hydroxychloroquine group than among who were not undergoing invasive mechanical
ventilation at baseline, the number of patients
who had progression to the prespecified com- 2035 n engl j med 383;21 nejm.org November 19, 2020 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. The new engl and jour nal of medicine Figure 2. Mortality at 28 Days. Death at 28 days (the primary outcome) occurred in 421 patients (27.0%)
in the hydroxychloroquine group and in 790 (25.0%) in the usual-care
group. The inset shows the same data on an expanded y axis. Mortality (%)
100
80
90
70
60
40
30
10
50
20
0
0
7
14
21
28
Days since Randomization
30
10
20
0
15
25
5
0
7
14
21
28
Rate ratio, 1.09 (95% CI, 0.97–1.23)
P=0.15 by log-rank test
No. at Risk
Hydroxychloroquine
Usual care
1561
3155
1337
2750
1227
2525
1169
2414
1137
2360
Hydroxychloroquine
Usual care atrioventricular block requiring intervention
(0.1% vs. 0.1%) (Table S4). Discussion In this analysis of the RECOVERY trial, we de-
termined that hydroxychloroquine was not an
effective treatment for patients hospitalized with
Covid-19. The lower boundary of the confidence
limit for the primary outcome ruled out any
reasonable possibility of a meaningful mortality
benefit. The results were consistent across sub-
groups according to age, sex, race, time since
illness onset, level of respiratory support, and
baseline-predicted risk. In addition, the results
suggest that the patients who received hydroxy-
chloroquine had a longer duration of hospital-
ization and, among those who were not under-
going mechanical ventilation at baseline, a higher
risk of invasive mechanical ventilation or death
than those who received usual care. Figure 2. Mortality at 28 Days. Death at 28 days (the primary outcome) occurred in 421 patients (27.0%)
in the hydroxychloroquine group and in 790 (25.0%) in the usual-care
group. The inset shows the same data on an expanded y axis. Death at 28 days (the primary outcome) occurred in 421 patients (27.0%)
in the hydroxychloroquine group and in 790 (25.0%) in the usual-care
group. The inset shows the same data on an expanded y axis. those in the usual-care group (risk ratio, 1.14;
95% CI, 1.03 to 1.27). Secondary Outcomes There was one report
of a serious adverse reaction that was deemed by
investigators to be related to hydroxychloro-
quine: a case of torsades de pointes, from which
the patient recovered without undergoing inter-
vention. Among the patients who were not re-
ceiving renal dialysis or hemofiltration at ran-
domization, the percentage who went on to
receive such treatment during the follow-up
period was the same in the hydroxychloroquine
group and the usual-care group (7.9% vs. 7.9%)
(Table S5). Mortality (%) The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission.
Copyright © 2020 Massachusetts Medical Society. All rights reserved. Other Prespecified Outcomes 0.75
1.0
2.0
1.5
Usual Care
Better
Hydroxychloroquine
Better
Age
<70 yr
≥70 to <80 yr
≥80 yr
Sex
Male
Female
Race or ethnic group
White
Black, Asian, or minority ethnic group
Days since symptom onset
≤7
>7
Respiratory support at randomization
No oxygen received
Oxygen only
Invasive mechanical ventilation
Baseline risk
<30%
≥30% to <45%
≥45%
All Participants
Hydroxychloroquine
Rate Ratio (95% CI)
Usual Care
Subgroup
0.50
no. of events/total no. (%)
160/925 (17.3)
314/1873 (16.8)
1.03 (0.85−1.25)
128/342 (37.4)
207/630 (32.9)
1.17 (0.93–1.47)
133/294 (45.2)
269/652 (41.3)
1.14 (0.92−1.42)
276/960 (28.8)
543/1974 (27.5)
1.05 (0.91−1.22)
145/601 (24.1)
247/1181 (20.9)
1.19 (0.96−1.47)
335/1181 (28.4)
610/2298 (26.5)
1.09 (0.95–1.25)
65/264 (24.6)
115/593 (19.4)
1.32 (0.96–1.81)
177/622 (28.5)
339/1275 (26.6)
1.10 (0.91−1.32)
242/930 (26.0)
445/1871 (23.8)
1.11 (0.94−1.30)
58/362 (16.0)
99/750 (13.2)
1.24 (0.89−1.73)
253/938 (27.0)
475/1873 (25.4)
1.08 (0.93−1.26)
110/261 (42.1)
216/532 (40.6)
1.03 (0.81−1.30)
146/994 (14.7)
274/1990 (13.8)
1.07 (0.88−1.32)
135/317 (42.6)
246/635 (38.7)
1.12 (0.90−1.40)
140/250 (56.0)
270/530 (50.9)
1.17 (0.95−1.45)
421/1561 (27.0)
790/3155 (25.0)
P=0.15
1.09 (0.97−1.23) Figure 3. Mortality at 28 Days, According to Subgroup. The size of the squares representing rate ratios is proportional to the amount of statistical information that was
available for each comparison. The method that was used for calculating the baseline-predicted risk in each sub-
group is described in the Supplementary Appendix. Race or ethnic group was recorded in the patient’s electronic
health record. 0.75
1.0
2.0
1.5
Usual Care
Better
Hydroxychloroquine
Better
Age
<70 yr
≥70 to <80 yr
≥80 yr
Sex
Male
Female
Race or ethnic group
White
Black, Asian, or minority ethnic group
Days since symptom onset
≤7
>7
Respiratory support at randomization
No oxygen received
Oxygen only
Invasive mechanical ventilation
Baseline risk
<30%
≥30% to <45%
≥45%
All Participants
Hydroxychloroquine
Rate Ratio (95% CI)
Usual Care
Subgroup
0.50
no. of events/total no. Other Prespecified Outcomes There was no difference between the hydroxy-
chloroquine group and the usual-care group in
28-day mortality that was ascribed to Covid-19
(24.0% vs. 23.5%). However, patients in the hy-
droxychloroquine group had a greater risk of
death from cardiac causes (mean [±SE] excess,
0.4±0.2 percentage points) and from non–SARS-
CoV-2 infection (mean excess, 0.4±0.2 percent-
age points) (Table S3). Data regarding the occur-
rence of new major cardiac arrhythmia were
collected for 735 of 1561 patients (47.1%) in the
hydroxychloroquine group and 1421 of 3155 pa-
tients (45.0%) in the usual-care group, after col-
lection of this information was added to the
follow-up form on May 12, 2020. Among these
patients, there were no significant differences
between the hydroxychloroquine group and the
usual-care group in the frequency of supraven-
tricular tachycardia (7.6% vs. 6.0%), ventricular
tachycardia or fibrillation (0.7% vs. 0.4%), or The RECOVERY trial is a large, pragmatic,
randomized, controlled platform trial designed
to assess the effect of potential treatments for
Covid-19 on 28-day mortality. Approximately
15% of the patients who were hospitalized with
Covid-19 in the United Kingdom during the trial
period were enrolled, and the percentage of pa-
tients in the usual-care group who died was
consistent with the hospitalized case fatality rate
among hospitalized patients in the United King-
dom and elsewhere.7,30,31 Only essential data were
collected at hospital sites, with additional infor-
mation (including long-term mortality) ascer-
tained through linkage with routine data sources. We did not collect information on physiologic,
electrocardiographic, laboratory, or virologic
measurements. Hydroxychloroquine has been proposed as a
treatment for Covid-19 largely on the basis of its 2036 n engl j med 383;21 nejm.org November 19, 2020 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 Figure 3. Mortality at 28 Days, According to Subgroup. The size of the squares representing rate ratios is proportional to the amount of statistical information that was
available for each comparison. The method that was used for calculating the baseline-predicted risk in each sub-
group is described in the Supplementary Appendix. Race or ethnic group was recorded in the patient’s electronic
health record. Other Prespecified Outcomes However, the 4-amino-
quinoline drugs are relatively weak antiviral
agents.15 The demonstration of therapeutic effi-
cacy of hydroxychloroquine in severe Covid-19
would require rapid attainment of efficacious
levels of free drug in the blood and respiratory
epithelium.32 Thus, to provide the greatest chance
of providing benefit in life-threatening Covid-19,
the dose regimen in our trial was designed to
result in rapid attainment and maintenance of
plasma levels that were as high as safely possi-
ble.15 These levels were predicted to be at the
upper end of those observed during steady-state
treatment of rheumatoid arthritis with hydroxy-
chloroquine.33 Our dosing schedule was based
on pharmacokinetic modeling of hydroxychloro-
quine that referenced a SARS-CoV-2 50% effec-
tive concentration of 0.72 μM, as scaled to
whole-blood levels and on the assumption that
cytosolic levels in the respiratory epithelium are
in dynamic equilibrium with blood levels.8,15,34 of very few events, but we did not observe ex-
cess mortality in the first 2 days of treatment
with hydroxychloroquine, the time when early
effects of dose-dependent toxicity might be ex-
pected. Furthermore, the data presented here
did not show any excess in ventricular tachycardia
or ventricular fibrillation in the hydroxychloro-
quine group. g
These findings indicate that hydroxychloro-
quine is not an effective treatment for hospital-
ized patients with Covid-19 but do not address
its use as prophylaxis or in patients with less
severe SARS-CoV-2 infection managed in the com-
munity. A review of Covid-19 treatment guide-
lines that was produced early in the pandemic
showed that chloroquine or hydroxychloroquine
was recommended in China, France, Italy, the
Netherlands, and South Korea.37 In the United
States, the use of chloroquine and hydroxychlo-
roquine was permitted in certain hospitalized pa-
tients under an Emergency Use Authorization
(EUA) of the Food and Drug Administration (FDA). A retrospective cohort study involving 1376 pa-
tients with Covid-19 who were admitted to the
hospital in New York City in March and April
2020 showed that 59% of the patients received
hydroxychloroquine.22,38 Since our preliminary re-
sults were made public on June 5, 2020, the FDA
has revoked the EUA for chloroquine and hydroxy-
chloroquine,39 and the World Health Organiza-
tion (WHO) and the National Institutes of Health
have ceased trials of its use in hospitalized pa-
tients on the grounds of a lack of benefit. Other Prespecified Outcomes (%)
160/925 (17.3)
314/1873 (16.8)
1.03 (0.85−1.25)
128/342 (37.4)
207/630 (32.9)
1.17 (0.93–1.47)
133/294 (45.2)
269/652 (41.3)
1.14 (0.92−1.42)
276/960 (28.8)
543/1974 (27.5)
1.05 (0.91−1.22)
145/601 (24.1)
247/1181 (20.9)
1.19 (0.96−1.47)
335/1181 (28.4)
610/2298 (26.5)
1.09 (0.95–1.25)
65/264 (24.6)
115/593 (19.4)
1.32 (0.96–1.81)
177/622 (28.5)
339/1275 (26.6)
1.10 (0.91−1.32)
242/930 (26.0)
445/1871 (23.8)
1.11 (0.94−1.30)
58/362 (16.0)
99/750 (13.2)
1.24 (0.89−1.73)
253/938 (27.0)
475/1873 (25.4)
1.08 (0.93−1.26)
110/261 (42.1)
216/532 (40.6)
1.03 (0.81−1.30)
146/994 (14.7)
274/1990 (13.8)
1.07 (0.88−1.32)
135/317 (42.6)
246/635 (38.7)
1.12 (0.90−1.40)
140/250 (56.0)
270/530 (50.9)
1.17 (0.95−1.45)
421/1561 (27.0)
790/3155 (25.0)
P=0.15
1.09 (0.97−1.23) Figure 3. Mortality at 28 Days, According to Subgroup. The size of the squares representing rate ratios is proportional to the amount of statistical information that was
available for each comparison. The method that was used for calculating the baseline-predicted risk in each sub-
group is described in the Supplementary Appendix. Race or ethnic group was recorded in the patient’s electronic
health record. he size of the squares representing rate ratios is proportional to the amount of statistical information that was
vailable for each comparison. The method that was used for calculating the baseline-predicted risk in each sub-
oup is described in the Supplementary Appendix. Race or ethnic group was recorded in the patient’s electronic
ealth record. Table 2. Primary and Secondary Outcomes. Outcome
Hydroxychloroquine
(N = 1561)
Usual Care
(N = 3155)
Rate or Risk Ratio
(95% CI)
no./total no. (%)
Primary outcome: 28-day mortality
421/1561 (27.0)
790/3155 (25.0)
1.09 (0.97–1.23)*
Secondary outcomes
Discharge from hospital in ≤28 days
931/1561 (59.6)
1983/3155 (62.9)
0.90 (0.83–0.98)*
Invasive mechanical ventilation or death†
399/1300 (30.7)
705/2623 (26.9)
1.14 (1.03–1.27)‡
Invasive mechanical ventilation
128/1300 (9.8)
225/2623 (8.6)
1.15 (0.93–1.41)
Death
311/1300 (23.9)
574/2623 (21.9)
1.09 (0.97–1.23)
* The between-group difference was calculated as a rate ratio. † Patients who were receiving invasive mechanical ventilation at randomization were excluded from this analysis. ‡ The between-group difference was calculated as a risk ratio. 2037 n engl j med 383;21 nejm.org November 19, 2020 The new engl and jour nal of medicine in vitro SARS-CoV-2 antiviral activity and on data
from observational studies reporting effective
reduction in viral loads. The views expressed in this article are those of the authors
and not necessarily those of the National Health Service (NHS),
the National Institute for Health Research (NIHR), or the De-
partment of Health and Social Care. n engl j med 383;21 nejm.org November 19, 2020
The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission.
Copyright © 2020 Massachusetts Medical Society. All rights reserved. Other Prespecified Outcomes The
WHO has released preliminary results from the
SOLIDARITY trial on the effectiveness of hy-
droxychloroquine in hospitalized patients with
Covid-19 that are consistent with the results from
the RECOVERY trial.40 The primary concern with short-term, high-
dose 4-aminoquinoline regimens is cardiovas-
cular toxicity. Hydroxychloroquine causes pre-
dictable prolongation of the corrected QT interval
on electrocardiography, which is exacerbated by
coadministration with azithromycin, as widely
prescribed in Covid-19 treatment.16-18 Although
torsades de pointes has been described, serious
cardiovascular toxicity has been infrequently re-
ported, despite the high prevalence of cardio-
vascular disease in hospitalized patients, the
common occurrence of myocarditis in Covid-19,
and the extensive use of hydroxychloroquine
and azithromycin together. The exception is a
Brazilian study that was stopped early because
of cardiotoxicity. However, in that study, chloro-
quine was administered at a base dose of 600 mg
twice daily for 10 days, a higher total dose than
those that were used in other trials, including
the RECOVERY trial.35,36 Pharmacokinetic mod-
eling in combination with information regarding
blood levels and mortality from a case series
involving 302 patients with chloroquine over-
dose predicts that a chloroquine regimen that
was equivalent to the hydroxychloroquine regi-
men used in our trial should have an acceptable
safety profile.36 There was a small absolute ex-
cess of cardiac mortality of 0.4 percentage points
in the hydroxychloroquine group on the basis The views expressed in this article are those of the authors
and not necessarily those of the National Health Service (NHS),
the National Institute for Health Research (NIHR), or the De-
partment of Health and Social Care. Supported by a grant (MC_PC_19056) to the University
of Oxford from UK Research and Innovation and the NIHR
and by core funding provided by NIHR Oxford Biomedical
Research Centre, Wellcome, the Bill and Melinda Gates Foun-
dation, the Department for International Development, Health
Data Research UK, the Medical Research Council Population
Health Research Unit, the NIHR Health Protection Unit in
Emerging and Zoonotic Infections, and NIHR Clinical Trials
Unit Support Funding. Tocilizumab was provided free of charge
for this study by Roche. AbbVie contributed some supplies of
lopinavir–ritonavir for use in the trial. The hydroxychloroquine
that was used in the trial was supplied by the NHS. Disclosure forms provided by the authors are available with
the full text of this article at NEJM.org. Appendix The authors’ full names and academic degrees are as follows: The RECOVERY Collaborative GroupPeter Horby, F.R.C.P., Marion Mafham,
M.D., Louise Linsell, D.Phil., Jennifer L. Bell, M.Sc., Natalie Staplin, Ph.D., Jonathan R. Emberson, Ph.D., Martin Wiselka, Ph.D., Andrew
Ustianowski, Ph.D., Einas Elmahi, M.Phil., Benjamin Prudon, F.R.C.P., Tony Whitehouse, F.R.C.A., Timothy Felton, Ph.D., John Wil-
liams, M.R.C.P., Jakki Faccenda, M.D., Jonathan Underwood, Ph.D., J. Kenneth Baillie, M.D., Ph.D., Lucy C. Chappell, Ph.D., Saul N. Faust, F.R.C.P.C.H., Thomas Jaki, Ph.D., Katie Jeffery, Ph.D., Wei Shen Lim, F.R.C.P., Alan Montgomery, Ph.D., Kathryn Rowan, Ph.D.,
Joel Tarning, Ph.D., James A. Watson, D.Phil., Nicholas J. White, F.R.S., Edmund Juszczak, M.Sc., Richard Haynes, D.M., and Martin J. Landray, Ph.D. The authors’ full names and academic degrees are as follows: The RECOVERY Collaborative GroupPeter Horby, F.R.C.P., Marion Mafham,
M.D., Louise Linsell, D.Phil., Jennifer L. Bell, M.Sc., Natalie Staplin, Ph.D., Jonathan R. Emberson, Ph.D., Martin Wiselka, Ph.D., Andrew
Ustianowski, Ph.D., Einas Elmahi, M.Phil., Benjamin Prudon, F.R.C.P., Tony Whitehouse, F.R.C.A., Timothy Felton, Ph.D., John Wil-
liams, M.R.C.P., Jakki Faccenda, M.D., Jonathan Underwood, Ph.D., J. Kenneth Baillie, M.D., Ph.D., Lucy C. Chappell, Ph.D., Saul N. Faust, F.R.C.P.C.H., Thomas Jaki, Ph.D., Katie Jeffery, Ph.D., Wei Shen Lim, F.R.C.P., Alan Montgomery, Ph.D., Kathryn Rowan, Ph.D.,
Joel Tarning, Ph.D., James A. Watson, D.Phil., Nicholas J. White, F.R.S., Edmund Juszczak, M.Sc., Richard Haynes, D.M., and Martin J. Landray, Ph.D. Hydroxychloroquine in Patients with Covid-19 A data sharing statement provided by the authors is available
with the full text of this article at NEJM.org. of Health and Social Care, the Intensive Care National Audit and
Research Centre, Public Health Scotland, National Records Ser-
vice of Scotland, the Secure Anonymised Information Linkage at
University of Swansea, and the NHS in England, Scotland, Wales,
and Northern Ireland; and the members of the independent data
monitoring committee: Peter Sandercock, Janet Darbyshire, David
DeMets, Robert Fowler, David Lalloo, Ian Roberts, and Janet Wittes. We thank the thousands of patients who participated in this trial;
the doctors, nurses, pharmacists, other allied health profession-
als, and research administrators at 176 NHS hospitals across the
United Kingdom who were assisted by the NIHR Clinical Research
Network, NHS DigiTrials, Public Health England, the Department Appendix y,
The affiliations of the members of the writing committee are as follows: the Centre for Tropical Medicine and Global Health, Nuffield
Department of Medicine (P.H., J.T., J.A.W., N.J.W.), Nuffield Department of Population Health (M.M., L.L., J.L.B., N.S., J.R.E., E.J.,
R.H., M.J.L.), the Medical Research Council (MRC) Population Health Research Unit (N.S., J.R.E., R.H., M.J.L.), University of Oxford,
the Oxford University Hospitals NHS Foundation Trust (K.J., M.J.L.), and the National Institute for Health Research (NIHR) Oxford
Biomedical Research Centre (M.J.L.), Oxford, University Hospitals of Leicester NHS Trust and University of Leicester, Leicester (M.W.),
the Regional Infectious Diseases Unit, North Manchester General Hospital (A.U.), University of Manchester (A.U., T.F.), and Manches-
ter University NHS Foundation Trust (T.F.), Manchester, the Research and Development Department, Northampton General Hospital,
Northampton (E.E.), the Department of Respiratory Medicine, North Tees and Hartlepool NHS Foundation Trust, Stockton-on-Tees
(B.P.), University Hospitals Birmingham NHS Foundation Trust and Institute of Microbiology and Infection, University of Birmingham,
Birmingham (T.W.), James Cook University Hospital, Middlesbrough (J.W.), North West Anglia NHS Foundation Trust, Peterborough
(J.F.), the Department of Infectious Diseases, Cardiff and Vale University Health Board, and the Division of Infection and Immunity,
Cardiff University, Cardiff (J.U.), Roslin Institute, University of Edinburgh, Edinburgh (J.K.B.), the School of Life Course Sciences,
King’s College London (L.C.C.), and the Intensive Care National Audit and Research Centre (K.R.), London, the NIHR Southampton
Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of
Southampton, Southampton (S.N.F.), the Department of Mathematics and Statistics, Lancaster University, Lancaster (T.J.), the MRC
Biostatistics Unit, University of Cambridge, Cambridge (T.J.), and the Respiratory Medicine Department, Nottingham University Hos-
pitals NHS Trust (W.S.L.), and the School of Medicine, University of Nottingham (A.M., E.J.), Nottingham — all in the United King-
dom; and the Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
(J.T., J.A.W., N.J.W.). Other Prespecified Outcomes 2038 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. References stratification of patients admitted to hos-
pital with covid-19 using the ISARIC WHO
Clinical Characterisation Protocol: devel-
opment and validation of the 4C Mortality
Score. BMJ 2020;370:m3339. stratification of patients admitted to hos-
pital with covid-19 using the ISARIC WHO
Clinical Characterisation Protocol: devel-
opment and validation of the 4C Mortality
Score. BMJ 2020;370:m3339. Clinical evidence for repurposing chloro-
quine and hydroxychloroquine as anti-
viral agents: a systematic review. Clin
Microbiol Infect 2020;26:979-87. stratification of patients admitted to hos-
pital with covid-19 using the ISARIC WHO
Clinical Characterisation Protocol: devel-
opment and validation of the 4C Mortality
Score. BMJ 2020;370:m3339. 1. Zhu N, Zhang D, Wang W, et al. A
novel coronavirus from patients with
pneumonia in China, 2019. N Engl J Med
2020;382:727-33. 14. Fantini J, Chahinian H, Yahi N. Syner-
gistic antiviral effect of hydroxychloro-
quine and azithromycin in combination
against SARS-CoV-2: what molecular dy-
namics studies of virus-host interactions
reveal. Int J Antimicrob Agents 2020;56:
106020. 2. Verity R, Okell LC, Dorigatti I, et al. Estimates of the severity of coronavirus
disease 2019: a model-based analysis. Lancet Infect Dis 2020;20:669-77. 8. Wang M, Cao R, Zhang L, et al. Rem-
desivir and chloroquine effectively inhibit
the recently emerged novel coronavirus
(2019-nCoV) in vitro. Cell Res 2020;30:
269-71. 3. Zhou F, Yu T, Du R, et al. Clinical
course and risk factors for mortality of
adult inpatients with COVID-19 in Wuhan,
China: a retrospective cohort study. Lan-
cet 2020;395:1054-62. 9. Lu R, Zhao X, Li J, et al. Genomic
characterisation and epidemiology of 2019
novel coronavirus: implications for virus
origins and receptor binding. Lancet 2020;
395:565-74. 15. White NJ, Watson JA, Hoglund RM,
Chan XHS, Cheah PY, Tarning J. COVID-19
prevention and treatment: a critical analy-
sis of chloroquine and hydroxychloroquine
clinical pharmacology. PLoS Med 2020;
17(9):e1003252. 4. Chen N, Zhou M, Dong X, et al. Epide-
miological and clinical characteristics of
99 cases of 2019 novel coronavirus pneu-
monia in Wuhan, China: a descriptive
study. Lancet 2020;395:507-13. 10. Vincent MJ, Bergeron E, Benjannet S,
et al. Chloroquine is a potent inhibitor of
SARS coronavirus infection and spread. Virol J 2005;2:69. 16. Rosenke K, Jarvis MA, Feldmann F,
et al. Hydroxychloroquine proves ineffec-
tive in hamsters and macaques infected
with SARS-CoV-2. June 11, 2020 (https://
www.biorxiv.org/content/10.1101/2020.06
.10.145144v1). preprint. 16. Rosenke K, Jarvis MA, Feldmann F,
et al. Hydroxychloroquine proves ineffec-
tive in hamsters and macaques infected
with SARS-CoV-2. Hydroxychloroquine in Patients with Covid-19 Hydroxychloroquine in Patients with Covid-19 Clinical and microbiological effect of a
combination of hydroxychloroquine and
azithromycin in 80 COVID-19 patients
with at least a six-day follow up: a pilot
observational study. Travel Med Infect Dis
2020;34:101663. 34. Yao X, Ye F, Zhang M, et al. In vitro
antiviral activity and projection of opti-
mized dosing design of hydroxychloro-
quine for the treatment of severe acute
respiratory syndrome coronavirus 2 (SARS-
CoV-2). Clin Infect Dis 2020;71:732-9. to moderate coronavirus disease 2019:
open label, randomised controlled trial. BMJ 2020;369:m1849. to moderate coronavirus disease 2019:
open label, randomised controlled trial. BMJ 2020;369:m1849. 26. Huang M, Tang T, Pang P, et al. Treat-
ing COVID-19 with chloroquine. J Mol
Cell Biol 2020;12:322-5. 35. Borba MGS, Val FFA, Sampaio VS, et al. Effect of high vs low doses of chloroquine
diphosphate as adjunctive therapy for pa-
tients hospitalized with severe acute re-
spiratory syndrome coronavirus 2 (SARS-
CoV-2) infection: a randomized clinical
trial. JAMA Netw Open 2020;3(4):e208857. 36. Watson JA, Tarning J, Hoglund RM,
et al. Concentration-dependent mortality
of chloroquine in overdose. Elife 2020;9:
e58631. 19. Million M, Lagier JC, Gautret P, et al. Early treatment of COVID-19 patients
with hydroxychloroquine and azithromy-
cin: a retrospective analysis of 1061 cases
in Marseille, France. Travel Med Infect
Dis 2020;35:101738. 27. Chen J, Liu D, Liu L, et al. A pilot study
of hydroxychloroquine in treatment of pa-
tients with moderate COVID-19. Zhejiang
Da Xue Xue Bao Yi Xue Ban 2020;49:215-9. (In Chinese.) Da Xue Xue Bao Yi Xue Ban 2020;49:215-9. (In Chinese.) 28. Chen Z, Hu J, Zhang Z, et al. Efficacy
of hydroxychloroquine in patients with
COVID 19 results of a randomized clinical 28. Chen Z, Hu J, Zhang Z, et al. Efficacy
of hydroxychloroquine in patients with
COVID-19: results of a randomized clinical
trial. April 10, 2020 (https://www.medrxiv
.org/content/10.1101/2020.03.22 20. Gao J, Tian Z, Yang X. Breakthrough:
chloroquine phosphate has shown appar-
ent efficacy in treatment of COVID-19
associated pneumonia in clinical studies. Biosci Trends 2020;14:72-3. .20040758v3). preprint. .20040758v3). preprint. 21. Yu B, Li C, Chen P, et al. Low dose of
hydroxychloroquine reduces fatality of criti-
cally ill patients with COVID-19. Sci China
Life Sci 2020 May 15 (Epub ahead of print). 22. Geleris J, Sun Y, Platt J, et al. Observa-
tional study of hydroxychloroquine in hos-
pitalized patients with Covid-19. N Engl J
Med 2020;382:2411-8. 37. Hydroxychloroquine in Patients with Covid-19 Dagens A, Sigfrid L, Cai E, et al. Scope, quality, and inclusivity of clinical
guidelines produced early in the covid-19
pandemic: rapid review. BMJ 2020;369:
m1936. 29. Cavalcanti AB, Zampieri FG, Rosa RG,
et al. Hydroxychloroquine with or without
azithromycin in mild-to-moderate Cov-
id-19. N Engl J Med 2020;383:2041-52. 30. Mekonnen Abate S, Ahmed Ali S,
Mantfardo B, Basu B. Rate of intensive
care unit admission and outcomes among
patients with coronavirus: a systematic
review and meta-analysis. PLoS One 2020;
15(7):e0235653. 38. Lenzer J. Covid-19: US gives emer-
gency approval to hydroxychloroquine
despite lack of evidence. BMJ 2020;369:
m1335. 23. Mahévas M, Tran V-T, Roumier M,
et al. Clinical efficacy of hydroxychloro-
quine in patients with covid-19 pneumo-
nia who require oxygen: observational
comparative study using routine care data. BMJ 2020;369:m1844. 39. Letter from the U.S. Food and Drug
Administration re: revocation of the Emer-
gency Use Authorization (EUA) letter of
March 20, 2020. June 15, 2020 (https://
www.fda.gov/media/138945/download). 39. Letter from the U.S. Food and Drug
Administration re: revocation of the Emer-
gency Use Authorization (EUA) letter of
March 20, 2020. June 15, 2020 (https://
www.fda.gov/media/138945/download). 40. World Health Organization. WHO dis-
continues hydroxychloroquine and lopina-
vir/ritonavir treatment arms for COVID-19. July 4, 2020 (https://www.who.int/news
-room/detail/04-07-2020-who-discontinues
-hydroxychloroquine-and-lopinavir
-ritonavir-treatment-arms-for-covid-19). Copyright © 2020 Massachusetts Medical Society. 31. Armstrong RA, Kane AD, Cook TM. Outcomes from intensive care in patients
with COVID-19: a systematic review and
meta-analysis of observational studies. Anaesthesia 2020;75:1340-9. 24. Molina JM, Delaugerre C, Le Goff J,
et al. No evidence of rapid antiviral clear-
ance or clinical benefit with the combina-
tion of hydroxychloroquine and azithro-
mycin in patients with severe COVID-19
infection. Med Mal Infect 2020;50:384. 32. Austin D, Okour M. Evaluation of po-
tential therapeutic options for COVID-19. J Clin Pharmacol 2020;60:976-7. 33. Carmichael SJ, Charles B, Tett SE. Population pharmacokinetics of hydroxy-
chloroquine in patients with rheumatoid
arthritis. Ther Drug Monit 2003;25:671-81. 25. Tang W, Cao Z, Han M, et al. Hydroxy-
chloroquine in patients with mainly mild 25. Tang W, Cao Z, Han M, et al. Hydroxy-
chloroquine in patients with mainly mild 2040 n engl j med 383;21 nejm.org November 19, 2020
The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. References June 11, 2020 (https://
www.biorxiv.org/content/10.1101/2020.06
.10.145144v1). preprint. 5. Cao J, Tu W-J, Cheng W, et al. Clinical
features and short-term outcomes of 102
patients with coronavirus disease 2019 in
Wuhan, China. Clin Infect Dis 2020;71:
748-55. 11. Zhou P, Yang X-L, Wang X-G, et al. A pneumonia outbreak associated with a
new coronavirus of probable bat origin. Nature 2020;579:270-3. 12. Keyaerts E, Vijgen L, Maes P, Neyts J,
Van Ranst M. In vitro inhibition of severe
acute respiratory syndrome coronavirus
by chloroquine. Biochem Biophys Res
Commun 2004;323:264-8. 17. Gautret P, Lagier J-C, Parola P, et al. Hydroxychloroquine and azithromycin as
a treatment of COVID-19: results of an
open-label non-randomized clinical trial. Int J Antimicrob Agents 2020;56:105949. 18. Gautret P, Lagier J-C, Parola P, et al. 6. Ruan Q, Yang K, Wang W, Jiang L,
Song J. Clinical predictors of mortality
due to COVID-19 based on an analysis of
data of 150 patients from Wuhan, China. Intensive Care Med 2020;46:846-8. 13. Rodrigo C, Fernando SD, Rajapakse S. 13. Rodrigo C, Fernando SD, Rajapakse S. 7. Knight SR, Ho A, Pius R, et al. Risk 2039 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 The New England Journal of Medicine
Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved.
|
https://openalex.org/W2774326815
|
https://europepmc.org/articles/pmc5718417?pdf=render
|
English
| null |
Fear of falling and postural reactivity in patients with glaucoma
|
PloS one
| 2,017
|
cc-by
| 7,190
|
RESEARCH ARTICLE Fa´bio B. Daga1,2,3, Alberto Diniz-Filho3, Erwin R. Boer3, Carolina P. B. Gracitelli2,3, Ricardo
Y. Abe3, Felipe A. Medeiros1,3* Fa´bio B. Daga1,2,3, Alberto Diniz-Filho3, Erwin R. Boer3, Carolina P. B. Gracitelli2,3, Ricardo
Y. Abe3, Felipe A. Medeiros1,3* Fa´bio B. Daga1,2,3, Alberto Diniz-Filho3, Erwin R. Boer3, Carolina P. B. Gracitelli2,3, Ricardo
Y. Abe3, Felipe A. Medeiros1,3* 1 Duke Eye Center and Department of Ophthalmology, Duke University, Durham, North Carolina, United
States of America, 2 Department of Ophthalmology and Vision Science, Federal University of São Paulo, São
Paulo, Brazil, 3 Department of Ophthalmology, University of California, San Diego, La Jolla, California, United
States of America * felipe.medeiros@duke.edu a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 Data Availability Statement: All relevant data are
within the paper and its Supporting Information
files. Data Availability Statement: All relevant data are
within the paper and its Supporting Information
files. Funding: National Institutes of Health/National Eye
Institute grant EY021818 (F.A.M), fellowship grant
from Brazilian National Council for Scientific and
Technological Development (CNPq) 233829/2014-
8 (A.D.F.). Financial support FAM: Alcon
Laboratories (Fort Worth, TX), Bausch & Lomb
(Garden City, NY), Carl Zeiss Meditec (Jena,
Germany), Heidelberg Engineering (Heidelberg,
Germany), Merck (White House Station, NJ), Editor: Manabu Sakakibara, Tokai University,
JAPAN Editor: Manabu Sakakibara, Tokai University,
JAPAN Received: August 4, 2017
Accepted: October 16, 2017
Published: December 6, 2017 Abstract
Purpose To investigate the relationship between postural metrics obtained by dynamic visual stimula-
tion in a virtual reality environment and the presence of fear of falling in glaucoma patients. Results Copyright: © 2017 Daga et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited. Subjects with glaucoma reported greater fear of falling compared to controls (-0.21 vs. 0.27;
P = 0.039). In glaucoma patients, postural metrics during dynamic visual stimulus were
more associated with fear of falling (R2 = 18.8%; P = 0.001) than static (R2 = 3.0%; P =
0.005) and dark field (R2 = 5.7%; P = 0.007) conditions. In the univariable model, fear of fall-
ing was not significantly associated with binocular standard perimetry mean sensitivity (P =
0.855). In the multivariable model, each 1 Nm larger SDTM in anteroposterior direction dur-
ing dynamic stimulus was associated with a worsening of 0.42 units in the fear of falling
questionnaire score (P = 0.001). Methods Citation: Daga FB, Diniz-Filho A, Boer ER, Gracitelli
CPB, Abe RY, Medeiros FA (2017) Fear of falling
and postural reactivity in patients with glaucoma. PLoS ONE 12(12): e0187220. https://doi.org/
10.1371/journal.pone.0187220 This cross-sectional study included 35 glaucoma patients and 26 controls that underwent
evaluation of postural balance by a force platform during presentation of static and dynamic
visual stimuli with head-mounted goggles (Oculus Rift). In dynamic condition, a peripheral
translational stimulus was used to induce vection and assess postural reactivity. Standard
deviations of torque moments (SDTM) were calculated as indicative of postural stability. Fear of falling was assessed by a standardized questionnaire. The relationship between a
summary score of fear of falling and postural metrics was investigated using linear regres-
sion models, adjusting for potentially confounding factors. Editor: Manabu Sakakibara, Tokai University,
JAPAN Introduction Allergan (Irvine, CA), Sensimed (Lausanne,
Switzerland), Topcon (Livermore, CA), Reichert
(Dewey, NY), National Eye Institute (Bethesda,
MD); Research support – Alcon Laboratories (Fort
Worth, TX), Allergan (Irvine, CA), Carl Zeiss
Meditec (Jena, Germany), Reichert (Dewey, NY);
Consultant – Allergan (Irvine, CA), Carl-Zeiss
Meditec, (Jena, Germany), Novartis (Basel,
Switzerland), nGoggle (San Diego, CA). The
funders had no role in study design, data collection
and analysis, decision to publish, or preparation of
the manuscript. Falls are one of the most common and potentially disabling issues among elderly people, jeop-
ardizing their health and independence.[1–7] Vision has an important role in balance control
and environment navigation, with previous studies demonstrating that conditions leading to
visual impairment are associated to higher risk of falling.[8–11] Glaucoma is a progressive
optic neuropathy characterized by degeneration of retinal ganglion cells and their axons and
previous studies have reported a higher risk of falling in patients with glaucoma compared to
normal subjects.[12–14] Glaucoma has also been related to greater fear of falling.[15–19] Fear of falling may have
major impact in older adults, since it leads to restriction of daily activities,[20] causing reduc-
tion in social interaction and mobility,[21,22] loss of confidence,[2,20,21] and depression.[23]
In addition, by restricting physical activity, fear of falling may result in further increase in risk
of falling. As actual falls may then lead to increased fear of falling, the process can become a
vicious circle.[24] Therefore, an assessment of fear of falling is important in order to under-
stand factors associated with fall risk and for development of assistive strategies. Competing interests: The authors have declared
that no competing interests exist Competing interests: The authors have declared
that no competing interests exist Although standard automatic perimetry (SAP) has been the gold standard test for assessing
visual function loss in glaucoma, the association with measures of fear of falling has been
inconsistent in the literature.[24] In SAP visual function is measured by assessing sensitivity to
detect a static white stimulus against a white background. Due to its simplicity, it is likely that
SAP testing does not fully capture certain dynamic aspects of vision that may be important in
performing daily activities, such as maintaining balance. Fear of falling and postural reactivity Introduction In a previous study, we developed a virtual reality paradigm to evaluate postural control
of glaucoma patients in response to dynamic visual stimulation.[11] Postural reactivity was
induced by presenting peripheral dynamic visual stimuli in an immersive virtual environment
using stereoscopic goggles, while assessing balance through a balance platform. Metrics
obtained under this testing paradigm performed significantly better to predict history of falls in
patients with glaucoma compared to SAP. However, the relationship between postural reactivity
metrics and fear of falling has not yet been investigated. Such relationship could be important
in understanding factors that are associated with increased fear of falling in glaucoma. The purpose of this study was to quantify fear of falling in a cohort of patients with glau-
coma and control subjects and investigate the relationship between fear of falling and metrics
of postural reactivity obtained using a virtual reality environment. Conclusion In glaucoma patients, postural reactivity to a dynamic visual stimulus using a virtual reality
environment was more strongly associated with fear of falling than visual field testing and
traditional balance assessment. 1 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 Methods This was a cross-sectional study. Written informed consent was obtained from all participants
(including controls and glaucoma patients). Institutional review board approval was obtained
and the study was conducted in adherence with the Declaration of Helsinki and to the Health
Insurance Portability and Accountability Act. Participants in this study underwent a comprehensive ophthalmologic examination, and
each visited included clinical examination, slit lamp biomicroscopy, visual acuity testing,
gonioscopy, dilated fundus examination, intraocular pressure measurement and stereophotog-
raphy. In addition, participants underwent visual field testing using the Swedish Interactive
Thresholding Algorithm Standard 24–2 strategy on a Humphrey Field Analyzer II-i (Carl
Zeiss Meditec, Dublin, CA), and they were required to have reliable visual field tests, which
was defined as having 33% fixation losses or false negative errors, or 15% of false positive
errors. Visual acuity was measured using Early Treatment Diabetic Retinopathy Study chart
and letter acuity was expressed as the logarithm of minimum angle of resolution. We included
only subjects with open angles on gonioscopy. We also investigated about previous systemic PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 2 / 13 Fear of falling and postural reactivity diseases (diabetes and hypertension), and also about the systemic use of β-blockers or α-ago-
nists. Subjects were excluded if they presented any other ocular or systemic disease that could
affect optic nerve or visual field. Subjects were also excluded if they presented with history of
systemic conditions affecting lower limbs, such as arthritis, gout, history of knee or hip
replacement, or any other pathology affecting the vestibular system. Glaucoma was defined by the presence of repeatable abnormal SAP tests (pattern standard
deviation with P < 0.05 and/or a Glaucoma Hemifield Test outside normal limits) and corre-
sponding optic nerve damage in at least one eye. Healthy control participants in this study
were recruited from the general population through advertisements and were required to be
normal on ophthalmological examination and normal appearance of the optic disc on masked
grading of stereophotographs. Severity of visual field defect was represented by the integrated
binocular mean sensitivity (MS) obtained from monocular SAP 24–2 tests. The integrated bin-
ocular MS was calculated as the average of sensitivities of the integrated binocular visual fields
obtained according to the binocular summation model described by Nelson-Quigg et al.[25] All subjects had measurements of weight and height obtained at the time of testing. Fear of falling evaluation Fear of falling was evaluated using the previously validated 16-item University of Illinois at
Chicago fear of falling scoring questionnaire (Fig 1).[28] Questionnaires were administered
orally to subjects during an in-person interview. Patients were asked about how much fear
they would have if they were to perform any of 16 different tasks, regardless of whether these
tasks had been performed recently. Three possible responses were accepted: not at all worried
(score 3), moderately worried (score 2), or very worried (score 1).[28] A partial credit item
response theory (IRT) model was used to summarize data from the questionnaires and a final
score of fear of falling was obtained. By taking into account item difficulty and discrimination,
summary scores of fear of falling were obtained for each subject. Scores ranged from -3 to +1,
with lower values associated with greater fear of falling. Methods These
were used to calculate body mass index (BMI) for each subject, as the quotient of mass (in kilo-
grams) divided by the square of height (in meters). Level of physical activity was investigated
using the Physical Activity Scale for the Elderly (PASE) questionnaire.[26] The scale ranges
from 0 to 400, with higher scores indicating greater level of physical activity.[26] History of
falls was acquired using the Elderly Fall Screening Test and the Multi-factor Falls Question-
naire.[27] Virtual reality environment for assessing postural reactivity Postural reactivity to visual information was assessed using an immersive virtual environment
with head-mounted stereoscopic goggles (Oculus Rift, Oculus VR, LLC, Irvine, CA) (Fig 2). Details of the testing procedure have been described previously.[11] The Oculus Rift was used
to present a stereoscopic 3D image on a binocular field of view of approximately 100 degrees
diagonal. Postural stability was evaluated using a force platform (AMTI Optima Human Per-
formance System, Advanced Mechanical Technology, Inc., Watertown, MA). Subjects were
supported by a harness system to prevent falling (Handrail and Harness Safety Structure, Ber-
tec Corp., Columbus, OH) (Fig 2). Subjects were required to remove their shoes and stand
upright on the center of the force platform with arms by their side and feet close together. Subjects underwent postural assessment under three conditions: 1. No Oculus Rift (static condition); 2. Oculus Rift in a dark field, without any visual stimulation; PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 3 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 Fear of falling and postural reactivity Fig 1. The 16-item University of Illinois at Chicago fear of falling measure scoring questionnaire. https://doi.org/10.1371/journal.pone.0187220.g001 3. Oculus Rift with translational stimulus (dynamic condition). 3. Oculus Rift with translational stimulus (dynamic condition). 3. Oculus Rift with translational stimulus (dynamic condition). 3. Oculus Rift with translational stimulus (dynamic condition). Postural stability was initially examined without the Oculus Rift. Subjects had both eyes
open and were instructed to fixate at a red dot on the wall. Patients were then instructed to put
on the Oculus Rift and keep their eyes always opened. Postural stability was then tested with
the Oculus Rift showing a completely dark field, i.e., a black screen without any visual stimula-
tion. As no visual input was present, this condition assessed the somatosensory and vestibular
contributions to postural control. In the dynamic condition, postural reactivity was assessed by presenting dynamic visual sti-
muli in order to induce the sensation of self-motion. This was done by presenting an ecolog-
ically valid peripheral background perturbation through the Oculus Rift, a peripheral
translational stimulus (tunnel) while the patient fixated down the tunnel. Ecological validity
refers to the fact that the visual scene moved as expected when the patients moved his/her
head and that the stimulus was what one would visually experience if moving through a tunnel. The peripheral stimulus was presented only in the region outside the central 10 degrees of
view, while the patient was instructed to keep fixation on a central red dot. The translational stimulus was comprised of a sum of four sinusoids with frequencies of
0.1167, 0.2833, 0.5167 and 0.9833 hertz. The amplitude of each sinusoid was inversely related PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 4 / 13 Fig 2. Patient performing the test on the virtual reality environment, while standing on th
platform and wearing the head-mounted goggles.
https://doi.org/10.1371/journal.pone.0187220.g002
Fear of falling and po
one 0187220
December 6 2017 Fear of falling and postural reactivity Fig 2. Patient performing the test on the virtual reality environment, while standing on the force
platform and wearing the head-mounted goggles. https://doi.org/10.1371/journal.pone.0187220.g002 Fig 2. Patient performing the test on the virtual reality environment, while standing on the force
platform and wearing the head-mounted goggles. Fig 2. Patient performing the test on the virtual reality environment, while standing on the force
platform and wearing the head-mounted goggles. https://doi.org/10.1371/journal.pone.0187220.g002 https://doi.org/10.1371/journal.pone.0187220.g002 5 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 Fear of falling and postural reactivity to its frequency to prevent that the highest frequency would dominate. The phases were
selected to minimize the difference between maximum magnitude of the combined signal and
its root mean square (RMS) magnitude; this process is called cresting and is used to avoid
salient signal characteristics caused by an excessively high signal magnitude or an excessively
long period of a low signal magnitude. The resulting signal was scaled to yield an amplitude
RMS of 0.4 meters and a velocity RMS of 0.5 meters/second for the tunnel stimulus. The bene-
fit of using sums-of-sinusoid stimuli is that the perturbation is unpredictable by the patient
unlike the single stimulus. Each test consisted of 15 seconds with a stationary peripheral stimu-
lus followed by 120 seconds of peripheral stimulation. The analysis was performed on the 120
seconds during which the peripheral stimulus was in motion. For each one of three test conditions described above, torque moments produced in the
mediolateral and anteroposterior directions around the center of the force plate were mea-
sured. The torque moments are generated when patient’s center of gravity moves causing a
change in the center of pressure on the force plate.[29] The standard deviations of the torque
moments (SDTM) were calculated as metrics indicative of postural stability and reported in
Newton meters (Nm). Standard deviations of the mediolateral and anteroposterior torque
moments were computed separately as well as the sum of them. Larger values of SDTM were
indicative of worse postural stability. Statistical analysis Descriptive statistics included mean and standard deviation of the variables. Normality
assumption was assessed by inspection of histograms and using Shapiro-Wilk test. Fisher’s
exact test was used for group comparison for categorical variables. Student t test was used for
group comparison for normally distributed variables and Wilcoxon rank-sum (Mann-Whit-
ney) test was used for group comparison for continuous non-normally distributed variables. The association between postural metrics and fear of falling was investigated using linear
regression models, where the summary score of fear of falling was used as the dependent vari-
able and the different postural metrics as independent variables. We initially ran univariable
models evaluating the association of each variable with the outcome. Subsequently, multivari-
able models were used adjusting for the potential confounding factors that had a P value < 0.2
in the univariable model. We also investigate the association between severity of visual field
defect on SAP and fear of falling. All statistical analyses were performed using commercially available software Stata, version
14 (StataCorp LP, College Station, TX). The alpha level (type I error) was set at 0.05. PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 Fear of falling and postural reactivity Table 1. Demographic and clinical characteristics of glaucoma and control subjects included in the study evaluating the relationship between
fear of falling and postural reactivity.*. Glaucoma (n = 35)
Control (n = 26)
P-value
Age, years
70.0 ± 11.2
67.2 ± 11.2
0.262a
Gender, n (%) female
15 (43)
17 (65)
0.120b
Race, n (%)
White
18 (51)
15 (58)
0.499b
African American
11 (31)
10 (39)
Asian
3 (9)
1 (3)
Other
3 (9)
0 (0)
Hypertension, n (%)
22 (68)
15 (68)
0.965b
Diabetes, n (%)
10 (31)
7 (31)
0.965b
Systemic β-blockers use, n (%)
18 (50)
7 (25)
Systemic α-agonists use, n (%)
16 (45)
0
Score of fear of falling
-0.21 ± 1.0
0.27 ± 0.7
0.039a
BMI, kg/m2
25.0 ± 4.0
25.1 ± 4.8
0.897c
Number of falls in past 12 months
0.94 ± 1.3
0.4 ± 0.6
0.013d
Summary score of PASE
156.6 ± 98.5
174.2 ± 96.7
0.526a
MD SAP 24–2 (worse eye), dB
-5.9 ± 7.8
-0.9 ± 1.9
<0.001a
MD SAP 24–2 (better eye), dB
-1.95 ± 4.4
0.3 ± 2.3
<0.001a
Binocular MS SAP 24–2, dB
28.5 ± 3.9
31.3 ± 1.6
<0.001a
Binocular visual acuity, logMAR
-0.02 ± 0.12
-0.07 ± 0.10
0.074c of glaucoma and control subjects included in the study evaluating the relationship between https://doi.org/10.1371/journal.pone.0187220.t001 the anteroposterior direction during dynamic condition was associated with a worsening of
0.32 units in the fear of falling questionnaire score (P = 0.009; R2 = 18.8%) (Table 2). SDTM in
the anteroposterior direction had a higher association with fear of falling than SDTM in the
mediolateral direction (P<0.001). When torque moments in the anteroposterior direction
were considered, postural metrics obtained during dynamic visual stimulation were signifi-
cantly more predictive of fear of falling than those obtained during static (R2 = 3.0%; P =
0.005) and dark field conditions (R2 = 5.7%; P = 0.007). Fear of falling was not significantly
associated with integrated binocular MS (R2 = 0.1%; P = 0.855) (Table 2). For glaucoma patients, number of falls in the past 12 months was significantly associated
with fear of falling (P = 0.035) (Table 2), with a 0.26 worse fear of falling score for each addi-
tional fall. Female gender was also associated with 0.82 units worsening in the fear of falling
score (P = 0.010) (Table 2). Results The study included 35 glaucoma patients and 26 control subjects. Table 1 presents demographic
and clinical characteristics of the studied population. There was no significant difference in
mean age between the glaucoma and control groups (70.0±11.2 vs. 67.2±11.2 years, respectively;
P = 0.262). There were also no statistically significant differences in gender, race, average BMI,
PASE scores, binocular visual acuity, and prevalence of hypertension or diabetes between the
two groups. As expected, the integrated binocular MS of SAP 24–2 showed worse values in glau-
coma patients compared with controls (28.5±3.9 vs. 31.3±1.6 dB, respectively; P<0.001). Sub-
jects with glaucoma reported worse mean scores of fear of falling compared to controls (-0.21
vs. 0.27, respectively; P = 0.039). Diagnosis of glaucoma was also associated with a 2.45 times
higher rate of falls in the past 12 months (rate ratio = 2.45; 95% CI: 1.20–4.97; P = 0.013). Postural metrics during dynamic visual stimulus presentation were significantly associated
with fear of falling in glaucoma patients. In the univariable model, each 1 Nm larger SDTM in PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 6 / 13 BMI = body mass index; kg/m2 = kilograms per square meter; PASE: Physical Activity Scale for the Elderly; MD = mean deviation; SAP = standard 2 = kilograms per square meter; PASE: Physical Activity Scale for the Elderly; MD = mean deviation; SAP = standar dB = decibels; MS = mean sensitivity; logMAR = logarithm of the minimum angle of resolution. https://doi.org/10.1371/journal.pone.0187220.t001 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 automated perimetry; dB = decibels; MS = mean sensitivity; logMAR = logarithm of the minimum angle of resolution *Values are presented as mean ± standard deviation, unless otherwise noted. as mean ± standard deviation, unless otherwise noted. rd deviation, unless otherwise noted. *Values are presented as mean ± standard deviation, unless otherwise noted. Fear of falling and postural reactivity Table 2. Results of the univariable and multivariable linear regression models for explaining fear of falling in glaucoma patients*. Characteristic
Univariable Model
Multivariable Model
Coefficient (95% CI)
P-value
Coefficient (95% CI)
P-value
Anteroposterior SDTM in Dynamic, per 1 Nm increase
-0.32 (-0.55 to -0.08)
0.009
-0.56 (-0.96 to -0.17)
0.007
Anteroposterior SDTM in Dark Field, per 1 Nm increase
-0.20 (-0.50 to 0.09)
0.007
0.20 (-0.23 to 0.64)
0.354
Age, per decade older
-0.03 (-0.06 to 0.00)
0.059
-0.16 (-0.38 to 0.06)
0.157
Gender, female
-0.82 (-1.43 to -0.21)
0.010
-1.04 (-1.61 to -0.47)
0.001
Race, African American
0.40 (-0.31 to 1.11)
0.258
Hypertension
0.19 (-0.49 to 0.86)
0.576
Diabetes
-0.19 (-0.86 to 0.49)
0.576
BMI, per 1 kg/m2 higher
Number of Falls in past 12 months
PASE score, per 100 points lower
-0.03 (-0.12 to 0.05)
-0.26 (-0.51 to -0.02)
0.31 (-0.01 to 0.64)
0.454
0.035
0.059
0.03 (-0.19 to 0.24)
-0.06 (0.20 to -0.32)
0.818
0.644
Binocular MS, per 1 dB lower
0.01 (-0.12 to 0.10)
0.855
Binocular visual acuity, per 0.1 logMAR higher
0.86 (-2.67 to 4.38)
0.621
CI = confidence interval; SDTM = standard deviations of the torque moments; Nm = Newton meter; BMI = body mass index; kg/m2 = kilogram per square
meter; PASE = Physical Activity Scale for the Elderly; MS = mean sensitivity; dB = decibel; logMAR = logarithm of the minimum angle of resolution. *Multivariable model was adjusted for age, gender, number of falls in the past 12 months and PASE score. https://doi org/10 1371/journal pone 0187220 t002 riable and multivariable linear regression models for explaining fear of falling in glaucoma patients*. CI = confidence interval; SDTM = standard deviations of the torque moments; Nm = Newton meter; BMI = body mass index; kg/m2 = kilogram per square
meter; PASE = Physical Activity Scale for the Elderly; MS = mean sensitivity; dB = decibel; logMAR = logarithm of the minimum angle of resolution. *Multivariable model was adjusted for age, gender, number of falls in the past 12 months and PASE score. For healthy subjects none of the postural metrics obtained during dynamic condition were sig-
nificantly associated with fear of falling. For healthy subjects none of the postural metrics obtained during dynamic condition were sig-
nificantly associated with fear of falling. PASE scores were associated with 0.31 units worsening in the fear
of falling questionnaire, but results did not reach statistical significance (P = 0.059). In a multi-
variable model that included age, gender, SDTM in the anteroposterior direction during dark
field condition, number of falls in past 12 months, and PASE score, each 1 Nm larger SDTM
in the anteroposterior direction during dynamic stimulus was associated with a worsening of
0.56 units in the fear of falling questionnaire score (P = 0.001). The multivariable model had
an adjusted R2 of 48.8% for predicting fear of falling in glaucoma subjects. (Table 2) (Fig 3). PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 7 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 Discussion In the present study, we found that metrics of postural reactivity in response to dynamic visual
stimulation presented in a virtual reality environment were significantly associated with fear of
falling in patients with glaucoma. The postural reactivity metrics showed stronger relationship
with fear of falling compared to traditional visual field assessment by SAP. To the best of our
knowledge, this is the first study to investigate the relationship between postural reactivity and
fear of falling in glaucoma patients. Our findings may help improve the understanding of fac-
tors associated with fear of falling in glaucoma and may also potentially assist in the develop-
ment of management strategies to decrease fear of falling and improve quality of life. In agreement with previous studies, patients with glaucoma had worse scores on the fear of
falling questionnaire compared to control subjects.[15,17] However, lower scores (i.e., worse
fear) reported by glaucoma patients were not significantly associated with visual field loss on
standard perimetry. Our results contrast to those of Ramulu and colleagues who found a sig-
nificant association between fear of falling and degree of visual field loss.[15] This could be
related to differences in the populations studied. The study by Ramulu and colleagues included
mostly patients with moderate and severe visual field loss, with median MD in the better eye of
-8dB. In contrast, our study included mostly patients with mild to moderate disease, with
median MD in the better eye of only approximately -2dB, although with a wide range from
-14.69dB to 2.97dB. Our results indicate that fear of falling in glaucoma patients with relatively
mild to moderate disease does not seem to be mediated only by their knowledge of the pres-
ence of disease, or by the degree of visual field loss, as indicated by the weak association with
SAP results. The parameter most strongly associated with fear of falling in our study was the SDTM in
the anteroposterior direction during dynamic visual stimulus presentation, with each 1 Nm
larger SDTM associated with a worsening of 0.32 units in the fear of falling questionnaire
score (P = 0.001). SDTM in response to dynamic visual stimuli was more associated with fear PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 8 / 13 Fig 3. Predicted fear of falling with 95% confidence interval for different values of standard deviation of torque moments (SDTM) in the
anteroposterior direction during dynamic visual stimulus presentation. PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 Discussion Predicted values were derived from the multivariable model adjusting for
confounding factors. Fear of falling and postural reactivity Fear of falling and postural reactivity Fi
3 P
di t d f
f f lli
ith 95%
fid
i t
l f
diff
t
l
f t
d
d d
i ti
f t
t (SDTM) i
th Fig 3. Predicted fear of falling with 95% confidence interval for different values of standard deviation of torque moments (SDTM) in the
anteroposterior direction during dynamic visual stimulus presentation. Predicted values were derived from the multivariable model adjusting for
confounding factors. Fig 3. Predicted fear of falling with 95% confidence interval for different values of standard deviation of torque moments (SDTM) in the
anteroposterior direction during dynamic visual stimulus presentation. Predicted values were derived from the multivariable model adjusting for
confounding factors. ith 95% confidence interval for different values of standard deviation of torque moments (SDTM) in the
g dynamic visual stimulus presentation. Predicted values were derived from the multivariable model adjusting for https://doi.org/10.1371/journal.pone.0187220.g003 https://doi.org/10.1371/journal.pone.0187220.g003 of falling than SDTM in the static condition. Previous studies have shown that under static con-
ditions central and peripheral visual fields appear to have equal importance in the control of
stance.[30] However, in the presence of dynamic information, peripheral vision plays a crucial
role in the control of stance by processing visual information on location and velocity and allow-
ing an adapted postural response to perceived perturbation.[31,32] As glaucoma has a relatively
larger effect on peripheral compared to central vision, this may help explain the better perfor-
mance of postural metrics obtained in dynamic versus static visual stimuli conditions in our
study. In fact, previous studies have suggested that differences in postural control may only be
detectable when the inducing environment is dynamic, rather than static.[33–35] Our results
also indicate that fear of falling in our sample of glaucoma patients does not seem to be mediated
by perceived weaknesses in somatosensory and vestibular systems, as indicated by the weaker
relationship to SDTM in the dark field condition, i.e., in the absence of any visual stimulation. We used a virtual reality environment to present dynamic visual stimuli that simulated a
tunnel moving in anteroposterior direction (translational stimuli). Discussion It is well known that the PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 9 / 13 Fear of falling and postural reactivity motion of the environment creates an illusion of self-motion (vection), which in turn induces
compensatory postural responses.[36] In a previous study, we have demonstrated that these
postural responses are significantly different in glaucoma compared to healthy subjects, with
glaucoma patients showing larger SDTM, i.e. greater postural instability in response to the
visual stimuli.[11] This increased instability in glaucoma patients may have several explana-
tions. The visual stimuli in our virtual reality paradigm are composed of a sum of sinusoids of
different spatial frequencies. In normal subjects, the high spatial frequencies may mask the
ability of lower spatial frequencies in effectively inducing vection and, therefore, postural
responses would be diminished. For glaucoma patients, it has been shown that retinal ganglion
cell loss may result in impaired motion detection, especially for higher spatial frequencies. [37,38] This would then “unmask” the vection-inducing low spatial frequencies, resulting in
greater vection and larger postural compensatory responses. Of note, if visual information pro-
cessing is slow as may happen in glaucoma patients,[39] these compensatory responses may be
deficient or inappropriate, leading to postural instability. It is interesting to note that postural perturbations in the anteroposterior direction (i.e.,
same direction as of the visual stimuli) were more strongly associated with fear of falling than
those in the mediolateral direction. This is in contrast to our previous study investigating the
relationship between postural reactivity and risk of falls using the same virtual reality para-
digm.[11] In our previous study, we showed that the SDTM in the mediolateral direction was
more strongly associated with history of falls than the SDTM in the anteroposterior direction,
for the same translational visual stimuli.[11] The higher association with history of falls for the
mediolateral SDTM is probably explained by the fact that increased postural perturbations in
the direction orthogonal to the visual stimuli may actually be a more important indicator of
overall destabilization of the subject and indicate greater risk of falls. However, fear of falling is
a subjective perception and, as such, may be more related to the greater sway of the patient
that is felt in the anteroposterior direction in response to translational stimuli. PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons
attribution license.
(ZIP) S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons
attribution license. (ZIP) S3 Fig. Signed PLOS consent form for publication of Fig 2 in a PLOS journal. (TIF) S1 Appendix. Dataset underlying the findings in the manuscript. (XLSX) Fear of falling and postural reactivity different instruments to assess fear of falling. As another limitation, it is possible that other
unmeasured variables, such as gait abnormalities, use of medications or other systemic condi-
tions, could also be associated with fear of falling in glaucoma and this issue requires further
investigations. In conclusion, evaluation of postural reactivity to a dynamic visual stimulus using a virtual
reality environment was more strongly associated with fear of falling in glaucoma patients
than visual field testing and traditional balance assessment. These results may contribute to the
knowledge of risk factors for fear of falling in glaucoma and may assist in the development of
strategies to reduce fear of falling and improve quality of life in patients affected by this condi-
tion. In addition, they suggest a promising role for virtual reality in replicating dynamic visual
conditions that might be superior to standard perimetry in assessing how vision impacts daily
activities in patients with glaucoma. S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons
attribution license. S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons
attribution license. S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons
attribution license. (ZIP) Supporting information S1 Fig. Front page of patient from Fig 2 license to publish under the creative commons
attribution license. Conceptualization: Felipe A. Medeiros. Data curation: Fa´bio B. Daga, Alberto Diniz-Filho, Carolina P. B. Gracitelli, Ricardo Y. Abe,
Felipe A. Medeiros. Formal analysis: Fa´bio B. Daga, Erwin R. Boer, Felipe A. Medeiros. Funding acquisition: Felipe A. Medeiros. Funding acquisition: Felipe A. Medeiros. Investigation: Felipe A. Medeiros. Investigation: Felipe A. Medeiros. Methodology: Fa´bio B. Daga, Felipe A. Medeiros. Project administration: Felipe A. Medeiros. Discussion The significant association between fear of falling and our proposed postural metrics could
indicate that these metrics might be useful tools to assess the efficacy of interventions designed
to reduce fear of falling and risk of falls in glaucoma patients, such as exercise-based interven-
tions. It should be noted, however, that fear of falling in an individual patient may have multi-
ple origins.[40,41] In fact, even the best postural reactivity metric in our study was able to
explain only approximately 20% of the variability in fear of falling scores in our sample of glau-
coma patients. Other factors were also associated with fear of falling in our study, such as pre-
vious history of falls and female gender, whereas age and physical activity were of borderline
statistical significance. Importantly, metrics of postural reactivity to dynamic visual stimula-
tion still had significant predictive value even in multivariable models, indicating an indepen-
dent contribution in explaining fear of falling. The multivariable model was able to explain
more than 50% of the variability of fear of falling scores, which could be considered a relatively
good predictive ability for such multifactorial and subjective outcome. Our study had limitations. Due to the cross-sectional design, we were not able to clearly
determine the temporal relationship between the proposed postural reactivity metrics and
development of fear of falling. In addition, we were not able to investigate the longitudinal
relationship between history of falls and fear of falling. However, such relationships are com-
plex and it is likely that simple causal effects cannot be demonstrated. Future longitudinal
studies should be able to clarify the role of postural reactivity metrics as proposed in our study
and risk of falls and fear of falling in glaucoma. As another limitation of our study, we used
only a single questionnaire to investigate and quantify the presence of fear of falling. Although
the questionnaire has been previously validated for this purpose, other scales and instruments
have also been developed. Future studies should attempt to validate our findings using PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 10 / 13 References 1. Nevitt MC, Cummings SR, Kidd S, Black D (1989) Risk factors for recurrent nonsyncopal falls. A pro-
spective study. JAMA 261: 2663–2668. PMID: 2709546 2. Tinetti ME, Speechley M, Ginter SF (1988) Risk factors for falls among elderly persons living in the com-
munity. N Engl J Med 319: 1701–1707. https://doi.org/10.1056/NEJM198812293192604 PMID:
3205267 3. Tinetti ME, Williams TF, Mayewski R (1986) Fall risk index for elderly patients based on number of
chronic disabilities. Am J Med 80: 429–434. PMID: 3953620 4. Campbell AJ, Reinken J, Allan BC, Martinez GS (1981) Falls in old age: a study of frequency and related
clinical factors. Age Ageing 10: 264–270. PMID: 7337066 5. Tobis JS, Reinsch S, Swanson JM, Byrd M, Scharf T (1985) Visual perception dominance of fallers
among community-dwelling older adults. J Am Geriatr Soc 33: 330–333. PMID: 3989198 6. Nickens H (1985) Intrinsic factors in falling among the elderly. Arch Intern Med 145: 1089–1093. PMID:
4004435 7. Glynn RJ, Seddon JM, Krug JH Jr., Sahagian CR, Chiavelli ME, Campion EW (1991) Falls in elderly
patients with glaucoma. Arch Ophthalmol 109: 205–210. PMID: 1993029 8. Haymes SA, Leblanc RP, Nicolela MT, Chiasson LA, Chauhan BC (2007) Risk of falls and motor vehicle
collisions in glaucoma. Invest Ophthalmol Vis Sci 48: 1149–1155. https://doi.org/10.1167/iovs.06-0886
PMID: 17325158 9. Lamoureux EL, Chong E, Wang JJ, Saw SM, Aung T, Mitchell P, et al. (2008) Visual impairment,
causes of vision loss, and falls: the singapore malay eye study. Invest Ophthalmol Vis Sci 49: 528–533. https://doi.org/10.1167/iovs.07-1036 PMID: 18234995 10. Tanabe S, Yuki K, Ozeki N, Shiba D, Tsubota K (2012) The association between primary open-angle
glaucoma and fall: an observational study. Clin Ophthalmol 6: 327–331. https://doi.org/10.2147/OPTH. S28281 PMID: 22399845 11. Diniz-Filho A, Boer ER, Gracitelli CP, Abe RY, van Driel N, Yang Z, et al. (2015) Evaluation of Postural
Control in Patients with Glaucoma Using a Virtual Reality Environment. Ophthalmology 122: 1131–
1138. https://doi.org/10.1016/j.ophtha.2015.02.010 PMID: 25892017 12. Wood JM, Lacherez P, Black AA, Cole MH, Boon MY, Kerr GK (2011) Risk of falls, injurious falls, and
other injuries resulting from visual impairment among older adults with age-related macular degenera-
tion. Invest Ophthalmol Vis Sci 52: 5088–5092. https://doi.org/10.1167/iovs.10-6644 PMID: 21474773 13. Black AA, Wood JM, Lovie-Kitchin JE (2011) Inferior field loss increases rate of falls in older adults with
glaucoma. Optom Vis Sci 88: 1275–1282. https://doi.org/10.1097/OPX.0b013e31822f4d6a PMID:
21873923 14. Project administration: Felipe A. Medeiros. Resources: Felipe A. Medeiros. Resources: Felipe A. Medeiros. Software: Felipe A. Medeiros. Supervision: Felipe A. Medeiros. Validation: Erwin R. Boer. Validation: Erwin R. Boer. Writing – original draft: Fa´bio B. Daga. Writing – original draft: Fa´bio B. Dag Writing – review & editing: Alberto Diniz-Filho, Erwin R. Boer, Carolina P. B. Gracitelli,
Ricardo Y. Abe, Felipe A. Medeiros. 11 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 Fear of falling and postural reactivity References Coleman AL, Stone K, Ewing SK, Nevitt M, Cummings S, Cauley JA, et al. (2004) Higher risk of multiple
falls among elderly women who lose visual acuity. Ophthalmology 111: 857–862. https://doi.org/10. 1016/j.ophtha.2003.09.033 PMID: 15121359 15. Ramulu PY, van Landingham SW, Massof RW, Chan ES, Ferrucci L, Friedman DS (2012) Fear of fall-
ing and visual field loss from glaucoma. Ophthalmology 119: 1352–1358. https://doi.org/10.1016/j. ophtha.2012.01.037 PMID: 22480738 16. Turano KA, Rubin GS, Quigley HA (1999) Mobility performance in glaucoma. Invest Ophthalmol Vis Sci
40: 2803–2809. PMID: 10549639 17. Yuki K, Tanabe S, Kouyama K, Fukagawa K, Uchino M, Shimoyama M, et al. (2013) The association
between visual field defect severity and fear of falling in primary open-angle glaucoma. Invest Ophthal-
mol Vis Sci 54: 7739–7745. https://doi.org/10.1167/iovs.13-12079 PMID: 24150761 18. Klein BE, Moss SE, Klein R, Lee KE, Cruickshanks KJ (2003) Associations of visual function with physi-
cal outcomes and limitations 5 years later in an older population: the Beaver Dam eye study. Ophthal-
mology 110: 644–650. https://doi.org/10.1016/S0161-6420(02)01935-8 PMID: 12689880 19. Wang MY, Rousseau J, Boisjoly H, Schmaltz H, Kergoat MJ, Moghadaszadeh S, et al. (2012) Activity
limitation due to a fear of falling in older adults with eye disease. Invest Ophthalmol Vis Sci 53: 7967–
7972. https://doi.org/10.1167/iovs.12-10701 PMID: 23132799 20. Maki BE, Holliday PJ, Topper AK (1991) Fear of falling and postural performance in the elderly. J Geron-
tol 46: M123–131. PMID: 2071833 21. Tinetti ME, Powell L (1993) Fear of falling and low self-efficacy: a case of dependence in elderly per-
sons. J Gerontol 48 Spec No: 35–38. PMID: 8409238 22. Vellas BJ, Wayne SJ, Romero LJ, Baumgartner RN, Garry PJ (1997) Fear of falling and restriction of
mobility in elderly fallers. Age Ageing 26: 189–193. PMID: 9223714 12 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 Fear of falling and postural reactivity 23. Suzuki M, Ohyama N, Yamada K, Kanamori M (2002) The relationship between fear of falling, activities
of daily living and quality of life among elderly individuals. Nurs Health Sci 4: 155–161. PMID:
12406202 23. Suzuki M, Ohyama N, Yamada K, Kanamori M (2002) The relationship between fear of falling, activities
of daily living and quality of life among elderly individuals. Nurs Health Sci 4: 155–161. PMID:
12406202 24. Friedman SM, Munoz B, West SK, Rubin GS, Fried LP (2002) Falls and fear of falling: which comes
first? References A longitudinal prediction model suggests strategies for primary and secondary prevention. J Am
Geriatr Soc 50: 1329–1335. PMID: 12164987 25. Nelson-Quigg JM, Cello K, Johnson CA (2000) Predicting binocular visual field sensitivity from monocu-
lar visual field results. Invest Ophthalmol Vis Sci 41: 2212–2221. PMID: 10892865 26. Washburn RA, Smith KW, Jette AM, Janney CA (1993) The Physical Activity Scale for the Elderly
(PASE): development and evaluation. J Clin Epidemiol 46: 153–162. PMID: 8437031 27. Lawson SN, Zaluski N, Petrie A, Arnold C, Basran J, Dal Bello-Haas V (2013) Validation of the Saska-
toon Falls Prevention Consortium’s Falls Screening and Referral Algorithm. Physiother Can 65: 31–39. https://doi.org/10.3138/ptc.2011-17 PMID: 24381379 28. Velozo CA, Peterson EW (2001) Developing meaningful Fear of Falling Measures for community dwell-
ing elderly. Am J Phys Med Rehabil 80: 662–673. PMID: 11523969 29. Caldwell GE, R D.G.E., Whittlesey SN (2004) Forces and their measurement. In: Robertson DGE, Cald-
well GE, Hamill J, Kamen G, Whittlesey SN, eds Research methods in biomechanics Champaign, IL:
Human Kinetics: 73–102. 30. Piponnier JC, Hanssens JM, Faubert J (2009) Effect of visual field locus and oscillation frequencies on
posture control in an ecological environment. J Vis 9: 13 11–10. 31. Berencsi A, Ishihara M, Imanaka K (2005) The functional role of central and peripheral vision in the con-
trol of posture. Hum Mov Sci 24: 689–709. https://doi.org/10.1016/j.humov.2005.10.014 PMID:
16337294 32. Habak C, Casanova C, Faubert J (2002) Central and peripheral interactions in the perception of optic
flow. Vision Res 42: 2843–2852. PMID: 12450509 33. Peterka RJ, Black FO (1990) Age-related changes in human posture control: sensory organization
tests. J Vestib Res 1: 73–85. PMID: 1670139 34. Peterka RJ, Black FO (1990) Age-related changes in human posture control: motor coordination tests. J Vestib Res 1: 87–96. PMID: 1670140 35. Ring C, Nayak US, Isaacs B (1988) Balance function in elderly people who have and who have not
fallen. Arch Phys Med Rehabil 69: 261–264. PMID: 3355354 36. Previc FH, Kenyon RV, Boer ER, Johnson BH (1993) The effects of background visual roll stimulation
on postural and manual control and self-motion perception. Percept Psychophys 54: 93–107. PMID:
8351192 37. Karwatsky P, Bertone A, Overbury O, Faubert J (2006) Defining the nature of motion perception deficits
in glaucoma using simple and complex motion stimuli. Optom Vis Sci 83: 466–472. https://doi.org/10. 1097/01.opx.0000225107.38719.0d PMID: 16840871 38. PLOS ONE | https://doi.org/10.1371/journal.pone.0187220
December 6, 2017 References Shabana N, Cornilleau Peres V, Carkeet A, Chew PT (2003) Motion perception in glaucoma patients: a
review. Surv Ophthalmol 48: 92–106. PMID: 12559330 39. Boer ER, Diniz A, Gracitelli C, Abe RY, Van Driel N, Yang ZY, et al. (2015) A Computational Visual-Ves-
tibular Balance Control Model with Peripheral Visual Input. Investigative Ophthalmology & Visual Sci-
ence 56. 40. Lach HW (2005) Incidence and risk factors for developing fear of falling in older adults. Public Health
Nurs 22: 45–52. https://doi.org/10.1111/j.0737-1209.2005.22107.x PMID: 15670324 41. Scheffer AC, Schuurmans MJ, van Dijk N, van der Hooft T, de Rooij SE (2008) Fear of falling: measure-
ment strategy, prevalence, risk factors and consequences among older persons. Age Ageing 37: 19–
24. https://doi.org/10.1093/ageing/afm169 PMID: 18194967 13 / 13
|
https://openalex.org/W4200308140
|
https://www.cambridge.org/core/services/aop-cambridge-core/content/view/14F9EC3B2B1CD5AB097D3671058A2F00/S0899823X2100502Xa.pdf/div-class-title-persistence-of-infectivity-in-elderly-individuals-diagnosed-with-severe-acute-respiratory-coronavirus-virus-2-sars-cov-2-infection-10-days-after-onset-of-symptoms-a-cross-sectional-study-div.pdf
|
English
| null |
Persistence of infectivity in elderly individuals diagnosed with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection 10 days after onset of symptoms: A cross-sectional study
|
Infection control and hospital epidemiology
| 2,021
|
cc-by
| 3,122
|
Population and setting In this prospective cross-sectional study, we included a conven-
ience sample of unvaccinated individuals aged >79 years with
COVID-19 confirmed by RT-PCR from 3 long-term care facili-
ties and 1 acute-care institution in Montreal, Canada, between
November 8, 2020, and January 25, 2021. Participants were
identified
using
institutional
infection
control
databases. Following verbal consent, a nasopharyngeal sample was col-
lected on day 10 after symptom onset using a flocked swab Infection Control & Hospital Epidemiology (2023), 44, 659–662 Infection Control & Hospital Epidemiology (2023), 44, 659–662
doi:10.1017/ice.2021.502 Infection Control & Hospital Epidemiology (2023), 44, 659–662
doi:10.1017/ice.2021.502 Infection Control & Hospital Epidemiology (2023), 44, 659–662
doi:10.1017/ice.2021.502 Abstract We performed viral culture of nasopharyngeal specimens in individuals aged 79 and older, infected with severe acute respiratory coronavirus
virus 2 (SARS-CoV-2), 10 days after symptom onset. A positive viral culture was obtained in 10 (45%) of 22 participants, including 4 (33%) of
12 individuals with improving symptoms. The results of this small study suggest that infectivity may be prolonged among older individuals. (Received 28 July 2021; accepted 22 November 2021; electronically published 6 December 2021) (Received 28 July 2021; accepted 22 November 2021; electronically published 6 December 2021) Coronavirus disease 2019 (COVID-19) is caused by the severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2).1 Infected indi-
viduals must be placed under isolation precautions until infectivity is
resolved.1 The current recommendation is based on studies that
used viral culture as an indicator of infectivity and requires isolation
for 10 days for nonsevere infections in immunocompetent individ-
uals, provided that symptoms are improving.1,2 However, these
studies enrolled relatively young individuals and may not be general-
izable to older patients.1,3,4 Furthermore, some studies have reported
a longer duration of SARS-CoV-2 RNA shedding by reverse tran-
scription polymerase chain reaction (RT-PCR) among older
patients.5 We assessed the presence of infectious SARS-CoV-2 virus
in elderly individuals with COVID-19, 10 days after symptom onset,
using viral culture as a surrogate for infectivity. (FLOQSwabs, Copan Italia, Brescia, Italy) and placed in 3 mL
universal viral transport media (Copan Italia). The samples
were kept at −80°C until RT-PCR and viral culture. Clinical
data (ie, immunosupression, date of symptom onset, symp-
tomatology, clinical outcomes) and the cycle threshold (Ct)
value of the first positive RT-PCR were extracted from patient
charts. (FLOQSwabs, Copan Italia, Brescia, Italy) and placed in 3 mL
universal viral transport media (Copan Italia). The samples
were kept at −80°C until RT-PCR and viral culture. Clinical
data (ie, immunosupression, date of symptom onset, symp-
tomatology, clinical outcomes) and the cycle threshold (Ct)
value of the first positive RT-PCR were extracted from patient
charts. Laboratory methods Viral cultures were performed on Vero E6 cells in 4-mL shell vials
as previously described using a 0.1-mL aliquot of specimen as inoc-
ulum.6 Cultures were kept for 15 days and monitored for a cyto-
pathic effect (CPE) every other day. On initial (day 0) samples, viral RNA was extracted using the
MagMAX Viral/Pathogen II Nucleic Acid Isolation Kit (Thermo
Scientific,
Waltham
MA). RT-PCR
was
performed
on
a
LightCycler LC480 (Roche) using TaqPath RT-qPCR Master Mix
(Thermo Scientific) and primers and probe targeting the E gene as
described previously.7 Samples collected on day 10 and culture super-
natants were processed with an in-house RT-PCR targeting the N
gene as previously described.6 We used the following forward, reverse
and
probe
sequences:
AACCAGAATGGAGAACGCAGTG,
CGGTGAACCAAGACGCAGTATTAT and CGATCAAAACAA
CGTCGGCCCCAAGGTTTAC.6 Persistence of infectivity in elderly individuals diagnosed with severe
acute respiratory coronavirus virus 2 (SARS-CoV-2) infection 10 days
after onset of symptoms: A cross-sectional study Persistence of infectivity in elderly individuals diagnosed with severe
acute respiratory coronavirus virus 2 (SARS-CoV-2) infection 10 days
after onset of symptoms: A cross-sectional study Yves Longtin MD1,2
, Leighanne O. Parkes MD1
, Hugues Charest PhD3,4,5, Stacy Rajarison RN, BScN1,
Gerasimos J. Zaharatos MD1,2, Judith Fafard MD3, Michel Roger MD, PhD3 and Gaston De Serres MD, PhD4
1Jewish General Hospital Sir Mortimer B. Davis, Montreal, Canada, 2Lady Davis Research Institute, Montreal, Canada, 3Laboratoire de Santé Publique du Québec,
Sainte-Anne-de-Bellevue, Canada, 4Institut National de Santé Publique du Québec, Quebec City, Canada and 5Département de microbiologie, infectiologie et
immunologie, Faculté de médecine, Université de Montréal, Montréal, Canada © The Author(s), 2021. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America. This is an Open Access article, distributed under the
terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original
article is properly cited. https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press mbridge University Press on behalf of The Society for Healthcare Epidemiology of America. This is an Open Access article, distributed under the
on licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original Author for correspondence: Dr Yves Longtin, E-mail: yves.longtin@mcgill.ca Statistical analyses The primary outcome was culture positivity, defined as the detec-
tion of a CPE combined with a RT-PCR Ct value on the superna-
tant that is lower than the Ct value of the original specimen. To
investigate factors associated with culture positivity, the Fisher Author for correspondence: Dr Yves Longtin, E-mail: yves.longtin@mcgill.ca
Cite this article: Longtin Y, et al. (2023). Persistence of infectivity in elderly individuals
diagnosed with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection 10
days after onset of symptoms: A cross-sectional study. Infection Control & Hospital
Epidemiology, 44: 659–662, https://doi.org/10.1017/ice.2021.502 © The Author(s), 2021. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America. This is an Open Access article, distributed under the
terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original
article is properly cited. © The Author(s), 2021. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America. This is an
terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distributi
article is properly cited. https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press 2 Published online by Cambridge University Press 660 Yves Longtin et al Table 1. Comparison of Patients With Positive or Negative Culture for SARS-CoV-2 on Day 10 of Infection Table 1. Comparison of Patients With Positive or Negative Culture for SARS-CoV-2 on Day 10 of Infection
Characteristic
Total (N=22),
No. (%)
Culture Positive (N=10),
No. (%)
Culture Negative (N=12),
No. Statistical analyses (%)
P Value
Sex, female
12 (55)
5 (50)
7 (58)
1.00
Age, median y (IQR)
90 (86–96)
90 (86–98)
90 (84–96)
.69
Immunosuppression
4 (18)
2 (20)
2 (17)
1.00
Reception of steroids
13 (59)
8 (80)
5 (42)
.10
Outcome
Hospitalized
8 (36)
5 (50)
3 (25)
.38
Death
7 (32)
3 (30)
4 (33)
1.00
Duration of isolation precautions, d (IQR)
13 (11–16)
14 (11–22)
12 (11–16)
.38
Symptoms1
Cough
16 (73)
8 (80)
8 (67)
.65
Fever
11 (50)
6 (60)
5 (42)
.67
Respiratory distress
7 (32)
4 (40)
3 (25)
.65
Other COVID-19–compatible symptoms2
16 (73)
7 (70)
9 (75)
1.00
Absence of risk factors for prolonged shedding3
4 (18)
2 (20)
2 (17)
1.00
Symptomatology on day 10 of infection
Resolved symptoms
8 (36)
3 (30)
5 (42)
.68
Persistent but improving symptoms
4 (18)
1 (10)
3 (25)
.59
Persistent and not improving symptoms
10 (45)
6 (60)
4 (33)
.39
Persistent fever4
4 (18)
2 (20)
2 (17)
1.00
Laboratory
Ct value on RT-PCR on day of diagnosis5 (IQR)
21 (16–27)
24 (15–27)
21 (18–29)
.73
Ct value on RT-PCR on day 10 of infection (IQR)6
21 (16–24)
17 (15–19)
23 (21–26)
.002 Specimens on day 10 had a median Ct of 21 (IQR, 16–24). A pos-
itive viral culture was obtained in 10 (45%) of 22 samples. Detection of a CPE occurred early; 6 (60%) of 10 samples demon-
strated a CPE by incubation day 3, and 9 (90%) of 10 by incubation
day 8. exact test and the Mann-Whitney U test were performed as appro-
priate. To investigate the capacity of Ct value on day 10 to predict
culture positivity, a receiver operating characteristics (ROC) curve
was plotted to determine the probability of a true positive result as a
function of the probability of a false positive result for all possible
Ct values. A P <.05 was considered significant. The study was
approved by the local research ethics committees. y
A positive culture was obtained for 6 (60%) of 10 individuals
whose symptoms were not improving on day 10 and for 4
(33%) of 12 of those with improving or resolved symptoms. Individuals with positive cultures tended to be more frequently
hospitalized than culture-negative individuals: 5 (50%) of 10 versus
3 (25%) of 12, respectively. Statistical analyses They were also more likely to have
received steroids than those with negative cultures: 8 (80%) of
10 versus 5 (42%) of 12. However, individuals with positive cul-
tures were less likely to die than those with negative cultures: 3
(30%) of 10 versus 4 (33%) of 12, respectively. Notably, these
differences were not statistically significant. Among patients with-
out a recognized risk factor for prolonged shedding, half (2 of 4)
had a positive culture on day 10. https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press Results Note. RT-PCR, detection of SARS-CoV-2 by reverse-transcription polymerase chain reaction. Fig. 1. Box plot showing the cycle threshold value of SARS-CoV-2 RT-PCR of nasopharyngeal swabs taken on the day of diagnosis and on day 10 after onset of symptoms from
elderly patients infected with COVID-19, stratified by persistence of infectivity on day 10 after onset of symptoms. The horizontal line in each box indicates the median, whereas the
top and bottom lines represent the 75th and 25th percentiles, respectively. Error bars represent 95% confidence intervals, and the dot represents an outlier. Note. RT-PCR, detection of SARS-CoV-2 by reverse-transcription polymerase chain reaction. culture on day 10, 24 vs 21; P = .73) (Fig. 1). In contrast, the Ct
value of the sample collected on day 10 predicted culture positivity
(median Ct of positive vs negative cultures, 17 (IQR, 15–19) vs 23
(IQR, 21–26), respectively; P = .003). The performance of the day-
10 Ct value in predicting culture positivity is shown through the
receiver operating characteristics (ROC) curve (Supplementary
Fig. 1 online). The area under the ROC curve was 0.90 (95% CI,
0.74–1.00). Using a cutoff Ct of 20.7 had 90% sensitivity (9 of
10 patients) and 90% specificity (9 of 10 patients) to predict culture
positivity. other predictors of prolonged infectivity. Cultures were performed
after a freeze–thaw cycle that may affect the integrity of the virus. We did not perform epidemiological investigations to correlate
culture positivity and transmissibility to other individuals. Most
individuals had risk factors for prolonged viral shedding. Still, per-
sistent infectivity in our elderly population was much more fre-
quent than previously reported among severe cases in younger
individuals in which ∼5% remain infectious by day 10.8 y
y
In conclusion, this investigation suggests that infectivity may be
longer than recognized among older individuals and appear to be
predicted by low Ct values on day 10 of infection. Further studies
are required to determine whether isolation precaution recom-
mendations should be modified among the older individuals. Discussion The belief that patients with COVID-19 remain infectious for <10
days stems from studies conducted among younger populations,
with an average or median age ranging from 33 to 57.3,4 This notion
may not be generalizable to patients over the age of 79; ∼50% of
individuals in our study were still shedding infectious viral par-
ticles 10 days after symptom onset. Furthermore, clinical improve-
ment was not predictive of loss of infectivity; ∼33% those with
resolved or improving symptoms remained infective. In contrast,
a lower cycle threshold (indicating a greater quantity of viral RNA
in the sample) was a predictor of culture positivity on day 10 of
COVID-19, as reported elsewhere.2,3,8 Supplementary material. To view supplementary material for this article,
please visit https://doi.org/10.1017/ice.2021.502 Acknowledgments. We thank the microbiology technicians of the virology
laboratory at the Laboratoire de Santé Publique du Québec for their assistance
in conducting the viral cultures. Financial support. Laboratoire de Santé Publique du Québec. Dr Yves
Longtin’s research is supported by the Fonds de Recherche du Québec en Santé. Financial support. Laboratoire de Santé Publique du Québec. Dr Yves
Longtin’s research is supported by the Fonds de Recherche du Québec en Santé. Conflicts of interest. Yves Longtin declares research grants outside of the sub-
mitted work from Merck, Gojo and Becton Dickinson. All other authors declare
no competing interests. Few studies have investigated infectivity specifically among
older individuals. In British long-term care homes, infectious virus
could be recovered for up to 13 days among residents (median age,
85) compared to up to 7 days among staff (median age, 47).9
Among nursing home residents in Washington, 4 of 8 samples col-
lected between days 7 and 13 after symptom onset were positive by
viral culture.2 By contrast, recovery of replication-competent
SARS-CoV-2 was 8 days or less after diagnosis in 8 of 9 nursing
home residents in Arkansas, although infectivity persisted for 19
days in 1 immunocompromised individual.10 https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press Results Overall, 22 participants were recruited. The median age was 90 years
old (interquartile range [IQR], 86–96) and 12 (55%) were female
(Table 1). Also, 4 patients (18%) were immunosuppressed, 13
(59%) received steroids to treat their infection, 8 (36%) were hospi-
talized, and 7 (32%) died. The initial sample to confirm the diagnosis
was taken within 1 day of symptom onset in 21 (95%) of 22 and had
a median RT-PCR Ct value of 21 (IQR, 16–27). By day 10 after symptom onset, 8 (36%) of 22 had no residual
symptom, 4 (18%) of 22 were still symptomatic but improving,
whereas 10 (45%) of 22 had no symptom improvement. The Ct value of the initial sample did not predict culture pos-
itivity (median Ct of participants with and without a positive 661 Infection Control & Hospital Epidemiology Fig. 1. Box plot showing the cycle threshold value of SARS-CoV-2 RT-PCR of nasopharyngeal swabs taken on the day of diagnosis and on day 10 after onset of symptoms from
elderly patients infected with COVID-19, stratified by persistence of infectivity on day 10 after onset of symptoms. The horizontal line in each box indicates the median, whereas the
top and bottom lines represent the 75th and 25th percentiles, respectively. Error bars represent 95% confidence intervals, and the dot represents an outlier. Note. RT-PCR, detection of SARS-CoV-2 by reverse-transcription polymerase chain reaction. Fig. 1. Box plot showing the cycle threshold value of SARS-CoV-2 RT-PCR of nasopharyngeal swabs taken on the day of diagnosis and on day 10 after onset of symptoms from
elderly patients infected with COVID-19, stratified by persistence of infectivity on day 10 after onset of symptoms. The horizontal line in each box indicates the median, whereas the
top and bottom lines represent the 75th and 25th percentiles, respectively. Error bars represent 95% confidence intervals, and the dot represents an outlier. Note. RT-PCR, detection of SARS-CoV-2 by reverse-transcription polymerase chain reaction. Fig. 1. Box plot showing the cycle threshold value of SARS-CoV-2 RT-PCR of nasopharyngeal swabs taken on the day of diagnosis and on day 10 after onset of symptoms from
elderly patients infected with COVID-19, stratified by persistence of infectivity on day 10 after onset of symptoms. The horizontal line in each box indicates the median, whereas the
top and bottom lines represent the 75th and 25th percentiles, respectively. Error bars represent 95% confidence intervals, and the dot represents an outlier. 02 Published online by Cambridge University Press 5. Owusu D, Pomeroy MA, Lewis NM, et al. Persistent SARS-CoV-2 RNA
shedding without evidence of infectiousness: a cohort study of individuals
with COVID-19. J Infect Dis 2021;224:1362–1371. 6. Longtin Y, Charest H, Quach C, et al. Infectivity of healthcare workers diag-
nosed with coronavirus disease 2019 (COVID-19) approximately 2 weeks
after onset of symptoms: a cross-sectional study. Infect Control Hosp
Epidemiol 2021. doi: 10.1017/ice.2020.1420. 4. Basile K, McPhie K, Carter I, et al. Cell-based culture of SARS-CoV-2
informs infectivity and safe de-isolation assessments during COVID-19.
Clin Infect Dis 2021;73:e2952–e2959. 4. Basile K, McPhie K, Carter I, et al. Cell-based culture of SARS-CoV-2
informs infectivity and safe de-isolation assessments during COVID-19.
Clin Infect Dis 2021;73:e2952–e2959.
5. Owusu D, Pomeroy MA, Lewis NM, et al. Persistent SARS-CoV-2 RNA
shedding without evidence of infectiousness: a cohort study of individuals
with COVID-19. J Infect Dis 2021;224:1362–1371.
6. Longtin Y, Charest H, Quach C, et al. Infectivity of healthcare workers diag-
nosed with coronavirus disease 2019 (COVID-19) approximately 2 weeks
after onset of symptoms: a cross-sectional study. Infect Control Hosp
Epidemiol 2021. doi: 10.1017/ice.2020.1420. https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press References 1. Kadire SR, Fabre V, Wenzel RP. Doctor, how long should I isolate? N Engl J
Med 2021;384:e47. 2. Arons MM, Hatfield KM, Reddy SC, et al. Presymptomatic SARS-CoV-2
infections and transmission in a skilled nursing facility. N Engl J Med
2020;382:2081–2090. 2. Arons MM, Hatfield KM, Reddy SC, et al. Presymptomatic SARS-CoV-2
infections and transmission in a skilled nursing facility. N Engl J Med
2020;382:2081–2090. 3. Gniazdowski V, Morris CP, Wohl S, et al. Repeat COVID-19 molecular test-
ing: correlation of SARS-CoV-2 culture with molecular assays and cycle
thresholds. Clin Infect Dis 2021;73:e860–e869. 3. Gniazdowski V, Morris CP, Wohl S, et al. Repeat COVID-19 molecular test-
ing: correlation of SARS-CoV-2 culture with molecular assays and cycle
thresholds. Clin Infect Dis 2021;73:e860–e869. Our study has several limitations. The small sample size limits
its generalizability. We did not collect data on comorbidities and 662 Yves Longtin et al Yves Longtin et al 4. Basile K, McPhie K, Carter I, et al. Cell-based culture of SARS-CoV-2
informs infectivity and safe de-isolation assessments during COVID-19. Clin Infect Dis 2021;73:e2952–e2959. 7. Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus
(2019-nCoV) by real-time RT-PCR. Euro Surveill 2020;25:2000045. 8. Kim MC, Cui C, Shin KR, et al. Duration of culturable SARS-CoV-2 in
hospitalized patients with COVID-19. N Engl J Med 2021;384:
671–673. 9. Ladhani SN, Chow JY, Janarthanan R, et al. Investigation of SARS-CoV-2
outbreaks in six care homes in London, April 2020. EClinicalMedicine
2020;26:100533. f
6. Longtin Y, Charest H, Quach C, et al. Infectivity of healthcare workers diag-
nosed with coronavirus disease 2019 (COVID-19) approximately 2 weeks
after onset of symptoms: a cross-sectional study. Infect Control Hosp
Epidemiol 2021. doi: 10.1017/ice.2020.1420. f
6. Longtin Y, Charest H, Quach C, et al. Infectivity of healthcare workers diag-
nosed with coronavirus disease 2019 (COVID-19) approximately 2 weeks
after onset of symptoms: a cross-sectional study. Infect Control Hosp
Epidemiol 2021. doi: 10.1017/ice.2020.1420. 10. Surie D, Huang JY, Brown AC, et al. Infectious period of severe acute res-
piratory syndrome coronavirus 2 in 17 nursing home residents—Arkansas,
June–August 2020. Open Forum Infect Dis 2021;8:ofab048.
|
https://openalex.org/W2728170331
|
https://europepmc.org/articles/pmc5492486?pdf=render
|
English
| null |
Extensively Drug-Resistant Klebsiella pneumoniae Causing Nosocomial Bloodstream Infections in China: Molecular Investigation of Antibiotic Resistance Determinants, Informing Therapy, and Clinical Outcomes
|
Frontiers in microbiology
| 2,017
|
cc-by
| 10,410
|
ORIGINAL RESEARCH
published: 30 June 2017
doi: 10.3389/fmicb.2017.01230 Extensively Drug-Resistant Klebsiella
pneumoniae Causing Nosocomial
Bloodstream Infections in China:
Molecular Investigation of Antibiotic
Resistance Determinants, Informing
Therapy, and Clinical Outcomes Wenzi Bi 1, 2, Haiyang Liu 1, Rhys A. Dunstan 3, Bin Li 1, Von Vergel L. Torres 3,
Jianming Cao 2, Lijiang Chen 1, Jonathan J. Wilksch 3, Richard A. Strugnell 4,
Trevor Lithgow 3* and Tieli Zhou 1* Keywords: antimicrobial resistance determinants, bacteraemia, clinical outcomes, Klebsiella pneumoniae, XDR 1 Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China, 2 School of
Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China, 3 Infection and Immunity Program,
Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia, 4 Department
of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, VIC, Australia Edited by:
Miklos Fuzi,
Semmelweis University, Hungary Reviewed by:
Xiaoting Hua,
Zhejiang University, China
Marcelo Tolmasky,
California State University, Fullerton,
United States Reviewed by:
Xiaoting Hua,
Zhejiang University, China
Marcelo Tolmasky,
California State University, Fullerton,
United States The rise in diversity of antimicrobial resistance phenotypes seen in Klebsiella pneumoniae
is becoming a serious antibiotic management problem. We sought to investigate the
molecular characteristics and clinical implications of extensively drug-resistant (XDR)
K. pneumoniae isolated from different nosocomial bloodstream infections (BSIs) patients
from July 2013 to November 2015. Even in combination treatment, meropenem did
not protect against mortality of BSIs patients (P = 0.015). In contrast, tigecycline in
combination with other antimicrobial agents significantly protected against mortality
(P = 0.016). Antimicrobial susceptibility tests, molecular detection of antibiotic resistance
determinants, conjugation experiments, multilocus sequence typing (MLST), S1-PFGE,
Southern blot, SDS-PAGE, immunoblot analysis, and pulsed-field gel electrophoresis
(PFGE) were used to characterize these isolates. These XDR K. pneumoniae strains
were resistant to conventional antimicrobials except tigecycline and polymyxin B and
co-harbored diverse resistance determinants. rmtB, blaKPC−2 as well as blaCTX−M−9
were located on a transferable plasmid of ∼54.2 kb and the most predominant replicon
type was IncF. 23 of the 35 isolates belonging the predominant clone were found
to incorporate the globally-disseminated sequence type ST11, but others including a
unique, previously undiscovered lineage ST2281 (allelic profile: 4-1-1-22-7-4-35) were
also found and characterized. The porins OmpK35 and OmpK36 were deficient in
two carbapenemase-negative carbapenem-resistant strains, suggesting decreased drug
uptake as a mechanism for carbapenem resistance. This study highlights the importance
of tracking hospital acquired infections, monitoring modes of antibiotic resistance to
improve health outcomes of BSIs patients and to highlight the problems of XDR
K. pneumoniae dissemination in healthcare settings. *Correspondence:
Trevor Lithgow
trevor.lithgow@monash.edu
Tieli Zhou
wyztli@163.com *Correspondence:
Trevor Lithgow
trevor.lithgow@monash.edu
Tieli Zhou
wyztli@163.com Specialty section:
This article was submitted to
Antimicrobials, Resistance and
Chemotherapy,
a section of the journal
Frontiers in Microbiology
Received: 24 April 2017
Accepted: 19 June 2017
Published: 30 June 2017 Specialty section:
This article was submitted to
Antimicrobials, Resistance and
Chemotherapy,
a section of the journal
Frontiers in Microbiology Specialty section:
This article was submitted to
Antimicrobials, Resistance and
Chemotherapy,
a section of the journal
Frontiers in Microbiology Received: 24 April 2017
Accepted: 19 June 2017
Published: 30 June 2017 Clinical Data Collection The Gram-negative bacterium Klebsiella pneumoniae is widely
distributed in the environment and increasingly reported
as a cause of invasive infections in healthcare settings,
particulary in immunocompromised patients (Bagley, 1985;
Lee et al., 2016; Paczosa and Mecsas, 2016; Wyres and
Holt, 2016). Antimicrobial resistance in K. pneumoniae is
increasing, particularly beta-lactamases and carbapenemases
having been well-characterized as increasing the infection
threat (Mathers et al., 2015; Campos et al., 2016; Lee et al.,
2016). This seriously antibiotic management problem is now
frequently seeing both nosocomial and community associated
infections. Infections caused by extensively drug-resistant (XDR)
K. pneumoniae, such as pneumonia, urinary tract infections,
and bloodstream infections (BSIs) (Bagley, 1985; Girometti
et al., 2014; Paczosa and Mecsas, 2016), have been closely
related to increased morbidity, mortality, long hospital stay,
and high healthcare costs (Giske et al., 2008; Bush et al.,
2011). From July 2013 to November 2015, a total of 131 BSIs patients
hospitalized in the First Affiliated Hospital of Wenzhou Medical
University were shown to carry K. pneumoniae. Among these,
35 patients were defined as XDR K. pneumoniae BSIs patients if
their blood cultures were positive for XDR K. pneumoniae and
with clinical signs of systemic inflammatory response syndrome. BSIs patients were further divided into two groups based
on clinical outcome of antimicrobial treatment: death group
(n = 14) and survivor group (n = 21). Medical records and
clinical data (patient age, gender, ICU length of stay, reasons
for ICU admission, intensive care procedures, comorbidities,
medical care measures before BSIs, antibiotic administration,
microbiological data, and outcomes) were collected and analyzed
and are presented in Table 1. All of the investigation protocols in this study were approved
by The Ethics Committee of The First Affiliated Hospital of
Wenzhou Medical University. Informed consent was waived
because this retrospective study with retrospective observational
nature mainly focused on bacteria and did no interventions to
patients. Antimicrobial
resistance
is
a
global
problem,
and
K. pneumoniae is recognized as a major pathogen of hospital-
acquired infections. In the past several years, Chinese clinicians
have witnessed a remarkable increase in the drug resistance
rate of K. pneumoniae strains isolated from clinical settings. For example, carbapenemase-producing K. pneumoniae was
first identified in China in 2007 and by 2013 a carbapenemase-
resistance cassette was carried by 13.4% of K. pneumoniae
isolated from hospital patients (Qi et al., 2011; Hu et al.,
2016). Citation: Citation:
Bi W, Liu H, Dunstan RA, Li B,
Torres VVL, Cao J, Chen L,
Wilksch JJ, Strugnell RA, Lithgow T
and Zhou T (2017) Extensively
Drug-Resistant Klebsiella pneumoniae
Causing Nosocomial Bloodstream
Infections in China: Molecular
Investigation of Antibiotic Resistance
Determinants, Informing Therapy, and
Clinical Outcomes. Front. Microbiol. 8:1230. doi: 10.3389/fmicb.2017.01230 June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 1 Bi et al. XDR K. Pneumoniae Causing BSIs Clinical Data Collection Now, a substantial portion of hospitalized patients
are
colonized
by
these
pathogens,
causing
outbreaks
of
nosocomial infections in various regions across the country
(Paczosa and Mecsas, 2016). K. pneumoniae is now seen as
one of the major pathogenic bacteria of BSIs, accounting for
11.3% between 2011 and 2012 in China (Lv et al., 2014). The
dissemination of XDR K. pneumoniae is now causing difficult-
to-treat infections worldwide, bringing with its tremendous
challenges to the clinical therapeutic options (Lim et al.,
2015). Although
carbapenems
possess
good
antibacterial
activity to Gram-negative bacteria, the rates of carbapenem
resistance among K. pneumoniae escalated from 0.7% in
2006 to 10% in 2013 (Hu et al., 2016). The availability of
alternative, effective antimicrobial agents is limited (Tang et al.,
2016). Bacterial Isolates Identification and
Antimicrobial Susceptibility Profiling p
y
g
This retrospective study was conducted at the First Affiliated
Hospital of Wenzhou Medical University, China. Based on the
standardized international definition for XDR described by Li
et al. (2012), 35 non-repetitive K. pneumoniae strains, isolated
from nosocomial BSIs patients that were found to be susceptible
to two or fewer antimicrobial categories, were collected. Initially,
bacterial identification and antimicrobial susceptibility tests were
conducted by the Vitek2 system (BioMèrieux, France). Then,
the isolates were stored in frozen condition at −80◦C with
30% glycerol. Subsequently, minimum inhibitory concentrations
(MICs) of tigecycline and polymyxin B were determined by broth
dilution method and interpreted by the recommendation of the
European Committee on Antimicrobial Susceptibility Testing
(EUCAST, 2015). Escherichia coli ATCC 25922 served as the
control strain for susceptibility testing. Frontiers in Microbiology | www.frontiersin.org Molecular Detection of Antibiotic
Resistance Determinants The
presence
of
resistant
mechanisms,
including
ESBLs
genes (blaCTX−M−1, blaCTX−M−9, blaTEM, blaSHV, blaVEB,
and blaPER), AmpC genes (blaCMY, blaFOX, blaMOX, blaDHA),
carbapenemase genes (blaKPC, blaSPM, blaIMP, blaVIM, blaGES,
blaNDM, blaOXA−23, blaOXA−48), PMQR genes [qnrA, qnrB,
qnrC, qnrD, qnrS, qepA, aac(6′)-Ib-cr, oqxA, oqxB, gyrA, parC],
AMEs [AAC(6′)-Ib, APH(3′)-Ia, AAC(3)-IV, ANT(2′′)-Ia], and
16S-RMTase genes (armA, rmtA, rmtB, rmtC, rmtD, rmtE) were
investigated by PCR and sequencing. For each isolate, DNA
was extracted from fresh bacterial colonies using an AxyPrep
Bacterial Genomic DNA Miniprep kit (Axygen Scientific,
Union city, CA, USA). PCR assays were performed on a Veriti Several
mechanisms
are
known
to
mediate
antibiotic
resistance to commonly used antimicrobial agents, including
extended-spectrum β-lactamases (ESBLs) and carbapenemases,
as well as plasmid-mediated quinolone resistance (PMQR)
genes,
aminoglycoside-modifying
enzymes
(AMEs),
and
16S rRNA methyltransferase (16S-RMTase) (Hu et al., 2014;
Findlay et al., 2015; Buruk et al., 2016). The current study
focused on pinpointing the antibiotic resistance determinants
of
XDR
K. pneumoniae
isolated
from
nosocomial
BSIs
patients
and
factors
closely
related
to
clinical
outcome,
with emphasis on determining appropriate antimicrobial drug
therapy. June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 2 Bi et al. Bi et al. XDR K. Pneumoniae Causing BSIs TABLE 1 | Clinical characteristics of nosocomial BSIs patients. Molecular Detection of Antibiotic
Resistance Determinants Characteristics of
BSIs patients
variable
All patients
(n = 35)
BSIs patients
P
Death group
Survivor group
(n = 14 )
(n = 21)
Age (years), median
(IOR)
60 (14–90)
65 (14–90)
59 (16–83)
Male
28 (80.0)
11 (31.4)
17 (48.6)
1
Type of ICU admission
Direct
13 (37.1)
6 (17.1)
7 (20.0)
0.724
Transfer
8 (22.9)
5 (14.3)
3 (8.6)
0.221
Reason for ICU admission
Respiratory failure
6 (17.1)
1 (2.8)
5 (14.3)
0.366
Shock
4 (11.4)
3 (8.6)
1 (2.8)
0.279
Coma
6 (17.1)
5 (14.3)
1 (2.8)
0.028
ICU intensive care procedures
Invasive mechanical
ventilation
16 (45.8)
8 (22.9)
8 (22.9)
0.317
Central venous
catheter
18 (51.4)
8 (22.9)
10 (28.5)
0.733
Urinary catheter
12 (34.3)
8 (22.9)
4 (11.4)
0.031
Pre-infection health care interventions
Surgery
8 (22.9)
5 (14.3)
3 (8.6)
0.221
Dialysis
6 (17.1)
2 (5.7)
4 (11.4)
1
Mechanical ventilation
17 (48.6)
8 (22.9)
9 (25.7)
0.5
Indwelling invasive devices
Central venous
catheter
28 (80.0)
13 (37.1)
15 (42.9)
0.203
Urinary catheter
20 (57.2)
12 (34.3)
8 (22.9)
0.007
Treatments administered
Corticosteroids
11 (31.4)
4 (11.4)
7 (20.0)
1
Chemotherapy,
radiotherapy
6 (17.1)
1 (2.8)
5 (14.3)
0.366
Comorbidities
Intracranial disease
7 (20.0)
6 (17.1)
1 (2.8)
0.01
Respiratory disease
27 (77.2)
10 (28.6)
17 (48.6)
0.685
Cardiovascular disease
11 (31.4)
4 (11.4)
7 (20.0)
1
Tumor, leukemia, and
lymphoma
5 (14.2)
1 (2.8)
4 (11.4)
0.627
Diabetes
8 (22.9)
3 (8.6)
5 (14.3)
1
Trauma
4 (11.4)
2 (5.7)
2 (5.7)
1
Kidney disease
11 (31.4)
4 (11.4)
7 (20.0)
1
Combination drug therapy
Combination including
tigecycline (50 mg/12 h)
14 (40.0)
2 (5.7)
12 (34.3)
0.016
Combination including
meropenem (1 g/8 h)
9 (25.7)
7 (20.0)
2 (5.7)
0.015
Length of stay
ICU length of stay, days
16 (1–58)
15 (1–58)
17 (3–57)
Hospital length of stay,
days
30 (1–86)
40 (1–60)
16 (6–86)
Data are presented as number (%) or median [IQR]. TABLE 1 | Clinical characteristics of nosocomial BSIs patients. available on request. BLAST was utilized to align drug-resistance
gene nucleotide sequences (http://blast.ncbi.nlm.nih.gov/Blast. cgi). Outer Membrane Proteins Analysis Outer Membrane Proteins Analysis
A crude outer membrane protein (OMP) fraction was isolated
by sonication, and OMPs were separated by sodium dodecyl
sulfate polyacrylamide gel electrophoresis (12% SDS-PAGE),
and OmpK35 and OmpK36 were detected by immunoblotting
(serum dilution 1:20,000). K. pneumoniae ATCC 13883 served
as a control strain for OMP profiling (Webb et al., 2012; Zhou
et al., 2015). For outer membrane purification, crude membranes
were isolated from K. pneumoniae ATCC 13883 and subjected
to sucrose density fractionation. Membrane fractions were then
subject to analysis by SDS-PAGE and Coomassie blue staining. Alternatively, fractions were analyzed by immunoblotting to
determine the localization of inner (F1β) and outer (BamB)
membrane proteins markers (Clements et al., 2009; Zhou et al.,
2015). Data are presented as number (%) or median [IQR]. Plasmid Analysis and Southern Blot Plasmid Analysis and Southern Blot
Major plasmid incompatibility groups: F, FIA, FIB, FIC, HI1,
HI2, I1, L/M, N, P, W, T, X, Y, K, A/C, B/O, FII, FrepB,
were detected by a PCR-based replicon typing (PBRT) scheme
(Carattoli et al., 2005). S1 nuclease converted supercoiled
plasmids into full-length linear molecules, and S1-PFGE can
be used to screen for megaplasmids simultaneously (Barton
et al., 1995). Total DNA from the K. pneumoniae donor strains
and E. coli transconjugants were isolated using an Axyprep
Bacterial Genomic DNA Miniprep kit, digested with S1 nuclease
(Takara Bio, Inc.) and analyzed in a CHEF-Mapper XA PFGE
system (Bio-Rad). The gel was then subject to Southern blot
analysis, after transfer to a positively charged nylon membrane
(Roche Diagnostics, Branford, USA) by the capillary method. The
membrane was subject to hybridization with labeled blaKPC−2,
rmtB, blaCTX−M−9 probes according to the instructions of
Detection Starter Kit II (Roche, Sant Cugat del Vallès, Spain). The
plasmids of Salmonella H9812 served as size markers (Zhou et al.,
2015). Conjugation Experiments To determine the transferability of resistance determinants,
Luria-Bertani (LB) mating experiments were implemented. Sodium azide-resistant E. coli J53 served as the recipient strain (Yi
et al., 2012). Transconjugants were selected on Mueller-Hinton
agar plates containing sodium azide (100 mg/L) and ertapenem
(0.5 mg/L). The resistance genes successfully transferred from
the donor strains were verified by PCR. MICs of antibiotics for
the transconjugants were compared to donors and E. coli J53 to
further confirm the transferable resistance genes. Distribution of Resistance Determinants Diverse resistance determinants were detected among the 35
XDR K. pneumoniae strains (Table 2). Of these, 33 strains
(94.3%) were detected as co-harboring three or more resistance
determinants. There is a global spread of KPC-2 carbapenemase
(Naas et al., 2008; Nordmann et al., 2009) that usually explains
such findings. However, two strains (FK688 and FK1934) did
not express KPC-2 carbapenemase (highlighted in Figure 1). Other β-lactamases were also prevalent, including CTX-M-type
ESBLs (31 isolates), SHV (28 isolates), and TEM (11 isolates). In addition, several strains harbored the β-lactamases CMY and
DHA-1. Additional genes conferring drug resistance were sequenced,
including the DNA gyrase encoding gyrA and the DNA
topoisomerase IV encoding parC. Amino acid substitutions
detected in 31 (88.6%) of the strains were gyrA (S83I, D87G) and
parC (S80I). In addition, mutations were detected in quinolone
resistance-determining regions (QRDRs). Intriguingly, 29 of the
30 major ST strains (ST11, ST656) among the fluoroquinolone-
resistant strains carried the favorable “double serine” mutations
in the gyrA and parC genes plus an additional-energetically less
favorable gyrA mutation. A single ST11 strain (2048/15) carried
just one favorable serine mutation without any less favorable Bacterial Clonal Relatedness the predominant clone (Table 2, Figure 1). This finding is
consistent with the epidemic dissemination of K. pneumoniae
carbapenemase (KPC)-producing K. pneumoniae in China
described in another study (Zhou et al., 2015). Another six
STs were also identified: ST1525 (FK688/13), ST290 (FK782/13),
ST2281 (FK1468/14), ST268 (FK2152/15), ST14 (FK2203/15),
ST656 (FK2180/15). The novel ST2281 (allelic profile: 4-1-1-22-
7-4-35) which was a multiple locus variant, has not previously
been documented and has been submitted to the MLST database. the predominant clone (Table 2, Figure 1). This finding is
consistent with the epidemic dissemination of K. pneumoniae
carbapenemase (KPC)-producing K. pneumoniae in China
described in another study (Zhou et al., 2015). Another six
STs were also identified: ST1525 (FK688/13), ST290 (FK782/13),
ST2281 (FK1468/14), ST268 (FK2152/15), ST14 (FK2203/15),
ST656 (FK2180/15). The novel ST2281 (allelic profile: 4-1-1-22-
7-4-35) which was a multiple locus variant, has not previously
been documented and has been submitted to the MLST database. been documented and has been submitted to the MLST database. The PFGE patterns of the 35 XDR K. pneumoniae isolates
show a major cluster of 23 closely related isolates that exhibited
>80% similarity: these are all KPC-2-producing resistant strains
and are all ST11 clones (Figure 1). The rest 12 isolates which
exhibited <80% similarity were assigned to seven STs (ST11,
ST1525, ST290, ST2281, ST268, ST14, and ST656). Eighteen XDR
K. pneumoniae isolated from ICU patients (directly admitted and
transferred) belong to the predominant cluster, and the other
five isolates belonging to the predominant cluster were separated
from other departments. A worrying finding is that the close
relatedness among the 23 XDR K. pneumoniae isolates suggests
a phenomenon of clone dissemination within the clinic and
the transfer of patients in different medical departments may
accelerate clonal spread of pathogens. Statistical Analysis Categorical variables were compared with the chi-square test
using SPSS software (version 17.0). Calculated p-values of < 0.05
were considered to be statistically significant. Susceptibilities of XDR K. pneumoniae Susceptibilities of XDR K. pneumoniae
MIC assays of the patient isolates revealed that each of the
XDR K. pneumoniae strains were highly resistant to at least one
of the β-lactams, carbapenems, aminoglycosides, quinolones, β-
lactam/inhibitor combinations, and other clinical antimicrobial
agents (Table 3). Consistent with the treatment success is the
observation that tigecycline exhibited superior bacteriostasis
activity in vitro. In addition, 33 isolates were susceptible to
polymyxin B (Table 3). Clinical Characteristics of BSIs Patients
There is a growing trend of mortality in hospital patients caused
by infections with K. pneumoniae (Paczosa and Mecsas, 2016). A total of 35 nosocomial BSIs patients (age 14–90 years; male:
female 4:1) were included in the present study (Table 1). These
patients had been admitted in the intensive care unit (60.0%),
hematology department (28.6%), and neurosurgery department
(11.4%), data not shown. The BSIs patients were primarily
elderly, suffered severe comorbidities and had been submitted
to invasive procedures, such as central venous catheterization
and urinary catheterization. As documented in Table 1, the BSIs
resulted in lengthy ICU stays (1–58 days; median 16 days),
within long overall hospital length of stay (1–86 days; median
30 days). The mortality rate attributed to BSIs caused by XDR
K. pneumoniae was 40.0%, i.e., 14 of the 35 patients died from
the BSI. Two groups of BSI patients had an increased risk of
death, those that received urinary catheterization (34.3% died
vs. 22.9% survived, P = 0.007), and patients with intracranial
disease (17.1% died vs. 2.8% survived, P = 0.01). In terms of their
treatment, combination therapy including meropenem proved to
be ineffective against mortality of BSIs patients caused by XDR
K. pneumoniae (P = 0.015), but tigecycline in combination with
other antimicrobial agents was significantly effective and reduced
the risk of death (P = 0.016). Furthermore, nine patients of
the survivor group were treated with fosfomycin combined with
more than three other antibiotics. Bacterial Clonal Relatedness Clonal relatedness for the 35 K. pneumoniae strains was
analyzed by pulsed-field gel electrophoresis (PFGE). Genomic
DNA was extracted using an AxyPrep Bacterial Genomic
DNA Miniprep kit, subjected to complete digestion with the
restriction endonuclease XbaI (Takara Bio, Dalian, China), and 96-well Thermal Cycler (Bio-Rad, USA) using specific primers,
corresponding to related studies (Jacoby, 2009; Yu et al., 2009; Li
et al., 2012; Ramirez and Tolmasky, 2013). Primer sequences are June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org Frontiers in Microbiology | www.frontiersin.org 3 XDR K. Pneumoniae Causing BSIs Bi et al. Bi et al. the diagnostic DNA fragments then separated in a PFGE CHEF-
Mapper XA system (Bio-Rad) using 0.5 × Tris-borate-EDTA
buffer at 120 V for 19 h, with pulse times ranging from 5
to 35 s. DNA fragments were stained with Gel Red (Biotium,
USA) and analyzed using Quality one software (Bio-Rad). The
DNA fingerprint patterns were analyzed according to the criteria
proposed by Tenover et al. (Hu et al., 2013) and strains with more
than 80% similarity were regarded as the same clone. Molecular
typing of XDR K. pneumoniae strains was performed according
to the protocol described on the Institut Pasteur K. pneumoniae
MLST website (http://bigsdb.web.pasteur.fr/klebsiella/klebsiella. html). The sequences of seven housekeeping genes (i.e., gapA,
infB, mdh, pgi, phoE, rpoB, and tonB) were amplified and
sequence types (STs) were assigned by the MLST database
according to Diancourt et al. (2005). The novel STs were
submitted to the MLST database. the diagnostic DNA fragments then separated in a PFGE CHEF-
Mapper XA system (Bio-Rad) using 0.5 × Tris-borate-EDTA
buffer at 120 V for 19 h, with pulse times ranging from 5
to 35 s. DNA fragments were stained with Gel Red (Biotium,
USA) and analyzed using Quality one software (Bio-Rad). The
DNA fingerprint patterns were analyzed according to the criteria
proposed by Tenover et al. (Hu et al., 2013) and strains with more
than 80% similarity were regarded as the same clone. Molecular
typing of XDR K. pneumoniae strains was performed according
to the protocol described on the Institut Pasteur K. pneumoniae
MLST website (http://bigsdb.web.pasteur.fr/klebsiella/klebsiella. html). The sequences of seven housekeeping genes (i.e., gapA,
infB, mdh, pgi, phoE, rpoB, and tonB) were amplified and
sequence types (STs) were assigned by the MLST database
according to Diancourt et al. (2005). The novel STs were
submitted to the MLST database. Genotypes and Clonal Relatedness of XDR
K. pneumoniae Molecular typing enables detection of nosocomial transmission
of bacterial pathogens, and can assist in identifying the
routes of transmission in hospital settings. Multilocus sequence
typing (MLST) identified seven different STs with ST11 being Frontiers in Microbiology | www.frontiersin.org June 2017 | Volume 8 | Article 1230 4 Bi et al. XDR K. Pneumoniae Causing BSIs ABLE 2 | Molecular characteristics and epidemiological analysis of XDR K. pneumoniae clinical isolates in Wenzhou, 2013–2015 (n = 35). Genotypes and Clonal Relatedness of XDR
K. pneumoniae olate/year
Resistance determinants
Epidemiological analysis
Carbape-
nemases
Other β-lactamases genes
Quinolone resistance genes
Aminoglycoside
resistance determinants
Size of blaKPC-2
plasmid (kb)
Transcon-
jugant
Replicon
types
STs
K 688/13
—
blaCMY, blaDHA−1
—
AAC(6′)-Ib, APH(3′)-Ia
—
—
1,525
K 729/13
KPC-2
blaCTX−M−14, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
—
—
IncFrepB
11
K 782/13
KPC-2
blaCTX−M−65, blaSHV−11
qnrS
AAC(6′)-Ib
—
—
—
290
K 1186/14a
KPC-2
blaCTX−M−65, blaSHV−11
qnrS, gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
54.7
J1186
IncFrepB
11
K 1271/14
KPC-2
—
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
—
—
IncFrepB
11
K 1425/14
KPC-2
blaCTX−M−14, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia,
—
—
IncFrepB
11
K 1468/14a
KPC-2
blaCTX−M−14, blaSHV−11
qnrB, gyrA (S83I, D87G)
AAC(6′)-Ib, AAC(3)-IV
54.7
J1468
—
2,281
K 1668/14
KPC-2
blaCTX−M−14, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
—
—
IncFrepB
11
K 1743/14a
KPC-2
blaCTX−M−65, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
167.1
J1743
IncFrepB
11
K 1855/14
KPC-2
blaCTX−M−14, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
—
—
IncFrepB
11
K 1869/14
KPC-2
blaCTX−M−65, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
—
—
IncFrepB
11
K 1919/15
KPC-2
blaCTX−M−14, blaSHV−11
aac(6′)-Ib-cr, gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
—
—
IncFrepB
11
K 2048/15
KPC-2
blaCTX−M−65, blaSHV−11
qnrS, parC (S80I)
AAC(6′)-Ib
—
—
IncFrepB
11
K 2104/15
KPC-2
blaCTX−M−65, blaSHV−11
aac(6′)-Ib-cr, gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
—
—
IncFrepB
11
K 2152/15a
KPC-2
blaCTX−M−15, blaSHV−11
qnrS
AAC(6′)-Ib
54.7
J2152
—
268
K 2200/15
KPC-2
blaCTX−M−65, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
—
—
IncFrepB
11
K 2203/15
KPC-2
blaCTX−M−15
—
AAC(6′)-Ib
—
—
—
14
K 2206/15
KPC-2
blaTEM−1, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
—
—
IncFrepB
11
K 2219/15
KPC-2
blaCTX−M−14
qnrB, gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
—
—
IncFrepB
11
K 2267/15
KPC-2
blaCTX−M−65, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
—
—
IncFrepB
11
K 2302/15a
KPC-2
blaCTX−M−15, blaCTX−M−65,
blaTEM−1, blaSHV−11
qnrS, gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
54.7
J2302
IncFrepB
11
K 2322/15a
KPC-2
blaCTX−M−14
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
54.7
J2322
—
11
K 2346/15a
KPC-2
blaCTX−M−65, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
54.7
J2346
IncFrepB
11
K 2348/15
KPC-2
blaCTX−M−65, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
—
—
IncFrepB
11
K 2578/15
KPC-2
blaCTX−M−14, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
—
—
IncFrepB
11
K 1881/15a
KPC-2
blaCTX−M−65, blaTEM−1, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
54.7
J1881
IncFrepB
11
K 1905/15
KPC-2
blaCTX−M−14, blaTEM−1, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia,
AAC(3)-IV, rmtB
—
—
IncFrepB
11
K 1934/15
—
blaSHV−11, blaDHA−1
aac(6′)-Ib-cr, gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia,
AAC(3)-IV, rmtB
—
—
—
11
K 1944/15
KPC-2
blaCTX−M−65, blaTEM−1, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, rmtB
—
—
IncFrepB
11
K 2076/15a
KPC-2
blaCTX−M−65, blaTEM−1
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
54.7
J2076
—
11
K 2016/15
KPC-2
blaCTX−M−14, blaTEM−1, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
—
—
IncFrepB
11
K 2047/15a
KPC-2
blaCTX−M−65, blaTEM−1, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6’)-Ib, APH(3′)-Ia,
AAC(3)-IV, rmtB
54.7
J2047
IncFrepB
11
K 2078/15
KPC-2
blaCTX−M−65, blaTEM−1
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
—
—
—
11
K 2142/15a
KPC-2
blaCTX−M−65, blaTEM−1, blaSHV−11
gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
54.7
J2142
IncFrepB
11
K 2180/15a
KPC-2
blaCTX−M−14, blaTEM−1, blaSHV−11
qnrB, aac(6′)-Ib-cr, gyrA (S83I, D87G), parC (S80I)
AAC(6′)-Ib, APH(3′)-Ia, rmtB
54.7
J2180
—
656
Strains that have successfully transferred carbapenem resistance genes blaKPC to E. June 2017 | Volume 8 | Article 1230 Genotypes and Clonal Relatedness of XDR
K. pneumoniae DNA fingerprints were revealed by Gel Red staining. For
MLST-based categorization of the strains, the sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were analyzed, and the
PFGE patterns have been organized according to a dendogram of 35 XDR K. pneumoniae isolates based on MLST analysis. In red text are those isolates with no
detectable carbapenemase genes. The gray box highlights the prevalence of the ST11 sequence type. but no transconjugants were recovered for the other 23 donor
strains, despite repeated attempts, may due to the lack of sex
factor F or conjugative plasmids which are key vehicles and
contain simultaneously important elements, including an origin
of transfer, DNA-processing factors (a relaxase and accessory
proteins), and mating pair formation proteins (Achtman et al.,
1971; Goessweiner-Mohr et al., 2014) (Table 2). The MIC values
for the transconjugants determined for β-lactam antibiotics
were consistent with the transfer of carbapenemase expression. Southern blot analysis revealed the presence of the blaKPC−2 in
the transconjugants and in 11 cases corresponded to a plasmid
of ∼50 kb (Figure 3), while strain J1743 carried the blaKPC−2
gene on a plasmid of ∼160 kb (Figure 3). These results are in
accordance with the S1-PFGE analysis of the isolates (Figure 2). Some of these strains were found to be FrepB-positive by PBRT,
showing that these plasmids belong to an IncF-type. mutations. In contrast, fluoroquinolone-resistant minor clone
strains either failed to harbor any gyrA or parC mutations
(ST1525, ST290, ST268, ST14) or harbored one favorable serine
mutation together with a less favorable mutation (ST2281)
(Table 2). The 16S-rRNA methylase encoding gene rmtB was
present in 28 (80%) of the strains, a gene that confers resistance to
most clinically relevant aminoglycosides. The plasmid-mediated
quinolone resistance genes qnrB, qnrS, and aac(6′)-Ib-cr were
also determined as present in 11 (31.4%) of the strains. 35
(100%) of the strains possessed AMEs, including AAC(6′)-
Ib (100%), APH(3′)-Ia (48.6%), AAC(3)-IV (11.4%), ANT(2′′)-
Ia (0%). Taken together, these results demonstrate carriage of
multiple genetic determinants for drug resistance in the BSI
strains. Genotypes and Clonal Relatedness of XDR
K. pneumoniae coli J53; “—” means undetected. June 2017 | Volume 8 | Article 1230 5 XDR K. Pneumoniae Causing BSIs Bi et al. FIGURE 1 | PFGE analysis of XDR K. pneumoniae isolates. In order to generate diagnostic genomic DNA fragmentation fingerprints, genomic DNA from each of the
XDR K. pneumoniae isolates was digested using XbaI and subjected to pulsed-field gel electrophoresis. DNA fingerprints were revealed by Gel Red staining. For
MLST-based categorization of the strains, the sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were analyzed, and the
PFGE patterns have been organized according to a dendogram of 35 XDR K. pneumoniae isolates based on MLST analysis. In red text are those isolates with no
detectable carbapenemase genes. The gray box highlights the prevalence of the ST11 sequence type. FIGURE 1 | PFGE analysis of XDR K. pneumoniae isolates. In order to generate diagnostic genomic DNA fragmentation fingerprints, genomic DNA from each of the
XDR K. pneumoniae isolates was digested using XbaI and subjected to pulsed-field gel electrophoresis. DNA fingerprints were revealed by Gel Red staining. For
MLST-based categorization of the strains, the sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were analyzed, and the
PFGE patterns have been organized according to a dendogram of 35 XDR K. pneumoniae isolates based on MLST analysis. In red text are those isolates with no
detectable carbapenemase genes. The gray box highlights the prevalence of the ST11 sequence type. FIGURE 1 | PFGE analysis of XDR K. pneumoniae isolates. In order to generate diagnostic genomic DNA fragmentation fingerprints, genomic DNA from each of the
XDR K. pneumoniae isolates was digested using XbaI and subjected to pulsed-field gel electrophoresis. DNA fingerprints were revealed by Gel Red staining. For
MLST-based categorization of the strains, the sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were analyzed, and the
PFGE patterns have been organized according to a dendogram of 35 XDR K. pneumoniae isolates based on MLST analysis. In red text are those isolates with no
detectable carbapenemase genes. The gray box highlights the prevalence of the ST11 sequence type. FIGURE 1 | PFGE analysis of XDR K. pneumoniae isolates. In order to generate diagnostic genomic DNA fragmentation fingerprints, genomic DNA from each of the
XDR K. pneumoniae isolates was digested using XbaI and subjected to pulsed-field gel electrophoresis. DS-Page of Outer Membrane Proteins SDS-Page of Outer Membrane Proteins
The major porins of E. coli, OmpF and OmpC, provide
for most of the flux of molecules up to ∼650 Da across
the outer membrane (Nikaido et al., 1983; Sugawara et al.,
2016) and thereby play a role in the susceptibility of E. coli to antibiotics (Nikaido, 2003; Zgurskaya et al., 2015). The homologous porins of K. pneumoniae, OmpK35 and
OmpK36, have been highlighted as the primary channels through KPC-2 and other resistance determinants are often carried
on plasmids (Kuai et al., 2014), and S1-PFGE revealed the
presence of one or more plasmids in each of the isolated
strains (Figure 2). The detected plasmids by S1-PFGE ranged
in size from ∼50 to ∼390 kb. For an initial assessment of the
plasmids, transconjugation experiments were established using
E. coli J53 as the recipient. Carbapenemase genes from 12
strains were successfully transferred to the recipient E. coli J53, June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 6 XDR K. Pneumoniae Causing BSIs Bi et al. TABLE 3 | Antibiotic susceptibility of XDR K. pneumoniae isolates. Antibiotics
MIC (mg/L)
Percentage
MIC50
MIC90
Range
Susceptible/Non-susceptible
β-lactams
CAZ
128
>128
64 to >128
0/100
CTX
>128
>128
32 to >128
0/100
β-lactam/Inhibitor
SAM
64
>128
64 to >128
0/100
TZP
>128
>128
64 to >128
0/100
Carbapenems
IPM
64
64
8 to >64
0/100
MEM
>64
>64
1 to >64
2.9/97.1
ETP
>64
>64
4 to >64
0/100
Aminoglycosides
AMK
>256
>256
1 to >256
5.7/94.3
GEN
>256
>256
8 to >256
0/100
TOB
256
>256
2 to >256
5.7/94.3
Quinolones
CIP
32
64
1 to 128
2.9/97.1
LEV
16
64
4 to 64
0/100
Other
FOS
>512
>512
64 to >512
0/100
PB
1
1
0.25 to 128
94.3/5.7
TGC
0.5
1
0.25 to 1
100/0
CAZ,
ceftazidime;
CTX,
cefotaxime;
SAM,
ampicillin/sulbactam;
TZP,
piperacillin/tazobactam;
IPM,
imipenem;
MEM,
meropenem;
ETP,
ertapenem;
AMK, amikacin; GEN, gentamicin; TOB, tobramycin; CIP, ciprofloxaxin; LEV, levofloxacin;
FOS, fosfomycin; PB, polymyxin B; TGC, tigecycline. BLE 3 | Antibiotic susceptibility of XDR K. pneumoniae isolates. a considerable cause of mortality in nosocomial infections
accounting for ∼14%, ranking immediately after respiratory
tract infections and incision infections in ICUs (Russotto et al.,
2015). In this period from 2013 to 2015, K. pneumoniae was
frequently isolated from these BSIs patients, and predominantly
with a multiple drug resistant phenotypes. DS-Page of Outer Membrane Proteins It is a growing
global reality, that XDR K. pneumoniae nosocomial infections
are associated with delays in appropriate therapy, and therefore
pose serious challenges to clinically effective therapeutic options
worldwide (Lim et al., 2015). The increasing prevalence and
global dissemination of these clinical XDR strains gravely
threatens public health (Zhao et al., 2015). While our study has been conducted in a single medical
center, the samples were sourced from the First Affiliated
Hospital of Wenzhou Medical University, which is one of the
largest comprehensive hospitals integrating medical care, clinical
practice teaching and scientific research. The hospitals outpatient
clinics service close to five million patients per annum, taking
responsibility for the medical care of a 30 million population in
southern Zhejiang and eastern Fujian areas. Environments such
as this provide a valuable resource to track new developments
in hospital acquired infections and monitor the dissemination of
new resistance genes for ongoing studies. Respiratory infections could be the key source of XDR
K. pneumoniae BSIs, which require a prolonged antibiotic
therapy and are considered as an important factor for acquired
resistance of pathogens (Ryan et al., 2015). The case-fatality
rate attributed to BSIs caused by XDR K. pneumoniae here was
40% (14/35), the higher than the overall mortality rate (15–20%)
associated with BSIs in previous studies (Russotto et al., 2015). The high ICU admission rate (n = 21, 60%) that was observed
in the present study, may relate to hypoimmunity resulting from
severe comorbidities and invasive care procedures (Woodford
et al., 2004; Bouza et al., 2013; Martelius et al., 2016). The clinical
retrospective data showed that 57% of cases received broad-
spectrum antibiotics, including third-generation cephalosporin,
carbapenems, and tigecycline. Recent studies have shown that
carbapenems are generally considered as part of combination
therapy when carbapenem MICs are <8 mg/L (Daikos et al.,
2014), and this had become a standard treatment regime. However, 34 of the 35 isolates of XDR K. pneumoniae in this study
were non-susceptible to meropenem and, even in combination
therapy, meropenem was not protective against mortality of BSIs
patients (P = 0.015). Thus, rapid typing and identification of
specific BSIs phenotypes is essential to avoid unnecessary and
inappropriate antimicrobial regimens. Our data showed that
an alternative treatment regime of tigecycline in combination
with other antimicrobial agents was significantly effective
(P = 0.016). which beta-lactams cross the outer membrane (Kaczmarek
et al., 2006). DS-Page of Outer Membrane Proteins OmpK35 and OmpK36 are highly abundant
proteins of the outer membrane in K. pneumoniae, and can
be readily detected by Coomassie blue staining after SDS-
PAGE analysis of the outer membranes (Rath et al., 2009). A procedure was optimized to purify outer membranes from
the control strain K. pneumoniae ATCC 13883, using sucrose
gradient fractionation to separate outer membranes from inner
membranes (Figure 4A). Immunoblotting for marker proteins
F1β and BamB served as controls for the fractions (Figure 4A). Comparative analysis of outer membrane fractions isolated from
the carbapenem-resistant, yet carbapenemase-negative strains
FK688 and FK1934 using antibodies specific for OmpK35 and
OmpK36 showed no detectable expression of OmpK35 and
OmpK36 (Figure 4B). PCR primers designed to amplify regions
of the corresponding loci failed to detect ompK35 and ompK36 in
FK688 and FK1934 (data not shown). which beta-lactams cross the outer membrane (Kaczmarek
et al., 2006). OmpK35 and OmpK36 are highly abundant
proteins of the outer membrane in K. pneumoniae, and can
be readily detected by Coomassie blue staining after SDS-
PAGE analysis of the outer membranes (Rath et al., 2009). A procedure was optimized to purify outer membranes from
the control strain K. pneumoniae ATCC 13883, using sucrose
gradient fractionation to separate outer membranes from inner
membranes (Figure 4A). Immunoblotting for marker proteins
F1β and BamB served as controls for the fractions (Figure 4A). Comparative analysis of outer membrane fractions isolated from
the carbapenem-resistant, yet carbapenemase-negative strains
FK688 and FK1934 using antibodies specific for OmpK35 and
OmpK36 showed no detectable expression of OmpK35 and
OmpK36 (Figure 4B). PCR primers designed to amplify regions
of the corresponding loci failed to detect ompK35 and ompK36 in
FK688 and FK1934 (data not shown). The emergence and spread of XDR K. pneumoniae over
the last decade is a major, global concern (Naparstek et al.,
2012), and the findings of this specific study are relevant
to problems faced by clinicians around the globe. In the
last several years, antibiotic resistance mediated by plasmids
has been increasing at a remarkable rate (Yang et al., 2011),
especially through genes encoding carbapenemase, PMQRs and
16S-RMTase. Strikingly, most of the isolates in this study Frontiers in Microbiology | www.frontiersin.org DISCUSSION Braenderup H9812 digested with XbaI; Lanes 2–12 represent transconjugants of the corresponding
number of donor isolates, all of the isolates code consistent with Table 3. (B) The corresponding Southern blot, hybridized with a DNA probe to the blaKPC−2
sequence. FIGURE 3 | Plasmid profiles of E. coli transconjugants. (A) In order to verify plasmids carried by the XDR K. pneumoniae isolates, transconjugation experiments were
established using E. coli J53 as a recipient strain. Genomic DNA was isolated from the transconjugants, digested using S1 nuclease and subjected to pulsed-field gel
electrophoresis. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI; Lanes 2–12 represent transconjugants of the corresponding
number of donor isolates, all of the isolates code consistent with Table 3. (B) The corresponding Southern blot, hybridized with a DNA probe to the blaKPC−2
sequence. FIGURE 3 | Plasmid profiles of E. coli transconjugants. (A) In order to verify plasmids carried by the XDR K. pneumoniae isolates, transconjugation experiments were
established using E. coli J53 as a recipient strain. Genomic DNA was isolated from the transconjugants, digested using S1 nuclease and subjected to pulsed-field gel
electrophoresis. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI; Lanes 2–12 represent transconjugants of the corresponding
number of donor isolates, all of the isolates code consistent with Table 3. (B) The corresponding Southern blot, hybridized with a DNA probe to the blaKPC−2
sequence. Using molecular analysis, we located blaKPC−2 on ∼50 and
∼160 kb transferable plasmids which co-harbored blarmtB and
blaCTX−M−9. In consideration of the problems that smaller
plasmids may not be detected by S1-PFGE, plasmids of randomly
selected 10 strains and 6 transconjugants were extracted and
separated by agarose gel electrophoresis. The result revealed the
presence of smaller plasmids which were not detected by S1-
PFGE in all of the 10 strains and 2 of the 6 transconjugants. The
gel was then subject to Southern blot analysis, after transfer to a
positively charged nylon membrane by the capillary method. The
membrane was subject to hybridization with labeled blaKPC−2
probes, nevertheless, hybridization signals were only observed in
large plasmids (>54.2 kb) (Figure S1). Figure S1 was available
in supplementary data, and demonstrate that smaller plasmids
didn’t mediate the widespread dissemination of resistant genes possessed KPC-2 and co-harbored three or more classes of
resistance genes. Frontiers in Microbiology | www.frontiersin.org DISCUSSION Between 2013 and 2015, the incidence rate of all nosocomial
infections in this major public hospital in southern China was
2.23%, comparable to other grade A tertiary hospitals that range
from 2 to 4% (Mu et al., 2015; Zhao, 2015). The current study was
motivated by the observation that bloodstream infection became Frontiers in Microbiology | www.frontiersin.org June 2017 | Volume 8 | Article 1230 7 Bi et al. XDR K. Pneumoniae Causing BSIs FIGURE 2 | Gel image of S1 PFGE result of all XDR K. pneumoniae isolates. Isolates were digested using S1 nuclease and subjected to pulsed-field gel
electrophoresis. The gel was subjected to Gel Red staining and analyzed in a CHEF-Mapper XA PFGE system. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI. FIGURE 3 | Plasmid profiles of E. coli transconjugants. (A) In order to verify plasmids carried by the XDR K. pneumoniae isolates, transconjugation experiments were
established using E. coli J53 as a recipient strain. Genomic DNA was isolated from the transconjugants, digested using S1 nuclease and subjected to pulsed-field gel
electrophoresis. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI; Lanes 2–12 represent transconjugants of the corresponding
number of donor isolates, all of the isolates code consistent with Table 3. (B) The corresponding Southern blot, hybridized with a DNA probe to the blaKPC−2
sequence. FIGURE 2 | Gel image of S1 PFGE result of all XDR K. pneumoniae isolates. Isolates were digested using S1 nuclease and subjected to pulsed-field gel
electrophoresis. The gel was subjected to Gel Red staining and analyzed in a CHEF-Mapper XA PFGE system. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI. FIGURE 2 | Gel image of S1 PFGE result of all XDR K. pneumoniae isolates. Isolates were digested using S1 nuclease and subjected to pulsed-field gel
electrophoresis. The gel was subjected to Gel Red staining and analyzed in a CHEF-Mapper XA PFGE system. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI. FIGURE 3 | Plasmid profiles of E. coli transconjugants. (A) In order to verify plasmids carried by the XDR K. pneumoniae isolates, transconjugation experiments were
established using E. coli J53 as a recipient strain. Genomic DNA was isolated from the transconjugants, digested using S1 nuclease and subjected to pulsed-field gel
electrophoresis. H = size marker strain Salmonella enterica ser. DISCUSSION The high prevalence rate of KPC-2 among these
isolates exceeded that found in other investigations across the
world (Bradford et al., 2004). Previous studies proposed that
blaKPC−2 resides on transmissible plasmids, which frequently
co-harbor other resistance elements (Endimiani et al., 2008),
leading to MDR and XDR pathogens. Even where carbapenemase
genes are not evident, carbapenem-resistant phenotypes were
observed; while they carried AmpC β-lactamase genes (blaCMY
and blaDHA−1), no carbapenemase genes were detected in two
strains from this study, FK688 and FK1934. Notably, these two
strains were not found to express OmpK35 and OmpK36. We
suggest that the absence of the major porins in the bacterial
outer membrane reduced permeability to carbapenem, thereby
enhancing carbapenem resistance. Frontiers in Microbiology | www.frontiersin.org June 2017 | Volume 8 | Article 1230 8 Bi et al. XDR K. Pneumoniae Causing BSIs Since multiple resistant determinants rendering almost all
antimicrobials ineffective and poor survival in patients infected
with XDR K. pneumoniae, tigecycline and polymyxin B seemed
to be the optional choices. Notably, multiple amino acid
substitutions, including both gyrA (S83I, D87G) and parC (S80I)
were observed among ST11 strains which was predominant
clone except a single ST11 strain (2048/15), being apparently
more than that detected in minor clone strains. Resistance
mutations decreased the affinity of gyrase and topoisomerase
IV for fluoroquinolones, and our findings also illustrate that
favorable mutations and consequently superior fitness, closely
associated with high-level resistance to fluoroquinolones, could
contribute to the promotion of the major international high-
risk clone (ST11) of multidrug-resistant K. pneumoniae. These
findings are in complete agreement with those published by Tóth
et al. (2014). FIGURE 4 | Remodeling of the outer membrane proteome in the XDR
K. pneumoniae isolates. (A) Total membranes were isolated from K. pneumoniae ATCC 13883 and subjected to sucrose density fractionation. Membrane fractions were subject to SDS-PAGE, and then Coomassie blue
staining (top panel) and immunoblotting (bottom panel) using antisera
recognizing known outer (BamB) and inner (F1β) membrane proteins. (B)
Whole cell lysates from K. pneumoniae ATCC 13883 and K. pneumoniae
clinical isolates FK688 and FK1934 were analyzed by SDS-PAGE and western
immunoblotting for OmpK35 and OmpK36. KPC-2-producing K. pneumoniae isolates have been reported
worldwide, and the dominant KPC-producing clone ST258 is
implicated in more than 70% of reported outbreaks in America
(Kitchel et al., 2009). Other STs (ST1525, ST290, ST14, ST268,
ST656, etc.) have not been reported to be MDR/XDR global
clones. Frontiers in Microbiology | www.frontiersin.org DISCUSSION The predominant clone now is ST11, which is a variant
of the pandemic ST258 clone and played an important role in
the epidemic dissemination of blaKPC−2 (Cuzon et al., 2010). High homology of KPC-2-producing K. pneumoniae ST11 has
been observed by PFGE, which indicated clonal dissemination in
our hospital in recent years, reinforcing the viewpoint speculated
by Qi et al. that ST11 K. pneumoniae could be considered as a
plasmid scavenger that amplifies plasmid dissemination (Qi et al.,
2011). FIGURE 4 | Remodeling of the outer membrane proteome in the XDR
K. pneumoniae isolates. (A) Total membranes were isolated from K. pneumoniae ATCC 13883 and subjected to sucrose density fractionation. Membrane fractions were subject to SDS-PAGE, and then Coomassie blue
staining (top panel) and immunoblotting (bottom panel) using antisera
recognizing known outer (BamB) and inner (F1β) membrane proteins. (B)
Whole cell lysates from K. pneumoniae ATCC 13883 and K. pneumoniae
clinical isolates FK688 and FK1934 were analyzed by SDS-PAGE and western
immunoblotting for OmpK35 and OmpK36. Smaller plasmids can be important resistance reservoirs
harboring multiple determinants, and many of them are high
copy number conferring the host bacterial strains high levels
of resistance. Therefore, comprehensive analysis and study
of smaller plasmids are essential for understanding the role
of smaller plasmids play in developing of XDR strains. In
addition, studying biology of virulence of XDR isolates, and
gene environment of the plasmids (∼50 and ∼160 kb) harboring
blaKPC−2 are worthwhile, and the lack of corresponding
researches are deficiencies of present study, further explorations
are still warranted in follow-up studies. blaKPC−2 in Wenzhou. However, investigation of other resistant
genes harbored by smaller plasmids are still warranted. The genetic environment surrounding the blaKPC−2 gene
which was located on various plasmids among the KPC-
producing Enterobacteriaceae iaolated from China is primarily
reported to be the integrin of Tn3-based transposon. The
truncated blaTEM gene fragment is the representative structure of
the Tn3 transposon (Luo et al., 2013). In present study, 6 isolates
carrying blaKPC−2 which located in ∼50 kb transferable plasmids
were detected to harbor blaTEM as well, so we speculate that
the blaKPC−2-surrounding nucleotide sequence contain integron
structure of Tn3-based transposon. REFERENCES produce beta-lactamase blaKPC−2 gene. Emerg. Infect. Dis. 16, 1349–1356. doi: 10.3201/eid1609.091389 produce beta-lactamase blaKPC−2 gene. Emerg. Infect. Dis. 16, 1349–1356. doi: 10.3201/eid1609.091389 Achtman, M., Willetts, N., and Clark, J. (1971). Beginning a genetic analysis of
conjugational transfer determined by the F factor in Escherichia coli by isolation
and characterization of transfer-deficient mutants. J. Bacteriol. 106, 529–538. Daikos, G. L., Tsaousi, S., Tzouvelekis, L. S., Anyfantis, I., Psichogiou, M.,
Argyropoulou,
A.,
et
al. (2014). Carbapenemase-producing
Klebsiella
pneumoniae
bloodstream
infections:
lowering
mortality
by
antibiotic
combination schemes and the role of carbapenems. Antimicrob. Agents
Chemother. 58, 2322–2328. doi: 10.1128/AAC.02166-13 Bagley, S. T. (1985). Habitat association of Klebsiella species. Infect. Control 6,
52–58. doi: 10.1017/S0195941700062603 Diancourt, L., Passet, V., Verhoef, J., Grimont, P. A., and Brisse, S. (2005). Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J. Clin. Microbiol. 43, 4178–4182. doi: 10.1128/JCM.43.8.4178-4182.2005 Barton, B. M., Harding, G. P., and Zuccarelli, A. J. (1995). A general method
for detecting and sizing large plasmids. Anal. Biochem. 226, 235–240. doi: 10.1006/abio.1995.1220 Doumith, M., Dhanji, H., Ellington, M. J., Hawkey, P., and Woodford, N. (2012). Characterization of plasmids encoding extended-spectrum beta-lactamases and
their addiction systems circulating among Escherichia coli clinical isolates in the
UK. J. Antimicrob. Chemother. 67, 878–885. doi: 10.1093/jac/dkr553 Bouza,
E.,
Eworo,
A.,
Fernandez
Cruz,
A.,
Reigadas,
E.,
Rodriguez-
Creixems,
M.,
and
Munoz,
P. (2013). Catheter-related
bloodstream
infections caused by Gram-negative bacteria. J. Hosp. Infect. 85, 316–320. doi: 10.1016/j.jhin.2013.08.008 Bradford, P. A., Bratu, S., Urban, C., Visalli, M., Mariano, N., Landman, D., et al. (2004). Emergence of carbapenem-resistant Klebsiella species possessing the
class A carbapenem-hydrolyzing KPC-2 and inhibitor-resistant TEM-30 beta-
lactamases in New York City. Clin. Infect. Dis. 39, 55–60. doi: 10.1086/421495 Endimiani, A., Carias, L. L., Hujer, A. M., Bethel, C. R., Hujer, K. M., Perez, F.,
et al. (2008). Presence of plasmid-mediated quinolone resistance in Klebsiella
pneumoniae isolates possessing blaKPC in the United States. Antimicrob. Agents
Chemother. 52, 2680–2682. doi: 10.1128/AAC.00158-08 EUCAST (2015). Breakpoint Tables for Interpretation of MICs and Zone Diameters. Version 5.0. Basel: European Committeeon Antimicrobial Susceptibility
Testing. Available onliine at: http://www.eucast.org. Buruk, C. K., Oztel Ocak, H., Bayramoglu, G., and Aydin, F. (2016). Investigation
of plasmid-mediated quinolone resistance genes in quinolone-resistant
Escherichia coli and Klebsiella spp. isolates from bloodstream infections. Mikrobiyoloji Bulteni 50, 186–195. doi: 10.5578/mb.20935 Findlay, J., Hopkins, K. L., Meunier, D., and Woodford, N. (2015). FUNDING The Supplementary Material for this article can be found
online
at:
http://journal.frontiersin.org/article/10.3389/fmicb. 2017.01230/full#supplementary-material This work was supported by research grants from the National
Natural Science Foundation of China (no. 81171614), the Health ACKNOWLEDGMENTS TZ, BL, and JC contributed to the design of the experiments. WB,
HL, RD, BL, VT, and LC performed the experiment. WB, HL, and
BL wrote the initial draft of the manuscript. TZ, TL, WB, HL,
RD, BL, VT, JC, LC, JW, and RS contributed to the acquisition,
analysis, interpretation of the data included in this manuscript. TZ, TL, WB, HL, BL, JC, LC, and RS revised the manuscript. All
authors approves of the final manuscript being submitted and
agree to be accountable for the work detailed in the submitted
manuscript. We thank the team of the curators of the Institute Pasteur
MLST system (Paris, France) for importing novel alleles, profiles
and/or isolates at http://bigsdb.web.pasteur.fr. We acknowledge
Dr. Takuya Shiota for antibodies recognizing OmpF/OmpK35
and OmpC/OmpK36. We thank Dr. Kerry Dunse for critical
comments on the manuscript. CONCLUSION In
summary,
the
complex
phenotypes
of
these
XDR
K. pneumoniae strains were associated with multiple resistance
determinants and remodeling of the outer membrane proteome. In addition, favorable gyrase and topoisomerase IV mutations
and consequently superior fitness contributed to the promotion
of
the
predominant
clone
(ST11)
of
multidrug-resistant
K. pneumoniae in Wenzhou, China. The dissemination and
epidemicity of clinical XDR K. pneumoniae strains result from
horizontal transmission of multiple resistance determinants
via IncF plasmids. KPC-2-producing K. pneumoniae ST11
played a crucial role. The clonal dissemination of XDR ST11
demonstrated that efficient screening, intensive surveillance,
strict disinfection procedure and prompt quarantine measures
are urgently needed to restrain the emergence and transmission The predominant blaKPC plasmid type was IncF, and was
associated with K. pneumoniae ST258 (Chen et al., 2013). We speculate that most (7/12) transferable blaCTX−M and
blaKPC−2 genes may be located on the IncF plasmid, which is
capable of clonal expansion and horizontal dissemination among
Enterobacteriaceae bacteria (Doumith et al., 2012). Previous
studies have shown that individual patients can be positive for
IncF plasmids for more than 3 years (Onnberg et al., 2014), which
might reflect either the persistence of the pathogen clone, or
persistence of the plasmid transmitted to other resident bacteria. ESBLs genes carried by plasmids are also detected in various
lineages of the Enterobacteriaceae (Tham et al., 2012). June 2017 | Volume 8 | Article 1230 9 Bi et al. XDR K. Pneumoniae Causing BSIs Department of Zhejiang Province of the People’s Republic of
China (no. 2011KYA106), the Zhejiang Provincial Program for
the Cultivation of High-level Innovative Health Talents (no. [2012]241), and Program Grant 1092262 from the National
Health and Medical Research Council, Australia. of XDR strains in hospital settings. The high mortality attributed
to BSIs caused by XDR K. pneumoniae is an alert to clinicians to
establish rational and effective combination drug therapy. REFERENCES 75, 373–376. doi: 10.1016/j.diagmicrobio.2013.01.006 ST1031 clinical isolates in China. Diagn. Microbiol. Infect. Dis. 75, 373–376. doi: 10.1016/j.diagmicrobio.2013.01.006 Nordmann, P., Cuzon, G., and Naas, T. (2009). The real threat of Klebsiella
pneumoniae carbapenemase-producing bacteria. Lancet Infect. Dis. 9, 228–236. doi: 10.1016/S1473-3099(09)70054-4 Hu, T. Y., Qu, J. Y., and Li, X. J. (2014). Detection of 16S rRNA methylase
genes and genotypes in ESBLs-producing enterobacteriaceae isolates from
urinary tract infections. Sichuan Da Xue Xue Bao Yi Xue Ban 45, 437–441. doi: 10.13464/j.scuxbyxb.2014.03.018 Onnberg, A., Soderquist, B., Persson, K., and Molling, P. (2014). Characterization
of CTX-M-producing Escherichia coli by repetitive sequence-based PCR and
real-time PCR-based replicon typing of CTX-M-15 plasmids. APMIS 122,
1136–1143. doi: 10.1111/apm.12270 Jacoby, G. A. (2009). AmpC beta-lactamases. Clin. Microbiol. Rev. 22, 161–182. doi: 10.1128/CMR.00036-08 Paczosa, M. K., and Mecsas, J. (2016). Klebsiella pneumoniae: going on the
offense with a strong defense. Microbiol. Mol. Biol. Rev. 80, 629–661. doi: 10.1128/MMBR.00078-15 Kaczmarek, F. M., Dib-Hajj, F., Shang, W., and Gootz, T. D. (2006). High-
level carbapenem resistance in a Klebsiella pneumoniae clinical isolate is
due to the combination of bla(ACT-1) beta-lactamase production, porin
OmpK35/36 insertional inactivation, and down-regulation of the phosphate
transport porin phoe. Antimicrob. Agents Chemother. 50, 3396–3406. doi: 10.1128/AAC.00285-06 Qi, Y., Wei, Z., Ji, S., Du, X., Shen, P., and Yu, Y. (2011). ST11, the dominant clone
of KPC-producing Klebsiella pneumoniae in China. J. Antimicrob. Chemother. 66, 307–312. doi: 10.1093/jac/dkq431 Ramirez, M. S., and Tolmasky, M. E. (2013). Aminoglycoside modifying enzymes. Drug Resist. Updat. 13, 151–171. doi: 10.1016/j.drup.2010.08.003 Kitchel, B., Rasheed, J. K., Patel, J. B., Srinivasan, A., Navon-Venezia, S.,
Carmeli, Y., et al. (2009). Molecular epidemiology of KPC-producing
Klebsiella pneumoniae isolates in the United States: clonal expansion of
multilocus sequence type 258. Antimicrob. Agents Chemother. 53, 3365–3370. doi: 10.1128/AAC.00126-09 Rath, A., Glibowicka, M., Nadeau, V. G., Chen, G., and Deber, C. M. (2009). Detergent
binding
explains
anomalous
SDS-PAGE
migration
of membrane proteins. Proc. Natl. Acad. Sci. U.S.A. 106, 1760–1765. doi: 10.1073/pnas.0813167106 Kuai, S., Shao, H., Huang, L., Pei, H., Lu, Z., Wang, W., et al. (2014). KPC-2 carbapenemase and DHA-1 AmpC determinants carried on the
same plasmid in Enterobacter aerogenes. J. Med. Microbiol. 63, 367–370. doi: 10.1099/jmm.0.054627-0 Russotto, V., Cortegiani, A., Graziano, G., Saporito, L., Raineri, S. M., Mammina,
C., et al. (2015). Bloodstream infections in intensive care unit patients:
distribution and antibiotic resistance of bacteria. Infect. Drug Resist. 8, 287–296. doi: 10.2147/IDR.S48810 Lee, C. R., Lee, J. REFERENCES H., Park, K. S., Kim, Y. B., and Jeong, B. C. (2016). Global dissemination of carbapenemase-producing Klebsiella pneumoniae:
epidemiology, genetic context, treatment options, and detection methods. Front. Microbiol. 7:895. doi: 10.3389/fmicb.2016.00895 Ryan, L., O’Mahony, E., Wrenn, C., FitzGerald, S., Fox, U., Boyle, B., et al. (2015). Epidemiology and molecular typing of VRE bloodstream isolates
in an Irish tertiary care hospital. J. Antimicrob. Chemother. 70, 2718–2724. doi: 10.1093/jac/dkv185 Li, B., Yi, Y., Wang, Q., Woo, P. C., Tan, L., Jing, H., et al. (2012). Analysis of drug resistance determinants in Klebsiella pneumoniae isolates
from a tertiary-care hospital in Beijing, China. PLoS ONE 7:e42280. doi: 10.1371/journal.pone.0042280 Sugawara, E., Kojima, S., and Nikaido, H. (2016). Klebsiella pneumoniae major
porins OmpK35 and OmpK36 allow more efficient diffusion of beta-lactams
than their Escherichia coli homologs OmpF and OmpC. J. Bacteriol. 198,
3200–3208. doi: 10.1128/JB.00590-16 Tang, H. J., Lai, C. C., Chen, C. C., Zhang, C. C., Weng, T. C., Chiu,
Y. H., et al. (2016). Colistin-sparing regimens against Klebsiella pneumoniae
carbapenemase-producing K. pneumoniae isolates: combination of tigecycline
or doxycycline and gentamicin or amikacin. J. Microbiol. Immunol. Infect. doi: 10.1016/j.jmii.2016.03.003. [Epub ahead of print]. Lim, T. P., Cai, Y., Hong, Y., Chan, E. C., Suranthran, S., Teo, J. Q., et al. (2015). In vitro pharmacodynamics of various antibiotics in combination
against extensively drug-resistant Klebsiella pneumoniae. Antimicrob. Agents
Chemother. 59, 2515–2524. doi: 10.1128/AAC.03639-14 Luo, Y., Yang, J., Ye, L., Guo, L., Zhao, Q., Chen, R., et al. (2013). Characterization
of KPC-2-producing Escherichia coli, Citrobacter freundii, Enterobacter cloacae,
Enterobacter aerogenes, and Klebsiella oxytoca isolates from a Chinese Hospital. Microb. Drug Resist. 20, 264–269. doi: 10.1089/mdr.2013.0150 Tham, J., Walder, M., Melander, E., and Odenholt, I. (2012). Duration of
colonization with extended-spectrum beta-lactamase-producing Escherichia
coli in patients with travellers’ diarrhoea. Scand. J. Infect. Dis. 44, 573–577. doi: 10.3109/00365548.2011.653582 Lv, Y., Li, Y., Xue, F., Zhang, X., Hu, Y., and Yu, T. (2014). Mohnarin
repert
of
2011-2012:
surveillance
for
resistance
of
bacteria
causing
bloodstream
infections. Chin. J. Clin. Pharmacol. 3,
278–288. doi: 10.13699/j.cnki.1001-6821.2014.03.004 Tóth, A., Kocsis, B., Damjanova, I., Kristóf, K., Jánvári, L., Pászti, J., et al. (2014). Fitness cost associated with resistance to fluoroquinolones is diverse
across clones of Klebsiella pneumoniae and may select for CTX-M-15 type
extended-spectrum β-lactamase. Eur. J. Clin. Microbiol. Infect. Dis. 33, 837–843. doi: 10.1007/s10096-013-2022-6 Martelius, T., Jalava, J., Karki, T., Mottonen, T., Ollgren, J., and Lyytikainen,
O. (2016). REFERENCES Nosocomial bloodstream infections caused by Escherichia coli and
Klebsiella pneumoniae resistant to third-generation cephalosporins, Finland,
1999–2013: trends, patient characteristics and mortality. Infect. Dis. 48,
229–234. doi: 10.3109/23744235.2015.1109135 Webb, C. T., Selkrig, J., Perry, A. J., Noinaj, N., Buchanan, S. K., and
Lithgow, T. (2012). Dynamic association of BAM complex modules includes
surface exposure of the lipoprotein BamC. J. Mol. Biol. 422, 545–555. doi: 10.1016/j.jmb.2012.05.035 Mathers, A. J., Peirano, G., and Pitout, J. D. (2015). The role of epidemic
resistance plasmids and international high-risk clones in the spread of
multidrug-resistant Enterobacteriaceae. Clin. Microbiol. Rev. 28, 565–591. doi: 10.1128/CMR.00116-14 Woodford, N., Tierno, P. M. Jr., Young, K., Tysall, L., Palepou, M. F.,
Ward, E., et al. (2004). Outbreak of Klebsiella pneumoniae producing a
new carbapenem-hydrolyzing class A beta-lactamase, KPC-3, in a New
York Medical Center. Antimicrob. Agents Chemother. 48, 4793–4799. doi: 10.1128/AAC.48.12.4793-4799.2004 Mu, J., Li, Z., and Shi, Y. (2015). Cross-sectional survey of prevalence of
nosocomial infections in a general hospital in 4 years. Chin. J. Nosocomiol. 21,
4891–4893. doi: 10.11816/cn.ni. 2015-141326 Wyres, K. L., and Holt, K. E. (2016). Klebsiella pneumoniae population
genomics and antimicrobial-resistant clones. Trends Microbiol. 24, 944–956. doi: 10.1016/j.tim.2016.09.007 Naas, T., Cuzon, G., Villegas, M. V., Lartigue, M. F., Quinn, J. P., and
Nordmann, P. (2008). Genetic structures at the origin of acquisition of the
beta-lactamase blaKPC gene. Antimicrob. Agents Chemother. 52, 1257–1263. doi: 10.1128/AAC.01451-07 Yang, J., Ye, L., Wang, W., Luo, Y., Zhang, Y., and Han, L. (2011). Diverse prevalence of 16S rRNA methylase genes armA and rmtB amongst
clinical multidrug-resistant Escherichia coli and Klebsiella pneumoniae isolates. Int. J. Antimicrob. Agents 8, 348–351. doi: 10.1016/j.ijantimicag.2011. 04.021 Naparstek, L., Carmeli, Y., Chmelnitsky, I., Banin, E., and Navon-Venezia,
S. (2012). Reduced susceptibility to chlorhexidine among extremely-drug-
resistant strains of Klebsiella pneumoniae. J. Hosp. Infect. 81, 15–19. doi: 10.1016/j.jhin.2012.02.007 Yi, H., Cho, Y. J., Yong, D., and Chun, J. (2012). Genome sequence of Escherichia
coli J53, a reference strain for genetic studies. J. Bacteriol. 194, 3742–3743. doi: 10.1128/JB.00641-12 Nikaido,
H. (2003). Molecular
basis
of
bacterial
outer
membrane
permeability
revisited. Microbiol. Mol. Biol. Rev. 67,
593–656. doi: 10.1128/MMBR.67.4.593-656.2003 Yu, F., Wang, L., Pan, J., Yao, D., Chen, C., Zhu, T., et al. (2009). Prevalence
of
16S
rRNA
methylase
genes
in
Klebsiella
pneumoniae
isolates from a Chinese teaching hospital: coexistence of rmtB and Nikaido, H., Rosenberg, E. Y., and Foulds, J. (1983). REFERENCES Evaluation
of three commercial assays for rapid detection of genes encoding clinically
relevant carbapenemases in cultured bacteria. J. Antimicrob. Chemother. 70,
1338–1342. doi: 10.1093/jac/dku571 Bush, K., Courvalin, P., Dantas, G., Davies, J., Eisenstein, B., Huovinen, P.,
et al. (2011). Tackling antibiotic resistance. Nat. Rev. Microbiol. 9, 894–896. doi: 10.1038/nrmicro2693 Girometti, N., Lewis, R. E., Giannella, M., Ambretti, S., Bartoletti, M., Tedeschi,
S., et al. (2014). Klebsiella pneumoniae bloodstream infection: epidemiology
and impact of inappropriate empirical therapy. Medicine 93, 298–309. doi: 10.1097/MD.0000000000000111 Campos, A. C., Albiero, J., Ecker, A. B., Kuroda, C. M., Meirelles, L. E., Polato,
A., et al. (2016). Outbreak of Klebsiella pneumoniae carbapenemase-producing
K. pneumoniae: a systematic review. Am. J. Infect. Control 44, 1374–1380. doi: 10.1016/j.ajic.2016.03.022 Carattoli, A., Bertini, A., Villa, L., Falbo, V., Hopkins, K. L., and Threlfall, E. J. (2005). Identification of plasmids by PCR-based replicon typing. J. Microbiol. Methods 63, 219–228. doi: 10.1016/j.mimet.2005.03.018 Giske, C. G., Monnet, D. L., Cars, O., and Carmeli, Y. (2008). Clinical
and economic impact of common multidrug-resistant gram-negative bacilli. Antimicrob. Agents Chemother. 52, 813–821. doi: 10.1128/AAC.01169-07 Goessweiner-Mohr, N., Arends, K., Keller, W., and Grohmann, E. (2014). Conjugation in gram-positive bacteria. Microbiol. Spectr. 2:PLAS-0004–2013. doi: 10.1128/microbiolspec.plas-0004-2013 Chen, L., Chavda, K. D., Melano, R. G., Jacobs, M. R., Levi, M. H., Bonomo, R. A., et al. (2013). Complete sequence of a bla(KPC-2)-harboring IncFII(K1)
plasmid from a Klebsiella pneumoniae sequence type 258 strain. Antimicrob. Agents Chemother. 57, 1542–1545. doi: 10.1128/AAC.02332-12 Agents Chemother. 57, 1542–1545. doi: 10.1128/AAC.02332-12 Hu, F. P., Guo, Y., Zhu, D. M., Wang, F., Jiang, X. F., Xu, Y. C., et al. (2016). Resistance trends among clinical isolates in China reported from
CHINET surveillance of bacterial resistance, 2005-2014. Clin Microbiol. Infect. 22(Suppl. 1), S9–S14. doi: 10.1016/j.cmi.2016.01.001 Clements, A., Bursac, D., Gatsos, X., Perry, A. J., Civciristov, S., Celik, N., et al. (2009). The reducible complexity of a mitochondrial molecular machine. Proc. Natl. Acad. Sci. U.S.A. 106, 15791–15795. doi: 10.1073/pnas.0908264106 Cuzon, G., Naas, T., Truong, H., Villegas, M. V., Wisell, K. T., Carmeli,
Y., et al. (2010). Worldwide diversity of Klebsiella pneumoniae that Hu, L., Zhong, Q., Tu, J., Xu, Y., Qin, Z., Parsons, C., et al. (2013). Emergence of blaNDM-1 among Klebsiella pneumoniae ST15 and novel Frontiers in Microbiology | www.frontiersin.org June 2017 | Volume 8 | Article 1230 10 Bi et al. Bi et al. XDR K. Pneumoniae Causing BSIs ST1031 clinical isolates in China. Diagn. Microbiol. Infect. Dis. Frontiers in Microbiology | www.frontiersin.org June 2017 | Volume 8 | Article 1230 REFERENCES Porin channels in Escherichia
coli: studies with beta-lactams in intact cells. J. Bacteriol. 153, 232–240. June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 11 Bi et al. Bi et al. XDR K. Pneumoniae Causing BSIs armA genes in the same isolate. Diagn. Microbiol. Infect. Dis. 64, 57–63. doi: 10.1016/j.diagmicrobio.2009.01.020 armA genes in the same isolate. Diagn. Microbiol. Infect. Dis. 64, 57–63. doi: 10.1016/j.diagmicrobio.2009.01.020 during a short period of time in a Chinese teaching hospital: epidemiology
study and molecular characteristics. Diagn. Microbiol. Infect. Dis. 82, 240–244. doi: 10.1016/j.diagmicrobio.2015.03.017 Zgurskaya, H. I., Weeks, J. W., Ntreh, A. T., Nickels, L. M., and Wolloscheck,
D. (2015). Mechanism of coupling drug transport reactions located in two
different membranes. Front. Microbiol. 6:100. doi: 10.3389/fmicb.2015.00100 Conflict of Interest Statement: The authors declare that the research was
conducted in the absence of any commercial or financial relationships that could
be construed as a potential conflict of interest. Zhao, F., Zhang, J., Fu, Y., Ruan, Z., and Xie, X. (2015). Dissemination
of extensively drug-resistant and KPC-2 producing Klebsiella pneumoniae
isolated from bloodstream infections. J. Infect. Dev. Ctries 9, 1016–1021. doi: 10.3855/jidc.6679 Copyright © 2017 Bi, Liu, Dunstan, Li, Torres, Cao, Chen, Wilksch, Strugnell,
Lithgow and Zhou. This is an open-access article distributed under the terms
of the Creative Commons Attribution License (CC BY). The use, distribution or
reproduction in other forums is permitted, provided the original author(s) or licensor
are credited and that the original publication in this journal is cited, in accordance
with accepted academic practice. No use, distribution or reproduction is permitted
which does not comply with these terms. Zhao,
X. (2015). Investigation
and
analysis
of
prevalence
rate
of
nosocomial
infections
in
a
three
level
of
first-class
hospital
of
traditional Chinese Medicine. Guangming J. Chin. Med. 24, 6110–6111. doi: 10.3969/j.issn.1003-8914.2015.06.027 Zhou, T., Zhang, Y., Li, M., Yu, X., Sun, Y., and Xu, J. (2015). An outbreak of
infections caused by extensively drug-resistant Klebsiella pneumoniae strains June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 12
|
https://openalex.org/W4289261419
|
https://www.researchsquare.com/article/rs-1893661/latest.pdf
|
English
| null |
The postoperative prognosis of elderly intertrochanteric fracture patients as evaluated by the Chang reduction quality criteria
|
Research Square (Research Square)
| 2,022
|
cc-by
| 5,713
|
The postoperative prognosis of elderly
intertrochanteric fracture patients as evaluated by
the Chang reduction quality criteria Chongqing Emergency Medical Center (Chongqing University Central Hospital)
xiaoxing Zhang
(
dszxx76@163.com
)
Chongqing Emergency Medical Center (Chongqing University Central Hospital) Results The mortality were 24.68% and 15.42% at 1 year and total follow-up, respectively. In the total follow-up
time and 1-year follow-up time, the mortality of CRQC-Excellent was significantly lower than that of CRQC-
Acceptable (p.adj < 0.05), and was significantly lower than that of CRQC-Poor (p.adj < 0.05). After multi-
factor adjustment, CRQC-Acceptable and Poor in were independent risk factors affecting the overall
mortality and 1-year mortality. In addition, advanced age, comorbidities ≥ 1, ASA3 + 4, and prolonged
preoperative waiting time were independent risk factors for survival in the total follow-up time. At 1-year
follow-up, only ASA3 + 4 and prolonged preoperative waiting time were independent risk factors for
survival. Subgroup analysis according to different characteristics at the total follow-up time and at the
one-year follow-up time showed that in most subgroups as CRQC decreased was significantly associated
with an increase in all-cause mortality (p for trend < 0.05). Conclusions This study highlights that CRQC-Acceptable and Poor are associated with increased all-cause mortality in
elderly intertrochanteric fractures. We should try to achieve good reduction of these fractures. Objective The aim of this study was to investigate the relationship between the Chang reduction quality criteria
(CRQC) and the outcome of elderly intertrochanteric fractures based on a subgroup of follow-up time. Methods Retrospective analysis of 389 elderly patients with intertrochanteric fractures treated surgically from
January 2019 to June 2021, including 130 males and 259 females; age 84.64 (77.50-89.74) years. Patient survival was followed by telephone between admission to hospital for fracture and death, or until
study deadline (June 1, 2022). According to the CRQC, were divided into Poor, Acceptable, Excellent three
groups. Based on total follow-up time and 1-year follow-up, univariate and multivariate Cox proportional
hazard models were used to assess the association between CRQC and all-cause mortality in elderly
intertrochanteric fractures. Further subgroup analysis was performed according to different clinical and
biological characteristics to make the results more accurate. Research Article Keywords: Chang reduction quality criteria, Elderly, Intertrochanteric fractures, Mortality
Posted Date: August 1st, 2022
DOI: https://doi.org/10.21203/rs.3.rs-1893661/v1
License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License Page 1/20 Page 1/20 Background Intertrochanteric fractures of the femur are more likely to occur in elderly individuals with osteoporosis,
most of which are unstable, with high mortality and disability rates. Clinical treatment of these fractures Page 2/20 is difficult to some extent. With the aging of the population, the incidence of intertrochanteric fractures
has been increasing annually [1-3]. Fixed early surgery is the current mainstream treatment and can allow
patients to engage in early functional exercise and outdoor activities, reduce complications and improve
quality of life, commonly used implants are typically attached to the marrow during include internal and
external fixation [4]. External fixation and intramedullary fixation provide good biomechanical stability
and are more suitable for elderly patients and patients with osteoporosis and unstable fractures, the latter
are commonly performed with PFNA and INTERTAN fixation systems [5,6]. The Guidelines of The National Institute for Health and Care Excellence (NICE) emphasize that getting
patients out of bed early after surgery can reduce mortality [7]. To achieve these goals, the fracture needs
to be fixed in a stable structure that will fully support load-bearing, thereby reducing pain and improving
function [8]. Poor stability after fracture fixation can lead to limb shortening, hip pain, dysfunction, and
even resurgery [9,10], resulting in a delay in getting patients out of bed. Reduction quality is one factor
determining stability after fracture fixation [11,12]. There are different criteria for evaluating the quality of intertrochanteric fracture reduction, the most
widely used of which are the criteria developed by Baumgaertner et al (Baumgaertner reduction quality
criteria, BRQC) [13,14]. Later, Chang et al, based on positive medial cortical support (PMCS, Fig. 1) and negative medial cortical support (NMCS, Fig. 1), proposed a new reset quality standard named the
Chang reduction quality criteria (CRQC) [15] (Table 1). Studies have shown that the CRQC is more reliable
than the BRQC in assessing stability after fracture fixation [16]. The main objective of this article is to assess the impact of reduction quality in regard to the CRQC on
patient survival after the intramedullary nail fixation of intertrochanteric femoral fractures in elderly
patients. To the best of our knowledge, there are no published studies on the CRQC in evaluating the reset
quality after femoral intertrochanteric fracture and thus in assessing the impact of reset quality on
mortality. Study design and patients A total of 389 patients with intertrochanteric fractures were admitted to the hospital between January
2019 and June 2021 for this study. All patients were fixed with INTERTAN or PFNA systems. The choice
of internal fixation was based on surgeon preference and experience. The inclusion criteria were as
follows: (1) diagnosis of intertrochanteric fracture (AO 31A1 or 31A2) [17]. (2) Age ≥ 65 years. (3) Low-
energy fractures, fresh fractures not older than 3 weeks. (4) Complete medical history. The
exclusion criteria were as follows: (1) Age < 65 years. (2) High energy fractures, old
fractures, and pathological fractures. (3) Prior conservative treatment. (4) Refusal of or loss to follow-up. Table 1 Chang reduction quality criteria (CRQC) Page 3/20 Page 3/20 Item
Score
I. Alignment
a. Anteroposterior view: normal or slightly valgus neck-shaft anglea
1
b. Lateral view: less than 20° of angulation
1
II. Displacement
a. Anteroposterior view: neutral or positive medial cortical supportb
1
b. Lateral view: smooth anterior cortical contactc
1
Reduction quality
Excellent
4
Acceptable
2 or 3
Poor
0 or 1 Item
Score
I. Alignment
a. Anteroposterior view: normal or slightly valgus neck-shaft anglea
1
b. Lateral view: less than 20° of angulation
1
II. Displacement
a. Anteroposterior view: neutral or positive medial cortical supportb
1
b. Lateral view: smooth anterior cortical contactc
1
Reduction quality
Excellent
4
Acceptable
2 or 3
Poor
0 or 1 Follow-up and study endpoint Patients were followed up by telephone once a month for the first three months after discharge, then
every three months until one year, and every six months thereafter. Follow-up time was defined as the
time between hospitalization and the date of death or the last follow-up visit (June 30, 2022). Data collection We retrospectively recorded age, sex, fracture type, fracture orientation, number of comorbidities,
American Society of Anesthesiologists (ASA) classification, type of anesthesia, preoperative waiting time,
blood transfusion, preoperative hemoglobin, and CRQC for the patients. The comorbidity data of these
patients were identified using the codes of the 10th Revision of the International Classification of
Diseases. Page 4/20 Page 4/20 The main exposure variable was the reset quality, as assessed by the CRQC. The CRQC were assessed by
two independent assessors (LJ and DX) blinded to each other's scores. Cases of disagreement were
resolved with the assistance of a third assessor (HM). Statistical analysis IBM SPSS 26.0 (IBM Corp. New York, USA) were used for statistical analyses. The significance level was
set to 0.05. Continuous variables are expressed as the mean ± standard deviation (SD) or median
(interquartile range, IQR). The Shapiro‒Wilk test was used to assess the normality of the distribution of
variables. The Kruskal‒Wallis H test was used for comparative analysis between the 3 groups of data
that did not conform to a normal distribution. One-way ANOVA was used for comparative analysis
between the 3 groups of normally distributed data. Categorical variables are expressed as frequencies
(percentages) and were compared by the χ2 test. Hazard ratios (HR) and 95% confidence intervals (CIs)
for the risk of death were calculated by one-way Cox regression analysis, incorporating the influencing
factors (p< 0.10) into a multifactorial Cox proportional risk model. We also performed subgroup analyses
for age, sex, fracture subtype, fracture orientation, number of comorbidities, ASA grade, blood transfusion,
and hemoglobin level. For the subgroup analyses, we did not perform multivariate adjustment because of
the very small number of events. Ethics approval This retrospective study involving human participants was conducted in accordance with the ethical
standards of the institutional and national research committee and with the 1964 Helsinki Declaration
and its later amendments or comparable ethical standards. The study was approved by the Ethics
Committee of the Central Hospital affiliated with Chongqing University. Informed consent was obtained
from all participants. Patient characteristics Page 5/20
A total of 389 patients with intertrochanteric fractures were included in this study, and their
characteristics are summarized in Table 1. The age of these participants was 84.64 (IQR, 77.50-89.74)
years, with females accounting for the majority of patients (66.58%). AO 31A2 intertrochanteric fractures
of the femur accounted for 79.69% of fractures, and 63.24% of fractures were on the right. The
proportions of patients with no, one, and two or more comorbid diseases were 21.85%, 35.73% and
42.42%, respectively. Regarding ASA grades, 11.05% and 88.95% of patients were grades 1+2 and grades Page 5/20 3+4, respectively. Among the types of anesthesia, general anesthesia, combined spinal and
epidural+spinal anesthesia, and nerve block were used on 37.28%, 59.64% and 3.08% of the patients,
respectively. The preoperative waiting time was 3 (IQR, 2-5) days. The preoperative hemoglobin level was
107 (IQR, 93-119) g/l. A total of 56.30% of the patients received blood transfusions. All-cause mortality
occurred in 96 patients during the total follow-up period (mortality rate: 24.68%). At the 1-year follow-up
time, all-cause death had occurred in 60 patients (mortality: 15.42%). As shown in Table 2, there were no statistically significant differences in the comparison of sex, age,
fracture subtype, orientation of the fracture, ASA score and preoperative waiting time among the 3 CRQC
groups (Poor, Acceptable, Excellent), whereas statistically significant differences were found in the
comparison of the number of comorbid diseases, mode of anesthesia, whether blood was transfused and
hemoglobin level (P<0.05). As shown in Table 1 and Figure 1, at the total follow-up, the morbidity of the
CRQC-Excellent group was significantly lower than that of the CRQC-Acceptable (16.67% vs. 31.91%,
p.adj<0.05) and CRQC-Poor groups (16.67% vs. 53.85%, p.adj<0.05). The mortality of the CRQC-
Acceptable group was lower than that of the CRQC-Poor group, but not significantly (31.91% vs. 53.85%,
p.adj>0.05). At the one-year follow-up, the CRQC-Excellent group had significantly lower mortality than the
CRQC-Acceptable (6.31% vs. 22.70%, p.adj<0.05) and CRQC-Poor groups (6.31% vs. 53.85%, p.adj<0.05),
and mortality in the CRQC-Acceptable group was significantly lower than that in the CRQC-Poor group
(22.70% vs. 53.85%, p.adj<0.05) (Fig. 2). Clinical variables predicting mortality The relationship between clinical variables and the prognosis of intertrochanteric fractures in elderly
patients is listed in Tables 3 and 4. At the total follow-up, according to univariate Cox analysis, increasing
age, fracture type (31A2), ≥1 comorbidity, ASA grades 3+4, longer preoperative waiting time, lower
hemoglobin level, blood transfusion and lower CRQC grade were significantly associated with increased
overall mortality (p< 0.10). At the 1-year follow-up, older age, fracture type (31A2), ASA grade 3+4,
prolonged preoperative waiting time, decreased hemoglobin levels, blood transfusions and lower CRQC
grade were found to be significantly associated with increased overall mortality by univariate Cox
analysis (p< 0.10). The influencing factors screened by univariate Cox regression analysis were incorporated into the
multivariate Cox proportional risk model. Increased age (HR 1.04, 95%CI 1.01-1.08), 1 comorbidity (HR
6.63, 95%CI 1.56-28.23), ≥2 comorbidities (HR 8.65, 95%CI 2.06-36.41), ASA grades 3+4 (HR 5.09, 95%CI
1.14-22.68), increased preoperative waiting time (HR 1.10, 95%CI 1.03-1.18), CRQC-Acceptable (HR 1.60,
95%CI 1.06-2.53), and CRQC-Poor (HR 6.67, 95%CI 3.48-12.77) were independent risk factors for all-cause
mortality during the total follow-up (Table 2). ASA grade 3+4 (HR 5.07, 95%CI 1.08-23.84), increased
preoperative waiting time (HR 1.12, 95%CI 1.03-1.21), and acceptable (HR 3.11, 95%CI 1.64-5.91) and
poor CRQC grades (HR 14.80, 95%CI 6.83-32.09) were independent risk factors for all-cause mortality
during the 1-year follow-up (Tables 3 and 4). Subgroup analyses Page 6/20 Page 6/20 To further verify whether the predictive values of the CRQC for mortality were consistent across
populations, we performed subgroup analyses using forest plots, as shown in Figure 4. Consistent with
the main analysis, subgroup analysis showed that in most subgroups, a lower CRQC grade was
significantly associated with increased all-cause mortality (p for trend<0.05). However, only two
subgroups, patients with ASA grades 1+2 (p=0.427) and patients with fracture type 31A2 (p=0.155), were
exceptions at the total follow-up. At the 1-year follow-up, only one subgroup, patients with ASA grades
1+2 (p=0.427), was the exception (Figs 3 and 4). Table 2 Patient characteristics according to CRQC grade Page 7/20 Variable
Total
(n=389)
CRQC grade
p value
Poor (n=26)
Acceptable (n=141)
Excellent (n=222)
Age (years)
84.64
(77.50-
89.74)
85 (71.83-
89.19)
84 (77.75-89.74)
84.64 (77.88-
89.74)
0.745a
Female, n(%)
259
(66.58)
18 (69.23)
90 (63.83)
151 (68.02)
0.681b
31A2, n (%)
310
(79.69)
24 (92.31)
116 (82.27)
170 (76.58)
0.107b
Right-side
fracture, n (%)
246
(63.24)
16 (61.54)
79 (56.03)
151 (68.02)
0.068b
Comorbidities, n
(%)
<0.001b
None
85
(21.85)
2 (7.69)
22 (15.60)
61 (27.48)
1
139
(35.73)
12 (46.15)
40 (28.37)
87 (39.19)
2 or more
165
(42.42)
12 (46.15)
79 (56.03)
74 (33.33)
ASA grade, n (%)
0.127b
1+2
43
(11.05)
6 (23.08)
13 (9.22)
24 (10.81)
3+4
346
(88.95)
20 (76.92)
128 (90.78)
198 (89.19)
Type of
anesthesia, n (%)
0.017b
General
145
(37.28)
10 (38.46)
60 (42.55)
75 (33.78)
Combined spinal
and
epidural+spinal
232
(59.64)
14 (53.85)
81 (57.45)
137 (61.71)
Nerve block
12 (3.08)
2 (7.69)
0 (0.00)
10 (4.50)
Preoperative
waiting time
(days)
3 (2-5)
4 (2-6.25)
3 (2-6)
3 (2-4)
0.097a
HB (g/l)
107 (93-
119)
92.5 (77-
112.75)
104 (93.5-116.5)
108.5 (94.75-
120)
0.017a 1-year death, n
(%)
60
(15.42)
14 (53.85)
32 (22.70)
14 (6.31)
<0.001b
Total death, n (%)
96
(24.68)
14 (53.85)
45 (31.91)
37 (16.67)
<0.001b Discussion The key to a stable fracture fixation is reduction quality. Many studies have included restoration quality,
but only as a confounding variable, rather than as the main object of research [18–22]. This study
focuses on the CRQC, which are a relatively new set of criteria for assessing the quality of reduction
following fracture fixation. We verified that compared with patients with excellent CRQC, those with
acceptable CRQC had a 0.6- and 1.1-times increase in mortality at the total postoperative and 1-year
follow-up, respectively, while those with poor CRQC showed a 5.67- and 13.80-times increase in mortality,
respectively. In other words, fracture reduction quality appears to be an important predictor of
postoperative mortality in elderly intertrochanteric fracture patients. Currently, however, when the patient's risk of death is high, the surgeon accepts a poor reduction,
considering continuing the fixation and shortening the operation time to be more important than
attempting to further improve the reduction. Similarly, the increased operative time, soft tissue dissection,
and blood loss associated with open reduction relative to closed reduction may not be in the patient's
best interest, or their functional needs may be lower, meaning they can better tolerate a poor reduction. The findings of this study urge us to better understand and focus more on the quality of the reduction. At present, there are two main standards for evaluating the postoperative reduction quality of
intertrochanteric fractures: the CRQC and BRQC [16]. The greatest innovation of the CRQC lies in the
introduction of the concepts of PMCS and NMCS [15, 23]. The CRQC require good reduction on
anteroposterior (AP) views, meeting two conditions: 1. a displacement less than the bone cortex
thickness; and 2. neutral or positive medial cortical support. The definition of good reduction thus
excludes two possibilities: NMCS with displacement less than the cortical thickness or PMCS with
displacement greater than the cortical thickness of the fracture. The CRQC require good reduction on
lateral views and a smooth anterior cortex, meaning that the displacement must be less than half of the
bone cortex thickness, emphasizing the strong support of the anterior cortex [24, 25]. Currently, most
internal fixation materials do not immobilize small trochanter fragments, so CRQC does not explicitly
require posterior cortical alignment [21]. The CRQC are also more reliable than the BRQC for three main
reasons. First, the use of the BRQC may result in the loss of some details. ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria,
HR, Hazard ratio, CI, Confidence interval ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria,
HR, Hazard ratio, CI, Confidence interval ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria,
HR, Hazard ratio, CI, Confidence interval aKruskal‒Wallis H test aKruskal‒Wallis H test bχ2 test ASA, American society of anesthesiologists, CRQC, Chang reduction quality criteria, HB, Hemoglobin Table 3 Univariate and multivariate Cox regression analyses of factors associated with total follow-up all-
cause mortality. Page 9/20 Variable
Univariate
Multivariate
HR (95% CI)
p
value
HR (95% CI)
p
value
Age (per 1 year increase)
1.05 (1.02-1.08)
<0.001
1.04 (1.01-
1.08)
0.006
Sex (Female vs. Male)
1.25 (0.83-1.88)
0.285
Fracture type (31A1 vs. 31A2)
1.86 (1.05-3.09)
0.033
1.63 (0.91-
2.92)
0.102
Fracture side (left vs. right)
0.82 (0.55-1.23)
0.342
Comorbidities
None
1.0 (Reference)
1.0 (Reference)
1
8.11 (1.93-
34.04)
0.004
6.63 (1.56-
28.23)
0.010
2 or more
16.86 (4.13-
68.91)
<0.001
8.65 (2.06-
36.41)
0.003
ASA grade (1+2 vs. 3+4)
6.77 (1.67-
27.50)
0.007
5.09 (1.14-
22.68)
0.033
Type of anesthesia
General
1.0 (Reference)
Combine spinal and epidural+spinal
0.76 (0.51-1.15)
0.192
Nerve block
0.74 (0.18-3.08)
0.681
Preoperative waiting time (per 1 day
increase)
1.12 (1.06-1.19)
<0.001
1.10 (1.03-
1.18)
0.005
HB (per 1 g/l increase)
0.99 (0.98-1.00)
0.010
1.00 (0.99-
1.01)
0.907
Blood transfusion (no vs. yes)
2.18 (1.40-3.38)
0.001
1.69 (1.00-
2.87)
0.052
CRQC grade
Excellent
1.0 (Reference)
1.0 (Reference)
Acceptable
2.15 (1.39-3.32)
0.01
1.60 (1.02-
2.53)
0.043
Poor
5.86 (3.16-
10.88)
<0.001
6.67 (3.48-
12.77)
<0.001
ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, Page 10/20
ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria,
HR, Hazard ratio, CI, Confidence interval esthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, Discussion For example, in the BRQC,
nonalignment includes three possible conditions: poor alignment only on the AP surface; poor alignment
only on the side; and poor AP and lateral alignment; the BRQC cannot distinguish between these Page 11/20 Page 11/20 Variable
Univariate
Multivariate
HR (95% CI)
p
value
HR (95% CI)
p
value
Age (per 1 year increase)
1.05 (1.01-1.08)
0.009
1.04 (1.00-
1.08)
0.066
Sex (Female vs. Male)
1.07 (0.63-1.82)
0.799
Fracture type (31A1 vs. 31A2)
2.46 (1.06-5.73)
0.036
1.94 (0.82-
4.56)
0.132
Fracture side (left vs. right)
0.75 (0.45-1.25)
0.275
Comorbidities
None
1.0 (Reference)
1
21624.41 (0-
2.59E+43
0.828
2 or more
55076.52 (0-
6.59E+43)
0.812
ASA grade (1+2 vs. 3+4)
3.87 (0.95-15.84)
0.060
5.07 (1.08-
23.84)
0.040
Type of anesthesia
General
1.0 (Reference)
Combine spinal and epidural+spinal
0.69 (0.41-1.16)
0.165
Nerve block
0.84 (0.20-3.54)
0.815
Preoperative waiting time (per 1 day
increase)
1.13 (1.05-1.22)
0.001
1.12 (1.03-
1.21)
0.007
HB (per 1 g/l increase)
0.98 (0.97-0.99)
0.001
0.99 (0.98-
1.01)
0.229
Blood transfusion (no vs. yes)
3.04 (1.65-5.62)
<0.001
1.63 (0.83-
3.19)
0.153
CRQC grade
Excellent
1.0 (Reference)
1.0 (Reference)
Acceptable
3.92 (2.09-3.32)
<0.001
3.11 (1.64-
5.91)
0.001
Poor
13.39 (6.37-7.35)
<0.001
14.80 (6.83-
32.09)
<0.001 Page 12/20
conditions. In contrast, the CRQC use a more ideal, 4-point scoring system and retains more details [16]. Second, the CRQC reasonably adopt the concept of PMCS, which provides cortical support between the two main fragments and prevents further lateral sliding of the femoral head and neck fragments [16]. Third, using one or half cortical thickness to describe the displacement is better than using the actual
distance of 4 mm because it can be measured directly with the naked eye through intraoperative C-arm
fluoroscopy without the use of special tools. two main fragments and prevents further lateral sliding of the femoral head and neck fragments [16]. Third, using one or half cortical thickness to describe the displacement is better than using the actual
distance of 4 mm because it can be measured directly with the naked eye through intraoperative C-arm
fluoroscopy without the use of special tools. Our study found that mortality increased with age and the number of comorbidities during the total
follow-up time. This conclusion has been confirmed in previous studies [26–29]. However, no
corresponding results were observed at the one-year follow-up, which may have been caused by
statistical error due to the small sample size. Discussion Some studies have reported that mortality is associated with higher ASA grades [30, 31]. Similarly, our
study further demonstrated that patients with ASA grades 3 + 4 had a higher risk of death at the total -
and 1-year follow-up than patients with ASA grades 1 + 2. However, this study had some limitations. This was a retrospective single-center study; large-sample,
multicenter, randomized controlled studies are needed to confirm the results. Second, we are only
evaluating medium-term outcomes because the number of deaths was relatively small, and it is
impossible to assess short-term outcomes. Conclusion In conclusion, we demonstrate that postoperative mortality in elderly intertrochanteric fracture patients is
associated with reduced reduction quality according to the CRQC. Therefore, we strongly recommend that
orthopedic surgeons consider reduction quality when treating elderly intertrochanteric fracture patients to
improve their outcomes. Availability of data and materials The datasets generated and/or analysed during the current study are not publicly available as they
contain information that could compromise the privacy of research participants but are available from
the corresponding author on reasonable request. Acknowledgements Page 13/20 Page 13/20 Not Applicable. Not Applicable. Funding Funding information is not available. Author details Department of Orthopaedic Surgery, Chongqing Emergency Medical Center (Chongqing University Central
Hospital), Chongqing 400010, China Ethics approval and consent to participate This retrospective study involving human participants was conducted in accordance with the ethical
standards of the institutional and national research committee and with the 1964 Helsinki Declaration
and its later amendments or comparable ethical standards. The study was approved by the Ethics
Committee of the Central Hospital affiliated with Chongqing University. Informed consent was obtained
from all participants. Author contributions All authors contributed to the study conception and design. Material preparation, data collection and
analysis were performed by HM and LJ. The first draft of the manuscript was written by HM, DX made
meaningful corrections to the structure of the article and guided the statistical methods and data
processing, and all authors commented on previous versions of the manuscript. ZXX participated in the
design of the study and proofread the manuscript as the corresponding author. All authors have read and
approved the manuscript. Consent for publication Not Applicable. Competing interests The authors declare that they have no competing interests. References Page 14/20 Page 14/20 Page 14/20 1. Yang X, Wu Q, Wang X. Investigation of perioperative hidden blood loss of unstable intertrochanteric
fracture in the elderly treated with different intramedullary fixations. Injury. 2017, 48(8): 1848-1852. 2. Angulo Tabernero M, Aguilar Ezquerra A, Ungria Murillo J, et al. Epidemiology of fractures of the
proximal third of the femur: 20 years follow-up]. Rev Fac Cien Med Univ Nac Cordoba. 2015, 72(3):
145-151. 3. Wang J, Wei J, Wang M. The risk factors of perioperative hemoglobin and hematocrit drop after
intramedullary nailing treatment for intertrochanteric fracture patients. J Orthop Sci. 2015, 20(1):
163-167. 4. Zhou F, Zhang ZS, Yang H, et al. Less invasive stabilization system (LISS) versus proximal femoral
nail anti-rotation (PFNA) in treating proximal femoral fractures: a prospective randomized study. J
Orthop Trauma. 2012, 26(3): 155-162. 5. Evaniew N, Bhandari M. Cochrane in CORR ®: Intramedullary nails for extracapsular hip fractures in
adults (review). Clin Orthop Relat Res. 2015, 473(3): 767-774. 6. Shen L, Zhang Y, Shen Y, Cui Z. Antirotation proximal femoral nail versus dynamic hip screw for
intertrochanteric fractures: a meta-analysis of randomized controlled studies. Orthop Traumatol Surg
Res. 2013, 99(4): 377-383. 7. National Institute for Health and Care Excellence Hip fracture–Management. London: Clinical
guideline CG124, 2017. 7. National Institute for Health and Care Excellence Hip fracture–Management. London: Clinical
guideline CG124, 2017. 8. Macdonald H, Brown R, Gronager M, Close J, Fleming T, Whitehouse M. Quality of fracture reduction
is associated with patient survival at one year, but not 30 days, following trochanteric hip fracture
fixation. A retrospective cohort study. Injury. 2022, 53(3): 1160-1163. 8. Macdonald H, Brown R, Gronager M, Close J, Fleming T, Whitehouse M. Quality of fracture reduction
is associated with patient survival at one year, but not 30 days, following trochanteric hip fracture
fixation. A retrospective cohort study. Injury. 2022, 53(3): 1160-1163. 9. Zlowodzki M, Brink O, Switzer J, et al. The effect of shortening and varus collapse of the femoral
neck on function after fixation of intracapsular fracture of the hip: a multi-centre cohort study. J Bone
Joint Surg [Br] 2008, 90-B:1487-1494. 9. Zlowodzki M, Brink O, Switzer J, et al. The effect of shortening and varus collapse of the femoral
neck on function after fixation of intracapsular fracture of the hip: a multi-centre cohort study. J Bone
Joint Surg [Br] 2008, 90-B:1487-1494. 10. Gordon M, Berntsson PO, Sjölund E, et al. Surg 2015, 135: 811-818. Surg 2015, 135: 811-818. 16. Mao W, Ni H, Li L, et al. Comparison of Baumgaertner and Chang reduction quality criteria for the
assessment of trochanteric fractures. Bone Joint Res. 2019, 8(10): 502-508. 17. Marsh JL, Slongo TF, Agel J, et al. Fracture and Dislocation Classififi- cation Compendium—2007:
orthopaedic trauma association classifification, database and outcomes committee. J Orthop
Trauma. 2007, 21(suppl 10): S1–S163. 18. Jiamton C, Boernert K, Babst R, Beeres F, Link B. The nail-shaft-axis of the of proximal femoral nail
antirotation (PFNA) is an important prognostic factor in the operative treatment of intertrochanteric
fractures. Arch Orthop Trauma Surg 2018, 138: 339-349. 19. De Bruijn K, den Hartog D, Tuinebreijer W, Roukema G. Reliability of predictors for screw cutout in
intertrochanteric hip fractures. J Bone Joint Surg [Am] 2012,94- A: 1266-1272. 20. Abram SG, Pollard TC, Andrade AJ. Inadequate 'three-point' proximal fixation predicts failure of the
Gamma nail. Bone Joint J 2013, 95-B: 825-830. 21. Buyukdogan K, Caglar O, Isik S, Tokgozoglu M, Atilla B. Risk factors for cut-out of double lag screw
fixation in proximal femoral fractures. Injury 2017, 48: 414-418. 22. Kashigar A, Vincent A, Gunton M, et al. Predictors of failure for cephalomedullary nailing of proximal
femoral fractures. Bone Joint J 2014, 96-B: 1029-1034. 23. Cho MR, Lee JH, Kwon JB, et al. The effect of positive medial cortical support in reduction of
pertrochanteric fractures with posteromedial wall defect using a dynamic hip screw. Clin Orthop Surg
2018, 10: 292-298. 24. Tsukada S, Okumura G, Matsueda M. Postoperative stability on lateral radiographs in the surgical
treatment of pertrochanteric hip fractures. Arch Orthop Trauma Surg 2012, 132: 839-846. 24. Tsukada S, Okumura G, Matsueda M. Postoperative stability on lateral radiographs in the surgical
treatment of pertrochanteric hip fractures. Arch Orthop Trauma Surg 2012, 132: 839-846. 25. Kozono N, Ikemura S, Yamashita A, et al. Direct reduction may need to be considered to avoid
postoperative subtype P in patients with an unstable trochanteric fracture: a retrospective study
using a multivariate analysis. Arch Orthop Trauma Surg 2014, 134: 1649-1654. 25. Kozono N, Ikemura S, Yamashita A, et al. Direct reduction may need to be considered to avoid
postoperative subtype P in patients with an unstable trochanteric fracture: a retrospective study
using a multivariate analysis. Arch Orthop Trauma Surg 2014, 134: 1649-1654. 26. Page 14/20 Loss of offset after pertrochanteric hip fractures affects hip
function one year after surgery with a short intramedullary nail. A prospective cohort study. Int
Orthop 2016, 40:799-806. 10. Gordon M, Berntsson PO, Sjölund E, et al. Loss of offset after pertrochanteric hip fractures affects hip
function one year after surgery with a short intramedullary nail. A prospective cohort study. Int
Orthop 2016, 40:799-806. 11. Biber R, Berger J, Bail HJ. The art of trochanteric fracture reduction. Injury 2016,47(Suppl 7): S3-S6. 11. Biber R, Berger J, Bail HJ. The art of trochanteric fracture reduction. Injury 2016,47(Suppl 7): S3-S6. 12. Socci AR, Casemyr NE, Leslie MP, Baumgaertner MR. Implant options for the treatment of
intertrochanteric fractures of the hip: rationale, evidence, and recommendations. Bone Joint J
2017,99-B:128-133. 13. Baumgaertner M, Curtin S, Lindskog D, Keggi J. The value of the tip-apex distance in predicting
failure of fixation of peritrochanteric fractures of the hip. J Bone Joint Surg [Am] 1995, 77-A: 1058-
1064. 14. Baumgaertner MR, Curtin SL, Lindskog DM. Intramedullary versus extramedullary fixation for the
treatment of intertrochanteric hip fractures. Clin Orthop Relat Res 1998, 348: 87-94. 14. Baumgaertner MR, Curtin SL, Lindskog DM. Intramedullary versus extramedullary fixation for the
treatment of intertrochanteric hip fractures. Clin Orthop Relat Res 1998, 348: 87-94. Page 15/20
15. Chang SM, Zhang YQ, Ma Z, et al. Fracture reduction with positive medial cortical support: a key
element in stability reconstruction for the unstable pertrochanteric hip fractures. Arch Orthop Trauma Page 15/20
15. Chang SM, Zhang YQ, Ma Z, et al. Fracture reduction with positive medial cortical support: a key
element in stability reconstruction for the unstable pertrochanteric hip fractures. Arch Orthop Trauma Surg 2015, 135: 811-818. Kumar P, Law S, Sriram KB (2017) Evaluation of platelet lymphocyte ratio and 90-day mortality in
patients with acute exacerbation of chronic obstructive pulmonary disease. J Thorac Dis 9(6): 1509–
1516. 27. Liu Y, Wang Z, Xiao W (2018) Risk factors for mortality in elderly patients with hip fractures: a meta-
analysis of 18 studies. Aging Clin Exp Res 30(4): 323–330. 27. Liu Y, Wang Z, Xiao W (2018) Risk factors for mortality in elderly patients with hip fractures: a meta-
analysis of 18 studies. Aging Clin Exp Res 30(4): 323–330. 28. Ercin E, Bilgili MG, Sarı C, et al. Risk factors for mortality in geriatric hip fractures: a compressional
study of different surgical procedures in 785 consecutive patients. Eur J Orthop Surg Traumatol
2017, 27: 101-6. 28. Ercin E, Bilgili MG, Sarı C, et al. Risk factors for mortality in geriatric hip fractures: a compressional
study of different surgical procedures in 785 consecutive patients. Eur J Orthop Surg Traumatol
2017, 27: 101-6. 29. Khan MA, Hossain FS, Ahmed I, Muthukumar N, Mohsen A. Predictors of early mortality after hip
fracture surgery. Int Orthop 2013, 37: 2119-24. 30. Gurger M. Factors impacting 1-year mortality after hip fractures in elderly patients: A retrospective
clinical study. Niger J Clin Pract 2019, 22: 648-51. Page 16/20 Page 16/20 31. Gremillet C, Jakobsson JG. Acute hip fracture surgery anaesthetic technique and 30-day mortality in
Sweden 2016 and 2017: A retrospective register study. F1000Res 2018, 7: 1009. 31. Gremillet C, Jakobsson JG. Acute hip fracture surgery anaesthetic technique and 30-day mortality in
Sweden 2016 and 2017: A retrospective register study. F1000Res 2018, 7: 1009. Figures Figure 1
Postoperative X-ray of intertrochanteric fracture. (A) X-ray showed positive medial cortical support,
meaning that the inferior edge of the medial cortex of the femoral head-neck fragment was medial to the
superior edge of the medial cortex of the femoral shaft with a displacement of less than one cortical
thickness. (B) X-ray showed negative medial cortical support, meaning that the inferior edge of the medial
cortex of the femoral head-neck fragment was lateral to the superior edge of the medial cortex of the
femoral shaft, regardless of displacement distance. (C) X-ray showed neutral medial cortical support,
meaning that the medial cortex of head–neck fragment and the femoral shaft were smoothly contacted. Postoperative X-ray of intertrochanteric fracture. (A) X-ray showed positive medial cortical support,
meaning that the inferior edge of the medial cortex of the femoral head-neck fragment was medial to the
superior edge of the medial cortex of the femoral shaft with a displacement of less than one cortical
thickness. (B) X-ray showed negative medial cortical support, meaning that the inferior edge of the medial
cortex of the femoral head-neck fragment was lateral to the superior edge of the medial cortex of the
femoral shaft, regardless of displacement distance. (C) X-ray showed neutral medial cortical support,
meaning that the medial cortex of head–neck fragment and the femoral shaft were smoothly contacted. Page 17/20 Figure 2
Column diagram comparing mortality in elderly intertrochanteric fracture patients at the 1 year and total
follow-up for different Chang reduction quality criteria (CRQC) grades were analyzed using the chi-square
test. Figure 2 Column diagram comparing mortality in elderly intertrochanteric fracture patients at the 1 year and total
follow-up for different Chang reduction quality criteria (CRQC) grades were analyzed using the chi-square
test. Page 18/20 Page 18/20 igure 3
orest plot of the subgroup analysis estimating the association between the C
riteria (CRQC) grade and total follow-up mortality based on different characte
etween subgroups were analyzed by Cox regression analysis. The black rhom
azard ratio (HR), and the black horizontal lines represent the 95% confidence Figure 3
Forest plot of the subgroup analysis estimating the association between the Chang reduction quality
criteria (CRQC) grade and total follow-up mortality based on different characteristics. Differences
between subgroups were analyzed by Cox regression analysis. The black rhombuses represent the
hazard ratio (HR), and the black horizontal lines represent the 95% confidence interval (CI). Figure 3 Figure 3 Forest plot of the subgroup analysis estimating the association between the Chang reduction quality
criteria (CRQC) grade and total follow-up mortality based on different characteristics. Differences
between subgroups were analyzed by Cox regression analysis. The black rhombuses represent the
hazard ratio (HR), and the black horizontal lines represent the 95% confidence interval (CI). Page 19/20 Figure 4
Forest plot of the subgroup analysis estimating the association between the Chang reduction quality
criteria (CRQC) grade and 1-year follow-up mortality based on different characteristics. Differences
between subgroups were analyzed by Cox regression analysis. The black rhombuses represent the
hazard ratio (HR), and the black horizontal lines represent the 95% confidence interval (CI). Forest plot of the subgroup analysis estimating the association between the Chang reduction quality
criteria (CRQC) grade and 1-year follow-up mortality based on different characteristics. Differences
between subgroups were analyzed by Cox regression analysis. The black rhombuses represent the
hazard ratio (HR), and the black horizontal lines represent the 95% confidence interval (CI). Page 20/20 Page 20/20
|
W4376614445.txt
|
https://journals.wlb-stuttgart.de/ojs/index.php/sh/article/download/6310/6199
|
de
|
Besonders vorbildliche Sanierungen
|
Schwäbische Heimat
| 2,023
|
cc-by
| 6,288
|
Ein repräsentativer Bau des 19. Jahrhunderts auf dem Land: der wiederbelebte Bahnhof Eckartshausen-Ilshofen
Besonders vorbildliche Sanierungen
Die fünf Preisträger des Denkmalschutzpreises Baden-Württemberg 2022
Gerhard Kabierske
Denkmalschutz und Denkmalpflege im Baden-Württemberg sind in den letzten Jahren nicht einfacher geworden.
Die unbefriedigende Stellensituation beim Landesamt für
Denkmalpflege macht eine ausreichende Beratungstätigkeit für Denkmaleigentümer schon geraume Zeit kaum
mehr möglich. Vorstöße, daran etwas zu ändern, haben
mit Verweis auf die Haushaltslage keine Chance umgesetzt zu werden. Die Covid-19-Pandemie hat die Situation
noch zugespitzt, denn wie sollte eine qualitative Denkmalpflege vom Homeoffice aus, ohne persönliche Inaugenscheinnahme der Kulturdenkmale und ohne den persönlichen Kontakt zur Bauherrschaft betrieben werden?
Und von Seiten der Politik und der Ministerialverwaltung
weht der Wind auch rau, wird doch neuerdings immer
18
stärker ein völlig ungerechtfertigter Widerspruch zwischen Umweltschutzbelangen und Denkmalpflege gesehen. Die geplante Änderung des Denkmalschutzgesetzes
wird mit ihrem undifferenzierten grünen Licht für Sonnenkollektoren, Windräder und Dämmmaßnahmen an
Kulturdenkmalen oder in deren Umgebung zwar wegen
ihres geringen Anteils von Denkmalen und Anlagen bei
den gesamten Baulichkeiten im Land an der Klimasituation nichts ändern, aber unsere historischen Stadtbilder
ganz wesentlich negativ beeinflussen. In einer gemeinsamen Stellungnahme haben der Schwäbische Heimatbund
und der Landesverein Badische Heimat gegen die Änderungen Stellung genommen – offensichtlich ohne Gehör
zu finden.
Schwäbische Heimat 2023|1
Umso wichtiger ist es für die beiden Vereine, den Denkmalschutz in Baden-Württemberg zu unterstützen und
ihre Anerkennung jenen privaten Eigentümern und
Eigentümerinnen auszusprechen, die besonders vorbildlich bei einer Gesamtsanierung oder Umnutzung ihres
historisch bedeutsamen Kulturdenkmals vorgegangen
sind und damit einen wichtigen Beitrag zur Tradierung
der vielfältigen Baukultur im Land geleistet haben. Der
bereits seit 1978 vergebene Denkmalschutzpreis soll dafür ein deutliches Zeichen setzen. Als Anerkennung erhalten die ausgezeichneten Eigentümer einen Geldpreis
in Höhe von 5.000 Euro sowie eine Bronzeplakette zur Anbringung an ihrem Gebäude. Zudem ist die Auszeichnung
mit Urkunden für sie sowie für beteiligte Architekten,
Restauratoren und Handwerker verbunden. Wie bereits
seit 2006 ist die Finanzierung des Preises, für den die Ministerin für Landesentwicklung und Wohnen Nicole Razavi die Schirmherrschaft übernommen hat, der großzügigen Unterstützung durch die Wüstenrot Stiftung zu verdanken.
Das Juryverfahren konnte 2022 glücklicherweise ohne
Corona-Einschränkungen stattfinden. Auf die Ausschreibung im Frühjahr gingen 65 Einsendungen ein. Die Jury,
die sich aus Dr. Anette Busse für die Wüstenrot Stiftung,
Prof. Dr. Ulrike Plate für das Landesamt für Denkmalpflege, Dr. Diana Wiedemann für die Architektenkammer Baden-Württemberg, Ulrich Gräf, Dr. Bernd Langner und Dr.
Karsten Preßler für den Schwäbischen Heimatbund, Dr.
Gerhard Kabierske für den Landesverein Badische Heimat
sowie Frank Mienhardt für den Städtetag BadenWürttemberg zusammensetzte, traf nach Vorprüfung und
Arbeitssitzung eine engere Wahl von elf Objekten. Diese
wurden bei einer dreitägigen Juryrundfahrt von über
tausend Kilometern vom Main bis zum Bodensee
besichtigt und schließlich die fünf Preisträger bestimmt:
das ehemalige Jägerhaus des Klosters Salem in Bermatingen, der Wildenhof in Lenzkirch-Raitenbuch, ein Fachwerkhaus in Maulbronn-Zaisersweiher, das frühere Pfarrhaus in Wangen-Oberwälden sowie der ehemalige Bahnhof Eckartshausen-Ilshofen. Die Preise werden im Rahmen einer Festveranstaltung am 24. April 2023 in der
Klosterkirche Salem überreicht, zu der der Schwäbische
Heimatbund und der Landesverein Badische Heimat alle
Interessierten herzlich einladen. Die Bauten und Sanierungen werden hier im Folgenden vorgestellt.
Zeugnis klösterlichen Bauens des 18. Jahrhunderts –
das sanierte Jägerhaus des Klosters Salem in Bermatingen
(Bodenseekreis)
»Wenn das einmal zum Verkauf steht, machen wir das«,
sagten sich Yvonne Eisele und Sven Nolle, die seit Jahren
in einem benachbarten Haus wohnten, in dem Yvonne
Eisele auch aufgewachsen war. Beim Traumobjekt des
Ehepaars handelte es sich nicht um irgendein Gebäude
des im nördlichen Hinterland des Bodensees gelegenen
Ortes Bermatingen, sondern um das sogenannte »Jägerhaus«, das zusammen mit dem auf dem Grundstück liegenden Backhaus und einer Torkelscheuer den lokalen
Klosterhof der nur wenige Kilometer entfernten Zisterzienserabtei Salem bildete. Deren Wohlstand noch im 18.
Jahrhundert dokumentieren nicht nur die monumentalen
Klosterbaulichkeiten in Salem, sondern ebenso die vielen
stattlichen Funktionsgebäude, die das Kloster auf seinem
Territorium errichten ließ. Beispiele für die besondere
Baukultur, die die Abtei entfaltete, sind auch das Rebleutehaus in Sipplingen und das Torkelgebäude in Mittelstenweiler, deren Sanierungen in den letzten Jahren bereits
mit dem Denkmalschutzpreis ausgezeichnet worden sind.
Vorbildlich restauriert und
als Wohnhaus weitergenutzt:
das ehemalige Jägerhaus des
Klosters Salem in Bermatingen.
Vorne der Zugang zum riesigen
Weinkeller unter dem Gebäude
Kulturerbe und Denkmalschutz
19
sich rechts und links die Räume reihen wie in der Klausur
eines barocken Klostergebäudes. Die Ausstattung überrascht in ihrer handwerklichen Solidität und der künstlerischen Ausstattung. Der Mittelflur zeigt kräftiges Sichtfachwerk und überaus üppig gestaltete Türen mit barocken Ohrgewänden und Verdachungen. Ein in den Flur
vorspringender ehemaliger Kamin trägt auf dem Sturz
der Ofenbedienungstür die Jahreszahl der Erbauung des
Hauses. Die seitlichen steinernen Wangen mit eingemeißeltem Beschlagwerk des 16. Jahrhunderts stammen
Überrascht durch seine Größe und Klarheit:
der Gewölbehalle des Weinkellers
Das 1721 errichtete Bermatinger Jägerhaus diente nicht
nur als Wohnung für den in Klosterdiensten stehenden
Jäger, sondern auch zur Verwaltung der unmittelbar
gegenüber ansteigenden weitläufigen Rebflächen am
Leopoldberg und zur Unterbringung der Rebleute, die
dort den Weinbau betrieben. Von der Bedeutung des
Weinbaus zeugt vor allem der mächtige Weinkeller, der
eindrucksvoll korbbogenförmig überwölbt ist und Licht
über hochgelegene Fenster in Stichkappen erhält. Hier
hatten riesige Holzfässer Platz. Von einem kleinen separaten Schutzhaus mit Satteldach und einem reich gestalteten Holztor direkt vor dem Jägerhaus führt eine breite
einläufige Treppe steil hinunter ins tiefe Gewölbe. Der
Keller bildet den langrechteckigen, podiumsartigen Sockel für das geräumige eingeschossige Fachwerkgebäude
mit hohem Walmdach, welches, nur von kleinen Schleppgaupen belichtet, unausgebaut ist. Das rot gestrichene
Fachwerk macht einen überaus schmucken Eindruck.
Eselsrücken zieren den Schwellbalken, und an den Hausecken in die Eckpfosten geschnitzte Abtsstäbe belegen
sinnfällig, wer einst hier der Bauherr und Eigentümer
war.
Das Innere ist, typisch für die Nutzbauten des Klosters,
über einen durchgehenden Mittelflur erschlossen, an dem
Funktion und Repräsentation:
der Mittelflur, der die Räume erschließt,
mit Sichtfachwerkwänden und Stuckdecke
Am Riedweg 1/1 Salem-Neufrach
Tel. 0 75 53-9 24 00
WWW.WIRTH-ET.DE
20
Schwäbische Heimat 2023|1
Der Dachstuhl als Fitnessraum:
offengelassen und nur der Boden
gedämmt. In der Mitte zwischen
den verzogenen Kaminen eine
alte Räucherkammer
ganz offensichtlich von einem älteren Klostergebäude
und sind hier wiederverwendet worden. Die Decken werden im Flur wie in den meisten Räumen von Hohlkehlen
eingefasst und von einfachen stuckgerahmten Rund- und
Vierpassformen akzentuiert.
Ohne Ausbau dient der Dachstuhl als Fitnessraum
2019 sollten sich die lang gehegten Hoffnungen von
Yvonne Eisele und Sven Nolle erfüllen. Im Zuge wirtschaftlicher Umstrukturierungen der Verwaltung des
markgräflich-badischen Hauses, das seit 1803 das Erbe
des aufgelösten Klosters Salem angetreten hatte, wurde
das Kulturdenkmal zum Kauf angeboten. Zuletzt war das
Gebäude zu Wohnzwecken sowie als Weinverkaufsstelle
genutzt worden; der Gewölbekeller ist jährlich Schauplatz
des großen Bermatinger Weinfests. Die Familie erwarb
das Anwesen und erwies sich, so die einhellige Meinung
der Jury, in ihrer denkmalbezogenen Einstellung als würdige Wahrerin der Haustradition.
Die Bereitschaft, das Haus nicht in mehrere Wohnungen
aufzuteilen, sondern es trotz des nicht alltäglichen
Grundrisses ohne größere Eingriffe selbst zu bewohnen,
ermöglichte es, die alte Struktur zu bewahren. Diese
konnte durch Entfernung einer später eingezogenen trennenden Wand im Flur sogar wieder deutlicher herausgeschält werden. Ebenso wurden im Bereich von Bad und
Toilette sowie im großen rückwärtigen Raum, der über
die gesamte Hausbreite reicht, spätere Veränderungen
rückgebaut. Beispielhaft ist vor allem auch der Verzicht
auf einen Ausbau des weiträumigen Dachstuhls mit seiner eindrucksvollen Holzkonstruktion. Er erhielt nur
einen kleinen containerartigen Einbau für eine Sauna
und die dafür notwendigen sanitären Einrichtungen. Passend dazu wird er unbeheizt als Fitnessraum genutzt.
Mit Hilfe des in Denkmalpflegefragen erfahrenen Teams
aus der Architektin Corinna Wagner, dem Zimmereibetrieb Holzbau Schmäh und dem Restaurator Jürgen
Schulz-Lorch sowie unter Beteiligung des Natursteinres-
Wir gratulieren zum
Denkmalschutzpreis
SWen
Markdorfer Straße 26
Kulturerbe und Denkmalschutz
|
88682 Salem-Neufrach
21
|
07553 / 7565
DAS FENSTER
Mehr als ein Loch in der Wand.
Eine Öffnung zur Erde, zum Wasser, zum Himmel.
Eine Öffnung zum Licht, zur Zuversicht, zur Hoffnung.
Eine Öffnung zu den Menschen, zum Leben, zur Liebe.
Eine Öffnung zu kostbaren Erinnerungen –
wir helfen Ihnen, diese Fenster für die Zukunft zu bewahren.
homa-rw.de
22
Schwäbische Heimat 2023|1
taurators Peter Wiest, des Malers Jürgen Dilpert und
des Stuckateurbetriebs Ziegler wurde das Haus 2020/21
nach einer genauen Bauanalyse und Schadenskartierung
vorbildlich saniert. Auch wenn der Bau in keinem besorgniserregenden Zustand war, zeigten sich doch beim Holzwerk und bei den Stufen der Eingangstreppe viele Schadstellen, die handwerklich vorbildlich repariert wurden.
Bei der Dämmung wurde auf natürliche Materialien Wert
gelegt. Die neuen Fenster wurden nach dem Vorbild eines
einzeln erhalten gebliebenen Beispiels wahrscheinlich
aus dem 19. Jahrhundert nachgebaut. Ausbauteile für
einen Windfang an der Haustür, die Küche und den Sanitärbereich wurden bewusst zeitgemäß gestaltet, ohne die
historische Substanz zu beeinträchtigen.
Langer Atem und engagierte Eigentümer – die Sanierung
des Wildenhofs in Lenzkirch-Raitenbuch (Landkreis
Breisgau-Hochschwarzwald)
Der Wildenhof in Raitenbuch zählt zu den eindrucksvollsten Höfen des Hochschwarzwalds: Er imponiert bereits
durch seine schiere Größe. Das gewaltige Dach, unter dem
er sich in einen Taleinschnitt schmiegt, misst nicht weniger als 1.100 Quadratmeter Fläche. Aber auch die geradezu archaisch-rustikale Anmutung der massiven StänderBohlenkonstruktion ist außergewöhnlich. Wie auch die
Inschrift über dem Eingang zum Wohnteil überliefert,
wurde der Hof im Jahr 1728 errichtet. Ursprünglich war
er Mittelpunkt eines großen Gutes mit Ackerbau und
Viehzucht. Der weitläufige hangseitige Bereich, der ursprünglich für Ställe genutzt wurde, zeugt noch heute davon, ebenso der riesige Raum der Tenne unter dem Dach,
in die Heuwagen von der Bergseite her einfahren konnten.
Die herausragende Stellung des Wildenhofs innerhalb der
Tradition der Schwarzwaldhöfe wurde früh erkannt. Bald
Ein mächtiges Zeugnis bäuerlicher Baukultur im
Schwarzwald: der Wildenhof in Lenzkirch-Raitenbuch
nach der Sanierung
nach dem Zweiten Weltkrieg wurde er als Kulturdenkmal
von besonderer Bedeutung eingetragen, war aber damals
schon ein Sorgenkind. Bereits für die 1860er-Jahre lässt
sich nachweisen, dass der zugehörige Landbesitz durch
Verkauf stark zusammengeschmolzen war. Die wechselnden Eigentümer konnten daher eine adäquate Bauunterhaltung nicht mehr gewährleisten. Zudem führten unzureichende Gründung sowie Hang- und Winddruck dazu,
dass sich die Holzkonstruktion dramatisch in Richtung
Tal verschob. Um 1,30 Meter hängt die talseitige Fassade
mit dem Krüppelwalm gegenüber der Vertikalen über, mit
vielen konstruktiven Folgen für das Baugefüge. So konnten die Ställe schon lange kaum mehr genutzt werden,
Das Herz des Wohnteils:
die große, in ihrer Dimension
wiederhergestellte Rauchküche
Kulturerbe und Denkmalschutz
23
Im quer durch das Haus
führenden Gang am besten zu
erkennen: die starke Verformung
des Hofes durch Berg- und
Winddruck, vor der statischen
Sicherung ein großes Problem
und ein Teil der Bohlenbalkenwände sowie vor allem die
Stubenausstattung des Wohnteils, der für zwei Familien
aufgeteilt worden war, gingen früh verloren. Mit Unterstützung der Denkmalpflege wurde 1956 die undichte
Schindeldachfläche mit Faserzementplatten überdeckt,
um wenigstens das Regenwasser abzuhalten. Immer noch
in bescheidenem Umfang landwirtschaftlich genutzt, befand sich der Hof in den späten 1980er-Jahren in einem
denkbar schlechten Zustand.
Martin Wider, Schreiner- und Zimmermeister sowie Restaurator im Handwerk, dem das Schicksal des Hofes am
Herzen lag, erwarb ihn 1990 und wagte eine ambitionierte Rettungsaktion. Auf Grundlage einer genauen Be-
Dem Bauherrn die Sicherheit zu geben, das Richtige zu tun
Seit über 30 Jahren steht der Name,
Martin Wider, für Denkmalpflege und
Bauen im Bestand im südwestdeutschen
Raum. Mit viel Leidenschaft und innovativem handwerklichem Knowhow war sein
Restauratorenbetrieb im Hochschwarzwald
federführend daran beteiligt, wertvolle
Bausubstanz zu restaurieren und zu modernisieren.
Nach der Übergabe der Zimmerei an seinen Sohn gründete Martin
Wider 2020 die Martin Wider BiB GmbH, in der er sein geballtes
Wissen und seine langjährige Erfahrung künftigen Bauherren zu
Verfügung stellt. Für öffentliche und private Bauherren
übernimmt er die Aufgaben von der Bauherrenvertretung bis zur
Bauprojektierung und Bauleitung. Dazu gehören ebenso die
professionelle Beratung in schwierigen Fragestellungen der
Denkmalpflege, das Aufstellen und die Verfolgung eines tragfähigen Kostenrahmens sowie die Begleitung in der termingerechten und qualitätsbewussten Umsetzung der Bauprojekte.
24
standsaufnahme und eines Sanierungskonzepts, das Ulrich Schnitzer, Spezialist für Schwarzwaldhöfe an der Universität Karlsruhe, mit Beteiligung des Landesdenkmalamts entwickelt hatte, sollte der Wildenhof statisch
gesichert, dabei seine überlieferte Struktur bewahrt und
ihm das historische Gesamtbild zurückgegeben werden.
Um dem Hof eine tragfähige wirtschaftliche Grundlage zu
ermöglichen, wurde in den innen neu gegliederten bergseitigen Stallteil und in die ehemaligen Knechtkammern
Widers Schreinerwerkstatt eingebaut und die riesige Tenne zu Lagerzwecken hergerichtet. In mehreren Etappen,
vor allem in den 1990er-Jahren und dann noch einmal
um 2006 und 2016, trieb Wider mit Engagement die um-
Martin Wider BiB GmbH
ERHALTEN BEWAHREN NUTZEN
– Beratung, Gutachten und Schadensanalysen
– Bauprojektierungen und Planung
– Definition von Nutzungsanforderungen
– Erarbeiten von Nutzungs- und Restaurierungskonzepten
– Bauleitung
– Vertretungs- und Unterstützungsmandate öffentlicher und
privater Bauherren
– Antragswesen (Denkmalförderungen und KfW – Anträge)
– Kostenschätzung und Kostenkontolle
Im Kaisergrund 8, 79859 Schluchsee, Tel: +49 176 1011 9811,
m.wider@wider-bib.de, www.wider-bib.de
Schwäbische Heimat 2023|1
fangreichen Arbeiten voran. Dabei wurden nachträgliche
An- und Einbauten entfernt, durch den Einbau von Stützkonstruktionen unter dem Dach die Statik in Ordnung gebracht. Im vorderen Bereich des Hauses wurden für die
privaten Wohnbedürfnisse Widers die Räume des ehemaligen Leibgedings für den Altbauern hergerichtet,
während die Sanierung der Stuben des eigentlichen
Wohnteils aus finanziellen Gründen liegenbleiben
musste.
Eine Außenwand musste neu aufgerichtet werden
2020 kaufte das Unternehmerehepaar Jürgen und Maria
Grieshaber den Hof. Mit großem persönlichem und finanziellem Engagement waren sie nun die Garanten für die
Fortführung des Projekts. Das ursprüngliche Sanierungskonzept von Ulrich Schnitzer wurde weiterverfolgt, die
Planung der 1990er-Jahre jedoch für die Wohnzwecke der
neuen Eigentümer durch Florian Rauch in Basel überarbeitet. Rauch selbst ist als Architekt am Denkmal kein
Unbekannter. Schon 2002 erhielt er für den eigenen
Schwarzwaldhof den Denkmalschutzpreis. Für die Realisierung zeichneten weiterhin Martin Wider und seine
Holzfirma verantwortlich, was Kontinuität gewährleistete.
Auch die abschließende Etappe der Sanierung des Wohnteils des Wildenhofs unter dem Ehepaar Grieshaber stellte sich als sehr anspruchsvoll und komplex dar. Der Gewölbekeller musste stabilisiert werden, bestehende Fundamente wurden ergänzt, die Primärkonstruktion statisch in Ordnung gebracht und die völlig verformte
Außenwand demontiert und neu aufgerichtet.
Besonderer Wert wurde dabei auch auf die Rekonstruktion der ursprünglichen Stubenfenster mit Schiebeflügeln
und auf deren Dichtigkeit gelegt. Überhaupt spielte der
Einbau moderner Haustechnik, die nicht ins Auge fallen
sollte, eine wichtige Rolle – von Dämmmaßnahmen, einer
neuen Holzpelletheizung mit Fußboden-, Fußleisten- und
Wandradiatoren bis hin zum Einbau einer die Bausubstanz schonenden und leicht rückbaubaren Sonderlösung
für einen behindertengerechten Aufzug, eine durch einen
Holzverschlag verkleidete Hebebühne.
Die Jury zeigte sich von dem Ergebnis der Sanierung
eines bedeutenden, aber besonders schwierigen Objekts
beeindruckt, die nur mit langem Atem und als Gesamtleistung von mehreren Eigentümern und beteiligten
Architekten und Handwerkern bewerkstelligt werden
konnte. Statische Sicherung, Erhaltung von Originalsubstanz, Rückbau von späteren Veränderungen, Rekonstruktion von Verlorenem, Adaption an heutige Funktionen
und Energiestandards, Qualität der handwerklichen Leistung sowie eine angemessene Gestaltqualität neuer Teile
erfolgten beim Wildenhof auf hohem Niveau, womit dem
Objekt eine besondere Beispielhaftigkeit zukommt. Abweichend von der üblichen Vergabe erhalten Jürgen und
Maria Grießhaber als die heutigen sowie Martin Wider als
frühere Eigentümer gemeinsam den Preis.
Kulturerbe und Denkmalschutz
Handwerklich perfekte Zimmermannsarbeit, inzwischen
schon wieder vom Wetter gezeichnet: der im ersten
Bauabschnitt der 1990er-Jahre wiederhergestellte
Außengang unter dem weit überstehenden Dach
Rekonstruktion nach erhaltenem Vorbild:
die Fenster der großen Eckstube
25
Vor dem Untergang gerettet – ein historisches Fachwerkhaus in Maulbronn-Zaisersweiher (Enzkreis)
2016 wurde Detlev Frodermann über eine Internetanzeige
auf ein Fachwerkhaus aufmerksam. Schon der erste Besuch in Zaisersweiher, einem Ortsteil von Maulbronn, begeisterte ihn und seine Frau. Der zweigeschossige Bau mit
hohem Satteldach und steilem Giebel zur Straße stellte
sich als das besonders schmucke Wohnhaus eines ehemaligen landwirtschaftlichen Anwesens im Ortskern unweit der Kirche heraus. Durch eine große Toreinfahrt gelangte man ursprünglich von der Straße in den rückwärtigen Bereich mit freistehendem Stall und Scheune. Der
Grundriss zeigt ein durch den Grundstückszuschnitt bedingtes verschobenes Rechteck. In Erwin Huxholds Publikation über das Bürgerhaus im Kraichgau war das Äußere
bereits gewürdigt worden als ein unversehrtes Beispiel
für Fachwerkfassaden der ersten Hälfte des 18. Jahrhunderts: Auffällig vor allem durch die aufwändigen Zierfachwerkbrüstungen unter den leicht erkerartig vortretenden
Fenstern des Obergeschosses, das zwar bäuerlich-derbe,
aber ungewöhnlich plastische Formen aufweist.
Beim Blick auf den Zustand des Hauses stellte sich 2016
freilich Ernüchterung ein. Seit nahezu vierzig Jahren war
das einst stolze Anwesen nicht mehr bewohnt worden und
entsprechend heruntergekommen. Mehrere Eigentümer
hatten sich in dieser Zeit die Klinke in die Hand gegeben
und waren mit verschiedenen Sanierungsüberlegungen
UNESCO-Welterbe
Kloster Maulbronn
Ganzjährig Führungen
Sonderführungen
Familienspaß
Museen in Maulbronn
Klostermuseum
Museum auf dem Schafhof
Steinhauerstube Schmie
Literaturmuseum
Kunstsammlung Heinrich
Märkte und Veranstaltungen
08.-10.04. Lebendiges
Kunsthandwerk
Mai-Sept. Klosterkonzerte
08./09.07. Fleckenfest Zaisersweiher
04.-06.08. WeinSommer Maulbronn
09./10.09. Kräuter- und Erntemarkt
08.10.
Erlebnistag im Kloster
09./10.12. Weihnachtsmarkt
Weitere Infos: Stadt Maulbronn, Tel.: 07043/103-0,
info@maulbronn.de, www.maulbronn-erleben.de
26
Oben ein Bild des Niedergangs: das Fachwerkhaus in
Maulbronn-Zaisersweiher vor der Sanierung, heute ist es
wieder ein Schmuckstück für den Ort.
gescheitert. Wasser drang über das kaputte Dach ins Innere, der hüfthohe Sockel aus Sandsteinquadern war brüchig und an den Ecken abgesunken, der Putz bröckelte
von den Fachen. Das Wetter hatte dem Holzwerk an den
Oberflächen stark zugesetzt. Doch trotz schwerer Schäden selbst an tragenden Teilen war das Gefüge noch einigermaßen stabil, da man für die Konstruktion ausschließlich Eichenbalken verwendet hatte. Für die zugehörige
Doppelscheune im hinteren Teil des Grundstücks gab es
jedoch keine Rettung mehr. Sie war nach einem Teileinsturz von den Denkmalbehörden zum Abbruch freigegeben worden. Da überdies auch das talseitige Nachbarhaus
abgerissen worden war, drohte dem Ortskern von Zaisersweiher an empfindlicher Stelle der Verlust des historisch
gewachsenen malerischen Straßenbilds.
Schwäbische Heimat 2023|1
Die Stube im Obergeschoss mit
alter Decke und reparierten
Fenstern
Frodermanns ließen sich von der auf den ersten Blick
hoffnungslosen Situation nicht abschrecken, nicht einmal
vom völlig vermüllten Hausinneren. Man hatte gute
Kenntnisse, was Holzbau anbelangt, und wusste zudem
den Bruder Thomas Frodermann mit im Boot. Gemeinsam besitzen sie in Stuttgart-Weilimdorf ein Zimmerergeschäft, das auf die Sanierung von Kulturdenkmalen spezialisiert ist. Die beiden Brüder fühlten sich von der
außergewöhnlichen Aufgabe herausgefordert und entschlossen sich zum Kauf des Objekts, um an ihm ihre
handwerklichen Fähigkeiten zu demonstrieren und es
denkmalgerecht zu sanieren.
Die Originalsubstanz war weitestgehend erhalten
Man ließ sich die dafür erforderliche Zeit. Die insgesamt
vierjährige Planungs- und Bauphase begann parallel zur
notwendigen Entrümpelung vorbildlich mit einer genauen Baudokumentation: verformungsgerechtes Aufmaß,
Farbbefunduntersuchung außen und innen, eine detaillierte Schadensdokumentation des Holzwerks sowie ein
vom Stuttgarter Architekturbüro Strebewerk erstelltes Instandsetzungskonzept bildeten für die Bauherren die
selbstverständliche Grundlage für die Realisierung der
Sanierungsmaßnahme. Dabei wurde dendrochronologisch auch die Datierung des Hauses geklärt. Das Holz
war 1731 geschlagen worden, die von Huxold angenommene Datierung bestätigte sich damit. Nachgewiesen
wurde gleichfalls, dass die Originalsubstanz weitestgehend ohne Umbauten erhalten geblieben war. Nur eine
Wand zwischen einem werkstattartigen Raum im Erdgeschoss und der innen liegenden Treppe war verschoben
worden, um im nicht unterkellerten Bau eine Grube
schaffen zu können. Diese Wand wurde an ihre ursprüng-
Kulturerbe und Denkmalschutz
Blick von der ehemaligen Durchfahrt auf die Treppe
27
liche Stelle zurückversetzt, um der Treppe wieder mehr
Raum zu verschaffen. Ansonsten wurden größere Eingriffe vermieden. Das Dach erhielt durch zwei neue Schleppgauben mehr Licht. Die Durchfahrt, bereits seit langem
geschlossen, wurde durch ein neues Tor zur Straße und
einen Glasabschluss zum Hof klimatisch dem Hausinneren zugeschlagen und durch zusätzliche Oberlichtöffnungen an der Längsseite besser belichtet. Der einzige große
Raum im Haus ist nun als Wohnbereich genutzt.
In allen Gewerken wurde nach den restauratorischen
Grundlagen auf besonders sorgfältige handwerkliche
Weise repariert. Die bestehenden bauzeitlichen Lehmausfachungen mit Staken konnten weitestgehend erhalten
werden, abgängige Fachen und solche mit modernen Baumaterialien des 20. Jahrhunderts wurden entfernt und
durch Lehmsteine ersetzt. Nachdem zwei originale, im
Umriss balusterartig gesägte Bretter der ursprünglichen
Treppenwangen gefunden worden waren, wurden diese
rekonstruiert. Natürlich wurde an Belange der Gegenwart
gedacht: Zur Wärmeisolierung wurden die reparierten alten Fenster zu Kastenkonstruktionen ausgebaut, an den
Außenwänden eine Innendämmschale angebracht und
mit Lehm verputzt. Der sichtbar gebliebene Dachstuhl erhielt eine außenseitige Bretterschalung mit Aufsparrendämmung, deren Erscheinungsbild am Giebelortgang
durch eine plastisch gegliederte Gestaltung geschickt minimiert wurde.
Das Haus ist wieder zu einem Schmuckstück für das Dorf
geworden und hat die Chance, auch weitere Generationen
zu beherbergen. Seit 2020 bewohnen Detlev Frodermann
und seine Frau das Haus, dessen Sanierung nach Meinung der Jury Schule machen sollte.
Reparatur als denkmalpflegerisches Ideal – das ehemalige
Pfarrhaus in Wangen-Oberwälden (Landkreis Göppingen)
Marlene und Johannes Widmann waren erst um die Dreißig, als sie 2017 das frühere Pfarrhaus in Oberwälden,
heute ein Ortsteil von Wangen bei Göppingen, erwarben.
Beide kannten das laut Bauinschrift am Kellerabgang
1787 errichtete Gebäude gut, da Marlene Widmann in
Oberwälden aufgewachsen war. Beide schätzen das malerische Ortsbild des Dorfes am Rand des Schurwaldes, zumal es sich stark abhebt von der verstädterten und zersiedelten Umgebung des nahen Fils- und Neckartals. Das
schlichte, wohlproportionierte spätbarocke Gebäude mit
seinem Krüppelwalmdach ist ein wichtiges Element des
baulichen Ensembles, das sich um die bis ins Mittelalter
zurückgehende Nikolauskirche und den Dorffriedhof
schart. In seinem engen Bezug zur Kirche bei gleichzeitiger Dominanz gegenüber den alten Bauernhäusern ist es
in Oberwälden bis heute geradezu ein Idealbild geblieben
für diese im Schwäbischen ehedem so wichtige Bauaufgabe. Hier war ein Mittelpunkt des kulturellen und religiösen Lebens im Dorf, in diesem Milieu war die 1823 gebo-
Der Enzkreis
Feiern Sie
Wir werden 50 mit uns!
Wir bedanken uns für die gute Zusammenarbeit
FRANKFURTER STRASSE 65, 75433 MAULBRONN
WWW.HEINRICH-BAUUNTERNEHMUNG.DE
TEL.: 07043-9253-0 FAX: 07043-9253-50
28
Die neue Badeinrichtung fügt sich in die alte Raumstruktur.
Schwäbische Heimat 2023|1
Das Pfarrhaus von Oberwälden
nach der behutsamen Sanierung:
noch immer ein Mittelpunkt
des Ortes, überragt von der
Turmspitze der Nikolauskirche
rene Luise Pichler als Pfarrerstochter aufgewachsen, die
später als Autorin historischer Romane bekannt werden
sollte.
Von der repräsentativen Front des zweigeschossigen Hauses mit seinem zentralen Eingang hat man zwischen den
zugehörigen Nebengebäuden von Pfarrscheuer und
Wasch- und Backhaus einen grandiosen Blick über unverbaute Natur auf den Hohenstaufen, den Rechberg und die
Schwäbische Alb. Hier zu wohnen war der Traum der jungen Familie. Das Haus gehörte der Gemeinde Wangen,
stand aber schon seit einigen Jahren leer, da man kein
Nutzungskonzept hatte. Zwar war es nicht in baufälligem
Zustand und noch bis in die 1980er-Jahre waren Maßnahmen zum Erhalt durchgeführt worden, doch wuchs schon
Efeu durch die Fenster. Außerdem gab es wegen der
Hanglage des unteren Geschosses in den Sockelzonen
Feuchtigkeitsprobleme, die bereits zu Schäden am Holzwerk führten. Eine Kostenschätzung für notwendige Sanierungsmaßnahmen schreckte die Ortsverwaltung über
Jahre ab, selbst tätig zu werden. Da die Widmanns Interesse anmeldeten, entschloss sich die Gemeinde, das Haus
gegen Höchstgebot zum Verkauf anzubieten. Es gelang
dem Ehepaar schließlich, den Zuschlag zu erlangen.
Mit alter Aura für moderne Wohnansprüche
Es kam dem Kulturdenkmal zugute, dass die neuen Eigentümer ein Gespür für den Wert der überkommenen Besonderheiten des Hauses besaßen und ihr Nutzungskonzept sich bestens mit der Struktur des Hauses vereinbaren ließ, dessen Bausubstanz sich auch im Inneren trotz
früherer Erneuerungen weitgehend erhalten hatte. Nur
die ursprüngliche Treppe war im späten 19. Jahrhundert
durch eine neue ersetzt worden. Im Erdgeschoss mit den
massiv gemauerten Außenwänden sollte neben der unge-
Kulturerbe und Denkmalschutz
wöhnlich großen Eingangshalle und den bestehenden
Wirtschaftsräumen eine kleine separate Wohnung geschaffen werden. Das aus verputztem Fachwerk bestehende Obergeschoss wurde für die großzügige Wohnung der
Eigentümer vorgesehen, bei der sich die Räume rechts
WIR BAUEN MIT HOLZ AUCH FÜR SIE
Fon 07331/83231, Hauptstraße 40, 73329 Kuchen
29
HERZLICHEN GLÜCKWUNSCH
Historische
Historische
Werte
Werte
erhalten
erhalten
ormati
Inf
ormati
Inf
nf
or
d
nf ern
or
dern
en en
on on
HIE
HIER
R
a
Foto: Gerhard Kabierske
Modernisieren Sie Ihre
historische
Immobilie
Modernisieren
Sie Ihremit
"Geprüften
Restauratoren
historische Immobilie
mit
im
Zimmererhandwerk".
"Geprüften
Restauratoren
Wir
verbinden traditionelles
im Zimmererhandwerk".
Handwerk
mit modernster
Wir verbinden
traditionelles
Technologie.
Handwerk mit modernster
Technologie.
a
Der Landkreis Göppingen gratuliert
den Preisträgern recht herzlich zum
Denkmalschutzpreis!
Preisgekrönte Denkmalsanierung
von Leibbrand.
Verband der Restauratoren
im Zimmererhandwerk
e.V.
Verband
der Restauratoren
im
Zimmererhandwerk
Helmuth-Hirth-Straße
7 e.V.
Verband
der Restauratoren
73760
Ostfildern 43 e.V.
im
Zimmererhandwerk
Hackländerstrasse
70184
Stuttgart
Telefon 0711-23996-50
Hackländerstrasse
43
Fax Stuttgart
0711-23996-60
70184
Telefon
0711-23996-50
E-Mail 0711-23996-60
info@restauratoren-verband.de
Fax
Telefon 0711-23996-50
Internet
www.restauratoren-verband.de
E-Mail info@restauratoren-verband.de
Fax
0711-23996-60
Internet
www.restauratoren-verband.de
E-Mail info@restauratoren-verband.de
Wir freuen uns mit den Besitzern über die
Auszeichnung mit dem Denkmalschutzpreis Baden-Württemberg 2022 für unsere
Arbeit am ehemaligen Pfarrhaus in WangenOberwälden. Unsere Restauratoren sanieren
nach den Richtlinen des WTA und haben
jahrzehntelange Erfahrung in der Sanierung
von Fachwerk- und Denkmalschutzobjekten.
U. Leibbrand GmbH Lutherstr. 65 · 73614 Schorndorf
Fon 07181·92015-0 · www.leibbrand.de
30
Schwäbische Heimat 2023|1
Der lichte große Wohnraum
mit umlaufender Lamperie
und aufgearbeitetem Parkett
im Obergeschoss: Der neue
Küchenblock wurde frei
hineingestellt, ohne den
Raumeindruck zu zerstören.
und links eines Mittelflurs reihen. Im bereits zuvor ausgebauten Dachgeschoss wurde eine weitere Wohnung eingerichtet, die wie jene im Erdgeschoss die Möglichkeit zur
Vermietung bietet. Veränderungen am Grundriss bestanden einzig in der Entfernung zweier nachträglich eingezogener Wände im Erd- und im Dachgeschoss und einem
Türdurchbruch an einer Stelle, an der früher wahrscheinlich bereits eine Öffnung bestanden hatte. Die Fachwerkkonstruktion der Innenwände wurde nicht angetastet,
ebenso blieb der Spitzboden unausgebaut, wobei am Dach
und im Bereich des Erdgeschosses bauphysikalisch richtige Dämmmaßnahmen mit Zellulosefasern und Lehmverputz zur Verbesserung der Energiebilanz durchgeführt
wurden, ohne das Erscheinungsbild zu beeinträchtigen.
Anstelle der alten Gasthermen im Haus wurde in der bereits früher sanierten und als Hobbywerkstatt genutzten
Pfarrscheuer ein umweltfreundlicher Kombikessel für
Scheitholz und Holzpellets installiert, der über eine Leitung das Gebäude zentral mit Wärme versorgt.
Der hinzugezogene Architekt Volker Sawall aus Geislingen
sowie die Handwerker erwiesen sich als äußerst kompetent im Umgang mit der vorhandenen Bausubstanz. Zunächst wurde durch die Verbesserung der Drainage der
Sockelzone das in den Außenmauern hochsteigende
Hangwasser vom Haus ferngehalten. Die weitere Sanierung ging durchweg von der Erhaltung und Reparatur des
Bestehenden aus. Ob die Verbundfenster aus den 1950erJahren, die Klappläden, die originalen Türen, die Dielenund Parkettböden aus verschiedenen Zeiten sowie die
umlaufenden Lamperien – das Holzwerk wurde handwerklich mit Sorgfalt aufgearbeitet. Die Beschläge aus
verschiedensten Zeiten wurden dabei wiederverwendet,
ob Türklinken aus der Erbauungszeit oder dem späten 19.
Jahrhundert oder die Fensteroliven der Nachkriegszeit.
Kulturerbe und Denkmalschutz
Putz und Stuck, aber auch unter späteren Bodenbelägen
zum Vorschein gekommene große Steinplatten wurden
ebenso fachgerecht ergänzt. Neue Teile wie beim Küchenoder Bädereinbau sind in bewusst modernen Formen gehalten, wobei eine zurückhaltende Gestaltung verhindert,
dass die Kontraste zwischen Alt und Neu zu stark ins Auge
springen.
Die Jury war von diesem vorbildlichen Beispiel des Umgangs mit einem Kulturdenkmal überzeugt, das durch
seine unaufdringliche Angemessenheit besticht. Das
Pfarrhaus wird einerseits in seiner alten Aura weitertradiert und gleichzeitig heutigen Wohnansprüchen gerecht.
Hier war Platz für Fässer: der Gewölbekeller unter einem
Teil des Gebäudes mit einem breiten Zugang von außen
und einer internen Treppe in den Eingangsbereich
31
Ausgezeichnet!
ESSEN, TAGEN, FEIERN UND GENIEßEN
im renovierten und stilvoll eingerichteten Bahnhof
| Restaurant und Barbetrieb
| Regionale Spezialitaten
| Hochzeiten und Familienfeste
| Firmenevents
| Vereinssitzungen
| Modern eingerichtete Apartments
mit komplett ausgestatteter Küche
| Kostenfreies W-Lan und Flat-TV
| Wöchentliche Reinigung
| Handtuch- und Bettwäschewechsel
Restaurant & Boardinghouse
Am Bahnhof 1
74532 Ilshofen-Eckartshausen
Tel. 07904 - 9438210
info@bahnhofmann.de
www.bahnhofmann.de
32
Schwäbische Heimat 2023|1
Ein »Tor zur Welt« – Wiederbelebung des Bahnhofs in
Eckartshausen-Ilshofen (Landkreis Schwäbisch Hall)
Für Claudia und Rüdiger Hofmann war es eine Herzensangelegenheit, den Bahnhof von Eckartshausen-Ilshofen
an der Bahnstrecke von Schwäbisch Hall nach Crailsheim
wieder zum Leben zu erwecken, zumal das relativ große
Gebäude, das auch als Bahnstation für das nahegelegene
Ilshofen und einen weiteren Einzugsbereich in Hohenlohe diente, heute noch in besonderer Weise das Ortsbild
des kleinen Eckartshausen prägt. Rüdiger Hofmann war
hier aufgewachsen, und für ihn hatte der Bahnhof in seiner Jugend, an der wichtigen Ostwestverbindung von
Heilbronn nach Nürnberg gelegen, nichts anderes als den
Anschluss an die weite Welt bedeutet. Die Bahnhofsgaststätte, die sich darin befand, empfand er als wichtigen
Mittelpunkt der Dorfgemeinschaft.
Dieser Bahnhof war 1864–67 im Zuge der Trassierung der
Kochertalbahn nach Plänen der Bahnbauverwaltung im
damals üblichen Stil der Funktionsbauten der KöniglichWürttembergischen Staatseisenbahnen errichtet worden:
mit Rundbogenfenstern und -türen im Erdgeschoss sowie
hochrechteckigen Fenstern im Obergeschoss, profiliert
eingeschnitten in die Verkleidung der Fassaden mit großen Steinquadern aus regionalem Sandstein. Über einem
zweiten, nur kniestockartigen Geschoss schließt ein flach
geneigtes und kräftig überstehendes Dach den kubischen
Baukörper ab. Im Erdgeschoss waren neben der Bahnhofsgaststätte der Schalter- und Warteraum untergebracht, in den Obergeschossen Wohnungen für Bahnbeamte und Bahnarbeiter. Mehr als 120 Jahre erfüllte der
Bahnhof seine Funktion, sah glänzende Tage, wenn der
württembergische König hier zu Manövern auf dem nahen Truppenübungsplatz ausstieg, aber auch tragische,
als gegen Ende des Zweiten Weltkriegs ein mit völlig entkräfteten KZ-Häftlingen beladener Güterzug hier tagelang
auf dem Gleis stand oder Tieffliegerangriffe auf die Bahnlinie erfolgten, von denen noch zahlreiche Einschusslöcher an den Fassaden zeugen.
Wie viele andere Landbahnhöfe war auch der Bahnhof in
Eckartshausen in den letzten Jahrzehnten vom Niedergang geprägt, obwohl die Bahntrasse keineswegs aufgege-
Kulturerbe und Denkmalschutz
Ein repräsentativer Bau des 19. Jahrhunderts
auf dem Land: der wiederbelebte Bahnhof
Eckartshausen-Ilshofen, vorne das sich unterordnende
neue Technikgebäude mit der Heizung
ben wurde. Zunächst nahmen Modernisierungen, wie
etwa der Einbau neuer Fenster, keine Rücksicht mehr auf
die bauliche und gestalterische Qualität der Architektur.
Dann zog sich die Deutsche Bahn mehr und mehr von der
zunehmend vernachlässigten Immobilie zurück, die ihre
ursprünglichen Aufgaben verlor. Schon 1994 wurde der
Schalterverkauf zugunsten eines simplen Automaten auf
dem Bahnsteig eingestellt, ebenso wurde die Bahnhofswirtschaft geschlossen. Direkt neben den Gleisen fiel der
Bahnhof für zwei Jahrzehnte in triste Agonie, was der
Bausubstanz nicht gut bekam. Massive Schäden am Holzwerk des Daches waren die Folge.
Das Unternehmerehepaar Hofmann verfolgte betrübt die
Entwicklung und ergriff sofort die Initiative, als bekannt
wurde, dass die Bahn das inzwischen denkmalgeschützte
Gebäude in Berlin versteigern lassen wollte. Sie steigerten
mit und erhielten den Zuschlag. Ihr Ziel war es, den Bahnhof so weit als möglich in seinen Ursprungszustand zu
versetzen und dabei eine wirtschaftliche wie denkmalver-
33
Nach Jahren der Leerstands:
die Bahnhofswirtschaft lädt
wieder zum Verweilen ein.
trägliche Nutzung zu finden. Erste Überlegungen für den
Umbau zu einem Hotel wurden nicht weiterverfolgt, als
klar wurde, dass dafür starke Eingriffe in die Substanz
notwendig und das Erscheinungsbild beeinträchtigende
Anbauten unerlässlich sein würden. Schließlich wurde
2016–18 eine Sanierung als Boardinghaus realisiert. Im
Erdgeschoss reaktivierte man die alte Bahnhofswirtschaft
und erweiterte sie um die Fläche der ehemaligen Schalterhalle und den Wartesaal. Die früheren Dienstwohnungen im Ober- und Dachgeschoss wurden zu kleineren
Wohneinheiten für temporäre Mietnutzungen umgebaut.
Sie werden vor allem von zeitweise in Ilshofen tätigen Mitarbeitern der international agierenden Metallbaufirma
genutzt, der Rüdiger Hofmann als Geschäftsführer vorsteht.
Spätere Veränderungen wurden rückgebaut, Befunduntersuchungen zur ursprünglichen Farbigkeit durchgeführt, verloren gegangene Gestaltqualität bei Fenstern
und Türen durch Nachbauten gemäß den noch vorhandenen originalen Elementen wiederhergestellt. Besonders
14
Erforschen und Erhalten
Jahresbericht der Bau- und Kunstdenkmalpflege 4/2021
15
Ruhe und Bewegung
– ein anmutiges Paar
Mutter mit Kind – ein Kooperationsprojekt zwischen Landesamt für
Denkmalpflege und Staatlicher Akademie der Bildenden Künste Stuttgart:
forschen – konservieren – erhalten
54
von Jochen Ansel
Erforschen und Erhalten
BAUDENKMALE &
KUNSTDENKMALE
Jahresbericht der Bau- und Kunstdenkmalpflege 4/2021
2
Klassizistisches
Kleinod
01
O B J E K T : Skulpturengruppe Maria mit Kind
S T A N D O R T : ehem. Klosterkirche St. Georg, Schlossbezirk 8, 88416 Ochsenhausen (Lkr. Biberach)
E I G E N T Ü M E R : Kath. Kirchengemeinde St. Georg
M A S S N A H M E : Untersuchung und Konservierung
B E T E I L I G T E : Institut für Konservierungswissenschaften an der Staatlichen Akademie der Bildenden
Künste, Prof. Dr. Wibke Neugebauer, Prof. Dr. Anna
von Reden, Dipl.-Rest. Peter Vogel, Anna Egeler und
Chiara Schweizer; Universität Konstanz, Lisa Braun
55
in Baden-Württemberg
Ochsenhausen
Zur Restaurierung der Wandmalereien im Spiegelsaal
des Leimener Rathauses
von Ruth Cypionka
◀1
BASILICA MINOR – FOLGEN DER
E R N E N N U N G Seit 2019 trägt die ehemalige
Klosterkirche St. Georg in Ochsenhausen den von
Papst Franziskus verliehenen Titel „Basilica minor“.
Die aus diesem Anlass in die Wege geleitete Neugestaltung des Altarbereichs lenkte die Aufmerksamkeit
auf die Skulptur der Maria mit Jesuskind, ein Werk des
Ulmer Schnitzers Niklaus Weckmann. Dieser wirkte
zwischen 1481 und 1526 und prägte den Ulmer Stil
maßgeblich. Von ihm geschaffene Schnitzretabel sind
im Alpenraum Italiens, Österreichs und der Schweiz
anzutreffen. Mit ihren mehr als 500 Jahren zählt die in
Ochsenhausen hochverehrte Marienfigur zu den ältesten Ausstattungsstücken der Kirche. Da der Einbau
der neuen Stufen- und Podestanlage im Altarraum der
Kirche umfangreiche Evakuierungs- und Sicherungsarbeiten an den Seitenaltären und am Kreuzaltar
bedingte, musste auch die Marienfigur ihren angestammten Platz verlassen, was eine Bewertung ihres
Erhaltungszustands nötig machte. Dabei stellten die
Restauratoren des Landesamts für Denkmalpflege Ablösungen in den Farblagen fest, viele Farbverluste
waren bereits eingetreten – ein Schadensprozess, den
es zu stoppen galt.
2
1
11
aufwändig erwies sich die Sanierung der Hausteinverkleidung der Fassaden, deren untere Teile stark verwittert
waren. Dabei wurde das passende Steinmaterial durch
Zweitverwendung von Quadern aus einer alten Mauer in
der Nachbarschaft des Bahnhofs gewonnen. Das Grundstück mit der Mauer hatte die Familie Hofmann dafür eigens hinzugekauft.
Die Jury beurteilt diese Sanierung als besonders beispielhaft, da sie zeigt, dass die Umnutzung eines Bahnhofs, die
häufig zu fragwürdigen Ergebnissen führt, in denkmalverträglicher Weise geschehen kann und nicht automatisch zu unwiederbringlichen Substanzverlusten führen
muss. Besonders gefiel, wie den strikten baurechtlichen
Auflagen für Brandschutz, Küchentechnik und Dämmmaßnahmen nachgekommen wurde, ohne das Gesamtbild zu stören. So wurde der zweite Fluchtweg durch den
Einbau einer weiteren inneren Treppe geschaffen, die
spiegelsymmetrisch zur bestehenden angelegt wurde und
weder von außen noch im Inneren in Erscheinung tritt.
Für die moderne holzbetriebene Heizungsanlage wurde
O B J E K T : Rathaus
P R O J E K T : Sanierung Rathaus
S T A N D O R T : Rathausstr. 8, 69181 Leimen (RheinNeckar-Kreis)
E I G E N T Ü M E R : Stadt Leimen
M A S S N A H M E : Restaurierung der Wandmalereien
B E T E I L I G T E J O C H E N : Ansel, Restaurator, LAD;
Böke & Fritz, Diplomrestauratoren für gefasste Holzobjekte und Wandmalerei, Eppingen; Stadt Leimen
F Ö R D E R U N G : Fördermittel des Landes und der
Denkmalstiftung Baden-Württemberg
Leimen
Das heutige Rathaus in Leimen – ein elfachsiger, zweigeschossiger Bau mit dreiachsigem Mittelrisalt und
vorgelagertem Balkon – besticht schon äußerlich
durch seine Größe und strenge klassizistische Gliederung mit rustiziertem Erdgeschoss und ebensolchen
Eckpilastern unter einem ausgebauten Mansarddach.
Der wohlhabende jüdische Hoffaktor Aaron Elias Seligmann (1747–1824) ließ sich 1794 diesen repräsentativen Bau errichten, der gestalterisch engen Bezug auf
Peter Anton von Verschaffelts Adelpalais Bretzenheim
in Mannheim nimmt. Seligmann, der nicht nur das
Salzmonopol für die Kurpfalz innehatte, sondern auch
die in Leimen florierende Tabakindustrie begründete,
setzte sich hiermit ein Denkmal, das nicht nur seinen
wirtschaftlichen, sondern auch gesellschaftlichen Aufstieg und die beginnende politische Emanzipation der
jüdischen Bevölkerung in der Epoche der Aufklärung
veranschaulichte.
1841 erwarb die Gemeinde Leimen das sogenannte
Palais Seligmann und richtete darin ihr Schul- und
Rathaus ein; die Rathausnutzung besteht bis heute.
D E R S P I E G E L S A A L Im Zentrum des Palais
liegt in der Beletage der über eine zweiläufige, repräsentative Treppenanlage erschlossene Festsaal mit
vorgelagertem Balkon. Er ist mit mythologischen
Wandgemälden auf Leinwand, die von gemalten Architekturgliederungen und Supraporten en grisaille
gerahmt werden, sowie mit zwei Kaminen und Spiegeln ausgestaltet. Die Malereien werden dem Mannheimer Maler Peter Ferdinand Deurer (1777–1844)
zugeschrieben.
Dieses eindrucksvolle klassizistische Kunstkabinett,
dessen Bildinhalte sich streng an antikes Formengut
anlehnen, war zu seiner Entstehungszeit äußerst modern und sollte die große Kunstkennerschaft und hohe
Bildung des Auftraggebers Seligmann zur Schau stellen.
2017 wurde entschieden, den vielgenutzten, vor allem
bei Hochzeitspaaren beliebten, aber in die Jahre gekommenen Saal zu restaurieren.
Der Jahresbericht der Bau- und Kunstdenkmalpflege in
Baden-Württemberg stellt jeweils bemerkenswerte Beispiele
aus dem Schatz von über 90.000 Bau- und Kunstdenkmalen
vor. Im aktuellen 4. Band (2021) sind Objekte aus allen
Epochen enthalten – vom mittelalterlichen Beinhaus in
Wertheim bis zur Bundesanwaltschaft in Karlsruhe.
Die Jahresberichte können auch zur Fortsetzung bestellt werden –
im Buchhandel sowie bei www.thorbecke.de
wm1226_anzeige.indd 1
Erforschen und Erhalten (2021)
256 Seiten, reich bebildert,
Paperback, 21 x 30 cm
€ 28,- [D] / ISBN 978-3-7995-1565-8
23.01.23 12:56
34
Schwäbische Heimat 2023|1
in deutlicher Entfernung vom Gebäude ein sich unterordnendes Funktionsgebäude errichtet. Ebenso positiv wurde bewertet, wie es durch kluge Planung im Obergeschoss
nur durch wenige Vermauerungen bzw. Türdurchbrüche
möglich war, kleinere Wohneinheiten zu schaffen, ohne
die ursprüngliche Struktur des Gebäudes grundlegend zu
beeinträchtigen.
Impulse für eine abwechslungsreiche Freizeit
Impulse für eine abwechslungsreiche Freizeit
Unsere schön gelegene Stadt
bietet:
Unsere schön
Stadt
Impulse
fürgelegene
eine abwechslungsreiche
Freizeit
• Gute Gastronomie- und
•
Reizvolle Ausflugs- und
bietet:
Unsere
schön
gelegene
Wandermöglichkeiten
Hotelbetriebe
• Reizvolle
AusflugsundStadt
• Gute
Gastronomie- und
bietet:
• Radfahren, Freibadbesuch, • Stauferburgruine Leofels
Wandermöglichkeiten
Hotelbetriebe
•
Gute
Gastronomie- und
• Reizvolle
Ausflugs- und
Tennis, Angeln
Infos
unter:
• Radfahren,
Freibadbesuch,
• Stauferburgruine
Leofels
Wandermöglichkeiten
HotelbetriebeIlshofen,
•
Theater, Ausstellungen,
Stadtverwaltung
Tennis,
Angeln
Infos
unter:
• Radfahren,
Stauferburgruine
Leofels
Haller
Str. 1, 74532 Ilshofen
Kleinkunst Freibadbesuch, •
• Theater,
Ausstellungen,
Stadtverwaltung
Ilshofen,
Tennis,
Angeln
Infos
•
Ilshofener
Herbst- und
Tel.:
0unter:
79 04/7 02-0
Haller Str. 1, 74532
Ilshofen
• Kleinkunst
Theater,
Ausstellungen,
Stadtverwaltung
Ilshofen,
Töpfermarkt,
Ostermarkt,
info@ilshofen.de
Haller
1, 74532
Kleinkunst
www.ilshofen.de
Stadtfest Herbst- und
Tel.: 0 Str.
79 04/7
02-0Ilshofen
• Ilshofener
• Töpfermarkt,
Ilshofener Herbstund
Tel.:
0 79 04/7 02-0
info@ilshofen.de
Ostermarkt,
Töpfermarkt, Ostermarkt,
info@ilshofen.de
www.ilshofen.de
Stadtfest
www.ilshofen.de
Stadtfest
Blick in die ehemalige Eingangshalle, nun auch
gastronomisch genutzt: restaurierte wandfeste
Ausstattung und nach Befund rekonstruierte Farbigkeit
Über den Autor
Gerhard Kabierske studierte Kunstgeschichte
und Provinzialrömische Archäologie an den
Universitäten Freiburg und München. Er promovierte bei Johannes Langner in Freiburg über
den badischen Jugendstil-Architekten Hermann
Billing. Von 1988 bis 1993 war er Stadtkonservator bei der Unteren Denkmalschutzbehörde
Karlsruhe und von 1993 bis 2020 tätig am
Südwestdeutschen Archiv für Architektur und
Ingenieurbau (saai) an der Universität Karlsruhe
bzw. am Karlsruher Institut für Technologie
Kulturerbe und Denkmalschutz
(KIT). Schwerpunkt seiner Arbeit bildeten der
Aufbau des Archivs zu einer der größten Einrichtungen seiner Art im deutschsprachigen
Bereich sowie Ausstellungen und Publikationen
zur Architektur des 19. und 20. Jahrhunderts.
Seit 2000 ist er Vertreter des Landesvereins
Badische Heimat in der Jury für den Denkmalschutzpreis Baden-Württemberg, seit 2006
deren Vorsitzender.
Einladung zur Preisverleihung
Der Festakt zur Verleihung des Denkmalschutzpreises findet in der Klosterkirche Salem am
24. April 2023 statt.
Details siehe im SHB Intern S. 101.
35
|
|
https://openalex.org/W4229043535
|
https://maplespub.co.in/assets/images/files/doc_1651721066.pdf
|
English
| null |
Human Papillomavirus (Hpv) Infection In Rural And Tribal Populations Of The World With A Special Focus On The Prevalence In India
|
Journal of Biomedical and Allied Research
| 2,022
|
cc-by
| 7,311
|
Journal of Biomedical and Allied Research
ISSN: 2582-4937
Rashid S, et al., 2022- J Biomed Allied Res
Review Article ISSN: 2582-4937
Rashid S, et al., 2022- J Biomed Allied Res
Review Article 2Jazan University, Jizan, Saudi Arabia *Corresponding Author: Dr. Shazia Rashid,
Ph.D. Assistant Professor, J3-412, Centre for
Medical Biotechnology, Amity Institute of
Biotechnology, Amity University, Noida, Uttar
Pradesh, India. Christina Choudhary1, Kanubha Sharma1, Sajad Ahmad
Dar2, Shazia Rashid1* Christina Choudhary1, Kanubha Sharma1, Sajad Ahmad
Dar2, Shazia Rashid1* Human
Papillomavirus
(HPV)
Infection in Rural and Tribal
Populations of the World with a
Special Focus on the Prevalence in
India 1Centre for Medical Biotechnology, Amity
Institute of Biotechnology, Amity University
Uttar Pradesh, India Abstract Received Date: 04-23-2022 Human papilloma virus (HPV) infection is one of the major
causes of cervical cancer which is one of the common causes
of death in women across the globe and is the fourth most
prevalent cancer in women representing 7.5% of female cancer
deaths globally and more than 85% of these occur in
underdeveloped regions. In India, cervical cancer is
responsible for the highest cancer deaths among women
which can be attributed to multiple pregnancies, open
relationships,
inadequate
sanitation
and
cleanliness,
behavioral habit and lifestyle, smoking, poor nutrition, and
long-term contraceptive use. These factors have been
associated as risk factors for cervical cancer. This review
discusses issues faced by women in tribal and rural areas of
India due to poor economic conditions, different lifestyles to mainstream population, socioc
and lack of access to healthcare facilities. The review also focusses on the tribal populations
the prevalence rates in these tribal groups. The current initiatives taken by government and n
organizations (NGOs) to prevent and control the HPV infection and reduce the cervical can
also been highlighted. The review emphasizes the urgent need for preferential care for wom
tribal communities of the world. Accepted Date: 05
Published Date: 05
Copyright© 2022 b
rights reserved. Th
distributed under
Commons Attribu
unrestricted
us
reproduction in a
original author and Accepted Date: 05-4-2022 Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Published Date: 05-20-2022 Copyright© 2022 by Choudhary C, et al. All
rights reserved. This is an open access article
distributed under the terms of the Creative
Commons Attribution License, which permits
unrestricted
use,
distribution,
and
reproduction in any medium, provided the
original author and source are credited. vical cancer; HPV; Risk factors; HPV prevalence; tribal; rural; Government initiatives; NGO- Keywords: Cervical cancer; HPV; Risk factors; HPV prevalence; tribal; rural; Government initiatives; NGO-
initiatives. Introduction underlying infectious diseases, smoking, poor
diet and long-term use of oral contraceptives
[8,9]. The population of the world is divided into
the urban, rural, and tribal populations. An
area is known as the rural sector when the
population of that area is less than 5,000, the
density of population less than 400 per sq km,
and more than 25% males are engaged in
agricultural areas. The tribal population
accounts for 5% of the global population [1]
and about 19.3% of the global population lives
in rural areas [2]. India is a diverse country
that has 29 States and 7 Union Territories. The current population of India according to
the 2019 Census is 1.37 billion, out of which 70
percent lives in a rural area [3,4]. India is
home to a large tribal population which is
approximately 8.6% of the Indian population
and about 65% people live in rural areas
whereas 35% people live in the urban area [5]. These factors are particularly more common
in the rural and tribal belts of India. Multiple pregnancies Some tribal communities live in open
relationships and in addition women are
prone to having successive pregnancies in a
year, which leads to higher parity, abortions,
poor health, and susceptibility to infections. In a study conducted among the tribal
adolescent girls of different tribes from three
different states of India–Madhya Pradesh
(Hoshangabad), Chhattisgarh (Narainpur and
Kondagaon) and Jharkhand (Jamshedpur) it
was found that they have persistent HPV
infection due to several factors among which
multiple pregnancies were also a major factor
[8,10]. One of the common causes of death across
the globe is cervical cancer. It is the fourth
most prevalent cancer in women representing
7.5% of female cancer deaths globally with
more than 85% of these occurring in
underdeveloped regions [6]. About 20% of
cancer deaths are caused due to Human
papilloma virus (HPV) infection and it is a
common cause of death for women belonging
to Eastern, Middle, and Western Africa,
Central America and South East Asia [7]. In
India, cervical cancer is responsible for
highest cancer deaths among women in rural
areas. Age is another important risk factor. In many
tribal communities, women become sexually
active at a very early age of 10-12 years. It has
been observed that women in their late teens
and mid-30s are more prone to cervical
cancer. Due to lack of education and poor
awareness, researchers propose that engaging
in sexual activity at a young age makes the
cervix highly vulnerable to HPV infection as a
result of the changes during puberty [11,12]. Women who undergo full-time pregnancy at
a very young age are more susceptible to
cervical cancer [8]. A study carried out in
different tribal areas of Madhya Pradesh,
Jharkhand, and Chhattisgarh, reported that
the mean age of women getting married was Risk factors of cervical cancer The common risk factors for HPV infection
are age, multiple sexual partners, multiple
pregnancies, poor sanitation and hygiene, Multiple partners It has been seen that some of the tribal
communities
mostly
live
in
open
relationships with multiple partners in
preference to the traditional one partner
marriage system, which increases their risk of
acquiring HPV infection [10]. According to
the study by Peedicayil et al in 2016, out of 809
women who took part in the study, 0.7% of
them had multiple partners and 3% of them
had used oral contraceptives [13]. A higher
HPV prevalence rate has been observed in
women
with
gynecological
symptoms
increasing their risk of developing cervical
cancer [14]. Poor sanitation and hygiene Due to poor economic conditions and
decreased awareness, women in rural and
tribal areas usually lack resources and
information to maintain sexual hygiene
particularly during menstruation. This makes
them vulnerable to poor sexual health and
prone to sexually transmitted infections, like
HPV leading to increased risk of cervical
cancer [9,15]. In a study conducted across the
tribal areas of Chhattisgarh, Madhya Pradesh,
Jharkhand, it was observed that most of the
women who were tested positive for HPV
infection had very poor sanitation and
hygiene particularly during the time of
menstruation, repeated use old cloth pieces
along with cow dung ash and other
unhygienic materials in their sanitary pad
during menstrual period making them more
susceptible to cervical cancer [10,16,17]. Behavioral pattern and lifestyle 18.1 years, and 43% of women became sexually
active before the age of 18 [10]. The prevalence of HPV in any area of
inhabitation depends on the lifestyle and
behavior of the inhabitants to a large extent. People living in tribal areas often live in
remote areas with lack contact with the
outside world [10]. Most of the rural and tribal
areas in India lack health care facilities
because they live in secluded and remote
areas. In addition, they are less likely to access
medical care due to their beliefs and prefer
natural
products
procured
locally
for
treatment [9,15]. Increased susceptibility to
diseases such as tuberculosis, pneumonia,
malaria, anemia and poor immune system are
reported in the tribal areas of Madhya
Pradesh,
Jharkhand,
and
Chhattisgarh. Chlamydia infection is a kind of bacterial
infection in the reproductive tract, which
helps the HPV to thrive on the cervix, leading
to a higher risk of cervical cancer [9,10,18,19]. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Poor diet Due to poor economic conditions in the tribal
areas, there is lack of nutritious food specially
required by women during pregnancy and
childbirth
which
may
cause
anemia,
malnutrition and weight loss in women and
could be linked to high prevalence of HPV
infection [10]. Smoking In rural areas, consumption of tobacco in
different forms is very common among men
and women. It has been observed that women
who smoke are more prone to cervical cancer
than non-smokers. Smoking tobacco and
other such substances damage the DNA of the
cervix and lower the immunity to fight HPV
infection
[19]. According,
to
a
study
conducted among tribal people, people in
these areas consume a lot of locally fermented
beverages called mahua and tadi which
contain toxic chemicals and hence, maybe the
reason for high HPV prevalence in this region
[18]. prolonged use of intrauterine contraceptive
devices can lead to actinomycosis, pelvic
inflammatory
disease
and
subsequent
possible malignancies [21]. However, Indian
tribal women have been reported to have no
or very limited knowledge about oral
contraception and the use of contraceptive
methods is also very limited [22]. Long term use of oral contraceptives There are limited studies carried out to
determine the HPV infection prevalence in
tribal population in India and on a global
level. Some major tribes/ tribal groups of
India and different continents are listed in
Table 1 and Table 2 respectively. Oral
contraceptives
are
the
hormonal
medications taken to prevent pregnancy. Various studies show that women using oral
contraceptives for 5 or more years are more
prone to cervical cancer, as these pills induce
a change in susceptibility of cervical cells and
result in persistent infection [20]. Moreover, Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024
result in persistent infection [20]. Moreover,
Indian States
Tribe/ Tribal Groups
Andhra Pradesh
Nakkala, Kurvikaran, Kondhs, Kodi, Kodhu, Desaya Kondhs, Dongria Kondhs,
Kuttiya Kondhs, Tikiria Kondhs, Yenity Kondhs, Kuvinga, Porja, Parangiperja
Arunachala Pradesh
Sulung Bangni, Sulung, Laju, Havi Tangsa, Liju Nocte, Lish Monpa
Assam
Syntheg, Chakma
Andaman & Nicobar Islands
Jarawas, Sentinelese, Shom Pens
Bihar
Banjara, Birhor, Parhayia, Korwa, Kora, Mudi-kora
Chhattisgarh
Saonta, Saunta
Dadra & Nagar Haveli
Naikda or Nayaka, Kathodi
Jammu & Kashmir
Bakarwal
Jharkhand
Parhaiya, Birhor, Savar, Baiga, Korwa
Kerala
Cholanaickan
Odisha
Mankirdia, Mankria, Mankidi, Koya, Gumba Koya, Koitur Koya, Kamar Koya,
Musara Koya, Dharua, Dhuruba, Dhurva, Korua, Parenga, Didayi, Didai Paroja,
Didai, Bondo Poraja, Bonda Paroja, Banda Paroja, Paroja, Parja, Bodo Paroja,
Barong Jhodia Paroja, Chhelia Paroja, Jhodia Paroja, Konda Paroja, Paraja, Ponga
Paroja, Sodia Paroja, Sano Paroja, Solia Paroja, Gandia, Omanatya, Omanatyo,
Amanatya
Rajasthan
Garasia(except Rajput in that region), Kathodi, Katkari, Dhor Kathodi, Dhor
Katkari, Son Kathodi, Son Katkari
Uttar Pradesh
Agariya, Baiga, Saharya, Raji
West Bengal
Gorait
Table 1: Tribes in each state of India [23]. Continent
Tribe/ Tribal Groups
References
Asia
Veddas (Sri Lanka), Jarawa (Andaman Islands, India), Naga (north-eastern
India and north-western Myanmar), Lhop (northwest Bhutan), Bodo (Nepal),
Giraavaru (Maldives). Long term use of oral contraceptives Burmans, Karen, Shan, Rakhine, Karenni, Chin, Kachin and Mon
(Burma/Myanmar)
Tibetans, Uighurs (China), Ainu, Okinawans (Japan), Orang asli (Malaysia),
Igorot, Lumad, Mangyan (Phillipines)
[24]
Africa
Zulu (South Africa), Maasai (East Africa), San Bushmen (Western Botswana
and Makgadikgadi), Yoruba (Nigeria and Southern Benin), Xhosa (Eastern-
Cape-Province of South Africa), Hausa (West Africa), Himba (Northern
Namibia), Oromo (southern parts of Ethiopia, Northern Kenya, some parts of
Somalia), Kalenjin (Western highlands of Kenya), Chaga (Tanzania)
[25]
Europe
Saami (Scandinavia and Russia)
[26]
South America
Mapuche, Kolla, Toba, Guarani, Wichi, Mocovi, Haurpe, Comechingen,
Tehuelche, Charrua, Pilaga (Argentina), Quechua, Aymara, Chiquitano,
Mojeno (Bolivia), Atacama (Chile), Awa, Chachi, Tsachila (Ecuador), Wayuu,
Pemon, Warao (Venezuela)
[27]
North America
Alaska natives, Pacific islands American (United States), Nahua Mazahua,
Otomi, Mixtecs (Mexico)
Table 2: Tribal groups present in different continents of the world. Tribe/ Tribal Groups Table 2: Tribal groups present in different continents of the world. tribal areas of southern coastal Karnataka,
reported a higher prevalence of HPV infection
among tribal women (40.6%) than general
population (14.3%) [31]. HPV infection with type 16
type was found in indigenous Nicobarese tribe, in
Andaman and Nicobar Islands, with a prevalence
of 2.3% [32]. In rural areas of West Bengal, a higher
prevalence of risk factors related to cervical cancer
was reported by Gupta et al, (2012). The prevalence
of HPV 16 and 18 in rural areas of eastern India was
found to be 7.5% and 9.6% respectively [33]. A
study carried out by Sharma et al. (2015) in tribal
areas of three Indian states: Madhya Pradesh,
Jharkhand and Chhattisgarh reported 12.9%
overall prevalence of HPV infection in tribal girls
of these regions with more than 65% of them
infected with HR-HPV types predominantly
HPV16 indicating. The study reported a very high
prevalence of HPV infection in adolescent and
young adult tribal girls possibly due to different
socio-sexual behavior, indicating a serious health Cervical cancer is one of the most common
cancers in women in India especially in rural and
tribal areas, where the HPV infection is increasing
at an alarming rate. However, the HPV prevalence
and incidence studies reported in rural and tribal
populations of India are limited. In India, the
initial reports of the incidence of cervical cancer
were reported from the rural areas of Barshi in
Maharashtra in 1987 [28]. Other rural areas
affected in the state of Maharashtra included
Paranda and Bhum Tahsils [28]. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Long term use of oral contraceptives In 2007, rural
areas of Ahmedabad and Gujrat were reported to
be affected by cervical cancer. About 700 different
cases were reported from Ratnagiri district in
Mumbai in 2009. In the following years, several
rural areas such as Sevagram, Konkan in
Maharashtra reported the incidence of cervical
cancer [29]. In Aizawl district of Mizoram, the
prevalence of HPV virus was reported to be 15.94%
and 11.08% in rural areas of Meghalaya [30]. A
population-based study was conducted in the Mozambique are affected by high incidences of
invasive cervical cancer and HPV appears to be
more common among women with normal
cytology than in more developed parts of the
world, with a prevalence of 24 percent on average
[39]. According to the WHO report, the rate of
cervical cancer is found to be higher in Eswatini,
followed by Malawi in-regions of sub-Saharan
Africa [40]. It was due to the lack of technical,
infrastructural, financial and human resources
needed for the cytological screening of HPV and
the method of Visual Inspection using acetic acid
(VIA) used for cytological screening due to low
income, resulting in higher HPV [41]. The main
reason for this difference in incidence rates is the
effective implementation of HPV screenings and
vaccination programs by the developed countries
compared to developing countries [42]. Table 3
lists the major studies carried out in the rural and
tribal populations of the world. concern for Indian tribal women. Apart from
India, cervical cancer is the second most common
cancer after breast cancer to affect women aged
15–44 years in the European Union with 33 000
cases of cervical cancer and 15 000 deaths each
year [34]. It is twice as high in Latin America
compared with the worldwide average and is
associated with 68,220 new cases of cervical cancer
per year with incidence rates range from 20 to 80
per 100,000 women and 31,712 cervical cancer-
associated deaths occur each year [35]. The
incident rates of HPV in sub-Saharan region are
very high, especially in Abuja, Nigeria, (with HPV
prevalence of 37%), where the proportion of HPV
positive women is same in all groups, from 10 years
to 65 years of age (or more) [36,37]. The higher
HPV rate was due to the high tobacco use, lack of
cervical
cancer
screening,
and
unattended
precancerous lesions [38]. Long term use of oral contraceptives The sub-Saharan Africa
regions of Guinea, Zambia, Tanzania, Malawi, and Continents/ Countries
Tribe/ Tribal Groups
Prevalence
Reference
Southeast Asia
Tibetan group, Hani women (China)
14%
[43]
South America
Guarani (Argentina)
64%
[44]
Tanzania (Eastern-Africa)
Mwanza
11.60%
[45]
Europe
North Sami (sami group) (Finland)
21%
[43,46]
Latin America
Alaska Native tribal women
16%
[43,47]
Table 3: Prevalence of HPV in different continents/ countries Table 3: Prevalence of HPV in different continents/ countries Table 3: Prevalence of HPV in different continents/ countries from various rural and urban registries [48]. This provides the map for designing and
implementing screening and management
programs effectively. Another committee that
works on the cancer control is the Indian
Academy of Pediatrics committee. Its purpose
is to raise awareness, educate patients and
parents on HPV infection and risk of cervical
cancer and sensitizing pediatricians to play an
active role in cervical cancer prevention
program
[49]. The
three
prophylactic
vaccines: quadrivalent HPV vaccine, bivalent
HPV vaccine, and the monovalent HPV Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Government
and
Non-Government
initiatives The government of India has developed
specific programs and initiatives to screen
and manage the increasing rate of HPV
infection among rural and tribal women in
India to reduce the cervical cancer burden in
this population. Indian Council of Medical
Research (ICMR) established the National
Cancer Registry program, which acts as a
surveillance system for cancer and collects
information about the cancer prevalence vaccines are available commercially are for
the prevention of HPV infection against HPV
genotypes 16,18,6 and 11 [50]. Gardasil,
Gardasil 9, and Cervarix are used for the
prevention of HPV infection from HPV
genotypes 16 and 18. Apart from these HPV
genotypes, Gardasil prevents infection caused
by HPV 6 and 11, which is responsible for 90%
of genital warts. Gardasil 9 prevents HPV
31,33,45,52, and 58 besides 6,11,16, and 18
[51,52]. In India, Gardasil was the first HPV
vaccine approved for use in 2006 [53]. HPV
vaccination is recommended for women from
9 to 26 years before the onset of any sexual
activity [54]. However, these vaccines provide
protection for only certain HPV types but not
all [54]. Also, some side effects like pain,
redness, or swelling in the arm where the shot
was given and fever, dizziness, nausea,
headache or feeling tired, muscle or joint pain
have been reported after the vaccination. rticle
be
discovered
only
after
the
true
implementation of these vaccines in India
[57]. Some of the states in India have initiated
HPV screening and vaccination programs. Delhi was the first state in India to launch free
HPV vaccination as a part of the Public
Health Program for girls of the age of 11-13
years at Delhi State Cancer Institute through
its framework in the east and west regions of
Delhi
[58]. WHO
has
supported
the
Government of Punjab (Bhatinda) for HPV
vaccination programme in 2016 [59]. In 2009,
a vaccination trial for cervical cancer was
conducted by Andhra Pradesh Minister for
Health and Family Welfare in collaboration
with
ICMR
and
PATH,
a
non-profit
organization in the USA in Khammam
district. A similar project was also launched
by the Gujrat government in Vadodara
district. Most of the vaccinated girls belonged
to the tribal communities whose parents were
agricultural laborers [60]. However, this trial
was suspended by the state governments
when six deaths of young girls were reported
in the weeks following the vaccination. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Government
and
Non-Government
initiatives It was
later discovered that the reason for their
death was due to other factors unrelated to
the HPV vaccine, such as poisoning,
drowning, malaria, or snakebite [55]. Various
non-governmental organizations (NGOs) like
Biocon Foundation and SAMA work to spread
awareness about HPV infection and its
vaccination. Biocon Foundation provides Pap
smears
tests
to
economically
poor
communities in India and it conducted its
first test in Karnataka in 2016. Since then, it
has been successful in screening more than
3000 women in India [55]. SAMA is a research
group that works for the health and welfare of
women. In 2010, SAMA reported the side In India, the National Technical Advisory
Group on Immunization recommended the
HPV vaccine for young women to be included
in the National Immunization Program [55]
to ensure easy access and affordability for the
economically and socially deprived sections
of the society. However, factors like high
vaccine costs, duration of vaccine use, vaccine
acceptance, and disease prioritization have
prevented the vaccine to become a part of the
National Immunization Program [56]. For a
mass HPV vaccination program, affordability
and accessibility are of major concern and for
region-specific issues; a cost-effective second-
generation vaccine may be needed [17]. WHO
recommends that HPV vaccination must be
included in the National Immunization
Program and the operational difficulties can vaccination as soon as enter seventh grade of
their school [65]. effects of the HPV vaccine given to young
girls, which included cramps, heavy bleeding,
and early onset of menstruation [53]. The Government schemes and initiative can
have both positive and negative impact on
people worldwide. The prophylactic vaccines
for HPV have met with mixed acceptance
globally. However, policy-level interventions
have been effective in increasing public
health benefit. Government policies and
mandates may result in improved HPV
vaccination coverage and reduced disease
burden and alternative policies that improve
unhindered access to HPV vaccination may
allow success as well [65]. The HPV vaccines
have been licensed almost in all the countries
across the globe. More than 80 countries have
introduced HPV vaccine in the National
Immunization Programs. In most programs, a
school-based approach is used to deliver the
vaccine to the targeted adolescents with
additional efforts using field clinics, and
primary health centers to cover girls who
missed vaccination and do not attend schools
[59,66]. Government
and
Non-Government
initiatives To encourage the research into HPV, the
National Institutes of Health, USA and
National Cancer Institutes, UK provides
grants and funds to enhance the healthcare
delivery system and studies its characteristics
[8]. Many countries across the world have
introduced HPV vaccination in their National
Immunization Program, including Australia,
Canada, USA, and various other European
countries [61]. In 2007, Australia commenced
the National HPV vaccination program and
National HPV vaccination Register (NHPVR)
that delivers HPV vaccine to young girls and
monitors and reports the coverage of HPV
vaccine [62]. Along with it, the National
Cervical
Screening
Program
was
also
introduced by the Australian government to
review cervical screening in different areas
[63]. In European countries, the Council of
the European Union recommends that the
screening programs for cervical cancer are
implemented using a systematic population-
based approach with quality assurance at all
appropriate levels and the test to be used
should be the pap test with age groups not
less than 20 and not more than 30 [64]. In the
United States, the Advisory Committee on
Immunization Practices recommends that all
the young girls (between age groups of 11-12)
should receive the HPV vaccine [61]. Following
this,
the
Cervical
Cancer
Prevention Act was also introduced which
proposed that girls should be given HPV Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 References 1. Basaninyenzi U. Indigenous people. The World Bank. 2021. 1. Basaninyenzi U. Indigenous people. The World Bank. 2021. 3. Area and population-Statistical yearbook 2018. Ministry of Statistics and Programme Implementation, Gov
India. 2019. 4. Census of India. Rural and Urban population distribution. Gov India. 2011. 4. Census of India. Rural and Urban population distribution. Gov India. 2011. 4. Census of India. Rural and Urban population distribution. Gov India. 2011. 5. Statistical Profile of Scheduled Tribes in India. Ministry of Tribal affairs statist 6. Ferlay J, Colombet M, Soerjomataram I, Mathers C, Parkin DM, Piñeros M, et al. Estimating the global cancer
incidence and mortality in 2018: GLOBOCAN sources and methods. Int J Cancer. 2019;144(8):1941-53. PubMed |
CrossRef 6. Ferlay J, Colombet M, Soerjomataram I, Mathers C, Parkin DM, Piñeros M, et al. Estimating the global cancer
incidence and mortality in 2018: GLOBOCAN sources and methods. Int J Cancer. 2019;144(8):1941-53. PubMed |
CrossRef 7. Sabeena S, Bhat PV, Kamath V, Arunkumar G. Global human papilloma virus vaccine implementation: An
update. J Obstet Gynaecol Res. 2018;44(6):989-97. PubMed | CrossRef 7. Sabeena S, Bhat PV, Kamath V, Arunkumar G. Global human papilloma virus vaccine implementation: An
update. J Obstet Gynaecol Res. 2018;44(6):989-97. PubMed | CrossRef 8. American Cancer Society, Risk Factors for Cervical Cancer. 2020. 9. Travasso C. Prevalence of HPV is high among Indian tribal girls and young women, study finds. BMJ. 2015;350. PubMed | CrossRef 9. Travasso C. Prevalence of HPV is high among Indian tribal girls and young women, study finds. BMJ. 2015;350. PubMed | CrossRef 10. Sharma K, Kathait A, Jain A, Kujur K, Raghuwanshi S, Bharti AC, et al. Higher prevalence of human
papillomavirus infection in adolescent and young adult girls belonging to different Indian tribes with varied
socio-sexual lifestyle. PLoS One. 2015;10(5). PubMed | CrossRef 10. Sharma K, Kathait A, Jain A, Kujur K, Raghuwanshi S, Bharti AC, et al. Higher prevalence of human
papillomavirus infection in adolescent and young adult girls belonging to different Indian tribes with varied
socio-sexual lifestyle. PLoS One. 2015;10(5). PubMed | CrossRef 11. Mabelele MM, Materu J, Ng’ida FD, Mahande MJ. Knowledge towards cervical cancer prevention and screening
practices among women who attended reproductive and child health clinic at Magu district hospital, Lake Zone
Tanzania: a cross-sectional study. BMC Cancer. 2018;18(1):1-8. PubMed | CrossRef 11. Mabelele MM, Materu J, Ng’ida FD, Mahande MJ. Conclusion The review highlights the status of HPV
prevalence in rural and tribal areas of India
and at global level. Most of the tribal
populations of the world live in secluded and
inaccessible areas and follow more open
sexual relationships with women becoming
sexually activity early, after menarche; and
have multiple sexual partners and are
multiparous. As these population groups are
located in distant areas and are economically
deprived, they have limited access to
healthcare facilities and may follow different social norms and religious beliefs which is
compounded
by
poverty,
illiteracy,
ignorance,
hostile
environment,
poor
sanitation, lack of safe drinking water, blind
beliefs
and
prejudices
particularly
in
developing and underdeveloped countries. As
the economic and socio-cultural milieu of this
population is different; the women are at an
increased risk of HPV infection. In order to
improve the health and reduce mortality in
women in these rural and tribal areas,
government organizations should adopt
rigorous measures to create awareness and
promote screening by setting up awareness workshops and screening camps about HPV
infection and cervical cancer and the
importance of maintaining good sexual
health and hygiene. The government should
develop policies to ensure the screening and
vaccination of adolescent girls and young
women in these areas and also improve the
health care facilities in the rural and tribal
areas of the country. The government
organizations can support and work along
with non-governmental organizations and
NGOs to promote the awareness and help
reduce cancer burden in rural and tribal
women. 1.
Basaninyenzi U. Indigenous people. The World Bank. 2021. |
4;
(
) |
p
J
4( )
4 |
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 2.
Census. New census data show differences between urban and rural populations. US Census Bureau. 2016.
3.
Area and population-Statistical yearbook 2018. Ministry of Statistics and Programme Implementation, Gov
India. 2019. References Knowledge towards cervical cancer prevention and screening
practices among women who attended reproductive and child health clinic at Magu district hospital, Lake Zone
Tanzania: a cross-sectional study. BMC Cancer. 2018;18(1):1-8. PubMed | CrossRef 12. Risk factors for Cervical Cancer. CCS. 2017. 13. Peedicayil A, Abraham P, Prasad J, Jeyaseelan L, Abraham S, Kurian S, et al. Community prevalence of human
papillomavirus by self-collected samples in South India. Indian J Gynecol Oncol. 2016;14(1):1-5. CrossRef 13. Peedicayil A, Abraham P, Prasad J, Jeyaseelan L, Abraham S, Kurian S, et al. Community prevalence of human
papillomavirus by self-collected samples in South India. Indian J Gynecol Oncol. 2016;14(1):1-5. CrossRef 14. De Sanjosé S, Diaz M, Castellsagué X, Clifford G, Bruni L, Muñoz N, et al. Worldwide prevalence and genotype
distribution of cervical human papillomavirus DNA in women with normal cytology: a meta-analysis. Lancet
Infect Dis. 2007;7(7):453-9. PubMed | CrossRef 14. De Sanjosé S, Diaz M, Castellsagué X, Clifford G, Bruni L, Muñoz N, et al. Worldwide prevalence and genotype
distribution of cervical human papillomavirus DNA in women with normal cytology: a meta-analysis. Lancet
Infect Dis. 2007;7(7):453-9. PubMed | CrossRef 15. Raychaudhuri S, Mandal S. Socio-demographic and behavioural risk factors for cervical cancer and knowledge,
attitude and practice in rural and urban areas of North Bengal, India. Asian Pac J Cancer Prev. 2012;13(4):1093-6. PubMed | CrossRef Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 16. Abulizi G, Li H, Mijiti P, Abulimiti T, Cai J, Gao J, et al. Risk factors for human papillomavirus infection prevalent
among Uyghur women from Xinjiang, China. Oncotarget. 2017;8(58):97955. PubMed | CrossRef 17. Srivastava AN, Misra JS, Srivastava S, Das BC, Gupta S. Cervical cancer screening in rural India: Status & current
concepts. Indian J Med Res. 2018;148(6):687. PubMed | CrossRef 18. Naik E, Karpur A, Taylor R, Ramaswami B, Ramachandra S, Balasubramaniam B, et al. Rural Indian tribal
communities: an emerging high-risk group for HIV/AIDS. BMC Int Health Hum Rights. 2005;5(1):1-7. PubMed |
CrossRef 19. Kashyap N, Krishnan N, Kaur S, Ghai S. Risk Factors of Cervical Cancer: A Case-Control Study. Asia Pac J Oncol
Nurs. 2019;6(3):308-314. PubMed | CrossRef 20. References PubMed | CrossRef 30. Bobdey S, Sathwara J, Jain A, Balasubramaniam G. Burden of cervical cancer and role of screening in India. Indian J Med Paediatr Oncol. 2016;37(04):278-85. PubMed | CrossRef 31. Ghosh S, Shetty RS, Pattanshetty SM, Mallya SD, Pandey D, Kabekkodu SP, et al. Human papilloma and other
DNA virus infections of the cervix: A population based comparative study among tribal and general population
in India. PLoS One. 2019;14(6). PubMed | CrossRef 31. Ghosh S, Shetty RS, Pattanshetty SM, Mallya SD, Pandey D, Kabekkodu SP, et al. Human papilloma and other
DNA virus infections of the cervix: A population based comparative study among tribal and general population
in India. PLoS One. 2019;14(6). PubMed | CrossRef 32. Parvez R, Hedau S, Bhattacharya D, Bhattacharjee H, Muruganandam N, Das BC, et al. High-risk HPV infection
among the tribal and non-tribal women of the Andaman and Nicobar Islands, India. Public Health. 2012;126(1):67-9. PubMed | CrossRef 32. Parvez R, Hedau S, Bhattacharya D, Bhattacharjee H, Muruganandam N, Das BC, et al. High-risk HPV infection
among the tribal and non-tribal women of the Andaman and Nicobar Islands, India. Public Health. 2012;126(1):67-9. PubMed | CrossRef 33. Duttagupta C, Sengupta S, Roy M, Sengupta D, Bhattacharya P, Laikangbam P, et al. Are Muslim women less
susceptible to oncogenic human papillomavirus infection? A study from rural eastern India. Int J Gynecol
Cancer. 2004;14(2). PubMed | CrossRef 33. Duttagupta C, Sengupta S, Roy M, Sengupta D, Bhattacharya P, Laikangbam P, et al. Are Muslim women less
susceptible to oncogenic human papillomavirus infection? A study from rural eastern India. Int J Gynecol
Cancer. 2004;14(2). PubMed | CrossRef 34. European Centre for Disease Prevention and Control, Factsheet about human papillomavirus. 20 35. Nogueira-Rodrigues A. HPV vaccination in Latin America: global challenges and feasible solutions. Am Soc Clin
Oncol Educ Book. 2019;39:e45-52. PubMed | CrossRef 35. Nogueira-Rodrigues A. HPV vaccination in Latin America: global challenges and feasible solutions. Am Soc Clin
Oncol Educ Book. 2019;39:e45-52. PubMed | CrossRef 36. Thomas JO, Herrero R, Omigbodun AA, Ojemakinde K, Ajayi IO, Fawole A, et al. Prevalence of papillomavirus
infection in women in Ibadan, Nigeria: a population-based study. Br J Cancer. 2004;90(3):638-45. PubMed |
CrossRef 36. Thomas JO, Herrero R, Omigbodun AA, Ojemakinde K, Ajayi IO, Fawole A, et al. Prevalence of papillomavirus
infection in women in Ibadan, Nigeria: a population-based study. Br J Cancer. 2004;90(3):638-45. PubMed |
CrossRef 37. References Moreno V, Bosch FX, Muñoz N, Meijer CJ, Shah KV, Walboomers JM, et al. International Agency for Research
on Cancer. Multicentric Cervical Cancer Study Group. Effect of oral contraceptives on risk of cervical cancer in
women with human papillomavirus infection: the IARC multicentric case-control study. Lancet. 2002;359(9312):1085-92. PubMed | CrossRef 21. Hegazy RA, Hegazy AA, Etman WM. Tubo-ovarian actinomycosis in perimenopausal woman with neglected
intrauterine device: A case report and review of literature. J Medical Case Repo. 2021;3(4):1-5. 21. Hegazy RA, Hegazy AA, Etman WM. Tubo-ovarian actinomycosis in perimenopausal woman with neglected
intrauterine device: A case report and review of literature. J Medical Case Repo. 2021;3(4):1-5. 22. Prusty RK. Use of contraceptives and unmet need for family planning among tribal women in India and selected
hilly states. J Health Popul Nutr. 2014;32(2):342. PubMed 22. Prusty RK. Use of contraceptives and unmet need for family planning among tribal women in India and selected
hilly states. J Health Popul Nutr. 2014;32(2):342. PubMed 23. Census of India. Scheduled area in Rajasthan. Gov Rajasthan. 2011. 24. WION Edge. 7 Unique Indigenous Tribes of South Asia. 2016. 25. Clay JW. Nation, tribe and ethnic group in Africa. Cultural Survival Quarterly. 1985;9(3):2-4. 26. Schooneveld, I.V. What is the oldest European Tribe? Sinchi Foundation. 2017. 26. Schooneveld, I.V. What is the oldest European Tribe? Sinchi Foundation. 2017. I di
L ti
A
i
i
th T
t
Fi t C
t
Th Fi t D
d
W
ld B
k 26. Schooneveld, I.V. What is the oldest European Tribe? Sinchi Foundation. 2017. 28. Jayant K, Nene BM, Badwe RA, Panse NS, Thorat RV, Khan FY. Rural cancer registry at Barshi, Maharashtra, and
its impact on cancer control. Natl Med J India. 2010;23(5):274. PubMed 28. Jayant K, Nene BM, Badwe RA, Panse NS, Thorat RV, Khan FY. Rural cancer registry at Barshi, Maharashtra, and 28. Jayant K, Nene BM, Badwe RA, Panse NS, Thorat RV, Khan FY. Rural canc
its impact on cancer control. Natl Med J India. 2010;23(5):274. PubMed 29. Nandakumar A. ICMR-NCPR-COD desk. Cancer Registry Abstract. 2011;16: 1-2. 29. Nandakumar A. ICMR-NCPR-COD desk. Cancer Registry Abstract. 2011;16: 1-2. 30. Bobdey S, Sathwara J, Jain A, Balasubramaniam G. Burden of cervical
Indian J Med Paediatr Oncol. 2016;37(04):278-85. PubMed | CrossRef 30. Bobdey S, Sathwara J, Jain A, Balasubramaniam G. Burden of cervical cancer and role of screening in India. Indian J Med Paediatr Oncol. 2016;37(04):278-85. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 References Akarolo-Anthony SN, Maso LD, Igbinoba F, Mbulaiteye SM, Adebamowo CA. Cancer burden among HIV-
positive persons in Nigeria: preliminary findings from the Nigerian AIDS-cancer match study. Infect Agent
Cancer. 2014;9(1):1-7. PubMed | CrossRef 37. Akarolo-Anthony SN, Maso LD, Igbinoba F, Mbulaiteye SM, Adebamowo CA. Cancer burden among HIV-
positive persons in Nigeria: preliminary findings from the Nigerian AIDS-cancer match study. Infect Agent
Cancer. 2014;9(1):1-7. PubMed | CrossRef |
38. Cancer of the cervix in the African Region, Regional Committee for Africa. WHO. 2011. 38. Cancer of the cervix in the African Region, Regional Committee for Africa. WHO. 2011. 39. De Vuyst H, Alemany L, Lacey C, Chibwesha CJ, Sahasrabuddhe V, Banura C, et al. The burden of human
papillomavirus infections and related diseases in sub-saharan Africa. Vaccine. 2013;31:32-46. PubMed | CrossRef
40. Cervical Cancer. WHO. 2020. 39. De Vuyst H, Alemany L, Lacey C, Chibwesha CJ, Sahasrabuddhe V, Banura C, et al. The burden of human
papillomavirus infections and related diseases in sub-saharan Africa. Vaccine. 2013;31:32-46. PubMed | CrossRef
40. Cervical Cancer. WHO. 2020. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 41. Aina IO, Raul SM, Padilla LA, Mthethwa-Hleta S, Preko PO, Jolly PE. Sociodemographic factors, health seeking
behaviors, reproductive history, and knowledge of cervical screening among women in Swaziland. Infect Agent
Cancer. 2020;15(1):1-9. PubMed | CrossRef 42. Chan CK, Aimagambetova G, Ukybassova T, Kongrtay K, Azizan A. Human papillomavirus infection and cervical
cancer: epidemiology, screening, and vaccination—review of current perspectives. J Oncol. 2019. PubMed |
CrossRef 43. Baloch Z, Yue L, Yuan T, Feng Y, Tai W, Liu Y, et al. Status of human papillomavirus infection in the ethnic
population in Yunnan Province, China. Biomed Res Int. 2015. PubMed | CrossRef 44. Tonon SA, Picconi MA, Zinovich JB, Nardari W, Mampaey M, Badano I, et al. Human papillomavirus cervical
infection in Guarani Indians from the rainforest of Misiones, Argentina. Int J Infect Dis. 2004;8(1):13-9. PubMed
| CrossRef 45. Houlihan CF, Baisley K, Bravo IG, Kapiga S, de Sanjosé S, Changalucha J, et al. The incidence of human
papillomavirus in Tanzanian adolescent girls before reported sexual debut. J Adolesc Health. 2016;58(3):295-301. PubMed | CrossRef 46. References Soininen L, Järvinen S, Pukkala E. Cancer incidence among Sami in northern Finland, 1979–1998. Int J Cancer. 2002;100(3):342-6. PubMed | CrossRef 47. Schmidt-Grimminger DC, Bell MC, Muller CJ, Maher DM, Chauhan SC, Buchwald DS. HPV infection among
rural American Indian women and urban white women in South Dakota: an HPV prevalence study. BMC Infect
Dis. 2011;11(1):1-8. PubMed | CrossRef 48. Summary report on HPV and cervical cancer statistics in India. WHO. HPV Info Centre. 2007 49. Choudhury P. Preventing cervical cancer: pediatricians role. Indian Pediatr. 2009. PubMed 50. Wang R, Pan W, Jin L, Huang W, Li Y, Wu D, et al. Human papillomavirus vaccine against cervical cancer:
Opportunity and challenge. Cancer Lett. 2020;471:88-102. PubMed | CrossRef 51. Chaturvedi AK, Engels EA, Pfeiffer RM, Hernandez BY, Xiao W, Kim E, et al. Human papillomavirus and rising
oropharyngeal cancer incidence in the United States. J Clin Oncol. 2011;29(32):4294. PubMed | CrossRef 5
,
g
,
,
,
,
,
p p
g
oropharyngeal cancer incidence in the United States. J Clin Oncol. 2011;29(32):4294. PubMed | CrossRef
52. Gillison ML, Chaturvedi AK, Lowy DR. HPV prophylactic vaccines and the potential prevention of noncervical 52. Gillison ML, Chaturvedi AK, Lowy DR. HPV prophylactic vaccines and the potential prevention of noncervical
cancers in both men and women. Cancer. 2008;113(10):3036-46. PubMed | CrossRef 53. Kumar N. Controversial vaccine studies: Why is Bill & Melinda Gates Foundation under fire from critics in India. The Economic Times. 2014. 54. Meites E, Szilagyi PG, Chesson HW, Unger ER, Romero JR, Markowitz LE. Human papillomavirus vaccination
for adults: updated recommendations of the Advisory Committee on Immunization Practices. MMWR Morb
Mortal Wkly Rep. 2019;19(11):3202-6. PubMed | CrossRef 55. Cousins S. A woman’s worth: health, stigma and discrimination in India. Sage Publications Pvt. L 55. Cousins S. A woman’s worth: health, stigma and discrimination in India. Sage Publications Pvt. Limited. 2020. 56. Chatterjee S, Chattopadhyay A, Samanta L. HPV and cervical cancer epidemiology-current status of HPV
vaccination in India. Asian Pac J Cancer Prev. 2016;17(8):3663-73. PubMed 56. Chatterjee S, Chattopadhyay A, Samanta L. HPV and cervical cancer epidemiology-current s
vaccination in India. Asian Pac J Cancer Prev. 2016;17(8):3663-73. PubMed 57. Rathi A, Singh SV. HPV Vaccine Scenario in India - A Short Report. Madridge J Vaccines. 2018;2(1):62-63. CrossRef 58. Mehrotra R, Hariprasad R, Rajaraman P, Mahajan V, Grover R, Kaur P, et al. |
4;
(
) |
p
J
4( )
4 |
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article
Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World
with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12.
DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 64. Stockholm, Guidance for the Introduction of HPV vaccines in EU countries. 2008. 63. Canfell K, Sitas F, Beral V. Cervical cancer in Australia and the United Kingdom: comparison of screening policy
and uptake, and cancer incidence and mortality. Med J Aust. 2006;185(9):482-6. PubMed | CrossRef 65. Brandt HM, Pierce JY, Crary A. Increasing HPV vaccination through policy for public health benefit. Hum Vaccin
Immunother. 2016;12(6):1623-5. PubMed | CrossRef References Stemming the wave of cervical
cancer: human papillomavirus vaccine introduction in India. J Glob Oncol. 2018;4. PubMed | CrossRef cancer: human papillomavirus vaccine introduction in India. J Glob Oncol. 2018;4. PubMed | CrossRef
59. Guide to introducing HPV vaccine into national immunization programmes. WHO. 2016. 59. Guide to introducing HPV vaccine into national immunization programmes. WHO. 2016. 60. Sarojini NB, Srinivasan S, Madhavi Y, Srinivasan S, Shenoi A. The HPV vaccine: science, ethics and regulation. Econ Pol Wkly. 2010;45(27):27-34. 61. Markowitz LE, Dunne EF, Saraiya M, Chesson HW, Curtis CR, Gee J, et al. Human papillomavirus vaccination:
recommendations of the Advisory Committee on Immunization Practices (ACIP). MMWR Recomm Rep. 2014;63(5):1-30. PubMed 62. Brotherton J, Gertig D, Chappell G, Rowlands L, Saville M. Catching up with the catch-up: HPV vaccination
coverage data for Australian women aged 18-26 years from the National HPV Vaccination Program Register. Commun Dis Intell Q Rep. 2011;35(2):197-201. PubMed 63. Canfell K, Sitas F, Beral V. Cervical cancer in Australia and the United Kingdom: comparison of screening policy
and uptake, and cancer incidence and mortality. Med J Aust. 2006;185(9):482-6. PubMed | CrossRef 64. Stockholm, Guidance for the Introduction of HPV vaccines in EU countries. 2008. 65. Brandt HM, Pierce JY, Crary A. Increasing HPV vaccination through policy for public health benefit. Hum Vaccin
Immunother. 2016;12(6):1623-5. PubMed | CrossRef 3 5
|
66. Hanson CM, Eckert L, Bloem P, Cernuschi T. Gavi HPV programs: application to implementation. Vaccines. 2015;3(2):408-19. PubMed | CrossRef 66. Hanson CM, Eckert L, Bloem P, Cernuschi T. Gavi HPV programs: application to implementation. Vaccines. 2015;3(2):408-19. PubMed | CrossRef
|
W2118568087.txt
|
https://ijbnpa.biomedcentral.com/counter/pdf/10.1186/1479-5868-7-83
|
en
|
Associations of quality of life with physical activity, fruit and vegetable consumption, and physical inactivity in a free living, multiethnic population in Hawaii: a longitudinal study
|
The international journal of behavioural nutrition and physical activity
| 2,010
|
cc-by
| 4,546
|
Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83
http://www.ijbnpa.org/content/7/1/83
RESEARCH
Open Access
Associations of quality of life with physical
activity, fruit and vegetable consumption, and
physical inactivity in a free living, multiethnic
population in Hawaii: a longitudinal study
Weiwen Chai1*, Claudio R Nigg2, Ian S Pagano1, Robert W Motl3, Caroline Horwath4, Rod K Dishman5
Abstract
Introduction: High intake of fruit and vegetables and being physically active are associated with reduced risk of
chronic diseases. In the current study, we examined the associations of physical activity, fruit and vegetable
consumption, and TV/video watching (indicator for physical inactivity) with perceived quality of life (QOL) in a
sample of free living adults.
Methods: A cohort (N = 139) from a random, multi-ethnic sample of 700 adults living in Hawaii was evaluated at
3-month intervals for the first year and 6-month intervals for the second year. QOL was assessed from self-reports
of mental or physical health at the end of the study.
Results: Overall, the cohort participants appeared to maintain relatively constant levels of physical activity, fruit and
vegetable intake, and TV/video watching. Physical activity was positively related to mental health (p-values < 0.05),
but not physical health, at all time points regardless of participants’ fruit and vegetable consumption and hours of
TV/video watching. Neither mental nor physical health was associated with fruit and vegetable intake or TV/video
watching.
Conclusion: Our study supports that physical activity is positively associated with mental health. Fruit and
vegetable consumption and TV/video watching may be too specific to represent an individual’s overall nutritional
status and physical inactivity, respectively.
Introduction
High intake of fruit and vegetables and being physically
active are associated with reduced risk of chronic diseases such as heart disease, diabetes, and cancers [1-5].
Despite interventions to increase physical activity in
the general population, only 30% of US adults aged 18
years or older are sufficiently active during their leisure
time according to recent surveys [6]. National campaigns such as 5-A-Day have increased awareness of
the health benefits associated with fruit and vegetables;
however, the increase in consumption of these foods
* Correspondence: wchai@crch.hawaii.edu
1
Cancer Research Center of Hawaii, University of Hawaii, (1236 Lauhala
Street), Honolulu, (HI 96813), USA
Full list of author information is available at the end of the article
has been relatively modest compared to the decrease in
fat intake [7].
Quality of life (QOL), a conceptualization reflecting an
individual’s physical and mental well-being, has emerged
as an important consideration in disease treatment and
prevention. Research on QOL and physical activity has
predominantly focused on elderly populations or populations with chronic diseases such as cardiovascular diseases, arthritis, pulmonary diseases, and cancer [1].
Although evidence consistently suggests a positive association between physical activity and QOL in these
populations [8,9], the relation may not be reproducible
in younger, disease-free individuals. In comparison to
the physical activity domain, fewer studies have assessed
the impact of fruit and vegetable intake on QOL and
© 2010 Chai et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.
Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83
http://www.ijbnpa.org/content/7/1/83
most of them were also conducted in diseased populations [10-14].
Physical inactivity has drawn far less research attention than physical activity; nevertheless, its adverse
health effects may be as important as the beneficial
effects of physical activity. It was reported that TV
watching, a commonly used indicator of inactivity was
associated with obesity [15,16]. Understanding behavioral patterns involving nutrition, physical activity, and
inactivity and how they influence QOL is essential to
public health as positive outcomes would provide the
general public with a motivation to adopt healthy lifestyles, thereby reducing risk and incidence of chronic
diseases. In the current study, we examined the associations of fruit and vegetables consumption, physical
activity, and inactivity with QOL in a sample of free living adults in Hawaii.
Methods
Participants and procedures
This longitudinal, cohort study used a random sample of
700 adults (18 years or older) from Hawaii. A sub-sample of 139 (20%) participants who completed QOL survey at the end of the study was used for analysis (QOL
cohort).
The detailed procedure was described previously [17].
In brief, the questionnaire was programmed into a computer assisted telephone interview system and participants were recruited using random digit dialing
procedures. A qualified individual whose birthday was
closest to the date of the phone call was asked to participate. A total of 700 adults were recruited and
informed consent was obtained from the participants.
The University of Hawaii Institutional Review Board
approved all study procedures. At baseline (T-1), 3month intervals (T-2, T-3, T-4, and T-5) for the first
year and 6-month intervals (T -6 and T-7) for the second year, assessments (30-minute interviews) regarding
participants’ physical activities and nutritional behaviors
were performed. A survey of QOL was sent out at the
end of the study (T-7); 139 (20%) participants completed
the survey.
Measures of physical activity
Physical activity was assessed using the International
Physical Activity Questionnaire (IPAQ) which records
physical activity as hours and additional minutes of participation during the past 7 days in activities rated
according to multiples of metabolic equivalents (METS).
IPAQ assesses frequency and duration of walking (3.3
METS) and moderate (4.0 METS) and vigorous (8.0
METS) physical activity, appropriate for categorization
of individuals as meeting public health guidelines for
sufficient regular physical activity. The total weekly
Page 2 of 6
physical activity levels, expressed as MET_hr/wk, were
calculated as the sum of walking and moderate and vigorous physical activity for the week. The IPAQ has
acceptable measurement properties for monitoring
population levels of physical activity among 18- to 65year-old adults in diverse settings [18].
Measures of physical inactivity
Physical inactivity/sedentary behavior was measured
according to the amount of time (hours) each participant spent on watching TV/video on an average day as
previously described [19]. Data suggest that TV/video
watching far exceeds the time spent in any other leisure
activity and represents the principal sedentary behavior
in the United States [20].
Measures of fruit and vegetable intake
The National Cancer Institute (NCI) Fruit and Vegetable screener was used in our study to assess the frequency and amount of consumption of 9 categories of
fruits and vegetables (fruit, fruit juices, salad, beans,
French fries, other potatoes, tomato sauce, vegetable
soups, and other vegetables) over the previous month
[21]. Computation of total daily servings of fruit
and vegetables was described elsewhere [21]. This questionnaire provides estimated median daily servings of
fruit and vegetables similar to those from 24-hour
recalls [21].
Measures of QOL
QOL was measured using a SF-12 Health Survey (SF12). The SF-12 is a multipurpose short-form with 12
questions, all selected from the SF-36 Health Survey
[22]. Scale sores were estimated for four health concepts
(physical functioning, role physical, role emotional, and
mental health) using two items each, whereas the
remaining four (bodily pain, general health, vitality, and
social functioning) were represented by a single item.
All 12 items were used to calculate the physical (PCS)
and mental (MCS) component summary scores by
applying a scoring algorithm empirically based on the
data of a US general population survey [22,23]. SF-12
was chosen in the current study since overall physical
and mental health were the key outcomes of interest.
Statistical analysis
Repeated-measures MIXED model was used to evaluate
if physical activity, fruit and vegetable intake, or hours
on TV/video watching were affected by time. Mean
values at T-2, 3, 4, 5, 6 or 7 were compared to that at
baseline (T-1).
Partial correlation was used to assess the associations
of QOL outcomes (MCS or PCS) with physical activity,
fruit and vegetable consumption, or TV/video watching.
Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83
http://www.ijbnpa.org/content/7/1/83
The basic model and the full model adjusted for ethnicity, gender, age (continuous), body mass index (BMI;
continuous), and education (continuous) were tested.
The results were similar for both models (data not
shown). We also used General Linear Model (GLM) to
examine the interactions between physical activity, fruit
and vegetable intake, and TV/video watching in relation
to MCS or PCS. T-test was used to assess the differences in the above three behavioral variables between
the total random sample and QOL cohort at baseline.
In order to examine whether QOL outcomes were associated with certain behavioral patterns, we classified study
participants into 9 profiles. The reason for this approach
was to further explore the potential/suggestive associations
which might not be detected by the above statistical analyses using continuous variables. The classification criteria
were described as follow. A participant was classified as
“average” if all his/her values (as means calculated from
the 7 time points) for physical activity, fruit and vegetable
intake, and TV/video watching were within 0.5 SD from
the corresponding cohort means. The remaining categories (for “non-average” participants) were defined
according to whether a participant’s value for a certain
behavioral variable was greater than 0.5 SD above or less
than 0.5 SD below the cohort mean (e.g., high for physical
activity, > cohort mean for physical activity + 0.5 SD; high
for fruit and vegetable intake, > cohort mean for fruit and
vegetable intake + 0.5 SD; low for TV/video watching,
Page 3 of 6
< cohort mean for TV/video watching - 0.5 SD). SAS software (SAS Institute, Cary, North Carolina) was used for all
analyses. All tests were two sided, and P < 0.05 was considered statistically significant.
Results
Table 1 shows baseline characteristics for the total random sample and QOL cohort. Although QOL cohort
participants were more likely to be older, females, and
Caucasians and less likely to be Pacific Islanders compared to the total random sample, there were no significant differences in baseline physical activity levels, fruit/
vegetable consumption, and hours of TV/video watching
between the two populations. It appeared that both
populations had relatively high fruit and vegetable
intakes at baseline (6.7 for QOL cohort and 7.4 for the
total random sample).
Overall, physical activity levels, fruit and vegetable
intake, and hours of TV/video watching remained relatively constant over the 2-year experimental period.
However, physical activity levels were significantly lower
at T-3 and T-6 than that at baseline. Participants also
had significantly lower fruit and vegetable intakes at T-4
and T-6 compared to baseline (Table 2).
Increasing weekly physical activity levels was significantly associated with increasing MCS at all time points
(T-1 to T-7; P-values < 0.05). There were no significant
associations between MCS and daily fruit and vegetable
Table 1 Selected baseline characteristics of the study participants
Characteristics
Age (y), mean (SD)
BMI (kg/m2), mean (SD)
Total random sample
(N = 700)
QOL cohort
(N = 139)
47.0 (17.1)
25.9 (5.6)
55.3 (15.5)
24.7 (4.7)
Education (y), mean (SD)
14.6 (2.8)
15.6 (2.9)
Median household income ($)
40-50,000
40-50,000
Gender, n (%)
Male
256 (36.6)
36 (25.9)
Female
438 (62.6)
103 (74.1)
Caucasian
Pacific islanders
261 (37.3)
155 (22.1)
59 (42.4)
20 (14.4)
Asian
218 (31.1)
43 (30.9)
Other
60 (8.6)
15 (10.8)
In excellent/very good/good/or fair health, n (%)
655 (95.0)
133 (95.7)
Physical activity (MET_hr/wk), mean (SD)
67.5 (66.2)
63.0 (59.2)
Fruit and vegetable (servings/d), mean (SD)
7.4 (6.5)
6.7 (4.2)
P = 0.10*
TV/video (hr/d), mean (SD)
2.5 (2.0)
2.3 (1.7)
Ethnicity, n (%)
P = 0.46*
P = 0.18*
Note. QOL = quality of life; BMI = body mass index; MET = metabolic equivalent.
* T-test was performed to examine the differences between the total random sample and QOL cohort in weekly physical activity levels, daily fruit and vegetable
consumption, and daily hours of TV/video watching at baseline.
Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83
http://www.ijbnpa.org/content/7/1/83
Page 4 of 6
Table 2 Levels of physical activity, fruit and vegetable intake, and TV/video watching for participants of QOL cohort
(N = 139) at the 7 time points
Time points
Physical activity
P*
(MET_hr/wk)
Baseline (T-1)
63.0 ± 4.7
3-month (T-2)
6-month (T-3)
55.6 ± 4.7
48.5 ± 4.8
Fruit and vegetable
P*
TV/video
(serving/d)
6.7 ± 0.4
0.11
0.001
P*
(hr/d)
2.3 ± 0.1
7.0 ± 0.4
6.7 ± 0.4
0.51
0.94
2.4 ± 0.1
2.2 ± 0.1
0.44
0.46
9-month (T-4)
58.5 ± 4.7
0.35
5.8 ± 0.4
0.04
2.3 ± 0.1
0.97
12-month (T-5)
56.0 ± 4.8
0.13
6.0 ± 0.4
0.12
2.3 ± 0.1
0.94
18-month (T-6)
54.0 ± 4.8
0.048
5.5 ± 0.4
0.01
2.3 ± 0.1
0.95
24-month (T-7)
61.9 ± 4.8
0.87
6.6 ± 0.4
0.79
2.2 ± 0.1
0.50
Note: Values are presented as mean ± SE; QOL = quality of life. MET = metabolic equivalent.
* P value for difference between T-1 (baseline) and T-2, T-3, T-4, T-5, T-6, or T-7 from repeated-measures MIXED model.
consumption. No significant associations were also
observed between MCS and daily hours of TV/video
watching except for T-3 and T-7, where an inverse association was observed. PCS was not associated with physical activity, fruit and vegetable intake, or hours of TV/
video watching (Table 3). There were no significant
interactions between physical activity, fruit and vegetable
consumption, and TV/video watching in relation to
MCS or PCS (P-values > 0.05).
The QOL outcomes for the 9 behavioral profiles were
listed in Table 4. We did not perform statistical analyses
due to small sample size for certain behavioral profiles.
Consistent with our overall findings, participants who
had average or above average physical activity levels
were also characterized by higher MCS scores regardless
of their status of fruit and vegetable consumption and/
or TV/video watching.
Discussion
Our results indicated that physical activity was predictive of positive mental health irrespective of participants’
other behaviors such as fruit and vegetable intake and
TV/video watching. This observation is in agreement
with other prospective studies that showed physically
active adults had lower risk of mental distress than inactive adults when measures like the SF-12, including its
parent measure, the SF-36, are used [1,24]. However,
those studies did not uniformly adjust for diet or sedentary behaviors that might confound the association
between perceived distress and physical activity [1,24].
The results are plausible given the large literature
from prospective cohort studies and randomized controlled trials that regular physical activity is associated
with reduced symptoms of depression and anxiety,
which represent the main content areas of the mental
health scale of the SF-12. Although limited, there is
emerging evidence to support neurobiological mechanisms whereby physical activity can reduce feelings of
Table 3 Correlations of physical activity, fruit and
vegetable intake, and TV/video watching with QOL
outcomes at the 7 time points*
Time points
MCS
PCS
r
P
r
P
Baseline
Physical activity
0.21
0.02
0.01
0.96
(T-1)
Fruit and Vegetable
-0.02
0.81
-0.02
0.79
TV/video
-0.00
0.99
0.02
0.82
3-month
Physical activity
0.21
0.02
0.06
0.50
(T-2)
Fruit and Vegetable
TV/video
0.02
-0.14
0.84
0.14
0.03
0.04
0.75
0.66
6-month
Physical activity
0.21
0.02
0.08
0.37
(T-3)
Fruit and Vegetable
0.09
0.28
-0.07
0.42
TV/video
-0.24
0.008
0.14
0.12
9-month
Physical activity
0.25
0.006
0.09
0.30
(T-4)
Fruit and Vegetable
TV/video
-0.06
-0.01
0.50
0.96
0.07
0.07
0.41
0.45
12-month
Physical activity
0.21
0.02
0.04
0.70
(T-5)
Fruit and Vegetable
0.13
0.14
-0.06
0.51
TV/video
-0.02
0.87
-0.07
0.45
18-month
Physical activity
0.24
0.009
0.12
0.21
(T-6)
Fruit and Vegetable
TV/video
0.12
-0.18
0.19
0.05
0.03
-0.06
0.71
0.49
24-month
Physical activity
0.24
0.01
0.05
0.56
(T-7)
Fruit and Vegetable
0.09
0.35
-0.04
0.65
TV/video
-0.21
0.02
-0.06
0.55
Note. QOL = quality of life; MCS = mental component summary for SF.-12;
PCS = physical component summary for SF-12; r = correlation coefficient
* Partial correlations were performed and results were adjusted for ethnicity,
gender, age, body mass index, and education.
Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83
http://www.ijbnpa.org/content/7/1/83
Page 5 of 6
Table 4 QOL outcomes for behavioral profiles
Behavioral profiles*
Behavioral parameters
mean (SD)
PA
FV
TV/video
low
low
low
11
23.6 (8.8)
3.4 (1.0)
1.7 (0.8)
49.9 (9.1)
44.1 (10.4)
low
low
low
high
high
low
13
16
15.6 (8.4)
21.3 (9.1)
2.7 (0.9)
7.8 (2.0)
3.7 (1.7)
1.6 (0.7)
48.4 (11.0)
44.5 (11.8)
48.7 (10.6)
49.0 (10.3)
low
high
high
14
23.3 (12.3)
7.1 (1.6)
3.7 (1.1)
48.7 (10.9)
45.6 (12.4)
high
high
high
10
134.8 (57.2)
7.8 (2.8)
3.6 (0.8)
47.0 (9.3)
54.5 (6.7)
high
high
low
32
92.6 (38.9)
8.6 (3.0)
1.3 (0.8)
48.3 (8.3)
53.7 (6.9)
high
low
high
6
80.1 (56.0)
4.4 (0.5)
4.1 (0.5)
51.0 (4.3)
54.2 (7.1)
high
low
low
3
44.9 (6.0)
3.0 (0.3)
0.6 (0.5)
46.9 (8.8)
54.6 (3.6)
34
54.6 (14.9)
5.8 (1.6)
2.0 (1.8)
50.4 (8.6)
51.9 (8.3)
Average†
N
PA
(MET_hr/wk)
FA
(serving/d)
QOL measures
mean (SD)
TV/video
(hr/d)
PCS
MCS
Note. QOL = quality of life; PA = physical activity; FV = fruit and vegetable intake; PCS = physical component summary for SF-12; MCS = mental component
summary for SF-12; MET = metabolic equivalent.
* ‘high’ refers to the participant’s value for PA, FV or TV/video was greater than 0.5 SD above the cohort mean for the respective variables; ‘low’ refers to the
participant’s value for PA, FV, or TV/video was less than 0.5 SD below the cohort mean for the respective variables.
†
Participants were classified as ‘average’ if their values for PA, FV, and TV/video were all within 0.5 SD from the corresponding cohort means.
depression or anxiety by positive influences on the central nervous system [25,26] Alternatively, physical activity may also influence mental health through social
interactions due to the mutual support and social relationships that are provided when engaging in physical
activity with others.
No associations were found between participants’ physical health and levels of physical activity. Previous
research conducted in elderly or chronically diseased
populations demonstrated strong evidence that exercise
improved individuals’ physical conditions [1]. It is suggested that older adults and those with chronic diseases
tend to have poorer physical health which creates challenges and requires specific needs concerning physical
activity [1]. Consequently, results obtained from these
populations may not be generalized to populations with
different age and physical conditions. The mean participant age in our study was 55.3 ± 15.5 years. Approximately 96% reported that their health was excellent,
very good, good, or fair. Thus, the lack of association
observed in the current study could be partially attributed to our younger and healthier study population
(essentially, a ceiling effect).
In our study, neither physical nor mental health was
associated with fruit and vegetable consumption. Similar
to physical activity domain, previous studies demonstrating positive associations between nutrition and QOL
were also predominately conducted in diseased populations. In our study, the average intakes of fruit and vegetables at each time point were high, all exceeding the
currently recommended 5 servings/day. As a consequence, the ability to detect the potential associations
may be limited due to the high intake (another ceiling
effect). Furthermore, food and nutrition can affect
people’s lives through many ways. Instead of focusing
on individual dietary component, we need to consider
the roles of other factors such as meal preparation, additional food groups, dinning environment, social interaction, and cultural aspects of food and diet.
Overall, TV/video watching was not associated with
mental or physical heath in the current study. The
inverse association with MCS observed at T-3 and T-7
is intriguing and requires further investigation. It was
suggested that depression and sedentary lifestyle have
bidirectional relationships [27]. Another study by Patten
et al. [28] showed that major depressive episodes were
associated with an increased risk of transition from an
active to an inactive pattern of activity. However, physical inactivity in the above studies was measured according to participant’s physical activity levels or daily
energy expenditure instead of quantifying the time spent
in sedentary behaviors such as TV/video watching.
There were several limitations to the current study. First,
although we used validated self-reported measures, objective indicators may provide more accurate evaluations of
behaviors. Second, QOL was only assessed at the end of
the study (T-7), resulting in a low response rate for the
survey (20%). However, in light of the evidence that participants maintained relatively constant levels of the behavioral parameters and the key variables from QOL cohort
were not considerably different from the entire sample, we
presume that our findings would persist over the 2-year
study period. Finally, we did not measure other sedentary
behaviors such as work-related physical inactivity which
could be relevant to QOL outcomes.
In conclusion, the results from this longitudinal study
indicated physical activity, superior to fruit and vegetable consumption and physical inactivity, is a main player
Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83
http://www.ijbnpa.org/content/7/1/83
influencing individual’s mental health. Our findings are
novel and support future investigations in a larger study
involving repeated measurements of QOL and multibehavioral frame work.
Abbreviations
QOL: Quality of life; SF-12: Short Form Health Survey; MCS: mental
component summary for SF-12; PCS: physical component summary for SF12; MET: metabolic equivalent; SD: standard deviation; SE: standard error.
Acknowledgements
Financial support for this study was received from the National Cancer
Institute Grant R01 CA109941 and R25 CA 90956.
Author details
1
Cancer Research Center of Hawaii, University of Hawaii, (1236 Lauhala
Street), Honolulu, (HI 96813), USA. 2Department of Public Health Studies,
University of Hawaii, (1960 East West Road), Honolulu, (HI 96822), USA.
3
Department of Kinesiology and Community Health, University of Illinois Champaign Urbana, (906 S. Goodwin Ave), Champaign, (IL 61820), USA.
4
Department of Human Nutrition, University of Otago, (33 Union Street),
Dunedin, New Zealand. 5Department of Kinesiology, University of Georgia,
(330 River Road), Athens, (GA 30602), USA.
Authors’ contributions
All of the authors made substantial contributions to the study concept and
design or analysis and interpretation of the data and have reviewed and
approved the final manuscript for submission. Specifically, WC designed the
analysis, analyzed the results, and was the primary author of every section of
the text. ISP aided in the design of the analysis and performed much of the
initial statistical analyses. CRN, RWM, CH, and RKD were instrumental in the
design of the study, and commented on and approved the manuscript.
Competing interests
The authors declare that they have no competing interests.
Received: 24 June 2010 Accepted: 22 November 2010
Published: 22 November 2010
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
References
1. Bize R, Johnson JA, Plotnikoff RC: Physical activity level and health-related
quality of life in the general adult population: a systematic review. Prev
Med 2007, 45:401-415.
2. Friedenreich CM, Orenstein MR: Physical activity and cancer prevention:
etiologic evidence and biological mechanisms. J Nutr 2002,
132:3456S-3464S.
3. Harding AH, Wareham NJ, Bingham SA, Khaw K, Luben R, Welch A,
Forouhi NG: Plasma vitamin C level, fruit and vegetable consumption,
and the risk of new-onset type 2 diabetes mellitus: the European
prospective investigation of cancer–Norfolk prospective study. Arch
Intern Med 2008, 168:1493-1499.
4. Ness AR, Powles JW: Fruit and vegetables, and cardiovascular disease: a
review. Int J Epidemiol 1997, 26:1-13.
5. Peto J: Cancer epidemiology in the last century and the next decade.
Nature 2001, 411:390-395.
6. Barnes P: Physical activity among adults: United States, 2000 and 2005.
Hyattsville, MD: US Department of Heath and Human Services, CDC; 2007.
7. Greene GW, Rossi SR: Stages of change for reducing dietary fat intake
over 18 months. J Am Diet Assoc 1998, 98:529-534, quiz 535-526.
8. Rejeski WJ, Brawley LR, Shumaker SA: Physical activity and health-related
quality of life. Exerc Sport Sci Rev 1996, 24:71-108.
9. Courneya KS, Friedenreich CM: Physical exercise and quality of life
following cancer diagnosis: a literature review. Ann Behav Med 1999,
21:171-179.
10. Pakiz B, Flatt SW, Mills KC, Jordan LJ, Carethers JM, Rock CL: Quality of life
and diet intervention in individuals at risk for recurrence of colorectal
adenomas. Psychooncology 2005, 14:85-93.
11. Toobert DJ, Glasgow RE, Strycker LA, Barrera M Jr, Radcliffe JL, Wander RC,
Bagdade JD: Biologic and quality-of-life outcomes from the
25.
26.
27.
28.
Page 6 of 6
Mediterranean Lifestyle Program: a randomized clinical trial. Diabetes
Care 2003, 26:2288-2293.
Plaisted CS, Lin PH, Ard JD, McClure ML, Svetkey LP: The effects of dietary
patterns on quality of life: a substudy of the Dietary Approaches to Stop
Hypertension trial. J Am Diet Assoc 1999, 99:S84-89.
Vallis M, Ruggiero L, Greene G, Jones H, Zinman B, Rossi S, Edwards L,
Rossi JS, Prochaska JO: Stages of change for healthy eating in diabetes:
relation to demographic, eating-related, health care utilization, and
psychosocial factors. Diabetes Care 2003, 26:1468-1474.
Corle DK, Sharbaugh C, Mateski DJ, Coyne T, Paskett ED, Cahill J, Daston C,
Lanza E, Schatzkin A: Self-rated quality of life measures: effect of change
to a low-fat, high-fiber, fruit and vegetable enriched diet. Ann Behav Med
2001, 23:198-207.
Andersen RE, Crespo CJ, Bartlett SJ, Cheskin LJ, Pratt M: Relationship of
physical activity and television watching with body weight and level of
fatness among children: results from the Third National Health and
Nutrition Examination Survey. JAMA 1998, 279:938-942.
Salmon J, Bauman A, Crawford D, Timperio A, Owen N: The association
between television viewing and overweight among Australian adults
participating in varying levels of leisure-time physical activity. Int J Obes
Relat Metab Disord 2000, 24:600-606.
Dishman RK, Thom NJ, Rooks CR, Motl RW, Horwath C, Nigg CR: Failure of
post-action stages of the transtheoretical model to predict change in
regular physical activity: a multiethnic cohort study. Ann Behav Med 2009,
37:280-293.
Craig CL, Marshall AL, Sjostrom M, Bauman AE, Booth ML, Ainsworth BE,
Pratt M, Ekelund U, Yngve A, Sallis JF, Oja P: International physical activity
questionnaire: 12-country reliability and validity. Med Sci Sports Exerc
2003, 35:1381-1395.
Buckworth J, Nigg C: Physical activity, exercise, and sedentary behavior
in college students. J Am Coll Health 2004, 53:28-34.
Dietz WH: The role of lifestyle in health: the epidemiology and
consequences of inactivity. Proc Nutr Soc 1996, 55:829-840.
Thompson FE, Subar AF, Smith AF, Midthune D, Radimer KL, Kahle LL,
Kipnis V: Fruit and vegetable assessment: performance of 2 new short
instruments and a food frequency questionnaire. J Am Diet Assoc 2002,
102:1764-1772.
Ware JE, Kosinski M: User’s manual for the SF-12v2™ Health Survey. 2007.
Kontodimopoulos N, Pappa E, Niakas D, Tountas Y: Validity of SF-12
summary scores in a Greek general population. Health Qual Life Outcomes
2007, 5:55.
Martin CK, Church TS, Thompson AM, Earnest CP, Blair SN: Exercise dose
and quality of life: a randomized controlled trial. Arch Intern Med 2009,
169:269-278.
Physical Activity Guidelines Advisory Committee: Physical Activity Guidelines
Advisory Committee Report, 2008. Washington, D.C.: U.S. Department of
Health and Human Services, 2008; 2008.
Dishman RK, O’Connor PJ: Lessons in exercise neuroloogy: The case of
endorphins. Mental Health and Physical Activity 2009, 2:4-9.
Roshanaei-Moghaddam B, Katon WJ, Russo J: The longitudinal effects of
depression on physical activity. Gen Hosp Psychiatry 2009, 31:306-315.
Patten SB, Williams JV, Lavorato DH, Eliasziw M: A longitudinal community
study of major depression and physical activity. Gen Hosp Psychiatry 2009,
31:571-575.
doi:10.1186/1479-5868-7-83
Cite this article as: Chai et al.: Associations of quality of life with
physical activity, fruit and vegetable consumption, and physical
inactivity in a free living, multiethnic population in Hawaii: a
longitudinal study. International Journal of Behavioral Nutrition and Physical
Activity 2010 7:83.
|
|
https://openalex.org/W3203006298
|
https://bmcimmunol.biomedcentral.com/track/pdf/10.1186/s12865-021-00456-2
|
English
| null |
Highly individual- and tissue-specific expression of glycoprotein group A and B blood antigens in the human kidney and liver
|
BMC immunology
| 2,021
|
cc-by
| 7,304
|
© The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Open Access Abstract Background: Currently, research on the quantitative distribution of ABO antigens in different organs and tissues
remains limited. We aimed to examine the individual characteristics of blood group glycoprotein A and B antigen
expression in human kidneys and livers. Methods: We obtained human samples, including the renal artery, renal vein, renal tissue, hepatic artery, hepatic
vein, portal vein, and hepatic tissue, from 24 deceased organ transplant donors. The expression of the blood group
antigens glycoprotein A and B was analysed and compared by Western blotting. Results: There was no significant difference in the expression between blood group glycoprotein A and B antigens
at any of the seven sites (p > 0.05). The expression of both A and B antigens was highest in renal tissue and the portal
vein and was lowest in the renal artery. A large difference in glycoprotein antigen expression was observed among
various donors or different regions of the same individual. Univariate analysis revealed that glycoprotein A/B antigens
were affected by the age and sex of donors and were significantly higher in males and in young people. Conclusions: Our study found that blood group glycoprotein antigen expression showed certain trends and distinct
distribution in the kidney, liver, and vessels among individuals and in different regions of the same individual, which
may explain the different clinical outcomes of patients who received ABO-incompatible transplantation. rds: ABO incompatible transplantation, Blood group antigen, Kidney, Liver, Western blot Keywords: ABO incompatible transplantation, Blood group antigen, Kidney, Liver, W complement activation [1]. Thus, pre-existing anti-donor
ABO antibodies in recipient blood must be removed
before ABOi transplantation, and antibody rebound must
be prevented after transplantation [2, 3]. Currently, clini-
cal preconditioning protocols exclusively consider the
anti-donor ABO antibody titre, which must be reduced
to the “safe” range (e.g., ≤ 1:16 in most transplant cen-
tres) on the transplant day [4–6]. Performing organ
transplantation in ABO-incompatible cases continues to
pose a significant challenge [7]. Even when the ABO anti-
body titre was “safe” on the day of transplantation, some
ABOi recipients still experienced AMR or even hyper-
acute rejection [8, 9]. In contrast, some ABOi allografts Highly individual‑ and tissue‑specific
expression of glycoprotein group A and B blood
antigens in the human kidney and liver Xianding Wang1,2†, Fan Zhang4†, Yamei Jiang3†, Zilin Xu4, Xiaobing Feng1,2, Linde Li1,2, Yu Fan1,2, Turun Song1,2,
Yunying Shi5, Zhongli Huang1,2 and Tao Lin1,2* Introductionh The transplantation of ABO-incompatible (ABOi) donor
allografts into recipients with naturally occurring anti-
A or B antibodies may sometimes result in antibody-
mediated rejection (AMR); this process is initiated by
antibodies binding to A or B antigens present on the
vascular endothelium within the graft and subsequent *Correspondence: kidney1234@163.com
†Xianding Wang, Fan Zhang are co-first authors
1 Department of Urology/Institute of Urology, West China Hospital,
Sichuan University, Number 37, Guoxue Alley, Chengdu 610041, Sichuan,
China Wang et al. BMC Immunol (2021) 22:66
https://doi.org/10.1186/s12865-021-00456-2 Wang et al. BMC Immunol (2021) 22:66
https://doi.org/10.1186/s12865-021-00456-2 *Correspondence: kidney1234@163.com
†Xianding Wang, Fan Zhang are co-first authors
1 Department of Urology/Institute of Urology, West China Hospital,
Sichuan University, Number 37, Guoxue Alley, Chengdu 610041, Sichuan,
China
Full list of author information is available at the end of the article For blood groups that were positive for antigen A,
namely, groups A and AB, further tests were performed
with anti-A1 lectin to determine the subtype of the blood
A antigen (A1 or A2). survived without AMR when the posttransplant ABO
antibody titre gradually increased to the preoperative
level [10, 11]. It is unclear why these two contrasting
events occur. To date, most studies have focused on the anti-donor
ABO antibody titre of recipients, and very little is known
about the influence of the donor expression pattern of
A/B antigens on posttransplant AMR incidence. It is
hypothesized that, in addition to ABO antibodies, the
onset and absence of AMR in these ABOi recipients may
also be attributed to the individual pattern of distribution,
subtype, and levels of ABO blood group antigens within
the allograft. Several previous studies have described the
expression pattern of organ- surface A/B antigens. On the
vascular endothelial cells of the human heart, only type II
A/B antigens were expressed, and type III/IV structures
were not detected. Conversely, in children who received
ABOi heart transplants, ABO antibodies specific for type
II antigens—the only A/B antigen subtypes expressed in
heart tissue—were absent, demonstrating the high speci-
ficity of B cell tolerance to donor blood group antigens
[12–14]. In the human renal vascular bed, a previous
study reported that there were three different A antigen
expression patterns (major, minor, and minimal staining
distribution), while all kidneys showed a B antigen pat-
tern that was similar to the major pattern of A antigen
but was slightly weaker [15]. These expression profiles
have important implications that should be considered in
clinical settings of ABOi transplantation. Eligibility criteria
Th
li ibili The eligibility criteria for deceased donors were as fol-
lows: (1) written consent obtained from the next of kin,
(2) 18–65 years old, (3) ABO blood group, (4) organ
donation after cardiac or brain death, (5) normal terminal
serum creatinine [< 110 µmol/l (female) or < 140 µmol/l
(male)], (6) normal terminal serum alanine aminotrans-
ferase [< 40 IU/L (female) or < 50 IU/L (male)], and (7)
the donated kidneys and livers were used for subsequent
ABO-compatible organ transplantation and had normal
graft function. Exclusion criteria included (1) acute kidney or liver
injury before donation, (2) a medical history of chronic
kidney disease or hepatitis B or C virus infection, (3)
active infection needing antibiotic treatment, and (4)
renal or liver parenchyma damage or lithiasis revealed by
ultrasound. However, these previous studies are limited because
A/B antigen quantification was performed with only
immunohistochemistry (IHC), which may be particu-
larly difficult to interpret. A/B antigens are expressed
in tissues as portions of glycolipids and glycoproteins. Highly individual- and tissue-specific expression of gly-
colipid group A and B blood antigens was found in previ-
ous studies [16], but no studies have used Western blot
analysis to quantify glycoprotein A/B antigens; previ-
ous studies used tissue samples in which red blood cells
(RBCs) were present at high levels, making it impossible
to distinguish between erythrocytic and tissue sources of
ABO blood group antigen expression with Western blot-
ting. Thus, the purpose of this study was to evaluate the
hypothesis that the quantitative glycoprotein A/B antigen
expression in RBC-free human kidneys and livers (the
two most common organs used for ABOi transplanta-
tion) varies greatly among individuals as well as among
different sites in an individual based on Western blotting. © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Wang et al. BMC Immunol (2021) 22:66 Page 2 of 9 (No. 2019SHEN282). All organ donation cases were con-
ducted according to the protocols for China Categories
I, II, and III donors [17]. All kidney [renal artery, renal
vein, renal tissue (by a 14-gauge BARD MAX-CORE
disposable core biopsy instrument)] and liver [hepatic
artery, hepatic vein, portal vein, hepatic tissue (by wedge
resection)] samples were obtained from deceased organ
transplant donors. The donor kidney and liver were per-
fused before and immediately after being removed surgi-
cally (to remove residual red blood cells) and preserved
in an RBC-free histidine-tryptophan-ketoglutarate solu-
tion. For blood groups that were positive for antigen A,
namely, groups A and AB, further tests were performed
with anti-A1 lectin to determine the subtype of the blood
A antigen (A1 or A2). (No. 2019SHEN282). All organ donation cases were con-
ducted according to the protocols for China Categories
I, II, and III donors [17]. All kidney [renal artery, renal
vein, renal tissue (by a 14-gauge BARD MAX-CORE
disposable core biopsy instrument)] and liver [hepatic
artery, hepatic vein, portal vein, hepatic tissue (by wedge
resection)] samples were obtained from deceased organ
transplant donors. The donor kidney and liver were per-
fused before and immediately after being removed surgi-
cally (to remove residual red blood cells) and preserved
in an RBC-free histidine-tryptophan-ketoglutarate solu-
tion. Western blot analysis Total protein was extracted from tissue samples, the tis-
sues were homogenized, and centrifuged at 4 °C. The
supernatants were used for Western blot assays. Proteins
were separated by 10% SDS-PAGE and then transferred
onto PVDF membranes (Amersham, GE Healthcare,
Chicago, IL). After being blocked with 5% nonfat milk,
membranes were incubated with an anti-blood group A
antibody (1:1000, BIOSCOT, Merck Millipore) at 4 °C
overnight, with a mouse monoclonal anti-β-actin anti-
body (1:10,000, ab8245) used as the internal reference,
followed by a subsequent incubation with a goat anti-
rabbit secondary antibody (1:8000, Santa Cruz Biotech-
nology, Santa Cruz, CA, USA). The visualization of the
protein bands was performed with enhanced chemilu-
minescence kits (Santa Cruz Biotechnology). The band
intensity was quantified using Image Lab 6.0.1 Software
(Bio-Rad Laboratories, Inc). The relative expression of
blood group antibodies is represented by the ratio of the Tissue samplesh This study protocol was reviewed and approved by the
Biomedical Ethics Committee, West China Hospital Wang et al. BMC Immunol (2021) 22:66 Wang et al. BMC Immunol (2021) 22:66 Page 3 of 9 Table 1 Clinical parameters of included deceased organ
transplant donors
BMI Body Mass Index
Feature
N = 24
Blood type [n (%)]
A
13 (54.2%)
B
6 (25%)
AB
2 (8.3%)
O
3 (12.5%)
Gender [n (%)]
Male
15 (62.5%)
Female
9 (37.5%)
Age (years) [mean ± sd]
50.29 ± 12.32
Height (meters) [mean ± sd]
1.64 ± 0.08
Weight (kilograms) [mean ± sd]
62.67 ± 12.76
BMI (kg/m2) [mean ± sd]
23.04 ± 4.00
Cause of death [n (%)]
Head trauma
13 (54.2%)
Stroke
10 (41.7%)
Central nervous system tumor
1 (4.2%) band intensity between the experimental band and inter-
nal reference. band intensity between the experimental band and inter-
nal reference. H&E and immunohistochemical staining Specimens from human kidneys and livers were fixed
in formalin and embedded in paraffin. For H&E stain-
ing, 4-µm slices were stained with H&E for histologi-
cal examination. For immunohistochemistry of blood
group A antigens, samples were rehydrated, washed with
TBS, and blocked with TBS containing 10% FCS and 1%
BSA, followed by incubation for 16 h in TBS containing
1% BSA and primary antibodies for blood group A or B
antigens. Tissue sections were washed twice with TBS,
and then HRP-conjugated anti-IgG secondary antibod-
ies were added to TBS. After washing twice, sections
were counterstained with Mayer’s haematoxylin, and
images were analysed with a Nikon eclipse 90i digital
microscope. Statistical analysis Experimental data are presented as the mean ± stand-
ard deviation (sd) or median (range). Mean values of the
groups with normally distributed data were compared
using Student’s t-tests or ANOVA, whereas Wilcoxon
rank-sum tests and Friedman M tests were used for com-
parisons of non-normally distributed data. All statistical
analyses were conducted using R (version 3.4.4), and a
P-value below 0.05 was considered significant. in the hepatic artery, 0.64 ± 0.53 in the hepatic vein,
0.71 ± 0.61 in the renal vein, 1.16 ± 0.90 in renal tissue,
and 1.56 ± 1.23 in the portal vein, in increasing order. The
mean intensities of B antigen among the 6 type B donors
and 2 type AB donors were 0.43 ± 0.36 in the renal artery,
0.61 ± 0.44 in hepatic tissue, 1.06 ± 0.78 in the renal vein,
1.10 ± 0.98 in the hepatic artery, 1.89 ± 1.10 in the por-
tal vein, 2.87 ± 3.20 in the hepatic vein, and 3.20 ± 2.92
in renal tissue, in increasing order. There was a 6.24-fold
difference in the mean glycoprotein A antigen intensity
between the lowest- and highest-intensity sites and a
corresponding 7.44-fold difference in the glycoprotein B
antigen intensity.f Results
h In this study, we obtained 168 tissue samples from 24
deceased organ donors, including 13 (54.2%) donors in
group A, 2 (8.3%) donors in group AB, 6 (25%) donors in
group B, and 3 (12.5%) donors in group O; there were 15
(62.5%) males and 9 (37.5%) females, with a mean age of
50.29 ± 12.32 years (Table 1). All the donors in groups A
and AB belonged to the A1 subtype. The mean height was
1.64 ± 0.08 m, and the mean weight was 62.67 ± 12.76 kg,
with a mean body mass index (BMI) of 23.04 ± 4.00 kg/
m2. The deceased donors died of a variety of causes: head
trauma (n = 13, 54.2%), stroke (n = 10, 41.7%), and central
nervous system tumours (n = 1, 4.2%). Much wider individual differences in blood group anti-
gen intensities were observed at the same site of various
donors as well as at different sites of the same donor. The
Friedman M test was then used and indicated that there
were differences in the distribution among the seven
sites of the glycoprotein A antigen group (p < 0.001), but
there was not a significant difference in the glycoprotein
B antigen group (p = 0.544). Individual differences were
significantly different in both the glycoprotein A antigen
group (p = 0.004) and B antigen group (p = 0.002). The
fold difference between the highest and lowest A antigen
intensities at the same site among the 13 type A donors
and 2 type AB donors was 98 (0.98/0.01) in the renal
artery, 213 (2.13/0.01) in the renal vein, 54.2 (3.25/0.06)
in renal tissue, 81.5 (1.63/0.02) in the hepatic artery, 10.2
(1.53/0.06) in the hepatic vein, 11.4 (5.00/0.44) in the
portal vein, and 10.2 (0.51/0.05) in hepatic tissue. The To eliminate false-positive errors, specimens from
blood group O were incubated with anti-blood group A
and B antibodies, and A/B antigens were not detected in
type O organs. In addition, B antigen expression was not
detected in blood group A specimens, and vice versa.h To eliminate false-positive errors, specimens from
blood group O were incubated with anti-blood group A
and B antibodies, and A/B antigens were not detected in
type O organs. In addition, B antigen expression was not
detected in blood group A specimens, and vice versa. The glycoprotein A and B antigen intensities at the
seven sites are displayed in Fig. 1. Results
h Western blot analysis
of blood group antigens from partial samples is shown in
Fig. 2. The mean intensities of A antigen among the 13
type A donors and 2 type AB donors were 0.25 ± 0.30 in
the renal artery, 0.25 ± 0.17 in hepatic tissue, 0.52 ± 0.50 The glycoprotein A and B antigen intensities at the
seven sites are displayed in Fig. 1. Western blot analysis
of blood group antigens from partial samples is shown in
Fig. 2. The mean intensities of A antigen among the 13
type A donors and 2 type AB donors were 0.25 ± 0.30 in
the renal artery, 0.25 ± 0.17 in hepatic tissue, 0.52 ± 0.50 Wang et al. BMC Immunol (2021) 22:66 Page 4 of 9 fold difference between the highest and lowest B antigen
intensities at the same site among the 6 type B donors
and 2 type AB donors was 56.5 (1.13/0.02) in the renal
artery, 36.2 (2.17/0.06) in the renal vein, 63.3 (8.23/0.13)
(
)
median fold difference between the highest and lowest A
antigen intensity at various sites in the same donor was
11.9 (range 4.15–317), while the median fold difference
between the highest and lowest B antigen intensity at var-
(
)
Fig. 1 Western blot results showing the relative expression of blood group A and B antigens in different tissues. The tissue samples included
88 samples from 15 blood group A donors and 49 samples from 8 blood group B donors. Research data are presented as the mean ± standard
deviation. PV: portal vein, RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; Renal: kidney tissue; Hepatica: liver tissue
Fig. 2 Western blot analysis of blood group antigens from two antigen A donors and two antigen B donors. PV: portal vein; RA: renal artery; RV:
renal vein; HA: hepatic artery; HV: hepatic vein; RE: kidney tissue; HE: liver tissue Fig. 1 Western blot results showing the relative expression of blood group A and B antigens in different tissues. The tissue samples included
88 samples from 15 blood group A donors and 49 samples from 8 blood group B donors. Research data are presented as the mean ± standard
deviation. PV: portal vein, RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; Renal: kidney tissue; Hepatica: liver tissue Fig. Results
h 1 Western blot results showing the relative expression of blood group A and B antigens in different tissues. The tissue samples included
88 samples from 15 blood group A donors and 49 samples from 8 blood group B donors. Research data are presented as the mean ± standard
deviation. PV: portal vein, RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; Renal: kidney tissue; Hepatica: liver tissue Fig. 2 Western blot analysis of blood group antigens from two antigen A donors and two antigen B donors. PV: portal vein; RA: renal artery; RV:
renal vein; HA: hepatic artery; HV: hepatic vein; RE: kidney tissue; HE: liver tissue Fig. 2 Western blot analysis of blood group antigens from two antigen A donors and two antigen B donors. PV: portal vein; RA: renal artery; RV:
renal vein; HA: hepatic artery; HV: hepatic vein; RE: kidney tissue; HE: liver tissue Fig. 2 Western blot analysis of blood group antigens from two antigen A donors and two antigen B donors. PV: portal vein; RA: renal artery; RV:
renal vein; HA: hepatic artery; HV: hepatic vein; RE: kidney tissue; HE: liver tissue median fold difference between the highest and lowest A
antigen intensity at various sites in the same donor was
11.9 (range 4.15–317), while the median fold difference
between the highest and lowest B antigen intensity at var-
ious sites in the same donor was 20.1 (range 4.03–70.75). Univariate analysis revealed that blood group glyco-
protein antigen expression in males was significantly fold difference between the highest and lowest B antigen
intensities at the same site among the 6 type B donors
and 2 type AB donors was 56.5 (1.13/0.02) in the renal
artery, 36.2 (2.17/0.06) in the renal vein, 63.3 (8.23/0.13)
in renal tissue, 21.7 (2.82/0.13) in the hepatic artery,
48.9 (10.26/0.21) in the hepatic vein, 9.88 (3.26/0.33) in
the portal vein, and 8.7 (1.31/0.15) in hepatic tissue. The median fold difference between the highest and lowest A
antigen intensity at various sites in the same donor was
11.9 (range 4.15–317), while the median fold difference
between the highest and lowest B antigen intensity at var-
ious sites in the same donor was 20.1 (range 4.03–70.75). g
Univariate analysis revealed that blood group glyco-
protein antigen expression in males was significantly Wang et al. BMC Immunol (2021) 22:66 Page 5 of 9 express A antigens on their RBCs. Results
h Similarly, blood group
B individuals express B antigens, group O individuals
express neither A nor B antigens, and group AB individu-
als express both [19]. In addition to RBCs, ABO blood
group antigens are also distributed on lymphocytes,
platelets, and most epithelial and endothelial cells. The
targets of blood group antibodies in ABOi transplanta-
tion are endothelial cells, but the antigen expression pat-
terns of endothelial cells are not faithfully modelled by
RBCs. Currently, there is little known about the endothe-
lial expression of blood group antigens in human organs. Vascularized allografts are the targets of blood group
antibodies, which, upon binding to endothelial cell sur-
faces, activate the complement system, which in turn
mediates AMR [20].hi higher than that in females (p = 0.048) in both the A and
B groups (Table 2). Furthermore, we found that glyco-
protein antigen expression was higher in young people
(p = 0.038). No association was observed between anti-
gen expression intensity and the BMI or transfusion his-
tory of the donor (Table 2). In all IHC sections, blood group antigen is shown in
red, and nuclei are represented in blue. The intensity and
distribution of the A antigen showed distinctly different
patterns in different tissues (Fig. 3). The renal tissue was
most strongly stained, and positivity was mainly found in
the glomerular and tubular capillaries. In the renal artery
and renal vein, the immunostaining was relatively weaker,
which was most obvious in the renal artery. In the renal
vein, portal vein, hepatic artery, and hepatic vein, positive
staining was mainly seen in the vascular bed, where the
endothelium was stained, whereas in liver tissue, positive
staining was mainly found in the venae centrales hepatis
and hepatic sinusoid. The intensity and distribution of
blood group antigens showed distinctly different patterns
in different tissues in both WB and IHC results. The amount of antigen displayed on a specific organ
may be of particular importance in ABOi transplan-
tation. Gehrie et al. performed IHC staining of blood
group A antigen in tissue blocks of 18 blood type A
cadaveric hearts obtained at autopsy [12]. Light micro-
scopic examination found that the endothelium stained
with a low intensity in 4 (22%) myocardial samples, an
intermediate intensity in 5 (28%) samples, and a high
intensity in 9 (50%) samples. PV portal vein; RA renal artery; RV renal vein; HA hepatic artery; HV hepatic vein; RE kidney tissue; HE liver tissue Results
h The digital analysis of IHC
staining intensity and percentage of the total surface
area of immunoreactivity revealed a 20-fold difference
between the lowest and highest expressing specimens,
and immunoreactivity was positively associated with Patients were grouped and then compared by male/female, transfusion history/no transfusion history, cut-off value of median age, or cu
value. P < 0.05 was regarded significantly different and marked in bold al artery; RV renal vein; HA hepatic artery; HV hepatic vein; RE kidney tissue; HE liver tissue Discussion This study also provided important experimental datato
further illustrate the mechanism of ABOi AMR. However, the major limitation of these previous studies
was that the IHC analysis of blood groups may be subject
to intra- and interobserver variability. Meanwhile, other
techniques for blood group antigen detection—such as
Western blotting—could have been affected by contami-
nating RBCs that are ubiquitous in autopsy and biopsy
specimens [20]. RBCs made it difficult to distinguish
between erythrocytic and tissue sources of blood group
antigen expression. The existence of RBCs may lead to
an overestimation of the relative expression in WB and
IHC results. Thus, autopsy samples cannot be used to
accurately quantify blood group antigens. Our study used
RBC-free histidine-tryptophan-ketoglutarate solution to
perfuse donor kidneys and livers to eliminate residual
RBCs. Thus, there should have been few, if any, resid-
ual RBCs in our tissue samples. A previous study found
highly individual- and tissue-specific expression of gly-
colipid group A and B blood antigens, but no studies have
analysed and compared glycoprotein A/B antigens. Thus,
we detected the relative expression of blood group glyco-
protein antigens in kidney and liver tissues with Western
blotting. Two weeks after ABOi transplantation, an antigen–
antibody reaction does not occur, and the ABOi allo-
grafts function normally, despite the presence of A/B
antigens on the graft and the existence of antibodies
directed against the corresponding antigens in the blood
of the recipient [23–25]. This type of tolerance is referred
to as “accommodation”, and its underlying mechanisms
remain to be elucidated. Accommodation may be due
to (1) a change in the antigen, leading to decreased anti-
body binding; (2) a change in antibodies, reducing their
cytotoxicity; or iii) a change in the graft, enabling it to
resist the injury mediated by the host immune system
[16, 26, 27]. During clinical transplantation accommo-
dation, these processes can manifest as the inhibition of
the activity of glycosyltransferase, resulting in decreased
antigenic immunogenicity. On the other hand, antigen
downregulation might underlie the process of accommo-
dation in which a graft survives and functions despite the Our study found that the mean intensity of glycopro-
tein A and B antigen was generally similar (p > 0.05). Furthermore, kidney tissue and the portal vein were the
two sites with the highest average intensity, and the renal
artery was the site with the lowest intensity. Discussion In the human renal vascular bed, three different A anti-
gen expression patterns with a major, minor, and minimal
staining distribution were observed. The major pattern
showed intense A antigen expression in the endothelium
of arteries, glomerular/peritubular capillaries, and veins. A minor pattern showed overall weaker antigen expres-
sion, whereas minimal had faint staining of peritubular
capillaries only. In all cases, the distal tubular epithelium
was focally stained, whereas proximal tubules were nega-
tive. The secretor gene did not influence renal A antigen
expression. All B kidneys showed a B antigen pattern
slightly weaker but similar to the major pattern of the A
antigen. pre-transplant preconditioning than ABOi liver trans-
plantation and why the incidence of AMR in ABOi kid-
ney transplantation was more higher than that in ABOi
liver transplantation. We also found a wide diversity of
blood group glycoprotein antigen intensities at the same
site from a cohort of different deceased donors as well
as at different sites from the same donor. These observa-
tions may explain why even when the ABO antibody titre
was “safe” on the transplant day, two allografts in our case
series of 48 ABOi recipients exhibited immediate failure
and pathology consistent with hyperacute rejection [21]. Thus, pre-transplant evaluation of the risk and sever-
ity of ABO blood group AMR may be important when
performing ABOi kidney transplantation and may allow
individualized preconditioning regimens based on A/B
antigen intensity and diversity. For example, when the
organ tissues and main vessels in a donor express a high
level of blood group antigens, the risk of AMR in the cor-
responding ABOi recipients may be likely to be higher,
and such recipients may need more intense precondition-
ing to decrease the ABO antibody titre to an even lower
level [22]. Worldwide, there are currently no safe, non-
invasive, and reliable methods that can be used to quan-
tify and inhibit ABO blood group antigen expression in
donor organs. As a result, the preconditioning regimen in
ABOi organ transplantation has been limited to decreas-
ing the blood group antibody titre in the recipients. Our
research revealed the prominent individual diversity of
glycoprotein intensity for the ABO antigen in different
organs and tissues by Western blotting. These results
are useful for the further study of risk stratification and
preconditioning regimens based on donor blood group
antigen expression levels in ABOi organ transplantation. Discussion ABO blood group antigens are carbohydrate chains
expressed on the cell membrane of RBCs. The H anti-
gen is the only ABO structure present in blood type O,
and A/B blood group antigens contain the H antigen as
a common precursor [18]. Blood group A individuals Table 2 Univariate analysis of clinical features related to blood group antigen expressionsff
Feature
P value
PV
RA
RV
HA
HV
RE
HE
Total
Sex
A
0.567
0.045
0.003
0.001
0.365
0.300
–
0.008
B
–
0.738
0.749
0.832
0.958
0.718
0.543
0.739
A&B
0.920
0.238
0.027
0.130
0.598
0.295
0.568
0.048
Transfusion
A
0.090
0.168
0.475
0.262
0.187
0.580
0.848
0.675
B
0.036
0.990
0.698
0.471
0.321
0.934
0.747
0.367
A&B
0.005
0.237
0.719
0.252
0.227
0.783
0.872
0.699
Age
A
0.648
0.382
0.309
0.178
0.678
0.646
0.050
0.459
B
0.890
0.504
0.042
0.009
0.446
0.165
–
0.029
A&B
0.690
0.908
0.121
0.065
0.464
0.204
0.809
0.038
BMI
A
0.722
0.380
0.351
0.850
0.714
0.885
–
0.874
B
–
0.124
0.133
0.006
0.266
0.177
0.255
0.009
A&B
0.926
0.940
0.153
0.208
0.398
0.143
0.350
0.054 Table 2 Univariate analysis of clinical features related to blood group antigen expressions
F
t
P
l Table 2 Univariate analysis of clinical features related to blood group antigen expressions Wang et al. BMC Immunol (2021) 22:66 Page 6 of 9 Fig. 3 Immunohistochemical staining of the renal artery (A), renal vein (B), portal vein (C), hepatic tissue (D), hepatic artery (E), hepatic vein (F),
renal tissue (G) of an A antigen donor and the renal tissue (H) of a blood type O donor. RA, renal artery; RV, renal vein; RE, renal tissue; HE, hepatic
tissue; HA, hepatic artery; HV, hepatic vein; PV, portal vein Fig. 3 Immunohistochemical staining of the renal artery (A), renal vein (B), portal vein (C), hepatic tissue (D), hepatic artery (E), hepatic vein (F),
renal tissue (G) of an A antigen donor and the renal tissue (H) of a blood type O donor. RA, renal artery; RV, renal vein; RE, renal tissue; HE, hepatic
tissue; HA, hepatic artery; HV, hepatic vein; PV, portal vein Wang et al. BMC Immunol (2021) 22:66 Page 7 of 9 patient age (p = 0.004). Breimer et al. examined the A/B
antigen expression of renal biopsy samples by IHC [15]. Availability of data and materials The datasets used and/or analysed during the current study are available from
the corresponding author on reasonable request. This study had several limitations. First, the statistical
power may have been limited due to the relatively small
sample size. Second, all individuals in the A and AB
blood groups had A1 subtypes because the frequency of
A2 in the Chinese population is < 1%, and no A2 individ-
uals were included in this study. Finally, all livers and kid-
neys from the deceased donors underwent subsequent
ABO-compatible but not ABOi organ transplantation. Thus, the association between A/B expression patterns
and blood group AMR remains to be elucidated. A large
prospective clinical trial is needed to confirm our current
findings and explore the association of A/B expression
patterns with AMR and graft function in ABOi organ
transplant recipients. Further studies might determine
whether there is a threshold of the expression of blood
group antigen that is likely to trigger AMR. Abbreviations ABOi: ABO-incompatible; AMR: Antibody-mediated rejection; IHC: Immunohis-
tochemistry; BMI: Body mass index; PV: Portal vein; RA: Renal artery; RV: Renal
vein; HA: Hepatic artery; HV: Hepatic vein; RE: Kidney tissue; HE: Liver tissue. 3. Flint S, Walker R, Hogan C, Haeusler M, Robertson A, Francis D, Millar R,
Finlay M, Landgren A, Cohney S. Successful ABO-incompatible kidney
transplantation with antibody removal and standard immunosuppres-
sion. Am J Transplant Off J Am Soc Transplant Am Soc Transplant Surg. 2011;11(5):1016–24. Author details
1 1 Department of Urology/Institute of Urology, West China Hospital, Sichuan
University, Number 37, Guoxue Alley, Chengdu 610041, Sichuan, China. 2 Organ Transplantation Center, West China Hospital, Sichuan University,
Chengdu, Sichuan, China. 3 Department of Urology/Shanghai Key Laboratory
of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai,
China. 4 West China School of Clinical Medicine, Sichuan University, Chengdu,
Sichuan, China. 5 Department of Nephrology, West China Hospital, Sichuan
University, Chengdu, Sichuan, China. Discussion It was not
surprising that the injury in renal tissue would be more
severe than that in the main renal vessels when blood
group AMR occurred. The high level of blood group anti-
gens in the portal vein may be related to the high inci-
dence of portal vein thrombosis and portal vein stenosis
after liver transplantation. Additionally, the compari-
son of the intensity in kidney versus liver tissues indi-
cated that there was a much higher expression level of
glycoprotein antigen in renal tissue than in liver tissue
from the same donor, which might partially explain why
ABOi kidney transplantation requires more aggressive Wang et al. BMC Immunol (2021) 22:66 Wang et al. BMC Immunol (2021) 22:66 Page 8 of 9 [grant number 2019-YF05-00084-SN]; and 1.3.5 Project for Disciplines of
Excellence-Clinical Research Incubation Project, West China Hospital, Sichuan
University [grant number 2018HXFH049, ZYJC18004, ZY2016104, 2019-075,
2021HXFH007]. The funders had no role in study design, data collection or
analysis, preparation of the manuscript, or the decision to publish. [grant number 2019-YF05-00084-SN]; and 1.3.5 Project for Disciplines of
Excellence-Clinical Research Incubation Project, West China Hospital, Sichuan
University [grant number 2018HXFH049, ZYJC18004, ZY2016104, 2019-075,
2021HXFH007]. The funders had no role in study design, data collection or
analysis, preparation of the manuscript, or the decision to publish. presence of anti-donor antibodies in the circulation of
the recipient. Ulfvin et al. analysed glycolipids extracted
from ABO-incompatible allografts that had become
accommodated and found the accommodated grafts had
reduced levels of antigen, suggesting that antigen down-
modulation might play a role in the long-term function of
the organs [28]. The authors have none to declare. 4. Koo T, Yang J. Current progress in ABO-incompatible kidney transplanta-
tion. Kidney Res Clin Pract. 2015;34(3):170–9. Conclusions Our study revealed substantial inter-individual variations
in blood group A and B antigens between human livers
and kidneys. These variations may explain differences in
the incidence and clinical severity of AMR in ABOi kid-
ney/liver transplantations and could theoretically be used
to risk-stratify ABOi organ transplant procedures. Future
studies may consider non-invasive detection methods
for the intensity of blood group antigens in a specific
donor organ, which could more accurately assess the risk
of AMR in ABOi transplantation recipients and help to
select more precise desensitization regimens to perform
ABOi organ transplantation safely. Received: 28 October 2020 Accepted: 23 September 2021 Consent for publication Consent for publication
Not applicable. Consent for publication
Not applicable. Not applicable. Authors’ contributions XW, FZ and YJ wrote the main manuscript text. The clinical tisses were col-
lected by ZX, XF, LL, YF, TS, YS, and ZH. Study was designed by TL and XW. The experiments were done by FZ and YJ. XW and FZ prepared Figs. 1, 2
and Tables 1, 2. All authors reviewed the manuscript. All authors read and
approved the final manuscript. 5. Uchida J, Kosoku A, Naganuma T, Tanaka T, Nakatani T. Latest insights on
ABO-incompatible living-donor renal transplantation. Int J Urol Off J Jpn
Urol Assoc. 2020;27(1):30–8. 6. Masterson R, Hughes P, Walker RG, Hogan C, Haeusler M, Robertson AR,
Millar R, Suh N, Cohney SJ. ABO incompatible renal transplantation with-
out antibody removal using conventional immunosuppression alone. Am
J Transplant. 2014;14(12):2807–13. Referencesf 1. Schiffer M, Kielstein J. ABO-incompatible renal transplantation: from
saline flushes to antigen-specific immunoadsorption-tools to overcome
the barrier. Korean J Hematol. 2011;46(3):164–8. 1. Schiffer M, Kielstein J. ABO-incompatible renal transplantation: from
saline flushes to antigen-specific immunoadsorption-tools to overcome
the barrier. Korean J Hematol. 2011;46(3):164–8. 2. Montgomery R, Locke J, King K, Segev D, Warren D, Kraus E, Cooper M,
Simpkins C, Singer A, Stewart Z, Melancon J, Ratner L, Zachary A, Haas
M. ABO incompatible renal transplantation: a paradigm ready for broad
implementation. Transplantation. 2009;87(8):1246–55. Ethics approval and consent to participate Informed consent was obtained from next of kin in accordance with the
Declaration of Helsinki and the Council for International Organizations of
Medical Sciences. This study protocol was reviewed and approved by the
Biomedical Ethics Committee, West China Hospital (No. 2019SHEN282). This
study protocol was reviewed and approved by the Biomedical Ethics Commit-
tee, West China Hospital (No. 2019SHEN282). All organ donation cases were
conducted according to the protocols for China Categories I, II, and III donors. Written consent to participate in the study was obtained from the donor’s
family. All tissues were obtained in West China Hospital, China and no tissues
were obtained from prisoners. Acknowledgements The authors have none to declare. Funding
Thi
k Aikawa A, Hadano T, Ohara T, Yamashita M, Arai K, Hirayama N, Mori Y,
Muramatsu M, Hasegawa A. Donor specific antibody suppression in ABO
incompatible kidney transplantation. Transplant Proc. 2001;33(1–2):395–7 13. Jeyakanthan M, Tao K, Zou L, Meloncelli P, Lowary T, Suzuki K, Boland D,
Larsen I, Burch M, Shaw N, Beddows K, Addonizio L, Zuckerman W, Afzali
B, Kim D, Mengel M, Shapiro A, West L. Chemical basis for qualitative and
quantitative differences between ABO blood groups and subgroups:
implications for organ transplantation. Am J Transplant Off J Am Soc
Transplant Am Soc Transplant Surg. 2015;15(10):2602–15. 25. Park WD, Grande JP, Ninova D, Nath KA, Platt JL, Gloor JM, Stegall
MD. Accommodation in ABO-incompatible kidney allografts, a novel
mechanism of self-protection against antibody-mediated injury. Am J
Transplant. 2003;3(8):952–60. 26. Park W, Grande J, Ninova D, Nath K, Platt J, Gloor J, Stegall M. Accom-
modation in ABO-incompatible kidney allografts, a novel mechanism of
self-protection against antibody-mediated injury. Am J Transplant Off J
Am Soc Transplant Am Soc Transplant Surg. 2003;3(8):952–60. 14. Jeyakanthan M, Meloncelli P, Zou L, Lowary T, Larsen I, Maier S, Tao K,
Rusch J, Chinnock R, Shaw N, Burch M, Beddows K, Addonizio L, Zucker-
man W, Pahl E, Rutledge J, Kanter K, Cairo C, Buriak J, Ross D, Rebeyka I,
West L. ABH-glycan microarray characterizes ABO subtype antibodies:
fine specificity of immune tolerance after ABO-incompatible transplanta-
tion. Am J Transplant Off J Am Soc Transplant Am Soc Transplant Surg. 2016;16(5):1548–58. 27. Takahashi K, Saito K, Takahara S, Okuyama A, Tanabe K, Toma H, Uchida
K, Hasegawa A, Yoshimura N, Kamiryo Y. Excellent long-term outcome
of ABO-incompatible living donor kidney transplantation in Japan. Am J Transplant Off J Am Soc Transplant Am Soc Transplant Surg. 2004;4(7):1089–96. 15. Breimer ME, Mölne J, Nordén G, Rydberg L, Thiel G, Svalander CT. Blood
group A and B antigen expression in human kidneys correlated to A1/
A2/B, Lewis, and secretor status. Transplantation. 2006;82(4):479–85. 28. Ogasawara K, Ueki J, Takenaka M, Furihata K. Study on the expression of
ABH antigens on platelets. Blood. 1993;82(3):993–9. 28. Ogasawara K, Ueki J, Takenaka M, Furihata K. Study on the expression of
ABH antigens on platelets. Blood. 1993;82(3):993–9. 28. Ogasawara K, Ueki J, Takenaka M, Furihata K. Study on the expression of
ABH antigens on platelets. Blood. 1993;82(3):993–9. 16. Ulfvin A, Bäcker A, Clausen H, Hakomori S, Rydberg L, Samuelsson B, Bre-
imer M. Funding
Thi
k This work was supported by grants from the National Natural Science Founda-
tion of China [grant number 81870513]; Sichuan Science and Technology Pro-
gram [grant number 2019YJ0133]; Chengdu Science and Technology Program 7. Scurt F, Ewert L, Mertens P, Haller H, Schmidt B, Chatzikyrkou C. Clinical outcomes after ABO-incompatible renal transplantation: Page 9 of 9 Wang et al. BMC Immunol (2021) 22:66 Wang et al. BMC Immunol (2021) 22:66 Wang et al. BMC Immunol (2021) 22:66 18. Milland J, Sandrin M. ABO blood group and related antigens, natural
antibodies and transplantation. Tissue Antigens. 2006;68(6):459–66. a systematic review and meta-analysis. Lancet (London, England). 2019;393(10185):2059–72. a systematic review and meta-analysis. Lancet (London, England). 2019;393(10185):2059–72. a systematic review and meta-analysis. Lancet (London, England). 2019;393(10185):2059–72. 8. Fryer J, Benedetti E, Perry E, Matas A. Antibody-mediated rejection of
an HLA-identical, ABO-incompatible kidney transplant after two failed
cadaver transplants. Transplantation. 1994;58(6):723–5. 19. Yamamoto F, McNeill P, Hakomori S. Genomic organization of human
histo-blood group ABO genes. Glycobiology. 1995;5(1):51–8. histo-blood group ABO genes. Glycobiology. 1995;5(1):51–8. 20. Garcia de Mattos Barbosa M, Cascalho M, Platt J. Accommodation in ABO-
incompatible organ transplants. Xenotransplantation. 2018;25(3):e12418. cadaver transplants. Transplantation. 1994;58(6):723–5. 9. Sugiyama K, Arai K, Aikawa A, Miyagi M, Ohara T, Hasegawa A, Muramatsu
M, Hirayama N, Tajima E, Kawamura T, Ogihara H, Hadano T, Nakano H. Reversibility from delayed hyperacute rejection in ABO-incompatible
renal transplantation: histopathological findings of renal allograft biopsy. Transpl Proc. 2005;37(2):701–4. 21. Wang XD, Liu JP, Fan Y, Song TR, Shi YY, Li YM, Lv YH, Li XH, Huang ZL, Lin T. Individualized preconditioning for ABO-incompatible living-donor kidney
transplantation: an initial report of 48 cases from China. Ann Transplant. 2020;25:e920224. 10. Warner P, Nester T. ABO-incompatible solid-organ transplantation. Am J
Clin Pathol. 2006;125:S87-94. 22. Kobayashi T, Saito K. A series of surveys on assay for anti-A/B antibody by
Japanese ABO-incompatible Transplantation Committee. Xenotransplan-
tation. 2006;13(2):136–40. 11. Montgomery J, Berger J, Warren D, James N, Montgomery R, Segev D. Outcomes of ABO-incompatible kidney transplantation in the United
States. Transplantation. 2012;93(6):603–9. 23. Shimmura H, Tanabe K, Ishikawa N, Tokumoto T, Takahashi K, Toma H. Role of anti-A/B antibody titers in results of ABO-incompatible kidney
transplantation. Transplantation. 2000;70(9):1331–5. 12. Gehrie E, Cates J, Nian H, Olson S, Young P. Blood Group A antigen expres-
sion on cardiac endothelium is highly individualized: possible implica-
tions for transplantation. Cardiovasc Pathol. 2013;22(4):251–6. 24. Funding
Thi
k Expression of glycolipid blood group antigens in single human
kidneys: change in antigen expression of rejected ABO incompatible
kidney grafts. Kidney Int. 1993;44(6):1289–97. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. 17. Huang J, Wang H, Fan ST, Zhao B, Zhang Z, Hao L, Huo F, Liu Y. The
national program for deceased organ donation in China. Transplantation. 2013;96(1):5–9. 17. Huang J, Wang H, Fan ST, Zhao B, Zhang Z, Hao L, Huo F, Liu Y. The
national program for deceased organ donation in China. Transplantation. 2013;96(1):5–9. •
fast, convenient online submission
•
thorough peer review by experienced researchers in your field
•
rapid publication on acceptance
•
support for research data, including large and complex data types
•
gold Open Access which fosters wider collaboration and increased citations
maximum visibility for your research: over 100M website views per year
•
At BMC, research is always in progress. Learn more biomedcentral.com/submissions
Ready to submit your research
Ready to submit your research ? Choose BMC and benefit from:
? Choose BMC and benefit from: •
fast, convenient online submission
•
thorough peer review by experienced researchers in your field
•
rapid publication on acceptance
•
support for research data, including large and complex data types
•
gold Open Access which fosters wider collaboration and increased citations
maximum visibility for your research: over 100M website views per year
•
At BMC, research is always in progress. Learn more biomedcentral.com/submissions
Ready to submit your research
Ready to submit your research ? Choose BMC and benefit from:
? Choose BMC and benefit from: •
fast, convenient online submission
•
thorough peer review by experienced researchers in your field
•
rapid publication on acceptance
•
support for research data, including large and complex data types
•
gold Open Access which fosters wider collaboration and increased citations
maximum visibility for your research: over 100M website views per year
•
At BMC, research is always in progress. Learn more biomedcentral.com/submissions
Ready to submit your research
Ready to submit your research ? Choose BMC and benefit from:
? Choose BMC and benefit from:
|
https://openalex.org/W4361871267
|
https://figshare.com/articles/journal_contribution/Supplementary_Figure_3_from_BRCA2_and_Nucleophosmin_Coregulate_Centrosome_Amplification_and_Form_a_Complex_with_the_Rho_Effector_Kinase_ROCK2/22386990/1/files/39832458.pdf
|
English
| null |
Supplementary Figure 1 from BRCA2 and Nucleophosmin Coregulate Centrosome Amplification and Form a Complex with the Rho Effector Kinase ROCK2
| null | 2,023
|
cc-by
| 218
|
Supplementary Figure S3 Wang et al. Wang et al. γ-Tubulin with
Hoechst
merge with
Hoechst
BRCA2 with
Hoechst
FLAG-
R3 BRCA2
FLAG-
R3 BRCA2
vector free
FLAG-vector
Fig. S3. NPM-BRCA2 interaction is critical for genomic stability. COS-7
cells were transfected with a FLAG-R3 BRCA2 (639–1508) expression vector or
the empty one. The cells were stained for γ-tubulin (red), BRCA2 (green), and
DNA (blue) Multinuclei are shown inside the white dotted line Arrows γ-Tubulin with
Hoechst
merge with
Hoechst
BRCA2 with
Hoechst
FLAG-
R3 BRCA2
FLAG-
R3 BRCA2 γ-Tubulin with
Hoechst
merge with
Hoechst
BRCA2 with
Hoechst
FLAG-
R3 BRCA2 γ-Tubulin with
Hoechst FLAG-
R3 BRCA2 G-
RCA2 FLAG-
R3 BRCA2 R3 BRCA2
vector free
FLAG-vector
Fig. S3. NPM-BRCA2 interaction is critical for genomic stability. COS-7
cells were transfected with a FLAG-R3 BRCA2 (639–1508) expression vector or
the empty one. The cells were stained for γ-tubulin (red), BRCA2 (green), and
DNA (blue). Multinuclei are shown inside the white dotted line. Arrows, vector free
FLAG-vector FLAG-vector Supplementary Figure S3 Supplementary Figure S3 vector free Fig. S3. NPM-BRCA2 interaction is critical for genomic stability. COS-7
cells were transfected with a FLAG-R3 BRCA2 (639–1508) expression vector or
the empty one. The cells were stained for γ-tubulin (red), BRCA2 (green), and
DNA (blue). Multinuclei are shown inside the white dotted line. Arrows,
centrosomes.
|
https://openalex.org/W1976446798
|
https://europepmc.org/articles/pmc2518853?pdf=render
|
English
| null |
Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks
|
PLOS computational biology/PLoS computational biology
| 2,008
|
cc-by
| 9,288
|
Introduction olites, and the slower motions reflect more physiologically relevant
transformations. Appreciation of this observation can result in
elucidating structure from the network and simplifying the
interactions. The reduction in dynamic dimensionality is based
on such pooling and the analysis of pooling is focused in the
underlying time scale hierarchy and its determinants. Under-
standing the time scale hierarchy and pooling structure of these
networks is critical to understanding network behavior and
simplifying it down to the core interactions. The network of interactions that occur between biological
components on a range of various spatial and temporal scales
confer hierarchical functionality in living cells. In order to
determine
how
molecular
events
organize
themselves
into
coherent physiological functions, in silico approaches are needed
to analyze how physiological functions emerge from the evolved
temporal structure of networks. Time scale decomposition is a
well-established, classical approach to dissecting network dynamics
and there is a notable history of analyzing the time scale hierarchy
in metabolic networks and matching the events that unfold on
each time scale with a physiological function [1–6]. This approach
enables the identification of the independent, characteristic time
scales for a dynamic system. In particular it has been possible
to decompose a cell-scale kinetic model of the human red blood
cell in time to show how its key metabolic demands are met
through a dynamic structure-function relationship. The underly-
ing principle is one of aggregation of concentration variables into
‘pools’ of concentrations that move in tandem on slower time
scales [5,7]. Top-down studies of dynamic characteristics of networks begin
with fully developed kinetic models that are formal representations
of large amounts of data about the chemistry and kinetics
component interactions. Network properties can be studied by
numerical simulations (that are condition-specific) or by analysis
(that often yield general model properties) of the model equations. Since
comprehensive
numerical
simulation
studies
become
intractable for larger networks and the identification of general
model properties are needed for the judicious simplification of
models, there is a need for analysis based methods in order to
characterize properties of dynamic networks. In this study we
present an in silico analysis method to determine pooling of
variables in complex dynamic models of biochemical reaction
networks. This method is used to study metabolic network models
and allows us to identify and analyze pool formation resulting from
the
underlying
stoichiometric,
thermodynamic,
and
kinetic
properties. Abstract The study of dynamic functions of large-scale biological networks has intensified in recent years. A critical component in
developing an understanding of such dynamics involves the study of their hierarchical organization. We investigate the
temporal hierarchy in biochemical reaction networks focusing on: (1) the elucidation of the existence of ‘‘pools’’ (i.e.,
aggregate variables) formed from component concentrations and (2) the determination of their composition and
interactions over different time scales. To date the identification of such pools without prior knowledge of their composition
has been a challenge. A new approach is developed for the algorithmic identification of pool formation using correlations
between elements of the modal matrix that correspond to a pair of concentrations and how such correlations form over the
hierarchy of time scales. The analysis elucidates a temporal hierarchy of events that range from chemical equilibration
events to the formation of physiologically meaningful pools, culminating in a network-scale (dynamic) structure–
(physiological) function relationship. This method is validated on a model of human red blood cell metabolism and further
applied to kinetic models of yeast glycolysis and human folate metabolism, enabling the simplification of these models. The
understanding of temporal hierarchy and the formation of dynamic aggregates on different time scales is foundational to
the study of network dynamics and has relevance in multiple areas ranging from bacterial strain design and metabolic
engineering to the understanding of disease processes in humans. Citation: Jamshidi N, Palsson B (2008) Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks. PLoS Comput Biol 4(9): e1000177. doi:10.1371/journal.pcbi.1000177 Received November 26, 2007; Accepted August 4, 2008; Published September 12, 2008 ceived November 26, 2007; Accepted August 4, 2008; Published September 12, 2008 Received November 26, 2007; Accepted August 4, 2008; Published September 12, 2008 Copyright: 2008 Jamshidi, Palsson. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. nding: This work was supported in part by a National Institutes of Health Training Grant to the Department of Bioengineering, Univ
ego. Competing Interests: The authors have declared that no competing interests exist. Competing Interests: The authors have declared that no competing interests exist. * E-mail: palsson@ucsd.edu * E-mail: palsson@ucsd.edu PLoS Computational Biology | www.ploscompbiol.org Neema Jamshidi, Bernhard Ø. Palsson* Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America Top-Down Analysis of Temporal Hierarchy in Biochemical
Reaction Networks Neema Jamshidi, Bernhard Ø. Palsson* September 2008 | Volume 4 | Issue 9 | e1000177 Citation: Jamshidi N, Palsson B (2008) Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks. PLoS Comput Biol 4(9): e1000177.
doi:10.1371/journal.pcbi.1000177 Method Development Dynamic description of networks. Linearizing the mass
conservation equations for a chemical reacting system around the
steady state yields the linear form of the dynamic mass balances, dx0 tð Þ
dt
~Jx0 tð Þ
ð1Þ Defining pools from modes. A column of the modal matrix
describes the participation of a concentration in each of the
linearly independent modes. When two concentrations (xi and xj)
become dynamically correlated beyond a particular time scale (say
after the kth time constant), the entries of the modal matrix in the
two corresponding columns are correlated with one another on the
subsequent time scales (Figure 2). This characteristic enables the
identification of the time scales that two concentrations would pool
together. ð1Þ where J is the n6n Jacobian matrix, and x9 ( = x2xss) is the
deviation vector of the concentration variables from the steady
state (xss). J describes the dynamical characteristics of the network
near the steady state. The properties of J can be analyzed using
matrix decomposition methods, and it is important for these
methods to capture the interactions between components across all
of the time scales of the network. where J is the n6n Jacobian matrix, and x9 ( = x2xss) is the
deviation vector of the concentration variables from the steady
state (xss). J describes the dynamical characteristics of the network
near the steady state. The properties of J can be analyzed using
matrix decomposition methods, and it is important for these
methods to capture the interactions between components across all
of the time scales of the network. Employing a geometric interpretation for this determination,
one can explicitly identify pool formation by calculating the angle
between columns (M21)i of the modal matrix, Temporal
decomposition. We
can
apply
a
similarity
transformation (see Materials and Methods) to J, J~M1L
1M1{1
ð2Þ ð2Þ H~cos qij
~
M{1
T
i : M{1
j
M{1
ð
ÞT
i
M{1
ð
Þj
ð5Þ ð5Þ where L is a diagonal matrix with the eigenvalues, that are the
negative reciprocal time constants [8]. The superscript star indicates
the possible presence of imaginary components in the matrices. Complex conjugate pairs can be removed by pre-multiplying by a
modified identity matrix with block diagonal ones at the rows and
columns in which the matrix has imaginary components. Author Summary Furthermore, different
steady states can be characterized as well, by recalculating the
Jacobian at the alternate steady states. Elucidating Network Pooling Structure Elucidating Network Pooling Structure dynamically independent ‘‘aggregates’’, or pooling of metabolites
into independent dynamic variables. Time scale decomposition can
be successfully performed only if the eigenvalues are well separated. When J is rank deficient, it implies the presence of dynamically
invariant pools reflecting chemically conserved moieties in the
network, whose sum total is constant. These vectors are not included
in the modal matrix. Author Summary Introduction The dynamics of biological networks characteristically span
large time scales (8 to 10 orders of magnitude), which contributes
to the challenge of analyzing and interpreting related models. However, there is structure in this dynamic hierarchy of events,
particularly in biochemical networks in which the fastest motions
generally correspond to the chemical equilibria between metab- September 2008 | Volume 4 | Issue 9 | e1000177 1 Author Summary Cellular metabolism describes the complex web of bio-
chemical transformations that are necessary to build the
structural components, to convert nutrients into ‘‘usable
energy’’ by the cell, and to degrade or excrete the by-
products. A critical aspect toward understanding metabo-
lism is the set of dynamic interactions between metabolites,
some of which occur very quickly while others occur more
slowly. To develop a ‘‘systems’’ understanding of how
networks operate dynamically we need to identify the
different processes that occur on different time scales. When
one moves from very fast time scales to slower ones, certain
components in the network move in concert and pool
together. We develop a method to elucidate the time scale
hierarchy of a network and to simplify its structure by
identifying these pools. This is applied to dynamic models of
metabolism for the human red blood cell, human folate
metabolism, and yeast glycolysis. It was possible to simplify
the structure of these networks into biologically meaningful
groups of variables. Because dynamics play important roles
in normal and abnormal function in biology, it is expected
that this work will contribute to an area of great relevance
for human disease and engineering applications. The modal matrix separates the dynamics of the network into a
series of dynamically independent motions [5,8], moving from the
fastest (top) modes to the slowest (bottom) modes as the time scales
lengthen (Figure 1B). Here we present an approach to the analysis
of the modal matrix that simplifies the elucidation of notable pools
without the need for intensive calculations of dynamic phase
portraits and auto-correlations functions in order to identify
biologically relevant interpretations of these modes as pools of
metabolites being created and consumed on different time scales
[2]. An illustrative ‘toy’ example of time scale decomposition is
described in the supplementary material (Figure S1). Table 2 summarizes some of the trade-offs between the
characterization of dynamics using the Jacobian matrix and
carrying out large numbers of dynamic simulations directly. Although carrying out dynamic simulations are not restricted to a
particular steady state, they are condition dependent (e.g. initial
conditions) and resource intensive. Hence for larger networks,
dynamic simulations are not a viable option. In contrast,
characterization of the pooling structure of networks via analysis
of the Jacobian requires only a single set of calculations to
characterize a particular steady state and this approach can be
applied to large and small networks alike. Method Development The
complex conjugate pairs arise in situations in which the motions of
these modes cannot be decomposed in time. The modal matrix,
M21, can then be used to define the modes, m, such that, in which M{1
i
refers to the magnitude of the ith column of the
modal matrix and qij refers to the angle between the ith and jth
columns of the modal matrix. However, if one were to simply
calculate the correlations between metabolites across all time
scales, in general no pooling would be observed among the
metabolites, even though there may be physiologically relevant
pooling between metabolites, that characteristically occur on
slower time scales. A simple illustration of this is depicted in by the
modal matrix in Figure 2, which highlights the need to
characterize aggregate pool formation of variables in the context
of progressively slower time scales. Hence this approach analyzes
progressive pooling across all of the network’s independent time
scales, in contrast to simulation based methods which are
dependent on a priori specification of the time scales of interest
for identifying correlations between metabolites. m~M{1x
ð3Þ ð3Þ which combined with Equation 1 results in, which combined with Equation 1 results in, dm
dt ~Lm
ð4Þ ð4Þ as described previously [5]. The rows in the modal matrix define as described previously [5]. The rows in the modal matrix define PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 2 Elucidating Network Pooling Structure Figure 1. Subspaces of the Jacobian matrix and different approaches for decomposing it into dynamically independent
interactions between metabolites. (A) The Jacobian acts as a linear operator mapping the dynamics onto the deviation variable. (B) The Modal
Matrix maps network dynamics onto independent time scales. Panels C and D illustrate two approaches to understanding the interactions between
metabolites on the different time scales. (C) Beginning from the fastest time scale and moving forward, components that move together on
subsequent time scales are lumped into an aggregate pool variable. The pooling pictorially for three different time scales in glycolysis and the
Rapoport-Leubering shunt in the red cell. The large blue dots indicate pool formation between two metabolites, signifying that these two
metabolites become coupled or correlated on slower times scales. Method Development In this case, glyceraldehyde 3-phosphate and dihydroxyacetone phosphate pool
together after the first time scale, the hexose phosphates pool together after the fourth time scale, and the triose phosphates pool together after the
eighth time scale. (D) Each time scale is analyzed independently and the interactions are defined in terms of the coefficients in the model and their
contribution to the cumulative sum of the modal coefficients. Analyzing all of the modes in this manner allows the identification of variables that are
dominant across multiple modes and identifying the time scales across which they are most active. Four fundamental subspaces are associated with J
and its mapping onto its time derivative. The key to temporal decomposition is the time-ordered removal of dynamic motions that lead to the step-
by-step increase in the null and left null spaces of J. doi:10.1371/journal.pcbi.1000177.g001 Figure 1. Subspaces of the Jacobian matrix and different approaches for decomposing it into dynamically independent
interactions between metabolites. (A) The Jacobian acts as a linear operator mapping the dynamics onto the deviation variable. (B) The Modal
Matrix maps network dynamics onto independent time scales. Panels C and D illustrate two approaches to understanding the interactions between
metabolites on the different time scales. (C) Beginning from the fastest time scale and moving forward, components that move together on
subsequent time scales are lumped into an aggregate pool variable. The pooling pictorially for three different time scales in glycolysis and the
Rapoport-Leubering shunt in the red cell. The large blue dots indicate pool formation between two metabolites, signifying that these two
metabolites become coupled or correlated on slower times scales. In this case, glyceraldehyde 3-phosphate and dihydroxyacetone phosphate pool
together after the first time scale, the hexose phosphates pool together after the fourth time scale, and the triose phosphates pool together after the
eighth time scale. (D) Each time scale is analyzed independently and the interactions are defined in terms of the coefficients in the model and their
contribution to the cumulative sum of the modal coefficients. Analyzing all of the modes in this manner allows the identification of variables that are
dominant across multiple modes and identifying the time scales across which they are most active. Four fundamental subspaces are associated with J
and its mapping onto its time derivative. Method Development The key to temporal decomposition is the time-ordered removal of dynamic motions that lead to the step-
by-step increase in the null and left null spaces of J. doi:10.1371/journal.pcbi.1000177.g001 metabolites, in which no aggregate pools form, there will be m sets of
pooling matrices. Conversely, for the extreme case in which all of the
metabolites form a single aggregate pool on a single time scale there
will only be a single pooling matrix. In order to identify the time scales at which pool formation
occurs, we compute the angle between two columns as a function
of an index k that runs from 1 to n time scales. As each row of the
modal matrix is removed (k increases by one) the angle is
recomputed to form a series of angles as a function of k; i.e., qij(k),
k = 1, 2, …, n. If the angle qij(k) is close to zero, the two columns
are correlated at and above that k value and the two corresponding
concentrations will move in tandem for the subsequent time scales,
thus forming an aggregate variable or a pool. The practical issue is
to determine when the angle is close enough to zero to make a call
on the formation of a pool. Defining dominant interactions for each mode. One can
quantitatively ascertain the contribution of each metabolite to each
mode by rank ordering the normalized mode and keeping only the
largest weights that add up to the specified cutoff percentage. At low
cut-off ranges, all metabolites with small contributions to the mode
will be zeroed out. The interactions across the modes can be mapped
on top of the interactions defined by the stoichiometric matrix in
order to compare and contrast the topological connectivity versus the
dynamic connectivity at time scales of interest. The pools can be described as a sum of matrix products over the
time scales of the network: Fts
i M{1Fm
i
ð6Þ PLoS Computational Biology | www.ploscompbiol.org Application of the Method ð6Þ The models studied here exhibit a significant span of time scales
(Table 1). A hierarchy pool formation on different time scales was
found in all networks based on the calculation of all pair wise qij(k)
in the models (Figures 1C and 2). The results can be presented in a
symmetric correlation tiled array, where each entry can be used to
represent k for a pair of concentrations. Figure 3 shows the result Fts
i is a binary diagonal matrix, with n2i non-zero elements on the
diagonal. Fm
i is a binary matrix with off-diagonal elements whenever
two columns meet a specific cutoff and can be combined into an
aggregate pool. Fts
i and Fm
i act on the modal matrix, by filtering out
modes or combining variables, respectively. For a network with m PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 3 Elucidating Network Pooling Structure Figure 2. Illustration of the progression correlation between two variables as fast time scales are removed. The set of dynamic
equations are linearized about a particular steady state. Applying a similarity transformation to the Jacobian, enables the calculation of the modal
matrix (depicted to the right). The rows of the matrix correspond to different time scales. When the ratios between two entries are constant, the two
metabolites pool together. After the second time scale, metabolites xi and xi+1 form an aggregate pool and after the fifth time scale, xi+2 joins the
pool. If the variables were compared across all time scales, no significant correlations would be observed. Hence, this simple example highlights the
need for a method to analyze correlations between metabolites with consideration of the characteristic time scales of the network. doi:10.1371/journal.pcbi.1000177.g002 Figure 2. Illustration of the progression correlation between two variables as fast time scales are removed. The set of dynamic
equations are linearized about a particular steady state. Applying a similarity transformation to the Jacobian, enables the calculation of the modal
matrix (depicted to the right). The rows of the matrix correspond to different time scales. When the ratios between two entries are constant, the two
metabolites pool together. After the second time scale, metabolites xi and xi+1 form an aggregate pool and after the fifth time scale, xi+2 joins the
pool. Application of the Method If the variables were compared across all time scales, no significant correlations would be observed. Hence, this simple example highlights the
need for a method to analyze correlations between metabolites with consideration of the characteristic time scales of the network. doi:10.1371/journal.pcbi.1000177.g002 Table 1. Summary of properties of the various kinetic models, particularly the Jacobian matrices of the networks. System
Dimension
Rank
Pooling
Conservation Pools
Effective Dimensionality
Time Scale Span
RBC
34
34
Complete
0
17
1.30E+10
Folate
10
9
Complete
1
6
4.88E+04
Yeast
20
20
Fragmented
0
13
7.50E+06
Pooling of the tiled modal arrays can be classified as complete (in which all elements pools together eventually) or fragmented. The number of conservation pools is
equal to the size of the left null space of the Jacobian. The effective dynamic dimensionality is the number of different time scales at which pooling occurs. The time
scale span is the ratio of the largest to smallest eigenvalue for each of the networks. doi:10.1371/journal.pcbi.1000177.t001 Pooling of the tiled modal arrays can be classified as complete (in which all elements pools together eventually) or fragmented. The number of conservation pools is
equal to the size of the left null space of the Jacobian. The effective dynamic dimensionality is the number of different time scales at which pooling occurs. The time
scale span is the ratio of the largest to smallest eigenvalue for each of the networks. doi:10.1371/journal.pcbi.1000177.t001 Pooling of the tiled modal arrays can be classified as complete (in which all elements pools together eventually) or fragmented. The number of conservation pools is
equal to the size of the left null space of the Jacobian. The effective dynamic dimensionality is the number of different time scales at which pooling occurs. The time
scale span is the ratio of the largest to smallest eigenvalue for each of the networks. doi:10 1371/journal pcbi 1000177 t001 Table 2. A comparison between the trade-offs for analyzing
the Jacobian around a particular steady state versus carrying
out dynamic simulations. Table 2. A comparison between the trade-offs for analyzing
the Jacobian around a particular steady state versus carrying
out dynamic simulations. of such an array for the human red cell. Since the array is
symmetric we can display both k and the modal coefficient ratio in
the pool (xi/xj) for each pair of concentrations; thus Table 2. Application of the Method A comparison between the trade-offs for analyzing
the Jacobian around a particular steady state versus carrying
out dynamic simulations. Jacobian Analysis
Dynamic Simulations
Generalized results
Conditions specific results
Scaleable
Intractable as the number of variables
increase
A single set of calculations will
characterize a particular steady state
Resource intensive, requires many
simulations in order to characterize
network pooling
Linear regime near a particular
steady state
May move from one steady state to
another
The approach presented here for analysis of the Jacobian in order to
characterize network dynamics allows generalized, comprehensive elucidation
of dynamics around a particular steady state directly and in a scaleable manner. In contrast, although the approach using dynamic simulations is not restricted
to a particular steady state, it is resource intensive and for larger networks it is
infeasible to characterize all of the different possible initial conditions, due to
combinatorial growth of the possible combinations. doi:10.1371/journal.pcbi.1000177.t002
PLoS Computational Biology | www ploscompbiol org N The lower left triangle of the tiled array indicates the time scale
k beyond which pooling occurs in the network. So for example,
G6P and F6P pool together after the fourth mode in the red
cell metabolic model. For the highly interconnected metabolic
network in the red cell, eventually, all of the metabolites pool
together. N The upper right triangle of the tiled array contains plots show
the ratios of the modal coefficients (xi/xj) for each of the
concentration pairs at all of the time scales above k for that
pair. For many of the concentration pairs, the ratio remains
fairly constant (glycolytic pools, pentose phosphate pools, etc)
past a certain time scale showing the relative contribution of
the compounds to a pool. N The pooling structure observed in Figure 3 is consistent with
the previous descriptions [2] and enable the simplification of
the network into equilibrium pools on fast time scales and
physiological ones on slower time scales (Figure 4). PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 PLoS Computational Biology | www.ploscompbiol.org 4 Elucidating Network Pooling Structure Figure 3. Time scale hierarchy of metabolic pool formation in the human red blood cell. The lower left triangle indicates the modes after
which pooling occurs between the corresponding metabolites (one being the fastest time scale). Application of the Method The upper right triangle are plots of the slopes
between the two metabolites for the remaining time scales after pool formation (the origin is always included in these approximations of the slopes),
color coded according to the time scale at which pooling occurs. Some of the metabolites such as the phosphoglycerates have fairly constant ratios
once they join aggregate pools. Others, such as ATP and ADP have varying ratios. These ratios change when interactions with other pathways
dominate on subsequent time scales, for example when glycolytic intermediates dominate on one time scale and nucleotide salvage metabolites
dominate on another, the respective interactions between ATP and ADP are affected differently. The cutoff value for cos(h) was 0.9. Abbreviations:
G6P, Glucose-6-phosphate; F6P, Fructose-6-phosphate; FDP. Fructose-1,6-bisphosphate; DHAP, Dihydroxyacetone phosphate; GAP, Glyceraldehyde-3-
phosphate; DPG13. 1,3-bisphosphoglycerate; DPG23, 2,3-bisphosphoglycerate; PG3, 3-phosphoglycerate; PG2, 2-phosphoglycerate; PEP,
Phosphoenolpyruvate; PYR, Pyruvate; LAC. Lactate; NADH, Nicotinamide adenine dinucleotide (reduced); GL6P. 6-Phospho-D-glucono-1,5-lactone;
GO6P, 6-Phospho-D-gluconate; NADPH, Nicotinamide adenine dinucleotide phosphate (reduced); GSH, glutathione (reduced); RU5P, Ribulose-5-
phosphate; R5P, Ribose-5-phosphate; X5P, Xylulose-5-phosphate; S7P, Sedoheptulose-7-phosphate; E4P, Erythrose-4-phosphate; ADO, Adenosine;
AMP, Adenosine monophosphate; ADP, Adenosine diphosphate; ATP, Adenosine triphohsphate; PRPP, 5-Phospho-D-ribose 1-diphosphate; IMP,
Inosine monophosphate; INO, Inosine; HX, Hypoxanthine; R1P, Ribose-1-phosphate; ADE, Adenine; NAI, Sodium; and KI, Potassium. doi:10.1371/journal.pcbi.1000177.g003 Figure 3. Time scale hierarchy of metabolic pool formation in the human red blood cell. The lower left triangle indicates the modes after
which pooling occurs between the corresponding metabolites (one being the fastest time scale). The upper right triangle are plots of the slopes
between the two metabolites for the remaining time scales after pool formation (the origin is always included in these approximations of the slopes),
color coded according to the time scale at which pooling occurs. Some of the metabolites such as the phosphoglycerates have fairly constant ratios
once they join aggregate pools. Others, such as ATP and ADP have varying ratios. These ratios change when interactions with other pathways
dominate on subsequent time scales, for example when glycolytic intermediates dominate on one time scale and nucleotide salvage metabolites
dominate on another, the respective interactions between ATP and ADP are affected differently. The cutoff value for cos(h) was 0.9. Abbreviations:
G6P, Glucose-6-phosphate; F6P, Fructose-6-phosphate; FDP. Fructose-1,6-bisphosphate; DHAP, Dihydroxyacetone phosphate; GAP, Glyceraldehyde-3-
phosphate; DPG13. 1,3-bisphosphoglycerate; DPG23, 2,3-bisphosphoglycerate; PG3, 3-phosphoglycerate; PG2, 2-phosphoglycerate; PEP,
Phosphoenolpyruvate; PYR, Pyruvate; LAC. Lactate; NADH, Nicotinamide adenine dinucleotide (reduced); GL6P. Application of the Method 6-Phospho-D-glucono-1,5-lactone;
GO6P, 6-Phospho-D-gluconate; NADPH, Nicotinamide adenine dinucleotide phosphate (reduced); GSH, glutathione (reduced); RU5P, Ribulose-5-
phosphate; R5P, Ribose-5-phosphate; X5P, Xylulose-5-phosphate; S7P, Sedoheptulose-7-phosphate; E4P, Erythrose-4-phosphate; ADO, Adenosine;
AMP, Adenosine monophosphate; ADP, Adenosine diphosphate; ATP, Adenosine triphohsphate; PRPP, 5-Phospho-D-ribose 1-diphosphate; IMP,
Inosine monophosphate; INO, Inosine; HX, Hypoxanthine; R1P, Ribose-1-phosphate; ADE, Adenine; NAI, Sodium; and KI, Potassium. doi:10.1371/journal.pcbi.1000177.g003 The time scale (k) for the formation of pools and the ratio between
a pair of concentrations are functions of three factors: network
stoichiometry (or topology), thermodynamics, and kinetic properties
of the transformations in the network. Viewing the dynamics of the
network in terms of the modal matrix and the pair-wise
concentration correlations on progressing time scales enables one
to consider the questions of (A) the thermodynamic versus kinetic
control of concentrations within the whole network and (B) the
delineation of kinetic versus topological decoupling in networks. making such thermodynamically neutral events lead to reduction in
effective dynamic dimensionality. Deviations from such behavior are
however observed, such as with 1,3 DPG and 2,3 DPG. Although the
free energy of formation of these two must are close (as approximated
by the group contribution method [9]), 2,3DPG does not pool
together with 1,3DPG until the 31st mode (Figure 3). Hence the
kinetic and allosteric regulatory ‘‘control’’ dominates. This ‘‘control’’
has physiological significance because 2,3DPG can regulate the
binding affinity of hemoglobin for oxygen and is maintained at a
higher concentration than the glycolytic intermediates. Other
examples in which kinetic ‘‘control’’ dominates include ATP and
NADPH, ADP and NADH, and G6P and ADP. Steady state kinetic versus thermodynamic equilibrium
effects. The thermodynamic equilibrium pools of the network can
be seen in Figure S2. Comparison of these pools with those in Figure 1
distinguishes between the equilibrium state and the kinetically driven
steady state. In many cases such comparisons show a thermodynamic
basis for pool formation, such as the hexose phosphates, the pentose
phosphates, and the triose phosphates. For metabolite pairs that are
thermodynamically close (with regards to the Gibbs free energy of
formation), the kinetics presumably have been adjusted to be fast, Kinetic and topological decoupling. Two striking features
of the tiled array are (1) the pooling between the majority of the
compounds occurs on the slowest time scales and (2) the slopes for
many of these are horizontal or vertical lines, implying dynami-
cally
independent
behavior. Application of the Method This
dynamically
independent
behavior may result from a lack of connectivity (topological PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 5 Elucidating Network Pooling Structure Figure 4. Converting human red cell metabolic network map into lumped pools according to time scale decomposition (adapted
from [26]). Pooling on fast time scales define the chemical equilibrium pools and on slower time scales the physiological pools. doi:10.1371/journal.pcbi.1000177.g004 Figure 4. Converting human red cell metabolic network map into lumped pools according to time scale decomposition (adapted
from [26]). Pooling on fast time scales define the chemical equilibrium pools and on slower time scales the physiological pools. doi:10.1371/journal.pcbi.1000177.g004 The tiled pooling array for folate metabolism was computed
(Figure 5). There were 7 independent time scales in the modal
matrix and one conserved folate moiety pool from the left null
space. From the array it is observed that the folate carrier branch decoupling) or from independent kinetics (e.g., kinetic decoupling
resulting from a zero order rate law). Thus, if compounds are
detected to be topologically decoupled in the tiling array they are
expected to dominate a particular mode. A kinetic or topologically decoupled compound will undergo the
largest changes in concentration and interactions with other
compounds during those time scales on which it plays a dominant
role the modes. After these time scales have been passed,
concentration changes are likely to be less significant and the
compounds could be viewed as joining an aggregate pool, but may
not be in a fixed ratio as would be dictated through strictly
thermodynamic or kinetic coupling. Figure 5. Tiled array of the hierarchical pool formation for
human folate metabolism (same layout and color coding as in
Figure 3). Abbreviations: 5MTHF, 5-methyltetrahydrofolate; THF,
tetrahydrofolate; DHF, dihydrofolate; CH2F, 5,10-methylenetrahydrofo-
late; CHF, 5,10-methenyltetrahydrofolate; 10FTHF, 10-formyltetrahydro-
folate; MET, methionine; SAM, S-adenosylmethionine; SAH, S-adenosyl-
homocysteine; and HCY, homocysteine. doi:10.1371/journal.pcbi.1000177.g005 Networks that are tightly connected in terms of stoichiometry
and kinetics will result in complete pooling of all metabolites on
the slowest time scales, which is seen in large part in the red cell
(Figure 1). There are examples of effectively uncoupled metabo-
lites in this model however. Sodium and potassium for example
are uncoupled from all metabolites except for the adenosine
phosphates, which results from topological decoupling, since the
only metabolites these ions interact with in the model are ATP and
ADP via the Na/K ATPase. PLoS Computational Biology | www.ploscompbiol.org Application of the Method On time scales slower than the minute time scales
(the sixth mode corresponds to ,6 minutes) the network boils
down to interactions between the folate pool and the methionine
pool. So on physiologically relevant time scales, the various
possible interactions depicted in Figure 7A simplify to shifting
between two carrier pools. (5MTHF, THF, DHF, CH2F, CHF, 10FTHF) of the network and
the methionine metabolism branch (MET, SAM, SAH, HCY) of
the network act fairly independently dynamically. S-adenosylme-
thionine (SAM) is the primary metabolite which joins the
interactions between the two branches. In order to identify if
these interactions are topologically driven, kinetically driven, or
combinations of both, one can plot the modes in which these
interactions are most significant (see Material and Methods). Figure 6 depicts the primary interactions on the slowest mode in
the network. It can be seen that SAM is not directly topologically
coupled to the folate branch, so the interactions between the two
branches,
mediated
by
SAM
is
driven
by
kinetic
effects. Additionally, note that although they pool together, SAM moves
in opposition to the folate carriers. The folate network is depicted
in Figure 7A and the progression of pooling over time is illustrated
in Figure 7B. On time scales slower than the minute time scales
(the sixth mode corresponds to ,6 minutes) the network boils
down to interactions between the folate pool and the methionine
pool. So on physiologically relevant time scales, the various
possible interactions depicted in Figure 7A simplify to shifting
between two carrier pools. Figure 6. An example of a graphical overlay of topological and
kinetic data for the dominant interacting metabolites for a
particular mode. The slowest mode in the folate network (,30 mi-
nute time scale) is shown. The green and red shaded elements reflect
the dynamic interactions between the metabolites on the 30 minute
time scale (the colors reflect positive and negative entries, respectively). The blue lines indicate topological connectivity (i.e. from the
stoichiometric matrix). doi:10.1371/journal.pcbi.1000177.g006 The tiled pooling array for the yeast glycolytic pathway was
computed (Figure 8). The pooling structure of the glycolytic pathway
is very similar to pool formation in the red cell, with glycolytic
intermediates aggregating together on the faster time scales. The doi:10.1371/journal.pcbi.1000177.g006 Figure 7. Human folate metabolism and hierarchical simplification into aggregate pools. (A) A map of the folate network described by
[23]. Application of the Method In contrast, pyruvate and lactate are
decoupled from the rest of glycolysis, even though they are
topologically connected to some of them, thus the decoupling is
driven by kinetic effects. Figure 5. Tiled array of the hierarchical pool formation for
human folate metabolism (same layout and color coding as in
Figure 3). Abbreviations: 5MTHF, 5-methyltetrahydrofolate; THF,
tetrahydrofolate; DHF, dihydrofolate; CH2F, 5,10-methylenetrahydrofo-
late; CHF, 5,10-methenyltetrahydrofolate; 10FTHF, 10-formyltetrahydro-
folate; MET, methionine; SAM, S-adenosylmethionine; SAH, S-adenosyl-
homocysteine; and HCY, homocysteine. doi:10.1371/journal.pcbi.1000177.g005 The tiled arrays can be used to define the ‘effective dynamic
dimensionality’ of the models by counting the number of different
time scales during which two or more variables form an aggregate
pool. For the networks considered, the effective dynamic dimension-
ality reduced the dimension by one-third to one-half (see Table 1). September 2008 | Volume 4 | Issue 9 | e1000177 PLoS Computational Biology | www.ploscompbiol.org 6 Elucidating Network Pooling Structure Figure 6. An example of a graphical overlay of topological and
kinetic data for the dominant interacting metabolites for a
particular mode. The slowest mode in the folate network (,30 mi-
nute time scale) is shown. The green and red shaded elements reflect
the dynamic interactions between the metabolites on the 30 minute
time scale (the colors reflect positive and negative entries, respectively). The blue lines indicate topological connectivity (i.e. from the
stoichiometric matrix). doi:10.1371/journal.pcbi.1000177.g006 (5MTHF, THF, DHF, CH2F, CHF, 10FTHF) of the network and
the methionine metabolism branch (MET, SAM, SAH, HCY) of
the network act fairly independently dynamically. S-adenosylme-
thionine (SAM) is the primary metabolite which joins the
interactions between the two branches. In order to identify if
these interactions are topologically driven, kinetically driven, or
combinations of both, one can plot the modes in which these
interactions are most significant (see Material and Methods). Figure 6 depicts the primary interactions on the slowest mode in
the network. It can be seen that SAM is not directly topologically
coupled to the folate branch, so the interactions between the two
branches,
mediated
by
SAM
is
driven
by
kinetic
effects. Additionally, note that although they pool together, SAM moves
in opposition to the folate carriers. The folate network is depicted
in Figure 7A and the progression of pooling over time is illustrated
in Figure 7B. Application of the Method (B) An illustration of progressive pool formation across the first 4 time scales for the folate network based on the results from Figure 5. Beyond
the first time scale pools form between CHF and CH2F; and 5MTHF, 10FTHF, SAM; and MET and SAH. DHF and THF form a pool beyond the second
time scale. Beyond the third time scale CH2F/CHF join the 5MTHF/10FTHF/SAM pool. Beyond the fourth time scale HCY joins the MET/SAH pool. Ultimately, on time scales on the order of a minute and slower, interactions between the pools of folate carriers and methionine metabolites interact. doi:10.1371/journal.pcbi.1000177.g007 Figure 7. Human folate metabolism and hierarchical simplification into aggregate pools. (A) A map of the folate network described by
[23]. (B) An illustration of progressive pool formation across the first 4 time scales for the folate network based on the results from Figure 5. Beyond
the first time scale pools form between CHF and CH2F; and 5MTHF, 10FTHF, SAM; and MET and SAH. DHF and THF form a pool beyond the second
time scale. Beyond the third time scale CH2F/CHF join the 5MTHF/10FTHF/SAM pool. Beyond the fourth time scale HCY joins the MET/SAH pool. Ultimately, on time scales on the order of a minute and slower, interactions between the pools of folate carriers and methionine metabolites interact. doi:10.1371/journal.pcbi.1000177.g007 September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 PLoS Computational Biology | www.ploscompbiol.org PLoS Computational Biology | www.ploscompbiol.org 7 Elucidating Network Pooling Structure Figure 8. Tiled array of the hierarchical pool formation for the yeast glycolytic pathway (same layout and color coding as in
Figure 3). Glycolytic intermediates and adenosine phosphates pool together on fast time scales. Fragmented pooling is also observed (i.e. there
were 0 entries in the slowest mode, indicating that on the slowest time scale, all of the components in the network do not move together in a
lumped pool). GLC, intracellular glucose; GLCX, extracellular glucose; G6P, glucose 6-phosphate; F6P, fructose 6-phosphate; FBP, fructose 1,6-
bisphosphate; GAP, glyceraldehyde 3-phosphate; DHAP, dihydroxyacetone phosphate; GLYC, intracellular glycerol; GLYCX, extracellular glycerol; BPG,
1,3-bisphosphoglycerate; PEP, phosphoenol pyruvate; PYR, pyruvate; ACA, intracellular acetaldehyde; ACAx, extracellular acetaldehyde; EtOH,
intracellular ethanol; EtOHx, extracellular ethanol; NADH, nicotinamide adenine dinucleotide (reduced form); ATP. adenosine triphosphate; ADP,
adenosine diphosphate. doi:10.1371/journal.pcbi.1000177.g008 Figure 8. Application of the Method Comparing
the
topological
versus
kinetic
interactions in a graphical format (not shown) illustrates that the
lack of interactions by acetate (ACA) and cyanide (CNX) with the
other components in the network are due to topological constraints. adenosine phosphates also pool together very quickly. A feature of
the tiled array not observed with the other models considered is
fragmentation of the pooling structure. This implies that unlike the
other two models considered, all of the metabolites do not eventually
move together in fixed ratios on the slowest time scales. These effects
can be driven by topological properties or kinetic properties of the
network
as
well. Comparing
the
topological
versus
kinetic
interactions in a graphical format (not shown) illustrates that the
lack of interactions by acetate (ACA) and cyanide (CNX) with the
other components in the network are due to topological constraints. The fragmented pooling reflects the fact that interactions between
ACA and CNX and the rest of the network can only occur during
particular time scales. These constraints however dictate much of the
overall behavior of the network. The fragmented pooling observed in
Figure 8 result in a simplified view of the network built around the
transporters, as seen in Figure 9. Figure 9. Simplified model of the yeast glycolytic pathway
dictated by the fragmented pooling of the network. The
glycolytic and redox potentials are similar to those in the red cell. The adenosine phosphate potential is only composed of ATP and ADP. The NADH/NAD ratio determines the redox interactions with glycolysis,
glycogen, and conversion between acetaldehyde and ethanol. doi:10.1371/journal.pcbi.1000177.g009 Taken together, in this study we: (1) developed top-down
approaches for the computationally driven delineation of pools, (2)
showed how to distinguish between topological, kinetic and
thermodynamic basis for pool formation, and (3) applied the methods
to analyze the dynamic structure of metabolic network models in
yeast and humans. The application of these methods enabled the
simplification of the networks based on the dynamic pooling of
metabolites on progressive time scales and the identification of the key
metabolic interactions on the slower time scales. Figure 9. Simplified model of the yeast glycolytic pathway
dictated by the fragmented pooling of the network. The
glycolytic and redox potentials are similar to those in the red cell. The adenosine phosphate potential is only composed of ATP and ADP. The NADH/NAD ratio determines the redox interactions with glycolysis,
glycogen, and conversion between acetaldehyde and ethanol. PLoS Computational Biology | www.ploscompbiol.org Application of the Method Tiled array of the hierarchical pool formation for the yeast glycolytic pathway (same layout and color coding as in
Figure 3). Glycolytic intermediates and adenosine phosphates pool together on fast time scales. Fragmented pooling is also observed (i.e. there
were 0 entries in the slowest mode, indicating that on the slowest time scale, all of the components in the network do not move together in a
lumped pool). GLC, intracellular glucose; GLCX, extracellular glucose; G6P, glucose 6-phosphate; F6P, fructose 6-phosphate; FBP, fructose 1,6-
bisphosphate; GAP, glyceraldehyde 3-phosphate; DHAP, dihydroxyacetone phosphate; GLYC, intracellular glycerol; GLYCX, extracellular glycerol; BPG,
1,3-bisphosphoglycerate; PEP, phosphoenol pyruvate; PYR, pyruvate; ACA, intracellular acetaldehyde; ACAx, extracellular acetaldehyde; EtOH,
intracellular ethanol; EtOHx, extracellular ethanol; NADH, nicotinamide adenine dinucleotide (reduced form); ATP. adenosine triphosphate; ADP,
adenosine diphosphate. doi:10 1371/journal pcbi 1000177 g008 doi:10.1371/journal.pcbi.1000177.g008 adenosine phosphates also pool together very quickly. A feature of
the tiled array not observed with the other models considered is
fragmentation of the pooling structure. This implies that unlike the
other two models considered, all of the metabolites do not eventually
move together in fixed ratios on the slowest time scales. These effects
can be driven by topological properties or kinetic properties of the
network
as
well. Comparing
the
topological
versus
kinetic
interactions in a graphical format (not shown) illustrates that the
lack of interactions by acetate (ACA) and cyanide (CNX) with the
other components in the network are due to topological constraints. The fragmented pooling reflects the fact that interactions between
ACA and CNX and the rest of the network can only occur during
particular time scales. These constraints however dictate much of the
overall behavior of the network. The fragmented pooling observed in
Figure 8 result in a simplified view of the network built around the
transporters, as seen in Figure 9. subsequent
time
scales. Furthermore,
metabolites
that
are
connected to multiple pathways are likely to have change ratios
even after they begin pooling. This is observed for ATP and ADP adenosine phosphates also pool together very quickly. A feature of
the tiled array not observed with the other models considered is
fragmentation of the pooling structure. This implies that unlike the
other two models considered, all of the metabolites do not eventually
move together in fixed ratios on the slowest time scales. These effects
can be driven by topological properties or kinetic properties of the
network
as
well. Materials and Methods The method developed above was developed, tested, and
implemented in Mathematica (Wolfram Research, Chicago, IL)
version 5.2. The models analyzed herein: the model of human red
cell metabolism [20–22], human folate metabolism [23], and yeast
glycolysis [24] were implemented in Mathematica. For each model, a stable steady state was identified by integrating
the equations over time until the concentration variables no longer
changed (error ,1610210, see Table S1). The Jacobian was then
calculated symbolically at that steady state condition. A growing number of large-scale kinetic models of biochemical
reaction networks are becoming available (e.g. http://www.cellml. org/, http://www.siliconcell.net/). There are also growing compi-
lations of information regarding enzyme kinetics (e.g., http://www. brenda-enzymes.info/,
http://sabio.villa-bosch.de/SABIORK/),
which portend the development and availability of more kinetic
models. Since dynamics simulations are not a viable approach for the
comprehensive characterization of pool formation for larger models,
there is a need for analysis based approaches to identify these general
characteristics in metabolic networks. Temporal decomposition was carried out as described in the
Results/Discussion section. Briefly for a general case, a similarity
transformation [8] of a square matrix, A, is given by A = DLD21
in which D is invertible (by definition) and L is a diagonal matrix. D is an orthogonal matrix composed of eigenvectors correspond-
ing to the entries of L (the eigenvalues). When the Jacobian matrix
for a first order differential equation with respect to time is
decomposed in this manner, the negative reciprocals of the
eigenvalues correspond to the characteristic time scales for the
corresponding
modes
[8]
(this
is
immediately
clear
upon
integration of Equation 4). All three of the models considered
here exhibited at least one pair of complex conjugate eigenvalues
at the steady states considered, hence the corresponding complex
conjugate modes were combined in order to eliminate oscillating
motions. The pooling approaches developed here were based on
identifying the dynamically independent times scales and their
corresponding modes. The principle pooling approach considered
here was based on a particular calculation given by the matrix
product, M{1
T M{1
ð7Þ ð7Þ The calculations for the correlations across progressive time
scales were carried out as described in Results/Discussion. Once
the modal matrix, M21, was calculated, all pairwise angles
between the metabolites (columns of the modal matrix) were
calculated (see Equation 5). The modal matrix is rank ordered
from the fastest (k = 1) to the slowest (k = n) modes. Materials and Methods The angles
between the columns of the modal matrix were recalculated n21
more times, in which an additional row of the modal matrix is
zeroed out at each iteration. For example at the third iteration
(k = 2), the first two rows of the modal matrix have been zeroed
out. The spectrum of correlation cut-off values for pooling were
considered from 10% to 99%. Cut-off values in the range 85% to
95% resulted in pooling of variables most consistent with the
known pooling structures of the human red cell [2,5]. A value of
90% was used as the correlation cutoff for the red cell, folate, and
yeast glycolysis models. The angle between two zero vectors was
classified as undefined and the angle between any zero vector and
another vector with at least one non-zero element was defined as
90u. Fragmentation of the pooling structure, in the strictest sense,
was identified by any 0 entry (or ,,10213) in the final row of the
metabolite modal matrix. In order to identify pools of metabolites, it was necessary to
sequentially eliminate rows and recalculate the product, however it
is worth noting that the matrix product in Equation 7 reflects the
‘dynamic connectivity’ of the network. These collective analyses of
the modal matrix allowed the subsequent identification of pools,
effective dimensionality reduction, differentiation between kinetic
and topological properties, and characterizing the component
condition numbers and strength of interactions between compo-
nents in the network. There has been an increased interest in the analysis of the
intrinsic characteristics of the growing number of available large-
scale kinetic biological network models [10–14]. The systematic,
algorithmic approach described herein demonstrated a general
approach to pool identification, thus demonstrating how top-down
analyses can be used to identify the hierarchical interactions
between components over the span of time scales and assist in the
simplification, analysis, and interpretation of network capabilities. This type of an analysis thus helps to link the component
interactions to the overall physiological functions and how such
functions can be affected by genetic parameters and how they
respond to environmental conditions. Values for the Gibbs standard free energies of formation for the
metabolites in the human red cell model were used from [25]. Elucidating Network Pooling Structure Elucidating Network Pooling Structure in the human red blood cell (Figure 3). These metabolites interact
with glycolysis, the pentose phosphates, and the nucleotide salvage
pathway and these interactions vary as the time scales are
dominated by the different pathways. Conversely, the ATP/ADP
ratio is fairly fixed and uniform in the yeast glycolytic model. This
appears to be a result of the fact that there is only one major
pathway that interacts with ATP and ADP. Further investigations
into when and why pooling ratios change may lead to a richer
appreciation of the integrated dynamic structure of metabolic
networks. Additionally it was observed that the pooling structure
may changes about different steady states. For example, in the
human red cell changing the magnitude of the energy load will
shift the time scale of the ATPase and hence alter the pooling of
the network (not shown). This is also an area in which further
investigation will yield an appreciation of altered dynamics
corresponding to different steady state conditions. ments of the fluxome and metabolome at various time points,
under different perturbations can be analyzed in terms of overall
dynamics and used to validate the model when computed and
measured results agree and alternatively used to highlight areas
where further revisions are needed when they disagree. This will
conceivably add a new dimension to the analysis of metabolism on
the genome-scale. Materials and Methods Recently, with the continued development of technologies and
experimental procedures to calculate cellular fluxes using iso-
topomer
data
and
to
carry
out
quantitative
metabolomic
measurements on a larger scale [15–19], a more complete
biochemical characterization of cells has become possible. The
approach and analysis presented herein, using the Jacobian to
characterize network and cellular level dynamics will benefit from
and serve to benefit the utility of these large datasets. Measure- PLoS Computational Biology | www.ploscompbiol.org Application of the Method doi:10.1371/journal.pcbi.1000177.g009 There were some observations in the results worth pointing to
suggest further areas worthy of investigation. The pooling ratios
between metabolites are not always constant and metabolites that
pool early on are more likely to have changing ratios on September 2008 | Volume 4 | Issue 9 | e1000177 8 References 15. Bartnik BL, Hovda DA, Lee PW (2007) Glucose metabolism after traumatic
brain injury: estimation of pyruvate carboxylase and pyruvate dehydrogenase
flux by mass isotopomer analysis. J Neurotrauma 24: 181–194. 1. Heinrich R, Schuster S, Holzhutter HG (1991) Mathematical analysis of
enzymic reaction systems using optimization principles. Eur J Biochem 201:
1–21. y
p
y
J
16. Brauer MJ, Yuan J, Bennett BD, Lu W, Kimball E, et al. (2006) Conservation of
the metabolomic response to starvation across two divergent microbes. Proc Natl
Acad Sci U S A 103: 19302–19307. 2. Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BO, Edwards JS (2002)
Description and analysis of metabolic connectivity and dynamics in the human
red blood cell. Biophys J 83: 646–662. 17. Schaub J, Mauch K, Reuss M (2007) Metabolic flux analysis in Escherichia coli
by integrating isotopic dynamic and isotopic stationary
13C labeling data. Biotechnol Bioeng 99: 1170–1185. 3. Kholodenko BN, Schuster S, Garcia J, Westerhoff HV, Cascante M (1998)
Control analysis of metabolic systems involving quasi-equilibrium reactions. Biochim Biophys Acta 1379: 337–352. 18. Vo TD, Paul Lee WN, Palsson BO (2007) Systems analysis of energy metabolism
elucidates the affected respiratory chain complex in Leigh’s syndrome. Mol
Genet Metab 91: 15–22. 4. Okino MS, Mavrovouniotis ML (1998) Simplification of mathematical models of
chemical reaction systems. Chem Rev 98: 391–408. 5. Palsson BO, Joshi A, Ozturk SS (1987) Reducing complexity in metabolic
networks: making metabolic meshes manageable. Fed Proc 46: 2485–2489. 19. Zhao J, Baba T, Mori H, Shimizu K (2004) Global metabolic response of
Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments
and the measurement of enzyme activities. Appl Microbiol Biotechnol 64:
91–98. 6. Heinrich R, Sonntag I (1982) Dynamics of non-linear biochemical systems and
the evolutionary significance of time hierarchy. Biosystems 15: 301–316. e evolutionary significance of time hierarchy. Biosystems 15: 301–316 7. Reich J, Selkov E (1981) Energy Metabolism of the Cell: A Theoretical Treatise. New York: Academic Press. 20. Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO (2001) Dynamic
simulation of the human red blood cell metabolic network. Bioinformatics 17:
286–287. 8. Strang G (2003) Introduction to Linear Algebra. Wellesley: Wellesley-Cam-
bridge. 21. Joshi A, Palsson BO (1989) Metabolic dynamics in the human red cell. Part I—a
comprehensive kinetic model. J Theor Biol 141: 515–528. 9. Mavrovouniotis ML (1991) Estimation of standard Gibbs energy changes of
biotransformations. J Biol Chem 266: 14440–14445. Acknowledgments We thank Dr. Christopher Henry for helpful correspondence and
determination of Gibbs free energy of formation calculations for various
metabolites. Supporting Information Figure S1
Illustrative example of time scale decomposition. An
Illustrative example of modal decomposition for a toy network. The dynamics of 3 reactions involving 6 metabolites is analyzed in
terms of the Jacobian matrix. Time scale decomposition is carried PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 9 Elucidating Network Pooling Structure out along with simulations and determination of the pooling
structure for this toy example. Table S1
Steady state concentrations and fluxes for folate, yeast,
and red blood cell. Found at: doi:10.1371/journal.pcbi.1000177.s003 (0.02 MB XLS) Found at: doi:10.1371/journal.pcbi.1000177.s001 (0.09 MB PDF) Found at: doi:10.1371/journal.pcbi.1000177.s001 (0.09 MB PDF) Figure
S2
Standard
free
energy
of
formation
ratios
for
metabolites in the human red blood cell. The lower left triangle
of the tiled array depicts a matrix with the ratios of the Gibbs free
energy of formation between the metabolites in the red blood cell
metabolic network. Ratios below 0.85 or above 1.15 were filtered
out and not shown. The remaining entries (blackened entries)
indicate expected pools if thermodynamic considerations alone
determined the behavior of the network in a closed system. Author Contributions Conceived and designed the experiments: NJ BOP. Performed the
experiments: NJ. Analyzed the data: NJ. Wrote the paper: NJ BOP. Conceived and designed the experiments: NJ BOP. Performed the
experiments: NJ. Analyzed the data: NJ. Wrote the paper: NJ BOP. Found at: doi:10.1371/journal.pcbi.1000177.s002 (0.06 MB PDF) PLoS Computational Biology | www.ploscompbiol.org References 22. Joshi A, Palsson BO (1990) Metabolic dynamics in the human red cell. Part III—
metabolic reaction rates. J Theor Biol 142: 41–68. 10. Famili I, Mahadevan R, Palsson BO (2005) k-Cone analysis: determining all
candidate values for kinetic parameters on a network scale. Biophys J 88:
1616–1625. 23. Reed MC, Nijhout HF, Neuhouser ML, Gregory JF III, Shane B, et al. (2006) A
mathematical model gives insights into nutritional and genetic aspects of folate-
mediated one-carbon metabolism. J Nutr 136: 2653–2661. 11. Holzhutter HG (2006) The generalized flux-minimization method and its
application to metabolic networks affected by enzyme deficiencies. Biosystems
83: 98–107. 24. Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, et al. (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the
constituent enzymes? Testing biochemistry. Eur J Biochem 267: 5313–5329. 12. Holzhutter S, Holzhutter HG (2004) Computational design of reduced
metabolic networks. ChemBioChem 5: 1401–1422. constituent enzymes? Testing biochemistry. Eur J Biochem 267: 5313 25. Henry CS, Broadbelt LJ, Hatzimanikatis V (2007) Thermodynamics-based
metabolic flux analysis. Biophys J 92: 1792–1805. 13. Klipp E (2007) Modelling dynamic processes in yeast. Yeast 24: 943–959. 14. Steuer R, Gross T, Selbig J, Blasius B (2006) Structural kinetic modeling of
metabolic networks. Proc Natl Acad Sci U S A 103: 11868–11873. 26. Jamshidi N (2000) A Model of the Human Red Blood Cell Metabolism: The In
Silico Erythrocyte. La Jolla: University of California San Diego. PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 10
|
https://openalex.org/W2003033471
|
https://europepmc.org/articles/pmc8477181?pdf=render
|
English
| null |
FOXO3a-mediated suppression of the self-renewal capacity of sphere-forming cells derived from the ovarian cancer SKOV3 cell line by 7-difluoromethoxyl-5,4′-di-n-octyl genistein
|
Molecular Medicine Reports
| 2,014
|
cc-by
| 625
|
Mol Med Rep 9: 1982‑1988, 2014; DOI: 10.3892/mmr.2014.2012 Mol Med Rep 9: 1982‑1988, 2014; DOI: 10.3892/mmr.2014.2012 Subsequently to the publication of this paper, an interested
reader drew to the authors’ attention that strikingly similar
western blot data were shown in Fig. 2 (to portray the Nagon
data in Fig. 2A and the CD133 data in Fig. 2B), and the same
data also appeared to have been included in Fig. 4 (to show the
p‑FOXO3a data). After having examined their original data,
the authors have realized that these figures were inadvertently
assembled incorrectly Figure 2. SKOV3 cell‑line‑derived SFCs possess properties of OCSLCs. (A) Western immunoblot analysis demonstrated that BMI1, Nagon and SOX2
were highly expressed in SFCs derived from SKOV3 cells compared with the
PC. (B) Western immunoblot analysis demonstrated that CD133, CD44 and
ADLH1 were highly expressed in SFCs derived from SKOV3 cells compared
with the PC. (C) H&E staining revealed that the histological features of
SFC‑derived xenografted tumors were similar to those identified for parental
SKOV3 cells (magnification, x100). SFCs, sphere‑forming cells; OCSLCs,
ovarian cancer stem‑like cells; PC, parental cells. The corrected versions of Figs. 2 and 4, showing the correct
data for the CD133 experiment in Fig. 2B and the p‑FOXO3a
experiment in Fig. 4, are shown opposite. Note that these errors
did not significantly affect the results or the conclusions
reported in this paper, and all the authors agree to this
Corrigendum. Furthermore, the authors apologize to the
readership for any inconvenience caused. Figure 4. DFOG reduces FOXO3a phosphorylation and CSC marker
expression of OCSLCs derived from SKOV3 cells. (A) The phosphorylated
form of the FOXO3a protein was highly expressed in SFCs derived from
SKOV3 cells compared with corresponding PCs. (B) Treatment with DFOG
downregulated the expression of phosphorylated FOXO3a in SFCs derived
from SKOV3 cells. (C) Treatment with DFOG downregulated the expression
of the self‑renewal associated proteins, including BMI1, Nagon and SOX2 in
SFCs derived from SKOV3 cells. (D) Treatment with DFOG downregulated
the expression of CSC markers, including CD133, CD44 and ALDH1 in
SFCs derived from SKOV3 cells. DFOG, 7‑difluoromethoxyl‑5,4’‑di‑n‑octyl
genistein; CSC, cancer stem cell; OCSLCs, ovarian cancer stem‑like cells;
SFCs, sphere‑forming cells; PCs, parental cells. Figure 4. DFOG reduces FOXO3a phosphorylation and CSC marker
expression of OCSLCs derived from SKOV3 cells. (A) The phosphorylated
form of the FOXO3a protein was highly expressed in SFCs derived from
SKOV3 cells compared with corresponding PCs. This work is licensed under a Creative Commons
Attribution 4.0 International (CC BY 4.0) License. CORRIGENDUM DOI: 10.3892/mmr.2021.12449 DOI: 10.3892/mmr.2021.12449 FOXO3a‑mediated suppression of the self‑renewal capacity
of sphere‑forming cells derived from the ovarian cancer
SKOV3 cell line by 7‑difluoromethoxyl‑5,4’‑di‑n‑octyl
genistein MOLECULAR MEDICINE REPORTS 24: 809, 2021 MOLECULAR MEDICINE REPORTS 24: 809, 2021 Figure 2. SKOV3 cell‑line‑derived SFCs possess properties of OCSLCs. (A) Western immunoblot analysis demonstrated that BMI1, Nagon and SOX2
were highly expressed in SFCs derived from SKOV3 cells compared with the
PC. (B) Western immunoblot analysis demonstrated that CD133, CD44 and
ADLH1 were highly expressed in SFCs derived from SKOV3 cells compared
with the PC. (C) H&E staining revealed that the histological features of
SFC‑derived xenografted tumors were similar to those identified for parental
SKOV3 cells (magnification, x100). SFCs, sphere‑forming cells; OCSLCs,
ovarian cancer stem‑like cells; PC, parental cells. Mol Med Rep 9: 1982‑1988, 2014; DOI: 10.3892/mmr.2014.2012 (B) Treatment with DFOG
downregulated the expression of phosphorylated FOXO3a in SFCs derived
from SKOV3 cells. (C) Treatment with DFOG downregulated the expression
of the self‑renewal associated proteins, including BMI1, Nagon and SOX2 in
SFCs derived from SKOV3 cells. (D) Treatment with DFOG downregulated
the expression of CSC markers, including CD133, CD44 and ALDH1 in
SFCs derived from SKOV3 cells. DFOG, 7‑difluoromethoxyl‑5,4’‑di‑n‑octyl
genistein; CSC, cancer stem cell; OCSLCs, ovarian cancer stem‑like cells;
SFCs, sphere‑forming cells; PCs, parental cells.
|
https://openalex.org/W2756478017
|
https://europepmc.org/articles/pmc5607599?pdf=render
|
English
| null |
Implementation of WHO multimodal strategy for improvement of hand hygiene: a quasi-experimental study in a Traditional Chinese Medicine hospital in Xi’an, China
|
Antimicrobial resistance and infection control
| 2,017
|
cc-by
| 5,766
|
* Correspondence: w.xq1123@163.com
1Department of Infection Control, Xi’an Hospital of Traditional Chinese Medicine,
No.69 Feng Cheng 8th Road, Weiyang District, Xi’an 710021, China
Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Implementation of WHO multimodal
strategy for improvement of hand hygiene:
a quasi-experimental study in a Traditional
Chinese Medicine hospital in Xi’an, China Li Shen1, Xiaoqing Wang1*
, Junming An2, Jialu An3, Ning Zhou1, Lu Sun1, Hong Chen1, Lin Feng4, Jing Han3
and Xiaorong Liu3 RESEARCH
Open Access
Implementation of WHO multimodal
strategy for improvement of hand hygiene:
a quasi-experimental study in a Traditional
Chinese Medicine hospital in Xi’an, China
Li Shen1, Xiaoqing Wang1*
, Junming An2, Jialu An3, Ning Zhou1, Lu Sun1, Hong Chen1, Lin Feng4, Jing Han3
and Xiaorong Liu3
Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98
DOI 10.1186/s13756-017-0254-4 RESEARCH
Open Access
Implementation of WHO multimodal
strategy for improvement of hand hygiene:
a quasi-experimental study in a Traditional
Chinese Medicine hospital in Xi’an, China
Li Shen1, Xiaoqing Wang1*
, Junming An2, Jialu An3, Ning Zhou1, Lu Sun1, Hong Chen1, Lin Feng4, Jing Han3
and Xiaorong Liu3
Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98
DOI 10.1186/s13756-017-0254-4 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98
DOI 10.1186/s13756-017-0254-4 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98
DOI 10.1186/s13756-017-0254-4 Part II: Observation of compliance and correctness before
and after intervention Part II: Observation of compliance and correctness before
and after intervention Part II: Observation of compliance and correctness before
and after intervention g
Healthcare-associated infection (HAI) represents a major
burden and safety issue for patients in the developing
countries, with severe and greatly underestimated effect
on patients and health care systems [1]. According to the
survey of National HAI Surveillance System, in 2014, at
least 26,972 cases of HAI arose in patients admitted to
hospital in China [2]. HAI resulted in prolonged length of
hospital stay, direct economic loss, morbidity and mortal-
ity among hospitalized patients [3]. A recent study in
China identified that the average cost of hospitalization in-
creased ¥13,839.16(€1792.64) due to HAI [4]. The hands
of healthcare workers (HCWs) can be a major mode of
transmission of microbial pathogens by touching the en-
vironment or patients’ skin during healthcare delivery,
which supports that hand hygiene (HH) is a critical com-
ponent of a bundle approaches for preventing and con-
trolling HAIs [5–9]. The World Health Organization
(WHO) launched a multimodal strategy in 2009 to im-
prove HH practice worldwide, which includes 5 important
components: (1) system change, (2) training and educa-
tion, (3) evaluation and feedback, (4) reminders in the
workplace (5) institutional safety climate [10]. It has been
demonstrated the implementation of WHO HH strategy
is feasible and effective to enhance hand hygiene compli-
ance, which leads to a reduction of HAI [11–14]. However, there have been few data on the implementation
of the WHO multimodal HH strategy in China. We initi-
ated this study of implementation of WHO multimodal
HH strategy in order to improve awareness of HAI and
enhance HH compliance and correctness among HCWs. In this part, detailed intervention measures were drawn
up and then implemented according to the multimodal
improvement strategy acquired from the results of ques-
tionnaire survey. We collected observational data on
compliance and correctness with HH before and after
intervention respectively. Observation sessions were performed by 9 trained stu-
dent nurses. The training course included HH indica-
tions and correct HH techniques recommended by
WHO. A standard form was used to record the HH
compliance and correctness. Observers were taught how
to complete the form and record the number of HH ac-
tions and HH opportunities. We defined an opportunity
as the occurrence of any indication during the observed
care sequences. Part I: Questionnaire survey In this part, we did a questionnaire survey on pos-
sible factors affecting HH behaviors of HCWs. Each
participant voted those factors contributing to HH
noncompliance from the questionnaire. On the basis
of the reasons for HH noncompliance summarized in
the questionnaire, multimodal improvement strategy
was developed accordingly. Part II: Observation of compliance and correctness before
and after intervention We recorded actions, either handwash-
ing or hand rubbing based on WHO “My Five Moments
for Hand Hygiene”: before touching a patient, before
clean/aseptic procedure, after body fluid exposure risk,
after touching a patient, and after touching patient sur-
roundings [15]. Since an indication for HH was related
to the risk of pathogen transmission from one surface to
another, we added two more WHO recommended indi-
cations in our study: if moving from a contaminated
body site to a clean body site during patient care, after
removing gloves [16]. An action with correct HH tech-
niques must satisfy three criteria: (1) rub hands with 6-
step HH techniques; (2) duration of the rub procedure
lasts 15 s at least; (3) dry hands with disposable paper
towels. Each observer monitored the HH practice of
HCWs for 45–60 min. Abstract Background: Hand hygiene (HH) is an essential component for preventing and controlling of healthcare-associated
infection (HAI), whereas compliance with HH among health care workers (HCWs) is frequently poor. This study aimed
to assess compliance and correctness with HH before and after the implementation of a multimodal HH improvement
strategy launched by the World Health Organization (WHO). Methods: A quasi-experimental study design including questionnaire survey generalizing possible factors affecting HH
behaviors of HCWs and direct observation method was used to evaluate the effectiveness of WHO multimodal HH
strategy in a hospital of Traditional Chinese Medicine. Multimodal HH improvement strategy was drawn up
according to the results of questionnaire survey. Compliance and correctness with HH among HCWs were
compared before and after intervention. Also HH practices for different indications based on WHO “My Five
Moments for Hand Hygiene” were recorded. Results: In total, 553 HCWs participated in the questionnaire survey and multimodal HH improvement strategy was
developed based on individual, environment and management levels. A total of 5044 observations in 23 wards were
recorded in this investigation. The rate of compliance and correctness with HH improved from 66.27% and 47.75% at
baseline to 80.53% and 88.35% after intervention. Doctors seemed to have better compliance with HH after intervention
(84.04%) than nurses and other HCWs (81.07% and 69.42%, respectively). When stratified by indication, compliance with
HH improved for all indications after intervention (P < 0.05) except for “after body fluid exposure risk” and “after touching
patient surroundings”. Conclusion: Implementing the WHO multimodal HH strategy can significantly improve HH compliance and correctness
among HCWs. Keywords: Hand hygiene, Compliance, Correctness, Healthcare-associated infection Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Page 2 of 7 Page 2 of 7 Page 2 of 7 Methods Compliance and correctness with HH were compared
before and after the implementation. HCWs including
doctors, nurses, technicians, interns and cleaners were
observed for HH actions and HH opportunities. Data of
technicians, interns and cleaners was combined as other
HCWs. We expressed HH compliance as the proportion
of predefined opportunities met by HH actions. And HH
correctness was regarded as the proportion of all HH ac-
tions met by HH actions with correct techniques. All the
data was analyzed with SPSS version 16.0. The Chi
square test was applied to test the statistical difference
in HH compliance and correctness before and after the
implementation. Also HH compliance stratified by pro-
fessional category and indication was calculated. Results
with P < 0.05 were considered statistically significant. The study was conducted in Xi’an Hospital of Traditional
Chinese
Medicine
(TCM),
Xi’an,
China,
between
September 2015 and August 2016. It is the largest
public hospital in north Xi’an, which is the capital
city of Shaanxi Province. This hospital has 1001 beds
in 27 clinical departments including acupuncture and
moxibustion, intensive care, emergency, surgical and
TCM subspecialties with 1377 HCWs. We performed
this
two-part
quasi-experimental
study
including
questionnaire survey of factors affecting HH behaviors
of HCWs and direct observation of compliance and
correctness with HH before and after intervention. Part I: Questionnaire survey Part I: Questionnaire survey
A total of 558 HCWs from 37 departments participated
in this survey. Of these, 553 (99.10%) completed the
baseline questionnaire. The general information of all
participants was summarized in Table 1. Each participant Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Page 3 of 7 Page 3 of 7 Table 1 The general information of 553 participants in the survey
N (cases)
Percentage (%)
Mean (±s)
Age
553
31.78 ± 8.120
Gender
Female
433
78.30
Male
120
21.70
Work experience
<1 year
104
18.81
1 ~ 5 years
139
25.13
5 ~ 10 years
155
28.03
≥10 years
155
28.03
Education level
Senior high
school
14
2.53
Junior college
181
32.73
College
273
49.37
Post graduate
85
15.37
Profession
Doctors
191
34.54
Nurses
300
54.25
Technicians
35
6.33
Interns
23
4.16
Cleaners
4
0.72 Table 1 The general information of 553 participants in the survey
N (cases)
Percentage (%)
Mean (±s)
Age
553
31.78 ± 8.120 For the individual reasons such as poor HH awareness,
full training campaign on HH techniques among HCWs
was carried out. Our management of infection control
department first participated in the training of WHO
“My Five Moments for Hand Hygiene” provided by Xi’an
Quality Control Center of Nosocomial Infection. Then
we shoot instructional videos on five key moments for
HH and correct HH techniques in our hospital wards
with our HCWs. After that they were called together to
study HH knowledge via videos and PPT (based on
WHO training slides). All the HCWs including doctors,
nurses, interns, student nurses, lab technicians and
cleaners should attend educational courses on HH every
year. A posttest format was used to assess training effi-
cacy after each course. Inadequate HH supplies and inconvenient HH facil-
ities was another cause for noncompliance with HH in
our hospital. We took a series of measures to improve
HH facilities: increasing supplies of pocket alcohol-based
hand rub (ABHR) and disposable paper towels; making
sure every wash basin equipped with disposable paper
towels and poster for correct handwashing techniques;
replacing water tap in nurse station with automatic elec-
tronic sensor tap; distributing skin care products to
HCWs. Colorful HH posters were placed in the doctor’s
office in each ward with WHO “My Five Moments for
Hand Hygiene”. A little tip for HH was placed at the
edge of the computer screen of nurse station. HH compliance by indication The rate of compliance with HH was statistically ele-
vated after intervention for all indications (P < 0.05) ex-
cept for “after body fluid exposure risk” and “after
touching patient surroundings”. The highest relative im-
provement appeared to be indication “if moving from a
contaminated body site to a clean body site during pa-
tient care”, from 30.61% to 59.82% (shown in Table 4). Part II: Observation of compliance and correctness before
and after intervention
HH compliance In our study, a total of 5044 opportunities for HH were
recorded in 23 wards before and after intervention. The
rate of compliance with HH improved from 66.27% at
baseline to 80.53% after intervention (shown in Table 2). After implementing the improvement strategy, doctors
had better HH compliance (84.04%) than nurses and
other HCWs (81.07% and 69.42%, respectively). The rate Part I: Questionnaire survey Visible re-
minders for HH were also set at the entrance of each
ward. To create a better environment for HH, we offered
large-scale HH improvement campaign to both HCWs voted those factors contributing to HH noncompliance
from the questionnaire. All the possible factors affecting
HH behaviors of HCWs were arranged in descending
order according to the number of votes (Fig. 1). The main
reasons for HH noncompliance were classified into indi-
vidual, environment and management levels. Multimodal
improvement strategy was drafted accordingly (Fig. 2)
and detailed intervention measures were drawn up at
the same time. Fig. 1 Possible factors affecting HH behaviors of HCWs in the questionnaire survey Fig. 1 Possible factors affecting HH behaviors of HCWs in the questionnaire survey Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Page 4 of 7 Fig. 2 Main reasons for HH noncompliance and corresponding improvement measures Fig. 2 Main reasons for HH noncompliance and corresponding improvement measures of compliance with HH was statistically increased after
intervention for each professional category (P < 0.05). of compliance with HH was statistically increased after
intervention for each professional category (P < 0.05). and patients with knowledge contest, visible display
boards, and live performance. In order to strengthen the supervision of HH practice
among HCWs, a seasonal feedback and evaluation sys-
tem was established. Management of infection control
department regularly reported HH compliance and HH
products consumption in the meeting of Nosocomial
Infection Control Management Committee, which in-
cluded hospital management, department heads, head
nurses and focal persons. Also HH compliance and HH
products consumption was directly related to the scores
of quality control of each department through HH re-
wards and punishment mechanism. Department with
noncompliant HCWs had to pay a fine. HH correctness A total of 2927 actions with correct HH techniques
were recorded. The rate of correctness with HH im-
proved
from
47.75%
to
88.35%
after
intervention
(shown in Table 3). The increase of correctness ap-
plied for all professional categories, which was statis-
tically significant (P < 0.05). Discussion We recog-
nized that compliance rates were above 70% for these
two indications before intervention, which suggested
that our HCWs intended to perform HH when they
thought there might be microbial contamination and in-
fection risk. In addition, compliance rates for “before”
related indications were promoted after intervention,
such as “before touching a patient” and “before clean/
aseptic procedures”. These findings revealed that HCWs
were inclined to wash their hands to protect themselves
rather than protect patients from potential infection,
which was noted in previous studies [31, 32]. As for in-
dication “after touching patient surroundings”, HH op-
portunities with this indication were most commonly
associated with lower levels of compliance than follow-
ing direct patient contact [33]. Traditional Chinese
Medicine treatments such as acupuncture and moxibus-
tion are often combined with diathermy machine and
herb fumigation device to get better curative effect. Most
of our HCWs could perform HH after therapy devices
were turned off. But when there was need to adjust the
setting of therapy devices, required HH practices were
not performed according to our observers. Multiple
studies indicated that HAI could be caused by many
pathogenic organisms present in the hospital environ-
ment and objects frequently touched by patients’ hands,
such as bed side rail, door knob, patient record, nurse
call button [34, 35]. Moreover, it was of vital import-
ance to strengthen the effectiveness of cleaning and
in order to prevent the transmission of pathogens
from patient surrounding environment to HCWs and
patients [36, 37]. T
ll
k
l d
h th
HCW
t
d Epidemiological evidence have shown that hand con-
tamination of nurses could cause cross-infection in a
direct or indirect way, especially in intensive care unit
and hemodialysis unit where nurses have many patient
contact opportunities [26, 27]. In our study, HH compli-
ance of doctors seemed superior to nurses when strati-
fied by professional category. There were far more
opportunities of HH for nurses in most departments
than for doctors. Then overcrowding workload of nurses
made them provide clinical care to multiple patients
without HH to finish their tasks faster. HH compliance
in other HCWs was generally lower than doctors and
nurses. Poor HH compliance was witnessed among tech-
nicians during physiotherapy [28]. Gloves were often
used during cleaning work to replace HH by cleaners,
which might increase the risk of transmission of bacteria
via contaminated gloved hands [29, 30]. Discussion Antimicrobial Resistance and Infection Control (2017) 6:98 Page 5 of 7 Table 4 Comparison of HH compliance before and after intervention of HCWs by indication
HH compliance before
intervention (%)
HH compliance after
intervention (%)
χ2
P
Before touching a patient
263/489 (53.78)
766/944 (81.14)
119.121
<0.001
After touching a patient
374/489 (76.48)
737/897 (82.16)
6.420
0.011
If moving from a contaminated body site
to a clean body site during patient care
15/49 (30.61)
134/224 (59.82)
13.837
<0.001
After body fluid exposure risk
65/84 (77.38)
172/209 (82.30)
0.937
0.333
Before clean/aseptic procedures
160/254 (62.99)
460/552 (83.33)
40.547
<0.001
After touching patient surroundings
150/190 (78.95)
339/415 (81.69)
0.631
0.427
After removing gloves
83/120 (69.17)
105/128 (82.03)
5.589
0.018 Table 4 Comparison of HH compliance before and after intervention of HCWs by indication irritation and dryness, which was a vital cause for non-
compliance with HH. In addition, irritated hands might
be more vulnerable to be colonized with pathogens [17]. Since cleaning hands frequently is essential for every
health care worker, it is important for health care set-
tings to provide proper HH products. Compared with
detergent and soap, ABHR has been reported to cause
less skin irritation, especially those with emollient prop-
erties [18, 19]. The application of skin care products can
preserve unimpaired skin, reduce the incidence of skin
irritation and dryness and ensure effective hand hygiene
[20]. In the last decades, there were concerns that skin
care products might pose a negative influence on the ef-
ficacy of hand disinfection [21, 22]. With the wide re-
search of well-formulated disinfectants with emollients
in recent years, it seems that the efficacy of disinfectants
would not be impaired when they are applied with se-
lected, compatible skin care products [23, 24]. In our
study, we provided skin care products to our HCWs to
minimize the influence on HH compliance due to skin
irritation and dryness. Moreover, we encourage our
HCWs to use skin care products before work, cleaning
and after work under recommendations [25]. to accomplish full training on HH. All in all, HH com-
pliance was improved in different professional categories
after intervention. Data of compliance by different HH indication was
also investigated in the present study. Compliance with
HH improved after intervention across all indications
except for “after body fluid exposure” and “after touch-
ing patient surroundings” in the observation. Discussion Our study identified that implementation of WHO
multimodal HH improvement strategy was effective to
enhance HH compliance and correctness among HCWs. In the questionnaire survey, over 50% of the participants
thought frequently washing hands led to hand skin Table 3 Comparison of HH correctness of HCWs before and after
intervention by professional category
HH correctness before
intervention (%)
HH correctness after
intervention (%)
χ2
P
Doctors
169/342 (49.42)
201/279 (72.04)
32.669
<0.001
Nurses
349/747 (46.72)
2030/2266 (89.59)
621.30
<0.001
Other
HCWs
12/21 (57.14)
166/168 (98.81)
59.123
<0.001
Overall
530/1110 (47.75)
2397/2713 (88.35)
723.76
<0.001 Table 2 Comparison of HH compliance of HCWs before and after
intervention by professional category
HH compliance before
intervention (%)
HH compliance after
intervention (%)
χ2
P
Doctors
342/459 (74.51)
279/332 (84.04)
10.362
0.001
Nurses
747/1081 (69.10)
2266/2795 (81.07)
64.538
<0.001
Other
HCWs
21/135 (15.56)
168/242 (69.42)
100.58
<0.001
Overall
1110/1675 (66.27)
2713/3369 (80.53)
123.99
<0.001
Table 3 Comparison of HH correctness of HCWs before and after
intervention by professional category
HH correctness before
intervention (%)
HH correctness after
intervention (%)
χ2
P
Doctors
169/342 (49.42)
201/279 (72.04)
32.669
<0.001
Nurses
349/747 (46.72)
2030/2266 (89.59)
621.30
<0.001
Other
HCWs
12/21 (57.14)
166/168 (98.81)
59.123
<0.001
Overall
530/1110 (47.75)
2397/2713 (88.35)
723.76
<0.001 Table 2 Comparison of HH compliance of HCWs before and after
intervention by professional category
HH compliance before
intervention (%)
HH compliance after
intervention (%)
χ2
P
Doctors
342/459 (74.51)
279/332 (84.04)
10.362
0.001
Nurses
747/1081 (69.10)
2266/2795 (81.07)
64.538
<0.001
Other
HCWs
21/135 (15.56)
168/242 (69.42)
100.58
<0.001
Overall
1110/1675 (66.27)
2713/3369 (80.53)
123.99
<0.001 Table 3 Comparison of HH correctness of HCWs before and after
intervention by professional category Table 2 Comparison of HH compliance of HCWs before and after
intervention by professional category Shen et al. Competing interests
Th
h
d
l
h p
g
The authors declare that they have no competing interests. p
g
The authors declare that they have no competing interests. Funding g
Project supported by Key Science and Technology R & D Program of Shaanxi
Province, China (Grant No.2016SF-213). Discussion Besides, the
growing mobility of cleaners and interns made it difficult To well acknowledge whether our HCWs mastered
the standard handwashing techniques, HH correctness Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Page 6 of 7 Page 6 of 7 Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Availability of data and materials The raw data supporting the results of this study are included within
the article and its additional files. Additional file 1, Additional file 2 and
Additional file 3. Authors’ contributions LS carried out the study and drafted the manuscript. XW conceived of the
study, participated in its design and coordination. JA contributed to the
design of the study. JA participated in the literature review and performed
statistical analysis. NZ, LS and HC provided training of hand hygiene indications
and correct hand hygiene techniques for observers and collected data. LF
organized workers to improve hand hygiene products and facilities. JH
and XL contributed to check and enter data. All authors read and approved the
final manuscript. Conclusions was investigated at the same time. In general, correct-
ness rate was far below our standards before interven-
tion. During the period of investigation, we found two
most commonly reasons for low HH correctness rate in
our hospital. Most of our HCWs knew the right HH
technique procedures but the duration of rubbing hands
did not meet our requirement (15 s at least). Inadequate
disposable paper towel was another cause for unpleasant
HH correctness rate. Therefore our infection control
staff took steps to promote correct HH techniques,
which included correct HH techniques training, increas-
ing supplies of pocket ABHR and disposable paper
towels. As a result, our HCWs’ HH correctness rates
were elevated after intervention. In conclusion, this intervention study has shown that
implementation
of
WHO
multimodal
improvement
strategy could significantly increase compliance and cor-
rectness with HH in our hospital. Further investigations
with sufficient sample size and larger multicenter series
are needed to validate the effectiveness of long-term per-
sistence of HH compliance improvement strategy. Consent for publication
Not applicable. Consent for publication
Not applicable. Additional files Additional file 1: HH raw data. (SAV 12 kb)
Additional file 2: Possible factors. (SAV 2 kb)
Additional file 3: Questionnaire survey raw data. (SAV 25 kb) Additional file 1: HH raw data. (SAV 12 kb)
Additional file 2: Possible factors. (SAV 2 kb)
Additional file 3: Questionnaire survey raw data. (SAV 25 kb) Additional file 1: HH raw data. (SAV 12 kb)
Additional file 2: Possible factors. (SAV 2 kb)
Additional file 3: Questionnaire survey raw data. (SAV 25 kb) In the last few years, domestic researches on im-
proving HH practice have been reported in succession
[38–44]. It is noteworthy that our study is the first
observational before-and-after intervention study on
improving HH compliance in Xi’an, Shaanxi province. Meanwhile it is the first study implementing WHO
multimodal strategy to promote HH practice in a
hospital of Traditional Chinese Medicine. HCWs have
many patient contact opportunities in the process of
Traditional Chinese Medicine treatments such as acu-
puncture
and
moxibustion,
massage,
cupping
and
other physical therapies. If standard HH practice were
not performed, it might increase the risk of cross-
infection. Our study summarized the reasons for non-
compliance with HH and provided scientific evidence
to promote HH practice for other hospitals of Trad-
itional Chinese Medicine. Nevertheless, this study also
had certain limitations. The entire observation of HH
compliance and correctness were only carried out in
general inpatient wards. We planned to observe HH
practice in critical departments for infection control
management such as emergency, intensive care unit
and hemodialysis unit. These places are characterized
by high patient volume, critically ill patients and more
invasive
operations. Improving
HH
compliance
in
such places would be meaningful for better infection
control. Furthermore, using student nurses as ob-
servers might have an impact on observation process. These student nurses observed HH practice of HCWs
in clinical wards during their clinical clerkships. Some
students told us they recognized their former teaching
nurses and classmates in the observation process and
thus
we
concerned
that
this
covert
investigation
might present the Hawthorn effect. In order to lessen
the influence of the Hawthorn effect on HH compli-
ance of HCWs, we plan to train every HCW in our
hospital to become a competent observer for HH
compliance of their co-workers. In this way every
HCW could be our covert observer and we could col-
lect reliable data of HH practice. Ethics approval and consent to participate Our study was approved by the Ethics Committee of Xi’an Hospital of Traditional
Chinese Medicine (No.XAZYYLS2015–05). The need for consent to participate was
waived as no individual person’s data were collected in any form. Our study was approved by the Ethics Committee of Xi’an Hospital of Traditional
Chinese Medicine (No.XAZYYLS2015–05). The need for consent to participate was
waived as no individual person’s data were collected in any form. Abbreviations ABHR: Alcohol-based hand rub; HAI: Healthcare-associated infection;
HCWs: Health care workers; HH: Hand hygiene; TCM: Traditional Chinese
Medicine; WHO: World Health Organization References Role of hand hygiene in healthcare-associated infection
prevention. J Hosp Infect. 2009;73:305–15. 7. Allegranzi B, Pittet D. Role of hand hygiene in healthcare-associated infection
prevention. J Hosp Infect. 2009;73:305–15. 8. Dancer SJ. The role of environmental cleaning in the control of hospital-
acquired infection. J Hosp Infect. 2009;73:378–85. 32. Patel B, Engelbrecht H, McDonald H, Morris V, Smythe W. A multifaceted
hospital-wide intervention increases hand hygiene compliance. S Afr Med J. 2016;106:32–5. 9. Weber DJ, Anderson D, Rutala WA. The role of the surface environment in
healthcare-associated infections. Curr Opin Infect Dis. 2013;26:338–44. 33. FitzGerald G, Moore G, Wilson AP. Hand hygiene after touching a patient's
surroundings: the opportunities most commonly missed. J Hosp Infect. 2013;84:27–31. 10. WHO. Guide to implementation: a guide to the implementation of the
WHO Multimodal Hand Hygiene Improvement Strategy. 2009. http://www. who.int/gpsc/5may/Guide_to_Implementation.pdf (Accessd Feb 7,2017). 34. Donskey CJ. Does improving surface cleaning and disinfection reduce health
care-associated infections? Am J Infect Control. 2013;41:S12–9. g
y
11. Allegranzi B, Gayet-Ageron A, Damani N, Bengaly L, McLaws ML, Moro ML, et al. Global implementation of WHO's multimodal strategy for improvement of hand
hygiene: a quasi-experimental study. Lancet Infect Dis. 2013;13:843–51. 35. Weber DJ, Rutala WA, Miller MB, Huslage K, Sickbert-Bennett E. Role of
hospital surfaces in the transmission of emerging health care-associated
pathogens: norovirus, Clostridium Difficile, and Acinetobacter species. Am J Infect Control. 2010;38:S25–33. 12. Arntz PR, Hopman J, Nillesen M, Yalcin E, Bleeker-Rovers CP, Voss A, et al. Effectiveness of a multimodal hand hygiene improvement strategy in the
emergency department. Am J Infect Control. 2016;44:1203–7. 36. Ramphal L, Suzuki S, McCracken IM, Addai A. Improving hospital staff
compliance with environmental cleaning behavior. Proc (Bayl Univ Med
Cent). 2014;27:88–91. 13. Farhoudi F, Sanaei Dashti A, Hoshangi Davani M, Ghalebi N, Sajadi G,
Taghizadeh R. Impact of WHO hand hygiene improvement program
implementation: a quasi-experimental trial. Biomed Res Int. 2016;2016:
7026169. 37. Kurashige EJ, Oie S, Furukawa H. Contamination of environmental surfaces
by methicillin-resistant Staphylococcus Aureus (MRSA) in rooms of inpatients
with MRSA-positive body sites. Braz J Microbiol. 2016;47:703–5. 14. Pfafflin F, Tufa TB, Getachew M, Nigussie T, Schonfeld A, Haussinger D, et al. Implementation of the WHO multimodal Hand Hygiene Improvement
Strategy in a University Hospital in Central Ethiopia. Antimicrob Resist
Infect Control. 2017;6:3. 38. Ji G, Yin H, Chen Y. Author details
1 1Department of Infection Control, Xi’an Hospital of Traditional Chinese Medicine,
No.69 Feng Cheng 8th Road, Weiyang District, Xi’an 710021, China. 2Department
of Acupuncture and Moxibustion, Xi’an Hospital of Traditional Chinese Medicine,
No.69 Feng Cheng 8th Road, Weiyang District, Xi’an 710021, China. 3Department
of Information Consultation, Library of Xi’an Jiaotong University, No.76 Yan Ta
West Road, Yanta District, Xi’an 710061, China. 4Department of Cadre Health Care,
Xi’an Hospital of Traditional Chinese Medicine, No.69 Feng Cheng 8th Road,
Weiyang District, Xi’an 710021, China. Page 7 of 7 Page 7 of 7 Page 7 of 7 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Received: 1 June 2017 Accepted: 4 September 2017 Received: 1 June 2017 Accepted: 4 September 2017 the efficacy of surgical hand disinfection and surgical glove perforation. BMC Infect Dis. 2014;14:315. the efficacy of surgical hand disinfection and surgical glove perforation. BMC Infect Dis. 2014;14:315. 25. Kampf G, Loffler H. Prevention of irritant contact dermatitis among health
care workers by using evidence-based hand hygiene practices: a review. Ind
Health. 2007;45:645–52. References 26. Duong MC, McLaws ML. Dangerous practices in a hemodialysis unit in Vietnam
identify from mixed methods. BMC Infect Dis. 2017;17:181. 1. Allegranzi B, Bagheri Nejad S, Combescure C, Graafmans W, Attar H,
Donaldson L, et al. Burden of endemic health-care-associated infection
in developing countries: systematic review and meta-analysis. Lancet. 2011;377:228–41. 27. Ghorbani A, Sadeghi L, Shahrokhi A, Mohammadpour A, Addo M, Khodadadi
E. Hand hygiene compliance before and after wearing gloves among intensive
care unit nurses in Iran. Am J Infect Control. 2016;44:e279–e81. 2. Ren N, Wen X, Wu A. Nationwide cross-sectional survey on healthcare-associated
infection in 2014. Chinese Journal of Infection Control. 2016;15:83–7. 2. Ren N, Wen X, Wu A. Nationwide cross-sectional survey on healthcare-associated
infection in 2014. Chinese Journal of Infection Control. 2016;15:83–7. 28. O'Donoghue M, Ng SH, Suen LK, Boost M. A quasi-experimental study to
determine the effects of a multifaceted educational intervention on hand
hygiene compliance in a radiography unit. Antimicrob Resist Infect Control. 2016;5:36. 3. Graves N, Weinhold D, Tong E, Birrell F, Doidge S, Ramritu P, et al. Effect of
healthcare-acquired infection on length of hospital stay and cost. Infect
Control Hosp Epidemiol. 2007;28:280–92. 3. Graves N, Weinhold D, Tong E, Birrell F, Doidge S, Ramritu P, et al. Effect of
healthcare-acquired infection on length of hospital stay and cost. Infect
Control Hosp Epidemiol. 2007;28:280–92. 29. McBryde ES, Bradley LC, Whitby M, McElwain DL. An investigation of contact
transmission of methicillin-resistant Staphylococcus Aureus. J Hosp Infect. 2004;
58:104–8. 4. Jia H, Hou T, Li W, Ma Q, Liu W, Yang Y, et al. Economic loss due to healthcare-
associated infection in 68 general hospitals in China. Chinese Journal of
Infection Control. 2016;15:637–41. 30. Snyder GM, Thom KA, Furuno JP, Perencevich EN, Roghmann MC, Strauss SM,
et al. Detection of methicillin-resistant Staphylococcus Aureus and
vancomycin-resistant enterococci on the gowns and gloves of healthcare
workers. Infect Control Hosp Epidemiol. 2008;29:583–9. 5. Allegranzi B, Pittet D. Preventing infections acquired during health-care delivery. Lancet. 2008;372:1719–20. 6. Chen P, Liu D. Epidemiological characteristics and preventive strategies of
nosocomial infection outbreak incidents in China in recent 30 years. Chinese Journal of Infection Control. 2010;9:387–92,99. 31. Lee A, Chalfine A, Daikos GL, Garilli S, Jovanovic B, Lemmen S, et al. Hand
hygiene practices and adherence determinants in surgical wards across
Europe and Israel: a multicenter observational study. Am J Infect Control. 2011;39:517–20. 7. Allegranzi B, Pittet D. References Prevalence of and risk factors for non-compliance with
glove utilization and hand hygiene among obstetrics and gynaecology
workers in rural China. J Hosp Infect. 2005;59:235–41. 15. WHO. About SAVE LIVES: Clean Your Hands. 2009. http://www.who.int/gpsc/
5may/background/5moments/en/ (Accessd Feb 7,2017). 39. Li LY, Zhao YC, Jia JX, Zhao XL, Jia HX. Investigation on compliance of hand
hygiene of healthcare workers. Zhongguo Yi Xue Ke Xue Yuan Xue Bao. 2008;30:546–9. 16. WHO. WHO guidelines on hand hygiene in health care: a summary. 2009. http://www.who.int/gpsc/information_centre/hand-hygiene-summary/en/
(Accessd Feb 7,2017). 40. Chau JP, Thompson DR, Twinn S, Lee DT, Pang SW. An evaluation of hospital
hand hygiene practice and glove use in Hong Kong. J Clin Nurs. 2011;20:1319–28. 17. Visscher MO, Randall WR. Hand hygiene compliance and irritant dermatitis:
a juxtaposition of healthcare issues. Int J Cosmet Sci. 2012;34:402–15. 41. Su D, Hu B, Rosenthal VD, Li R, Hao C, Pan W, et al. Impact of the international
nosocomial infection control consortium (INICC) multidimensional hand
hygiene approach in five intensive care units in three cities of China. Public
Health. 2015;129:979–88. 18. Boyce JM, Kelliher S, Vallande N. Skin irritation and dryness associated with
two hand-hygiene regimens: soap-and-water hand washing versus hand
antisepsis with an alcoholic hand gel. Infect Control Hosp Epidemiol. 2000;
21:442–8. 42. Mu X, Xu Y, Yang T, Zhang J, Wang C, Liu W, et al. Improving hand hygiene
compliance among healthcare workers: an intervention study in a Hospital
in Guizhou Province. China Braz J Infect Dis. 2016;20:413–8. 19. Larson E, Girard R, Pessoa-Silva CL, Boyce J, Donaldson L, Pittet D. Skin
reactions related to hand hygiene and selection of hand hygiene products. Am J Infect Control. 2006;34:627–35. 43. Chen P, Yuan T, Sun Q, Jiang L, Jiang H, Zhu Z, et al. Role of quality control
circle in sustained improvement of hand hygiene compliance: an observational
study in a stomatology hospital in Shandong. China Antimicrob Resist Infect
Control. 2016;5:54. 20. Bissett L. Skin care: an essential component of hand hygiene and infection
control. Br J Nurs. 2007;16:976–81. 21. Walsh B, Blakemore PH, Drabu YJ. The effect of handcream on the antibacterial
activity of chlorhexidine gluconate. J Hosp Infect. 1987;9:30–3. 44. Cheng VC, Tai JW, Li WS, Chau PH, So SY, Wong LM, et al. Implementation
of directly observed patient hand hygiene for hospitalized patients by hand
hygiene ambassadors in Hong Kong. Am J Infect Control. 2016;44:621–4. activity of chlorhexidine gluconate. References J Hosp Infect. 1987;9:30–3. 22. Benson L, LeBlanc D, Bush L, White J. The effects of surfactant systems and
moisturizing products on the residual activity of a chlorhexidine gluconate
handwash using a pigskin substrate. Infect Control Hosp Epidemiol. 1990;11:
67–70. 23. Heeg P. Does hand care ruin hand disinfection? J Hosp Infect. 2001;48(Suppl A):
S37–9. 24. Harnoss JC, Brune L, Ansorg J, Heidecke CD, Assadian O, Kramer A. Practice
of skin protection and skin care among German surgeons and influence on
|
https://openalex.org/W3128249030
|
https://link.springer.com/content/pdf/10.1007/s11109-021-09683-0.pdf
|
English
| null |
Propaganda, Presumed Influence, and Collective Protest
|
Political behavior
| 2,021
|
cc-by
| 12,032
|
Abstract Political propaganda can reduce citizens’ inclinations to protest by directly influenc-
ing their preferences or beliefs about the government. However, given that protest
is risky in authoritarian societies and requires collective participation, propaganda
can also reduce citizens’ inclination to protest by making them think that other citi-
zens, rather than themselves, may have been influenced by propaganda and are, as a
result, unwilling to protest. We test this indirect mechanism of propaganda using a
survey experiment with Chinese internet users from diverse backgrounds and find
that they do believe propaganda affects other citizens’ support for and beliefs about
the government more than their own support and beliefs. Moreover, they believe
that propaganda reduces other citizens’ willingness to protest, which in turn reduces
their own willingness to protest. Therefore, the power of propaganda may sometimes
lie more in the social perceptions and uncertainty it creates than in its direct indi-
vidual effects. Keywords Propaganda · Protest · Presumed influence · Third-person effect Accepted: 21 January 2021 / Published online: 8 February 2021
© The Author(s) 2021 Accepted: 21 January 2021 / Published online: 8 February 2021
© The Author(s) 2021 Accepted: 21 January 2021 / Published online: 8 February 2021
© The Author(s) 2021 Political Behavior (2022) 44:1789–1812
https://doi.org/10.1007/s11109-021-09683-0 Political Behavior (2022) 44:1789–1812
https://doi.org/10.1007/s11109-021-09683-0 ORIGINAL PAPER NAL PAPER Haifeng Huang1 · Nicholas Cruz1 Haifeng Huang1 · Nicholas Cruz1 1
Department of Political Science, University of California at Merced, CA, USA Introduction How does political propaganda affect citizen behavior, particularly protest, in an
authoritarian society? Standard research on this question focuses on how propa-
ganda directly affects individuals’ political preferences or beliefs. For example,
most existing studies regard propaganda as persuasion and argue that propaganda
works by persuading citizens about the merits of the government or its policies,
thereby increasing citizens’ support of the regime and reducing their inclination
to dissent (Adena et al. 2015; Cantoni et al. 2017; Gehlbach and Sonin 2014; * Haifeng Huang
hhuang24@ucmerced.edu
https://www.hhuang.org/
Nicholas Cruz
ncruz5@ucmerced.edu
1
Department of Political Science, University of California at Merced, CA, USA (0123456789)
1 3 456789)
3 456789)
3 Political Behavior (2022) 44:1789–1812 1790 Guriev and Treisman 2020; Peisakhin and Rozenas 2018; Rozenas and Stukal
2019). Other works treat propaganda as signaling and suggest that propaganda
does not necessarily affect individuals’ political support, but instead signals
the power and capacity of the government through the act of propaganda itself,
thereby intimidating citizens and dampening their inclination to protest (Huang
2015b; Svolik 2012; Wedeen 1999). Both propaganda as persuasion and propaganda as signaling are direct and
individual-based mechanisms. Mass protests, however, are inherently collective
actions. Given that protest is risky under an authoritarian regime and that partici-
pants of a failed protest are subject to potentially severe punishment, most indi-
viduals’ decisions about whether to protest depend not only on their own prefer-
ences or beliefs about the government but also on their perceptions of whether or
how many other people will turn out to protest, which then determines how likely
the protest will be to succeed (Chwe 2003; Egorov et al. 2009; Lohmann 1994). In other words, protest is a game of complementarity in which individuals will be
more (less) willing to participate the more (less) likely they think other people
will participate (e.g., Gehlbach et al. 2016; Bueno De Mesquita 2010; Edmond
2013). Introduction Incorporating the logic of collective protest into theories of propaganda
thus introduces an alternative channel by which regimes can manipulate citizen
behavior: Even if propaganda does not directly persuade individuals about the
merits of government or influence their beliefs about its power and capacity, it
can still make them less willing to protest if they believe that propaganda has suc-
cessfully persuaded or intimidated other people not to protest.l In other words, propaganda can sometimes work not by influencing individ-
uals’ own preferences or beliefs but by making them think that other people’s
preferences or beliefs may have been influenced. This mechanism of propaganda
hinges on its indirect effect at the collective level rather than its direct effect at
the individual level. We build our theory on the “influence of presumed influ-
ence” model in communication studies, which argues that the effects of media
are often indirect and occur through the channel of presumed media influence
on other people (Gunther and Storey 2003; Tal-Or et al. 2009). A closely related
idea, the “third-person effect,” which can be considered a special case of the
“influence of presumed influence” model, makes an even more specific predic-
tion: Individuals tend to believe that media and communications have a stronger
effect on others than on themselves, and then they react to the presumed effect on
others (Davison 1983; Perloff 2009; Sun et al. 2008). Curiously, although prop-
aganda is a key motivating example in Davison ’s (1983) original formulation
of the third person effect hypothesis, there have been few empirical investiga-
tions of propaganda’s indirect effect, especially in the authoritarian setting. Most
studies of the influence of presumed influence instead focus on media effects in
democratic societies. This study provides such an investigation in the case of
contemporary China to enrich theories of political propaganda. In addition, most
existing studies under the influence of presumed media influence framework, par-
ticularly those on the third-person effect, use surveys and ask people directly how
they think media affects themselves and others. In contrast, we experimentally 1 3 Political Behavior (2022) 44:1789–1812 1791 compare propaganda’s presumed effect on others with its actual effect on oneself,
and how the former may affect individuals’ participation in protest more than the
latter. compare propaganda’s presumed effect on others with its actual effect on oneself,
and how the former may affect individuals’ participation in protest more than the
latter. Introduction Using an online survey experiment featuring real propaganda messages from Chi-
na’s state media, we find that propaganda exposure has a greater effect on respond-
ents’ beliefs about other citizens’ support for the regime than on their own support
for the regime. Propaganda exposure also has a greater effect on the respondents’
beliefs about other citizens’ assessments of the power and stability of the regime
than their own assessment. In addition, propaganda reduces the respondents’ beliefs
about other people’s willingness to protest, which in turn has a negative effect on
their own willingness to protest.i Our findings suggest that, due to the nature of collective protest, authoritarian
propaganda can work not (just) by manipulating what individual citizens think
about the regime or their own propensity to protest against the regime, but (also) by
manipulating the information and perceptions that citizens have about each other,
creating social uncertainty. In other words, political authorities can use their vantage
point as an agenda setter to create a mirage surrounding propaganda; citizens’ con-
cern that other citizens could have been influenced by propaganda can sometimes be
sufficient to deter them from challenging the authorities. Our results are consistent
with the classic game-theoretic argument about the critical role of common knowl-
edge in shaping social interactions. They not only provide micro-level empirical
support for the ideas of pluralistic ignorance and preference falsification sustaining
authoritarian rule (Chwe 2003; Havel 1985; Kuran 1991) but also explicate a spe-
cific and critical mechanism for the phenomenon. i
The next section lays out our theory and hypotheses. Section 3 explains the
experimental design and data. Section 4 presents the results on both the perceptual
and behavioral components of the influence of presumed influence of propaganda. The last section discusses our results and concludes. 1 For similar definitions, see Huang (2018) and Jowett and O’Donnell (2018). 2 We focus attention on the typical repressive authoritarian setting rather than on settings where there
is a high degree of civil liberty and where punishment for protest participation is traditionally rare, as in
Cantoni et al. ’s (2019) study.
3 The process can even go one step further. Given the complementarity of collective protest, both “all
people protest” and “no one protests” are potential equilibria. Propaganda may simply serve as a coordi-
nation device and make the “no one protests” outcome the focal point and thus the resulting equilibrium,
even if people’s preferences and beliefs about the regime are not influenced by propaganda and they do
not think other people are influenced. This possibility can be examined in future research. Influence of the Presumed Influence of Propaganda Propaganda is the deliberate dissemination of inaccurate, exaggerated, or fabricated
information that favors a political cause or player.1 Our theoretical framework about
authoritarian propaganda posits that it operates on both the individual and collec-
tive levels. At the individual level, propaganda can manipulate the preferences of
individuals directly, by persuading them about the merits of the regime, its lead-
ers, or its policies and thus increasing their support of the regime; this is the stand-
ard theory of propaganda as persuasion (Adena et al. 2015; Cantoni et al. 2017;
Gehlbach and Sonin 2014; Guriev and Treisman 2020; Peisakhin and Rozenas 2018;
Rozenas and Stukal 2019). At the same time, some propaganda is not persuasive but
heavy-handed and even ridiculous, but by demonstrating the state’s ability to com-
mand great resources and the organizational capacity to impose such (unpersuasive 1 3 1792 Political Behavior (2022) 44:1789–1812 and unpopular) propaganda messages on the society, the regime can signal its power
and capacity in social control, and thus deter the public from challenging it. In other
words, instead of shaping individuals’ political preferences, propaganda can work
by influencing their beliefs about the power of the state; this is the theory of propa-
ganda as signaling (Huang 2015b, 2018). At the collective level, regardless of whether propaganda can change individu-
als’ own support of the regime or beliefs about the regime’s power, it may affect
their perceptions of other people’s support for the regime or their beliefs about the
regime’s power, since it is possible that other people have been influenced by propa-
ganda. Because a single person’s protest can be easily defeated by the regime, effec-
tive protest almost necessarily requires collective participation. In particular, strate-
gic complementarity “characterizes mass protests” (Gehlbach et al. 2016, p. 579);
the fewer people who participate in a protest, the less likely it will succeed (Bueno
De Mesquita 2010; Chwe 2003; Edmond 2013). Influence of the Presumed Influence of Propaganda The literature has examined a variety of explanations
for the prevalent self-other perceptual gap: motivational explanations that center on
people’s motivations for self-enhancement and the feeling that they are better and
less gullible than others, and cognitive explanations in which people act as naive
social scientists and create simple theories about the effects of media on society (see
Tal-Or et al. 2009, for a review of the literature). Regardless of the specific sources
of self-other perceptual gaps, it should be emphasized that the existence of the per-
ceptual component of the presumed media influence model enjoys robust empirical
support. This study does not consider the cognitive or psychological sources of the
perception that media and communications may have stronger effects on others than
oneself, only that the effect can exist in some form and be exploited by propaganda. f
Drawing on individual-level theories of propaganda and the perceptual compo-
nent of the influence of presumed influence framework, we offer two hypotheses
about the presumed influence of propaganda. Given that propaganda is traditionally
understood as efforts by regimes to increase citizen support through persuasion, our
first hypothesis (H1) is that individuals believe that propaganda would increase other
people’s support of the regime; in fact, propaganda’s presumed influence on others’
support for the regime will be stronger than its effects on one’s own support for the
regime. Note that here we compare individuals’ perceptions of propaganda’s effect
on others with its actual effect on oneself. In the traditional third-person effect litera-
ture, the comparison is between individuals’ perceptions of media’s effects on others
and their perceptions of media’s effects on themselves (but see Cohen et al. 1988). Since people’s perceptions of media’s effects on themselves may not be accurate,
it is more useful to use the actual effect as a comparison. This difference will be
reflected in our research design, to be discussed in the next section. l
Our second hypothesis (H2) is based on the more recent literature on propaganda
as signaling, and it posits that propaganda will make individuals believe that propa-
ganda would increase other people’s assessment of the regime’s power and capac-
ity to maintain social stability; in fact, propaganda’s presumed influence on others’
assessment of the regime’s capacity to maintain stability will be stronger than its
effect on their own assessment of the regime’s capacity. Influence of the Presumed Influence of Propaganda Therefore, given the risk and poten-
tially severe negative consequences of participating in a failed protest against an
authoritarian government, people will be less likely to protest the less they think
other people will participate in protest.2 Propaganda can thus reduce citizens’ protest
inclination by making them think that other people (may) have been influenced by
propaganda (and consequently support the government or believe the government is
too powerful to oppose), even if the effect of propaganda on themselves is limited.3
Our focus in this study is on this indirect, collective-level effect of propaganda, i.e.,
the influence of presumed influence of propaganda (IPIP). It is important to note
that IPIP does not deny that propaganda can influence individuals directly. It argues,
however, that even if there is little individual-level direct effect, propaganda may
still work through its indirect effect at the collective level.ll f
We build our theory of IPIP on the “influence of presumed influence” frame-
work of media effects (Gunther and Storey 2003), including the third-person effect
hypothesis (Davison 1983), which has been one of the most influential theoretical
frameworks in communication studies (Perloff 2009). The influence of presumed
influence model has two components. First, people perceive some influence of a
message on others, and this presumed influence on others may well be stronger than
the message’s perceived effect on themselves (the perceptual component); Second,
people react to their perceptions of the message’s influence on others (the behavioral
component). In other words, a media message can have indirect influences on indi-
viduals’ behavior through their perceptions of its effect on other people. f
The literature in communication studies and social psychology has found robust
evidence for the perceptual component of the indirect media influence framework 1 3 Political Behavior (2022) 44:1789–1812 1793 across a wide variety of contexts, such as media violence and pornography, adver-
tising, news coverage, and entertainment, as well as across various study designs
(e.g., Cohen et al. 1988; Mutz 1989; Perloff 1999; Peiser and Peter 2000; Price and
Tewksbury 1996; Sun et al. 2008). Recent work has extended the research to new
areas, such as fake news, polling, social media, and international news, and similarly
found that individuals often perceive others to be more influenced than themselves
by such messaging and platforms (e.g., Chung et al. 2017; Jang and Kim 2018; Tsay-
Vogel 2016; Wei et al. 2017). Influence of the Presumed Influence of Propaganda Note again, here we are
comparing individuals’ perceptions of propaganda’s effect on others with its actual
effect on themselves.f f
Our third and perhaps most important hypothesis is about the behavioral effects
of propaganda’s presumed influence. While earlier research in the third-person effect
literature using the self-other perceptual gap to predict individuals’ behavior has
yielded mixed results (Perloff 1999; Xu and Gonzenbach 2008), the influence of
presumed influence model emphasizes media’s presumed influence on others rather 1 3 Political Behavior (2022) 44:1789–1812 1794 than perceptual differences between self and others (Gunther and Storey 2003),4 and
here the evidence has been considerably stronger (Chung and Moon 2016; Dohle
et al. 2017; Tal-Or et al. 2009; Wei et al. 2017). But existing research on the influ-
ence of presumed media influence has focused on individuals’ support for censor-
ship and restrictions of media content that are perceived to have a negative influence
on others, e.g., hate speech, fake news, and pornography. Even in other contexts,
such as voting and online political discussion, the behavioral consequence of the
third-person effect is usually thought to be that individuals take actions to correct
or balance the perceived negative effect of media messaging on others (Golan et al. 2008; Rojas 2010).fl We study the effect of the presumed influence of propaganda on collective protest
in the authoritarian setting, where the consequence of government messaging is that
individuals may take actions to conform to the expected behavior of others who are
thought to have been influenced by the messaging rather than to counterbalance the
effect of the messaging on others. In addition, dealing with collective action rather
than individual behavior, our focus is not just on how the presumed influence of
propaganda on other people’s attitudes affects individuals’ behavior, as is commonly
the case in existing studies of the influence of presumed influence and third-per-
son effects, but on how the expected behavior of other people, due to propaganda,
affects individuals’ own behavior. In other words, given the complementarity of pro-
test behavior, we focus on how propaganda affects individuals’ coordination motives
rather than their correction or counterbalance motives (Little 2017; Tal-Or et al. 2009). We therefore hypothesize that propaganda exposure will create the expectation
that propaganda has made other citizens less willing to protest (H3a), and this expec-
tation will negatively affect individuals’ own willingness to protest (H3b). 4 Even in Davison ’s (1983) original thesis about third-person effects, for the behavioral component he
emphasized the presumed influence on others rather than the self-other perceptual gap (Chung and Moon
2016). Influence of the Presumed Influence of Propaganda In other
words, we propose an indirect channel through which propaganda reduces protest:
by affecting how individuals perceive their peers’ willingness to protest, thereby
inhibiting their own willingness to participate in collective action. Here, perceptions
of other citizens’ willingness to protest serves as a mediating variable between prop-
aganda exposure and individuals’ willingness to protest.fl Our analysis of the behavioral effect of the presumed influence of propaganda
is related to a few recent studies of media effects. Jin et al. (2018) study how blog
posts about the Fukushima nuclear accident’s contamination risks affected people’s
seafood consumption behavior and their perceptions of others’ behavior, and how
their own behavior and others’ behavior affected each other. Similarly, Tewksbury
et al. (2004) study how anxieties about the Y2K computer problem and percep-
tions of other people’s overreactions to it (e.g., bank withdrawals and food hoard-
ing) influenced individuals’ own protective behavior. These studies, however, do
not explain the theoretical foundations of the interaction between self-behavior and
other-behavior, e.g., why in the individualistic consumption (as opposed collective 1 3 3 Political Behavior (2022) 44:1789–1812 1795 action) setting, after controlling for anxiety levels, people would reduce eating sea-
food in response to other people’s reduced seafood consumption, or why other peo-
ple’s over-hoarding of cash and food would reduce one’s own protective behavior. Little (2017) provides a game-theoretic model in which some citizens are credulous,
and informed citizens who know the government is lying would nevertheless behave
as if they believe its propaganda since they want to coordinate their behavior with
credulous citizens. The coordination motive is also essential in our collective protest
setting, but, in our setting, citizens can be homogeneous (and all disbelieve propa-
ganda) rather than having divergent information capacity. Our theory is consistent with the classic formal-theoretic literature about the
crucial roles of common knowledge, preference falsification, and pluralistic igno-
rance in affecting regime stability. Propaganda breaks down public communications,
without which it will be hard to form common knowledge about citizens’ politi-
cal attitudes (Chwe 2003). More specifically, in accordance with Kuran ’s (1991)
account of preference falsification, propaganda (together with repression) makes
citizens hide their true and private preferences and leads to a public discourse that
prevents citizens from knowing the real distribution of anti-government sentiments
in the society (see also Havel 1985). Such pluralistic ignorance is the wellspring of
authoritarian stability. Influence of the Presumed Influence of Propaganda In the more recent global game literature, Edmond (2013) has
shown that even though citizens are aware of propaganda, they cannot completely
discount the government’s exaggeration of its strength when neither the govern-
ment’s actual level of strength nor the amount of propaganda is perfectly observed. Further, since citizen actions are strategic complements, information manipulation
will reduce every citizens’ incentive to participate in anti-government collective
actions if it reduces some citizens’ incentive. Our study provides micro-level empiri-
cal evidence in support of these theoretical insights and explicates a specific and
critical mechanism, the influence of the presumed influence of propaganda, which
leads to preference falsification, pluralistic ignorance, and the breakdown of com-
mon knowledge. Study Design To test the above hypotheses, we conducted a survey experiment in July-August
2018 with 895 Chinese internet users from diverse backgrounds (see more below). The experiment proceeded as follows. Participants were first asked a battery of
background questions about their social and political attitudes, including life satis-
faction, national pride, political interest, pro-Western orientation, and evaluation of
China’s current political system. See Online Appendix 1 for question wording. They
were then randomly assigned into one of five groups: a control group that did not
receive any propaganda treatment and four treatment groups that each received a dif-
ferent propaganda message (see below). The experiment was designed to compare
individuals who were exposed to propaganda with individuals who were not. We use
four different propaganda treatments simply because there exists a wide variety of 1 3 3 1796 Political Behavior (2022) 44:1789–1812 propaganda, and we do not want to unnecessarily limit our analysis to a particular
message.i propaganda, and we do not want to unnecessarily limit our analysis to a particular
message.i Afterwards, all respondents were asked two sets of outcome questions, the first
about their own opinions about China’s current overall current situation, China’s
future prospects, the government’s ability in governing the country, its responsive-
ness to citizen demands, its ability to maintain social and political stability, and,
finally, their willingness to participate in protest against government malfeasance
and injustice in their region. Due to the political sensitivity of the last question,
we used the term “collective walk,” a widely understood codeword on the Chinese
internet, to refer to protest. The questions on China’s overall current situation, the Chinese government’s
governance, its responsiveness, and China’s future prospects were all intended to
measure respondents’ support for the government, so they were summed into an
aggregate variable regime support to avoid the issue of multiple hypothesis testing.5
The question on the Chinese government’s ability to maintain stability was intended
to measure its perceived power and capacity, in light of the signaling theory of
propaganda. The last question on “collective walk” simply measures willingness to
protest.6 The second set of outcome questions asked the respondents how they thought
an average person (“yiban ren”) in the society would answer the above questions
if they had been exposed to the same materials during the survey. 5 Cronbach’s alpha for the index is 0.796, indicating fairly good inter-item reliability. Cronbach’s alpha
for the index when measuring the respondents’ perceptions of other people’s support for the government
(see below) is even higher: 0.848.
6 The topics of willingness to protest and the regime’s stability-maintaining capacity were potentially
more politically sensitive than other questions. To increase the respondents’ willingness to complete the
survey and reduce their wariness, the survey only asked one question for each of the two topics. Study Design (For the control
group, participants were simply asked how they thought an average person would
answer the questions they had just answered). For example, in the first set of ques-
tions, respondents were asked about their willingness to protest, and, in the second
set, respondents were asked what they believed an average citizen’s willingness to
protest was. To avoid priming, the set of questions on the respondents’ own attitudes
and beliefs was asked before any questions on their perceptions of other people’s
attitudes and beliefs began. Finally, demographic information was collected. Given the between-subject experimental design, in the analysis below we will
compare answers to the self questions between the treatment and control groups to
obtain the “self effect” of propaganda (see Cohen et al. 1988, for a similar approach). This is the actual effect of propaganda on oneself rather than its perceived effect
on oneself. We will also compare answers to the other questions between the treat-
ment and control groups to obtain the “other effect” of propaganda. This is the pre-
sumed effect of propaganda on others. Naturally, individuals do not know the actual
effect of propaganda on others, and therefore we measure their perceptions of propa-
ganda’s effect on others. To examine the potentially different effects of propaganda
on individuals’ self attitudes and their perceptions of other people’s attitudes, we
will compare the differences between answers to the self and other questions in the 1 3 Political Behavior (2022) 44:1789–1812 1797 treatment groups and the differences in the control group, in addition to comparing
the self and other effects of propaganda.f treatment groups and the differences in the control group, in addition to comparing
the self and other effects of propaganda.f f
This approach differs from how most existing studies measure the self-other
perceptual differences. Existing studies typically use surveys, and respondents are
directly asked how they think a particular media message would respectively affect
themselves and others. But people might not have an accurate perception of a mes-
sage’s effect on themselves; for example, they sometimes under-report the amount
of actual change in their own opinions produced by media messages (Chung et al. 2017). In addition, direct questioning may have a social desirability problem. 7 The video can be viewed at http://www.chinanews.com/gn/shipin/2018/03-12/news760210.shtml (last
accessed December 30, 2020).
8 See http://world.huanqiu.com/article/2018-05/12116405.html (last accessed December 30, 2020) for
the article in Chinese.
9 See http://www.qstheory.cn/dukan/qs/2017-11/15/c_1121947684.htm (last accessed December 30,
2020) for the article in Chinese. Data The participants in the experiment were recruited through a market survey company,
with each unique user and IP address allowed only once in a survey to prevent repet-
itive participation. The respondents were directed to a US-based survey website to
take the survey anonymously, which also allowed us to maintain full control over the
survey, and the survey company did not have access to the data. There are several
reasons why conducting the survey experiment with an online sample is appropriate
for this study. First, online anonymity can make the respondents more truthful with
their answers than face-to-face or telephone surveys, which is crucial here, given the
sensitivity of our survey questions. Second, over half of China’s population are now
online, and the internet has become the center of activism and collective action in
the country, with the middle class broadly preferring digital forms of engagement
over traditional forms of political participation (Huang 2015a; Yang 2009). Under-
standing the internet population’s political attitudes and potential behavior is there-
fore particularly important. As shown in Online Appendix 1, the participants had
diverse sociodemographic backgrounds: They came from all walks of life, from var-
ious education backgrounds and age groups, and from all over China. In fact, their
gender, regional, urban/rural, and occupational distributions are broadly comparable
to China’s general internet population. They were younger and better educated on
average than the general population, but such characteristics may also be particularly
important for our topic: protest. Table 1 shows the summary statistics of the independent and dependent variables
across the experimental groups. With regards to the pre-treatment independent vari-
ables, all the demographic variables are balanced across the groups. Most of the pre-
treatment dispositional variables are also well balanced, with national pride being
the main exception. In the statistical regressions below, we control the demographic
and other pre-treatment covariates.i As for the dependent variables, Table 1 indicates that there are no significant dif-
ferences in the mean values of the self variables between the groups, but there are
significant differences in the mean values of the other regime support and other sta-
bility. This is mainly driven by the differences between the self variables and other
variables in the control group, as their differences in the treatment groups are much
smaller. 10 See http://media.people.com.cn/n1/2018/0129/c40606-29791511.html (last accessed December 30,
2020) for the article in Chinese. Study Design They should all feel ashamed,” which lauds the
achievements of China’s space program and its willingness to share the use of Chi-
na’s planned space station with foreign countries, in contrast to some other coun-
tries’ refusal to allow China to participate in the International Space Station project,
with some vivid examples (space treatment).8 The third treatment was an article
from the Seeking Truth magazine, titled “China is the world’s largest democracy,”
which argues that China actually has a democratic system and is the world’s largest
democracy due to its population (democracy treatment).9 The final treatment was 1 3 Political Behavior (2022) 44:1789–1812 1798 an article from the People’s Daily titled “The Whole World is Reading this Book:
Xi Jinping on Governance in China,” which touts the alleged popularity of said
book around the world (book treatment).10 Again, it is important to note that we are
not interested in comparing the effects of different treatments; rather, our goal is to
understand the differences between the treatment and the control conditions. an article from the People’s Daily titled “The Whole World is Reading this Book:
Xi Jinping on Governance in China,” which touts the alleged popularity of said
book around the world (book treatment).10 Again, it is important to note that we are
not interested in comparing the effects of different treatments; rather, our goal is to
understand the differences between the treatment and the control conditions. Study Design Indeed, studies have shown that messages viewed as socially desirable often elicit a
first-person effect: Respondents state that the positive messages have greater effects
on themselves than on others (e.g., Duck et al. 1995; Gunther and Thorson 1992). The social desirability problem may be particularly acute in an authoritarian coun-
try, where it is undesirable and even risky to directly reveal the lack of effect of
government messages—on themselves or others. Similarly, people’s reports of their
own level of support for the regime cannot be taken at face value. Indeed, some
recent studies on Chinese public opinion have shown that people often misrepresent
their true opinions on politically sensitive questions when asked directly (Jiang and
Yang 2016; Li et al. 2018). Our approach did not ask respondents directly how they
think propaganda affected themselves or others; rather, it measures propaganda’s
effects indirectly and unobtrusively through inter-group comparisons of political
attitudes and perceptions. Similarly, when analyzing self-other differences in politi-
cal attitudes, we do not focus on within-subject differences, since either self attitudes
or other attitudes (but particularly the former) may be misrepresented. Instead, we
focus on the inter-group differences in the self-other differences. ff
The four treatments were selected to cover the breadth of state media propaganda
in contemporary China. The first treatment was a short and artistically appealing
video, titled “China in One Minute,” made by China’s premier official newspaper
People’s Daily, that describes the country’s recent economic and social achieve-
ments (video treatment).7 The second treatment was an article from Global Times,
titled “China is just generous. Entries are group means for each variable. Standard deviations in parentheses Data For example, the difference between self regime support and other regime
support in the control group is about 0.27 on a five-point scale ( p < 0.001 ), but
they are at most around 0.1 in the treatment groups (specifically, in the case of the 1 3 Political Behavior (2022) 44:1789–1812 1799 Table 1 Summary statistics Table 1 Summary statistics
Entries are group means for each variable. Standard deviations in parentheses
Control
Video
Book
Democracy
Space
Min
Max
F
Prob > F
N = 175
N = 169
N = 204
N = 180
N = 167
Independent vari-
ables
Female
0.589
0.538
0.539
0.539
0.509
0
1
0.57
0.686
(0.493)
(0.500)
(0.500)
(0.500)
(0.501)
Age group
2.983
2.947
3.088
3.100
3.222
1
10
0.95
0.432
(1.603)
(1.436)
(1.314)
(1.506)
(1.335)
Education
4.343
4.420
4.407
4.239
4.521
1
6
1.96
0.099
(1.1015)
(1.078)
(0.929)
(0.982)
(0.904)
Income level
4.394
4.426
4.588
4.639
4.563
1
7
1.68
0.153
(1.055)
(1.100)
(1.021)
(1.181)
(1.117)
CCP member
0.117
0.207
0.240
0.150
0.174
0
1
1.50
0.201
(0.383)
(0.406)
(0.428)
(0.358)
(0.380)
Urban
0.617
0.609
0.598
0.606
0.605
0
1
0.04
0.997
(0.487)
(0.489)
(0.492)
(0.490)
(0.490)
Life satisfaction
3.549
3.621
3.721
3.456
3.437
0
5
2.18
0.070
(1.107)
(1.112)
(1.048)
(1.115)
(1.090)
Political interest
2.863
2.769
2.887
2.828
2.784
1
4
0.75
0.555
(0.776)
(0.845)
(0.724)
(0.746)
(0.807)
National pride
3.726
3.553
3.681
3.556
3.593
1
4
2.82
0.024
(0.508)
(0.724)
(0.613)
(0.749)
(0.678)
Pro-west orienta-
tion
2.837
2.926
2.870
2.917
2.916
1
4
0.61
0.653
(0.626)
(0.658)
(0.621)
(0.688)
(0.644)
System evaluation
3.474
3.361
3.466
3.372
3.365
1
4
1.07
0.369
(0.702)
(0.752)
(0.690)
(0.784)
(0.779)
Dependent variables
Self regime sup-
port
3.124
3.178
3.290
3.204
3.204
0.5
4
1.44
0.217
(0.681)
(0.737)
(0.645)
(0.695)
(0.681)
Other regime
support
2.840
3.249
3.199
3.083
3.207
0
4
8.64
<0.001
(0.826)
(0.673)
(0.701)
(0.775)
(0.752)
Self regime stabil-
ity
4.274
4.337
4.324
4.344
4.347
1
5
0.30
0.878
(0.761)
(0.723)
(0.752)
(0.663)
(0.711)
Other regime
stability
3.989
4.302
4.230
4.222
4.311
1
5
5.10
0.001
(0.864)
(0.662)
(0.756)
(0.706)
(0.806)
Self protest
2.377
2.337
2.441
2.350
2.473
1
4
0.65
0.624
(0.968)
(0.925)
(1.023)
(0.948)
(0.943)
Other protest
2.749
2.509
2.578
2.550
2.515
1
4
1.93
0.104
(0.919)
(0.901)
(0.962)
(0.923)
(0.950) 3 1800 Political Behavior (2022) 44:1789–1812 Fig. 1 Treatment effects on regime support. 11 It is also interesting that in the baseline (control) condition, the respondents’ self-reported regime sup-
port and assessment of regime stability are higher than their perception of other people’s regime sup-
port and assessment of regime stability, and their self-reported willingness to protest is lower than their
perception of other people’s protest willingness. However, due to the political desirability of overstating
one’s support for the regime and understating willingness to dissent, we do not take this self-reported
self-other difference within each group at face value. Instead, we focus on the inter-group differences. Data These are regression coefficients of the treatments, showing
their effects on the respondents’ own regime support (left), their perceptions of other people’s regime
support (middle), and the differences between their perceptions of other people’s regime support and
their own regime support (right). “TREATED” represents a separate model where all treatment groups
were pooled as the “treated” group. Regime support is re-scaled to range from 0 to 1. The horizontal
lines represent 95% confidence intervals Fig. 1 Treatment effects on regime support. These are regression coefficients of the treatments, showing
their effects on the respondents’ own regime support (left), their perceptions of other people’s regime
support (middle), and the differences between their perceptions of other people’s regime support and
their own regime support (right). “TREATED” represents a separate model where all treatment groups
were pooled as the “treated” group. Regime support is re-scaled to range from 0 to 1. The horizontal
lines represent 95% confidence intervals democracy group, p = 0.009 ). Essentially, it appears the treatments increased the
values of the other variables, without similarly increasingly the values of the self
variables.11 The next section will take a closer look into the differences. Presumed Influence of Propaganda We first report the results about propaganda’s effects on individuals’ preferences and
beliefs about the government, their perceptions of propaganda’s effects on other peo-
ple’s preferences and beliefs, and the self-other differences. Figure 1 plots the effects 1 3 Political Behavior (2022) 44:1789–1812 1801 of the treatments on regime support, with and without controlling for demographic
and attitudinal covariates (see Tables S2 and S3 in Online Appendix for numerical
regression results). The left panel of Fig. 1 shows that, without controlling for the
covariates, only the treatment about Xi Jinping’s book significantly increased the
respondents’ self regime support relative to the control condition, while the other
three treatments did not change self regime support. When the covariates are con-
trolled, all four treatments increased the respondents’ self regime support. Using the
omnibus variable “TREATED,” which indicates whether a respondent received any
treatment, the effect size of the treatments on self regime support was 3.9 percentage
points (with covariates controlled, see Table S2). The middle panel of Fig. 1 shows
that, whether controlling for the covariates or not, all four treatments significantly
increased the respondents’ perceptions of other people’s regime support. The effect
size of the TREATED variable for other regime support when the covariates are
controlled was 9.2 percentage points, more than twice as large as the effect size for
self regime support.if This suggests the treatments had a significantly greater effect on the respond-
ents’ assessment of other people’s regime support than on their own regime sup-
port. The right panel of Fig. 1 shows this is indeed the case. Here the estimand is
the difference between the respondents’ perceptions of other people’s regime sup-
port and their own regime support. The panel shows that the other-self discrepancies
are significantly larger in all treatment groups except the democracy group than in
the control group. In other words, not only did the respondents believe propaganda
increased other people’s support for the regime, but the messages had a stronger
effect on their perceptions of other citizens’ regime support than on their own sup-
port, consistent with H1.f Figure 2 plots the effects of the treatments on the respondents’ assessment of
regime stability (see Tables S4 and S5 in Online Appendix for numerical regression
results). Presumed Influence of Propaganda The left panel shows that, none of the four propaganda treatments increased
the respondents’ own assessment of regime stability relative to the control condi-
tion, whether controlling for the covariates or not. The middle panel, on the other
hand, shows that all four propaganda messages increased their perceptions of other
people’s assessment of regime stability. The effect size of the omnibus TREATED
variable for other regime stability is 6.7 percentage points. This suggests that propa-
ganda has stronger effects on the respondents’ perceptions of other people’s assess-
ment of regime stability than on their own assessment of regime stability. The right
panel of Fig. 2 shows that this is indeed the case. Here the estimand is the difference
between the respondents’ perceptions of other people’s assessment of regime stabil-
ity and their own assessment of regime stability. The panel shows that the other-self
discrepancies are larger in all treatment groups except the democracy group, where
the difference misses the .05 significance level, than in the control group. This is
because propaganda increased the respondents’ perceptions of other people’s assess-
ment of regime stability without similarly increasing their own assessment of regime
stability. The results are consistent with H2.ff To further test the difference between the treatments’ effects on self attitudes
and on other attitudes, we conduct coefficient equality tests for regime support
and assessment of regime stability using seemingly unrelated regressions (SUR), 1 3 3 3 Political Behavior (2022) 44:1789–1812 1802 Fig. 2 Treatment effects on assessment of regime stability. These are regression coefficients of the treat-
ments, showing their effects on the respondents’ own assessment of regime stability (left), their per-
ceptions of other people’s assessment of regime stability (middle), and the differences between their
perceptions of other people’s assessment of regime stability and their own assessment of regime sta-
bility (right). “TREATED” represents a separate model where all treatment groups were pooled as the
“treated” group. Assessment of regime stability is re-scaled to range from 0 to 1. The horizontal lines
represent 95% confidence intervals Fig. 2 Treatment effects on assessment of regime stability. These are regression coefficients of the treat-
ments, showing their effects on the respondents’ own assessment of regime stability (left), their per-
ceptions of other people’s assessment of regime stability (middle), and the differences between their
perceptions of other people’s assessment of regime stability and their own assessment of regime sta-
bility (right). Presumed Influence of Propaganda “TREATED” represents a separate model where all treatment groups were pooled as the
“treated” group. Assessment of regime stability is re-scaled to range from 0 to 1. The horizontal lines
represent 95% confidence intervals which estimate self attitudes and other attitudes as a system of equations and
allow the errors in different equations to be correlated. The top panel of Table 2
shows that except for the democracy treatment, the coefficients of all other treat-
ments as well as the omnibus TREATED variable are larger for other regime sup-
port than for self regime support. The bottom panel shows that the coefficients of
all treatments are larger for other regime stability than for self regime stability,
although the difference is only significant at .1 percent level for the democracy
treatment. The results are consistent with Figs. 1 and 2 and once more indicate
that propaganda has differential effects on the respondents’ own regime support
and assessment of regime stability than on their perceptions of others. The results above lend strong support to both H1 and H2. Propaganda makes
the respondents perceive that other people are now more supportive of the regime
and that the regime’s ability to maintain stability is now stronger in other peo-
ple’s assessment. This presumed influence on other peoples’ regime support and
assessment of regime stability is stronger than propaganda’s influence on the
respondents’ own regime support and assessment of regime stability. 1 3 Political Behavior (2022) 44:1789–1812 1803 Table 2 Coefficient equality
tests for regime support and
assessment of regime stability Table 2 Coefficient equality
tests for regime support and
assessment of regime stability Equality of coefficient tests with seemingly unrelated regressions,
controlling for demographic and pre-treatment attitudinal covariates. “TREATED” represents a separate model where all treatment groups
were pooled together as the “treated” group
Treatment
Coefficient
Standard error
P
Other regime support – self regime support
Video
0.080
0.017
0.000
Democracy
0.026
0.017
0.129
Book
0.047
0.016
0.004
Space
0.062
0.017
<0.001
TREATED
0.053
0.014
<0.001
Other regime stability – self regime stability
Video
0.059
0.019
0.002
Democracy
0.035
0.019
0.070
Book
0.047
0.018
0.010
Space
0.058
0.019
0.003
TREATED
0.049
0.015
0.001 Treatment
Coefficient
Standard error
P Equality of coefficient tests with seemingly unrelated regressions,
controlling for demographic and pre-treatment attitudinal covariates. Presumed Influence of Propaganda “TREATED” represents a separate model where all treatment groups
were pooled together as the “treated” group One potential concern about our results is that since our sample is not representa-
tive of Chinese society, when the respondents answered questions about what an
average person (“yiban ren”) in the society would think about the government, they
might have in mind someone different from themselves. In particular, the average
person in the society may be less well educated and have lower income than our
sample. Indeed, while most of the self-other perceptual gaps in the third person
effect literature can be interpreted as biases, Shen et al. (2018) argue that some self-
other perceptual gaps may reflect accurate differences, rather than biases, because
the individuals in question are comparing themselves to a different group of people. f
One way to address the issue is to recognize that because people tend to interact
more with and live among people who are like themselves, they tend to overestimate
their own representativeness in the population. As a result, when they think about
“an average person in the society,” the person they have in mind would be more sim-
ilar to themselves than an actual average person in the society. In that sense, what
the actual average person is like is not as crucial as people’s perception of what an
average person is like. Nevertheless, to mitigate the concern that our respondents might be thinking
about people very different from themselves in demographic characteristics when
answering questions about the “average person,” we divided the participants into
those with college education and those without, and those with high income and
those with low income (based on the median values). We then interact the treat-
ments with both education and income, and regress the outcome variables on the
interaction terms. As Tables S8–S11 in Online Appendix show, the coefficients of
the interaction terms were never statistically significant, meaning that the college-
educated did not react to the treatments differently from the non-college-educated,
and that the high-income people did not react to the treatments differently from 1 3 3 3 1804 Political Behavior (2022) 44:1789–1812 Fig. 3 Treatment effects on willingness to protest. Presumed Influence of Propaganda These are regression coefficients of the treatments,
showing their effects on the respondents’ willingness to protest (left), their perceptions of other people’s
willingness to protest (middle), and the differences between other people’s presumed willingness to pro-
test and the respondents’ own willingness to protest (right). “TREATED” represents a separate model
where all treatment groups were pooled as the “treated” group. Willingness to support is re-scaled to
range from 0 to 1. The horizontal lines represent 95% confidence intervals Fig. 3 Treatment effects on willingness to protest. These are regression coefficients of the treatments,
showing their effects on the respondents’ willingness to protest (left), their perceptions of other people’s
willingness to protest (middle), and the differences between other people’s presumed willingness to pro-
test and the respondents’ own willingness to protest (right). “TREATED” represents a separate model
where all treatment groups were pooled as the “treated” group. Willingness to support is re-scaled to
range from 0 to 1. The horizontal lines represent 95% confidence intervals the low-income people, with regards to either self attitudes or perceptions of other
attitudes. This suggests that responses to the “average person” questions were not
affected by the lack of representativeness of the online sample. 12 In line with much of the literature on the third-person effect and influence of presumed influence, we
use behavioral intentions or attitudes toward behavior to measure behavioral effects. Behavioral Effects of Propaganda’s Presumed Influence We now examine propaganda’s effect on individuals’ willingness to protest, their
perceptions of other citizens’ willingness to protest, and how the latter may affect
the former.12 Corresponding to Figs. 1, 2, and 3 plots the effects of the treatments
on the respondents’ own willingness to protest and their perceptions of others’
willingness to protest (see Tables S6 and S7 for numerical regression results). The left and middle panels show that the propaganda treatments did not affect the
respondents’ willingness to protest relative to the control condition, but they did
reduce their perceptions of other people’s willingness to protest, which is natural, 1 3 Political Behavior (2022) 44:1789–1812 1805 Table 3 Coefficient equality
tests for protest willingness Table 3 Coefficient equality
tests for protest willingness Equality of coefficient tests with seemingly unrelated regressions. “TREATED” represents a separate model where all treatment groups
were pooled as the “treated” group
Treatment
Coefficient
Standard error
P
Other protest willingness – self protest willingness
Video
− 0.052
0.023
0.024
Democracy
− 0.037
0.023
0.100
Book
− 0.060
0.022
0.006
Space
− 0.082
0.023
<0.001
TREATED
− 0.058
0.018
0.001 Coefficient
Standard error
P Equality of coefficient tests with seemingly unrelated regressions. “TREATED” represents a separate model where all treatment groups
were pooled as the “treated” group Fig. 4 Direct and indirect effects of propaganda on willingness to protest Fig. 4 Direct and indirect effects of propaganda on willingness to protest given propaganda’s presumed influence on other people’s regime support and
assessment of regime stability, and consistent with H3a. The right panel of Fig. 3
and the coefficient equality tests in Table 3 indicate that the treatments indeed
have differential effects on self protest willingness and other protest willingness.i ff
While the above result confirms H3a, it does not address a critical part of our
third hypothesis, namely whether individuals’ perceptions of other citizens’ will-
ingness to protest would affect their own willingness to protest (H3b). In particu-
lar, the null total effects of propaganda on the respondents’ self protest willing-
ness, shown in Fig. 3, is a combination of the direct effect of propaganda on their
own protest willingness and the indirect effect of propaganda on their willingness
to protest through its impact on other citizens’ presumed willingness to protest
(the mediator), as illustrated in Fig. 4. Behavioral Effects of Propaganda’s Presumed Influence We need to separate the two effects to
understand how changes in other people’s presumed willingness to protest affect
individuals’ own willingness to protest.f Therefore, to test H3b and unpack the indirect effect of propaganda on individu-
als’ protest willingness through its effect on their perceptions of other people’s pro-
test willingness, we employ mediation analysis (Imai et al. 2010, 2011). This method 1 3 Political Behavior (2022) 44:1789–1812 1806 Table 4 Mediation analysis: propaganda’s effect on self protest with other protest as the mediator
ACE is average causal mediation effect, and ADE is average direct effect. Robust standard errors in
parentheses. ***p < 0.001 , **p < 0.01 , * p < 0.05
Video
Democracy
Book
Space
TREATED
ACME
− 0.036*
− 0.030*
− 0.029*
− 0.031*
− 0.032**
(0.015)
(0.014)
(0.029)
(0.015)
(0.012)
ADE
0.029
0.008
0.041*
0.061**
0.034*
(0.020)
(0.023)
(0.021)
(0.022)
(0.017)
Total effect
− 0.007
− 0.022
0.013
0.030
0.002
(0.025)
(0.026)
(0.025)
(0.026)
(0.021) separates the average treatment effect (total effect) into two components: the Aver-
age Causal Mediation Effect (ACME) and the Average Direct Effect (ADE). The
former represents the indirect effect of the treatment on the outcome through the
mediator, while the latter represents the direct effect of the treatment on the outcome
with no mediator. The method is intended to ascertain if the treatment explains any
variation in the mediator and if that variation in turn explains any variation in the
outcome. separates the average treatment effect (total effect) into two components: the Aver-
age Causal Mediation Effect (ACME) and the Average Direct Effect (ADE). The
former represents the indirect effect of the treatment on the outcome through the
mediator, while the latter represents the direct effect of the treatment on the outcome
with no mediator. The method is intended to ascertain if the treatment explains any
variation in the mediator and if that variation in turn explains any variation in the
outcome. Our mediation model has propaganda exposure as the treatment, individuals’
perceptions of other people’s protest willingness as the mediator, and individuals’
own protest willingness as the outcome. Table 4 presents the results of the mediation
analysis. The ACMEs of the Video, Democracy, Book, and Space propaganda treat-
ments as well as the omnibus TREATED variable are all negative and significant. 13 The result also suggests that the perceived self-other discrepancy in media and propaganda effects
may reflect not just magnitude but also direction. Behavioral Effects of Propaganda’s Presumed Influence This
essentially translates to assuming that there are no unmeasured pre-treatment or
post-treatment covariates that confound the relationship between the mediator and
outcome. It is this latter component of the mediation model that potentially poses a
threat to our inference.i Recall that the survey experiment first exposed participants to propaganda mes-
sages, then asked them about their own willingness to protest, and later asked them
about their perceptions of others’ willingness to protest. Because the outcome is
measured before the mediator, this raises the potential that a question ordering effect
is creating endogeneity between the outcome and mediator. In other words, it could
be the case that a correlation between self protest and other protest is a causal effect
of the former on the latter via a priming effect. However, in our survey, the question
measuring the respondents’ own willingness to protest (self protest) did not immedi-
ately precede the question measuring their perceptions of other people’s willingness
to protest (other protest). The set of questions on the respondent’s own attitudes and
behavior was asked before the set of questions on others began, so there was consid-
erable space between the questions measuring self protest and other protest. There-
fore, any question ordering effects are likely to be minimal.f f
Nevertheless, to offer evidence about the appropriateness of the mediation analy-
sis, we conduct a sensitivity analysis and analyze additional, re-specified, media-
tion models. Figure 5 presents the sensitivity analysis for the mediation models of
Table 4. The sensitivity analysis tests for the degree to which the confidence interval
for an indirect effect is sensitive to the correlation between the residuals of the medi-
ator and outcome regressions, which is defined as 휌 . In other words, this test esti-
mates the degree of correlation between these two sets of residuals that is necessary
to make the confidence interval around the indirect effect contain zero. In effect,
this tests for how sensitive the ACME is to a confounding variable. For our models,
the sensitivity analysis estimates a 휌 of approximately 0.6, which indicates that the
estimates of our mediation model are relatively robust to the presence of a potential
confounding variable. For further robustness, we estimated additional mediation models, but this time
the mediating and outcome variables were swapped. Behavioral Effects of Propaganda’s Presumed Influence This provides strong evidence that propaganda exposure indirectly reduces individu-
als’ protest willingness by reducing their perceptions of others’ protest willingness,
as stated in H3b. The ADEs of the Video and Democracy treatments cannot be dis-
tinguished from zero, but interestingly the Book and Space treatments have posi-
tive direct effects on protest willingness, suggesting that propaganda messages may
sometimes unwittingly cause citizens to want to protest, a kind of backfire effect. In
our experiment, this is perhaps because the propaganda messages about the great-
ness of China and its leader encourage the respondents to express willingness to dis-
sent against injustice and government malfeasance, which are holding China back.13
But regardless of propaganda’s direct effect, people’s concern about other citizens’
interpretation of and reactions to propaganda pulled them back and reduced their
desire to protest to the null condition, as reflected in the insignificant total effect of
propaganda on protest willingness.i The finding of the mediation model does come with one important caveat,
however. As Imai et al. (2011) show, use of a mediation model to infer causality
must satisfy one key assumption: sequential ignorability. This assumption has two
components. First, given the observed pre− treatment confounders, the treatment 1 3 1 3 Political Behavior (2022) 44:1789–1812 1807 assignment is statistically independent of potential outcomes and potential media-
tors. In other words, we are assuming that there are no omitted variables confound-
ing the relationship between the treatment and the mediator and the relationship
between the treatment and the outcome. This first component of the assumption
holds because treatment assignment is randomized. Second, the observed mediator
is ignorable given the actual treatment status and pre-treatment confounders. This
essentially translates to assuming that there are no unmeasured pre-treatment or
post-treatment covariates that confound the relationship between the mediator and
outcome. It is this latter component of the mediation model that potentially poses a
threat to our inference.i assignment is statistically independent of potential outcomes and potential media-
tors. In other words, we are assuming that there are no omitted variables confound-
ing the relationship between the treatment and the mediator and the relationship
between the treatment and the outcome. This first component of the assumption
holds because treatment assignment is randomized. Second, the observed mediator
is ignorable given the actual treatment status and pre-treatment confounders. Discussion and Conclusion This study experimentally shows that people often believe that propaganda increases
other people’s support for a regime or their beliefs about a regime’s capacity to
maintain stability. In fact, the presumed influence of propaganda on other people’s
support for and beliefs about a regime are usually stronger than propaganda’s actual
influence on oneself. Consequently, propaganda can reduce people’s perceptions of
other people’s willingness to protest, which in turn dilutes their own propensity to
protest due to its risky nature under authoritarian regimes. Thus, propaganda can
stave off dissent not by directly changing individuals’ own attitudes and intentions
but, instead indirectly, by altering people’s perceptions of other people’s attitudes
and behavioral intentions.i These findings imply that, due to the complementarity of participation in mass
protest, authoritarian regimes have a special advantage by being the agenda setters
in the propaganda game. Propaganda does not have to directly change individuals’
own willingness to protest to be effective. As long as propaganda reduces individu-
als’ perceptions of other people’s willingness to protest, or just makes them uncer-
tain if other citizens have been influenced by it, they will be more timid in challeng-
ing the regime. Propaganda can achieve much of its function for the regime simply
by sowing uncertainty among citizens about what they think others think and will
do. Different from what conventional wisdom often assumes, the power of propa-
ganda may sometimes lie more in the social perception and uncertainty it creates
than in changes it induces in individuals’ own political attitudes and beliefs. The study thus enriches theories of authoritarian propaganda, which have so far
focused on propaganda’s direct effect on individuals’ themselves. The results also
contrast with findings in the existing literature that in democratic and semi-dem-
ocratic societies, where basic rights of expression and association are guaranteed,
stronger perception of other people’s willingness to participate in protest or voting,
or perceptions of protest news’s effects on other people, are associated with a lower
willingness to participate (Banning 2006; Cantoni et al. 2019; Lo et al. 2017). In
these societies, participation is more of a public good that demands a threshold level
of contribution: Perception of other people’s participation reduces the need for one-
self to participate in order to meet the threshold and, thus, could drive down one’s
own willingness to participate. In other words, these are games of substitutes. Behavioral Effects of Propaganda’s Presumed Influence If it is indeed the case that indi-
viduals’ own willingness to protest is driving their perceptions of others’ willingness
to protest, then it should be the case that the propaganda exposure explains some
variation in self willingness to protest, and that variation in turn explains some vari-
ation in others’ presumed willingness to protest. However, these alternative mod-
els failed to identify a significant ACME. As Table 5 shows, the ACME is consist-
ently indistinguishable from zero for all treatment conditions, suggesting that the
variations in self protest that were caused by treatment exposure did not explain the
variations in other protest. Additionally, consistent with our earlier finding that treat-
ment exposure caused a reduction in other protest, the ADE and total effect of these 1 3 3 3 1808 Political Behavior (2022) 44:1789–1812 Fig. 5 Protest mediation sensitivity Fig. 5 Protest mediation sensitivity Table 5 Alternative mediation analysis: propaganda’s effect on other protest with self protest as the
mediator Table 5 Alternative mediation analysis: propaganda’s effect on other protest with self protest as th
mediator ACE is average causal mediation effect, and ADE is average direct effect. Robust standard errors in
parentheses. ***p < 0.001 , **p < 0.01 , * p < 0.05
Video
Democracy
Book
Space
TREATED
ACME
− 0.004
− 0.012
0.007
0.016
0.001
(0.017)
(0.014)
(0.013)
(0.014)
(0.011)
ADE
− 0.058**
− 0.044*
− 0.058**
− 0.073***
− 0.056***
(0.020)
(0.021)
(0.020)
(0.022)
(0.017)
Total effect
− 0.062*
− 0.056*
− 0.051*
− 0.057*
− 0.055**
(0.025)
(0.025)
(0.024)
(0.026)
(0.021) ACE is average causal mediation effect, and ADE is average direct effect. Robust standard errors in
parentheses. ***p < 0.001 , **p < 0.01 , * p < 0.05 alternative mediation models are significantly negative in all cases. These results
suggest that the possibility of a confounding priming effect is negligible. Our initial
mediation analysis results are therefore fairly robust: Perceptions of others’ reduced 1 Political Behavior (2022) 44:1789–1812 1809 willingness to protest due to propaganda would drive down people’s own willing-
ness to protest. willingness to protest due to propaganda would drive down people’s own willing-
ness to protest. Discussion and Conclusion Col-
lective protests in authoritarian settings, however, are strategic games of comple-
ments (Chwe 2003; Edmond 2013; Gehlbach et al. 2016): The more/less willing
other people are to participate, the more/less willing are individuals themselves. It
is in this strategic setting that propaganda can inhibit people’s willingness to protest
by reducing their perceptions of other people’s willingness to protest. And it is this
mechanism that contributes to preference falsification, pluralistic ignorance, and the
breakdown of common knowledge (Chwe 2003; Havel 1985; Kuran 1991). 1 3 1810 Political Behavior (2022) 44:1789–1812 Besides enriching our understanding of authoritarian propaganda, this study
also contributes to the literature on the influence of presumed media influence. The
standard literature on the influence of presumed influence focuses on people’s per-
ceptions of media’s influence on others, without comparing the influence on others
with influence on oneself. The third-person effect literature, on the other hand, focus
on the discrepancy between media’s presumed influence on oneself and on others,
without considering wither the presumed effect on oneself is accurate, or whether
the presumed influence of media is really stronger than its actual influence on one-
self. We show that propaganda’s presumed effects on others can be stronger than its
actual effects on oneself, not just stronger than its presumed effects on oneself. It
is this “real” presumed influence of propaganda that leads to one’s perceptions of
propaganda’s influence on other people’s behavior, which in turn affects one’s own
behavior.f One limitation of the study is that the propaganda messages had negative effects
on the respondents’ perceptions of other people’s protest willingness, hence nega-
tive indirect effects on their own protest willingness, but the messages had either
null or positive direct effects on the respondents’ protest willingness. As discussed
above, the positive direct effect is likely because the propaganda messages about the
greatness of China and its leader encouraged the respondents to express willingness
to dissent against injustice and government malfeasance, which were holding China
back. Self-other perceptual discrepancies have always been recognized in the third-
person effect literature as a kind of inconsistency or bias. Our study suggests the
self-other discrepancies may be larger than typically understood: A media message’s
self and other effects may differ not just in magnitude but also in direction. Acknowledgements The authors would like to thank Zhaotian Luo, Arturas Rozenas, Minh Trinh, audi-
ence members at APSA and MPSA, and several anonymous reviewers for helpful comments. Replication
data are available at https://doi.org/10.7910/DVN/ZEYLMH Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,
which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as
you give appropriate credit to the original author(s) and the source, provide a link to the Creative Com-
mons licence, and indicate if changes were made. The images or other third party material in this article
are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons licence and your intended use is
not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission
directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licen
ses/by/4.0/. Adena, M., Enikolopov, R., Petrova, M., Santarosa, V., & Zhuravskaya, E. (2015). Radio and the Rise of
the Nazis in Prewar Germany. The Quarterly Journal of Economics, 130(4), 1885–1939. Discussion and Conclusion Under-
standing the causes and/or prevalence of the directional divergence goes beyond the
scope of this study, but it is potentially an important issue for future research. Supplementary Information The online version contains supplementary material available at https://doi. org/10.1007/s11109-021-09683-0. Acknowledgements The authors would like to thank Zhaotian Luo, Arturas Rozenas, Minh Trinh, audi-
ence members at APSA and MPSA, and several anonymous reviewers for helpful comments. Replication
data are available at https://doi.org/10.7910/DVN/ZEYLMH References Adena, M., Enikolopov, R., Petrova, M., Santarosa, V., & Zhuravskaya, E. (2015). Radio and the Rise of
the Nazis in Prewar Germany. The Quarterly Journal of Economics, 130(4), 1885–1939. 1 3 1 3 1 3 Political Behavior (2022) 44:1789–1812 1811 Banning, S. A. (2006). Third-person effects on political participation. Journalism & Mass Communica-
tion Quarterly, 83(4), 785–800. Bueno De Mesquita, E. (2010). Regime change and revolutionary entrepreneurs. American Political Sci-
ence Review, 104(3), 446–466. Cantoni, D., Chen, Y., Yang, D. Y., Yuchtman, N., & Zhang, Y. J. (2017). Curriculum and ideology. Jour-
nal of Political Economy, 125(2), 338–392. Cantoni, D., Yang, D. Y., Yuchtman, N., & Zhang, Y. J. (2019). Protests as strategic games: Experimen-
tal evidence from Hong Kong’s antiauthoritarian movement. The Quarterly Journal of Economics,
134(2), 1021–1077.f Chung, S., Heo, Y.-J., & Moon, J.-H. (2017). Perceived versus actual polling effects: Biases in percep-
tions of election poll effects on candidate evaluations. International Journal of Public Opinion
Research, 30(3), 420–442.f Chung, S., & Moon, S.-I. (2016). Is the third-person effect real? A critical examination of rationales, test-
ing methods, and previous findings of the third-person effect on censorship attitudes. Human Com-
munication Research, 42(2), 312–337. Chwe, M. S.-Y. (2003). Rational ritual: Culture, coordination, and common knowledge. Princeton:
Princeton University Press. Cohen, J., Mutz, D., Price, V., & Gunther, A. (1988). Perceived impact of defamation: An experiment on
third-person effects. Public Opinion Quarterly, 52(2), 161–173.f f
Davison, W. P. (1983). The third-person effect in communication. Public Opinion Quarterly, 47(1), 1–15. Dohle, M., Bernhard, U., & Kelm, O. (2017). Presumed media influences and demands for restric-
tions: Using panel data to examine the causal direction. Mass Communication and Society, 20(5),
595–613.l Duck, J. M., Terry, D. J., & Hogg, M. A. (1995). The perceived influence of AIDS advertising: Third-
person effects in the context of positive media content. Basic and Applied Social Psychology, 17(3),
305–325. Edmond, C. (2013). Information manipulation, coordination, and regime change. Review of Econom
Studies, 80(4), 1422–1458. Egorov, G., Guriev, S., & Sonin, K. (2009). Why resource-poor dictators allow freer media: A theory an
evidence from panel data. American Political Science Review, 103(4), 645–668. p
Gehlbach, S., & Sonin, K. (2014). Government control of the media. Journal of Public Economics, 118,
163–171. Gehlbach, S., Sonin, K., & Svolik, M. W. (2016). Formal models of nondemocratic politics. Annual
Review of Political Science, 19, 565–584. Golan, G. J., Banning, S. References Research & Politics, 5(1), 1–8. Little, A. (2017). Propaganda and credulity. Games and Economic Behavior, 102, 224–232.f Lo, V.-H., Wei, R., & Lu, H.-Y. (2017). Issue importance, third-person effects of protest news, and par-
ticipation in Taiwan’s sunflower movement. Journalism & Mass Communication Quarterly, 94(3),
682–702. Lohmann, S. (1994). The dynamics of information cascades: The Monday demonstrations in Leipzi
East Germany, 1981–91. World Politics, 47(1), 42–101.llf Mutz, D. C. (1989). The influence of perceptions of media influence: Third person effects and the public
expression of opinions. International Journal of Public Opinion Research, 1(1), 3–23.f Peisakhin, L., & Rozenas, A. (2018). Electoral effects of biased media: Russian television in Ukraine. American Journal of Political Science, 62(3), 535–550. Peisakhin, L., & Rozenas, A. (2018). Electoral effects of bia
American Journal of Political Science, 62(3), 535–550. Peiser, W., & Peter, J. (2000). Third-person perception of television-viewing behavior. Journal of Com-
munication, 50(1), 25–45.ff Perloff, R. M. (1999). The third person effect: A critical review and synthesis. Media Psychology, 1(4),
353–378.ff Perloff, R. M. (2009). Mass media, social perception, and the third-person effect. In J. Bryant & M. B. Oliver
(Eds.), Media effects: Advances in theory and research (3rd ed., pp. 252–268). Abingdon: Routledge.f Price, V., & Tewksbury, D. (1996). Measuring the third-person effect of news: The impact of questio
order, contrast and knowledge. International Journal of Public Opinion Research, 8(2), 120–141.f Rojas, H. (2010). Corrective actions in the public sphere: How perceptions of media and media effec
shape political behaviors. International Journal of Public Opinion Research, 22(3), 343–363. Rozenas, A., & Stukal, D. (2019). How autocrats manipulate economic news: Evidence from Russia’s
state-controlled television. Journal of Politics, 81, 982–996. Shen, L., Sun, Y., & Pan, Z. (2018). Not all perceptual gaps were created equal: Explicating the third-
person perception (TPP) as a cognitive fallacy. Mass Communication and Society, 21(4), 399–424. Sun, Y., Pan, Z., & Shen, L. (2008). Understanding the third-person perception: Evidence from a met
analysis. Journal of Communication, 58(2), 280–300. y
Svolik, M. W. (2012). The politics of authoritarian rule. Cambridge: Cambridge University Press. T l O
N T f ti Y & G
th
A C (2009) Th i fl
f
d
di i fl
O i i Tal-Or, N., Tsfati, Y., & Gunther, A. C. (2009). The influence of presumed media influence: Origins and
implications of the third-person perception. In R. L. Nabi & M. B. References A., & Lundy, L. (2008). Likelihood to vote, candidate choice, and the third-per-
son effect: Behavioral implications of political advertising in the 2004 Presidential Election. Ameri-
can Behavioral Scientist, 52(2), 278–290.f Gunther, A. C., & Thorson, E. (1992). Perceived persuasive effects of product commercials and pub-
lic service announcements: Third-person effects in new domains. Communication Research, 19(5),
574–596.ll Gunther, A. C., & Storey, J. D. (2003). The influence of presumed influence. Journal of Communicatio
53(2), 199–215. Guriev, S., & Treisman, D. (2020). A theory of informational autocracy. Journal of Public Economic
186, 104158. Havel, V. (1985). The power of the powerless: Citizens against the State in Central-Eastern Europe. Armonk: M.E. Sharpe. Huang, H. (2015a). International knowledge and domestic evaluations in a changing society: The case
China. American Political Science Review, 109(3), 613–634. Huang, H. (2015b). Propaganda as signaling. Comparative Politics, 47(4), 419–444. Huang, H. (2018). The pathology of hard propaganda. The Journal of Politics, 80(3), 1034–1038. Imai, K., Keele, L., & Tingley, D. (2010). A general approach to causal mediation analysis. Psychological
Methods, 15(4), 309. Imai, K., Keele, L., Tingley, D., & Yamamoto, T. (2011). Unpacking the black box of causality: Learning
about causal mechanisms from experimental and observational studies. American Political Science
Review, 105(4), 765–789. ,
( ),
Jang, S. M., & Kim, J. K. (2018). Third person effects of fake news: Fake news regulation and media lit-
eracy interventions. Computers in Human Behavior, 80, 295–302. 1 3 1812 Political Behavior (2022) 44:1789–1812 Jiang, J., & Yang, D. L. (2016). Lying or believing? Measuring preference falsification from a politic
purge in China. Comparative Political Studies, 49(5), 600–634.l Jin, B., Chung, S., & Byeon, S. (2018). Media influence on intention for risk-aversive behaviors: The
direct and indirect influence of blogs through presumed influence on others. International Journal
of Communication, 12, 2443–2460. Jowett, G. S., & O’Donnell, V. (2018). Propaganda & Persuasion. Newbury Park: Sage Publications. Jowett, G. S., & O’Donnell, V. (2018). Propaganda & Persuasion. Newbury Park: Sage Publications. Kuran, T. (1991). Now out of never: The element of surprise in the East European revolution of 1989. World Politics, 44(1), 7–48. Kuran, T. (1991). Now out of never: The element of surprise in the East European revolution of 198
World Politics, 44(1), 7–48. Li, X., Shi, W., & Zhu, B. (2018). The face of internet recruitment: Evaluating the labor markets of online
crowdsourcing platforms in China. References Oliver (Eds.) The SAGE Hand-
book of Media Processes and Effects. SAGE Publications chapter 7 (pp. 99–112). f
Tewksbury, D., Moy, P., & Weis, D. S. (2004). Preparations for Y2K: Revisiting the behavioral comp
nent of the third-person effect. Journal of Communication, 54, 138–155.f f
Tsay-Vogel, M. (2016). Me versus Them: Third-person effects among Facebook users. New Media
Society, 18(9), 1956–1972. Wedeen, L. (1999). Ambiguities of domination: Politics, rhetoric, and symbols in contemporary Syria. Chicago: University of Chicago Press.l Wei, R., Lo, V., & Golan, G. (2017). Examining the relationship between presumed influence of US
news about China and the support for the Chinese Government’s Global Public relations campaigns. International Journal of Communication, 11, 2964–2981. Xu, J., & Gonzenbach, W. J. (2008). Does a perceptual discrepancy lead to action? A meta-analysis of the
behavioral component of the third-person effect. International Journal of Public Opinion Research,
20(3), 375–385. Yang, G. (2009). The power of the Internet in China: Citizen activism online. New York: Columbia Uni-
versity Press. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published
maps and institutional affiliations. 1 3
|
https://openalex.org/W2766918855
|
https://aacr.figshare.com/articles/journal_contribution/Supplementary_Information_from_Interleukin-27_Exerts_Its_Antitumor_Effects_by_Promoting_Differentiation_of_Hematopoietic_Stem_Cells_to_M1_Macrophages/22417611/1/files/39863718.pdf
|
English
| null |
Interleukin-27 Exerts Its Antitumor Effects by Promoting Differentiation of Hematopoietic Stem Cells to M1 Macrophages
|
Cancer research
| 2,018
|
cc-by
| 1,068
|
Supplementary Information
Supplemental Table 1. Primers used in this study.
Name
Direction
Sequence 5' to 3'
iNOS
forward
reverse
CAAGCTGAACTTGAGCGAGGA
TTTACTCAGTGCCAGAAGCTGGA
IRF8
forward
reverse
CTGCTCAGGCAGGTGTCAGAAG
AGGCCAGCCATTAGTGGTGAAG
IL-12p40
forward
reverse
ACTCACATCTGCTGCTCCACAAG
CACGTGAACCGTCCGGAGTA
Arg-1
forward
reverse
AGCTCTGGGAATCTGCATGG
ATGTACACGATGTCTTTGGCAGATA
Ym1
forward
reverse
GATGGCCTCAACCTGGACTG
CGTCAATGATTCCTGCTCCTG
Fizz1
forward
reverse
CAGCTGATGGTCCCAGTGAA
CAAGCACACCCAGTAGCAGTC
PD-L1
forward
reverse
TGTGTCCGTCGTGGATCTGA
TTGCTGTTGAAGTCGCAGGAG
TIM-3
forward
reverse
AGCTCTGGGAATCTGCATGG
ATGTACACGATGTCTTTGGCAGATA
PD-1
forward
reverse
GATGGCCTCAACCTGGACTG
CGTCAATGATTCCTGCTCCTG
TGF-β1
forward
reverse
CAGCTGATGGTCCCAGTGAA
CAAGCACACCCAGTAGCAGTC
GAPDH
forward
reverse
TGTGTCCGTCGTGGATCTGA
TTGCTGTTGAAGTCGCAGGAG Supplementary Information
Supplemental Table 1. Primers used in this study. Name
Direction
Sequence 5' to 3'
iNOS
forward
reverse
CAAGCTGAACTTGAGCGAGGA
TTTACTCAGTGCCAGAAGCTGGA
IRF8
forward
reverse
CTGCTCAGGCAGGTGTCAGAAG
AGGCCAGCCATTAGTGGTGAAG
IL-12p40
forward
reverse
ACTCACATCTGCTGCTCCACAAG
CACGTGAACCGTCCGGAGTA
Arg-1
forward
reverse
AGCTCTGGGAATCTGCATGG
ATGTACACGATGTCTTTGGCAGATA
Ym1
forward
reverse
GATGGCCTCAACCTGGACTG
CGTCAATGATTCCTGCTCCTG
Fizz1
forward
reverse
CAGCTGATGGTCCCAGTGAA
CAAGCACACCCAGTAGCAGTC
PD-L1
forward
reverse
TGTGTCCGTCGTGGATCTGA
TTGCTGTTGAAGTCGCAGGAG
TIM-3
forward
reverse
AGCTCTGGGAATCTGCATGG
ATGTACACGATGTCTTTGGCAGATA
PD-1
forward
reverse
GATGGCCTCAACCTGGACTG
CGTCAATGATTCCTGCTCCTG
TGF-β1
forward
reverse
CAGCTGATGGTCCCAGTGAA
CAAGCACACCCAGTAGCAGTC
GAPDH
forward
reverse
TGTGTCCGTCGTGGATCTGA
TTGCTGTTGAAGTCGCAGGAG Supplementary Information 1 1 Supplementary Figure Legends Supplementary Figure S1. Gating strategy in flow cytometry analysis of mast cells,
basophils, neutrophils, and macrophages together with M1 and M2 macrophages. On
day 19 after tumor implantation, the LSK cell population in the BM was purified (A)
and their multipotency was examined under in vitro myeloid cell differentiation
conditions into mast cells and basophils (B), and neutrophils and macrophages (C). Supplementary Figure S2. IL-27 augments the infiltration of CD11b+ myeloid cells
into MC38 tumor. MC38-IL-27 or MC38-Vector tumor was implanted and tumor
growth was monitored (A). Data are shown as mean ± SEM (n = 3 or 4) and are
representative of more than three independent experiments. On day 20, tumor was
harvested, single-cell suspension was prepared and subjected to flow cytometer analysis. Representative dot plots of macrophage population are shown (B), and the cell numbers
of individual populations were counted (C). Data are shown as mean ± SEM (n = 3 or 4)
and are representative of more than two independent experiments. *P < 0.05, **P <
0.01, ***P < 0.001. Supplementary Figure S3. IL-27 promotes the differentiation into M1 macrophages in
MC38 tumor-bearing mice. Single-cell suspensions prepared from tumor on day 20
after tumor implantation were analyzed by flow cytometry. Representative dot plots of
Gr-MDSCs, Mo-MDSCs, and macrophages are shown, and their cell numbers were
counted (A and B). (C) Representative dot plots of M1 and M2 macrophages are shown,
their cell numbers were counted, and ratio of M1/M2 macrophages was calculated. Data
are shown as mean ± SEM (n = 3 or 4) and are representative of more than two
independent experiments. (D) mRNA expression of markers for M1 and M2
macrophages in purified CD11b+ myeloid cells was analyzed by real-time RT-PCR. Data are shown as mean ± SEM (n = 4) and are representative of more than four
independent experiments. *P < 0.05, **P < 0.01, ***P < 0.001. 2 2 Supplementary Figure S4. IL-27 much less but significantly augments the infiltration
of M1 macrophages into B16F10 tumor when the tumor size in B16F10-IL-27
tumor-bearing mice reaches the similar tumor size to that in control tumor-bearing mice. B16F10-IL-27 tumor (2 × 107 cells/mouse) or B16F10-Vector tumor (5 × 104
cells/mouse) was implanted and tumor growth was monitored. When the tumor size
reached the same size 13 days after tumor implantation, the tumor-infiltrating cells were
analyzed by flow cytometry. Supplementary Figure Legends Representative dot plots of macrophages (A) and M1/M2
macrophages (B) are shown. Their cell numbers were counted per tumor volume, and
ratio of M1/M2 macrophages was calculated (C-F). Their cell numbers were also
counted per tumor weight, and ratio of M1/M2 macrophages was calculated (G-J). Data
are shown as mean ± SEM (n = 5) and are representative of two independent
experiments. *P < 0.05, **P < 0.01. Supplementary Figure S5. IL-27 inhibits the differentiation into immunosuppressive
macrophages in MC38 tumor-bearing mice. On day 20 after tumor implantation,
mononuclear cells were purified from tumor masses, and CD11b+ myeloid cells were
further purified and subjected to immunosuppressive activity, which was assessed by
the ability to inhibit OVA-specific CD8+ T-cell proliferation. Data are shown as mean ±
SEM (n = 3) and are representative of more than three independent experiments. *P <
0.05, **P < 0.01, ***P < 0.001. Supplementary Figure S6. Therapeutic potential of the CD11b+ myeloid cells purified
from tumors of B16F10-IL-27 tumor-bearing mice on pre-existing tumor model. Mice
were implanted with B16F10-IL-27 tumor (2 × 107 cells/mouse) or B16F10-Vector
tumor (5 × 105 cells/mouse), and CD11b+ myeloid cells were purified from their tumors
8 days after implantation. When mice were implanted with parental B16F10 tumor (5 × 3 3 105 cells/mouse) and their tumor size reached 5 mm in diameter on day 5, these CD11b+
myeloid cells (5 × 105 cells/50 µl/mouse) were both intravenously and intratumorally
injected into these mice with the pre-existing tumor. Tumor growth was monitored with
time course. Data are shown as mean ± SEM (n = 5) and are representative of two
independent experiments. *P < 0.05. Supplementary Figure S7. IL-27-induced MC38 tumor-infiltrating myeloid cells exert
direct antitumor effects by killing tumor through NO. (A) CD11b+ myeloid cells
purified from tumor of MC38-IL-27 or MC38-Vector tumor-bearing mice were
admixed with parental MC38 tumor, and tumor growth was monitored with time course. Data are shown as mean ± SEM (n = 4 or 5) and are representative of more than two
independent experiments. On day 20 after tumor implantation, killing activity of
CD11b+ myeloid cells against parental MC38 tumor was measured by 51Cr release assay
(B), and NO production in the culture supernatant was measured in the presence or
absence of NOS inhibitor, L-NMMA (C). (D) The effects of inhibition of NOS activity
by L-NMMA on the killing activity were examined. Supplementary Figure Legends Data are shown as mean ± SEM (n
= 4 or 5) and are representative of more than four independent experiments. *P < 0.05,
**P < 0.01, ***P < 0.001. Supplementary Figure S8. Enhanced mRNA expression of immune checkpoint
molecules and TGF-β1 in CD11b+ myeloid cells in IL-27-expressing tumor-bearing
mice. B16F10-IL-27 and B16F10-Vector tumor or MC38-IL-27 and MC38-Vector
tumor were implanted and tumor growth was monitored. On day 18, tumor was
harvested, and CD11b+ myeloid cells were purified from tumor and subjected to
real-time RT-PCR. Blood was also collected and its serum TGF-β1 level was
determined by its specific ELISA. Data are shown as mean ± SEM (n = 4) and are
representative of three independent experiments. *P < 0.05, ***P < 0.001. 4
|
https://openalex.org/W2947203071
|
https://europepmc.org/articles/pmc6603559?pdf=render
|
English
| null |
Susceptibility Profiles of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) to Deltamethrin Reveal a Contrast between the Northern and the Southern Benin
|
International journal of environmental research and public health/International journal of environmental research and public health
| 2,019
|
cc-by
| 8,087
|
Susceptibility Profiles of Helicoverpa armigera
(Hübner) (Lepidoptera: Noctuidae) to Deltamethrin
Reveal a Contrast between the Northern and the
Southern Benin Eric Tossou 1,2,*, Ghislain Tepa-Yotto 1,3, Ouorou K. Douro Kpindou 1, Ruth Sandeu 4,
Benjamin Datinon 1, Francis Zeukeng 4
, Romaric Akoton 1,2, Généviève M. Tchigossou 1,2,
Innocent Djègbè 5, John Vontas 6,7, Thibaud Martin 8,9, Charles Wondji 10, Manuele Tamò 1
,
Aimé H. Bokonon-Ganta 2 and Rousseau Djouaka 1,* 1
International Institute of Tropical Agriculture (IITA), 08 P.O. Tri-Postal, Box 0932 Cotonou, Benin;
g.tepa-yotto@cgiar.org (G.T.-Y.); d.kpindou@cgiar.org (O.K.D.K.); b.datinon@cgiar.org (B.D.);
romaricakoton88@gmail.com (R.A.); tchigossougenevieve@yahoo.fr (G.M.T.); m.tamo@cgiar.org (M.T.) 1
International Institute of Tropical Agriculture (IITA), 08 P.O. Tri-Postal, Box 0932 Cotonou, Benin;
g.tepa-yotto@cgiar.org (G.T.-Y.); d.kpindou@cgiar.org (O.K.D.K.); b.datinon@cgiar.org (B.D.); 2
Direction of Plant Production, University of Abomey-Calavi, P.O. Box 526 Abomey-Calavi, Benin;
aimehbg@gmail.com g g
3
School of Crop and Seed Production, National University of Agriculture (UNA-Benin),
P.O. Box 43 Kétou, Benin Faculty of Science, Department of Biochemistry, University of Yaoundé I, P.O. Box 812 Yaoundé, Cameroon
d
2009@
h
(R S )
f
k07@
h
(F Z ) 4
Faculty of Science, Department of Biochemistry, University of Yaoundé I, P.O. Box 812 Yaoundé, Cam
sandeu2009@yahoo.com (R.S.); zeusfranck07@yahoo.com (F.Z.) 4
Faculty of Science, Department of Biochemistry, University of Ya
sandeu2009@yahoo.com (R.S.); zeusfranck07@yahoo.com (F.Z.) 5
Life And Earth Sciences, National University of Science, Technology, Engineering and Mathematics,
P.O. Box 2282 Abomey, Benin; djegbe1@yahoo.fr 6
Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, N Plastira 100,
70013 Crete, Greece; vontas@imbb.forth.gr g
7
Pesticide Science, Agricultural University of Athens, Ieraodos 75, 11855 Athens, Greece 7
Pesticide Science, Agricultural University of Athens, Ieraodos 75, 11855 Athens, Greece
8
Cirad UR Hortsys, Université Montpellier, Campus international de Baillarguet, 34 398 Montpellier, France;
thibaud.martin@cirad.fr 8
Cirad UR Hortsys, Université Montpellier, Campus international de Baillarguet, 34 398 Montpellier, Fra
thibaud.martin@cirad.fr 9
Biosciences Unit, University Houphouet Boigny, Cocody 01 BP 6483Abidjan, Côte d’Ivoire 10
Vector group, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; charles.wondji@lstmed.ac.uk
*
Correspondence: eric.tossou82@gmail.com (E.T.); r.djouaka@cgiar.org (R.D.); *
Correspondence: eric.tossou82@gmail.com (E.T.); r.djouaka@cgiar.org (R.D.);
Tel.: +229-9563-4911 (E.T.); +229-9620-4924 (R.D.) *
Correspondence: eric.tossou82@gmail.com (E.T.); r.djouaka@cgiar.org
Tel.: +229-9563-4911 (E.T.); +229-9620-4924 (R.D.) p
g
j
g
g
Tel.: +229-9563-4911 (E.T.); +229-9620-4924 (R.D.)
International Journal of
Environmental Research
and Public Health International Journal of
Environmental Research
and Public Health www.mdpi.com/journal/ijerph Int. J. Environ. Res. Public Health 2019, 16, 1882; doi:10.3390/ijerph16111882 1. Introduction The cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) is a key polyphagous
pest infesting several crops such as cotton, tomato, maize, sorghum, chickpea, pigeon pea, pulses,
vegetables and tomato crops worldwide [1]. This pest causes an estimated loss of over US$ 5 billion
annually in Africa despite application of pesticides [2]. In contrast to many other arthropod pests,
H. armigera has a wide geographical range of host plants and can adapt to new environments [3]. New publications on H. armigera in South America [4,5] created suspicions of the presence of other
species of Helicoverpa in Africa given the proximity between the two continents. Species identification
remains complex with possibilities of misidentification due to morphological similarities between
H. armigera and Heliothinae species (such as Helicoverpa zea (Boddie)) [6]. The restriction fragment length
polymorphism (RFLP)-PCR method is used to determine a genetic variation between the populations. PCR-RFLP amplifies specific partial regions of the mitochondrial DNA (mtDNA) genome followed by
the digestion of PCR products with specific endonucleases to distinguish between combining patterns
of partial regions of the mitochondrial gene [7]. This technique has been optimised for confirming
H. armigera [7]. Economic damage caused by H. armigera is very significant worldwide [2]. Over the past decades,
management of H. armigera has become increasingly difficult due to its high reproductive and damage
potentials [8]. The strong tendency of H. armigera to move from one fruit to another without consuming
it completely, explains why this pest causes extensive damages to crops even when the number of
larvae is relatively low [9]. y
Synthetic insecticides have shown promising control of chewing and sucking insect pests in
the early 1980s, these compounds are applicable to Helicoverpa pests. Cotton and tomato, the main
Helicoverpa host plants, are generally protected from pest damage by application of insecticides such
as carbamates, organophosphates and synthetic pyrethroids [10,11]. In comparison to carbamates
and organophosphates, synthetic pyrethroids are effective at low dosages for controlling H. armigera
at extremely low cost [10,12]. Excessive and continuous applications of pyrethroid insecticides
for H. armigera control initiated since the mid-1980s in most countries have led to resistance
selection pressure in several field populations of this insect [10,13,14]. With this development
of insecticide resistance, the control of H. armigera has become critical in many regions worldwide [8,15]. Recent studies have reported the increased resistance of H. Received: 4 March 2019; Accepted: 3 May 2019; Published: 28 May 2019 Abstract: Helicoverpa armigera is an indigenous species in Africa and has been reported in the
destruction of several crops in Benin. Management of H. armigera pest is mainly focused on the use
of synthetic pyrethroids, which may contribute to resistance selection. This study aimed to screen
the susceptibility pattern of field populations of H. armigera to deltamethrin in Benin. Relevant
information on the type of pesticides used by farmers were gathered through surveys. Collected
samples of Helicoverpa (F0) were reared to F1. F0 were subjected to morphological speciation followed
by a confirmation using restriction fragment length polymorphism coupled with a polymerase chain
reaction (RFLP-PCR). F1 (larvae) were used for insecticide susceptibility with deltamethrin alone and
in the presence of the P450 inhibitor Piperonyl Butoxide (PBO). Deltamethrin and lambda-cyhalothrin
were the most used pyrethroids in tomato and cotton farms respectively. All field-sampled Helicoverpa
were found to be H. armigera. Susceptibility assays of H. armigera to deltamethrin revealed a high
resistance pattern in cowpea (resistance factor (RF) = 2340), cotton (RF varying from 12 to 516) and
tomato (RF=85) farms which is a concern for the control of this major polyphagous agricultural
pest. There was a significant increase of mortality when deltamethrin insecticide was combined
with piperonyl butoxide (PBO), suggesting the possible involvement of detoxification enzymes such
as oxidase. This study highlights the presence of P450 induced metabolic resistance in H. armigera
populations from diverse cropping systems in Benin. The recorded high levels of deltamethrin Int. J. Environ. Res. Public Health 2019, 16, 1882; doi:10.3390/ijerph16111882 2 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 resistance in H. armigera is a concern for the control of this major agricultural pest in Benin as the
country is currently embarking into economical expansion of cotton, vegetables and grain-legumes
cropping systems. resistance in H. armigera is a concern for the control of this major agricultural pest in Benin as the
country is currently embarking into economical expansion of cotton, vegetables and grain-legumes
cropping systems. Keywords: H. armigera; pyrethroid resistance; Benin 1. Introduction armigera control in
different host crops and in different localities in Benin. 2.3. Insects Sampling, Molecular Speciation and Insecticide Susceptibility Testing 2.3. Insects Sampling, Molecular Speciation and Insecticide Susceptibility Testing 2.1. Study Sites Benin is located between the Equator and the Tropic of Cancer at latitudes ranging from 6◦30’ N
to 12◦30’ N and longitude ranging from 1◦E to 3◦40’ E. This country shares boundaries with Togo in
the West, Burkina Faso and Niger in the North, and Nigeria in the East. Four main agro-ecological
zones are found in the country. The North-Sudanese, the Atacorian, the Sub-Sudanese and the
Sub-Equatorial climatic zones. A total of 6 agricultural settings were surveyed in these agro-ecosystems. Field populations of Helicoverpa spp. were sampled in the following 6 localities. Kassakou in the
North-Sudanese area, characterized by one long dry season and a short rainy season, with relatively
low humidity and rainfall (800 to 1000 mm per year), and high temperatures (up to 45◦C during dry
seasons). The localities of Yarra and Zaffé both in the Sub-Sudanese area with a long rainy season and
a short dry season. Rainfalls ranging between 900 and 1200 mm, less hilly localities with wet savanna
vegetation types. Finally, three localities (Djidja, Kokrokinho, Abomey-Calavi) in the Sub-Equatorial
area that spans the southern part of the country and extends up to coastal areas of Benin. Two rainy
and two dry seasons are recorded in these localities. The relative humidity is high, temperatures are
relatively low, and the vegetation is a mosaic of coastal wetlands, forest, and wet savanna (Figure 1). 1. Introduction armigera to pyrethroids in Pakistan [16],
South India [17], Spain [18] and West Africa [19]. Durigan et al. [20] pointed to metabolic
resistance mechanisms and showed that the quantities of cytochrome P450 (CYP337B1, CYP337B2
and CYP337B3) are greater in resistant strains compare to susceptible strains after exposure to
deltamethrin. Furthermore, Martin et al. [21] also demonstrated that P450 enzymes contribute to
deltamethrin resistance in H. armigera populations from West Africa. These results were further
confirmed by Brun-Barale et al. [19] who identified the modified P450 genes. Insecticide resistance
development usually occurs with the appearance of genetic mutations and/ or increased enzymatic
detoxification [20,22]. Recent studies indicate that metabolic resistance is primarily responsible for
pyrethroid resistance in H. armigera. Elevated oxidative detoxification (P450-based resistance) was
confirmed as the major resistance mechanism to pyrethroids in Australia and Asia [20,23,24]. Very little is known about the susceptibility profiles of H. armigera to the commonly used
agricultural insecticide deltamethrin across agro-ecological areas in Benin. Although many studies 3 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 have been conducted worldwide on H. armigera [1,12,17,19,24], very few of these research works have
been carried out in the western part of Africa [11,19,21]. In Benin for example, no study had extensively
and simultaneously mapped the insecticide resistance profiles of this pest on several cropping systems
such as cotton, vegetable and grain legumes currently under intensification. In addition to this lack of
information on resistance mapping in Benin, no research had attempted to provide information on
potential mechanisms conferring observed phenotypic resistance profiles in several cropping systems. Taking into account the current nationwide economic options made by the Benin government to
promote the development of cotton, vegetables and grain legumes farming, there is a great need to
regularly document and update information on insecticide resistance profiles and related resistance
mechanisms developed by H. armigera nationwide. Data from this research will support strategic
policies on the selection of cost-effective insecticides for better control of this polyphagous pest. This research documents on the control of H. armigera pest in various host plants, provides information
on the extent of H. armigera resistance to deltamethrin in the South-North transect of Benin, investigates
possible role of detoxifiers (P450 enzymes) in recorded phenotypic resistances. Information generated
will help to improve decision making on the type of insecticides to be used for H. 2.2. Insecticide Utilisation by Farmers in Surveyed Localities 2.2. Insecticide Utilisation by Farmers in Surveyed Localities The knowledge of farmers on the use of chemical pesticides for H. armigera control was assessed
in surveyed tomato, cotton, and cowpea farms from November 2016 to November 2017. Relevant
information on the use of chemical pesticides for H. armigera control were gathered through focus group
discussions, direct field observations and in-depth interviews. Information collected included: the
types of pesticides used by farmers, the concentrations/doses applied and the application frequencies. Based on the number of farmers in each farm, we determined the minimal acceptable size of farmers
to be interviewed in each locality. A total of 180 volunteer farmers consented this survey in the six
studied localities. 2.3.1. Laboratory Strain A susceptible strain of H. armigera (SoucheVrac Sensible, SVS) was obtained from the Entomology
laboratory of the Agricultural Research Institute for Development in Cameroon (IRAD-Garoua, 4 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 Cameroon). SVS was transferred to the International Institute of Tropical Agriculture (IITA-Benin)
insectary at pupae stage, and was reared following laboratory conditions and steps described
by Nibouche [25]. This strain was used as the standard susceptible colony during insecticide
susceptibility assays. Figure 1. Map of Benin showing localities where H. armigera populations were found. ld Sampling of Wild Populations of Helicoverpa Figure 1. Map of Benin showing localities where H. armigera populations were found. 2.3.2. Field Sampling of Wild Populations of Helicoverpa 2.3.2. Field Sampling of Wild Populations of Helicoverpa Field populations of Helicoverpawere collected during rainy seasons in 6 agricultural localities
namely (Kassakou, Yarra, Zaffé, Djidja, Kokrokinho and Abomey-Calavi) (Table 1; Figure 1). Collected
samples of Helicoverpa (F0) were reared to F1. The parents (F0) were preserved in suitable containers
filled with ethanol (100%), and stored at −20◦C. These samples (F0) were later subjected to molecular
speciation using RFLP-PCR [7]. F0 progenies (third instar larvae) were used for insecticide susceptibility
assays (topical assays) with deltamethrin alone and in the presence of the P450 inhibitor piperonyl
butoxide (PBO). Insects collected in the field were introduced into cylindrical plastic cups (4cm diameter; Field populations of Helicoverpawere collected during rainy seasons in 6 agricultural localities
namely (Kassakou, Yarra, Zaffé, Djidja, Kokrokinho and Abomey-Calavi) (Table 1; Figure 1). Collected
samples of Helicoverpa (F0) were reared to F1. The parents (F0) were preserved in suitable containers
filled with ethanol (100%), and stored at −20◦C. These samples (F0) were later subjected to molecular
speciation using RFLP-PCR [7]. F0 progenies (third instar larvae) were used for insecticide susceptibility
assays (topical assays) with deltamethrin alone and in the presence of the P450 inhibitor piperonyl
butoxide (PBO). Insects collected in the field were introduced into cylindrical plastic cups (4cm diameter; 5 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 5cm height) with a cover punched with holes to allow ventilation for breathing of larvae. Each cup
was filled with 4g of solid agar media for feeding larvae throughout their transportation from the field
to the IITA-Benin insectary. Table 1. Geolocalization of surveyed localities for H. armigera sampling. 2.3.3. Laboratory Rearing of H. Armigera Both laboratory and field strains of H. armigera were reared at 25±1◦C, 75% Relative Humidity
(RH), and a photoperiod of 12:12 Light:Darkness (L:D) in the insectary as described by Nibouche [25]. Briefly, larvae were reared on an artificial diet composed of maize flour (120 g/L), brewer yeast (40 g/L),
white cowpea flour (172 g/L), honey (20 g/L), sorbic acid (2 g/L), ascorbic acid (6 g/L), agar (25 g/L),
40% formaldehyde (2 mL/L), erythrocin (0.05g/L) and acyclovir (1.2g/L). The fourth instar larvae
were obtained and individualized into cylindrical plastic cups containing artificial diet (4g) to avoid
cannibalism. Pupae were collected, disinfected and, morphological identifications were carried out
before emergence of adults. Emerging adult males and females from F0 larvae were pooled for matting. Eggs from this matting were incubated for hatching and, larvae (F1) from hatched eggs were placed on
artificial diet and reared to L3-larva stage; the developmental stage used for insecticide susceptibility
assays (Topical assays) with deltamethrin insecticide. 2.3.4. Molecular Speciation of Sampled Helicoverpa spp. 2.3.1. Laboratory Strain Collection Site
Region (Agro Ecosystem)
Host Plant
Latitude Longitude
Sample Strains
Zaffé
Central (Sub-Sudanese)
Cotton
07◦55.343’
ZAF.16
002◦15.256’
Kokrokinho
South (Sub-equatorial)
Tomato
06◦57.377’
KOK.16
002◦37.868’
Abomey-Calavi
South (Sub-equatorial)
Cowpea
06◦25.260’
AB-C.16
002◦19.684’
Kassakou
North (North-Sudanese)
Cotton
11◦4.520’
KAS.17
002◦54.127’
Yarra
North (Sub-Sudanese)
Cotton
10◦30.447’
YAR.17
002◦28.569’
Djidja
Central (Sub-equatorial)
Cotton
07◦19.495’
DJI.17
001◦56.393′
Benoue and Mayo Rey
North
Cotton
-
‘SVS’
- Table 1. Geolocalization of surveyed localities for H. armigera sampling. 2.3.3. Laboratory Rearing of H. Armigera 2.4. Synergist Test with Piperonyl Butoxide (PBO) For this assay, 135 to 233 larvae of H. armigera from each locality were pre-exposed to the P450
inhibitor piperonyl butoxide 90% (PBO) (20 µg/µL) for one hour and immediately after, these larvae
were exposed to deltamethrin at five concentrations thrice replicated of the technical grade (0.01DD,
0.1DD, DD, 10DD, and 100DD) so as to cover the full dose range bioassay. Acetone solution was added
to serve as the control solution. The diagnostic concentration was used for plotting the graph showing
the effect of the PBO synergist on larvae. Larval mortality was monitored every 24 h after exposure
until 72 h. 2.3.5. Insecticide Susceptibility Assays (Topical Assays) 2.3.5. Insecticide Susceptibility Assays (Topical Assays) As documented in most published papers, this assay was conducted on larval stages as they are
the most cropsdamaging stages [9]. The selection of larvae for insecticide susceptibility analysis was
supported by several published papers and standards [17,27]. Technical grade of deltamethrin 99%
(Sigma-Aldrich, Taufkirchen, Germany) was used in this assay. Susceptibility of third instar larvae
of H. armigera (F1 offspring) to deltamethrin was tested using topical application technique [10,27]. Two-fold serial dilutions were prepared in pure acetone according to Kranthi [28] and the following
concentrations were obtained for bioassays with the susceptible strain: (0.01454; 0.02908; 0.05816;
0.1163; 0.2326; 0.4653; 0.9306 µg/g). A log-probit dose (dose-mortality) curve was drawn from this
strain and a diagnostic dose (DD) of 2181µg/g was obtained. Five concentrations thrice replicated of
the technical grade (0.01DD, 0.1DD, DD, 10DD, and 100DD) and a control with no insecticide (0DD)
were then prepared for bioassays with the field strains of H. armigera (144 to 349 larvae). Each exposed
larva had a body weight between 30–40 mg. One microliter of deltamethrin was applied topically to
the pro-thoraxic dorsum of the pest. Larvae were tested individually in plastic cups (4cm diameter;
5cm height) containing 4g of artificial diet and punched at the top. Pure acetone was used as control. The mortality was assessed every 24 h post exposure and was monitored for a total of 72 h for both
test and control samples. Larvae were considered dead when unable to move if prodded with a blunt
probe or brush [10,27]. 2.3.4. Molecular Speciation of Sampled Helicoverpa spp. PCR-RFLP was used in this speciation. Total genomic DNA was extracted from sampled F0
individuals (parents) after they had produced their progenies (F1). Samples (F0) were analysed for
molecular speciation and for predicting the species profiles of offspring to be submitted to insecticide
susceptibility tests. Total DNA was obtained after crushing the whole insect and following the
extraction protocoldescribed by Livak [26]. Extracted DNA was quantified using a nanodrop 8000
(Thermo Scientific, Mississauga, ON, Canada) and a working DNA solution of 40–50 ng/µL was
prepared for amplification. Amplifications were carried out in 50µL reaction containing cytochrome
oxidase I (COI) and cytochrome b (Cytb) (Table 2) according to Behere et al. [7]. DNA amplification was confirmed by running 5µL of the post-PCR products on 1.5% agarose
gel stained with 1% Midori green. Two restriction enzymes (BstZ17I and HphI) were used for
discriminating H. armigera species. The pattern of product sizes on the agarose gel was used for
identifying H. armigera species following Behere et al. protocol [7] (Table 3). 6 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 Table 2. Primers used for amplifying H. armigerasequences. Primers
Primer Sequences
COI
COI-F02
5′CTC AAA TTA ATT ACT CCC CAT C′3′
COI-R02
5′GGA GGT AAG TTT TGG TAT CAT T3′
Cytb
Cytb-F02
5′GAA TCC TTT AAT TTA AAA TAT AC3′
Cytb-R02
5′AAA TAT GGG TTA GTT AAA GTT AA3′ Table 2. Primers used for amplifying H. armigerasequences. Table 3. Expected sizes of digested PCR products for H. armigera identification. Extraction
Amplifications
Digestion Enzymes
Digestion Products (pb)
Helicoverpa spp. DNA
Amplified product (COI)
BstZ17I
318 + 193
Amplified product (CYTB)
HphI
280 + 154 Table 3. Expected sizes of digested PCR products for H. armigera identification. 3.1. Insecticides Used for Cotton and Tomato Farming in Benin We conducted interviews and group discussions with a total of one hundred and eighty farmers (140
for interviews and 40 for group discussions) from tomato and cotton farms to identify insecticide families
used for H. armigera control. Different classes of insecticides were identified namely: pyrethroids,
organophosphates, carbamates and biopesticides (Bacillus thuringiensis, Neem) (Figure 2). Figure 2. Insecticide use in cotton and tomato farming in Benin. Figure 2. Insecticide use in cotton and tomato farming in Benin. Synthetic pyrethroids (deltamethrin, lambda-cyhalothrin and cypermethrin) were identified as
the main insecticides (60%) used against H. armigera. Deltamethrin and lambda-cyhalothrin were
the most used pyrethroids in tomatoes farming (50.9%) and cotton farming (28.7%) respectively. Organophosphates (chlorpyrifos and dimethoate) were also mentioned by farmers and used either as
single or in combinations with pyrethroids. Information provided by farmers revealed that tomato
farms are sprayed once every 10 days, whereas cotton farms are treated two times per month. Despite
the use of these insecticides, cases of plants and fruits attack by insects were still reported by cotton and
tomato farmers, raising the failure of these synthetic insecticides for tomato and cotton plants protection. 2.5. Data Analysis Mortality curves for different tested concentrations of deltamethrin were computed using probit
analysis (WinDL50software; CIRAD, Montpellier, France). Results were expressed as percentage
mortalities. Abbott’s formula was used for correcting the recorded mortalities. Resistance factors (RFs)
were determined as the ratio of the lethal dose for 50% (LD50) of field collected populations of insects
and the susceptible strain. RFs were used to classify levels of insecticide resistance as: susceptible (RF
= 0–1), low resistance (RF = 2–10), moderate resistance (RF = 11–30), high resistance (RF = 31–100), 7 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 very high resistance (RF > 100) following descriptions made by Torres-Vila et al. [18]. The level of
significance was set at p < 0.05. very high resistance (RF > 100) following descriptions made by Torres-Vila et al. [18]. The level of
significance was set at p < 0.05. 3.2. Molecular Validation of Morphologically Identification of Helicoverpaarmigera. COI and Cytb genes fragments were successfully amplified in one hundred and twenty Helicoverpa
samples. 20 samples of F0 adult were analysed from each surveyed agricultural setting. Following
digestions of amplified PCR products with restriction endonucleases (BstZ17I and HphI). All analysed
samples from the 6 surveyed localities were identified using molecular techniques as H. armigera
(Table 3 and Figure 3). 8 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 Figure 3. Agarose gel electrophoresis of PCR products digested with BstZ17I and HphI restriction
enzymes, showing different restriction fragment length polymorphism (RFLP) patterns of analysed
samples of H. armigera. M: molecular weight markers. Lanes 1-2, 3-4, 5-6, 7-8, 9-10 and 11-12:H. armigera
specimens from Kassakou, Zaffé, Kokrokinho, Djidja, Abomey-calavi and Yarra respectively. 3. Bioassays Figure 3. Agarose gel electrophoresis of PCR products digested with BstZ17I and HphI restriction
enzymes, showing different restriction fragment length polymorphism (RFLP) patterns of analysed
samples of H. armigera. M: molecular weight markers. Lanes 1-2, 3-4, 5-6, 7-8, 9-10 and 11-12:H. armigera
specimens from Kassakou, Zaffé, Kokrokinho, Djidja, Abomey-calavi and Yarra respectively. Figure 3. Agarose gel electrophoresis of PCR products digested with BstZ17I and HphI restriction
enzymes, showing different restriction fragment length polymorphism (RFLP) patterns of analysed
samples of H. armigera. M: molecular weight markers. Lanes 1-2, 3-4, 5-6, 7-8, 9-10 and 11-12:H. armigera
specimens from Kassakou, Zaffé, Kokrokinho, Djidja, Abomey-calavi and Yarra respectively. Bioassays 3.3.1. Susceptibility of H. armigera to Deltamethrin Following susceptibility assays conducted with deltamethrin, the LD50 of the susceptible strain
of H. armigera (SVS) was 0.064 µg/g (Table 4), while the diagnostic dose (DD: LD99.9) was 2.181 µg/g. When field samples (L3 from the F1) were exposed to same serial dilutions of deltamethrin, lower
mortality rates which correspond to high levels of resistance were observed. Mortality rates of 9.7%
and a LD50 = 149.780 µg/g were recorded with H. armigera from the Abomey-calavi farms; mortality
rates of 14.36% and LD50 = 20.378 µg/g recorded with H. armigera from the Zaffé farms; mortality rates
of 31.77% and LD50 = 36.16 µg/g for samples from Djidja; mortality rates of 34.35% and LD50 = 5.428
µg/g for samples from Kokrokinho; mortality rates of 43.3% and LD50 = 2.105 µg/g for samples from
Yarra; mortality rates 52.9% and DL50 = 0.800 µg/g for H. armigera from the Kassakou farm (Table 4). Table 4. Recorded LD50 with laboratory and field samples of H.armigera when exposed to Deltamethrin. Strain
Host Plant
Region (Agro Ecosystem)
n
LD50 (µg/g) (95% FL)
Slope ± SE
‘SVS’
Cotton
North
668
0.064
(0.035–0.064)
1.91 ± 2.29
KOK.16
(Kokrokinho)
Tomato
South (Sub-equatorial)
248
5.428 *
(2.62–8.81)
1.02 ± 0.75
ZAF.16
(Zaffe)
Cotton
Central (Sub-Sudanese)
South (Sub-equatorial)
240
20.378 *
(12.88–34.07)
1.10 ± 1.44
KAS.17
(Kassakou)
Cotton
North (North-Sudanese)
150
0.800 *
(0.132–4.85)
0.61 ± 0.06
YAR.17
(Yarra)
Cotton
North (Sub-Sudanese)
150
2.105 *
(0.236–18.7)
0.56 ± 0.181
AB-C.16
(Abomey-Calavi)
Cowpea
South (Sub-equatorial)
349
149.780 *
(31.12–720.84)
0.76 ± 1.65
DJI.17
(Djidja)
Cotton
Central (Sub- equatorial)
144
36.16 *
(1.23–181.16)
0.32 ± 0.48
N = number of tested larvae (third instar), LD50 = dose that kills 50% of the tested sample, * = LD50 significantly
different from that of the susceptible ‘SVS’ strain; 95% FL = Fidicial limits (95%). Table 4. Recorded LD50 with laboratory and field samples of H.armigera when exposed to Deltamethrin. Determined Resistance Factors (RF) from recorded mortalities were 12.5; 32.89; 318.41; and 565
folds higher for Kassakou, Yarra, Zaffé and Djidja cotton farms respectively, as compared to the
susceptible laboratory strain SVS (Figure 4). For H. armigera collected in tomato farms, RF was 84.81 9 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 folds higher (samples from Kokrokinho) than the susceptible strain “SVS”. 4.2. Molecular Identification of H. armigera Molecular speciation using COI and Cytb targets coupled with digestion by BstZ17I and HphI
respectively helped confirming the presence of H. armigerain the 6 surveyed sites in Benin. Previous
studies based on morphological characters such as forewings of noctuid moths have shown several
limitations for differentiating some members of Helicoverpa family. In this research, we have used for
the first time in Benin a published DNA based protocol [7] for confirming the presence of H. armigera
in different host plants in the North-South transect of the country. This molecular based identification
of H. armigera in addition to traditional morphological methods described by Matthews [31] constitute
effective combinations for improved speciation of H. armigera and better control of this polyphagous pest. 4.1. The Use of Insecticide for H. armigera Control This study revealed that up to 60% of tomato and cotton producers in Benin use pyrethroids to
control H. armigera in their farms. Deltamethrin and lambda-cyhalothrin are the main insecticides
used against H. armigera in tomato and cotton production respectively. In cotton farming systems,
Lambda-cyhalothrin is most often combined with Chlorpyriphos- ethyl for H. armigera control. Data from this survey also revealed that despite the newly approved national Integrated Pest
Management (IPM) strategy which replaces the use of deltamethrin by either lambda cyhalothrin
(pyrethrinoid) or chlorpyriphos-ethyl (organophosphate) [29], many farmers continue to actively use
deltamethrin for fighting H. armigera in cotton fields. As recorded in tomato farming, Decis 12,5 CE
(deltamethrin) is also intensively used by cowpea farmers (Frequency: 6 days/1L/ha) [30]; this could
explain high resistance profiles observed in H. armigera populations harvested in cowpea farms. 3.3.1. Susceptibility of H. armigera to Deltamethrin As for samples from
cowpea farms of Abomey-Calavi, we recorded a RF of 2340.31 folds higher than the susceptible strain
“SVS” (Figure 4). Overall, the results of this research revealed higher levels of deltamethrin resistance
in cowpea farms. We also recorded an increased resistance pattern as we move down from the North
to the southern part of Benin (Figure 4). Figure 4. Map of Benin showing the resistance profile of H. armigerapopulations to deltamethrin in the
North-South transect. The resistance profile is expressed in term of resistance factor (RF) calculated
from the DL50. 3 2 Mortality Rates of H armigera When Exposed to Combinations of PBO Synergist and Figure 4. Map of Benin showing the resistance profile of H. armigerapopulations to deltamethrin in the
North-South transect. The resistance profile is expressed in term of resistance factor (RF) calculated
from the DL50. 3.3.2. Mortality Rates of H. armigera When Exposed to Combinations of PBO Synergist and
Deltamethrin 3.3.2. Mortality Rates of H. armigera When Exposed to Combinations of PBO Synergist and
Deltamethrin When PBO was combined with deltamethrin insecticide, the recovery of susceptibility was
observed for all H. armigera tested (Table S1). The susceptibility was total for H. armigera populations
from cotton farms of Kassakou and Yarra with mortality rates reaching 100% (Figure 5). With populations
from the cotton farm of Djidja, 81.2% mortality was recorded with the combination PBO and deltamethrin
whereas, 76.2% mortality was observed with H. armigera populations from the surveyed cowpea
farm of Abomey-Calavi (Figure 5). Resistance profiles recorded in cotton farms (North of Benin)
were mostly metabolic whereas in cowpea and tomato farms (South of Benin) several mechanisms
which include increase activities of oxidase detoxification were observed. No synergist test was
performed on H. armigera from Zaffé and Kokrokinho farms due to the low number of larvae collected
in these localities. 10 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 10 of 15 Figure 5. Recorded mortalities of H. armigera populations following exposures to diagnostic dose of
deltamethrin in the presence or absence of piperonyl butoxide (PBO) synergist. n = number of tested
larvae (third instar), NT = No tested. Figure 5. Recorded mortalities of H. armigera populations following exposures to diagnostic dose of
deltamethrin in the presence or absence of piperonyl butoxide (PBO) synergist. n = number of tested
larvae (third instar), NT = No tested. 4.3. Susceptibility of Helicoverpa armigera to Deltamethrin in Benin IPM strategies implemented in most cropping systems in Benin are mainly based on the use
of synthetic chemicals such as pyrethroids, organochlorines and organophosphates [11]. Of these
insecticide families, two pyrethroids (deltamethrin and lambda-cyhalothrin) are mostly used for
protecting tomato and cotton crops against the polyphagous H. armigera as reported in Benin and other
West African countries [32–35]. This regular use of pyrethroids by farmers against this pest of high
economic interest has less been backed by a constant monitoring of their susceptibility patterns to
insecticides. This research revealed that farmers are continuing to use deltamethrin for H. armigera
control despite the fact that this insect has already developed high resistance levels to this insecticide. 11 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 This study highlights the need to provide evidence-based information to farmers on the resistance
profiles of the main agricultural pests to guide their insecticide usage. Data generated revealed a
high resistance of H. armigera to deltamethrin in cowpea farms (RF = 2340) followed by tomato farms
(RF = 84.81) and finally cotton farms (RF ranged 12.5 to 515.94). This high resistance to deltamethrin
could be attributed to the overuse and miss-use of this insecticide during many decades in vegetable
(tomato), grain legumes (cowpea) and cotton fields across the country [14,33,34]. In addition to the
misuse and overuse of insecticides by farmers, the poor quality of pesticides used for pest control
has also been documented as favouring the selection of resistance in wild population of pests [36,37]. Resistance levels of H. armigera populations from cotton fields was lower than previously reported
in other localities of Benin [11,19] and, in some west African countries such as: Burkina Faso and
Ivory Coast [29]. The relatively low resistance recorded in cotton farms could be related to recent
modifications made nationwide on IPM strategies such as the alternative use of insecticide families for
cotton pest control [29]. In Benin for example, the treatment of cotton plants starts with two spraying
of organophosphate followed by a combination of pyrethroids and organophosphate during the last
four spraying passages. Such alternative use of different families of insecticides make difficult the
development of high resistance levels in surveyed cotton farms. In Contrast, alternative treatments
are neither conducted in tomato farms nor in cowpea cropping systems hence, the relatively high
resistance profiles recorded with Helicoverpa populations from these two commodities. 4.3. Susceptibility of Helicoverpa armigera to Deltamethrin in Benin In tomato
and cowpea farms, deltamethrin remains the insecticide of choice for H. armigera control [30,35]. Resistance selection observed could be primarily due to the permanent use of this insecticide by
farmers or, through use of poor quality deltamethrin for pests control as documented by some
authors [33,34]. Very surprisingly, we recorded high resistance levels in the cotton farms of Djidja
and Zaffé in the South Benin; contradicting data from the surveyed cotton farms of Kassakou and
Yarra in the North Benin. As a matter of fact, both cotton farms of Djidja and Zaffé are surrounded
by tomato, and cowpea farms which are regularly under pyrethroid treatments. It is possible that
Helicoverpa populations of Djidja/Zaffé cotton farms in addition to receiving insecticides residues
from cotton treatments also get exposed to pyrethroid insecticides leaching from surrounding tomato
and cowpea farms during rainfalls. This combined selection pressure from cotton insecticides and
leached insecticides from neighbouring tomato and cowpea farms could explain the higher resistance
levels recorded in cotton farms of Djidja and Zaffé contrary to other cotton farms surveyed in the
northern Benin (Figure 4). High resistance profiles were globally recorded in the Southern part of
Benin compare to North. These high resistance profiles of insects in the Southern Benin had also been
documented by Djouaka et al. [38] and other scientists working on insecticide resistance in malaria
mosquitoes [36,37,39]. These high resistance levels recorded in southern Benin, compared to northern
part of the country, could be associated to combinations of resistance selection factors such as the
wide range of agrochemicals misused and overused by farmers, and other environmental pollutants
(xenobiotics) which are still to be well identified. The overuse and misuse of pyrethroids lead to a
loss of effectiveness of this insecticide as most pests will gradually develop resistance to the selection
pressure; this will further increase the financial cost of pests treatment. This misuse of insecticides
also leads to environmental pollution causing the imbalance of ecosystems [40]. The importance of
conducting insecticide resistance studies on H. armigera resides on the current nationwide need of
boosting cotton, vegetables and grain legumes production for increased communities income in Benin. Maps on insecticide resistance spread generated will support strategic policies on the selection of more
effective insecticides for better control of this polyphagous pest on different cropping systems and in
d ff
l
l 5. Conclusions This research focused on the use of synthetic chemicals in diverseagro-ecosystems forimproved
pest control strategies. Results from this study revealed high levels of pyrethroid resistance in several
populations of H. armigera in the North- South transect of Benin. An increasing resistance pattern was
observed as we moved from the North to the southern Benin. A resistance contrast was also recorded
in between populations of H. armigera from cotton, tomato and cowpea. The involvement of P450s
metabolizers in the observed deltamethrin resistance was documented. Further investigation is being
conducted into: assessing insecticide resistance profiles of H. armigera to other insecticides, screen for
developed resistance mechanism pathways and study related fitness costs. This scientific evidence
isimportant for the development of more tailored, cost effective and sustainable IPM strategies against
this highly polyphagous pest. Supplementary Materials: The following are available online at http://www.mdpi.com/1660-4601/16/11/188
Table S1: LD50 for deltamethrin with PBO on susceptible and resistant strains of H. armigera in Benin. Author Contributions: E.T., R.D. and M.T. designed the study; E.T., F.Z., G.T.-Y., R.D., O.K.D.K., R.A., G.T., R.S.,
B.D. and A.H.B.-G. conducted experiments; E.T., R.D. wrote the manuscript and I.D., J.V., T.M., C.W., M.T., G.T.-Y. and A.H.B.-G. crosschecked the manuscript prior to submission. Funding: This research received funding from the Wellcome Trust International Intermediate Fellowship
214201/Z/18/Z awarded to Rousseau Djouaka. It also received support from Fp5-A4NH program of the CGIAR
coordinated by Bernard Bett, Jo Line and JeffWaage. Acknowledgments: The AgroEcoHealth platform of International Institute of Tropical Agriculture–Benin
supported this research. The authors are indebted to Théodore LAWE (Sodecoton/IRAD Cameroon) for providing
the ‘SVS’ strain, Robert AHOMANGNON for his assistance in the collection and rearing of field strains of H. armigera in Benin. All thanks to Elie DANNON (IITA-Benin) for his contributions to the discussion section of
this manuscript. Conflicts of Interest: The authors declare no conflict of interest. 4.4. Resistance Mechanisms Developed by H. Armigera Populations to Deltamethrin When field populations of H. armigera were exposed to PBO synergists prior to deltamethrin
bio-assays, we recorded a significant increase in observed mortalities; implying the consistent
involvement of P450-mediated detoxification enzymes in observed resistance mechanisms. These results 12 of 15 12 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 are similar to those reported by Durigan et al. [20] in Brazil; Achaleke et al. [41] and Brun-Barale et al. [19]
in Central Africa and West Africa respectively. However, the fact that mortalities below 100% were
recorded in Djidja and Abomey-Calavi even in the presence of synergist PBO may indicate the possible
presence of other mechanisms of resistance in these H. armigera populations. Previous studies had
revealed the involvement of esterase enzymes in highly resistant populations of Helicoverpa spp. from farms under IPM [42,43]. This research further highlights the implication of several families of
metabolizers in recorded pyrethroid resistance in H. armigera populations in Benin. The effectiveness
of synergists as recorded in this research suggests a possible combination of PBO and pyrethroids
for improved performance of current treatments of cotton, vegetable and grain legumes farms in
Benin. More investigations are needed for a better understanding of developed resistance mechanism
pathways as these evidences are necessary for a better management of this pest and for reducing
related economic losses. 3.
Djihinto, A.C.; Katary, A.; Djaboutou, M.C.; Prudent, P.; Menozzi, P.; Atachi, P. Variation in biological
parameters of cypermethrin resistant and susceptible strains of Helicoverpa armigera from Benin Republic,
West Africa. Int. J. Biol. Chem. Sci. 2012, 6, 931–940. [CrossRef] References Behere, G.T.; Tay, W.T.; Russell, D.A.; Batterham, P. Molecular markers to discriminate among four pest
species of Helicoverpa (Lepidoptera: Noctuidae). Bull. Entomol. Res. 2008, 98, 599–603. [CrossRef] 8. Chaturvedi, I. Status of insecticide resistance in the cotton bollworm, Helicoverpa armigera (Hubner). J. Cent. Eur. Agric. 2007, 8, 171–182. 9. Zalucki, M.P.; Daglish, G.; Firempong, S.; Twine, P. The biology and ecology of Heliothisarmigera (Hiibner)
and H. punctiger a wallengren (Lepidoptera: Noctuidae) in Australia: What do we know? Aust. J. Zool. 1986, 34,
779–814. [CrossRef] 10. Martin, T.; Ochou, G.O.; Hala-N’klo, F.; Vassal, J.M.; Vaissayre, M. Pyrethroid resistance in the cotton
bollworm, Helicoverpa armigera (Hubner), in West Africa. Pest Manag. Sci. 2000, 56, 549–554. [CrossRef] 10. Martin, T.; Ochou, G.O.; Hala-N’klo, F.; Vassal, J.M.; Vaissayre, M. Pyrethroid resistance in the cotton
bollworm, Helicoverpa armigera (Hubner), in West Africa. Pest Manag. Sci. 2000, 56, 549–554. [CrossRef]
11. Djihinto, A.C.; Katary, A.; Prudent, P.; Vassal, J.-M.; Vaissayre, M. Variation in resistance to pyrethroids in
H li
i
f
B
i
R
bli
W
t Af i
J E
E t
l 2009 102 1928 1934 [C
R f] 1. Djihinto, A.C.; Katary, A.; Prudent, P.; Vassal, J.-M.; Vaissayre, M. Variation in resistance to pyrethroid
Helicoverpa armigera from Benin Republic, West Africa. J. Econ. Entomol. 2009, 102, 1928–1934. [CrossRe 12. Vaissayre, M.; Ochou, G.O.; Hema, O.S.A.; Togola, M. Changing strategies for sustainable management of
cotton pests in sub–Saharan Africa. Cah. Agric. 2006, 15, 80–84. 13. Brévault, T.; Achaleke, J.; Sougnabé, S.P.; Vaissayre, M. Tracking pyrethroid resistance in the polyphagous
bollworm, Helicoverpa armigera (Lepidoptera: Noctuidae), in the shifting landscape of a cotton-growing
area. Bull. Entomol. Res. 2008, 98, 565–573. [CrossRef] 14. Yadouleton, A.W.M.; Asidi, A.; Djouaka, R.F.; Braïma, J.; Agossou, C.D.; Akogbeto, M.C. Development of
vegetable farming: A cause of the emergence of insecticide resistance in populations of Anophelesgambiae in
urban areas of Benin. Malar. J. 2009, 8, 103. [CrossRef] 15. Tabashnik, B.E.; Mota-Sanchez, D.; Whalon, M.E.; Hollingworth, R.M.; Carrière, Y. Defining terms for
proactive management of resistance to bt crops and pesticides. J. Econ. Entomol. 2014, 107, 496–507. [CrossRef] [PubMed] 16. Ahmad, M.; Arif, I.M.; Ahmad, Z. Monitoring insecticide resistance of Helicoverpa armigera (Lepidoptera:
Noctuidae) in Pakistan. J. Econ. Entomol. 1995, 88, 771–776. [CrossRef] 17. Ramasubramanian, T.; Regupathy, A. Magnitude and mechanism of insecticide resistance in Helicoverpa
armigera hub. population of Tamil Nadu, India. Asian J. Plant Sci. 2004, 3, 94–100. [CrossRef] 18. References 1. Regupathy, A.; Kranthi, K.P.; Asokan, G.; Armes, N.J.; Rao, N.V.; Soundarajan, R.P.; Russel, D.A. Mechanisms
of insecticide resistance in field populations of Helicoverpa armigera in India. In Proceedings of the International
Conference of Integrated Approaching to Combating Resistance, Harpenden Herts, UK, 14–16 April 1997;
p. 117. 1. Regupathy, A.; Kranthi, K.P.; Asokan, G.; Armes, N.J.; Rao, N.V.; Soundarajan, R.P.; Russel, D.A. Mechanisms
of insecticide resistance in field populations of Helicoverpa armigera in India. In Proceedings of the International
Conference of Integrated Approaching to Combating Resistance, Harpenden Herts, UK, 14–16 April 1997;
p. 117. 2. Sharma, H.C. Heliothis/Helicoverpa Management: Emerging Trends and Strategies for Future Research; Oxford &
IBH Publishing Co. Pvt. Ltd: New Delhi, India, 2005; Available online: https://www.cabdirect.org/cabdirect/
abstract/20053129730 (accessed on 25 February 2019). 2. Sharma, H.C. Heliothis/Helicoverpa Management: Emerging Trends and Strategies for Future Research; Oxford &
IBH Publishing Co. Pvt. Ltd: New Delhi, India, 2005; Available online: https://www.cabdirect.org/cabdirect/
abstract/20053129730 (accessed on 25 February 2019). 3. Djihinto, A.C.; Katary, A.; Djaboutou, M.C.; Prudent, P.; Menozzi, P.; Atachi, P. Variation in biological
parameters of cypermethrin resistant and susceptible strains of Helicoverpa armigera from Benin Republic,
West Africa. Int. J. Biol. Chem. Sci. 2012, 6, 931–940. [CrossRef] 3. Djihinto, A.C.; Katary, A.; Djaboutou, M.C.; Prudent, P.; Menozzi, P.; Atachi, P. Variation in biological
parameters of cypermethrin resistant and susceptible strains of Helicoverpa armigera from Benin Republic,
West Africa. Int. J. Biol. Chem. Sci. 2012, 6, 931–940. [CrossRef] 13 of 15 13 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 4. Pinto, F.A.; Mattos, M.V.V.; Silva, F.W.S.; Rocha, S.L.; Elliot, S.L. The spread of Helicoverpa armigera (Lepidoptera:
Noctuidae) and coexistence with Helicoverpa zea in Southeastern Brazil. Insects 2017, 8, 87. [CrossRef] [PubMed] 4. Pinto, F.A.; Mattos, M.V.V.; Silva, F.W.S.; Rocha, S.L.; Elliot, S.L. The spread of Helicoverpa armigera (Lepidoptera:
Noctuidae) and coexistence with Helicoverpa zea in Southeastern Brazil. Insects 2017, 8, 87. [CrossRef] [PubMed]
5. Jones, C.M.; Parry, H.; Tay, W.T.; Reynolds, D.R.; Chapman, J.W. Movement ecology of pest Helicoverpa: 5. Jones, C.M.; Parry, H.; Tay, W.T.; Reynolds, D.R.; Chapman, J.W. Movement ecology of pest Helicoverpa:
Implications for ongoing spread. Annu. Rev. Entomol. 2019, 64, 277–295. [CrossRef] 6. Pogue, M.G. A new synonym of Helicoverpa zea (Boddie) and differentiation of adult males of H. zea; and H. armigera (Hübner) (Lepidoptera: Noctuidae: Heliothinae). Ann. Entomol. Soc. Am. 2004, 97, 1222–1226. [CrossRef] 7. References Torres-Vila, L.M.; Rodríguez-Molina, M.C.; Lacasa-Plasencia, A.; Bielza-Lino, P. Insecticide resistance of
Helicoverpa armigera to endosulfan, carbamates and organophosphates: The Spanish case. Crop Prot. 2002, 21,
1003–1013. [CrossRef] 19. Brun-Barale, A.; Héma, O.; Martin, T.; Suraporn, S.; Audant, P.; Sezutsu, H.; Feyereisen, R. Multiple P450
genes overexpressed in deltamethrin-resistant strains of Helicoverpa armigera. Pest Manag. Sci. 2010, 66,
900–909. [CrossRef] [PubMed] 20. Durigan, M.R.; Corrêa, A.S.; Pereira, R.M.; Leite, N.A.; Amado, D.; de Sousa, D.R.; Omoto, C. High frequency
of CYP337B3 gene associated with control failures of Helicoverpa armigera with pyrethroid insecticides in
Brazil. Pestic. Biochem. Physiol. 2017, 143, 73–80. [CrossRef] [PubMed] 21. Martin, T.; Ochou, G.O.; Vaissayre, M.; Fournier, D. Organophosphorus insecticides synergize pyrethroids
in the resistant strain of cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) from West
Africa. J. Econ. Entomol. 2003, 96, 468–474. [CrossRef] 22. Li, X.; Schuler, M.A.; Berenbaum, M.R. Molecular mechanisms of metabolic resistance to synthetic and
natural xenobiotics. Annu. Rev. Entomol. 2007, 52, 231–253. [CrossRef] 23. Oakeshott, J.G.; Farnsworth, C.A.; East, P.D.; Scott, C.; Han, Y.; Wu, Y.; Russell, R.J. How many genetic
options for evolving insecticide resistance in heliothine and spodopteran pests? Pest Manag. Sci. 2013, 69,
889–896. [CrossRef] 24. Yang, Y.; Li, Y.; Wu, Y. Current status of insecticide resistance in Helicoverpa armigera after 15 years of bt cotton
planting in China. J. Econ. Entomol. 2013, 106, 375–381. [CrossRef] [PubMed] Int. J. Environ. Res. Public Health 2019, 16, 1882 14 of 15 25. Nibouche, S. Cycle Évolutif de Helicoverpa armigera (Hubner, 1808) (Lepidoptera, Noctuidae) Dans L’ouest
du Burkina Faso: Biologie, Écologie et Variabilité Géographique des Populations. 1994. Available online:
http://agritrop.cirad.fr/312599/ (accessed on 25 February 2019). 26. Livak, K.J. Organization and mapping of a sequence on the Drosophila melanogaster X and Y chromosomes
that is transcribed during spermatogenesis. Genetics 1984, 107, 611–634. Available online: http://www.ncbi. nlm.nih.gov/pubmed/6430749 (accessed on 26 February 2019). [PubMed] 27. Gunning, R.V.; Easton, C.S.; Greenup, L.R.; Edge, V.E. Pyrethroid resistance in Heliothis armigera (Hübner)
(Lepidoptera: Noctuidae) in Australia. J. Econ. Entomol. 1984, 77, 1283–1287. [CrossRef] 28. Kranthi, K.R. Insecticide Resistance Monitoring, Mechanisms and Management Manual; Central Institute for
Cotton Research: Nagpur, India, 2005. 29. Martin, T.; Chandre, F.; Ochou, G.O.; Vaissayre, M.; Fournier, D. Pyrethroid resistance mechanisms in the
cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) from West Africa. Pestic. Biochem. Physiol. 2002,
74, 17–26. [CrossRef] 30. Mehinto, J.T.; Atachi, P.; Elégbédé, M.; Kobi, O.; Kpindou, D. References Efficacité comparée des insecticides de natures
différentes dans la gestion des insectes ravageurs du niébé au Centre du Bénin. J. Appl. Biosiences. 2014, 84,
7674–7681. [CrossRef] 31. Matthews, M. Heliothine Moths of Australia. A Guide to Pest Bollworms and Related Noctuid Groups; CSIRO
Publishing: Collingwood, Australia, 1999; Available online: https://www.cabdirect.org/cabdirect/abstract/
19991111459 (accessed on 25 February 2019). 32. Ahouangninou, C.; Fayomi, B.E.; Martin, T. Évaluation des risques sanitaires et environnementaux des
pratiques phytosanitaires des producteurs maraîchers dans la commune rurale de Tori-Bossito (Sud-Bénin). Cah. Agric. 2011, 20, 216–222. [CrossRef] 33. Azandémè-Hounmalon, G.Y.; Affognon, H.D.; Komlan, F.A.; Tamò, M.; Fiaboe, K.K.M.; Kreiter, S.; Martin, T. Farmers’ control practices against the invasive red spider mite, Tetranychusevansi Baker & Pritchard in Benin. Crop Prot. 2015, 76, 53–58. [CrossRef] 34. Akogbeto, M.C.; Djouaka, R.; Noukpo, H. [Use of agricultural insecticides in Benin]. Bull. Soc. Pathol. Exot. 2005, 98, 400–405. Available online: https://www.researchgate.net/publication/7346565_Use_of_agricultural_
insecticides_in_Benin (accessed on 25 February 2019). 35. Martin, T.; Ochou, G.O.; Djihinto, A.; Traore, D.; Togola, M.; Vassal, J.M.; Vaissayre, M.; Fournier, D. Controlling an insecticide-resistant bollworm in West Africa. Agric. Ecosyst. Environ. 2005, 107, 409–411. [CrossRef] 36. Corbel, V.; N’Guessan, R.; Brengues, C.; Chandre, F.; Djogbenou, L.; Martin, T.; Akogbéto, M.; Hougard, J.M.;
Rowland, M. Multiple insecticide resistance mechanisms in Anopheles gambiae and Culex quinquefasciatus
from Benin, West Africa. Acta Trop. 2007, 101, 207–216. [CrossRef] [PubMed] 37. Djègbè, I.; Boussari, O.; Sidick, A.; Martin, T.; Ranson, H.; Chandre, F.; Akogbéto, M.; Corbel, V. Dynamics of
insecticide resistance in malaria vectors in Benin: First evidence of the presence of L1014S kdr mutation in
Anopheles gambiae from West Africa. Malar. J. 2011, 10, 261. [CrossRef] 38. Djouaka, R.; Akoton, R.I.; Tchigossou, G.M.; Atoyebi, S.M.; Irving, H.; Kusimo, M.O.; Djegbe, I.; Riveron, J.M.;
Tossou, E.; Yessoufou, A.; et al. Mapping the distribution of Anopheles funestus across Benin highlights a sharp
contrast of susceptibility to insecticides and infection rate to Plasmodium between southern and northern
populations. Wellcome Open Res. 2017, 1, 28. [CrossRef] 39. Djogbénou, L.; Noel, V.; Agnew, P. Costs of insensitive acetylcholinesterase insecticide resistance for the
malaria vector Anopheles gambiae homozygous for the G119S mutation. Malar. J. 2010, 9, 12. [CrossRef] 40. Ratan, M.; Rafiq, L.; Javid, M.; Razia, S. Imbalance due to Pesticide Contamination in Different
Ecosystems. Int. J. Theor. Appl. Sci. 2018, 10, 239–246. Available online: https://www.researchgate. net/publication/325945183_Imbalance_due_to_Pesticide_Contamination_in_Different_Ecosystems (accessed
on 11 April 2019). 41. 42.
Gunning, R.V.; Moores, G.D.; Devonshire, A.L. Esterase inhibitors synergise the toxicity of pyrethroids in
Australian Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae). Pestic. Biochem. Physiol. 1999, 63, 50–62.
[CrossRef]
43.
Young, S.J.; Gunning, R.V.; Moores, G.D. The effect of piperonyl butoxide on pyrethroid-resistance-associated
esterases in Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae). Pest Manag. Sci. 2005, 61, 397–401.
[CrossRef] [PubMed]
© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/). © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/). References Achaleke, J.; Martin, T.; Ghogomu, R.T.; Vaissayre, M.; Brévault, T. Esterase-mediated resistance to pyrethroids
in field populations of Helicoverpa armigera (Lepidoptera: Noctuidae) from Central Africa. Pest Manag. Sci. 2009,
65, 1147–1154. [CrossRef] [PubMed] 15 of 15 15 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 42. Gunning, R.V.; Moores, G.D.; Devonshire, A.L. Esterase inhibitors synergise the toxicity of pyrethroids in
Australian Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae). Pestic. Biochem. Physiol. 1999, 63, 50–62. [CrossRef]
43. Young, S.J.; Gunning, R.V.; Moores, G.D. The effect of piperonyl butoxide on pyrethroid-resistance-associated
esterases in Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae). Pest Manag. Sci. 2005, 61, 397–401. [CrossRef] [PubMed]
© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/).
|
https://openalex.org/W4256640301
|
https://www.qeios.com/read/7TSGJH/pdf
|
English
| null |
HPV-Mediated (p16-Positive) Oropharyngeal Cancer Pathologic Primary Tumor TNM Finding v8
|
Definitions
| 2,020
|
cc-by
| 93
|
Qeios · Definition, February 2, 2020 Open Peer Review on Qeios Open Peer Review on Qeios HPV-Mediated (p16-Positive)
Oropharyngeal Cancer Pathologic Primary
Tumor TNM Finding v8 National Cancer Institute National Cancer Institute Qeios ID: 7TSGJH · https://doi.org/10.32388/7TSGJH Source National Cancer Institute. HPV-Mediated (p16-Positive) Oropharyngeal Cancer
Pathologic Primary Tumor TNM Finding v8. NCI Thesaurus. Code C132861. A pathologic finding about one or more characteristics of HPV-mediated (p16-positive)
oropharyngeal cancer, following the rules of the TNM AJCC v8 classification system as
they pertain to staging of the primary tumor. Qeios ID: 7TSGJH · https://doi.org/10.32388/7TSGJH 1/1
|
W4240969670.txt
|
https://www.qeios.com/read/LNL7Y4/pdf
|
de
|
MET Protein Variant
|
Definitions
| 2,020
|
cc-by
| 56
|
Qeios · Definition, February 8, 2020
Ope n Pe e r Re v ie w on Qe ios
MET Protein Variant
National Cancer Institute
Source
National Cancer Institute. MET Protein Variant. NCI T hesaurus. Code C136286.
A variation in the amino acid sequence for the hepatocyte growth factor receptor
protein.
Qeios ID: LNL7Y4 · https://doi.org/10.32388/LNL7Y4
1/1
|
|
https://openalex.org/W2056863276
|
https://zenodo.org/records/1538070/files/article.pdf
|
English
| null |
On the Bacteriology of Initial Dental Caries: A Reply to the Foregoing Statement by Dr. J. Leon Williams
|
Journal of dental research
| 1,919
|
public-domain
| 949
|
permission.
at Univ of Connecticut / Health Center / Library on April 12, 2015 For personal use only. No other uses without
jdr.sagepub.com
Downloaded from ON THE BACTERIOLOGY OF INITIAL DENTAL CARIES
O
O
GO
G WILLIAM J. GIES
Biochemical Laboratory of Columbia University, at the College of Physicians and Surgeons,
New York City WILLIAM J. GIES
Biochemical Laboratory of Columbia University, at the College of Physicians and Surgeons,
New York City WILLIAM J. GIES
Biochemical Laboratory of Columbia University, at the College of Physicians and Surgeons,
New York City Dr. Williams is quite correct in his assumption, as stated in the
paper preceding this, that we have been working without detailed
knowledge of what he has done in dental bacteriology. In our first
review of the situation in this field, my collaborator, Dr. Lothrop (1),
referred to a paper, by Dr. Williams (2), in which Dr. Williams de-
scribed Vincentini's Leptothrix racemosa. It was said, in that review,
that L. racemosa is probably a fungus. We knew of Goadby's com-
ment in this relation, as follows (3): "This organism (L. racemosa),
according to Vincentini and Leon Williams, belongs to a higher order
than the bacteria or schizomycetes, and it is suggested that it should
be placed among the fungi. Williams thinks that the process of
sporulation that he has seen is nearly allied to the uridineae or rusts." In our earlier laboratory observations in this connection, my col-
laborator, Dr. Kligler, identified and cultivated two species of Lepto-
thrix from dental deposits. One of them, L. buccalis, was referred
to as follows (4): "L. buccalis. Fifteen strains of the true Leptothrix
were studied in detail. They correspond with the description usually
given for the typical organism. They all showed the same mor-
phology and resembled microscopically both the L. buccalis of Miller
and the L. racemosa of Vincentini and Williams." In our next publication on this subject, in an early issue of this
JOURNAL, we shall present a full review of Dr. Williams' work in this
relation, with particular reference to its bearing on the present status
of dental bacteriology. It has been a part of our plan, from the beginning, to include the
type of study and photomicrographic demonstration that Dr. Williams
mentions as a deficiency in our reports to date. We have found it 27 28 WILLIAM J. GIES impossible to progress as rapidly or as comprehensively as we hoped,
because of lack of financial resources on which to proceed. impossible to progress as rapidly or as comprehensively as we hoped,
because of lack of financial resources on which to proceed. It is very gratifying to receive Dr. permission.
at Univ of Connecticut / Health Center / Library on April 12, 2015 For personal use only. No other uses without
jdr.sagepub.com
Downloaded from WILLIAM J. GIES
Biochemical Laboratory of Columbia University, at the College of Physicians and Surgeons,
New York City Williams' proffer of a gift of
$500 to this JOURNAL, to promote the purpose of the JOURNAL itself,
to assist us in our bacterio-chemical study, and to help us to prepare,
for educational purposes, dental specimens showing the mucin plaque
in situ. I have assured Dr. Williams that his generosity is very
greatly appreciated and that we shall be happy to endeavor to execute
all his suggestions. I have before me, as I write, the two excellent reproductions, in
Goadby's book (5), of photomicrographs of specimens made by Dr. Williams showing "a section of enamel with layer of attached organ-
isms and formation of pits between enamel rods" (p. 135), and "dental
caries affecting dentine under enamel pit" (p. 144). It is evident,
from the effectiveness of these photomicrographs, that Dr. Williams'
experience in work of this kind will be of the greatest possible assist-
ance to us in our endeavor to make similar specimens, for permanent
use in dental schools and for study in our research. With Goadby's book still before me I note further, with pleasure,
the following comment, on p. 137: "Leon Williams has demonstrated
the plaques of microorganisms on the enamel surface of teeth, and
the incipient caries occurring under these plaques." Readers of my reports to the First District Dental Society of the
State of New York, on the dentifricial efficacy of food-acid media, as
published in the Journal of the Allied Dental Societies since the issue
of December, 1910, will doubtless be interested in the following com-
ment by Goadby, in the same book, p. 139, quoting Dr. Williams:
"Dr. Leon Williams tells me that the Sicilians, who are particularly
free from caries, are large consumers of lemons." The generous attitude of Dr. Williams, as expressed in the pre-
ceding paper, toward the furtherance of dental research and the pro-
motion of dental education, is very gratifying evidence of his abiding
active interest in the advancement of his profession. It is a pleasure and an honor to accept, and to try to merit, for the
JOURNAL OF DENTAL RESEARCH, such a valued and stimulating
practical expression of idealism as Dr. Williams presents
to the
readers of this JOURNAL. 29 permission.
at Univ of Connecticut / Health Center / Library on April 12, 2015 For personal use only. No other uses without
jdr.sagepub.com
Downloaded from LITERATURE CITED (1) LOTHROP
1911
Journal of the Allied Dental Societies, vi, p. 305. (1) LOTHROP
1911
Journal of the Allied Dental Societies, vi, p. 305. ( )
(2) WILLIAMS
1899
Dental Cosmos, xli, p. 317. (3) GOADBY
1903
Mycology of the mouth, p. 187. (4) KLIGLER AND GIES
1915
Journal of the Al (4) KLIGLER AND GIES
1915
Journal of the Allied Dental Societies, x, p. 328. (5) GOADBY
1903
Mycology of the mouth.
|
https://openalex.org/W4313799967
|
https://www.research.ed.ac.uk/files/325704712/gkac1232.pdf
|
English
| null |
Cryo-EM structure of the fully assembled Elongator complex
|
Nucleic acids research
| 2,023
|
cc-by
| 20,199
|
General rights
C
i h f
h General rights
Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s)
and / or other copyright owners and it is a condition of accessing these publications that users recognise and
abide by the legal requirements associated with these rights. Edinburgh Research Explorer Digital Object Identifier (DOI):
10.1093/nar/gkac1232 Document Version:
Publisher's PDF, also known as Version of record Published In:
Nucleic Acids Research Cryo-EM structure of the fully assembled elongator complex Citation for published version:
Jaciuk, M, Scherf, D, Kaszuba, K, Gaik, M, Rau, A, Kościelniak, A, Krutyhołowa, R, Rawski, M, Indyka, P,
Graziadei, A, Chramiec-Głąbik, A, Biela, A, Dobosz, D, Lin, T-Y, Abbassi, N-E-H, Hammermeister, A,
Rappsilber, J, Kosinski, J, Schaffrath, R & Glatt, S 2023, 'Cryo-EM structure of the fully assembled
elongator complex', Nucleic Acids Research, vol. 51, no. 5, gkac1232, pp. 2011-2032. https://doi.org/10.1093/nar/gkac1232 Citation for published version: Citation for published version:
Jaciuk, M, Scherf, D, Kaszuba, K, Gaik, M, Rau, A, Kościelniak, A, Krutyhołowa, R, Rawski, M, Indyka, P,
Graziadei, A, Chramiec-Głąbik, A, Biela, A, Dobosz, D, Lin, T-Y, Abbassi, N-E-H, Hammermeister, A,
Rappsilber, J, Kosinski, J, Schaffrath, R & Glatt, S 2023, 'Cryo-EM structure of the fully assembled
elongator complex', Nucleic Acids Research, vol. 51, no. 5, gkac1232, pp. 2011-2032. https://doi.org/10.1093/nar/gkac1232 Take down policy Take down policy
The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer
content complies with UK legislation. If you believe that the public display of this file breaches copyright please
contact openaccess@ed.ac.uk providing details, and we will remove access to the work immediately and
investigate your claim. Download date: 24. Oct. 2024 Nucleic Acids Research, 2023
1
https://doi.org/10.1093/nar/gkac1232 NAR Breakthrough Article
Cryo-EM structure of the fully assembled Elongator
complex Marcin Jaciuk1, David Scherf2, Karol Kaszuba3,4, Monika Gaik
1, Alexander Rau5,
Anna Ko´scielniak1, Ro´scisław Krutyhołowa1, Michał Rawski1,6, Paulina Indyka1,6,
Andrea Graziadei5, Andrzej Chramiec-Gł˛abik1, Anna Biela1, Dominika Dobosz1,
Ting-Yu Lin1, Nour-el-Hana Abbassi1,7, Alexander Hammermeister1,2, Juri Rappsilber
5,8,
Jan Kosinski
3,4,9, Raffael Schaffrath
2 and Sebastian Glatt
1,* 1Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland, 2Institute for Biology,
Department for Microbiology, University of Kassel, Kassel 34132, Germany, 3European Molecular Biology Laboratory
Hamburg, Hamburg 22607, Germany, 4Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany,
5Bioanalytics, Institute of Biotechnology, Technische Universit¨at Berlin, Berlin 13355, Germany, 6National
Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland, 7Postgraduate School of
Molecular Medicine, Medical University of Warsaw, Warsaw 02-091, Poland, 8Wellcome Centre for Cell Biology,
University of Edinburgh, Edinburgh EH9 3BF, UK and 9Structural and Computational Biology Unit, European
Molecular Biology Laboratory, Heidelberg 69117, Germany Received August 22, 2022; Revised November 22, 2022; Editorial Decision November 23, 2022; Accepted Dec C⃝The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. *To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902; Email: sebastian.glatt@uj.edu.pl
Present address: Ro´scisław Krutyhołowa, Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland. ABSTRACT fully assembled mouse Elongator complex at 5.9 ˚A
resolution. Our results confirm the structural con-
servation of Elongator and its intermediates among
eukaryotes. Furthermore, we complement our analy-
ses with the biochemical characterization of the as-
sembled human Elongator. Our results provide the
molecular basis for the assembly of Elongator and
its tRNA modification activity in eukaryotes. ar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Transfer RNA (tRNA) molecules are essential to de-
code messenger RNA codons during protein synthe-
sis. All known tRNAs are heavily modified at mul-
tiple positions through post-transcriptional addition
of chemical groups. Modifications in the tRNA an-
ticodons are directly influencing ribosome decod-
ing and dynamics during translation elongation and
are crucial for maintaining proteome integrity. In eu-
karyotes, wobble uridines are modified by Elonga-
tor, a large and highly conserved macromolecular
complex. Elongator consists of two subcomplexes,
namely Elp123 containing the enzymatically active
Elp3 subunit and the associated Elp456 hetero-
hexamer. The structure of the fully assembled com-
plex and the function of the Elp456 subcomplex have
remained elusive. Here, we show the cryo-electron
microscopy structure of yeast Elongator at an overall
resolution of 4.3 ˚A. We validate the obtained struc-
ture by complementary mutational analyses in vitro
and in vivo. In addition, we determined various struc-
tures of the murine Elongator complex, including the eceived August 22, 2022; Revised November 22, 2022; Editorial Decision November 23, 2022; Accepted Decemb INTRODUCTION strate (31). Of note, the structure of yeast Elp3 resembles
previously resolved crystal structures of bacterial and ar-
chaeal Elp3 proteins (32,33). In detail, the Elp3 subunit
specifically binds the tRNA anticodon stem loop (ASL) in
the vicinity of its radical S-adenosyl methionine (rSAM)
and lysine acetyltransferase (KAT) domains to modify the
well-positioned U34 nucleotide (32–34). tRNA binding is
aided by additional contacts in the CTD of Elp1, which was
previously shown to be heavily phosphorylated (35) and in-
volved in tRNA binding (36). Transfer RNAs (tRNA) are one of the most essential
biomolecules in all living organisms. Together with mes-
senger RNAs (mRNA), they are responsible for the cor-
rect transfer of information from the genomic DNA into
functional polypeptide chains. tRNAs undergo significant
post-transcriptional modifications, which confer stabiliza-
tion of the folded tRNA, regulate the interaction with other
molecules or tune the codon-anticodon pairing during the
mRNA translation process within the ribosome (1). In eu-
karyotes, almost all wobble uridines at position 34 (U34),
are carboxymethylated on the fifth carbon of their base
(cm5) by the activity of the highly conserved Elongator
complex aided by its accessory proteins Kti11, Kti12, Kti13,
Kti14 and Sit4 (2–6). Subsequently, cm5 is further modi-
fied by other enzymes to 5-methoxycarbonylmethyl (mcm5),
5-carbamoylmethyl (ncm5) or 5-methoxy-carbonyl-methyl-
2-thio (mcm5s2) (7,8). These modifications regulate proper
tRNA binding in the A-site of translating ribosomes during
the elongation phase (9–11) and thus maintain an optimal
speed during polypeptide synthesis, supporting proper co-
translational folding of the nascent proteins. Decreased lev-
els of wobble uridine modifications lead to ribosome paus-
ing, incorrect protein folding and consequently trigger in-
tracellular protein aggregation and proteotoxic stress (12–
14). Furthermore, Elongator is a clinically highly relevant
enzyme, as mutations that disturb the structure or func-
tion of the complex result in severe human diseases (15),
like familial dysautonomia (16), rolandic epilepsy (17), in-
tellectual disability (18), amyotrophic lateral sclerosis (19),
other neurodevelopmental diseases (20–22) and childhood
medulloblastoma (23). g (
)
Despite all previous efforts, several fundamental ques-
tions concerning Elongator’s function remain elusive. For
instance, the tRNA modification reaction has not been re-
constituted in vitro (37,38), which leaves the exact molecu-
lar mechanisms and the observed substrate specificity unan-
swered. INTRODUCTION One of the main open questions concerns the func-
tional role of the Elp456 subcomplex, which interacts with
Elp123 and is essential for the activity of Elongator in yeast
(39). To address these outstanding questions, we investi-
gated the cryo-EM structures of the yeast Elongator com-
plex in its native and bis(sulfosuccinimidyl)suberate (BS3)
stabilized state. Next, we validated the functional relevance
of the newly identified structural features in vivo using es-
tablished phenotypic assays. Furthermore, we were able to
confirm the high structural conservation of Elongator and
its active site by determining structures of Elp123, Elp123–
tRNA and Elongator complexes from yeast and mouse. Finally, through biochemical characterization of human
Elp123 and Elp456 we can propose a detailed reaction
mechanism and suggest a role for the Elp456 subcomplex
during the reaction cycle of the Elongator. GRAPHICAL ABSTRACT e
-
-
e
n
ll
c-
o
-
e
GRAPHICAL ABSTRACT
ax: +48 12 664 6902; Email: sebastian.glatt@uj.edu.pl
f Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland. 23 containing the enzymatically active
t and the associated Elp456 hetero-
e structure of the fully assembled com-
function of the Elp456 subcomplex have
sive. Here, we show the cryo-electron
structure of yeast Elongator at an overall
4.3 ˚A. We validate the obtained struc-
plementary mutational analyses in vitro
n addition, we determined various struc-
murine Elongator complex, including the
GRAPHICAL ABSTRACT
ondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902; Email: sebastian.glatt@uj.edu.pl
´scisław Krutyhołowa, Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland. *To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902; Email: sebastian.glatt@uj.edu.pl
Present address: Ro´scisław Krutyhołowa, Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland. 2 Nucleic Acids Research, 2023 MATERIALS AND METHODS The Elongator complex harbors two copies of each of
its six subunits, namely Elongator proteins 1–6 (Elp1–Elp6)
(24). The complex can be divided into two discrete sub-
complexes - the larger catalytic Elp123 and the smaller hex-
americ ring-shaped Elp456 (25,26). Studies applying nega-
tive stain electron microscopy, revealed that Saccharomyces
cerevisiae Elp123 (ScElp123) adopts a symmetric ‘moth’-
like shape, with two distinguishable lobes that are sepa-
rated by a cleft and connected by an arch region. In con-
trast, the structure of the fully assembled Elongator com-
plex seems asymmetric as Elp456 only binds to one lobe
of the dimeric Elp123 subcomplex (27,28). Based on these
initial low-resolution reconstructions the following subunit
arrangement of the Elp123 subcomplex was proposed – the
two N-terminal WD40 domains of Elp1 and Elp2 (29), en-
compass the enzymatically active Elp3 subunit from op-
posite directions creating a lobe of Elp123. The remaining
C-terminal domain (CTD) of Elp1 consisting of tetratri-
copeptide repeats (TPRs) and the CTD of the second copy
of Elp1 dimerize into an arch-like structure that connects
two Elp123 lobes, respectively (30). Subsequent single par-
ticle cryo-electron microscopy (cryo-EM) studies resulted
in high-resolution structures of yeast Elp123 in its free and
tRNA-bound states. Intriguingly, these structures revealed
the spatial organization of the active site in the eukaryotic
Elp3 protein, including the coordination of an iron-sulfur
cluster, the S-adenosyl-methionine (SAM) cleavage product
5′-deoxyadenosine (5′-dA) and the respective tRNA sub- Bulk yeast tRNA isolation To obtain yeast bulk tRNA, S. cerevisiae strains were grown
in YPD (Yeast Extract–Peptone–Dextrose) to an OD600 nm
of 1, harvested, washed and resuspended in NucleoZOL
(Machery Nagel). Cells were lysed by bead beating in 6 cy-
cles each 60 s, 20% v/v volume of chloroform was added
and samples were vigorously vortexed for another 60 s. Sub-
sequently, the suspension was incubated for 15 min at 4◦C
and centrifugated for 30 min at 21 000 × g. The aqueous
RNA-containing phase was transferred into a new reaction
tube and large RNAs were precipitated for 3 h at −20◦C us-
ing 2/3 volume of 8 M LiCl. Large RNAs were pelleted for
30 min at 4◦C and 21 000 × g. To increase tRNA purity, the
LiCl precipitation step was repeated. The tRNA-containing
supernatant was precipitated with 10% v/v 3 M sodium
acetate pH 5.2 and 2.5 volumes 100% ethanol overnight
at −20◦C. The tRNA containing pellet was washed twice
with 75% v/v ethanol, air dried and resuspended in 10 mM
sodium acetate pH 5.2. tRNA concentrations were deter-
mined using the Epoch (Agilent BioTek) spectrophotome-
ter and stored at −80◦C. Protein production and purification DS1-2b yeast cells (MAT his3-Δ200, leu2-Δ1, trp1-Δ63,
ura3-52), co-transformed with the constructs expressing all
six Elongator genes, were grown on synthetic drop-out (SD)
media plates (2% w/v agar and 2% w/v glucose) lacking
tryptophan, leucine and uracil. Cells were grown shaking
overnight at 30◦C in the SD media (2% w/v glucose), reinoc-
ulated (3:50 ratio) on the next day into fresh SD medium
and further incubated overnight at 30◦C with shaking. For
protein overproduction, cells were inoculated (1:20) in fresh
SD media containing 2% w/v raffinose and incubated for
5–7 h at 30◦C while shaking. ELP genes expression was
induced by addition of galactose to a final concentration
of 2% w/v and cells were left shaking for 21 h at 30◦C. Cells were harvested by centrifugation, resuspended in lysis
buffer (250 mM HEPES (pH 7.5), 100 mM NaCl, 10% v/v
glycerol, 0.1% v/v Tween 20, 1 mM sodium orthovanadate,
20 mM sodium fluoride, aprotinin (2 g/ml), leupeptin (5
g/ml), 1 M pepstatin A, and 1 mM PMSF) and small
cell suspensions droplets were flash frozen in liquid nitro-
gen. Droplets were lysed by cryo-milling (Qiagen TissueL-
yser II) and stored as a powder at −80◦C until use. All pu-
rification steps were performed at 4◦C or on ice. 12 ml of
fresh lysis buffer was added per 40 g of dry yeast pellet
and thawed for 1 h under agitation. Lysates were clarified
by two consecutive centrifugation steps at 21 000 × g for
30 min. Cell extracts were incubated for 30 min with 3 ml
of IgG Sepharose™6 Fast Flow resin (GE Healthcare) and
washed three times with lysis buffer. Proteins were eluted in
5 ml lysis buffer by TEV protease cleavage (1 mg) in pres-
ence of 1 mM dithiothreitol (DTT) for 1 h. Subsequently,
the eluent was applied to a 1 ml StrepTrap HP column
(GE Healthcare) and eluted with 20 mM D-desthiobiotin. The complex was concentrated using an Amicon Ultra-
15 centrifugal filter (100 kDa cut-off) and the Elonga-
tor was further purified on a Superose 6 Increase 10/300
GL column (GE Healthcare) equilibrated with 20 mM
HEPES (pH 7.5), 100 mM NaCl and 3 mM DTT. Selected
fractions were pooled and concentrated with an Amicon
Ultra-0.5 centrifugal filter (100 kDa cut-off). Aliquots were
frozen in liquid nitrogen and stored at −80◦C for further
use. Preparation of expression constructs Eluates were concentrated using Amicon Ultra-
15 centrifugal filters (100 kDa cut-off) and subjected to a
Superose S6 Increase 10/300 GL column (GE Healthcare)
equilibrated with 20 mM HEPES (pH 7.5), 100 mM NaCl
and 5 mM DTT. Purity, integrity, protein quality and all
complexes stoichiometry were monitored during every step
by SDS-PAGE analysis and visualization with Coomassie
stain. and pBig1b plasmids to obtain ELP123 and ELP456, re-
spectively (41). Mutagenesis in human ELP1, ELP4 and
ELP5 were carried out using the QuikChange method. All
genetic constructs were confirmed by DNA sequencing and
moved to the insect cells expression system using standard
Bac-to-Bac protocols. Preparation of expression constructs The ORFs of Saccharomyces cerevisiae ELP1 to ELP6 were
amplified by polymerase chain reactions (PCRs) and cloned
in pairs into three individual vectors with inducible GAL1
and GAL10 promoters to allow for simultaneous expres-
sion of two gene products from a single vector (40). Yeast
cells co-transformed with all three constructs, were selected
for tryptophan, leucine and uracil prototrophy. Coding se-
quences for FLAG and Twin-Strep-tag (IBA Lifesciences)
were added in frame to ELP1 and ELP3, respectively. In
addition, Elp6 was overproduced with a Staphylococcus au-
reus protein A tag and a tobacco etch virus (TEV) pro-
tease cleavage site to facilitate the purification from yeast
cells. All sequences were introduced at the 3′ end of the
individual ORFs. Mus musculus and Homo sapiens biG-
Bac (41,42) constructs containing the ORFs of ELP123
and ELP456 were prepared using a similar tagging strat-
egy. After PCR amplification all expression cassettes (ex-
cept for ELP2) were cloned separately into pFastBac1 plas-
mids. ELP3 was cloned in frame with a Twin-Strep-Tag se-
quence and ELP6 with FLAG-TEV-Protein A sequence at
their 3′ ends. ELP2 genes were cloned into pFastBac-HTA
with a 6xHis-tag sequence at its 5′ end. All genes were am-
plified from the pFastBac plasmids by PCR using primers
with predefined 5′ and 3′ overhangs in each gene, followed
by Gibson assembly reactions (43,44) (NEB) using pBig1a Nucleic Acids Research, 2023 3 methylsulfonyl fluoride in presence of DNase I by three
freeze-thaw cycles and sonication. Lysates were clarified by
two consecutive centrifugation steps at 4◦C and 63 000 × g
for 30 and 60 min. Elp123 subcomplexes were purified from
cell extracts using a 5 ml StrepTrap HP column (GE Health-
care) and eluted with 10 mM d-desthiobiotin. Next, Elp123
subcomplexes were further purified on a 5 ml HiTrap Hep-
arin HP column (GE Healthcare) and eluted with a linear
KCl gradient (50 mM HEPES pH 7.5, 1000 mM KCl, 1 mM
DTT). The final purification step was carried out on a Su-
perose 6 Increase 10/300 GL column (GE Healthcare) equi-
librated with 20 mM HEPES (pH 7.5), 100 mM NaCl and
5 mM DTT. Mouse and human Elp456 subcomplexes were
purified from cell extracts using IgG Sepharose™6 Fast
Flow resin equilibrated with 50 mM HEPES (pH 7.5), 300
mM NaCl, 1 mM DTT and 5% v/v glycerol. Elution from
the resin was accomplished by TEV protease cleavage (1
mg/5 ml). Human bulk tRNA isolation Mouse and human Elp123 were overproduced in Super
Sf9-1, Sf9-3 respectively, while both Elp456 in Hi-5 cells. Cells were cultured in ESF921 medium (Expression Sys-
tems) to a density of 800 000 cells/ml for Super Sf9-1/Sf9-3
and 500 000 cells/ml for Hi-5 cells, followed by baculovirus
infection with the multiplicity of infection (MOI) of 1 and
grown for 3 days at 27◦C while shaking. Cell pellets were
harvested and lysed in 50 mM HEPES (pH 7.5), 100 mM
NaCl for Elp123 and 300 mM NaCl for Elp456, 2 mM
MgCl2, 2 mM DTT, 5% v/v glycerol, aprotinin (2 g/ml),
leupeptin (5 g/ml), 1 M pepstatin A, 1 mM phenyl- HEK293T cells cultured on 15-cm Petri dishes were washed
with PBS and lysed for 5 min in 250 l RNA lysis buffer (10
mM Tris–HCl (pH 7.5), 100 mM NaCl, 10 mM MgCl2, 1%
TritonX-100 v/v, 0.5% v/v sodium deoxycholate, 0.5 mM
DTT) at 4◦C. The lysate was mixed with MiliQ water at a
1:1 ratio v/v and the RNA was isolated three times with 1
volume of acid-phenol:chloroform (1:1 ratio v/v), followed
by an additional step using 1 volume chloroform. After each
step the sample was vortexed and centrifugated for 10 min
at 4500 × g at 4◦C and the aqueous phases were collected, 4 Nucleic Acids Research, 2023 WARP 1.0.9 (46) for ScElongator, and cryoSPARC (47)
for MmElp123–tRNA and MmElongator. Averaged micro-
graphs for all datasets were imported into cryoSPARC and
the contrast transfer function (CTF) was corrected. Blob
picking was performed on 10–15% of micrographs to select
an initial set of particles for template picking (MmElp123–
tRNA) and to train the TOPAZ particle picker (48). For
ScElp456 and MmElp123 two separate trainings were per-
formed for different orientations. The resulting TOPAZ
models were used next to pick particles from all micro-
graphs of respective data sets. A similar approach was ap-
plied for the MmElongator dataset, where two TOPAZ
picking jobs were used during the analysis. Extracted par-
ticles were binned as indicated in respective processing
pipeline panels and particle curation was performed via 2D
classification and ab-initio reconstructions. All Elongator-
related particles, except for MmElp123–tRNA, were next
converted with pyem (49) and imported into Relion for fur-
ther sub-classification. For ScElongator and MmElongator,
masked 3D classifications around Elp456 were applied
to improve the densities of the smaller subcomplex. Model building, refinement and validation Atomic models for both, yeast and mouse structures, were
prepared via SWISS-MODEL homology model building
(50–58), using PDB entries 6QK7 and 4A8J as templates. The model of the yeast Elp3 subunit from Elp123–tRNA
was replaced with the AlphaFold2 model (59) to include
the previously missing N-terminus. After rigid body fitting
into the cryo-EM density map, the models were manually
curated and corrected in Coot (60) and further fitted by
molecular dynamic flexible fit using MDFF (61) and Nam-
dinator (62). The obtained atomic models were refined in
Phenix (63,64), analyzed in Coot and validated with Mol-
Probity (65) (Table 1). Figures were prepared using PyMOL
(The PyMOL Molecular Graphics System, Version 2.5.1
Schr¨odinger, LLC) and UCSF ChimeraX (66). Elongator reconstitution and pull-down assays Mouse or human Elp123 were incubated with the respec-
tive Elp456 subcomplex for 30 min at 25◦C with 1:2 weight
ratio and subsequent purification on a Superose 6 In-
crease 10/300 GL column (GE Healthcare) equilibrated
with 20 mM HEPES (pH 7.5), 100 mM NaCl and 5 mM
DTT. For the pull-down experiments 10 g of bait and
20 g of prey were used. Elp123 was immobilized on
StrepTactin™Sepharose™(Cytiva) beads via Twin-Strep-
tagged Elp3 or in case of Elp456 via anti-DYKDDDDK Human bulk tRNA isolation The precipitate, was
centrifuged at 8000 × g for 30 min at 4◦C and the super-
natant was discarded. The pellet was resuspended in 100
l equilibration buffer without TritonX-100 (10 mM Bis–
Tris (pH 6.3), 15% ethanol v/v, 200 mM KCl). RNA con-
centration was measured using a NanoDrop spectropho-
tometer and the sample was stored at −80◦C until use. To
isolate bulk tRNA 900 g of total RNA (diluted in 2 ml
equilibration buffer without TritonX-100) was loaded on
an equilibrated NucleoBond AX100 column (10 mM Bis–
Tris (pH 6.3), 15% v/v ethanol, 200 mM KCl, 0.15% v/v
TritonX-100) and washed twice with 12 ml washing buffer
(10 mM Bis–Tris (pH 6.3), 15% v/v ethanol, 500 mM KCl)
tRNA was eluted with 12 ml elution buffer (10 mM Bis–
Tris (pH 6.3), 15% v/v ethanol, 800 mM KCl) and mixed
with 2.5 volumes of 100% ethanol, 1 l of glycogen and in-
cubated overnight at −80◦C. After precipitation, the sam-
ple was centrifuged for 30 min at 8000 × g (4◦C), and the
supernatant was discarded. The tRNA pellet was washed
with 40 ml 80% v/v EtOH by vortexing. Afterward, the
tRNA was centrifuged for 30 min at 8000 × g (4◦C). Subse-
quently, the tRNA pellet was air dried and resuspended in
30 l RNAse free water. tRNA concentration was measured
using a NanoDrop spectrophotometer and the sample was
stored at −80◦C for later use. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Electron microscopy QUANTIFOIL® R 2/1 copper grids (200 mesh) were glow-
discharged on a Leica EM ACE 200 glow discharger (8
mA, 60 s). 2.5 l of the sample at 0.4–0.6 mg/ml con-
centration was plunge-frozen using a Vitrobot Mark IV
(Thermo Fisher) set to 100% humidity and 4◦C with the
following blotting parameters −15 s wait time, blot force
5 and 5 s blot time. tRNA was used at 3–5 molar ex-
cess with 15 min incubation on ice for ScElp123–tRNA
and 37◦C for mouse Elp123 (MmElp123)–tRNA samples. ScElp123–tRNA micrographs were acquired at 300 kV us-
ing a Titan Krios 2 (FEI; EMBL, Germany) equipped with
a Gatan Quantum energy filter and a K2 Summit direct
electron detector. 11,080 micrographs were collected with
0.81 ˚A pixel size and 0.8–2 m under-focus for a total
of 40 frames accumulating 42.45 e−/ ˚A2 dose. The remain-
ing datasets were collected on Titan Krios G3i (Thermo
Fisher; Solaris, Poland) equipped with a Gatan Quan-
tum energy filter and a K3 Summit direct electron detec-
tor. The used under-focus range was 0.9–3 m for a total
of 40 frames accumulating an overall dose of 40 e−/ ˚A2. 6339, 4716, 6415, 7000 and 5232 micrographs were col-
lected for ScElongator, ScElp456, MmElp123, MmElp123–
tRNA and MmElongator, respectively with a pixel size of
1.1 ˚A for ScElp456 and 0.86 ˚A for the remaining data
sets. Human bulk tRNA isolation For
ScElp123–tRNA masked tRNA 3D classification followed
by CTF refinement and Bayesian polishing were performed
to improve the tRNA density. For the MmElp123 active
site, a masked 3D classification was performed that resulted
in an improved density around the bound SAM molecule. The final maps after post-processing were obtained at
the following resolutions −4.35 ˚A for ScElongator, 3.96
˚A for ScElp123–tRNA, 3.7 ˚A for ScElp456, 4.01 ˚A for
MmElp123 and 5.92 ˚A for MmElongator, respectively. The analysis of MmElp123–tRNA was exclusively per-
formed in cryoSPARC resulting in an overall resolution of
4.35 ˚A. combined and mixed with 10% volume of 3 M sodium ac-
etate pH 5.5, three volumes of 100% ethanol, 1 l of glyco-
gen and incubated overnight at −80◦C. The precipitate, was
centrifuged at 8000 × g for 30 min at 4◦C and the super-
natant was discarded. The pellet was resuspended in 100
l equilibration buffer without TritonX-100 (10 mM Bis–
Tris (pH 6.3), 15% ethanol v/v, 200 mM KCl). RNA con-
centration was measured using a NanoDrop spectropho-
tometer and the sample was stored at −80◦C until use. To
isolate bulk tRNA 900 g of total RNA (diluted in 2 ml
equilibration buffer without TritonX-100) was loaded on
an equilibrated NucleoBond AX100 column (10 mM Bis–
Tris (pH 6.3), 15% v/v ethanol, 200 mM KCl, 0.15% v/v
TritonX-100) and washed twice with 12 ml washing buffer
(10 mM Bis–Tris (pH 6.3), 15% v/v ethanol, 500 mM KCl)
tRNA was eluted with 12 ml elution buffer (10 mM Bis–
Tris (pH 6.3), 15% v/v ethanol, 800 mM KCl) and mixed
with 2.5 volumes of 100% ethanol, 1 l of glycogen and in-
cubated overnight at −80◦C. After precipitation, the sam-
ple was centrifuged for 30 min at 8000 × g (4◦C), and the
supernatant was discarded. The tRNA pellet was washed
with 40 ml 80% v/v EtOH by vortexing. Afterward, the
tRNA was centrifuged for 30 min at 8000 × g (4◦C). Subse-
quently, the tRNA pellet was air dried and resuspended in
30 l RNAse free water. tRNA concentration was measured
using a NanoDrop spectrophotometer and the sample was
stored at −80◦C for later use. combined and mixed with 10% volume of 3 M sodium ac-
etate pH 5.5, three volumes of 100% ethanol, 1 l of glyco-
gen and incubated overnight at −80◦C. Image processing Frame alignment and dose weighting were performed
with Relion 3.1 (45) implementation of motion correc-
tion for ScElp123–tRNA, ScElp456 and MmElp123; with Nucleic Acids Research, 2023 5 Table 1. Cryo-EM data collection, refinement and validation statistics
ScElongator
EMD-15622
PDB ID 8ASV
ScElp456
EMD-15635
PDB ID 8AT6
ScElp123–tRNA
EMD-15623
PDB ID 8ASW
MmElp123
EMD-15682
PDB ID 8AVG
MmElp123–tRNA
EMD-15625
MmElongator
EMD-15626
Data collection and
processing
Magnification
105 000×
81 000×
165 000×
105 000×
105 000×
105 000×
Voltage (keV)
300
300
300
300
300
300
Electron exposure
(e-/ ˚A2)
40
40
42.45
40
40
40
Defocus range
−0.9 to −3.0
−0.9 to −3.0
−0.8 to −2.0
−0.9 to −3.0
−0.9 to −1.5
−0.9 to −3.0
Pixel size ( ˚A)
0.86
1.1
0.81
0.86
0.86
0.86
Symmetry imposed
C1
C1
C1
C1
C1
C1
Initial particle
images (no.)
188 389
364 424
693 585
364 424
161 871
581 666
Final particle
images (no.)
12 514
128 593
16 809
42 894
24 829
27 128
Map resolution ( ˚A)
4.35
3.7
3.96
4.01
4.35
5.9
FSC threshold
0.143
0.143
0.143
0.143
0.143
0.143
Map resolution
range ( ˚A)
3.9 to >10
3.6 to 6.6
3.7 to 9.7
3.8 to >10
2.8 to >10
4.4 to >10
Refinement
Initial model used
6QK7 and 4A8J
4A8J
6QK7
6QK7
Model resolution
( ˚A)
3.5
3.7
3.5
3.5
FSC threshold
0.143
0.143
0.143
0.143
Model resolution
range ( ˚A)
n/a
n/a
n/a
n/a
Map sharpening B
factor ( ˚A2)
−141.69
−129.16
−67.83
−131.78
Model composition
Non-hydrogen
atoms
35 795
12 587
24 783
13 749
Protein residues
4478
1580
2897
1732
Nucleotide
residues
73
Ligands
1
0
2
2
B factors ( ˚A2)
Protein
99.05
107.76
97.38
84.42
Nucleotide
254.23
Ligands
60.85
61.57
55.04
R.m.s. deviations
Bond lengths ( ˚A)
0.004
0.004
0.006
0.004
Bond angles (◦)
0.990
0.974
1.014
0.989
Validation
MolProbity score
2.13
1.92
2.35
2.17
Clashscore
12.59
9.75
19.37
13.21
Poor rotamers
(%)
0.02
0.00
0.71
0.07
Ramachandran
Favored (%)
90.93
93.80
89.25
90.48
Allowed (%)
9.00
5.88
10.51
9.34
Disallowed (%)
0.07
0.32
0.24
0.18
CC volume
0.65
0.85
0.76
0.71
(Pierce™) resin and FLAG-tagged Elp6. The respective sub-
complex was added and incubated for 30–60 min at 4◦C,
followed by three wash steps with 20 mM HEPES (pH
7.5), 100 mM NaCl, 1 mM DTT, 0.05% v/v Tween 20. Microscale thermophoresis (MST) and gel shift for tRNA
binding assay
The internally Cy5-labeled tRNA ArgUCU (0.2 M) or
tRNA AlaUGC (0.3 M) were incubated for 5 min at 37◦C
with serial dilutions of Elp123, Elp456 or Elongator vari-
ants (starting from 10 M) in MST Buffer (20 mM HEPES
(pH 7.5), 100 mM NaCl, 5 mM DTT, 0.0125% v/v Tween
20). Measurements were performed at 60% excitation power
in Premium Coated capillaries on the Monolith NT.115
(Nanotemper Technologies) at 37◦C. Obtained data were
analyzed and dissociation constant values were calculated Yeast genetic manipulations and phenotypic characterization PCR-based deletions of ELP1, ELP3, ELP4, ELP5 and
ELP6 genes were generated in the UMY2893 wild type
strain (2) using a KlURA3 marker (67) for later counters-
election (68). In order to generate the individual mutations
in ELP1, ELP3, ELP4, ELP5 and ELP6, each gene was
amplified using a primer pair that binds 200 bp up- and
downstream of the ORF from UMY2893 strain and lig-
ated into the pJET1.2 blunt vector. Mutations were intro-
duced via site-directed mutagenesis and further verified by
DNA sequencing. Subsequently, a KlTRP1 marker cassette
was integrated in the 3′UTR of all mutants constructs us-
ing homologous recombination (69). Mutant alleles were
reintroduced into the corresponding knockout strains and
transformants were selected for the loss of KlURA3 marker
gene by 5-fluoroorotic acid resistance and tryptophan pro-
totrophy. Mutants were further confirmed by PCR and ver-
ified by DNA sequencing. To analyze Elongator function
in the generated mutant alleles, growth behavior on media
was analyzed as previously described (70). Introduction of
ELP1-(c-myc)3 and ELP5-(FLAG)3 into the genome was
facilitated by homologous recombination of the desired tag
together with a KlLEU2 (67) or clonNAT marker cassette
(71). Descriptions and genotypes of all yeast strains are
listed in Supplementary Table S1. Yeast protein extraction, co-immunoprecipitation and west-
ern blot analysis To probe for in vivo acetyl-CoA carboxylase (Acc1) in-
teraction, co-immunoprecipitation was carried out as de-
scribed before (70). 8 mg lysate was incubated with 8 g
antibody coupled Dynabeads (Invitrogen, USA) or anti-
FLAG M2 magnetic beads (Sigma-Aldrich, USA) over
night. Unbound protein was removed via a magnetic rack
and precipitated proteins were washed three times with
1 ml B60 buffer (50 mM HEPES–KOH pH 7.3, 60 mM
KAc, 5 mM Mg(Ac)2, 0.1% v/v TritonX-100, 10% v/v glyc-
erol, 1 mM NaF, 20 mM ß-glycerolphosphate, 1 mM DTT,
cOmplete™protease inhibitor cocktail (Roche, Germany)). Bound protein was eluted with elution buffer (50 mM Tris
pH 8.0, 0.2% w/v SDS, 0.1% v/v Tween 20) at 50◦C for
15 min and subsequent incubation of 1× Laemmli buffer
at 98◦C for 5 min. Proteins were separated on a 10% SDS-
PAGE and analysed by Western blotting on a 0.45 M pore
sized polyvinylidene difluoride (Merck, Germany) mem-
brane. Proteins were detected using anti-c-myc (9E10 hy-
bridoma supernatant kindly provided by Prof. Dr M. Ma-
niak), anti-GFP antibody (sc-9996 Santa Cruz, USA), anti-
FLAG antibody (F7425 Sigma-Aldrich, USA) and anti-
Cdc19 serum (kindly provided by Dr. J. Thorner, University
of California, Berkley, USA). Image processing Microscale thermophoresis (MST) and gel shift for tRNA
binding assay
The internally Cy5-labeled tRNA ArgUCU (0.2 M) or
tRNA AlaUGC (0 3 M) were incubated for 5 min at 37◦C
Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February Table 1. Cryo-EM data collection, refinement and validation statistics 0.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Microscale thermophoresis (MST) and gel shift for tRNA
binding assay (Pierce™) resin and FLAG-tagged Elp6. The respective sub-
complex was added and incubated for 30–60 min at 4◦C,
followed by three wash steps with 20 mM HEPES (pH
7.5), 100 mM NaCl, 1 mM DTT, 0.05% v/v Tween 20. Elution from StrepTactin or anti-DYKDDDK resin was
carried out in the same buffer containing either 5 mM d-
desthiobiotin or 3× FLAG peptide at a concentration of
300 ng/l. Input controls and pull-downs were analyzed
on a SDS-PAGE and visualized with Coomassie or sil-
ver staining. ATP and bulk tRNA were used at indicated
concentrations. 6 Nucleic Acids Research, 2023 using MO. Affinity software (Nanotemper Technologies)
from at least three independent experiments (n > 3). For
gel shift experiments internally Cy5-labled tRNA AlaUGC
(0.2 M) was incubated with 0.05–1 M wild type Elp123,
Elongator or Elp123Elp11132–1224 variant at 4◦C for 15 min. Next samples were separated on NativePAGE™4–16% Bis–
Tris Protein Gels at 4◦C for 90 min and 150 V. Gels were
imaged on BIO-RAD ChemiDoc™MP Imaging System in
Cy5 detection mode. mM NaCl, 2 mM DTT and 1 mg/ml lysozyme. After soni-
cation, the lysate was cleared at 40 000 × g for 30 min and
the supernatant was cycled on a Protino® 5ml GST/4B col-
umn overnight. The column was washed with lysis buffer
omitting lysozyme and eluted in the same buffer containing
20 mM glutathione. Eluted fractions were further purified
on a Superdex 75 16/600 (GE Healthcare) column, concen-
trated, and dialyzed into a storage buffer (50 mM Tris–HCl
(pH 7.5) at 4◦C, 150 mM NaCl, 2 mM DTT). GST--toxin purification The GST--toxin construct was expressed in the Es-
cherichia coli BL21 (DE3) pRARE strain. Cultures were
grown at 37◦C in autoinduction media (72) and were shifted
after 5–6 h to 18◦C for overnight induction. Cells were lysed
in buffer containing 50 mM Tris–HCl (pH 7.5) at 4◦C, 300 Acetyl-CoA hydrolysis assay To probe for the mcm5s2U34 modification status of Elon-
gator mutants an in vitro cleavage assay using GST--toxin
was applied as previously described (73). In detail, tRNA
levels were adjusted to the same concentration in cleavage
buffer containing 20 mM Tris–HCl (pH 8.0) at 4◦C, 150 mM
NaCl, 2 mM EDTA and 2 mM DTT. Purified GST--toxin
or GST was added to the tRNAs at a final concentration of
4 M and incubated for 30 min at 30◦C. Next, samples were
denatured in loading buffer 20 mM Tris–HCl (pH 8.0) at
4◦C, 4 M urea, 20 mM boric acid, 2 mM EDTA, 0.02% w/v
xylencyanol ff, 0.01% w/v bromophenol blue at 90◦C for
5 min and resolved on an 10% urea-PAGE (100 mM Tris–
HCl (pH 8.0) at 4◦C, 100 mM boric acid, 1 mM EDTA, 10%
acrylamide w/v (acrylamide/bis-acrylamide 19:1), 5.12 M
urea) at 180 V for 35 min in TBE buffer (100 mM Tris–HCl
(pH 8.0) at 4◦C, 100 mM boric acid, 2 mM EDTA). tRNA
and cleavage products were stained with SYBR™Gold (In-
vitrogen). The assay was performed as previously described (31). In
detail, 0.3 M of Elongator variants were mixed with 2
M human bulk tRNA in presence of 100 M acetyl-CoA
(ACO) in 1× acetyl-CoA assay buffer and incubated in a
thermocycler for 3 h at 37◦C. Next, the samples were fil-
tered by a 3 kDa cut-off concentrator (EMD Millipore) and
the collected flow-through, of each reaction, was distributed
into a 96-well plate. ACO quantity of each sample was
determined using the Acetyl-CoA Assay Kit (MAK039,
Merck) according to the manufacturer’s instructions. Fluo-
rescence intensity was measured on a plate reader (TECAN)
at probe-specific excitation (535 nm) and emission (587 nm)
wavelengths. Hydrolysis rates were calculated from at least
three independent experiments. Sample photo-crosslinking for mass spectrometry The results were then filtered to a false dis-
covery rate (FDR) of 3% on the residue-pair level, result-
ing in 1047 residue pairs (119 heteromeric). FDR settings
at lower error levels were optimised by enabling boosting
for heteromeric crosslinks. Single particle cryo-EM structure of yeast Elongator The endogenous Elongator complex is constitutively ex-
pressed in yeast cells, but its low abundance has previously
complicated the purification of the stoichiometric complex
in quantities required for comprehensive structural and bio-
chemical analyses (37,84). To overcome this technical limi-
tation, we adapted an advanced overexpression system for
S. cerevisiae Elongator (ScElongator) enabling us to simul-
taneously overexpress the full-length versions of Elp1, Elp2,
Elp3, Elp4, Elp5 and Elp6 in suitable yeast strains (Supple-
mentary Figure S1A). The incorporation of specific affinity
tags for Elp1, Elp3 and Elp6 allowed us to establish a ro-
bust purification protocol that reproducibly resulted in pure
and homogenous samples of fully assembled ScElongator
containing all six subunits (Figure 1A, B and Supplemen-
tary Figure S1B). We typically obtained 5–15 g of purified
complex per liter of yeast culture, which was sufficient for
biochemical and structural analyses by single particle cryo-
EM. The purified stoichiometric complex eluted from a size
exclusion chromatography column at a calculated molecu-
lar weight of ∼850 kDa. Like the endogenous complex (85),
the recombinant Elongator contains two copies of each sub-
unit. The 260/280 nm absorption ratio indicates that the
purified complex had no co-purified endogenous tRNAs
nor other nucleic acids (Figure 1A). We observed a higher
molecular weight protein at ∼250 kDa, which we identi-
fied as Acetyl-CoA carboxylase 1 (Acc1) by mass spec-
trometry. Acc1 is a multifunctional homodimeric enzyme
of approximately 500 kDa that catalyses the formation of
malonyl-coenzyme A from ACO (86). To check whether
yeast Acc1 interacts with the Elongator in vivo, we tagged
endogenous Elp1 (c-myc), Elp5 (FLAG) in an Acc1 (GFP) Crosslinking mass spectrometry data acquisition For the liquid chromatography–tandem mass spectrometry
(LC–MS/MS) analysis, an Ultimate 3000 RSLCnano sys-
tem (Dionex, Thermo Fisher Scientific) connected to an Or-
bitrap Fusion Lumos Tribrid mass spectrometer (Thermo
Fisher Scientific) was used. Each SEC fraction was resus-
pended in 1.6% v/v ACN and 0.1% v/v formic acid be-
fore injection onto a 50-cm EASY-Spray C18 LC column
(Thermo Scientific, 50◦C operating temperature). The flow
rate during sample loading and separation was 0.3 l/min. The mobile phase consisted of solvent A (0.1% v/v formic
acid) and B (80% v/v ACN, 0.1% v/v formic acid). A 2–55%
gradient of B was applied over the course of 90–100 min
(optimised per SEC fraction) with a final increase to 95%
B within 2.5 min. An EASY-Spray source (Thermo Scien-
tific) ionised the eluting peptides before introducing them
to the mass spectrometer. For each SEC fraction, two ac-
quisitions were carried out. Data-dependent MS data were
acquired in cycles of 2.5 s using the top-speed setting and
the full scan mass spectrum was recorded in the Orbitrap
with a resolution of 120 000. Ions with a charge state from
3+ to 7+ were selected for fragmentation by stepped higher-
energy collisional dissociation (26%, 28% and 30%) using a
decision tree (76). Spectra of fragments were recorded in the
Orbitrap with a resolution of 60 000. Peaks were excluded
after a single repeat for the duration of 60 s (dynamic exclu-
sion). Sample photo-crosslinking for mass spectrometry The search was performed with the ‘Open’
pre-set workflow but with Crystal-C disabled. Crosslinked
peptides were identified using xiSEARCH (version 1.7.6.4;
(80)) using a database comprising 100 proteins with the
highest intensity-based absolute quantification identified in
the same experiments by MaxQuant (version 2.0.3.0; (81)). The search was performed using the following parame-
ters: Enyzme: Trypsin; Missed Cleavages: 3; Missing Mono-
Isotopic Peaks: 2; Cross-Linker ¦ Mass: NonCovalent ¦ 0,
SDA Knterm ¦ 82; MS Tolerance: 3 ppm; MS2 Tolerance:
5 ppm; Fixed Modifications: carbamidomethylation (C);
Variable Modifications: SDA-hydro (K, S, T, Y), SDA-loop
(K, S, T, Y), acetylation (K, C, S, T, N-terminus), acetalde-
hyde + 26 (H, K, N-terminus), carboxyamidomethylation
(M, C, U), deamidation (N, R, Q), amidination (K, N-
terminus). Search results were filtered using xiFDR (version
2.1.5.6; (82,83)). Prior to FDR calculation, prefilters were
applied on both target and decoy matches (peptide1 unique
matched conservative > 2.0; peptide2 unique matched con-
servative > 2.0; peptide1 unique crosslinked matched non
lossy > 0.0; peptide2 unique crosslinked matched non
lossy > 0.0). The results were then filtered to a false dis-
covery rate (FDR) of 3% on the residue-pair level, result-
ing in 1047 residue pairs (119 heteromeric). FDR settings
at lower error levels were optimised by enabling boosting
for heteromeric crosslinks. 4.3.0; (78,79). The search was performed with the ‘Open’
pre-set workflow but with Crystal-C disabled. Crosslinked
peptides were identified using xiSEARCH (version 1.7.6.4;
(80)) using a database comprising 100 proteins with the
highest intensity-based absolute quantification identified in
the same experiments by MaxQuant (version 2.0.3.0; (81)). The search was performed using the following parame-
ters: Enyzme: Trypsin; Missed Cleavages: 3; Missing Mono-
Isotopic Peaks: 2; Cross-Linker ¦ Mass: NonCovalent ¦ 0,
SDA Knterm ¦ 82; MS Tolerance: 3 ppm; MS2 Tolerance:
5 ppm; Fixed Modifications: carbamidomethylation (C);
Variable Modifications: SDA-hydro (K, S, T, Y), SDA-loop
(K, S, T, Y), acetylation (K, C, S, T, N-terminus), acetalde-
hyde + 26 (H, K, N-terminus), carboxyamidomethylation
(M, C, U), deamidation (N, R, Q), amidination (K, N-
terminus). Search results were filtered using xiFDR (version
2.1.5.6; (82,83)). Prior to FDR calculation, prefilters were
applied on both target and decoy matches (peptide1 unique
matched conservative > 2.0; peptide2 unique matched con-
servative > 2.0; peptide1 unique crosslinked matched non
lossy > 0.0; peptide2 unique crosslinked matched non
lossy > 0.0). Sample photo-crosslinking for mass spectrometry 85 g of ScElongator complex at 2.22 M concentration
was crosslinked with sulfo-SDA (sulfosuccinimidyl 4,4′- Nucleic Acids Research, 2023 7 azipentanoate, Thermo Scientific) at 1:500 and 1:1000 sam-
ple:crosslinker molar ratios. The reaction was incubated
at room temperature for 60 min irradiated with UV light
at 365 nm using a Luxigen34 LZ1 LED emitter (Osram
Sylvania Inc.) for 10 s, and quenched with a final con-
centration of 50 mM ammonium bicarbonate (ABC). The
crosslinked complex was separated from single subunits
on a Novex Bis–Tris 4–12% SDS-PAGE gel (Life Tech-
nologies). Gel pieces containing the crosslinked complex
were excised. The sample was reduced with DTT and free
sulfhydryl groups were alkylated using iodoacetamide (74). Proteins were digested overnight at 37◦C with 1 g trypsin
(Thermo Scientific Pierce) per 20 g of protein sample. The
digested peptides were recovered and desalted using C18
StageTips (75). The eluates of the StageTips were pooled
and fractionated by size exclusion chromatography (SEC)
using a Superdex™30 Increase 3.2/300 column (GE Health-
care) and a mobile phase consisting of 30% v/v ACN and
0.1% v/v trifluoric acid at a flow rate of 10 l/min. The
first six fractions (50 l each) containing peptides were
collected and the solvent was removed using a vacuum
concentrator. azipentanoate, Thermo Scientific) at 1:500 and 1:1000 sam-
ple:crosslinker molar ratios. The reaction was incubated
at room temperature for 60 min irradiated with UV light
at 365 nm using a Luxigen34 LZ1 LED emitter (Osram
Sylvania Inc.) for 10 s, and quenched with a final con-
centration of 50 mM ammonium bicarbonate (ABC). The
crosslinked complex was separated from single subunits
on a Novex Bis–Tris 4–12% SDS-PAGE gel (Life Tech-
nologies). Gel pieces containing the crosslinked complex
were excised. The sample was reduced with DTT and free
sulfhydryl groups were alkylated using iodoacetamide (74). Proteins were digested overnight at 37◦C with 1 g trypsin
(Thermo Scientific Pierce) per 20 g of protein sample. The
digested peptides were recovered and desalted using C18
StageTips (75). The eluates of the StageTips were pooled
and fractionated by size exclusion chromatography (SEC)
using a Superdex™30 Increase 3.2/300 column (GE Health-
care) and a mobile phase consisting of 30% v/v ACN and
0.1% v/v trifluoric acid at a flow rate of 10 l/min. The
first six fractions (50 l each) containing peptides were
collected and the solvent was removed using a vacuum
concentrator. 4.3.0; (78,79). Crosslinking mass spectrometry data processing MS2 peak lists were generated from the mass spectromet-
ric raw data with the MSConvert module of ProteoWiz-
ard (version 3.0.11729). Precursor and fragment m/z val-
ues were recalibrated based the average mass error of lin-
ear peptide spectrum matches. Additional peptide modifi-
cations were identified using FragPipe (version 18.0) with
MSFragger (version 3.4; (77)) and philosopher (version 8 Nucleic Acids Research, 2023 Nucleic Acids Research, 2023
gure 1. Cryo-EM structure of yeast Elongator. (A) Purification chromatogram profile of yeast Elongator. Red and blue lines represent UV260 and UV280
sorbance, respectively. The peak corresponding to Elongator is indicated with a black arrow. (B) SDS-PAGE representing the final purification quality
the Elongator sample. (C) Reference-free 2D class averages of yeast Elongator data set, scale bar 100 ˚A. (D) Cryo-EM reconstruction of yeast Elongator
4.35 ˚A resolution visualized at indicated map contouring with the atomic model at two orientations (upper and lower right). A schematic representation
the complex is shown in the middle with Elp456 highlighted in color on the cryo-EM reconstruction and all subunits colored in accordance with the
heme on the atomic model. Front view on the density and atomic model of Elp456 (lower left). Double lobe low-resolution cryo-EM reconstruction of
ongator (upper left), coloring corresponds to the atomic model of native ScElongator. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac e/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Figure 1. Cryo-EM structure of yeast Elongator. (A) Purification chromatogram profile of yeast Elongator. Red and blue lines represent UV260 and UV280
absorbance, respectively. The peak corresponding to Elongator is indicated with a black arrow. (B) SDS-PAGE representing the final purification quality
of the Elongator sample. (C) Reference-free 2D class averages of yeast Elongator data set, scale bar 100 ˚A. (D) Cryo-EM reconstruction of yeast Elongator
at 4.35 ˚A resolution visualized at indicated map contouring with the atomic model at two orientations (upper and lower right). A schematic representation
of the complex is shown in the middle with Elp456 highlighted in color on the cryo-EM reconstruction and all subunits colored in accordance with the
scheme on the atomic model. Front view on the density and atomic model of Elp456 (lower left). Double lobe low-resolution cryo-EM reconstruction of
Elongator (upper left), coloring corresponds to the atomic model of native ScElongator. Figure 1. Cryo-EM structure of yeast Elongator. (A) Purification chromatogram profile of yeast Elongator. Crosslinking mass spectrometry data processing As mentioned above, we did not observe a sta-
bilization of the second Elp123 lobe upon recruitment of
Elp456 to the Elp123 dimer. As previously anticipated, the
two copies of the largest subunit, namely Elp1 (∼150 kDa),
act as the central scaffold for the lobe and the whole Elonga-
tor assembly. The two N-terminal WD40 domains of each
Elp1 molecule create a platform for the catalytic Elp3 sub-
unit, which is clamped from the opposite side by Elp2. In
our map, we observed an additional unaccommodated den-
sity in the proximity of the rSAM domain of Elp3, into
which we fit a previously uncharacterized loop region of
the first WD40 domain of Elp1 (aa191–237). This unantic-
ipated loop stretches from the third -sheet of the WD40
domain along Elp3 towards the base of Elp2 and returns
to the fourth -sheet of the same WD40 domain (Figure
2B). Characteristic densities for the iron-sulfur cluster are
clearly recognizable in both native and crosslinked struc-
tures of ScElongator. However, we were not able to iden-
tify densities for bound SAM or 5′-dA molecules, which
were present in proximity to the cluster in the previous
cryo-EM structure of the Elp123 subcomplex (Figure 1D)
(92). Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gka (
)
Our Elongator cryo-EM structure reveals that the hetero-
hexameric Elp456 occupies a position that faces the active
site of Elp3 and bridges between the enzymatic subunit and
the C-terminal region of Elp1. Both copies of Elp4 and one
copy of Elp5 and Elp6 each are interacting with the Elp123
subcomplex. Although Elp2 does not seem to be directly
involved in Elp456 binding, it might contribute indirectly
by stabilizing the Elp123 lobe (93). Furthermore, the re-
solved structure of Elongator is in full agreement with spa-
tial restraints derived from a cross-linking mass spectrom-
etry analysis of TAP-tag purified endogenous Elongator
complex (27). In detail, Elp123 and Elp456 subcomplexes
interact with each other at three individual contact points
involving Elp1, Elp3, Elp4, Elp5, and Elp6. The first contact
point (CP1) is formed between less conserved residues of
the Elp3 rSAM domain (Trp341 and Lys342) and a loop re-
gion in Elp4 (Tyr369, Ser371, Gln372, Lys375 and Glu401). The second contact point (CP2) is formed between a loop
region of Elp4 (aa172-195) and helices 27 and 28 of the
dimerization domain of Elp1 (Asp1160, Gln1164, Arg1171,
Tyr1254, Arg1261 and Arg1265). Crosslinking mass spectrometry data processing The maps from both approaches show a very similar over-
all shape of the complex, independently confirming the po-
sition of Elp456 after two different routes of sample prepa-
ration (Supplementary Figure S2B). The dimensions of the
complex are ∼200 × 162 × 140 ˚A, in line with the estima-
tion from a previous low-resolution negative stain recon-
struction (27). The local resolution estimation indicates that
the center of the Elp123 lobe extends to 3.9 ˚A, whereas
parts of Elp456 as well as the TPR and dimerization re-
gion of Elp1 are less well resolved. Similar to our previous
high-resolution reconstructions of yeast Elp123 (with and
without bound tRNA), the density of the second Elp123
lobe is not clearly visible. In addition, 2D class averages al-
ready show that the second Elp123 lobe is blurred after im-
age averaging, suggesting relatively high flexibility between
the two Elp123 lobes, which is also observable in presence
of Elp456. Nevertheless, we managed to reconstruct a map
for the complete complex with both lobes visible at an esti-
mated overall resolution of 17.2 ˚A, when stabilized with BS3
(Figure 1D). As we could only visualize the second lobe at
low map thresholds and did not see any density of Elp456
in the second lobe, we decided to exclude the empty lobe
from subsequent refinement procedures. In summary, our
results reveal the overall arrangement of the yeast Elongator
complex at an unprecedented resolution. Furthermore, the
cryo-EM structure(s) independently confirm that the hex-
americ ring-shaped Elp456 subcomplex is indeed asymmet-
rically localized on only one lobe. The high quality of our
cryo-EM map shows details of the complex and allows us to
unambiguously determine the orientation of the ScElp456
subcomplex. Additionally, the presented maps allow for the
precise structural characterization of all individual Elonga-
tor subunits, their relative position and their interaction net-
work within the fully assembled complex at high resolution
(Figure 1D). remain flexible also in the fully assembled complex. In ad-
dition, we compared the structure of the Elp123 subcom-
plex after binding of Elp456 with the previously determined
Elp123 subcomplex in absence and presence of tRNA (31). We did not detect any major rearrangements of the Elp123
subcomplex after binding of Elp456 (Supplementary Figure
S3C), although the lobe adopts a slightly less compacted
topology. Crosslinking mass spectrometry data processing Red and blue lines represent UV260 and UV280
absorbance, respectively. The peak corresponding to Elongator is indicated with a black arrow. (B) SDS-PAGE representing the final purification quality
of the Elongator sample. (C) Reference-free 2D class averages of yeast Elongator data set, scale bar 100 ˚A. (D) Cryo-EM reconstruction of yeast Elongator
at 4.35 ˚A resolution visualized at indicated map contouring with the atomic model at two orientations (upper and lower right). A schematic representation
of the complex is shown in the middle with Elp456 highlighted in color on the cryo-EM reconstruction and all subunits colored in accordance with the
scheme on the atomic model. Front view on the density and atomic model of Elp456 (lower left). Double lobe low-resolution cryo-EM reconstruction of
Elongator (upper left), coloring corresponds to the atomic model of native ScElongator. as potential Elongator binding partners in other studies
(29,89–91). background (87) and conducted co-immunoprecipitation
(co-IP) assays. As we did not observe any interaction of
Acc1 with Elongator in these assays (Supplementary Fig-
ure S1C), we conclude that Acc1 is an co-purifying con-
taminant in our preparations. Of note, we also co-purified
sub-stoichiometric amounts of Kti11 and Kti12, whereas
other regulatory proteins known to temporarily associate
with yeast Elongator were undetectable (88). Furthermore,
we did not find any hits for actin, tubulin, RNA poly-
merase subunits or histones, which have been proposed Next, we prepared cryo-EM grids with the freshly pu-
rified sample and analyzed the structure of the complex
using single particle cryo-EM. After vitrification and grid
optimization, we collected a dataset of 6339 micrographs
on a Titan Krios microscope. We analyzed the complete
dataset by applying basic image curation steps as well as it-
erative rounds of particle picking, 2D/3D classification rou-
tines and refinement procedures. Thereby, we determined Nucleic Acids Research, 2023 9 the structure of ScElongator at an overall resolution of 4.35
˚A (Figure 1C, D, Supplementary Figure S2A and Table 1). The reconstruction shows an additional, unambiguous den-
sity for the ScElp456 ring next to one of the two Elp123
lobes. In an attempt to further improve the resolution of
the reconstruction, we stabilized the sample with a low con-
centration of BS3. However, the stabilized sample resulted
in a reconstruction at a lower overall resolution of 6.6 ˚A. Crosslinking mass spectrometry data processing This larger interface also
involves the N-terminus of Elp5 and a not well-defined loop
region of Elp1 (aa1176-1251) known to carry functionally
relevant phosphorylation sites (35). The third contact point
(CP3) is an interface that is created at the three-way junc-
tion between the KAT domain of Elp3 and the C-terminal
residues of Elp6 (Figure 2B). Noteworthy, the N-terminus
of Elp4 (Elp4 1–66), which was shown to contribute to the
interaction with Elp1 (27), was not visible in our densi-
ties and did not participate in any long-range interactions
with Elp1. All interacting residues of Elp456 are involved
only once in the interaction with Elp123, and the respec- Crosslinking mass spectrometry data processing The maps from both approaches show a very similar over-
all shape of the complex, independently confirming the po-
sition of Elp456 after two different routes of sample prepa-
ration (Supplementary Figure S2B). The dimensions of the
complex are ∼200 × 162 × 140 ˚A, in line with the estima-
tion from a previous low-resolution negative stain recon-
struction (27). The local resolution estimation indicates that
the center of the Elp123 lobe extends to 3.9 ˚A, whereas
parts of Elp456 as well as the TPR and dimerization re-
gion of Elp1 are less well resolved. Similar to our previous
high-resolution reconstructions of yeast Elp123 (with and
without bound tRNA), the density of the second Elp123
lobe is not clearly visible. In addition, 2D class averages al-
ready show that the second Elp123 lobe is blurred after im-
age averaging, suggesting relatively high flexibility between
the two Elp123 lobes, which is also observable in presence
of Elp456. Nevertheless, we managed to reconstruct a map
for the complete complex with both lobes visible at an esti-
mated overall resolution of 17.2 ˚A, when stabilized with BS3
(Figure 1D). As we could only visualize the second lobe at
low map thresholds and did not see any density of Elp456
in the second lobe, we decided to exclude the empty lobe
from subsequent refinement procedures. In summary, our
results reveal the overall arrangement of the yeast Elongator
complex at an unprecedented resolution. Furthermore, the
cryo-EM structure(s) independently confirm that the hex-
americ ring-shaped Elp456 subcomplex is indeed asymmet-
rically localized on only one lobe. The high quality of our
cryo-EM map shows details of the complex and allows us to
unambiguously determine the orientation of the ScElp456
subcomplex. Additionally, the presented maps allow for the
precise structural characterization of all individual Elonga-
tor subunits, their relative position and their interaction net-
work within the fully assembled complex at high resolution
(Figure 1D). the structure of ScElongator at an overall resolution of 4.35
˚A (Figure 1C, D, Supplementary Figure S2A and Table 1). The reconstruction shows an additional, unambiguous den-
sity for the ScElp456 ring next to one of the two Elp123
lobes. In an attempt to further improve the resolution of
the reconstruction, we stabilized the sample with a low con-
centration of BS3. However, the stabilized sample resulted
in a reconstruction at a lower overall resolution of 6.6 ˚A. The interaction interfaces between Elp123 and Elp456 are
crucial for Elongator’s tRNA modification activity We generated numerous yeast strains that carry specific sin-
gle amino acid substitutions or deleted regions in Elp1,
Elp3, Elp4, Elp5 and Elp6. Next, we tested these strains
in previously established phenotypical assays that indi-
rectly probe the tRNA modification activity of Elongator
in vivo (2,94,95). In addition, we used an in vitro -toxin
tRNA cleavage assay to further validate the observed phe-
notypes of the structure-guided mutations (73) (Supple-
mentary Figure S4A). -toxin (the active tRNase subunit
of trimeric killer toxin zymocin) acts as a nuclease that re-
quires the mcm5s2U34 modification to cleave tRNAs at the
anticodon. Therefore, any mutation that reduces or abol-
ishes the tRNA modification activity of Elongator, leads to
reduced mcm5s2U34 modification levels in vivo and protects
tRNAs from cleavage by -toxin (95,96). Since the readout
of the aforementioned -toxin-based assays predominantly
samples the modification status of tRNA GluUUC, we also
monitored the Elongator dependent mcm5U34 modification
of the SUP4 nonsense suppressor tRNA TyrUUA via its ef-
ficiency of ochre stop codon readthrough (2). As expected,
gene deletions of elp1, elp3, elp4, elp5, and elp6 were found
to be resistant to zymocin and the toxic arginine analogue
canavanine in a SUP4 tRNA and can1-100 allele containing
background (for more details, see (2)), Figure 2C and Sup-
plementary Figure S4B, C). Furthermore, we show that the
newly identified loop (aa191–237) from the first WD40 of
Elp1 and the unstructured N-terminal region of Elp4 (aa1–
66) are crucial for Elongator function in vivo. g
p
To further validate our structural model we carried out
a photo-crosslinking mass spectrometry (XL-MS) analysis
of the purified yeast Elongator complex. 638 out of 883
detected cross links are in agreement (30 ˚A distance) with
our structural model (Supplementary Figure S5A). In ad-
dition, 125 out of 189 crosslinks that disagree with our
model are located in loop regions of Elp1, namely aa191–
237 and aa1176–1251. Therefore, it seems these loops can
become flexible, which is in agreement with the previous
high-resolution reconstruction of yeast Elp123 (92) where
no density was detectable for them. We also checked for any
specific crosslinks between Elongator and Acc1, but only a
single crosslink was detected, indicating that the two com-
plexes indeed do not interact or share a large interface. The interaction interfaces between Elp123 and Elp456 are
crucial for Elongator’s tRNA modification activity Al-
though, the second Elp123 lobe is not well-resolved in our
maps the presence of a few crosslinks indicated that the two
Elp123 lobes could get in close proximity of each other also
in the presence of Elp456. Hence, we used additional 3D
variability and masked 3D classification analyses to check
whether the second lobe can obtain any specific conforma-
tions upon Elp456 binding (Supplementary Figure S5B). We indeed managed to partially enhance the density of the
second lobe, but due to reduced number of particles the res-
olution decreased (Supplementary Figure S5B). None of
the obtained reconstructions revealed a complete second
lobe or specific conformation, which is consistent with the
low resolution of the two-lobed BS3 stabilized Elongator
complex (Figure 1D). These additional results further sup-
port our notion that the second lobe stays flexible in the
fully assembled Elongator complex. 0.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 )
g
Next, we analyzed the structure-guided mutation in
the three identified contact points CP1, CP2 and CP3 to
understand the importance of these regions individually. The mutations of Elp3 residues ( W341A/K342A) and
Elp4 (E401A, Y369A/S371A and Q372A/K375A) in CP1
show no measurable effects on the tRNA modification
activity of Elongator. Strikingly, all tested mutations
in CP2 nearly abolished Elongator’s tRNA modifica-
tion activity. Mutations and deletions of the identified
residues in Elp1 (Δ191–237, Y1254A/R1261A/R1265A,
D1160A/Q1164A/R1171A,
Δ1176–1200,
Δ1201–1225,
Δ1226–1251), Elp4 (Δ172–195, Δ357–376) and Elp5
(Δ1–20) display tRNA hypo-modification phenotypes that
are indistinguishable from their respective gene deletion
mutants, in all conducted in vivo and in vitro tRNA modi-
fication assays (Figure 2C and Supplementary Figure S4). The third and most central interface (CP3) appears to be
as important for Elongator activity as CP2. Mutations
in Elp3 (R399A/D402A/L403A) and Elp6 (Δ271–273,
T226A/F228A/K230A) are resistant to growth inhibition
by zymocin. Of note, mutants in Elp123 demonstrate iden-
tical phenotypes in all applied assays, whereas individual
mutations in Elp456 (e.g. elp4 Δ172–195, elp5 Δ1–7, elp6
Δ271–273
and
elp6
T226A/F228A/K230A)
exhibited Elp456 bridges between Elp3 and the C-terminus of Elp1 The cryo-EM structure of yeast Elp456 in complex with
Elp123 almost perfectly resembles the previously solved
structures of the truncated Elp456 hexamer determined
by macromolecular crystallography (85,90). As we ob-
served unbound ring-shaped Elp456 particles in one of our
datasets, we also determined the cryo-EM structure of free
full-length ScElp456 at 3.7 ˚A overall resolution (Figure 2A,
Supplementary Figure S3A and Table 1). The newly ob-
tained structures of full-length Elp456 are almost identi-
cal to the truncated crystal structure of the Elp456 sub-
complex (Supplementary Figure S3B). The structure con-
firms that Elp456 contains two copies of Elp4, Elp5 and
Elp6, forming a symmetric dimer of trimers. However, the
N- and C-terminal extensions of Elp4 and Elp5 (including
a small predicted domain at the C-terminus of Elp5 (85)) 10 Nucleic Acids Research, 2023 10 Nucleic Acids Research, 2023
Figure 2. Functional validation of yeast Elongator. (A) Cryo-EM map and atomic model of the apo ScElp456 subcomplex. (B) Front view on the atomic
model of yeast Elongator (left). Atomic model in surface representation at different orientations with a position of selected mutations represented in
sticks (point mutation) and cartoon (deletion or truncation). Colouring corresponds to the affiliation of the particular position to the given subunit. (C)
Phenotypic analyses of various yeast strains carrying variations in Elp1, Elp3, Elp4, Elp5 and Elp6 using zymocin resistance assays. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1 g Figure 2. Functional validation of yeast Elongator. (A) Cryo-EM map and atomic model of the apo ScElp456 subcomplex. (B) Front view on the atomic
model of yeast Elongator (left) Atomic model in surface representation at different orientations with a position of selected mutations represented in
y
y
g
y Figure 2. Functional validation of yeast Elongator. (A) Cryo-EM map and atomic model of the apo ScElp456 subcomplex. (B) Front view on the atomic
model of yeast Elongator (left). Atomic model in surface representation at different orientations with a position of selected mutations represented in
sticks (point mutation) and cartoon (deletion or truncation). Colouring corresponds to the affiliation of the particular position to the given subunit. (C)
Phenotypic analyses of various yeast strains carrying variations in Elp1, Elp3, Elp4, Elp5 and Elp6 using zymocin resistance assays. Elp456 bridges between Elp3 and the C-terminus of Elp1 Nucleic Acids Research, 2023 11 tive second copy of the residues within the ring appear to
be irrelevant for the respective interactions. Therefore, we
were able to mutate selected residues and regions to ana-
lyze their specific role for the in vivo function of Elongator
(Figure 2B, C). a slightly divergent phenotype. These variations mostly
affect mutants that display intermediate phenotypes and
might occur due to different sensitivity of performed assay
formats. These results also support the recent observation
that Elp456 function might only be relevant for a subset of
cellular tRNAs (22). All zymocin and canavanine-sensitive
mutants and the latter mentioned variable phenotype
mutants are susceptible to in vivo and in vitro -toxin
cleavage. In conclusion, our data show that interfaces of
CP2 and CP3 are crucial for Elongator’s tRNA modi-
fication activity, whereas the CP1 region, between Elp3
and Elp4 appears to be functionally dispensable. These
results directly validate our structural model that depicts
the complicated interaction network between individual
subunits of the assembled Elongator complex. The interaction interfaces between Elp123 and Elp456 are
crucial for Elongator’s tRNA modification activity The structure of the Elp123 subcomplex is highly conserved
among eukaryotes Surprisingly, we could identify
an intact SAM molecule bound to the iron-sulfur cluster of
MmElp123, which was co-purified from the host cells. The
coordination of this ligand is similar to the 5′-dA molecule
found in ScElp123. At the current stage, it remains unclear
if the difference results from different catalytic rates, ap-
plied classification schemes or from the fact that we iso-
late ScElp123 from yeast cells, whereas MmElp123 was pro-
duced in insect cells, though in case of archaeal Elp3 SAM
remained uncleaved in the absence of tRNA (34). Nonethe-
less, the structural similarities between the subcomplexes
(pre and post SAM cleavage), suggest that the cleavage reac-
tion itself does not induce major rearrangements in the ac-
tive site of Elp3 or in the coordination of the adenosine moi-
ety. Thus, our detailed analyses of the active sites in ScElp3
and MmElp3 further highlight the homology of yeast and
mouse Elongator complexes. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac To determine the structure of MmElp123, we vitrified
freshly purified samples in absence and presence of in
vitro transcribed mouse tRNA ArgUCU. We optimized the
sample preparation procedure, collected large datasets and
solved structures that are with and without tRNA at 4.35 ˚A
and 4.0 ˚A resolutions, respectively (Supplementary Figure
S7A,B and Table 1). Meanwhile, we also collected a dataset
for ScElp123 in complex with yeast tRNA AlaUGC and ob-
tained a reconstruction at an improved resolution of 3.96 ˚A
(Supplementary Figure S8 and Table 1). This new tRNA-
bound structure of ScElp123 allowed us to build a more re-
liable atomic model of the tRNA-bound complex (Figure
3A), which facilitated the structural comparison of individ-
ual regions in ScElp123 and MmElp123. Both, yeast and
mouse Elp123–tRNA structures, contain characteristic L-
shaped tRNA densities, spanning from the center of Elp3
to the C-terminus of Elp1 (Figure 3A and Supplementary
Figure S9). tRNA molecules are positioned in both com-
plexes in a similar conformation – the ASL is inserted in the
active site of Elp3 and the T-arm is in contact with the CTD
of Elp1, while the acceptor stem points away from the com-
plex. The second Elp123 lobe remains flexible and poorly
defined, in both structures. Thus, tRNA binding does not
affect the relative orientation between the two lobes, and the
second lobe was excluded from the subsequent refinement
process. The structure of the Elp123 subcomplex is highly conserved
among eukaryotes Like in yeast, the murine Elongator consists of six sub-
units. However, the sequence similarity and identity of the
mouse proteins vary between the subunits compared to
their yeast counterparts. Although Elp1, Elp2, Elp3 and
Elp4 proteins show high sequence identity, Elp5 and Elp6
display surprisingly low sequence similarity among eukary-
otes (84). Therefore, we asked whether the Elongator com-
plex is structurally and functionally conserved in higher eu-
karyotes, particularly in mammals. We employed the biG-
Bac expression system to overproduce mouse subcomplexes
by co-expressing MmElp123 and MmElp456 genes sepa-
rately in insect cells. The incorporation of affinity tags on 12 Nucleic Acids Research, 2023 12 Elp3 (TST) and Elp6 (FLAG) facilitated the purification
of the individual subcomplexes using standard affinity and
size exclusion chromatography. The gel filtration profiles of
MmElp123 (∼610 kDa) and MmElp456 (∼220 kDa) show
that they all elute at the expected elution volume (Supple-
mentary Figure S6) demonstrating that the mouse complex
also form dimers like the yeast counterparts. tural details of the active sites of ScElp123 and MmElp123
(Figure 3B). Both complexes harbor an iron-sulfur-cluster
[4Fe4S] involved in the generation of a 5′-dA radical, which
is necessary for the U34 modification reaction, and the
cluster is coordinated by three highly conserved cysteine
residues, which contact the respective iron atoms of the clus-
ter. Although we did not supplement the sample with SAM
before vitrification, we identified a bound 5′-dA molecule
in the yeast active site next to the cluster. Gln257 contacts
one of the hydroxyl groups in 5′-dA and positions the radi-
cal carrying methyl group in close proximity to Tyr136 and
Tyr327, which both are positioned in a similar distance to
the base of U34 and to the methyl group of 5′-dA. Further-
more, we observed that the density of Tyr136 connects to
the one of U34, suggesting direct interaction. This tyrosine
possibly pulls the uridine closer to the iron-sulfur cluster
and the 5′-dA molecule. As for the fourth iron atom of the
cluster, it is not coordinated by any cysteine residue but it
is bordered by an additional, adjacent density, which most
likely can be attributed to bound methionine. Methionine
is the second cleavage product of SAM which was also re-
ported in crystal structures of the bacterial rSAM proteins
RlmN (97) and MiaB (98). The structure of the Elp123 subcomplex is highly conserved
among eukaryotes Of note, we used masked 3D classification to iden-
tify a subfraction of particles that shows a tRNA-like den-
sity also in the second Elp123 lobe. Nonetheless, due to nec-
essary subclassification procedures the resulting maps lack
the quality to ultimately confirm that mouse Elp123 can si-
multaneously bind tRNAs in each of its lobes, like yeast
Elp123 (92). As for the mouse apo Elp123 structure, the
obtained density is significantly smaller and only the core
lobe of the subcomplex is structured, resulting in decreased
overall dimensions (∼140 × 100 × 65 ˚A; Figure 3A). In
detail, the spatial arrangement of Elp2, Elp3 and the N-
terminal region of Elp1 are very similar to the tRNA-bound
MmElp123 and the ScElp123 structures (92). Strikingly, the
CTD of MmElp1, which is visible in the yeast Elp123, re-
mains flexible in MmElp123 in the absence of tRNA (Fig-
ure 3A). This observation indicates that yeast Elp123 is
inherently more stable in the absence of tRNAs and that
the binding of tRNAs induces structural rearrangements in
the Elp1 CTD of mammals. Nonetheless, both yeast and
murine Elp123 appear very similar in its tRNA bound form. Our comparative analyses of the tRNA-bound ScElp123
and MmElp123 show that both subcomplexes bind their
tRNA substrates in an almost identical fashion and that the
involvement of several regions in tRNA binding might have
contributed to the high sequence conservation in Elp1 and
Elp3 amongst eukaryotes. As aforementioned, the enzymatically active Elp3 sub- The structure of the fully assembled Elongator is highly con-
served among eukaryotes Finally, we also investigated whether in mouse Elp456 inter-
acts with Elp123 in a similar way as in yeasts. For this, we
reconstituted the Elongator in vitro from individually pu-
rified MmElp123 and MmElp456 subcomplexes and ana-
lyzed the obtained complex by single particle cryo-EM (Fig-
ure 4, Supplementary Figures S10 and S11A). In detail, we
observed efficient complex formation after combing both
purified subcomplexes without the addition of other co-
factors. The reconstituted complex shows a stoichiometric
composition of all six subunits, indicating that the bi-lobal
Elp123 in mouse Elongator also preferentially binds only
one hetero-hexameric Elp456 subcomplex. Subsequently,
we used the reconstituted and re-purified complex after gel-
filtration to prepare cryo-EM grids. After sample optimiza-
tion and data collection, we determined the cryo-EM struc-
ture of the mouse Elongator at an overall resolution of 5.9 ˚A
(Table 1). The structure of MmElongator is very similar to
yeast Elongator, with a clearly distinguishable lobe, an arch As aforementioned, the enzymatically active Elp3 sub-
unit shows a high overall sequence conservation. This simi-
larity becomes even more evident, by comparing the struc- Nucleic Acids Research, 2023 13 r structural conservation in eukaryotes. (A) Cryo-EM reconstructions of MmElp123–tRNA (upper left), MmElp123 (lower left) and
upper right) complexes with atomic models in the same orientation. tRNA colored in deep teal. (B) Comparison of the active site of
nd MmElp123. Selected, structurally conserved residues in stick representation, with densities shown for iron-sulfur clusters (ScElp123–
, 5′-dA (ScElp123–tRNA) and SAM (MmElp123). Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 Febru Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Figure 3. Elongator structural conservation in eukaryotes. (A) Cryo-EM reconstructions of MmElp123–tRNA (upper left), MmElp123 (lower left) and
ScElp123–tRNA (upper right) complexes with atomic models in the same orientation. tRNA colored in deep teal. (B) Comparison of the active site of
ScElp123–tRNA and MmElp123. Selected, structurally conserved residues in stick representation, with densities shown for iron-sulfur clusters (ScElp123–
tRNA/MmElp123), 5′-dA (ScElp123–tRNA) and SAM (MmElp123). g
y
y
g Figure 3. Elongator structural conservation in eukaryotes. (A) Cryo-EM reconstructions of MmElp123–tRNA (upper left), MmElp123 (lower left) and
ScElp123–tRNA (upper right) complexes with atomic models in the same orientation. tRNA colored in deep teal. (B) Comparison of the active site of
ScElp123–tRNA and MmElp123. The structure of the fully assembled Elongator is highly con-
served among eukaryotes tion showed that the tRNA molecule would fit without any
significant clashes into the space formed between the two
subcomplexes and that the binding of the ASL in the ac-
tive site of Elp3 would be unaffected. Moreover, the rela-
tively long and not well-structured loop region (aa169–233)
in Elp4, which binds the CTD of Elp1, might provide addi-
tional flexibility to accommodate a tRNA molecule. In ad-
dition, our ScElongator model also clearly shows that the
tRNA binding loop (aa1176–1251) of Elp1 is displaced by
Elp456 and would not be able to interact with the T-arm of
tRNAs (Figure 5A). This observation is in line with the fact
that ScElongator has a lower tRNA binding affinity com-
pared to the ScElp123 subcomplex (31). Of note, the second
lobe of Elp123, which is not occupied by Elp456, would in tion showed that the tRNA molecule would fit without any
significant clashes into the space formed between the two
subcomplexes and that the binding of the ASL in the ac-
tive site of Elp3 would be unaffected. Moreover, the rela-
tively long and not well-structured loop region (aa169–233)
in Elp4, which binds the CTD of Elp1, might provide addi-
tional flexibility to accommodate a tRNA molecule. In ad-
dition, our ScElongator model also clearly shows that the
tRNA binding loop (aa1176–1251) of Elp1 is displaced by
Elp456 and would not be able to interact with the T-arm of
tRNAs (Figure 5A). This observation is in line with the fact
that ScElongator has a lower tRNA binding affinity com-
pared to the ScElp123 subcomplex (31). Of note, the second
lobe of Elp123, which is not occupied by Elp456, would in The structure of the fully assembled Elongator is highly con-
served among eukaryotes Selected, structurally conserved residues in stick representation, with densities shown for iron-sulfur clusters (ScElp123–
tRNA/MmElp123), 5′-dA (ScElp123–tRNA) and SAM (MmElp123). We would like to highlight that although the fully as-
sembled Elongator binds tRNAs (31), despite our intense
experimental efforts, we were still not able to attain the
yeast or mouse tRNA-bound Elongator structure. To ex-
plore whether Elongator could in principle accommodate
tRNA molecules in an Elp456-occupied Elp123 lobe, we su-
perimposed ScElp123–tRNA on ScElongator via its Elp3
subunit (RMSD 1.22 ˚A2) (Figure 5A). The superimposi- region between the lobes and an asymmetrically positioned
Elp456 ring on one of the two Elp123 lobes. The quality
of the obtained map allowed the unambiguous placement
of the Elp456 subcomplex, revealing the same three contact
points formed between the subcomplexes in yeast. However,
the limited resolution of our reconstruction prevented us
from analyzing the molecular details of the active site in the
fully assembled mouse Elongator complex. region between the lobes and an asymmetrically positioned
Elp456 ring on one of the two Elp123 lobes. The quality
of the obtained map allowed the unambiguous placement
of the Elp456 subcomplex, revealing the same three contact
points formed between the subcomplexes in yeast. However,
the limited resolution of our reconstruction prevented us
from analyzing the molecular details of the active site in the
fully assembled mouse Elongator complex. 14 Nucleic Acids Research, 2023 ure 4. Mouse Elongator complex. Cryo-EM reconstructions of MmElongator complex with an atomic model in the same orientation. Elp456 is colored
accordance to the scheme from Figure 1D. For comparison, yeast density and model are in the same orientation above. p
p
g
y
y Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Figure 4. Mouse Elongator complex. Cryo-EM reconstructions of MmElongator complex with an atomic model in the same orientation. Elp456 is colored
in accordance to the scheme from Figure 1D. For comparison, yeast density and model are in the same orientation above. Figure 4. Mouse Elongator complex. Cryo-EM reconstructions of MmElongator complex with an atomic model in th
in accordance to the scheme from Figure 1D. For comparison, yeast density and model are in the same orientation a principle be able to bind tRNA, strongly complicating the
interpretation of the results from the binding assays. The CTD of Elp1 is responsible for tRNA binding and sub-
complex interaction We further investigated the importance of these structural
rearrangements by complementary biochemical analyses. We used human Elongator subcomplexes produced in in-
sect cells and reconstituted them as we did with the mouse
Elongator sample (Supplementary Figures S6B and S11A). First, we measured the binding affinity of mouse and hu-
man Elp123 and Elongator towards in vitro transcribed
(IVT) tRNAs. Like yeast Elp123 (31), mouse and human
Elp123 bound mouse tRNA AlaUGC with higher affinity Nucleic Acids Research, 2023 15 Figure 5. Biochemical and functional characterization of Elongator complex from higher eukaryotes. (A) Superposition of ScElp123–tRNA and
ScElongator in two orientations, showing a possibility of the tRNA (deep teal) binding by the latter complex (above). Below: yeast CP2 comparison
etween ScElp123–tRNA and ScElongator complexes showing Elp1 tRNA binding loop displacement. (B) Microscale thermophoresis measurements,
espective fits, and calculated dissociation constant (Kd) values for the mouse (top) and human (bottom) Elp123 (red) and Elongator (black). In both cases,
he Hill coefficient is close to 1, indicating the presence of independent binding sites. n = 3. (C) SDS-PAGE gel comparing in vitro reconstitution of human
Elongator complex with the use of Elp1, Elp4 and Elp5 functional variants of CP2 structural features presented in the previous panel. Twin-Strep-tag
ndicated on Elp3 subunit. (D) EMSA assay using wild type human Elp123 (left), human Elp123Elp11132–1224 (right), and fluorescently labeled tRNA
AlaUGC. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 Febr Downloaded from https://academic.oup.com/nar/advance article/doi/10 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Figure 5. Biochemical and functional characterization of Elongator complex from higher eukaryotes. (A) Superposition of ScElp123–tRNA and
ScElongator in two orientations, showing a possibility of the tRNA (deep teal) binding by the latter complex (above). Below: yeast CP2 comparison
between ScElp123–tRNA and ScElongator complexes showing Elp1 tRNA binding loop displacement. (B) Microscale thermophoresis measurements,
respective fits, and calculated dissociation constant (Kd) values for the mouse (top) and human (bottom) Elp123 (red) and Elongator (black). In both cases,
the Hill coefficient is close to 1, indicating the presence of independent binding sites. n = 3. (C) SDS-PAGE gel comparing in vitro reconstitution of human
Elongator complex with the use of Elp1, Elp4 and Elp5 functional variants of CP2 structural features presented in the previous panel. The CTD of Elp1 is responsible for tRNA binding and sub-
complex interaction Twin-Strep-tag
indicated on Elp3 subunit. (D) EMSA assay using wild type human Elp123 (left), human Elp123Elp11132–1224 (right), and fluorescently labeled tRNA
AlaUGC. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. Figure 5. Biochemical and functional characterization of Elongator complex from higher eukaryotes. (A) Superposition of ScElp123–tRNA and
ScElongator in two orientations, showing a possibility of the tRNA (deep teal) binding by the latter complex (above). Below: yeast CP2 comparison
between ScElp123–tRNA and ScElongator complexes showing Elp1 tRNA binding loop displacement. (B) Microscale thermophoresis measurements,
respective fits, and calculated dissociation constant (Kd) values for the mouse (top) and human (bottom) Elp123 (red) and Elongator (black). In both cases,
the Hill coefficient is close to 1, indicating the presence of independent binding sites. n = 3. (C) SDS-PAGE gel comparing in vitro reconstitution of human
Elongator complex with the use of Elp1, Elp4 and Elp5 functional variants of CP2 structural features presented in the previous panel. Twin-Strep-tag
indicated on Elp3 subunit. (D) EMSA assay using wild type human Elp123 (left), human Elp123Elp11132–1224 (right), and fluorescently labeled tRNA
AlaUGC. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. than the fully assembled Elongator complex, but when we
used mouse or human tRNA ArgUCU we observed no dif-
ferences in affinity (Figure 5B). These data again support
the notion that Elp456 might discriminate between sub-
pools of tRNAs (22). Second, we examined whether the
recombinantly produced mouse and human Elongator as-
semblies hydrolyze (ACO) faster upon tRNA binding (33). Initially, we employed HEK293 cells-derived human bulk tRNA for the assay, and it did not stimulate the ACO ac-
tivity of yeast Elongator (Supplementary Figure S11B). To
exclude any incompatibility of ScElongator with human-
specific tRNA modification patterns, we then tested yeast
samples with extracted yeast bulk tRNA. Our results show
that all used Elongator complexes can hydrolyze ACO in the
presence of tRNAs to different degree. Elongator displays
slightly lower activity than their respective Elp123 coun- 16 Nucleic Acids Research, 2023 16 We also performed the experiments for both mouse and hu-
man proteins in the presence of purified bulk tRNA to test
if any minor tRNA species or tRNAs carrying modification
intermediates may affect the reconstitution. The CTD of Elp1 is responsible for tRNA binding and sub-
complex interaction Again, the full
complex assembly is independent of tRNA, ATP or com-
binations thereof (Figure 6B and Supplementary Figure
S12B, C). As the presence of ATP influences tRNA binding
ability of Elp456, but not the assembly of the full complex,
we further determined the impact of ATP on tRNA bind-
ing of the fully assembled reconstituted complex. The gel
shift assay showed that the fully assembled human Elonga-
tor complex has slightly lower affinity towards tRNA in the
presence of ATP (Figure 6C). The ATP effect on decrease
of tRNA binding is also found in the Elp123. Based on this
finding we would like to propose a molecular mechanism,
in which Elp456 acts as a molecular extruder that binds
tRNA with greater affinity and pulls it away from Elp123. A stronger Elp456–tRNA complex may fall apart upon suc-
cessful ATP hydrolysis, releasing the tRNA and prepare
Elp456 for another round of the reaction cycle, which in
principle could promote the overall fidelity of tRNA modi-
fication. (Figure 7). terparts, but a high batch-to-batch variation and the use
of different bulk tRNAs limit the outcome of these analy-
ses (Supplementary Figure S11C). Third, we produced sev-
eral human Elongator variants that lack the regions impor-
tant for tRNA or other subcomplex binding (i.e. CP2). In
detail, we produced variants lacking (i) the tRNA binding
loop of Elp1 (Elp11132–1224), (ii) the Elp1 binding loop of
Elp4 (Elp4133–175) and (iii) the very N-terminus of Elp5
(Elp51–9). The pull-down assays showed that all mutations
moderately affect Elongator reconstitution, with stronger
effects for Elp11132–1224 and Elp4133–175 and less promi-
nent reduction of binding by the Elp5 truncation (Figure
5C and Supplementary Figure S11D). These data indicated
that the regions creating CP2 indeed affect the complex for-
mation and that the loop region in Elp1, which was previ-
ously shown to contact the bound tRNA molecule is also in-
volved in Elp456 recruitment. They also confirm a close link
between tRNA binding and Elp456 recruitment. However,
electrophoretic mobility shift assay (EMSA) showed that
the 1132–1224 deletion in Elp1 displayed no significant
effect on affinity of Elp123 variant toward mouse tRNA
AlaUGC compared to wild type subcomplex (Figure 5D). DISCUSSION tRNA anticodon modifications by Elongator have a broad
implication for biomedicine and translational research, as
its dysfunction is associated with a variety of severe human
diseases. Yet, details of its mechanistic mode of action have
remained elusive, leaving some of the most important ques-
tions related to this large macromolecular complex unan-
swered. In this work, we developed novel protocols that allow
overexpression and purification of the whole Elongator
complex from yeast cells for the first time. Furthermore,
we managed to overproduce, purify and reconstitute mouse
and human Elongator complexes using advanced insect
cell expression systems. We have determined several high-
resolution cryo-EM structures for yeast and mouse Elonga-
tor complexes in the presence and absence of tRNAs. Fore-
most, the comparison of our cryo-EM structures demon-
strates high similarities between yeast and mouse Elonga-
tor and their intermediates. Our results reveal how both
subcomplexes interact with each other and that in both
cases, the Elp456 ring binds to only one Elp123 lobe, leav-
ing the second one unoccupied. As the reconstitutions of
the mammalian Elongator complexes were carried out in
excess of the smaller subcomplex the possibility existed
that both Elp123 lobes would bind one Elp456 ring, re-
sulting in a 1:2 stoichiometry of the subcomplexes. Yet,
in our MmElongator structure the ring again binds only
to one Elp123 lobe with a 1:1 stoichiometry, suggesting
that the alternative scenario with two Elp456 rings bind-
ing both lobes of Elp123 at the same time appears rather
unlikely. The poorly defined density of the second Elp123
lobe in both the ScElongator and MmElongator struc-
tures indicates its high flexibility, even in the presence of
Elp456. Surprisingly, the CTD of Elp1 remains disordered
in MmElp123. Nonetheless, binding of either tRNA or
Elp456 do not cause major structural rearrangement but
instead lead to a more compact and rigid complex. There- The CTD of Elp1 is responsible for tRNA binding and sub-
complex interaction This is likely due to that tRNA binding seems to be dom-
inated by Elp3 and the second contact site located in the
Elp1 CTD might simply sense the presence of a tRNA or
serves a role during specific transition states. This could
explain our observation that the CTD loop deletion in-
deed displays functional importance in vivo even though
there is no significant contribution to tRNA binding in the
in vitro assay. It should also be noted that we were only
able to test individual mutations and the observed inter-
faces are rather large. Hence, the remaining sites in a re-
spective mutant (Elp11132–1224) might be sufficient to main-
tain tRNA binding. Finally, tRNA binding might not be af-
fected by the tested mutants as the second Elp456-free lobe
of Elp123 could mediate tRNA binding in the presence of
Elp456. Nonetheless, the biochemical analyses of human
Elongator support our structural findings, and several as-
pects need to be addressed by additional analyses in the
future. High ATP concentration stimulates tRNA binding of Elp456 It was previously shown that yeast Elp456 binds tRNA in
an ATP hydrolysis regulated manner (26). To verify whether
mouse and human Elp456 behave in a similar fashion,
we measured the binding affinity towards mouse tRNA
AlaUGC using MST assays with varying ATP concentra-
tions (Figure 6A). Similar to yeast Elp456, low ATP con-
centration indeed decreases the affinity of both mammalian
Elp456 complexes towards tRNA in comparison to samples
without ATP. When physiologically relevant ATP concen-
trations (e.g. 2.5 mM) (99–101) were used, we detected a
dramatic increase in binding affinities (Figure 6A). As our
data show that Elp456 cannot only release tRNA upon hy-
drolysis of ATP but also bind strongly to tRNA at higher
ATP concentration, we next investigated whether the inter-
action between human Elp123 and Elp456 could be ATP-
dependent. The pull-down interaction assay showed no dif-
ferences in the full complex assembly in the presence of var-
ious concentrations of ATP (Supplementary Figure S12A). Nucleic Acids Research, 2023 17 re 6. Biochemical and functional characterization of Elp456. (A) Microscale thermophoresis measurements, respective fits, and calculated dissociation
tant (Kd) values for mouse and human Elp456 at varying ATP concentrations. n = 3, n = 4 for mouse Elp456 and 0 mM ATP. (B) SDS-PAGE gel
vitro reconstitution of human Elongator under varying ATP concentration and bulk tRNA presence. Twin-Strep-tag indicated on Elp3 subunit. (C)
SA assay using fluorescently labeled tRNA AlaUGC (0.2 M), human Elp123 (top) and Elongator (bottom) (0.05–1 M) in the absence and presence
TP. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. Downloaded from https://academic.oup.com/nar/advance article/doi/10.1093/nar/gkac1232/6970223 by Unive Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Figure 6. Biochemical and functional characterization of Elp456. (A) Microscale thermophoresis measurements, respective fits, and calculated dissociation
constant (Kd) values for mouse and human Elp456 at varying ATP concentrations. n = 3, n = 4 for mouse Elp456 and 0 mM ATP. (B) SDS-PAGE gel
of in vitro reconstitution of human Elongator under varying ATP concentration and bulk tRNA presence. Twin-Strep-tag indicated on Elp3 subunit. (C)
EMSA assay using fluorescently labeled tRNA AlaUGC (0.2 M), human Elp123 (top) and Elongator (bottom) (0.05–1 M) in the absence and presence
of ATP. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. High ATP concentration stimulates tRNA binding of Elp456 fore, the rather flexible mammalian Elongator complexes
at the start of the reaction might undergo unanticipated
structural rearrangements upon substrate binding, absent
in yeast Elongator. It is noteworthy that we resolved a
loop region (aa184–238) in yeast Elp1, which is essential
for the modification activity in vivo and seems to sup-
port the integrity of the Elp123 subcomplex. As this loop
is not visible in any of the previous cryo-EM structures
and produces several violating crosslinks, it might become
structured only under certain conditions indicating a dy-
namic component of complex assembly also for the yeast
complex. leagues proposed a catalytic reaction mechanism based on
the biochemical characterizations of archaeal Elp3. The
Elp3 utilizes its rSAM domain to accommodate and cleave
SAM to produce a 5′-dA radical. The 5′-dA radical is then
used to generate an acetyl radical where the acetyl group
comes from the hydrolyzed ACO product or from a cova-
lent acetyl-Elp3 intermediate (34). An unresolved issue is
how the radical is transferred. The radical transfer may be
similar to some ribonucleotide reductases, which are known
to transfer generated radicals through a tyrosine relay sys-
tem over a distance of ∼30 ˚A (102). Indeed, two struc-
turally highly conserved tyrosine residues, namely Tyr136
and Tyr327, are present in yeast Elp3 active site, which are
juxtaposed to the radical carrying methyl group of 5′-dA. For the full catalytic reaction to finish, it still requires the
hydrolyzed acetyl group from the KAT domain to be trans-
ferred to the proposed Lys325 residue, which is residing in
the rSAM domain. We speculate that Tyr327 might mediate
the acetyl radical formation by bridging between the 5′-dA leagues proposed a catalytic reaction mechanism based on
the biochemical characterizations of archaeal Elp3. The
Elp3 utilizes its rSAM domain to accommodate and cleave
SAM to produce a 5′-dA radical. The 5′-dA radical is then
used to generate an acetyl radical where the acetyl group
comes from the hydrolyzed ACO product or from a cova-
lent acetyl-Elp3 intermediate (34). An unresolved issue is
how the radical is transferred. The radical transfer may be
similar to some ribonucleotide reductases, which are known
to transfer generated radicals through a tyrosine relay sys-
tem over a distance of ∼30 ˚A (102). High ATP concentration stimulates tRNA binding of Elp456 After the cre-
ation of acetyl radical on Lys325, the C5 atom of U34 is ide-
ally positioned to be modified, resulting in cm5U34. More-
over, our structures represent snapshots at certain stages
of the catalytic reaction. First, the MmElp123 harbors a
SAM molecule that is bound to the iron-sulfur cluster, in-
dicating that SAM binding occurs before tRNA binding. Second, the ScElp123 in complex with tRNA harbors the
SAM cleavage products, namely 5′-dA and methionine, in
its catalytic site. Third, we could not identify any SAM
molecule in the full Elongator, suggesting SAM is con-
sumed. Hence, we depict the catalytic reaction as follows: (i)
the Elp123 structure with intact SAM represents the initial
state prior to tRNA binding and SAM cleavage; (ii) subse-
quently Elp123 mediates SAM cleavage upon tRNA bind-
ing (i.e. the Elp123–tRNA structure) which represents the
stage of a radical generation just before its transfer from 5′-
dA; (iii) the SAM free-Elongator depicts the post state of
the catalytic reaction. radical and the acetyl group (Figure 7). Of note, Tyr327 is
crucial for Elongator’s activity in yeast (31). After the cre-
ation of acetyl radical on Lys325, the C5 atom of U34 is ide-
ally positioned to be modified, resulting in cm5U34. More-
over, our structures represent snapshots at certain stages
of the catalytic reaction. First, the MmElp123 harbors a
SAM molecule that is bound to the iron-sulfur cluster, in-
dicating that SAM binding occurs before tRNA binding. Second, the ScElp123 in complex with tRNA harbors the
SAM cleavage products, namely 5′-dA and methionine, in
its catalytic site. Third, we could not identify any SAM
molecule in the full Elongator, suggesting SAM is con-
sumed. Hence, we depict the catalytic reaction as follows: (i)
the Elp123 structure with intact SAM represents the initial
state prior to tRNA binding and SAM cleavage; (ii) subse-
quently Elp123 mediates SAM cleavage upon tRNA bind-
ing (i.e. the Elp123–tRNA structure) which represents the
stage of a radical generation just before its transfer from 5′-
dA; (iii) the SAM free-Elongator depicts the post state of
the catalytic reaction.i sufficient structural details to provide pseudo-atomic mod-
els. Based on these structure analyses, we further biochem-
ically characterized the role of Elp456 during the Elonga-
tor reaction cycle. High ATP concentration stimulates tRNA binding of Elp456 Indeed, two struc-
turally highly conserved tyrosine residues, namely Tyr136
and Tyr327, are present in yeast Elp3 active site, which are
juxtaposed to the radical carrying methyl group of 5′-dA. For the full catalytic reaction to finish, it still requires the
hydrolyzed acetyl group from the KAT domain to be trans-
ferred to the proposed Lys325 residue, which is residing in
the rSAM domain. We speculate that Tyr327 might mediate
the acetyl radical formation by bridging between the 5′-dA Apart from the overall structural similarities between
fungal and murine Elongator, the spatial organization of
their active sites is highly conserved as well. As the molecu-
lar mechanism of the tRNA modification reaction is still
not fully characterized, we analyzed the conserved fea-
tures of the various active sites in all our structures to
understand the underlying principles. Selvadurai and col- 18 Nucleic Acids Research, 2023 Figure 7. Elongator’s reaction scheme. A schematic overview of the individual reaction intermediates of the eukaryotic Elongator complex. In higher
mammalians highly flexible Elp123 binds tRNA substrate, SAM and Ac-CoA to modify U34. Bound tRNA substrate tethers the lobe with the CTD of
Elp1. Next, SAM is cleaved to methionine and 5′-dA radical. The radical is passed on acetylated lysine with the help of tyrosine residue. Acetyl radical
can then react with C5 of U34. After U34 modification, Elp456 assists in the release of certain tRNA species via Elp1 tRNA binding loop displacement. To allow tRNA binding to the Elp123 lobe occupied by Elp456 the smaller subcomplex needs to dissociate. How this occurs needs further investigation. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Figure 7. Elongator’s reaction scheme. A schematic overview of the individual reaction intermediates of the eukaryotic Elongator complex. In higher
mammalians highly flexible Elp123 binds tRNA substrate, SAM and Ac-CoA to modify U34. Bound tRNA substrate tethers the lobe with the CTD of
Elp1. Next, SAM is cleaved to methionine and 5′-dA radical. The radical is passed on acetylated lysine with the help of tyrosine residue. Acetyl radical
can then react with C5 of U34. After U34 modification, Elp456 assists in the release of certain tRNA species via Elp1 tRNA binding loop displacement. To allow tRNA binding to the Elp123 lobe occupied by Elp456 the smaller subcomplex needs to dissociate. How this occurs needs further investigation. radical and the acetyl group (Figure 7). Of note, Tyr327 is
crucial for Elongator’s activity in yeast (31). DATA AVAILABILITY veniently explained why we have not obtained a structure
of the fully assembled complex with tRNA and that the full
complex shows a decreased affinity for certain tRNAs. Af-
ter comparing the structures of Elp123-tRNA and Elonga-
tor, we nevertheless had to realize that also the full complex
would be able to accommodate a single tRNA molecule in
the space formed between the Elp123 lobe and the Elp456
ring. Although, the tRNA binding loop in the CTD of Elp1
would not be able to interact with the elbow region of the
bound tRNA, as it is displaced by the bound Elp456 ring. To gain further insights, we introduced specific mutations
in human Elp1, which either remove the whole loop re-
gion or target specific regions of the loop (1176–1200,
1201–1225 and 1226–1251). All three deletions in vivo
in yeast Elp1 result in the inactivation of the Elongator
pathway, but its removal in human Elp123 is not suffi-
cient to diminish tRNA binding to Elp123, clearly prov-
ing that tRNA binding mainly occurs through the ASL
bound in the active site of Elp3. The mechanistic rational
behind tRNA selectivity and detailed intramolecular relay
of tRNA remain elusive, but as Elp123 does not require
Elp456 to bind tRNAs, we believe that Elp456 is impor-
tant for the late stages of the modification reaction. Strik-
ingly, we found that at physiologically relevant ATP con-
centration the affinity of mammalian Elp456 towards tR-
NAs exceeds the one measured for Elp123, respectively. As neither ATP nor tRNA influenced the interaction of
Elp123 and Elp456, we speculate that ATP-binding might
trigger the transition of an already modified tRNA to the
Elp456 complex, which then releases the tRNA after ATP
hydrolysis (Figure 7). As we were not able to detect any
SAM molecule in the Elongator structures from mouse
and yeast, we conclude that the Elp456-bound intermedi-
ate, represents the latest stage of the modification reaction
and that after release from the Elp456 ring, the next reac-
tion is initiated by binding of SAM, ACO and a modifiable
tRNA.i The models and cryo-EM densities map have been de-
posited in the EMData Bank (EMDB) and the Protein Data
Bank (PDB) – yeast Elongator (PDB ID 8ASV and EMD-
15622), mouse Elongator (EMD-15626), yeast Elp456
(PDB ID 8AT6 and EMD-15635), mouse Elp123 (PDB
ID 8AVG and EMD-15682), yeast Elp123–tRNA (PDB
ID 8ASW and EMD-15623), mouse Elp123–tRNA (EMD-
15625). High ATP concentration stimulates tRNA binding of Elp456 It is interesting to see that the Elp456
ring occupies a similar region as the tRNA suggesting
that Elp456 could spatially compete with a bound tRNA
substrate. However, by super-positioning the structures of
Elp123–tRNA and Elongator, we had to realize that tRNA
still can spatially fit between Elp123 and Elp456. Despite
the extensive efforts, we still could not manage to obtain
any Elongator–tRNA structure. We further present that the
CTD of Elp1 is essential for the catalytic activity and it has
dual interacting targets, tRNA and Elp456. It seems that the
interaction is discriminated to one or the other. However,
the tRNA interaction with CTD is not crucial for tRNA
recruitment. tRNA binding to Elp123 is an independent event that
does not require the presence of Elp456. However, the full
Elongator complex displays different affinities to individ-
ual tRNA targets, suggesting a role for Elp456. The most
obvious model, where binding of Elp456 directly competes
with a bound tRNA molecule in Elp123, would have con- y
This is the first study to present the interaction of the
Elp123 and Elp456 subcomplexes at high-resolution with Nucleic Acids Research, 2023 19 veniently explained why we have not obtained a structure
of the fully assembled complex with tRNA and that the full
complex shows a decreased affinity for certain tRNAs. Af-
ter comparing the structures of Elp123-tRNA and Elonga-
tor, we nevertheless had to realize that also the full complex
would be able to accommodate a single tRNA molecule in
the space formed between the Elp123 lobe and the Elp456
ring. Although, the tRNA binding loop in the CTD of Elp1
would not be able to interact with the elbow region of the
bound tRNA, as it is displaced by the bound Elp456 ring. To gain further insights, we introduced specific mutations
in human Elp1, which either remove the whole loop re-
gion or target specific regions of the loop (1176–1200,
1201–1225 and 1226–1251). All three deletions in vivo
in yeast Elp1 result in the inactivation of the Elongator
pathway, but its removal in human Elp123 is not suffi-
cient to diminish tRNA binding to Elp123, clearly prov-
ing that tRNA binding mainly occurs through the ASL
bound in the active site of Elp3. High ATP concentration stimulates tRNA binding of Elp456 The mechanistic rational
behind tRNA selectivity and detailed intramolecular relay
of tRNA remain elusive, but as Elp123 does not require
Elp456 to bind tRNAs, we believe that Elp456 is impor-
tant for the late stages of the modification reaction. Strik-
ingly, we found that at physiologically relevant ATP con-
centration the affinity of mammalian Elp456 towards tR-
NAs exceeds the one measured for Elp123, respectively. As neither ATP nor tRNA influenced the interaction of
Elp123 and Elp456, we speculate that ATP-binding might
trigger the transition of an already modified tRNA to the
Elp456 complex, which then releases the tRNA after ATP
hydrolysis (Figure 7). As we were not able to detect any
SAM molecule in the Elongator structures from mouse
and yeast, we conclude that the Elp456-bound intermedi-
ate, represents the latest stage of the modification reaction
and that after release from the Elp456 ring, the next reac-
tion is initiated by binding of SAM, ACO and a modifiable
tRNA.i Supplementary Data are available at NAR Online. Supplementary Data are available at NAR Online. DATA AVAILABILITY All XL-MS data are available at https://repository. jpostdb.org/entry/JPST001914 (ID JPST001914). All other
data generated in this study are available from correspond-
ing authors on reasonable request. ACKNOWLEDGEMENTS We thank all members of the Glatt and Schaffrath labo-
ratories for discussion and suggestions. The GST--toxin
construct was a kind gift from Anders S. Bystr¨om. This
publication was developed under the provision of the Pol-
ish Ministry of Education and Science project: ‘Support
for research and development with the use of research in-
frastructure of the National Synchrotron Radiation Centre
SOLARIS’ under contract nr 1/SOL/2021/2. We acknowl-
edge SOLARIS Centre for the access to the Titan Krios,
where the measurements were performed. Part of this work
used iNEXT Discovery platform to gain access to the Cryo-
Electron Microscopy Imaging Centre at EMBL Heidelberg. Finally, this research was partially supported by PLGrid In-
frastructure (Academic Computer Centre Cyfronet AGH). The open-access publication of this article was funded by
the Priority Research Area BioS under the program ‘Initia-
tive of Excellence – Research University’ at the Jagiellonian
University in Krakow. oi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Based on previous findings, we conclude that Elongator
can bind all types of tRNAs, but only the recognition of
specific bases in certain tRNAs triggers ACO hydrolysis in
the KAT domain and SAM cleavage in the rSAM domain. In mammals, the binding of tRNAs induces large structural
rearrangements in the arch domain, which might confer ad-
ditional selectivity and create a second contact at the elbow
region of the bound tRNA molecule. All modifiable tRNAs
would receive cm5 at U34 by the activity of the Elp123, but
some tRNAs additionally require the assistance of Elp456
to be unloaded from the complex after the modification re-
action. To release certain modified tRNAs from Elp123, the
smaller subcomplex would bind again and displace the loop
in the Elp1 CTD allowing the tRNA to be released. We
speculate that the affinity of certain tRNAs is simply too
high for a release from Elp123 and that the displacement
of the loop, facilitates the ATP-dependent transfer of tR-
NAs to the Elp456 ring. How the transfer from Elp123 to
Elp456 exactly happens will require additional studies. In
summary, our data provide novel insights into the structural
and functional conservation of Elongator in eukaryotes and
our work paves the way for further analyses of the intrinsic
dynamics of Elongator and the specific differences between
its tRNA substrate molecules. FUNDING OPUS16 grant [2018/31/B/NZ1/03559 to M.J., R.K.,
N.H.A., S.G.] from the National Science Centre; Eu-
ropean Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation pro-
gramme [101001394 to S.G.]; MCB structural biology
core facility (supported by the TEAM TECH CORE
FACILITY/2017–4/6) grant from Foundation for Polish
Science to M.R., P.I., S.G.]; PhD scholarship support by
the Otto Braun-Fonds (B. Braun, Melsungen AG, Ger-
many to D.S.); Deutsche Forschungsgemeinschaft, Ger-
many [SCHA750/20, SCHA750/25 to R.S.]. Funding for
open access chrge: Priority Research Area BioS under the
program ‘Initiative of Excellence––Research University’ at
the Jagiellonian University in Krakow. C
fli t f i t
t t t
t N
d
l
d 1. Machnicka,M.A., Olchowik,A., Grosjean,H. and Bujnicki,J.M.
(2014) Distribution and frequencies of post-transcriptional
modifications in tRNAs. RNA Biol., 11, 1619–1629. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. REFERENCES 1. Machnicka,M.A., Olchowik,A., Grosjean,H. and Bujnicki,J.M. (2014) Distribution and frequencies of post-transcriptional
modifications in tRNAs. RNA Biol., 11, 1619–1629. 20 Nucleic Acids Research, 2023 Chramiec-Gł˛abik,A. et al. (2021) Elp2 mutations perturb the
epitranscriptome and lead to a complex neurodevelopmental
phenotype. Nat. Commun., 12, 19. 2. Huang,B., Johansson,M.J.O. and Bystr¨om,A.S. (2005) An early step
in wobble uridine tRNA modification requires the Elongator
complex. RNA, 11, 424–436. 3. Huang,B.O., Lu,J. and Bystro,A.S. (2008) A genome-wide screen
identifies genes required for formation of the wobble nucleoside in
Saccharomyces cerevisiae. RNA, 14, 2183–2194. 22. Gaik,M., Kojic,M., Stegeman,M.R., ¨Onc¨u- ¨Oner,T., Ko´scielniak,A.,
Jones,A., Mohamed,A., Chau,P.Y.S., Sharmin,S.,
Chramiec-Gł˛abik,A. et al. (2022) Functional divergence of the two
Elongator subcomplexes during neurodevelopment. EMBO Mol. Med., 14, 396–401. 4. Glatt,S., Zabel,R., Vonkova,I., Kumar,A., Netz,D.J., Pierik,A.J.,
Rybin,V., Lill,R., Gavin,A.-C.A.C., Balbach,J. et al. (2015) Structure
of the Kti11/Kti13 heterodimer and its double role in modifications
of tRNA and eukaryotic elongation factor 2. Structure, 23, 149–160. 23. Waszak,S.M., Giles,W., Gudenas,B.L., Smith,K.S., Forget,A.,
Kojic,M., Garcia-lopez,J., Hadley,J., Hamilton,K.V, Indersie,E. et al. (2020) Germline Elongator mutations in Sonic Hedgehog
medulloblastoma. Nature, 580, 396–401. 5. Kolaj-Robin,O., McEwen,A.G., Cavarelli,J. and Seraphin,B. (2015)
Structure of the Elongator cofactor complex Kti11/Kti13 provides
insight into the role of Kti13 in Elongator-dependent tRNA
modification. FEBS J., 282, 819–833. 24. NJ Krogan,J.G. (2001) Characterization of a six-subunit
holo-Elongator complex required for the regulated expression of a
group of genes in Saccharomyces cerevisiae. Mol. Cell. Biol., 21,
8203–8212. 6. Jablonowski,D., Fichtner,L., Stark,M.J.R. and Schaffrath,R. (2004)
The yeast elongator histone acetylase requires Sit4-dependent
dephosphorylation for toxin-target capacity. Mol. Biol. Cell, 15,
1459–1469. 25. Winkler,G.S., Petrakis,T.G., Ethelberg,S., Tokunaga,M.,
Erdjument-bromage,H., Tempst,P. and Svejstrup,J.Q. (2001) RNA
polymerase II elongator holoenzyme is composed of two discrete
subcomplexes. J. Biol. Chem., 276, 32743–32749. 7. Karlsborn,T., T¨ukenmez,H., Mahmud,A.K.M.F., Xu,F., Xu,H. and
Bystr¨om,A.S. (2014) Elongator, a conserved complex required for
wobble uridine modifications in eukaryotes. RNA Biol., 11,
1519–1528. 26. Glatt,S., L´etoquart,J., Faux,C., Taylor,N.M.I., S´eraphin,B. and
M¨uller,C.W. (2012) The Elongator subcomplex Elp456 is a
hexameric RecA-like ATPase. Nat. Struct. Mol. Biol., 19, 314–320. 27 D
d
M I K
i
ki J K l j R bi
O D
f
A O i A 8. Johansson,M.J.O., Xu,F. and Bystr¨om,A.S. (2018) Elongator––a
tRNA modifying complex that promotes efficient translational
decoding. Biochim. Biophys. Acta - Gene Regul. Mech., 1861,
401–408. 27. Dauden,M.I., Kosinski,J., Kolaj-Robin,O., Desfosses,A., Ori,A.,
Faux,C., Hoffmann,N.A., Onuma,O.F., Breunig,K.D., Beck,M. et al. (2017) Architecture of the yeast Elongator complex. EMBO
Rep., 18, 264–279. REFERENCES 9. Vendeix,F.A.P., Iv,F.V.M., Cantara,W.A., Gustilo,E.M., Sproat,B.,
Malkiewicz,A. and Agris,P.F. (2012) Human tRNA Lys3 UUU is
pre-structured by natural modifications for cognate and wbble codon
binding through keto–enol tautomerism. J. Mol. Biol., 416, 467–485. 28. Setiaputra,D.T., Cheng,D.T., Lu,S., Hansen,J.M., Dalwadi,U.,
Lam,C.H., To,J.L., Dong,M. and Yip,C.K. (2017) Molecular
architecture of the yeast Elongator complex reveals an unexpected
asymmetric subunit arrangement. EMBO Rep., 18, 280–291. 10. Anissa,V., Rezgui,N., Tyagi,K., Ranjan,N., Konevega,A.L. and
Mittelstaet,J. (2013) tRNA tKUUU,tQUUG, and tEUUC wobble
position modification fine-tune protein translation by promoting
ribosome A-site binding. Proc. Natl Acad. Sci., 110, 12289–12294.i 29. Dong,C., Lin,Z., Diao,W., Li,D., Chu,X., Wang,Z., Zhou,H.,
Xie,Z., Shen,Y. and Long,J. (2015) The elp2 subunit is essential for
elongator complex assembly and functional regulation. Structure,
23, 1078–1086. 11. Ranjan,N. and Rodnina,M.V. (2017) Thio-modification of tRNA at
the wobble position as regulator of the kinetics of decoding and
translocation on the ribosome. J. Am. Chem. Soc., 139, 5857–5864. 30. Xu,H., Lin,Z., Li,F., Diao,W., Dong,C., Zhou,H., Xie,X., Wang,Z.,
Shen,Y. and Long,J. (2015) Dimerization of elongator protein 1 is
essential for Elongator complex assembly. Proc. Natl. Acad. Sci. U. S. A., 112, 10697–10702. 12. Rodnina,M.V, Fischer,N., Maracci,C., Stark,H. and Rodnina,M.V
(2017) Ribosome dynamics during decoding. Philos. Trans. R. Soc. L. B. Biol. Sci., 372, 20160182. 31. Dauden,M.I., Jaciuk,M., Weis,F., Lin,T.-Y., Kleindienst,C.,
Abbassi,N.E.H., Khatter,H., Krutyholowa,R., Breunig,K.D.,
Kosinski,J. et al. (2019) Molecular basis of tRNA recognition by the
Elongator complex. Sci. Adv., 5, eaaw2326. 13. Thommen,M., Holtkamp,W. and Rodnina,M.V (2017)
Co-translational protein folding: progress and methods. Curr. Opin. Struct. Biol., 42, 83–89. 14. Nedialkova,D.D. and Leidel,S.A. (2015) Optimization of codon
translation rates via tRNA modifications maintains proteome
integrity. Cell, 161, 1606–1618. 32. Glatt,S., Zabel,R., Kolaj-Robin,O., Onuma,O.F., Baudin,F.,
Graziadei,A., Taverniti,V., Lin,T., Baymann,F., S´eraphin,B. et al. (2016) Structural basis for tRNA modification by Elp3 from
Dehalococcoides mccartyi. Nat. Struct. Mol. Biol., 23, 794–802. 15. Hawer,H., Hammermeister,A., Ravichandran,K.E., Glatt,S.,
Schaffrath,R. and Klassen,R. (2018) Roles of Elongator dependent
tRNA modification pathways in neurodegeneration and cancer. Genes (Basel.)., 10, 1–23. i
halococcoides mccartyi. Nat. Struct. Mol. Biol., 23, 794–80 33. Lin,T.-Y., Abbassi,N.E.H., Zakrzewski,K., Chramiec-Gł˛abik,A.,
Jemioła-Rzemi´nska,M., R´o˙zycki,J. and Glatt,S. (2019) The
Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. Nat. Commun., 10, 625. 16. Anderson,S.L., Coli,R., Daly,I.W., Kichula,E.A., Rork,M.J.,
Volpi,S.A., Ekstein,J. and Rubin,B.Y. (2001) Familial dysautonomia
is caused by mutations of the IKAP gene. Am. J. Hum. Genet., 68,
753–758. 34. Selvadurai,K., Wang,P., Seimetz,J. and Huang,R.H.H. REFERENCES (2014)
Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5
via a radical mechanism. Nat. Chem. Biol., 10, 810–812. 17. Strug,L.J.J., Clarke,T., Chiang,T., Chien,M.C., Baskurt,Z., Li,W.L.,
Dorfman,R., Bali,B., Wirrell,E., Kugler,S.L.L. et al. (2009)
Centrotemporal sharp wave EEG trait in rolandic epilepsy maps to
Elongator Protein Complex 4 (ELP4). Eur. J. Hum. Genet., 17,
1171–1181. 35. Abdel-Fattah,W., Jablonowski,D., Di Santo,R., Th¨uring,K.L.,
Scheidt,V., Hammermeister,A., ten Have,S., Helm,M., Schaffrath,R. and Stark,M.J.R. (2015) Phosphorylation of Elp1 by Hrr25 is
required for elongator-dependent tRNA modification in yeast. PLos
Genet., 11, e1004931. 18. Cohen,J.S., Srivastava,S., Farwell,K.D., Lu,H.M.H., Zeng,W.,
Chao,E.C. and Fatemi,A. (2015) ELP2 is a novel gene implicated in
neurodevelopmental disabilities. Am. J. Med. Genet. A, 167,
1391–1395. 36. Di Santo,R., Bandau,S. and Stark,M.J.R. (2014) A conserved and
essential basic region mediates tRNA binding to the Elp1 subunit of
the Saccharomyces cerevisiae Elongator complex. Mol. Microbiol.,
92, 1227–1242.i 19. Simpson,C.L., Lemmens,R., Miskiewicz,K., Broom,W.J.,
Hansen,V.K., van Vught,P.W.J.J., Landers,J.E., Sapp,P., van Den
Bosch,L., Knight,J. et al. (2009) Variants of the elongator protein 3
(ELP3) gene are associated with motor neuron degeneration. Hum. Mol. Genet., 18, 472–481. 37. Lin,T.-Y. and Glatt,S. (2018) tRNA modification by Elongator
Protein 3 (Elp3). In: Scott,R.A. (ed.) Encyclopedia of Inorganic and
Bioinorganic Chemistry. Wiley Online Library, eibc2623. 38. Abbassi,N.E.H., Biela,A., Glatt,S. and Lin,T.Y. (2020) How
elongator acetylates trna bases. Int. J. Mol. Sci., 21, 1–13. 20. Kojic,M., Gaik,M., Kiska,B., Salerno-Kochan,A., Hunt,S.,
Tedoldi,A., Mureev,S., Jones,A., Whittle,B., Genovesi,L.A. et al. (2018) Elongator mutation in mice induces neurodegeneration and
ataxia-like behavior. Nat. Commun., 9, 3195. 39. Glatt,S., Letoquart,J., Faux,C., Taylor,N.M.I., Seraphin,B. and
Muller,C.W. (2012) The Elongator subcomplex Elp456 is a
hexameric RecA-like ATPase. Nat. Struct. Mol. Biol., 19, 314–320. ataxia-like behavior. Nat. Commun., 9, 3195. 40. Gaik,M., Flemming,D., Von Appen,A., Kastritis,P., M¨ucke,N.,
Fischer,J., Stelter,P., Ori,A., Bui,K.H., Baßler,J. et al. (2015) 21. Kojic,M., Gawda,T., Gaik,M., Begg,A., Salerno-Kochan,A.,
Kurniawan,N.D., Jones,A., Dro˙zd˙zyk,K., Ko´scielniak,A., Nucleic Acids Research, 2023 21 Nucleic Acids Research, 2023 21 Structural basis for assembly and function of the Nup82 complex in
the nuclear pore scaffold. J. Cell Biol., 208, 283–297. Structural basis for assembly and function of the Nup82 complex in
the nuclear pore scaffold. J. Cell Biol., 208, 283–297. 61. Trabuco,L.G., Villa,E., Mitra,K., Frank,J. and Schulten,K. (2008)
Flexible fitting of atomic structures into electron microscopy maps
using molecular dynamics. Structure, 16, 673–683. 41. Weissmann,F., Petzold,G., VanderLinden,R., Huis in ’t Veld,P.J.,
Brown,N.G., Lampert,F., Westermann,S., Stark,H., Schulman,B.A. and Peters,J.-M. py
(
)
,
https://doi.org/10.5281/zenodo.3576630. 50. Waterhouse,A., Bertoni,M., Bienert,S., Studer,G., Tauriello,G.,
Gumienny,R., Heer,F.T., Beer,T.A.P.De, Rempfer,C., Bordoli,L. et al. (2018) SWISS-MODEL: homology modelling of protein
structures and complexes. 46, 296–303. 70. Krutyhołowa,R., Hammermeister,A., Zabel,R., Abdel-Fattah,W.,
Reinhardt-Tews,A., Helm,M., Stark,M.J.R., Breunig,K.D.,
Schaffrath,R. and Glatt,S. (2019) Kti12, a PSTK-like tRNA
dependent ATPase essential for tRNA modification by Elongator. Nucleic. Acids. Res., 47, 4814–4830. .1093/nar/gka 51. Bienert,S., Waterhouse,A., De Beer,T.A.P., Tauriello,G., Studer,G.,
Bordoli,L. and Schwede,T. (2017) The SWISS-MODEL
repository––new features and functionality. Nucleic. Acids. Res., 45,
D313–D319. 71. Goldstein,A.L. and McCusker,J.H. (1999) Three new dominant
drug resistance cassettes for gene disruption in Saccharomyces
cerevisiae. Yeast, 15, 1541–1553. ac1232/ 52. Guex,N., Peitsch,M.C. and Schwede,T. (2009) Automated
comparative protein structure modeling with SWISS-MODEL and
Swiss-PdbViewer: a historical perspective. Electrophoresis, 30,
S162–S173. ,
,
72. Studier,F.W. (2005) Protein production by auto-induction in high
density shaking cultures. Protein Expr. Purif., 41, 207–234. /6970 73. Lentini,J.M., Ramos,J. and Fu,D. (2018) Monitoring the
5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification in
eukaryotic tRNAs via the -toxin endonuclease. RNA, 24, 749–758. 0223 by U 53. Studer,G., Tauriello,G., Bienert,S., Biasini,M., Johner,N. and
Schwede,T. (2021) ProMod3 - a versatile homology modelling
toolbox. PLoS Comput. Biol., 17, 1–18. eukaryotic tRNAs via the -toxin endonuclease. RNA, 2 74. Chen,Z.A., Jawhari,A., Fischer,L., Buchen,C., Tahir,S.,
Kamenski,T., Rasmussen,M., Lariviere,L., Bukowski-Wills,J.C.,
Nilges,M. et al. (2010) Architecture of the RNA polymerase
II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J., 29, 717–726. University of 54. Studer,G., Rempfer,C., Waterhouse,A.M., Gumienny,R., Haas,J. and Schwede,T. (2020) QMEANDisCo––distance constraints
applied on model quality estimation. Bioinformatics, 36, 1765–1771. d
i
i i
d
h
d
(
) A
i
h l
l 55. Studer,G., Biasini,M. and Schwede,T. (2014) Assessing the local
structural quality of transmembrane protein models using statistical
potentials (QMEANBrane). Bioinformatics, 30, 505–511. 75. Rappsilber,J., Ishihama,Y. and Mann,M. (2003) Stop and Go
Extraction tips for matrix-assisted laser desorption/ionization,
nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem., 75, 663–670. Edinburgh 56. Benkert,P., Biasini,M. and Schwede,T. (2011) Toward the estimation
of the absolute quality of individual protein structure models. Bioinformatics, 27, 343–350. 76. Kolbowski,L., Mendes,M.L. and Rappsilber,J. (2017) Optimizing
the parameters governing the fragmentation of cross-linked peptides
in a tribrid mass spectrometer. Anal. Chem., 89, 5311–5318. h user on 57. Bertoni,M., Kiefer,F., Biasini,M., Bordoli,L. and Schwede,T. (2017)
Modeling protein quaternary structure of homo- and
hetero-oligomers beyond binary interactions by homology. Sci. Rep., 7, 1–15. 77. Kong,A.T., Leprevost,F.V., Avtonomov,D.M., Mellacheruvu,D. and
Nesvizhskii,A.I. (2017) MSFragger: ultrafast and comprehensive
peptide identification in mass spectrometry-based proteomics. Nat. REFERENCES (2016) biGBac enables rapid gene assembly for the
expression of large multisubunit protein complexes. Proc. Natl. Acad. Sci. U.S.A., 113, E2564–E2569. 62. Kidmose,R.T., Juhl,J., Nissen,P., Boesen,T., Karlsen,J.L. and
Pedersen,B.P. (2019) Namdinator - automatic molecular dynamics
flexible fitting of structural models into cryo-EM and
crystallography experimental maps. IUCrJ., 6, 526–531. crystallography experimental maps. IUCrJ., 6, 526–53 42. Weissmann,F. and Peters,J. (2018) Expressing multi-subunit
complexes using Bigbac. Methods Mol Biol., 1764, 329–343. 63. Afonine,P.V, Ralf,W., Headd,J.J. and Thomas,C. (2012) Towards
automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. Sect. D., 68, 352–367. 43. Gibson,D.G., Young,L., Chuang,R., Venter,J.C., Iii,C.A.H.,
Smith,H.O. and America,N. (2009) Enzymatic assembly of DNA
molecules up to several hundred kilobases. Nat Methods., 6,
343–345. 64. Liebschner,D., Afonine,P.V., Baker,M.L., Bunkoczi,G., Chen,V.B.,
Croll,T.I., Hintze,B., Hung,L.W., Jain,S., McCoy,A.J. et al. (2019)
Macromolecular structure determination using X-rays, neutrons and
electrons: recent developments in Phenix. Acta Crystallogr. Sect. D
Struct. Biol., 75, 861–877. ed from https 44. Gibson,D.G., Glass,J.I., Lartigue,C., Noskov,V.N., Chuang,R.,
Algire,M.A., Benders,G.A., Montague,M.G., Ma,L., Moodie,M.M. et al. (2010) Creation of a bacterial cell controlled by a chemically
synthesized genome. Science, 329, 52–57. 65. Davis,I.W., Leaver-Fay,A., Chen,V.B., Block,J.N., Kapral,G.J.,
Wang,X., Murray,L.W., Arendall,W.B., Snoeyink,J., Richardson,J.S. et al. (2007) MolProbity: all-atom contacts and structure validation
for proteins and nucleic acids. Nucleic Acids Res., 35, W375–W383. dd
d
h y
g
45. Scheres,S.H.W. (2012) RELION: implementation of a Bayesian
approach to cryo-EM structure determination. J. Struct. Biol., 180,
519–530. 66. Pettersen,E.F., Goddard,T.D., Huang,C.C., Meng,E.C., Couch,G.S.,
Croll,T.I., Morris,J.H. and Ferrin,T.E. (2021) UCSF ChimeraX:
structure visualization for researchers, educators, and developers. Protein Sci., 30, 70–82. ic.oup.com 46. Tegunov,D. and Cramer,P. (2019) Real-time cryo-electron
microscopy data preprocessing with Warp. Nat. Methods, 16,
1146–1152. 47. Punjani,A., Rubinstein,J.L., Fleet,D.J. and Brubaker,M.A. (2017)
CryoSPARC: algorithms for rapid unsupervised cryo-EM structure
determination. Nat. Methods, 14, 290–296. 67. Gueldener,U., Heinisch,J., Koehler,G.J., Voss,D. and
Hegemann,J.H. (2002) A second set of loxP marker cassettes for
Cre-mediated multiple gene knockouts in budding yeast. Nucleic
Acids Res., 30, e23. m/nar/adva 48. Bepler,T., Morin,A., Rapp,M., Brasch,J., Shapiro,L., Noble,A.J. and Berger,B. (2019) Positive-unlabeled convolutional neural
networks for particle picking in cryo-electron micrographs. Nat. Methods, 16, 1153–1160. 68. Boeke,J.D., La Croute,F. and Fink,G.R. (1984) A positive selection
for mutants lacking orotidine-5′-phosphate decarboxylase activity in
yeast: 5-fluoro-orotic acid resistance. MGG Mol. Gen. Genet., 197,
345–346. ance-article 49. Asarnow,D., Palovcak,E. and Cheng,Y. (2019) asarnow/pyem:
UCSF pyem v0.5 (v0.5). Zenodo,
https://doi.org/10.5281/zenodo.3576630. 69. Jacobus,A.P. and Gross,J. REFERENCES (2015) Optimal cloning of PCR fragments
by homologous recombination in Escherichia coli. PLoS One, 10,
1–17. e/doi/10 py
(
)
,
https://doi.org/10.5281/zenodo.3576630. Methods, 14, 513–520. n 08 Febru 58. Mariani,V., Biasini,M., Barbato,A. and Schwede,T. (2013) IDDT: a
local superposition-free score for comparing protein structures and
models using distance difference tests. Bioinformatics, 29,
2722–2728. 78. da Veiga Leprevost,F., Haynes,S.E., Avtonomov,D.M., Chang,H.Y.,
Shanmugam,A.K., Mellacheruvu,D., Kong,A.T. and
Nesvizhskii,A.I. (2020) Philosopher: a versatile toolkit for shotgun
proteomics data analysis. Nat. Methods, 17, 869–870. 59. Jumper,J., Evans,R., Pritzel,A., Green,T., Figurnov,M.,
Ronneberger,O., Tunyasuvunakool,K., Bates,R., ˇZ´ıdek,A.,
Potapenko,A. et al. (2021) Highly accurate protein structure
prediction with AlphaFold. Nature, 596, 583–589. 79. Yu,F., Teo,G.C., Kong,A.T., Haynes,S.E., Avtonomov,D.M.,
Geiszler,D.J. and Nesvizhskii,A.I. (2020) Identification of modified
peptides using localization-aware open search. Nat. Commun., 11,
4065. prediction with AlphaFold. Nature, 596, 583–589. 60. Emsley,P., Lohkamp,B., Scott,W.G. and Cowtan,K. (2010) Features
and development of Coot. Acta Crystallogr. Sect. D Biol. Crystallogr., 66, 486–501. 80. Mendes,M.L., Fischer,L., Chen,Z.A., Barbon,M., O’Reilly,F.J.,
Giese,S.H., Bohlke-Schneider,M., Belsom,A., Dau,T., Combe,C.W. 22 Nucleic Acids Research, 2023 et al. (2019) An integrated workflow for crosslinking mass
spectrometry. Mol. Syst. Biol., 15, e8994. et al. (2019) An integrated workflow for crosslinking mass
spectrometry. Mol. Syst. Biol., 15, e8994. 92. Dauden,M.I.M.I., Jaciuk,M., Weis,F., Lin,T.-Y.T.-Y.T.-Y.,
Kleindienst,C., Abbassi,N.E.H.N.E.H.N.E.H., Khatter,H.,
Krutyholowa,R., Breunig,K.D.K.D., Kosinski,J. et al. (2019)
Molecular basis of tRNA recognition by the Elongator complex. Sci. Adv., 5, eaaw2326. 81. Tyanova,S., Temu,T. and Cox,J. (2016) The MaxQuant
computational platform for mass spectrometry-based shotgun
proteomics. Nat. Protoc., 11, 2301–2319. 82. Fischer,L. and Rappsilber,J. (2017) Quirks of error estimation in
cross-linking/mass spectrometry. Anal. Chem., 89, 3829–3833. 93. Dalwadi,U., Mannar,D., Zierhut,F. and Yip,C.K. (2022)
Biochemical and structural characterization of human core
Elongator and its subassemblies. ACS Omega, 7, 3424–3433. 83. M¨uller,F., Fischer,L., Chen,Z.A., Auchynnikava,T. and
Rappsilber,J. (2018) On the reproducibility of label-free quantitative
cross-linking/mass spectrometry. J. Am. Soc. Mass Spectrom., 29,
405–412. 94. Frohloff,F., Fichtner,L., Jablonowski,D., Breunig,K.D. and
Schaffrath,R. (2001) Saccharomyces cerevisiae Elongator mutations
confer resistance to the Kluyveromyces lactis zymocin. EMBO J., 20,
1993–2003. 84. Dauden,M.I., Jaciuk,M., Muller,C.W. and Glatt,S. (2017) Structural
asymmetry in the eukaryotic Elongator complex. FEBS Lett., 592,
502–515. 95. Lu,J., Huang,B.O., Esberg,A., Johansson,M.J.O. and Bystr¨om,A.S. (2005) The Kluyveromyces lactis -toxin targets tRNA anticodons. RNA, 11, 1648–1654. 85. Glatt,S., Letoquart,J., Faux,C., Taylor,N.M., Seraphin,B. and
Muller,C.W. (2012) The Elongator subcomplex Elp456 is a
hexameric RecA-like ATPase. Nat. Struct. Mol. Biol., 19, 314–320. 96. Jablonowski,D., Zink,S., Mehlgarten,C., Daum,G. and
Schaffrath,R. (2006) tRNAGlu wobble uridine methylation by Trm9
identifies Elongator’s key role for zymocin-induced cell death in
yeast. Mol. Microbiol., 59, 677–688. 86. Zhang,H., Yang,Z., Shen,Y. and Tong,L. py
(
)
,
https://doi.org/10.5281/zenodo.3576630. (2003) Crystal structure of
the carboxyltransferase domain of acetyl-coenzyme a carboxylase. Science (80-.), 299, 2064–2067. 97. Schwalm,EricaL., Grove,TylerL., Squire,J., Booker,A.K.B.,
Schwalm,E.L., Grove,T.L., Booker,S.J. and Boal,A.K. (2016)
Crystallographic capture of a radical S-adenosylmethionine enzyme
in the act of modifying tRNA. Science, 352, 309–312. 87. Huh,W.K., Falvo,J.V., Gerke,L.C., Carroll,A.S., Howson,R.W.,
Weissman,J.S. and O’Shea,E.K. (2003) Global analysis of protein
localization in budding yeast. Nature, 425, 686–691. 88. Krutyhołowa,R., Zakrzewski,K. and Glatt,S. (2019) Charging the
code –– tRNA modification complexes. Curr. Opin. Struct. Biol., 55,
138–146. 98. Esakova,O.A., Grove,T.L., Yennawar,N.H., Arcinas,A.J., Wang,B.,
Krebs,C., Almo,S.C. and Booker,S.J. (2021) Structural basis for
tRNA methylthiolation by the radical SAM enzyme MiaB. Nature,
597, 566–570. 89. Creppe,C., Malinouskaya,L., Volvert,M.L., Gillard,M., Close,P.,
Malaise,O., Laguesse,S., Cornez,I., Rahmouni,S., Ormenese,S. et al. (2009) Elongator controls the migration and differentiation of
cortical neurons through acetylation of alpha-tubulin. Cell, 136,
551–564. vance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 99. Larcombe-McDouall,J., Buttell,N., Harrison,N. and Wray,S. (1999)
In vivo pH and metabolite changes during a single contraction in rat
uterine smooth muscle. J. Physiol., 518, 783–790. 100. Gribble,F.M., Loussouarn,G., Tucker,S.J., Zhao,C., Nichols,C.G. and Ashcroft,F.M. (2000) A novel method for measurement of
submembrane ATP concentration. J. Biol. Chem., 275, 30046–30049. 90. Lin,Z., Zhao,W., Diao,W., Xie,X., Wang,Z., Zhang,J., Shen,Y. and
Long,J. (2012) Crystal structure of elongator subcomplex Elp4-6. J. Biol. Chem., 287, 21501–21508. 101. Zimmerman,J.J., von Saint Andr´e-von Arnim,A. and McLaughlin,J. (2011) Cellular Respiration. 4th edn. Elsevier. 91. Wittschieben,B.O., Otero,G., De Bizemont,T., Fellows,J.,
E dj
t B
H Ohb R Li Y Alli C D T 91. Wittschieben,B.O., Otero,G., De Bizemont,T., Fellows,J.,
Erdjument-Bromage,H., Ohba,R., Li,Y., Allis,C.D., Tempst,P. and
Svejstrup,J.Q. (1999) A novel histone acetyltransferase is an integral
subunit of elongating RNA polymerase II holoenzyme. Mol. Cell, 4,
123–128. 102. Kang,G., Taguchi,A.T., Stubbe,J. and Drennan,C.L. (2020)
Structure of a trapped radical transfer pathway within a
ribonucleotide reductase holocomplex. Science, 368, 424–427.
|
https://openalex.org/W2902145381
|
https://dspace.lib.cranfield.ac.uk/bitstream/1826/13705/4/Assessment_of_silt_from_sand_and_gravel_processing-2018.pdf
|
English
| null |
Assessment of silt from sand and gravel processing as a suitable sub-soil material in land restoration: A glasshouse study
|
Chemosphere
| 2,019
|
cc-by
| 8,929
| ERROR: type should be string, got "https://doi.org/10.1016/j.chemosphere.2018.11.155\n0045-6535/© 2018 Elsevier Ltd. All rights reserved. a r t i c l e\ni n f o Annually, sand and gravel processing generates approximately 20 million tonnes of non-commercial by-\nproduct as fine silt particles (<63 mm) which constitutes approximately 20% of quarry production in the\nUK. This study is significant as it investigated the use of quarry silt as a sub-soil medium to partially\nsubstitute soil-forming materials whilst facilitating successful post-restoration crop establishment. In a\nglasshouse pot experiment, top-soil and sub-soil layering was simulated, generating an artificial sub-soil\nmedium by mixing two quarry non-commercial by-products, i.e. silt and overburden. These were\nblended in three ratios (100:0, 70:30, 50:50). Pots were packed to two bulk densities (1.3 and 1.5 g cm-3)\nand sown with three cover crops used in the early restoration process namely winter rye (Secale cereale),\nwhite mustard (Sinapis alba) and a grassland seed mixture (Lolium perenne, Phleum pratense, Poa\npratensis, Festuca rubra). Three weeks into growth, the first signs of nitrogen (N) deficiency were\nobserved in mustard plants, with phosphorus (P) and potassium (K) deficiencies observed at 35 days. Rye\nexhibited minor N deficiency symptoms four weeks into growth, whilst the grassland mixture showed\nno deficiency symptoms. The 70:30 silt:overburden sub-soil blend resulted in significantly higher Root\nMass Densities of grassland seed mixture and rye in the sub-soil layer as compared with the other blends. The innovation in this work is the detailed physical, chemical and biological characterisation of silt:o-\nverburden blends and effects on root development of plants commonly used in early restoration to bio-\nengineer soil structural improvements. 2018 El\ni\nL d All i h\nd Article history:\nReceived 30 August 2018\nReceived in revised form\n11 November 2018\nAccepted 23 November 2018\nAvailable online 1 December 2018 Article history:\nReceived 30 August 2018\nReceived in revised form\n11 November 2018\nAccepted 23 November 2018\nAvailable online 1 December 2018\nKeywords:\nQuarry silt\nCover crops\nRestoration\nRoot mass density\nNutrients Article history:\nReceived 30 August 2018\nReceived in revised form\n11 November 2018\nAccepted 23 November 2018\nAvailable online 1 December 2018 Keywords:\nQuarry silt\nCover crops\nRestoration\nRoot mass density\nNutrients © 2018 Elsevier Ltd. All rights reserved. h i g h l i g h t s \u0001 Silt is not fully utilised in quarries as a resource. \u0001 Silt is not fully utilised in quarries as a resource. \u0001 Root development of mustard tap roots was restricted compared to grass. \u0001 Quarry silt blended with growing medium is a suitable subsoil medium for grass and rye. \u0001 Root development of mustard tap roots was restricted compared to grass. \u0001 Quarry silt blended with growing medium is a suitable subsoil medium for grass and rye. Assessment of silt from sand and gravel processing as a suitable\nsub-soil material in land restoration: A glasshouse study Lucie Ma\u0001skov\u0003a a, Robert W. Simmons a, Sarah De Baets a, Enrique Moran Montero b,\nAude Delmer b, Ruben Sakrabani a, * a School of Water, Energy and Environment, Cranfield University, Building 52a, Cranfield Bedfordshire, MK43 0AL, UK\nb Tarmac Ltd., Panshanger Park, Hertford, Hertfordshire, SG14 2NA, UK * Corresponding author.\nE-mail address: r.sakrabani@cranfield.ac.uk (R. Sakrabani). Contents lists available at ScienceDirect Contents lists available at ScienceDirect * Corresponding author.\nE-mail address: r.sakrabani@cranfield Chemosphere 219 (2019) 58e65 Chemosphere 219 (2019) 58e65 E-mail address: r.sakrabani@cranfield.ac.uk (R. Sakrabani). * Corresponding author.\nE-mail address: r.sakrab © 2018 Elsevier Ltd. All rights reserved. 2.3. Winter rye The aim of this project was to determine the suitability of non-\ncommercial by-product such as quarry silt from mining lagoons in\ncombination with overburden as a replacement for sub-soil to\nfacilitate cover crop establishment on restoration sites and whole\nprofile bio-remediation of soil structure. Outcomes will inform\nrecommendations for the successful use of non-commercial by-\nproducts such as quarry silt and overburden in future restoration\nprojects by mineral operators. Seeding rates for Winter Rye depend on local climate conditions\nand seeding method being either drill or broadcast. Values as low as\n62e67 kg ha\u00041\n(Government\nof\nAlberta,\n2016)\nand\nup\nto\n56e224 kg ha\u00041 (Casey, 2012) can be used. Based on this, a seeding\nrate of 90 kg ha\u00041 was used, as an approximate average value for\nthis experiment. Winter Rye can germinate in temperatures as low as 1 \u0005C\nallowing seeding as late as September, the end of October, or even\nDecember (AGRAVIS, 2017; Rosenfeld and Rayns, 2011). It is the\nmost frost tolerant of all cereals (Oelke et al., 1990). It prefers well-\ndrained light loams and sandy soils, but can also be established on\nheavy clays (Bj€orkman and Shail, 2014; Oelke et al., 1990). It has a\ndense, fibrous branching root system that grows especially vigor-\nously in the upper 0.3 m of soil. 2.2. Experimental design In typical quarry restorations conducted by Tarmac Ltd, a 0.6 m\nlayer of sub-soil would be capped with a 0.3 m layer of top-soil\nstripped from the surface prior to sand and gravel extraction. This\nsubstrate layering ratio was also simulated in the pot experiment. As a sub-soil medium, 3 quarry silt:overburden blend ratios were\nselected, 100:0, 70:30 and 50:50, aiming for a high quarry silt\ncontent. Quarry restoration can result in spatial variation in sub-soil and\ntop-soil bulk densities (BD). Bulk density values normally vary from\n1.1 to 1.8 g cm\u00043, whilst in extreme conditions surface soil layers\nmay have BD as low as 0.5 g cm\u00043 and heavily compacted soils may\nexceed 2.0 g cm\u00043 (Cresswell and Hamilton, 2002). A value of\n1.3 g cm\u00043 was chosen for top-soil BD and the sub-soil materials\nwere packed at a BD of either 1.3 or 1.5 g cm\u00043 in order to represent\na low and a high degree of sub-soil compaction. Cover crops possess traits that can effectively remediate com-\npacted soils (Kirkegaard et al., 2008). Research has also demon-\nstrated that the generation of biopores through a ‘bio-drilling’\neffect of cover crops in compacted soils can result in increased yield\nof follow-on crops (Chen and Weil, 2010; Cresswell and Kirkegaard,\n1995; Kirkegaard et al., 2008). Plant roots engineer soil structure\ndirectly by penetrating and displacing soil, depositing adhesive\ncompounds which encourage aggregation, and indirectly via a\nrange of other root deposits which provide energy and nutrient\nsources for soil biota (White and Kirkegaard, 2010). 1.1. Quarry restorations At the end of the operating life of sand and gravel quarries, the\nresulting voids have to be levelled and graded to achieve landscape\nand landform objectives stated in restoration plans to allow agreed\nupon restoration objectives (CEMEX, 2014; DCLG, 2014). Quarry silt\nlagoons would normally be restored into wetland habitats, or\ncapped with a \u00031 m thick layer of overburden and planted with\nwillow rods (Tarmac Ltd., 2008). However, quarries often face a\nshortage of top-soil and sub-soil forming materials. Moreover, it is a\npriority to use materials available on-site to minimise the high\ntransport costs associated with importing materials (Tarmac Ltd.,\n2008). A possible solution would be the use of non-commercial\nby-product such as quarry silt and overburden as a partial\nreplacement for sub-soil in restorations. The suitability of quarry\nfor use in artificial soils was evaluated by (Mitchell et al., 2004) who\ninvestigated several types of quarry fine blends as a growing me-\ndium for grass species. However biomass was restricted primarily\ndue to nutrient deficiencies. Three restoration cover crops were evaluated in this study. These included white mustard (Sinapis alba) a tap rooted species;\nwinter rye (Secale cereale) as a cereal representative; and a grass-\nland seed mixture (Lolium perenne, Phleum pratense, Poa pratensis,\nFestuca rubra) as a reference crop already used in Tarmac Ltd res-\ntorations. No fertilizers were applied to simulate natural restoration\nprocesses. Each treatment was replicated in triplicate. 1. Introduction crushing and screening of the material to separate sand and gravel\naggregates from fines (<0.063 mm), which consist of silt, clay and\nother non-quartz particles (British Geological Survey, 2013). These\nfines are collected in water, giving rise to a suspension, which is\nthen pumped into lagoons and allowed to settle out (British\nGeological Survey, 2013). The resultant suspension remains in\nsemi-liquid, anaerobic state for many years, or even decades (Jarvis\nand Walton, 2010). This product is then usually referred to as\n‘quarry silt’. Quarry silt, which is generated during sand and gravel pro-\ncessing, is an un-avoidable and significant proportion of quarry\noutputs (Mitchell, 2007). The amount of quarry silt varies between\n5 and 30% of the total volume extracted, averaging around 10e15%\n(Harrison et al., 2001). Mineral processing involves washing, Quarry silt is currently defined as a non-commercial by-product\nas there is currently no market, nevertheless it should be noted that L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 59 quarry silt is an inert and non-hazardous material (Mitchell, 2007). Overburden, which is a layer of material lying above the product to\nbe extracted, is also regarded as a non-commercial by-product. The\nneed to minimise the amount of quarry non-commercial by-\nproduct is driven by environmental and social considerations and\nregulatory compliances (Mitchell, 2007). Quarry silt production can\nexceed storage capacity on site and require excavation in order to\nincrease lagoon capacity, which causes both economical and\nlogistical problems to the quarry operators (Mitchell, 2007). Reduction of quarry non-commercial by-product production usu-\nally starts at source, with an optimisation audit of the processing\ntechnology where emphasis is usually placed on good practice and\nmodernization of the crushing plant (Mitchell, 2007). The main use\nof sand and gravel non-commercial by-products is as a backfill or\nsub-soil material in site landscaping and restoration (Harrison et al.,\n2001). Another possible use of quarry non-commercial by-products\naccording to Mitchell (2007) is as vegetated tips around the quarry\nsite to screen the workings. Reusing mineral non-commercial by-\nproducts such a quarry silt contributes to efficient use of resources,\nreduces environmental impacts, and improves sustainability for\nlocal communities (Mitchell et al., 2004). using excavators. Top-soil was sourced from a compacted vegetated\nbund lining Blashford Quarry using trowels. An 8-point 120 kg top-\nsoil (0e0.3 m depth) sample was collected. 2.1. Study area Materials for this study were obtained from two different\nquarries operated by Tarmac Ltd, where there was an excess pro-\nduction of quarry silt and overburden. Blashford Quarry was the\nsource of the quarry silt sub-soil material and top-soil, and\nMountsorrel Quarry provided overburden. Mountsorrel Quarry is a\ngranite quarry located between the villages of Mountsorrel and\nQuorn in Leicestershire. A total of 80 kg of overburden from this site\nwas collected from 10 randomly selected points. Blashford Quarry\nis located in Hampshire, south of Salisbury with an annual quarry\nsilt production of >20,000 m3. A 10 point 210 kg composite quarry\nsilt sample (0e0.3 m depth) was collected from two silt lagoons 2.6. Glasshouse experiment set-up For both pot experiment and laboratory analyses, growing me-\ndiums (top-soil, quarry silt and overburden) were air dried and\nsieved to <2 mm. It should be noted, that in order to minimise\nheterogeneity between experimental replicates, the coarse aggre-\ngate fraction >2 mm, was removed during sample preparation. Post\nair-drying, quarry silt and overburden were ground to <2 mm using\na mechanical sieved soil grinder. EC was determined on 1:5 soil:water extract, based on the\nBritish Standard BS 7755: Section 3.4:1995. SOM content was\nanalysed using the loss on ignition method following British\nStandard BS EN 13039:2000. Soil pH was determined on a 1:5\nsuspension of soil in water, based on the British Standard BS ISO\n10390:2005. PSD was measured using the sieving and sedimentation\nmethod based on the British Standard BS 7755 Section 5.4:1998. Soil\nmineral-N was measured using KCl extract based on MAFF\nReference Book RB427 (1986). Sub-soil medium was mixed to the desired ratios of 100:0, 70:30\nand 50:50 of quarry silt:overburden. To represent the restoration\nlayering ratio, the sub-soil layer was packed to a depth of 12 cm\nfrom the bottom of the pot, leaving the next 5 cm for the top-soil\nlayer. Sub-soil was packed at two bulk densities (BD), representing\nlow and\nhigh\ncompaction. The\nhighest\nBD\nachievable\nwas\n1.5 g cm\u00043, with the lower value set at 1.3 g cm\u00043. All pots were then\ncapped with a 5 cm layer of top-soil (previously acquired from\nBlashford Quarry) at a BD of 1.3 g cm\u00043 to reach a total pot volume\nof 2313 cm3. 2.8. Statistical analyses Results were analysed using the STATISTICA 12.0 software. Soil\nproperties were analysed using factorial analysis of variance\n(ANOVA) to determine the effects of multiple categorical variables,\nnamely bulk density (BD), quarry silt:overburden ratio (sub-soil\nblend T1, T2 and T3) and cover crop (CC) treatment. One-way and\ntwo-way ANOVA were used to analyse single categorical indepen-\ndent values for either BD or sub-soil blend, where significance for\nthe CC was not proved. Significant values were analysed following\npost-hoc Fisher LSD analysis to show differences between mean\nvalues. Normality was checked and significance was set at p \u0006 0.05. Spearman correlation was carried out on key parameters as shown\nin Table 4. Pots were placed in the Cranfield University Glasshouse in a\ncompletely randomised layout and wetted to field capacity from\nthe base via capillary rise. Cover crop seeds (winter rye, white\nmustard and grassland seed mixture) were broadcasted on the 16th\nof June 2017 (adopted from Tarmac Ltd seeding methods). However\ndue to unexpectedly hot weather (~30 \u0005C, seeds had to be incor-\nporated to a depth of <0.5 mm. Uniform pot watering was under-\ntaken approximately every two days, depending on weather\nconditions to assure crop survival. The experiment was terminated\napproximately 6 weeks after set-up. Pot layout was changed twice\nin order to randomize possible variation in growing conditions\nwithin the glasshouse. During the pot trial, mustard plants were\naffected by several insect species including aphids (Lipaphis ery-\nsimi), mustard leaf miner (Chromatomyia horticola) and large white\nbutterfly (Pieris brassicae). The rye and grass mixture treatments\nhad no pest infestation issues. in Table 4. 2.5. Grassland seed mixture A standard seed mixture for quarry restoration adopted by\nTarmac Ltd when restoring back to an agricultural end-use is a\ngrassland seed mixture. It is commonly used in the first 2e3 years\nwithin a mandatory 5-year aftercare period. Seeding is usually\ncarried out during MarcheApril or SeptembereOctober at a rate of\n34 kg ha\u00041 (Walnes Seeds, 2017). Mixtures containing the same or\nsimilar grass species (Table 1) are usually designed as a damage\nresistant paddock mixture for grazing and hay production (Walnes\nSeeds, 2017). RMD ¼ MD\nV\n\u0001\nkg m\u00043\u0003\n(1) RMD ¼ MD\nV\n\u0001\nkg m\u00043\u0003 (1) Prior to packing in pots a 6-point composite sub-sample of top-\nsoil was collected and analysed at the Cranfield University's Envi-\nronmental Analytics Facility, following Standard Operating Pro-\ncedures based on British Standard Methods. At termination, fresh\nsub-soil blends and top-soil samples were collected and analysed\nfor nitrate and ammonium as plant available nitrogen (N) in a\ncommercial external laboratory. Blended treatments T1-T3 and top-\nsoil was air dried, sieved to <2 mm and analysed for electrical\nconductivity (EC), soil organic matter (SOM), pH and particle size\ndistribution (PSD). has a tap rooting architecture and is frost sensitive. has a tap rooting architecture and is frost sensitive. has a tap rooting architecture and is frost sensitive. penetration through the top-soil and sub-soil layers. One quarter of\neach pot was the used to assess root development. Roots were\nextracted following the root washing method of De Baets et al. (2007). To determine the root mass density (RMD), roots had to\nbe oven-dried at 65 \u0005C for 24 h. Dry root mass (MD (kg)) was then\ndivided by the volume of the soil sample (V (m3)) (De Baets et al.,\n2007) to obtain RMD. 2.5. Grassland seed mixture 2.7. Laboratory analyses In accordance with BS 3882:2015 (BSI, 2015), the texture of the\ntop-soil derived from Blashford Quarry used in the pot experiment\nis classified as a silt loam. With a clay content of 17.9%, soil pH of\n5.7e6.7 and OM of 2.97% the top-soil is defined as a low fertility\ntop-soil (BSI, 2015) (Table 2; Table 4). At termination, the soil was carefully extruded intact from the\npots a cut in half using a palette knife to visually asses root Table 1\nTarmac's standard grassland seed mixture. Common name\nVariety\nScientific name\n%\nPerennial ryegrass\nTemprano\n(Lolium perenne L.)\n32\nPerennial ryegrass\nElital\n(Lolium perenne L.)\n29\nTimothy\nAlma\n(Phleum pratense L.)\n7\nSmooth stalk meadow grass\nPanduro\n(Poa pratensis L.)\n29\nCreeping red fescue\nReport strong\n(Festuca rubra L.)\n3 2.4. Mustard Mustard can be sown from March to September (Rosenfeld and\nRayns, 2011). It prefers fertile, loamy, well drained soils and does\nnot tolerate waterlogging and dry sandy soils (Oplinger et al., 1991). Seeding rates for mustard vary from 10 kg ha\u00041 (Bodner et al., 2010)\nup to 20 kg ha\u00041 (Rosenfeld and Rayns, 2011). A commercially\nadopted seeding rate of 20 kg ha\u00041 was used in this study. Mustard\nseedlings emerge rapidly but continue to grow slowly thereafter. It L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 60 3.2.1. Available N Cover crops significantly influenced the amount of nitrate in\nboth TS and SS, and available N in TS. Different SS blends only had Fig. 1. Visual assessment of mustard root development (T3 (50:50), BD 1.5). Marked correlations are significant at p < 0.05. Table 4 Spearman correlation coefficients between key variables. RMD (kg m\u00043) is for root\nmass density, OM (%) is organic matter, EC (mS cm\u00041) is electrical conductivity, pH is\nsoil acidity, TS stands for topsoil and SS for subsoil. The most significant dependence was found for the TS:SS ratio\n(Table 6). Highest ratios, which indicate uneven root distribution,\nwere observed on mustard treatments. The lowest values for TS:SS\nratio were obtained on rye. RMD (kg\nm\u00043)\nOM (%)\nEC (mS cm\u00041)\nSoil pH\nTS:SS\nTS\nSS\nTS\nSS\nTS\nSS\nTS\nSS\nRMD TS\nRMD SS\n0.82\nOM TS\n\u00040.02\n0.02\nOM SS\n0.00\n\u00040.07\n0.76\nEC TS\n\u00040.17\n\u00040.18\n\u00040.22\n\u00040.33\nEC SS\n0.16\n0.29\n\u00040.56\n\u00040.78\n\u00040.04\npH TS\n0.29\n0.31\n0.37\n0.19\n\u00040.40\n\u00040.55\npH SS\n\u00040.20\n\u00040.13\n\u00040.19\n\u00040.52\n0.17\n0.25\n\u00040.06\nTS:SS\n\u00040.54\n\u00040.89\n\u00040.17\n0.01\n\u00040.01\n\u00040.25\n\u00040.34\n0.13\nBD\n\u00040.04\n\u00040.10\n0.03\n\u00040.02\n0.27\n0.32\n0.36\n\u00040.03\n0.10\nMarked correlations are significant at p < 0.05. Table 2\nMean (n of significant relationships was the SS blend. Root mass densities\nwere most affected by type of cover crop (CC) (Table 5). The RMD of\nSS was also significantly affected by BD. Further, the TS:SS RMD\nratio was significantly affected by CC type. Table 2\nMean (n ¼ 4) particle size distribution (PSD) of blended sub-soil treatments. Sand - 0.6 mm\n- 0.063 mm (%)\nSilt - 0.063 mm\n- 0.002 mm (%)\nClay <0.002\nmm (%)\nTop-soil\n6.66 (±0.90)\n75.4 (±0.66)\n17.9 (±0.49)\nT1\n5.39 (±0.62)\n33.7 (±0.73)\n61.0 (±0.92)\nT2\n6.26 (±0.95)\n46.5 (±0.93)\n47.3 (±0.98)\nT3\n5.08 (±1.01)\n55.1 (±1.26)\n39.8 (±0.75)\nT1 ¼ Sub-soil blend with 100% silt; T2 ¼ 70% silt and 30% overburden; T3 ¼ 50% silt\nand 50% overburden. Values in parentheses indicated ±1 SE. Table 2\nMean (n ¼ 4) particle size distribution (PSD) of blended sub-soil treatments. Correlation coefficients shown in the Table 4 indicate, that there\nis a high correlation between RMD TS/RMD SS and the TS:SS ratio. Also OM TS/SS correlates with EC SS, OM TS correlates with OM SS\nand pH SS correlates with OM SS. Sub-soil blend (quarry silt:overburden ratio) had a significant\neffect on all of the metrics measured. RMD of SS was significantly\nhigher\nin\nSS\nblend\nT2\n(0.1 kg m\u00043)\nas\ncompared\nwith\nT1\n(0.06 kg m\u00043) and T3 (0.06 kg m\u00043), which had comparable values\n(Table 4). 3.2. Soil-root interaction To quantify the root distribution between substrate layers,\nvalues for RMD were used to create a top-soil:sub-soil (TS:SS) ratio. To quantify the root distribution between substrate layers,\nvalues for RMD were used to create a top-soil:sub-soil (TS:SS) ratio. Low TS:SS values represent a balanced root distribution between\nthe TS and SS, high TS:SS ratio values correspond to few or no roots\nfound within the SS layer, hence root mass being mostly restricted\nto the TS layer. Low TS:SS values represent a balanced root distribution between\nthe TS and SS, high TS:SS ratio values correspond to few or no roots\nfound within the SS layer, hence root mass being mostly restricted\nto the TS layer. y\nSignificant relationships between soil and root properties are\nshown in Table 3. The categorical variable with the largest number Fig. 1. Visual assessment of mustard root development (T3 (50:50), BD 1.5). Table 3 Categorical significant responses for all three variables and their combinations. RMD\n(kg m¡3) is for root mass desity, OM (%) is organic matter, EC (mS cm\u00041) is electrical\nconductivity, pH is soil acidity, TS stands for topsoil and SS for subsoil. Cover crop significantly (p \u0006 0.001) influenced RMD in both the\nTS and SS layers (Table 3). A balanced root distribution (TS:SS) was\nnoted\nfor\nrye\ntreatments,\nfollowed\nby\nthe\ngrassland\nmix. Conversely, a significantly lower TS:SS was observed for the\nmustard cover crop treatments (Table 5). This corresponds with the\nvisual assessment of pots where in most cases, mustard roots did\nnot penetrate into the SS layer (Fig. 4). Bulk density significantly\ninfluenced the RMD of the SS (Table 5). RMD (kg\nm\u00043)\nOM (%)\nEC (mS\ncm\u00041)\nSoil pH\nTS:SS\nTS\nSS\nTS\nSS\nTS\nSS\nTS\nSS\nSub-soil blend\n**\n***\n***\n**\n***\nBD\n***\n*\nCC\n***\n***\n**\n***\n***\nBD*CC\n*\n**\n*\nSub-soil blend*BD*CC\n***\nMean values significant at *p \u0006 0.05, **p \u0006 0.01, ***p \u0006 0.001. The combination of CC and BD variables significantly influenced\nRMD of both TS and SS, which is reflected in the TS:SS (Table 6). Mustard had in general significantly lower RMDs as compared with\nrye and grassland cover crop treatments (Table 6). High BD\n(1.5 g cm\u00043) of the SS was associated with increased RMD of TS in\npots with mustard and rye as compared to the low BD treatments\n(1.3 g cm\u00043). High BD (1.5 g cm\u00043) of the SS in grassland mixture\ntreatments was conversely followed by decrease in RMD of TS. Table 1 In accordance with BS 2601:2013 (BSI, 2013), the texture of the\nT1 (100:0) sub-soil blend corresponds to a clay, while both the T2\n(70:30) and T3 (50:50) sub-soil blends are defined a s a silty clay. T1\nand T3 blends are, with pH values of 5.4e8.5 slightly below re-\nquirements (5.5e8.5) for multipurpose sub-soil (Table 4). The T2\nsub-soil blend with a pH of 7.9e8.0 falls within the calcareous sub-\nsoil category. L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 61 Within the same column values followed by the same letter(s) are not significantly different following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses\nindicated ±1 SE. Table 5 grassland mixture showed only minor signs of nutrient deficiency. At the time of termination of the pot trial, mustard plants were fully\nexhausted (Fig. 2). Fig. 3. Mustard plant showing N deficiency signs e stunned growth and chlorosis on\nolder leaves (27 days after sowing) (left) and possible P deficiency signs e purple\npetioles (35 days after sowing) (right) (Berry, 2006; Kumar and Sharma, 2013). 3.3. Plant response In general, roots avoided the sub-soil layer by growing in the\nspace between the soil and the pot. Mustard roots were almost\nalways unable to penetrate into the sub-soil (Fig. 1). 4.1. Cover crop treatment response an effect on the ammonium content (Table 7). In general, mustard\ntreatments were associated with significantly higher amounts of\navailable N in top-soil as compared to rye and grass mixture\ntreatments. Sub-soil blend T1 had the highest amounts of ammo-\nnium\nas\ncompared\nwith\nT2\nand\nT3\nirrespective\nof\nCC\ntreatment(Table 7). Cover crops are used as a temporary measure to facilitate the\nstabilisation and recover of soils and hydrology post restoration\n(BWSR, 2012). In a restoration context, a soil profile is re-created\nusing materials, which might have been kept under anaerobic\nconditions for years, such as quarry silts. Essential first steps for\neffective rehabilitation of restored soil profiles are improving the\nsoil structure and enhancing hydrological and gaseous connectivity\nbetween soil horizons. Planting a mixture of species can be ad-\nvantageous to ensure soil cover and increase organic matter\nthroughout the profile due to different root systems architectures\n(BWSR, 2012; Cresswell and Kirkegaard, 1995). Cover crops influ-\nence soil properties through the decomposition of crop residues\n(Radicetti et al., 2016). If used correctly, they can enhance soil\nproperties by capturing, fixing and recycling nutrients, increase\nSOM, improve soil structure, enhance soil microbiology, mitigate N-\nleaching and protect soil from erosion (Bodner et al., 2010). Table 5 Table 5\nMean (n ¼ 18) significant root mass densities (RMD, kg m\u00043) and soil physico-chemical characteristics between blended treatments. OM (%) is organic matter, EC (mS cm\u00041) is\nelectrical conductivity, pH is soil acidity, TS stands for topsoil and SS for subsoil. Table 5\nMean (n ¼ 18) significant root mass densities (RMD, kg m\u00043) and soil physico-chemical characteristics between blended treatments. OM (%) is organic matter, EC (mS cm\u00041) is\nelectrical conductivity, pH is soil acidity, TS stands for topsoil and SS for subsoil. RMD e SS (kg m\u00043)\nOM - SS (%)\npH - SS\nEC e TS (mS cm\u00041)\nEC e SS (mS cm\u00041)\nT1\n0.06a (±0.014.5)\n4.37b (±0.31)\n5.7b (±0.16)\n8.86a (±0.84)\n19.1a (±0.96)\nT2\n0.1b (±21.1)\n3.80ab (±0.31)\n8.0a (±0.01)\n10.3ab (±1.27)\n27.8a (±1.65)\nT3\n0.06a (±18.4)\n3.15a (±0.35)\n7.9a (±0.16)\n13.8b (±1.70)\n21.3b (±2.16)\nWithin the same column values followed by the same letter(s) are not significantly different following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses\nindicated ±1 SE. Mean (n ¼ 18) significant root mass densities (RMD, kg m\u00043) and soil physico-chemical characteristics between blended treatments\nelectrical conductivity, pH is soil acidity, TS stands for topsoil and SS for subsoil. MD, kg m\u00043) and soil physico-chemical characteristics between blended treatments. OM (%) is organic matter, EC (mS cm\u00041) is\nnds for topsoil and SS for subsoil. RMD e SS (kg m\u00043)\nOM - SS (%)\npH - SS\nEC e TS (mS cm\u00041)\nEC e SS (mS cm\u00041)\nT1\n0.06a (±0.014.5)\n4.37b (±0.31)\n5.7b (±0.16)\n8.86a (±0.84)\n19.1a (±0.96)\nT2\n0.1b (±21.1)\n3.80ab (±0.31)\n8.0a (±0.01)\n10.3ab (±1.27)\n27.8a (±1.65)\nT3\n0.06a (±18.4)\n3.15a (±0.35)\n7.9a (±0.16)\n13.8b (±1.70)\n21.3b (±2.16) L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 62 Fig. 2. Effects of nutrient deficiency on mustard plants 36 days (left) and 47 days\n(right) after sowing. Fig. 4. Mustard leaf showing possible K-deficiency symptoms (35 days after sowing)\n(Kumar and Sharma, 2013). Fig. 2. Effects of nutrient deficiency on mustard plants 36 days (left) and 47 days\n(right) after sowing. Fig. 3. Mustard plant showing N deficiency signs e stunned growth and chlorosis on\nolder leaves (27 days after sowing) (left) and possible P deficiency signs e purple\npetioles (35 days after sowing) (right) (Berry, 2006; Kumar and Sharma, 2013). Fig. 4. Mustard leaf showing possible K-deficiency symptoms (35 days after sowing)\n(Kumar and Sharma, 2013). Table 7 Another advantage of a rye-legume mixture is that rye holds\nN while improving soil structure and legumes fix N, making some\nof it available for rye (Kammermeyer, 2016). Rye can also be useful\nin restoration projects taking place in the autumn, as late seeding is\nrequired, owing to its ability to germinate at low temperatures and\nproduce sufficient soil cover for the winter (AGRAVIS, 2017; CEMEX,\n2014). root length and root anatomy of 7-day old cereals. Materechera\net al. (1991) grew seedlings of twenty-two plant species for 10\ndays and observed that soil compaction reduced root elongation by\n90% while increasing root diameters. Strongly compacted soils are\nusually only penetrated by roots through cracks and/or pre-existing\nbiopores (Gła̧b, 2008). This may in large part explain the RMD re-\nsults observed for rye treatments in this study. Nevertheless, it is\nimportant to note that in this pot study, rye roots avoided pene-\ntrating the SS mainly by growing through the macro-pore space at\nthe soil-pot interface. Evidence suggest that yields of some grasses\nmight be unaffected by compaction (Gła̧b, 2013, 2008). Vallance\nand Sonogan (1995) stated that fibrous roots of rye grow espe-\ncially well in the first 30 cm of soil, however, Chen and Weil (2010)\nclaim that rye roots are strongly affected by soil compaction. Scholefield and Hall (1985) claim that the ability of grasses to\npenetrate highly compacted soils by becoming constricted can be\nconsidered as a compensation of radial pressure. Growing rye may\nhowever be considered in mixtures with other grass species, or\nlegumes. According to Clark (2007), a rye-legume mixture is able to\nadjust to different N levels, meaning that in soils rich on N, rye\ntends to grow better while in soils poor on N, the legume grows\nbetter. Another advantage of a rye-legume mixture is that rye holds\nN while improving soil structure and legumes fix N, making some\nof it available for rye (Kammermeyer, 2016). Rye can also be useful\nin restoration projects taking place in the autumn, as late seeding is\nrequired, owing to its ability to germinate at low temperatures and\nproduce sufficient soil cover for the winter (AGRAVIS, 2017; CEMEX,\n2014). Adaptation for local environmental conditions and suitability\nfor the specific agro-ecological target are however essential\n(Bodner et al., 2010). Materechera et al. Table 7 (1991) have observed, that\nroots of larger diameters such as taproots of dicotyledonous plants\npenetrated soil more than those with smaller diameters. Perkons\net al. (2014) also found, that tap-root plant species create larger\nbiopores thus allow subsequent crop roots to penetrate to deeper\nsoil layers. Yu et al. (2016) claim, that especially for annual plants,\nroot thickness is very important for improving soil structure. Nonetheless, Cresswell and Kirkegaard (1995) suggest that tap\nrooted annual crops are unlikely to improve porosity of deeper,\ncompacted soil horizons. At the higher BD (1.5 g cm\u00043) of SS blends, RMD of rye in the TS\nincreased, with a corresponding decrease in RMD in the SS. This\ncould be explained by the inability of rye to penetrate into the\ncompacted SS, hence the root mass remained limited to the TS\nlayer. Root growth rate is minimally affected by BDs below\n1.4 g cm\u00043, however, values above together with the absence of pre-\nexisting biopores considerably decreases root elongation rate\n(Gaiser et al., 2013). Contrary to this, the TS:SS ratio of rye was\nsignificantly lower (low TS:SS ratio represents even root distribu-\ntion throughout the pot) as compared with mustard, which can be\nexplained by a proportion of the rye roots growing in the space\nbetween the pot and the soil, distorting the RMD ratio. 3.4. Nutrient deficiency Signs of N-deficiency were assessed by visual analysis against\nimages in Berry (2006), visible on mustard plants three weeks after\nsowing (Fig. 3). Four weeks into the experiment all mustard plants\nexhibited significant visible signs of N as well as potential phos-\nphorus (P) and potassium (K) deficiencies (Berry, 2006; Kumar and\nSharma, 2013), (Fig. 4). At four weeks, rye also started displaying N\nnutrient deficiency symptoms through yellowing leaf tips, the Cover crops encourage soil aggregation indirectly via root de-\nposits which provide energy and nutrient sources for soil biota\n(White and Kirkegaard, 2010). These biota improve the architecture\nof the soil by mechanisms including adhesion, kinetic restructuring\nand filamentous binding (Miransari, 2014). Herrera et al. (2017) also L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 63 Table 6\nEffect of cover crop treatment and subsoil blend bulk density (BD) on topsoil (TS) and subsoil (SS) root mass densities (RMDs) and topsoil:subsoil ratio (TS:SS ratio). COVER CROP\nBD (g cm\u00043)\nRMD e TS (kg m\u00043)\nRMD e SS (kg m\u00043)\nTS:SS\nGrassland\nBD 1.3\n0.76bc (±121)\n0.08c (±10.7)\n10.5a (±1.76)\nGrassland\nBD 1.5\n0.56b (±70.3)\n0.04b (±5.55)\n18.5ab (±5.43)\nMustard\nBD 1.3\n0.17a (±22.7)\n0.01a (±1.05)\n45.9c (±9.00)\nMustard\nBD 1.5\n0.21a (±30.8)\n0.01ab (±5.51)\n29.8b (±5.55)\nRye\nBD 1.3\n0.86c (±82.9)\n0.19e (±24.6)\n5.24a (±1.57)\nRye\nBD 1.5\n1.13d (±169)\n0.14d (±14.3)\n8.94a (±1.90)\nWithin the same column values followed by the same letter(s) are not significantly different following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses\nindicated ±1 SE. Table 6\nEffect of cover crop treatment and subsoil blend bulk density (BD) on topsoil (TS) and subsoil (SS) root mass densities (RMDs) and topsoil:subsoil ratio (TS:SS ratio). COVER CROP\nBD (g cm\u00043)\nRMD e TS (kg m\u00043)\nRMD e SS (kg m\u00043)\nTS:SS\nGrassland\nBD 1.3\n0.76bc (±121)\n0.08c (±10.7)\n10.5a (±1.76)\nGrassland\nBD 1.5\n0.56b (±70.3)\n0.04b (±5.55)\n18.5ab (±5.43)\nMustard\nBD 1.3\n0.17a (±22.7)\n0.01a (±1.05)\n45.9c (±9.00)\nMustard\nBD 1.5\n0.21a (±30.8)\n0.01ab (±5.51)\n29.8b (±5.55)\nRye\nBD 1.3\n0.86c (±82.9)\n0.19e (±24.6)\n5.24a (±1.57)\nRye\nBD 1.5\n1.13d (±169)\n0.14d (±14.3)\n8.94a (±1.90)\nWithin the same column values followed by the same letter(s) are not significantly different following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses\nindicated ±1 SE. Table 7\nSoil N values, significantly dependent (p \u0006 0.05) on CC and sub-soil blends. Table 7 a The amount of soil N as kg ha\u00041 has been estimated assuming the standard Tarmac TS depth of 0.3 m for soil N profiling; Within the same column values followed by the\nsame letter(s) are not significantly different (p \u0006 0.05) following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses indicated ±1 SE. a The amount of soil N as kg ha\u00041 has been estimated assuming the standard Tarmac TS depth of 0.3 m for soil N profiling; W\nsame letter(s) are not significantly different (p \u0006 0.05) following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in observed that the choice of CC influences the C and N input into the\nsoil via root decomposition dynamics and variable root biomass\nproduction. Brennan and Acosta-Martinez (2017), observed that\nfrequent cover cropping can have more significant beneficial im-\npacts on soil microbiology than using compost. root length and root anatomy of 7-day old cereals. Materechera\net al. (1991) grew seedlings of twenty-two plant species for 10\ndays and observed that soil compaction reduced root elongation by\n90% while increasing root diameters. Strongly compacted soils are\nusually only penetrated by roots through cracks and/or pre-existing\nbiopores (Gła̧b, 2008). This may in large part explain the RMD re-\nsults observed for rye treatments in this study. Nevertheless, it is\nimportant to note that in this pot study, rye roots avoided pene-\ntrating the SS mainly by growing through the macro-pore space at\nthe soil-pot interface. Evidence suggest that yields of some grasses\nmight be unaffected by compaction (Gła̧b, 2013, 2008). Vallance\nand Sonogan (1995) stated that fibrous roots of rye grow espe-\ncially well in the first 30 cm of soil, however, Chen and Weil (2010)\nclaim that rye roots are strongly affected by soil compaction. Scholefield and Hall (1985) claim that the ability of grasses to\npenetrate highly compacted soils by becoming constricted can be\nconsidered as a compensation of radial pressure. Growing rye may\nhowever be considered in mixtures with other grass species, or\nlegumes. According to Clark (2007), a rye-legume mixture is able to\nadjust to different N levels, meaning that in soils rich on N, rye\ntends to grow better while in soils poor on N, the legume grows\nbetter. 3.4. Nutrient deficiency CC\nNitrate N (þ) (mg kg\u00041)\nAvailable N (þ) 30 cm profilea (kg N ha\u00041)\nSub-soil blend\nAmmonium (þ) (mg kg\u00041)\nTS\nSS\nTS\nSS\nGrassland\n0.58a (±0.50)\n0.19a (±0.00)\n5.22a (±1.82)\nT1\n0.90b (±0.05)\nRye\n1.56a (±0.35)\n0.07a (±0.10)\n8.12a (±1.44)\nT2\n0.50a (±0.15)\nMustard\n5.85b (±0.11)\n0.62b (±0.08)\n24.5b (±0.44)\nT3\n0.51a (±0.07)\na The amount of soil N as kg ha\u00041 has been estimated assuming the standard Tarmac TS depth of 0.3 m for soil N profiling; Within the same column values followed by the\nsame letter(s) are not significantly different (p \u0006 0.05) following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses indicated ±1 SE. Table 6 Table 7\nSoil N values, significantly dependent (p \u0006 0.05) on CC and sub-soil blends. CC\nNitrate N (þ) (mg kg\u00041)\nAvailable N (þ) 30 cm profilea (kg N ha\u00041)\nSub-soil blend\nAmmonium (þ) (mg kg\u00041)\nTS\nSS\nTS\nSS\nGrassland\n0.58a (±0.50)\n0.19a (±0.00)\n5.22a (±1.82)\nT1\n0.90b (±0.05)\nRye\n1.56a (±0.35)\n0.07a (±0.10)\n8.12a (±1.44)\nT2\n0.50a (±0.15)\nMustard\n5.85b (±0.11)\n0.62b (±0.08)\n24.5b (±0.44)\nT3\n0.51a (±0.07)\na The amount of soil N as kg ha\u00041 has been estimated assuming the standard Tarmac TS depth of 0.3 m for soil N profiling; Within the same column values followed by the\nsame letter(s) are not significantly different (p \u0006 0.05) following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses indicated ±1 SE. 5. Conclusions EC values for the T1-T3 treatments varied between 9 and\n28 mS cm\u00041, which is classified as non-saline and is typical for\nnormal surface soils (Hazelton and Murphy, 2007). To accelerate\nthe process of silt-water separation within silt lagoons, some\nquarries choose to use anionic flocculants such as iron (Fe) and\naluminium (Al) salts to accelerate water and silt separation. This\ncould influence EC values of quarry silt as well as be one of possible\ncauses of highly restricted mustard root development. Testing silt\nfor flocculants or other potentially phytotoxic elements is therefore\nrecommended. Across all cover crop types, the best preforming sub-soil blend\nwas the T2 (70:30) treatment in terms of significantly higher RMD\nin the sub-soil. Mustard with tap roots performed poorly in com-\nparison to the rye and grassland mix treatments which are asso-\nciate\nwith\ndense\nfine\nroots. Therefore,\nmustard\ncannot\nbe\nrecommended as a suitable cover crop for restoration projects\nwhere quarry silt is used in a blended sub-soil medium. Both the\ngrassland mixture and winter rye had significantly better perfor-\nmance, as compared to mustard with a different root type. It can be\nsuggested that improving top-soil/sub-soil connectivity could be\nachieved if rye and grasses were grown together in a mix, or in\nconjunction with legume species to facilitate successful biological\nand hydrological connectivity in restored soils. The results indicate\nthat quarry silt can be used for this purpose, nevertheless, due to its\nhigh clay content, blending quarry silt with overburden, or PAS 100\norganic compost is highly advisable. Soil pH may be used as an indicator for suitability for specific\ngrass or crop species (Hazelton and Murphy, 2007). Baize (1993)\nsuggests that optimum pH should be between 6.5 and 7.5. As\nsub-soil blends T2 and T3 resulted in a pH typical for alkaline soils\n(7.9 and 8.0, respectively), this should be approached with caution. Soil pH above 7 reduces bioavailability of trace metals such as Cu,\nZn and Ni, (Han, 2007). Nevertheless, according to Hazelton and\nMurphy (2007), pH values of the T1-T3 SS blends and TS used in\nthis study should not affect availability of N, P, K, S, Ca, or Mg as they\nwere always >5.0 and < 8.5, with the exception of availability of Fe\nbeing reduced in pH < 7.5, which applies for both T2 and T3. Acknowledgements The authors would like to express their gratitude and thanks to\nTarmac Ltd., for providing the funding and study materials. 4.3. Nutrient deficiency associated with experimental treatments N, P and K, also known as primary nutrients, are essential\nmacronutrients promoting growth, energy storage and higher\nplants cell wall strength (Kumar and Sharma, 2013). In restored\nsoils blended with quarry non-commercial by-product, a lack of\nnutrients should be expected (Mitchell et al., 2004). N-deficiency\nwas visible on mustard plants as early as 3 weeks into growth. The\nlack of N was noticeable through retarded growth and leaf symp-\ntoms. These symptoms were first observed in older leaves owing to\ntranslocation of N through the plant to younger tissues, leaving\nlower leaves yellow chlorotic and in later stages necrotic (Kumar\nand Sharma, 2013). This nutrient deficiency was aggravated by\nbuds being visible at week four. Typically in mustards, buds are\nusually visible after 5 weeks and flowers appear 7e10 days later\n(Oplinger et al., 1991). Early flowering of mustard results in short\nlived preservation of accumulated N, as stated by Herrera and\nLiedgens\n(2009). According\nto\nRosenfeld\nand\nRayns\n(2011),\nmustard will start to flower once its canopy reaches 0.5e0.7 m of\nheight and continues to grow even after that, exceeding 1 m. In this\nstudy, the average height of mustard plants in bloom was only\n0.38 m as a result of stunted growth induced by lack of essential\nnutrients. According to (Kumar and Sharma, 2013), lack of N is\nlikely to occur in waterlogged conditions, and soils with pH < 6.0 or\npH > 8.0. Most plants absorb N as ammonium (NH4þ) or nitrate\n(NO3\u0004), which is also soluble in water and therefore easily leachable\n(Hosier and Bradley, 1999). Laboratory results showed that pots\ntreated with mustard had significantly higher NO3\u0004 concentrations\nin both TS and SS as compared with other CC treatments. This\nsuggests that mustard is not effective in scavenging nutrients due\nto its root structure lacking fine roots. Phosphorus P deficiencies on\nmustard plants were also visible across all blended treatments as\npurple petioles, dwarfed plants (P promotes root development) and\nmarginal and interveinal chlorosis (Berry, 2006; Kumar and\nSharma, 2013). 4.2. Growing media characteristics Soil compaction does not only increase BD, resulting in greater\nmass per volume, it also changes soil properties, such as water\nretention, hydraulic conductivity, nutrient transport and uptake, N\nmineralization, soil gases movement etc. (Guaman et al., 2016;\nLipiec et al., 2003; Miransari et al., 2009; Wolkowski and Lowery,\n2008). Most importantly, soil compaction may alter root penetra-\ntion between restored soil layers, or even limit root growth to the\nTS only, thereby considerably reducing water and nutrient avail-\nability to plants, resulting in plant growth reduction (Lipiec et al.,\n2003; Miransari et al., 2009; Pabin et al., 2003; Wolkowski and\nLowery, 2008). According to results of the PSD, quarry silt contains a large\nproportion of clay sized particles. Clays tend to be chemically and\nphysically active, which means that their ability to hold water and\nnutrients is increased (Hazelton and Murphy, 2007). High clay\ncontent however increases susceptibility to compaction (Frost,\n1988). Critical BDs, which are likely to severely affect plant growth and\nroot penetration, are different for different soil textures. For clay\nloam and clay soils, the critical values are >1.6 and > 1.4 g cm\u00043\n(Hazelton and Murphy, 2007). This may in large part explain the\nobservation that for blends T1, T2 and T3, the higher SS BD Lipiec et al. (2012) observed that soil compaction (Soil pene-\ntration resistance exceeding 2 MPa at field capacity) directly affects L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 64 significantly reduced RMD of rye. significantly reduced RMD of rye. used as sub-soil media. Results from the research project ‘Minerals\nfrom Waste’ suggest that quarry non-commercial by-products can\nbe successfully used; especially if mixed with a green waste\ncompost in order to prevent any possible nutrient depletion and\nimprove the initial soil structure (Mitchell et al., 2004). Quarry silt from Blashford Quarry contained not only fine par-\nticles, but also a coarse fraction of cobbles and boulders (>63 mm),\nwhich is not uncommon for a quarry silt (Harrison et al., 2001). Under field conditions, this may positively influence root penetra-\ntion by creating macro pores and voids within the substrate. References AGRAVIS, 2017. Winter Rye (Secale Cereale) [WWW Document]. URL. https://www. agravis.de/en/pflanzen/saatgut/getreide/winterroggen/index.html\n(accessed\n7.14.18). i\n1993 S il S i\nA\nl\nG id\nC\nil\nS Baize, D., 1993. Soil Science Analyses - a Guide to Current Use. Wiley, Surrey. Berry, W., 2006. Symptoms of deficiency in essential minerals. In: Taiz, L., Zeiger, E ,\n,\ny\ny,\ny\nBerry, W., 2006. Symptoms of deficiency in essential minerals. In: Taiz, L., Zeiger, E.,\nMøller, I.M., Murphy, A. (Eds.), Plant Physiology and Development. Sinauer\nAssociates, Massachusetts. y\ny\np\ny\ng\nMøller, I.M., Murphy, A. (Eds.), Plant Physiology and Development. Sinauer\nAssociates, Massachusetts. Bj€orkman, T., Shail, J.W., 2014. Cornell Cover Crop Guide for Rye, Ver. 1.080324. Cornell University. Bodner, G., Himmelbauer, M., Loiskandl, W., Kaul, H.-P., 2010. Improved evaluation\nof cover crop species by growth and root factors. Agron. Sustain. Dev. 30,\n455e464. https://doi.org/10.1051/agro/2009029. Brennan, E.B., Acosta-Martinez, V., 2017. Cover cropping frequency is the main\ndriver of soil microbial changes during six years of organic vegetable produc-\ntion. Soil Biol. Biochem. 109, 188e204. https://doi.org/10.1016/j.soilbio.2017.01. 014. British\nGeological\nSurvey,\n2013. Construction\nAggregates. Mineral\nPlanning\nFactsheet. BSI, 2013. BS 8601:2013 Specification for Subsoil and Requirements for Use. BSI\nStandards Limited 2013. BSI, 2015. BS 3882:2015 Specification for Topsoil. BSI Standards Limited 2015. BWSR, 2012. Planting Temporary Cover Crops - Technical Guidance Document. Casey, A.P., 2012. Plant Guide for Cereal Rye (Secale Cereale). USDA-Natural Re-\nsources Conservation Service, Elsberry. CEMEX, 2014. East Leake Quarry Landscaping. Restoration CEMEX, 2014. East Leake Quarry Landscaping. Restoration and Aftercare. Chen, G., Weil, R.R., 2010. Penetration of cover crop roots through compacted soils. Plant Soil 331, 31e43. https://doi.org/10.1007/s11104-009-0223-7. Clark, A., 2007. Managing cover crops profitably. In: Handbook Series. Sustainable\nAgriculture Research and Education (SARE), third ed. https://doi.org/10.1017/\nCBO9781107415324.004 Cresswell, H.P., Hamilton, G.J., 2002. Bulk density and pore space relations. In:\nMcKenzie, N.J., Cresswell, H.P., Coughlan, K.J. (Eds.), Soil Physical Measurement\nand\nInterpretation\nfor\nLand\nEvaluation. CSIRO\nPublishing,\nCollingwood,\npp. 35e58. Cresswell, H.P., Kirkegaard, J.A., 1995. Subsoil amelioration by plant rootsdthe\nprocess and the evidence. Aust. J. Soil Res. https://doi.org/10.1071/SR9950221. id\nh\nl\ni\nf\ni\nl\ni\ni\nl\nki\nd DCLG, 2014. Guidance on the Planning for Mineral Extraction in Plan Making and\nthe\nApplication\nProcess\n[WWW\nDocument]. URL. https://www.gov.uk/\nguidance/minerals (accessed 7.21.17). De Baets, S., Poesen, J., Knapen, A., Galindo, P., 2007. Impact of root architecture on\nthe erosion-reducing potential of roots during concentrated flow. Earth Surf. References Harrison, D.J., Bloodworth, A.J., Eyre, J.M., Scott, P.W., MacFarlane, M., 2001. Uti-\nlisation of Mineral Waste: a Scoping Study. Pabin, J., Lipiec, J., Włodek, S., Biskupski, A., 2003. Effect of different tillage systems\nand straw management on some physical properties of soil and on the yield of\nwinter rye in monoculture. Int. Agrophys. 17. Hazelton, P., Murphy, B., 2007. Interpreting Soil Test Results: what Do All the\nNumbers Mean? CSIRO PUBLISHING, Collingwood. Perkons, U., Kautz, T., Uteau, D., Peth, S., Geier, V., Thomas, K., Lutke Holz, K.,\nAthmann, M., Pude, R., Kopke, U., 2014. Root-length densities of various annual\ncrops following crops with contrasting root systems. Soil Tillage Res. 137,\n50e57. https://doi.org/10.1016/j.still.2013.11.005. g\nHerrera, J.M., Liedgens, M., 2009. Leaching and utilization of nitrogen during a\nspring wheat catch crop succession. J. Environ. Qual. 38, 1410. https://doi.org/\n10.2134/jeq2008.0267. Herrera, J.M., Büchi, L., Rubio, G., Torres-Guerrero, C., Wendling, M., Stamp, P.,\nPellet, D., 2017. Root decomposition at high and low N supply throughout a crop\nrotation. Eur. J. Agron. 84, 105e112. https://doi.org/10.1016/j.eja.2016.12.012. Radicetti, E., Mancinelli, R., Moscetti, R., Campiglia, E., 2016. Management of winter\ncover crop residues under different tillage conditions affects nitrogen utiliza-\ntion efficiency and yield of eggplant (Solanum melanogena L.) in Mediterranean\nenvironment. Soil Tillage Res. 155, 329e338. https://doi.org/10.1016/j.still.2015. 09.004. Hosier, S., Bradley, L., 1999. Guide to Symptoms of Plant Nutrient Deficiencies\n[WWW Document]. URL. https://extension.arizona.edu/sites/extension.arizona. edu/files/pubs/az1106.pdf (accessed 7.1.17). Rosenfeld, A., Rayns, F., 2011. Sort Out Your Soil - a Practical Guide to Green Ma-\nnures. COTSWOLD Grass Seeds. Jarvis,\nD.,\nWalton,\nG.,\n2010. Restoration\nof\nAggregate\nQuarry\nLagoons\nfor\nBiodiversity. Scholefield, D., Hall, D.M., 1985. Constricted growth of grass roots through rigid\npores. Plant Soil 85, 153e162. https://doi.org/10.1007/BF02139621. Kammermeyer, K., 2016. Rye-secale Cereale [WWW Document]. URL. https://www. pennington.com/resources/agriculture/wildlife/articles/rye-secale-cereale\n(accessed 7.7.17). Vallance, N., Sonogan, R., 1995. Growing Cereal Rye [WWW Document]. URL. http://\nagriculture.vic.gov.au/agriculture/grains-and-other-crops/crop-production/\ngrowing-cereal-rye (accessed 7.14.17). Kirkegaard, J., Christen, O., Krupinsky, J., Layzell, D., 2008. Break crop benefits in\ntemperate wheat production. Field Crop. Res. 107, 185e195. https://doi.org/10. 1016/j.fcr.2008.02.010. Walnes Seeds, 2017. Grass Seed [WWW Document]. URL. http://www.walnesseeds. com/grass-seed/ (accessed 7.14.17). /j\nKumar, P., Sharma, M.K., 2013. Nutrient Deficiencies of Field Crops: Guide to\nDiagnosis and Management. CABI. White, R.G., Kirkegaard, J.A., 2010. The distribution and abundance of wheat roots in\na dense, structured subsoil - implications for water uptake. Plant Cell Environ. 33, 133e148. https://doi.org/10.1111/j.1365-3040.2009.02059.x. g\ng\nLipiec, J., Arvidsson, J., Murer, E., 2003. References Process Landforms https://doi org/10 1002/esp 1470 The additional of supplementary nutrient sources should be\nconsidered if quarry silt as non-commercial by-products are to be Process. Landforms. https://doi.org/10.1002/esp.1470. Frost, J.P., 1988. Effects on crop yields of machinery traffic and soil loosening Part 1. L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 65 seedling roots of different plant species. Plant Soil 135, 31e41. https://doi.org/\n10.1007/BF00014776. seedling roots of different plant species. Plant Soil 135, 31e41. https://doi.org/\n10.1007/BF00014776. Effects on grass yield of traffic frequency and date of loosening. J. Agric. Eng. Res. 39, 301e312. https://doi.org/10.1016/0021-8634(88)90151-5. Miransari, M., 2014. Plant growth promoting rhizobacteria. J. Plant Nutr. 37,\n2227e2235. https://doi.org/10.1080/01904167.2014.920384. Gaiser, T., Perkons, U., Küpper, P.M., Kautz, T., Uteau-Puschmann, D., Ewert, F.,\nEnders, A., Krauss, G., 2013. Modeling biopore effects on root growth and\nbiomass production on soils with pronounced sub-soil clay accumulation. Ecol. Model. 256, 6e15. https://doi.org/10.1016/j.ecolmodel.2013.02.016. Miransari, M., Bahrami, H.A., Rejali, F., Malakouti, M.J., 2009. Effects of arbuscular\nmycorrhiza, soil sterilization, and soil compaction on wheat (Triticum aestivum\nL.) nutrients uptake. Soil Tillage Res. 104, 48e55. https://doi.org/10.1016/j.still. 2008.11.006. Gła̧b, T., 2008. Effects of tractor wheeling on root morphology and yield of lucerne\n(Medicago sativa L.). Grass Forage Sci. 63, 398e406. https://doi.org/10.1111/j. 1365-2494.2008.00647.x. Mitchell, C., 2007. Quarry Fines and Waste [WWW Document]. URL. http://nora. nerc.ac.uk/6290/1/Quarry_Fines_and_Waste.pdf (accessed 7.21.17). Gła̧b, T., 2013. Impact of soil compaction on root development and yield of\nmeadow-grass. Int. Agrophys. 27, 7e13. https://doi.org/10.2478/v10247-012-\n0062-2. Mitchell, C.J., Harrison, D.J., Robinson, H.L., Ghazireh, N., 2004. Minerals from Waste:\nrecent BGS and Tarmac experience in finding uses for mine and quarry waste. Miner. Eng. 17, 279e284. https://doi.org/10.1016/j.mineng.2003.07.020. Government of Alberta, 2016. Fall Rye Production. Alberta Agriculture and Rural\nDevelopment, Edmonton. Oelke, E.A., Oplinger, E.S., Bahri, H., Durgan, B.R., Putnam, D.H., Doll, J.D.,\nKelling, K.A., 1990. Rye - Alternative Field Crops Manual [WWW Document]. URL. www.hort.purdue.edu/newcrop/afcm/rye.html (accessed 7.7.17). Guaman, V., Båth, B., Hagman, J., Gunnarsson, A., Persson, P., 2016. Short time effects\nof biological and inter-row subsoiling on yield of potatoes grown on a loamy\nsand, and on soil penetration resistance, root growth and nitrogen uptake. Eur. J. Agron. 80, 55e65. https://doi.org/10.1016/j.eja.2016.06.014. Oplinger, E.S., Oelke, E.A., Putnam, D.H., Kelling, K.A., Kaminsid, A.R., Teynor, T.M.,\nDoll, J.D., Durgan, B.R., 1991. Mustard - Alternative Field Crops Manual [WWW\nDocument]. URL. www.hort.purdue.edu/newcrop/afcm/mustard.html (accessed\n7.8.17). Han, F.X., 2007. Biogeochemistry of Trace Elements in Arid Environments. Springer\nScience & Business Media, Netherlands. Cranfield University\nCERES Research Repository\nhttps://dspace.lib.cranfield.ac.uk/\nSchool of Water, Energy and Environment (SWEE)\nStaff publications (SWEE)\nAssessment of silt from sand and gravel\nprocessing as a suitable sub-soil\nmaterial in land restoration: A\nglasshouse study\nMašková, Lucie\n2018-12-01\nAttribution 4.0 International\nMašková L, Simmons RW, De Baets S, et al. (2019) Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil material in land restoration: A glasshouse study.\nChemosphere, Volume 219, March 2019, pp. 58-65\nhttps://doi.org/10.1016/j.chemosphere.2018.11.155\nDownloaded from CERES Research Repository, Cranfield University Cranfield University\nCERES Research Repository Cranfield University\nCERES Research Repository https://dspace.lib.cranfield.ac.uk/ School of Water, Energy and Environment (SWEE) Staff publications (SWEE) Mašková L, Simmons RW, De Baets S, et al. (2019) Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil material in land restoration: A glasshouse study.\nChemosphere, Volume 219, March 2019, pp. 58-65\nhttps://doi.org/10.1016/j.chemosphere.2018.11.155\nDownloaded from CERES Research Repository, Cranfield University References Review of modelling crop growth, movement\nof water and chemicals in relation to topsoil and subsoil compaction. Soil\nTillage Res. 73, 15e29. https://doi.org/10.1016/S0167-1987(03)00096-5. Wolkowski, R., Lowery, B., 2008. Soil Compaction : Causes, Concerns, and Cures. Madison. g\n,\np //\ng/\n/\n(\n)\nLipiec, J., Horn, R., Pietrusiewicz, J., Siczek, A., 2012. Effects of soil compaction on\nroot elongation and anatomy of different cereal plant species. Soil Tillage Res. 121, 74e81. https://doi.org/10.1016/j.still.2012.01.013. MAFF Reference Book RB427, 1986. Method 53 Analysis of Agricultural Materials. Materechera, S.A., Dexter, A.R., Alston, A.M., 1991. Penetration of very strong soils by g\np //\ng/\n/\n(\n)\nLipiec, J., Horn, R., Pietrusiewicz, J., Siczek, A., 2012. Effects of soil compaction on\nroot elongation and anatomy of different cereal plant species. Soil Tillage Res. 121, 74e81. https://doi.org/10.1016/j.still.2012.01.013. Yu, Y., Loiskandl, W., Kaul, H.P., Himmelbauer, M., Wei, W., Chen, L., Bodner, G., 2016. Estimation of runoff mitigation by morphologically different cover crop root\nsystems. J. Hydrol. 538, 667e676. https://doi.org/10.1016/j.jhydrol.2016.04.060. MAFF Reference Book RB427, 1986. Method 53 Analysis of Agricultural Materials. Materechera, S.A., Dexter, A.R., Alston, A.M., 1991. Penetration of very strong soils by Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil\nmaterial in land restoration: A\nglasshouse study Mašková, Lucie\n2018-12-01\nAttribution 4.0 International Mašková, Lucie\n2018-12-01\nAttribution 4.0 International Attribution 4.0 International Mašková L, Simmons RW, De Baets S, et al. (2019) Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil material in land restoration: A glasshouse study. Chemosphere, Volume 219, March 2019, pp. 58-65\nhttps://doi.org/10.1016/j.chemosphere.2018.11.155\nDownloaded from CERES Research Repository, Cranfield University Mašková L, Simmons RW, De Baets S, et al. (2019) Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil material in land restoration: A glasshouse study. Chemosphere, Volume 219, March 2019, pp. 58-65\nhttps://doi.org/10.1016/j.chemosphere.2018.11.155\nDownloaded from CERES Research Repository, Cranfield University"
|
https://openalex.org/W1970043862
|
http://rcin.org.pl/Content/147074/PDF/WA488_182663_19746_s1913.pdf
|
English
| null |
THE EPIGAMIC BEHAVIOUR OF THE TERMITE MICROTERMES SUDAN ENSIS SJST. OBSERVED AT KAGELU, YEI, EQUATORIAL PROV., ANGLO‐EGYPTIAN SUDAN. ECONOMIC IMPORTANCE OF TERMITES TO THE NATIVE AZANDE.
|
Proceedings of the Royal Entomological Society of London. Series A, General Entomology
| 1,938
|
public-domain
| 936
|
THE EPIGAMIC BEHAVIOUR OF THE TERMITE M1CROTERMES
SUDANENSIS SJST. OBSERVED AT KAGELU, YEI, EQUATORIAL
PROV., ANGLO-EGYPTIAN SUDAN. ECONOMIC IMPORTANCE
OF TERMITES TO THE NATIVE AZANDE.
By Dr J
G
M
D S By Dr. J. G. My e r s, D.Sc . [Th e following interesting notes were sent by my friend Dr. Myers, together
with tubes of specimens bearing the locality and the number 6401. All were
kindly named by Mr. F. G. M. Westropp in the Brit. Mus. (Nat. Hist.), where they
were compared with a co-type of Microtermes sudanensis.—E. B. Po u l t o n .] Kagelu, Yei, Equatorial Province, Sudan. 25 June, 1937. I send under separate cover some termites illustrating the habit of biting
the female during courtship. I never saw anything like it in Invertebrates
before. It is mentioned in a recent note in our Proceedings. It is real “ cave
man ” stuff. The following is transcribed from my journal:—
“ K
l
30 M
h
1937
Wi
d
i g
y j
“ Kagelu : 30 March, 1937.—Winged termites at light between 7 and 8
p.m. At least half chasing each other or holding on, with mandibles, to the
tip or side—mostly tip—of the females’ abdomens, like bulldogs : several
males often on one female, each interlocked group being preserved in a separ
ate tube. Some of the males are still maintaining their hold in the alcohol
after being killed with cyanide. Even when completely suspended and
entangled in spiders’ webs males were still fighting for a place at a female’s
side or still hanging on. Sometimes the males were winged and the females
de-alated, or vice versa. In one instance two males were pursuing one female,
trying hard to get a grip, but she always fought violently, even turning complete
somersaults. When I disturbed them by removing the female, they turned
on each other and attacked furiously, each trying to take hold on or near the
mandibles of the other, thus proving that each was not mistaking the other
for a female. Their mandibles clashed like stags’ horns, and one could almost
fancy that the sound was audible. I have made no microscopic examination,
but assumed the sexes from the behaviour. All can be checked, as fighting
and mating sets are all kept separate. There is also included a tubeful col
lected at random for identification.” [The sets of termites received from Dr. Myers were in five tubes andhave been
sexed by Dr. B. M. Hobby. Each tube contained 1 £, the numbers of males
being, 1, 2, 2, 3, 3, respectively. THE EPIGAMIC BEHAVIOUR OF THE TERMITE M1CROTERMES
SUDANENSIS SJST. OBSERVED AT KAGELU, YEI, EQUATORIAL
PROV., ANGLO-EGYPTIAN SUDAN. ECONOMIC IMPORTANCE
OF TERMITES TO THE NATIVE AZANDE.
By Dr J
G
M
D S The random collection contained 7 £<$, 5
one male being mutilated so that its sex was difficult to determine. No tube
contained only males. In these very interesting records Dr. Myers confirms and extends the
observations recorded by Prof. G. D. Hale Carpenter in 1936, Proc. R. ent. Soc. Lond. (A) 11: 93-94 : viz. those of Burtt on an unnamed termite in Tangan
yika Territory; Kofoid; and Fuller on four S. African species. All the observa
tions, including those of Dr. Myers, appear to concern the methods of courtship
alone, and not to include copulation which may perhaps take place underground. —E. B. P.] Incidentally termites of many kinds are immensely important in the
economy of the Azande, among whom I have just been working. One of the
PROC. R. ENT. SOC. LOND. (a ) 13. PTS. 1-3. (MAR. 1938.) r
rcin.org.pl Dr. J. G. Myers on the behaviour of a termite. 8 greatest problems the administration faces with the Azande is diet-deficiency,
especially in animal proteins. For sleeping-sickness control they have all
been concentrated on the roads; so that hunting covers a much smaller area,
and tsetse debars them keeping livestock while the Government prevents them
from eating each other. In these circumstances termites form their chief
animal food and they know far more about the swarming habits, which seem
to be very specific, than any entomologist. They collect them in incredible
quantities. I have tasted them roasted with a little salt’ and they are excellent
—much better than shrimps—entirely free from the cockroachy odour and taste
I somehow expected. In addition to eating the termites themselves they press
out an excellent, odourless yellow oil, which at least in some considerable
sections is the chief cooking fat throughout the year, used far more extensively
than sesame. I am getting some of it analysed officially. Who knows what
potent vitamins it may contain ! In addition to the use of termites as food, the natives consult them as oracles. They take two small sticks of two different kinds of wood and thrust them,
with, the appropriate spells, into an opened gallery of a large termitarium,
but only one built by certain species. According as one or other stick is gnawed
(or both) in the morning the answer to the question put is negative or affirma
tive, or qualified. This is described in minute detail by Evans-Pritchard
in his absorbing and magnificent work, Witchcraft, Oracles and Magic Among the
Azande (Oxford, 1937). (
)
I have collected about 15 species, with Azande names and lore, and sent them
for identification direct to Dr. Snyder, of Washington. I have some other very interesting pinned insects, including a huge Drilid
I am now in the middle of studying, which tackles large snails, 3 inches long
and more, with no subtilty but a direct attack.
|
https://openalex.org/W3015307007
|
https://ri.conicet.gov.ar/bitstream/11336/127198/2/CONICET_Digital_Nro.0e720c21-34ed-4e76-9a33-7af19046746e_A.pdf
|
English
| null |
Efficient Selection of New Immunobiotic Strains With Antiviral Effects in Local and Distal Mucosal Sites by Using Porcine Intestinal Epitheliocytes
|
Frontiers in immunology
| 2,020
|
cc-by
| 13,900
|
ORIGINAL RESEARCH
published: 08 April 2020
doi: 10.3389/fimmu.2020.00543 Efficient Selection of New
Immunobiotic Strains With Antiviral
Effects in Local and Distal Mucosal
Sites by Using Porcine Intestinal
Epitheliocytes Leonardo Albarracin1,2†, Valeria Garcia-Castillo1,3†, Yuki Masumizu2, Yuhki Indo2,
Md Aminul Islam2, Yoshihito Suda4, Apolinaria Garcia-Cancino3, Hisashi Aso5,6,
Hideki Takahashi7,8, Haruki Kitazawa2,6* and Julio Villena1,2* Leonardo Albarracin1,2†, Valeria Garcia-Castillo1,3†, Yuki Masumizu2, Yuhki Indo2,
Md Aminul Islam2, Yoshihito Suda4, Apolinaria Garcia-Cancino3, Hisashi Aso5,6,
Hideki Takahashi7,8, Haruki Kitazawa2,6* and Julio Villena1,2* *Correspondence:
Haruki Kitazawa Previously, we evaluated the effect of the immunobiotic strain Lactobacillus rhamnosus
CRL1505 on the transcriptomic response of porcine intestinal epithelial (PIE) cells
triggered by the challenge with the Toll-like receptor 3 (TLR-3) agonist poly(I:C) and
successfully identified a group of genes that can be used as prospective biomarkers
for the screening of new antiviral immunobiotics. In this work, several strains of
lactobacilli were evaluated according to their ability to modulate the expression of IFNα,
IFNβ, RIG1, TLR3, OAS1, RNASEL, MX2, A20, CXCL5, CCL4, IL-15, SELL, SELE,
EPCAM, PTGS2, PTEGES, and PTGER4 in PIE cells after the stimulation with poly(I:C). Comparative analysis of transcripts variations revealed that one of the studied bacteria,
Lactobacillus plantarum MPL16, clustered together with the CRL1505 strain, indicating
a similar immunomodulatory potential. Two sets of in vivo experiments in Balb/c mice
were performed to evaluate L. plantarum MPL16 immunomodulatory activities. Orally
administered MPL16 prior intraperitoneal injection of poly(I:C) significantly reduced the
levels of the proinflammatory mediators tumor necrosis factor α (TNF-α), interleukin 6
(IL-6), and IL-15 in the intestinal mucosa. In addition, orally administered L. plantarum
MPL16 prior nasal stimulation with poly(I:C) or respiratory syncytial virus infection
significantly decreased the levels of the biochemical markers of lung tissue damage. In addition, reduced levels of the proinflammatory mediators TNF-α, IL-6, and IL-8 were
found in MPL16-treated mice. Improved levels of IFN-β and IFN-γ in the respiratory
mucosa were observed in mice treated with L. plantarum MPL16 when compared to
control mice. The immunological changes induced by L. plantarum MPL16 were not *Correspondence:
Haruki Kitazawa
haruki.kitazawa.c7@tohoku.ac.jp
Julio Villena
jcvillena@cerela.org.ar †These authors have contributed
equally to this work Specialty section:
This article was submitted to
Nutritional Immunology,
a section of the journal
Frontiers in Immunology Received: 30 November 2019
Accepted: 10 March 2020
Published: 08 April 2020 1 Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucuman, Argentina, 2 Food
and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku
University, Sendai, Japan, 3 Laboratory of Bacterial Pathogenicity, Faculty of Biological Sciences, University of Concepción,
Concepción, Chile, 4 Department of Food, Agriculture and Environment, Miyagi University, Sendai, Japan, 5 Cell Biology
Laboratory, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan, 6 Livestock Immunology Unit,
International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural
Science, Tohoku University, Sendai, Japan, 7 Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku
University, Sendai, Japan, 8 Plant Immunology Unit, International Education and Research Centre for Food and Agricultural
Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan Edited by:
Lijuan Yuan,
Virginia Tech, United States Virginia Tech, United States
Reviewed by:
Francisco José Pérez-Cano,
University of Barcelona, Spain
Lei Shi,
Georgia State University,
United States Reviewed by:
Francisco José Pérez-Cano,
University of Barcelona, Spain
Lei Shi, Georgia State University,
United States Georgia State University,
United States INTRODUCTION randomized controlled trial conducted in children younger than
5 years, it was demonstrated that the immunobiotic CRL1505
strain is capable to enhance mucosal immunity and reduced the
incidence and severity of intestinal and respiratory infections (2). Of note, our studies in mice models have clearly shown that
the immunomodulatory capacities of L. rhamnosus CRL1505 are
a strain-specific property because other immunobiotic strains
such as Lactobacillus plantarum CRL1506 can stimulate only the
intestinal immunity after their oral administration (7–10). More than a third of child deaths worldwide are attributed to
malnutrition and its profound impact on the immune system
and the host resistance to infections. In this sense, pneumonia
and diarrhea remain the leading causes of death of children. Together, these two infectious diseases account for 29% of
all deaths of children younger than 5 years and result in
the loss of 2 million young lives annually (1). In 2009, the
World Health Organization (WHO) separately published two
strategies for the control of pneumonia and diarrhea. Since these
strategies were implemented globally, it has been recognized
that pneumonia and diarrhea could be treated more effectively
in a coordinated manner. Thus, WHO-UNICEF published in
2013 an Integrated Global Action Plan for the Prevention
and Control of Pneumonia and Diarrhea (GAPPD), which
proposes a cohesive approach to ending deaths from preventable
pneumonia and diarrhea in children (1). The GAPPD proposes
interventions to create healthy environments, promotes practices
to protect children from infectious diseases, and ensures that
all children have access to appropriate preventive and treatment
measures. The document emphasizes the importance of healthy
nutrition to reduce the incidence and severity of pneumonia and
diarrhea simultaneously. y
(
)
It is well known that intestinal epithelial cells (IECs) had
a central role in determining the type of immune response
triggered by antigens in the intestinal mucosa through their
interactions with immune cells (11, 12). In this regard,
studies have reported that immunomodulatory LAB modulate
intestinal immune responses by regulating the functions of IECs
(13). Therefore, we hypothesized that transcriptomic analysis
evaluating the effect of L. rhamnosus CRL1505 and L. plantarum
CRL1506 on IECs could bring valuable information about
their capacity of modulating the intestinal innate antiviral
immune response, as well as provide some clues about their
differential ability to influence immunity in the respiratory
tract. INTRODUCTION By using porcine intestinal epithelial (PIE) cells that
express the pattern recognition receptor (PRR) Toll-like receptor
3 (TLR-3) and respond to poly(I:C) stimulation (14, 15);
we studied the similarities and differences of L. rhamnosus
CRL1505 and L. plantarum CRL1506 in terms of their ability
to modulate the immunotranscriptomic response of epithelial
cells (16). The transcriptional profiling performed in PIE
cells allowed us to characterize the immune and immune-
related genes involved in their response to TLR3 activation,
which included type I interferons (IFNs), antiviral factors,
cytokines, chemokines, adhesion molecules, enzymes involved in
prostaglandin biosynthesis, PRRs, and negative regulators of the
TLR signaling pathway. In addition, we were able to confirm
that the CRL1505 and CRL1506 strains differently regulated
the immunotranscriptomic response of poly(I:C)-challenged
PIE cells (16). Quantitative and qualitative differences in the
expression of immune and immune-related genes in PIE cells
were found when L. rhamnosus CRL1505 and L. plantarum
CRL1506 treatments were compared. Moreover, the comparative
analysis of the effect of the two strains allowed us to identify a
group of genes that could be used as potential biomarkers for the
efficient selection of new antiviral immunobiotics in PIE cells,
which could beneficially influence both the intestinal and the
respiratory antiviral immunity. Various clinical trials and studies in animal models have
demonstrated the ability of probiotic lactic acid bacteria
(LAB) with immunomodulatory activities, also known as
immunobiotics, to improve the resistance to intestinal viral
infections (2, 3). Although most of the research related to the
beneficial effect of immunobiotics on the host’s immune system
has focused on the stimulation of intestinal immunity to protect
against viral infections (4), it has also been shown that the oral
administration of some immunobiotics strains can beneficially
modulate not only the local intestinal immunity but also immune
responses in distant mucosal sites such as the respiratory tract
(5, 6). Then, it is believed that appropriate immunobiotic
LAB strains can be effectively used as preventive therapies
to improve antiviral defenses and reduce the complications
from the deregulated inflammatory responses in both the
intestine and the respiratory tract. Therefore, the efficient
selection of immunobiotic strains that orally administered
are capable of favorably modulating intestinal and respiratory
antiviral immunity could contribute to reducing the risk of
viral infections, having a simultaneous impact on resistance to
pneumonia and diarrhea. Citation: Albarracin L, Garcia-Castillo V,
Masumizu Y, Indo Y, Islam MA,
Suda Y, Garcia-Cancino A, Aso H,
Takahashi H, Kitazawa H and Villena J
(2020) Efficient Selection of New
Immunobiotic Strains With Antiviral
Effects in Local and Distal Mucosal
Sites by Using Porcine Intestinal
Epitheliocytes. April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 1 Albarracin et al. Selection of Antiviral Immunobiotics in PIE Cells different from those previously reported for the CRL1505 strain in in vitro and in vivo
studies. The results of this work confirm that new immunobiotic strains with the ability of
stimulating both local and distal antiviral immune responses can be efficiently selected
by evaluating the expression of biomarkers in PIE cells. Keywords: porcine intestinal epithelial cells, TLR3, Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum
MPL16, antiviral response, respiratory immunity Keywords: porcine intestinal epithelial cells, TLR3, Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum
MPL16, antiviral response, respiratory immunity Frontiers in Immunology | www.frontiersin.org PIE Cells The PIE cell line was originally derived from intestinal
epithelia isolated from an unsuckled neonatal swine (17). Porcine intestinal epithelial cells are intestinal non-transformed
cultured cells that assume a monolayer with a cobblestone
and
epithelial-like
morphology
and
with
close
contact
between cells during culture (14, 17, 18). Porcine intestinal
epithelial cells were maintained in Dulbecco modified eagle
medium (DMEM) (Invitrogen Corporation, Carlsbad, CA,
United States) supplemented with 10% fetal calf serum,
100 mg/mL streptomycin and 100 U/mL penicillin at 37◦C in an
atmosphere of 5% CO2 (16, 18–20). Microorganisms Lactobacillus rhamnosus CRL1505, L. plantarum CRL1506,
L. rhamnosus CRL576, and L. plantarum CRL681 belong to
CERELA Culture Collection; L. rhamnosus IBL07 belongs to the
Infection Biology Laboratory of IMMCA-CONICET-UNT and
was kindly given by Dr. Vizoso-Pinto. Lactobacillus plantarum
MPL16 belongs to the Food and Feed Immunology Group
Culture Collection, These strains were grown in Man–Rogosa–
Sharpe broth at 37◦C. For the in vitro immunomodulatory assays,
overnight cultures were harvested by centrifugation, washed
three times with sterile phosphate-buffered saline (PBS), counted
in a Petroff–Hausser counting chamber, and resuspended
in DMEM until use. Two sets of experiments were performed in treated and
control mice. In the first set of experiments, mice were challenged
by the intraperitoneal route with 100 µL of PBS containing 30 µg
poly(I:C) according to our previous publication (8). Biochemical
markers of injury as well as intestinal cytokines’ concentrations
were evaluated 2 days after poly(I:C) administration as described
below. In the second set of experiments, mice were lightly
anesthetized, and 100 µL of PBS, containing 250 µg poly(I:C)
(equivalent to 10 mg/kg body weight), was administered via the
nares according to our previous publication (7). Mice received
three doses of poly(I:C) with 24-h rest period between each
administration. INTRODUCTION Lactobacillus rhamnosus CRL1505, orally administered to
mice, is able to differentially modulate both intestinal (7, 8)
and respiratory (9, 10) antiviral immunity. Moreover, in a In this work, we tested this hypothesis by evaluating
the
influence
of
several
immunomodulatory
and
non-
immunomodulatory lactobacilli strains in the expression of April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 2 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. IFNα, IFNβ, RIG1, TLR3, OAS1, RNASEL, MX2, A20, CXCL5,
CCL4, IL-15, SELL, SELE, EPCAM, PTGS2, PTEGES, and
PTGER4 in poly(I:C)-challenged PIE cells and by studying
in vivo the effect of orally administered lactobacilli on the
intestinal and respiratory antiviral innate immune responses. cDNAs according to the manufacturer’s recommendations. Real-
time qPCR was carried out using a 7300 real-time PCR system
(Applied Biosystems, Warrington, United Kingdom) and the
Platinum SYBR green qPCR SuperMix uracil-DNA glycosylase
with 6-carboxyl-X-rhodamine (ROX) (Invitrogen). The primers
used for the study of IFNα, IFNβ, RIG1, TLR3, OAS1, RNASEL,
MX2, A20, CXCL5, CCL4, IL-15, SELL, SELE, EPCAM, PTGS2,
PLA2G4A, PTEGES, and PTGER4 expressions in this study were
described before (16, 20, 21). The PCR cycling conditions were
2 min at 50◦C, followed by 2 min at 95◦C, and then 40 cycles of
15 s at 95◦C, 30 s at 60◦C, and 30 s at 72◦C. The reaction mixtures
contained 5 µL of sample cDNA and 15 µL of master mix,
which included the sense and antisense primers. According to the
minimum information for publication of quantitative real-time
PCR experiments guidelines, β-actin was used as a housekeeping
gene because of its high stability across porcine various tissues
(14, 15, 21). Expression of β-actin was used to normalize cDNA
levels for differences in total cDNA levels in the samples. Animals, Feeding Procedures, and
Poly(I:C) Challenge Male 6-week-old BALB/c mice were obtained from the closed
colony kept at CERELA-CONICET. Animals were housed
in plastic cages in a controlled atmosphere (22◦C ± 2◦C
temperature, 55% ±2% humidity) with a 12-h light/dark cycle. Lactobacilli were orally administered to different groups of mice
for five consecutive days at a dose of 108 cells/mouse per day in
the drinking water (22, 23). The treated groups and the untreated
control mice were fed a conventional balanced diet ad libitum. Respiratory Syncytial Virus Infection Respiratory Syncytial Virus Infection
Infection with human respiratory syncytial virus (RSV) strain
A2 was performed as described previously (9). Briefly, RSV was
grown in Vero cells for 3 h at 37◦C, 5% CO2 at multiplicity of
infection of 1 in 5 mL of DMEM. After cell lysis, virus supernatant
was sucrose density gradient purified and stored in 30% sucrose
at −80◦C. For infection, mice were lightly anesthetized with
isoflurane and intranasally challenged with 3.1 × 106 plaque
forming units (PFU) of RSV (9). Immunomodulatory Effect of Lactobacilli
in PIE Cells The study of the immunomodulatory capacity of lactobacilli was
performed in PIE cells as described previously (15, 16, 18, 20). Porcine intestinal epithelial cells were seeded at 3 × 104 cells per
well in 12-well type I collagen-coated plates (Sumitomo Bakelite
Co., Tokyo, Japan) and cultured for 3 days. After changing
medium, lactobacilli (5 × 108 cells/mL) were added, and 48 h
later, each well was washed vigorously with medium at least
three times to eliminate all stimulants. Then cells were stimulated
with poly(I:C) (60 µg/mL) for 12 h for reverse transcription–
polymerase chain reaction (RT-PCR) studies. Quantitative Expression Analysis by
Two-Step Real-Time Quantitative PCR Two-step real-time quantitative PCR (qPCR) was performed
to characterize the expression of selected genes in PIE cells as
described previously (16). TRIzol reagent (Invitrogen) was used
for total RNA isolation from each PIE cell sample, and Quantitect
RT kit (Qiagen, Tokyo, Japan) was used for the synthesis of all For the evaluation of viral infection, the RSV immunoplaque
assay was performed (9). In brief, lung tissue was removed
from mice, homogenized using a pellet pestle, and centrifuged at
2,600 × g for 10 min at 4◦C to clarify supernatant. Serial dilutions
of lung tissue–clarified supernatants were added into fresh Vero April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 3 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. cells monolayers and incubated at 37◦C, 5% CO2 for 3 h. All
samples were run in triplicate. After incubation and removal
of supernatant, 1 mL of fresh DMEM medium containing
10% fetal bovine serum, 0.1% penicillin-streptomycin, and
0.001% ciprofloxacin was added to monolayers. When extensive
syncytia developed, monolayers were fixed with 1 mL of ice-cold
acetone:methanol (60:40). Then, wells were treated with primary
RSV anti-F (clones 131-2A; Chemicon, Temecula, CA, United
States) and anti-G{mouse monoclonal [8C5 (9B6)] to RSV
glycoprotein; Abcam} antibodies for 2 h, followed by secondary
horseradish peroxidase anti–mouse immunoglobulin antibody
(anti–mouse immunoglobulin G, horseradish peroxidase–linked
antibody #7076; Cell Signaling Technology, Danvers, MA, United
States) for 1 h. Plates washed twice with PBS containing 0.5%
Tween 20 (Sigma, St. Louis, MO, United States) after each
antibody incubation step. Individual plaques were developed
using a DAB substrate kit (ab64238; Abcam, Cambridge, United
Kingdom) following the manufacturer’s specifications. Results
were expressed as log10 PFU/g of lung. 10 min at 900 × g; the pellet was discarded, and the fluid was
frozen at −70◦C for subsequent analyses. Albumin content
was determined colorimetrically based on albumin binding to
bromocresol green using an albumin diagnostic kit (Wiener
Lab). Lactate dehydrogenase activity, expressed as units per liter
of BAL fluid, was determined by using the Wiener reagents and
procedures (Wiener Lab) (7). Lung wet-to-dry weight ratio was measured as previously
described (7, 9). Wet-to-dry weight ratio was calculated as an
index of intrapulmonary fluid accumulation, without correction
for blood content. Statistical Analysis Statistical analyses were performed using GLM and REG
procedures available in the SAS computer program (SAS,
1994). Comparisons between mean values were carried out
using one-way analysis of variance and Fisher least significant
difference test. For these analyses, P < 0.05 and P < 0.01 were
considered significant. All experiments were carried out in compliance with the
Guide for Care and Use of Laboratory Animals and approved
by the Ethical Committee of Animal Care at CERELA, Argentina
(protocol no. BIOT-CRL/14 and BIOT-CRL/11) (7, 8). Cytokine Concentrations Serum and BAL samples were obtained as described before (9). Briefly, blood samples were obtained by cardiac puncture under
anesthesia. For BAL samples, the trachea was exposed surgically
and intubated with a catheter. A small incision was made in
the trachea, and two sequential lavages were performed in each
mouse by injecting sterile PBS with 1% heparin. The recovered
fluid was centrifuged for 10 min at 300 revolutions/min, and
the supernatant was recovered. Intestinal fluid samples were
obtained according to our previous publication (8). Briefly, the
small intestine was flushed with 5 mL of PBS, and the fluid was
centrifuged (10,000 × g, 4◦C 10 min) to separate particulate
material. The serum, BAL and intestinal supernatant samples
were kept frozen at −80◦C until use. Frontiers in Immunology | www.frontiersin.org Markers of Injury Lactate dehydrogenase (LDH) and aspartate aminotransferase
(AST) activities were determined in the serum to evaluate general
toxicity of poly(I:C) in mice challenged by the intraperitoneal
injection. Blood samples were obtained through cardiac puncture
under anesthesia. LDH and AST activities, expressed as units per
liter of serum, were determined by measuring the formation of
the reduced form of nicotinamide adenine dinucleotide using
the Wiener reagents and procedures (Wiener Lab, Buenos Aires,
Argentina) (8). Ethics Statement Animals were housed in plastic cages and environmental
conditions were kept constant, in agreement with the standards
for animal housing. Animal welfare was in charge of researchers
and special stafftrained in animal care and handling at CERELA. The minimal number of animals required for an appropriate
statistical analysis was calculated with the help of the Biostatistics
Laboratory of CERELA. Tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), IL-
10, IL-15, IFN-β, and IFN-γ concentrations in serum, intestinal
fluid, and BAL samples were measured with commercially
available enzyme-linked immunosorbent assay technique kits
following the manufacturer’s recommendations (R&D Systems,
Minneapolis, MN, United States). Animals were housed individually during the experiments. All efforts were made to minimize the number of animals and
their suffering. Animal health and behavior were monitored
twice a day. Animals were euthanized immediately after the time
point was reached by using xylazine and ketamine. No signs of
discomfort or pain and no deaths were observed before mice
reached the endpoints. Modulation of TLR3-Induced
Immunotranscriptome Changes in PIE
Cells by Lactobacilli Previously, we analyzed the effect of L. rhamnosus CRL1505 and
L. plantarum CRL1506 on the innate immune response of PIE
cells after the challenge with poly(I:C) by using a transcriptomic
approach (16). From that study, we were able to select a set
of potential biomarkers that would allow us to efficiently select
new immunobiotic strains with antiviral capabilities including
IFNα, IFNβ, RIG1, TLR3, OAS1, RNASEL, MX2, A20, CXCL5,
CCL4, IL-15, SELL, SELE, EPCAM, PTGS2, PLA2G4A, PTEGES,
and PTGER4. Then, in order to validate this assumption,
PIE cells were stimulated with different lactobacilli including Albumin
content,
a
measure
to
quantitate
increased
permeability of the bronchoalveolar–capillarity barrier, and LDH
activity, an indicator of general cytotoxicity, were determined
in bronchoalveolar lavage (BAL) fluid. Bronchoalveolar lavage
samples were obtained as described previously (7, 15). Briefly,
the trachea was exposed and intubated with a catheter, and
two sequential lavages were performed by injecting sterile PBS
in each mouse lung. The recovered fluid was centrifuged for April 2020 | Volume 11 | Article 543 4 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. immunomodulatory (L. rhamnosus CRL1505, L. plantarum
CRL1506, L. rhamnosus IBL07, and L. plantarum MPL16) (8,
16, 24, 25) and non-immunomodulatory (L. rhamnosus CRL576
and L. plantarum CRL681) strains and then challenged with
poly(I:C). The expression of the biomarkers was then evaluated. When the expressions of type I IFNs, antiviral factors, and
the negative regulator A20 were analyzed, a strain-dependent
effect was observed (Figure 1, Supplementary Figure S1). The
CRL1505, CRL1506, and MPL16 strains were highly efficient
for increasing IFNα, MX2, OAS1, and TLR3 expression. In
addition, L. rhamnosus CRL1505, and L. plantarum MPL16
were the lactobacilli with the highest capacity to increase the
expression of IFNβ and RNASEL (Figure 1). Lactobacillus
rhamnosus IBL07 was capable of enhancing the mRNA levels
of IFNα, IFNβ, OAS1, TLR3, and RNASEL, but it was not as
efficient as the CRL1505 and MPL16 strains. RIG-1 was enhanced
by all the immunomodulatory strains CRL1505, CRL1506,
IBL027, and MPL16, whereas the non-immunomodulatory
strains CRL681 and CRL576 were not able to induce changes
in the expression of type I IFNs or antiviral factors (Figure 1,
Supplementary Figure S1). Lactobacillus rhamnosus CRL1505,
L. plantarum CRL1506, and L. plantarum MPL16 significantly
reduced the expression of A20 in poly(I:C)-challenged PIE
cells, whereas no effect was observed for the other studied
strains (Figure 1). Modulation of TLR3-Induced
Immunotranscriptome Changes in PIE
Cells by Lactobacilli The CRL1505 and MPL16 strains were highly efficient in
enhancing the expression of CCL4, CXCL5, EPCAM, and SELE
(Figure 2). The CRL1506 and IBL027 augmented the expression
of CCL4, but the levels of this mRNA were significantly lower
than in the CRL1505 or MPL16 groups (Figure 2). The four
immunomodulatory strains increased SELL expression, being
L. plantarum MPL16 the most efficient to achieve this effect. The non-immunomodulatory strains CRL681 and CRL576 were
not able to induce changes in the expression of chemokines
and adhesion molecules (Figure 2). Lactobacillus rhamnosus
CRL1505, L. plantarum CRL1506, and L. plantarum MPL16
significantly reduced the expression of IL-15 in poly(I:C)-
challenged PIE cells, whereas no effect was observed for the other
studied strains (Figure 2). The
expressions
of
PTGS2,
PLA2G4A,
and
PTEGES
were enhanced, and PTGER4 was reduced by the four
immunomodulatory
strains
(Supplementary
Figure
S2). However, L. rhamnosus CRL1505 and L. plantarum MPL16 were
more efficient than L. plantarum CRL1506 and L. rhamnosus
IBL027 to increase the expression of PTGS2, PLA2G4A,
and PTEGES and reduce PTGER4 in poly(I:C)-challenged
PIE cells. The non-immunomodulatory strains CRL681 and
CRL576 were not able to induce changes in the expression
of
the
enzymes
involved
in
prostaglandins
biosynthesis
(Supplementary Figure S2). FIGURE 1 | Expression of interferon (IFN)-β, antiviral factors (MX2 and RNASEL), and the negative regulator A20 genes in porcine intestinal epithelial (PIE) cells
treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or
L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine intestinal
epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 1 | Expression of interferon (IFN)-β, antiviral factors (MX2 and RNASEL), and the negative regulator A20 genes in porcine intestinal epithelial (PIE) cells
treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or
L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine intestinal
epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. Modulation of TLR3-Induced
Immunotranscriptome Changes in PIE
Cells by Lactobacilli April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 5 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 2 | Expression of chemokines [interleukin 15 (IL-15), CCL4, and CXCL5] and adhesion molecules (EPCAM, SELE, and SELL) genes in porcine intestinal
epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum
MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine
ntestinal epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent
experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 3 | Heat map analysis of the differentially regulated genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505,
L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral
molecular–associated pattern poly(I:C). FIGURE 2 | Expression of chemokines [interleukin 15 (IL-15), CCL4, and CXCL5] and adhesion molecules (EPCAM, SELE, and SELL) genes in porcine intestinal
epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum
MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine
intestinal epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent
experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 2 | Expression of chemokines [interleukin 15 (IL-15), CCL4, and CXCL5] and adhesion molecules (EPCAM, SELE, and SELL) genes in porcine intestinal
epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum
MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine
intestinal epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent
experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 3 | Heat map analysis of the differentially regulated genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505,
L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. Modulation of TLR3-Triggered
Respiratory Immune Response in Mice
by Lactobacilli y
We
have
previously
reported
that
orally
administered
L. rhamnosus CRL1505 is able to beneficially modulate the
respiratory immune response triggered by TLR3 activation (7)
and improve the resistance against influenza virus (10) and RSV
(9). We also showed that the capacity of orally administered
CRL1505 strain to modulate immunity in distal mucosal sites
is not sheared by the immunomodulatory strain L. plantarum
CRL1506. Then, taking into considerations the similarities
found in this work between the CRL1505 and MPL16 strains,
we were interested in finding out whether orally administered
L. plantarum MPL16 was able to influence respiratory tract
immunity. For this purpose, lactobacilli were given orally
to different groups of mice, and the serum and respiratory
cytokine profile was evaluated before (basal levels) and after
the nasal challenge with poly(I:C). The changes in the profile of
cytokines induced in the BAL (Supplementary Figure S6) and
serum (Supplementary Figure S7) by lactobacilli indicated a
clear strain-dependent effect. When the levels of the different
cytokines were analyzed in BAL, it was shown that only
L. rhamnosus CRL1505 and L. plantarum MPL16 enhanced the
concentrations of IFN-β. In addition, CRL1505, MPL16 and
IBL027 increased the basal levels of IFN-γ and IL-10. However,
L. rhamnosus IBL027 was less efficient than the CRL1505
and MPL16 to induce the up-regulation of those cytokines
(Supplementary Figure S6). The basal levels of respiratory
TNF-α were increased by L. rhamnosus CRL1505, L. plantarum
MPL16, and L. plantarum CRL1506, whereas the CRL681 and
CRL576 treatments induced no changes in any of the cytokines
evaluated in the respiratory tract (Supplementary Figure S6). We evaluated the biochemical markers LDH and AST in order
to study the inflammatory damage after poly(I:C) administration
(Figure 4). As we reported previously (8), the intraperitoneal
challenge with poly(I:C) significantly increased LDH and AST
activities in serum samples. The four immunomodulatory
strains decreased serum LDH and AST, whereas the non-
immunomodulatory strains CRL681 and CRL576 did not modify
the levels of those markers (Figure 4). g
In addition, the intraperitoneal administration of poly(I:C)
significantly
increased
the
levels
of
IFN-β;
IFN-γ;
the
proinflammatory
cytokines
TNF-α,
IL-6,
and
IL-15;
and
the regulatory cytokine IL-10 in the intestinal fluid (Figure 5). The four immunomodulatory strains were able to enhance
the intestinal levels of IFN-β and IFN-γ after TLR3 activation. Modulation of TLR3-Induced
Immunotranscriptome Changes in PIE
Cells by Lactobacilli plantarum CRL681 and challenged with the viral
molecular–associated pattern poly(I:C). FIGURE 3 | Heat map analysis of the differentially regulated genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505,
L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral
molecular–associated pattern poly(I:C). FIGURE 3 | Heat map analysis of the differentially regulated genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505,
L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral
molecular–associated pattern poly(I:C). with similar immunomodulatory properties in the context
of TLR3 activation. As shown in Figure 3, the treatments
with immunomodulatory lactobacilli plus poly(I:C) clustered We performed a cluster analysis to depict the transcriptomic
patterns of differentially modulated genes between lactobacilli-
treated and control PIE cells, in order to find the strains April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 6 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. Again, we performed a cluster analysis to depict the
differentially modulated cytokines and injury markers between
lactobacilli-treated and control mice, in order to find the
strains with similar immunomodulatory properties in the in vivo
mice model. As shown in Figure 6, a clear strain-dependent
effect was observed in the ability of lactobacilli to modulate
cytokines before and after poly(I:C) challenge. Interestingly,
L. rhamnosus CRL1505 and L. plantarum MPL16 clustered
together and separated from the other immunomodulatory
strains L. plantarum CRL1506 and L. rhamnosus IBL027. These
results allow us to speculate that L. plantarum MPL16 would
have the ability to differentially regulate the intestinal innate
immune response in poy(I:C)-challenged mice and protect
against the inflammatory damage (Supplementary Figure S5) in
a way comparable to that previously reported for L. rhamnosus
CRL1505 (8). together and separated from the non-immunomodulatory
strains. Moreover, L. rhamnosus CRL1505 and L. plantarum
MPL16 were separated from L. plantarum CRL1506 and
L. rhamnosus IBL027. These results indicate that L. plantarum
MPL16 would have the ability to differentially regulate the
immunotranscriptomic response in poy(I:C)-challenged PIE cells
(Supplementary Figure S3) in a way comparable to that
previously reported for L. rhamnosus CRL1505 (16, 20). Modulation of TLR3-Triggered Intestinal
Immune Response in Mice by
Lactobacilli Next, we were interested in finding out whether the differences
in the immunomodulatory activities of CRL1505, MPL16,
CRL1506, and IBL027 observed in PIE cells could be also found in
an in vivo model. Then, lactobacilli were given orally to different
groups of mice, and the intestinal cytokine profile was evaluated
before (basal levels) and after the intraperitoneal challenge with
poly(I:C). As observed in Supplementary Figure S4, a strain-
dependent ability in the modulation of the basal levels of
intestinal cytokines was detected. The four immunomodulatory
strains increased the intestinal levels of IFN-β, IFN-γ, and IL-10;
however, L. rhamnosus CRL1505 and L. plantarum MPL16 were
more efficient than the other strains to augment IFN-γ and IL-
10. The non-immunomodulatory strains CRL681 and CRL576
did not modify the levels of intestinal IFN-β. Interestingly,
L. plantarum CRL681 increased the levels of intestinal IFN-γ
and IL-10 (Supplementary Figure S4). All the lactobacilli strains
with the exception of L. rhamnosus CRL576 increased TNF-α,
whereas the CRL1505, MPL16, IBL027, and CRL681 enhanced
the intestinal levels of IL-6 (Supplementary Figure S4). The basal
concentration of IL-15 was under the detection limits in all the
experimental groups (data not shown). Modulation of TLR3-Triggered
Respiratory Immune Response in Mice
by Lactobacilli The CRL1505, MPL16, CRL1506, and IBL027 strain were
also capable of significantly reducing the concentrations of
TNF-α, IL-6, and IL-15 and increasing the levels of IL-10 in the
intestine when compared to control mice (Figure 5). Of note,
L. rhamnosus CRL1505 and L. plantarum MPL16 were more
efficient than the other strains to reduce TNF-α and IL-15. The
non-immunomodulatory strains CRL681 and CRL576 did not
modify the levels of IFN-β, IFN-γ, TNF-α, IL-6, IL-15, or IL-10
when compared to controls (Figure 5). All the immunomodulatory strains were capable of enhancing
the concentrations of IFN-β, IFN-γ, TNF-α, and IL-10 in
serum when compared to controls. However, L. rhamnosus
CRL1505 and L. plantarum MPL16 were more efficient than
the other immunomodulatory strains to increase the basal levels
of serum IFN-γ, TNF-α, and IL-10. Lactobacillus rhamnosus
CRL576 and L. plantarum CRL681 did not induce significant April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org Frontiers in Immunology | www.frontiersin.org 7 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 4 | Levels of serum injury markers [lactate dehydrogenase (LDH) and aspartate aminotransferase (AST)] in mice orally treated with Lactobacillus rhamnosus
CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per
day for five consecutive days) and then challenged by the intraperitoneal route with 30 µg of the viral molecular–associated pattern poly(I:C). Mice with no lactobacilli
treatment and challenged with poly(I:C) were used as controls. Serum injury markers were evaluated on day 2 after poly(:C) administration. The results represent data
from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 4 | Levels of serum injury markers [lactate dehydrogenase (LDH) and aspartate aminotransferase (AST)] in mice orally treated with Lactobacillus rhamnosus
CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per
day for five consecutive days) and then challenged by the intraperitoneal route with 30 µg of the viral molecular–associated pattern poly(I:C). Mice with no lactobacilli
treatment and challenged with poly(I:C) were used as controls. Serum injury markers were evaluated on day 2 after poly(:C) administration. The results represent data
from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. Modulation of TLR3-Triggered
Respiratory Immune Response in Mice
by Lactobacilli FIGURE 5 | Levels of intestinal interferons (IFN-β and IFN-γ), proinflammatory cytokines [TNF-α and interleukin 6 (IL-6)] and IL-10 in mice orally treated with
Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum
CRL681 (108 cells/mouse per day for 5 consecutive days) and then challenged by the intraperitoneal route with 30 µg of the viral molecular–associated pattern
poly(I:C). Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Immune factors were evaluated on day 2 after poly(:C)
administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 5 | Levels of intestinal interferons (IFN-β and IFN-γ), proinflammatory cytokines [TNF-α and interleukin 6 (IL-6)] and IL-10 in mice orally treated with
Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum
CRL681 (108 cells/mouse per day for 5 consecutive days) and then challenged by the intraperitoneal route with 30 µg of the viral molecular–associated pattern
poly(I:C). Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Immune factors were evaluated on day 2 after poly(:C)
administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. levels of IFN-β, IFN-γ, TNF-α, and IL-10. Lactobacillus
rhamnosus CRL1505 and L. plantarum MPL16 enhanced the
levels of IFN-β and IFN-γ in both serum and BAL, whereas
L. rhamnosus IBL027 was capable of increasing only BAL
IFN-γ. The four immunomodulatory strains were capable of
reducing serum and BAL levels of TNF-α, however; the CRL1505
and MPL16 strains were more effective to down-regulate this
inflammatory cytokine in the respiratory tract (Figure 8). In
addition, the four immunomodulatory strains increased IL-10
in serum (Supplementary Figure S8), but only L. rhamnosus
CRL1505 and L. plantarum MPL16 enhanced the levels of this
immunoregulatory cytokine in the respiratory tract (Figure 8). changes in serum cytokines when compared to controls
(Supplementary Figure S7). We also evaluated the levels of the biochemical markers
albumin and LDH in BAL as indicators of lung injury
(7, 9, 10). Frontiers in Immunology | www.frontiersin.org Modulation of TLR3-Triggered
Respiratory Immune Response in Mice
by Lactobacilli The nasal challenge of mice with poly(I:C)
significantly altered lungs function and induced lung injuries
as demonstrated by the increased levels of BAL albumin and
LDH (Figure 7), reflecting alteration of the alveolar–capillary
barrier and local cellular damage. Only L. rhamnosus CRL1505
and L. plantarum MPL16 treatments were able to significantly
reduce the levels of BAL LDH and albumin when compared to
controls (Figure 7). We performed a cluster analysis to depict the differentially
modulated serum and BAL cytokines and lung injury markers The nasal administration poly(I:C) significantly increased
serum (Supplementary Figure S8) and respiratory (Figure 8) April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 8 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 6 | Heat map analysis of the differentially regulated intestinal immune factors and serum injury markers before (basal) and after poly(I:C) challenge. Mice
were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16,
or L. plantarum CRL681, and then challenged by the intraperitoneal route with the viral molecular–associated pattern poly(I:C). FIGURE 6 | Heat map analysis of the differentially regulated intestinal immune factors and serum injury markers before (basal) and after poly(I:C) challenge. Mice
were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16,
or L. plantarum CRL681, and then challenged by the intraperitoneal route with the viral molecular–associated pattern poly(I:C). FIGURE 7 | Levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus
CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day
for five consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for 3 consecutive days. Mice with no
lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage injury markers were evaluated on day 2 after the last poly(:C)
administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 6 | Heat map analysis of the differentially regulated intestinal immune factors and serum injury markers before (basal) and after poly(I:C) challenge. Mice
were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. Modulation of TLR3-Triggered
Respiratory Immune Response in Mice
by Lactobacilli rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16,
or L. plantarum CRL681, and then challenged by the intraperitoneal route with the viral molecular–associated pattern poly(I:C). FIGURE 7 | Levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus
CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day
for five consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for 3 consecutive days. Mice with no
lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage injury markers were evaluated on day 2 after the last poly(:C)
administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 7 | Levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus
CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day
for five consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for 3 consecutive days. Mice with no
lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage injury markers were evaluated on day 2 after the last poly(:C)
administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. between lactobacilli-treated and control mice. As shown in
Figure 9, a clear strain-dependent effect was observed in the
ability of lactobacilli to modulate immunity in the respiratory
tract. Of note, L. rhamnosus CRL1505 and L. plantarum
MPL16 clustered together and separated from the other
immunomodulatory strains. These results allow us to speculate that L. plantarum MPL16 would have the ability to differentially
regulate the systemic and respiratory innate immune response
in poy(I:C)-challenged mice and protect against the lung
inflammatory damage (Supplementary Figure S9) in a way
comparable to that previously reported for L. rhamnosus
CRL1505 (7). April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org Frontiers in Immunology | www.frontiersin.org 9 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. Modulation of TLR3-Triggered
Respiratory Immune Response in Mice
by Lactobacilli plantarum MPL16, or L. plantarum CRL681 (108
cells/mouse per day for 5 consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for three
consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage immune factors were evaluated o
day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences
(P < 0.05), a < b < c. The MPL16 and CRL1505 strains significantly increased the
respiratory levels of TNF-α, being L. rhamnosus CRL1505
more effective than L. plantarum MPL16 to achieve this
effect (Figure 11). Enhancement of the Resistance Against
RSV Infection by L. plantarum MPL16 The MPL16 and CRL1505 strains significantly increased the
respiratory levels of TNF-α, being L. rhamnosus CRL1505
more effective than L. plantarum MPL16 to achieve this
effect (Figure 11). y
p
Finally, we aimed to test whether the oral administration of
L. plantarum MPL16 was able to confer protection against
a respiratory virus challenge. For this purpose, mice were
fed the MPL16 strain and then nasally challenged with RSV. Lactobacillus rhamnosus CRL1505 and L. plantarum CRL1506
were used as positive and negative controls, respectively,
according to our previous work demonstrating their different
ability to protect against this viral pathogen (9). As shown
in Figure 10, both L. rhamnosus CRL1505 and L. plantarum
MPL16 were equally effective in reducing RSV lung titers,
whereas the CRL1506 strain did not induce changes when
compared to control mice. In addition, the MPL16 and CRL1505
strains significantly reduced the levels of the markers of lung
damage, whereas L. plantarum CRL1506 was not able to
achieve this effect (Figure 10). The levels of respiratory IFN-
β, IFN-γ, TNF-α, and IL-10 were also evaluated after the
challenge with RSV (Figure 11). Both L. rhamnosus CRL1505
and L. plantarum MPL16 enhanced the levels of IFN-β, IFN-
γ, and IL-10 in BAL, whereas L. plantarum CRL1506 was
not capable of increasing these cytokines when compared to
controls. The CRL1506 strain did not induce changes in the
levels of BAL TNF-α when compared to the control group. Modulation of TLR3-Triggered
Respiratory Immune Response in Mice
by Lactobacilli FIGURE 8 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus
rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108
cells/mouse per day for 5 consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for three
consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage immune factors were evaluated on
day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences
(P < 0.05), a < b < c. FIGURE 8 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus
rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108
cells/mouse per day for 5 consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for three
consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage immune factors were evaluated on
day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences
(P < 0.05), a < b < c. FIGURE 8 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus
rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108
cells/mouse per day for 5 consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for three
consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage immune factors were evaluated on
day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences
(P < 0.05), a < b < c. FIGURE 8 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus
rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. DISCUSSION Moreover, MPL16-treated
mice also showed higher levels of intestinal IFN-γ as observed
by L. rhamnosus CRL1505. It was reported that infection with
rotavirus in suckling mice induces a significant up-regulation
of different types of IFNs in the intestine including IFN-γ by
T cells and type I IFNs by dendritic cells (DCs) and IECs
(30). Interferons binding to their cognate cell surface receptors
activate positive feedback loops that amplify the expression of
IFNs as well as more than 300 different IFN-stimulated genes
(31). This IFNs release then efficiently amplify the expression
of antiviral proteins targeting a variety of viral replication steps
in uninfected bystander cells. It was also shown in in vitro
studies that the addition of purified exogenous IFNs after
rotavirus infection of human IECs does not significantly hamper around the world to reduce the incidence and severity of
intestinal and pulmonary infections caused by viruses. Such
selection, in addition to being efficient, should be performed
using in vitro systems in order to minimize the use of
experimental animals. Bifidobacterium infantis MCC12 (15) increased the expression
of IFN-β and antiviral factors by reducing the expression of
A20. The down-regulation of A20 gene expression in poly(I:C)-
challenged PIE cells results in the improved activation of IRF3
and NF-κB signaling pathways, which increase the expression
of not only IFN-α, IFN-β, MX2, OAS1, and RNASEL but in
addition several other antiviral factors including OASL, MX1,
OAS2, RNASE4, IFIT1, IFIT3, IFIT2, and IFIT5 (Supplementary
Figure S3) (16). The in vivo experiments in mice performed
here also demonstrated that L. plantarum MPL16 is able to
enhance the intestinal levels of IFN-β. Moreover, MPL16-treated
mice also showed higher levels of intestinal IFN-γ as observed
by L. rhamnosus CRL1505. It was reported that infection with
rotavirus in suckling mice induces a significant up-regulation
of different types of IFNs in the intestine including IFN-γ by
T cells and type I IFNs by dendritic cells (DCs) and IECs
(30). Interferons binding to their cognate cell surface receptors
activate positive feedback loops that amplify the expression of
IFNs as well as more than 300 different IFN-stimulated genes
(31). This IFNs release then efficiently amplify the expression
of antiviral proteins targeting a variety of viral replication steps
in uninfected bystander cells. DISCUSSION In middle- and low-income countries, intestinal and respiratory
viral infections are the most common and deadly diseases
in children (26–28). The use of functional foods such as
those containing immunomodulatory probiotic lactobacilli has
been proposed to stimulate the intestinal and the respiratory
immune system, improving the outcome of viral diarrhea
and pneumonia simultaneously. An example of the high
probability
of
success
of
this
strategy
is
the
“Yogurito
Nutritional Program” implemented in Argentina (2, 29). The
program uses a probiotic yogurt containing the immunobiotic
strain L. rhamnosus CRL1505 to prevent respiratory and
gastrointestinal diseases by enhancing the immunological system
of children attending public schools. Then, the selection of
new immunobiotic strains that have different biotechnological
properties but the same or better immunomodulatory capacities
than L. rhamnosus CRL1505 could enhance the development
of various types of functional foods that could be used April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 10 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 9 | Heat map analysis of the differentially regulated serum and bronchoalveolar lavage (BAL) immune factors and BAL injury markers before (basal) and after
poly(I:C) challenge. Mice were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum
CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and then challenged by the nasal route with the viral molecular–associated pattern poly(I:C) for three
consecutive days. FIGURE 9 | Heat map analysis of the differentially regulated serum and bronchoalveolar lavage (BAL) immune factors and BAL injury markers before (basal) and after
poly(I:C) challenge. Mice were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum
CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and then challenged by the nasal route with the viral molecular–associated pattern poly(I:C) for three
consecutive days. Bifidobacterium infantis MCC12 (15) increased the expression
of IFN-β and antiviral factors by reducing the expression of
A20. The down-regulation of A20 gene expression in poly(I:C)-
challenged PIE cells results in the improved activation of IRF3
and NF-κB signaling pathways, which increase the expression
of not only IFN-α, IFN-β, MX2, OAS1, and RNASEL but in
addition several other antiviral factors including OASL, MX1,
OAS2, RNASE4, IFIT1, IFIT3, IFIT2, and IFIT5 (Supplementary
Figure S3) (16). The in vivo experiments in mice performed
here also demonstrated that L. plantarum MPL16 is able to
enhance the intestinal levels of IFN-β. Frontiers in Immunology | www.frontiersin.org DISCUSSION Respiratory syncytial virus titers and injury markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments
(n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 10 | Lung respiratory syncytial virus (RSV) titers, lung wet-to-dry ratio, and levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate
dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse
per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Respiratory syncytial virus titers and injury markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments
(n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 10 | Lung respiratory syncytial virus (RSV) titers, lung wet-to-dry ratio, and levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate
dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse
per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Respiratory syncytial virus titers and injury markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments
(n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. viral replication; however, IFN treatment of cells prior to viral
challenge is required to achieve an efficient restriction of rotavirus
replication (32). intestinal mucosa can contribute to the local damage mediated
by the inflammatory and oxidative stress (35). In addition, it
was reported that purified dsRNA from rotavirus is able to
induce severe intestinal damage in mice through the activation of
TLR3 signaling pathway (36). Moreover, it was also demonstrated
that the intraperitoneal administration of the synthetic dsRNA
poly(I:C) to mice mimics the inflammatory intestinal immune
response elicited by rotavirus and induce mucosal erosion, villous
atrophy, intestinal wall attenuation, and diarrhea (8, 36, 37). Frontiers in Immunology | www.frontiersin.org DISCUSSION It was also shown in in vitro
studies that the addition of purified exogenous IFNs after
rotavirus infection of human IECs does not significantly hamper In this work, we demonstrated that the study of biomarkers
expression in poly(I:C)-challenged PIE cells is a very effective tool
for the selection of immunobiotics with the ability to modulate
intestinal and respiratory antiviral immunity. The transcriptional
profiling performed in vitro in poly(I:C)-challenged PIE cells
in this work allowed us to select a new immunobiotic strain,
L. plantarum MPL16, with the ability to stimulate in vivo the local
(intestinal) and distal (respiratory) mucosal immune systems. Lactobacillus rhamnosus CRL1505 and L. plantarum MPL16
similarly modulated gene expression in poly(I:C)-challenged PIE
cells inducing significant increases of both IFN-α and IFN-β and
in the antiviral factors MX2, OAS1, and RNASEL. Our previous
studies in PIE cells showed that rotavirus can be detected by this
cell line through TLR3, inducing the expression of IFN-β and up-
regulating the antiviral genes MxA and RNASEL (15). Moreover,
those studies demonstrated that immunobiotics strains with
the ability to enhance IFN-β, MxA, and RNASEL were also
capable of reducing rotavirus replication. We demonstrated that
immunobiotic strains such as L. rhamnosus CRL1505 (16) and April 2020 | Volume 11 | Article 543 11 Albarracin et al. Selection of Antiviral Immunobiotics in PIE Cells FIGURE 10 | Lung respiratory syncytial virus (RSV) titers, lung wet-to-dry ratio, and levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate
dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse
per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Respiratory syncytial virus titers and injury markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments
(n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 10 | Lung respiratory syncytial virus (RSV) titers, lung wet-to-dry ratio, and levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate
dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse
per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. DISCUSSION Immune markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. lymphocytes (IELs) and promote epithelial destruction through
the RAE1–NKG2D interaction (Supplementary Figure S5) (38). We reported previously that L. rhamnosus CRL1505 is able
to significantly reduce the expression of IL-15 and RAE1 in
poly(I:C)-challenged PIE cells (16) and to reduce the levels
of intestinal TNF-α and IL-15 and diminish the gut damage
mediated by CD3+NK1.1+CD8αα+ IELs in mice after TLR3
activation (8). Here, we found that L. plantarum MPL16 is
able to modulate the cytokine profile expression triggered by
TLR3 activation in PIE cells as well as in mice intestinal
mucosa, in a way similar to that observed for the CRL1505
strain. Then, it is tempting to speculate that L. plantarum
MPL16 would have the ability to beneficially regulate intestinal
inflammation in the context of TLR3 activation; however,
more detailed studies using viral challenges are necessary to
demonstrate this effect. Our results allow us to speculate that L. plantarum MPL16
would be capable to modulate IECs innate immune response,
improve the resistance to rotavirus infection, and reduce
the severity of inflammatory-mediated damage, as we have
previously demonstrated in vitro (16, 20), in vivo (8), and in
clinical trials (2, 29) for the CRL1505 strain. lymphocytes (IELs) and promote epithelial destruction through
the RAE1–NKG2D interaction (Supplementary Figure S5) (38). We reported previously that L. rhamnosus CRL1505 is able
to significantly reduce the expression of IL-15 and RAE1 in
poly(I:C)-challenged PIE cells (16) and to reduce the levels
of intestinal TNF-α and IL-15 and diminish the gut damage
mediated by CD3+NK1.1+CD8αα+ IELs in mice after TLR3
activation (8). Here, we found that L. plantarum MPL16 is
able to modulate the cytokine profile expression triggered by
TLR3 activation in PIE cells as well as in mice intestinal
mucosa, in a way similar to that observed for the CRL1505
strain. Then, it is tempting to speculate that L. plantarum
MPL16 would have the ability to beneficially regulate intestinal
inflammation in the context of TLR3 activation; however,
more detailed studies using viral challenges are necessary to
demonstrate this effect. We
also
demonstrated
here
that
orally
administered
L. plantarum MPL16 is able to differentially modulate the
respiratory antiviral immune response. DISCUSSION Interestingly, it was shown that the intestinal damage triggered by
dsRNA-TRL3 interaction is mediated by the increased expression
of IL-15 and retinoic acid early inducible 1 (RAE1) in IECs, which
induce the activation of CD3+NK1.1+CD8αα+ intraepithelial The excessive activation of the inflammatory response or the
failure in the mechanisms that control it significantly contributes
to the injury of the infected tissue during viral infections. Intestinal epithelial cells produce a variety of cytokines and
chemokines in response to the viral attack, including IL-6, IL-8,
TNF-α, and granulocyte-macrophage colony-stimulating factor. The production of those inflammatory factors is important
for the protection against the viral infection through their
direct antiviral effects (33) or the recruitment and activation of
phagocytes (34). However, infiltration of immune cells to the April 2020 | Volume 11 | Article 543 12 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 11 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus
rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the
nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Immune markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 11 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus
rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the
nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Immune markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 11 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus
rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the
nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Frontiers in Immunology | www.frontiersin.org DISCUSSION plantarum MPL16
significantly reduced the respiratory injury markers after RSV
challenge and differentially modulated the levels of respiratory
proinflammatory and anti-inflammatory cytokines induced by
the viral infection. Those effects were similar to the previously
described for the CRL1505 strain (Supplementary Figure S9)
(7, 9, 10, 39). different immune cell populations such as DCs and macrophages,
as well as more detailed molecular and genomic characterization
of both lactobacilli strains, could contribute significantly to the
understanding of the molecular mechanisms involved in the
ability of immunobiotics to stimulate distant mucosal sites such
as the respiratory tract. Of note, the biotechnological properties of the two strains
are different. Whereas L. rhamnosus CRL1505 has been used
mainly in the development of dairy functional products (2, 44),
the MPL16 strain has shown a remarkable ability to growth
and ferment wakame (Undaria pinnatifida) that is the most
popular and economically important edible brown algae in Asian
countries (24, 45). Then, the different biotechnological properties
of L. plantarum MPL16 could potentiate the development of
non-dairy functional foods or feeds with the ability to improve
antiviral immunity in the intestine and the respiratory tract. AUTHOR CONTRIBUTIONS JV and HK designed the study and manuscript writing. LA,
VG-C, YI, and MI did the laboratory work. LA, MI, and
YS did the statistical analysis. AG-C, HA, HT, JV, and HK
contributed to data analysis and interpretation. All authors read
and approved the manuscript. The results of this work confirm that new immunobiotics
strains with the ability of stimulating both local and distal
antiviral immune responses when orally administered can be
efficiently selected by evaluating the expression of appropriate
biomarkers of the transcriptomic profile of poly(I:C)-challenged
PIE cells. The comparison of the transcriptomic patterns
of differentially modulated genes in PIE cells treated with
different lactobacilli allowed us to select the MPL16 strain that
clustered together with the immunobiotic strain L. rhamnosus
CRL1505, which has been proved to differentially modulate
the intestinal and the respiratory antiviral responses and
protect against enteric and respiratory viruses (2, 7, 9, 10). The in vivo studies performed here conclusively demonstrated
that L. plantarum MPL16 modulated the profiles of intestinal,
serum, and respiratory cytokines; reduced the inflammatory
damage triggered by TLR3 activation in both the intestinal
and respiratory mucosa; and improved the resistance to RSV
infection. The immunological changes induced by L. plantarum
MPL16 were not different from those previously reported for
the CRL1505 strain. Further mechanistic studies evaluating
comparatively the effects of CRL1505 and MPL16 strains in DISCUSSION We reported previously
that the improvement of IFN-β production by CD11c+SiglecF+
alveolar macrophages and IFN-γ by CD3+CD4+ T cells is related
to the ability of immunobiotic treatments to enhance resistance
to respiratory virus (39, 40), in line with studies demonstrating
that these immune cell populations are the main producer of
IFNs during pulmonary viral infections (36, 37). The increased
levels of respiratory IFN-γ and IFN-β found in L. plantarum April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org Frontiers in Immunology | www.frontiersin.org 13 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. MPL16–treated mice correlated with the improved resistance of
mice to RSV infection. On the other hand, we have extensively
used a mice experimental model of lung inflammation based
on the nasal administration of poly(I:C) in order to mimic
the respiratory innate antiviral immune response triggered by
RSV and to evaluate the beneficial effects of immunobiotic
bacteria (7, 9, 10, 39, 40). The respiratory priming with the TLR3
agonist induces a marked inflammatory damage characterized
by impaired alveolar–capillary barrier function and epithelial cell
death as well as increased levels of TNF-α, IL-6, IL-8, and MCP-1. Prominent improvements of the IL-8, MIP-1, RANTES, MCP-1,
TNF-α, and IL-6 have been reported in both experimentally
RSV-infected mice and naturally RSV-infected children (41). The
increase in the respiratory levels of those inflammatory factors,
especially TNF-α, contributes to clearance of the virus during
the early stages of RSV infection; however, their continued
production exacerbates lung injuries during the late stages
of infection (41, 42). Then, the appropriate regulation of the
respiratory immune response is also essential for the protection
of RSV-infected hosts. In this regard, it was demonstrated
that IL-10 has a crucial role in regulating the severity of RSV
infection (42, 43). The deficiency of IL-10 does not affect RSV
load in lungs, but significantly enhances the inflammatory cells
influx into the lung, promotes lung damage, and increases
weight loss of infected mice (42, 43). The results of this work
demonstrated that orally administered L. plantarum MPL16 is
able to reduce the levels of inflammatory factors, increase IL-10,
and significantly diminish the markers of lung tissue damage
after the nasal administration of poly(I:C). Moreover, we also
demonstrated here that orally administered L. ETHICS STATEMENT The
animal
study
was
reviewed
and
approved
by
the
Ethical
Committee
of
Animal
Care
CERELA-CONICET,
Tucuman, Argentina. DATA AVAILABILITY STATEMENT The datasets generated for this study are available on request to
the corresponding author. Frontiers in Immunology | www.frontiersin.org REFERENCES 8. Tada A, Zelaya H, Clua P, Salva S, Alvarez S, Kitazawa H, et al. Immunobiotic
Lactobacillus strains reduce small intestinal injury induced by intraepithelial
lymphocytes after Toll-like receptor 3 activation. Inflamm Res. (2016) 65:771–
83. doi: 10.1007/s00011-016-0957-7 1. WHO/UNICEF. Ending Preventable Deaths from Pneumonia and Diarrhoea
by 2025. New York, NY: UNICEF. (2013). doi: ISBN978-92-415-0523-9 1. WHO/UNICEF. Ending Preventable Deaths from Pneumonia and Diarrhoea
by 2025. New York, NY: UNICEF. (2013). doi: ISBN978-92-415-0523-9 9. Chiba E, Tomosada Y, Vizoso-Pinto MG, Salva S, Takahashi T, Tsukida K, et al. Immunobiotic Lactobacillus rhamnosus improves resistance of infant mice
against respiratory syncytial virus infection. Int Immunopharmacol. (2013)
17:373–82. doi: 10.1016/j.intimp.2013.06.024 2. Villena J, Salva S, Núñez M, Corzo J, Tolaba R, Faedda J, et al. Probiotics for
everyone! The novel immunobiotic Lactobacillus rhamnosus CRL1505 and the
beginning of social probiotic programs in Argentina. Int J Biotechnol Wellness
Ind. (2012) 1:189–98. doi: 10.6000/1927-3037/2012.01.03.05 3. Kitazawa H, Villena J. Modulation of respiratory TLR3-anti-viral response
by probiotic microorganisms: lessons learned from Lactobacillus rhamnosus
CRL1505. Front Immunol. (2014) 5:201. doi: 10.3389/fimmu.2014.00201 10. Zelaya H, Tsukida K, Chiba E, Marranzino G, Alvarez S, Kitazawa H,
et al. Immunobiotic Lactobacilli reduce viral-associated pulmonary damage
through the modulation of inflammation-coagulation interactions. Int
Immunopharmacol. (2014) 19:161–73. doi: 10.1016/j.intimp.2013.12.020 4. Villena J, Vizoso-Pinto MG, Kitazawa H. Intestinal innate antiviral immunity
and immunobiotics: beneficial effects against Rotavirus infection. Front
Immunol. (2016) 7:563. doi: 10.3389/fimmu.2016.00563 11. Parashar UD, Gibson CJ, Bresee JS, Glass RI. Rotavirus and severe childhood
diarrhea. Emerg Infect Dis. (2006) 12:304–6. doi: 10.3201/eid1202.050006 12. Greenberg HB, Estes MK. Rotaviruses: from pathogenesis to vaccination. Gastroenterology. (2009) 136:1939–51. doi: 10.1053/j.gastro.2009.02.076 5. Villena J, Oliveira MLS, Ferreira PCD, Salva S, Alvarez S. Lactic acid bacteria
in the prevention of pneumococcal respiratory infection: future opportunities
and challenges. Int Immunopharmacol. (2011) 11:1633–45. doi: 10.1016/j. intimp.2011.06.004 13. Villena J, Kitazawa H. Modulation of intestinal TLR4-inflammatory signaling
pathways by probiotic microorganisms: lessons learned from Lactobacillus
jensenii TL2937. Front Immunol. (2014) 4:512. doi: 10.3389/fimmu.2013. 00512 6. Zelaya H, Alvarez S, Kitazawa H, Villena J. Respiratory antiviral immunity and
immunobiotics: beneficial effects on inflammation-coagulation interaction
during influenza virus infection. Front Immunol. (2016) 7:633. doi: 10.3389/
fimmu.2016.00633 14. Hosoya S, Villena J, Shimazu T, Tohno M, Fujie H, Chiba E, et al. Immunobiotic lactic acid bacteria beneficially regulate immune response
triggered by poly(I:C) in porcine intestinal epithelial cells. Vet Res. (2011)
42:111. doi: 10.1186/1297-9716-42-111 7. SUPPLEMENTARY MATERIAL FIGURE S5 | Global overview of the effect of L. rhamnosus CRL1505 and
L. plantarum MPL16 on the intestinal inflammatory injury induced by poly(I:C) and
mediated by the activation of CD3+NK1.1+CD8αα+ intraepithelial lymphocytes
(IELs) that promote epithelial destruction through the RAE1–NKG2D interaction. Detailed immunomodulatory mechanisms were previously studied for
L. rhamnosus CRL1505 (8). The Supplementary Material for this article can be found
online at: https://www.frontiersin.org/articles/10.3389/fimmu. 2020.00543/full#supplementary-material FIGURE S6 | Levels of bronco-alveolar lavages (BAL) interferons (IFN-β and
IFN-γ), TNF-α and IL-10 in mice orally treated with Lactobacillus rhamnosus
CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum
CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse/day for
five consecutive days). Mice with no lactobacilli treatment were used as controls. Immune factors were evaluated on day 6. The results represent data from three
independent experiments (n = 6 per group). Letters indicate significant differences
(P < 0.05), a < b < c. FIGURE S1 | Expression of interferon (IFN)-α, and antiviral factors (TLR3, RIG-1
and OAS1) genes in porcine intestinal epithelial (PIE) cells treated with
Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus
CRL576, Lactobacillus plantarumC RL1506, L. plantarum MPL16, or L. plantarum
CRL681 and challenged with the viral molecular associated pattern poly(I:C),
analyzed by qPCR. PIE cells with no lactobacilli treatment and stimulated with
poly(I:C) were used as controls. The results represent data from three independent
experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S1 | Expression of interferon (IFN)-α, and antiviral factors (TLR3, RIG-1
and OAS1) genes in porcine intestinal epithelial (PIE) cells treated with
Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus
CRL576, Lactobacillus plantarumC RL1506, L. plantarum MPL16, or L. plantarum
CRL681 and challenged with the viral molecular associated pattern poly(I:C),
analyzed by qPCR. PIE cells with no lactobacilli treatment and stimulated with
poly(I:C) were used as controls. The results represent data from three independent
experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S1 | Expression of interferon (IFN)-α, and antiviral factors (TLR3, RIG-1
and OAS1) genes in porcine intestinal epithelial (PIE) cells treated with FIGURE S7 | Levels of serum interferons (IFN-β and IFN-γ), TNF-α and IL-10 in
mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus
IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum
MPL16, or L. plantarum CRL681 (108 cells/mouse/day for five consecutive days). Selection of Antiviral Immunobiotics in PIE Cells Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. SUPPLEMENTARY MATERIAL plantarum MPL16 and challenged with poly(I:C). Detailed immunomodulatory
mechanisms were previously studied for L. rhamnosus CRL1505 (16, 20). FIGURE S4 | Levels of intestinal interferons (IFN-β and IFN-γ), proinflammatory
cytokines (TNF-α and IL-6) and IL-10 in mice orally treated with Lactobacillus
rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576,
Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681
(108 cells/mouse/day for five consecutive days). Mice with no lactobacilli treatment
were used as controls. Immune factors were evaluated on day 6. The results
represent data from three independent experiments (n = 6 per group). Letters
indicate significant differences (P < 0.05), a < b < c. FIGURE S9 | Global overview of the effect of L. rhamnosus CRL1505 and
L. plantarum MPL16 on the respiratory innate immune response triggered by
poly(I:C). Detailed immunomodulatory mechanisms were previously studied for
L. rhamnosus CRL1505 (7, 9). FIGURE S9 | Global overview of the effect of L. rhamnosus CRL1505 and
L. plantarum MPL16 on the respiratory innate immune response triggered by
poly(I:C). Detailed immunomodulatory mechanisms were previously studied for
L. rhamnosus CRL1505 (7, 9). (108 cells/mouse/day for five consecutive days). Mice with no lactobacilli treatment
were used as controls. Immune factors were evaluated on day 6. The results
represent data from three independent experiments (n = 6 per group). Letters
indicate significant differences (P < 0.05), a < b < c. SUPPLEMENTARY MATERIAL Mice with no lactobacilli treatment were used as controls. Immune factors were
evaluated on day 6. The results represent data from three independent
experiments (n = 6 per group). Letters indicate significant differences
(P < 0.05), a < b < c. FIGURE S2 | Expression of genes involved in prostaglandins biosynthesis
(PTGS2, PLA2G4A, PTGER4 and PTGES) in porcine intestinal epithelial (PIE) cells
treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027,
L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16,
or L. plantarum CRL681 and challenged with the viral molecular associated
pattern poly(I:C), analyzed by qPCR. PIE cells with no lactobacilli treatment and
stimulated with poly(I:C) were used as controls. The results represent data from
three independent experiments. Letters indicate significant differences
(P < 0.05), a < b < c. FIGURE S2 | Expression of genes involved in prostaglandins biosynthesis
(PTGS2, PLA2G4A, PTGER4 and PTGES) in porcine intestinal epithelial (PIE) cells
treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027,
L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16,
or L. plantarum CRL681 and challenged with the viral molecular associated
pattern poly(I:C), analyzed by qPCR. PIE cells with no lactobacilli treatment and
stimulated with poly(I:C) were used as controls. The results represent data from
three independent experiments. Letters indicate significant differences
(P < 0.05), a < b < c. FIGURE S8 | Levels of serum interferons (IFN-β and IFN-γ), TNF-α and IL-10 in
mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus
IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum
MPL16, or L. plantarum CRL681 (108 cells/mouse/day for five consecutive days),
and then challenged by the nasal route with 250 µg of the viral molecular
associated pattern poly(I:C) for three consecutive days. Mice with no lactobacilli
treatment and challenged with poly(I:C) were used as controls. Serum immune
factors were evaluated on day 2 after the last poly(:C) administration. The results
represent data from three independent experiments (n = 6 per group). Letters
indicate significant differences (P < 0.05), a < b < c. FIGURE S3 | Global overview of the signaling pathways and immune genes
differentially regulated in PIE cells treated with L. rhamnosus CRL1505 or
L. plantarum MPL16 and challenged with poly(I:C). Detailed immunomodulatory
mechanisms were previously studied for L. rhamnosus CRL1505 (16, 20). FIGURE S3 | Global overview of the signaling pathways and immune genes
differentially regulated in PIE cells treated with L. rhamnosus CRL1505 or
L. FUNDING This study was supported by ANPCyT–FONCyT Grant PICT-
2016-0410 to JV, Grant-in-Aid for Scientific Research (A)
(19H00965), and Open Partnership Joint Projects of JSPS
Bilateral Joint Research Projects from the Japan Society for the
Promotion of Science (JSPS) to HK. This research was also
supported by grants from the project of NARO Bio-oriented
Technology
Research
Advancement
Institution
(research
program on the development of innovative technology, No. 01002A) to HK and JSPS Core-to-Core Program, A. Advanced
Research Networks entitled Establishment of international
agricultural
immunology
research-core
for
a
quantum
improvement in food safety. This study was also supported
by grants for Scientific Research on Innovative Areas from the
Ministry of Education, Culture, Science, Sports, and Technology
(MEXT) of Japan (16H06429, 16K21723, and 16H06435) to HT. April 2020 | Volume 11 | Article 543 14 REFERENCES Villena J, Chiba E, Tomosada Y, Salva S, Marranzino G, Kitazawa H,
et al. Orally administered Lactobacillus rhamnosus modulates the respiratory
immune response triggered by the viral pathogen-associated molecular pattern
poly(I:C). BMC Immunol. (2012) 13:53. doi: 10.1186/1471-2172-13-53 15. Ishizuka T, Kanmani P, Kobayashi H, Miyazaki A, Soma J, Suda Y, et al. Immunobiotic bifidobacteria strains modulate rotavirus immune response in April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 15 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. porcine intestinal epitheliocytes via pattern recognition receptor signaling. PLoS One. (2016) 11:e0152416. doi: 10.1371/journal.pone.0152416 porcine intestinal epitheliocytes via pattern recognition receptor signaling. PLoS One. (2016) 11:e0152416. doi: 10.1371/journal.pone.0152416 32. Bass DM. Interferon gamma and interleukin 1, but not interferon alfa, inhibit
rotavirus entry into human intestinal cell lines. Gastroenterology. (1997)
113:81–9. doi: 10.1016/S0016-5085(97)70083-0 16. Albarracin L, Kobayashi H, Iida H, Sato N, Nochi T, Aso H, et al. Transcriptomic analysis of the innate antiviral immune response in porcine
intestinal epithelial cells: influence of immunobiotic Lactobacilli. Front
Immunol. (2017) 8:57. doi: 10.3389/fimmu.2017.00057 33. Hakim MS, Ding S, Chen S, Yin Y, Su J, van der Woude CJ, et al. TNF-α exerts potent anti-rotavirus effects via the activation of classical
NF-κB pathway. Virus Res. (2018) 253:28–37. doi: 10.1016/j.virusres.2018. 05.022 17. Moue M, Tohno M, Shimazu T, Kido T, Aso H, Saito T, et al. Toll-like receptor
4 and cytokine expression involved in functional immune response in an
originally established porcine intestinal epitheliocyte cell line. Biochim Biophys
Acta Gen Subj. (2008) 1780:134–44. doi: 10.1016/j.bbagen.2007.11.006 34. Gandhi GR, Santos VS, Denadai M, da Silva Calisto VK, de Souza Siqueira
Quintans J, de Oliveira e Silva AM, et al. Cytokines in the management of
rotavirus infection: a systematic review of in vivo studies. Cytokine. (2017)
96:152–60. doi: 10.1016/j.cyto.2017.04.013 18. Shimazu T, Villena J, Tohno M, Fujie H, Hosoya S, Shimosato T, et al. Immunobiotic Lactobacillus jensenii elicits anti-inflammatory activity in
porcine intestinal epithelial cells by modulating negative regulators of the
Toll-like receptor signaling pathway. Infect Immun. (2012) 80:276–88. doi:
10.1128/IAI.05729-11 35. Broggi A, Tan Y, Granucci F, Zanoni I. IFN-λ suppresses intestinal
inflammation by non-translational regulation of neutrophil function. Nat
Immunol. (2017) 18:1084–93. doi: 10.1038/ni.3821 36. Zhou R, Wei H, Sun R, Tian Z. Recognition of double-stranded RNA by TLR3
induces severe small intestinal injury in mice. J Immunol. (2007) 178:4548–56. doi: 10.4049/jimmunol.178.7.4548 19. REFERENCES Tomosada Y, Villena J, Murata K, Chiba E, Shimazu T, Aso H, et al. Immunoregulatory effect of bifidobacteria strains in porcine intestinal
epithelial cells through modulation of ubiquitin-editing enzyme A20
expression. PLoS One. (2013) 8:e59259. doi: 10.1371/journal.pone.0059259 37. Araya RE, Jury J, Bondar C, Verdu EF, Chirdo FG. Intraluminal administration
of Poly I:C causes an enteropathy that is exacerbated by administration of
oral dietary antigen. PLoS One. (2014) 9:e99236. doi: 10.1371/journal.pone. 0099236 20. Villena J, Chiba E, Vizoso-Pinto M, Tomosada Y, Takahashi T, Ishizuka T,
et al. Immunobiotic Lactobacillus rhamnosus strains differentially modulate
antiviral immune response in porcine intestinal epithelial and antigen
presenting cells. BMC Microbiol. (2014) 14:126. doi: 10.1186/1471-2180-14-
126 38. Zhou R, Wei H, Sun R, Zhang J, Tian Z. NKG2D recognition mediates Toll-
like receptor 3 signaling-induced breakdown of epithelial homeostasis in the
small intestines of mice. Proc Natl Acad Sci USA. (2007) 104:7512–5. doi:
10.1073/pnas.0700822104 21. Kobayashi H, Albarracin L, Sato N, Kanmani P, Kober AKMH, Ikeda-
Ohtsubo
W,
et
al. Modulation
of
porcine
intestinal
epitheliocytes
immunetranscriptome response by Lactobacillus jensenii TL2937. Benef
Microbes. (2016) 7:769–82. doi: 10.3920/BM2016.0095 39. Clua P, Kanmani P, Zelaya H, Tada A, Humayun Kober AKM, Salva S,
et al. Peptidoglycan from immunobiotic Lactobacillus rhamnosus improves
resistance of infant Mice to respiratory syncytial viral infection and secondary
pneumococcal pneumonia. Front Immunol. (2017) 8:948. doi: 10.3389/fimmu. 2017.00948 22. Macpherson C, Audy J, Mathieu O, Tompkins TA. Multistrain probiotic
modulation of intestinal epithelial cells’ immune response to a double-
stranded RNA ligand, poly(i·c). Appl Environ Microbiol. (2014) 80:1692–700. doi: 10.1128/AEM.03411-13 40. Kanmani P, Clua P, Vizoso-Pinto MG, Rodriguez C, Alvarez S, Melnikov V,
et al. Respiratory commensal bacteria Corynebacterium pseudodiphtheriticum
improves resistance of infant mice to respiratory syncytial virus and
Streptococcus pneumoniae superinfection. Front Microbiol. (2017) 8:1613. doi: 10.3389/fmicb.2017.01613 23. Bagchi P, Nandi S, Chattopadhyay S, Bhowmick R, Halder UC, Nayak MK,
et al. Identification of common human host genes involved in pathogenesis of
different rotavirus strains: an attempt to recognize probable antiviral targets. Virus Res. (2012) 169:144–53. doi: 10.1016/j.virusres.2012.07.021 41. McNamara PS, Smyth RL. The pathogenesis of respiratory syncytial virus
disease in childhood. Br Med Bull. (2002) 61:13–28. doi: 10.1093/bmb/61.1.13 24. Masumizu Y, Zhou B, Kober AKMH, Islam MA, Iida H, Ikeda-Ohtsubo W,
et al. Isolation and immunocharacterization of Lactobacillus salivarius from
the Intestine of Wakame-Fed pigs to develop novel “Immunosynbiotics”. Microorganisms. (2019) 7:167. doi: 10.3390/microorganisms7060167 42. REFERENCES Sun J, Cardani A, Sharma AK, Laubach VE, Jack RS, Müller W, et al. Autocrine
regulation of pulmonary inflammation by effector T-cell derived IL-10 during
infection with respiratory syncytial virus. PLoS Pathog. (2011) 7:e1002173. doi: 10.1371/journal.ppat.1002173 25. Arce LP, Raya Tonetti MF, Raimondo MP, Müller MF, Salva S, Álvarez S,
et al. Oral vaccination with Hepatitis E virus capsid protein and immunobiotic
bacterium-like particles induce intestinal and systemic immunity in mice. Probiotics Antimicrob Proteins. (2019):doi: 10.1007/s12602-019-09598-7 43. Loebbermann J, Schnoeller C, Thornton H, Durant L, Sweeney NP, Schuijs
M, et al. Openshaw PJ. IL-10 regulates viral lung immunopathology during
acute respiratory syncytial virus infection in mice. PLoS One. (2012) 7:e32371. doi: 10.1371/journal.pone.0032371 26. Bardach A, Ciapponi A, Garcia-Marti S, Glujovsky D, Mazzoni A, Fayad
A, et al. Epidemiology of acute otitis media in children of Latin America
and the Caribbean: a systematic review and meta-analysis. Int J Pediatr
Otorhinolaryngol. (2011) 75:1062–70. doi: 10.1016/j.ijporl.2011.05.014 44. Salva S, Nuñez M, Villena J, Ramón A, Font G, Alvarez S. Development of
a fermented goats’ milk containing Lactobacillus rhamnosus: in vivo study
of health benefits. J Sci Food Agric. (2011) 91:2355–62. doi: 10.1002/jsfa. 4467 27. Edmond K, Scott S, Korczak V, Ward C, Sanderson C, Theodoratou E,
et al. Long term sequelae from childhood pneumonia; systematic review and
meta-analysis. PLoS One. (2012) 7:e31239. doi: 10.1371/journal.pone.0031239 45. Villena J, Saavedra L, Hebert EM, Suda Y, Masumizu Y, Albarracin
L, et al. Draft genome sequence of Lactobacillus plantarum MPL16,
a
wakame-utilizing
immunobiotic
strain
isolated
from
swine
feces. Genome
Announc. (2017)
5:e00006–17. doi:
10.1128/genomeA. 00006-17 28. Gentile A, Bardach A, Ciapponi A, Garcia-Marti S, Aruj P, Glujovsky D,
et al. Epidemiology of community-acquired pneumonia in children of Latin
America and the Caribbean: a systematic review and meta-analysis. Int J Infect
Dis. (2012) 16:e5–15. doi: 10.1016/j.ijid.2011.09.013 Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. 29. Bortz G, Thomas H. Biotechnologies for inclusive development: scaling up,
knowledge intensity and empowerment. (the case of the probiotic yoghurt
‘Yogurito’ in Argentina). Innov Dev. (2017) 7:37–61. doi: 10.1080/2157930X. 2017.1281206 Copyright © 2020 Albarracin, Garcia-Castillo, Masumizu, Indo, Islam, Suda,
Garcia-Cancino, Aso, Takahashi, Kitazawa and Villena. This is an open-access article
distributed under the terms of the Creative Commons Attribution License (CC BY). REFERENCES The use, distribution or reproduction in other forums is permitted, provided the
original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. No
use, distribution or reproduction is permitted which does not comply with these terms. Copyright © 2020 Albarracin, Garcia-Castillo, Masumizu, Indo, Islam, Suda,
Garcia-Cancino, Aso, Takahashi, Kitazawa and Villena. This is an open-access article
distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the
original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. No
use, distribution or reproduction is permitted which does not comply with these terms. 30. Sen A, Rothenberg ME, Mukherjee G, Feng N, Kalisky T, Nair N, et al. Innate
immune response to homologous rotavirus infection in the small intestinal
villous epithelium at single-cell resolution. Proc Natl Acad Sci USA. (2012)
109:20667–72. doi: 10.1073/pnas.1212188109 f
(
)
The use, distribution or reproduction in other forums is permitted, provided the
original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. No
use, distribution or reproduction is permitted which does not comply with these terms. 31. Hoffmann HH, Schneider WM, Rice CM. Interferons and viruses: an
evolutionary arms race of molecular interactions. Trends Immunol. (2015)
36:124–38. doi: 10.1016/j.it.2015.01.004 April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 16
|
https://openalex.org/W2909404937
|
https://europepmc.org/articles/pmc6334337?pdf=render
|
English
| null |
Genome-Based Approach Delivers Vaccine Candidates Against Pseudomonas aeruginosa
|
Frontiers in immunology
| 2,019
|
cc-by
| 8,620
|
Genome-Based Approach Delivers
Vaccine Candidates Against
Pseudomonas aeruginosa
Irene Bianconi 1†, Beatriz Alcalá-Franco 1†, Maria Scarselli 2†, Mattia Dalsass 2,3,
Scilla Buccato 2, Annalisa Colaprico 2, Sara Marchi 2, Vega Masignani 2‡ and
Alessandra Bragonzi 1*‡ 1 Infection and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele
Scientific Institute, Milan, Italy, 2 GSK, Siena, Italy, 3 Dipartimento di Scienze Cliniche e Biologiche, Universitá degli Studi di
Torino, Turin, Italy PA5340 combined
with PA3526-MotY gave the maximum protection. Both proteins were surface exposed
by immunofluorescence and triggered a specific immune response. Combination of
these two protein antigens could represent a potential vaccine to prevent P. aeruginosa
infection Edited by:
Pedro A. Reche,
Complutense University of Madrid,
Spain Reviewed by:
Paola Massari,
Tufts University School of Medicine,
United States
Giampiero Pietrocola,
University of Pavia, Italy *Correspondence:
Alessandra Bragonzi
bragonzi.alessandra@hsr.it †These authors have contributed
equally to this work and share first
authorship ‡These authors have contributed
equally to this work and share senior
authorship Specialty section:
This article was submitted to
Vaccines and Molecular Therapeutics,
a section of the journal
Frontiers in Immunology Specialty section:
This article was submitted to
Vaccines and Molecular Therapeutics,
a section of the journal
Frontiers in Immunology Keywords: Pseudomonas aeruginosa, reverse vaccinology, vaccine, respiratory infection, mouse model Received: 17 September 2018
Accepted: 06 December 2018
Published: 09 January 2019 ORIGINAL RESEARCH
published: 09 January 2019
doi: 10.3389/fimmu.2018.03021 High incidence, severity and increasing antibiotic resistance characterize Pseudomonas
aeruginosa infections, highlighting the need for new therapeutic options. Vaccination
strategies to prevent or limit P. aeruginosa infections represent a rational approach to
positively impact the clinical outcome of risk patients; nevertheless this bacterium remains
a challenging vaccine target. To identify novel vaccine candidates, we started from
the genome sequence analysis of the P. aeruginosa reference strain PAO1 exploring
the reverse vaccinology approach integrated with additional bioinformatic tools. The
bioinformatic approaches resulted in the selection of 52 potential antigens. These
vaccine candidates were conserved in P. aeruginosa genomes from different origin
and among strains isolated longitudinally from cystic fibrosis patients. To assess the
immune-protection of single or antigens combination against P. aeruginosa infection,
a vaccination protocol was established in murine model of acute respiratory infection. Combinations of selected candidates, rather than single antigens, effectively controlled
P. aeruginosa infection in the in vivo model of murine pneumonia. Five combinations were
capable of significantly increase survival rate among challenged mice and all included
PA5340, a hypothetical protein exclusively present in P. aeruginosa. PA5340 combined
with PA3526-MotY gave the maximum protection. Both proteins were surface exposed
by immunofluorescence and triggered a specific immune response. Combination of
these two protein antigens could represent a potential vaccine to prevent P. aeruginosa
infection High incidence, severity and increasing antibiotic resistance characterize Pseudomonas
aeruginosa infections, highlighting the need for new therapeutic options. Vaccination
strategies to prevent or limit P. aeruginosa infections represent a rational approach to
positively impact the clinical outcome of risk patients; nevertheless this bacterium remains
a challenging vaccine target. To identify novel vaccine candidates, we started from
the genome sequence analysis of the P. aeruginosa reference strain PAO1 exploring
the reverse vaccinology approach integrated with additional bioinformatic tools. The
bioinformatic approaches resulted in the selection of 52 potential antigens. These
vaccine candidates were conserved in P. aeruginosa genomes from different origin
and among strains isolated longitudinally from cystic fibrosis patients. To assess the
immune-protection of single or antigens combination against P. aeruginosa infection,
a vaccination protocol was established in murine model of acute respiratory infection. Combinations of selected candidates, rather than single antigens, effectively controlled
P. aeruginosa infection in the in vivo model of murine pneumonia. Five combinations were
capable of significantly increase survival rate among challenged mice and all included
PA5340, a hypothetical protein exclusively present in P. aeruginosa. Keywords: Pseudomonas aeruginosa, reverse vaccinology, vaccine, respiratory infection, mouse model P. aeruginosa Antigens Selection by
Genome-Wide Screening P. aeruginosa Antigens Selection by
Genome-Wide Screening Genome Wide Screening
Among 5,570 open reading frames (ORFs) encoded by P. aeruginosa PAO1 strain (5), we predicted a total of 2,430 surface
or membrane-associated proteins by using high throughput
bioinformatics
localization
prediction
tools. In
particular,
subcellular localization was predicted by PsortB software. In the case of predicted non-cytoplasmic polypeptides the
presence of signal peptide and localization of cleavage site
were predicted with SignalP. N-terminal signatures predictive
of lipoproteins were identified by using the LipoP server and
putative transmembrane regions were predicted with Tmpred. Among them, 307 were classified as outer membrane proteins
or lipoproteins, 583 as periplasmic proteins, and 2,109 as inner
membrane proteins. The remaining 2,562 ORFs were predicted
to encode cytoplasmic proteins. Since inner membrane proteins
are barely exposed on the outside of the bacterium and are
difficult to express and purify, all were discarded from selection
except those with sequence similarities to known virulence
factors or extracellular proteins from other bacterial pathogens. The final selection totaled 950 ORFs (Figure 1). In recent years, remarkable progress has been made in
the identification of P. aeruginosa virulence factors and their
variations among different infection processes. It has been more
accurately recognized that P. aeruginosa is an antigenically
variable microorganism that adapts easily to different growth
conditions and escapes host immune recognition. The high
variability of the proteins among different P. aeruginosa strains
and within the same strain, grown in diverse environmental
conditions, may represent a serious obstacle to the development
of a globally effective anti–P. aeruginosa vaccine (10). So
far, P. aeruginosa vaccine candidates have been found by
classical approach—by identifying more abundant surface
proteins and oligosaccharides or by selecting specific virulence
factors, according to their relevance in the disease outcome. Integrated genomics and proteomics approaches have been
recently used to predict vaccine candidates against P. aeruginosa
(11). Although several vaccine formulations have been tested
clinically, none has been licensed (10, 12). P. aeruginosa
vaccines tested so far in humans consisted of antigens targeting
single rather than multiple virulence mechanisms—OprF-
OprI fusion (13), flagella (14), O antigen-conjugated vaccines
(15), high molecular weight alginate (16). Further success in
P. aeruginosa vaccine development may require a different
approach, including bacterial genome evaluation to identify
novel antigen combinations potentially addressing multiple
virulence mechanisms, such as initial bacterial colonization,
immune evasion, colony aggregation and cytotoxicity. Citation: Bianconi I, Alcalá-Franco B,
Scarselli M, Dalsass M, Buccato S,
Colaprico A, Marchi S, Masignani V
and Bragonzi A (2019)
Genome-Based Approach Delivers
Vaccine Candidates Against
Pseudomonas aeruginosa. Front. Immunol. 9:3021. doi: 10.3389/fimmu.2018.03021 P. aeruginosa infections are among the most severe public health issues. This opportunistic
bacterium belongs to the multi-drug resistant (MDR) ESKAPE pathogens, along with
Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and
Enterobacter. According to data from Centers for Disease Control, P. aeruginosa is responsible
for millions of infections each year in the community, 10–15% of all healthcare-associated
infections, with more than 300,000 cases annually in the EU, USA and Japan (1). Patients
hospitalized in intensive care units (ICU) run a high risk of acquiring P. aeruginosa as they January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org P. aeruginosa Vaccine Bianconi et al. may develop ventilator-associated pneumonia (VAP) and sepsis
(2–4). Other risk groups are patients with a compromised
immune system, either from immunosuppressive therapies and
underlying diseases such as cancer, AIDS or hereditary cystic
fibrosis (CF). This high prevalence is partly due to the vast
arsenal of virulence factors that facilitates acute infections and
the propensity of P. aeruginosa to form highly structured biofilm
communities that cause chronic infections (5). serogroup B Neisseria meningitidis (MenB), now licensed in
several countries worldwide (19, 20). Reverse vaccinology aims
at identifying surface exposed proteins, ideally playing a relevant
role in pathogenesis, which can serve as targets of the host
immune system. This approach has not yet been implemented
for P. aeruginosa. In this study, reverse vaccinology approach
was combined with advanced genomic technologies to select
new protein antigens against P. aeruginosa. We report that
combinations of selected candidates, more than single antigens,
effectively control P. aeruginosa infections in a mouse model of
acute pneumonia. Taking the severity of the illness into account, current
treatment guidelines for the management of bacterial infection
recommend single antibiotic or combination therapy. Despite
the wide arsenal of drugs for P. aeruginosa infections available
on the market, inefficacy of these treatments is commonplace. Resistance rapidly emerges, usually linked to intrinsic bacterial
resistance mechanisms, development of new antibiotic resistance,
and/or limited penetration of antibiotics into biofilms (3,
6). Development of antibiotics with a novel mode of action
and/or alternative therapies remains an urgent need for
patients. Citation: Antibacterial agents launched in recent decades were
modifications of existing molecules; the development of entirely
new classes of antibiotics has been largely abandoned (7). Immunotherapy for preventing pulmonary infection has also
been tested (8), but clinical efficacy has been disappointing (9,
10). Immunization strategies do not cover P. aeruginosa infection
in healthcare practices. Frontiers in Immunology | www.frontiersin.org P. aeruginosa Antigens Selection by
Genome-Wide Screening g
In a second step of prioritization and to avoid selection
of potential self-antigens, we excluded all proteins containing
domains with sequence similarity (E-value>1e-10) to human
and/or mouse proteins, narrowing the selection to 824 proteins. To identify proteins more directly related to P. aeruginosa
pathogenesis and fitness, and to avoid widespread bacterial
housekeeping factors, sequence comparison to E. coli K12 whole
proteome was performed; we discarded P. aeruginosa proteins
sharing more than 40% sequence similarity over at least 70% of
the length of the E. coli counterpart. As sequence conservation
is highly desirable for broad-spectrum vaccine candidates, a
comparative analysis was performed with the genome sequence
of seven published P. aeruginosa strains including clinical isolates
of different origins (PA14, LESB58, PA7, 2192, C3719, PACS2,
RP73); only proteins belonging to the core genome were kept. Candidate selection was also refined by removing short peptides
(<150 aa long), eventually leading to a total of 531 hits. To further
prioritize the candidates and reduce the final pool of proteins for
experimental testing, a PSI-Blast analysis was conducted; results
were manually curated to remove any residual protein putatively
involved in intermediate metabolism, DNA synthesis, translation During the past two decades, reverse vaccinology has
revolutionized the approach to vaccine research (17, 18),
ultimately leading to the development of new generation
vaccines based on antigens previously unrecognized by other
approaches. One is 4CMenB, the first universal vaccine against January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 2 Bianconi et al. P. aeruginosa Vaccine FIGURE 1 | Schematic workflow of antigen selection in silico. The complete PAO1 proteome has been analyzed as described in the text. Distribution of ORFs
according to predicted sub-cellular localization using Psort is summarized at the top. Below, selection steps succession is reported, indicating the number of
candidates (hits) selected after each step. C: cytoplasm; IN: inner membrane; P: periplasm; OM: outer membrane. FIGURE 1 | Schematic workflow of antigen selection in silico. The complete PAO1 proteome has been analyzed as described in the text. Distribution of ORFs
according to predicted sub-cellular localization using Psort is summarized at the top. Below, selection steps succession is reported, indicating the number of
candidates (hits) selected after each step. C: cytoplasm; IN: inner membrane; P: periplasm; OM: outer membrane. challenged intratracheally (i.t.) with 5 × 106 CFU/lung of P. P. aeruginosa Antigens Selection by
Genome-Wide Screening aeruginosa reference strain PAO1 and monitored twice a day
for 1 week for health parameters indicative of animal wellness. In this model, all mice immunized with Alum alone (negative
control group) consistently showed symptoms of a severe clinical
disease and died within 48 h, whereas mice immunized with
whole cell inactivated PAO1 bacteria were consistently protected
by homologous challenge in a dose-dependent manner. Of the
30 antigens tested, 10 showed a modest increase in survival
compared to the negative control (up to 20% at day 5) and were
investigated further (Table 1 and Figure 2). The other 20 proteins
tested did not differ substantially from the negative control and
were discarded (data not shown). Survival of mice vaccinated
with OprF-OprI fusion (10.7%) was comparable to that observed
by vaccination with the 10 selected proteins. and repair, protein synthesis and transport, and more generally,
in any cellular process confined to the bacterial cytoplasm. The
final pool of in silico selected candidates included 52 antigens—
31 proteins of known and 21 of unknown functions (Figure 1
and Table S1). The presence of well-known virulence factors like
ExoA and ExoT, as well as relevant outer membrane proteins
like OprF and OprH in the final list of candidates confirmed the
reliability of the selection strategy. When tested against an extended panel of 104 P. aeruginosa
complete genomes, it emerged that all candidates share a mean
identity/coverage ratio ranging from 0.78 to 1.00 (Figure S1)
confirming that a vast proportion of epitopes potentially
presented by each candidate to the immune system is conserved
across the natural P. aeruginosa population. Frontiers in Immunology | www.frontiersin.org Evaluation of Combinations of Candidates
in a Murine Model of Pneumonia C57Bl/6 male mice were challenged with PAO1 (5*106
cfu) 2 weeks after last vaccination with ten single antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1
heat-inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at FIGURE 2 | Survival curves of groups of mice immunized with single antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1 (5*106
cfu) 2 weeks after last vaccination with ten single antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1
heat-inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at
least two/three independent experiments (n = 16–40). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative
control group. N refers to the number of animals. FIGURE 2 | Survival curves of groups of mice immunized with single antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1 (5*106
cfu) 2 weeks after last vaccination with ten single antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1
heat-inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at
least two/three independent experiments (n = 16–40). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative
control group. N refers to the number of animals. PA0328-AaaA,
PA2407-FpvC,
PA3526-MotY,
PA4082-
CupB5, PA4765-OmlA, PA5047, and PA5340) the antisera
obtained
immunizing
with
recombinant
proteins
were
used in Western Blot and immunofluorescence microscopy
(Table 1
and
Figure 4). All
the
antisera
recognized
the
recombinant proteins, the homologous P. aeruginosa strain
PAO1 and the heterologous clinical isolate MDR-RP73; this
demonstrates the capacity of the vaccine candidates to induce
specific antibody production that can recognize the native
proteins. PA0328-AaaA,
PA2407-FpvC,
PA3526-MotY,
PA4082-
CupB5, PA4765-OmlA, PA5047, and PA5340) the antisera
obtained
immunizing
with
recombinant
proteins
were
used in Western Blot and immunofluorescence microscopy
(Table 1
and
Figure 4). All
the
antisera
recognized
the
recombinant proteins, the homologous P. aeruginosa strain
PAO1 and the heterologous clinical isolate MDR-RP73; this
demonstrates the capacity of the vaccine candidates to induce
specific antibody production that can recognize the native
proteins. Evaluation of Combinations of Candidates
in a Murine Model of Pneumonia 0.015, and 0.015, respectively) and mean survival time (one-way
ANOVA p-value < 0.01) when compared with negative controls
(Figure 3 and Figure S2). The best antigens combination was
PA5340+PA3526-MotY, with survival increased up to 50%. Three combinations described above, PA5340+PA3526-motY,
PA5340+PA5112-EstA, and PA5340+PA0328-AaaA, increased
survival significantly when compared with OprF-OprI (Mantel-
Cox test 0.0091, 0.0009, and 0.012, respectively). Interestingly,
an increase in survival rate was also observed (though not
statistically significant) when OprF-OprI was combined with
PA5340, going from 10.7% of the fusion alone to 40% when
tested in combination (Mantel-Cox test 0.058). To determine whether the selected proteins were effectively
expressed and exposed on the surface of bacterial cells, a double
immunofluorescence was carried out with the murine antisera
and a specific antibody for P. aeruginosa anti-cell wall as initial
characterization. Co-localization of the two signals could suggest
that the proteins were present at the bacterial cell surface. As expected, sera of naïve mice did not recognize antigens
while antisera of mice immunized with whole cell inactivated Evaluation of Combinations of Candidates
in a Murine Model of Pneumonia Of 52 P. aeruginosa vaccine candidates (Table S1), 30 ORFs
(57.7%) were successfully expressed in E. coli BL21 as His-tag
fusions. OprF-OprI fusion, designed according to the known
construct used in the recent clinical trial (21), was included in this
study. Ability of these antigens to protect against P. aeruginosa
infection was tested in a mouse model of acute pneumonia
(22). C57Bl/6 mice were immunized intraperitoneally (i.p.) with
10 ug of each protein formulated with aluminum hydroxide
(Alum) as adjuvant at 0, 21, and 35 days. At day 50, mice were In order to increase the survival rate of vaccinated mice,
proteins conferring higher protection were pooled in group
of two, and 22 combinations were tested. Five combinations,
all containing the antigen candidate PA5340, were the most
promising
(PA5340+PA1178-OprH,
PA5340+PA3526-motY,
PA5340+PA5112-EstA,
PA5340+PA5047,
PA5340+PA0328-
AaaA). These combinations showed a significant increase in both
survival curves (Mantel-Cox test p < 0.0002, 0.0019, 0.0027, January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 3 P. aeruginosa Vaccine Bianconi et al. TABLE 1 | Top line vaccine candidates of P. aeruginosa. Locus_tag
Protein annotation
Surface exposure(a)
Antigenic potential(b)
Sequence conservation(c)
Sequence conservation(d)
PA0328
arginine-specific autotransporter AaaA
Yes
Yes
99.3% ± 0.2%
99.2% ± 0.3%
PA1178
outer membrane protein OprH precursor
Yes
Yes
100% ± 0%
99.9% ± 0.2%
PA1248
outer membrane protein AprF precursor
Yes
Yes
99.6%± 0.3%
99.2%± 4.6%
PA2407
putative adhesion protein FpvC
Yes
Yes
100% ± 0%
98.3% ± 10.4%
PA3526
outer membrane protein precursor MotY
Yes
Yes
99.1% ± 0.8%
99.7% ± 0.5%
PA4082
adhesive protein CupB5
Yes
Yes
98.8% ± 0.5%
98.5% ± 2.9%
PA4765
outer membrane lipoprotein OmlA precursor
Yes
Yes
99.7% ± 0.3%
98.9% ± 7.2%
PA5047
putative Zn-dependent protease
Yes
Yes
99.9% ± 0.1%
99.2% ± 7.1%
PA5112
esterase EstA
No
Yes
99.8% ± 0.2%
99.1% ± 7.2%
PA5340
hypothetical protein
Yes
Yes
98.8% ± 0.3%
99.2% ± 0.3%
aSurface exposure suggested by immunofluorescence microscopy co-localization (see text). bEvaluated by Western Blot against recombinant proteins, P. aeruginosa strain PAO1 and
clinical isolate MDR-RP73 (see text). Sequence conservation expressed as mean percentage of amino acid identity ± standard deviation calculated among a collection of CF clinical
strains cand on the public collection of 104 completed P. aeruginosa genomes available in GenBank (see text)d. TABLE 1 | Top line vaccine candidates of P. aeruginosa. Evaluation of Combinations of Candidates
in a Murine Model of Pneumonia |
p
g
Locus_tag
Protein annotation
Surface exposure(a)
Antigenic potential(b)
Sequence conservation(c)
Sequence conservation(d)
PA0328
arginine-specific autotransporter AaaA
Yes
Yes
99.3% ± 0.2%
99.2% ± 0.3%
PA1178
outer membrane protein OprH precursor
Yes
Yes
100% ± 0%
99.9% ± 0.2%
PA1248
outer membrane protein AprF precursor
Yes
Yes
99.6%± 0.3%
99.2%± 4.6%
PA2407
putative adhesion protein FpvC
Yes
Yes
100% ± 0%
98.3% ± 10.4%
PA3526
outer membrane protein precursor MotY
Yes
Yes
99.1% ± 0.8%
99.7% ± 0.5%
PA4082
adhesive protein CupB5
Yes
Yes
98.8% ± 0.5%
98.5% ± 2.9%
PA4765
outer membrane lipoprotein OmlA precursor
Yes
Yes
99.7% ± 0.3%
98.9% ± 7.2%
PA5047
putative Zn-dependent protease
Yes
Yes
99.9% ± 0.1%
99.2% ± 7.1%
PA5112
esterase EstA
No
Yes
99.8% ± 0.2%
99.1% ± 7.2%
PA5340
hypothetical protein
Yes
Yes
98.8% ± 0.3%
99.2% ± 0.3%
aSurface exposure suggested by immunofluorescence microscopy co-localization (see text). bEvaluated by Western Blot against recombinant proteins, P. aeruginosa strain PAO1 and
clinical isolate MDR-RP73 (see text). Sequence conservation expressed as mean percentage of amino acid identity ± standard deviation calculated among a collection of CF clinical
strains cand on the public collection of 104 completed P. aeruginosa genomes available in GenBank (see text)d. FIGURE 2 | Survival curves of groups of mice immunized with single antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1 (5*106
cfu) 2 weeks after last vaccination with ten single antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1
heat-inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at
least two/three independent experiments (n = 16–40). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative
control group. N refers to the number of animals. Surface exposure(a)
Antigenic potential(b)
Sequence conservation(c)
Sequence conservation(d) aSurface exposure suggested by immunofluorescence microscopy co-localization (see text). bEvaluated by Western Blot against recombinant proteins, P. aeruginosa strain PAO1 and
clinical isolate MDR-RP73 (see text). Sequence conservation expressed as mean percentage of amino acid identity ± standard deviation calculated among a collection of CF clinical
strains cand on the public collection of 104 completed P. aeruginosa genomes available in GenBank (see text)d. FIGURE 2 | Survival curves of groups of mice immunized with single antigens selected as vaccine candidates. January 2019 | Volume 9 | Article 3021 In vitro Characterization of Selected
Antigens To characterize antigenic potential and cellular localization of
selected antigens (PA1178-OprH, PA1248-AprF, PA5112-EstA, January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 4 P. aeruginosa Vaccine Bianconi et al. FIGURE 3 | Survival curves of groups of mice immunized with combined antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1
(5*106 cfu) 2 weeks after last vaccination with combined antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1
heat inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at
least two/three independent experiments (n = 17–33). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative
control group: *p < 0.05, **p < 0.01, ***p < 0.001. N refers to the number of animals. FIGURE 4 | Cellular localization of vaccine candidates PA5340 and PA3526-MotY and controls by immunofluorescence microscopy. Immunofluorescence staining
with confocal microscopy shows the localization of antigens (green) (A–E) and the PAO1 cell wall (red) (F–J). For antigens localization the antisera of naïve mice (A) or
immunized with PA3526-MotY (B), PA5340 (C), OprF-OprI (D) or heat inactivated PAO1 (E) were used. Merged images show the co-localization of the two signals
(yellow) (K–O) suggesting that proteins could be surface exposed. Detailed co-localization of antigens of interest is shown in the magnification (L, M, N). FIGURE 3 | Survival curves of groups of mice immunized with combined antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1
(5*106 cfu) 2 weeks after last vaccination with combined antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1
heat inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at
least two/three independent experiments (n = 17–33). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative
control group: *p < 0.05, **p < 0.01, ***p < 0.001. N refers to the number of animals. FIGURE 3 | Survival curves of groups of mice immunized with combined antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1
(5*106 cfu) 2 weeks after last vaccination with combined antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1
heat inactivated (h.i.) groups (positive control). In vitro Characterization of Selected
Antigens An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at
least two/three independent experiments (n = 17–33). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative
control group: *p < 0.05, **p < 0.01, ***p < 0.001. N refers to the number of animals. FIGURE 4 | Cellular localization of vaccine candidates PA5340 and PA3526-MotY and controls by immunofluorescence microscopy. Immunofluorescence staining
with confocal microscopy shows the localization of antigens (green) (A–E) and the PAO1 cell wall (red) (F–J). For antigens localization the antisera of naïve mice (A) or
immunized with PA3526-MotY (B), PA5340 (C), OprF-OprI (D) or heat inactivated PAO1 (E) were used. Merged images show the co-localization of the two signals
(yellow) (K–O) suggesting that proteins could be surface exposed. Detailed co-localization of antigens of interest is shown in the magnification (L, M, N). FIGURE 4 | Cellular localization of vaccine candidates PA5340 and PA3526-MotY and controls by immunofluorescence microscopy. Immunofluorescence staining
with confocal microscopy shows the localization of antigens (green) (A–E) and the PAO1 cell wall (red) (F–J). For antigens localization the antisera of naïve mice (A) or
immunized with PA3526-MotY (B), PA5340 (C), OprF-OprI (D) or heat inactivated PAO1 (E) were used. Merged images show the co-localization of the two signals
(yellow) (K–O) suggesting that proteins could be surface exposed. Detailed co-localization of antigens of interest is shown in the magnification (L, M, N). PAO1 showed a strong co-localization signal. The same staining
was performed with the antisera of mice immunized with the
10 selected antigens and OprF-OprI (Table 1 and Figure 4). According to immunofluorescence microscopy results, all the
selected antigens co-localized with the cell surface antibody,
with the exception of PA5112-EstA. In particular, a similar January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 5 P. aeruginosa Vaccine Bianconi et al. co-localization pattern was observed with antisera of PA5340,
PA3526-MotY, and OprF-OprI. co-localization pattern was observed with antisera of PA5340,
PA3526-MotY, and OprF-OprI. is an antigenically variable microorganism and can undergo
phenotypic variation under changing environmental conditions,
such as the airways in CF patients (23). In particular,
the
adaptation
process
generates
unique
lineages
of
P. aeruginosa
pathogenic
variants
that
differ
systematically
from environmentally-acquired strains and can escape immune
recognition (24). In vitro Characterization of Selected
Antigens We considered this question worthy of
investigation and expanded the comparative sequence analysis
on a collection of 19 clinical strains isolated from CF patients
at the onset of infection and after years of chronic colonization
(25, 26). The selected antigens were conserved among CF clinical
isolates indicating that the corresponding genes were not under
positive selection and these antigens could be useful for targeting
both the initial infecting strains and those promoting progression
toward chronic infection. Considering the epidemiology of P. aeruginosa infection, both environmental-to-host and patient-
to-patient transmission have been described and it appears likely
that highly conserved not-adapted antigens might have superior
clinical relevance. Frontiers in Immunology | www.frontiersin.org Conservation Profile of Selected Antigens
Among a Collection of CF Clinical Isolates Conservation of the selected antigens among P. aeruginosa
genomes was initially considered as selection criteria and the
candidates were checked in the ensemble of publicly available
complete genome sequences. Moreover, we investigated the
sequence conservation of the ten most protective antigens in
a collection of 19 clinical strains isolated from CF patients at
the onset of infection and after years of chronic colonization
(Figure S3). Full-length sequences of the ten genes were obtained
by PCR from most of the 19 strains. Nucleotide sequences were
translated into the amino acid (aa) sequences and compared
with PAO1 protein sequence. Overall, identity conservation levels
were higher than 98% (Table 1 and Table S2), confirming a
strong potential of these proteins to induce effective and cross-
protective immunity among P. aeruginosa circulating strains. Previous studies that tested P. aeruginosa antigens provided
valuable information on the feasibility of vaccination but
were limited by either the number of antigens tested and by
redundancy in their selection (10). Abundant surface proteins
and oligosaccharides, particular virulence factors have been
previously considered. However, none of these started from a
large scale screening, performed comparative analysis of the
P. aeruginosa protein antigens and tested in animal models
for preclinical studies. Our screening identified 52 antigens
distributed as having known (31) or unknown functions (21). The
presence of known virulence factors in the final list of candidates
confirmed the reliability of this general selection strategy. We
identified a number of proteins, like ExoA and ExoT, as well
as relevant outer membrane proteins, like OprF, and OprH,
already shown to be required for virulence in P. aeruginosa. The outer membrane protein PscC precursor (PA1716) identified
in this study was previously identified by integrated genomics
and proteomics approach (11). Furthermore, different proteins
involved in the chaperone/usher pathways (CupA-E) were
identified in this study and Rashid et al. (11). Half of the
candidate antigens identified belonged to the functional category
of hypothetical, unknown, and unclassified genes (21 genes,
35.8% of the total), suggesting that there is still a large proportion
of potentially immunogenic antigens to be discovered within the
unexplored part of the P. aeruginosa. DISCUSSION As an alternative treatment to antibiotics, immunotherapy
should represent an option to prevent MDR infections by
P. aeruginosa. A universal protein-based vaccine against P. aeruginosa remains a critical unmet medical need. To identify
possible antigens suitable for the development of a P. aeruginosa
vaccine, we explored the reverse vaccinology approach integrated
with additional genomic and bioinformatic approaches. This
strategy involved an initial screening of target antigens on
the basis of their putative cellular localization; this identified
a large number of proteins (2,430 ORFs) predicted to be
surface or membrane-associated to various extents. Note that
the P. aeruginosa genome is larger than most sequenced
bacteria (6.3 Mb) (5) and the resulting high number of 5,570
predicted protein encoding genes challenges this approach. Hence, additional criteria were included for antigen selection,
with the aim of reducing the pool to a reasonable number of
candidates and to rationalize the subsequent experimental steps. In particular, the absence of sequence similarity to proteins
encoded by the commensal E. coli K12 strain, as well as sequence
similarity to proteins involved in primary house-keeping and cell
metabolism functions have been used as cutting edge to narrow
the shortlist of antigens. Proteins displaying epitopes very similar
to those present in widely-conserved proteins from human and
mouse origin were also excluded as candidates, as they might be
poorly immunogenic and have a high probability of behaving as
self-antigens. Several diverse animal models have been used in preclinical
studies of vaccination to evaluate in vivo protection against P. aeruginosa infection. Mouse models, including burned animals,
those with immunocompromised intraperitoneal infection, or
with acute pneumonia, have primarily been used in the
past. These models were used for preclinical evaluation of
candidates like the flagellum, the alginate exopolysaccharide
conjugated to tetanus toxoid, polysaccharides, and outer
membrane protein such as OprF and OprI. (27–31). Based
on our previous experience we consider respiratory infection
in immunocompetent mice a highly robust and appropriate
model to predict efficacy of vaccine candidates for further
clinical testing in patients at risk of respiratory infection, Considering that large sequence diversity characterizes P. aeruginosa genome, we tested the conservation of selected
candidates among the P. aeruginosa complete genome sequences
available on public databases. This analysis confirmed the
presence and conservation of selected antigens in the core
genome. Further
genomic
analysis
considered
sequence
intraclonal diversity of selected antigens in clinical strains
isolated from CF patients. It is recognized that P. Gene Sequencing Reference strain PAO1 (5) and 19 P. aeruginosa clinical
strains isolated from CF patients attending the Medizinische
Hochschule Hannover and described previously (25, 26) were
used to sequence the genes of vaccine candidates. PCR genes
amplification was carried out using the list of primers detailed
in the Supplementary Information. Cloning, Expression, and Purification of P.
aeruginosa Recombinant Proteins Polypeptides antigens from P. aeruginosa PAO1 were PCR-
amplified using specific oligonucleotides and P. aeruginosa
chromosomal DNA as templates. Resulting PCR products were
cloned in pET15b (Novagen) using the PIPE method (44). To express cloned proteins, BL21(DE3)T1r clones containing
pET15b constructs were grown in LB medium containing
100 µg/ml Ampicilin at 37◦C until OD600 = 0.5. Protein
expression was induced by adding 1 mM IPTG and growing at
the same temperature for additional 3 hrs. Conventional protein
extractions and SDS-Page were performed to check protein
expression. Western Blot was used to confirm proper expression
of tested P. aeruginosa antigens. Protein
purification
has
been
performed
as
reported
previously (45). Briefly, bacteria cells undergone to mechanical
or chemical lysis and recombinant polypeptides were recovered
from crude cell extracts by immobilized-metal ion affinity
chromatography (IMAC) using His MultiTrapTM HP 50 mL
NiSepharose High-Performance 96 well-vacuum plates (GE
Healthcare). Polypeptides expressed as insoluble inclusion
bodies were solubilized in 50 mM Tris–HCl elution buffer,
pH 8.8 containing 8 MUrea, 1 mM TCEP-HCl, and 250 mM
imidazole. Renaturation was performed by dialysis in 50 mM
NaH2PO4, pH 8.8 containing 10% (v/v) glycerol, 0.5 M
arginine, 5.0 mM of reduced glutathione, 0.5 mM of oxidized
glutathione in the presence of 4, 2, or 0 M urea. Protein
concentration was determined using the Micro BCA protein
assay reagent kit (Pierce). Protein purity was checked by
SDS-PAGE CRITERION XT Precast Gel (Biorad) followed by
Coomassie blue staining. DISCUSSION In
this work, C57Bl/6 mice succumbed following infection with
high dose of PAO1 virulent P. aeruginosa strain. Vaccination
with whole cell inactivated P. aeruginosa induced an effective
immunological response as demonstrated by full protection of
the mice. Conversely, mice immunization with the adjuvant
alone did not provide any protection as all mice showed severe
clinical disease. These data strongly support the choice of this
robust mouse model for screening and selecting the best vaccine
candidates. Vaccination with the ten purified soluble proteins
on our short list demonstrated distinct disease phenotypes,
ranging from severe pneumonia to partial protection from a
lethal dose of P. aeruginosa infection. We report that half
of the vaccine candidates screened in this study were more
effective when compared to OprF/OprI. It is worth noting
that OprF/OprI fusion was one of the treatments evaluated in
clinical trial although clinical efficacy has been disappointing
(36). Given that vaccines containing several antigens have been
shown to confer better protection than those containing only
one antigen (20, 37), we decided to assess antigen combinations. Selection of antigens to combine was made from the shortlist
of the ten most promising antigens and tested to further
increase the vaccine efficacy and survival rate in murine models. This systematic screening identified five combinations, capable
of significantly increasing the survival rate among challenged
mice. All combinations included PA5340, a hypothetical protein
exclusively present in P. aeruginosa. The maximum proportion
of mice protected against challenge was 50%, achieved with
PA5340 combined with PA3526-MotY. These two proteins were
capable of triggering a specific immune response and initial
characterization could indicate surface exposure. Nevertheless,
as their function is still undetermined, it is unlikely that either
protein would ever be selected by a traditional approach. Overall
this study confirms the capability of reverse vaccinology to give
new impetus in the research of vaccines against P. aeruginosa
infection through the rapid identification of novel vaccine
candidates. analysis against the sequenced genomes was performed using
BLAST. The amino acid sequence of strain PAO1 was aligned
against the protein translation of complete genome sequences
with BLASTp (BLAST 2.2.26+) and against the genome of
human and mouse with VAXGEN (http://www.violinet.org/
vaxgen/index.php) (43). Ethics Statement Animal studies adhered to the Italian Ministry of Health
guidelines for the use and care of experimental animals (protocol
#443). The use of the clinical data is in line with study no. 3739 that was approved by the Ethics Commission of Hannover
Medical School. DISCUSSION aeruginosa January 2019 | Volume 9 | Article 3021 6 P. aeruginosa Vaccine Bianconi et al. such as VAP or CF (22, 32). The mouse model of acute
infection has been extensively employed as the standard in P. aeruginosa pathogenesis and efficacy studies (24, 33–35). In
this work, C57Bl/6 mice succumbed following infection with
high dose of PAO1 virulent P. aeruginosa strain. Vaccination
with whole cell inactivated P. aeruginosa induced an effective
immunological response as demonstrated by full protection of
the mice. Conversely, mice immunization with the adjuvant
alone did not provide any protection as all mice showed severe
clinical disease. These data strongly support the choice of this
robust mouse model for screening and selecting the best vaccine
candidates. Vaccination with the ten purified soluble proteins
on our short list demonstrated distinct disease phenotypes,
ranging from severe pneumonia to partial protection from a
lethal dose of P. aeruginosa infection. We report that half
of the vaccine candidates screened in this study were more
effective when compared to OprF/OprI. It is worth noting
that OprF/OprI fusion was one of the treatments evaluated in
clinical trial although clinical efficacy has been disappointing
(36). Given that vaccines containing several antigens have been
shown to confer better protection than those containing only
one antigen (20, 37), we decided to assess antigen combinations. Selection of antigens to combine was made from the shortlist
of the ten most promising antigens and tested to further
increase the vaccine efficacy and survival rate in murine models. This systematic screening identified five combinations, capable
of significantly increasing the survival rate among challenged
mice. All combinations included PA5340, a hypothetical protein
exclusively present in P. aeruginosa. The maximum proportion
of mice protected against challenge was 50%, achieved with
PA5340 combined with PA3526-MotY. These two proteins were
capable of triggering a specific immune response and initial
characterization could indicate surface exposure. Nevertheless,
as their function is still undetermined, it is unlikely that either
protein would ever be selected by a traditional approach. Overall
this study confirms the capability of reverse vaccinology to give
new impetus in the research of vaccines against P. aeruginosa
infection through the rapid identification of novel vaccine
candidates. such as VAP or CF (22, 32). The mouse model of acute
infection has been extensively employed as the standard in P. aeruginosa pathogenesis and efficacy studies (24, 33–35). FUNDING whole cell heat-inactivated PAO1 strain at different doses (105-
107 CFU). To obtain the antisera, mice were bled at day -
1, 34, and 49. At day 50, mice were challenged with 5 ×
106 CFU of P. aeruginosa PAO1 strain by acute infection and
monitored every 12 h for general wellness as detailed in the
Supplementary Information. This work was sponsored by Novartis Vaccines and Diagnostics
Srl; in March 2015 the Novartis non-influenza Vaccines
business was acquired by the GSK group of companies. The
sponsor was involved in all stages of the study conduct
and analysis. This work was supported in part by the
Italian Cystic Fibrosis Research Foundation (FFC#08/2006
and FFC#10/2009) to AB with the contribution of the
Delegazioni FFC of Como, Catania, Vittoria Ragusa, Latina
and LIFC onlus Associazione regionale siciliana, in memory of
Simone. This work was sponsored by Novartis Vaccines and Diagnostics
Srl; in March 2015 the Novartis non-influenza Vaccines
business was acquired by the GSK group of companies. The
sponsor was involved in all stages of the study conduct
and analysis. This work was supported in part by the
Italian Cystic Fibrosis Research Foundation (FFC#08/2006
and FFC#10/2009) to AB with the contribution of the
Delegazioni FFC of Como, Catania, Vittoria Ragusa, Latina
and LIFC onlus Associazione regionale siciliana, in memory of
Simone. SUPPLEMENTARY MATERIAL AB and VM: conceiving and designing the experiments. BA-F,
IB, MS, SB, SM, AC, and MD: performing experiments. AB, AB and VM: conceiving and designing the experiments. BA-F,
IB, MS, SB, SM, AC, and MD: performing experiments. AB,
BA-F, IB, MS, and VM: analyzing data and interpretation of
the experiments results. AB, BA-F, IB, MS, and VM: writing the
manuscript. IB, MS, SB, SM, AC, and MD: performing experiments. AB,
BA-F, IB, MS, and VM: analyzing data and interpretation of
the experiments results. AB, BA-F, IB, MS, and VM: writing the
manuscript. The Supplementary Material for this article can be found
online at: https://www.frontiersin.org/articles/10.3389/fimmu. 2018.03021/full#supplementary-material Western Blot and Immunofluorescence
Microscopy Specific antisera from immunized mice were used to confirm
protein expression by Western Blot and surface localization
of
antigens
by
immunofluorescence
as
detailed
in
the
Supplementary Information. In silico Analysis and Computational Tools In silico Analysis and Computational Tools
PSORTb (38) was used for the subcellular localization prediction,
SingnalP (39) to predict the SPs and their probable cleavage site
in secreted proteins, the TatP prediction server to predict the
presence of bacterial Tat signal peptides (40), LipoP (41) predict
lipoproteins, TMpred to predict transmembrane segments (42). C57BL/6NCrlBR 5 week-old male mice (Charles River) were
immunized i.p. at day 0, 21, and 35 with recombinant proteins
formulated with Alum, either individually or as a combination
of proteins. The formulations were optimized for pH and
osmolarity. Each antigen was used at 10 µg/formulation/animal. The final concentration of Alum was 2 mg/ml in 10 mM histidine
buffer (pH 6.5). Negative control mice were immunized with
Alum alone, while positive control mice were boosted with To check presence and conservation of vaccine candidates
in other P. aeruginosa genomes, comparative protein sequence January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 7 P. aeruginosa Vaccine Bianconi et al. REFERENCES 13. Westritschnig K, Hochreiter R, Wallner G, Firbas C, Schwameis M, Jilma
B, et al. A randomized, placebo-controlled phase I study assessing the safety
and immunogenicity of a Pseudomonas aeruginosa hybrid outer membrane
protein OprF/I vaccine (IC43) in healthy volunteers. Hum Vacc Immunother. (2014) 10:170–83. doi: 10.4161/hv.26565 1. Boucher HW, Talbot GH, Bradley JS, Edwards JE, Gilbert D, Rice LB, et al. Bad
bugs, no drugs: no ESKAPE! an update from the infectious diseases society of
america. Clin Infect Dis. (2009) 48:1–12. doi: 10.1086/595011 1. Boucher HW, Talbot GH, Bradley JS, Edwards JE, Gilbert D, Rice LB, et al. Bad
bugs, no drugs: no ESKAPE! an update from the infectious diseases society of
america. Clin Infect Dis. (2009) 48:1–12. doi: 10.1086/595011 2. Williams
BJ,
Dehnbostel
J,
Blackwell
TS. Pseudomonas
aeruginosa:
host
defence
in
lung
diseases. Respirology
(2010)
15:1037–56. doi: 10.1111/j.1440-1843.2010.01819.x 2. Williams
BJ,
Dehnbostel
J,
Blackwell
TS. Pseudomonas
aeruginosa:
host
defence
in
lung
diseases. Respirology
(2010)
15:1037–56. doi: 10.1111/j.1440-1843.2010.01819.x 14. Doring G, Meisner C. Stern M. A double-blind randomized placebo-
controlled phase III study of a Pseudomonas aeruginosa flagella vaccine
in cystic fibrosis patients. Proc Natl Acad Sci USA. (2007) 104:11020–5. doi: 10.1073/pnas.0702403104 3. Gellatly
SL,
Hancock
RE. Pseudomonas
aeruginosa:
new
insights
into pathogenesis and host defenses. Pathog Dis. (2013) 67:159–73. doi: 10.1111/2049-632X.12033 3. Gellatly
SL,
Hancock
RE. Pseudomonas
aeruginosa:
new
insights
into pathogenesis and host defenses. Pathog Dis. (2013) 67:159–73. doi: 10.1111/2049-632X.12033 15. Cryz SJ Jr, Lang A, Rüdeberg A, Wedgwood J, Que JU, Fürer E, et al. Immunization of cystic fibrosis patients with a Pseudomonas aeruginosa
O-polysaccharide-toxin a conjugate vaccine. Behring Inst Mitt. (1997)
98:345–9. 4. Chastre J, Fagon JY. Ventilator-associated pneumonia. Am J Respir Crit Care
Med. (2002) 165:867–903. doi: 10.1164/ajrccm.165.7.2105078 4. Chastre J, Fagon JY. Ventilator-associated pneumonia. Am J Respir Crit Care
Med. (2002) 165:867–903. doi: 10.1164/ajrccm.165.7.2105078 5. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ,
et al. Complete genome sequence of Pseudomonas aeruginosa PA01, an
opportunistic pathogen. Nature (2000) 406:959–64. doi: 10.1038/35023079 5. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ,
et al. Complete genome sequence of Pseudomonas aeruginosa PA01, an
opportunistic pathogen. Nature (2000) 406:959–64. doi: 10.1038/35023079 16. Pier GB, DesJardin D, Grout M, Garner C, Bennett SE, Pekoe G, et al., Human
immune response to Pseudomonas aeruginosa mucoid exopolysaccharide
(alginate) vaccine. Infec Immunity (1994) 62:3972–9. 6. Page MG, Heim J. Statistical Analysis The authors thank B. Tummler (Klinische Forschergruppe,
Medizinische Hochschule Hannover, Germany) for supplying
the P. aeruginosa clinical strain and G. B. Pier for providing
specific rabbit anti P. aeruginosa cell wall antibody (Brigham and
Women’s Hospital, Channing Labs, Boston, USA). Statistical calculations and tests were performed using Mantel-
Cox test and one-way ANOVA, considering p < 0.05 as the limit
of statistical significance. REFERENCES Prospects for the next anti-Pseudomonas drug. Curr Opin
Pharmacol. (2009) 9:558–65. doi: 10.1016/j.coph.2009.08.006 17. Mora M, Veggi D, Santini L, Pizza M, Rappuoli R. Reverse vaccinology.Drug
Discov Today (2003) 8:459–64. doi: 10.1016/S1359-6446(03)02689-8 6. Page MG, Heim J. Prospects for the next anti-Pseudomonas drug. Curr Opin
Pharmacol. (2009) 9:558–65. doi: 10.1016/j.coph.2009.08.006 7. Projan SJ, Youngman PJ. Antimicrobials: new solutions badly needed. Curr
Opin Microbiol. (2002) 5:463–5. doi: 10.1016/S1369-5274(02)00364-8 7. Projan SJ, Youngman PJ. Antimicrobials: new solutions badly needed. Curr
Opin Microbiol. (2002) 5:463–5. doi: 10.1016/S1369-5274(02)00364-8 18. Scarselli M, Giuliani MM, Adu-Bobie J, Pizza M, Rappuoli R. The
impact of genomics on vaccine design. Trends Biotechnol. (2005) 23:84–91. doi: 10.1016/j.tibtech.2004.12.008 8. Holder IA. Pseudomonas immunotherapy: a historical overview. Vaccine
(2004) 22:831–9. doi: 10.1016/j.vaccine.2003.11.028 8. Holder IA. Pseudomonas immunotherapy: a historical overview. Vaccine
(2004) 22:831–9. doi: 10.1016/j.vaccine.2003.11.028 19. Grifantini R, Bartolini E, Muzzi A, Draghi M, Frigimelica E, Berger
J, et al. Previously unrecognized vaccine candidates against group B
meningococcus identified by DNA microarrays. Nat Biothecnol. (2002)
20:914–20. doi: 10.1038/nbt728 9. Sedlak-Weinstein E, Cripps AW, Kyd JM, Foxwell AR. Pseudomonas
aeruginosa: the potential to immunise against infection. Expert Opin Biol Ther. (2005) 5:967–82. doi: 10.1517/14712598.5.7.967 10. Döring G, Pier GB. Vaccines and immunotherapy against Pseudomonas
aeruginosa. Vaccine (2008) 26:1011–24. doi: 10.1016/j.vaccine.2007.12.007 20. Giuliani MM, Adu-Bobie J, Comanducci M, Aricò B, Savino S, Santini L, et al. A universal vaccine for serogroup B meningococcus. Proc Natl Acad Sci USA
(2006) 103:10834–9. doi: 10.1073/pnas.0603940103 11. Rashid MI, Naz A, Ali A, Andleeb S. Prediction of vaccine candidates
against Pseudomonas aeruginosa: an integrated genomics and proteomics
approach. Genomics
(2017)
109:274–83. doi:
10.1016/j.ygeno.2017. 05.001 21. Gabelsberger J, Knapp B, Bauersachs S, Enz UI, von Specht BU, Domdey
H. et al. A hybrid outer membrane protein antigen for vaccination against
Pseudomonas aeruginosa. Behring Inst Mitt. (1997) 98:302–14. 12. Sharma A, Krause A, Worgall S. Recent developments for Pseudomonas
vaccines. Hum
Vaccin. (2011)
7:999–1011. doi:
10.4161/hv.7.10. 16369 22. Bragonzi A. Murine models of acute and chronic lung infection with
cystic fibrosis pathogens. IJMM (2010) 300:584–93. doi: 10.1016/j.ijmm.2010. 08.012 January 2019 | Volume 9 | Article 3021 8 Frontiers in Immunology | www.frontiersin.org Bianconi et al. P. aeruginosa Vaccine of Pseudomonas aeruginosa Pneumonia. Antimicrob Chemother. (2016)
60:4991–5000. doi: 10.1128/AAC.00390-16 23. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR, D’Argenio
DA, et al. Genetic adaptation by Pseudomonas aeruginosa to the airways
of cystic fibrosis patients. REFERENCES Proc Natl Acad Sci USA (2006) 103:8487–92
doi: 10.1073/pnas.0602138103 36. Rello J, Krenn CG, Locker G, Pilger E, Madl C, Balica L, et al. A randomized
placebo-controlled phase II study of a Pseudomonas vaccine in ventilated ICU
patients. Crit Care (2017) 21:22. doi: 10.1186/s13054-017-1601-9 24. Cigana C, Lorè NI, Riva C, De Fino I, Spagnuolo L, Sipione B, et al.,
Tracking the immunopathological response to Pseudomonas aeruginosa
during respiratory infections. Sci Rep. (2016) 6:21465. doi: 10.1038/srep
21465 37. Olin P, Rasmussen F, Gustafsson L, Hallander HO, Heijbel H. Randomised
controlled trial of two-component, three-component, and five-component
acellular pertussis vaccines compared with whole-cell pertussis vaccine. Ad
Hoc group for the study of pertussis vaccines. Lancet (1997) 350:1569–77. doi: 10.1016/S0140-6736(97)06508-2 25. Bragonzi A, Wiehlmann L, Klockgether J, Cramer N, Worlitzsch D, Döring
G, et al. Sequence diversity of the mucABD locus in Pseudomonas aeruginosa
isolates from patients with cystic fibrosis. Microbiology (2006) 152:3261–9. doi: 10.1099/mic.0.29175-0 38. Gardy JL, Brinkman FS. Methods for predicting bacterial protein subcellular
localization. Nat Rev Microbiol. (2006) 4:741–51. doi: 10.1038/nrmicro1494 26. Bragonzi A, Wiehlmann L, Klockgether J, Cramer N, Worlitzsch D, Döring
G, et al. Pseudomonas aeruginosa microevolution during cystic fibrosis lung
infection establishes clones with adapted virulence. Am J Res Crit Care Med. (2009) 180:138–45. doi: 10.1164/rccm.200812-1943OC 39. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating
signal peptides from transmembrane regions. Nat Methods (2011) 8:785–6. doi: 10.1038/nmeth.1701 40. Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S. Prediction
of
twin-arginine
signal
peptides. BMC
Bioinform. (2005)
6:167. doi: 10.1186/1471-2105-6-167 27. Zuercher AW, Horn MP, Wu H, Song Z, Bundgaard CJ, Johansen HK, et al. Intranasal immunisation with conjugate vaccine protects mice from systemic
and respiratory tract infection with Pseudomonas aeruginosa. Vaccine (2006)
24:4333–42. doi: 10.1016/j.vaccine.2006.03.007 41. Juncker AS WH, Von Heijne G, Brunak S, Nielsen H, Krogh A. Prediction
of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci. (2003)
12:1652–62. doi: 10.1110/ps.0303703 28. Behrouz B, Hashemi FB, Fatemi MJ, Naghavi S, Irajian G, Halabian R,
et al. Immunization with bivalent flagellin protects mice against fatal
Pseudomonas aeruginosa pneumonia. J Immunol Res. (2017) 2017:5689709. doi: 10.1155/2017/5689709 42. Hofmann KSW. TMbase - a database of membrane spanning proteins
segments. Biol Chem. Hoppe-Seyler (1993) 374:166. 43. He Y, Racz R, Sayers S, Lin Y, Todd T, Hur J, et al. Updates on the web-
based VIOLIN vaccine database and analysis system. Nucleic Acids Res. (2014)
42:D1124–32. REFERENCES doi: 10.1093/nar/gkt1133 29. Kashef N, Behzadian-Nejad Q, Najar-Peerayeh S, Mousavi-Hosseini K,
Moazzeni M, Djavid GE, et al. Synthesis and characterization of Pseudomonas
aeruginosa alginate-tetanus toxoid conjugate. J Med Microbiol. (2006) 55(Pt
10):1441–6. doi: 10.1099/jmm.0.46696-0 44. Bonacci S, Buccato S, Maione D, Petracca R. Successful completion of a
semi-automated enzyme-free cloning method. J Struct Funct Genom. (2016)
17:57–66. doi: 10.1007/s10969-016-9207-z 30. von Specht BU, Knapp B, Muth G, Bröker M, Hungerer KD, Diehl KD,
et al. Protection of immunocompromised mice against lethal infection with
Pseudomonas aeruginosa by active or passive immunization with recombinant
P. aeruginosa outer membrane protein F and outer membrane protein I fusion
proteins. Infec Immun. (1995) 63:1855–62. 45. Palumbo E1, Fiaschi L, Brunelli B, Marchi S, Savino S, Pizza M. Antigen identification starting from the genome: a “Reverse Vaccinology”
approach applied to MenB. Methods Mol Biol. (2012) 799:361–403. doi: 10.1007/978-1-61779-346-2_21 31. ScarffJM, Goldberg JB. Vaccination against Pseudomonas aeruginosa
pneumonia in immunocompromised mice. Clin Vacc Immunol. (2008)
15:367–75. doi: 10.1128/CVI.00419-07 Conflict of Interest Statement: MS, SM, SB, AC, and VM were employees of
Novartis Vaccines and Diagnostics Srl at the time of the study (now part of
the GSK group of companies). They are now employees of the GSK group of
companies. MD is a student at the University of Torino and participated in a post
graduate studentship program at GSK. 32. Kukavica-Ibrulj I, Facchini M, Cigana C, Levesque RC, Bragonzi A. Assessing
Pseudomonas aeruginosa virulence and the host response using murine
models of acute and chronic lung infection. Methods Molecul Biol. (2014)
1149:757–71. doi: 10.1007/978-1-4939-0473-0_58 The remaining authors declare that the research was conducted in the absence of
any commercial or financial relationships that could be construed as a potential
conflict of interest. 33. Lore NI, Cigana C, De Fino I, Riva C, Juhas M, Schwager S, et al. Cystic
fibrosis-niche
adaptation
of
Pseudomonas
aeruginosa
reduces
virulence
in
multiple
infection
hosts. PLoS
ONE
(2012)
7:e35648. doi: 10.1371/journal.pone.0035648 34. De Simone M, Spagnuolo L, Lorè NI, Rossi G, Cigana C, De Fino I, et al. Host
genetic background influences the response to the opportunistic Pseudomonas
aeruginosa
infection
altering
cell-mediated
immunity
and
bacterial
replication. PLoS ONE (2014) 9:e106873. doi: 10.1371/journal.pone.01
06873 Copyright © 2019 Bianconi, Alcalá-Franco, Scarselli, Dalsass, Buccato, Colaprico,
Marchi, Masignani and Bragonzi. This is an open-access article distributed under the
terms of the Creative Commons Attribution License (CC BY). Frontiers in Immunology | www.frontiersin.org January 2019 | Volume 9 | Article 3021 35. Cigana C, Bernardini F, Facchini M, Alcalá-Franco B, Riva C, De Fino
I, et al. Efficacy of the novel antibiotic POL7001 in preclinical models REFERENCES The use, distribution
or reproduction in other forums is permitted, provided the original author(s) and
the copyright owner(s) are credited and that the original publication in this journal
is cited, in accordance with accepted academic practice. No use, distribution or
reproduction is permitted which does not comply with these terms. 35. Cigana C, Bernardini F, Facchini M, Alcalá-Franco B, Riva C, De Fino
I, et al. Efficacy of the novel antibiotic POL7001 in preclinical models January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 9
|
https://openalex.org/W2563867472
|
https://europepmc.org/articles/pmc5323497?pdf=render
|
English
| null |
Pastoralists as Optimal Foragers? Reoccupation and Site Selection in the Deserts of Post-Soviet Kazakhstan
|
Human ecology
| 2,016
|
cc-by
| 14,779
|
* S. Robinson
sarah.robinson09@gmail.com Pastoralists as Optimal Foragers? Reoccupation and Site
Selection in the Deserts of Post-Soviet Kazakhstan S. Robinson1,2
& C. Kerven1 & R. Behnke1 & K. Kushenov3 & E. J. Milner-Gulland1,4 Published online: 24 December 2016
# The Author(s) 2016. This article is published with open access at Springerlink.com Published online: 24 December 2016
# The Author(s) 2016. This article is published with open access at Springerlink.com Published online: 24 December 2016
# The Author(s) 2016. This article is published with open access at Springerlink.com Keywords Pastoralism . Kazakhstan . Optimal foraging . Central place . Grazing Keywords Pastoralism . Kazakhstan . Optimal foraging . Central place . Grazing Abstract This study explores the drivers of site selection
amongst livestock owners under conditions of increasing an-
imal numbers following a low point in the 1990s. Our major
goal was to understand whether livestock owners are acting as
‘optimal foragers,’ targeting areas of highest forage availabil-
ity as they colonise previously empty areas. The results pre-
sented here suggest that they do not. Initially, distance from
home settlement was the dominant determinant of site occu-
pancy, with closer sites occupied earlier regardless of other
characteristics. Some owners remained on depleted vegetation
for longer than would be predicted under conditions of opti-
mal foraging, indicating that distance-related costs
constrained resource matching. In the latter period, increases
in livestock wealth encouraged the occupation of distant sites
exhibiting higher vegetation density and water quality, but
some owners still occupied highly depleted sites. Improved
transport and water supply infrastructure are needed if pasto-
ralists are to optimise resource use across the landscape. 1
Imperial College London, Silwood Park, Buckhurst Road, Ascot,
Berks SL5 7PY, UK Hum Ecol (2017) 45:5–21
DOI 10.1007/s10745-016-9870-5 Hum Ecol (2017) 45:5–21
DOI 10.1007/s10745-016-9870-5 2
La Cousteille, 09400 Saurat, France 3
Centre for Livestock and Veterinary Research, Dzhandosov Str. 31,
Almaty, Kazakhstan 480035 Electronic supplementary material The online version of this article
(doi:10.1007/s10745-016-9870-5) contains supplementary material,
which is available to authorized users. 4
Department of Zoology, University of Oxford, South Parks Road,
Oxford OX1 3PS, UK Introduction The country as a whole suffers from a winter feed
deficit (Government of Kazakhstan and the World Bank
2004) and in semi-arid areas, which comprise 80% of total
grazing lands, supplementary fodder cannot be grown. It is
here, particularly in key wintering areas, that optimal use of
natural forage resources would bring the greatest benefits. In an equilibrium environment, in which all patches are
occupied, optimal foraging results in an ideal free distribution,
which predicts that the ratio of individuals between two for-
aging sites will match the ratio of resources in those two sites,
i.e., a matching of foragers and forage resources at the popu-
lation level (Fretwell and Lucas 1970). Our study area is one of the most important winter pastures
in Kazakhstan and access brings significant economic benefits
through a reduction in winter feed costs (Milner-Gulland et al. 2006). It is thus important to understand what is driving, and
constraining, the process of re-colonization of such key pas-
tures. The second issue of interest is pasture degradation. This
is of concern in Central Asia because, although animal num-
bers are now low, mobility has declined, leading to high local-
ised stocking densities with severe impact on soils and vege-
tation (Alimaev et al. 2008; Robinson 2016). We are interested in whether our human agents respond to
forage-related factors as the primary criteria for site selection
in order to maximise food intake of their livestock, or whether
other factors such as water availability or costs related to dis-
tance from the home settlement may be more important. The
predictions of MVT are thus a convenient starting point from
which to explore the factors determining herder decision
making. Most grazing systems in Kazakhstan contain multiple veg-
etation types, and these pastures are used at different seasons
(Zhambakin 1995). Our study system is no exception and
consists of four seasonal pasture types located in different
ecological zones. Large scale movement between these zones
is discussed elsewhere (Kerven et al. 2016a; Robinson et al. 2016). Here, we investigate the re-colonization of well-based
sites by livestock herds and flocks across a large desert pasture
in one of these ecological zones. The case constitutes an un-
usual natural experiment in which people retracted from a
fully exploited landscape to concentrate their herds around
settlements and then moved back out over a period of decades. Introduction 1 Operation of the classic marginal value theorem. As animals
forage for longer in a given patch, intake is assumed to increase at a
decreasing rate. The optimal residency time within a patch (Topt)
depends on the relationship between travel time and the slope of the
curve relating intake to foraging time. Where the marginal rate of intake
(slope of the curve) is equal to the slope of the cost (travel time between
patches), it is optimal for the animal to leave for the next patch. Therefore
when travel time is longer (t2) the animal should spend longer in the patch
than when the travel time is shorter (t1). Adapted from Charnov (1976)
and De Boer and Prins (1989) Fig. 1 Operation of the classic marginal value theorem. As animals
forage for longer in a given patch, intake is assumed to increase at a
decreasing rate. The optimal residency time within a patch (Topt)
depends on the relationship between travel time and the slope of the
curve relating intake to foraging time. Where the marginal rate of intake
(slope of the curve) is equal to the slope of the cost (travel time between
patches), it is optimal for the animal to leave for the next patch. Therefore
when travel time is longer (t2) the animal should spend longer in the patch
than when the travel time is shorter (t1). Adapted from Charnov (1976)
and De Boer and Prins (1989) Introduction Extensive pastoralism is a key livelihood strategy in arid re-
gions where few other forms of land use are feasible (Thornton
et al. 2002), and relies on the ability of animals to exploit spatial
and temporal variation in forage resources, traditionally
achieved through mobile animal husbandry systems. Yet glob-
ally livestock mobility is declining (Boone et al. 2008; Dong
et al. 2011). Kazakhstan is no exception to this pattern and has
suffered from a particularly extreme contraction in livestock
mobility (Kerven et al. 2006) following the collapse of collec-
tive agriculture and a 75% drop in livestock numbers associated
with the end of the Soviet Union (Behnke 2003). Economic
conditions remain difficult - the costs of moving livestock now
fall on individual households rather than large institutions, lead-
ing to loss of economies of scale. Although Kazakhstan has the
fifth largest grazing resource in the world (FAOSTAT 2015), it
has been estimated that only around 30% is currently grazed
(Tazhibaev et al. 2014). Livestock numbers are now increasing. By 2013, total live-
stock numbers (in sheep equivalents) had risen by 80% from
their nadir in 1999, but still lie at around half of Soviet-era
inventories (FAOSTAT 2015). Whilst this increase has not, in
the few cases documented, brought about a full scale return to
mobile pastoralism, some migrations including high mountain
pastures have persisted (Ferret 2013) and re-colonization of
abandoned desert areas is now occurring in some areas
(Kerven et al. 2016b). This is not the result of state planning,
but of individual decision making. The Kazakh government
would like to encourage the increased use of remote pastures,
seeing these as a way of reducing supplementary feed costs * S. Robinson
sarah.robinson09@gmail.com 4
Department of Zoology, University of Oxford, South Parks Road,
Oxford OX1 3PS, UK Hum Ecol (2017) 45:5–21 6 compared to landscape averages). They will leave a patch
when the marginal intake rate drops to the average for the
habitat. This type of individual-level behaviour is captured in
the marginal value theorem (MVT) (Charnov 1976): The
richer the occupied patch is compared to the landscape aver-
age, the longer the patch residence time should be. (Ministry of Agriculture of the Republic of Kazakhstan 2013,
2014). Introduction One similar case is the re-colonisation of the Longone flood
plain in Cameroon, in which re-flooding resulted in an influx
of pastoralists, shown by the authors to occur roughly in pro-
portion to increasing grazing resources (Scholte et al. 2006). In our case, pastoralists started from a central point (the set-
tlement) from which they re-colonized sites defined by avail-
ability of water. We explore the factors underlying site selec-
tion by observing this re-colonization experiment over time. Given the related phenomena of pasture overstocking and
abandonment that have been documented in Kazakhstan, we
are particularly interested in whether herders are ‘optimal for-
agers’, targeting areas of highest forage availability as they
colonise previously empty areas. In order to understand this
process, we use theoretical frameworks from the discipline of
ecology, which predict how animals make decisions about
where to forage in space and time. Bringing costs of accessing patches into the equation
changes the predicted behaviour. For example, as travel time
between patches increases, the time spent in a given patch is
predicted to increase, because the costs of leaving are higher
(Fig. 1). Such a relationship would suggest that greater travel
times would lead to higher depletion of resources as animals
spend more time on patches. If there are two sites, one rich in resources but further
from the settlement, and one poor in resources but close
by, then two processes are operating to retain animals in
the richer patch. As well as higher travel costs leading to
higher residency time, the higher initial resource density
means that the site will be grazed for longer before it
reaches the landscape average resource density. Thus, Fig. 1 Operation of the classic marginal value theorem. As animals
forage for longer in a given patch, intake is assumed to increase at a
decreasing rate. The optimal residency time within a patch (Topt)
depends on the relationship between travel time and the slope of the
curve relating intake to foraging time. Where the marginal rate of intake
(slope of the curve) is equal to the slope of the cost (travel time between
patches), it is optimal for the animal to leave for the next patch. Therefore
when travel time is longer (t2) the animal should spend longer in the patch
than when the travel time is shorter (t1). Adapted from Charnov (1976)
and De Boer and Prins (1989) Fig. Optimal Foraging It has long been suggested that animals primarily concerned
with maximising their food intake will behave as ‘optimal
foragers’. In an unconstrained space within which resources
are patchy and travel costs are negligible, these foragers will
firstly target resources of highest value (resource density Hum Ecol (2017) 45:5–21 7 and Prins 1989; Moritz et al. 2010; Rozen-Rechels et al. 2015;
Shrader et al. 2012; Turner et al. 2005). and Prins 1989; Moritz et al. 2010; Rozen-Rechels et al. 2015;
Shrader et al. 2012; Turner et al. 2005). foragers will travel further (bear more costs) for a richer
patch where higher initial resource density compensates
for the time travelled. This study looks at site selection, not around camps, but
between multiple camps distributed at distances of several
kilometres across a total area of hundreds of square
kilometres, from year to year. We are therefore working at
the landscape scale – or Bailey et al.’s Bhome range.^ Only
a few studies have mapped or modelled herded livestock at
this scale (Boone et al. 2008; McCarthy 2007; Moritz et al. 2014; Scholte et al. 2006; Vanselow et al. 2012). Some (e.g.,
Moritz et al. 2014) have tested for an ideal free distribution
(IFD) at the population level. An IFD would be the predicted
result of optimal foraging decisions by individual herders in
an equilibrium environment where the ratio of gain to cost is
the same across the landscape. But our expanding non-
equilibrium environment means that an ideal free distribution
is unlikely to have yet emerged. We are thus able to expose the
processes involved in site selection over time in a way that is
not possible in an equilibrium situation. Our study system is
also rather different to those to which MVT is usually applied. Its defining characteristics are common in pastoral systems
but rarely appear in ecological studies on wildlife (Table 1). This theory helps us to investigate resource depletion and
the potential for pasture degradation, because resource density
metrics (e.g., vegetation cover or NDVI) are often easier to
measure than forage intake by animals. For this reason, giving
up density (GUD), the resource density at which animals leave
a patch, is often measured in studies of MVTas an indicator of
the intake rate at which patches are left (Brown 1988). Scale Bailey et al. (1996) have defined six scales at which the for-
aging behaviour of large herbivores may be studied: bite,
feeding station, patch, feeding site, camp, and home range. Most studies of herbivore foraging behaviour are conducted
at the lower end of this scale, over minutes or hours and
between individual patches of vegetation. It is only recently
that studies have been up-scaled to look at seasonal move-
ments over landscapes (Owen-Smith et al. 2010). Most stud-
ies at the upper end concern wildlife; few deal with herded
livestock under human decision making. Optimal Foraging For this
study, GUD is interesting in itself – because very low GUDs
may be associated with high levels of resource depletion and
pasture degradation. Key MVT predictions have been validated in domestic
animals under controlled conditions (Laca et al. 1993;
Utsumi et al. 2009), in wildlife (Astrom et al. 1990; Fryxell
et al. 2004), and in human foragers such as hunter gatherers
and fruit pickers (Hill et al. 1987; Wolfe 2013). As predicted,
these authors found that total intake rate decreases as distance
between patches increases, and that patch residence time in-
creases with patch size (a proxy for resource density) and with
distance between patches. De Boer and Prins (1989) found
that these predictions also partially apply to herders of domes-
tic animals, reporting that herders tended to evaluate trade-offs
between travel time, foraging time and intake over the day
rather than on a patch by patch basis, but that over a longer
time frame they did optimise forage intake within the limits
imposed by the need to return to the homestead at night. This
brings up issues of spatial and temporal scale and of the effects
of having a central place to return to, both of which we will
now examine in more detail. The study area has an added advantage in that ‘patches’ are
self-defining. MVT describes resource consumption in a
patchy habitat. But patchiness is a relatively difficult concept
to pin down in grassland habitats in which resources may be
continuously distributed in space and time (Fryxell 2008). In
our case, each well and its associated grazing radius may be
construed as a discrete ‘patch.’ This makes it conceptually
simple to define both patch occupation and patch abandon-
ment as presence and absence at wells. Wells may be used for the whole year or just part of the
year. Livestock owners may use several wells in the same
year, or one alone, but the set of wells to be used over the year
is decided in advance because rental contracts for sites must
be made at the beginning of the year or earlier. Thus, decision
making events occur in advance and the temporal scale at
which site selection must be studied is multi-annual. Central Place Considerations Costs of bringing supplies are
incurred many times over grazing period
Group foraging effects
Larger herd sizes likely to reduce costs of movement per animal
Predation
Possibly a factor, but not of high significance between sites within
the desert Group foraging effects
Predation (ii)
Considering the expanding nature of site selection over
time and ignoring the cost of travel, we predict that sites
occupied earlier have a higher resource density than
those occupied later, or at least this would have been true
during the early stages of re-occupation. distance and environmental quality – e.g., if forage is denser
further out from central points. In our system, patch quality is
indeed likely to be positively correlated with distance from
settlements. Large distance-related costs in a central place foraging
scenario could delay leaving times of patches closer to the
settlement and decrease the GUD of those patches, despite
denser patches further out, contrary to the expectations of
MVT when there is no central patch to return to. This
would result in a situation much like that of a piosphere,
in which closer sites would become depleted and distant
sites would become relatively richer, resulting in positive
correlations between distance from settlement, total in-
take, and environmental quality. If travel costs are much higher than the MOC of not mov-
ing, then livestock will deplete resources to far below the
average level for the landscape, leading to very low GUDs. In such cases, we would expect to see that hypotheses (i) and
(ii) would be refuted. In addition we would expect to observe
the following conditions: In such cases, we would expect to see that hypotheses (i) and
(ii) would be refuted. In addition we would expect to observe
the following conditions: (iii)
Higher levels of relative depletion (not absolute re-
source density) outwards from wells at occupied sites
than unoccupied sites; Close to home, GUD and forage intake rates when the
patch is left are low because the short distances compensate
for the high missed opportunity costs (MOC) of the better
forage in distant patches. Once MOC become larger than
distance-related costs, it is worth changing patches. Herd size
is likely to offset distance by reducing costs through econo-
mies of scale. We use this model to set up our hypotheses. Central Place Considerations Our theory so far would predict that total intake increases with
environmental quality but that the GUD is the same for all
patches, unless costs are higher at some patches than at others. Although we are not addressing grazing patterns within
piospheres, our system also exhibits certain central place char-
acteristics. In terms of primary family residence, livestock
owners are based in three settlements. Those using several
wells over the year may try to ensure that these are located
close to each other, but it seems likely that the primary con-
sideration will be distance from the home settlement. Within a
landscape we would expect to find a relationship between
distance and total intake if there is a relationship between Studies of foraging amongst domestic livestock in semi-
arid environments often concern herds or flocks congregating
around central places, to which they return at night and which
represent water or shelter, rather than food resources. This
results in the generation of a piosphere or grazing gradient
around the central point (Lange 1969). Most studies
concerning the foraging patterns of domestic animals (herded
or not) concern daily movements around these central points,
corresponding to the camp level (Coppolillo 2000; De Boer Hum Ecol (2017) 45:5–21 8 Table 1 Defining characteristics
of the study site relevant to studies
of foraging cteristics
to studies
Currency to be optimised
Profit
Spatial scale
Landscape or home range
Patch definition
Wells, to which livestock are restricted at a radius of around 6 km
Temporal scale
Multi-annual: the set of wells to be used is decided in advance on
an annual basis. Grazing periods at wells usually last months
Central place effects
The distance from home villages to wells is more likely to
influence site selection than distance between wells used by the
same livestock owner
Costs
Most costs co-vary with distance. Metabolic costs are incurred
once a year during migration. Central Place Considerations (iv)
Lower depletion levels at more recently occupied sites
than sites occupied for several years or occupied and
then abandoned; (v)
An overriding role for distance in the system: sites close to
our putative central point, the village, would be colonized
first regardless of forage availability considerations; (vi)
Amongst occupied sites and over time we would expect
to see a positive relationship between vegetation density
and distance from villages, as the ratio of gain to cost
should start to equalise over the landscape. We would
also find negative relationships between forage deple-
tion and distance as forage is depleted closer to villages; Table 1 Defining characteristics
of the study site relevant to studies
of foraging Hypotheses The non-equilibrium situation means that there is unlikely to
be a direct relationship between resource density and stocking
rate, but the situation of expansion across a single zone is
suitable to test the following two hypotheses, which relate to
the beginning of the expansion process and would hold if gain
is strongly correlated with resource density and if travel-
related costs are low: (vii)
Lastly, if herd sizes have a mitigating effect on costs, we
would expect to see a positive relationship between
herd size and distance from the central point. These hypotheses may be tested straightforwardly in an
environment in which patch quality (before grazing) is distrib-
uted randomly. Yet patch quality distribution is not random,
but exhibits gradients across the landscape. Moreover, forage
density is certainly not the only site characteristic of possible (i)
Resource density may be higher at occupied sites than
unoccupied sites if herders are targeting higher vegetation
density under optimal foraging conditions and have not
yet depleted patches to the landscape average. Hum Ecol (2017) 45:5–21 9 interest to herders. Water quality (salinity) and accessibility
(depth) have been shown to influence site selection, whilst
snow cover and relief affect vegetation and site accessibility
(Kerven et al. 2016b) and also exhibit gradients across the
study area. We also explore how the spatial distribution of
these additional factors influences site selection. (Fig. 2), most owners now base their livestock along the river
Chu or in the Moiynkum desert, and use one or both of these
areas over the year. The study area includes three former sovkhoz (Soviet era
state collective farms), Chu, Moiynkum and Baital, whose
populations were concentrated in the settlements of Ulan
bel’, Malye Kamkale, and Sary Ozek respectively (Fig. 3a). Chu and Moiynkum have today been merged to form a single
administrative sub-district (Chu), whilst Baital now forms half
of the adjacent Karabuget sub-district to the east. Methods We take an interdisciplinary approach using qualitative data
from interviews with herders, local officials and livestock pro-
fessionals, quantitative data on stocking metrics and a set of
bio-physical variables to examine each hypothesis. By the 1980s, the Moiynkum desert was highly degraded,
with severe deflation around wells (Bizhanova 1999;
Dzhanpeisov et al. 1990). Today, livestock numbers are
around only 15–20% of Soviet-era levels, and pasture condi-
tion is likely to have recovered to some extent. Since the
collapse of the sovkhoz, some herders have established long-
term bases around wells. In spring and summer, users may
move animals from these bases to temporary encampments
in open access areas along the Chu river and in Betpak-dala. By contrast, the bases in the Moiynkum are located on formal-
ly leased pasture and often have investments in infrastructure
such as barns and houses (Kerven et al. 2016b). Base sites
may be occupied for many years, and yet site abandonment
and re-occupation was also common during our study. The
sample of occupied and unoccupied wells is large enough The Study Area 3 Site occupation and resource density in the Moiynkum desert, (a)
Well distribution and occupation in 2003 and 2011–2014 (b) Mean NDVI
in 2012 across the study area (c) Relationship between mean annual for basic statistical investigation but not for multi-variate anal-
ysis, so the role of resource density and other factors that
possibly determine site selection was examined separately. for basic statistical investigation but not for multi-variate anal-
ysis, so the role of resource density and other factors that
possibly determine site selection was examined separately. was available for 80 owners in 2003 and 84 in 2012 (58
appeared in both years). According to the census data, 49
owners used the Moiynkum desert at some period of the year
in 2002-2003, and 30 in 2011–2012 (note that due to the
practice of collective herding several owners may use the
same sites, just as one owner may use more than one site). The information on stock type, numbers, water source, and
monthly location name were entered into a database. Numbers
were converted to standard livestock units (LU) often used by
pasture scientists in Central Asia and similar to cattle-sheep
ratios used on rangelands elsewhere (USDA/NRCS 2003):
one sheep or goat is one LU; one cow, horse or camel is five
LU. These units were multiplied by the number of days at the The Study Area The Moiynkum is a sandy desert located in Dzhambul prov-
ince of south-central Kazakhstan just south of the river Chu
(Fig. 2). It originally constituted the wintering pasture of a
much larger migratory system in which livestock spent the
summer over 300 km north of the river Chu (Fig. 3a), along
which the human population and associated settlements are
based. Today, although some livestock are moved a reduced
distance to the north into the clay desert of Betpak-dala Fig. 2 Location of Moiynkum desert in Kazakhstan Fig. 2 Location of Moiynkum desert in Kazakhstan Fig. 2 Location of Moiynkum desert in Kazakhstan Hum Ecol (2017) 45:5–21 10 for basic statistical investigation but not for multi-variate anal-
ysis, so the role of resource density and other factors that
possibly determine site selection was examined separately. Data Collection and Processing
was available for 80 owners in 2003 and 84 in 2012 (58
appeared in both years). According to the census data, 49
owners used the Moiynkum desert at some period of the year
in 2002-2003, and 30 in 2011–2012 (note that due to the
practice of collective herding several owners may use the
same sites just as one owner may use more than one site)
Fig. 3 Site occupation and resource density in the Moiynkum desert, (a)
Well distribution and occupation in 2003 and 2011–2014 (b) Mean NDVI
in 2012 across the study area (c) Relationship between mean annual
NDVI at 6km radius from wells and distance from Chu valley
settlements at used and unused sites: b1 = 2.676e-04 (se = 1.893e-05);
R2 = 0.49; p < 0.0001
10
Hum Ecol (2017) 45:5 21 Fig. 3 Site occupation and resource density in the Moiynkum desert, (a)
Well distribution and occupation in 2003 and 2011–2014 (b) Mean NDVI
NDVI at 6km radius from wells and distance from Chu valley
settlements at used and unused sites: b1 = 2 676e-04 (se = 1 893e-05); NDVI at 6km radius from wells and distance from Chu valley
settlements at used and unused sites: b1 = 2.676e-04 (se = 1.893e-05);
R2 = 0.49; p < 0.0001 Fig. Data Collection and Processing Outside these bound-
aries, false absences are possible as the knowledge of our
informants regarding these outlying areas may have been in-
complete, and some wells may have been used for herds from
other administrative areas. Livestock from Sary Ozek make
little use of the desert and so the dynamic process of site
occupation examined in this study principally concerns Chu
and Moiynkum, corresponding to modern Chu sub-district. Therefore, some analyses were also performed on this subset
of sites alone, concerning 102 potential sites. Most of these
have been re-occupied from Ulan bel’ village as Malye
Kamkale is virtually abandoned. During interviews conducted in 2013 and in spring 2014 a
number of additional occupied wells were recorded, including
some which were newly occupied and a small number missed
during the original census, but exact dates of use and livestock
numbers were not recorded. Thus, livestock presence data
were available for wells occupied in 2002–03 and between
the end of 2011 and the start of 2014 (concerning mainly the
years 2012 and 2013), whilst density (stocking rate) informa-
tion was available on a monthly basis for two single year
periods running from the months of October 2002 and 2011. Concerning the exact locations of used sites, many of the
surveys and interviews were conducted at grazing sites, re-
corded by GPS. Livestock owners and other knowledgeable
interviewees identified additional used locations on a set of
1:50,000 Soviet era topographical maps. The majority of these
sites were then visited by vehicle with key informants and
recorded by GPS. The locations of those sites that could not
be visited were digitised directly from the georeferenced to-
pographical maps on which all wells are shown, many with
names. Most such locations were verified on the maps by
more than one interviewee. All locations, with their coordi-
nates, were inputted into a relational database, thus providing
exact locations for every site listed in the livestock survey
table. Overall, livestock were present at 26 locations in 2002/
2003 and 40 during the full fieldwork period of 2011–2014
(of which 37 were within former sovkhoz boundaries and 30 in
Chu sub-district). Twenty-seven of these were recorded with
full livestock number information for our specific census pe-
riod October 2011–October 2012. The rest were recorded as
having livestock presence at some point between October
2011 and April 2014. Data Collection and Processing Livestock Data Formal questionnaire censuses were conduct-
ed with all livestock owners present in the study area in 2003
and 2012. The census asked owners to list pasture locations
and water sources used by their large stock and small stock
(separately) over 12 month periods starting from October
2002 and October 2011. Overall, 118 unique livestock owners
were recorded. Of these, full livestock ownership information 11 Hum Ecol (2017) 45:5–21 major sites likely to have been used as bases in the past; others
consisted of isolated wells and may have been occupied for
shorter periods on a temporary basis. Both sets of sites were
used in analysis for comparison, but the set of sites with in-
frastructure was considered to be the most conservative esti-
mate of potential livestock locations existing during the later
Soviet period (Fig. 3a). Not all of these have working water
supply facilities today, many having been destroyed, dried up
or become too expensive to exploit. location during the relevant time period to give a single com-
parable figure for each location expressed in ‘livestock unit
years’ (LUY). This metric is equivalent to one head of sheep
grazing at a location for one year. location during the relevant time period to give a single com-
parable figure for each location expressed in ‘livestock unit
years’ (LUY). This metric is equivalent to one head of sheep
grazing at a location for one year. Open-ended interviews were conducted with 97 individuals
(many interviewed more than once) during five fieldwork pe-
riods between 2012 and 2014. Interviewees included livestock
owners, shepherds, village mayors, veterinary officers, former
employees of the state livestock farm, and employees of the state
forestry department. Interviews were used to gather livestock
owners’ perceptions on site selection and to identify important
variables affecting decision-making. The results are discussed in
detail elsewhere (Kerven et al. 2016b) and summarised here
briefly in relation to our hypotheses and findings. In addition to the set of 282 potential sites, a number of
geographical subsets were used during analysis including the
restricted set of 130 sites1 within former sovkhoz boundaries,
where we can be virtually certain that we have no false ab-
sences - i.e., any users of these wells from outside were also
recorded and included in the census. 1 All potential site numbers concern those with infrastructure on the
maps. Well and Livestock Distributions in the Moiynkum Desert Wells with infrastructure in the sand desert portion of our three
sovkhoz territories were located on average 3.5 km apart (well
below the radius at which animals graze) so the area was
essentially ‘full up’ with potential sites in Soviet times. The
distribution of wells (with infrastructure) mapped within all
sovkhoz boundaries is close to a distributed regular pattern
(n = 130, nearest neighbour ratio = 1.7, z-score = 1.72,
p = 0.08) and within Chu sub-district alone follows a highly
distributed pattern (n = 102, nearest neighbour ratio = 1.14, z-
score = 2.7, p < 0.01). The equivalent analysis using all wells
reveals a random pattern, suggesting that a planned effort was
made to regularly space sites with infrastructure and
confirming that the presence of infrastructure might be the
best metric to define absences (potential yet unoccupied sites). These findings also suggest that either underlying environ-
mental factors did not influence well distribution, or that these
factors do not display a spatial gradient or clustering pattern. Resource Depletion In many arid areas of Central Asia, for-
age is relatively homogeneous around wells; wells and shelter
are located in the same place and forage availability tends to
increase, and grazing pressure to decrease, away from this
single central point (Alimaev et al. 2008; Kanchaev et al. 2003; Nechaeva et al. 1979). Differences between NDVI at
0-2 km and 3-5 km from wells, or NDVI gradients, were
measured using the annual average NDVI data for 2003 and
2012. These gradients may be interpreted as a measure of
resource depletion and have been shown to be closely related
to stocking density metrics elsewhere in the region (Behnke
et al. 2016). Water Availability Both well depth and salinity have been
found to influence site selection, the influence of depth acting
through the cost of pumping (Kerven et al. 2016b). Water
quality was estimated by livestock owners as good, average,
or salty for a subset of 41 wells, and interviewees also provid-
ed depth information for 39 wells. Today, large areas of the Moiynkum desert are unoccupied
but the number of occupied sites has risen from 26 in 2002–3
to 40 in 2012–13, with 15 sites occupied in both periods. Some sites are occupied all year but others only seasonally. Well and Livestock Distributions in the Moiynkum Desert Seasonal use is now highly variable, ranging from one to four
seasons rather than in spring/autumn (north of the desert) and
winter (southern desert) which characterised the Soviet period
(Fig. S2, supplementary materials 3). Other Variables Affecting Site Selection It was assumed that
travel costs to occupied sites from home settlements were
proportional to distance, which was measured using the
ARCMAP point distance tool. Products from the MODIS in-
strument were processed to produce multi-annual snow cover
images at a resolution of 5 degrees (see supplementary mate-
rials 1). Relief, in the form of sand dunes, was mapped at a
30 m resolution using visual enhancement and interpretation
of an ASTER Digital Elevation Model (DEM). Data Collection and Processing Statistical Analysis Relationships between distance from set-
tlement and NDVI, date of first occupation and NDVI, stock-
ing rate and NDVI gradient, and well depth and first date of
occupation were explored by ordinary least squares linear re-
gression. Differences in mean NDVI, NDVI gradient, distance
from settlement, well depth and snow cover between locations
with stock presence and absence were assessed using Welch’s
t-test; differences in these variables between the four site
stocking categories (used in 2003 alone, 2011–14 alone, both
periods or unused) were assessed using one-way ANOVA. All
statistical analyses were carried out in R (R Core Team 2014). Image processing and analysis were carried out using the
Raster package for R (Hijmans and van Etten 2013) and
ARCGIS (ESRI 2011). We have not attempted to match the season of use of the
Moiynkum desert to NDVI values at time of use. In the mi-
gratory system as a whole movements are partly influenced by
seasonal variations in vegetation availability which occur be-
tween vegetation zones (Robinson et al. 2016). However,
within the Moiynkum vegetation types are more homoge-
neous. These sites constitute primary bases from which other,
more temporary moves may be made. By integrating NDVI
over the year, we are looking at the overall attractiveness of a
site as a ‘base’ regardless of the season in which it was used at
the time of the study. Data Collection and Processing These data represent two snapshots of
well occupation in a complex 20 year-long process of well
occupation and abandonment. Our data do not include infor-
mation on the exact dates and length of occupation periods
between the two study periods. However, the year of first
occupation since the collapse of the sovkhoz was obtained
for a subset of 29 wells for more detailed investigation of site
sequencing. The sets of occupied sites are different in the two
time periods, altering the choice of unoccupied sites. This is
addressed by explicitly comparing site characteristics between
sites occupied in 2011–2014 alone, occupied in 2003 and then
abandoned, and occupied in both periods. Livestock presences were recorded as locations having any
stock presence over the year, whilst absences were defined as
locations having wells that existed in the Soviet era, but which
were not recorded as occupied either in 2002–3, or between
2011 and 2014. These may be considered potential sites, and
were digitised from the topographic maps (which show all
wells and outbuildings existing during the 1980s, after which
no new infrastructure was built). Over the past few years, livestock owners whose animals
are based at settlements along the Chu have started to move
them to wells outside former sovkhoz boundaries. For this
reason the maximum extent of our analysis was set to cover
an area stretching up to 30 km from these boundaries. Within
this area, of the total of 445 occupied and potential sites, 282
had infrastructure (buildings, barns) and were considered to be Resource Density The remote-sensing derived Normalised
Difference Vegetation Index (NDVI) is used worldwide as
an indicator of green biomass (Pettorelli et al. 2011). We 12 Hum Ecol (2017) 45:5–21 employed a gapless 250 m 16 day NDVI dataset generated
from the MODIS MOD13Q1 product (Vuolo et al. 2012) for
the years 2001–2012, from which we extracted annual aver-
ages both over the entire period and for the years 2003 and
2012 alone (see supplementary materials 1). Average NDVI
values were extracted around each location (usually where the
livestock were watered or spent the night) at a radius of 6 km,
shown to be the typical extent of grazing impact around desert
wells in Kazakhstan (Karnieli et al. 2008). Vegetation compo-
sition was also investigated using a vegetation map (Fig. S1
supplementary materials 2) generated from a MODIS-based
classification (see supplementary materials 1). Resource Density Our first hypothesis was that occupied sites may be those with
higher long term average resource density. We examined this
by comparing average annual NDVI (2001–2012) at occupied
and unoccupied wells. Taking livestock occupancy during the
2011–2014 period, there was no significant difference in mean
NDVI values between the 37 occupied and 93 unoccupied
locations within the three former sovkhoz boundaries at a
6 km radius from the well (t = 0.87, p = 0.39). But at a radius
of 1 km, where grazing pressure is greatest, occupied sites had
significantly lower NDVI (t = 2.46, p < 0.05). The 2003 set of
occupied sites exhibits very strong differences in NDVI when
compared with sites unoccupied at that time, even at 6 km
radius from wells, with occupied sites having significantly
lower NDVI (n = 130 wells of which 26 occupied; t = 4.2,
p < 0.0005). These differences were also noted using NDVI in
the year of use instead of 12 year annual average NDVI. Thus
site selection decisions made in individual years are unlikely
to depend on resource density characteristics in that specific
year, and resource densities in a given year do not differ rad-
ically from long term averages. Biomass NDVI appears to increase towards the east of the
study area and in some parts of the southeast (Fig. 3b). This
follows a precipitation gradient. Average annual precipitation
ranges from 150 mm close to the Chu river to 180–200 mm in
the central Moiynkum (Kurochkina and Osmanova 1973) and
294 mm in the south (Bizhanova and Kurochkina 1989). The
existence of a biomass gradient independent of resource de-
pletion by grazers is evident (Fig. 3c), which indicates a strong
relationship between NDVI and distance (to the south) from
settlements, not only for occupied sites, but also for sites un-
occupied in either study period. Water and Snow Our sample of wells, representing those for
which respondents had knowledge, exhibited decreasing sa-
linity towards the south from settlements, a factor identified as
important in site selection by herders (Kerven et al. 2016b and
supplementary materials Table S1). Those wells having aver-
age or good quality water tend to be deeper close to Ulan bel’
and shallower to the south and east (Fig. S3). Characterising Resource Gradients across the Study Area The occupation of new sites has occurred mostly to the south
and east (Fig. 3a). There are large groups of sites, particularly
to the south of Ulan Bel’ and northern parts of former sovkhoz
Moiynkum, which are unoccupied. We discuss how forage 13 Hum Ecol (2017) 45:5–21 resources, and other natural factors possibly influencing site
selection, vary across the desert. resources, and other natural factors possibly influencing site
selection, vary across the desert. higher precipitation, snow cover is also lower to the south
and east, probably influenced by higher temperatures, partic-
ularly in early spring (Fig. S4, supplementary materials 5). Vegetation and Soils The north of the desert, which has clay
takyr-like soils, has few wells because the ground water is
salty. This area is covered by vegetation dominated by
Artemisia and Haloxylon spp. (see vegetation type 1,
Fig. S1, supplementary materials). This pasture makes poor
grazing outside the autumn and only two occupied wells were
located here. Further south, the soil becomes progressively
sandier (Fig. 3b). Transitional areas dominated by
Ceratoides (vegetation type 2 in Fig. S1) give way to vegeta-
tion dominated by shrubs such as Calligonum, Haloxylon,
Astragalus spp. which, together with an understory including
Ceratoides, Kochia and Atriplex spp., provide good forage all
year round. By far the majority of wells are located in this
vegetation type on sandy soils (south of the clay/sand border
in Fig. 3b and corresponding to type 3 in Fig. S1), which is
rather homogeneous, apart from areas affected by fire, visible
as patches of low NDVI in the southeast of Fig. 3b. The
increasingly sandy soils to the south present transport difficul-
ties as deeper sand combined with higher dune size increase
both fuel costs and the risk of vehicles becoming stuck, thus
requiring heavier and more expensive transportation. Distance The role of distance from settlements as a constraint
to site occupation is evident (Fig. 3a). More recently occupied
sites appear to be located further away from settlements, a
phenomenon even more exaggerated when we consider that
in fact most expansion is from the settlement of Ulan bel’
alone. However, the expansion appears rather directional to-
wards the south and east, so distance, whilst important, must
interact with other factors. We now turn to a more formal analysis of relationships
between these factors and site occupation. Resource Density Post hoc com-
parisons using the Tukey HSD test indicated that the difference in mean
NDVI gradient between newly occupied sites (2011–14) verses sites oc-
cupied in both periods is significant (p < 0.001); difference between sites
occupied in 2003 alone and in 2011–14 alone is insignificant (p = 0.9);
difference between sites used in both years and sites never used is signif-
icant (p < 0.0001). Note: boxplots shown here (and all subsequent
boxplots) show median values (horizontal lines in box centre), and the
1st and 3rd quartiles (top and bottom of boxes). The whiskers extend to
values of 1.5 x Q3-Q1. Outliers are shown as dots and represent values >
Q1–1.5*IQR and < Q3 + 1.5*IQR where IQR = Q3 - Q1. a) Fig. 4 a Regression of annual average NDVI (2001–2012) against year
of first re-occupation after collapse of the sovkhoz (n = 29): β1 = 0.001
(se = 0.00028); R2 = 0.327; p < 0.005. b NDVI at sites used in 2003,
2011–14, both periods and unused sites, within sovkhoz boundaries
(n = 11, 22, 15, 82). There was a significant difference in group means
(F = 4.4; p < 0.01). Post hoc comparisons using the Tukey HSD test
indicate no difference between mean NDVI at sites used in 2011–14
and unused sites (p = 0.99); significant differences between unused sites
and those used in 2003 (p < 0.05) and near significance between sites
used in 2011–2014 and in 2003 alone (p = 0.064). A t-test on these latter
two group means is significant: t = −3.1, p < 0.005. c 2012 NDVI gradient
at occupied and unoccupied sites within former sovkhoz boundaries in
2011–2012 alone (census year only; present n = 27; absent n = 103). A
positive gradient implies that NDVI increases out from the well (a mea-
sure of resource depletion); negative gradients imply that NDVI decreases
out from the well. The difference in mean gradient is significant: t = −4.8,
p < 0.0001. Taking all sites used from 2011 to 2014 (present n = 37, Fig. 4 a Regression of annual average NDVI (2001–2012) against year
of first re-occupation after collapse of the sovkhoz (n = 29): β1 = 0.001
(se = 0.00028); R2 = 0.327; p < 0.005. b NDVI at sites used in 2003,
2011–14, both periods and unused sites, within sovkhoz boundaries
(n = 11, 22, 15, 82). Resource Density Thus, for a
livestock owner based at Ulan bel’, although most nearby
wells are relatively shallow, many are of poor quality, while
the deeper good quality wells are expensive to use. Further
away in former Moiynkum and Baital sovkhozes, those wells
known to respondents tended to be both shallow and of good
or average quality. These particularly attractive wells are now
occupied by owners based at Sary Ozek and Malye Kamkale;
others are occupied by owners from Ulan bel’ who have also
tended to move greater distances in recent years. Despite Our second hypothesis was that most resource dense sites
would be occupied earlier. Here, we regressed annual average
NDVI against year of first occupation of sites since the col-
lapse of the sovkhoz. Whilst no relationships were evident at
6 km radius, a weak relationship did emerge closer to wells
(Fig. 4a), but again the direction of the relationship is the
inverse of that predicted by MVT, with those sites occupied
first exhibiting lower NDVI than sites occupied later on. Relationships between resource density and the order of
site occupation were explored further by comparing NDVI
at the sets of sites occupied in 2003 alone, those occupied in
2011–2014 alone, and sites occupied in both years (Fig. 4b). Sites occupied after 2003 (i.e., appearing in the 2011–2014
dataset only) have mean NDVI levels very close to those of
unoccupied sites, whilst those occupied in 2003 and during
both periods have much lower NDVI values. Hum Ecol (2017) 45:5–21 14 14 Fig. 4 a Regression of annual average NDVI (2001–2012) against year
of first re-occupation after collapse of the sovkhoz (n = 29): β1 = 0.001
(se = 0.00028); R2 = 0.327; p < 0.005. b NDVI at sites used in 2003,
2011–14, both periods and unused sites, within sovkhoz boundaries
(n = 11, 22, 15, 82). There was a significant difference in group means
(F = 4.4; p < 0.01). Post hoc comparisons using the Tukey HSD test
indicate no difference between mean NDVI at sites used in 2011–14
and unused sites (p = 0.99); significant differences between unused sites
and those used in 2003 (p < 0.05) and near significance between sites
used in 2011–2014 and in 2003 alone (p = 0.064). A t-test on these latter
two group means is significant: t = −3.1, p < 0.005. Resource Density c 2012 NDVI gradient
at occupied and unoccupied sites within former sovkhoz boundaries in
2011–2012 alone (census year only; present n = 27; absent n = 103). A
positive gradient implies that NDVI increases out from the well (a mea-
sure of resource depletion); negative gradients imply that NDVI decreases
out from the well. The difference in mean gradient is significant: t = −4.8,
p < 0.0001. Taking all sites used from 2011 to 2014 (present n = 37,
absent n = 93) the relationship is weaker as many of these were used
for the first time t = −3.0, p < 0.005. The equivalent test for 2003 data
(n = 26; 104) is significant: t = −4.1, p < 0.0005. d 2012 NDVI gradients
at sites used in 2003, 2011–14, both periods and unused sites, within
former sovkhoz boundaries (n = 11, 22, 15, 82). There was a significant
difference between group means (F = 10.44; P < 0.0001). Post hoc com-
parisons using the Tukey HSD test indicated that the difference in mean
NDVI gradient between newly occupied sites (2011–14) verses sites oc-
cupied in both periods is significant (p < 0.001); difference between sites
occupied in 2003 alone and in 2011–14 alone is insignificant (p = 0.9);
difference between sites used in both years and sites never used is signif-
icant (p < 0.0001). Note: boxplots shown here (and all subsequent
boxplots) show median values (horizontal lines in box centre), and the
1st and 3rd quartiles (top and bottom of boxes). The whiskers extend to
values of 1.5 x Q3-Q1. Outliers are shown as dots and represent values >
Q1–1.5*IQR and < Q3 + 1.5*IQR where IQR = Q3 - Q1. a)
14
Hum Ecol (2017) 45:5–21 absent n = 93) the relationship is weaker as many of these were used
for the first time t = −3.0, p < 0.005. The equivalent test for 2003 data
(n = 26; 104) is significant: t = −4.1, p < 0.0005. d 2012 NDVI gradients
at sites used in 2003, 2011–14, both periods and unused sites, within
former sovkhoz boundaries (n = 11, 22, 15, 82). There was a significant
difference between group means (F = 10.44; P < 0.0001). Resource Density There was a significant difference in group means
(F = 4.4; p < 0.01). Post hoc comparisons using the Tukey HSD test
indicate no difference between mean NDVI at sites used in 2011–14
and unused sites (p = 0.99); significant differences between unused sites
and those used in 2003 (p < 0.05) and near significance between sites
used in 2011–2014 and in 2003 alone (p = 0.064). A t-test on these latter
two group means is significant: t = −3.1, p < 0.005. c 2012 NDVI gradient
at occupied and unoccupied sites within former sovkhoz boundaries in
2011–2012 alone (census year only; present n = 27; absent n = 103). A
positive gradient implies that NDVI increases out from the well (a mea-
sure of resource depletion); negative gradients imply that NDVI decreases
out from the well. The difference in mean gradient is significant: t = −4.8,
p < 0.0001. Taking all sites used from 2011 to 2014 (present n = 37, absent n = 93) the relationship is weaker as many of these were used
for the first time t = −3.0, p < 0.005. The equivalent test for 2003 data
(n = 26; 104) is significant: t = −4.1, p < 0.0005. d 2012 NDVI gradients
at sites used in 2003, 2011–14, both periods and unused sites, within
former sovkhoz boundaries (n = 11, 22, 15, 82). There was a significant
difference between group means (F = 10.44; P < 0.0001). Post hoc com-
parisons using the Tukey HSD test indicated that the difference in mean
NDVI gradient between newly occupied sites (2011–14) verses sites oc-
cupied in both periods is significant (p < 0.001); difference between sites
occupied in 2003 alone and in 2011–14 alone is insignificant (p = 0.9);
difference between sites used in both years and sites never used is signif-
icant (p < 0.0001). Note: boxplots shown here (and all subsequent
boxplots) show median values (horizontal lines in box centre), and the
1st and 3rd quartiles (top and bottom of boxes). The whiskers extend to
values of 1.5 x Q3-Q1. Outliers are shown as dots and represent values >
Q1–1.5*IQR and < Q3 + 1.5*IQR where IQR = Q3 - Q1. Resource Density a) Hum Ecol (2017) 45:5–21 15 The above analyses suggest that differences in resource
density between occupied and unoccupied wells, both in space
and over time, are related to vegetation depletion caused by
grazing at various periods during the 12 years over which the
NDVI data are averaged. In this scenario, our theory predicts
that when travel costs are high, sites are occupied beyond the
point at which the forage acquisition rate drops below the
landscape average. In this case, site occupancy determines
vegetation density rather than the reverse. Additional evidence
for such a scenario is that NDVI differences between occupied
and unoccupied sites in 2012 and 2003 are larger (with higher
statistical significance) when the full set of sites with wells
(not only those having infrastructure) are included in the anal-
ysis. Whilst wells with infrastructure are likely to have been
occupied in the past, those without infrastructure may have
been little or never occupied, thus amplifying the potential
difference in accumulated grazing pressure between occupied
and unoccupied sites. This also suggests that past grazing
effects are detectable for long periods. weedy species may persist for many years after NDVI gradients
are no longer detectable. It should be noted that although we have found relationships
between livestock presence and resource depletion, relationships
were not found between actual livestock density (annualised
stocking rate) and the extent or size of the gradient in either
2003 or 2012. This may be because stocking rates are not vari-
able enough to cause detectable differences in depletion level. Overall, at least by 2012, site occupation appears more
likely to be causing resource depletion than to constitute a
response to variability in vegetation density, consistent with
the scenario that distance-related costs were the dominant fac-
tor determining site selection. However, although the MVT
prediction that the most resource dense sites would be occu-
pied first has not been shown to be correct, it is difficult to
refute convincingly because we are essentially dealing with
two temporal ‘snapshots.’ Our dataset does not have the fine
temporal detail of occupation and abandonment dates which
could perhaps have been used with associated NDVI data at
dates of initial occupation to untangle these two factors. If
relationships between resource density and date of first occu-
pation do exist, they are most likely to be negative, as those
sites occupied first are furthest north, where precipitation is
lowest. Resource Density Those sites occupied in 2003, but abandoned before
the subsequent study period, have low NDVI gradients (little
depletion) in 2012 (Fig. 4d), but also have low long-term
average absolute NDVI values (Fig. 4b), suggesting that these
sites may be generally resource-poor in a way not related to
depletion alone. This may also explain why the difference
between NDVI at occupied and unoccupied sites was so much
greater for the 2003 dataset (significant at 6 km) than for the
2011–14 dataset (non-significant at 6 km). However, we have seen that there is also a north-south
gradient in ‘natural’ vegetation density related to climatic fac-
tors rather than livestock grazing. Our most recently occupied
sites, as well as many unoccupied sites, appear to be located
further south. Thus we must examine not only absolute re-
source density, but relative depletion levels around wells in
order to better understand the process behind the observed
patterns. Resource Depletion We now therefore turn to our hypotheses concerning NDVI
gradients outwards from wells. As hypothesised, average
NDVI gradients were steeper at occupied than at unoccupied
sites in both 2003 and 2012 (Fig. 4c). Secondly, we examined
average NDVI gradients in 2012, at sites with different occu-
pation histories, to address the hypothesis that more recently
occupied, or more briefly occupied, sites should exhibit less
resource depletion. Within sovkhoz boundaries, sites occupied
only in recent times (appearing in the 2011–2014 dataset alone)
exhibited no discernible difference in NDVI gradient in 2012
from unoccupied sites, which, as would be expected, have a
median gradient of around zero (Fig. 4d). Sites occupied in both
periods exhibited high levels of depletion. The difference be-
tween sites occupied in both periods and those appearing only
in the 2011–2014 dataset is particularly strong. However, de-
pletion at sites occupied in 2003 but subsequently abandoned is
slight, and mean gradients are statistically indistinguishable
from those at sites occupied only recently (Fig. 4d). These
results suggest that (i) the effects of depletion require several
years of site occupation to become evident as NDVI gradients,
and (ii) the impact of past grazing appears to decrease over the
timescale at which we are working. We should remember here
that NDVI gradients are not measuring the quality of grazing - A second prediction of classical MVT, that movement
away from sites would occur once they had been grazed down
to the landscape average resource density, appears not to be
supported, at least for the 2003 dataset. Even in recent years,
although some herders have recently colonised un-depleted
sites, others have stayed on patches long past the GUD pre-
dicted by MVT, again supporting the idea that costs of move-
ment are high. We now turn to hypothesis (v) concerning
distance from the home settlement (Table 2). Other Factors Other factors that interviews with herders and local profes-
sionals suggested were important determinants of the cost or
attractiveness of particular sites were water quality (saline or
not), depth and type of the well (which may affect extraction
cost), topography (which may affect travel cost), and snow
cover (which may impede grazing in winter but provide im-
portant moisture in spring) (see Kerven et al. 2016b). As we
have seen, the water quality of wells varies with distance from
settlements, such that less saline wells are further away
(Table S1 in supplementary materials). Of the 41 wells for
which salinity scores were given, 24 of the 25 wells listed as
good or average were occupied between 2011 and 2014,
whilst the 16 saline wells were occupied and unoccupied in
equal proportion. In 2003 there was no difference in the pro-
portion of occupied saline and non-saline wells, suggesting
that selectivity for water quality may have increased over time. Likewise, no relationship was detected between water quality
and date of first occupation for our subset of 29 wells for
which year of first occupation after collapse of the sovkhoz
was available. If costs increase with distance then we would expect GUD
to be lower closer to settlements and higher farther away, as
the ratio of cost to gain starts to equalise over the landscape
(hypothesis vi). By the end of our study period, we would thus
expect to see a gradient of resource density outwards from
settlements at sites occupied during our study period, but not
at unoccupied sites. However, this hypothesis cannot be con-
firmed due to the natural north-south increase in resource den-
sity evident at both occupied and unoccupied sites (Fig. 2c). It
is in 2013 and within sovkhoz boundaries alone that there is
most likely to be equalising of cost-gain ratio. We did indeed
find a strong positive relationship between distance from the
home settlement and NDVI at sites that had been occupied at
any time during the study period (n = 48; β1 = 7.2e-04
(se = 6.0e-05); R2 = 0.76, p < 0.0001). However, there is also
a strong relationship between NDVI and distance for sites that
were not occupied in either period (n = 82; β1 = 7.6e-04
(se = 7.3e-05); R2 = 0.57; p < 0.0001), albeit with a lower
slope. Distance According to this hypothesis, if other factors were equal then
we would expect the sites closest to villages to be settled first. This question is explored for Ulan bel’ sub-district (former
Chu and Moiynkum sovkhoz) alone, as so few stock from
Sary Ozek are located outside the settlement. In this sub-
district most livestock are coming from the settlement of
Ulan bel’. Results confirm that indeed occupied sites were
significantly closer to Ulan bel’ than unoccupied sites in
2003 (Table 2). However, by 2012 there was no significant Hum Ecol (2017) 45:5–21 16 Table 2 Distance from Ulan bel’
and livestock presence and
absence (for sites within the
boundaries of Chu sub-district). Year
n
(absence)
n
(presence)
Mean distance,
km (absence)
Mean distance,
km (presence)
t
p
2003
78
24
49.6
37.2
4.3
<0.0001
2012
72
30
46.6
46.9
-0.081
ns (0.9359) difference between occupied and unoccupied sites. It thus ap-
pears that either suitable sites closer to Ulan bel’ are all occu-
pied or a reduced importance of travel costs (e.g., lower fuel
costs or higher returns from meat sales) means that factors
other than distance are increasingly important in site selection. Certainly 11 of the sites occupied in 2003 close to Ulan bel’
were subsequently abandoned, and there are still many empty
wells throughout the study area, so reduced travel costs may
be more important. No relationships between stocking rate
and distance from Ulan bel’ were found. related to distance from the village. We explored the
relationship between both average herd size over the
months each site was occupied, and annualised stocking
rate (in LUY) and distance from village for the year
2012. No relationships were apparent here for either
variable, however the sample size of sites for which
stocking information was available was small (n = 27). The difference in herd size between sites occupied in
2012 and sites occupied in both 2003 and 2012 was
also non-significant. Yet the impact of distance on site selection still had conse-
quences during the later study period. If we compare sites
occupied in 2011–14 with the theoretical larger universe of
unoccupied sites across the wider Moiynkum zone, then
NDVI values at sites occupied in 2011–14 are significantly
lower than those of other sites, even at a radius of 6 km (242
wells of which 40 occupied; t = 4.2, df = 68.12, p < 0.001). Distance This is because there are many unoccupied sites in the highly
vegetated south of the sandy massif. These sites are potentially
available and indeed a few were occupied by 2013. Other Factors Sites unused in either period not included as sample size n = 3 is too small Fig. 5 a Well depth and year of first occupation (n = 23): β1=-0.8494
(se = 0.2522); R2 = 0.35, p < 0.005. Note: two very deep outliers (80 m)
have been removed. b Well depth and use period category. Sites used in
2003 only: mean = 19 m, n = 5. In 2011–2014 only: mean = 13 m, n = 17. In both periods: mean = 24 m; n = 14. T-test for difference in mean depths
of wells used in 2003 or both years verses those used in 2011–2014 alone
(n = 19; 17, means =22.7 m & 12.7 m) is significant: t = 3.8, p < 0.001. Sites unused in either period not included as sample size n = 3 is too small lower at more recently occupied sites (2011–14 only) compared
to those occupied in 2003 alone, but the absolute mean differ-
ences are very small (Fig. S6, supplementary materials 7). Moreover, more snow may be positive for spring growth, thus
in interviews some herders considered snow to be an important
factor determining site selection whilst others did not, depending
on season of use. This factor is also likely to be confounded with
geographical location, which as we have seen, correlates with
other factors varying along the same north-south gradient. those which were in fact occupied later on (hence existence of
knowledge about these wells in 2012–2014 interviews). There
are very few data for wells unoccupied in either period. This is
because herders are unsure about the status of wells that have
not been visited for a long time. However, interviews do con-
firm that pumping costs increase with well depth and that
water quality is an important pull factor in site selection
(Kerven et al. 2016b). Lastly, we examined the effect of water source type on live-
stock presence. The Soviet-era grazing plan of Ulan bel’ shows
all major shaft wells and bore holes (n = 58). Sites having only
bore holes may be the least likely to be occupied today as they
require the most powerful pumps. Indeed, of the 25 sites at which
bore holes alone are indicated, only five were occupied in either
2003 or 2011–14 (of which three have been occupied since
2012). Other Factors We would also expect to find negative relationships
between forage depletion and distance from settlement at oc-
cupied sites, as forage is depleted closer to settlements (again
calculating distances as above). Here although a slightly neg-
ative relationship was observed, it is extremely weak
(b1 = −9.6e-05 (se = 4.5e-05); R2 = 0.08, p < 0.05). There were no significant differences in well depth be-
tween occupied and unoccupied wells in 2011–14, but the
sample size of unoccupied wells (8) for which depth data were
available was small. In 2003, occupied wells were significant-
ly deeper (n = 39; unoccupied n = 20, occupied n = 19; means
=12.5 m and 22.7 m; t = −4.06, p < 0.0005). The possible
conclusion that shallower wells tend to be occupied later on is
supported by weak relationships between well depth and both
date of first occupation and use period category (Fig. 5). These data are circumstantial at best – the set of wells for
which information could be gathered represents that for which
informants had knowledge, and the limit of our research re-
sources. Most data for wells unoccupied in 2003 concern Lastly, we expected that if economies of scale could
mitigate travel costs, herd size should be positively 17 Hum Ecol (2017) 45:5–21 Fig. 5 a Well depth and year of first occupation (n = 23): β1=-0.8494
(se = 0.2522); R2 = 0.35, p < 0.005. Note: two very deep outliers (80 m)
have been removed. b Well depth and use period category. Sites used in
2003 only: mean = 19 m, n = 5. In 2011–2014 only: mean = 13 m, n = 17. In both periods: mean = 24 m; n = 14. T-test for difference in mean depths
of wells used in 2003 or both years verses those used in 2011–2014 alone
(n = 19; 17, means =22.7 m & 12.7 m) is significant: t = 3.8, p < 0.001. Sites unused in either period not included as sample size n = 3 is too small In both periods: mean = 24 m; n = 14. T-test for difference in mean depths
of wells used in 2003 or both years verses those used in 2011–2014 alone
(n = 19; 17, means =22.7 m & 12.7 m) is significant: t = 3.8, p < 0.001. Other Factors Of the 33 sites with shaft wells or both types, 18 (54%)
were occupied (X2 = 7.1, p < 0.005). Most unoccupied sites lie
directly south of Ulan bel’ nearer to the metalled road. The fact
that most of them are bore holes may explain why those sites,
despite being easily accessed, are rarely occupied (Fig. 2a,
Fig. S5, supplementary materials 6). In this area, livestock
owners also mentioned transport difficulties related to sand depth
and dune height (Kerven et al. 2016b). Sandy soils may increase
travel costs related to the occupation of all southern wells, but
those in the south west may be particularly hard to reach (sup-
plementary materials 6). To summarise, it appears that over time, herders have been
increasingly targeting shallower and less saline wells in areas
with higher vegetation density. Discussion and Conclusions False in 2012 However, even unoccupied sites may have continued to exhibit
depletion from heavy use in the Soviet era; at the start of the
study the time scale needed for more recent grazing activity to
become detectable was unknown - the effects of grazing in
2012 were not detectable in the NDVI data at 6 km radius. equalise, is only one of the processes occurring here. The
other is that the ratio of costs to profit is changing over
time, thus the depressing effect of cost on GUD may also
lessen over time. This is indeed illustrated by the declining
influence of distance on site selection between our two
study periods. Livestock have stayed at these sites longer than would be
predicted under conditions of optimal foraging, and have thus
grazed vegetation to levels lower than would be expected if they
were just responding to differences in forage availability between
sites. GUDs are low, suggesting that costs of movement are high. These costs tend to co-vary with distance from settlements and
were clearly the overriding factor determining site selection, at
least during in the initial phase of expansion. Distance imposes
costs not only in the one-off movement of livestock at the start of
the grazing period, but in the many trips back and forth for
supplies and family visits (Kerven et al. 2006). Part of this decrease in costs may be related to an increase
in livestock numbers, which operates to decrease economies
of scale (Kerven et al. 2004, 2006, 2008). Although we have
shown in previous work that herd size is strongly related to the
number of ecological zones occupied by migratory livestock
(Robinson et al. 2016), we have not been able to demonstrate
relationships between herd size and distance within the single
zone studied here. However, the number of small stock in our
study area roughly doubled from 2003 to 2012. This increase
has translated both into a greater number of flocks using the
Moiynkum desert, and to an increase in median flock size
belonging to individuals, by around 70% over our study peri-
od (Kerven et al. 2016b). Higher meat prices and lower
pumping costs have also contributed to general increased
wealth of herders in recent years. Secondly, sites occupied later on have on average, both
higher vegetation densities and lower depletion levels than
those occupied at the start of our study period. Discussion and Conclusions A major goal of this paper was to understand whether live-
stock owners are acting as ‘optimal foragers,’ targeting areas
of highest forage availability as they colonise previously emp-
ty areas. The results presented here suggest that they do not
follow the classical MVT (hypotheses i and ii, Table 3). Rather, it appears that travel costs are potentially critical de-
terminants of site occupation, meaning that animals stay lon-
ger at sites than would be expected under classical MVT,
leading to resource depletion (hypotheses iii–vi, Table 3). This is despite the continued existence of many unoccupied
sites in the study area. Historically, one of the values of the Moiynkum desert as a
winter grazing area lay in its relatively low snow cover. Today,
although many sites are also occupied in other seasons (Fig. S2,
supplementary materials 3), winter is still a key grazing period. Snow cover as measured by satellite imagery is significantly We found that occupied sites have significantly lower veg-
etation density and higher NDVI gradients than unoccupied
sites. Such a pattern may seem rather predictable in semi-arid
systems in which livestock are constrained to water points. Hum Ecol (2017) 45:5–21 18 Table 3 Results of hypothesis
testing
№
Hypothesis
Results
(i)
Resource density is higher at used sites than at unused sites (IFD)
False in 2003 & 2012. (ii)
Order of site occupation by individual herders since the collapse
of the sovkhoz is positively related to resource density (IFD)
False
(iii)
Resource depletion is higher at sites where livestock are present
than at those where they are absent. True in 2003 & 2012
(iv)
Resource depletion is lower at more recently occupied sites than
(a) sites used for many years and (b) sites used and then
abandoned. (a) True
(b) False
(v)
Within specified spatial boundaries, sites at which livestock are
present are closer to settlements than sites from which they
are absent. 2003: True
2012: False
(vi)
For the later dataset we expect: (a) positive relationship between
forage density and distance from villages; (b) negative
relationship between forage depletion and distance from
settlements
(a) True
(b) Inconclusive
(vii)
If larger herd sizes mitigate costs of movement we would expect
to find positive relationships between herd size and distance
from settlements. Table 3 Results of hypothesis
testing References Alimaev, I. I., Kerven, C., Torekhanov, A., Behnke, R., Smailov, K.,
Yurchenko, V., Sisatov, Z., and Shanbaev, K. (2008). The impact
of livestock grazing on soils and vegetation around settlements in
Southeast Kazakhstan. In Behnke, R. (ed.), The Socio-economic
Causes and Consequences of Desertification in Central Asia,
Springer. (
y
g
)
This study has shown the dominance of economic
considerations over forage-related issues in herders’ de-
cisions about how best to use resources, in contrast to a
pastoral system in Africa which has been subject to sim-
ilar analyses (Scholte et al. 2006). Such a situation is
likely to be the case in pastoral systems that are increas-
ingly subject to sedentarisation of households in a central
place and reliance on mechanised transport. In terms of
policy, the Kazakh government could intervene in a
number of ways to reduce the high costs related to low
GUDs and high levels of resource depletion. These in-
clude improving transport links, increasing the attractive-
ness of distant sites by repairing wells and other infra-
structure and ensuring that administrative and other
transaction costs of land access are as low as possible. It could also act to incentivise seasonal movement out of
the Moiynkum desert, as much of the strongest depletion
comes from livestock kept in the desert in the summer. Overall, the government needs to weigh the cost efficien-
cy of such policies, in terms of improved access to nat-
ural forage, against its current policies which favour the
intensification of livestock production. Astrom M., Lunberg P., and Danell K. (1990). Partial Prey Consumption
by Browsers: Trees as Patches. Journal of Animal Ecology 59: 287–
300. Bailey D. W., Gross J. E., Laca E. A., Rittenhouse L. R., Coughenour M. B., Swift D. M., and Sims P. L. (1996). Mechanisms that Result in
Large Herbivore Grazing Distribution Patterns. Journal of Range
Management 49: 386–400. Behnke R. (2003). Reconfiguring property rights in livestock production
systems of western Almaty oblast, Kazakstan. In Kerven C. (ed.),
Prospects for Pastoralism in Kazakstan and Turkmenistan: From
State Farms to Private Flocks, Routledge Curzon, London. Behnke R., Robinson S., and Milner-Gulland E. J. (2016). Governing
Open Access: Livestock Distributions and Institutional Control in
the Karakum Desert of Turkmenistan. Land Use Policy 52: 103–
119. Bizhanova, G. K. (1999). Discussion and Conclusions Thus over time,
depletion may indeed be driving livestock to new sites with
high vegetation density, located further from the central point
of departure. However, these sites do not just exhibit high
levels of un-depleted vegetation. As we noted, they also tend
to host sweet and shallow wells. Well salinity and snow cover
vary along the same spatial gradient as vegetation density so it
is difficult to untangle their relative importance. Herders’
perceptions suggest that water-related factors are impor-
tant in site selection and abandonment, with depletion
also a notable ‘push factor.’ Absolute vegetation density
was less commonly given as a ‘pull factor.’ Whichever
predominates, livestock owners have clearly selected
more attractive sites in 2012 than in 2003. This may have relaxed constraints originally imposed by
distance, allowing livestock owners to target better sites. Such
a proposition is supported by the fact that the colonisation of
increasing numbers of sites has been accompanied by a simul-
taneous process of site abandonment, as evidenced by the
group of wells occupied in 2003 alone, and suggesting that
the factors favouring the initial choice of certain sites subse-
quently changed over time. Resource depletion at early-
occupied sites, a suite of positive characteristics of unoccupied
sites, and a decrease in distance-related costs may have all led
to the observed patterns of site occupation over time. The operation of the MVT, predicting movement from
depleted patches to new patches once costs and gains Despite these processes, and the recent colonisation of many
new sites with low depletion and high vegetation density, a Hum Ecol (2017) 45:5–21 19 Zharas; Nurgul and Nazgul Zhumasheva. We appreciate the comments
and suggestions from two anonymous reviewers. large proportion of sites occupied in 2003 continue to be occu-
pied today, and this set of sites in particular still exhibits strong
depletion – indicating very low GUDs and high cost to gain
ratios. In order to use sites in the Moiynkum, considerable
investments must be made to restore wells, winter houses and
barns. Even if owners were able to Bsell^ these assets, the costs
of rebuilding them at a new and more distant sites is likely to be
high. Although recent trends suggest movement out of depleted
areas, these have not yet resulted in optimal foraging patterns
across the landscape. It remains to be seen whether such pat-
terns will emerge as livestock numbers rise still further. Discussion and Conclusions Compliance with Ethical Standards
Research reported here was
funded by the Leverhulme Trust in an award to Imperial College
London, Department of Life Sciences, entitled BExclusion vs Mobility:
Limits to Ideal Free Distributions in Pastoralist Systems^ (grant number
RPG 251). The authors are solely responsible for the interpretation of the
results, and for any errors contained in this paper. Conflict of Interest
The authors declare that they have no conflict of
interest. Open Access This article is distributed under the terms of the Creative
Commons Attribution 4.0 International License (http://
creativecommons.org/licenses/by/4.0/), which permits unrestricted use,
distribution, and reproduction in any medium, provided you give
appropriate credit to the original author(s) and the source, provide a link
to the Creative Commons license, and indicate if changes were made. The use of the MVT to structure our investigations
has been useful because it allows us to weigh up the
opposing ‘pull factors’ of resource density (and other
attractive site characteristics) against the constraints im-
posed by distance. The relative outcome of these two
opposing forces is measured in our specific factor of
interest – resource depletion, interpreted in the theory
through the concept of GUD. This approach has allowed
us to show empirically over a large area what range
scientists in Kazakhstan have observed since indepen-
dence – an uneven use of rangeland resources leading
to a combination of localised overuse and abandonment
(Alimaev et al. 2008; Rachkovskaya and Bragina 2012). References Predictive
Models of Movement by Serengeti Grazers. Ecology 85: 2429–
2435. Moritz M., Soma E., Scholte P., Xiao N., Taylor L., Juran T., and Saïdou
K. (2010). An Integrated Approach to Modeling Grazing Pressure in
Pastoral Systems: the Case of the Logone Floodplain (Cameroon). Human Ecology 38: 775–789. Government of Kazakhstan and the World Bank (2004). Supporting
Revival of the Livestock Sector in Kazakhstan, Programme for
Collaborative Economic Research of the Government of,
Kazakhstan, Washington. Moritz M., Hamilton I. A., Chen Y., and Scholte P. (2014). Mobile
Pastoralists in the Logone Floodplain Distribute Themselves in an
Ideal Free Distribution. Current Anthropology 55: 115–122. Hijmans, R. J., and van Etten, J. (2013). Raster Package for R. 2.1 ed. Nechaeva N. T., Antonova K. G., Karshenas C. D., Mukhammedov G.,
and Hurberdiev M. (1979). Vegetation Productivity in the Central
Karakum and Implications for User Regimes [Produktivnost′ rastitel
′nosti tsentral′nykh Karakumov v sviazi s razlichnym rezhimom
ispol′zovaniia], Nauka, Moscow. Hill K., Kaplan K., Hawkes K., and Hurtado A. (1987). Foraging
Decisions Amongst Ache Hunter-Gatherers: New Data and
Implications for Optimal Foraging. Human Ecology 13: 29–47. Kanchaev K., Kerven C., and Wright I. A. (2003). The limits of the land:
pasture and water conditions. In Kerven C. (ed.), Prospects for
Pastoralism in Kazakhstan and Turkmenistan: From State Farms to
Private Flocks, Routledge Curzon, London. Owen-Smith N., Fryxell J. M., and Merill E. M. (2010). Foraging Theory
Upscaled: the Behavioural Ecology of Herbivore Movement. Philosphical Transactions of the Royal Society 365: 2267–2278. Pettorelli N., Ryan S., Mueller T., Bunnefeld N., Jedrzejewska B., Lima
M., and Kausrud K. (2011). The Normalized Difference Vegetation
Index (NDVI): Unforeseen Successes in Animal Ecology. Climate
Research 46: 15–27. Karnieli A., Gilad U., Ponzet M., Svoray T., Mirzadinov R., and Fedorina
O. (2008). Assessing Land-Cover Change and Degradation in the
Central Asian Deserts Using Satellite Image Processing and
Geostatistical Methods. Journal of Arid Environments 72: 2093–
2105. Rachkovskaya, E. I., and Bragina, T. M. (2012). Steppes of Kazakhstan:
diversity and present state. In Werger, M. J. A., and Van Staalduinen,
M. A. (eds.), Eurasian Steppes. Ecological Problems and
Livelihoods in a Changing World, Springer. Kerven C., Alimaev I. I., Behnke R., Davidson G., Franchois L.,
Malmakov N., Mathijs E., Smailov A., Temirbekov S., and Wright
I. A. (2004). Retraction and Explansion of Flock Mobility in Central
Asia: Costs and Consequences. African Journal of Range and
Forage Science 21: 91–102. Robinson, S. References An estimation of the extent of desertification of
psammophytic vegetation of Kazakhstan [Otsenka stepeni
opustynivaniya psammofitnovo rastitel’nosti Kazakhstana] In
Baitulin, I. O., Ogar, N. P., and Bragina, T. M. (eds.),
Transformation of Natural Ecosytems and their Components during
Desertification [Transformatsiya Prirodnykh Ekosistem i ikh
Komponentov pri Opustynivanii], Almaty. Russian. Bizhanova G., and Kurochkina L. Y. (1989). Mapping of Human-Induced
Change in the Pastures of the Moiynkum [Antropogennye Smeny
Pastbishch Moiynkumov i ikh Kartografirovanie], Nauka, Alma-
Ata. Boone, R. B., Burnsilver, S. B., Gavin, K. A., and Hobbs, N. T. (2008). Large scale movements of large herbivores: livestock following
changes in seasonal forage supply. In Prins, H. H. T., and Van
Langevelde, F. (eds.), Resource Ecology: Spatial and Temporal
Dynamics of Foraging, Springer. Acknowledgements
This paper is a contribution to Imperial College’s
Grand Challenges in Ecosystems and the Environment initiative. We are
very grateful to the following individuals for their support, advice, and
assistance: Resgul Adushov; Ilya Ilytch Alimaev; Kydrbai Atabaev and
all his family; Cara Kerven; Bulgyn Koitai; Igor Lysenko; Zheksinbai
Sisatov; Aidos Smailov; Sayat Temirbekov; Sean Webber; Aigul Brown J. S. (1988). Patch Use as an Indicator of Habitat Preference,
Predation Risk and Competition. Behavioural Ecology and
Sociobiology 22: 3–47. 20 Hum Ecol (2017) 45:5–21 arid rangelands. In Behnke, R. (ed.), The Socio-Economic
Consequences of Desertification in Central Asia, Springer. arid rangelands. In Behnke, R. (ed.), The Socio-Economic
Consequences of Desertification in Central Asia, Springer. Charnov E. L. (1976). Optimal Foraging, the Marginal Value Theorum. Theoretical Population Biology 9: 129–136. Coppolillo P. B. (2000). The Landscape Ecology of Pastoral Herding:
Spatial Analysis of Land Use and Livestock Production in East
Africa. Human Ecology 28: 527–560. Kerven, C., Robinson, S., Behnke, R., Kashenov, K., and Milner-
Gulland, E. J. (2016a). Horseflies, Wolves and Wells: Biophysical
and Socio-economic Factors Influencing Livestock Distribution in
Kazakhstan’s Rangelands. Land Use Policy. Core Team R. (2014). A language and environment for statistical com-
puting, R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/ Kerven C., Robinson S., Behnke R., Kushenov K., and Milner-Gulland
E. J. (2016b). A Pastoral Frontier: from Chaos to Capitalism and the
Recolonisation of the Kazakh Rangelands. Journal of Arid
Environments 127: 106–119. De Boer W. F., and Prins H. H. T. (1989). Decisions of Cattle Herdsmen
in Burkina Faso and Optimal Foraging Models. Human Ecology 17:
445–464. Kurochkina L. Y., and Osmanova L. T. (1973). References Pastures of Sandy Deserts
of Kazakhstan [Pastbishcha Peschanykh Pustyn’ Kazakhstana],
Alma-Ata, Kainar. Dong S., Wen L., Liu S., Zhang X., Lassoie J. P., Yi S., Li X., Li J., and Li
Y. (2011). Vulnerability of Worldwide Pastoralism to Global Change
and Interdisciplinary Strategies for Sustainable Pastoralism. Ecology and Society 16: 10. Laca E. A., Distel R. A., Griggs T. C., Deo G. P., and Demment M. W. (1993). Field Test of Optimal Foraging with Cattle: the Marginal
Value Theorem Successfully Predicts Patch Selection and
Utilization, International Grasslands Congress, Rock Hampton. Dzhanpeisov R., Alimbaev A. K., Minyat V. E., and Smagulov T. A. (1990). Degradation of Soils of Mountain and Desert Pastures in
Kazakhstan. Problems of Desert Development 4: 19–26. Lange R. T. (1969). The Pioshpere: Sheep Track and Dung Patterns. Journal of Range Management 22: 396–400. ESRI (2011). ArcGIS Desktop, 10 edn., Environmental Systems
Research Institute, Redlands. McCarthy N. (2007). Climate Variability and Flexibility in Resource Use
Access: the Case of Pastoral Mobility in Northern Kenya. Environment and Development Economics 12: 403–421. FAOSTAT (2015). Database available at http://faostat.fao.org/. Food and
Agriculture Organization of the United Nations. Milner-Gulland E. J., Kerven C., Behnke R., Wright I. A., and Smailov A. (2006). A Multi-agent System Model of Pastoralist Behavior in
Kazakhstan. Ecological Complexity 3: 23–36. Ferret, C. (2013). Today’s mobile pastoralism in south-eastern
Kazakhstan. A case study in Rajymbek district In A. Bissenova,
Schoeberlein, J., and Mcguire, G. (eds.), The Steppe and the
Sown, XIII Biennial Conference of the European Society for
Central Asian Studies (ESCAS), Astana, Kazakhstan. Ministry of Agriculture of the Republic of Kazakhstan (2013). Programme for the Development of the Agroindustrial Complex in
the Kazakh Republic 2013–2020 “Agribusiness 2020” [Programma
po razvitiu agropromyshlennovo kompleksa v Respubliki
Kazakhstana na 2013–2020 gody - “Agrobiznes-2020”]. Astana. Fretwell S. D., and Lucas H. L. (1970). On Territorial Behaviour and
Other Factors Influencing Habitat Distribution in Birds. I. Theoretical Development. Acta Biotheoretica 19: 16–36. Ministry of Agriculture of the Republic of Kazakhstan (2014). Master
plan for meat livestock sector development in the Republic of
Kazakhstan till 2020 [Master plan rasvitiya otrasli myasnogo
skotovodstvo v Respubliki Kazakhstana do 2020 Goda]. Astana. Fryxell, J. M. (2008). Predictive modelling of patch use by terrestrial
herbivores. In: Prins, H. H. T., and Van Langevelde, F. (eds.),
Resource Ecology: Spatial and Temporal Dyamics of Foraging. Springer. Fryxell J. M., Wilmhurst J. F., and Sinclair A. R. E. (2004). References (2016). Land degradation in Central Asia: evidence, percep-
tion and policy. In: Behnke, R. (ed.), The End of Desertification? Disputing Environmental Change in the Drylands. Springer Earth
System Science. Kerven, C., Alimaev, I. I., Behnke, R., Davidson, G., Malmakov, N.,
Smailov, A., and Wright, I. A. (2006). Fragmenting Pastoral
Mobility: Changing Grazing Patterns in Post-Soviet Kazakhstan. USDA Forest Service Proceedings RMRSP-39, pp. 99–110. Robinson S., Kerven C., Behnke R., Kashenov K., and Milner-Gulland E. J. (2016). The Changing Role of Biophysical and Socio-economic
Drivers in Determining Livestock Distributions: a Historical
Perspective from Kazakhstan. Agricultural Systems 143: 169–182. Kerven, C., Shanbaev, K., Alimaev, I. I., Smailov, A., and Smailov, K. (2008). Livestock mobility and degradation in Kazakhstan’s semi- Hum Ecol (2017) 45:5–21 21 USDA/NRCS (2003). National Range and Pasture Handbook. Fort
Worth, Texas, USA: Natural Resources Conservation Service’s
Grazing Lands Technology Institute (GLTI). Rozen-Rechels D., van Beest F. M., Richard E., Uzal A., Medill S. A.,
and McLoughlin P. D. (2015). Densitydependent, Central Place
Foraging in a Grazing Herbivore: Competition and Tradeoffs in
Time Allocation Near Water. Oikos 124: 1142–1150. Utsumi S. A., Cagniano C. A., Galli J. R., McEachern M. B., Demment
M. W., and Laca E. (2009). Resource Heterogeneity and Foraging
Behaviour of Cattle Across Spatial Scales. BMC Ecology 9. Scholte P., Kari S., Moritz M., and Prins H. (2006). Pastoralist Responses
to Floodplain Rehabilitation in North Cameroon. Human Ecology
34: 27–51. Vanselow K., Kraudzun T., and Samimi C. (2012). Grazing Practises and
Pasture Tenure in the Eastern Pamirs. Mountain Research and
Development 32: 324–336. Shrader A. M., Kerley G. I. H., Brown J. S., and Kotler B. P. (2012). Patch
Use in Free-Ranging Goats: Does a Large Mammalian Herbivore
Forage Like Other Central Place Foragers? Ethology 118: 1–8. Vuolo, F., Mattiuzzi, M., Klisch, A., and Atzberger, C. (2012). Data
service platform for MODIS Vegetation Indices time series process-
ing at BOKU Vienna: current status and future perspectives. Proc. SPIE Earth Resources and Environmental Remote Sensing/GIS
Applications III, 85380A (October 25, 2012) Tazhibaev S., Musabekov K., Yesbolova A., Ibraimova S.,
Mergenbayeva A., Sabdenova Z., and Seidahmetov M. (2014). Issues in the Development of the Livestock Sector in Kazakhstan. Procedia Social and Behavioural Sciences 143: 610–614. Thornton P. K., Kruska R. L., Henninger N., Kristjanson P. M., Reid R. S., Atieno F., Odero A. N., and Ndegwa T. (2002). References Mapping Poverty
and Livestock in the Developing World, International Livestock
Research Institute, Nairobi. Wolfe J. M. (2013). When is it Time to Move to the Next Raspberry
Bush? Foraging Rules in Human Visual Search. Journal of Vision
13: 1–17. Turner M., Hiernaux P., and Schlecht E. (2005). The Distribution of
Grazing Pressure in Relation to Vegetation Resources in Semi-arid
West Africa: the Role of Herding. Ecosystems 8: 668–681. Zhambakin Z. A. (1995). Pastures of Kazakhstan [Pastbishcha
Kazakhstana], Kainar, Almaty.
|
https://openalex.org/W2527710167
|
https://europepmc.org/articles/pmc5055691?pdf=render
|
English
| null |
Risk of selection bias in randomized trials: further insight
|
Trials
| 2,016
|
cc-by
| 4,016
|
Correspondence: vb78c@nih.gov
National Cancer Institute and University of Maryland Baltimore County,
Biometry Research Group, National Cancer Institute, 9609 Medical Center
Drive, Rockville, MD 20850, USA © 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Background appropriate allocation concealment, but, rather, have
(at best) only partial allocation concealment. Cleary,
allocation concealment is not a binary phenomenon [2],
and its success depends on addressing both threats, direct
observation and prediction. In other words, improper
randomization constitutes a violation of allocation con-
cealment [3]. These are not two distinct dimensions of
trial quality, and should not be treated as such. Kahan, Rehal, and Cro [1] are to be congratulated for
drawing attention to a rather important problem in trial
design, namely how to reduce or eliminate the risk of
selection bias. The remedial methods discussed include
(1) masking recruiters, (2) the use of unrestricted
randomization, (3) not stratifying by site in multicenter
trials, (4) avoiding permuted blocks when stratifying by
site, and (5) making better use of prognostic covariates. Among the major findings are that 3 % of the trials used
unrestricted randomization, 35 % did not specify how
they randomized at all, and 58 % of those that stratified
by site used permuted blocks. We wish to focus on these
findings, and also on another opportunity to curb selec-
tion bias, namely post-trial auditing as a disincentive. Berger Trials (2016) 17:485
DOI 10.1186/s13063-016-1597-5 Berger Trials (2016) 17:485
DOI 10.1186/s13063-016-1597-5 Open Access Risk of selection bias in randomized trials:
further insight Vance W. Berger Vance W. Berger Abstract The quality of randomization is an under-appreciated facet of trial design. The present piece represents an advance
in our collective understanding of how allocation concealment and randomization relate to risk of selection bias in
randomized trials, and other measures are also considered. Though the overwhelming majority of the advice given
is timely and correct, it is more instructive to focus on the relatively narrow sliver of advice that is incorrect (namely,
that trials should not stratify by site, and that unrestricted randomization is a solution to the problem of selection
bias), so it is in this context that the comments here must be understood. In no way is this intended to be a
rebuttal of the excellent work we have before us. Rather, it is a refinement. Keywords: Allocation concealment, Berger-Exner test, Conditional unrestricted randomization, Maximal procedure Unrestricted randomization: is 3 % too much, or
too little? The authors put forth unrestricted randomization as a
method to eliminate selection bias, and indeed it is. But
when we bear in mind that we can prevent all carpal
tunnel syndrome instantly by amputating all hands as a
preventative measure, we recognize that eliminating one
problem is not enough. The solution must also not intro-
duce additional problems. Unfortunately, unrestricted
randomization does precisely that, and this is why nobody
has ever used it, or ever would use it in an actual trial. The 3 % is not, as suggested, too small a figure; it is, on
the contrary, too large a figure. The true nature of allocation concealment It is stated that even with appropriate allocation conceal-
ment, prediction may still be possible. This misguided
statement represents a misunderstanding of allocation
concealment, and needs to be refuted since the notion is
so prevalent. As one might guess from the name itself,
allocation concealment means that the allocations are
concealed. If they can be predicted, then we do not have This may sound like an audacious claim. How can
we state that unrestricted randomization has never
been used when the authors report that 3 % figure? In fact what is used when authors claim unrestricted
randomization is not actually unrestricted randomization,
as we shall explain. They instead use a vaguely defined Correspondence: vb78c@nih.gov
National Cancer Institute and University of Maryland Baltimore County,
Biometry Research Group, National Cancer Institute, 9609 Medical Center
Drive, Rockville, MD 20850, USA Berger Trials (2016) 17:485 Page 2 of 5 Page 2 of 5 variation we shall refer to as conditional unrestricted
randomization. One major problem with unrestricted
randomization is chronological bias, or the possibility of
many more early patients ending up in one treatment
group and many more later patients ending up in the
other treatment group [4, 5]. In fact, this chronological
bias is the primary reason that restricted randomization is
used (as it should be) [6]. However, we shall focus instead
on another issue with unrestricted randomization. Just as
a normal distribution for heights means that, sooner or
later, we will encounter an individual with a negative
height [7], so too is it the case that with true unrestricted
randomization we will, sooner or later, see an allocation
sequence comprised entirely of only one treatment group. condition) [4, 5, 9]. As it turns out, these MTI procedures
are not only expressed more precisely (and honestly) than
unrestricted randomization, but they are also far more
suitable for actual trials by virtue of controlling chrono-
logical bias and eliminating the possibility of unfortunate
outcomes of the type we described earlier. So the authors are correct in spirit. We do need
randomization procedures with fewer restrictions. But
the solution is not to swing the pendulum all the
way to the other side. We do still need some restrictions,
namely the MTI. But the call should be for no additional
restrictions above and beyond this, and also for larger
MTI values than those that are typically used in practice,
plus dropping the requirement of terminal balance. The true nature of allocation concealment q
p
y
y
g
p
We do not believe that any clinical trial researcher
would ever, under any circumstances, accept such an
unfortunate outcome. If confronted by this, they would
“throw it back” and try again. But this discretion to do
that calls into question just which allocation sequences
would be considered admissible? We do not get around
this consideration by appeal to the fact that we did not
have to throw the first one back, nor by the old adage
about not being able to define it but knowing it when
we see it. In a world of precise definitions, this simply
will not cut it. Knowledge of the sampling properties of
the randomization procedure is possible only when we
actually know what the randomization procedure is. So
would we have accepted a split of 95:5? What about
90:10? Where exactly is the line drawn? And even if we
are not only OK but also thrilled with the ideal ratio of
50:50, are we still OK with a 50:50 sequence that is
segregated, with the first half of the allocations all
going to the same group, and then the rest going to
the other group to balance out the numbers at the
end? No, we are not. Failure to specify how the trial was randomized
The authors are correct that failure to specify how the
trial was randomized is simply unacceptable. And yet
this occurred in 35 % of the trials evaluated. One can
only imagine a conversation between a patient (P), a
prescribing physician (PP), and a statistician (S): P: Is this treatment you prescribed the best option
given my condition? PP: The evidence suggests that it is. P: I understand that medical studies are conducted to
the highest and most rigorous standards possible? PP: Yes, they are. The stakes are too high for anything
less than the best. P: And this is why the highest level of evidence is
reserved for randomized trials? Berger Trials (2016) 17:485 Berger Trials (2016) 17:485 Berger Trials (2016) 17:485 Page 3 of 5 Page 3 of 5 S: That is correct. to recommend its use, given its drawbacks on the other
dimension. But that is not the case when stating that the
MTI procedures are superior to blocked randomization. Here, the superiority is in an overall sense, and not just
in one isolated dimension. There is no compensation by
appeal to other dimensions. The MTI procedures match
blocked randomization for control of chronological bias,
and beat it soundly for control of selection bias, in fact
in more ways than one [9]. As such, the use of permuted
block randomization is indefensible. P: And instead of calling these authors to account, you
just assume that they randomized correctly, and then
you act accordingly in your prescribing decisions? Don’t
ask, don’t tell? Even if that means that patients may then
get exposed to harmful treatments? And this is where our hypothetical dialogue ends, but
I would be curious to know how real physicians might
respond at this point. The enormous influence on trial
quality and the reliability of the precise method of
randomization cannot be overstated. The potential for
misleading evidence resulting from flawed randomization
methods has been well-documented [5]. And yet even
given how important this information is, over one third of
the trial authors could not be bothered to supply it, and
over one third of the journal review teams could not be
bothered to insist on it as a condition for publication. The
very essence of evidence-based medicine is trust but verify
(and that trust part is optional), yet consumers of medical
research are put in a position of having to take it on faith
that the research teams conducted rigorous research
despite the fact that these very same research teams
clearly were not rigorous at all in their reporting? This is
not even a matter of trust. Trust would be believing the
claim, but here, no claim is even offered. They do not even
claim to have randomized correctly. Credibility in a sys-
tem that allows for this cavalier attitude towards the lives
and health of actual patients might be misplaced. Berger Trials (2016) 17:485 One
reviewer
pointed
out
that
permuted
block
randomization should be fine in masked trials, since
even an occasional unmasked allocation would likely
occur after the block is complete, and also for multi-
center trials for which no one investigator can keep
track of all allocations, since some will occur at other
centers. This is, in fact, a widely held view, and likely
contributes to the reluctance to switch from permuted
block randomization to MTI randomization, so it does
merit a thoughtful response. g
p
First, in multicenter trials, randomization is generally
stratified by center, so that in fact an investigator can
keep track of how the allocation is progressing, at least
at his or her center, but then this is all that is relevant
for prediction anyway. Second, even if randomization
were not so stratified, investigators can still predict
successfully, even without certainty, based on how many
patients have so far been randomized to each group. True, this can be done with MTI randomization too, but
then it will be less successful than it will be with
permuted blocks. Moreover, some unmasking in trials
that are planned as masked can be immediate, as with
injection site reactions [11]. And even if masking is
retained perfectly throughout, so that selection bias of
the type we consider is not an issue, there is still no
benefit in using permuted block randomization. In that
case, it is just as good as, but not better than, MTI
randomization [9]. So we are comparing two procedures,
one of which is clearly better in one situation and is just
as good in the other situation, and we would not know
ahead of time which situation we would be in. PP: Exactly. PP: Exactly. PP: Exactly. P: Are all types of randomization equally rigorous, or
are some better than others? PP: This is a question for the statistician. S: Some methods of randomization are better than
others. The
worst
ones,
such
as
permuted
block
randomization, can be easily deciphered and subverted. Hopefully, it is clear that “unrestricted randomization”
is a procedure that nobody would ever use in an actual
clinical trial and, moreover, it is sufficiently poorly defined
that when it is claimed we cannot decipher what proced-
ure actually was used. If pressed, then a researcher who
claimed to use unrestricted randomization would have to
come to grips with just how large an imbalance in
group sizes he or she would tolerate. In fact, there is a
class of randomization procedures that explicitly takes
into account this maximally tolerated imbalance (MTI),
namely the MTI procedures, including the big stick
(essentially unrestricted randomization until the MTI
is reached, at which point the allocation is forced to
restore balance) [6], Chen’s procedure (a refinement of
the big stick in which a biasing probability is specified
so as to encourage a move towards balance without
forcing it, at least until the MTI is reached) [8], and
the maximal procedure (which selects randomly from
among the allocation sequences that adhere to the MTI P: I see! Well, in that case, it’s a good thing that the
trials whose results have informed your decision on how
to treat me did not use permuted block randomization! p
S: Well, they may have. We actually don’t know if they
did or didn’t. P: I understand. I would not expect you to memorize
all the details of every study. But for my peace of mind,
can you please check on that when you go back to your
office and have the studies available? S: No, I happen to have the articles right here with me. It is not that I cannot remember. We do not know
because the articles did not specify how they randomized. P: So you are telling me that they may have used a valid
randomization procedure, and they may not have? We have
no way to know? And if they didn’t, then the trial results
may bear little or no resemblance to the reality governing
how effective this treatment is for my condition? Permuted blocks It is pointed out [1] that 58 % of the stratified trials used
permuted blocks. We can all agree that this is way too
high, and the ideal proportion would be somewhere
close to zero. Even one trial using permuted blocks is
one too many. But what about trials that are not strati-
fied by center? Are permuted blocks OK in these? The
answer is still no. Just as the MTI procedures are far su-
perior to unrestricted randomization by virtue of their
better ability to handle chronological bias, so too are
they far superior to permuted block randomization, but
here due to their superior ability to control selection bias
[9, 10]. The best randomization procedure for eliminat-
ing selection bias is unrestricted randomization, yet for
the reasons articulated above, we are still opposed to its
use in practice. Might the same argument be offered to
justify using permuted block randomization even though
the MTI methods are superior? No, it cannot. This discussion makes clear that permuted block
randomization should not be used. It does not, however,
support the use of MTI randomization, since it would be
a false dichotomy to believe that these are the only two
options. Clearly, they are not. Proschan [12] discusses
some other types of randomization that might be used,
and, indeed, these too would be preferable to permuted
block randomization. However, in other work we have
found MTI randomization to be optimal, so it is these
procedures that we focus on, and recommend for use in
practice. Future work will extend the MTI procedures to
unequal allocation, and more than two treatment groups,
but for now, at least we can point out that it does seem The comparison of any two randomization methods,
whether we are comparing unrestricted randomization
to the maximal procedure or whether we are comparing
blocked randomization to the big stick, must necessarily
account for both selection bias and chronological bias. The fact that unrestricted randomization wins on only
one of these comparisons is, as we have seen, insufficient Berger Trials (2016) 17:485 Berger Trials (2016) 17:485 Page 4 of 5 Page 4 of 5 prudent to replace permuted block randomization with
MTI randomization, at least for trials with two arms and a
1:1 allocation. treatment in fact is no more effective than the control
(or placebo). Abbreviations MTI: Maximally tolerated imbalance; P: Patient; PP: Prescribing physician;
S: Statistician Competing interests
The author declares that he has no competing interests. p
g
The author declares that he has no competing interests. Received: 17 September 2015 Accepted: 11 September 2016 References Permuted blocks So while inertia remains a huge problem in
getting researchers to upgrade their methodologies [15],
it is not the only problem. There is more at play here,
including a perverse system of incentives that works to
reward researchers for using flawed research method-
ology. What possible incentive do researchers have to
get it right when doing so will hurt their bottom line
and, moreover, given that it is optional anyway? Why
report honest trial results when doing so will put you at
a strategic disadvantage relative to your competitors,
some of whom may be using blocked randomization and
any other trick they can get away with? Post-trial auditing One ideal opportunity to control selection bias was not
touched upon, but should have been. It seems pretty
close to research malpractice to not specify how the
randomization was conducted, and it is just as bad to
not formally test for selection bias after the fact. This
widespread failure to even consider selection bias allows
offending investigators to fly under the radar and to
carry on without any fear of any real consequence. There
simply is no disincentive to engage in this type of
behavior. Clearly, this needs to change if trial results are
to remain credible even after the public comes to
understand just how easy the results are to manipulate. They will need to be assured that while it is theoretically
possible to manipulate trial results, actual trials are
immune because only best practices are used. Presently,
we are not even close to being able to claim this. Clearly, self-policing does not work. It is time for an
external agency to step in and clean up the mess. Only when
true accountability is demanded of all medical researchers
can we expect, first, better reporting of randomization
methods, and second, better randomization methods. The
first step has to be zero tolerance for failure to report the
randomization method used in a trial, and zero tolerance for
failure to audit the trial for selection bias after the fact. Short
of these steps, the public has every reason to withdraw
whatever trust it has left in the medical establishment. Post-trial auditing needs to be standard and routine. It
should not be triggered only when there is some basis
for suspicion [13], unless the inherent vested interests
the researchers have when conducting the trials them-
selves constitute a firm basis for suspicion, as clearly
they should. The most reliable method for testing for
selection bias in a randomized trial is the Berger-Exner
test [14], which is based on a comparative analysis of
those patients who could have been anticipated to end
up in the active treatment group versus those who ended
up there by chance. One can only wonder how many of
the trials considered conducted this analysis, although
the silence on this issue speaks volumes and we pretty
much already know the answer. References
h 1. Kahan BC, Rehal S, Cro S. Risk of selection bias in randomised trials. Trials. 2015. In press. Acknowledgements The review team offered helpful comments that greatly improved the
presentation. The review team offered helpful comments that greatly improved the
presentation. 12.
Proschan M. Influence of selection bias on type I error rate under random
permuted block designs. Stat Sin. 1994;4:219–31.
13.
Berger VW. Do not test for baseline imbalances unless they are known to
be present? Qual Life Res. 2009;18:399.
14.
Berger VW, Exner DV. Detecting selection bias in randomized clinical trials.
Control Clin Trials. 1999;20(4):319–27.
15.
Berger VW. Conflicts of interest, selective inertia, and research malpractice in
randomized clinical trials: an unholy trinity. Sci Eng Ethics. 2014. in press. Berger Trials (2016) 17:485 Conclusions 2. Berger VW. Is allocation concealment a binary phenomenon? Med J Aust. 2005;183(3):165. There is a major disconnect between the perception of
medical research as a pristine beacon of hope working
to save us all, and the reality of medical research as a
business conducted at least partially to enrich those
engage in it. Certain outcomes are more profitable, and
the trials are conducted, for the most part, by the very
parties who stand to gain or lose based on the trial
outcomes. Moreover, these same parties with the vested
interests
also
enjoy
almost
unfettered discretion
to
conduct the trials as they see fit, subject to some
constraints but, as we have seen, constraints that still
allow for discretion in deciding, among other things,
to randomize properly or not. This key component of
trial quality is left as a personal decision. 3. Berger VW, Do AC. Allocation concealment continues to be misunderstood. J Clin Epidemiol. 2010;63(4):468–70. 4. Berger VW, Ivanova A, Deloria-Knoll M. Minimizing predictability while
retaining balance through the use of less restrictive randomization
procedures. Stat Med. 2003;22(19):3017–28. 5. Berger VW. Selection bias and covariate imbalances in randomized clinical
trials. Chichester: Wiley; 2005. 6. Soares JF, Wu CFJ. Some restricted randomization rules in sequential
designs. Commun Stat Theor Methods. 1983;12:2017–34. 7. Perlman P, Possen BH, Legat VD, Rubenacker AS, Bockiger U, Stieben-Emmerling L
When will we see people of negative height. Significance. 2013;10(1):46–8. 8. Chen YP. Biased coin design with imbalance tolerance. Communicat Stat
Stoch Models. 1999;15:953–75. 8. Chen YP. Biased coin design with imbalance tolerance. Communicat Stat
Stoch Models. 1999;15:953–75. 9. Berger VW, Agnor RC, Bejleri K. Comparing MTI randomization procedures
to blocked randomization. Stat Med. 2016;35(5):685–94. 10. Zhao W, Weng Y, Wu Q, Palesch Y. Quantitative comparison of
randomization designs in sequential clinical trials based on treatment
balance and allocation randomness. Pharm Stat. 2012;11:39–48. doi:10.1002/pst.493. Improper randomization, such as permuted block
randomization, invites the type of selection bias that can
masquerade
as
a
treatment
effect
even
when
the 11. Berger VW, Agnor RC. Delayed unmasking and selection bias. Stat Med. 2016;35(12):2111–2. 11. Berger VW, Agnor RC. Delayed unmasking and selection bias. Stat Med. 2016;35(12):2111–2. 15.
Berger VW. Conflicts of interest, selective inertia, and research malpractice in
randomized clinical trials: an unholy trinity. Sci Eng Ethics. 2014. in press. Berger Trials (2016) 17:485 Page 5 of 5 Berger Trials (2016) 17:485 Berger Trials (2016) 17:485 Page 5 of 5 • We accept pre-submission inquiries
• Our selector tool helps you to find the most relevant journal
• We provide round the clock customer support
• Convenient online submission
• Thorough peer review
• Inclusion in PubMed and all major indexing services
• Maximum visibility for your research
Submit your manuscript at
www.biomedcentral.com/submit
Submit your next manuscript to BioMed Central
and we will help you at every step: • We accept pre-submission inquiries
• Our selector tool helps you to find the most relevant journal
• We provide round the clock customer support
• Convenient online submission
• Thorough peer review
• Inclusion in PubMed and all major indexing services
• Maximum visibility for your research
Submit your manuscript at
www.biomedcentral.com/submit
Submit your next manuscript to BioMed Central
and we will help you at every step: • We accept pre-submission inquiries
• Our selector tool helps you to find the most relevant journal
• We provide round the clock customer support
• Convenient online submission
• Thorough peer review
• Inclusion in PubMed and all major indexing services
• Maximum visibility for your research
Submit your manuscript at
www.biomedcentral.com/submit
Submit your next manuscript to BioMed Central
and we will help you at every step: Submit your next manuscript to BioMed Central
and we will help you at every step:
|
https://openalex.org/W3216860791
|
http://www.scielo.br/pdf/rbsmi/v8n3/a10v8n3.pdf
|
Portuguese
| null |
Effects of the consumption of "multimixture" on nutritional status: a community trial involving children from a slum district on the outskirts of Maceió, State of Alagoas, Brazil
|
Revista Brasileira de Saúde Materno Infantil
| 2,008
|
cc-by
| 6,737
|
ARTIGOS ORIGINAIS / ORIGINAL ARTICLES ARTIGOS ORIGINAIS / ORIGINAL ARTICLES Resumo Objectives: to investigate the impact of the
consumption of "multimixture" (a bran-based cereal
mixture) on the nutritional status of children at risk of
malnutrition. Objetivos: verificar o impacto do consumo da multi-
mistura sobre as condições de nutrição e saúde de
crianças em situação de risco. Métodos: ensaio comunitário envolvendo crianças
(6 a 60 meses) de uma favela de Maceió, Alagoas, Brasil,
aleatoriamente alocadas para o Grupo Controle (n=50)
ou Grupo Multimistura (n=48). Neste, a suplementação
consistiu de duas colheres de sopa/dia. Avaliações
antropométricas foram realizadas antes e após a fase
experimental (10 meses). A incidência de agravos à
saúde foi investigada pela realização de inquéritos
quinzenais de morbidade. O consumo alimentar foi ana-
lisado por inquérito recordatório de 24 horas (três dias
alternados). Os níveis de hemoglobina (Hemocue ) e de
retinol sérico (HPLC) foram aferidos apenas no final da
fase experimental. As medidas de desfecho foram
comparadas entre os grupos usando-se testes
paramétricos ou não-paramétricos, conforme cada situ-
ação. Diferenças foram consideradas como estatistica-
mente significativas quando p<0,05. Methods: a community trial involving children (6
to 60 months) from a slum area in the city of Maceió,
State of Alagoas, Brazil, randomly assigned to the
Control Group (n=60) or to the "multimixture" Group
(n=48). The supplement consisted of two tablespoons
of "multimixture" per day. Anthropometric measure-
ments were taken before and after the experimental
phase (10 months). The incidence of health problems
was investigated on a biweekly basis. Food consump-
tion was assessed by way of 24 hour dietary recall (on
three alternate days). Hemoglobin (HemoCue®) and
serum retinol (HPLC) were determined at the end of
the experimental phase. The resulting measurements
for the two groups were compared using parametric
or non-parametric statistics in according with the
situation. Differences were considerate as significa-
tive statistically when p<0.05. Resultados: não foram observadas diferenças
(p>0,05) entre os resultados obtidos na avaliação
antropométrica, dietética, bioquímica e na incidência de
diarréia, vômitos e febre. Todavia, as infecções respi-
ratórias incidiram de forma mais intensa sobre as
crianças do Grupo Controle (24,3% vs. 16,9%;
OR=1,59; IC95%=1,13-2,24; p<0,01). Results: no differences were observed (p>0.05)
between the results obtained from anthropometric
measurements and dietary intake, between levels of
hemoglobin and serum retinol or in the incidence of
diarrhea, vomiting or fever. However, there was a
higher incidence of respiratory infections among the
children in the Control Group (24.3% vs.16.9%;
OR=1.59; 95%CI = 1.13-2.24; p<0.01). Efeitos do consumo da multimistura sobre o
estado nutricional: ensaio comunitário
envolvendo crianças de uma favela da
periferia de Maceió, Alagoas, Brasil Haroldo da Silva Ferreira 1
Sybelle de Araújo Cavalcante 2
Cyro Rego Cabral Jr. 3
Adriana Toledo de Paffer 4 Haroldo da Silva Ferreira 1
Sybelle de Araújo Cavalcante 2
Cyro Rego Cabral Jr. 3
Adriana Toledo de Paffer 4 1-4 Faculdade de Nutrição. Universidade Federal de Alagoas. Campus A. C. Simões, BR 104-Norte, Km 97, Cidade
Universitária. Maceió, AL, Brasil. CEP: 57.072-970. E-mail: haroldo.ufal@gmail.com 1-4 Faculdade de Nutrição. Universidade Federal de Alagoas. Campus A. C. Simões, BR 104-Norte, Km 97, Cidade
Universitária. Maceió, AL, Brasil. CEP: 57.072-970. E-mail: haroldo.ufal@gmail.com Effects of the consumption of
"multimixture" on nutritional status: a
community trial involving children from a
slum district on the outskirts of Maceió,
State of Alagoas, Brazil Palavras-chave Palavras-chave
Antropometria,
Anemia, Alimentação alternativa, Infecções respiratórias Alimentação alternativa, Infecções respiratórias Resumo Conclusões: a suplementação com multimistura não
alterou o perfil antropométrico ou a freqüência de
anemia e hipovitaminose A entre as crianças. Conclusions: the "multimixture" food supplement
did not alter the anthropometric profile or the
frequency of anemia or hypervitaminosis A among the
children. Métodos Trata-se de um estudo do tipo ensaio comunitário,
constituído de um grupo experimental e um grupo
controle, envolvendo crianças na faixa etária de 6 a
60 meses, residentes na favela Cidade de Lona, no
município de Maceió, Alagoas, Brasil. A favela Cidade de Lona possui aproximada-
mente 600 domicílios. A fim de proceder a alocação
das crianças em um dos grupos de estudo, dividiu-se
a área em dois setores, A e B, tomando como refe-
rência uma rua central da localidade. Após uma
avaliação antropométrica de todas as crianças da
faixa etária-alvo, foi escolhido, para cada setor, um
grupo de 50 crianças com menor escore z para o
índice peso para idade. Por meio de sorteio, definiu-
se que tais crianças dos setores A e B formariam,
respectivamente, os grupos controle e multimistura. A investigação foi procedida no período de janeiro a
outubro de 2006. Segundo Mahler,5 sendo a desnutrição uma
conseqüência da pobreza e da privação, só poderá
ser erradicada mediante uma ação política orientada
a reduzir as desigualdades entre países e entre os
habitantes de um mesmo país. Na ausência dessa
política, a sociedade civil organizada busca soluções
alternativas para o problema. Todos os pais ou responsáveis foram informados
quanto aos detalhes da pesquisa, autorizaram e assi-
naram o Termo de Consentimento Livre e
Esclarecido, conforme definido no projeto subme-
tido e aprovado pelo Comitê de Ética em Pesquisa
da Universidade Federal de Alagoas. No contexto dessas ações, surgiu a proposta da
alimentação alternativa, tendo por base a premissa
que folhas, cascas e sementes descartadas como lixo,
seriam potencialmente nutritivas.6 Esse conceito
teve como principal desdobramento a elaboração da
chamada multimistura (MM), um farelo formulado a
partir desses subprodutos e usado como suplemento
à alimentação habitual de crianças, o qual vem sendo
utilizado por profissionais de saúde em grande
número de municípios brasileiros.7 Não foram incluídas no sorteio aquelas crianças
que atendessem uma ou mais das seguintes
condições: a) não autorização dos pais ou respon-
sáveis; b) criança portadora de desnutrição grave (z
<-3 para quaisquer dos índices antropométricos
formados com as variáveis peso, altura, sexo e
idade); e c) criança portadora de malformações ou
enfermidades (acamadas, hospitalizadas, com febre
no início do estudo, entre outras condições). Key words Key words
Anthropometry, Anemia, Alternative
feeding, Respiratory tract infections 309 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Ferreira HS et al. Introdução entre os resultados obtidos.7 entre os resultados obtidos.7 Diante do exposto, justifica-se a realização de
estudos epidemiológicos controlados que possam
avaliar a eficácia das intervenções que vêm sendo
adotadas em várias localidades brasileiras, baseadas
na utilização da multimistura. Apesar das evidências de que o Brasil passa por um
processo de transição nutricional e das reiteradas
vezes em que os países membros das Nações Unidas
têm reafirmado o compromisso de garantir o direito
de todo ser humano em não padecer de fome, a
desnutrição infantil continua sendo um grave pro-
blema de saúde pública em nosso país.1 O objetivo deste trabalho foi avaliar se o
consumo regular da multimistura contribui para a
promoção da melhoria das condições de nutrição e
saúde de crianças submetidas à situação de risco
nutricional. A partir 1974, quando ocorreu o primeiro
inquérito nutricional de abrangência nacional, a
prevalência de desnutrição em crianças apresentou
um declínio da ordem de 72%. No entanto, ainda
existem diferenciais importantes entre as regiões
geográficas brasileiras. No último inquérito, rea-
lizado em 1996, a prevalência de desnutrição obser-
vada no Centro-Sul do país foi de 5,6% enquanto
que, no Nordeste, essa prevalência era de 17,9% de
crianças desnutridas.2 Esses dados, baseados em
proporções populacionais, mascaram a gravidade
com que a desnutrição acomete determinados
grupos, especialmente aqueles submetidos à insegu-
rança alimentar. Em estudos conduzidos em favelas
de Alagoas, têm-se encontrado quase 50% das
crianças com déficit estatural importante3 e mais de
93% acometidas pela anemia.4 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Métodos No entanto, tal proposição tem recebido muitas
críticas no meio acadêmico em virtude da alegação
de falta de comprovação científica de seus efeitos,
ausência de controle sanitário, bem como pela sua
inadequação para consumo humano, isso devido à
possível existência de toxinas e fatores antinutri-
cionais.8-12 Além desses critérios, definiu-se que seriam
excluídas do estudo as crianças que, tendo sido intro-
duzidas no Grupo Multimistura, tenham durante o
transcorrer da coleta de dados: a) deteriorado seu
estado nutricional atingindo a condição de desnu-
trição grave; b) desenvolvido qualquer agravo que
pudesse ser atribuído ao uso da multimistura, ainda No intuito de contribuir para o esclarecimento
dessa problemática, várias pesquisas têm sido rea-
lizadas; no entanto, ainda existem muitas divergên-
cias sobre o assunto em virtude das discrepâncias 310 Efeitos do consumo da multimistura que de forma especulativa; c) a autorização dos pais
para participação no estudo fosse retirada; e d) não
tenham participado de todas as etapas do estudo. adequação tendo como referencial os valores
recomendados
nas
Recommended
Dietary
Allowances (RDAs).15 Adicionalmente, comparou-
se o percentual de crianças que não atingiram a meta
de ingestão individual (RDA), no grupo experi-
mental e controle. A multimistura foi preparada e fornecida pela
Pastoral da Criança de Maceió. Era composta de
farelo de trigo (80%), folha de mandioca (10%) e pó
de casca de ovo (10%). Esses ingredientes passavam
por um tratamento térmico durante 5 a 10 minutos
em fogo baixo, mexendo-se com colher de pau com
a finalidade de destruir microrganismos e substân-
cias tóxicas. Em seguida, eram trituradas em moinho
e depois peneiradas a fim de facilitar a homo-
geneização. Embora não fosse objetivo deste trabalho avaliar
o padrão alimentar das crianças, houve a necessidade
de introdução desse procedimento, visando-se
garantir que possíveis diferenças encontradas nos
indicadores utilizados no estudo pudessem ser
atribuídas à suplementação utilizada e não a
discrepâncias na ingestão dietética dos grupos
envolvidos. O controle de qualidade do produto final foi efe-
tuado pelo Laboratório Central do Estado de Alagoas
(LACEN) e, paralelamente, pelo Laboratório de
Microbiologia de Alimentos da Faculdade de
Nutrição da Universidade Federal de Alagoas. Foram realizadas duas avaliações antropomé-
tricas, uma antes do início do seguimento e outra no
final da fase experimental. Os dados relativos às
variáveis de idade, sexo, massa corporal e estatura
foram processados por meio do Epi-Info 3.3.2, de
modo a constituir os índices peso-para-idade, peso-
para-altura e altura-para-idade. Métodos O referencial antro-
pométrico utilizado foi o do Center for Disease
Control and Prevention (CDC) do National Center
for Health Statistics, 2000, que se encontra incorpo-
rado ao programa Epi-info. Obviamente, apenas as crianças do grupo experi-
mental (Grupo Multimistura) recebiam o suple-
mento. Para cada criança, era fornecida multimistura
em embalagem específica, contendo a quantidade
aproximada para consumo quinzenal. Ao final deste
período, um membro da equipe retornava ao
domicílio recolhendo o recipiente com as eventuais
sobras, fornecendo novo recipiente com multimis-
tura, para consumo na quinzena seguinte. Esses
procedimentos tiveram os seguintes objetivos: a)
evitar o consumo de multimistura com validade
vencida; e b) observar se a mesma estava sendo de
fato consumida. A massa corporal foi obtida por meio de balança
antropométrica digital portátil, com capacidade para
180 kg e sensibilidade de 100 g (balança Marte
PP180 ). O comprimento das crianças menores de dois
anos foi verificado na posição de decúbito dorsal
sobre um estadiômetro de madeira, dotado de fita
métrica, com sensibilidade de 0,1cm. As crianças
com idade superior a dois anos foram medidas em
posição ortostática em estadiômetro dotado de fita
métrica com as mesmas características acima
referidas. A Multimistura era oferecida na proporção de
duas colheres de sopa por dia, fracionadas na
alimentação habitual da criança, durante um período
de 10 meses (fase experimental). A ingestão habitual das crianças foi estimada
com base na média do consumo obtida em três
inquéritos recordatórios de 24 horas aplicados em
intervalos não inferiores a 30 dias. As informações
foram sempre prestadas pelas respectivas mães. Como recurso para ajudá-las a recordar as porções
de alimentos consumidos foi utilizado o álbum de
registro fotográfico de alimentos de Zabotto.13 Os dados foram coletados por estudantes do
curso de graduação em nutrição, devidamente
treinados e supervisionados, seguindo as recomen-
dações do Ministério da Saúde.16 O inquérito bioquímico envolveu todas as
crianças do estudo (Grupos Controle e Multimistura)
e foi constituído de exame de hemoglobina (Hb) e
determinação do retinol sérico. Por questões éticas,
essas determinações só foram procedidas ao final da
fase experimental, de modo a garantir tratamento
adequado a todas as crianças que apresentassem
anemia e/ou hipovitaminose A. O inquérito bioquímico envolveu todas as
crianças do estudo (Grupos Controle e Multimistura)
e foi constituído de exame de hemoglobina (Hb) e
determinação do retinol sérico. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Resultados As condições de vida verificadas na localidade estu-
dada eram de extrema miséria. Todos os domicílios
eram barracos feitos de caibros cobertos com plás-
tico ou papelão. O piso não tinha revestimento. Não
existia banheiro, de modo que os dejetos eram
jogados a céu aberto, juntamente com o lixo em
geral. A água era obtida da rede pública, através de
algumas torneiras colocadas em pontos estratégicos
da favela, sendo armazenada em recipientes como
tonéis, baldes ou latões. A maioria dos adultos não
estava inserida no mercado de trabalho formal, de
modo que os homens faziam "biscaites" e as
mulheres, quando trabalhavam, exerciam funções
como as de empregada doméstica ou lavadeira, si-
tuação em parte explicada pelo baixo nível de esco-
laridade vigente (50,7% dos adultos eram analfa-
betos). Portanto, a amostra estudada foi retirada de
uma população em situação de extrema insegurança
alimentar. Na análise, somaram-se todos os eventos ocor-
ridos durante o período de avaliação, segundo o tipo
de ocorrência e grupo de estudo. As respectivas
freqüências foram, então, comparadas. As crianças de ambos os grupos receberam anti-
helmíntico polivalente no início do estudo e também
ao final do mesmo. Aquelas que, por ocasião dos inquéritos de
morbidade, estavam acometidas por diarréia, rece-
biam atenção específica baseada na terapia de
reidratação oral. Para isso foram distribuídas
colheres-medida e as respectivas orientações de
como preparar e administrar o soro caseiro. Adicionalmente, foi distribuído hipoclorito de sódio
em todos os domicílios, visando melhorar a quali-
dade sanitária da água consumida. Ao final do período experimental de dez meses,
o grupo controle permaneceu com as 50 crianças que
iniciaram o estudo, enquanto o Grupo Multimistura
ficou com 48. Neste grupo, duas crianças foram
excluídas, em virtude de não terem utilizado a multi-
mistura com a regularidade recomendada. Os pacotes estatísticos Epi-Info, versão 3.3.2 e
SPSS, versão 14.0, foram usados para as análises
estatísticas. Para verificar o atendimento aos pressu-
postos paramétricos foram utilizados o teste de
Levene (para homogeneidade das variâncias dos
erros) e o teste de Shapiro-Wilk (para normalidade
na distribuição dos resíduos), admitindo-se para
ambos p<0,05. Houve necessidade de ajuste apenas
para as variáveis dietéticas, exceto para o ferro e o
zinco. A energia e o cálcio foram ajustados por trans-
formação logarítmica. Os valores de proteína foram
transformados em raiz quadrada mais 0,5. Para a
vitamina A não se obteve ajuste em nenhum dos
procedimentos testados. Métodos Por questões éticas,
essas determinações só foram procedidas ao final da
fase experimental, de modo a garantir tratamento
adequado a todas as crianças que apresentassem
anemia e/ou hipovitaminose A. Para os cálculos da ingestão (média dos três
inquéritos) de energia, proteínas, ferro, vitamina A,
cálcio e zinco, os dados obtidos foram processados
no software NutWin®.14 Objetivando transformar os dados em uma
unidade padrão que permitisse a comparação das
ingestões do conjunto das crianças, haja vista a
impossibilidade de comparação direta em virtude das
diferentes recomendações nutricionais segundo as
distintas faixas etárias, os respectivos valores de
ingestão foram transformados em percentual de A determinação da Hb foi procedida em uma
gota de sangue capilar, obtida por punção da polpa
digital, em um fotômetro portátil (HemoCuea®). Foram consideradas anêmicas as crianças com níveis
de Hb<11g/dl.17 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 311 Ferreira HS et al. Ferreira HS et al. Para a determinação do retinol sérico, após jejum
noturno de 12 horas, foram coletados cerca de 3 mL
de sangue venoso em seringas descartáveis, trans-
ferindo o material para tubos de ensaio. Após
centrifugação, o soro foi acondicionado em tubos
Eppendorf e mantido sob congelamento até o
momento das análises, procedidas por método
cromatográfico (cromatografia líquida de alta
resolução-HPLC). Durante todas as etapas, tomou-se
o cuidado de manter as amostras ao abrigo da luz,
em virtude da fotossensibilidade do retinol. Foram
consideradas portadoras de hipovitaminose A as
crianças com retinol sérico <20 µg/dL.18 pendentes (exceto para a vitamina A que, por não
atender aos pressupostos paramétricos, foi analisada
por meio do teste de Mann-Whitney). Quando a
análise envolvia três ou mais médias, usou-se a
análise de variância (ANOVA) pelo Teste F de
Snedecor, seguida do Teste de Tukey (HSD; p<0,05)
para comparações múltiplas das médias. Na comparação entre as freqüências das variá-
veis categóricas usou-se o Teste do Qui-quadrado de
Pearson (χ2) para verificação de diferença significa-
tiva (p<0,05) e como medida de associação, a razão
de chances (Odds ratio). Após três meses do início da fase experimental,
procederam-se inquéritos quinzenais de morbidade
referida, com auxílio de formulário específico, no
intuito de caracterizar a presença de agravos à saúde,
tais como diarréia, infecções respiratórias, febre e
vômitos. Este inquérito era repetido a cada 15 dias
durante o transcorrer da fase experimental e seguiu a
metodologia descrita por Cesar et al.19 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; *=obtido pelo coeficiente de associação phi (ϕ)
entre os grupos de estudo; ns=não significativo (p>0,05). **=diferença estatisticamente significativa. Resultados Os resultados referentes aos inquéritos antro-
pométricos encontram-se expressos na Tabela 1,
enquanto aqueles relativos às determinações de
hemoglobina e retinol sérico são apresentados na
Tabela 2. Em nenhuma das situações observaram-se
diferenças significativas (p>0,05). O consumo da multimistura não alterou a
incidência de diarréia, vômito e febre durante a fase
experimental, já que as diferenças entre os grupos
não foram significativas (p>0,05). Quanto às
infecções respiratórias, ocorreu maior incidência
sobre o grupo controle (24,3% versus 16,9%;
OR=1,59; IC95%=1,1-2,2; p=0,006) conforme Para verificar a existência de diferença significa-
tiva (p<0,05) entre as médias obtidas em cada grupo
utilizou-se o teste t de Student para amostras inde- 312 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Efeitos do consumo da multimistura Tabela 1 Índices antropométricos (Escores z médios) em crianças de 0 a 60 meses de idade, antes e após a suplementação
(Grupo multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade de Lona", Maceió, Alagoas, 2005. Índice antropométrico
Inquérito
Grupos de estudo Valor p (ANOVA)
Controle
Multimistura
Altura-para-idade
inicial
-1,19±1,41
-1,44±1,35
0,46
final
-1,17±1,35
-1,53±1,28
Peso-para-idade
inicial
-1,03±1,18
-1,25±1,11
0,60
final
-0,96±1,17
-1,17±1,09
Peso-para-altura
inicial
-0,32±0,87
-0,44±0,83
0,88
final
-0,29±1,05
-0,31±0,92
Tabela 2
Hemoglobina e retinol sérico (Média ± DP) e prevalência de anemia e hipovitaminose A em crianças de 0 a 60 meses
após 10 meses de suplementação (Grupo Multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade
de Lona", Maceió, Alagoas, 2005
Grupo
Hb (g/dL)
Retinol (µg/dL)
Anemia* (%)
Hipovitaminose A** (%)
Controle
12,4±2,3
26,0±5,9
16,1
11,9
Multimistura
12,8±1,7
24,4±4,4
8,3
21,6
Significância estatística
pa=0,41ns
pa=0,18ns
OR=2,12
OR=0,49
IC95%=0,3-17,7
IC95%=0,1-1,9
pb=0,45ns
pc=0,24ns
*=Hemoglobina <11 g/dL; **=retinol sérico <20 µg/dL; a=Teste t de Student; b =Teste de Fischer; c=teste do qui-
quadrado; OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; ns=não significativo (p>0,05). Índices antropométricos (Escores z médios) em crianças de 0 a 60 meses de idade, antes e após a suplementação
(Grupo multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade de Lona", Maceió, Alagoas, 2005. Índice antropométrico
Inquérito
Grupos de estudo Valor p (ANOVA)
Controle
Multimistura
Altura-para-idade
inicial
-1,19±1,41
-1,44±1,35
0,46
final
-1,17±1,35
-1,53±1,28
Peso-para-idade
inicial
-1,03±1,18
-1,25±1,11
0,60
final
-0,96±1,17
-1,17±1,09
Peso-para-altura
inicial
-0,32±0,87
-0,44±0,83
0,88
final
-0,29±1,05
-0,31±0,92 Índices antropométricos (Escores z médios) em crianças de 0 a 60 meses de idade, antes e após a suplementação
(Grupo multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade de Lona", Maceió, Alagoas, 2005. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Tabela 4 Características do consumo alimentar de crianças menores de cinco anos, segundo alocação no Grupo Controle ou no
Grupo Multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. Componente dietético
Grupo
Adequação percentual em relação à Proporção (%) de crianças que
recomendação*
não atingiram a meta de
ingestão individual*
mediana
(p25-p75)
pa
(%)
pb
Energia
Controle
67,7
(52,1-84,9)
0,707
88,9
0,35
Multimistura
66,3
(52,9-79,4)
77,4
Proteína
Controle
186,2
(140,3-269,8)
0,104
5,6
0,65
Multimistura
237,2
(181,5-341,4)
9,7
Cálcio
Controle
51,4
(29,2-96,6)
0,203
77,8
0,09
Multimistura
44,1
(21,8-66,9)
93,5
Ferro
Controle
77,6
(56,3-98,4)
0,934
75,0
0,95
Multimistura
75,2
(60,9-92,3)
77,4
Vitamina A
Controle
60,3
(29,7-107,0)
0,807
73,5
0,77
Multimistura
49,4
(29,5-92,0)
76,7
Zinco
Controle
43,6
(29,4-59,9)
0,147
100,0
0,21
Multimistura
51,3
(37,9-69,2)
93,5
*=RDA=Recommended Dietary Allowances;15 a=teste t de Student para amostras independentes, exceto para vitamina
A (Mann-Whitney); b=Teste do qui-quadrado (χ2); p>0,05 (diferença não-significativa). Características do consumo alimentar de crianças menores de cinco anos, segundo alocação no Grupo Controle ou no
Grupo Multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. *=RDA=Recommended Dietary Allowances;15 a=teste t de Student para amostras independentes, exceto para vitamina
A (Mann-Whitney); b=Teste do qui-quadrado (χ2); p>0,05 (diferença não-significativa). *=RDA=Recommended Dietary Allowances;15 a=teste t de Student para amostras independentes, exceto para vitamina
A (Mann-Whitney); b=Teste do qui-quadrado (χ2); p>0,05 (diferença não-significativa). Tabela 2 Tabela 2
Hemoglobina e retinol sérico (Média ± DP) e prevalência de anemia e hipovitaminose A em crianças de 0 a 60 meses
após 10 meses de suplementação (Grupo Multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade
de Lona", Maceió, Alagoas, 2005
Grupo
Hb (g/dL)
Retinol (µg/dL)
Anemia* (%)
Hipovitaminose A** (%)
Controle
12,4±2,3
26,0±5,9
16,1
11,9
Multimistura
12,8±1,7
24,4±4,4
8,3
21,6
Significância estatística
pa=0,41ns
pa=0,18ns
OR=2,12
OR=0,49
IC95%=0,3-17,7
IC95%=0,1-1,9
pb=0,45ns
pc=0,24ns
*=Hemoglobina <11 g/dL; **=retinol sérico <20 µg/dL; a=Teste t de Student; b =Teste de Fischer; c=teste do qui-
quadrado; OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; ns=não significativo (p>0,05). Hemoglobina e retinol sérico (Média ± DP) e prevalência de anemia e hipovitaminose A em crianças de 0 a 60 meses
após 10 meses de suplementação (Grupo Multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade
de Lona", Maceió, Alagoas, 2005 *=Hemoglobina <11 g/dL; **=retinol sérico <20 µg/dL; a=Teste t de Student; b =Teste de Fischer; c=teste do qui-
quadrado; OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; ns=não significativo (p>0,05). Incidência de eventos nosológicos entre crianças de 6 a 60 meses, segundo o consumo ou não da Multimistura. Favela
"Cidade de Lona", Maceió, Alagoas, 2005
Agravos
Grupos de estudo
OR (IC95%)
Valor p*
Controle (%)
Multimistura (%)
Diarréia
10,9
10,5
1,04
0,86ns
(0,67-1,62)
Infecção respiratória
24,3
16,9
1,59
0,006**
(1,13-2,24)
Vômito
2,6
2,9
0,89
0,77ns
(0,38 - 2,10)
Febre
16,7
14,4
1,19
0,35ns
(0,81-1,74)
OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; *=obtido pelo coeficiente de associação phi (ϕ)
entre os grupos de estudo; ns=não significativo (p>0 05) **=diferença estatisticamente significativa Incidência de eventos nosológicos entre crianças de 6 a 60 meses, segundo o consumo ou não da Multimistura. Favela
"Cidade de Lona", Maceió, Alagoas, 2005 OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; *=obtido pelo coeficiente de associação phi (ϕ)
entre os grupos de estudo; ns=não significativo (p>0,05). **=diferença estatisticamente significativa. 313 Ferreira HS et al. Tabela 4 Figura 1 50,0
40,0
20,0
10,0
0
Frequência (%)
Vômito
Fase experimental (mês)
Multimistura
Controle
4
5
6
7
8
9
10
50,0
40,0
20,0
10,0
0
Frequência (%)
Febre
Fase experimental (mês)
Multimistura
Controle
4
5
6
7
8
9
10
g
Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a
multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a
multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. 50,0
40,0
20,0
10,0
0
Frequência (%)
Vômito
Fase experimental (mês)
Multimistura
Controle
4
5
6
7
8
9
10
50,0
40,0
20,0
10,0
0
Frequência (%)
Febre
Fase experimental (mês)
Multimistura
Controle
4
5
6
7
8
9
10
Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a
multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. demonstrado na Tabela 3. A Figura 1 ilustra a
evolução desses agravos ao longo do experimento,
destacando-se a sazonalidade de suas ocorrências. fora discreta, no entanto eliminaram-se as formas
graves que antes acometiam 16% das crianças.20
Apesar de o trabalho ter sido descontinuado, pode
ter contribuído, em longo prazo, para a redução aos
níveis ora observados. A utilização da multimistura,
por sua vez, a julgar pelos resultados aqui apresen-
tados, parece não ter interferido no sentido de incre-
mentar os níveis de hemoglobina e/ou reduzir a
prevalência de anemia. O inquérito dietético revelou que os dois grupos
tinham consumo alimentar semelhantes, não tendo
sido observadas diferenças significativas (p>0,05)
na proporção de crianças que não atingiram a meta
de ingestão individual para nenhum dos compo-
nentes dietéticos analisados, bem como na ade-
quação percentual em relação às RDAs (Tabela 4). Resultado semelhante foi obtido em 2002, por
Neumann,21 em pesquisa realizada nas creches do
município de Pelotas, Rio Grande do Sul. Cerca de
1200 crianças de um a sete anos participaram do
estudo, sendo que metade recebeu a multimistura
(farelo de trigo: 30%, farelo de arroz: 30%, farinha
de milho: 15%, farinha de trigo: 10%, casca de ovo:
5% e sementes de abóbora ou girassol: 5% e pó de
folha de mandioca:5%). Ao final de seis meses, não
havia diferença quanto à anemia entre as crianças
que receberam e as que não receberam a multimis-
tura. Figura 1 A partir desse estudo, conduzido por um dos
coordenadores da Pastoral da Criança, principal
instituição promotora da utilização desse suplemento
no Brasil, houve uma reorientação das estratégias de
ação dessa Organização em relação à anemia,
passando-se ao seu pessoal de campo a seguinte
recomendação: "A multimistura não funciona para
crianças com anemia e, portanto, não deve ser Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Figura 1 50,0
40,0
20,0
10,0
0
Frequência (%)
Diarréia
Fase experimental (mês)
Multimistura
Controle
4
5
6
7
8
9
10
50,0
40,0
20,0
10,0
0
Frequência
Infecções Respiratórias
Fase experimental (mês)
Multimistura
Controle
4
5
6
7
8
9
10
g
Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a
multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. continua Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a
multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. Fase experimental (mês)
7
8 continua Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 314 Efeitos do consumo da multimistura Figura 1 Discussão A prevalência geral de anemia observada no
conjunto das crianças (12,3%) foi surpreendente-
mente baixa considerando-se o contexto ambiental
em que vivem. Pesquisa realizada por Ferreira et al.4
nessa mesma comunidade, no ano de 2002, encon-
trou uma freqüência de 96,4% entre as crianças da
mesma faixa etária. Imediatamente após esse
trabalho, iniciou-se um projeto de extensão onde
foram desenvolvidas diversas atividades dire-
cionadas à prevenção e ao controle do problema, tais
como a educação nutricional e tratamento com
sulfato ferroso e anti-helmíntico polivalente. Seis
meses após a implantação desses procedimentos,
verificou-se que a redução da prevalência de anemia 315 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Ferreira HS et al. utilizada com esta intenção."22 utilizada com esta intenção."22 que consumiu a mesma dieta, sem multimistura. Após seis meses de intervenção, verificou-se que as
ações gerais de saúde causaram efeito benéfico na
condição nutricional das crianças, tendo em vista
que melhoraram seus parâmetros hematológicos,
independentemente da multimistura. No entanto, os
valores médios para o índice estatura para idade
foram significantemente mais elevados no grupo
submetido à suplementação. Concluíram que a
suplementação de dietas deficientes com multimis-
tura contribuiu para a melhoria da estatura de
crianças. No presente estudo, a multimistura também não
se revelou efetiva no sentido de elevar os níveis
séricos de retinol e/ou reduzir a prevalência de
hipovitaminose A. A World Health Organization23 classifica os indi-
víduos, segundo os níveis de retinol, em quatro cate-
gorias: Deficiente (<10,0 µg/dL); Baixo (de 10,0 a
19,9 µg/dL); Aceitável (de 20,0 a 29,9 µg/dL); e
Normal (>30,0µg/dL). Com base nessa classificação,
considera-se que prevalências de 2% a 10% de
baixos níveis (10,0 a 19,9 µg/dL) na população
representa um problema de saúde pública leve. Quando entre 10,1% a 19,9%, qualifica-se o pro-
blema como moderado. Acima dessa freqüência,
caracteriza-se a situação como grave problema de
saúde pública. Considerando o conjunto das crianças
avaliadas neste estudo, a prevalência de crianças
com baixos níveis foi de 16,5%. Como a análise
estatística indicou que as diferenças observadas
entre os grupos não podem ser atribuídas ao
consumo da multimistura, pode-se inferir que essa
proporção possa ser extrapolada para o conjunto das
crianças residentes na favela Cidade de Lona. Assim,
a hipovitaminose A representaria um problema de
saúde pública em nível moderado nessa comunidade. Discussão Em nosso estudo a utilização da multimistura não
alterou a prevalência de agravos à saúde, exceto em
relação às infecções respiratórias. Esse dado parece
contraditório na medida em que não foram obser-
vadas diferenças nos níveis séricos de retinol, fator
reconhecidamente protetor contra as infecções.26
Essa observação remete a uma limitação desta inves-
tigação, que foi a de não controlar a avaliação do
retinol sérico pela presença de infecção, determi-
nando-se, concomitantemente, por exemplo, a
proteína C reativa.27 Diante da condição ambiental
degradante em que viviam as crianças, infecções
constantes representa uma rotina entre elas. A
presença desse tipo de agravo pode afetar a síntese
da Retinol Binding Protein (RBP), contribuindo para
a diminuição dos níveis circulantes do retinol, ainda
que possam haver reservas hepáticas adequadas
desse nutriente, o que determinaria uma classifi-
cação errada (falsos-positivos) de hipovitaminose A. Embora o nível de retinol sérico seja um dos indi-
cadores mais utilizados atualmente para detectar a
carência de vitamina A em nível epidemiológico,
admite-se certa limitação em sua utilização pelo fato
de que ele não reflete com fidedignidade as reservas
orgânicas desse nutriente.28 Tal como ocorreu em relação aos níveis de
hemoglobina e de retinol sérico, o consumo da
multimistura também não se mostrou efetivo na
melhoria do perfil antropométrico das crianças. Resultados semelhantes foram encontrados por
Oliveira et al.24 ao avaliaram o impacto da suple-
mentação da dieta com multimistura sobre o estado
nutricional de pré-escolares matriculados em quatro
creches no Estado da Paraíba. As crianças foram
dividas em três grupos, cada um recebendo, respecti-
vamente, placebo, 5 g e 10 g de multimistura. Concluíram que não houve alteração significativa no
estado nutricional após dois meses de suplemen-
tação. Gigante et al.25 também concluíram pela
inefetividade da multimistura ao conduzirem estudo
de intervenção, longitudinal e controlado, incluindo
crianças de 24 escolas de educação infantil que
foram comparadas antes e depois da intervenção,
tendo como indicadores parâmetros antropométricos
e o nível de hemoglobina. Esse aspecto pode ter mascarado os possíveis
efeitos da multimistura especificamente em relação
ao seu potencial em prover quantidades importantes
de vitamina A. Estudo realizado em nossos labo-
ratórios7 avaliou a efetividade da multimistura como
suplemento vitamínico e/ou mineral na recuperação
ponderal de ratos submetidos à desnutrição pós-
natal, concluindo que a mesma atendeu às necessi-
dades de vitaminas, mas apenas parte das necessi-
dades de minerais dos animais. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Discussão Siqueira et al.26 investigaram a efetividade da
suplementação dietética com a multimistura,
concomitantemente com outras ações destinadas a
melhorar a saúde de crianças. Trinta e um estudantes
matriculados em uma escola rural foram examinados
(antropometria e hematologia), antes e após o
consumo da multimistura. Os resultados foram
comparados com aqueles do grupo controle (n=26), Estudos bromatológicos têm encontrado altas
concentrações de minerais (ferro, cálcio, zinco,
cobre, manganês, selênio) e vitaminas (A, B2, B6, C,
ácido fólico, ácido pantotênico e biotina) na multi-
mistura ou em seus componentes.29 Contudo, existe
a possibilidade de uma baixa biodisponibilidade 316 Efeitos do consumo da multimistura acreditam que crianças menores de cinco anos não
sejam susceptíveis a um efeito psicológico (efeito
placebo) por estarem recebendo uma alimentação
adicionada de um determinado suplemento. desses minerais, pelo fato de que o zinco, o ferro, o
cobre e o cálcio, em determinadas concentrações
relativas, interferirem mutuamente nas suas taxas de
utilização. Adicionalmente, a multimistura possui
teores importantes de fitatos, oxalatos e de fibra
dietética, que podem reduzir a biodisponibilidade
dos minerais.30 Diante do exposto, pode-se concluir que a adição
de multimistura à alimentação habitual de crianças
de
uma
favela,
caracterizada
por
extrema
precariedade ambiental e socioeconômica, não
alterou seu perfil antropométrico, a freqüência de
anemia ou a de hipovitaminose A. Em relação às
morbidades, parece ter reduzido a incidência de
infecções respiratórias, resultado este que necessita
ser visto com cuidado, considerando a falta de justi-
ficativa fisiológica para esse achado. No presente estudo, não foi possível fazer a
comparação dos níveis de hemoglobina e de retinol
sérico no início e ao final do trabalho, tal como se
fez com a antropometria. Por questões éticas, tais
procedimentos foram realizados apenas no final da
fase experimental, uma vez que os casos de anemia
e/ou hipovitaminose A detectados teriam que ser
devidamente tratados pelos métodos convencionais
(sulfato ferroso e/ou megadose de vitamina A
prescritos por médica da equipe e fornecidos pela
coordenação do projeto). Assim, embora todo estudo
experimental seja longitudinal por natureza, esse
procedimento, especificamente, teve caráter trans-
versal, de forma que os autores não conheciam a
condição inicial das crianças. No entanto, em virtude
da homogeneidade das famílias residentes na favela
"Cidade de Lona" em termos socioeconômicos e
ambientais, é altamente plausível supor que os
grupos eram semelhantes entre si no início do
estudo. Discussão A alta prevalência de infecções e má-nutrição
observada na comunidade deve-se às precárias
condições socioeconômicas e péssima qualidade de
vida prevalecentes na localidade. A não disponibili-
dade de água de boa qualidade, ausência de sanea-
mento básico, inadequado destino do lixo e dos
dejetos, a baixa escolaridade e profissionalização
dos adultos, o difícil ou inexistente acesso à
assistência à saúde, entre outros fatores, são pro-
blemas que precisam ser resolvidos para que se
garanta, efetivamente, um melhor nível de saúde
para aquela comunidade, sobretudo, para as suas
crianças. Nesta investigação não foi utilizado placebo no
Grupo Controle em virtude da dificuldade de encon-
trar substrato que mimetizasse a multimistura e que,
adicionalmente, não promovesse qualquer incre-
mento nutritivo à refeição. Pensou-se em usar
farinha de mandioca ou farinha láctea, mas decidiu-
se por não fazê-lo, pois esses ingredientes possuem
características nutricionais que não permitem
considerá-los como "inertes". Além disso, os autores Agradecimentos À Fundação de Amparo à Pesquisa do Estado de
Alagoas (FAPEAL) e ao Conselho Nacional de
Desenvolvimento Científico e Tecnólogico (CNPq)
pela concessão, respectivamente, de bolsa de
mestrado (Processo No. 20050230427-7) e de inici-
ação científica. 4. Ferreira HS, Assunção ML, Vasconcelos VS, Melo FP,
Oliveira CG, Santos TO. Saúde de populações marginal-
izadas: desnutrição, anemia e enteroparasitoses em crianças
de uma favela do Movimento dos Sem-Teto, Maceió,
Alagoas. Rev Bras Saúde Matern Infant. 2002; 2: 177-85. 3. Ferreira HS, Albuquerque MFM, Ataide TR, Morais MGC,
Mendes MCR, Siqueira TCA, Silva GJ. Estado nutricional
de crianças residentes em invasão do movimento dos Sem-
Terra. Fazenda Conceição, Porto Calvo, Alagoas. Cad
Saúde Pública. 1997; 13: 137-9. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 2. Monteiro CA. A dimensão da pobreza, da desnutrição e da
fome no Brasil. Est Avançados. 2003;17: 7-20. Referências 1. Monte CMG. Desnutrição: um desafio secular à nutrição
infantil. J Pediatr. (Rio de J) 2000; 76 (Supl. 3): S285-S97. 5. Mahler H. Present status of WHO's initiative, health for all
by the year 2000. Ann Rev Public Health. 1988; 9: 71-97. 2. Monteiro CA. A dimensão da pobreza, da desnutrição e da
fome no Brasil. Est Avançados. 2003;17: 7-20. 6. Brandão CT, Brandão RF. Alimentação alternativa. Brasília: INAN, 1996. 7. Ferreira HS, Assunção ML, França AOS, Cardoso EP,
Moura FA. Efetividade da multimistura como suplemento
de dietas deficientes em vitaminas e/ou minerais na recu-
peração ponderal de ratos submetidos à desnutrição pós-
natal. Rev Nutr. 2005; 18: 63-74. 4. Ferreira HS, Assunção ML, Vasconcelos VS, Melo FP,
Oliveira CG, Santos TO. Saúde de populações marginal-
izadas: desnutrição, anemia e enteroparasitoses em crianças
de uma favela do Movimento dos Sem-Teto, Maceió,
Alagoas. Rev Bras Saúde Matern Infant. 2002; 2: 177-85. 8. Amâncio OMS, Lajolo FM, Santoro M, Nóbrega FJ,
Queiroz SS, Farfan JA. Recuperação nutricional de grupos
populacionais de baixa renda: análise crítica. Cad Nutr. 1995; 9: 1-4. 317 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Ferreira HS et al. 21. Neumann NA. Multimistura de farelos não combate a
anemia. J Pastoral Criança.[periódico online] 2005. [acesso
em 26 jun 2006] 105: 14. Disponível em: http://www. pastoraldacrianca.com.br/jornal/107/pag14.pdf. 9. Azeredo VB. Multimistura: uma alternativa alimentar? Rio
de Janeiro: Universidade Federal Fluminense; 1999. 10. Bittencourt SA. Uma alternativa para a política nutricional
brasileira? Cad Saúde Pública. 1998; 14: 629-39. 22. Coordenação Nacional da Pastoral da Criança. Multimistura de alimentos, resgate do conceito original:
quanto mais colorido for o prato de comida, melhor! [16 jun
2006] Disponível em: http://www.pastoraldacrianca.org.br/
htmltonuke.php?filnavn=dicas/dicas_multimistura.htm. 11. CFN (Conselho Federal de Nutricionistas). Multimistura: a
posição do CFN. Rev Cons Nac Nutr. 2002; 6: 9. 12. Farfan JA. Alimentação alternativa: análise crítica de uma
proposta de intervenção nutricional. Cad Saúde Pública. 1998; 14: 205-11. 23. WHO (World Health Organization). Control of vitamin A
deficiency and xerophthalmia: Geneva; 1982. (WHO:
Technical Report Series, 672). 13. Zabotto CB. Registro fotográfico para inquéritos dietéticos. Goiânia: Ed. UFG; 1996. 14. Anção MS, Cuppari L, Draibe SA, Sigulem D. Programa de
Apoio à Nutrição - NutWin, versão 1.5 [CD-ROM]. São
Paulo: Departamento de Informática em Saúde da Escola
Paulista de Medicina da Universidade Federal de São
Paulo; 2002 24. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Recebido em 4 de setembro de 2007
Versão final apresentada em 4 de julho de 2008
Aprovado em 7 de julho de 2008 Referências Oliveira SMS, Costa MJC, Rivera MAA, Santos LMP,
Ribeiro MLC, Soares GSF, Asciutti LS, Costa SFG. Impacto da multimistura no estado nutricional de pré-esco-
lares matriculados em creches. Rev Nutr. 2006; 19: 169-76. 25. Gigante DP, Buchweitz M, Helbig E, Almeida AS, Araújo
CL, Neumann NA, Victora C. Ensaio randomizado sobre o
impacto da multimistura no estado nutricional de crianças
atendidas em escolas de educação infantil. J Pediatr. (Rio J)
2007; 83: 363-9 15. National Research Council. Commission on Life Sciences. Subcommittee on the 10 Edition of the Recommended
Dietary Allowances,
Food
and
Nutrition
Board. Recommended dietary allowances. 10. ed. Washington, DC:
National Academy Press; 1989. 26. Siqueira EMA, Azevedo IT, Arruda SF, Lima SMD,
Gonçalves CA, Souza EMT. Regional low-cost diet supple-
ment improves the nutritional status of school children in a
semi-arid region of Brazil. Nutr Res. 2003; 23: 703-12. 16. Fagundes AA, Barros DC, Duar HA, Sardinha LMV,
Pereira MM, Leão MM. Vigilância alimentar e nutricional -
SISVAN: orientações básicas para a coleta, processamento,
análise de dados e informação em serviços de saúde. Brasília, DF: Ministério da Saúde; 2004. 27. Aukrust P, Müller F, Ueland T, Svardal AM, Berge RK,
Frøland SS. Decreased vitamin A levels in common vari-
able immunodeficiency: vitamin A supplementation in vivo
enhances immunoglobulin production and downregulates
inflammatory responses. Eur J Clin Invest. 2000; 30: 252-9. 17. WHO (World Health Organization). Iron deficiency
anaemia. Assessment, prevention and control: a guide for
programme managers. Geneva; 2001. 18. WHO (World Health Organization). Indicators for assessing
vitamin A deficiency and their application in monitoring
and evaluating intervention programmes. Geneva; 1996. (Micronutrient Series). 28. Stephensen CB, Gildengorin G. Serum retinol, the acute
phase response, and the apparent misclassification of
vitamin A status in the III National Health and Nutrition
Examination Survey. Am J Clin Nutr. 2000; 72: 1170-8. 19. Cesar CLG, Figueiredo GM, Westphal MF, Cardoso MRA,
Costa MZ, Gattás VL. Morbidade referida e utilização de
serviços de saúde em localidades urbanas brasileiras:
metodologia. Rev Saúde Pública. 1996; 30: 153-60. 29. Madruga MS, Câmara FS. The chemical composition of
"multimistura" as a food supplement. Food Chem. 2000;
68: 41-4. 30. Cozollino SMF. Biodisponibilidade de minerais. Rev Nutr. 1997; 10: 87-98. 20. Ferreira HS. Mulheres obesas de baixa estatura e seus filhos
desnutridos. Est Avançados. 2006; 20: 159-66. 318
|
https://openalex.org/W4389620510
|
https://www.nature.com/articles/s41598-023-49398-2.pdf
|
English
| null |
Deriving expert-driven seismic and wind fragility functions for non-engineered residential typologies in Batanes, Philippines
|
Scientific reports
| 2,023
|
cc-by
| 13,348
|
OPEN Arvin Hadlos *, Aaron Opdyke & S. Ali Hadigheh Natural hazards inflict significant damage to dwellings in the Philippines where housing is often
the most valued asset of households. Residential fragility functions estimate structural damage to
mitigate risk but these are challenging to derive when empirical and analytical data are lacking, as
is common in rural areas. Too often, conventional fragility estimates overlook the characteristics of
informally built or non-engineered dwellings common in rural areas. We used a heuristic alternative of
deriving fragility functions relying on experts’ judgements to understand the housing performance of
non-engineered residential typologies in the Province of Batanes in the Philippines. Drawing on field
surveys in the Municipality of Itbayat, we identified and defined seven prominent typologies. Based
on the Applied Technology Council’s expert-driven method of deriving fragility functions, 18 experts
estimated the damage states of these typologies against the impacts of earthquakes and typhoons
which are the two most prominent hazards in the region. Our findings provide first-generation fragility
functions for Batanes as a step towards more localised risk assessment in the Philippines. More
broadly, these functions can be used for typologies identified beyond Batanes where similar structural
characteristics are prevalent. Building back safer after disasters has been a consistent mantra for post-disaster reconstruction efforts under the
Sendai Framework for Disaster Risk Reduction1. Dwellings in low- and middle-income countries are the most
valued assets of households but these also tend to be the most disaster-affected2. To safeguard these assets, it is
imperative to understand their structural performance against the impacts of hazards. The derivation of fragility
functions captures structural performance of a building when it is subjected to an environmental excitation3–6. Fragility functions, often depicted graphically as a series of fragility curves, appraise risk by quantifying the rela-
tionship between a hazard intensity (e.g., seismic intensity or wind speed) and the probability of a component
or structure reaching or exceeding a certain damage state3–6.h g
g
g
The availability of fragility functions can support modelling natural hazard impacts and more informed
targeting of structural safety programs. For example, deriving these functions can reveal vulnerable structural
typologies in a building stock leading to risk prioritisation interventions. Hence, risk and loss estimation methods
are usually anchored on deriving these functions, such as those developed by the United States Federal Emergency
Management Agency (FEMA)4,7–9. www.nature.com/scientificreports www.nature.com/scientificreports School of Civil Engineering, The University of Sydney, Camperdown, NSW 2006, Australia. *email: arvin.hadlos@
sydney.edu.au Scientific Reports | (2023) 13:22008 www.nature.com/scientificreports/ performance when assessed against competing impacts on structures. Building-level disaster risk reduction
(DRR) measures have shown how multi-hazard trade-offs and asynergies complicate building more resilient
dwellings. That is, where construction practices may reduce the impact of risk to one hazard, such can exacerbate
the risk to another hazard13,14. Depending on the available sources of damage data, fragility functions can be derived in various ways5,15. When documented post-disaster damage data is available, empirical methods can be used. If resources allow for
the simulation or modelling of structural typologies, analytical methods can be employed. When both resources
are lacking, a heuristic alternative is to solicit experts’ opinions to derive the functions. A fourth approach is
a hybrid of at least two methods. Further discussion about these four methods, including an overview of past
studies using specific approaches, can be found in Maio and Tsionis et al.16 and Rossetto et al.17. Previous atten-
tion to deriving these functions has primarily focused on a structure’s performance to a single hazard. Recently,
there has been a growing emphasis in academic, policy, and practice environments to incorporate multi-hazard
approaches to realise effective DRR strategies14,18,19.f f
Hazards impact a structure differently thereby requiring a combination of strategies and approaches to reduce
or mitigate risk13,14. Deriving multi-hazard fragility functions can therefore offer insights on how to optimise
trade-offs in construction decisions. The scarcity of data and technical resources are, however, roadblocks in
rural contexts in low- and middle-income countries. The expert-driven approach is often the only possible
method in the absence of empirical and analytical data16,20–22. Elicitation of experts’ opinions has been used
in various disciplines to produce the fragility functions of components of interests, extending from structural
engineering20,23–25, hydrology10,22, and civil engineering26. The ATC-58 project of the Applied Technology Council
(ATC) aimed to develop next-generation seismic design assessment standards, and the expert-driven method
is adopted among other approaches to derive fragility functions as formalised through a proposed method of
solicitation and aggregation of experts’ opinions27,28. The main strength of this approach is that experts can
include in their assessment all factors affecting the response of a structure against hazards, unlike empirical and
analytical methods where these are limited to the quantity and quality of available data15. The major drawback
of expert-driven methods is the subjectivity associated with experts’ experience and trust in their judgement15. www.nature.com/scientificreports/ However, when dealing with non-engineered residential typologies, experts’ experience is beneficial to capture
the varied structural performance arising from the inherent variability of the design and construction of these
building classes.h g
The objective of this study was to derive fragility functions for non-engineered residential typologies in the
Province of Batanes—the storm-battered northernmost part of the Philippines. We drew on field surveys in the
Municipality of Itbayat to identify relevant typologies for the Province of Batanes. The remote island municipal-
ity of Itbayat was home to vernacular stone-and-lime houses, like elsewhere in Batanes, built out of tradition
to withstand typhoon impacts. Unfortunately, these dwellings were extensively damaged following the series of
destructive earthquakes (magnitudes (Mw) 5.4, 5.9, 5.8) in 201929,30. These disasters redefined the construction
practices in the area with a departure from the stone-and-lime character of the building stock. We surveyed the
existing building stock three years later and identified the most prominent typologies that households chose to
build to replace these vernacular dwellings. Based on the expert-driven approach of deriving fragility functions
developed in ATC-58, a pool of experts estimated the seismic and wind performance of both the vernacular
and replacement typologies.hh y
g
The rest of the paper is structured as follows. The Methods section characterises the research procedures and
protocols undertaken for this study. Next, under the Results section, we present the identified housing typologies
and the derived fragility functions. The Discussion section then provides insights gleaned in using the expert-
driven approach in deriving fragility functions. Lastly, in the Conclusion section, we summarise the theoretical
and practical implications of this study. Methods
B l Below, we outline how we surveyed the housing typologies, followed by the process of soliciting and aggregating
experts’ estimates. We then present how we derived the fragility functions. Lastly, we provide information on the
research ethics protocols and permits obtained for this study. OPEN However, in the context of resource-constraint communities, the limited data
on past disaster damage and unregulated construction practices inhibit the derivation of fragility functions. While
these functions are a foundational tool to understand structural safety and are useful for disaster preparedness,
they are too often lacking in hazard-prone regions where they are critically important10. yt
g
p
g
y
y
p
In rural areas in low- and middle-income countries, dwellings built informally by residents are common. These are either patterned from longstanding vernacular practices, borne out of the immediate need to have
shelter (e.g., urgent reconstruction due to disaster impacts), or as a compromise to rising construction costs. In
these cases, the construction of dwellings is usually non-engineered, with the absence or limited oversight of
qualified building professionals11. As a result, housing typologies often exhibit a high variance of characteristics
compared to conventional building typologies designed and constructed based on prevailing building codes and
standards. While these non-engineered structures are not prejudiced to be deficient in structural safety and may,
in fact, reveal sound locally developed building practices12, their structural performance is less documented and
certain. Furthermore, the exposure of dwellings to multiple natural hazards hinders our understanding of their Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ Identification of housing typologiesi Identifying a building typology is the first step in building-level risk estimation as this serves as the object of
analysis for fragility functions. A typology, usually labelled with a taxonomy (string), characterises a building
class from attributes posing vulnerability to the impacts of natural hazards4,31. For example, for earthquake risk,
structures are classified according to the (i) type of lateral load-resisting system, (ii) material of lateral load-
resisting system, (iii) building height, and (iv) seismic code level (or the period of construction of a structure
vis-à-vis the enforcement of seismic regulations). Such attributes are the core parameters used in risk analysis
by many organisations, such as FEMA for HAZUS7 and the Global Earthquake Model (GEM)31. For typhoon
risk, the same set of attributes are relevant, but with wind-induced damage concentrated on walls and roofs32,33,
building envelope materials and roof profile are usually considered in conjunction34. In this study, we used all
these attributes—except for the seismic code level—to inform the development of a rapid visual survey to assess
the attributes of a building stock. The seismic code level was omitted because the housing typologies surveyed
were non-engineered, with formal seismic regulations having limited applicability to these types of structures. Th
d
l
d
d
h fi
b
ld
b
h g
g
g
y
y
The rapid visual surveys were conducted in January 2023 using the five building attributes as the parameters
of the assessment. For lateral load-resisting systems, we referred to the expanded classifications and defini-
tions of the GEM taxonomy35 since their database accounts for the structural characteristics of non-engineered
construction31. The field study aimed to understand the housing reconstruction strategies of households after Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 Solicitation of experts’ opiniont p
p
After identifying the predominant housing typologies, we selected a pool of experts to estimate the damage
states of these typologies. In qualifying “expertise”, we recognised both the inputs of those who are locally based
(“local experts”) and those who are not but with relevant insights on the housing performance of non-engineered
typologies in the country (“specialists”). Local experts included the municipal engineers for all six municipalities
in Batanes and district engineers at the provincial level. These roles assume building regulatory responsibilities in
the targeted jurisdictions encompassing extensive experience with local damage impacts from past earthquakes
and typhoons in Batanes. yp
For the specialists, their expertise was sought because of their familiarity with the dynamics of the typologies
of interest. While the impacts of hazards vary in different geographical contexts, the specialists’ judgements were
considered reliable if they were acquainted with the common damage mechanisms or expected performance of
these structures in the Philippine setting. We relied on academic publications and technical reports focused on
seismic and wind field assessments as the basis for identifying specialists. We identified documents on Google
Scholar and Scopus employing a permutation of the following keywords: “housing”, “damage”, “Philippines”, “dis-
aster”, “shelter”, “assessment”, “wind OR typhoon”, and “seismic OR earthquake”. From this query, we shortlisted
relevant documents, and then conducted literature snowballing to trace other documents not captured by the
keyword search. The authors of these documents were then compiled. Finally, we shortlisted those with civil,
structural, or construction engineering backgrounds. g
g
g
Porter et al.27 developed a method to systematically solicit and aggregate experts’ opinions to derive fragil-
ity functions. This is among the methods of damage analysis developed for the ATC for its next-generation
probabilistic assessment of structures adapted from the Pacific Earthquake Engineering Research Centre27. Unlike behavioural means of aggregating experts’ opinions wherein participants interact with each other and
arrive at a consensus, this proposed method uses a mathematical approach to consolidate distinct inputs of
participants17. Consultation with experts and combining their individual judgements provide a worthwhile basis
for assessment41 since consensus-based approaches might reflect mere conformity among experts rather than
genuine agreement24. While developed for seismic applications, the expert-driven method for ATC explicitly
focuses on aggregating experts’ opinions. It can therefore be adaptable if the required information on component
types, damage states, and engineering demand parameters (EDPs) are contextualised to the impacts of hazards of
interest. Solicitation of experts’ opiniont Hence, we used this method in deriving both the fragility functions against the impacts of earthquakes
and typhoons. The procedure asks experts to estimate the (median and lower-bound) values of a specified EDP
with respect to the presented component type and damage states, alongside their self-assessed level of expertise. The use of EDP, however, is less relevant when the components of interest are low-rise non-engineered hous-
ing typologies. For example, inter-story drift ratio, being one of the most common EDPs42,43, is best suited for
multi-story components because of the need to analyse relative translational displacement of floor levels. In this
regard, it was imperative to substitute EDP with the intensity measure of a hazard. g
p
y
A survey form adapted from Porter et al.27 was developed for this study. For earthquakes, we used the Philip-
pine Institute of Volcanology and Seismology (PHIVOLCS) Earthquake Intensity Scale (PEIS) as the intensity
measure, ranging from numeral I (weakest, “scarcely perceptible”) to X (strongest, “completely devastating”)44. This intensity scale, developed by PHIVOLCS, considers the common building construction types in the Philip-
pines and the population’s perception of shaking strength, thus making it the official intensity scale in the country
since 199645. PEIS is comparable to the widely used Modified Mercalli Intensity (MMI) scale in that intensities I
to VII represent the same effect of ground shaking, while PEIS VIII is similar to MMI VIII–IX; PEIS IX to MMI
X–XI; and PEIS X to MMI XII45,46. We opted to use earthquake intensity instead of Peak Ground Acceleration
(PGA) because the local engineers surveyed were more familiar with damage relationships with instrumental
intensities. This is due to the lack of localised seismic hazard maps until recently and the limited use of PGA as a
design parameter in the current National Structural Code of the Philippines. In addition, instrumental intensi-
ties can be converted to PGA when conversion equations of intensities and ground motion become available47
with applicability to the geographical context of interest. With the absence of such conversion equations for the
Philippines for the time being, using PEIS is logical since building damageability has been long attributed to
instrumental intensities within the country. www.nature.com/scientificreports/ www.nature.com/scientificreports/ the 2019 earthquakes in the Municipality of Itbayat, located in the Province of Batanes in the Philippines (see
Fig. 1). Hence, we focused the surveys on the emergent (or replacement) typologies constructed by households
who were living in vernacular stone-and-lime houses before the earthquakes but were forced to rebuild due to the
extensive damage to this typology. This pre-earthquake typology was also surveyed. Out of the 153 households
identified from the joint report of the Municipal Disaster Risk Reduction Office (MDRRMO) and the Municipal
Planning and Development Office (MPDO) in Itbayat, we were able to survey 101 structures. The remaining
houses were not surveyed due to the unavailability of households despite multiple attempts at the time of the
survey (n = 35) or where households did not reconstruct their houses and have either migrated to a different
municipality or living with relatives (n = 17). In surveying the attributes of the stone-and-lime housing typol-
ogy, we relied on households’ recollection about the features of their past dwelling. We also triangulated these
features via archival research (e.g., photo documentation from the National Commission on Indigenous Peoples
(NCIP)), desk research (e.g., publications36–40), and field visits to a few standing archetypes in the municipality. For the emergent housing typologies after the earthquakes, these were surveyed as all the necessary information
was observable onsite. 3
Vol (012
ports | (2023) 13:22008 |
https://doi.org/10.1038/s41598-023-49398-2
Figure 1. Map of Itbayat, Batanes in the Philippines. Figure 1. Map of Itbayat, Batanes in the Philipp Figure 1. Map of Itbayat, Batanes in the Philippines. https://doi.org/10.1038/s41598-023-49398-2 https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ Solicitation of experts’ opiniont We explained the median as, “What hazard intensity can bring the
specified damage state to 50% of the residential structures having the same typology?” For the lower bound, it
was explained as, “What hazard intensity can bring the specified damage state to 10% of the residential structures
having the same typology?” Lastly, experts were also asked to rate their level of confidence with the range of
estimates they provided for each typology, ranging from 1 (low) to 5 (high). Note that we used the term level of
confidence instead of level of expertise to emphasise that we were interested in the trust in their estimates and
not with their professional standing as this was pre-assessed before invitation using the methods described above.h of the 2019 earthquakes in Itbayat (and the felt intensities in surrounding municipalities)30 was provided to help
orient the respondents about the intensity measure used. Similarly, for the third part, information about the
known intensities of Typhoon Ferdie (Meranti) in 2016 and Typhoon Yolanda (Haiyan) in 2013 was supplied with
a sample of the regional wind hazard map of the Philippines. For both the second and third part, the respective
damage states were presented, leading to the assessment section. The experts were asked to estimate what PEIS
intensity (for earthquake) and 3-s peak gust wind speed (for typhoon) will yield each of the damage states (DS1
to DS5) for each of the typologies. The experts were asked to provide both median and lower-bound intensities,
following the method of Porter et al.27,28. We explained the median as, “What hazard intensity can bring the
specified damage state to 50% of the residential structures having the same typology?” For the lower bound, it
was explained as, “What hazard intensity can bring the specified damage state to 10% of the residential structures
having the same typology?” Lastly, experts were also asked to rate their level of confidence with the range of
estimates they provided for each typology, ranging from 1 (low) to 5 (high). Note that we used the term level of
confidence instead of level of expertise to emphasise that we were interested in the trust in their estimates and
not with their professional standing as this was pre-assessed before invitation using the methods described above. Th
d
d
l
f
l
l
h p
g
p
g
The surveys were conducted online from May 2023 to July 2023. Solicitation of experts’ opiniont Forcing the use of PGA considering such context would introduce
significant, and in our view—unjustified, uncertainty in the fragility functions.hit gi
ji
y
g
y
The damage states defined by FEMA for earthquake loss estimation4,7 were used after contextualising them
to the structural properties of the identified typologies. We used these damage states because of their specificity
in describing structural conditions. Thus, these well-delineated descriptions of structural failure for each dam-
age state helped eliminate ambiguity in assessing stages of structural failure6. These are categorised within five
damage states (DS), namely: no/very minor (DS1), minor (DS2), moderate (DS3), extensive (DS4), and complete
(DS5) (see Table 1). For typhoons, we used 3-s peak gust wind speed in kilometres per hour (km/h) as the intensity measure, rang-
ing from 0 to 400 km/h. The maximum value was capped at 400 km/h—a reasonable and realistic upper bound
based on the intensity ranges of the strongest typhoons recorded in the country. For example, Typhoon Haiyan
(Yolanda), one of the strongest typhoons to hit the country, had an estimated peak gust of 324 to 378 km/h48. The
damage states for wind impacts were based on FEMA8,9 for the same reason that they have specific delineations
of structural conditions. The damage states are categorised into five, namely: no/very minor (DS1), minor (DS2),
moderate (DS3), extensive (DS4), and complete (DS5) (see Table 1).h p
The content of the expert survey form was divided into three parts: (1) information on the housing typologies,
(2) earthquake assessment, and (3) typhoon assessment. For the first part, actual images of the typologies taken
onsite were provided, alongside descriptions of the type and materials of their lateral load-resisting systems,
building height, wall materials, and roof profile. For the second part, information about the recorded intensities Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ www.nature.com/scientificreports/ p
Damage State (DS)
Earthquake
Typhoon
DS1–No/very minor damage
None or very minor damage
None to very minor damage. Roof cover loss of less than 2% with no or
limited water penetration
DS2–Minor damage
Small (≤ 1/8 inch or ≤ 3 mm) cracks or hairline cracks at corners of doors,
windows, wall ceiling intersections, connections (e.g., on welds, beam
and column joints, etc.), wall surfaces; spalling at a few locations (for
typologies with concrete components)
Roof cover loss of 2% to 15% of the roof area but can be temporarily cov-
ered to prevent water seepage. Solicitation of experts’ opiniont In total, we sent 57 survey invites to the roster
of local experts and specialists we identified earlier. Eighteen (18) agreed to participate, five declined, and 34 did
not respond. The respondents comprised seven local experts and 11 specialists. Two local experts decided to
provide a single response while two specialists expressed confidence in answering only either the earthquake or
typhoon assessment. We therefore collected 16 unique responses per assessment. In using expert judgement to
quantify scientific uncertainty, it is suggested that 8–15 experts are reasonable, with diminishing returns becom-
ing evident from having 20 or more participants49. Recent studies that used expert judgement for engineering
applications have relied on this range of the number of experts involved10,20,24. Additionally, comprehensive
insights of experts can be derived despite a limited size of cohort if and when participants are selected system-
atically based on their expertise aligning with the context of the assessment49. Finally, in the method utilised for
this study, fragility functions derived through experts’ estimates are considered to be of medium quality (the
highest benchmark specified) when at least three experts have ≥ 3 level of confidence27,28. Solicitation of experts’ opiniont Roof structure remains intact. Maximum
of one window/door failure. No failure of wall structure but marks/dents
are visible which can be repaired by painting/patching
DS3 – Moderate damage
Large (> 1/8 inch or > 3 mm) cracks at corners of doors and windows,
connections (e.g., on welds, beam and column joints, etc.), wall surfaces;
permanent rotation at connections are likely; spalling at wall ends (for
typologies with concrete components)
Roof cover loss of above 15% to 50% of the roof area. Roof structure
remains intact. Moderate window breakage. Water penetration causes
some interior damage to the structure. No failure of wall structure
DS4–Extensive damage
Partial collapse, characterised by failed connections/critical elements,
permanent lateral movement of floors, roof, beams, etc., extensive large/
through-the-wall cracks (for concrete/masonry components) or out-of-
plane failure
Roof cover loss of more than 50%. Roof structure remains intact. Major
window damage. Water penetration causes extensive damage to the
interior of structure. No failure of wall structure
DS5–Complete damage
Total collapse, or in imminent danger of collapse, due to failed lateral-
load resisting system
Complete roof failure and/or failure of wall structure Table 1. Damage states for earthquake and typhoon impacts. Adapted from Kircher et al.4, FEMA7,8, and
Vickery et al.9. Table 1. Damage states for earthquake and typhoon impacts. Adapted from Kircher et al.4, FEMA7,8, and
Vickery et al.9. of the 2019 earthquakes in Itbayat (and the felt intensities in surrounding municipalities)30 was provided to help
orient the respondents about the intensity measure used. Similarly, for the third part, information about the
known intensities of Typhoon Ferdie (Meranti) in 2016 and Typhoon Yolanda (Haiyan) in 2013 was supplied with
a sample of the regional wind hazard map of the Philippines. For both the second and third part, the respective
damage states were presented, leading to the assessment section. The experts were asked to estimate what PEIS
intensity (for earthquake) and 3-s peak gust wind speed (for typhoon) will yield each of the damage states (DS1
to DS5) for each of the typologies. The experts were asked to provide both median and lower-bound intensities,
following the method of Porter et al.27,28. Plotting of fragility functions
l
f
d fi
h
b b Fragility functions define the probability of a damage state ds being exceeded or reached for a component, given
a particular value of intensity measure im, such that P[DS ≥ ds | IM = im]. In this expression, lowercase notations
indicate particular values of the uppercase variables. Fragility functions are most commonly idealised through a
lognormal cumulative distribution function5,6,50 (see Eq. 5). Each fragility function needs a median value (xm) of
the intensity measure representing the threshold and the variability of a damage state, and a logarithmic standard
deviation (β) describing the total variability of the damage states4. (5)
P[DS ≥ds|IM = im] = φ
ln(im/xm)
β (5) where ds = specific damage state; im = particular value of intensity measure; ϕ = standard normal cumulative
distribution function; xm = median value of distribution (as derived in Eq. 1); β = logarithmic standard deviation
(as derived in Eq. 3). In plotting the fragility functions, we used the plnorm() function in RStudio which idealises the lognormal
cumulative distribution function. We used the calculated xm and β values from Eqs. (1) and (3). For the xm inputs,
we first calculated their lognormal values to standardise on the log scale before feeding them into the function. For one typology (LW-B), we encountered a minor crossing of two functions (damage states). Crossing of curves
implies a meaningless negative probability and this was addressed using Eqs. (6) and (7) to adjust xm and β values
as proposed by Porter et al.27,28. Where functions i and j cross having medians xmj > xmi and βi ≠ βj, the adjusted
values x’mi and β’i were calculated. (6)
β′
i = 1
N
N
i=1
βi for all i (6) (7)
x′mi = exp(1.28(β′ −βi) + lnxmi) (7) Aggregation of experts’ opinionh gg
g
p
p
The median and lower-bound values of experts’ estimates of hazard intensities and the corresponding levels of
confidence were used as inputs for Eqs. (1, 2, 3) which are part of the method developed by Porter et al.27,28. These
equations are based on probability encoding and expert qualification and a full transcript of their derivation is
found in Porter et al.28. If Eq. (3) produces β < 0.4, either justify the β, or use Eq. 2 and Eq. 4:
(1)
xm =
N
i=1 wα
i xmi
N
i=1 wα
i
(2)
xl =
N
i=1 wα
i xli
N
i=1 wα
i
(3)
β =
ln
xm
xl
1.28 (1) (2) (3) If Eq. (3) produces β < 0.4, either justify the β, or use Eq. 2 and Eq. 4: If Eq. (3) produces β < 0.4, either justify the β, or use Eq. 2 and Eq. 4: https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ β = 0.4
xm = 1.67xl (4) where N = number of experts providing judgment about a value; i = index of experts, i {1, 2,…N}; xmi = estimated
median intensity measure of expert i; xli = estimated lower-bound intensity measure of expert i; wi = level of
expertise of expert i; α = 1.5hih These equations weight experts’ estimates based on their levels of confidence. The constant value of α renders
that estimates with an assigned level of confidence of 3 are weighted five times more than just a confidence of 1,
while a confidence of 5 is weighted around twice as much as 3. The constant values in Eq. (3) and (4) anchor the
dispersion between the median and lower-bound values to suggest a reasonable range within these. For this study,
we did not use Eq. (4) and instead just used the calculated β. At least for the context of this assessment, there is
no plausible argument to have a definitive threshold to maintain a reasonable gap between the solicited median
and lower-bound values. For example, a difference of just 1 PEIS intensity can have pronounced implications for
housing damage, as with a 0.5 difference, depending on how these structures are built. For wind speeds, a dif-
ference of 10 km/h might already bring lower-bound and median probabilities of damage to certain typologies,
while for others, higher wind speeds bring more pronounced housing damage. Ethics and inclusion statement All procedures performed involving human subjects were in accordance with the Human Research Ethics Com-
mittee of The University of Sydney under the approved protocol 2022/705. The field study site was located on
the ancestral domain of the Indigenous people of Itbayat. A free prior-informed consent was obtained from the
National Commission on Indigenous Peoples under Certificate of Precondition R2-IKSP-2022–12-21. Identified housing typologies i
g
Unreinforced masonry Lightweight Lightweight
Two variations of lightweight structures were identified, both having post-and-beam lateral load-resisting sys-
tems. The first variation (“LW-A”) features timber beams and timber columns for primary (corner) posts, where
the columns do not have footings and are only driven underground. The beam-to-column connections vary
with the use of bolts, nails, and improvised hooks made from reinforcing steel bars (RSB). The second variation
(“LW-B”) of lightweight structures has primary (corner) posts made of 4-inch to 5-inch diameter steel pipes with
RC footing and with timber beams. These components are connected via bolts, improvised hooks made from
RSB, and in some instances, the beams are notched and clipped inside the steel pipes. Both lightweight typolo-
gies are one-story structures having gable roof profiles, where their roof eaves rarely exceed 300 mm. Roof and
walls are enveloped by corrugated galvanised iron (CGI) sheets fastened every other one or two corrugations
on wooden frames using common wire nails with improvised rubber washers. Additional timber posts as inter-
mediate supports are used. CGI or plywood covers for door openings are common and the same for windows
alongside jalousie (louvred) glass. Of the surveyed residential building stock, 17% and 25% account for LW-A
and LW-B, respectively. www.nature.com/scientificreports/ organisations. Six prominent housing typologies were identified replacing URM which account for 91% of the
surveyed building stock. These include variations of lightweight, semi-concrete, and reinforced concrete (RC)
dwellings (see Figs. 2 and 3). organisations. Six prominent housing typologies were identified replacing URM which account for 91% of the
surveyed building stock. These include variations of lightweight, semi-concrete, and reinforced concrete (RC)
dwellings (see Figs. 2 and 3). Unreinforced masonry f
y
Before the series of earthquakes in 2019, unreinforced masonry (“URM”) dwellings were the vernacular housing
archetype in the municipality of Itbayat like elsewhere in the province of Batanes. This typology is characterised
by thick (0.80—1 m in width) coral limestone walls bounded by quicklime mortar and roofed with layered cogon. Unique in Batanes, this typology is of Spanish colonial influence adapted by the Ivatans in response to frequent
typhoons38,40. With wind-induced damages common in this context, features to safeguard the structure include
solid wooden panels with shutters to cover openings, a low stature of the structure for better wind resistance,
and a blank wall facing the direction where wind blows strongest. Whilst responsive against wind impacts as
per locals’ experience, this typology proved vulnerable to ground shaking—evident on the extensive damage
experienced following the maximum intensity of PEIS VII from the 2019 earthquakes30. A conservative estimate
based on field data suggests that there are fewer than ten structures remaining of such typology in Itbayat, though
much can still be seen in most municipalities in Batanes. Post-earthquake, the household-led reconstruction
resulted in a departure from the vernacular construction styles. New typologies emerged due to regulatory restric-
tions affecting traditional resource extraction of building materials (e.g., hardwood, limestones, and cogon), the
favourability of contemporary construction methods, and the presence of modern shelter materials donated by https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ Semi‑concrete For semi-concrete structures, two variations were surveyed, both having hybrid lateral load-resisting systems. These typologies have post-and-beam systems in combination with half-height RC walls at the base of the struc-
ture providing additional lateral stiffness. The first variation of semi-concrete structure (“SC-A”) has primary
(corner) posts made of 4-inch to 5-inch diameter steel pipes with RC footing and with timber beams. The beam-
to-column connections vary with the use of bolts, improvised hooks made from RSB, and in some instances, the
beams are just notched and clipped inside the steel pipes. The second variation (“SC-B”) has RC columns with
RC footing. The columns have dowels on top used to wrap and fasten the timber beams (and sometimes together
with roof members). Both semi-concrete typologies are one-story structures having gable roof profiles, where
their roof eaves rarely exceed 300 mm. Roof and walls are enveloped by CGI sheets fastened every other one
or two corrugations on wooden frames using common wire nails with improvised rubber washers. Additional
timber posts as intermediate supports are used. CGI or plywood covers for door openings are common and Figure 2. The surveyed housing typologies in Itbayat. (a) Unreinforced masonry (URM). (b) Lightweight with
wooden posts (LW-A). (c) Lightweight with steel posts (LW-B). (d) Semi-concrete with steel posts (SC-A). (e)
Semi-concrete with RC posts (SC-B). (f) RC structure with lightweight roofing (RC-A) where in some instances,
inside gutters are common to conceal the edges of roofing sheets as shown in (g). (h) RC structure with RC slab
roofing (RC-B). Figure 2. The surveyed housing typologies in Itbayat. (a) Unreinforced masonry (URM). (b) Lightweight with
wooden posts (LW-A). (c) Lightweight with steel posts (LW-B). (d) Semi-concrete with steel posts (SC-A). (e)
Semi-concrete with RC posts (SC-B). (f) RC structure with lightweight roofing (RC-A) where in some instances,
inside gutters are common to conceal the edges of roofing sheets as shown in (g). (h) RC structure with RC slab
roofing (RC-B). https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ Figure 3. Structural details documented across the typologies surveyed. (a) Roof-to-wall connection where
thick logs are embedded in stone walls and (b) layered thatch (cogon) roofing with reed matting are features
of URM. (c) Improvised rubber washers for nail fasteners are used for typologies with CGI sheets. For LW-A,
common post-and-beam connections are (d) bolted, (e) hooked with reinforcing steel bars, and (f) nailed. Semi‑concrete For
LW-B and SC-A, common post-and-beam connections are (g) bolted, (h) notched and clipped, and (i) hooked
with reinforcing steel bars. For SC-B, typical post-and-beam connections are (j, k) dowels wrapped around
beams and roof members. For RC-A, (l) roof-to-wall connections are common to be via dowels from reinforcing
steel bars wrapping the wooden roof members. For RC-B, (m) beams and columns are reinforced concrete
supporting the slab roof. Figure 3. Structural details documented across the typologies surveyed. (a) Roof-to-wall connection where
thick logs are embedded in stone walls and (b) layered thatch (cogon) roofing with reed matting are features
of URM. (c) Improvised rubber washers for nail fasteners are used for typologies with CGI sheets. For LW-A,
common post-and-beam connections are (d) bolted, (e) hooked with reinforcing steel bars, and (f) nailed. For
LW-B and SC-A, common post-and-beam connections are (g) bolted, (h) notched and clipped, and (i) hooked
with reinforcing steel bars. For SC-B, typical post-and-beam connections are (j, k) dowels wrapped around
beams and roof members. For RC-A, (l) roof-to-wall connections are common to be via dowels from reinforcing
steel bars wrapping the wooden roof members. For RC-B, (m) beams and columns are reinforced concrete
supporting the slab roof. the same for windows alongside jalousie (louvred) glass. SC-A has a 17% share of the surveyed building stock,
while SC-B has 14%. Reinforced concrete f
Two types of RC structures were identified—one with lightweight roofing (“RC-A”) and the other one with RC
slab roofing (“RC-B”). RC-A has a gable roof configuration with eaves rarely exceeding 300 mm. The CGI roof
panels are fastened to wooden roof members using common wire nails with improvised rubber washers. Mean-
while, RC-B has a flat slab with eaves typically exceeding 300 mm. Both RC typologies are one-story structures
having RC posts (including footings), beams, and walls. As such, these are considered to have hybrid lateral
load-resisting systems characterised by their moment frame connections in combination with RC walls provid-
ing additional lateral stiffness. CGI or plywood covers for door openings are common and the same for windows
alongside jalousie (louvred) glass. Of the surveyed residential building stock, 9% are RC-A and 9% are RCB.i g
j
g
y
g
All the typologies identified in this study are considered non-engineered due to limited regulatory building
oversight. For URM, building codes and standards were not yet in place, or perhaps limited, when these structures
were constructed (circa ~ 1900s). In 2019 after the earthquakes, the housing reconstruction phase coincided with
the typhoon season, and although the need for a building permit was not explicitly waived, the sense of urgency
dictated the thrust of the household-led rebuilding influenced by the resources available to households. For
example, those who chose to build LW-A and LW-B initially envisioned these as temporary, intending to build
more permanent dwellings later, but financial limitations precluded this from happening. Nevertheless, building
materials were carefully selected in some instances. For example, local hardwood was favoured over commercial
timber for main structural elements such as rafters and beams. For those who chose to build concrete typolo-
gies, imported commercial aggregates from mainland Luzon were desired for their quality. However, since the Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ importation of materials would inflate building costs, households used local aggregates (crushed coral limestones)
for walls while commercial aggregates were used for beams and columns. importation of materials would inflate building costs, households used local aggregates (crushed coral limestones)
for walls while commercial aggregates were used for beams and columns. Fragility functionsh g
y
The fragility functions derived in this study, presented in Figs. 4 and 5, are based on the calculated xm and β
values shown in Table 2. For seismic impacts, URM has a 27% probability of reaching or exceeding very minor
damage (DS1) at PEIS III. This intensity is of weak shaking comparable to the vibration of a passing light truck. 9
Vol (01234
23) 13:22008 |
https://doi.org/10.1038/s41598-023-49398-2
The fragility functions derived in this study, presented in Figs. 4 and 5, are based on the calculated xm and β
values shown in Table 2. For seismic impacts, URM has a 27% probability of reaching or exceeding very minor
damage (DS1) at PEIS III. This intensity is of weak shaking comparable to the vibration of a passing light truck. Figure 4. Fragility functions against seismic impacts derived from experts’ estimates. Figure 4. Fragility functions against seismic impacts derived from experts’ estimates. Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ Figure 5. Fragility functions against wind impacts derived through experts’ estimates. Figure 5. Fragility functions against wind impacts derived through experts’ estimates. The rest of the typologies have negligible probabilities (almost 0%) to any damage state at this intensity. At PEIS
V, described as strong shaking with a rocking effect on buildings, all typologies except for URM show a 45%
to 69% probability of meeting or exceeding DS1 and a likelihood of ≤ 30% of DS2 (minor damage) and DS3
(moderate damage). Meanwhile, at a very destructive shaking (PEIS VIII) where many well-built buildings are
expected to be considerably damaged, URM structures have a 95% probability of reaching or exceeding DS4
(extensive damage) and 81% for complete damage (DS5). For lightweight typologies, there are 78% (LW-A) and https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ Table 2. xm and β values of the fragility functions. Fragility functionsh Considering a 200 km/h peak gust, URM,
RC typologies, and SC-B have very low to negligible probabilities of reaching or exceeding DS5 unlike LW-A,
LW-B, and SC-A where there are 22%, 17%, and 8% chances of meeting or exceeding DS5, respectively. This
wind intensity corresponds roughly to an estimated 20-year return period in the Province of Batanes, meaning
that it has a 5% possibility to happen in a given year, based on the regional severe wind hazard maps for the
Philippines51. At 300 km/h, corresponding to a 500-year return period (0.2% chance to happen in a given year),
URM structures have 87% and 65% probabilities of reaching or exceeding DS4 and DS5, respectively. RC-A is
expected to perform similarly with 87% and 69% probabilities of DS4 and DS5, respectively. Meanwhile, RC-B
shows an 11% probability of reaching or exceeding DS4 and a 3% probability for DS5. For lightweight typologies,
DS4 has a likelihood of 97% (LW-A and LW-B), while DS5 corresponds with 92% (LW-A) and 91% (LW-B). For
semi-concrete typologies, DS4 shows 92% (SC-A) and 89% (SC-B) probabilities of exceedance, and 81% (SC-A)
to 74% (SC-B) for DS5. At 400 km/h, all typologies have > 99% probability of exceedance for DS5, except for
RC-B having a 79% likelihood of reaching or exceeding this damage state. Studies on the derivation of fragility functions in the Philippines are presently very limited. Cross-comparison
of our functions to the available studies is challenging given the differences of how typologies and damage states
are characterised including the nuanced assumptions considered in deriving these functions. Given these limita-
tions, we were only able to draw comparisons to the works of Pacheco et al.52 and Naguit et al.53 on the fragility
functions derived for lightweight, wooden-framed structures. This typology is comparable to LW-A (lightweight
with wooden posts) in this study characterised by wooden post and beam systems. Other typologies from these
studies exhibit different structural characteristics from the ones we surveyed. For example, low-rise concrete-
framed typologies described by both studies cannot be used for direct comparison since in their works, these
are described as concrete moment-framed structures with (hollow block) masonry walls whereas those surveyed
in this study were concrete moment-framed structures with RC walls, adding lateral stiffness to the structure. Fragility functionsh Typology
Earthquake
Typhoon
DS1
DS2
DS3
DS4
DS5
DS1
DS2
DS3
DS4
DS5
URM
xm: 3.49
4.28
5.17
6.14
7.20
xm:136.87
177.26
222.60
256.70
285.18
β: 0.25
0.22
0.19
0.16
0.12
β: 0.16
0.15
0.15
0.14
0.13
LW-A
xm: 4.63
5.45
6.34
7.17
7.96
xm:104.12
130.13
158.80
201.53
230.30
β: 0.19
0.16
0.16
0.14
0.12
β: 0.18
0.14
0.18
0.21
0.19
LW-B
xm: 4.86
5.90
6.54
7.43
8.33
xm:110.18
137.59
165.86
207.47
236.83
β: 0.12
0.15
0.14
0.11
0.09
β: 0.18
0.14
0.20
0.20
0.18
SC-A
xm: 4.87
5.60
6.52
7.40
8.32
xm:122.14
149.67
178.05
222.68
256.26
β: 0.17
0.12
0.12
0.11
0.09
β: 0.18
0.14
0.21
0.21
0.18
SC-B
xm: 4.62
5.43
6.16
7.26
8.17
xm:125.02
157.52
190.12
243.92
270.10
β: 0.16
0.15
0.10
0.11
0.11
β: 0.18
0.18
0.17
0.17
0.16
RC-A
xm: 5.11
5.89
6.82
7.59
8.43
xm:145.23
181.70
210.73
255.46
281.16
β: 0.16
0.13
0.12
0.10
0.08
β: 0.20
0.17
0.17
0.14
0.13
RC-B
xm: 4.85
5.55
6.42
7.36
8.18
xm:230.27
266.00
298.31
338.73
366.65
β: 0.17
0.14
0.14
0.12
0.11
β: 0.08
0.12
0.12
0.10
0.11 Table 2. xm and β values of the fragility functions. 75% (LW-B) probabilities of meeting or exceeding DS4, and 52% (LW-A) and 33% (LW-B) likelihood for DS5. For semi-concrete typologies, still considering PEIS VIII, there is 76% (SC-A) and 81% (SC-B) probabilities of
reaching or exceeding DS4, and 33% (SC-A) and 42% (SC-B) probabilities for DS5. For RC typologies, DS4 has
70% (RC-A) and 76% (RC-B) chances of being reached or exceeded, while 25% (RC-A) and 42% (RC-B) for DS5. Generally, URM tends to be the most vulnerable typology to seismic impacts while the other typologies perform
better, either because of low structure weights (LW-A, LW-B), more robust lateral force resisting systems (RC-A,
RC-B), or a combination of these features (SC-A, SC-B). ),
(
,
)
While URM might be vulnerable to seismic impacts, it generally tends to perform better against wind along-
side RC typologies. At 100 km/h 3-s peak gust, URM has a 2% likelihood of reaching or exceeding DS1, RC-A
has a 3% probability and RC-B has a negligible probability. At the same wind intensity, lightweight typologies
show 41% (LW-A) and 30% (LW-B) probabilities of meeting or exceeding DS1, while semi-concrete typolo-
gies show 13% (SC-A) and 11% (SC-B) probabilities of exceedance. Fragility functionsh Pacheco et al.52 derived their functions using a hybrid approach (computational and heuristic) while Naguit
et al.53 generated their functions using empirical methods using data collected by communities. g
g
p
g
y
Comparing seismic fragilities of lightweight wooden structures (see Fig. 6), our functions provide higher
probabilities for complete damage or collapse. Whereas Naguit et al.’s53 functions estimate ~ 50% probabilities
of exceedance for collapse and Pacheco et al.’s52 functions estimate ~ 85% for complete damage at the maximum
seismic intensity possible (PEIS X / MMI XII), our functions assume complete damage at this intensity close to
100% probability of exceedance. Our functions also indicate that slight damage may start to manifest between
Intensities II and III, close to Naguit et al.’s53 which suggest minor cracks starting to manifest around Intensity
II. Meanwhile, Pacheco et al.’s52 functions indicate slight damage starting to become possible at Intensity IV. For
wind comparisons (see Fig. 7), both our functions and Pacheco et al.’s52 suggest > 75% probabilities of exceedance
for complete damage for wind speeds greater than 350 km/h. For both functions, slight/minor and moderate Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ e.com/scientificreports/
damage start to arise around 100 km/h but ours have steeper curves suggesting a more rapid change in prob-
abilities with the increase of wind speed. In comparing functions, caution should be taken since differences can
Figure 6. Comparison of seismic fragility functions to other studies for lightweight, wooden-framed typology. (Note: PEIS stands for PHIVOLCS Earthquake Intensity Scale while MMI stands for Modified Mercalli
Intensity). Figure 7. Comparison of wind fragility functions to other studies for lightweight, wooden-framed typology. p
Figure 6. Comparison of seismic fragility functions to other studies for lightweight, wooden-framed typology. (Note: PEIS stands for PHIVOLCS Earthquake Intensity Scale while MMI stands for Modified Mercalli
Intensity). Figure 6. Comparison of seismic fragility functions to other studies for lightweight, wooden-framed typology. (Note: PEIS stands for PHIVOLCS Earthquake Intensity Scale while MMI stands for Modified Mercalli
Intensity). Figure 6. Comparison of seismic fragility functions to other studies for lightweight, wooden-framed typology. (Note: PEIS stands for PHIVOLCS Earthquake Intensity Scale while MMI stands for Modified Mercalli
Intensity). Figure 7. Comparison of wind fragility functions to other studies for lightweight, wooden-framed typology. Figure 7. www.nature.com/scientificreports/ of 3 or greater (out of 5). As shown in Table 3, there was variation in experts’ confidence in their assessments. The median of confidence level for wind assessments for each typology is 3 across all typologies. Meanwhile, for
seismic assessments, heavier typologies (URM, RC-A, and RC-B) have a median confidence rating of 4 while
the rest, which are the lighter weight counterparts, have a median confidence level of 3. Considering experts’
unweighted (or raw) inputs, standard deviations across damage states for earthquake intensities range from
PEIS 0.83–PEIS 1.54, while for typhoon wind speeds, they range from 43.29 to 105.65 km/h. The minimum and
maximum values of the consolidated estimates from both local experts and specialists are presented in Table 3
and these values show the variation of inputs solicited for this assessment.i of 3 or greater (out of 5). As shown in Table 3, there was variation in experts’ confidence in their assessments. The median of confidence level for wind assessments for each typology is 3 across all typologies. Meanwhile, for
seismic assessments, heavier typologies (URM, RC-A, and RC-B) have a median confidence rating of 4 while
the rest, which are the lighter weight counterparts, have a median confidence level of 3. Considering experts’
unweighted (or raw) inputs, standard deviations across damage states for earthquake intensities range from
PEIS 0.83–PEIS 1.54, while for typhoon wind speeds, they range from 43.29 to 105.65 km/h. The minimum and
maximum values of the consolidated estimates from both local experts and specialists are presented in Table 3
and these values show the variation of inputs solicited for this assessment. p
To summarise, respondents were more confident in their assessments of heavier typologies for both hazards. However, for typhoon hazards, variance of responses increased from light to heavy typologies, suggesting wider
variation in expert assessments. In general, we argue that the variability of experts’ inputs should be consid-
ered an advantage for the context of this assessment because such variability encompasses the broad scenario-
based observations of housing performance. This consideration is beneficial most especially where construction
resources are used less prescriptively against building codes and standards requiring less straightforward appraisal
of housing performance. Table 3. Ranges of consolidated experts’ estimates shown through minimum and maximum values, including
the median. *Confidence levels are ordinal ratings from 1 to 5. **IM stands for intensity measure. www.nature.com/scientificreports/ For
earthquake, it is expressed in PHIVOLCS Earthquake Intensity Scale (PEIS). For typhoon, it is expressed in
kilometres per hour (km/h). Table 3. Ranges of consolidated experts’ estimates shown through minimum and maximum values, including
the median. *Confidence levels are ordinal ratings from 1 to 5. **IM stands for intensity measure. For
earthquake, it is expressed in PHIVOLCS Earthquake Intensity Scale (PEIS). For typhoon, it is expressed in
kilometres per hour (km/h). Fragility functionsh Comparison of wind fragility functions to other studies for lightweight, wooden-framed typology damage start to arise around 100 km/h but ours have steeper curves suggesting a more rapid change in prob-
abilities with the increase of wind speed. In comparing functions, caution should be taken since differences can
emanate from the varied characterisations adopted by authors. For example, the use three-tier damage scale (e.g.,
Naguit et al.53) can result to a different set of functions when applying more granular observations to visualise
or represent five damage states.fii damage start to arise around 100 km/h but ours have steeper curves suggesting a more rapid change in prob-
abilities with the increase of wind speed. In comparing functions, caution should be taken since differences can
emanate from the varied characterisations adopted by authors. For example, the use three-tier damage scale (e.g.,
Naguit et al.53) can result to a different set of functions when applying more granular observations to visualise
or represent five damage states.fii i
Benchmarking the accuracy of the functions derived in this study is difficult as these are the first to be derived
for this geographical context. In the interim, these functions can be considered as medium quality having satisfied
the criteria of Porter et al.27,28 to have at least three experts whose confidence ratings are ≥ 3. For the expert-driven
approach in ATC-58, only low and medium-quality benchmarks are provided in reporting on the quality of the
derived functions. At least 68% of the responses for every typology for each hazard received confidence ratings https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ i
g
y
earthquake, it is expressed in PHIVOLCS Earthquake Intensity Scale (PEIS). For typhoon, it is expressed in
kilometres per hour (km/h). Table 3. Ranges of consolidated experts’ estimates shown through minimum and maximum values, including
he median. *Confidence levels are ordinal ratings from 1 to 5. **IM stands for intensity measure. For www.nature.com/scientificreports/ Earthquake intensity (PEIS)
Typhoon intensity (km/h)
URM
LW-A
LW-B
SC-A
SC-B
RC-A
RC-B
URM
LW-A
LW-B
SC-A
SC-B
RC-A
RC-B
Confidence levels*
Min
1
1
3
1
1
1
1
1
1
1
1
1
1
1
Max
4
4
4
5
5
5
4
5
5
5
5
5
5
5
Median
4
3
3
3
3
4
4
3
3
3
3
3
3
3
DS 1
Median IM**
Min
2
1
3
2
2
4
3
50
30
30
60
60
45
70
Max
6
4
8
8
7
7
7
300
225
225
300
300
300
400
Median
3
3
5
4
4
5
4.5
100
100
100
100
100
120
150
Lower bound IM
Min
1
1
2
1
1
1
2
30
20
25
50
55
30
60
Max
5
7
8
7
6
6
5
250
200
200
250
250
250
400
Median
2
3
4
3
3
4
4
80
60
70
80
80
100
130
DS 2
Median IM
Min
3
3.5
4
3
2.5
4.5
3
70
40
40
75
80
55
90
Max
6
8
8
8
8
8
8
325
250
250
325
325
325
400
Median
4
5
6
5
5
5.75
5.5
150
120
126
135
140
150
200
Lower bound IM
Min
2
2
3
2
1
2
2
40
25
30
60
70
45
70
Max
5
7
8
8
7
7
6
275
225
225
275
275
275
400
Median
3
4
5
4
4
5
5
120
100
100
100
100
125
155
DS 3
Median IM
Min
3
4
4.5
3.5
3
5
4
75
60
60
90
90
75
160
Max
7
9
9
9
8
9
8
350
275
275
350
350
350
400
Median
5
6
6.75
6
6
7
6.75
180
155
155
160
180
200
300
Lower bound IM
Min
2
3
4
3
2
4
2
50
40
45
60
60
50
100
Max
6
8
8
8
8
8
7
300
250
250
300
300
300
400
Median
4
5
5.5
5
5
6
5.5
160
115
120
125
145
150
200
DS 4
Median IM
Min
4
5
6
4
4
6
5
80
90
90
140
140
90
220
Max
8
10
10
9
9
10
9
375
300
300
375
375
375
400
Median
6
7
7.25
7
7
7.5
7.5
200
200
200
200
205
240
350
Lower bound IM
Min
3
3
4
3
2
4
3
70
80
90
100
100
75
160
Max
7
9
9
8
9
9
8
325
275
275
325
325
325
400
Median
5
6
6.25
6
6
7
6.5
175
150
150
150
175
200
300
DS 5
Median IM
Min
5
6
6.5
5
5
7
6
90
110
110
150
150
100
250
Max
9
10
10
10
10
10
10
400
325
325
400
400
400
400
Median
7
8
8
8
8
8
8
250
245
250
250
240
260
400
Lower bound IM
Min
4
5
6
4
3
5
5
60
90
100
100
100
85
180
Max
8
9
9
9
9
10
9
375
300
300
350
350
350
400
Median
6.5
7
7.25
7
7
7.5
7.25
200
180
185
200
200
222.5
325 Table 3. Discussion
d However,
in some instances, there is no definite historical upper bound of hazard intensities for wind events due to previ-
ous data limitations. For example, recorded peak gusts of Typhoon Meranti (Ferdie) in 2016 are unavailable in
Itbayat where it made landfall54. Likewise, peak gusts of Typhoon Haiyan (Yolanda) were not recorded across
some weather stations in the Visayas region due to the damage sustained by the weather instruments48,55,56. To
compensate for such limitations, intensity readings of neighbouring international weather agencies were used. Additionally, estimated intensities evident from impact signs to infrastructure as derived in some studies were
referenced55–57. However, without officially recorded intensity readings of some of the largest typhoons in the
Philippines, estimates will always be confined within the proxied or assumed values. For seismic impacts, a fac-
tor to consider as raised by one specialist is the possibility of circular logic between PEIS intensities and damage
states. That is, PEIS ground shaking is at least partly pegged to certain descriptors of building damage. h
f h
d
h
bl
l
h
l
l
d
l d h
On the use of the expert-driven approach as a viable alternative where analytical and empirical data are
currently impractical to acquire, we realise that expertise can also be a rare commodity. Local expertise might
be limited at a municipal level especially in small, geographically remote areas. We have addressed this issue
by broadening the jurisdiction to the provincial level where district engineers compensated for this limitation. Additionally, while there is a reasonable number of specialists who could be prospective respondents, their
availability was not guaranteed, and response rates mainly dictated the sampling of the respondents. Therefore,
robustly qualifying who gets involved was the priority more than reaching a certain quota of respondents with
a focus on quality over quantity of participant selection.hih These three insights guided our derivation of the first-generation fragility functions in Batanes. The non-
engineered nature of the typologies surveyed makes it a challenge to definitively assess the variability inherent
to this building stock. This study, however, advanced this pursuit by acknowledging the nuanced characteristics
of non-engineered typologies, which could have otherwise been categorised within existing generic taxonomies. In the Philippines, previous efforts to generate fragility or vulnerability functions for residential typologies have
been conducted for Greater Metro Manila Area52, Bohol53, and Cebu58, with contributions in the GEM database. Discussion
d In conducting the expert-driven approach of deriving fragility functions, we gleaned three insights to consider
when using this heuristic alternative for damage analysis. These insights include how disaster sub-culture influ-
ences experts’ estimates, some caveats to be aware of when relying on hazard intensities published by agencies,
and the logistical challenges of soliciting experts’ opinions. In areas like Batanes where people have perennial encounters with hazards, disaster preparedness practices
instinctively emerge to become part of their disaster sub-culture. For example, before a typhoon hits, houses are
tied up with ropes to secure their envelopes (a practice called kap’yakuyakut in Itbayat and kapanpet in mainland
Batanes). Meanwhile, windows are covered with an additional layer of improvised shutters (tapangko). During
the solicitation of experts’ opinions, a local expert commented that his estimates were guided by how the houses
perform in conjunction with these prevailing disaster preparedness practices in the area. These considerations
provide a layered understanding of housing performance embedded in local settings—and why the develop-
ment of localised fragility functions is important. Conventional approaches to damage analysis would suggest
equal, unifying assumptions for assessments. However, understanding these local practices requires context and
nuance not captured by decoupling building elements and preparedness activities. Commanding local experts to
“disregard” such considerations is counterintuitive given that the core basis of their estimates is on actual obser-
vations. Beyond the expert-driven approach, there is an opportunity to consider these types of non-traditional
measures in computational fragility modelling done experimentally. These disaster preparedness practices will
also have an impact on future empirical data collected in Batanes since housing damage will likely be reflective
of the housing performance in conjunction with such practices. Damage estimates based on experts’ opinions are guided by actual observations of housing performance
based on past disaster events. These observations are most likely referenced with impactful hazard intensities as
broadcasted by agencies. Since damage estimates are relative or “framed” within agency-interpreted intensities,
any errors, limitations, or discrepancies in how these intensities are interpreted affect the experts’ estimates. On
the survey forms, we provided information sheets that contained ranges of hazard intensities of notable disaster
events in the Philippines from different data sources to guide respondents in situating their estimates. The inten-
tion was to confine their estimates within reasonable hazard intensities that were actually recorded. Discussion
d This study branched out further north to consider the rural context of a small island geography which has been
pressured to address multi-hazard housing safety due to the competing impacts of extreme events. The functions
derived are fundamental tools for practitioners to understand the vulnerability of non-engineered structures and
offer targeted structural mitigation and preparedness programmes contextualised in the area. It is suggested that
when more empirical data becomes available, the possibility of combining new and existing functions should
be explored50,59. www.nature.com/scientificreports/ Ranges of consolidated experts’ estimates shown through minimum and maximum values, including
the median. *Confidence levels are ordinal ratings from 1 to 5. **IM stands for intensity measure. For
earthquake, it is expressed in PHIVOLCS Earthquake Intensity Scale (PEIS). For typhoon, it is expressed in
kilometres per hour (km/h). Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ References 25(10), 1241–1263. https://doi.org/10.1016/S0141-0296(03)00060-9 (2003). g
g
6. Maio, R. & Tsionis, G. Seismic Fragility Curves for the European Building Stock: Review and Evaluation of Existing Fragility Curves
(Publications Office, Luxembourg, 2015).i fi
17. Rossetto, T., D’Ayala, D., Ioannou, I. and Meslem, A. ‘Evaluation of existing fragility curves’, in SYNER-G: Typology Definition and
Fragility Functions for Physical Elements at Seismic Risk, vol. 27, Pitilakis, K., Crowley, H. and Kaynia, A. M. Eds., in Geotechni‑
cal, Geological and Earthquake Engineering, vol. 27, Dordrecht: Springer Netherlands, 2014, pp. 47–93. https://doi.org/10.1007/
978-94-007-7872-6_3. 18. De Angeli, S. et al. A multi-hazard framework for spatial-temporal impact analysis. Int. J. Disaster Risk Reduct. 73, 102829. htt
doi.org/10.1016/j.ijdrr.2022.102829 (2022). g
j j
9. Kappes, M. S., Keiler, M., von Elverfeldt, K. & Glade, T. Challenges of analyzing multi-hazard risk: A review. Nat. Hazards 64(2)
1925–1958. https://doi.org/10.1007/s11069-012-0294-2 (2012). p
g
20. Jaiswal, K., Wald, D., Perkins, D., Aspinall, W. and Kiremidjian, A. ‘Estimating structural collapse fragility of generic building
typologies using expert judgment’, in Safety, Reliability, Risk and Life-Cycle Performance of Structures and Infrastructures, G. Deo-
datis, B. Ellingwood, and D. Frangopol, Eds., CRC Press, 2014, pp. 879–886. https://doi.org/10.1201/b16387-130. g
g p
pp
p
g
21. Jaiswal, K. S., Aspinall, W. P. Perkins, D., Wald, D. and Porter, K. A. ‘Use of expert judgment elicitation to estimate seismic vulner-
ability of selected building types’, in Proceedings of the 15th World Conference on Earthquake Engineering, Lisbon, Portugal, (2012). ll
h
l
l
h d
f
l
d
f
l
d
k 22. Martello, M. V., Whittle, A. J. & Lyons-Galante, H. R. Depth-damage curves for rail rapid transit infrastructure. J. Flood Risk M
https://doi.org/10.1111/jfr3.12856 (2022). p
g
j
(
)
23. Applied Technology Council, ‘ATC-13 Earthquake Damage Evaluation Data for California’, Redwood City, CA, (1985). gy
g
y
24. Ioannou, I., Aspinall, W., Rush, D., Bisby, L. & Rossetto, T. Expert judgment-based fragility assessment of reinforced con
buildings exposed to fire. Reliab. Eng. Syst. Saf. 167, 105–127. https://doi.org/10.1016/j.ress.2017.05.011 (2017). oannou, I., Aspinall, W., Rush, D., Bisby, L. & Rossetto, T. Expert judgment-based fragility assessment of reinforced concrete
uildings exposed to fire Reliab Eng Syst Saf 167 105 127 https://doi org/10 1016/j ress 2017 05 011 (2017) i
25. Miura, H., Midorikawa, S., Fujimoto, K., Pacheco, B. M. & Yamanaka, H. Earthquake damage estimation in Metro Manila, Phil-
ippines based on seismic performance of buildings evaluated by local experts’ judgments. References A., Patelli, E. and Au, I. S.-K. Eds., Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 1–29. (2021) https://doi.org/10
1007/978-3-642-36197-5_256-1. 7. FEMA, Hazus Earthquake Model Technical Manual. (2020) 8. FEMA, Hazus Hurricane Model Technical Manual. (2021). ,
(
)
9. Vickery, P. J. et al. HAZUS-MH hurricane model methodology. II: Damage and loss estimation. Nat. Hazards Rev. 7(2), 94–103. https://doi.org/10.1061/(ASCE)1527-6988(2006)7:2(94) (2006). 9. Vickery, P. J. et al. HAZUS-MH hurricane model methodology. II: Damage and loss estimation. Nat. Hazards Rev. 7(2), 94–
https://doi.org/10.1061/(ASCE)1527-6988(2006)7:2(94) (2006). 9. Vickery, P. J. et al. HAZUS-MH hurricane model methodology. II: Damage and l
https://doi.org/10.1061/(ASCE)1527-6988(2006)7:2(94) (2006). p
g
0. Pita, G. L., Albornoz, B. S. & Zaracho, J. I. Flood depth-damage and fragility functions derived with structured expert judgment
J. Hydrol. 603, 126982. https://doi.org/10.1016/j.jhydrol.2021.126982 (2021). p
g
10. Pita, G. L., Albornoz, B. S. & Zaracho, J. I. Flood depth-damage and fragility functions de
J. Hydrol. 603, 126982. https://doi.org/10.1016/j.jhydrol.2021.126982 (2021). 11. Charleson A. et al., Towards resilient non-engineered construction: guide for risk-informed policy-making. United Nations Educa-
tional, Scientific, and Cultural Organisation, (2016). 11. Charleson A. et al., Towards resilient non-engineered construction: guide for risk-informed policy-making. United Nations Educa-
tional, Scientific, and Cultural Organisation, (2016). tional, Scientific, and Cultural Organisation, (2016). i
g
2. Hadlos, A., Opdyke, A. & Hadigheh, S. A. Where does local and indigenous knowledge in disaster risk reduction go from here? A
i li
i
I
J Di
Ri k R d
79 103160 h
//d i
/10 1016/j ijd
2022 103160 (2022) i
12. Hadlos, A., Opdyke, A. & Hadigheh, S. A. Where does local and indigenous knowledge in disaster risk reduction go from here? A systematic literature review. Int. J. Disaster Risk Reduct. 79, 103160. https://doi.org/10.1016/j.ijdrr.2022.103160 (2022).hl i
12. Hadlos, A., Opdyke, A. & Hadigheh, S. A. Where do y
J
,
p
g
j j
(
)
3. de Ruiter, M. C. et al. The asynergies of structural disaster risk reduction measures: Comparing floods and earthquakes. Earth’
Future https://doi.org/10.1029/2020EF001531 (2021). y
13. de Ruiter, M. C. et al. The asynergies of structural disa
Future https://doi.org/10.1029/2020EF001531 (2021). h
y
g
Future https://doi.org/10.1029/2020EF001531 (2021) g
14. Li, Y., Ahuja, A. & Padgett, J. E. Review of methods to assess, design for, and mitigate multiple hazards. J. Perform. Constr. Facil. 26(1), 104–117. https://doi.org/10.1061/(ASCE)CF.1943-5509.0000279 (2012). g
15. Rossetto, T. & Elnashai, A. Derivation of vulnerability functions for European-type RC structures based on observational data. Eng. Struct. Data availability
Th d
d
d y
The datasets used and analysed in this study are available from the corresponding author upon reasonable request Received: 2 August 2023; Accepted: 7 December 2023 Received: 2 August 2023; Accepted: 7 December 2023 Received: 2 August 2023; Accepted: 7 December 2023 References 1. UNISDR, ‘Sendai Framework for Disaster Risk Reduction 2015 - 2030’, (2015). 1. UNISDR, ‘Sendai Framework for Disaster Risk Reduction 2015 - 2030’, (2015). 1. UNISDR, ‘Sendai Framework for Disaster Risk Reduction 2015 - 2030’, (2015) med, I. An overview of post-disaster permanent housing reconstr 2. Ahmed, I. An overview of post-disaster permanent housing reconstruction in developing countries. Int. J. Disaster Resil. Buil
Environ. 2(2), 148–164. https://doi.org/10.1108/17595901111149141 (2011). 2. Ahmed, I. An overview of post-disaster permanent housing reconstruction in developing coun
Environ. 2(2), 148–164. https://doi.org/10.1108/17595901111149141 (2011). 2. Ahmed, I. An overview of post-disaster permanent housing reconstruction in dev
Environ. 2(2), 148–164. https://doi.org/10.1108/17595901111149141 (2011). ron. 2(2), 148–164. https://doi.org/10.1108/17595901111149141 ( p
g
3. Kaynia, A., Iervolino, I., Taucer, F. and Hancilar, U. Guidelines for deriving seismic fragility functions of elements at risk: buildings,
lifelines, transportation networks and critical facilities. LU: Publications Office of the European Union, 2013. Accessed: Dec. 18,
2022. [Online]. Available: https://data.europa.eu/doi/https://doi.org/10.2788/19605 p
g
3. Kaynia, A., Iervolino, I., Taucer, F. and Hancilar, U. Guidelines for deriving seismic fragility functions of elements at risk: buildings
lifelines, transportation networks and critical facilities. LU: Publications Office of the European Union, 2013. Accessed: Dec. 18
2022. [Online]. Available: https://data.europa.eu/doi/https://doi.org/10.2788/19605 3. Kaynia, A., Iervolino, I., Taucer, F. and Hancilar, U. Guidelines for deriving seismic fragility functions of elements at risk: buildings,
lifelines, transportation networks and critical facilities. LU: Publications Office of the European Union, 2013. Accessed: Dec. 18,
2022. [Online]. Available: https://data.europa.eu/doi/https://doi.org/10.2788/19605 [
]
p
p
p
g
4. Kircher, C. A., Whitman, R. V. & Holmes, W. T. HAZUS earthquake loss estimation methods. Nat. Hazards Rev. 7(2), 45–59
https://doi.org/10.1061/(ASCE)1527-6988(2006)7:2(45) (2006). p
p
p
g
4. Kircher, C. A., Whitman, R. V. & Holmes, W. T. HAZUS earthquake loss estimation methods. Nat. Hazards Rev. 7(2), 45–59. https://doi.org/10.1061/(ASCE)1527-6988(2006)7:2(45) (2006). p
g
5. Negulescu, C. and Gehl, P. ‘Mechanical Methods: Fragility Curves and Pushover Analysis’, in Seismic Vulnerability of Structures
P. Gueguen, Ed., Hoboken, NJ USA: John Wiley & Sons, Inc., (2013), pp. 63–110. https://doi.org/10.1002/9781118603925.ch2. g
y
pp
p
g
6. Porter, K. ‘A beginner’s guide to fragility, vulnerability, and risk’, in Encyclopedia of Earthquake Engineering, Beer, M., Kougioumt-
zoglou, I. A., Patelli, E. and Au, I. S.-K. Eds., Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 1–29. (2021) https://doi.org/10.
1007/978-3-642-36197-5_256-1. g
y
pp
p
g
6. Porter, K. ‘A beginner’s guide to fragility, vulnerability, and risk’, in Encyclopedia of Earthquake Engineering, Beer, M., Kougioumt-
zoglou, I. Conclusion Using fragility functions in risk assessments is fundamental to model anticipated structural housing damage
against the impacts of natural hazards. We used an expert-driven approach to derive wind and seismic fragility
functions for the Province of Batanes. Theoretically, this study provides new estimates of the performance of non-
engineered housing in the Philippines, which would traditionally be discounted by conventional fragility assess-
ments relying on generic building taxonomies. This region-specific evaluation is a step to advance more localised
risk assessments. Practically, the set of fragility functions derived in this study is seen to assist practitioners in
exploring risk preparedness and mitigation measures applicable in Batanes. On a national scale, we fill gaps on
the lacking representation of building archetypes in rural and remote areas as most attention to understanding
building-level risk reduction has, to date, focused in urban centres where data are more accessible. Our functions https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ lay a foundation for more holistic and contextualised approaches to risk modelling nationwide considering the
inclusion of neglected geographic areas. As new damage data and analysis emerge in the future, our functions
can aid hybrid approaches to generate the next generation of fragility estimates. lay a foundation for more holistic and contextualised approaches to risk modelling nationwide considering the
inclusion of neglected geographic areas. As new damage data and analysis emerge in the future, our functions
can aid hybrid approaches to generate the next generation of fragility estimates. www.nature.com/scientificreports/ ‘Tropical cyclone passage report’, typhoon committee, (2016). Accessed: Jul. 12, 2023. [Online]. Available: https://
typhooncommittee.org/docs/Passage%20Reports/2016/1614-MERANTE-Philippines.pdf typhooncommittee.org/docs/Passage%20Reports/2016/1614-M 5. Agar, J. C., Mata, W. L. & Hernandez, J. Jr. Estimating typhoon haiyan’s wind speeds using windicators. Philipp. Eng. J. 39(1), 29–42
(2018). 6. Aquino, R. E., Mata, W. and Valdez, J. J. ‘Brief Report on Observed Wind Damages in Leyte and Samar due to Typhoon Yolanda
of 2013’, (2014). 56. Aquino, R. E., Mata, W. and Valdez, J. J. ‘Brief Report on Observed Wind Damages in Leyte and Samar due to Typhoon Yolanda
of 2013’, (2014). 57. Hernandez, J. Jr., Aquino, R. E., Pacheco, B. & Cruz, E. Damage caused by typhoon haiyan in the philippines, review of structural
regulations and practice, and research developments in wind engineering wind engineers. JAWE 40(3), 270–274 (2015). 58. Agar, J. C. et al. Component-based severe wind vulnerability analysis of wooden buildings in the Philippines. AEJ 12(2), 219–225. 57. Hernandez, J. Jr., Aquino, R. E., Pacheco, B. & Cruz, E. Damage caused by typhoon haiyan in the philippines, review of structural
regulations and practice, and research developments in wind engineering wind engineers. JAWE 40(3), 270–274 (2015). 58. Agar, J. C. et al. Component-based severe wind vulnerability analysis of wooden buildings in the Philippines. AEJ 12(2), 219–225. https://doi.org/10.11113/aej.v12.17463 (2022). p
g
j
(
)
59. Jaiswal, K., Wald, D. & D’Ayala, D. Developing empirical collapse fragility functions for global building types. Earthq. Spectra 27(3),
775–795. https://doi.org/10.1193/1.3606398 (2011). p
g
j
9. Jaiswal, K., Wald, D. & D’Ayala, D. Developing empirical collapse fragility functions for global building types. Earthq. Spectra 27(3)
775–795. https://doi.org/10.1193/1.3606398 (2011). Acknowledgements g
We thank the Local Government Unit (LGU) of Itbayat and the National Commission on Indigenous Peoples
(NCIP) in Batanes for their support in facilitating the regulatory approvals in conducting this study. In particular,
we would like to acknowledge the help extended by the Council of Elders of Itbayat, LGU Mayor Sabas de Sagon,
Department of Interior and Local Government Officer Ms Charmaine Gato, and NCIP personnel Mr Eduardo
Delfin, Mr Gilbert Ruiz, and Mrs Marilyn Galolo. www.nature.com/scientificreports/ www.nature.com/scientificreports/ 33. Venable, C., Liel, A. B., Kijewski-Correa, T. & Javernick-Will, A. Wind performance assessment of postdisaster housing in the
Philippines. Nat. Hazards Rev. 22(4), 04021033. https://doi.org/10.1061/(ASCE)NH.1527-6996.0000491 (2021). l
l
h
d
k
f
k f
l
l h
d
h
( ) 34. Sevieri, G. et al. A multi-hazard risk prioritisation framework for cultural heritage assets. Nat. Hazards Earth Syst. Sci. 2
1391–1414. https://doi.org/10.5194/nhess-20-1391-2020 (2020). p
g
(
)
35. GEM Foundation, ‘Glossary for GEM Taxonomy’. Accessed: Feb. 11, 2023. [Online]. Available: https://taxonomy.openquake 35. GEM Foundation, ‘Glossary for GEM Taxonomy’. Accessed: Feb. 11, 2023. [Online]. Available: https://taxonomy.openquake.org/ y
y
p
y p
q
g
6. Adami, F. The traditional ivatan house in barangay itbud today’, Ivatan Stud. J., vol. II, III, IV, no. 1995–1997, pp. 216–231, 1998 36. Adami, F. The traditional ivatan house in barangay itbud today’, Ivatan Stud. J., vol. II, III, IV, R. A Visual Dictionary on Filipino Architecture (University of San y
y
g
8. Hornedo, F. Traditional Ivatan Shelter and Architecture, Part Two, The Classic Traditional Ivatan House: Emergence and Prospects
Ivatan Studies Journal, vol. XIII–XIV, no. 2015–2016, pp. 39–112, 2015. pp
9. National Historical Commission of the Philippines. Ivatan Traditional House: A Construction and Maintenance Manual (Nationa
Historical Commission of the Philippines, Manila, 2018). pp
)
40. National Historical Commission of the Philippines. Vahay: Documenting the Story of the Ivatan House (National Historical Com-
mission of the Philippines, Manila, 2018). pp
1. Clemen, R. T. & Winkler, R. L. Combining probability distributions from experts in risk analysis. Risk Anal. 19(2), 187–203. https://
doi.org/10.1111/j.1539-6924.1999.tb00399.x (1999). g
j
(
)
2. Moehle, J. and Deierlein, G. A Framework Methodology for Performance-Based Earthquake Engineering, presented at the 13th
World Conference on Earthquake Engineering, Vancouver, B.C., Canada, (2004).t g
g
3. Skolnik, D. A. & Wallace, J. W. Critical assessment of interstory drift measurements. J. Struct. Eng. 136(12), 1574–1584. https://
doi.org/10.1061/(ASCE)ST.1943-541X.0000255 (2010). g
4. Philippine Institute of Volcanology and Seismology, ‘PHIVOLCS Earthquake Intensity Scale (PEIS)’. Accessed: Jul. 10, 2023
[Online]. Available: https://www.phivolcs.dost.gov.ph/index.php/earthquake/earthquake-intensity-scale g
y
5. Lasala, M. et al. Establishment of earthquake intensity meter network in the Philippines. J. Disaster Res. 10(1), 43–50. https://doi
org/10.20965/jdr.2015.p0043 (2015).i g
j
p
46. Japan International Cooperation Agency, Pacific Consultants International, OYO International Corporation, and PASCO Corpora-
tion, ‘Earthquake Impact Reduction Study for Metropolitan Manila, Republic of the Philippines’, Volume 1, (2004). y
47. Cua, G. et al. www.nature.com/scientificreports/ Best Practices for using macroseismic intensity and ground motion intensity conversion equations for hazard
l
d l
’
d
l
h
l
(
) 47. Cua, G. et al. Best Practices for using macroseismic intensity and ground motion intensity conversion equations for hazard and
loss models in GEM1’, GEM Foundation, Pavia, Italy, GEM Technical Report 2010-04, (2010). 47. Cua, G. et al. Best Practices for using macroseismic intensity and ground motion intensity conversion equations for hazard and
loss models in GEM1’, GEM Foundation, Pavia, Italy, GEM Technical Report 2010-04, (2010). y
p
(
)
8. Yang, Q., Gao, R., Bai, F., Li, T. & Tamura, Y. Damage to buildings and structures due to recent devastating wind hazards in Eas
Asia. Nat. Hazards 92(3), 1321–1353. https://doi.org/10.1007/s11069-018-3253-8 (2018).i ds 92(3), 1321–1353. https://doi.org/10.1007/s11069-018-3253-8 (2 p
g
49. Aspinall, W. P. and Cooke, R. M. Quantifying scientific uncertainty from expert judgement elicitation, in Risk and Uncertainty
Assessment for Natural Hazards, 1st ed., Rougier, J., Sparks, S., and Hill, L. J. Eds., Cambridge University Press, 2013, pp. 64–99. https://doi.org/10.1017/CBO9781139047562.005. p
g
0. Lallemant, D., Kiremidjian, A. & Burton, H. Statistical procedures for developing earthquake damage fragility curves. Earthq
Engng. Struct. Dyn. 44(9), 1373–1389. https://doi.org/10.1002/eqe.2522 (2015). g g
y
p
g
q
51. Philippine Atmospheric, Geophysical, and Astronomical Services, ‘Regional Severe Wind Hazard Maps’. Accessed: Jul. 17, 2
[O l
] A
l bl
h
//
d
h/
d
d
/
d 51. Philippine Atmospheric, Geophysical, and Astronomical Services, ‘Regional Severe Wind Hazard Maps’. Accessed: Jul. 17, 2023. [Online]. Available: https://www.pagasa.dost.gov.ph/products-and-services/severe-wind-maps [Online]. Available: https://www.pagasa.dost.gov.ph/products-a p
p g
g
p
p
p
52. Pacheco, B. et al. Development of Vulnerability Curves of Key Building Types in the Greater Metro Manila Area, Philippines
Report (University of the Philippines Diliman, Philippines, Quezon City, Philippines, 2014). g
g
t al. Development of Vulnerability Curves of Key Building Types in 52. Pacheco, B. et al. Development of Vulnerability Curves of Key Building Types in the Greater Metro Manila Area, Philippines
Report (University of the Philippines Diliman, Philippines, Quezon City, Philippines, 2014). p
y
y
53. Naguit, M. et al. From source to building fragility: Post-event assessment of the 2013 M7.1 Bohol, Philippines, earthquake. Earthq. Spectra 33(3), 999–1027. https://doi.org/10.1193/0101716eqs173m (2017). p
y
y
53. Naguit, M. et al. From source to building fragility: Post-event assessment of the 201
Spectra 33(3), 999–1027. https://doi.org/10.1193/0101716eqs173m (2017). p
p
g
q
54. Paciente, R. Competing interests h p
g
The authors declare no competing interests. References Soil Dynam. Earthq. Eng. 28(10–11),
764–777. https://doi.org/10.1016/j.soildyn.2007.10.011 (2008).l p
g
j
y
6. Winter, M. G. et al. An expert judgement approach to determining the physical vulnerability of roads to debris flow. Bull. Eng
Geol. Environ. 73(2), 291–305. https://doi.org/10.1007/s10064-014-0570-3 (2014). p
g
7. Porter, K., Kennedy, R. & Bachman, R. Creating fragility functions for performance-based earthquake engineering. Earthq. Spectra
23(2), 471–489. https://doi.org/10.1193/1.2720892 (2007). p
g
28. Porter, P. K., Kennedy, R. and Bachman, R. Developing fragility functions for building components for ATC-58’, Applied Technol-
ogy Council, Redwood City, CA, (2006). gy
y
29. International Federation of Red Cross and Red Crescent Societies, ‘Philippines: Batanes Eart
l ‘
f h
l
d
(
)
d
b gy
y
29. International Federation of Red Cross and Red Crescent Societies, ‘Philippines: Batanes Earthquake’, (2020). 30 Perez J et al ‘Impacts of the 27 July 2019 Magnitudes (Mw) 5 4 5 9 and 5 8 Itbayat Batanes Earthquakes’ Dep 29. International Federation of Red Cross and Red Crescent Societies, ‘Philippines: Batanes Earthquake’, (2020). 30. Perez J. et al., ‘Impacts of the 27 July 2019 Magnitudes (Mw) 5.4, 5.9, and 5.8 Itbayat, Batanes Earthquakes’, Department of Scie
and Technology
Philippine Institute of Volcanology and Seismology (2019) pp
q
30. Perez J. et al., ‘Impacts of the 27 July 2019 Magnitudes (Mw) 5.4, 5.9, and 5.8 Itbayat, Batanes Earthquakes’, Department of Science
and Technology - Philippine Institute of Volcanology and Seismology, (2019). 30. Perez J. et al., ‘Impacts of the 27 July 2019 Magnitudes (Mw) 5.4, 5.9, and 5.8 Itbayat, Batanes E
and Technology - Philippine Institute of Volcanology and Seismology, (2019).i 30. Perez J. et al., Impacts of the 27 July 2019 Magnitudes (Mw) 5.4, 5.9, and 5.8 Itbayat, Batanes Earthquakes, Department of Sc
and Technology - Philippine Institute of Volcanology and Seismology, (2019).i gy
pp
gy
gy (
)
31. Silva, V. et al. A building classification system for multi-hazard risk assessment. Int. J. Disaster Risk Sci. 13(2), 161–177. https://
doi.org/10.1007/s13753-022-00400-x (2022). 32. Venable, C., Javernick-Will, A., Liel, A. B. and Koschmann, M. A. Revealing (mis)alignments between household perceptions and
engineering assessments of post-disaster housing safety in typhoons, Int. J. Disaster Risk Reduct., 53, (2021), https://doi.org/10.
1016/j.ijdrr.2020.101976. https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | Author contributions A.H. wrote the main manuscript text, conducted the field visits, data collection, and analysis. A.O. provided
primary supervision while S.A.H. provided secondary supervision. A.H. and A.O. edited the manuscript. All
authors conceptualised the project and reviewed the manuscript. Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the
Creative Commons licence, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons licence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Additional information Correspondence and requests for materials should be addressed to A.H. Correspondence and requests for materials should be addressed to A.H. Reprints and permissions information is available at www.nature.com/reprints. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and
nstitutional affiliations. https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ www.nature.com/scientificreports/ Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the
Creative Commons licence, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons licence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2023 https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 |
|
https://openalex.org/W4221017390
|
https://hal.archives-ouvertes.fr/hal-03578475/file/Sharma-2021-Mitochondrial%20Transport%2C%20Partitioning%20and%20Quality%20Control_preprints202106.0657.v1.pdf
|
English
| null |
Mitochondrial transport, partitioning, and quality control at the heart of cell proliferation and fate acquisition
|
American journal of physiology. Cell physiology
| 2,022
|
cc-by
| 13,323
|
To cite this version: Rakesh Kumar Sharma, Abderrahman Chafik, Giulia Bertolin. Mitochondrial transport, partitioning,
and quality control at the heart of cell proliferation and fate acquisition. American Journal of Physi-
ology - Cell Physiology, 2022, 322 (2), pp.C311-C325. 10.1152/ajpcell.00256.2021. hal-03578475 Distributed under a Creative Commons Attribution 4.0 International License To cite this version: Rakesh Kumar Sharma, Abderrahman Chafik, Giulia Bertolin. Mitochondrial Transport, Partitioning
and Quality Control at the Heart of Cell Proliferation and Fate Acquisition. 2021. hal-03383673 Mitochondrial Transport, Partitioning and Quality
Control at the Heart of Cell Proliferation and Fate
Acquisition
Rakesh Kumar Sharma, Abderrahman Chafik, Giulia Bertolin Rakesh Kumar Sharma, Abderrahman Chafik, Giulia Bertolin HAL Id: hal-03578475
https://hal.science/hal-03578475v1
Submitted on 17 Feb 2022 L’archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d’enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés. HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers. Distributed under a Creative Commons Attribution 4.0 International License Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Correspondence should be addressed to GB: giulia.bertolin@univ-rennes1.fr; Tel: +330223237516 Correspondence should be addressed to GB: giulia.bertolin@univ-rennes1.fr; Tel: +330223237516 Rakesh Kumar Sharma1,*, Abderrahman Chafik1,* and Giulia Bertolin1 akesh Kumar Sharma1,*, Abderrahman Chafik1,* and Giulia Bertolin1 1Univ Rennes, CNRS, IGDR (Genetics and Development Institute of Rennes), UMR 6290, F-35000
Rennes, France
* * These authors equally contributed to this work. * These authors equally contributed to this work. HAL Id: hal-03383673
https://hal-univ-rennes1.archives-ouvertes.fr/hal-03383673
Preprint submitted on 18 Oct 2021 L’archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d’enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés. HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers. Distributed under a Creative Commons Attribution| 4.0 International License Introduction Mitochondria are found in most of the eukaryotic cells and they contribute to many functions
such as ATP generation, β oxidation of fatty acids, and cellular metabolism (1). Mitochondria
are also implicated, among other functions, in reactive oxygen species (ROS) generation and
turnover, in apoptotic pathways, and in calcium signaling (1). Mitochondria are dynamic and
motile organelles (2, 3) that constantly fragment (a mechanism also known as fission) and fuse
(3, 4). Mitochondria also undergo turnover, which comprises selective clearance by mitophagy
when organelles are damaged and biogenesis events to increase the mass of the mitochondrial
network (4). Mitochondrial fission is driven by the binding of Dynamin-1-like protein
(Drp1/DNM1L) to its receptor proteins MFF (mitochondrial fission factor), MID49/51, and/or
FIS1 on the mitochondrial outer membrane (4, 5). Oligomerized DNM1L wraps around
mitochondria by forming a ring that causes Outer Mitochondrial Membrane deformation and
scission (6). Daughter mitochondria obtained after fission may undergo re-fusion with the rest
of the network, or they can be subjected to mitophagy in case their activity is compromised,
such as after the accumulation of deleterious mtDNA mutations, of ROS, or of misfolded
proteins (7). In contrast to fission, mitochondrial fusion is a mechanism in which two
mitochondria fuse together, and the two mitochondrial units share tRNAs, rRNAs, proteins and
matrix metabolites (8). Fusion between Inner Mitochondrial Membranes is mediated by Optic
Atrophy Protein 1 (OPA1), while on the Outer Mitochondrial Membranes (OMM) Mitofusin1
(MFN1), and Mitofusin2 (MFN2) are the key players (9). Mitochondrial fusion and fission
processes are collectively known as mitochondrial dynamics and influence nearly all
mitochondrial functions including respiration, calcium buffering, bioenergetic adaptation, and
apoptosis (10, 11). Here, we will review our current state of the art on how mitochondrial dynamics is involved in
and required for the transport of mitochondria within the cell, and for the effective clearance
of mitochondria under physiological conditions. We will also recapitulate our current
knowledge on the consequences of mitochondrial transport, dynamics and mitophagy failures
for mitochondrial homeostasis, cell stemness and fate acquisition. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Abstract Mitochondria are essential to cell homeostasis, and alterations in mitochondrial distribution,
segregation or turnover have been linked to complex pathologies such as neurodegenerative
diseases or cancer. Understanding how these functions are coordinated in specific cell types is
a major challenge to discover how mitochondria globally shape cell functionality. In this
review, we will first describe how mitochondrial transport and dynamics are regulated
throughout the cell cycle in yeast and in mammals. Second, we will explore the functional
consequences of mitochondrial transport and partitioning on cell proliferation, fate acquisition,
stemness, and on the way cells adapt their metabolism. Last, we will focus on how
mitochondrial clearance programs represent a further layer of complexity for cell
differentiation, or in the maintenance of stemness. Defining how mitochondrial transport,
dynamics and clearance are mutually orchestrated in specific cell types may help our
understanding of how cells can transition from a physiological to a pathological state. 1 Mitochondrial transport and inheritance during cell cycle progression As introduced above, mitochondria play multiple functions and their proper distribution during
cell division is essential for cell survival. However, these organelles can only be generated by
an increase in mitochondrial mass, followed by the separation of pre-existing mitochondria
from the network (16). Therefore, the maintenance of the mitochondrial pool must be
coordinated throughout the cell cycle to ensure the proper distribution of these organelles in
the daughter cells. Mutations in genes encoded by the mitochondrial genome are lethal in
higher vertebrates, thereby limiting our capacity to explore how these mutations might affect
mitochondrial inheritance. To overcome this issue, early studies on mitochondrial inheritance
were performed in baker's yeast (Saccharomyces cerevisiae), and showed that organelle
inheritance is well coordinated with the cell cycle. Actin cables – bundles of F-actin acting as a track for the bidirectional movement of cargo –
are responsible for the transfer of mitochondria from the mother to the bud. In addition, these
cables also arise from the bud tips and undergo continuous movements toward the mother cell
tip. This backwards movement is called retrograde cable flow (RCAF) and as described below,
increased RCAF rates for mitochondria are linked with the fitness of the mitochondria that are
transferred to the bud. In the early stage of the G1 phase, actin starts to polarize, and
mitochondria align with the mother-bud axis. In the S phase and until the G2 phase,
mitochondrial movement occurs towards the bud tip by anterograde linear excursions, and
towards the mother tip by retrograde linear excursions (17, 18). This bidirectional movement
leads to the accumulation of mitochondria into both bud and mother cell tips in an actin-
dependent manner. During the M phase instead, mitochondria are shed from actin and
distributed throughout the bud (17, 18). The mutant yeast strain tpm1∆ lacking a functional
actin stabilizing tropomyosin 1 gene (TPM1) shows abnormal mitochondrial distribution and
morphology (17). Mutations in the actin-encoding gene ACT1 (19), or in the chaperone-
encoding genes CCT4 and CCT6 which are essential for actin folding, cause defects in
mitochondrial morphology and unequal distribution of mitochondria to the daughter cell (19–
21). During cell division, mitochondrial inheritance mechanisms ensure the transfer of
metabolically active mitochondria to the daughter cell, while mitochondria with a highly-
oxidized redox potential are retained in the mother cell and maintain the mother-daughter age
asymmetry in yeast (18, 22). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 with the cytoskeletal protein Kinesin 5 on the other hand (13). MIRO proteins also interact
with the mitochondrial fusion proteins MFN1 and MFN2, thereby linking mitochondrial
dynamics and transport (12, 14). This link is further corroborated by the observation that the
motor protein dynein is critical for DNM1L-mediated fission (15). The disruption of dynein
functions in HeLa cells dramatically changes the organization of the mitochondrial network
and inhibits organelle fission, causing extensive branching and tubular mitochondria (15). However, what are the consequences on cell physiology, metabolism and proliferation if
mitochondrial transport and dynamics are impaired? The interplay of mitochondrial transport and dynamics ensures faithful organelle
distribution. Mitochondria move along the cytoskeleton with the help of the motor proteins and this function
is critical for organelles to orchestrate fission, fusion and quality control events. In specialized
cells as neurons, mitochondrial movements towards the axonal ends are critical for fulfilling
the energy required at synapses. In mammals, mitochondrial movements occur on the
microtubules with the help of motor proteins such as kinesins and dyneins (12, 13). The
recruitment of the motor proteins on the mitochondrial surface is essential for mitochondrial
transport. Typically, these motor proteins are opposite in nature, and the kinesins transport the
mitochondria to the plus end of the microtubule (anterograde), while dynein to the minus end
(retrograde). The adaptor proteins Milton/TRAK help in the anchoring of mitochondria by
motor proteins, as they interact directly with the OMM proteins MIRO 1/2 on one hand, and 2 2 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 essential for the normal RCAF and for mitochondrial inheritance during cell division. Any
perturbation of its functions causes the transfer of mitochondria containing high reactive
oxygen species to daughter cells and reduces yeast lifespan (18, 22, 23). essential for the normal RCAF and for mitochondrial inheritance during cell division. Any
perturbation of its functions causes the transfer of mitochondria containing high reactive
oxygen species to daughter cells and reduces yeast lifespan (18, 22, 23). Last, Altmann et al. showed that the class V myosin motor protein Myo2 is essential for actin-
mediated mitochondrial transport (24). They showed that Myo2 facilitates the binding of
mitochondria to actin, and it helps mitochondrial motility during cell division. Moreover,
mutations in Myo2 that alter the binding of mitochondria to actin cables cause the abnormal
accumulation of mitochondria in the mother cell (24). Although a significant body of evidence
illustrated that mitochondrial delivery and quality control in yeast is mediated by actin
throughout the cell cycle, the majority of the molecular motors involved beyond Myo2 still
remains to be discovered. Last, Altmann et al. showed that the class V myosin motor protein Myo2 is essential for actin-
mediated mitochondrial transport (24). They showed that Myo2 facilitates the binding of
mitochondria to actin, and it helps mitochondrial motility during cell division. Moreover,
mutations in Myo2 that alter the binding of mitochondria to actin cables cause the abnormal
accumulation of mitochondria in the mother cell (24). Although a significant body of evidence
illustrated that mitochondrial delivery and quality control in yeast is mediated by actin
throughout the cell cycle, the majority of the molecular motors involved beyond Myo2 still
remains to be discovered. In mammalian cells, mitochondrial segregation also occurs during mitosis. However, a cross-
talk between the mitochondrial dynamics and the cell cycle machinery begins as early as a cell
commits to cell cycle entry (G0-G1), and both cell cycle progression and mitochondrial division
occur in parallel. During the G1 phase, the biosynthesis of the mitochondrial complexes occurs (25, 26). As the
cell progresses towards the S phase, the levels of Cyclin E increase together with the Cyclin
E-dependent inhibition of DNM1L (27, 28). Mitochondrial transport and inheritance during cell cycle progression Deleting the Mmr1p protein, a member of the DSL1 family that
assists the tethering of mitochondria to the bud, was shown to compromise the quality of
mitochondria delivered to the daughter cell (22). Yeast Sirtuin (SIRT2) was also found to be 3 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/prep Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 causes the aggregation of mitochondria and alter the mitochondrial positioning at this cell cycle
phase (37). These discrepancies may be due to differential incubations with latrunculin A (10
min (34) or 1 h (37)), or they might be intrinsic to the resolution power of the microscopy
setups used to image the samples (Airyscan high-resolution microscopy (37) or conventional
confocal microscopy (34)). Overall, mitochondrial segregation at mitosis is a complex, but well-coordinated process in
mammalian cells: after the release of mitochondria from motor proteins during the early stages
of mitosis, actin cables ensure the uniform distribution of mitochondria prior to cell division. The requirements for mitochondrial transport in proliferating cells and in cells largely in
quiescence share functional similarities, although in specific cell types as neurons the
mechanisms of mitochondrial transport on cytoskeletal tracks have been better characterized. Neurons mostly rely on mitochondrial ATP for their survival, and they maintain a
comparatively higher number of mitochondria than other cell types. Neurons typically have
higher ATP demands at synapses, and this finding is supported by the high amount of
mitochondria that can be found at these locations following their transport from the cell body. Similarly, the dependence of mitochondria on the nuclear genome for organelle-specific
turnover programs necessitates the transport of damaged mitochondria back from the axon and
dendrites to the cell body (38). As in other cell types, mitochondria in neurons travel long-distance along the microtubule
cytoskeleton, and short-distance along the actin network (39). The long-distance transport of
mitochondria along microtubules is facilitated by kinesins and dynein (40). There are three
classes of kinesin motors: the major transporter class Kinesin-1 family (KIF5s – KIF5A, KIF5B
and KIF5C–), the Kinesin-3 family (KIF1B-α) and Kinesin-Like Protein 6 (KLP6) (41, 42). As
introduced above, the loading of kinesins on mitochondria is performed with the help of the
adaptor protein Milton in Drosophila, or the TRAK proteins in mammals. Milton links the
OMM protein dMiro in Drosophila /MIRO1 and MIRO2 in mammals (43) to the cargo binding
domain of KIF5. This complex constituted by MIRO (receptor), KIF5 (motor), and
Milton/TRAKs (adaptors) facilitates the anterograde mitochondrial movement of mitochondria
(36, 42). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 This tips the mitochondrial dynamics balance
towards fusion, and mitochondria appear as a hyper-fused and compact tubular network (27,
28), together with high ATP synthesis capabilities needed for the cell cycle to progress (29). During the S phase, mitochondrial DNA content also increases, thereby reflecting a strong
coordination between nuclear and mitochondrial DNA synthesis processes (30). As the cell
progresses toward mitosis, the levels of Cyclin B increase and the CDK1 (Cyclin-dependent
kinase 1)/Cyclin B complex phosphorylates DNM1L on Ser585 (31) and on Ser616 (32). The
phosphorylation of DNM1L is critical to activate its GTPase activity, leading to the activation
of mitochondrial fission programs during cell division (33) (Fig. 1). From the beginning of the G1 phase and until mitosis, mitochondria are associated with motor
proteins for their transport. After fission at mitosis, mitochondria are released from
microtubules upon the phosphorylation of dynein by CDK1, and of kinesin-1 (Kinesin Heavy
Chain or KHC) by Aurora A/AURKA (31, 34, 35). Interestingly, motor proteins were shown
to be required for mitochondrial fission events during early mitosis. After fission is achieved,
motor shedding is necessary for the symmetric distribution of mitochondria in mammalian cells
(34). The forced attachment of kinesin to mitotic mitochondria causes an asymmetric
mitochondrial distribution in the daughter cells, while the attachment of dynein-bound
mitochondria to the mitotic spindle arrests cell at mitosis (34). This strongly supports the notion
that the release of motor proteins from the mitochondrial membrane is crucial for successful
progression through mitosis (Fig. 2). However, the mechanism of mitochondrial distribution
after the release of motor proteins remains controversial (12, 34, 36). Chung et al. showed that
mitochondrial distribution occurs passively after the release of the motor proteins during
mitosis, and treatment of cultured cells with the actin-depolymerizing agent latrunculin A did
not alter mitochondrial partitioning into the two daughter cells (34). However, Moore et al
showed that mitochondria were associated with a dynamic wave of actin filament during
mitosis, and depolymerizing the actin meshwork with either latrunculin A or cytochalasin D 4 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 TCTEX1 favors the binding of dynein with the OMM protein voltage-dependent anion-
selective channel (VDAC) (50). Then, dynactin binds directly to dynein, and it also binds to
microtubules through its p150Glued component (51). Dynein in complex with dynactin is then
capable to interact with Milton/TRAK2 and MIRO to mediate retrograde mitochondrial
transport (36, 52) (Fig. 3A and B). TCTEX1 favors the binding of dynein with the OMM protein voltage-dependent anion-
selective channel (VDAC) (50). Then, dynactin binds directly to dynein, and it also binds to
microtubules through its p150Glued component (51). Dynein in complex with dynactin is then
capable to interact with Milton/TRAK2 and MIRO to mediate retrograde mitochondrial
transport (36, 52) (Fig. 3A and B). Although most mitochondrial transport takes place on microtubule tracks with the help of
kinesins and dynein, the short distance movements in dendritic spines are orchestrated by
myosins on the actin network (53). As introduced above, myosins are ATP-dependent motor
proteins and out of 18 classes of myosin proteins, Myo-19 (53, 54) and Myo-5 were associated
with mitochondrial transport in mammalian cells, with Myo-5 acting through the SPIRE1 actin-
nucleating protein (55, 56). Both Myo-19 and Myo-5 were shown to bind to MIRO proteins to
facilitate the mitochondrial transport (36) (Fig. 3C). However, the involvement of these motors
in specific cells as neurons remains to be fully elucidated. Mitochondrial transport is crucial for the survival of neurons and for the maintenance of
synapses. Perturbations of mitochondrial transport have been linked to neurodegenerative
diseases such as Alzheimer’s (57–61) and Parkinson's (62–66), amyotrophic lateral sclerosis
(67–70), schizophrenia (71, 72) and Huntington's diseases (73–75). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/prep Although the complete mechanism of mitochondrial transport by KIF1B-α and KLP6
motor proteins is not well understood yet, their loading on mitochondria appears to be
facilitated by the adaptor protein KBP (kinesin binding protein) (44, 45). Impairing the function
of KLP6 by RNAi in C. elegans was shown to cause an alteration of mitochondrial morphology
(46). Similarly, HeLa and Neuro-2a cells expressing a mutant KLP6 construct lacking the
motor domain showed altered mitochondrial morphology and an inhibited transport of
mitochondria in neurites of differentiated Neuro-2a cells (46) (Fig. 3A). The retrograde mitochondrial motion in neurons is driven by the dynein motor complex and its
partner dynactin (47). The dynein motor is a multimeric protein consisting of two heavy chains
(DHC), several intermediate chains (DICs) and dynein light intermediate chains (DLICs), and
dynein light chains (DLC) (47–49). The dynein heavy chains act as the motor, and the other
subunits participate to the association of the dynein motor with the cargo and in regulating the
mobility of dynein along the microtubule tracks. However, the large structure of dynein
complexifies experimental analyses, and the dynein-mediated mitochondrial transport
mechanism has not been fully elucidated yet. One study suggests that the DLC protein 5 The transport of mitochondria among cell populations as a potential route to adapt cell
metabolism and contribute to chemoresistance in cancer The transport of mitochondria among cell populations as a potential route to adapt cell
metabolism and contribute to chemoresistance in cancer Metabolic adaptation is an essential aspect for survival in the adverse tumor microenvironment,
where every cell is undergoing multiple rounds of uncontrolled cell division. In such a
competitive environment for nutrients availability, it is challenging to fulfill both substrate and
energy requirements. Mitochondria play an essential role by fueling the energy requirements
of the cancer cell by using various substrates, maintaining a pool of cancer stem cells, and
helping in the development of metastasis (79–81). However, it is not clear whether the role(s)
of mitochondria in these processes is played by the entire mitochondrial network within a
particular cell population, or it is due to an exchange of mitochondria among the various cell
populations constituting a tumor. It has been shown that mitochondria can be transferred from
adult stem cells and/or somatic cells to defective cells with no mitochondrial DNA (r0 cells)
(82, 83). This transfer restores aerobic respiration in r0 cells, and provided the first evidence
of mitochondrial transfer between two cell populations (82). After this report, mitochondrial
transfer was shown to occur under various paradigms: from the pluripotent mesenchymal stem
cells to lung epithelial cells to protect from cigarette smoke-induced damage (84); from
mesenchymal stem cells to epithelial cells to protect the injured cells in ischemia-reperfusion
models (85, 86); from mesenchymal stem cells to rotenone-stressed mitochondrial myopathy,
encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) fibroblasts to rescue
their bioenergetics capabilities (87). Furthermore, the transfer of dysfunctional mitochondria
from neurons to astrocytes and the consequent clearing of defective mitochondria within the
astrocytes (88) was shown to provide neuroprotection in an animal model of stroke. In the
context of cancer, the transfer of mitochondria was shown to occur from endothelial cells to
cancer cells (89), and from bone marrow stromal cells to leukemic cells (90). This transfer
protects the cancer cells from apoptosis and increases its chemoresistance. Last, the
intracellular transfer of functional mitochondria from a highly invasive bladder cancer cells
increases their metastatic and invasive properties, and results in an increased tumor size in a
T24 xenograft mice model (91). The transport of mitochondria to active sites of inflammation or metastasis was also shown to
be key to disease progression. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.06 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 different sets of “aged” mitochondria (78). Based on the relative content of aged mitochondria,
lymphocytes will enter separate metabolic pathways. The cells that follow PI3K-dependent
catabolic pathways were shown to contain “younger” mitochondria, to clear damaged
organelles more efficiently and self-renew as naive stem cells. On the contrary, cells following
AMPK-related anabolic pathways contain more “aged” mitochondria and undergo senescence
(78). Although the respective molecular mechanisms and the player involved still remain to be
fully understood, these studies show that the asymmetric partitioning of mitochondria is key to
cell metabolism, together with the capacity of the cell to maintain stemness in specific cell
types. Asymmetric mitochondrial inheritance during mitosis and its link to stemness In general, somatic cell division show a symmetric distribution of mitochondria into the two
daughter cells, which receive comparable amounts of mitochondria with similar membrane
potential levels. DNM1L-mediated mitochondrial fission is critical for the correct distribution
of mitochondria in the daughter cells. AURKA and the Cyclin B/CDK1 complex, together with
RALA (small Ras-like GTPase) and its adaptor and RALBP1 were shown to be key for
mitochondrial fission at mitosis. AURKA phosphorylates RALA at Ser194 and upon
phosphorylation, RALA localizes to mitochondria and favors the localization of its effector
RALBP1 and of DNM1L itself to this compartment (32). Impairing this cascade of events alters
DNM1L-dependent mitochondrial fission, resulting in the asymmetric segregation of
mitochondria in the two daughter cells (32). Unlike in somatic cells, the uneven distribution of “aged” mitochondria often occurs during the
asymmetric cell division of stem cells. One of the daughter cells receives the majority of newly-
synthesized mitochondria and maintains the stem cell fate, while the daughter cell receiving a
higher proportion of “aged” mitochondria will acquire a differentiated, non-stem fate (76). In
addition, the inhibition of DNM1L-mediated mitochondrial fission events in the stem cell
blocks the asymmetrical distribution of “old” mitochondria, leading to the loss of stem cell
properties (76). Therefore, mitochondrial fission is also crucial for the maintenance of the stem
cell phenotype. A similar study showed that the alteration of mitochondrial dynamics, or the
presence of mitochondrial stress during the division of hematopoietic stem cells (HSCs) causes
the asymmetric distribution of mitochondria in the daughter cells (77). The cells receiving
dysfunctional mitochondria fail to manage the biosynthetic demands needed to progress
throughout the cell cycle, and undergo replicative senescence (77). Another study illustrated
that LPS-activated lymphocytes divide asymmetrically, and give rise to daughter cells having 6 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 However, the involvement of mitochondrial transport and its role in providing ATP for
cell migration has been neglected. A study on epithelial breast cancer cell lines shows that the
localization of mitochondria to the leading edge of the migrating cell increases the migration
velocity and helps directional persistence (99). Similarly to the impact of mitochondrial fission
for lymphocyte migration (94), promoting mitochondrial fusion by overexpressing OPA1,
blocking fission by overexpressing a dominant-negative form of DNM1L (DNM1LK38A) or
impairing mitochondrial transport using a MIRO1 shRNA slow down the migration of cancer
cells (99). These data further corroborate the importance of mitochondrial dynamics and
transport in cancer metastasis, although our current view of the importance of their interplay
for cancer progression is still partial. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 process that requires high quantities of ATP for lymphocytes to adhere, contract and perform
protrusions. In this light, mitochondria play a crucial role in lymphocyte migration (94):
mitochondrial fission and redistribution were shown to be critical for migration, while an
increase in mitochondrial fusion slows down this process (94). process that requires high quantities of ATP for lymphocytes to adhere, contract and perform
protrusions. In this light, mitochondria play a crucial role in lymphocyte migration (94):
mitochondrial fission and redistribution were shown to be critical for migration, while an
increase in mitochondrial fusion slows down this process (94). process that requires high quantities of ATP for lymphocytes to adhere, contract and perform
protrusions. In this light, mitochondria play a crucial role in lymphocyte migration (94):
mitochondrial fission and redistribution were shown to be critical for migration, while an
increase in mitochondrial fusion slows down this process (94). Similarly, cell migration is a characteristic feature of cancer cells that allows them to
metastasize away from the primary site of the tumor (95). Cytoskeletal proteins are known to
be crucial for cell migration and cancer metastasis, and many dugs developed to target
cytoskeletal stability and functions are under investigation and show promising results (96–
98). However, the involvement of mitochondrial transport and its role in providing ATP for
cell migration has been neglected. A study on epithelial breast cancer cell lines shows that the
localization of mitochondria to the leading edge of the migrating cell increases the migration
velocity and helps directional persistence (99). Similarly to the impact of mitochondrial fission
for lymphocyte migration (94), promoting mitochondrial fusion by overexpressing OPA1,
blocking fission by overexpressing a dominant-negative form of DNM1L (DNM1LK38A) or
impairing mitochondrial transport using a MIRO1 shRNA slow down the migration of cancer
cells (99). These data further corroborate the importance of mitochondrial dynamics and
transport in cancer metastasis, although our current view of the importance of their interplay
for cancer progression is still partial. Similarly, cell migration is a characteristic feature of cancer cells that allows them to
metastasize away from the primary site of the tumor (95). Cytoskeletal proteins are known to
be crucial for cell migration and cancer metastasis, and many dugs developed to target
cytoskeletal stability and functions are under investigation and show promising results (96–
98). The transport of mitochondria among cell populations as a potential route to adapt cell
metabolism and contribute to chemoresistance in cancer Lymphocyte migration is vital for adequate immunological
response at the site of injury or inflammation, and it is guided by the cytokines or chemokines
released at the site of the injury (92, 93). Lymphocyte migration is an energy-consuming 7 Mechanisms of mitophagy in red blood cells The maturation of erythroblasts into mature red blood cells is a process commonly known as
terminal erythropoiesis. It starts in the bone marrow within erythroblastic islands, which consist
of a central macrophage surrounded by erythroblasts, and it ends in the bloodstream, where
reticulocytes complete their maturation in approximately two days (106, 107). The maturation
of erythroblasts into red blood cells leads to profound changes in cell morphology, such as the
loss of nearly 20% of the plasma membrane surface area, an overall reduced cell volume, the
increased association of the cytoskeleton with the outer plasma membrane, enucleation and the
loss of all residual cytoplasmic organelles, such as the Golgi apparatus, the endoplasmic
reticulum (ER), mitochondria and ribosomes (106). The disappearance of mitochondria during terminal erythropoiesis gathered significant
attention after the discovery that the main mechanism of mitochondrial clearance in
erythroblast maturation is mitophagy (107). During the final step of erythroid differentiation
LC3, an ubiquitin-like modifier required for the growth of autophagosomal membranes is
converted from its unmodified form – known as LC3-I – to a lipidated form, LC3-II (108). The
presence of autophagy during erythroid differentiation was confirmed by the work of
Mortensen et al, where it was shown that the conditional knockout of the essential autophagy
gene ATG7 in mouse erythrocytes induces the accumulation of damaged mitochondria with
altered membrane potential (ΔΨm), increased susceptibility to cell death and anemia (109). During erythroblast maturation, it was shown that the outer mitochondrial membrane protein
NIP3-like protein X (NIX), also named Bcl-2/adenovirus E1B 19 kDa interacting protein 3-
like (BNIP3L) induces a loss of ΔΨm and the recruitment of LC3 to mitochondria (110). These
events target mitochondria to autophagosomes for clearance during erythroid maturation. At
the molecular level, NIX plays the role of a mitophagy receptor by recruiting LC3 and its
cognate protein GABARAP, to damaged mitochondria through its amino-terminal LC3-
interacting region (LIR) (111). Mice lacking the NIX:LC3/GABARAP interaction showed an
altered mitochondrial clearance in maturing reticulocytes, a restored ΔΨm, altered erythroid
maturation, and anemia. Other proteins were also shown to play a role in erythroid maturation, such as the serine-
threonine kinase ULK1 (Uncoordinated 51-Like Autophagy Activating Kinase 1). ULK1
deficiency was shown to delay the clearance of mitochondria in mouse reticulocytes and
embryonic fibroblasts (112). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 In the sections below, we will review our current knowledge on the main mechanisms of basal
mitophagy, and explore the consequences of impaired mitophagy for cell proliferation,
stemness and fate acquisition. In the sections below, we will review our current knowledge on the main mechanisms of basal
mitophagy, and explore the consequences of impaired mitophagy for cell proliferation,
stemness and fate acquisition. Mitochondrial quality control as a requirement for cell differentiation, fate acquisition
and stemness. As introduced above, the capacity of cells to activate and achieve the clearance of dysfunctional
mitochondria is key to cell physiology, and organelle turnover heavily relies on mitochondrial
dynamics and transport (100). Mitochondria are selectively cleared by mitophagy, an
organelle-specific autophagy pathway (101, 102). In mitophagy, dysfunctional mitochondria
are engulfed in a double-membrane vesicles known as autophagosomes and then degraded by
lysosomes. Mitochondrial quality control begins before the entry into the cell cycle, as cells
with defective mitochondria were shown to remain in G0 (103). Interestingly, an in vivo study
in Drosophila showed that the disruption of mitochondrial complex I functions can
compromise mitochondrial membrane potential, ATP synthesis, and it causes G1-S arrest
(104). A recent report linked the PINK1/PARKIN mitophagy pathway and a successful cell
cycle progression. Upon widespread mitochondrial dysfunction, induced by incubating cells
with an oligomycin/antimycin cocktail, the PINK1/PARKIN pathway was shown to sequester
the mitotic Tank Binding Kinase 1 (TBK1) to damaged mitochondria. Genetic ablation or
pharmacological inhibition of TBK1 triggered cell cycle arrest at mitosis (105). These studies
suggest that mitochondrial quality control is a prerequisite for cell cycle entry and progression. Whether these events are important also in physiological paradigms of mitophagy, and whether
the mitochondrial transport machinery is involved in basal quality control events is currently a
matter of intense investigation in the field. 8 8 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/prepr Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 as RB1CC1, the formation of BECN1-PtdIns3K complexes, and it ultimately inhibits
mitophagy. Mitochondria not undergoing mitophagy display excessive mitochondrial ROS
levels and overall oxidative stress, which was proposed to cause the destruction of erythrocytes
by hemolysis. Although ATG7 and ULK1 were shown to play key roles in mitophagy during
terminal erythropoiesis, their absence does not completely abolish mitochondrial turnover, and
it suggests the existence of an alternative pathway that can be implicated in this process (112,
114, 115). In this optic, RAB9A, a member of the Rab GTPase family implicated in endosome
trafficking (116), was shown to trigger mitophagy activation in erythroid leukemic cell lines
and in vivo even when the canonical, ATG7-dependent autophagy pathway is blocked (115,
117) (Fig. 4). However, further studies are required to understand the spatiotemporal activation
of these two pathways in physiological conditions. Mitochondrial elimination by mitophagy during the maturation of red blood cells is an
important process, and its deficiency is associated with many diseases such as myelodysplastic
syndromes anemia and sickle cell disease (118, 119). This is why investigating the mechanisms
and actors implicated in the clearance of mitochondria from red blood cells is necessary to
unravel how this process is compromised in patients, and may help developing new therapeutic
strategies. Mechanisms of mitophagy in red blood cells The mitophagy-inducing function of ULK1 during erythroid
maturation was shown to require AMPK activity, and more specifically the activity of the a1
isoform (PRKAA1) (113). The lack of PRKAA1 activity (by PRKAA1 inactivation or gene
deletion in mice erythroid precursors) decreases ULK1 phosphorylation on Ser555, a key
modification required for the nucleation of autophagic vesicles. The absence of this
phosphorylation prevents the direct association of ULK1 with autophagy-related partners such 9 Basal mitophagy in Drosophila, C. elegans and mice: paternal mitophagy after fertilization Despite the fact that spermatozoan mitochondria are found in the oocyte upon fertilization, only
maternal mitochondria are inherited in the majority of eukaryotic species (128). Several reports
have shown that paternal mitochondria sperm-derived (PMS) are eliminated shortly after
fertilization. In mice, PMS disappear from embryos during the 4-cell to 8-cell stage transition
(129). In 2011, Sato and Sato demonstrated that the elimination of PMS in C. elegans requires
autophagy, as PMS were maintained in zygotes with defective autophagy, and they were
detectable even at the first larval stage (130). By following the expression of LGG-1 and LGG-
2, the C. elegans homologs of LC3, Rawi et al. showed that the entry of the spermatozoan
organelles into the oocyte upon fertilization triggers an autophagy response (131). Under these
conditions, structures positive for LGG-1 and LGG-2 were found to surround PMS. Similarly,
several autophagosomal markers such as LC3, GABARAP, SQSTM1 and Lys63-positive
ubiquitin chains were found in the vicinity of ubiquitinated PMS in the fertilized mouse oocyte
and corroborating the role of autophagy for the clearance of paternal mitochondria (131). However, the molecular mechanisms of mitochondrial turnover seem to partially differ among
species, as mammalian PMS are ubiquitinated while C. elegans sperm mitochondria are not
(131, 132). The elimination of paternal mitochondria has been also shown to occur in Drosophila. Transgenic flies with fluorescently-tagged sperm mitochondria revealed that PMS disappear
90 minutes after egg laying (133). Eggs fertilized by DJ-GFP, a fluorescent sperm-specific
mitochondrial protein, and maternally expressing the fluorescent autophagy reporter mCherry-
Atg8, the Drosophila homolog of LC3, showed a localization of Atg8-positive vesicles in the
vicinity of DJ-positive paternal mitochondria, which start to be degraded 30 minutes after egg
laying. In contrast to C. elegans, ubiquitination seems to be required for paternal mitochondrial
clearance in Drosophila. Directly after fertilization, PMS are ubiquitinated and SQSTM1, an
autophagy receptor recognizing ubiquitylated proteins (134), is recruited to the PMS. While
PARKIN does not appear to be involved in the paternal clearance of mitochondria
in Drosophila, it seems to be required for the mammalian turnover of PMS (133, 135). Recently, Prohibitin 2 (PHB2) an inner mitochondrial membrane protein has been found to
function as a key mitophagy receptor for PARKIN-mediated mitophagy in mammalian cells
and to play a critical role in the elimination of paternal mitochondria in C. elegans (136). By
following the fate of paternal mitochondria stained by MitoTracker Red in fertilized C. Mitophagy in Stem Cell Maintenance and Differentiation As described above, the correct maintenance of the blood system is critical to homeostasis. In
addition to the mitophagy mechanisms regulating terminal erythropoiesis, HSCs continuously
repress oxidative metabolism and eliminate active mitochondria via mitophagy to remain in a
quiescent state (120). HSCs were shown to rely on anaerobic glycolysis for their energy needs,
and this is a potential strategy used by the stem cell to prevent the accumulation of high levels
of ROS that can lead to blood aging phenotypes (121, 122). It has been demonstrated that
mitophagy in HSCs involves the autophagy factor ATG12 (120). The knockout of ATG12 in
mice HSCs induces an increase in the total number of mitochondria, which were shown to
adopt an elongated morphology. Under these conditions, HSCs also display an increased
mitochondrial membrane potential compared to the controls, revealing an accumulation of
active mitochondria which cannot undergo ATG12-mediated autophagic degradation. In a
parallel study, Ito et al. have demonstrated that Tie2+ HSCs, a subpopulation of mouse HSCs,
can maintain their stemness potential by upregulating a PINK1/PARKIN-dependent mitophagy
program (123). Complementary data show that the absence of PINK1 in mouse embryonic
fibroblasts (MEFs) lowers their capacity to be reprogrammed into induced pluripotent stem
cells (iPSCs) and conversely, PINK1-deficient iPSCs tend to spontaneously differentiate and
to lose their ability to maintain stemness proprieties (124). In addition, the overall
reprogramming of MEFs into iPSCs was recently associated with a decrease in mitochondrial
mass and an increase of BNIP3L/NIX-dependent mitophagy, and this independently of a ΔΨm
loss (125). Mitophagy has also been shown to be implicated in the differentiation of mouse neuroblast
stem cells into retinal ganglion cells (RGCs). This process has been found to involve NIX- 10 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprint Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 dependent mitophagy induced by hypoxia to eliminate mitochondria and shift their metabolism
from mitochondrial respiration towards glycolysis (126). In muscle differentiation, mitophagy
was also found to play a role in differentiating primitive myoblasts into mature myotubes (127). This was shown to require mitochondrial network remodeling and the induction of SQSTM1
(sequestosome1)-mediated mitophagy. Mitophagy in this model temporally occurs before the
biogenesis of new mitochondria, and this transition parallels a metabolic shift: myoblasts were
found to be mainly in a glycolytic state, while mature myotubes switch to oxidative
phosphorylation. Basal mitophagy in Drosophila, C. elegans and mice: paternal mitophagy after fertilization Basal mitophagy in Drosophila, C. elegans and mice: paternal mitophagy after fertilization Conclusions and open questions. Our knowledge on how mitochondrial dynamics, transport and mitophagy are orchestrated in
specific cell types and in physiological conditions is core to our understanding of how cell
homeostasis is maintained. These functions are not only required to maintain proper
mitochondrial functionality, but they also allow the correct partitioning of the mitochondrial
pool to daughter cells during cell division. In addition, the molecular machineries involved in
maintaining these mitochondrial functions were shown to directly participate to the acquisition
of cell fate and stemness, and to regulate the overall metabolic capacity of the cell. Failure in
regulating these functions by altering the abundance of the molecular players involved has been
linked to pathological conditions, such as neurodegenerative disorders or cancer. Although the importance of mitochondrial dynamics, transport or clearance is increasingly
clear, our knowledge of how these functions are mutually connected at the physiological level
remains partial. Recent data shed light on paradigms and molecular actors of basal, piecemeal
mitophagy in mammalian cells, which appears to be turned on when cells rely on oxidative
phosphorylation for ATP production (138, 139). So far, the major players appear to be ATG8
proteins, SQSTM1 and the import protein SAMM50, while no involvement of PINK1 or of
DNM1L has been found (138, 139). Therefore, piecemeal mitophagy seems to be different
from the physiological clearance of paternal mitochondria, which utilizes the PINK1/PARKIN
pathway and mitochondrial dynamics actors instead (135). However, differences in the
abundance of proteins regulating mitochondrial dynamics can be observed in SAMM50-
induced piecemeal mitophagy (139). Whether this is directly linked to a mitochondrial
transport impairment or a chronic protein import deficiency still remains to be ruled out. Together, it appears that several paradigms of physiological mitophagy exist, each of them
being activated in specific cell types or metabolic conditions, and each of them showing a
unique set of molecular actors only partially shared with the other ones. Whether these
paradigms all rely on an efficient transport machinery still remains to be determined. In conclusion, the link between physiological paradigms of mitophagy and their relationship to
organelle transport still remains to be fully elucidated, together with the importance that these
processes have for mitochondrial segregation at cell division in both symmetrically- and
asymmetrically-dividing cells. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 oocytes, it has been shown, that the knockdown of PHB2 in spermatozoids impaired paternal
mitochondrial clearance. In this study, it was shown that PHB2 has an LC3-interacting motif
allowing it to bind to LC3 during mitophagy. However, PHB2 is an inner mitochondrial
membrane protein and its interaction with LC3 requires its exposure to the cytosol. Indeed, it
was demonstrated that a proteasome-dependent OMM rupture is necessary for the interaction
between PHB2 and active, lipidated LC3 (LC3-II) (136). These findings were further
corroborated in vivo, as paternal mitochondria were shown to undergo depolarization and a
ruptured OMM upon the entry of the PMS into the oocyte in C. elegans (137). Basal mitophagy in Drosophila, C. elegans and mice: paternal mitophagy after fertilization elegans 11 Conclusions and open questions. Last, future studies are needed to explore how the adaptation of
cellular and mitochondrial metabolism can shape mitochondrial transport and basal mitophagy
pathways, and the consequences that this metabolic adaptation has for cell proliferation or 12 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 doi:10.20944/preprints202106.0657.v1 quiescence, differentiation or stemness, and fate acquisition in physiological and pathological
conditions. quiescence, differentiation or stemness, and fate acquisition in physiological and pathological
conditions. 13 reprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Figures and figure legends
Fig. 1. Changes in mitochondrial dynamics during cell cycle. The levels of Cyclin E increase
during S phase, and this inhibits DNM1L-mediated mitochondrial fission in favor of fusion. The resulting hyper-fused mitochondria have high ATP synthesis capabilities, that sustain
cycle progression. At mitosis, Cyclin B/CDK1 activate DNM1L by phosphorylating it on
Ser585 and Ser616 residue. These modifications cause mitochondrial fission, which is
mandatory for cells to progress throughout mitosis. Figure assembled using templates freely
available on https://bioicons.com/ and on https://smart.servier.com/) Fig. 1. Changes in mitochondrial dynamics during cell cycle. The levels of Cyclin E increase
during S phase, and this inhibits DNM1L-mediated mitochondrial fission in favor of fusion. The resulting hyper-fused mitochondria have high ATP synthesis capabilities, that sustain
cycle progression. At mitosis, Cyclin B/CDK1 activate DNM1L by phosphorylating it on
Ser585 and Ser616 residue. These modifications cause mitochondrial fission, which is
mandatory for cells to progress throughout mitosis. Figure assembled using templates freely
available on https://bioicons.com/ and on https://smart.servier.com/) 14 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Fig. 2. The release of motor proteins from mitochondria during mitosis is essential for
successful cell cycle progression (A) CDK1 causes the phosphorylation of dynein, which
causes release of mitochondria from this motor. (B) Inhibiting the release of mitochondria from
dynein, or the forced attachment of dynein to mitochondria causes cell cycle arrest at mitosis. (C) Aurora A/AURKA causes phosphorylation of kinesins, which causes the release of
mitochondria from the motor protein. (D) Inhibiting the release of mitochondria from kinesins,
or the forced attachment of kinesins to mitochondria causes the asymmetric distribution of Fig. 2. The release of motor proteins from mitochondria during mitosis is essential for
successful cell cycle progression (A) CDK1 causes the phosphorylation of dynein, which
causes release of mitochondria from this motor. Conclusions and open questions. (B) Inhibiting the release of mitochondria from
dynein, or the forced attachment of dynein to mitochondria causes cell cycle arrest at mitosis. (C) Aurora A/AURKA causes phosphorylation of kinesins, which causes the release of
mitochondria from the motor protein. (D) Inhibiting the release of mitochondria from kinesins,
or the forced attachment of kinesins to mitochondria causes the asymmetric distribution of 15 mitochondria at mitosis. Figure assembled using templates freely available on
https://bioicons.com/ and on https://smart.servier.com/)
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 doi:10.20944/preprints202106.0657.v1 mitochondria at mitosis. Figure assembled using templates freely available on
https://bioicons.com/ and on https://smart.servier.com/) mitochondria at mitosis. Figure assembled using templates freely available on
https://bioicons.com/ and on https://smart.servier.com/) mitochondria at mitosis. Figure assembled using templates freely available on
https://bioicons.com/ and on https://smart.servier.com/) 16 16 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Fig. 3. Mitochondrial transport in neurons. (A) Mitochondrial transport is carried by dynein
and kinesins. Due to the difference in polarity of microtubules in axon, mitochondrial
anterograde movement is carried by kinesins, and retrograde movement by dynein. (B)
Microtubule in dendrite have mixed polarity and unlike in axons, both anterograde and
retrograde movements are facilitated by dynein. (C) Short-distance mitochondrial transport in
the actin-rich dendritic spines is performed by myosins. Mitochondria previously traveling on Fig. 3. Mitochondrial transport in neurons. (A) Mitochondrial transport is carried by dynein
and kinesins. Due to the difference in polarity of microtubules in axon, mitochondrial
anterograde movement is carried by kinesins, and retrograde movement by dynein. (B)
Microtubule in dendrite have mixed polarity and unlike in axons, both anterograde and
retrograde movements are facilitated by dynein. (C) Short-distance mitochondrial transport in
the actin-rich dendritic spines is performed by myosins. Mitochondria previously traveling on 17 doi:10.20944/preprints202106.0657.v1 microtubule tracks can be transferred to myosin motors, which facilitate their anchoring on
actin tracks. Figure assembled using templates freely available on https://bioicons.com/ and on
https://smart.servier.com/) microtubule tracks can be transferred to myosin motors, which facilitate their anchoring on
actin tracks. Figure assembled using templates freely available on https://bioicons.com/ and on
https://smart.servier.com/) 18 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Fig. 4. Mitochondrial elimination by mitophagy during the maturation of red blood cells. Conflicts of Interest The authors declare no conflict of interest. Funding This work was supported by the Centre National de la Recherche Scientifique (CNRS), the
Ligue Contre le Cancer Comités d’Ille et Vilaine, et du Finistère, and the Association pour la
Recherche Contre le Cancer (ARC) to G.B. R.K.S. was supported by a fellowship from the
Brittany region, France (Région Bretagne). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Author Contributions Author Contributions
R.K.S. and A.C. wrote the manuscript; G.B. conceptualized, wrote and reviewed the
manuscript and provided funding. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Conclusions and open questions. When red blood cell maturation is not perturbed, mitochondrial elimination by mitophagy
occurs following two pathways: a NIX/BNI3PL-dependent mitophagy, and a RAB9A-
dependent clearance. NIX/BNI3PL induces mitochondrial depolarization and recruitment of
LC3 on autophagosomal membranes, followed by degradation of the cargo. RAB9A-dependent
mitophagy was also shown to occur in parallel. In case of ATG7 deficiency, altered and
depolarized mitochondria accumulate in erythrocytes, while ULK1 deficiency results in
delayed mitochondrial clearance. Mitochondria not undergoing mitophagy display excessive
mitochondrial ROS levels and overall oxidative stress, which was proposed to be the leading
cause for the destruction of erythrocytes by hemolysis and anemia. Figure assembled using
templates freely available on https://bioicons.com/ and on https://smart.servier.com/) ndrial elimination by mitophagy during the maturation of red blood cells. Fig. 4. Mitochondrial elimination by mitophagy during the maturation of red blood cells. When red blood cell maturation is not perturbed, mitochondrial elimination by mitophagy
occurs following two pathways: a NIX/BNI3PL-dependent mitophagy, and a RAB9A-
dependent clearance. NIX/BNI3PL induces mitochondrial depolarization and recruitment of
LC3 on autophagosomal membranes, followed by degradation of the cargo. RAB9A-dependent
mitophagy was also shown to occur in parallel. In case of ATG7 deficiency, altered and
depolarized mitochondria accumulate in erythrocytes, while ULK1 deficiency results in
delayed mitochondrial clearance. Mitochondria not undergoing mitophagy display excessive
mitochondrial ROS levels and overall oxidative stress, which was proposed to be the leading
cause for the destruction of erythrocytes by hemolysis and anemia. Figure assembled using
templates freely available on https://bioicons.com/ and on https://smart.servier.com/) 19 References 1. Osellame LD, Blacker TS, Duchen MR. Cellular and molecular mechanisms of
mitochondrial function. Best Pract Res Clin Endocrinol Metab 26: 711–723, 2012. doi:
10.1016/j.beem.2012.05.003. 2. Lewis MR, Lewis WH. Mitochondria (and other cytoplasmic structures) in tissue cultures. Am J Anat 17: 339–401, 1915. doi: https://doi.org/10.1002/aja.1000170304. 3. Tilokani L, Nagashima S, Paupe V, Prudent J. Mitochondrial dynamics: overview of
molecular mechanisms. Essays Biochem 62: 341–360, 2018. doi: 10.1042/EBC20170104. 4. Murata D, Arai K, Iijima M, Sesaki H. Mitochondrial division, fusion and degradation. J
Biochem (Tokyo) 167: 233–241, 2020. doi: 10.1093/jb/mvz106. 5. Twig G, Elorza A, Molina AJA, Mohamed H, Wikstrom JD, Walzer G, Stiles L, Haigh
SE, Katz S, Las G, Alroy J, Wu M, Py BF, Yuan J, Deeney JT, Corkey BE, Shirihai OS. Fission
and selective fusion govern mitochondrial segregation and elimination by autophagy. EMBO J 27:
433–446, 2008. doi: 10.1038/sj.emboj.7601963. 6. Kraus F, Ryan MT. The constriction and scission machineries involved in mitochondrial
fission. J Cell Sci 130: 2953–2960, 2017. doi: 10.1242/jcs.199562. 7. Ni HM, Williams JA, Ding WX. Mitochondrial dynamics and mitochondrial quality control. Redox Biol 4: 6–13, 2015. doi: 10.1016/j.redox.2014.11.006. 8. Youle RJ, Bliek AM van der. Mitochondrial Fission, Fusion, and Stress. Science 337: 1062–
1065, 2012. doi: 10.1126/science.1219855. 9. Westermann B. Mitochondrial fusion and fission in cell life and death. Nat Rev Mol Cell Biol
11: 872–884, 2010. 10. Twig G, Shirihai OS. The interplay between mitochondrial dynamics and mitophagy. Antioxid Redox Signal 14: 1939–1951, 2011. doi: 10.1089/ars.2010.3779. 11. Suen D-F, Norris KL, Youle RJ. Mitochondrial dynamics and apoptosis. Genes Dev 22:
1577–1590, 2008. doi: 10.1101/gad.1658508. 12. Moore AS, Holzbaur EL. Mitochondrial-cytoskeletal interactions: dynamic associations that
facilitate network function and remodeling. Curr Opin Physiol 3: 94–100, 2018. doi: 20 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 10.1016/j.cophys.2018.03.003. 13. Fransson \AAsa, Ruusala A, Aspenström P. The atypical Rho GTPases Miro-1 and Miro-2
have essential roles in mitochondrial trafficking. Biochem Biophys Res Commun 344: 500–510, 2006. doi: 10.1016/j.bbrc.2006.03.163. 14. Misko A, Jiang S, Wegorzewska I, Milbrandt J, Baloh RH. Mitofusin 2 Is Necessary for
Transport of Axonal Mitochondria and Interacts with the Miro/Milton Complex. J Neurosci 30: 4232–
4240, 2010. doi: 10.1523/JNEUROSCI.6248-09.2010. 15. Varadi A, Johnson-Cadwell LI, Cirulli V, Yoon Y, Allan VJ, Rutter GA. Cytoplasmic
dynein regulates the subcellular distribution of mitochondria by controlling the recruitment of the
fission factor dynamin-related protein-1. J Cell Sci 117: 4389–4400, 2004. doi: 10.1242/jcs.01299. 16. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 mitochondrial state achieved at G1-S regulates cyclin E buildup and entry into S phase. Proc Natl
Acad Sci U S A 106: 11960–11965, 2009. doi: 10.1073/pnas.0904875106. mitochondrial state achieved at G1-S regulates cyclin E buildup and entry into S phase. Proc Natl
Acad Sci U S A 106: 11960–11965, 2009. doi: 10.1073/pnas.0904875106. 28. Horbay R, Bilyy R. Mitochondrial dynamics during cell cycling. Apoptosis 21: 1327–1335,
2016. doi: 10.1007/s10495-016-1295-5. 29. Sweet S, Singh G. Changes in mitochondrial mass, membrane potential, and cellular
adenosine triphosphate content during the cell cycle of human leukemic (HL- 60) cells. J Cell Physiol
180: 91–96, 1999. doi: 10.1002/(SICI)1097-4652(199907)180:1<91::AID-JCP10>3.0.CO;2-6. 30. Lee S, Kim S, Sun X, Lee JH, Cho H. Cell cycle-dependent mitochondrial biogenesis and
dynamics in mammalian cells. Biochem Biophys Res Commun 357: 111–117, 2007. doi:
10.1016/j.bbrc.2007.03.091. 31. Taguchi N, Ishihara N, Jofuku A, Oka T, Mihara K. Mitotic Phosphorylation of Dynamin-
related GTPase Drp1 Participates in Mitochondrial Fission*. J Biol Chem 282: 11521–11529, 2007. doi: 10.1074/jbc.M607279200. 32. Kashatus DF, Lim KH, Brady DC, Pershing NLK, Cox AD, Counter CM. RALA and
RALBP1 regulate mitochondrial fission at mitosis. Nat Cell Biol 13: 1108–1117, 2011. doi:
10.1038/ncb2310. 33. Kashatus DF, Lim KH, Brady DC, Pershing NLK, Cox AD, Counter CM. RALA and
RALBP1 regulate mitochondrial fission at mitosis. Nat Cell Biol 13: 1108–1117, 2011. doi:
10.1038/ncb2310. 34. Chung JYM, Steen JA, Schwarz TL. Phosphorylation-Induced Motor Shedding Is Required
at Mitosis for Proper Distribution and Passive Inheritance of Mitochondria. Cell Rep 16: 2142–2155,
2016. doi: 10.1016/j.celrep.2016.07.055. 35. Lee S, Kim S, Sun X, Lee JH, Cho H. Cell cycle-dependent mitochondrial biogenesis and
dynamics in mammalian cells. Biochem Biophys Res Commun 357: 111–117, 2007. doi:
10.1016/j.bbrc.2007.03.091. 36. López-Doménech G, Covill-Cooke C, Ivankovic D, Halff EF, Sheehan DF, Norkett R,
Birsa N, Kittler JT. Miro proteins coordinate microtubule- and actin-dependent mitochondrial
transport and distribution. EMBO J 37: 321–336, 2018. doi: 10.15252/embj.201696380. 37. Moore AS, Coscia SM, Simpson CL, Ortega FE, Wait EC, Heddleston JM, Nirschl JJ,
Obara CJ, Guedes-Dias P, Boecker CA, Chew T-L, Theriot JA, Lippincott-Schwartz J,
Holzbaur ELF. Actin cables and comet tails organize mitochondrial networks in mitosis. Nature 591:
659–664, 2021. doi: 10.1038/s41586-021-03309-5. 38. Scarpulla RC. Nucleus-encoded regulators of mitochondrial function: Integration of
respiratory chain expression, nutrient sensing and metabolic stress. Biochim Biophys Acta BBA - Gene
Regul Mech 1819: 1088–1097, 2012. doi: 10.1016/j.bbagrm.2011.10.011. 39. References Nunnari J, Walter P. Regulation of Organelle Biogenesis. Cell 84: 389–394, 1996. doi:
10.1016/S0092-8674(00)81283-0. 17. Simon VR, Karmon SL, Pon LA. Mitochondrial inheritance: Cell cycle and actin cable
dependence of polarized mitochondrial movements in saccharomyces cerevisiae. Cell Motil
Cytoskeleton 37: 199–210, 1997. doi: 10.1002/(SICI)1097-0169(1997)37:3<199::AID-
CM2>3.0.CO;2-2. 18. Higuchi R, Vevea JD, Swayne TC, Chojnowski R, Hill V, Boldogh IR, Pon LA. Actin
dynamics affect mitochondrial quality control and aging in budding yeast. Curr Biol 23: 2417–2422,
2013. doi: 10.1016/j.cub.2013.10.022. 19. Lazzarino DA, Boldogh I, Smith MG, Rosand J, Pon LA. Yeast Mitochondria Contain
ATP-sensitive , Reversible Actin-binding Activity. 5: 807–818, 1994. 20. Altmann K, Westermann B. Role of Essential Genes in Mitochondrial Morphogenesis in
Saccharomyces cerevisiae □. 16: 5410–5417, 2005. doi: 10.1091/mbc.E05. 21. Boldogh IR, Pon LA. Interactions of mitochondria with the actin cytoskeleton. Biochim
Biophys Acta - Mol Cell Res 1763: 450–462, 2006. doi: 10.1016/j.bbamcr.2006.02.014. 22. McFaline-Figueroa JR, Vevea J, Swayne TC, Zhou C, Liu C, Leung G, Boldogh IR, Pon
LA. Mitochondrial quality control during inheritance is associated with lifespan and mother-daughter
age asymmetry in budding yeast. Aging Cell 10: 885–895, 2011. doi: 10.1111/j.1474-
9726.2011.00731.x. 23. Swayne TC, Zhou C, Boldogh IR, Mcfaline-figueroa R, Charalel JK, Thoms S, Yang C,
Leung G, Mcinnes J, Erdmann R, Pon LA. Report Role for cER and Mmr1p in Anchorage of
Mitochondria at Sites of Polarized Surface Growth in Budding Yeast. . 24. Altmann K, Frank M, Neumann D, Jakobs S, Westermann B. The class V myosin motor
protein, Myo2, plays a major role in mitochondrial motility in Saccharomyces cerevisiae. J Cell Biol
181: 119–130, 2008. doi: 10.1083/jcb.200709099. 25. Van den Bogert C, Muus P, Haanen C, Pennings A, Melis TE, Kroon AM. Mitochondrial
biogenesis and mitochondrial activity during the progression of the cell cycle of human leukemic
cells. Exp Cell Res 178: 143–153, 1988. doi: 10.1016/0014-4827(88)90385-0. 26. Martínez-Diez M, Santamaría G, Ortega ÁD, Cuezva JM. Biogenesis and dynamic of
mitochondria during the cell cycle: Significance of 3’UTRs. PLoS ONE 1: 1–12, 2006. doi:
10.1371/journal.pone.0000107. 27. Mitra K, Wunder C, Roysam B, Lin G, Lippincott-Schwartz J. A hyperfused 21 21 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 model for neuron disease. Proc Natl Acad Sci 111: E3631–E3640, 2014. 42. Lin M-Y, Sheng Z-H. Regulation of mitochondrial transport in neurons. Exp Cell Res 334:
35–44, 2015. doi: 10.1016/j.yexcr.2015.01.004. 43. Fransson Å, Ruusala A, Aspenström P. The atypical Rho GTPases Miro-1 and Miro-2 have
essential roles in mitochondrial trafficking. Biochem Biophys Res Commun 344: 500–510, 2006. doi:
10.1016/j.bbrc.2006.03.163. 44. Wozniak MJ, Melzer M, Dorner C, Haring H-U, Lammers R. The novel protein KBP
regulates mitochondria localization by interaction with a kinesin-like protein. BMC Cell Biol 6: 35,
2005. doi: 10.1186/1471-2121-6-35. 45. Lyons DA, Naylor SG, Mercurio S, Dominguez C, Talbot WS. KBP is essential for axonal
structure, outgrowth and maintenance in zebrafish, providing insight into the cellular basis of
Goldberg-Shprintzen syndrome. Development 135: 599–608, 2008. doi: 10.1242/dev.012377. 46. Tanaka K, Sugiura Y, Ichishita R, Mihara K, Oka T. KLP6: a newly identified kinesin
that regulates the morphology and transport of mitochondria in neuronal cells. J Cell Sci 124: 2457–
2465, 2011. doi: 10.1242/jcs.086470. 47. Schnapp BJ, Reese TS. Dynein is the motor for retrograde axonal transport of organelles. Proc Natl Acad Sci 86: 1548–1552, 1989. 48. Asai DJ, Koonce MP. The dynein heavy chain: structure, mechanics and evolution. Trends
Cell Biol 11: 196–202, 2001. doi: 10.1016/S0962-8924(01)01970-5. 49. Sheng Z-H, Cai Q. Mitochondrial transport in neurons: impact on synaptic homeostasis and
neurodegeneration. Nat Rev Neurosci 13: 77–93, 2012. doi: 10.1038/nrn3156. 50. Schwarzer C, Barnikol-Watanabe S, Thinnes FP, Hilschmann N. Voltage-dependent
anion-selective channel (VDAC) interacts with the dynein light chain Tctex1 and the heat-shock
protein PBP74. Int J Biochem Cell Biol 34: 1059–1070, 2002. doi: 10.1016/S1357-2725(02)00026-2. 51. Schroer TA. Dynactin. Annu Rev Cell Dev Biol 20: 759–779, 2004. doi:
10.1146/annurev.cellbio.20.012103.094623. 52. van Spronsen M, Mikhaylova M, Lipka J, Schlager MA, van den Heuvel DJ, Kuijpers
M, Wulf PS, Keijzer N, Demmers J, Kapitein LC, Jaarsma D, Gerritsen HC, Akhmanova A,
Hoogenraad CC. TRAK/Milton Motor-Adaptor Proteins Steer Mitochondrial Trafficking to Axons
and Dendrites. Neuron 77: 485–502, 2013. doi: 10.1016/j.neuron.2012.11.027. 53. Quintero OA, DiVito MM, Adikes RC, Kortan MB, Case LB, Lier AJ, Panaretos NS,
Slater SQ, Rengarajan M, Feliu M, Cheney RE. Human Myo19 Is a Novel Myosin that Associates
with Mitochondria. Curr Biol 19: 2008–2013, 2009. doi: 10.1016/j.cub.2009.10.026. 54. Rohn JL, Patel JV, Neumann B, Bulkescher J, Mchedlishvili N, McMullan RC,
Quintero OA, Ellenberg J, Baum B. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Ligon LA, Steward O. Role of microtubules and actin filaments in the movement of
mitochondria in the axons and dendrites of cultured hippocampal neurons. . 40. Lovas JR, Wang X. The meaning of mitochondrial movement to a neuron’s life. Biochim
Biophys Acta - Mol Cell Res 1833: 184–194, 2013. doi: 10.1016/j.bbamcr.2012.04.007. 41. Nguyen TT, Oh SS, Weaver D, Lewandowska A, Maxfield D, Schuler M-H, Smith NK,
Macfarlane J, Saunders G, Palmer CA, Debattisti V, Koshiba T, Pulst S, Feldman EL,
Hajnóczky G, Shaw JM. Loss of Miro1-directed mitochondrial movement results in a novel murine 22 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 57. Flannery PJ, Trushina E. Mitochondrial dynamics and transport in Alzheimer’s disease. Mol Cell Neurosci 98: 109–120, 2019. doi: 10.1016/j.mcn.2019.06.009. 58. Vossel KA, Zhang K, Brodbeck J, Daub AC, Sharma P, Finkbeiner S, Cui B, Mucke L. Tau Reduction Prevents Aβ-Induced Defects in Axonal Transport. Science 330: 198–198, 2010. doi:
10.1126/science.1194653. 59. Wang X, Su B, Zheng L, Perry G, Smith MA, Zhu X. The role of abnormal mitochondrial
dynamics in the pathogenesis of Alzheimer’s disease. J Neurochem 109 Suppl 1: 153–159, 2009. doi:
10.1111/j.1471-4159.2009.05867.x. 60. Rui Y, Tiwari P, Xie Z, Zheng JQ. Acute impairment of mitochondrial trafficking by beta-
amyloid peptides in hippocampal neurons. J Neurosci Off J Soc Neurosci 26: 10480–10487, 2006. doi: 10.1523/JNEUROSCI.3231-06.2006. 61. Stokin GB, Lillo C, Falzone TL, Brusch RG, Rockenstein E, Mount SL, Raman R,
Davies P, Masliah E, Williams DS, Goldstein LSB. Axonopathy and Transport Deficits Early in the
Pathogenesis of Alzheimer’s Disease. Science 307: 1282–1288, 2005. doi: 10.1126/science.1105681. 62. Hsieh CH, Shaltouki A, Gonzalez AE, Bettencourt da Cruz A, Burbulla LF, St. Lawrence E, Schüle B, Krainc D, Palmer TD, Wang X. Functional Impairment in Miro
Degradation and Mitophagy Is a Shared Feature in Familial and Sporadic Parkinson’s Disease. Cell
Stem Cell 19: 709–724, 2016. doi: 10.1016/j.stem.2016.08.002. 63. Weihofen A, Thomas KJ, Ostaszewski BL, Cookson MR, Selkoe DJ. Pink1 forms a
multiprotein complex with Miro and Milton, linking Pink1 function to mitochondrial trafficking. Biochemistry 48: 2045–2052, 2009. doi: 10.1021/bi8019178. 64. Lee H-J, Khoshaghideh F, Lee S, Lee S-J. Impairment of microtubule-dependent trafficking
by overexpression of α-synuclein. Eur J Neurosci 24: 3153–3162, 2006. doi: 10.1111/j.1460-
9568.2006.05210.x. 65. Yang F, Jiang Q, Zhao J, Ren Y, Sutton MD, Feng J. Parkin Stabilizes Microtubules
through Strong Binding Mediated by Three Independent Domains*. J Biol Chem 280: 17154–17162,
2005. doi: 10.1074/jbc.M500843200. 66. Gillardon F. Leucine-rich repeat kinase 2 phosphorylates brain tubulin-beta isoforms and
modulates microtubule stability – a point of convergence in Parkinsonian neurodegeneration? J
Neurochem 110: 1514–1522, 2009. doi: 10.1111/j.1471-4159.2009.06235.x. 67. Sasaki S, Iwata M. Impairment of fast axonal transport in the proximal axons of anterior
horn neurons in amyotrophic lateral sclerosis. Neurology 47: 535–540, 1996. doi:
10.1212/WNL.47.2.535. 68. De Vos KJ, Chapman AL, Tennant ME, Manser C, Tudor EL, Lau K-F, Brownlees J,
Ackerley S, Shaw PJ, McLoughlin DM, Shaw CE, Leigh PN, Miller CCJ, Grierson AJ. Familial
amyotrophic lateral sclerosis-linked SOD1 mutants perturb fast axonal transport to reduce axonal
mitochondria content. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Myo19 Ensures Symmetric Partitioning of Mitochondria and
Coupling of Mitochondrial Segregation to Cell Division. Curr Biol 24: 2598–2605, 2014. doi:
10.1016/j.cub.2014.09.045. 55. Manor U, Bartholomew S, Golani G, Christenson E, Kozlov M, Higgs H, Spudich J,
Lippincott-Schwartz J. A mitochondria-anchored isoform of the actin-nucleating spire protein
regulates mitochondrial division. eLife 4: e08828, 2015. doi: 10.7554/eLife.08828. 56. Straub F, Welz T, Alberico H, Brandão RO, Huber A, Samol-Wolf A, Brakebusch C,
Woods D, Kollmar M, Martin-Gonzalez J, Kerkhoff E. The SPIRE1 actin nucleator coordinates 23 0.
Shi P, Ström A-L, Gal J, Zhu H. Effects of ALS-related SOD1 mutants on dynein- and Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 KIF5-mediated retrograde and anterograde axonal transport. Biochim Biophys Acta BBA - Mol Basis
Dis 1802: 707–716, 2010. doi: 10.1016/j.bbadis.2010.05.008. KIF5-mediated retrograde and anterograde axonal transport. Biochim Biophys Acta BBA - Mol Basis
Dis 1802: 707–716, 2010. doi: 10.1016/j.bbadis.2010.05.008. 71. Rezin GT, Amboni G, Zugno AI, Quevedo J, Streck EL. Mitochondrial Dysfunction and
Psychiatric Disorders. Neurochem Res 34: 1021, 2008. doi: 10.1007/s11064-008-9865-8. 72. Flippo KH, Strack S. An emerging role for mitochondrial dynamics in schizophrenia. Schizophr Res 187: 26–32, 2017. doi: 10.1016/j.schres.2017.05.003. 73. Caviston JP, Ross JL, Antony SM, Tokito M, Holzbaur ELF. Huntingtin facilitates
dynein/dynactin-mediated vesicle transport. Proc Natl Acad Sci U S A 104: 10045–10050, 2007. doi:
10.1073/pnas.0610628104. 74. Colin E, Zala D, Liot G, Rangone H, Borrell-Pagès M, Li X-J, Saudou F, Humbert S. Huntingtin phosphorylation acts as a molecular switch for anterograde/retrograde transport in
neurons. EMBO J 27: 2124–2134, 2008. doi: 10.1038/emboj.2008.133. 75. Trushina E, Dyer RB, Badger JD, Ure D, Eide L, Tran DD, Vrieze BT, Legendre-
Guillemin V, McPherson PS, Mandavilli BS, Van Houten B, Zeitlin S, McNiven M, Aebersold
R, Hayden M, Parisi JE, Seeberg E, Dragatsis I, Doyle K, Bender A, Chacko C, McMurray CT. M t
t h
ti
ti i
i
l t ffi ki
i
li
i
i
d i
it
M l C ll 75. Trushina E, Dyer RB, Badger JD, Ure D, Eide L, Tran DD, Vrieze BT, Legendre-
Guillemin V, McPherson PS, Mandavilli BS, Van Houten B, Zeitlin S, McNiven M, Aebersold
R, Hayden M, Parisi JE, Seeberg E, Dragatsis I, Doyle K, Bender A, Chacko C, McMurray CT. Mutant huntingtin impairs axonal trafficking in mammalian neurons in vivo and in vitro. Mol Cell
Biol 24: 8195–8209, 2004. doi: 10.1128/MCB.24.18.8195-8209.2004. ,
,
,
,
,
,
R, Hayden M, Parisi JE, Seeberg E, Dragatsis I, Doyle K, Bender A, Chacko C, McMurray CT. Mutant huntingtin impairs axonal trafficking in mammalian neurons in vivo and in vitro. Mol Cell
Biol 24: 8195–8209, 2004. doi: 10.1128/MCB.24.18.8195-8209.2004. 76. Katajisto P, Döhla J, Chaffer CL, Pentinmikko N, Marjanovic N, Iqbal S, Zoncu R,
Chen W, Weinberg RA, Sabatini DM. Asymmetric apportioning of aged mitochondria between
daughter cells is required for stemness. Science 348: 340–343, 2015. doi: 10.1126/science.1260384. 77. Hinge A, He J, Bartram J, Javier J, Xu J, Fjellman E, Sesaki H, Li T, Yu J, Wunderlich
M, Mulloy J, Kofron M, Salomonis N, Grimes HL, Filippi M-D. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Hum Mol Genet 16: 2720–2728, 2007. doi: 10.1093/hmg/ddm226. 69. Magrané J, Hervias I, Henning MS, Damiano M, Kawamata H, Manfredi G. Mutant
SOD1 in neuronal mitochondria causes toxicity and mitochondrial dynamics abnormalities. Hum Mol
Genet 18: 4552–4564, 2009. doi: 10.1093/hmg/ddp421. 70. Shi P, Ström A-L, Gal J, Zhu H. Effects of ALS-related SOD1 mutants on dynein- and 24 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 83. Cho YM, Kim JH, Kim M, Park SJ, Koh SH, Ahn HS, Kang GH, Lee J Bin, Park KS,
Lee HK. Mesenchymal stem cells transfer mitochondria to the cells with virtually no mitochondrial
function but not with pathogenic mtDNA mutations. PLoS ONE 7: 0–7, 2012. doi:
10.1371/journal.pone.0032778. 84. Li X, Zhang Y, Yeung SC, Liang Y, Liang X, Ding Y, Ip MSM, Tse HF, Mak JCW, Lian
Q. Mitochondrial transfer of induced pluripotent stem cell-derived mesenchymal stem cells to airway
epithelial cells attenuates cigarette smoke-induced damage. Am J Respir Cell Mol Biol 51: 455–465,
2014. doi: 10.1165/rcmb.2013-0529OC. 85. Liu K, Ji K, Guo L, Wu W, Lu H, Shan P, Yan C. Mesenchymal stem cells rescue injured
endothelial cells in an in vitro ischemia-reperfusion model via tunneling nanotube like structure-
mediated mitochondrial transfer. Microvasc Res 92: 10–18, 2014. doi: 10.1016/j.mvr.2014.01.008. 86. Cowan DB, Yao R, Akurathi V, Snay ER, Thedsanamoorthy JK, Zurakowski D,
Ericsson M, Friehs I, Wu Y, Levitsky S, Del Nido PJ, Packard AB, McCully JD. Intracoronary
delivery of mitochondria to the ischemic heart for cardioprotection. PLoS ONE 11: 1–19, 2016. doi:
10.1371/journal.pone.0160889. 87. Lin TK, Chen S Der, Chuang YC, Lan MY, Chuang JH, Wang PW, Hsu TY, Wang FS,
Tsai MH, Huang ST, Wang XW, Tsai PC, Lin HY, Liou CW. Mitochondrial transfer of wharton’s
jelly mesenchymal stem cells eliminates mutation burden and rescues mitochondrial bioenergetics in
rotenone-stressed MELAS fibroblasts. Oxid Med Cell Longev 2019, 2019. doi:
10.1155/2019/9537504. 88. Hayakawa K, Esposito E, Wang X, Terasaki Y, Liu Y, Xing C, Ji X, Lo EH. Transfer of
mitochondria from astrocytes to neurons after stroke. Nature 535: 551–555, 2016. doi:
10.1038/nature18928. 89. Pasquier J, Guerrouahen BS, Ghiabi P, Maleki M, Al Sulaiti H, Le Foll F, Rafii A. Tunneling nanotubes mediate preferential transfer of mitochondria from endothelial to cancer cells
and confer chemoresistance. Qatar Found Annu Res Forum Proc : BMP88, 2012. doi:
10.5339/qfarf.2012.bmp88. 90. Moschoi R, Imbert V, Nebout M, Chiche J, Mary D, Prebet T, Saland E, Castellano R,
Pouyet L, Collette Y, Vey N, Chabannon C, Recher C, Sarry JE, Alcor D, Peyron JF,
Griessinger E. Protective mitochondrial transfer from bone marrow stromal cells to acute myeloid
leukemic cells during chemotherapy. Blood 128: 253–264, 2016. doi: 10.1182/blood-2015-07-
655860. 91. Lu J, Zheng X, Li F, Yu Y, Chen Z, Liu Z, Wang Z, Xu H, Yang W. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Asymmetrically Segregated
Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive
HSC Attrition. Cell Stem Cell 26: 420-430.e6, 2020. doi: 10.1016/j.stem.2020.01.016. 78. Adams WC, Chen Y-H, Kratchmarov R, Yen B, Nish SA, Lin W-HW, Rothman NJ,
Luchsinger LL, Klein U, Busslinger M, Rathmell JC, Snoeck H-W, Reiner SL. Anabolism-
Associated Mitochondrial Stasis Driving Lymphocyte Differentiation over Self-Renewal. Cell Rep 17:
3142–3152, 2016. doi: 10.1016/j.celrep.2016.11.065. 79. Ko YH, Lin Z, Flomenberg N, Pestell RG, Howell A, Sotgia F, Lisanti MP, Martinez-
Outschoorn UE. Glutamine fuels a vicious cycle of autophagy in the tumor stroma and oxidative
mitochondrial metabolism in epithelial cancer cells: Implications for preventing chemotherapy
resistance. Cancer Biol Ther 12: 1085–1097, 2011. doi: 10.4161/cbt.12.12.18671. 80. Shin MK, Cheong JH. Mitochondria-centric bioenergetic characteristics in cancer stem-like
cells. Arch Pharm Res 42: 113–127, 2019. doi: 10.1007/s12272-019-01127-y. 81. Tan AS, Baty JW, Dong LF, Bezawork-Geleta A, Endaya B, Goodwin J, Bajzikova M,
Kovarova J, Peterka M, Yan B, Pesdar EA, Sobol M, Filimonenko A, Stuart S, Vondrusova M, Kluckova K, Sachaphibulkij K, Rohlena J, Hozak P, Truksa J, Eccles D, Haupt LM, Griffiths
LR, Neuzil J, Berridge M V. Mitochondrial genome acquisition restores respiratory function and
tumorigenic potential of cancer cells without mitochondrial DNA. Cell Metab 21: 81–94, 2015. doi:
10.1016/j.cmet.2014.12.003. 82. Spees JL, Olson SD, Whitney MJ, Prockop DJ. Mitochondrial transfer between cells can
rescue aerobic respiration. Proc Natl Acad Sci U S A 103: 1283–1288, 2006. doi:
10.1073/pnas.0510511103. 25 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints20210 doi:10.20944/preprints202106.0657.v1 95. Seyfried TN, Huysentruyt LC. On the Origin of Cancer Metastasis. Crit Rev Oncog 18,
2013. doi: 10.1615/CritRevOncog.v18.i1-2.40. 96. Ong MS, Deng S, Halim CE, Cai W, Tan TZ, Huang RY-J, Sethi G, Hooi SC, Kumar
AP, Yap CT. Cytoskeletal Proteins in Cancer and Intracellular Stress: A Therapeutic Perspective. Cancers 12, 2020. doi: 10.3390/cancers12010238. 97. Ali MRK, Wu Y, Tang Y, Xiao H, Chen K, Han T, Fang N, Wu R, El-Sayed MA. Targeting cancer cell integrins using gold nanorods in photothermal therapy inhibits migration
through affecting cytoskeletal proteins. Proc Natl Acad Sci 114: E5655–E5663, 2017. 98. Stehn JR, Haass NK, Bonello T, Desouza M, Kottyan G, Treutlein H, Zeng J,
Nascimento PRBB, Sequeira VB, Butler TL, Allanson M, Fath T, Hill TA, McCluskey A,
Schevzov G, Palmer SJ, Hardeman EC, Winlaw D, Reeve VE, Dixon I, Weninger W, Cripe TP,
Gunning PW. A Novel Class of Anticancer Compounds Targets the Actin Cytoskeleton in Tumor
Cells. Cancer Res 73: 5169–5182, 2013. 99. Desai SP, Bhatia SN, Toner M, Irimia D. Mitochondrial localization and the persistent
migration of epithelial cancer cells. Biophys J 104: 2077–2088, 2013. doi: 10.1016/j.bpj.2013.03.025. 100. Safiulina D, Kuum M, Choubey V, Hickey MA, Kaasik A. Mitochondrial transport
proteins RHOT1 and RHOT2 serve as docking sites for PRKN-mediated mitophagy. Autophagy 15:
930–931, 2019. doi: 10.1080/15548627.2019.1586260. 101. Nakatogawa H, Suzuki K, Kamada Y, Ohsumi Y. Dynamics and diversity in autophagy
mechanisms: lessons from yeast. Nat Rev Mol Cell Biol 10: 458–467, 2009. doi: 10.1038/nrm2708. 102. Youle RJ, Narendra DP. Mechanisms of mitophagy. Nat Rev Mol Cell Biol 12: 9–14, 2011. doi: 10.1038/nrm3028. 103. Schieke SM, McCoy JP, Finkel T. Coordination of mitochondrial bioenergetics with G1
phase cell cycle progression. Cell Cycle 7: 1782–1787, 2008. doi: 10.4161/cc.7.12.6067. 104. Owusu-Ansah E, Yavari A, Mandal S, Banerjee U. Distinct mitochondrial retrograde
signals control the G1-S cell cycle checkpoint. Nat Genet 40: 356–361, 2008. doi:
10.1038/ng.2007.50. 105. Sarraf SA, Sideris DP, Giagtzoglou N, Ni L, Kankel MW, Sen A, Bochicchio LE, Huang
C-H, Nussenzweig SC, Worley SH, Morton PD, Artavanis-Tsakonas S, Youle RJ, Pickrell AM. PINK1/Parkin Influences Cell Cycle by Sequestering TBK1 at Damaged Mitochondria, Inhibiting
Mitosis. Cell Rep 29: 225-235.e5, 2019. doi: 10.1016/j.celrep.2019.08.085. 106. Palis J. Primitive and definitive erythropoiesis in mammals. Front Physiol 5, 2014. doi:
10.3389/fphys.2014.00003. 107. Moras M, Lefevre SD, Ostuni MA. From Erythroblasts to Mature Red Blood Cells:
Organelle Clearance in Mammals. Front Physiol 8, 2017. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Tunneling nanotubes
promote intercellular mitochondria transfer followed by increased invasiveness in bladder cancer
cells. Oncotarget 8: 15539–15552, 2017. doi: 10.18632/oncotarget.14695. 92. Shachar I, Karin N. The dual roles of inflammatory cytokines and chemokines in the
regulation of autoimmune diseases and their clinical implications. J Leukoc Biol 93: 51–61, 2013. doi:
10.1189/jlb.0612293. 93. D’ambrosio D, Mariani M, Panina-Bordignon P, Sinigaglia F. Chemokines and Their
Receptors Guiding T Lymphocyte Recruitment in Lung Inflammation. Am J Respir Crit Care Med
164: 1266–1275, 2001. doi: 10.1164/ajrccm.164.7.2103011. 94. Campello S, Lacalle RA, Bettella M, Mañes S, Scorrano L, Viola A. Orchestration of
lymphocyte chemotaxis by mitochondrial dynamics. J Exp Med 203: 2879–2886, 2006. doi:
10.1084/jem.20061877. 26 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 110. Sandoval H, Thiagarajan P, Dasgupta SK, Schumacher A, Prchal JT, Chen M, Wang J. Essential role for Nix in autophagic maturation of erythroid cells. Nature 454: 232–235, 2008. doi:
10.1038/nature07006. 111. Novak I, Kirkin V, McEwan DG, Zhang J, Wild P, Rozenknop A, Rogov V, Löhr F,
Popovic D, Occhipinti A, Reichert AS, Terzic J, Dötsch V, Ney PA, Dikic I. Nix is a selective
autophagy receptor for mitochondrial clearance. EMBO Rep 11: 45–51, 2010. doi:
10.1038/embor.2009.256. 112. Kundu M, Lindsten T, Yang C-Y, Wu J, Zhao F, Zhang J, Selak MA, Ney PA,
Thompson CB. Ulk1 plays a critical role in the autophagic clearance of mitochondria and ribosomes
during reticulocyte maturation. Blood 112: 1493–1502, 2008. doi: 10.1182/blood-2008-02-137398. 113. Zhu H, Foretz M, Xie Z, Zhang M, Zhu Z, Xing J, Leclerc J, Gaudry M, Viollet B, Zou
M-H. PRKAA1/AMPKα1 is required for autophagy-dependent mitochondrial clearance during
erythrocyte maturation. Autophagy 10: 1522–1534, 2014. doi: 10.4161/auto.29197. 114. Zhang J, Randall MS, Loyd MR, Dorsey FC, Kundu M, Cleveland JL, Ney PA. Mitochondrial clearance is regulated by Atg7-dependent and -independent mechanisms during
reticulocyte maturation. Blood 114: 157–164, 2009. doi: 10.1182/blood-2008-04-151639. 115. Nishida Y, Arakawa S, Fujitani K, Yamaguchi H, Mizuta T, Kanaseki T, Komatsu M,
Otsu K, Tsujimoto Y, Shimizu S. Discovery of Atg5/Atg7-independent alternative macroautophagy. Nature 461: 654–658, 2009. doi: 10.1038/nature08455. 116. Stenmark H. Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol 10: 513–
525, 2009. doi: 10.1038/nrm2728. 117. Wang J, Fang Y, Yan L, Yuan N, Zhang S, Xu L, Nie M, Zhang X, Wang J. Erythroleukemia cells acquire an alternative mitophagy capability. Sci Rep 6: 24641, 2016. doi:
10.1038/srep24641. 118. Jiang H, Yang L, Guo L, Cui N, Zhang G, Liu C, Xing L, Shao Z, Wang H. Impaired
Mitophagy of Nucleated Erythroid Cells Leads to Anemia in Patients with Myelodysplastic
Syndromes. Oxid Med Cell Longev 2018: e6328051, 2018. doi: 10.1155/2018/6328051. 119. Martino S, Arlet J-B, Odièvre M-H, Jullien V, Moras M, Hattab C, Lefebvre T, Gouya
L, Ostuni MA, Lefevre SD, Kim CLV. Deficient mitophagy pathways in sickle cell disease. Br J
Haematol n/a, [date unknown]. doi: https://doi.org/10.1111/bjh.17416. 120. Ho TT, Warr MR, Adelman ER, Lansinger OM, Flach J, Verovskaya EV, Figueroa ME,
Passegué E. Autophagy maintains the metabolism and function of young and old stem cells. Nature
543: 205–210, 2017. doi: 10.1038/nature21388. 121. Ito K, Suda T. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints20210 doi: 10.3389/fphys.2017.01076. 108. Schweers RL, Zhang J, Randall MS, Loyd MR, Li W, Dorsey FC, Kundu M, Opferman
JT, Cleveland JL, Miller JL, Ney PA. NIX is required for programmed mitochondrial clearance
during reticulocyte maturation. Proc Natl Acad Sci U S A 104: 19500–19505, 2007. doi:
10.1073/pnas.0708818104. 109. Mortensen M, Ferguson DJP, Edelmann M, Kessler B, Morten KJ, Komatsu M, Simon
AK. Loss of autophagy in erythroid cells leads to defective removal of mitochondria and severe
anemia in vivo. Proc Natl Acad Sci U S A 107: 832–837, 2010. doi: 10.1073/pnas.0913170107. 27 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 E, Rodriguez-Gallego E, Fernández-Arroyo S, Joven J, Baekelandt V, Menendez JA. Mitophagy-driven mitochondrial rejuvenation regulates stem cell fate. Aging 8: 1330–1352, 2016. doi: 10.18632/aging.100976. 125. Xiang G, Yang L, Long Q, Chen K, Tang H, Wu Y, Liu Z, Zhou Y, Qi J, Zheng L, Liu
W, Ying Z, Fan W, Shi H, Li H, Lin X, Gao M, Liu J, Bao F, Li L, Duan L, Li M, Liu X. BNIP3L-dependent mitophagy accounts for mitochondrial clearance during 3 factors-induced somatic
cell reprogramming. Autophagy 13: 1543–1555, 2017. doi: 10.1080/15548627.2017.1338545. 126. Esteban-Martínez L, Sierra-Filardi E, McGreal RS, Salazar-Roa M, Mariño G, Seco E,
Durand S, Enot D, Graña O, Malumbres M, Cvekl A, Cuervo AM, Kroemer G, Boya P. Programmed mitophagy is essential for the glycolytic switch during cell differentiation. EMBO J 36:
1688–1706, 2017. doi: 10.15252/embj.201695916. 127. Sin J, Andres AM, Taylor DJR, Weston T, Hiraumi Y, Stotland A, Kim BJ, Huang C,
Doran KS, Gottlieb RA. Mitophagy is required for mitochondrial biogenesis and myogenic
differentiation of C2C12 myoblasts. Autophagy 12: 369–380, 2016. doi:
10.1080/15548627.2015.1115172. 128. Ankel-Simons F, Cummins JM. Misconceptions about mitochondria and mammalian
fertilization: Implications for theories on human evolution. Proc Natl Acad Sci U S A 93: 13859–
13863, 1996. 129. Cummins JM, Wakayama T, Yanagimachi R. Fate of microinjected spermatid
mitochondria in the mouse oocyte and embryo. Zygote 6: 213–222, 1998. doi:
10.1017/S0967199498000148. 130. Sato M, Sato K. Degradation of Paternal Mitochondria by Fertilization-Triggered Autophagy
in C. elegans Embryos. Science 334: 1141–1144, 2011. doi: 10.1126/science.1210333. 131. Rawi SA, Louvet-Vallée S, Djeddi A, Sachse M, Culetto E, Hajjar C, Boyd L, Legouis R,
Galy V. Postfertilization Autophagy of Sperm Organelles Prevents Paternal Mitochondrial DNA
Transmission. Science 334: 1144–1147, 2011. doi: 10.1126/science.1211878. 132. Sutovsky P, Moreno RD, Ramalho-Santos J, Dominko T, Simerly C, Schatten G. Ubiquitin tag for sperm mitochondria. Nature 402: 371–372, 1999. doi: 10.1038/46466. 133. Politi Y, Gal L, Kalifa Y, Ravid L, Elazar Z, Arama E. Paternal Mitochondrial Destruction
after Fertilization Is Mediated by a Common Endocytic and Autophagic Pathway in Drosophila. Dev
Cell 29: 305–320, 2014. doi: 10.1016/j.devcel.2014.04.005. 134. Vadlamudi RK, Joung I, Strominger JL, Shin J. p62, a phosphotyrosine-independent
ligand of the SH2 domain of p56lck, belongs to a new class of ubiquitin-binding proteins. J Biol
Chem 271: 20235–20237, 1996. doi: 10.1074/jbc.271.34.20235. 135. Rojansky R, Cha M-Y, Chan DC. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Metabolic requirements for the maintenance of self-renewing stem cells. Nat
Rev Mol Cell Biol 15: 243–256, 2014. doi: 10.1038/nrm3772. 122. Khacho M, Slack RS. Mitochondrial activity in the regulation of stem cell self-renewal and
differentiation. Curr Opin Cell Biol 49: 1–8, 2017. doi: 10.1016/j.ceb.2017.11.003. 123. Ito K, Turcotte R, Cui J, Zimmerman SE, Pinho S, Mizoguchi T, Arai F, Runnels JM,
Alt C, Teruya-Feldstein J, Mar JC, Singh R, Suda T, Lin CP, Frenette PS, Ito K. Self-renewal of
a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearance. Science 354:
1156–1160, 2016. doi: 10.1126/science.aaf5530. 124. Vazquez-Martin A, Van den Haute C, Cufí S, Corominas-Faja B, Cuyàs E, Lopez-Bonet 28 139.
Abudu YP, Shrestha BK, Zhang W, Palara A, Brenne HB, Larsen KB, Wolfson DL,
Dumitriu G, Øie CI, Ahluwalia BS, Levy G, Behrends C, Tooze SA, Mouilleron S, Lamark T,
Johansen T. SAMM50 acts with p62 in piecemeal basal- and OXPHOS-induced mitophagy of SAM
and MICOS components. J Cell Biol 220, 2021. doi: 10.1083/jcb.202009092. 138.
Guerroué FL, Eck F, Jung J, Starzetz T, Mittelbronn M, Kaulich M, Behrends C.
Autophagosomal Content Profiling Reveals an LC3C-Dependent Piecemeal Mitophagy Pathway. Mol
Cell 68: 786-796.e6, 2017. doi: 10.1016/j.molcel.2017.10.029. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Elimination of paternal mitochondria in mouse embryos
occurs through autophagic degradation dependent on PARKIN and MUL1. eLife 5, 2016. doi:
10.7554/eLife.17896. 136. Wei Y, Chiang W-C, Sumpter R, Mishra P, Levine B. Prohibitin 2 Is an Inner
Mitochondrial Membrane Mitophagy Receptor. Cell 168: 224-238.e10, 2017. doi:
10.1016/j.cell.2016.11.042. 137. Wang Y, Zhang Y, Chen L, Liang Q, Yin X-M, Miao L, Kang B-H, Xue D. Kinetics and
specificity of paternal mitochondrial elimination in Caenorhabditis elegans. Nat Commun 7: 12569,
2016. doi: 10.1038/ncomms12569. 29 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 138. Guerroué FL, Eck F, Jung J, Starzetz T, Mittelbronn M, Kaulich M, Behrends C. Autophagosomal Content Profiling Reveals an LC3C-Dependent Piecemeal Mitophagy Pathway. Mol
Cell 68: 786-796.e6, 2017. doi: 10.1016/j.molcel.2017.10.029. 138. Guerroué FL, Eck F, Jung J, Starzetz T, Mittelbronn M, Kaulich M, Behrends C. Autophagosomal Content Profiling Reveals an LC3C-Dependent Piecemeal Mitophagy Pathway. Mol
Cell 68: 786-796.e6, 2017. doi: 10.1016/j.molcel.2017.10.029. 139. Abudu YP, Shrestha BK, Zhang W, Palara A, Brenne HB, Larsen KB, Wolfson DL,
Dumitriu G, Øie CI, Ahluwalia BS, Levy G, Behrends C, Tooze SA, Mouilleron S, Lamark T,
Johansen T. SAMM50 acts with p62 in piecemeal basal- and OXPHOS-induced mitophagy of SAM
and MICOS components. J Cell Biol 220, 2021. doi: 10.1083/jcb.202009092. 30
|
https://openalex.org/W2094818343
|
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0123765&type=printable
|
English
| null |
An Analytical Comparison of the Opinions of Physicians Working in Emergency and Trauma Surgery Departments at Tabriz and Vienna Medical Universities Regarding Family Presence during Resuscitation
|
PloS one
| 2,015
|
cc-by
| 5,800
|
OPEN ACCESS Citation: Soleimanpour H, Behringer W, Tabrizi JS,
Sarahrudi K, Golzari SEJ, Hajdu S, et al. (2015) An
Analytical Comparison of the Opinions of Physicians
Working in Emergency and Trauma Surgery
Departments at Tabriz and Vienna Medical
Universities Regarding Family Presence during
Resuscitation. PLoS ONE 10(4): e0123765. doi:10.1371/journal.pone.0123765 * soleimanpourh@tbzmed.ac.ir An Analytical Comparison of the Opinions of
Physicians Working in Emergency and
Trauma Surgery Departments at Tabriz and
Vienna Medical Universities Regarding
Family Presence during Resuscitation Hassan Soleimanpour1*, Wilhelm Behringer2, Jafar Sadegh Tabrizi1, Kambiz Sarahrudi3,
Samad E J Golzari4, Stefan Hajdu3, Maryam Rasouli5, Mehdi Nikakhtar6,
Robab Mehdizadeh Esfanjani7 Hassan Soleimanpour1*, Wilhelm Behringer2, Jafar Sadegh Tabrizi1, Kambiz Sarahrudi3,
Samad E J Golzari4, Stefan Hajdu3, Maryam Rasouli5, Mehdi Nikakhtar6,
Robab Mehdizadeh Esfanjani7 1 Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz-
51664, I.R., Iran, 2 Department of Emergency Medicine, Medical University of Vienna, Vienna General
Hospital, Waehringer Guertel 18–20, 1090 Vienna, Austria, 3 Department of Traumatology, Medical
University of Vienna, Waehringer Guertel 18–20, A-1090 Vienna, Austria, 4 Cardiovascular Research
Center, Tabriz University of Medical Sciences, Tabriz-51664, I.R., Iran, 5 Students’ Research Committee,
Tabriz University of Medical Sciences, Tabriz-51664, I.R., Iran, 6 Department of Emergency Medicine,
Tabriz University of Medical Sciences, Tabriz-51664, I.R., Iran, 7 Neurosciences Research Center, Tabriz
University of Medical Sciences, Tabriz-51664, I.R., Iran RESEARCH ARTICLE Abstract Most physicians at Vienna and Tabriz Medical universities were not open towards family
members’ presence during resuscitation. Introduction Conventionally, throughout the resuscitation procedure, in case of in-hospital cardiac arrest,
patients’ relatives are guided to a separate room in which an experienced nurse advises them of
the patient’s status. Permitting patients’ relatives to witness the resuscitation has always been a
controversial issue. In general, relatives are rarely asked to be present in the resuscitation room,
unless they are eager to be [1–5]. Throughout the international meeting of the American College of Chest Physicians in 2000,
experts from all over the world presented numerous perspectives on dealing with Family Pres-
ence during Resuscitation (FPDR). At this conference, scholars emphasized that FPDR is an
ethnic and cultural issue and that the results obtained from related research are country-specif-
ic and not universally applicable [6]. Given the global challenge posed by FPDR in the field of cardiopulmonary resuscitation
(CPR), we resolved to evaluate the opinions of physicians working in the emergency depart-
ments of Austrian and Iranian medical universities regarding the presence of patients’ relatives
during resuscitation. Our primary hypothesis was that the opinions of physicians working in
the emergency and trauma surgery departments of Tabriz and Vienna medical universities
(serving as models for developing and developed countries, respectively) and, therefore, within
different cultures and societies, vary with regard to approval of FPDR relatives’ witnessing of
patients’ resuscitation. Abstract The present study evaluated the opinions of physicians working in the emergency and trau-
ma surgery departments of Vienna Medical University, in Austria, and Tabriz Medical Uni-
versity, in Iran, regarding the presence of patients’ relatives during resuscitation. In a
descriptive-analytical study, the data obtained from questionnaires that had been distribut-
ed randomly to 40 specialists and residents at each of the participating universities were an-
alyzed. The questionnaire consisted of two sections aimed at capturing the participants’
demographic data, the participants’ opinions regarding their support for the family’s pres-
ence during resuscitation, and the multiple potential factors affecting the participants’ atti-
tudes, including health beliefs, triggers that could facilitate the procedure, self-efficacy,
intellectual norms, and perceived behavioral control. The questionnaire also included a di-
rect question (Question 16) on whether the participants approved of family presence. Each
question could be answered using a Likert-type scale. The results showed that the mean
scores for Question 16 were 4.31 ± 0.64 and 3.57 ± 1.31 for participants at Vienna and Ta-
briz universities, respectively. Moreover, physicians at Vienna University disapproved of the
presence of patients’ families during resuscitation to a higher extent than did those at Tabriz
University (P = 0.018). Of the studied prognostic factors affecting the perspectives of Vienna
Medical University’s physicians, health beliefs (P = 0.000; B = 1.146), triggers (P = 0.000; B
= 1.050), and norms (P = 0.000; B = 0.714) were found to be significant. Moreover, of the
studied prognostic factors affecting the perspectives of Tabriz Medical University’s Academic Editor: Chang-Qing Gao, Central South
University, CHINA Received: December 26, 2014
Accepted: February 20, 2015
Published: April 23, 2015 Copyright: © 2015 Soleimanpour et al. This is an
open access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited. Data Availability Statement: Data are from the
published FPDR study whose authors may be
contacted at H_MOFID1357@YAHOO.COM. Competing Interests: The authors have declared
that no competing interests exist. 1 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 Family Presence during Resuscitation physicians, health beliefs (P = 0.000; B = 0.875), triggers (P = 0.000; B = 1.11), self-efficacy
(P = 0.001; B = 0.5), and perceived behavioral control (P = 0.03; B = 0.713) were significant. PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 (1)
(2)
(3)
(4)
(5)
Q6
Patients’ relatives have the right to be in the resuscitation room. (1)
(2)
(3)
(4)
(5)
Q7
There are many people in our department who support FPDR. (1)
(2)
(3)
(4)
(5)
Q8
My clinical practice is affected by the presence of a patient’s family. (5)
(4)
(3)
(2)
(1)
Q9
My supervisor expects me to allow patients’ relatives to be present during
resuscitation. (1)
(2)
(3)
(4)
(5)
Q10
The resuscitation team’s stress levels will increase as a result of the presence
of a patient’s family. (5)
(4)
(3)
(2)
(1)
Q11
Ending the resuscitation process would be difficult in the presence of a patient’s
family. (5)
(4)
(3)
(2)
(1)
Q12
The patient’s relatives may believe that the resuscitation process was
disorganized. (5)
(4)
(3)
(2)
(1)
Q13
FPDR would increase the likelihood of litigation. (5)
(4)
(3)
(2)
(1)
Q14
If absent, relatives would be angry at staff, due to the belief that they did not
exhaust their efforts. (5)
(4)
(3)
(2)
(1)
Q15
FPDR is a privacy breach, regardless of the patient’s prior consent. (5)
(4)
(3)
(2)
(1)
Q16
I support the legalization of FPDR. (1)
(2)
(3)
(4)
(5)
Q17
If I were a patient’s relative, I would like to be present during resuscitation. (1)
(2)
(3)
(4)
(5)
Q18
If I were a patient undergoing resuscitation, I would like my relatives to be
present during resuscitation. (1)
(2)
(3)
(4)
(5)
doi:10.1371/journal.pone.0123765.t001
PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015
3 doi:10.1371/journal.pone.0123765.t001 participants’ general opinions regarding their support for FPDR and multiple factors possibly
affecting their attitudes (Table 1). g
(
)
Valid behavioral theories and models that informed the questionnaire items included the
Health Belief Model [7], Theory of Reasoned Action [8], programmed behavior [9], and the
Theory of Self-Efficacy [10]. Since no solid theory or model has ever been used to predict be-
havioral patterns, we combined several behavioral theories to design the questionnaire, which
was based on questionnaires that had been validated in a previous study [11]. Questions 1, 2, 3,
4, 17, and 18 are related to health beliefs (i.e., if health experts believe that FDOR is useful to
the patients’ health and/or the family’s psychological health). Questions 5, 6, and 7 evaluated
the triggers that could facilitate FPDR initiation. Methods Using a descriptive-analytical approach, the data obtained from 40 questionnaires that had
been distributed randomly among specialists and residents in emergency and trauma surgery
departments of Imam Reza Hospital, Tabriz University of Medical Sciences, Iran and Vienna
General Hospital, Vienna University of Medical Sciences, Austria were captured and analyzed. The questionnaire is shown in Table 1. Tabriz Imam Reza Hospital is a 300-bed tertiary general
hospital and Vienna General Hospital is a 2500-bed tertiary hospital. Overall, 32 and 35 ques-
tionnaires were returned and analyzed in Vienna General Hospital and Tabriz Imam Reza
Hospital, respectively. The response rate was 80% (32/40) for Vienna General Hospital and
87.5% (35/40) for Tabriz Imam Reza Hospital. This study was approved by the Ethics Committee of Tabriz University of Medical Sciences
and the Research Committee of the Vienna Emergency Medicine Department. Prior to the
completion of the questionnaire, the participants received information on FPDR through a
typed letter attached to the distributed questionnaires. Written informed consent was obtained
by the first author of this manuscript (HS). FPDR was defined as the presence of a family member or relative in the CPR room environ-
ment, providing them with the opportunity to witness the CPR procedure. The questionnaire
consisted of the following two sections: Section 1, which was aimed at collecting the partici-
pants’ demographic data, and Section 2, which consisted of 18 questions evaluating 2 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 Question 8 evaluated if clinical practice is af-
fected by the presence of a patient’s family. Question 9 focuses on the intellectual norms of the
participants (i.e., experiencing pressure from a superior to allow FPDR). Questions 10–15,
which evaluate perceived behavioral control, reflect the participants’ conceptualization of ob-
stacles and risks associated with their approval of FPDR. In Question 16, the participants were
directly asked as to whether they approved of FPDR or not. Each of the 18 questions was rated
on a Likert scale (1 = strongly support, 2 = support, 3 = indifferent, 4 = do not support, and
5 = do not support at all) [7]. To test for consistency in the participants’ responses, some of the
questions were reverse-scored. Table 1 presents the real scores assigned to all the questions. The effect of each predictor (i.e., health beliefs, triggers, self-efficacy, and intellectual norms)
on participants’ attitudes towards FPDR was presented as the mean of the Likert score for each
corresponding question. Linear regression was used to determine the effect of the independent Valid behavioral theories and models that informed the questionnaire items included the
Health Belief Model [7], Theory of Reasoned Action [8], programmed behavior [9], and the
Theory of Self-Efficacy [10]. Since no solid theory or model has ever been used to predict be-
havioral patterns, we combined several behavioral theories to design the questionnaire, which
was based on questionnaires that had been validated in a previous study [11]. Questions 1, 2, 3,
4, 17, and 18 are related to health beliefs (i.e., if health experts believe that FDOR is useful to
the patients’ health and/or the family’s psychological health). Questions 5, 6, and 7 evaluated
the triggers that could facilitate FPDR initiation. Question 8 evaluated if clinical practice is af-
fected by the presence of a patient’s family. Question 9 focuses on the intellectual norms of the
participants (i.e., experiencing pressure from a superior to allow FPDR). Questions 10–15, which evaluate perceived behavioral control, reflect the participants’ conceptualization of ob-
stacles and risks associated with their approval of FPDR. In Question 16, the participants were
directly asked as to whether they approved of FPDR or not. Each of the 18 questions was rated
on a Likert scale (1 = strongly support, 2 = support, 3 = indifferent, 4 = do not support, and
5 = do not support at all) [7]. Family Presence during Resuscitation Table 1. Likert scores (in parentheses) for answers to each questionnaire item. Table 1. Likert scores (in parentheses) for answers to each questionnaire item. Strongly
agree
Agree
Indifferent
Disagree
Strongly
disagree
Q1
Patients’ relatives endure grief after experiencing FPDR. (1)
(2)
(3)
(4)
(5)
Q2
Patients’ relatives will have a better understanding of the resuscitation process. (1)
(2)
(3)
(4)
(5)
Q3
Patients’ relatives can talk to the dying patient. (1)
(2)
(3)
(4)
(5)
Q4
Seeing the resuscitation process is a traumatic experience for family members. (5)
(4)
(3)
(2)
(1)
Q5
The following question should be included in our departmental checklist: Does
the patient’s family want to be present during CPR or not? (1)
(2)
(3)
(4)
(5)
Q6
Patients’ relatives have the right to be in the resuscitation room. (1)
(2)
(3)
(4)
(5)
Q7
There are many people in our department who support FPDR. (1)
(2)
(3)
(4)
(5)
Q8
My clinical practice is affected by the presence of a patient’s family. (5)
(4)
(3)
(2)
(1)
Q9
My supervisor expects me to allow patients’ relatives to be present during
resuscitation. (1)
(2)
(3)
(4)
(5)
Q10
The resuscitation team’s stress levels will increase as a result of the presence
of a patient’s family. (5)
(4)
(3)
(2)
(1)
Q11
Ending the resuscitation process would be difficult in the presence of a patient’s
family. (5)
(4)
(3)
(2)
(1)
Q12
The patient’s relatives may believe that the resuscitation process was
disorganized. (5)
(4)
(3)
(2)
(1)
Q13
FPDR would increase the likelihood of litigation. (5)
(4)
(3)
(2)
(1)
Q14
If absent, relatives would be angry at staff, due to the belief that they did not
exhaust their efforts. (5)
(4)
(3)
(2)
(1)
Q15
FPDR is a privacy breach, regardless of the patient’s prior consent. (5)
(4)
(3)
(2)
(1)
Q16
I support the legalization of FPDR. (1)
(2)
(3)
(4)
(5)
Q17
If I were a patient’s relative, I would like to be present during resuscitation. (1)
(2)
(3)
(4)
(5)
Q18
If I were a patient undergoing resuscitation, I would like my relatives to be
present during resuscitation. (1)
(2)
(3)
(4)
(5)
doi:10 1371/journal pone 0123765 t001 participants’ general opinions regarding their support for FPDR and multiple factors possibly
affecting their attitudes (Table 1). Valid behavioral theories and models that informed the questionnaire items included the
Health Belief Model [7], Theory of Reasoned Action [8], programmed behavior [9], and the
Theory of Self-Efficacy [10]. Since no solid theory or model has ever been used to predict be-
havioral patterns, we combined several behavioral theories to design the questionnaire, which
was based on questionnaires that had been validated in a previous study [11]. Questions 1, 2,
4, 17, and 18 are related to health beliefs (i.e., if health experts believe that FDOR is useful to
the patients’ health and/or the family’s psychological health). Questions 5, 6, and 7 evaluated
the triggers that could facilitate FPDR initiation. Question 8 evaluated if clinical practice is af
fected by the presence of a patient’s family. Question 9 focuses on the intellectual norms of th
participants (i.e., experiencing pressure from a superior to allow FPDR). Questions 10–15,
which evaluate perceived behavioral control, reflect the participants’ conceptualization of ob-
stacles and risks associated with their approval of FPDR. In Question 16, the participants wer
directly asked as to whether they approved of FPDR or not. Each of the 18 questions was rate
on a Likert scale (1 = strongly support, 2 = support, 3 = indifferent, 4 = do not support, and
5 = do not support at all) [7]. To test for consistency in the participants’ responses, some of th
questions were reverse-scored. Table 1 presents the real scores assigned to all the questions. The effect of each predictor (i.e., health beliefs, triggers, self-efficacy, and intellectual norms)
on participants’ attitudes towards FPDR was presented as the mean of the Likert score for eac
corresponding question. Linear regression was used to determine the effect of the independen
Table 1. Likert scores (in parentheses) for answers to each questionnaire item. Strongly
agree
Agree
Indifferent
Disagree
Strongly
disagree
Q1
Patients’ relatives endure grief after experiencing FPDR. (1)
(2)
(3)
(4)
(5)
Q2
Patients’ relatives will have a better understanding of the resuscitation process. (1)
(2)
(3)
(4)
(5)
Q3
Patients’ relatives can talk to the dying patient. (1)
(2)
(3)
(4)
(5)
Q4
Seeing the resuscitation process is a traumatic experience for family members. (5)
(4)
(3)
(2)
(1)
Q5
The following question should be included in our departmental checklist: Does
the patient’s family want to be present during CPR or not? Results Of the 32 respondents at Vienna Medical University, 7 (21.9%) were emergency medicine spe-
cialists, 21 (65.6%) were trauma surgeons, and 4 (12.5%) were emergency medical residents. Of
the 35 respondents at Tabriz Medical University, 10 (28.6%) were emergency medicine special-
ists and 25 (71.4%) were residents (Table 2). The responses to each of the 18 questions are presented in Table 3. No significant relationship was observed between Iranian and Austrian physicians’ (repre-
sented by Tabriz and Vienna Medical universities, respectively) age and FPDR (P = 0.5 and
P = 0.9, respectively). The mean Likert score obtained for Question 16 was 4.31 ± 0.64 and
3.57 ± 1.31 for the participants at Vienna and Tabriz Medical universities, respectively. Vienna
physicians disapproved of FPDR more so than did Tabriz physicians; this result was significant
(P = 0.018). Of the studied prognostic factors affecting the views of the Vienna physicians re-
garding FPDR, health beliefs (P = 0.000; B = 1.146), triggers (P = 0.000; B = 1.050), and intellec-
tual norms (P = 0.000; B = 0.714) were found to be significant. This means that these three
factors significantly influenced Vienna physicians’ aversion towards FPDR. In contrast, of the
studied prognostic factors affecting the views of the Tabriz physicians regarding FPDR, health
beliefs (P = 0.000; B = 0.875), triggers (P = 0.000; B = 1.11), self-efficacy (P = 0.001; B = 0.5),
and perceived behavioral control (P = 0.03; B = 0.713) proved significant. This means that
these three factors significantly influenced Tabriz physicians’ aversion towards FPDR. The
mean Likert scores obtained for each prognostic factor by the participants from the two groups
are presented in Table 3. A comparison of the two groups revealed a statistically significant dif-
ference for triggers (P = 0.0001), self-efficacy (P = 0.003), intellectual norms (P = 0.0001), and
perceived behavioral control (P = 0.001). mean Likert scores obtained for each prognostic factor by the participants from the two groups
are presented in Table 3. A comparison of the two groups revealed a statistically significant dif-
ference for triggers (P = 0.0001), self-efficacy (P = 0.003), intellectual norms (P = 0.0001), and
perceived behavioral control (P = 0.001). Family Presence during Resuscitation variables (i.e., health beliefs, triggers, self-efficacy, and intellectual norms) on the dependent
variable (approval of FPDR). The Mann-Whitney U-test was used to compare the attitudes of
participants from Tabriz Medical University and Vienna Medical University. A P-value of less
than 0.05 was considered statistically significant. To test for consistency in the participants’ responses, some of the
questions were reverse-scored. Table 1 presents the real scores assigned to all the questions. The effect of each predictor (i.e., health beliefs, triggers, self-efficacy, and intellectual norms)
on participants’ attitudes towards FPDR was presented as the mean of the Likert score for each
corresponding question. Linear regression was used to determine the effect of the independent 3 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 Family Presence during Resuscitation Table 3. Number (%) of participants subscribing to each response category and means obtained for each question. City
Strongly
agree
Agree
Indifferent
Disagree
Strongly
disagree
Likert
score
P-value
Health beliefs
Tabriz
3.45 ± 1.10
0.374
Vienna
3.81 ± 0.44
Q1
Patients’ relatives endure the grief process after
experiencing FPDR. Tabriz
2 (5.7)
1 (2.9)
6 (17.1)
16 (45.7)
10 (28.6)
3.88 ± 1.65
0.056
Vienna
0 (0)
1 (3.1)
0 (0)
18 (56.3)
13 (40.6)
4.34 ± 0.65
Q2
Patients’ relatives will have a better
understanding of the resuscitation process. Tabriz
3 (8.6)
16
(17.1)
5 (14.3)
11 (31.4)
10 (28.6)
3.54 ± 1.31
0.153
Vienna
0 (0)
1 (3.1)
0 (0)
26 (81.3)
5 (15.6)
4.09 ± 0.53
Q3
Patients’ relatives can touch or talk to the dying
patient. Tabriz
3 (8.6)
6
(17.1)
7 (20)
7 (20)
12 (34.3)
3.54 ± 1.35
0.022
Vienna
0 (0)
0 (0)
2 (6.3)
17 (53.1)
13 (40.6)
4.34 ± 0.60
Q4
Seeing the resuscitation process is a traumatic
experience for family members. Tabriz
3 (8.6)
13
(37.1)
6 (17.1)
7 (20)
6 (17.1)
3 ± 1.28
0.001
Vienna
0 (0)
1 (3.1)
1 (3.1)
30 (93.8)
0 (0)
2.09 ± 0.39
Q17
If I were a patient’s relative, I would like to be
present during resuscitation. Tabriz
5 (14.3)
7 (20)
1 (2.9)
7 (20)
15 (42.9)
3.57 ± 1.55
0.547
Vienna
1 (3.1)
1 (3.1)
0 (0)
21 (65.6)
9 (28.1)
4.12 ± 0.83
Q18
If I were a patient undergoing resuscitation, I
would like my relatives to be present during
resuscitation. Tabriz
7 (20)
8
(22.9)
2 (5.7)
7 (20)
11 (31.4)
3.200 ± 1.58
0.084
Vienna
2 (6.3)
2 (6.3)
6 (18.8)
9 (28.1)
13 (40.6)
3.90 ± 1.20
Triggers
Tabriz
3.22 ± 0.78
0.0001
Vienna
4.21 ± 0.53
Q5
The following question should be included in
our departmental checklist: Does the patient’s
family want to be present during CPR or not? Tabriz
3 (8.6)
1 (2.9)
8 (22.9)
13 (37.1)
10 (28.6)
3.74 ± 1.17
0.017
Vienna
1 (3.1)
0 (0)
0 (0)
17 (53.1)
14 (43.8)
4.34 ± 0.78
Q6
Patients’ relatives have the right to be present
in the resuscitation room. Discussion The results obtained from our study showed that most physicians at Vienna and Tabriz Medical
universities disapprove of/strongly disapprove of FPDR; however, the proportion is much lower
among physicians at Vienna Medical University (60% for Tabriz Medical University and 96.9%
for Vienna Medical University; Table 3). Despite the fact that physicians at Tabriz Medical Uni-
versity had a generally more positive attitude toward FPDR than did Vienna Medical Univer-
sity’s physicians, most still did not approve of FPDR. Health beliefs and intellectual norms were
identified as the most important factors influencing disagreement regarding FPDR, followed by
self-efficacy and perceived behavioral control among physicians at Tabriz Medical University. Table 2. Participants’ demographic characteristics according to affiliation. Vienna
Tabriz
P-value
Sex
Male
25 (78.1%)
21 (60%)
0.11
Female
7 (21.9%)
14 (40%)
Experience
Percentile 25
3
2
0.005
Percentile 50
5
3
Percentile 75
14
6
Age
35.67 ± 7.76
33.88 ± 6.72
0.32
doi:10.1371/journal.pone.0123765.t002
PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015
4 / 8 Table 2. Participants’ demographic characteristics according to affiliation. 4 / 8 Tabriz
2 (5.7)
7 (20)
4 (11.4)
12 (34.3)
10 (28.6)
3.600 ± 1.26
0.079
Vienna
0 (0)
0 (0)
1 (3.1)
23 (71.9)
8 (25)
4.21 ± 0.49
Q7
There are many people in our department who
support FPDR. Tabriz
7 (20)
16
(45.9)
6 (17.1)
5 (14.3)
1 (2.9)
2.34 ± 1.05
0.0001
Vienna
0 (0)
1 (3.1)
1 (3.1)
24 (75)
6 (18.8)
4.09 ± 0.58
Self efficacy
Tabriz
2.88 ± 1.36
0.003
Vienna
1.93 ± 0.50
Q8
My clinical practice is affected by the presence
of a patient’s family. Tabriz
4 (11.4)
10
(28.6)
7 (20)
6 (17.1)
8 (22.9)
2.88 ± 1.36
0.003
Vienna
0 (0)
1 (3.1)
0 (0)
17 (53.1)
14 (43.8)
1.93 ± 0.50
Norms
Tabriz
3.37 ± 0.91
0.0001
Vienna
4.40 ± 0.55
Q9
My supervisor expects me to allow patients’
relatives to be present during resuscitation. Tabriz
1 (2.9)
5
(14.3)
11 (31.4)
16 (45.7)
2 (5.7)
3.37 ± 0.9
0.0001
Vienna
0 (0)
0 (0)
1 (3.1)
17 (53.1)
14 (43.8)
4.40 ± 0.55
Perceived behavioral control
Tabriz
2.91 ± 0.88
0.001
Vienna
2.34 ± 0.31
Q10
The emotional stress of the resuscitation team
will increase as a result of the presence of a
patient’s family. Tabriz
5 (14.3)
7 (20)
4 (11.4)
11 (31.4)
8 (22.9)
2.71 ± 1.40
0.081
Vienna
0 (0)
0 (0)
1 (3.1)
31 (96.9)
0 (0)
2.03 ± 0.17
Q11
Ending the resuscitation process would be
difficult in the presence of a patient’s family. Tabriz
3 (8.6)
6
(17.1)
2 (5.7)
15 (42.9)
9 (25.7)
2.40 ± 1.28
0.649
Vienna
0 (0)
2 (6.3)
0 (0)
28 (87)
2 (6.3)
2.06 ± 0.56
(Continued) articipants subscribing to each response category and means obtained for each question. 5 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 Family Presence during Resuscitation Table 3. (Continued) Table 3. (Continued)
City
Strongly
agree
Agree
Indifferent
Disagree
Strongly
disagree
Likert
score
P-value
Q12
The patient’s relatives may believe that the
resuscitation process was disorganized. Tabriz
1 (2.9)
9
(25.7)
5 (14.3)
14 (40)
6 (17.1)
2.57 ± 1.14
0.01
Vienna
5 (15.6)
26
(81.3)
0 (0)
1 (3.1)
0 (0)
1.90 ± 0.53
Q13
FPDR would increase the likelihood of litigation. Tabriz
3 (8.6)
13
(37.1)
8 (22.9)
4 (11.4)
7 (20)
3.02 ± 1.29
0.001
Vienna
0 (0)
0 (0)
1 (3,1)
27 (84.4)
4 (12.5)
1.90 ± 0.39
Q14
If absent, relatives would be angry at staff, due
to the belief that they did not exhaust their
efforts. Tabriz
9 (25.7)
14
(40)
7 (20)
4 (11.4)
37 (13.4)
3.74 ± 1.06
0.0001
Vienna
13 (40.6)
13
(40.6)
3 (9.4)
3 (9.4)
0 (0)
4.12 ± 0.94
Q15
FPDR is a privacy breach, regardless of the
patient’s prior consent. Tabriz
3 (8.6)
13
(37.1)
8 (22.9)
5 (14.3)
6 (17.1)
3.05 ± 1.25
0.0001
Vienna
0 (0)
0 (0)
1 (3.1)
29 (90.6)
1 (1.3)
2.00 ± 0.25
Support for FPDR
Tabriz
3.57 ± 1.31
0.018
Vienna
4.31 ± 0.64
Q16
I support the legalization of FPDR. Tabriz
4 (11.4)
3 (8.6)
7 (20)
11 (31.4)
10 (28.6)
3.57 ± 1.31
0.018
Vienna
0 (0)
1 (3.1)
0 (0)
19 (59.4)
12 (37.5)
4.31 ± 0.64
Vienna
2 (6.3)
2 (6.3)
6 (18.8)
9 (28.1)
13 (40.6)
3.90 ± 1.20
doi:10 1371/journal pone 0123765 t003 doi:10.1371/journal.pone.0123765.t003 In other words, the most important factor determining their negative attitudes toward FPDR
was their skepticism regarding the efficacy of FPDR, as well as their colleagues’ disagreement re-
garding FPDR. No significant difference was found between the physicians at the two universi-
ties regarding health beliefs; however, triggers, norms, self-efficacy, and perceived behavioral
control were found to be more predictive of Vienna Medical University physicians’ negative at-
titudes toward FPDR than Tabriz Medical University’s physicians attitudes. A previous study
by Jabre et al. suggested that FPDR does not affect a medical team’s level of emotional stress
and does not result in medico-legal claims [12]. Similar to many previous studies, the results ob-
tained from our study revealed that FPDR is associated with increased fear of litigation, particu-
larly among Tabriz Medical University’s physicians. This could explain these physicians’
aversion to FPDR [13]. PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 Conclusion In contrast to our hypothesis, emergency medicine and trauma surgery physicians in both Vi-
enna and Tabriz medical universities disapproved of FPDR; however, this disapproval was
more significant among Vienna than Tabriz physicians. FPDR should be assessed in every
country, in consideration of country-specific traditions, culture, and religion. Therefore,
knowledge of the different factors contributing towards physicians’ disapproval of FPDR in
Iran and Austria would facilitate the removal of the obstacles hindering the execution of FPDR
in those countries and enable health policymakers to implement related, required measures. Family Presence during Resuscitation similar results to ours, most physicians and nurses did not approve of FPDR in the cases of
both pediatric and adult patients, believing that it would be of no benefit to the family during
the grieving process [16, 17]. Although it is widely accepted that FPDR has a positive impact on the relatives witnessing
CPR, in our study, the physicians in both countries tended not to accept this fact. Physicians at
Tabriz Medical University seemed less reluctant to accept FPDR than those at Vienna Medical
University. Based on the results obtained (Table 3), contributing factors for Austrian physi-
cians were as follows: (1) significant disbelief in the argument, that relatives witnessing CPR
would benefit from either talking to or touching the patient; (2) the assumption that the head
of the department would disapprove of FPDR; and (3) the fear that most relatives would think
of CPR as a disorganized procedure. Interestingly, the deterring factors were found to be differ-
ent for Iranian physicians; these included fear of legislation, invasion of the patient’s privacy,
reduced performance by the CPR team, traumatization of the witnessing relatives, and the as-
sumption that the relatives would not doubt or question if the physicians did all they could. Limitations of the study: The number of the attending professors was more than the resi-
dents in Vienna Medical University and also the number of the residents was more than the at-
tending professors in Tabriz Medical University; this might have affected the significant
differences observed between both studied groups. Our study was conducted in only two cen-
ters and it was of a relatively small sample size. Hence, the conclusion derived from this study
might be ungeneralizable to all populations. S2 Dataset. Demographic characteristics data for each participant according to affiliation.
(SAV) S1 Questionnaire. Blank copy of the questionnaire. (DOC) S1 Questionnaire. Blank copy of the questionnaire. (DOC) Supporting Information S1 Dataset. Data for each participant according to answers to each questionnaire item and
subscribing to each response category and means obtained for each question. (SAV) S2 Dataset. Demographic characteristics data for each participant according to affiliation. (SAV) S2 Dataset. Demographic characteristics data for each participant according to affiliation. (SAV) However, considering the results of Jabre et al.’s study, physicians
should cast aside their fear of medico-legal claims when performing family-witnessed CPR in
their daily practice. Furthermore, in Jabre et al.’s study, FPDR was had apparent positive impli-
cations for the psychological aspects of the family members [12]. Most studies tend to focus on the experience of FPDR, with very few having focused on
medical staff’s views in this regard. Most have stated that clear and precise policies are required
regarding FPDR, so that sufficient psychological support can be provided to family members
who choose to be present during CPR [14]. In a study by Duran et al., it was suggested that
medical staff are mostly in favor of FPDR, which is in contrast with the results of our study
[15]. This could have been due to the fact that, in addition to attending specialists, Duran
et al.’s study involved other healthcare providers, such as nurses and non-attending specialists,
who held more positive attitudes regarding FPDR. In our study, however, only the attitudes of
the attending specialists and residents involved in FPDR were evaluated. According to the
guidelines of the American Heart Association (AHA), medical staff should seriously consider
the implementation of FPDR [14]. This is in sharp contrast with our study’s findings, in which
the medical staff in both sub-groups did not seem open towards FPDR. In another study with 6 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 References 1. Boehm J. Family presence during resuscitation. 2008; 3(5). Available: http://www.zoll.com/
CodeCommunicationsNewsletter/CCNL05_08/CodeCommunications05_08.pdf. 2. Meyers TA, Eichhorn DJ, Guzzetta CE. Do families want to be present during CPR? A retrospective
survey. J Emerg Nurs. 1998; 24(5): 400–405. PMID: 9814254 3. Boyd R. Witnessed resuscitation by relatives. Resuscitation. 2000; 43(3): 171–176. PMID: 10711485 4. Offord RJ. Should relatives of patients with cardiac arrest be invited to be present during cardiopulmo-
nary resuscitation? Intensive Crit Care Nurs. 1998; 14(6): 288–293. PMID: 10196912 5. Shaner K, Eckle N. Implementing a program to support the option of family presence during resuscita-
tion. ACCH Advocate. 1997; 3(1): 3–7. 6. American Heart Association. American Heart Association guidelines for cardiopulmonary resuscitation
and emergency cardiovascular care. Circulation. 2005; 112(Supp): IV-1–IV-211. 7. Rosenstock I. The health belief model: explaining health behavior through expectancies. In: Glanz K,
Lewis FM, Rimer BK, editors. Health behavior and health education: theory research and practice. San
Francisco: Jossey-Bass; 1990. pp. 39–61. 8. Fishbein M, Middlestadt S. Using the theory of reasoned action to develop educational intervention: ap-
plications to illicit drug use. Health Educ Res. 1987; 2(4): 361–371. 9. Schifter DE, Ajzen I. Intention, perceived control, and weight loss: an application of the theory of
planned behavior. J Pers Soc Psychol. 1985; 49(3): 843–851. PMID: 4045706 10. Schwarzer R. Self-efficacy in the adoption and maintenance of health behaviors: theoretical ap-
proaches and a new model. In: Schwarzer R. editor. Self-efficacy: thought control of action. Washing-
ton (DC): Hemisphere Publishing; 1992. pp. 217–243. 11. Lam DSY, Wong SN, Hui H, Lee W, So KT. Attitudes of doctors and nurses to family presence during
paediatric cardiopulmonary resuscitation. HK J Paediatr (new series). 2007; 12: 253–259. 12. Jabre P, Belpomme V, Azoulay E, Jacob L, Bertrand L, Lapostolle F, et al. Family presence during car-
diopulmonary resuscitation. N Engl J Med. 2013; 368(11): 1008–1018. doi: 10.1056/NEJMoa1203366
PMID: 23484827 13. Baird G, Sammy I, Nunes P, Paul J. Attitudes and practices regarding resuscitation in emergency de-
partments in Trinidad and Tobago. Emerg Med J. 2014 Nov; 31(11):889–93. doi: 10.1136/emermed-
2012-201472 PMID: 23851033 14. The American Heart Association in collaboration with the International Liaison Committee on Resusci-
tation. Guidelines 2000 for cardiopulmonary resuscitation and emergency cardiovascular care. Part 10:
pediatric advanced life support. Circulation. 2000; 102(8 Suppl): I291–1342. PMID: 10966679 15. Duran CR, Oman KS, Abel JJ, Koziel VM, Szymanski D. Family Presence during Resuscitation forming part of Maryam Rasouli’s specialty thesis, entitled “An analytical comparison between
the opinions of physicians working in Emergency Departments in Tabriz-Iran and Vienna-
Austria regarding the Family Presence during Resuscitation." It is registered at Tabriz Universi-
ty of Medical Sciences (No: 91.3–6.12) and was presented in June 2014. Author Contributions Conceived and designed the experiments: HS WB. Performed the experiments: JST KS SH. An-
alyzed the data: RME ER. Contributed reagents/materials/analysis tools: MR MN. Wrote the
paper: HS WB SG. Critical revisions of the manuscript: WB. PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 Acknowledgments The authors would like to express their gratitude towards participating physicians from Tabriz
Medical University and Vienna Medical University. We would also like to thank Dr. Minou
Gharehbaglou, at the Faculty of Architecture and urbanism, Tabriz Islamic Art University, Ta-
briz, Iran, and Dr. Aida Maleki Gavgani, at the Department of Building Physics and Building
Ecology, Vienna University of Technology, Karlsplatz 13, 1040 Vienna, Austria, for their assis-
tance with the preparation of the electronic questionnaire. This article is based on a dataset 7 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015 References Attitudes toward and beliefs about family pres-
ence: a survey of healthcare providers, patients’ families, and patients. Am J Crit Care. 2007; 16(3):
270–279. PMID: 17460319 16. Twibell RS, Siela D, Riwitis C, Wheatley J, Riegle T, Bousman D, et al. Nurses’ perceptions of their self-
confidence and the benefits and risks of family presence during resuscitation. Am J Crit Care. 2008; 17
(2): 101–111. PMID: 18310646 17. Soleimanpour H, Tabrizi JS, Farnam A, Nikakhtar M, Mokhtarpour M, Golzari SE, et al. Attitudes of
emergency medicine physicians towards family presence during resuscitation. Resuscitation. 2013; 84
(12): e149–150. doi: 10.1016/j.resuscitation.2013.07.031 PMID: 23973750 8 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765
April 23, 2015
|
https://openalex.org/W3082030877
|
https://bmcemergmed.biomedcentral.com/track/pdf/10.1186/s12873-020-00363-6
|
English
| null |
Characteristics and outcomes of patients with dyspnoea as the main symptom, assessed by prehospital emergency nurses- a retrospective observational study
|
BMC emergency medicine
| 2,020
|
cc-by
| 7,932
|
Kauppi et al. BMC Emergency Medicine (2020) 20:67
https://doi.org/10.1186/s12873-020-00363-6 Kauppi et al. BMC Emergency Medicine (2020) 20:67
https://doi.org/10.1186/s12873-020-00363-6 Open Access Characteristics and outcomes of patients
with dyspnoea as the main symptom,
assessed by prehospital emergency nurses-
a retrospective observational study Wivica Kauppi1,2*
, Johan Herlitz1,2, Carl Magnusson1,3, Lina Palmér2 and Christer Axelsson1,2 Abstract Background: Dyspnoea (breathing difficulty) is among the most commonly cited reasons for contacting
emergency medical services (EMSs). Dyspnoea is caused by several serious underlying medical conditions and,
based on patients individual needs and complex illnesses or injuries, ambulance staff are independently responsible
for advanced care provision. Few large-scale prehospital studies have reviewed patients with dyspnoea. This study
aimed to describe the characteristics and final outcomes of patients whose main symptom was classified as
dyspnoea by the prehospital emergency nurse (PEN). Methods: This retrospective observational study included patients aged > 16 years whose main symptom was
dyspnoea. All the enrolled patients were assessed in the south-western part of Sweden by PENs during January and
December, 2017. Of 7260 assignments (9% of all primary missions), 6354 fulfilled the inclusion criteria. Analysis was
performed using descriptive statistics, and the tests used were odds ratios and Kaplan-Meier analysis. Results: The patients mean age was 73 years, and approximately 56% were women. More than 400 different final
diagnostic codes (International Statistical Classification of Diseases and Related Health Problems [ICD]-10th edition)
were observed, and 11% of the ICD-10 codes denoted time-critical conditions. The three most commonly observed
aetiologies were chronic obstructive pulmonary disease (20.4%), pulmonary infection (17.1%), and heart failure
(15%). The comorbidity values were high, with 84.4% having previously experienced dyspnoea. The overall 30-day
mortality was 11.1%. More than half called EMSs more than 50 h after symptom onset. Conclusions: Among patients assessed by PENs due to dyspnoea as the main symptom there were more than 400
different final diagnoses, of which 11% were regarded as time-critical. These patients had a severe comorbidity and
11% died within the first 30 days. Keywords: Dyspnoea, Epidemiology, Aetiology, Major incidents, Prevention, Emergency medical service, Prehospital
emergency nurse, Ambulance * Correspondence: wivica.kauppi@hb.se Correspondence: wivica.kauppi@hb.se
1PreHospen- Centre for Prehospital Research, Faculty of Caring, Work Life and
Social Welfare, University of Borås, SE- 501 90 Borås, Sweden
2Faculty of Caring Science, Work Life and Social Welfare, University of Borås,
Borås, Sweden
Full list of author information is available at the end of the article * Correspondence: wivica.kauppi@hb.se
1PreHospen- Centre for Prehospital Research, Faculty of Caring, Work Life and
Social Welfare, University of Borås, SE- 501 90 Borås, Sweden
2Faculty of Caring Science, Work Life and Social Welfare, University of Borås,
Borås, Sweden
Full list of author information is available at the end of the article Competence of Swedish ambulances, and the associated
guidelines and triage system Since 2005, all ambulances in Sweden have at least one
registered nurse and one ambulance technician [13]. A
majority of all such nurses have completed a three-year
nursing course followed by a one-year Master’s course
focusing on prehospital emergency care and have the
professional title ‘PEN’. PENs provide assessment and
treatment according to national and local guidelines. In Sweden, prehospital emergency nurses (PENs) have
an important role in the assessment and triaging of
dyspnoea patients at the scene. The treatment of dys-
pnoea begins with the management of the underlying
condition, due to which the diagnosis of acute dyspnoea
is crucial in EMS settings to ensure the provision of ap-
propriate treatment and care [7]. Patients with dyspnoea
constitute a complex group, as the presence of additional
health problems makes it difficult to identify the under-
lying cause of the condition. In addition to the physio-
logical perspective, severe anxiety and fear are observed
commonly in connection with dyspnoea. This denotes
that PENs have the responsibility of providing care
aimed at increasing patients strength and focusing on
their existential needs [8–10]. Previous studies have
described the epidemiology and outcomes of patients
with dyspnoea who are transported by EMSs to emergency
departments (EDs) in Denmark, Australia/New Zealand
and the United States [8, 11, 12]. However, few large-scale
EMS studies have been conducted in such settings till date. In the present study, we aimed to describe the characteris-
tics and final outcomes, overall and in relation to sex of
patients receiving care from PENs and whose main symp-
tom was dyspnoea. In order to assess and prioritise patients degree of pre-
hospital care required, PENs perform triage classification
according to the Rapid Emergency Triage and Treat-
ment System for adults (RETTS- A) [14]. RETTS-A
codes are divided into the following types: 1) vital signs
(VS) and 2) 53 emergency signs and symptoms (ESS)
codes [see Additional file 1: Red and orange VS and ESS
code 04, dyspnoea]. Both types allow for the allocation
of patients separately to a severity/triage level in which
the highest level is used for the final assessment. The se-
verity/triage level is assigned one of five different colours
(red, orange, yellow, green, and blue) according to the
time from assessment to the time a patient must be seen
by a physician. Background inhabitants in urban, suburban, and rural areas. During
2017, the two EMS organisations had 123,614 ambulance
missions with a priority level of 1 to 3. Of these, 87,611
missions involved an initial patient assessment defined as
the primary mission (Fig. 1). Dyspnoea (breathing difficulty) is among the most com-
monly cited reasons for contacting emergency medical
services (EMSs) [1]. The American Thoracic Society
defines dyspnoea as “a subjective experience of breathing
discomfort that consists of qualitatively distinct sensa-
tions that vary in intensity” [2]. It manifests itself in
various ways such as shortness of breath, air hunger, and
chest tightness [3]. Dyspnoea is caused by several medical
conditions [4, 5], and respiratory failure is among the most
severe time-critical conditions for which the provision of
immediate prehospital care by EMSs can have a highly
valuable impact [6]. © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,
which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give
appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if
changes were made. The images or other third party material in this article are included in the article's Creative Commons
licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons
licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain
permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the
data made available in this article, unless otherwise stated in a credit line to the data. Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Page 2 of 11 Competence of Swedish ambulances, and the associated
guidelines and triage system Red and orange indicate the most urgent
cases whereas yellow and green denote the absence of
individual medical risk even if patients are made to wait
to undergo physician assessment. The colour blue is not
used in the prehospital triage. In ESS code 04 (dyspnoea
as the main symptom), it is mandatory for the PENs to
evaluate ECG in all patients. In addition of all prehospi-
tal severe ill patients, it is also mandatory to evaluate the
P-Glucose level. Inclusion and exclusion criteria The inclusion criteria were as follows: 1) a primary
mission in which a patient (or e.g. a family member that
represents the patient) calls the dispatch centre, an
ambulance is dispatched and 2) the assignment of an
ESS code of 04 (dyspnoea) is made by the PEN. The
exclusion criteria were as follows: 1) lack of a personal
identity number, 2) transportation to hospitals outside
the research area, 3) age < 16 years, 4) duplicate EMS
records, 5) missing record or lack of information, 6)
incorrect triage (ESS), and 7) secondary transport use. A
total of 7260 patients were initially identified from the
sample (9% of all assignments). After a manual review,
908 patients were excluded due to various exclusion
criteria, and a total of 6354 patients were finally included
in the study (Fig. 1). Among the 6354 patients, a total of A
quantitative,
exploratory,
descriptive
design
was
employed based on a consecutive retrospective review of
EMS and hospital records. The study included all patients
over a one-year time-period who called the emergency
number (112) in Sweden, had an ambulance dispatched
and were assessed by the prehospital emergency nurses
(PENs) with the main symptom of dyspnoea. Endpoints The primary endpoint was the aetiology according to the
final diagnosis. Secondary endpoints were comorbidity
according to patients previous history and the 30- day
mortality. Tertiary endpoints were the patients delay
time from symptom onset until calling for EMS and
clinical findings on arrival of PENs. Time-critical conditions are defined as conditions
where prompt management and medical interventions
are crucial to avoid severe complications and early death
[16, 17]. Population The study was conducted within two EMS organisations,
which together include 16 ambulance stations in the south-
western part of Sweden. The two EMS organisations cover
a combined area of 7400 km2, with a population of 962,000 Page 3 of 11 Kauppi et al. BMC Emergency Medicine Kauppi et al. BMC Emergency Medicine (2020) 20:67 Fig. 1 Flow chart of the studied patients, assessed as the main symptom of dyspnoea the ICD-10 which comprises 22 chapters (I–XXII). In all
the ambulances, only 12 lead ECG was used. In order to
achieve the best possible data quality, data on ECG inter-
pretations were collected first from prehospital records,
second from ED notes, and third, in cases in which no
interpretation was documented but an ECG was recorded,
by the author (WK). ECG deviations comprise atrial fibrilla-
tion/flutter, ST-elevation, ST-depression, T-wave inversion,
and left bundle branch block. Other deviations include AV-
block I, II, III, ectopic atrial rhythm/tachycardia, and
ventricular tachycardia. P-glucose levels were measured
through a capillary test performed by the PEN, and a value
≥9.5 mmol/l was defined as high [15]. 3665 patients had one EMS contact during the study
period and 2689 patients had multiple contacts. A total
of 4587 unique patients were included in the survival
analysis of which 922 patients were randomly selected
from the patients with multiple contacts. Statistics In the tables, results are presented as number (percent-
age), median (25th, 75th percentiles), or mean (standard
deviation). For two-group comparisons, crude odds
ratios with their correspondent confidence intervals were
calculated. A Kaplan-Meier survival curve stratified by
sex was plotted (Fig. 2), while the lifelines survival func-
tion was used to report differences by sex for 30-day
mortality. All tests are two-sided, and due to the number
of
tests
performed,
p-values
< 0.01
were
considered
significant. Confidence intervals computed at the 99% level
were used. Data processing and statistical analyses were
performed using SPSS version 24 (Armonk, NY, USA: IBM
Corp.) and Python version 3.7 (Python software foundation)
with lifelines package (Cameron Davidson-Pilon, Jonas
Kalderstam, Paul Zivich, et al. CamDavidsonPilon/lifelines:
v0.23.9. 2020). Results Totally, 7262 EMS missions fulfilled the inclusion cri-
teria, and 908 cases (13%) were excluded due to reasons
shown in Fig. 1. Overall, patients with the ESS code 04
(dyspnoea as the main symptom) conformed 9% of all
primary EMS missions and more than 60% of those
patients were hospitalised (Fig. 1). Symptoms and clinical findings In all, 23.1% of the patients had pain, 1.2% had syncope,
and 1.6% showed alcohol/drug-related issues. Abnormal
vital parameters were seen with the following rates
(according to the RETTS-A): respiratory rate < 8/min or >
25/min (48.7%), oxygen saturation < 90% (35.2%), heart
rate < 40/min or > 120/min (11.5%), systolic blood pres-
sure < 90 mmHg (1.8%), body temperature < 35 or > 41 de-
grees (0.5%), and degree of consciousness > RLS 2 (1.6%). An ECG was recorded in 74% of the cases; 70.8% of them
showed a sinus rhythm, whereas 22.8% showed atrial fib-
rillation/flutter. Signs of possible myocardial ischemia
were revealed as ST-elevation (2.5%), ST-depression
(13.9%), T-wave inversion (9.5%), and left bundle branch
block (6%). P-glucose levels were measured in 31.3% of
the cases, of whom 37.6% showed elevated values. Men
had more often deviation of the systolic blood pressure
and atrial fibrillation than women (Table 2). Data collection The patients in this study were consecutively included
by assignment through an EMS record database (Ambu-
link) and followed-up by hospital records (Melior) accord-
ing to the directions for inclusion and exclusion. Ambulink
contains the RETTS-A triage classification and Melior con-
tains the International Classification of Diseases (ICD) code. Medical history and final diagnoses were categorised using These were defined by our research group consisting
of a cardiologist and number of PENs based on the avail-
able literature and clinical experience. This definition
has been previously described [16]. However, a few
further diagnoses (e.g. acute respiratory failure with Page 4 of 11 Page 4 of 11 Kauppi et al. BMC Emergency Medicine (2020) 20:67 hypercapnia or hypoxia, ketoacidosis and lactacidosis)
fulfilling the above criteria appeared in the analyses of
the present study cohort and have therefore been added. hypercapnia or hypoxia, ketoacidosis and lactacidosis)
fulfilling the above criteria appeared in the analyses of
the present study cohort and have therefore been added. dyspnoea. A large proportion had a history of cardiovascu-
lar disease including hypertension (46.5%), heart failure
(30%), atrial fibrillation (29%), ischemic heart disease (26%). Furthermore, 47.5% had a history of pulmonary disease,
18.8% had diabetes and 19.4% had cancer. Men had a
higher prevalence of previous heart disease, diabetes and
renal disease whereas women had a higher prevalence of
previous pulmonary disease, system disease and psychiatric
disease (Table 1). Discussion Discussion
In this study, dyspnoea was classified as the main
symptom in approximately 9% of all the EMS-assigned
patients, similar to previous findings [1, 9, 12]. The most
novel
information
was
that
among
patients
with
dyspnoea there were more than 400 different final diag-
noses. (ICD-10 codes) and 11% of them were assessed as
time critical. Many of the patients had a severe comor-
bidity and 11% were dead within 30 days. Despite this,
only half of the patients dialled 112 within 50 h after
onset of symptoms. Distribution of patients according to the final diagnosis
(ICD-10 code) among groups more than 30 patients The patients showed 473 different ICD-10 codes pointing
to the primary aetiology. The three most commonly ob-
served aetiologies were Chronic Obstructive Pulmonary
Disease (COPD) (20.4%), pulmonary infection (17.1%),
and heart failure (15%). Totally, 11% of the ICD-10 codes
showed time-critical conditions. After combining these
ICD-10 codes, the three most common conditions were
cardiovascular disease, followed by infection and pulmon-
ary disease. Women more often had pulmonary disease
(Table 4). The three most commonly observed disease groups
were those of the respiratory system; those of the
circulatory system; and symptoms, signs, and abnormal
clinical findings not elsewhere classified. This finding is
similar to that of a recent Danish study [8], with the
exception for diseases of the circulatory system, which
were more frequently noted in our study (23% versus
13%). Moreover, the three most commonly observed
aetiologies
were
COPD
(20%),
pulmonary
infection
(17%), and heart failure (15%). In the United States, a
lower frequency of COPD (13%) was observed [12],
whereas a study from Australia/New Zealand showed
higher rates of pulmonary infections (23%) and heart
failure (20%) [11]. Age, sex, and previous history The three most commonly observed disease groups
were: diseases of the respiratory system (49.1%); diseases The patients’ mean age was 73 years, and 56% of them were
women. A majority (84.4%) had previously experienced Fig. 2 Kaplan-Meier survival plot of patients assessed by the PEN as the main symptom of dyspnoea and stratified by women and men er survival plot of patients assessed by the PEN as the main symptom of dyspnoea and stratified by women and men Kauppi et al. BMC Emergency Medicine (2020) 20:67 Page 5 of 11 Table 1 Age, sex and previous history
All patients
Women
Men
Missing
n
6354
3538
2816
All
Women
Men
Age - years
Mean (±SD)
72.9 (17.5)
73.3 (18.1)
72.5 (16.6)
Median (25th,75th percentile)
77 (66,86)
78 (67,86)
76 (66,85)
Previous history - n(%)
Dyspnoea
4971 (84.4)
2766 (84.0)
1.07 [0.89,1.29]a
467
247
220
Pulmonary diseaseb
2966 (47.5)
1762 (50.6)
0.76 [0.66,0.86]
116
59
57
Hypertension
2948 (46.5)
1718 (48.6)
0.82 [0.72,0.94]
8
5
3
Heart failure
1894 (30.0)
961 (27.4)
1.32 [1.15,1.52]
38
27
11
Atrial fibrillation
1838 (29.0)
945 (26.8)
1.27 [1.10,1.47]
14
8
6
Ischaemic heart disease
1642 (26.0)
785 (22.3)
1.54 [1.33,1.79]
40
16
24
Psychiatric disorderc
1337 (21.2)
862 (24.5)
0.63 [0.53,0.74]
34
20
14
Cancer
1226 (19.4)
669 (19.0)
1.06 [0.90,1.25]
23
15
8
Diabetes
1190 (18.8)
550 (15.6)
1.60 [1.35,1.89]
12
7
5
Renal disease
759 (12.0)
310 (8.8)
1.97 [1.61,2.42]
12
8
4
System disease
393 (6.2)
286 (8.1)
0.45 [0.33,0.61]
17
12
5
Other diseased
4412 (69.5)
2458 (69.6)
1.00 [0.87,1.15]
8
4
4
aOdds ratio and 99% - confidence interval
bChronic obstructive pulmonary disease, asthma bronchiale, other pulmonary disease
cPanic disorder, anxiety disorder, depression, bipolar disease, schizofrenia, other psychiatric disorder
dOther disease: e.g. peripheral vascular diseases, other heart conditions, previous pulmonary embolism bChronic obstructive pulmonary disease, asthma bronchiale, other pulmonary disease
cPanic disorder, anxiety disorder, depression, bipolar disease, schizofrenia, other psychiatric disorder
dOther disease: e.g. peripheral vascular diseases, other heart conditions, previous pulmonary embolism of the circulatory system (23.1%); and symptoms, signs,
and abnormal clinical findings not elsewhere classified
(13.4%). Women had more often a respiratory disease
(Table 3). Mortality The overall 30-day, and 1-year mortality values were
11.1, and 21.5%, respectively. Men had a higher 1-year
mortality than women (p < 0.005)(Fig. 2). The three most
common final diagnoses among all patients who died
within 30 days were pneumonia, followed by heart failure
and COPD with acute exacerbation. The three most
common final diagnoses among patients with time-
critical conditions who died within 30 days were stroke,
sepsis followed by acute respiratory insufficiency. The patients in whom dyspnoea was the main symp-
tom represent an older population (median age 77 years)
with a high comorbidity. Such findings have also been Kauppi et al. Mortality BMC Emergency Medicine (2020) 20:67 Page 6 of 11 Table 2 Symptoms and clinical findings Table 2 Symptoms and clinical findings
All patients
Women
Men
Missing
n
6354
3538
2816
All
Women
Men
Time interval - median hh:mma
Symptom onset - call for EMS
51:08 (3:57,145:02)
50:58 [47:49,55:18]
51:11 [47:47,55:59]
438
245
193
Symptoms - n(%)
Pain
1402 (23.1)
806 (23.9)
0.91 [0.78,1.07]b
292
162
130
If yes, VAS mediana
4 (2,6)
3 [2,4]
4 [3,5]
1149
660
489
Syncope
77 (1.2)
47 (1.3)
0.80 [0.44,1.47]
24
14
10
Affected by alcohol, drugs
103 (1.6)
46 (1.3)
1.57 [0.94,2.63]
36
17
19
Vital signs; first recording – medianc
Respiratory rate (breaths/min)
25 (20,32) 48.7
25 (20,32) 49.1
0.96 [0.84,1.01]
137
70
67
Oxygen saturation (%)
93 (86,97) 35.2
93 (85,97) 36.0
0.92 [0.81,1.06]
120
55
65
Heart rate (beats/min)
92 (80,110) 11.5
94 (80,110) 11.7
0.95 [0.77,1.17]
122
58
64
Systolic blood pressure (mmHg)
140 (120,160) 1.8
140 (120,160) 1.2
2.15 [1.30,3.57]
236
132
104
Diastolic blood pressure (mmHg)
80 (70,90) 0.3
80 (70,90) 0.3
1.26 [0.37,4.25]
870
482
388
Body temperature (°C)
37.0 (36.6,37.4) 0.5
37.0 (36.6,37.5) 0.5
1.34 [0.55,3.29]
234
128
106
Degree of consciousness (RLS)
1 (1,1) 1.6
1 (1,1) 1.7
0.91 [0.51,1.60]
1110
616
494
ECG recorded in ambulance - n(%)
4693 (74.0)
2540 (71.9)
1.28 [1.10,1.49]
8
4
4
ECG rhythm - n(%)d
873
512
361
Sinus rythm
3882 (70.8)
2257 (74.6)
0.67 [0.57,0.79]
Atrial fibrillation/flutter
1249 (22.8)
648 (21.4)
1.19 [1.01,1.41]
Other rythme
350 (6.4)
121 (4.0)
2.47 [1.83,3.33]
ECG pattern - n(%)d
957
569
388
ST-elevation
137 (2.5)
67 (2.3)
1.29 [0.82,2.01]
ST-depression
748 (13.9)
420 (14.1)
0.95 [0.77,1.16]
T-wave inversion
511 (9.5)
270 (9.1)
1.10 [0.87,1.40]
Left bundle branch block
325 (6.0)
181 (6.1)
0.97 [0.72,1.31]
Blood Glucose measured - n(%)
1991 (31.3)
1034 (29.2)
1.25 [1.08,1.43]
Blood glucose elevation ≥9.5 mmol/l
749 (37.6)
402 (38.9)
0.89 [0.70,1.14]
aAll patients category denoted with 25th and 75th percentiles, women and men with 99% - confidence intervals;VAS: visual analogue scale
bOdds ratio and 99% - confidence interval
cAll patients and women category denoted with median (25th,75th percentiles) and percetage of deviating vital signs. Mortality Odds ratio and 99%-confidence intervals
calculated on number of deviating vital signs
Deviating vital signs: Respiratory rate < 8 or > 25 breaths/min; Oxygen saturation < 90%; Heart rate < 40/min or > 120/min; Systolic blood pressure < 90 mm/Hg;
Diastolic blood pressure > 140 mm/hg; Body temperature (°C) < 35 or > 41; Reaction level scale (RLS) > 2
d almost three times as high as in the total EMS popula-
tion in the same area [19]. Furthermore, our result also
found that men with dyspnoea as the main symptom
had a higher mortality rate than women. We have no
clear explanation to this finding. There was no signifi-
cant difference between women and men in terms of
their final diagnosis with the exception of a lower rate of
pulmonary disease among women. But men had a more
severe comorbidity and more frequently suffered from a
previous history of a cardiovascular disease and renal
disease. This may have contributed the higher mortality
among men. From an overall population perspective reported in previous studies [8, 11, 12]. This is not
unexpected since the incidence of chronic conditions
associated with dyspnoea (e.g. COPD, heart failure, and
coronary artery disease) increase with age [18]. Surpris-
ingly, the majority had previously experienced dyspnoea. In our result, more than 60% of all patients were hospi-
talised. This is more than the entire EMS population in
the same sampling area where the median age was 69
years and 50% of those taken to the ED were hospita-
lised [19]. Overall, 11% of our study patients died within 30 days,
similar to previous studies [8, 9]. The mortality risk was Kauppi et al. Mortality BMC Emergency Medicine (2020) 20:67 Page 7 of 11 Table 3 Distribution of patients across the 23 major ICD-10 code groups
All patientsa
Women
Men
Chapters - n(%)
6354
3538
2816
I Certain infections and parasites diseases A00 – B99
161 (3.0)
75 (2.6)
1.40 [0.92,2.10]b
II Neoplasm C00 – D48
131 (2.5)
62 (2.1)
1.35 [0.85,2.12]
III Diseases of the blood and blood forming organs
and certain diseases involving the
immuno-mechanisms D50 – D89
34 (0.6)
16 (0.6)
1.35 [0.56,3.29]
IV Endocrine, nutritional and metabolic diseases
E00 – E90
42 (0.8)
25 (0.9)
0.82 [0.36,1.84]
V Mental and behavioural disorders F00 – F99
91 (1.7)
50 (1.7)
0.98 [0.57,1.70]
VI Diseases of the nervous system G00 – G99
29 (0.5)
17 (0.6)
0.85 [0.32,2.24]
VII Diseases of the eye and adnexa H00 – H59
0 (0.0)
0 (0.0)
0 [0,0]
VIII Diseases of the eye and mastoid process
H60 – H95
0 (0.0)
0 (0.0)
0 [0,0]
IX Diseases of the circulatory system I00 – I99
1230 (23.1)
647 (22.3)
1.11 [0.94,1.31]
X Diseases of the respiratory system J00 – J99
2615 (49.1)
1476 (50.8)
0.86 [0.75,0.99]
XI Diseases of the digestive system K00 – K93
65 (1.2)
33 (1.1)
1.17 [0.61,2.22]
XII Diseases of the skin and subcutaneous tissue
L00 – L99
6 (0.1)
3 (0.1)
1.20 [0.15,9,85]
XIII Diseases of the musculoskeletal tissue and
connective tissue M00 – M99
51 (1.0)
37 (1.3)
0.45 [0.20,1.02]
XIV Diseases of the genitourinery system N00 – N99
69 (1.3)
30 (1.0)
1.57 [0.84,2.95]
XV Pregnancy, childbirth and puerperium O00 – O99
1 (< 0.1)
1 (< 0.1)
0 [0,0]
XVI Certain conditions originating from the perinatal
period P00 – P96
0 (0.0)
0 (0.0)
0 [0,0]
XVII Congenital malformations, deformation and
chromosomal malformations Q00 – Q99
1 (< 0.1)
0 (0.0)
0 [0,0]
XVIII Symptoms, signs and abnormal clinical findings,
not elsewhere classified R00 – R99
711 (13.4)
382 (13.2)
1.04 [0.84,1.28]
XIX Injury, Poisoning and certain other consequences
of external causes S00 – T98
33 (0.6)
23 (0.8)
0.52 [0.20,1.38]
XX External causes of morbidity and mortality
V00 – V99
1 (< 0.1)
1 (< 0.1)
0 [0,0]
XXI External causes to disease and death Y01 – Y98
1 (< 0.1)
1 (< 0.1)
0 [0,0]
XXII Factors influencing health status and contact
with health services Z00 – Z99
48 (0.9)
23 (0.8)
1.31 [0.62,2.76]
XXIII Codes for special purposes U00-U99
4 (0.1)
3 (0.1)
0.40 [0.20,7.84]
aMissing diagnosis in 1030 patients (women 633, men 397)
bOdds ratio and 99% - confidence interval Table 3 Distribution of patients across the 23 major ICD-10 code groups XIII Diseases of the musculoskeletal tissue and
connective tissue M00 – M99 XIV Diseases of the genitourinery system N00 – N99 XV Pregnancy, childbirth and puerperium O00 – O99 XVI Certain conditions originating from the perinatal
period P00 – P96 aMissing diagnosis in 1030 patients (women 633, men 397)
bOdds ratio and 99% - confidence interval [20], it has been denoted that men have a greater vulner-
ability to cardiovascular diseases which is a reason to
their higher mortality rate in general. Mortality the five First Hour Quinted emergency time-related
pathologies. This means that immediate prehospital
treatment and early diagnosis may be crucial in reducing
the morbidity and mortality risk [6]. Patients attending EMS due to dyspnoea appear to
have a five times higher risk of death than those with
chest pain [9, 21]. This is in agreement with other
reports saying that regardless of the aetiology, patients
who have dyspnoea in combination with other condi-
tions have a poor prognoses [22]. Thus, dyspnoea should
be perceived as a high-risk symptom and a strong
predictor of an increased mortality risk [9, 11, 23, 24]. Further, respiratory failure has been defined as among This should be attributed to the fact that patients only
call EMSs when they cannot manage the situation them-
selves and indeed half of patients waited more than
2 days after symptom onset in our study. In one previ-
ous study [25], patients tried to ignore their symptoms
or manage them (working through), leading to delays in
calling EMSs; some of these patients even took a
“waiting approach”, while others were frustrated by their Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine Page 8 of 11 Table 4 Distribution of patients according to final diagnosis (ICD-10 code) among groups more than 30 patients
All patientsa
Women
Men
Final diagnosis - n(%)
6354
3538
2816
1. Cardiovascular disease
1316 (24.7)
694 (23.9)
1.10 [0.94,1.30]b
a. Heart failure
801 (15.0)
402 (13.8)
399 (16.5)
b. Ischemic heart disease
154 (2.9)
70 (2.4)
84 (3.5)
c. Arrhythmia
142 (2.7)
87 (3.0)
55 (2.3)
d. Pulmonary embolism
123 (2.3)
81 (2.8)
42 (1.7)
2. Pulmonary disease
1311 (24.6)
780 (26.9)
0.77 [0.65,0.91]
a. Chronic obstructive pulmonary disease
1088 (20.4)
656 (22.6)
432 (17.9)
b. Asthma bronchiale
127 (2.4)
87 (3.0)
40 (1.7)
c. Other pulmonary diseases
94 (1.8)
37 (1.3)
57 (2.4)
3. Infection
1172 (22.0)
607 (20.9)
1.15 [0.97,1.37]
a. Pulmonary
912 (17.1)
469 (16.1)
443 (18.3)
b. Sepsis
97 (1.8)
43 (1.5)
54 (2.2)
c. Ear, nose and throat and upper airways
81 (1.5)
52 (1.8)
29 (1.2)
d. Other infection
74 (1.4)
40 (1.4)
34 (1.4)
4. Symptom diagnosis
662 (12.4)
353 (12.2)
1.06 [0.85,1.31]
5. Cancer
138 (2.6)
66 (2.3)
1.32 [0.85,2.01]
a. Pulmonary
89 (1.7)
49 (1.7)
40 (1.7)
b. Other localisation
31 (0.6)
13 (0.4)
18 (0.7)
6. Mortality Respiratory insufficiency
129 (2.4)
79 (2.7)
0.76 [0.47,1.21]
7. Psychiatric disorder
90 (1.7)
49 (1.7)
1.01 [0.58,1.74]
9. Urinary disease
69 (1.3)
30 (1.0)
1.57 [0.84,2.95]
10. Pleura Disease
54 (1.0)
32 (1.1)
0.82 [0.40,1.69]
11. Muscle skeletal pain
44 (0.8)
32 (1.1)
0.45 [0.19,1.07]
12. Organ failure
39 (0.7)
23 (0.8)
0.84 [0.36,1.95]
13. Gastrointestinal disease
33 (0.6)
18 (0.6)
1.00 [0.41,2.47]
14. Anaemia
33 (0.6)
15 (0.5)
1.44 [0.59,3.56]
aMissing diagnosis in 1030 patients (women 633, men 397)
bOdds ratio with 99% - confidence interval, subcategories with percentage Table 4 Distribution of patients according to final diagnosis (ICD-10 code) among groups more than 30 patients
All patientsa
Women
Men Table 4 Distribution of patients according to final diagnosis (ICD-10 code) among groups more than 30 patients ents according to final diagnosis (ICD-10 code) among groups more than 30 patients aMissing diagnosis in 1030 patients (women 633, men 397)
bOdds ratio with 99% - confidence interval, subcategories with percentage Almost one in four patients had atrial fibrillation and
a few had signs of myocardial ischemia on ECG, indicat-
ing that a cardiac pathology was not uncommon. This is
most likely explained by the high degree of cardiovascu-
lar comorbidity reported in such populations [26–29]. Atrial fibrillation and acute heart failure are often seen
in combination, and since heart failure is one of the
dominating aetiologies behind dyspnoea, this was an
expected finding. Based on previous history, one may
assume that when atrial fibrillation occurred, it was most
often previously known. Dyspnoea due to acute heart
failure and the presence of ECG-related abnormalities,
such as ventricular or supraventricular arrhythmia, brady-
cardia, or ongoing myocardial ischemia, may all be indica-
tors of an increased risk of early hospital death [30]. symptoms. This information is vital for consideration in
the meeting between the PEN and patient. The dyspnoea experience varies across people, and
one can assume that some degree of tolerance to
dyspnoea already existed in our patient group due to
their comorbidities (e.g. COPD, heart failure, and
hypertension). This is supported by earlier studies
[10, 23] in which this patient group was characterised
by poor health. Dyspnoea, to some extent, is a part of
natural ageing and results in a decreasing degree of
physical capacity; thus, it is not always explained by a
specific illness or related to comorbidity presence. Mortality It
may also be that elderly people are more tolerant and
do not want to interfere or be perceived as disruptive. Thus, they may understate their symptom experience
and severity when finally calling for help. This makes
it even more difficult for both dispatchers and the
PEN to determine disease severity [11]. One in four patients experienced pain, which may be
important from a diagnostic as well as therapeutic
perspective. The pain experience was mostly related to Page 9 of 11 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Furthermore, due to the study design, the data had to
be retrospectively collected from patient records, and
important clinical parameters such as VS may have been
measured but never recorded. In both EMS and hospital
records, the documentation was sometimes insufficient. Likewise, it is possible that patients with other main
symptoms who still have dyspnoea may have been classi-
fied into other ESS codes (not only ESS 04) by the PEN,
as dyspnoea is also present in other conditions such as
chest pain. breathing-related chest discomfort, thoracic pain, chest
wall pain, shoulder pain, or pain due to other unclear
reasons. The presence of pain in dyspnoea patients has
previously been reported [9, 21, 22, 31], mostly in the
form of chest pain as a result of underlying causes
including pulmonary embolism myocardial infarction,
pneumonia and panic disorder. A large proportion had hyperglycaemia. This may be
an alarming sign also among patients with dyspnoea. Hyperglycaemia is a marker of acute stress response
which, especially in nondiabetic patients, is associated
with
higher
rates
of
in-hospital
complications
and
mortality [15, 32]. Information on the final diagnosis was missing in 1030
of all missions. Such cases were those left on- scene in
whom there was no information on final diagnosis and
patients who were brought to hospital and directly sent
home from the Emergency Department, since some of
them were never assessed by a physician. However, the
present study was conducted in accordance with a paper
by Kaji et al. [37], with the aim of reducing the bias
associated with medical record reviews. Clinical implications Our results suggest that 11% of all patients seen by PENs
due to dyspnoea have time critical diagnosis and 11%
will die during the subsequent 30 days. Available infor-
mation from age, sex, comorbidity and clinical findings
including
vital
parameters,
ECG
recordings,
blood
glucose measurements and other symptoms may form
the basis for the building of future decision support tools
in order to differentiate patients with high and low risk
for future adverse events. Supplementary information
Supplementary information accompanies
1186/s12873-020-00363-6. Supplementary information
Supplementary information accompanies this paper at https://doi.org/10. 1186/s12873-020-00363-6. Conclusions Dyspnoea, as the main symptom, constituted approxi-
mately 9% of all the EMS missions in our study. A major-
ity of the patients taken to hospital with dyspnoea as the
main symptom were hospitalised and more than 400
different final diagnoses were observed, of which 11% were
regarded as time-critical. A very high proportion (84%)
had previously suffered from dyspnoea, which may explain
why more than half showed delays greater than 2 days
from symptom onset to EMS contact. High comorbidity
values may contribute to this finding. Likewise, that pa-
tients call for help only when the situation is truly unman-
ageable makes them even more vulnerable. Dyspnoea, as
the main symptom, is associated with a high risk of death,
and 11% of all patients were dead within 30 days. However, more than half of these patients had abnormal
vital parameters at the time of PEN assessment. This
knowledge is important, not only for EMSs, but also for
clinicians and those responsible for the provision of
education in different emergency courses. Strengths and limitations Additional file 1. The supplementary file describes in more detail
deviating vital signs Red/Orange level according to RETTS-A (2017
version) and RETTS ESS 04 (main symptom of dyspnoea). The major strength of our study is that data were
collected from a relatively large representative sample. While the data were collected from a mix of urban and
rural areas, the study itself is limited to a specific region
of Sweden (southwest) which may impede the degree of
generalisability of the findings to other settings. People
living in the northern part of Sweden have greater diffi-
culties in accessing EMSs and longer transport distances,
which may lead to result variations. Mortality Although only 11% had time critical final diagnoses, a
much
larger
proportion
of
these
patients
will
be
regarded as having a time-critical condition in the acute
phase since the majority had abnormal VS, primarily an
abnormal respiratory rate and oxygen saturation. This
requires advanced knowledge from the PENs who is
caring for patients with dyspnoea, as abnormal vital
parameters may be a sign of a number of different
serious conditions; both cardiogenic, pulmonary and
other aetiologies of acute respiratory failure. This high-
lights the importance of early recognition of the patients
condition and directed treatment already at an early
stage by EMS, as it might be crucial for the final out-
come [33–35]. It has previously been reported that acute
ill patients (including those with dyspnoea) admitted
thorough ED [36] with abnormal vital parameters, have
an increased risk of death. The most powerful predictors
were abnormal respiratory rate, oxygen saturation and
Glasgow Coma scale (GCS). Ethics approval and consent to participate The design of the study was approved by the Regional Ethics Committee in
Gothenburg, Sweden (Dnr 989-17). All the procedures performed in this
study were in accordance with the ethical standards of the Declaration of
Helsinki [38]. Consent were obtained from chief executive officers in the
participating EMS organisations for reviewing patient records and to use the
data for analysis. Informed consent for participation was not required. This is
mostly not recommended by Ethical Review Boards in Sweden for the
following reasons: 13. Suserud BO. A new profession in the pre-hospital care field--the ambulance
nurse. Nurs Crit Care. 2005;10:269–71. 13. Suserud BO. A new profession in the pre-hospital care field--the ambulance
nurse. Nurs Crit Care. 2005;10:269–71. 14. Widgren BR, Jourak M. Medical emergency triage and treatment system
(METTS): a new protocol in primary triage and secondary priority decision in
emergency medicine. J Emerg Med. 2011;40:623–8. 14. Widgren BR, Jourak M. Medical emergency triage and treatment system
(METTS): a new protocol in primary triage and secondary priority decision in
emergency medicine. J Emerg Med. 2011;40:623–8. 15. Sud M, Wang X, Austin PC, Lipscombe LL, Newton GE, Tu JV, et al. Presentation blood glucose and death, hospitalization, and future
diabetes risk in patients with acute heart failure syndromes. Eur Heart J. 2015;36:924–31. 15. Sud M, Wang X, Austin PC, Lipscombe LL, Newton GE, Tu JV, et al. Presentation blood glucose and death, hospitalization, and future
diabetes risk in patients with acute heart failure syndromes. Eur Heart J. 2015;36:924–31. 1)
Individual patients could never be identified since their identification
number was translated to a code. Their integrity, therefore, remained
intact. 1)
Individual patients could never be identified since their identification
number was translated to a code. Their integrity, therefore, remained
intact. 16. Wibring K, Magnusson C, Axelsson C, Lundgren P, Herlitz J, Andersson HM. Towards definitions of time-sensitive conditions in prehospital care. Scand J
Trauma Resusc Emerg Med. 2020;28:7. 16. Wibring K, Magnusson C, Axelsson C, Lundgren P, Herlitz J, Andersson HM. Towards definitions of time-sensitive conditions in prehospital care. Scand J
Trauma Resusc Emerg Med. 2020;28:7. 2)
Some of the most seriously ill patients could never be contacted
retrospectively, since they had either died or were in a very poor
clinical condition. This would increase the risk of selection bias,
thereby, hampering the reliability of the data. 17. Sovso MB, Christensen MB, Bech BH, Christensen HC, Christensen EF,
Huibers L. Abbreviations COPD: Chronic obstructive pulmonary disease; ECG: Electrocardiogram;
ED: Emergency department; EMS: Emergency medical service;
ESS: Emergency signs and symptoms; ICD-10: International Statistical
Classification of Diseases and Related Health Problems – 10th revision;
PEN: Prehospital emergency nurse; RETTS-A: Rapid emergency triage and
treatment system for adults; VS: Vital signs Page 10 of 11 Page 10 of 11 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 3. Pooler C. Living with chronic lower pulmonary disease: disruptions of the
embodied phenomenological self. Glob Qual Nurs Res. 2014;1:
2333393614548762. Funding
WK
i WK received funding from the University of Borås, Sweden. The funder did
not have any role in the study design, aim, or process. Open access funding
provided by University of Boras. 10. Hayen A, Herigstad M, Pattinson KT. Understanding dyspnea as a complex
individual experience. Maturitas. 2013;76:45–50. 11. Kelly AM, Holdgate A, Keijzers G, Klim S, Graham CA, Craig S, et al. Epidemiology, prehospital care and outcomes of patients arriving by
ambulance with dyspnoea: an observational study. Scand J Trauma Resusc
Emerg Med. 2016;24:113. Consent for publication
Not applicable. Not applicable. 19. Magnusson C, Herlitz J, Axelsson C. Patient characteristics, triage utilisation,
level of care, and outcomes in an unselected adult patient population seen
by the emergency medical services: a prospective observational study. BMC
Emerg Med. 2020;20:7. Acknowledgements The authors wish to acknowledge the Ambulance and Prehospital
Emergency Care, Sahlgrenska University Hospital in Gothenburg, Sweden
and Ambulance and Prehospital Emergency Care, Södra Älvsborg hospital in
Borås, Sweden for providing data on EMS assignments. We also
acknowledge the help extended by Jonny Lindqvist, Region Västra Götaland,
Gothenburg, Sweden in creating the data protocol. 4. Berliner D, Schneider N, Welte T, Bauersachs J. The differential diagnosis of
dyspnea. Dtsch Arztebl Int. 2016;113:834–45. and Ambulance and Prehospital Emergency Care, Södra Älvsborg hospital in
Borås, Sweden for providing data on EMS assignments. We also acknowledge the help extended by Jonny Lindqvist, Region Västra Götaland,
Gothenburg, Sweden in creating the data protocol. 5. Gori CS, Magrini L, Travaglino F, Di Somma S. Role of biomarkers in patient
with dyspnea. Eur Rev Med Pharmacol Sci. 2011;15:229–40. 5. Gori CS, Magrini L, Travaglino F, Di Somma S. Role of biomarkers in patients
with dyspnea. Eur Rev Med Pharmacol Sci. 2011;15:229–40. 6. Krafft T, Garcia Castrillo-Riesgo L, Edwards S, Fischer M, Overton J,
Robertson-Steel I, et al. European emergency data project (EED project):
EMS data-based health surveillance system. Eur J Pub Health. 2003;13:85–90. Availability of data and materials The datasets analysed during the current study are available from the
corresponding author on reasonable request. 12. Prekker ME, Feemster LC, Hough CL, Carlbom D, Crothers K, Au DH, et al. The epidemiology and outcome of prehospital respiratory distress. Acad
Emerg Med. 2014;21:543–50. Received: 24 March 2020 Accepted: 21 August 2020 Received: 24 March 2020 Accepted: 21 August 2020 22. McConaghy JR, Oza RS. Outpatient diagnosis of acute chest pain in adults. Am Fam Physician. 2013;87:177–82. 23. Huijnen B, van der Horst F, van Amelsvoort L, Wesseling G, Lansbergen M,
Aarts P, et al. Dyspnea in elderly family practice patients. Occurrence,
severity, quality of life and mortality over an 8-year period. Fam Pract. 2006;
23:34–9. Authors’ contributions WK, CA, JH, and LP developed the design and the research protocol. WK, CA,
and JH created the data forms. WK collected the data. CM supervised the
statistical analyses and was discussed with WK, CA and JH. WK and JH wrote
the first draft of the manuscript. WK, CA, JH, LP, and CM supervised and
analysed the data and their interpretation. All the authors participated in the
final drafting of the manuscript and have read and approved the final
manuscript. 7. Christie A, Costa-Scorse B, Nicholls M, Jones P, Howie G. Accuracy of
working diagnosis by paramedics for patients presenting with dyspnoea. Emerg Med Australas. 2016;28:525–30. 8. Lindskou TA, Pilgaard L, Sovso MB, Klojgard TA, Larsen TM, Jensen FB, et al. Symptom, diagnosis and mortality among respiratory emergency medical
service patients. PLoS One. 2019;14:e0213145. analysed the data and their interpretation. All the authors participated in the
final drafting of the manuscript and have read and approved the final
manuscript. 9. Botker MT, Stengaard C, Andersen MS, Sondergaard HM, Dodt KK, Niemann
T, et al. Dyspnea, a high-risk symptom in patients suspected of myocardial
infarction in the ambulance? A population-based follow-up study. Scand J
Trauma Resusc Emerg Med. 2016;24:15. Author details
1 20. Crimmins EM, Shim H, Zhang YS, Kim JK. Differences between men and
women in mortality and the health dimensions of the morbidity process. Clin Chem. 2019;65:135–45. 1PreHospen- Centre for Prehospital Research, Faculty of Caring, Work Life and
Social Welfare, University of Borås, SE- 501 90 Borås, Sweden. 2Faculty of
Caring Science, Work Life and Social Welfare, University of Borås, Borås,
Sweden. 3Department of Molecular and Clinical Medicine, Sahlgrenska
Academy, University of Gothenburg, Gothenburg, Sweden. 21. Pedersen CK, Stengaard C, Friesgaard K, Dodt KK, Sondergaard HM,
Terkelsen CJ, et al. Chest pain in the ambulance; prevalence, causes and
outcome - a retrospective cohort study. Scand J Trauma Resusc Emerg Med. 2019;27:84. Competing interests The authors declare that they have no competing interests. Ethics approval and consent to participate Contacting out-of-hours primary care or emergency medical
services for time-critical conditions - impact on patient outcomes. BMC
Health Serv Res. 2019;19:813. 3)
Approaching patients with these issues may create more anxiety than
satisfaction and may, therefore, be regarded as unethical. 18. Kelly AM, Keijzers G, Klim S, Graham CA, Craig S, Kuan WS, et al. An
observational study of dyspnea in emergency departments: the Asia,
Australia, and New Zealand dyspnea in emergency departments study
(AANZDEM). Acad Emerg Med. 2017;24:328–36. 18. Kelly AM, Keijzers G, Klim S, Graham CA, Craig S, Kuan WS, et al. An
observational study of dyspnea in emergency departments: the Asia,
Australia, and New Zealand dyspnea in emergency departments study
(AANZDEM). Acad Emerg Med. 2017;24:328–36. References 1. Pittet V, Burnand B, Yersin B, Carron PN. Trends of pre-hospital emergency
medical services activity over 10 years: a population-based registry analysis. BMC Health Serv Res. 2014;14:380. 1. Pittet V, Burnand B, Yersin B, Carron PN. Trends of pre-hospital emergency
medical services activity over 10 years: a population-based registry analysis. BMC Health Serv Res. 2014;14:380. 24. Berraho M, Nejjari C, El Rhazi K, Tessier JF, Dartigues JF, Barberger-Gateau P,
et al. Dyspnea: a strong independent factor for long-term mortality in the
elderly. J Nutr Health Aging. 2013;17:908–12. 2. Parshall MB, Schwartzstein RM, Adams L, Banzett RB, Manning HL, Bourbeau
J, et al. An official American Thoracic Society statement: update on the
mechanisms, assessment, and management of dyspnea. Am J Respir Crit
Care Med. 2012;185:435–52. 25. McCabe PJ, Rhudy LM, Chamberlain AM, DeVon HA. Fatigue, dyspnea, and
intermittent symptoms are associated with treatment-seeking delay for Page 11 of 11 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 symptoms of atrial fibrillation before diagnosis. Eur J Cardiovasc Nurs. 2016;
15:459–68. symptoms of atrial fibrillation before diagnosis. Eur J Cardiovasc Nurs. 2016;
15:459–68. 26. Odigie-Okon E, Jordan B, Dijeh S, Wolff A, Dadu R, Lall P, et al. Cardiac injury
in patients with COPD presenting with dyspnea: a pilot study. Int J Chron
Obstruct Pulmon Dis. 2010;5:395–9. 27. Wilhelmsen L, Rosengren A, Lappas G. Hospitalizations for atrial fibrillation in
the general male population: morbidity and risk factors. J Intern Med. 2001;
250:382–9. 28. Ariansen I, Edvardsen E, Borchsenius F, Abdelnoor M, Tveit A, Gjesdal K. Lung function and dyspnea in patients with permanent atrial fibrillation. Eur
J Intern Med. 2011;22:466–70. 29. Vanfleteren LE, Franssen FM, Uszko-Lencer NH, Spruit MA, Celis M, Gorgels
AP, et al. Frequency and relevance of ischemic electrocardiographic findings
in patients with chronic obstructive pulmonary disease. Am J Cardiol. 2011;
108:1669–74. 30. Beygui F, Castren M, Brunetti ND, Rosell-Ortiz F, Christ M, Zeymer U, et al. Pre-hospital management of patients with chest pain and/or dyspnoea of
cardiac origin. A position paper of the Acute Cardiovascular Care
Association (ACCA) of the ESC. Eur Heart J Acute Cardiovasc Care. 2015;9:
59–81. 31. Johansson EL, Ternesten-Hasseus E, Olsen MF, Millqvist E. Respiratory
movement and pain thresholds in airway environmental sensitivity, asthma
and COPD. Respir Med. 2012;106:1006–13. 32. Schuetz P, Kennedy M, Lucas JM, Howell MD, Aird WC, Yealy DM, et al. References Initial management of septic patients with hyperglycemia in the noncritical
care inpatient setting. Am J Med. 2012;125:670–8. 33. Mebazaa A, Tolppanen H, Mueller C, Lassus J, DiSomma S, Baksyte G, et al. Acute heart failure and cardiogenic shock: a multidisciplinary practical
guidance. Intensive Care Med. 2016;42:147–63. 34. Hensel M, Strunden MS, Tank S, Gagelmann N, Wirtz S, Kerner T. Prehospital
non-invasive ventilation in acute respiratory failure is justified even if the
distance to hospital is short. Am J Emerg Med. 2019;37:651–6. 35. Nielsen VM, Madsen J, Aasen A, Toft-Petersen AP, Lubcke K, Rasmussen BS,
et al. Prehospital treatment with continuous positive airway pressure in
patients with acute respiratory failure: a regional observational study. Scand
J Trauma Resusc Emerg Med. 2016;24:121. 36. Barfod C, Lauritzen MM, Danker JK, Soletormos G, Forberg JL, Berlac PA,
et al. Abnormal vital signs are strong predictors for intensive care unit
admission and in-hospital mortality in adults triaged in the emergency
department - a prospective cohort study. Scand J Trauma Resusc Emerg
Med. 2012;20:28. 37. Kaji AH, Schriger D, Green S. Looking through the retrospectoscope:
reducing bias in emergency medicine chart review studies. Ann Emerg
Med. 2014;64:292–8. 37. Kaji AH, Schriger D, Green S. Looking through the retrospectoscope:
reducing bias in emergency medicine chart review studies. Ann Emerg
Med. 2014;64:292–8. 38. World Medical A. World medical association declaration of Helsinki: ethical
principles for medical research involving human subjects. JAMA. 2013;310:
2191–4. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations.
|
https://openalex.org/W3163893482
|
https://bmcgastroenterol.biomedcentral.com/track/pdf/10.1186/s12876-021-01813-6
|
English
| null |
Primary intestinal lymphangiectasia presenting as limb hemihyperplasia: a case report and literature review
|
BMC gastroenterology
| 2,021
|
cc-by
| 3,575
|
Khayat BMC Gastroenterol (2021) 21:225
https://doi.org/10.1186/s12876-021-01813-6 Khayat BMC Gastroenterol (2021) 21:225
https://doi.org/10.1186/s12876-021-01813-6 Abstract Background: Primary intestinal lymphangiectasia is an exceedingly rare disorder. Epidemiology is unknown. It usu-
ally presents with lower extremity swelling, diarrhea, ascites, and protein-losing enteropathy. Since the pathogenesis
of edema is usually due to hypoalbuminemia; both extremities are typically involved. The edema can rarely be due to
abnormal lymphatic circulation, causing lymphedema, which usually involves both extremities as well. Diagnosis is
made by the constellation of clinical, biochemical, endoscopic, and histological findings. Treatment involves dietary
modification, to reduce lymphatic dilation in response to dietary fat. Other pharmacologic (e.g., octreotide) and
replacement measures may be indicated as well. The most serious long-term complication is intestinal lymphoma. Herein is a case of Primary intestinal lymphangiectasia presenting with unilateral lower limb swelling. Case presentation: A 4-year-old boy presents with left foot swelling since the age of 4 months, in addition to inter-
mittent diarrhea, and abdominal swelling. The foot swelling had been evaluated by different health care professionals
in the past, and was mislabeled as either cellulitis, or congenital hemihyperplasia. Physical examination revealed mild
ascites, and a non-pitting foot edema with a positive Stemmer’s sign (lymphedema). Blood work revealed hypoalbu-
minemia (albumin 2 g/dl), and hypogammaglobulinemia. Endoscopy showed dilated lacteals throughout the duo-
denum. Histopathologic examination revealed massively dilated lamina propria lymphatics in the duodenal biopsies. The patient was diagnosed with primary intestinal lymphangiectasia. He was treated with high-protein and low-fat
diet, and supplemental formula high in medium chain triglycerides. On follow-up, the patient’s diarrhea completely
resolved, and his ascites and edema improved significantly. Conclusions: The presence of unilateral lower limb edema should not preclude the diagnosis of systemic disor-
ders, and a high index of suspicion is required in atypical presentations. A good knowledge about Primary intestinal
lymphangiectasia manifestations, and physical examination skills to differentiate edema or lymphedema from tissue
overgrowth can significantly aid in the diagnosis. Keywords: Lymphedema, Intestinal lymphangiectasis, Primary intestinal lymphangiectasia, Saudi Arabia,
Hemihyperplasia, Case report Primary intestinal lymphangiectasia
presenting as limb hemihyperplasia: a case
report and literature review Ammar A. Khayat* © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Background Primary intestinal lymphangiectasia (PIL) was first
described by Waldman et al. in 1961, when they noticed
an association between hypoproteinemia and gut protein
loss [1]. Since then, sporadic cases from around the world
have been reported on this rare disease [2, 3]. Prevalence
is unknown, with most studies being limited to case *Correspondence: aakhayat@uqu.edu.sa
Department of Pediatrics, Gastroenterology Unit, Department
of Pediatrics, Faculty of Medicine, Umm AL Qura University, King
Abdulaziz University, 24381 Al‑Abdiyyah, Makkah, Saudi Arabia © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Khayat BMC Gastroenterol (2021) 21:225 Page 2 of 5 Page 2 of 5 Left foot examination revealed a significantly swollen
dorsal aspect of the foot and toes confirming presence
of edema up to the level of his ankle. The edema was
minimally pitting, with a positive Stemmer’s sign (Fig. 1). Ankle joint examination was otherwise unremarkable. reports and series [4]. The majority of patients present in
the first 3 years of life [4, 5]. The most common reported
presentation is bilateral lower limb edema, with or with-
out ascites, and often with diarrhea [4, 5]. PIL typically
responds well to dietary modification [4, 5]. Herein is
a case of PIL presenting with unilateral edema, initially
mislabeled as limb hemihyperplasia (hemihypertrophy),
and ascites. Laboratory workup showed a low albumin at 2 g/
dl (normal range 3.5–5.5 g/dl), total protein at 2.9 g/
dl (normal range 6–8 g/dl), total IgG at 147 mg/dl (nor-
mal range 565–1765 mg/dl), IgM at 16 mg/dl (normal
range 55–375 mg/dl), and IgA at 30 mg/dl (normal range
85–385 mg/dl). Other tests were essentially within nor-
mal limits including a negative urine protein, normal liver
enzyme levels, and a negative tissue transglutaminase
IgA antibody. Upper and lower gastrointestinal endos-
copies were performed and showed the classic appear-
ance of white spots or dilated “lacteals” in the duodenum
(Fig. 2). The colon showed lymphoid nodular hyperplasia. Otherwise, endoscopy was unremarkable. Histopatho-
logic examination showed a remarkably dilated lamina
propria lymphatic vessels in the duodenum (Fig. 3). Oth-
erwise, no other significant abnormalities were observed. Lymphoscintigraphy of his left foot showed failure of
progression to the proximal lymph nodes confirming the
presence of massively dilated lymphatics.h Case presentation 2 Endoscopic image of the duodenum at the level of the second part, showing the mucosa completely covered with white spots or dilated
“lacteals” Fig. 2 Endoscopic image of the duodenum at the level of the second part, showing the mucosa completely covered with white spots or dilated
“lacteals” age of the duodenum at the level of the second part, showing the mucosa completely covered with white spots or dilated Fig. 2 Endoscopic image of the duodenum at the level of the second part, showing the mucosa completely covered with
“lacteals” Fig. 2 Endoscopic image of the duodenum at the level of the second part, showing the mucosa completely covered with white spots or dilated
“lacteals” Fig. 4 A and B: Photographic images of the patient’s left foot
showing the edema prior to dietary modification (a) and the
significant improvement after dietary modification (b) Fig. 3 Hematoxylin and Eosin stain of duodenal mucosal biopsy at
10X magnification, showing massively dilated lymphatic vessels in
lamina propria, glandular and surface epithelium are unremarkable
otherwise. Podoplanin stain highlighting the lymphatic vascular
endothelium of duodenal mucosal biopsy at 10X magnification is
shown in inset, again redemonstrating the massive dilation Fig. 4 A and B: Photographic images of the patient’s left foot
showing the edema prior to dietary modification (a) and the
significant improvement after dietary modification (b) Fig. 3 Hematoxylin and Eosin stain of duodenal mucosal biopsy at
10X magnification, showing massively dilated lymphatic vessels in
lamina propria, glandular and surface epithelium are unremarkable
otherwise. Podoplanin stain highlighting the lymphatic vascular
endothelium of duodenal mucosal biopsy at 10X magnification is
shown in inset, again redemonstrating the massive dilation Case presentation A 4-year-old boy with no known medical condition
presents to an outpatient clinic with history of left foot
swelling and diarrhea. The swelling was noted by par-
ents at the age of 4 months, which had been evaluated
by medical professionals and attributed to a local infec-
tion according to parents. It had never disappeared com-
pletely, despite a waxing and waning course, which led
parents to believe it was a congenital condition. During
the course, a physician mislabeled the swelling as hemi-
hyperplasia (hemihypertrophy), due to the stark differ-
ence in the size of the feet. More recently, the patient
started complaining of intermittent watery to semi-
formed stools, 3–6 times per day, that were aggravated by
fatty diet, and were occasionally difficult to flush. He was
noted to have poor subcutaneous fat in his face and arms
but did not lose weight. Family history was negative for
lymphedema, or any other genetic disorder. The diagnosis of primary intestinal lymphangiectasia
was made based on the constellation of clinical, biochem-
ical, endoscopic, and histological findings.h On examination, he was vitally stable. He looked
undernourished even though his weight was on the 90th
centile, likely due to ascites. Abdominal examination
revealed mild ascites, normal bowel sounds, and no orga-
nomegaly. Cardiac and respiratory examinations were
unremarkable. His right foot showed almost no edema. i
The patient was started on high protein, minimal fat
diet, along with supplemental high medium chain triglyc-
eride (MCT) formula. On follow up, his weight remained on the 90th cen-
tile, however, his mid-arm circumference was on
the 75th centile. His bowel movement frequency, Fig. 1 a and b Photographic images of the patient’s left foot (a), showing a positive Stemmer’s sign: the skin on the dorsum of the second toe
cannot be easily pinched, compared to the right foot (b) Fig. 1 a and b Photographic images of the patient’s left foot (a), showing a positive Stemmer’s sign: the skin on the dorsum of the second toe
cannot be easily pinched, compared to the right foot (b) Fig. 1 a and b Photographic images of the patient’s left foot (a), showing a positive Stemmer’s sign: the skin on the dorsum of the second toe
cannot be easily pinched, compared to the right foot (b) Khayat BMC Gastroenterol (2021) 21:225 Page 3 of 5 Fig. Discussion and conclusion Unilateral limb swelling has a wide array of differential
diagnoses, such as different types of lymphedema (pri-
mary and secondary) [6, 7]. True Hemihyperplasia is
seen in syndromes such as Beckwith-Weidemann syn-
drome, or could be an isolated disorder [8]. Hemihy-
perplasia differs from lymphedema where there is a true
tissue overgrowth in the former, whereas only accumula-
tion of excess interstitial fluid in the latter [7–9]. and consistency improved immediately, and so did
his subcutaneous fat eventually. His ascites resolved
completely, and his left leg swelling was significantly
improving as well (Fig. 4), with persistence of Stem-
mer’s sign however. His Albumin and total protein lev-
els improved as well. l
primary lymphedema without systemic manifes-
tations or visceral involvement (i.e., PIL, or chylous Khayat BMC Gastroenterol (2021) 21:225 Khayat BMC Gastroenterol (2021) 21:225 Page 4 of 5 Treatment focuses mainly on dietary modification [4, 5,
11]. dietary fat induces dilation of lymphatics even in the
normal intestines. Therefore, avoidance of fat decreases
excessive dilation and risk of rupture in lymphangiectasia
[5, 13]. High MCT containing formulas, and fat restric-
tion along with high protein diet are the cornerstones of
treatment for infants, and older children respectively [4,
5, 11]. MCTs are absorbed directly into the portal venous
circulation and do not require lymphatic flow for absorp-
tion [21]. Octreotide use for the treatment of chylous
effusions has been described in the literature [22]. Its
effect on the intestines is unclear, but it is hypothesized
that it decreases triglycerides absorption, and induces
splanchnic vasoconstriction [5]. Albumin and intrave-
nous immunoglobulin (IVIG) infusions are frequently
indicated as replacement therapies, depending on the
levels and clinical scenarios [5]. Other treatment meas-
ures include managing any nutritional deficiencies, spe-
cifically fat-soluble vitamins [5, 23]. effusions) also occurs in a familial pattern and is often
due to a genetic disorder [7]. The onset can be con-
genital, or present later in life, and can be localized to
the lower extremities or other body parts, including
upper extremities and face [7]. The edema can be uni-
lateral, but more commonly bilateral, as seen in Meige,
and Melroy syndromes [7, 10]. PIL in comparison, com-
monly presents as an isolated, or non-familial disorder
[5, 11]. Rarely, it may occur in a familial or a syndro-
mic pattern, where there is a widespread lymphatic
malformations or dysplasia [5, 11]. Authors’ contributions AK has worked on drafting the manuscript, gathering data, obtaining consent,
and critically revising the final manuscript. All authors read and approved the
final manuscript. Acknowledgements I would like to thank Dr Layla Abdullah, and Dr Dania Saleh from the depart-
ment of Pathology for providing me with high quality histopathology images,
and Dr. Abdulhameed Ibrahim, as well as the patient’s father for providing
clinical photographs. PIL diagnosis is usually made by endoscopic, and his-
topathologic findings of the small intestines, showing
the typical dilated lymphatic vessels in the lamina pro-
pria and submucosa [4, 5]. Limb lymphatic vessels can
be examined by various radiographic techniques, which
can aid in the diagnosis, and to rule out secondary
causes of limb lymphedema or chylous effusions [5, 20]. Examples include lymphoscintigraphy, lymphangiogra-
phy, and magnetic resonance lymphangiography [5, 20]. Abbreviations
IVIG I IVIG: Intravenous immunoglobulin.; MCT: Medium chain triglycerides.; PIL:
Primary intestinal lymphangiectasia.. Discussion and conclusion Examples include
Turner, Noonan, and Hennekam syndromes [5, 12]. The
lymphedema associated with PIL (whether syndromic
or isolated) is typically bilateral [4, 5]. Hypoalbuminemia is another mechanism of edema in
PIL, which in fact, is more common than lymphedema
[1, 5]. The underlying pathophysiology is lymph loss
in bowel lumen, from excessive dilation and eventually
rupture of the already ectatic lymphatic vessels of small
bowels [1, 5]. Intestinal lymph is rich in long chain tri-
glycerides, lymphocytes, and proteins [13]. The result
of excessive lymph loss is the characteristic steatorrhea,
lymphopenia, edema, and hypoproteinemia including
hypogammaglobulinemia [1, 4, 5, 13]. Interestingly, the
case herein predominantly had a combined pitting and
non-pitting unilateral edema, despite presenting with-
systemic manifestations and visceral involvement (PIL
and ascites). i
The most serious but rare long-term complication
reported in PIL is intestinal B cell lymphoma [4, 24]. Other complications include nutritional deficiencies,
lower extremity cellulitis, and the effects of chronic foot
swelling on quality of life [5, 23]. In conclusion, PIL is a rare disorder that typically pre-
sents with protein-losing enteropathy, diarrhea, and
bilateral lower limb edema. Nonetheless, unilateral lower
limb edema (non-pitting more so than pitting) should not
preclude the diagnosis of a systemic disorder, and a high
index of suspicion is required in atypical presentations. A good knowledge about PIL, and physical examination
skills to differentiate edema or lymphedema from tissue
overgrowth can significantly aid in the diagnosis. PIL
responds well to dietary modification, but needs long-
term monitoring into adulthood, for potentially serious
complications. The most common clinical presentation in PIL
includes bilateral lower extremity edema and intermit-
tent or chronic diarrhea [4, 5, 14]. As discussed earlier,
The edema is mainly pitting; due to hypoalbuminemia,
but could rarely be non-pitting as well, when it is due to
lymphedema [5, 11, 15, 16]. It is oftentimes difficult to
distinguish them, especially when both are present [5]. Stemmer’s sign can be helpful in such cases, where a
positive sign (the inability to pinch the skin at the dor-
sum of the second toe) indicates lymphedema, rather
than pitting edema [5, 17]. Other clinical manifesta-
tions of PIL including abdominal mass, chylous effusion
(ascitic, pleural, or pericardial), generalized anasarca,
and intestinal mechanical obstruction have been rarely
reported [5, 18, 19]. Declarations and pharmacological perspective. Open Access Macedonian J Med Sci. 2018;6:1682–4. and pharmacological perspective. Open Access Macedonian J Med Sci. 2018;6:1682–4. Ethics approval and consent to participate
Not applicable. 11. Vardy PA, Lebenthal E, Shwachman H. Intestinal lymphagiectasia: a reap-
praisal. Pediatrics. 1975;55:842–51. 12. Hennekam RC, Geerdink RA, Hamel BC, et al. Autosomal recessive
intestinal lymphangiectasia and lymphedema, with facial anomalies and
mental retardation. Am J Med Genet. 1989;34:593–600. intestinal lymphangiectasia and lymphedema, with facial References Very late onset small intestinal B cell lymphoma associated with
primary intestinal lymphangiectasia and diffuse cutaneous warts. Gut. 2000;47:296–300. 8. Hoyme HE, Seaver LH, Jones KL, Procopio F, Crooks W, Feingold M. Isolated hemihyperplasia (hemihypertrophy): report of a prospective
multicenter study of the incidence of neoplasia and review. Am J Med
Genet. 1998;79:274–8. 9. Clericuzio CL, Martin RA. Diagnostic criteria and tumor screening for
individuals with isolated hemihyperplasia. Genetics Med 2009;11:220–2. Consent for publication mental retardation. Am J Med Genet. 1989;34:593–600. I have obtained a written consent from the patient’s legal guardian to
publish the case. 13. Alexander JS, Ganta VC, Jordan PA, Witte MH. Gastrointestinal lymphatics
in health and disease. Pathophysiology. 2010;17:315–35. 13. Alexander JS, Ganta VC, Jordan PA, Witte MH. Gastrointe in health and disease. Pathophysiology. 2010;17:315–35. 14. Mushtaq I, Cheema HA, Malik HS, Waheed N, Hashmi MA, Malik HS. Causes of chronic non-infectious diarrhoea in infants less than 6 months
of age: rarely recognized entities. JAMC. 2017;29:78–82. Funding No funding received for this work. Khayat BMC Gastroenterol (2021) 21:225 Page 5 of 5 Khayat BMC Gastroenterol Received: 28 October 2020 Accepted: 11 May 2021 Received: 28 October 2020 Accepted: 11 May 2021 festations. J Am Acad Dermatol. 2017;77:1009–20. 16. Boursier V, Vignes S. [Limb lymphedema as a first manifestation of
primary intestinal lymphangiectasia (Waldmann’s disease)]. J Maladies
Vascul. 2004;29:103–6. 17. Goss JA, Greene AK. Sensitivity and specificity of the stemmer sign for
lymphedema: a clinical lymphoscintigraphic study. Plast Reconst Surg
Global Open. 2019;7:e2295. References 1. Waldmann TA, Steinfeld JL, Dutcher TF, Davidson JD, Gordon RS. Jr. The
role of the gastrointestinal system in “idiopathic hypoproteinemia”. Gas-
troenterology. 1961;41:197–207. 1. Waldmann TA, Steinfeld JL, Dutcher TF, Davidson JD, Gordon RS. Jr. The
role of the gastrointestinal system in “idiopathic hypoproteinemia”. Gas-
troenterology. 1961;41:197–207. 18. Lenzhofer R, Lindner M, Moser A, Berger J, Schuschnigg C, Thurner J. Acute jejunal ileus in intestinal lymphangiectasia. Clin Investigator. 1993;71:568–71. 2. Isa HM, Al-Arayedh GG, Mohamed AM. Intestinal lymphangiectasia in
children. A favorable response to dietary modifications. Saudi Med J. 2016;37:199–204. 19. Rao R, Shashidhar H. Intestinal lymphangiectasia presenting as abdomi
nal mass. Gastrointest Endosc. 2007;65:522–3 (discussion 3) 19. Rao R, Shashidhar H. Intestinal lymphangiectasia presenting as abdomi-
nal mass. Gastrointest Endosc. 2007;65:522–3 (discussion 3) 3. Valdovinos-Oregón D, Ramírez-Mayans J, Cervantes-Bustamante R, et al. [Primary intestinal lymphangiectasia: twenty years of experience at a
Mexican tertiary care hospital]. Rev Gastroenterol Mexico. 2014;79:7–12. 20. Kamble RB, Shetty R, Diwakar N, Madhusudan G. Technical note: MRI
lymphangiography of the lower limb in secondary lymphedema. Indian J
Radiol Imaging. 2011;21:15–7. 4. Wen J, Tang Q, Wu J, Wang Y, Cai W. Primary intestinal lymphangi-
ectasia: four case reports and a review of the literature. Dig Dis Sci. 2010;55:3466–72. 21. Łoś-Rycharska E, Kieraszewicz Z, Czerwionka-Szaflarska M. Medium chain
triglycerides (MCT) formulas in paediatric and allergological practice. Przeglad gastroenterologiczny. 2016;11:226–31. 5. Vignes S, Bellanger J. Primary intestinal lymphangiectasia (Waldmann’s
disease). Orphanet J Rare Dis. 2008;3:5. 22. Bui A, Long CJ, Breitzka RL, Wolovits JS. Evaluating the use of octreotide
for acquired chylothorax in pediatric critically Ill patients following cardiac
surgery. JPPT. 2019;24:406–15. 6. Tiwari A, Cheng K-S, Button M, Myint F, Hamilton G. Differential diagnosis,
investigation, and current treatment of lower limb lymphedema. Arch
Surg. 2003;138:152–61. g
y
23. Braamskamp MJ, Dolman KM, Tabbers MM. Clinical practice. Protein-
losing enteropathy in children. Eur J Pediatrics. 2010;169:1179–85. 23. Braamskamp MJ, Dolman KM, Tabbers MM. Clinical practice. Protein-
losing enteropathy in children. Eur J Pediatrics. 2010;169:1179–85. 7. Jones GE, Mansour S. An approach to familial lymphoedema. Clin Med. 2017;17:552–7. 24. Bouhnik Y, Etienney I, Nemeth J, Thevenot T, Lavergne-Slove A, Matuchan-
sky C. Very late onset small intestinal B cell lymphoma associated with
primary intestinal lymphangiectasia and diffuse cutaneous warts. Gut. 2000;47:296–300. 24. Bouhnik Y, Etienney I, Nemeth J, Thevenot T, Lavergne-Slove A, Matuchan-
sky C. Conflict of interest
None to declare. g
y
g
15. Grada AA, Phillips TJ. Lymphedema. Pathophysiology and clinical man
festations. J Am Acad Dermatol. 2017;77:1009–20. 15. Grada AA, Phillips TJ. Lymphedema. Pathophysiology a Publisher’s Note
S
N Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. 10. Meshram GG, Kaur N, Hura KS. Unilateral primary congenital
lymphedema of the upper limb in an 11-month-old infant: a clinical •
fast, convenient online submission
•
thorough peer review by experienced researchers in your field
•
rapid publication on acceptance
•
support for research data, including large and complex data types
•
gold Open Access which fosters wider collaboration and increased citations
maximum visibility for your research: over 100M website views per year
•
At BMC, research is always in progress. Learn more biomedcentral.com/submissions
Ready to submit your research
Ready to submit your research ? Choose BMC and benefit from:
? Choose BMC and benefit from: •
fast, convenient online submission
•
thorough peer review by experienced researchers in your field
•
rapid publication on acceptance
•
support for research data, including large and complex data types
•
gold Open Access which fosters wider collaboration and increased citations
maximum visibility for your research: over 100M website views per year
•
At BMC, research is always in progress. Learn more biomedcentral.com/submissions
Ready to submit your research
Ready to submit your research ? Choose BMC and benefit from:
? Choose BMC and benefit from:
|
https://openalex.org/W4213052826
|
https://sosains.greenvest.co.id/index.php/sosains/article/download/352/685
|
Indonesian
| null |
Analisis Pengetahuan, Sikap dan Perilaku Berisiko Tertular Human Immunodeficiency Virus/Acquired Immuno Deficiency Syndrome (Hiv/Aids)
|
Jurnal sosial dan sains/Jurnal Sosial dan Sains
| 2,022
|
cc-by-sa
| 2,935
|
ABSTRAK ,
Latar Belakang : Human immunodeficiency virus (HIV) menargetkan sistem kekebalan
tubuh dan melemahkan sistem pertahanan manusia terhadap infeksi dan beberapa jenis
kanker. Ketika virus merusak fungsi sel-sel kekebalan, individu yang terinfeksi secara
bertahap menjadi imunodefisiensi. Tujuan : Meningkatkan kerentanan terhadap
berbagai infeksi, kanker, dan penyakit lain yang dapat dilawan oleh orang dengan sistem
kekebalan tubuh yang sehat. Metode : Metode penelitian yang digunakan yaitu desain
penelitian deskriptif. Penentuan responden menggunakan purposive sampling dan
diperoleh sebanyak 89 responden. Pengumpulan data berupa pengisian kuesioner dan
studi dokumentasi. Dalam penelitian ini telah dilakukan uji etik oleh Lembaga Etik
STIKes Budi Luhur Cimahi. Hasil : Hasil penelitian menunjukkan bahwa dalam rumah
tahanan negara kelas I Bandung Hampir setengahnya memiliki tingkat pengetahuan
yang cukup dengan jumlah responden sebanyak 36 responden, Sebagian besar memiliki
sikap mendukung untuk mencegah penularan HIV/AIDS dengan jumlah responden 54
responden, Sebagian besar memiliki berisiko tertular HIV/AIDS dengan jumlah
responden 48 responden. Kesimpulan : Analisis tingkat Pengetahuan terhadap warga
binaan hampir setengahnya memiliki tingkat pengetahuan yang cukup dengan jumlah
responden sebanyak 36 responden. Keywords:
Pengetahuan,
Sikap dan
Perilaku Berisiko,
HIV/AIDS,
Warga binaan Info Artikel :
Diterima : 29 Januari 2022 Info Artikel :
Diterima : 29 Januari 2022 Keywords:
Knowledge,
Attitudes and
risk behavior,
HIV/AIDS,
Assisted
residents JURNAL 1,2,3Program Studi D3 Kebidanan, STIKes Budi Luhur Cimahi, Indonesia
Corresponding Author : Sri Wahyuni¹
Email : uni.budiluhur@gmail.com1, g
widya.p.astuti@gmail.com2 dan imamsamadji@gmail.com3 Keywords:
Pengetahuan,
Sikap dan
Perilaku Berisiko,
HIV/AIDS,
Warga binaan PENDAHULUAN Secara global hingga pertengahan tahun 2015 terdapat 15,8 juta orang yang hidup
dengan HIV dan 2,0 juta orang baru terinfeksi HIV serta terdapat 1,2 juta orang meninggal
karena penyebab terkait HIV (Ardhiyanti, Lusiana, & Megasari, 2015). Diperkirakan 0,8%
dari orang dewasa berusia 15-49 tahun di seluruh dunia hidup dengan HIV. Berdasarkan
Laporan Perkembangan HIV/AIDS dan Infeksi Seksual Menular tahun 2017 oleh
Kementerian Kesehatan Republik Indonesia, jumlah kumulatif infeksi HIV sampai dengan
Desember 2017 di Indonesia adalah sebanyak 280.263 kasus, dengan jumlah kumulatif
AIDS sebanyak 102.667 kasus terhitung dari tahun 1987 hingga Desember 2017 (Yusran
& Rezal, n.d.). Dalam laporan yang sama juga ditemukan bahwa jumlah penemuan kasus
infeksi baru HIV dan AIDS mengalami peningkatan setiap tahunnya. Data ini
mengindikasikan peningkatan jumlah penularan infeksi HIV di Indonesia. HIV AIDS dapat
menyerang setiap orang, dengan komunitas Lesbian, Gay, Bisexual, and Transgender
(LGBT), pekerja seksual, pengguna jarum suntik bersama, dan penghuni lapas sebagai
populasi kunci yang memiliki risiko penularan tinggi (Sembiring & Yeni, 2021). Berdasarkan data yang diterima dari Dinas Kesehatan Jawa Barat kumulatif kasus
HIV/AIDS di Jawa Barat dari tahun 2006-2017 mengalami kenaikan signifikan. Dan jika
dibagi menjadi per Kabupaten/Kota ternyata Kota Bandung menduduki peringkat pertama
dengan 945 kasus sepanjang 2018. Berdasarkan data dari Dinas Kesehatan Kota Bandung periode 2017-2019 yang
ditemukan dalam kondisi HIV ialah 935 kasus dan yang ditemukan dalam keadaan AIDS
adalah 380 kasus, yang meninggal sebanyak 22 orang sisanya sedang dalam perawatan. Menurut data dari Sistem Database Permasyarakatan (SDP) diambil dari seluruh Kantor
Wilayah Seluruh Indonesia di awal bulan Februari 2020 terdapat 894 warga binaan yang
terkena HIV/AIDS dan 9.601 yang berisiko terkena HIV/AIDS. Sedangkan di tingkat
kantor wilayah Jawa Barat terdapat 117 warga binaan yang terkena HIV/AIDS dan 300
yang berisiko terkena HIV/AIDS. Lebih mendalam lagi terhadap RUTAN yang berada di
Jawa Barat yaitu RUTAN Kelas I Bandung terdapat 7 warga binaan yang terkena
HIV/AIDS dan 10 yang berisiko terkena HIV/AIDS akibat penggunaan narkoba suntik. Pengetahuan merupakan hasil dari tahu, dan ini terjadi setelah orang melakukan
pengindraan terhadap suatu objek tertentu. Pengindraan terhadap obyek terjadi melalui
panca indra manusia yakni penglihatan, pendengaran, penciuman, rasa dan raba dengan
sendiri (Indah, Aswitami, & Diantari, 2020). Sikap merupakan reaksi atau respon seseorang
yang masih tertutup terhadap stimulus atau objek (Ayu & Kurniawati, 2017). ABSTRACT Background : Human immunodeficiency virus (HIV) targets the immune system and
weakens the human defense system against infections and some types of cancer. When
the virus impairs the function of immune cells, the infected individual gradually becomes
immunodeficient. Purpose : Increases susceptibility to various infections, cancers, and
other diseases that people with healthy immune systems can fight off. Method : The
research method used is descriptive research design. Determination of respondents
using purposive sampling and obtained as many as 89 respondents. Data collection is
in the form of filling out questionnaires and studying documentation. In this study, an
ethical test was carried out by the Budi Luhur Cimahi Institute of Ethics for STIKes. Results : The results showed that in class I state detention centers in Bandung, almost
half of them had a sufficient level of knowledge with 36 respondents, most had a
supportive attitude to prevent HIV/AIDS transmission with 54 respondents, most were 244 http://sosains.greenvest.co.id 2022 Analisis Pengetahuan, Sikap dan Perilaku Beresiko
Tertular Human Immunodeficiency Virus/Acquired
Immuno Deficiency Syndrome (HIV/AIDS) at risk of contracting HIV/AIDS. with the number of respondents 48 respondents. Conclusion : Knowledge level analysis of the inmates Almost half of them have a
sufficient level of knowledge with a total of 36 respondents. at risk of contracting HIV/AIDS. with the number of respondents 48 respondents. Conclusion : Knowledge level analysis of the inmates Almost half of them have a
sufficient level of knowledge with a total of 36 respondents. Sri Wahyuni, Widya Putriastuti dan Imam Samiadji PENDAHULUAN Sikap adalah predisposisi untuk melakukan atau tidak melakukan suatu perilaku
tertentu, sehingga sikap bukan hanya kondisi internal psikologis yang murni dari individu,
sikap merupakan kesadaran yang sifatnya individual (Fadlilah & Rahil, 2019). Artinya
proses ini terjadi secara subjektif dan unik pada diri setiap individu. Perilaku adalah respon
individu terhadap suatu stimulus atau suatu tindakan yang dapat diamati dan mempunyai
frekuensi spesifik, durasi dan tujuan baik disadari maupun tidak (Kurniawati & Wardani,
2020). Perilaku merupakan kumpulan berbagai faktor yang saling berinteraksi. Sehubungan dengan hal tersebut penulis tertarik untuk melakukan penelitian dengan judul
“Analisis Pengetahuan, Sikap dan Perilaku Berisiko tertular Human Immunodeficiency
Virus / Acquired Immuno Deficiency Syndrome (HIV/AIDS) Di Rumah Tahanan Negara
Kelas I Bandung Tahun 2020”. Penelitian ini dimaksudkan untuk mengetahui analisis Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 245 Volume 2, Nomor 2, Februari 2022
p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022
p-ISSN 2774-7018 ; e-ISSN 2774-700X pengetahuan, sikap dan perilaku berisiko tertular Hu man Immunodeficiency Virus /
Acquired Immuno Deficiency Syndrome (HIV/AIDS) di Rumah Tahanan Negara Kelas I
Bandung. Tujuan penelitian ini adalah Meningkatkan kerentanan terhadap berbagai infeksi,
kanker, dan penyakit lain yang dapat dilawan oleh orang dengan sistem kekebalan tubuh
yang sehat. pengetahuan, sikap dan perilaku berisiko tertular Hu man Immunodeficiency Virus /
Acquired Immuno Deficiency Syndrome (HIV/AIDS) di Rumah Tahanan Negara Kelas I
Bandung. Tujuan penelitian ini adalah Meningkatkan kerentanan terhadap berbagai infeksi,
kanker, dan penyakit lain yang dapat dilawan oleh orang dengan sistem kekebalan tubuh
yang sehat. Analisis Pengetahuan, Sikap dan Perilaku Beresiko
Tertular Human Immunodeficiency Virus/Acquired
Immuno Deficiency Syndrome (HIV/AIDS) Analisis Pengetahuan, Sikap dan Perilaku Beresiko
Tertular Human Immunodeficiency Virus/Acquired
Immuno Deficiency Syndrome (HIV/AIDS) 2022 1. Pengetahuan Berdasarkan hasil penelitian yang tercantum tentang tingkat pengetahuan pada
warga binaan didapatkan bahwa dari analisa tentang tingkat pengetahuan pada warga
binaan didapatkan bahwa dari 89 responden, sebagian responden memiliki tingkat
pengetahuan baik sebanyak 27 responden (30,3%) sedangkan responden memiliki tingkat
pengetahuan cukup sebanyak 36 responden (40,4%) dan responden yang memiliki tingkat
pengetahuan kurang sebanyak 26 responden (29,2%). Hasil penelitian tersebut menjelaskan
bahwa sebagian besar responden memiliki tingkat pengetahuan yang cukup. Adapun
kejadian tingkat pengetahuan yang baik sebanyak 27 responden dan tingkat pengetahuan
yang kurang sebanyak 26 responden. Pengetahuan tentang HIV/AIDS ditemukan cukup,
namun masih ada kesalahpahaman tentang HIV/AIDS pada warga binaan sehingga masih
diperlukan edukasi untuk memperbaiki hal tersebut (Ristianadewi, Septimar, & Wibisono,
2021). Individu mampu mengingatkan kesehatan dengan cara meningkatkan pengetahuan. Teori tersebut menekankan pada kemampuan warga binaan untuk beradaptasi dalam
meningkatkan pengetahuan tentang HIV/AIDS dengan cara menanyakan kepada teman
seruangan maupun kepada petugas. Seseorang yang terpaksa tinggal di lembaga
permasyarakatan karena menjalani hukuman akan mempengaruhi kondisinya. Mereka akan
mengalami kesulitan untuk menyesuaikan kehidupan nya di lembaga permasyarakatan,
tetapi mereka harus tetap mengikuti aturan-aturan yang berlaku di lembaga
permasyarakatan. Selain itu, mereka juga harus terpisah dari keluarganya, teman
sebayanya, kehilangan kebebasan untuk tinggal diluar. Hal tersebut akan menyebabkan
seseorang mendapat tekanan karena hidup di lembaga permasyarakatan, untuk
meningkatkan pengetahuan warga binaan tentang bahayanya tertular HIV/AIDS maka
disini harus dilakukan edukasi dan penyuluhan kesehatan oleh petugas untuk menambah
wawasan mengenai bahayanya tertular HIV/AIDS (Irawan, 2018). METODE PENELITIAN Penelitian ini menggunakan rancangan desain penelitian deskriptif. Metode
penelitian deskriptif ini dilakukan untuk mengetahui keberadaan variabel mandiri, baik
hanya pada satu variabel atau lebih (variabel yang berdiri sendiri atau variabel bebas) tanpa
membuat perbandingan variabel itu sendiri dan mencari hubungan dengan variabel lain
(Sugiyono, 2013). Populasi dalam penelitian ini adalah warga binaan sebanyak 828
responden. Teknik pengambilan sampel yang digunakan yaitu purposive sampling dengan
jumlah sampel sebanyak 89 responden. Penelitian dilakukan di Rumah Tahanan Negara
Kelas I Bandung. Analisis data pada penelitian ini menggunakan analisa univariat, analisa
univariat adalah analisis yang bertujuan untuk mendeskripsikan atau menjelaskan
karakteristik setiap variabel penelitian. Untuk mencegah timbulnya masalah etik, maka
peneliti telah melakukan izin etik dan penelitian ini telah terdaftar di komisi Etik Penelitian
dan Pengembangan Kesehatan Nasional (KEPPKN) Kementrian Kesehatan Republik
Indonesia, dalam surat keterangan nomor :31/D/KEPK-STIKes/VIII/2020 dengan nomor
kodefikasi : 3277042S, melakukan informed concent, menjaga kerahasiaan responden,
memberikan manfaat terhadap penelitian yang sudah dilakukan dan menjaga keadilan
antara responden yang satu dengan responden yang lainnya. HASIL DAN PEMBAHASAN
Tabel 1. Hasil frekuensi tingkat Pengetahuan
Tingkat Pengetahuan
Frekuensi
Persentase (%)
Baik
27
30,3 %
Cukup
36
40,4 %
Kurang
26
29,2%
Total
89
100 %
Sumber : Data Primer 2020
Tabel 2. Hasil frekuensi Sikap
Sikap
Frekuensi
Persentase (%)
Mendukung
54
60,7 %
Kurang Mendukung
35
39,3 %
Total
89
100 %
Sumber : Data Primer 2020
Tabel 3. Hasil frekuensi Perilaku Berisiko
Sikap
Frekuensi
Persentase (%)
Tidak Berisiko
41
46,1 %
Berisiko
48
53,9 %
Total
89
100 %
Sumber : Data Primer 202 HASIL DAN PEMBAHASAN Tabel 1. http://sosains.greenvest.co.id 246 Analisis Pengetahuan, Sikap dan Perilaku Beresiko
Tertular Human Immunodeficiency Virus/Acquired
Immuno Deficiency Syndrome (HIV/AIDS) Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 2. Sikap Berdasarkan hasil penelitian yang tercantum tentang sikap pada warga binaan
didapatkan bahwa dari analisa tentang sikap pada warga binaan didapatan bahwa dari 89
responden, sebagian besar responden memiliki sikap mendukung sebanyak 54 responden
(60,7%) dan sebagian responden sebanyak 35 (39,3 %) memiliki sikap kurang mendukung. Hasil penelitian tersebut menjelaskan bahwa sebagian besar responden memiliki sikap
yang mendukung sebanyak 54 responden adapun 35 responden yang lainnya memiliki
sikap kurang mendukung. Hasil ini sesuai dengan yang di paparkan oleh Nur Arifatun dan
Dyah mahendrasari yang menyatakan bahwa warga binaan memiliki sikap yang
mendukung. Berdasarkan hasil jawaban yang diperoleh sebagian besar responden memiliki
sikap yang mendukung yaitu sebanyak 36 responden (55,4%) warga binaan setuju
berperilaku sehat agar terhindar dari penularan HIV/AIDS dan responden yang memiliki
sikap kurang mendukung sebanyak 29 responden (44,6) (Fachmi, Miharja, & Harianto,
2016). Teori Sister Callista Roy menjelaskan tentang bagaimana individu mampu
mengingkatkan kesehatan dengan cara mempertahankan sikap yang mendukung. Teori tersebut menekankan pada kemampuan warga binaan untuk beradaptasi dalam
meningkatkan sikap yang mendukung tentang HIV/AIDS. Seseorang yang terpaksa tinggal
di lembaga permasyarakatan karena menjalani hukuman akan mempengaruhi kondisinya
(Fajarani, 2017). Mereka akan mengalami kesulitan untuk menyesuaikan kehidupan nya di
lembaga permasyarakatan, tetapi mereka harus tetap mengikuti aturan-aturan yang berlaku
di lembaga permasyarakatan. Selain itu, mereka juga harus terpisah dari keluarganya,
teman sebayanya, kehilangan kebebasan untuk tinggal diluar. Hal tersebut akan Sri Wahyuni, Widya Putriastuti dan Imam Samiadji Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 247 Volume 2, Nomor 2, Februari 2022
p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022
p-ISSN 2774-7018 ; e-ISSN 2774-700X menyebabkan seseorang mendapat tekanan karena hidup di lembaga permasyarakatan,
untuk meningkatkan sikap yang mendukung untuk tidak tertular HIV/AIDS. Proses
komunkasi yang terjalin antar warga binaan yang satu dengan yang lainnya ataupun dengan
petugas rumah tahanan serta kerabat yang datang untuk menjenguk berindikasi terhadap
segala bentuk proses perubahan komunikasi seorang warga binaan di rumah tahanan. Komunikasi tidak terlepas dari peran komunikator, dalam hal ini komunikasi seorang
warga binaan di rumah tahanan melalui komunkasi yang saling mengungkapkan perasaan
emosi, pendapat dan tujuan. Sehingga terjalin komunkasi yang efektik didalamnya untuk
bersikap mendukung supaya tidak terkena HIV/AIDS selama di dalam rumah tahanan,
sedangkan jika seorang warga binaan kurang komunkasi antar teman sesama warga
binaan,petugas maupun kerabat akan dipastikan warga binaan mempunyai sikap yang
kurang mendukung terhadap penularan HIV/AIDS di rumah tahanan. KESIMPULAN Berdasarkan pembahasan dari hasil penelitian yang berjudul “Analisis Pengetahuan,
Sikap dan Perilaku Berisiko tertular Human Immunodeficiency Virus/Acquired Immuno
Deficiency Syndrome (HIV/AIDS) di Rumah Tahanan Negara Kelas I Bandung” yang
dilakukan pada tanggal 22-29 Juni 2020 terhadap 89 responden dengan tujuan umum untuk
mengetahui Analisis Pengetahuan, Sikap dan Perilaku Berisiko tertular Human
Immunodeficiency Virus/ Acquired Immuno Deficiency Syndrome (HIV/AIDS) di Rumah
Tahanan Negara Kelas I Bandung dan untuk menafsirkan persepsi jawab dibuat pedoman
tafsiran yang diambil dari sughiyono, maka dapat disimpulkan bahwa: Analisis tingkat
Pengetahuan terhadap warga binaan Hampir setengahnya memiliki tingkat pengetahuan
yang cukup dengan jumlah responden sebanyak 36 responden. Analisis Sikap pada warga
binaan Sebagian besar memiliki sikap mendukung untuk mencegah penularan HIV/AIDS
dengan jumlah responden 54 responden. Analisis Perilaku Berisiko pada warga binaan
sebagian besar memiliki berisiko tertular HIV/AIDS dengan jumlah responden 48
responden. Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 3. Perilaku Berisiko Berdasarkan hasil penelitian yang tercantum tentang perilaku berisiko pada warga
binaan didapatkan bahwa dari analisa tentang perilaku berisiko pada warga binaan
didapatkan bahwa dari 89 responden, sebagian besar responden berisiko tertular HIV/AIDS
dengan perilaku menggunakan jarum suntik secara bergantian dan membuat tindik secara
bergantian sebanyak 48 responden (53,9%) dan sebagian responden sebanyak 41(46,1%)
tidak berisiko tertular HIV/AIDS. Hasil penelitian tersebut menjelaskan bahwa sebagian
besar responden berjumlah 89 orang yang berisiko tertular HIV/AIDS (tindakan
penggunaan jarum suntik NAPZA, tindakan terkait hubungan seksual berisiko, dan
tindakan lainnya) sebanyak 48 responden (53,9%) berisiko terkena HIV/AIDS sedangkan
sebagian kecil responden sebanyak 41 orang (46,1%) tidak berisiko terkena HIV/AIDS. Hasil ini sesuai dengan yang di paparkan oleh Mondesari,dkk (2016) yang menyatakan
bahwa warga binaan yang berisiko tertular HIV/AIDS masih banyak. Berdasarkan hasil
penelitian dapat diketahui bahwa responden yang berisiko tertular HIV/AIDS yaitu
sebanyak 50 orang (93%), sedangkan yang tidak melakukan berisiko tertular HIV/AIDS
sebanyak 4 orang (7%). Model adaptasinya dalam tatanan pelayanan keperawatan terdiri dari tujuan
keperawatan dan aktivitas keperawatan. Kebutuhan akan pelayanan keperawatan timbul
saat klien tidak dapat beradaptasi dengan tekanan lingkungan internal maupun eksternal. Warga binaan yang baru ataupun lama juga melakuan proses adaptasi, dimana warga
binaan tersebut harus melakukan tindakan pencegahan mengenai perilaku berisiko agar
tidak terkena penyakit HIV/AIDS. Hal ini sesuai dengan yang diungkapkan Nur Arifatun
dan Dyah mahendrasari (2017) yang menyatakan bahwa 21 orang berperilaku berisiko dan
44 orang tidak berisiko, ini disebabkan sering diadakan nya penyuluhan tentang HIV/AIDS
dan NAPZA secara rutin dan merata kepada semua warga binaan, meningkatkan kegiatan
penanggulangan HIV/AIDS oleh petugas terutama pada awal napadina pertama kali masuk
menjadi warga binaan rumah tahanan. Populasi warga binaan (narapidana) di lapas adalah
juga merupakan salah satu populasi kunci yang penting dalam penyebaran HIV di
Indonesia. Perilaku menggunakan narkotika suntik, pengaruhnya sangat kuat dan bermakna
secara statistik terhadap risiko terkena infeksi HIV. Secara keseluruhan, faktor-faktor
(determinan) yang dapat meningkatkan risiko terinfeksi HIV secara bermakna di kalangan
para warga binaan dilapas/rutan di Indonesia adalah: berbagi jarum suntik tidak steril,
kontak seksual dengan sesama warga binaan, terinfeksi PMS (khususnya sifilis) dan
memakai tato dan tindik. 248 http://sosains.greenvest.co.id 2022 Analisis Pengetahuan, Sikap dan Perilaku Beresiko
Tertular Human Immunodeficiency Virus/Acquired
Immuno Deficiency Syndrome (HIV/AIDS) REFERENCES Ardhiyanti, Yulrina, Lusiana, Novita, & Megasari, Kiki. (2015). Bahan ajar AIDS pada
asuhan kebidanan. Yogyakarta: Deepublish. Ayu, Suci Musvita, & Kurniawati, Tri. (2017). Hubungan Tingkat Pengetahuan Remaja
Putri Tentang Aborsi Dengan Sikap Remaja Terhadap Aborsi Di Man 2 Kediri Jawa
Timur. Unnes Journal of Public Health, 6(2), 97–100. Fachmi, Sintha Noor, Miharja, Ediyar, & Harianto, Joanggi. (2016). Hubungan antara
Tingkat Kecemasan dengan Sikap Perawat dalam Penanganan Kekambuhan Pasien
Perilaku Kekerasan di RSJD Atma Husada Mahakam Samarinda Tahun 2016. Fadlilah, Siti, & Rahil, Nazwar Hamdani. (2019). Faktor-Faktor Yang Berhubungan
Dengan Perilaku Pencegahan Cidera Muskuloskeletal Pada Pemain Futsal. Jurnal
Keperawatan BSI, 7(1). Fajarani, Anggit Saktika. (2017). Tingkat stres dan harga diri narapidana wanita di lembaga
pemasyarakatan kelas II A Kota Bogor. Jurnal Riset Kesehatan Poltekkes Depkes
Bandung, 9(2), 26–33. Indah, Pande Putu Indah Purnamayanthi, Aswitami, Ni Gusti Ayu Pramita, & Diantari, Ni
Putu Ayu Mita. (2020). Gambaran Tingkat Pengetahuan Ibu Hamil Trimester III
Tentang Tanda Bahaya Persalinan. Journal Center of Research Publication in
Midwifery and Nursing, 4(2), 28–32. Irawan, Doni. (2018). Pengaruh Pendidikan Kesehatan Dengan Metode Pembelajaran
Didaktif (Ceramah) Dan Sokratik (Buzz Group) Terhadap Tingkat Pengetahuan
Mengenai Bahaya Perilaku Merokok Pada Peserta Didik Madrasah Tsanawiyah Al-
Hidayah Sukawening. Kurniawati, Novi, & Wardani, Riska Aprilia. (2020). Hubungan Persepsi Remaja Tentang
Perilaku Seksual Pranikah Dan Perilaku Seksual Pranikah Pada Remaja. Jurnal
Keperawatan, 13(2), 11. Ristianadewi, Hannny Putri, Septimar, Zahrah Maulidia, & Wibisono, Ahmad Yusuf
Gunawan. (2021). Perilaku Berisiko Dan Perilaku Pencegahan Tertular Penyakit
Hiv/Aids Di Lembaga Pemasyarakatan Pada Tahun 2020. Nusantara Hasana Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 249 Volume 2, Nomor 2, Februari 2022
p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022
p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022
p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022
p-ISSN 2774-7018 ; e-ISSN 2774-700X Journal, 1(2), 130–137. Sembiring, Rony Pramana, & Yeni, Yeni. (2021). Analisis Faktor Yang Berhubungan
Dengan Pencegahan Penularan Hiv/Aids Pada Warga Binaan Pemasyarakatan
(Wbp) Di Lembaga Pemasyarakatan Kelas I Palembang Sumatera Selatan. Palembang: Sriwijaya University. Sugiyono, Dr. (2013). Metode penelitian pendidikan pendekatan kuantitatif, kualitatif dan
R&D. Yusran, Sartiah, & Rezal, Farit. (n.d.). Kajian Empiris Stigma terhadap ODHA pada
Masyarakat di Kota Kendari. Jurnal Wawasan Promosi Kesehatan, 1(1). This work is licensed under a Creative Commons Attribution-ShareAlike
4.0 International License. 250 http://sosains.greenvest.co.id
|
https://openalex.org/W4241726080
|
https://repozytorium.biblos.pk.edu.pl/redo/resources/30699/file/suwFiles/KozlowskiT_ArchitecturalSculpture.pdf
|
English
| null |
Architectural sculpture
|
Brill’s New Pauly
| 2,014
|
cc-by
| 3,021
|
* Ph.D. Arch. Tomasz Kozłowski, Department of Housing Architecture and Architectural Composition,
Faculty of Architecture, Cracow University of Technology. ARCHITECTURAL SCULPTURE
ARCHITEKTONICZNA RZEŹBA A b s t r a c t
The paper presents the links between the different fields of art: painting, music, sculpture
and architecture. The great influence of expressionist sculpture on architecture is emphasized. Modern buildings often look like built monuments. Architects like Zaha Hadid and Frank
Ghery can distance themselves from their predecessors, but it seems to be evident that they
unintentionally continue what was ‘born’ in the early twentieth century. A b s t r a c t The paper presents the links between the different fields of art: painting, music, sculpture
and architecture. The great influence of expressionist sculpture on architecture is emphasized. Modern buildings often look like built monuments. Architects like Zaha Hadid and Frank
Ghery can distance themselves from their predecessors, but it seems to be evident that they
unintentionally continue what was ‘born’ in the early twentieth century. Keywords: architecture, expressionism, new forms S t r e s z c z e n i e
Tekst stara się pokazać powiązanie różnych dziedzin sztuki: malarstwa, muzyki, rzeźby i ar-
chitektury. Wpływ, jaki rzeźba ekspresjonistyczna miała na architekturę, jest wielki. Współ-
czesne budynki wyglądają niekiedy jak zbudowane pomniki. Architekci, tacy jak Zahy Hadid
czy Franka Ghery, mogą odżegnywać się od poprzedników, ale może mimowolnie kontynuują
to, co narodziło się na początku XX wieku. S t r e s z c z e n i e Tekst stara się pokazać powiązanie różnych dziedzin sztuki: malarstwa, muzyki, rzeźby i ar-
chitektury. Wpływ, jaki rzeźba ekspresjonistyczna miała na architekturę, jest wielki. Współ-
czesne budynki wyglądają niekiedy jak zbudowane pomniki. Architekci, tacy jak Zahy Hadid
czy Franka Ghery, mogą odżegnywać się od poprzedników, ale może mimowolnie kontynuują
to, co narodziło się na początku XX wieku. Słowa kluczowe: ekspresjonizm, architektura, rzeźba, dekompozycja * Ph.D. Arch. Tomasz Kozłowski, Department of Housing Architecture and Architectural Composition,
Faculty of Architecture, Cracow University of Technology. 48 It is difficult to define expressionist sculpture as a uniform style. The authors
of The Encyclopedia of Expressionism tried to find two artistic trends making it easier to
state its definition precisely. “One outlook prevailed among the German critics: sculpture
revealed a considerable dose of openness to expressionism or rejected the existing
conventions. According to the other outlook, expressionism means intensive expressiveness
of forms going to such extremes as deformation and abstraction which results from
an artist’s inner need”1. Expressionist sculpture created by artists belonging to the Die
Brücke group, remained under the influence of primitive art. These authors explained
their interest with the “primeval” expression of such works. Their creations often imitated
African statuettes in a literal manner. Here again, artists talked about abandoning the past,
meaning the immediate past, as usual. “The entire art of the late nineteenth century called
art pompier, characterized by shameless odalisques, the nudity of classical deities as well
as exaggerated historical references, can be easily identified as kitsch”2. Twentieth-century
creation was expected to be different, free from passeism, more ideological, unorthodox
and original. We can assume that an artist’s desire for the internal dynamics of a given
work became a shared feature. That kind of art combined various creative tendencies
and included the achievements of such authors as Picasso, Barlach or Archipenko. Such a “primitive” style, which rejected the existing conventions of picturing destruction,
ruins and absence in a metaphorical but also literal manner, can be exemplified by Ossip
Zadkine’s sculpture entitled The Torn City also known as The Destroyed City (1951‒1953). The artist, defined as a post-cubist, created it by drilling the volumes deeply and producing
a profoundly bombastic form3. Zadkine’s monument shows a human figure decomposed
in the cubistic manner. In this case, we can say that the dramatic monument to the ruined
city is a ruin or perhaps an expression itself. 1 L. Richard, Encyklopedia ekspresjonizmu, Warsaw 1996, 136.
2 U. Eco, Historia brzydoty, Poznan 2007, 400.
3 A. Borzeskowska, Całkiem nowe ruiny. Między romantyzmem a postmodernizmem, „Arteon” 2002,
No. 5, 44-45.
4 A. Kotula, P. Krakowski, Rzeźba współczesna, Warsaw 1980, 117. S t r e s z c z e n i e Certainly, this work is expressive and full
of curves – it bears the artist’s humane message concerning World War II and the bombings
of the centre of Rotterdam in 1940. “Today’s young sculptor will borrow the daring concept
of spontaneity and genuine freedom from Negro art in order to reach EXPRESSION”4. In 1994, Philip Johnson designed the visitor pavilion Glass House in New Canaan,
Connecticut. The author called this building, or maybe sculpture, Da Monsta which means
a monster in hip-hop slang. It was constructed from plastered concrete laid upon a steel
net. Provides an introduction to Johnson’s work. The entire estate together with some
pavilion houses, a guesthouse, a painting gallery, a sculpture gallery and a library act as
a museum these days. The entrance building itself consists of two intermingling irregular
volumes with sharp edges. The middle is just the waiting room and the projection room. The author admits that he was inspired by Hermann Finsterlin’s art. However, it may be
his authorial interpretation of the expressionism of the early twentieth century. The bodies
forming a part of this composition as well as the colours of the “elevations” become
aggressive. Their redness and greyness help a visitor to find the shapes which formed this 49 pavilion. The work proves that a new monument need not be large – it can have a “regular”
human scale. In the other outlook, one can search out some inspirations for the minimalist sculpture
The Broken Obelisk (1967) created in Houston by an artist from the circle of abstract
expressionism – Barnett Newman. It shows an elegant composition of “post-elementary”
volumes against the background of an equally smart modernist architecture without causing
discomfort through its instability. The artist moves towards abstraction but the onlooker’s
attention is temporarily occupied by the “chipped” top of the slender quadratic prism which
crowns the composition with its unreliable spot support. The following questions arise: Is this
the beginning of an interrupted composition or the closing of a ruined one? Was the whole
the basis for something bigger or can this thing be continued like The Endless Column by
Constantine Brancusi? The present time has given architects some tools for creating new
structures that could not be built by the expressionists of the early twentieth century. 5 M. Misiągiewicz, O prezentacji idei architektonicznej, Krakow 1999, 114.
6 D. Sharp, Modern Architecture and Expressionism, New York 1966, 98. S t r e s z c z e n i e Coop Himmelb(l)au’s Pavilion 21 MINI Opera 50 Space (2008‒2010) was built for the needs of the Munich Opera Festival 2010. Władysław
Tatarkiewicz’s comments explaining various meanings of the word “beauty” could be its
motto. The philosopher presented it as five definitions which best match the theory of beauty. “Namely: 1) Beauty is a simple quality characteristic of some things; 2) it is a particular
shape characteristic of some things; 3) it is what arouses certain special emotions in people;
4) it is the manifestation of a commonplace (typical, ideal) factor in a thing; 5) it is
expression”7. The building is small and lacks decorations in the ordinary sense of the word. However, it becomes the essence of ornamentation itself. Its form is to correspond with the
assignments it received. It is to be a place for a quest for new ways of perceiving art. The area
is not big (560 m²) and has seats for 300 people only. The volume was shaped – as the authors
claim – with a computer simulation of Jimi Hendrix’s song Purple Haze and the passages
from Mozart’s Don Giovanni. Ideologically, this work resembles the Philips expositional
pavilion designed by Le Corbusier in 1958. The building is an eyesore just like Finsterlin’s
sculptures. On one hand, it encourages the passers-by to come closer and look at themselves
in the polished metal; on the other hand, it scares them away like a fortress. However,
the authors do not distance themselves from the functional explanation of the form of their
work which is supposed to absorb the noise from the neighbouring streets. The musical
connotations are also important here considering the fleetingness of this work which, despite
its considerable size, was disassembled and moved to another location to create a new
category: “mobile architecture”. Referring to Wolf D. Prix’s words “Architecture should
embrace, be passionate, smooth, hard, with sharp corners. It must be brutal, rounded, gentle,
colourful, obscene, tempting, dreaming, alluring, surpassing, wet, dry, with a heartbeat. It has
to be vital or lifeless. If it is cold, it must be stone-cold; if it is hot, it has to be as hot as fire. Architecture must burn”8, we could add that it should be an eyesore, too. In 1921, Walter Gropius designed Denkmal der Märzgefallenen (The Monument
to the Casualties of the Kapp Putsch) whose form resembles an overturned obelisk with
a pyramid on top. S t r e s z c z e n i e Philip
Johnson and John Burgee raised twin towers Puerta de Europa I and Puerta de Europa
II – two leaning prisms, 114 metres tall, 15 degrees off the vertical – on one of Madrid’s
boulevards. The chequered elevation of dark glass is decorated with a glittering frame in
the corners of the building and in its centre. The slanting elevations are reinforced with
some intersecting elements. Both towers are supported by enormous counterweights which
facilitated construction. The structures were conceived as one spatial layout jointly creating
a gateway to Europe and a new street perspective. A struggle against the gravitational forces
forms the first leaning skyscrapers. Similarly to The Broken Obelisk, they fight with nature
and win. Maria Misiągiewicz describes Hermann Finsterlin’s achievements: “…He treated
a structure as a pointless and unequaled game of sublime forces included in rough matter
frozen at the moment of the most profound reflection”5. As a young architect, Finsterlin created
a number of utopian house designs. He was not an architect by profession. He decided to take
up art after he had climbed Mount Watzmann at night and discovered the beauty of nature. In 1919, Walter Gropius invited him to take part in an exhibition of the Unknown Architects
organized in Berlin. Similarly to Scharoun, Finsterlin created utopian designs but – contrary
to Scharoun – he never managed to realize his visions. His designs were presented as clay
sculptures, sharp, pointed, without right angles, sometimes resembling crystals. As Dennis
Sharp writes, Finsterlin treated a building as a work of all the arts, a gigantic empty sculpture
with unlimited possibilities of shaping the outside and the inside as well as only one requirement
of esthetical balance.6 Such gesamtkunstwerk is expressed in a combination of various
domains of art: literature, painting, music, architecture. Finsterlin was also a poet, an essayist
and a composer after all. The new approach to design was caused by his prophetic dream
where he saw a completely new type of architecture with colourful bent walls, so different
from the primitive cuboidal dwelling structure. The impact of such an outlook on architecture
is still noticeable. While admiring the designs of The Mausoleum (1919) or The Little
Guesthouse (1921), an association with some implemented designs by Coop Himmelb(l)au,
Zaha Hadid or Frank Gehry comes to mind. 7 W. Tatarkiewicz, Dzieje sześciu pojęć, Warsaw 1975, 138.
8 Coop Himmelb(l)au, Architektur muß brennen, Graz 1980, V.M. Lampugnani, op. cit., 116.
9 P. Francastel, Sztuka a technika, Warsaw 1966, 275. S t r e s z c z e n i e However, it was built of concrete instead of stone. It was conceived
to present a thunderbolt as a symbol of life. It was raised in 1922 and then destroyed by
the fascists; its replica still stands on the grounds of the cemetery in Weimar. This work
can make the prototype for Pavilion 21. Its form is uncompromising – with no ornaments,
sharp, indicating the direction toward the sky. It could be explained with Pierre Francastel’s
words: “Thus, a work of art is essentially an object of special nature, an imaginary object,
i.e. a kind of sign transmitter which is not a pattern, an image which appeared in an artist’s
mind, a picture he formed at the end of his work or an original image that emerges in every
onlooker’s head. Since it includes this margin of indefiniteness, it can show specific yet
fragmentary starting points. Moreover, it can express communicative reactions making
us aware of one of the crucial features of a work of art and one of the possible tangent points
between such apparently distant forms as an image and a building”9. In this case, a sculpture
appears somewhere between an image and a building. The work looks as if it was moving
– it is dynamic like in a motion picture. We do not know if this form goes up or down; 51 it becomes an expression of movement. The recipient feels like coming nearer and sustaining
the monument to save it from inescapable destruction. Perhaps it is a reminiscence
of the strictly expressionist painting The Sea of Ice (1823‒1824) by the Romantic German
artist Caspar David Friedrich. Looking at it, we are also uncertain if the ship was destroyed
by the ice banks or absorbed by the concrete car park at the supermarket. “The assignment
of art is not to facilitate general harmony but to come as a shock”10. These words uttered by
the writer and poet Walter Husenclaver could act as the motto of contemporary art. Expressionist sculpture had a strong impact on architecture. Hans Poelzig’s design
of Grosses Schauspielhaus (1919) in Berlin is one huge monument. Hermann Finsterlin’s
buildings assumed the form of sculptural models only. Mendelsohn’s design of Einsteinturm
includes independent sculptures instead of an architectural model. Both Zaha Hadid and
Frank Gehry’s contemporary buildings are already constructed expressionist sculptures
distinguished by their monumental scale, not by their form. W. Husenclaver, Zadania teatru, in Ekspresjonizm w teatrze europejskim, Warsaw 1993, 250.i 10 W. Husenclaver, Zadania teatru, in Ekspresjonizm w teatrze europejskim, Warsaw 1993, 250.
11 E.H. Gombrich, Pisma o sztuce i kulturze, selected and edited by R. Woodfield, Krakow 2011, 84.
12 E. Viollet-le-Duc, Dictionnaire raisonné de l’architecture française du XIe au XVIe siècle
E. Porębska, M. Poprzęcka, Teoretycy, artyści i krytycy o sztuce 1700‒1870, Warsaw 1989, 470-471 H. Gombrich, Pisma o sztuce i kulturze, selected and edited by R. Woodfield, Krakow 2011, 84. ,
,
yi
,
,
12 E. Viollet-le-Duc, Dictionnaire raisonné de l’architecture française du XIe au XVIe siècle,
E. Porębska, M. Poprzęcka, Teoretycy, artyści i krytycy o sztuce 1700‒1870, Warsaw 1989, 470-471. S t r e s z c z e n i e The present day always pretends
that it is not looking for the origins, but this is nothing but an artistic delusion. Creators try to
avoid being accused of copying things which is understandable but we are always left with
some aftersights, with a fugitive inspiration drawn from what used to be. Obviously, it is
a blurred image – we are not always capable of seeing the original because we can remember
the shape yet in different colours. If we treat the present state of architecture as evolution,
we must not forget that evolution has no purpose. What we are observing right now was
unpredictable to those who lived and worked in the early twentieth century. Let us quote
Heinrich Wölfflin’s words cited by Ernst Gombrich in his ruminations on the psychology
and mystery of styles which may become the motto of the return to expressionist art:
“Not everything is possible at every time”11, or Viollet-le-Duc’s statement: “If the Gothic
constructors had been able to use cast iron in large bars, they would have willingly mastered
this technique necessary for making buttresses as slender and durable as possible. Perhaps
they would have applied them more appropriately than we do”12. These days, owing to new
building technologies and computers, we can fulfill our predecessors’ dreams. Contemporary
architects have joined the artistic community, whereas the models of their houses or stadiums
can be exhibited at museums beside sculptures created by the futurists and expressionists
of the early twentieth century with no shame at all. We might venture a thesis on the appearance
of a new tendency in contemporary art – architectural sculpture as an esthetical category
unrelated to the function or scale of a work but related to its form. 52 Ill. 1. Ossip Zadkine, The Torn City of Rotterdam, The Netherlands 1953 (Rotterdam Der neubau
einer Stadt, edited by C. Van Traa) Ill. 1. Ossip Zadkine, The Torn City of Rotterdam, The Netherlands 1953 (Rotterdam Der neubau
einer Stadt, edited by C. Van Traa) Ill. 2. Philip Johnson, Visitor’s pavilion, New Canaan, Connecticut, 1994 (“Domus”, February 1996) . Philip Johnson, Visitor’s pavilion, New Canaan, Connecticut, 1994 (“Domus”, February 1996 53 Ill. 3. Barnett Newman, The Broken Obelisk, Houston, 1967 (Wojciech Włodarczyk, W poszukiwaniu
istoty. Minimal-art i konceptualizm, [In:] Sztuka świata, tom 10, Warszawa 1996) Ill. 3. Barnett Newman, The Broken Obelisk, Houston, 1967 (Wojciech Włodarczyk, W poszukiwaniu
istoty. S t r e s z c z e n i e Minimal-art i konceptualizm, [In:] Sztuka świata, tom 10, Warszawa 1996) Ill. 4. Hermann Finsterlin, Mausoleum, 1919 (Dennis Sharp, Modern Architecture and Expressionism,
New York 1966) Ill. 4. Hermann Finsterlin, Mausoleum, 1919 (Dennis Sharp, Modern Architecture and Expressionism,
New York 1966) 54 Ill. 5. Coop Himmelb(l)au, Pavilion 21 MINI Opera Space (Munich Opera Festival 2010, Munich,
Germany, 2008‒2010) Ill. 5. Coop Himmelb(l)au, Pavilion 21 MINI Opera Space (Munich Opera Festival 2010, Munich,
Germany, 2008‒2010) Ill. 6. Walter Gropius, The Monument to the Casualties of the Kapp Putsch, 1921 (Werlag Gerd Hatje,
Bauhaus Weimar 1919‒1925 Dessau 1925‒28, Stuttgart 1955) Ill. 6. Walter Gropius, The Monument to the Casualties of the Kapp Putsch, 1921 (Werlag Gerd Hatje,
Bauhaus Weimar 1919‒1925 Dessau 1925‒28, Stuttgart 1955) 55 Ill. 7. Caspar David Friedrich, The Sea of Ice, 1823‒1824, oil paint Ill. 7. Caspar David Friedrich, The Sea of Ice, 1823‒1824, oil paint
|
https://openalex.org/W4376138152
|
https://researchonline.lshtm.ac.uk/id/eprint/4669681/1/Tapsoba-etal-2023-Do-Out-of-Pocket-Payments-for-Care-for-Children-under-5-Persist-Even-in-a-Context-of-Free-Healthcare-in-BurkinaFaso.pdf
|
English
| null |
Do Out-of-Pocket Payments for Care for Children under 5 Persist Even in a Context of Free Healthcare in Burkina Faso? Evidence from a Cross-Sectional Population-Based Survey
|
Healthcare
| 2,023
|
cc-by
| 8,703
|
Citation: Tapsoba, L.D.G.; Yara, M.;
Nakovics, M.I.; Somda, S.M.A.;
Lohmann, J.; Robyn, P.J.; Hamadou,
S.; Hien, H.; De Allegri, M. Do
Out-of-Pocket Payments for Care for
Children under 5 Persist Even in a
Context of Free Healthcare in
Burkina Faso? Evidence from a
Cross-Sectional Population-Based
Survey. Healthcare 2023, 11, 1379. https://doi.org/10.3390/
healthcare11101379 Keywords: free healthcare; out-of-pocket payments; children under 5; Burkina Faso healthcare healthcare healthcare healthcare Article
Do Out-of-Pocket Payments for Care for Children under 5
Persist Even in a Context of Free Healthcare in Burkina Faso?
Evidence from a Cross-Sectional Population-Based Survey
Ludovic D. G. Tapsoba 1,*
, Mimbouré Yara 1, Meike I. Nakovics 2, Serge M. A. Somda 1,3
, Julia Lohmann 2,4,
Paul J. Robyn 5, Saidou Hamadou 5, Hervé Hien 1 and Manuela De Allegri 2 1
Centre MURAZ, National Institute of Public Health, Bobo-Dioulasso 390, Burkina Faso
2
H id lb
I
i
f Gl b l H
l h M di
l F
l
d U i
i
H
i
l U i
i
f H id lb 1
Centre MURAZ, National Institute of Public Health, Bobo-Dioulasso 390, Burkina Faso
2
Heidelberg Institute of Global Health, Medical Faculty and University Hospital, University of Heidelberg,
69120 Heidelberg, Germany 1
Centre MURAZ, National Institute of Public Health, Bobo-Dioulasso 390, Burkina Faso
2
Heidelberg Institute of Global Health, Medical Faculty and University Hospital, University of Heidelberg,
69120 Heidelberg, Germany 3
UFR Exact and Applied Sciences, Nazi Boni University, Bobo-Dioulasso BP 1091, Burkina Faso
4
Department of Global Health and Development, London School of Hygiene & Tropical Medicine,
Keppel Street, London WC1E 7HT, UK pp
,
,
5
The World Bank Group, 1818 H St. NW, Washington, DC 20433, USA pp
5
The World Bank Group, 1818 H St. NW, Washington, DC 20433, USA *
Correspondence: ludo_deo@yahoo.fr *
Correspondence: ludo_deo@yahoo.fr *
Correspondence: ludo_deo@yahoo.fr Abstract: Background: In April 2016, Burkina Faso began free healthcare for children aged from 0 to
5 years. However, its implementation faces challenges, and the goal of this study is to estimate the
fees paid for this child care and to determine the causes of these direct payments. Methods: Data
gathering involved 807 children aged from 0 to 5 years who had contact with the public healthcare
system. The estimation of the determinants of out-of-pocket health payments involved the application
of a two-part regression model. Results: About 31% of the children made out-of-pocket payments for
healthcare (an average of 3407.77 CFA francs per case of illness). Of these, 96% paid for medicines
and 24% paid for consultations. The first model showed that out-of-pocket payments were positively
associated with hospitalization, urban area of residence, and severity of illness, were made in the
East-Central and North-Central regions, and were negatively associated with the 7 to 23 month age
range. The second model showed that hospitalization and severity of illness increased the amount of
direct health payments. Conclusion: Children targeted by free healthcare still make out-of-pocket
payments. The dysfunction of this policy needs to be studied to ensure adequate financial protection
for children in Burkina Faso. 1. Background Academic Editor: Mustafa Z. Younis An increasing number of countries in Sub-Saharan Africa have recently implemented
policies to waive/reduce the cost of healthcare for the poorest members of their populations
or for specific sections of the populations such as pregnant women and children under
five [1]. These policies vary from country to country in terms of the services covered
and the social groups benefiting. For example, in 2006, Senegal introduced a policy of
eliminating user fees for childbirth care at the national level; in 2005 Mali introduced a
policy of eliminating fees for cesarean sections. Several studies have shown that out-of-
pocket payments can be a barrier to the use of health services [2,3]. Fee removal/reduction
policies aim to increase access to healthcare facilities, thereby contributing to the reduction
of maternal and neonatal mortality and helping to achieve the Sustainable Development
Goals [4]. The adoption of these policies is not an easy task, as public policy development
and implementation in most African countries are fraught with difficulties [5]. Received: 2 March 2023
Revised: 24 April 2023
Accepted: 5 May 2023
Published: 10 May 2023 Copyright:
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article
distributed
under
the
terms
and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/). p
g
The studies of fee removal/reduction policies have mostly focused on the impact on
healthcare service utilization rather than on financial protection. They show that these https://www.mdpi.com/journal/healthcare Healthcare 2023, 11, 1379. https://doi.org/10.3390/healthcare11101379 Healthcare 2023, 11, 1379 2 of 12 policies increase the use of healthcare services [6]. However, studies have shown that
out-of-pocket health payments still remain in free care settings, but the studies are not
sufficiently representative of the country’s population [7–12]. y
p
y
p p
In Burkina-Faso, a series of measures to waive user fees have been taken since the 2000s. In 2005, the management of severe malaria cases was fully subsidized [13]. Impregnated
mosquito nets have also been subsidized and distributed throughout the country since
2010. In the area of maternal health, a subsidy of 60 to 80%, depending on the services
offered, is provided for complicated and elective deliveries. The Government of Burkina
Faso has initiated the total exemption of healthcare fees for women and children aged from
0 to 5 years as of 1 June 2016 after successful pilot experiences. This free care strategy
aims to significantly reduce preventable deaths among children aged from 0 to 5 years
and women [14]. As part of this policy, many sub-Saharan countries are reimbursing
health facilities [15]. However, Burkina Faso has started the financial management of this
policy by pre-positioning funds for the covered services in accounts opened specifically for
the free healthcare policy. This strategy was adopted to avoid delays in reimbursement,
which encouraged out-of-pocket payments. Few studies have examined the drivers of
out-of-pocket expenditure (OOPE) in a context of free care delivery [16,17]. This study aims at filling an existing gap in the literature as one of the first to exam-
ine the effects of the national free healthcare policy on out-of-pocket spending for child
healthcare services. Prior impact evaluations have either referred to pilot experiences [18]
or examined the impact on payments for maternal care services [16]. This study builds on
household data from 24 districts to measure out-of-pocket expenditure for children aged 0
to 5 years more than one year after the launch of the free healthcare policy. 2.1. Framework of the Study Burkina Faso is a low-income country with an agricultural vocation. Its economy is
subject to climatic hazards, fluctuations in world trade conditions, and the exchange rate
(INSD, Demographic and Health Survey and Multiple Indicators “EDSBF-MICS IV”, 2010). The 2014 Continuous Multisectoral Survey (CMS) reveals that 40.1% of the Burkinabe
population is poor [19]. As one of the poorest countries in the world, the country has been
making economic progress in recent years thanks to relatively high annual economic growth
(+6.51% in 2018). However, Burkina Faso has a long way to go on the road to development. The GDP per capita is only XOF444,817.96 (US$740.75 (1 XOF = 0.0017 US$ (April 2023))
(2018). This makes it difficult for people to access basic social services and increases
unemployment. In addition, the country suffers from high morbidity and mortality, mainly
due to acute infectious diseases (acute malaria, acute respiratory infections, diarrhea, etc.)
and high infant and maternal mortality rates (World Health Organization, 2015; African
Health Observatory, 2016). As a result, the country ranks 185 out of 188 countries on the
2016 Human Development Index (HDI) (United Nations Development Program, 2016) [20]. Burkina Faso is a low-income country with an agricultural vocation. Its economy is
subject to climatic hazards, fluctuations in world trade conditions, and the exchange rate
(INSD, Demographic and Health Survey and Multiple Indicators “EDSBF-MICS IV”, 2010). The 2014 Continuous Multisectoral Survey (CMS) reveals that 40.1% of the Burkinabe
population is poor [19]. As one of the poorest countries in the world, the country has been
making economic progress in recent years thanks to relatively high annual economic growth
(+6.51% in 2018). However, Burkina Faso has a long way to go on the road to development. The GDP per capita is only XOF444,817.96 (US$740.75 (1 XOF = 0.0017 US$ (April 2023))
(2018). This makes it difficult for people to access basic social services and increases
unemployment. In addition, the country suffers from high morbidity and mortality, mainly
due to acute infectious diseases (acute malaria, acute respiratory infections, diarrhea, etc.)
and high infant and maternal mortality rates (World Health Organization, 2015; African
Health Observatory, 2016). As a result, the country ranks 185 out of 188 countries on the
2016 Human Development Index (HDI) (United Nations Development Program, 2016) [20]. The healthcare structure is organized in three levels. The first level is the health district,
which encompasses two parts. 2.2. The Free Care Policy for Children from 0 to 5 Years 2.2. The Free Care Policy for Children from 0 to 5 Years On 2 March 2016, Burkina-Faso adopted a policy of free care for children aged from 0
to 5 years, which was implemented on 2 April 2016, by the health districts of the Center,
Sahel, and Hauts-Bassins regions. On 1 May 2016, the hospitals in the aforementioned
regions also started the implementation. As of the 1 June 2016, the implementation was
extended to all the other facilities in the other regions. Free care is offered in public health
facilities and private health facilities that have signed an agreement with the Ministry
of Health. The targeted populations benefit from free care whatever the medical or surgical specialty g
p p
g
p
y
Healthcare for children aged from 0 to 5 years is preventive, diagnostic, and curative
in both outpatient and inpatient/observation settings for all common conditions targeted
by the IMCI (Integrated Management of Childhood Illness) strategy to reduce infant and
child mortality [22]. 2.3. Data and Data Sources Data for this study were gathered from the Final Household Survey for the impact
evaluation of the Results-Based Financing (Fbr), financed by the World Bank between April
and June 2017. The sample is composed of 7935 households in 24 districts (intervention and
control) in the six project regions (Boucle of Mouhoun, North-Central, West-Central, North,
South-West, and East-Central). These households were selected in two phases: in the first
phase, villages were selected randomly from the health areas. One village was randomly
selected for each HSPC. In the second phase, 15 households were randomly selected in
each village based on a complete list of households. This list consisted of households with
at least one pregnant woman or one woman who had given birth in the last 24 months. For this study, we used the household module, namely the sections on socioeconomic
and demographic characteristics of households, education, and health, particularly health-
care expenditures for acute illnesses. In each household, the respondents were the head of
the household, pregnant women, or women who had given birth in the last 24 months, and
all children aged from 0 to 5 years. Our study therefore focuses on children aged from 0 to
5 years. 2.1. Framework of the Study The first level includes the Health and Social Promotion
Centers (HSPC), which is the first contact point for a wide range of primary care services
for children aged 0–5 years. The second level is the Medical and Surgical Centers (MSC). In
2020, there were 70 health districts with 2041 Health and Social Promotion Centers (HSPC)
and 46 Medical and Surgical Centers (MSC) in operation. In 2020, the second level included
nine Regional Hospital Centers (RHC) serving as references for the CMAs, and the third
level consists of six University Hospital Centers. In addition, Burkina Faso has 641 private
facilities concentrated in the cities of Ouagadougou and Bobo-Dioulasso [21]. The healthcare structure is organized in three levels. The first level is the health district,
which encompasses two parts. The first level includes the Health and Social Promotion
Centers (HSPC), which is the first contact point for a wide range of primary care services
for children aged 0–5 years. The second level is the Medical and Surgical Centers (MSC). In
2020, there were 70 health districts with 2041 Health and Social Promotion Centers (HSPC)
and 46 Medical and Surgical Centers (MSC) in operation. In 2020, the second level included
nine Regional Hospital Centers (RHC) serving as references for the CMAs, and the third
level consists of six University Hospital Centers. In addition, Burkina Faso has 641 private
facilities concentrated in the cities of Ouagadougou and Bobo-Dioulasso [21]. Out-of-pocket health payments accounted for 35.8% of current health expenditures in
2018 (National Health Accounts 2018). This figure is high by WHO standards (the WHO
stipulates that the percentage of out-of-pocket payments on current health expenditures
should not exceed 20%). Healthcare 2023, 11, 1379 3 of 12 2.4. Description of the Sample We focused on children aged from 0 to 5 years who reported having a non-chronic
illness or injury and whose parents sought care. The data allowed us to identify those
children who reported contact with the formal public healthcare system for care as in
previous studies [16]. This target was taken because we are interested in the free healthcare
policy that is implemented in our study in public healthcare facilities in Burkina Faso. The
identification steps of our sub-sample are visible in the flow chart (Figure 1). 2.5.1. Variable of Interest The “Out-of-pocket expenditure” is the main variable of interest. It aggregates all
health expenditures made by the household for children aged from 0 to 5 who were sick
in the last 24 months and who used healthcare in a public health facility. This package
of care concerns only those in the free basket (including hospitalization) when a child
aged 0–5 is cared for in a public health facility. These expenditures include consultation
fees, laboratory/radiography and surgical fees (examinations), purchase of medicines, and
hospitalization fees. Informal payments without receipts and transportation costs were
therefore not included in the calculations of out-of-pocket health payments. Calculations
were made at the individual, not the household, level. This avoids the risk of double-
counting costs. Some of these costs might have been paid outside the health facility, namely
those related to the purchase of drugs and examination fees. Expenditures were calculated
in the local currency of the country, i.e., in XOF. Indirect costs were not considered. 4 of 12 Healthcare 2023, 11, 1379 1
Children under five years old:
15,323
No acute illness or injury: 14,308
acute illness or injury:
1015
Steps to get treatment :
889
No steps to get treatment:
126
contact with the formal
public health care system:
807
Private and no contact with
the formal public health care
system: 82
Expenses for health care:
248
No expenses for health care:
559
Figure 1. Sample identification chart. 2.5.2. Explanatory (Control) Variables
The research of factors associated with out-of-pocket expenditure highlights the
demographic data of patients and their mothers (age, place of residence, mother’s le Children under five years old:
15 323 Children under five years old:
15,323 No acute illness or injury: 14,308 acute illness or injury:
1015 No steps to get treatment:
126 Steps to get treatment :
889 Steps to get treatment :
889 Private and no contact with
the formal public health care
system: 82 contact with the formal
public health care system:
807 No expenses for health care:
559 Expenses for health care: Figure 1. Sample identification chart. 2.5.2. Explanatory (Control) Variables 1= (0–6); 2= (7–23); 3 =(24–59)
0 = Boy; 1 = Girl
0 = No effect on activities; 1 = Any effect on activities
0 = No; 1 = Yes
0= ≤5 km; 1= > 5 km
0 = Rural; 1 = Urban
0 = Other; 1 = Poor (Socio-economic status/quintile 1)
0= Uneducated; 1= Educated
0 = No; 1 = Yes
1 = Boucle du Mouhoun; 2 = Center est; 3 = Center nord;
4 = Center ouest; 5= Nord; 6 = Sud ouest Age (months)
Sex
Perceived illness severity
Hospitalization
Distance from household to nearest health facility (km)
Place of residence
Poverty status (SES)
Mother’s level of education in the household
District Fbr
Region We categorized “disease severity” into no effect on activities and some effect on
activities (leisure, school, being able to eat, etc.). 2.5.2. Explanatory (Control) Variables 2.5.2. Explanatory (Control) Variables 1
The research of factors associated with out-of-pocket expenditure highlights the socio-
demographic data of patients and their mothers (age, place of residence, mother’s level of Healthcare 2023, 11, 1379 5 of 12 5 of 12 education, economic status) and those related to the health system (health district, region,
distance from the health center) as control variables (Table 1). education, economic status) and those related to the health system (health district, region,
distance from the health center) as control variables (Table 1). The “economic status” ranks households in the poorest quintile of socio-economic
status (SES) against the other four richer quintiles. This approach follows the logic of the
most vulnerable exemption policy that started its experimentation since 2008 with the
collaboration of a German NGO (HELP). Socio-economic status (SES) was calculated as a
continuous variable using the Multiple Component Analysis (MCA) method to aggregate
information on assets, household housing characteristics, and other parameters, and was
divided into quintiles [23,24]. Table 1. Variables and measurements. Mesurements and Categorization
Variables of Interest
Probability of out-of-pocket expenditure
0 = No; 1 = Yes
Out-of-pocket expenditure [FRS CFA]
Continuous
Explanatory variables
Age (months)
1= (0–6); 2= (7–23); 3 =(24–59)
Sex
0 = Boy; 1 = Girl
Perceived illness severity
0 = No effect on activities; 1 = Any effect on activities
Hospitalization
0 = No; 1 = Yes
Distance from household to nearest health facility (km)
0= ≤5 km; 1= > 5 km
Place of residence
0 = Rural; 1 = Urban
Poverty status (SES)
0 = Other; 1 = Poor (Socio-economic status/quintile 1)
Mother’s level of education in the household
0= Uneducated; 1= Educated
District Fbr
0 = No; 1 = Yes
Region
1 = Boucle du Mouhoun; 2 = Center est; 3 = Center nord;
4 = Center ouest; 5= Nord; 6 = Sud ouest Table 1. Variables and measurements. 2.6. Analytical Approach Our objective was to identify how many children face an out-of-pocket expenditure,
quantify its amount, and determine the associated factors. First, we computed mean
values, standard deviation (SD), median, min and max values. To correct for outliers,
we applied winsorizing, replacing 5 to 25% of outlier expenditure data items [25]. This
method preserves the power of the sample in the regression analysis and avoids bias in the
calculation of the mean value and variance by retaining higher values in the sample [26]. y
g
g
p
Second, we examined which factors were associated with a positive expenditure and
with the magnitude of the expenditure. To address usual challenges related to the large
number of zeros, skewness, and possible bias due to heteroscedasticity, several authors
have recommended a two-part model approach [27]. Accordingly, the probability of facing
a positive direct health payment was modeled first (Pr (Y > 0|X)) and followed by modeling
the amounts of out-of-pocket health payments for those who paid (E (Y|Y > 0, X)) [27], as
expressed in the equation below: E (Y|X) = Pr (Y > 0|X) × E (Y|Y > 0, X). Hence, for the first part, a logit regression was done to identify the “probability of
incurring OOPE” because the interpretation of its results is quite simple. For the second
part, the Box-Cox test (p = 0 for λ = 0) showed that the data are not suitable for the use
of the generalized linear model (GLM) with a log link. Therefore, the OLS model with
log transformation of Y was used to identify the “determinants of out-of-pocket health
payments” in the second part. For the gross scale back transformation, the restrictive Healthcare 2023, 11, 1379 6 of 12 assumption of normal distribution of log scale errors was not imposed. The estimator of
Duan (1983) was used in preference [27,28]. The data analysis was performed with STATA
version 13. assumption of normal distribution of log scale errors was not imposed. The estimator of
Duan (1983) was used in preference [27,28]. The data analysis was performed with STATA
version 13. 3.2. Direct Childcare Services Payments 3.2. Direct Childcare Services Payments About 31% (n = 248) of those who had contact with the formal public healthcare system
faced direct childcare service payments that averaged XOF3407.77 (US$ 5.67) (min: 100 frs
and max: 10,000 frs) per illness episode (Table 2). The highest average expenditure was
observed for hospitalization (concerning 4%), laboratory/radiology and surgical services
(concerning 2%), and consultations (concerning 24%). The most frequent expenditures
were for medical drugs (96%) and for consultation fees (24%). Additional expenses outside
the free care package were noted. These are transportation expenses for 109 children (44%)
whose parents declared that they had paid for transportation out of their own pockets
with an average of XOF728 (US$1.21). This gives an indication of the financial burden
on households. The highest variance is for hospitalization (SD = XOF16,358.74) and for
consultation (XOF3459.1) Table 2. Adjusted out-of-pocket expenditures (OOPE) 1 among those who used formal. Table 2. Adjusted out-of-pocket expenditures (OOPE) 1 among those who used formal. j
p
p
(
)
g
N
%
Average (Frs CFA)
SD (Frs CFA)
Median (Frs CFA)
Min (Frs CFA)
Max (Frs CFA)
Probability of OOPE among
those who used formal services
(n = 807)
OOP = 0
559
69
NA
NA
NA
NA
NA
OOP > 0
248
31
3407.77
2839.53
3200
100
10,000
Components of OOPE (n = 248)
Consultation fees
59
24
3269.06
3459.1
1500
100
10,100
Laboratory/radiography and
surgery costs (examinations)
5
2
4100
1341.64
5000
2000
5000
Drugs
237
96
2895.33
2388.14
2000
100
8000
Hospitalization costs
11
4
12,209.09
16,358.74
5050
750
50,000
Total direct health payments
248
100
3407.77
2839.53
3200
100
10,000
Transports
109
44
728.73
210.70
700
300
1000
SD: Standard Deviation. Corresponds to the costs of transport spent by those who made OOP. PS: these costs are
not parts of the free health care basket. 2.7. Ethical Considerations The study received the favorable opinion of the ethics committee of the University of
Heidelberg (S-272/2013) and the national ethics committee for health research of Burkina
Faso (N◦2013-7-066 and N◦2015-5-071). Respondents gave their informed consent, and
their confidentiality was ensured by the anonymity used in the data collection tools. 3.1. Characteristics of Sample The sample included a total of 15,323 children aged from 0 to 5 years (Figure 1). Of
these, 1015 children reported a non-chronic illness or injury in the four weeks preceding the
survey date. Of these, 807 sick children aged 0 to 5 years had contact with the formal public
healthcare system. Most of these children did not come from poor households and lived
in rural areas (n = 807, 90.46%) with an average distance from the household to the health
facility of less than or equal to 5 km. These children were from FBR districts for 79.18% and
went to primary healthcare facilities (HSPC, maternity) to receive care (97.40%). 3.3. Factors Associated with OOP Payments The percentage of children aged from 0 to 5 years who paid for care differed signif-
icantly according to the child’s age group, severity of illness, economic status, place of
residence, and region. The following factors have no impact on childcare service payments:
mother’s level of education in the household, proximity to the health center, and district
FBR. Table 3 presents the proportions of free and paid care services according to children Healthcare 2023, 11, 1379 7 of 12 7 of 12 aged from 0 to 5 years characteristics. This table allowed us to select the variables of the
two-part model, taking variables as significant at the 20% level. aged from 0 to 5 years characteristics. This table allowed us to select the variables of the
two-part model, taking variables as significant at the 20% level. Table 4 presents the adjusted results of the two-part model that included 807 obser-
vations in the first part and 248 in the second part. In the logistic regression (first part),
hospitalization, place of residence, region of residence, child’s age group, economic sta-
tus, and severity of illness were significantly associated with out-of-pocket payments for
children aged from 0 to 5 years. As a result, those who are hospitalized are 4.53 times
more (95% CI= 1.92–8.88) likely to pay for childcare services than those not hospitalized. Compared with those in rural places, those in urban places paid for childcare services
3.47 times more often (95% CI = 1.88–5.34). People with an illness that affects any activity
are 1.53 times more likely (95% CI = 1.07–2.09) to pay for childcare services than those
whose illness does not affect their activities. Compared with the South-West region, those
that lived in the East-Central and North-Central were 4.50 times (95% CI = 2.18–9.29) and
2.43 times (95% CI = 1.16–5.08) more likely to pay for childcare services for children aged
from 0 to 5 years, respectively. In addition, children in the 7- to 23-month age group are
48 percent (95% CI= 0.35–0.83) less likely to pay for childcare services than those in the
0- to 6-month age group. The poorest section of the population (quintile 1) are 33 percent
(95% CI= 0.44–1.07) less likely to pay for childcare services. Thus, the poor are protected. Table 3. A proportion of children aged 0–5 years who paid and who did not pay for services. 3.3. Factors Associated with OOP Payments Two-part model for the determinants of out-of-pocket expenditure (First part: logit, second
part: OLS with log transformation; n = 807). In the log-transformed OLS regression (second part), hospitalization significantly
increased the amount of out-of-pocket health payments for children aged from 0 to 5 years
(coef = 0.78; p < 0.001). The amount was higher for people with an illness that affects any
activity (coef = 0.24; p = 0.047). In addition, locations such as the East-Central, North-Central,
and West-Central region saw increased the amounts of out-of-pocket health payments when
there was a direct childcare services payment (coef= 0.60; 0.59; 0.76 and p = 0.029; 0.04; 0.01)
compared with the South-West region. 3.3. Factors Associated with OOP Payments Characteristics
Children Who Paid (n = 248)
Children Who Did not Pay (n = 559)
P
n
%
n
%
Age groups (months)
0.012
(0–6)
58
40.28
86
59.72
(7–23)
119
27.17
319
72.83
(24–59)
71
31.56
154
68.44
Perceived illness severity
0.099
No effect
92
27.54
242
72.46
Effect
156
32.98
317
67.02
Poverty indices
0.009
Not poor
216
32.73
444
67.27
Poor (the poorest)
32
21.77
115
78.23
Mother’s level of education in the household
0.708
Uneducated
195
30.42
446
69.58
Educated
53
31.93
113
68.07
Place of residence
0.000
Rural
206
28.22
524
71.78
Urban
42
54.55
35
45.45
Proximity to a health center (distance in km)
0.472
≤5 km
187
31.43
408
68.57
>5 km
61
28.77
151
71.23
District Fbr
0.621
No
49
29.17
119
70.83
Yes
199
31.14
440
68.86
Region
0.000
Boucle du Mouhoun
30
26.79
82
73.21
Center Est
67
48.2
72
51.8
Center Nord
44
32.35
92
67.65
Center Ouest
38
27.74
99
72.26
Nord
56
26.17
158
73.83
Sud Ouest
13
18.84
56
81.16 Table 3. A proportion of children aged 0–5 years who paid and who did not pay for services. Healthcare 2023, 11, 1379 8 of 12 Table 4. Two-part model for the determinants of out-of-pocket expenditure (First part: logit, second
part: OLS with log transformation; n = 807). Part 1: Likelihood of Having a Direct Payment (n = 807)
Part 2: Determinants of the Amount of OOPE (n = 248)
Explanatory Variables
OR
95% CI
p-Value
Coeff
95% CI
p-Value
Age group (months)
(0–6 months)
1
0
(7–23 months)
0.52
0.35–0.83
0.003 ***
−0.09
−0.39–0.19
0.51
(24–59 months)
0.62
0.39–1.01
0.052 *
−0.015
−0.33–0.30
0.92
Hospitalization
No
1
0
Yes
4.53
1.92–8.88
<0.001 ***
0.78
0.38–1.17
<0.001 ***
Perceived illness severity
No effect
1
0
Effect
1.53
1.07–2.09
0.018 **
0.24
−0.003–0.49
0.047 **
Place of residence
Rural
1
0
Urban
3.47
1.88–5.34
<0.001 ***
0.34
−0.032–0.66
0.031 **
Poverty Indices
Not poor
1
0
Poor
0.67
0.44–1.07
0.098 *
0.09
−0.25–0.45
0.61
Regions
South-West
1
0
Boucle du Mouhoun
1.51
0.70–3.28
0.288
−0.02
−0.63–0.58
0.945
Central-East
4.50
2.18–9.29
<0.001 ***
0.60
0.06–1.14
0.029 **
Central-North
2.43
1.16–5.08
0.018 **
0.59
0.02–1.16
0.040 **
Centre-West
1.60
0.75–3.37
0.216
0.76
0.18–1.34
0.01 **
North
1.71
0.84–3.48
0.137
0.23
−32–0.78
0.409
* Significance at 10%; ** Significance at 5%; *** Significance at 1%. Table 4. 4. Discussion Our study is one of the first ones to estimate the level and determinants of out-of-
pocket payments for care among children aged 0 to 5 years of age in the context of the
gratuité, the free healthcare policy launched nationwide in 2016 in Burkina Faso. Our study
makes an important contribution to the literature by providing evidence on the efficacy
of the policy in removing user charges at point of use during its early implementation
phase, building on a representative population-based sample and covering over a third
of the country. Prior studies measuring OOP expenditure in the context of free healthcare
policies in Burkina Faso have traditionally drawn from pilot experiences or focused on
expenditures for maternal care [16,18]. p
First, our results show that one year into the implementation, one third of all children
aged 0 to 5 years of age who reported an episode of illness or injury and who sought care
in the formal public healthcare system incurred direct health payments in the process of
seeking care. Among those who incurred a payment, the amount averaged XOF 3407.77
(US$5.67) per episode of care. This amount is considerable in a country where, even in
the formal sector, the minimum wage is equivalent to XOF 34,664 and where 44% of the
population lives in extreme poverty on less than US$2 per day [29]. While our study has
not investigated how families cope with these high payments, we can only speculate that
past strategies (including asset erosion and borrowing) persist and contribute to further
household impoverishment [30,31]. Our results are consistent with what has been observed
in prior studies, suggesting that the introduction of free healthcare policies alone is not
sufficient to remove all payments at point of use [12,16,32,33]. Prior research has indicated
that challenges related to the implementation of healthcare policies, including insufficient
knowledge among implementers and funding, which are often responsible for residual
fees [34–36]. Further research is needed to investigate the root causes of our observations. 9 of 12 Healthcare 2023, 11, 1379 Second, our analysis shows that hospitalization, laboratory/radiology services, and
surgery, although infrequent events, were key cost drivers. This suggests a failure on
behalf of the system to provide free healthcare consistently across all levels of care. Similar
patterns have been observed elsewhere in the presence of free healthcare policies. 4. Discussion For
instance, in Zambia, almost all children accessed care free of charge after the introduction
of the free healthcare policy, but nearly 10% were left to pay catastrophic amounts [9]. This
suggests that healthcare systems are unable to implement the policy consistently and are
unable to apply purchasing models that meet different needs, leading to a breakdown of
supply chains. Further investments are needed a priori in the systems to not jeopardize the
potential of free healthcare policies. p
p
Our findings indicate that expenditure on medications remained considerable at an
average of XOF2, 895 (US$4.82). This observation is consistent with prior studies, having
shown that in a context of free healthcare, frequent expenses are related to medications [12]. Several factors could explain why seeking care at public facilities still results in a high
expenditure on medications. For instance, previous studies have suggested that stock-outs
of medicines and medical consumables at public facilities push patients to purchase drugs
at private facilities, driving expenditure on drugs. According to the Ministry of Health of
Burkina Faso, only 60 percent of drug orders were fulfilled by the company responsible for
supplying public health facilities with essential generic drugs in 2017. This is likely to have
forced patients to resort to the private sector, resulting in direct payments in spite of a free
healthcare setting in the public system [16,37]. Further research is needed to understand
and strengthen the supply of stocks at the Centrale d’Achat des Médicaments Essentiels
Génériques (CAMEG). Looking in-depth at the results of the two-part regression model, we noted that
children have a higher probability of incurring a direct payment if they were hospitalized,
live in an urban place, suffer from a severe condition, and live in the East-Central, North-
Central, or West-Central region. More specifically, it is not surprising that a severe illness,
since it limits daily activities and has a strong association with hospitalization, increases
the likelihood of making an expenditure [11,38,39]. In line with prior studies [32,40,41], we
found that OOP payments were higher among children of higher socio-economic status. This may reflect a higher ability to pay for items not directly covered by the free healthcare
system, such as speciality instead of generic drugs [42,43]. 4. Discussion Likewise, OOP payments are
higher in urban settings, possibly suggesting different costs between rural and urban
settings [44] and access to more opportunities for spending on additional services in urban
settings not covered by the free healthcare policy. Contrary to what has been observed
in other settings [45,46], we observed higher spending on children of a younger age
(0 to 6 month), suggesting that there may be more gaps in the policy coverage among
this age group. g g
p
It also needs to be noted that beyond direct medical costs, 44% of the children who
reported out-of-pocket expenditure for care also reported spending an average of XOF728
(US$1.21) for transportation. This finding underlines the high costs associated with seeking
care beyond direct medical costs. A great deal has been written highlighting distance as
one of the main barriers to accessing care in Burkina Faso, as well as in other developing
countries [47]. In order to fully remove financial barriers to access, policy makers need to
include a lump sum to cover transport to health facilities so that distance does not impose
an additional cost. Methodological Considerations Beyond its policy contribution, we noted a few methodological limitations related
to the nature of the data we used for our study. First, we acknowledge that the data we
used were six years old by the time we submitted the article for publication. We are aware
of the potential bias derived from the age of the data, as a lot could have changed in
either direction, producing increases or decreases in OOP payments in Burkina Faso in
the meantime. Nonetheless, we note that at the time of submission, no other large-scale Healthcare 2023, 11, 1379 10 of 12 10 of 12 population-based dataset was available in the country since the Demographic Health
Survey has not been released for several years. Therefore, our estimates of OOP payments
in the country remain the most relevant ones in the context of the gratuité. Second, the
questionnaire was not developed to assess the determinants of spending for children aged
0 to 5 years of age [11]. As a result, information on the causes of the different sources
of out-of-pocket payments is missing and could not be used to complement evidence
from our analysis. Third, data were collected retrospectively, so information on out-
of-pocket payments is likely to be less accurate because it is subject to recall bias [48]. Fourth, by considering children aged 0 to 5 years of age who had contact with the formal
public healthcare system, we purposely truncated the sample to include only children who
sought care in the public healthcare system. This is in line with our research question to
determine the role of the gratuité in curbing OOP payments but may obviously lead to an
underestimation of the overall magnitude of OPP for children under 5 in the country, since
it captures only care encounters covered by the gratuité. Last, we recognize our inability
to account for facility characteristics in our model as potential drivers of out-of-pocket
expenditure due to the impossibility to link household survey data to facility data. This
has limited the potential for causal inference on the role of health system characteristics in
driving OOP payments under the gratuité. 5. Conclusions Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. 1.
Richard, F.; Witter, S.; de Brouwere, V. Innovative Approaches to Reducing Financial Barriers to Obstetric Care in Low-Income
Countries. Am. J. Public Health 2010, 100, 1845–1852. [CrossRef] [PubMed] 5. Conclusions The study revealed that a considerable proportion of children aged from 0 to 5 years,
who are the target of the current free healthcare policy, continue to pay for access to health-
care. These payments are largely due to the purchase of drugs and medical consumables,
probably due to stock-outs and the prescription of drugs not available in the pharmacy of
public health facilities. Further research is needed to understand why these payments at
point of use persist, and efforts are needed to ensure greater efficiency implementation to
guarantee better financial protection. Author Contributions: Conceptualization, L.D.G.T., H.H. and M.D.A.; Methodology, L.D.G.T., M.Y. and M.D.A.; Validation, L.D.G.T., M.I.N., S.M.A.S., J.L. and S.H.; Formal analysis, L.D.G.T., M.Y.,
M.I.N., S.M.A.S., J.L., P.J.R. and M.D.A.; Data curation, L.D.G.T. and M.Y.; Writing—original draft,
L.D.G.T.; Writing—review & editing, M.Y., M.I.N., S.M.A.S., J.L., P.J.R., S.H., H.H. and M.D.A.;
Visualization, L.D.G.T., M.Y., M.I.N. and S.M.A.S.; Supervision, L.D.G.T., J.L., P.J.R., S.H., H.H. and
M.D.A. All authors have read and agreed to the published version of the manuscript. Author Contributions: Conceptualization, L.D.G.T., H.H. and M.D.A.; Methodology, L.D.G.T., M.Y. and M.D.A.; Validation, L.D.G.T., M.I.N., S.M.A.S., J.L. and S.H.; Formal analysis, L.D.G.T., M.Y.,
M.I.N., S.M.A.S., J.L., P.J.R. and M.D.A.; Data curation, L.D.G.T. and M.Y.; Writing—original draft,
L.D.G.T.; Writing—review & editing, M.Y., M.I.N., S.M.A.S., J.L., P.J.R., S.H., H.H. and M.D.A.;
Visualization, L.D.G.T., M.Y., M.I.N. and S.M.A.S.; Supervision, L.D.G.T., J.L., P.J.R., S.H., H.H. and
M.D.A. All authors have read and agreed to the published version of the manuscript. Funding: This study used data from the endline survey of the impact evaluation of the Performanc
Based Financing Program in Burkina Faso, a study funded by the World Bank’s Health Results
Innovation Trust Fund. All authors, however, contributed their own time towards preparation of this
article. The World Bank provided no direct funding for preparation of this article. Institutional Review Board Statement: The study was conducted in accordance with the Declaration
of Helsinki, and approved by the Ethics Committee of the University of Heidelberg (S-272/2013) and
the national ethics committee for health research of Burkina Faso (N◦2013-7-066 and N◦2015-5-071). Informed Consent Statement: Informed consent was obtained from all subjects involved in
the study. Data Availability Statement: Data is available on request for reasons of confidentiality and ethics. The data presented in this study are available on request from the principal investigators of the
project who provided the data. 2.
Shahrawat, R.; Rao, K.D. Insured yet vulnerable: Out-of-pocket payments and India’s poor. Health Policy Plan. 2012, 27, 213–221.
[CrossRef] [PubMed] References 1. Richard, F.; Witter, S.; de Brouwere, V. Innovative Approaches to Reducing Financial Barriers to Obstetric Care in Low-Income
Countries. Am. J. Public Health 2010, 100, 1845–1852. [CrossRef] [PubMed]
2. Shahrawat, R.; Rao, K.D. Insured yet vulnerable: Out-of-pocket payments and India’s poor. Health Policy Plan. 2012, 27, 213–221. [CrossRef] [PubMed] 11 of 12 11 of 12 Healthcare 2023, 11, 1379 3. Saksena, P.; Hsu, J.; Evans, D.B. Financial Risk Protection and Universal Health Coverage: Evidence and Measurement Challenges. PLoS Med. 2014, 11, e1001701. [CrossRef] [PubMed] 4. Hercot, D.; Meessen, B.; Ridde, V.; Gilson, L. Removing user fees for health services in low-income countries: A multi-country
review framework for assessing the process of policy change. Health Policy Plan. 2011, 26, ii5–ii15. [CrossRef] [PubMed] g
p
p
y
g
y
5. Ridde, V.; Morestin, F. A scoping review of the literature on the abolition of user fees in health care services in Africa. Health
Policy Plan. 2011, 26, 1–11. [CrossRef] 6. Lagarde, M.; Palmer, N. The impact of user fees on access to health services in low- and middle-income countries. Cochrane
Database Syst. Rev. 2011, CD009094. [CrossRef] y
7. Dalinjong, P.A.; Wang, A.Y.; Homer, C.S.E. Has the free maternal health policy eliminated out of pocket payments for maternal
health services? Views of women, health providers and insurance managers in Northern Ghana. PLoS ONE 2018, 13, e0184830. [CrossRef] [PubMed] [
] [
]
8. Kaonga, O.; Banda, C.; Masiye, F. Hardship financing of out-of-pocket payments in the context of free healthcare in Zambia. PLoS
ONE 2019, 14, e0214750. [CrossRef] 9. Masiye, F.; Kaonga, O.; Kirigia, J.M. Does User Fee Removal Policy Provide Financial Protection from Catastrophic Health Care
Payments? Evidence from Zambia. PLoS ONE 2016, 11, e0146508. [CrossRef] at, J.; Audibert, M.; Belem, S. Analyzing the Financial Sustainability of User Fee Removal Policies: A R 10. Mathonnat, J.; Audibert, M.; Belem, S. Analyzing the Financial Sustainability of User Fee Removal Policies: A Rapid First
Assessment Methodology with a Practical Application for Burkina Faso. Appl. Health Econ. Health Policy 2020, 18, 767–780. Available online: http://link.springer.com/10.1007/s40258-019-00506-2 (accessed on 13 January 2020). [CrossRef] p
p
g
(
J
y
)
11. Nakovics, M.I.; Brenner, S.; Robyn, P.J.; Tapsoba, L.D.G.; De Allegri, M. Determinants of individual healthcare expenditure:
A cross-sectional analysis in rural Burkina Faso. Int. J. Health Plan. Manag. 2019, 34, e1478–e1494. Available online: http:
//doi.wiley.com/10.1002/hpm.2812 (accessed on 26 July 2019). References [CrossRef] [PubMed] //
y
/
/ p
(
J
y
) [
] [
]
12. Ridde, V.; Diarra, A.; Moha, M. User fees abolition policy in Niger: Comparing the under five years exemption implementation in
two districts. Health Policy 2011, 99, 219–225. [CrossRef] [PubMed] y
p
y
12. Ridde, V.; Diarra, A.; Moha, M. User fees abolition policy in Niger: Com
two districts. Health Policy 2011, 99, 219–225. [CrossRef] [PubMed] 13. Zombré, D.; De Allegri, M.; Ridde, V. Immediate and sustained effects of user fee exemption on healthcare utilization among
children under five in Burkina Faso: A controlled interrupted time-series analysis. Soc. Sci. Med. 2017, 179, 27–35. [CrossRef]
[PubMed] [
]
14. Ministère de la Santé et de la Prévention. Burkina Faso Stratégie Nationale de Mise en Oeuvre de la Politique Nationale de Gratuité des
Soins (2018–2022); Ministère de la Santé et de la Prévention: Paris, France, 2017. 15. Richard, F.; Antony, M.; Witter, S.; Kelley, A.; Kafando, Y.; Meessen, B. Fee Exemption for Maternal Care in Sub-Saharan Africa: A
Review of 11 Countries and Lessons for the Region. Glob. Health Gov. 2013, 6, 52–72. 16. Meda, I.B.; Baguiya, A.; Ridde, V.; Ouédraogo, H.G.; Dumont, A.; Kouanda, S. Out-of-pocket payments in the context of a free
maternal health care policy in Burkina Faso: A national cross-sectional survey. Health Econ. Rev. 2019, 9, 1–14. Available online:
https://healtheconomicsreview.springeropen.com/articles/10.1186/s13561-019-0228-8 (accessed on 5 May 2019). [CrossRef] p
p
g
p
y
17. Ridde, V.; Agier, I.; Jahn, A.; Mueller, O.; Tiendrebéogo, J.; Yé, M.; De Allegri, M. The impact of user fee removal policies on
household out-of-pocket spending: Evidence against the inverse equity hypothesis from a population based study in Burkina
Faso. Eur. J. Health Econ. 2015, 16, 55–64. [CrossRef] 18. Nguyen, H.T. Economic Evaluation of User-Fee Exemption Policies for Maternal Healthcare in Burkina Faso: Evidence From a
Cost-Effectiveness Analysis. VALUE Health 2020, 23, 300–308. [CrossRef] 19. KI, E. Le Taux de Pauvreté Passe de 47% à 40.1% au Burkina Faso. Available online: http://www.ecodufaso.com/le-taux-de-
pauvrete-passe-de-47-a-401-au-burkina-faso/ (accessed on 11 May 2018). 20. Ecofin, A. Le Classement des Pays Africains Dans L’édition 2016 de L’indice de Développement Humain du PNUD. Avail-
able online: https://www.agenceecofin.com/economie/2403-45994-le-classement-des-pays-africains-dans-l-edition-2016-de-
l-indice-de-developpement-humain-du-pnud (accessed on 28 March 2018). pp
p
21. Ministère de la Santé du Burkina Faso. Annuaire Statistique Ministère de la Santé. Available online: https://www.sante.gov.bf/
fileadmin/annuaire_2020_mshp.pdf (accessed on 28 March 2022). p p
22. References Deb, P.; Norton, E.C.; Manning, W.G. Health Econometrics Using Stata. Available online: https://www.routledge.com/Health-
Econometrics-Using-Stata-1st-Edition/Deb-Norton-Manning/p/book/9781597182287 (accessed on 11 July 2020). g
g p
(
y
)
29. World Bank. Poverty & Equity Data Portal. Poverty & Equity Data Portal—Burkina Faso. Available online: http://povertydata. worldbank.org/poverty/country/BFA (accessed on 9 November 2018). g p
y
y
30. Meessen, B.; Zhenzhong, Z.; Damme, W.V.; Devadasan, N.; Criel, B.; Bloom, G. Iatrogenic poverty. Trop. Med. Int. Health 2003,
8, 581–584. [CrossRef] [PubMed] 31. Sauerborn, R.; Adams, A.; Hien, M. Household strategies to cope with the economic costs of illness. Soc. Sci. Med. 1982 1996,
43, 291–301. [CrossRef] 32. Asante, F.; Chikwama, C.; Daniels, A.; Armar-Klemesu, M. Evaluating the Economic Outcomes of the Policy of Fee Exemption for
Maternal Delivery Care in Ghana. Ghana Med. J. 2007, 41, 110–117. [CrossRef] 33. Kruk, M.E.; Mbaruku, G.; Rockers, P.C.; Galea, S. User fee exemptions are not enough: Out-of-pocket pay
services in rural Tanzania. Trop. Med. Int. Health 2008, 13, 1442–1451. [CrossRef] 34. Carasso, B.S.; Lagarde, M.; Cheelo, C.; Chansa, C.; Palmer, N. Health worker perspectives on user fee removal in Zambia. Hum. Resour. Health 2012, 10, 40. [CrossRef] 35. Ridde, V.; Leppert, G.; Hien, H.; Robyn, P.J.; De Allegri, M. Street-level workers’ inadequate knowledge and application of
exemption policies in Burkina Faso jeopardize the achievement of universal health coverage: Evidence from a cross-sectional
survey. Int. J. Equity Health 2018, 17, 5. [CrossRef] y
q
y
36. Sato, M.; Gilson, L. Exploring health facilities’ experiences in implementing the free health-care policy (FHCP) in Nepal: How
did organizational factors influence the implementation of the user-fee abolition policy? Health Policy Plan. 2015, 30, 1272–1288. [CrossRef] [
]
37. Opwora, A.; Waweru, E.; Toda, M.; Noor, A.; Edwards, T.; Fegan, G.; Molyneux, S.; Goodman, C. Implementation of patient
charges at primary care facilities in Kenya: Implications of low adherence to user fee policy for users and facility revenue. Health
Policy Plan. 2015, 30, 508–517. [CrossRef] [PubMed] y
[
] [
]
38. Castellani, J.; Mihaylova, B. Out-of-Pocket Costs and Other Determinants of Access to Healthcare for Children with Febrile
Illnesses: A Case-Control Study in Rural Tanzania. PLoS ONE 2015, 10, e0122386. [CrossRef] 39. Hendrix, N.; Bar-Zeev, N.; Atherly, D.; Chikafa, J.; Mvula, H.; Wachepa, R.; Crampin, A.C.; Mhango, T.; Mwansambo, C.;
Heyderman, R.S.; et al. The economic impact of childhood acute gastroenteritis on Malawian families and the healthcare system. References Ketsela, T.; Habimana, P.; Martines, J.; Mbewe, A.; Williams, A.; Sabiiti, J.N.; Thiam, A.; Narayanan, I.; Bahl, R. Prise en charge
intégrée des maladies de l’enfance (PCIME). In Donnons Sa Chance à chaque Nouveau-né de L’Afrique; 2010; Volume 10. Available 22. Ketsela, T.; Habimana, P.; Martines, J.; Mbewe, A.; Williams, A.; Sabiiti, J.N.; Thiam, A.; Narayanan, I.; Bahl, R. Prise en charge
intégrée des maladies de l’enfance (PCIME). In Donnons Sa Chance à chaque Nouveau-né de L’Afrique; 2010; Volume 10. Available
online: https://www.who.int/pmnch/media/publications/oanfr_III_5.pdf (accessed on 28 March 2023). online: https://www.who.int/pmnch/media/publications/oanfr_III_5.pdf (accessed on 28 March 2023). 23. Kolenikov, S.; Angeles, G. Socioeconomic Status Measurement with Discrete Proxy Variables: Is Principal Component Analysis a
Reliable Answer? Rev. Income Wealth 2009, 55, 128–165. [CrossRef] p
p
p
p
23. Kolenikov, S.; Angeles, G. Socioeconomic Status Measurement with Discrete Proxy Variables: Is Principal Component Analysis a
Reliable Answer? Rev. Income Wealth 2009, 55, 128–165. [CrossRef] 23. Kolenikov, S.; Angeles, G. Socioeconomic Status Measurement with Discrete Proxy Variables: Is Princip
Reliable Answer? Rev. Income Wealth 2009, 55, 128–165. [CrossRef] 24. Vyas, S.; Kumaranayake, L. Constructing socio-economic status indices: How to use principal components analysis. Health Policy
Plan. 2006, 21, 459–468. [CrossRef] [
]
M.; Etzel, C.J.; Fernández, J.R.; Chen, J.; Allison, D.B.; Amos, C.I. Effect of Winsorization on Power and Type 1 25. Shete, S.; Beasley, T.M.; Etzel, C.J.; Fernández, J.R.; Chen, J.; Allison, D.B.; Amos, C.I. Effect of Winsorization on Power and Type 1
Error of Variance Components and Related Methods of QTL Detection. Behav. Genet. 2004, 34, 153–159. [CrossRef] [PubMed]
h
l
A O’
A
h
S G
f
l
h d f
l
h
l h
d 25. Shete, S.; Beasley, T.M.; Etzel, C.J.; Fernández, J.R.; Chen, J.; Allison, D.B.; Amos, C.I. Effect of Winsorization on Power and Type 1
Error of Variance Components and Related Methods of QTL Detection. Behav. Genet. 2004, 34, 153–159. [CrossRef] [PubMed]
26. Mihaylova, B.; Briggs, A.; O’Hagan, A.; Thompson, S.G. Review of statistical methods for analysing healthcare resources and
costs. Health Econ. 2010, 21, 897–916. [CrossRef] [PubMed] p
26. Mihaylova, B.; Briggs, A.; O’Hagan, A.; Thompson, S.G. Review of statistical methods for analysi
costs. Health Econ. 2010, 21, 897–916. [CrossRef] [PubMed] 27. Belotti, F.; Deb, P.; Manning, W.G.; Norton, E.C. Twopm: Two-Part Models. Stata J. Promot. Commun. Stat. Stata 2015, 15, 3–20. [CrossRef] 12 of 12 12 of 12 Healthcare 2023, 11, 1379 28. References Open Access 2017, 7, e017347. [CrossRef] [PubMed] 40. Laokri, S. Assessing out-of-pocket expenditures for primary health care: How responsive is the Democratic Republic of Congo
health system to providing financial risk protection? BMC Health Serv. Res. 2018, 18, 451. [CrossRef] [PubMed]
41
T ff
N Ch
G D
i
f h
l h
ki
f
hildh
d ill
i
N i
bi l
T
M d I t H
lth 2005 40. Laokri, S. Assessing out-of-pocket expenditures for primary health care: How responsive is the Democratic Republic of Congo
health system to providing financial risk protection? BMC Health Serv. Res. 2018, 18, 451. [CrossRef] [PubMed]
41. Taffa, N.; Chepngeno, G. Determinants of health care seeking for childhood illnesses in Nairobi slums. Trop. Med. Int. Health 2005,
10, 6. [CrossRef] [PubMed] 41. Taffa, N.; Chepngeno, G. Determinants of health care seeking for childhood illnesses in Nairobi slums. Trop. Med. Int. Health 2005,
10, 6. [CrossRef] [PubMed] Hélène-Pelage, J.; Moueza, N.; Lamy, S.; Carrère, P. “No generics, Doctor!” The perspective of general
French regions. BMC Health Serv. Res. 2017, 17, 707. [CrossRef] 42. Riner, B.; Bussy, A.; Hélène-Pelage, J.; Moueza, N.; Lamy, S.; Carrère, P. “No generics, Doctor!” Th
practitioners in two French regions. BMC Health Serv. Res. 2017, 17, 707. [CrossRef] 43. Dunne, S.S.; Dunne, C.P. What do people really think of generic medicines? A systematic review and critical appraisal of literature
on stakeholder perceptions of generic drugs. BMC Med. 2015, 13, 173. [CrossRef] p
p
g
g
44. Sauerborn, R.; Berman, P.; Nougtara, A. Age bias, but no gender bias, in the intra-household resource allocation for health care in
rural Burkina Faso. Health Transit. Rev. 1996, 23, 131–145. 45. Mugisha, F.; Kouyate, B.; Gbangou, A.; Sauerborn, R. Examining out-of-pocket expenditure on health care in Nouna, Burkina
Faso: Implications for health policy. Trop. Med. Int. Health 2002, 7, 10. [CrossRef] 45. Mugisha, F.; Kouyate, B.; Gbangou, A.; Sauerborn, R. Examining out-of-pocket expenditure on health care in Nouna, Burkina
Faso: Implications for health policy. Trop. Med. Int. Health 2002, 7, 10. [CrossRef] 46. Hjortsberg, C. Why do the sick not utilise health care? The case of Zambia. Health Econ. 2003, 12, 755 770. [CrossRef]
47. Tey, N.; Lai, S. Correlates of and Barriers to the Utilization of Health Services for Delivery in South Asia and Sub-Saharan Africa. Sci. World J. 2013, 2013, 423403. [CrossRef] [PubMed] 47. Tey, N.; Lai, S. References Correlates of and Barriers to the Utilization of Health Services for Delivery in South Asia and Sub-Saharan Africa. Sci. World J. 2013, 2013, 423403. [CrossRef] [PubMed] 48. Heijink, R.; Xu, K.; Saksena, P.; Evans, D.; WHO. Validity and Comparability of Out of Pocket Health Expenditure from Household
Surveys a Review of the Literature and Current Survey Instruments. 2011. Available online: http://www.who.int/health_
financing/documents/covdp_e_11_01oop_errors/en/ (accessed on 10 September 2018). 48. Heijink, R.; Xu, K.; Saksena, P.; Evans, D.; WHO. Validity and Comparability of Out of Pocket Health Expenditure from Household
Surveys a Review of the Literature and Current Survey Instruments. 2011. Available online: http://www.who.int/health_
financing/documents/covdp_e_11_01oop_errors/en/ (accessed on 10 September 2018). Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual
author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to
people or property resulting from any ideas, methods, instructions or products referred to in the content.
|
https://openalex.org/W2888664982
|
https://europepmc.org/articles/pmc6140119?pdf=render
|
English
| null |
A Brain without Brakes: Reduced Inhibition Is Associated with Enhanced but Dysregulated Plasticity in the Aged Rat Auditory Cortex
|
ENeuro
| 2,018
|
cc-by
| 15,706
|
New Research Sensory and Motor Systems Sensory and Motor Systems Author Contributions: JMC and EdV designed research; JMC, LO, and BK
performed research; JMC and EdV analyzed data; JMC and EdV wrote the
paper. Received February 1, 2018; accepted June 29, 2018; First published August
21, 2018.
The authors declare no competing financial interests. Abstract During early developmental windows known as critical periods (CPs) of plasticity, passive alterations in the quality
and quantity of sensory inputs are sufficient to induce profound and long-lasting distortions in cortical sensory
representations. With CP closure, those representations are stabilized, a process requiring the maturation of
inhibitory networks and the maintenance of sufficient GABAergic tone in the cortex. In humans and rodents,
however, cortical inhibition progressively decreases with advancing age, raising the possibility that the regulation
of plasticity could be altered in older individuals. Here we tested the hypothesis that aging results in a
destabilization of sensory representations and maladaptive dysregulated plasticity in the rat primary auditory
cortex (A1). Consistent with this idea, we found that passive tone exposure is sufficient to distort frequency tuning
in the A1 of older but not younger adult rats. However, we also found that these passive distortions decayed
rapidly, indicating an ongoing instability of A1 tuning in the aging cortex. These changes were associated with a
decrease in GABA neurotransmitter concentration and a reduction in parvalbumin and perineuronal net expres-
sion in the cortex. Finally, we show that artificially increasing GABA tone in the aging A1 is sufficient to restore
representational stability and improve the retention of learning. Key words: Aging; auditory cortex; cortical plasticity; GABA; inhibition; training DOI:http://dx.doi.org/10.1523/ENEURO.0051-18.2018 1Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal QC H3A
2B4, Canada and 2Centre for Research on Brain, Language, and Music, Montreal QC H3G 2A8, Canada Significance Statement In this study, we examined brain plasticity in the auditory cortex of young adult and older adult rats in the
context of different types of auditory stimulation and training. Surprisingly, older brains retained an equal or
even higher potential for plasticity compared to young adults. In older brains, however, changes elicited by
auditory stimulation and training were rapidly lost, suggesting that such increased plasticity might be
detrimental, as the older brains were unable to consolidate these changes. This increased but poorly
regulated plasticity was associated with a reduction in cortical inhibition, which normally maintains the
stability of sensory representations in the young adult brain. Importantly, increasing inhibition artificially with
clinically available drugs restored stability and improved the retention of learning. rat primary auditory cortex (A1; Hensch, 2005; de Villers-
Sidani et al., 2007). On closure of the CP, these
experience-dependent alterations are consolidated, and
A1 tuning becomes relatively resistant to passive sound J. Miguel Cisneros-Franco,1,2
Lydia Ouellet,1 Brishna Kamal,1 and
Etienne de Villers-Sidani1,2 J. Miguel Cisneros-Franco,1,2
Lydia Ouellet,1 Brishna Kamal,1 and
Etienne d DOI:http://dx.doi.org/10.1523/ENEURO.0051-18.2018 Received February 1, 2018; accepted June 29, 2018; First published August
21, 2018.
The authors declare no competing financial interests.
July/August 2018, 5(4) e0051-18.2018 1–15 Mapping the auditory cortex learning (Maffei and Turrigiano, 2008; Caroni et al., 2012). Cortical inhibitory circuits are almost invariably affected
by natural aging, as evidenced by a reduction of inhibitory
tone and specific inhibitory interneurons such as PV and
somatostatin-positive (SST) cells in older brains (Cas-
pary et al., 2008; Stanley et al., 2012; Ouellet and de
Villers-Sidani, 2014). Given the importance of inhibitory
processes in the regulation of plasticity and learning, it is
reasonable to speculate that aging could have a signifi-
cant impact on the mechanisms of learning in the brain
(Caspary et al., 2008; Liguz-Lecznar et al., 2014). Loss of
inhibition could lead to a state of cortical instability where
sensory representations are easily distorted by nonspe-
cific passive experiences, as is the case with the CP (Zhou
et al., 2011). Such impairments could likely explain the
noisy sensory processing and less effective learning and
recovery observed in older rodents (Liguz-Lecznar et al.,
2014) and humans (Boyke et al., 2008; Knoflach et al.,
2012). Here, we tested these ideas using a combination of
controlled passive pure tone exposure, pharmacological
experiments, and behavioral training in young and old
rats. We found that experience-dependent plasticity is
paradoxically enhanced but unstable in old rats compared
to young controls. Such instability was found even for
relatively short 10 minute-long exposures and was paral-
leled by a reduction in the number of PV cells and PNNs. Finally, we also demonstrated that this instability is asso-
ciated with a more rapid decay of learning that can be
reversed by artificially enhancing GABA tone in the brain. For A1 mapping, the rats were premedicated with dexa-
methasone (0.2 mg/kg) to minimize brain edema. They
were anesthetized with ketamine/xylazine/acepromazine
(65/13/1.5 mg/kg, i.p.) followed by a continuous delivery
of isoflurane 1% in oxygen delivered via endotracheal
intubation and mechanical ventilation. Vital signs were
monitored using a MouseOx device (Starr Life Sciences). Body temperature was monitored with a rectal probe and
maintained at 37°C with a homeothermic blanket system. The rats were held by the orbits in a custom-designed
head holder, leaving the ears unobstructed. The cisterna
magna was drained of cerebrospinal fluid to further min-
imize brain edema. The left temporalis muscle was re-
flected, auditory cortex (AC) was exposed, and the dura
was resected. The cortex was maintained under a thin
layer of silicone oil to prevent desiccation. Cortical responses were recorded with 32–64-channel
tungsten microelectrode arrays (Neuronexus). Gouvernement du Canada | Canadian Institutes of Health Research (CIHR)
grant MOP-133426 to EdV, and CIHR Vanier Canada Graduate Scholarship
and CONACYT fellowship to JMC.
Acknowledgments: We are grateful to M. Thomas and P. Voss for useful
comments on this manuscript.
Correspondence should be addressed to J. Miguel Cisneros-Franco, 3801
University Rm 753, Montreal, QC, H3A2B4, Canada. E-mail: mike.cisneros-
franco@mail.mcgill.ca.
DOI:http://dx.doi.org/10.1523/ENEURO.0051-18.2018
Copyright © 2018 Cisneros-Franco et al.
This is an open-access article distributed under the terms of the Creative
Commons Attribution 4.0 International license, which permits unrestricted use,
distribution and reproduction in any medium provided that the original work is
properly attributed. Materials and Methods exposures. CP closure in sensory cortices is associated
with the maturation of functional and structural inhibitory
elements (Hensch, 2005; Fritschy and Panzanelli, 2014),
including the maturation of parvalbumin positive (PV)
interneurons (Kuhlman et al., 2013) and perineuronal nets
(PNN; Wang and Fawcett, 2012). In the adult brain, plastic
changes of the magnitude observed in the CP can be
induced by down-regulating cortical inhibition (Fagiolini
and Hensch, 2000) or disrupting elements involved in the
stabilization of cortical representations such as PNNs
(Pizzorusso et al., 2002; Carulli et al., 2010; Wang and
Fawcett, 2012). Plastic changes of this magnitude other-
wise still occur in the mature brain, but regulation mech-
anisms restrict them mainly to the context of behavior
(Blake et al., 2006; Polley et al., 2006; Caroni et al., 2012). This tight gating of plasticity and resulting relative stability
in the mature brain contribute to the consolidation and
retention of new perceptuo-motor skills acquired through
learning (Maffei and Turrigiano, 2008; Caroni et al., 2012). All experimental procedures used in this study were
approved by the Animal Care Committee and follow es-
tablished guidelines. Twenty-three immature Long-Evans
rats of either sex [age postnatal 10 days (P10) to P24], 24
Long-Evans young adult rats of either sex (age 6–8 mo),
and 28 Long-Evans old adult rats of either sex (22–24 mo)
were used for this study. Finally, we also demonstrated that this instability is asso-
ciated with a more rapid decay of learning that can be
reversed by artificially enhancing GABA tone in the brain. Passive sound exposure The tone pip-exposed rats were housed for 1 or 2
consecutive weeks (24 h/d, 7 d/wk) in a sound attenuated
chamber equipped with a speaker. The exposure se-
quences were generated using custom Matlab routines
and contained repetitive trains of six 25-ms-long 5- or
10-kHz pips with 5-ms cosine gates presented at a rate of
5 p.p.s. at an intensity of 70 dB SPL. exposures. CP closure in sensory cortices is associated
with the maturation of functional and structural inhibitory
elements (Hensch, 2005; Fritschy and Panzanelli, 2014),
including the maturation of parvalbumin positive (PV)
interneurons (Kuhlman et al., 2013) and perineuronal nets
(PNN; Wang and Fawcett, 2012). In the adult brain, plastic
changes of the magnitude observed in the CP can be
induced by down-regulating cortical inhibition (Fagiolini
and Hensch, 2000) or disrupting elements involved in the
stabilization of cortical representations such as PNNs
(Pizzorusso et al., 2002; Carulli et al., 2010; Wang and
Fawcett, 2012). Plastic changes of this magnitude other-
wise still occur in the mature brain, but regulation mech-
anisms restrict them mainly to the context of behavior
(Blake et al., 2006; Polley et al., 2006; Caroni et al., 2012). This tight gating of plasticity and resulting relative stability
in the mature brain contribute to the consolidation and
retention of new perceptuo-motor skills acquired through
learning (Maffei and Turrigiano, 2008; Caroni et al., 2012). Cortical inhibitory circuits are almost invariably affected
by natural aging, as evidenced by a reduction of inhibitory
tone and specific inhibitory interneurons such as PV and
somatostatin-positive (SST) cells in older brains (Cas-
pary et al., 2008; Stanley et al., 2012; Ouellet and de
Villers-Sidani, 2014). Given the importance of inhibitory
processes in the regulation of plasticity and learning, it is
reasonable to speculate that aging could have a signifi-
cant impact on the mechanisms of learning in the brain
(Caspary et al., 2008; Liguz-Lecznar et al., 2014). Loss of
inhibition could lead to a state of cortical instability where
sensory representations are easily distorted by nonspe-
cific passive experiences, as is the case with the CP (Zhou
et al., 2011). Such impairments could likely explain the
noisy sensory processing and less effective learning and
recovery observed in older rodents (Liguz-Lecznar et al.,
2014) and humans (Boyke et al., 2008; Knoflach et al.,
2012). Here, we tested these ideas using a combination of
controlled passive pure tone exposure, pharmacological
experiments, and behavioral training in young and old
rats. We found that experience-dependent plasticity is
paradoxically enhanced but unstable in old rats compared
to young controls. Such instability was found even for
relatively short 10 minute-long exposures and was paral-
leled by a reduction in the number of PV cells and PNNs. Introduction During early developmental epochs known as critical
periods (CPs) of plasticity, passive exposure to environ-
mental sounds profoundly shapes frequency tuning in the July/August 2018, 5(4) e0051-18.2018 1–15 New Research
2 of 15 Gouvernement du Canada | Canadian Institutes of Health Research (CIHR)
grant MOP-133426 to EdV, and CIHR Vanier Canada Graduate Scholarship
and CONACYT fellowship to JMC. DOI:http://dx.doi.org/10.1523/ENEURO.0051-18.2018 Acknowledgments: We are grateful to M. Thomas and P. Voss for useful
comments on this manuscript. Copyright © 2018 Cisneros-Franco et al. This is an open-access article distributed under the terms of the Creative
Commons Attribution 4.0 International license, which permits unrestricted use,
distribution and reproduction in any medium provided that the original work is
properly attributed. GABA microdialysis Immediately after craniotomy (see Methods: Electro-
physiology), a microdialysis probe (CMA 12 Microdialysis
probe, Harvard Apparatus) was implanted in the AC using
the stereotaxic coordinates (Paxinos and Watson, 2007):
bregma AP, –4.5 mm; ML, –7 mm; DV, 4.5 mm. The pump
rate was set at 0.09 mL/h (PHD ultra 4400 Syringe pump,
Harvard Apparatus). Samples were manually collected
and frozen at –80°C until analysis with high performance
liquid chromatography (Reinhoud et al., 2013). Normalized responses to standard and oddball tones
were obtained by dividing the average firing rate recorded
in the 50 ms after the occurrence of each tone presenta-
tion by the average firing rate observed during the 50 ms
after the first standard or oddball tone in the sequence. Asymptotes for standard and oddball responses were
calculated by fitting exponential functions with a least
squares method to the normalized response data from
each recorded neuron. Simple linear regression of the
normalized responses to the standard tone for the interval
from event no. 150 to event no. 1200 was performed. The
slope of the resulting best fit line was computed to deter-
mine the level of adaptation for each recorded site. was classified as either “go” (producing a nose poke
behavior) or “no-go.” For a given trial, the rat could elicit
one of four reinforcements produced by the combinations
of responses (go or no-go) and stimulus properties (target
or nontarget). Go responses within 5 s of a target were
scored as a hit; a failure to respond within this time
window was scored as a miss; a go response within 5 s of
a nontarget stimulus was scored as a false positive; the
absence of a response was scored as a withhold. A hit
triggered the delivery of a food pellet. A miss or false
positive initiated a 5-s time-out period during which time
the house lights were turned off and no stimuli were
presented. A withhold did not produce a reward or a
time-out. Psychometric functions and stimulus target rec-
ognition indexes (D-prime) were calculated for each train-
ing session by plotting the percentage of go responses as
a function of the total number of target stimuli (i.e., hit
ratio) and the percentage of false positives as a function of
the total number of foils (i.e., false-positive ratio). Learning
curves were reconstructed by plotting the D-prime mea-
sure reached over successive days of training. pseudo-randomly distributed oddball frequencies presented
20% of the time with no repetition. The oddball frequencies
in the train had a constant separation of 1 octave. Immunohistochemistry y
Immediately following the end of recording sessions,
rats received a high dose of pentobarbital (85 mg/kg i.p.)
and were perfused intracardially with 4% paraformalde-
hyde in 0.1 M PBS at pH 7.2. Immediately after perfusion,
rat brains were removed and placed in the same fixative
overnight for further fixation and then transferred to a 30%
sucrose solution, snap-frozen, and stored at –80°C until
sectioning. Fixed material was cut in the coronal plane
along the tonotopic axis of A1 on a freezing microtome at
40 µm. Tissue was incubated overnight at 4°C in
either monoclonal or polyclonal antisera (for anti-PV: #P-
3088, dilution 1:10,000, Sigma-Aldrich; for PNN, fluores-
cein wisteria floribunda lectin #FL-1351, dilution 1:200,
Vector Laboratories). Tissue samples were always pro-
cessed in pairs during immunostaining procedures to limit
variables relative to antibody penetration, incubation time,
and post-sectioning age/condition of tissue. A Zeiss LSM
510 Meta confocal microscope was used to assess fluo-
rescence in the immunostained sections. Quantification of
PV cells and PNN optical density was performed in
ImageJ (National Institutes of Health) and MetaMorph
imaging software (Molecular Devices Systems), respec-
tively. Digital images of A1 cortical sections were taken
with a 40 objective (Zeiss LSM 510). All quantification
was assessed in 300–400-µm-wide A1 sectors
(rostral, middle, caudal) extending from layer 1 to the un-
derlying white matter by an experimenter blind to the age of Electrophysiological data analysis The characteristic frequency (CF) of a cortical site was
defined as the frequency at the tip of the V-shaped tuning
curve. For flat-peaked tuning curves, the CF was defined
as the midpoint of the plateau at threshold. For tuning
curves with multiple peaks, the CF was defined as the
frequency at the most sensitive tip (i.e., with lowest
threshold). The CF and threshold were determined using
an automated routine developed in the Matlab environ-
ment (The MathWorks). To generate A1 maps, Voronoi tessellation (a Matlab
routine) was performed to create tessellated polygons
with electrode penetration sites at their centers. Each
polygon was assigned the characteristics (i.e., CF) of the
corresponding penetration site. In this way, every point on
the surface of the AC was linked to the characteristics
experimentally derived from its closest sampled cortical
site. Primary AC (A1) was identified based on its rostral-
to-caudal tonotopy, reliable short-latency tone-evoked
neuronal responses, and relatively sharp V-shaped RF. To
examine A1 map plasticity, we compared the percentage
of A1 sites with CFs in 12 bins (width octave) span-
ning the spectrum of presented tones. Mapping the auditory cortex The micro-
electrode array was lowered orthogonally into the cortex
to a depth of 470–600 µm (layers 4/5) where vig-
orous stimulus-driven responses were obtained. The ex-
tracellular neural action potentials were amplified, filtered
(0.3–5 kHz), sorted, and monitored on-line. Acoustic stim-
uli were generated using TDT System III (Tucker-Davis
Technologies) and delivered in a free-field manner to the
right ear through a calibrated speaker (Tucker-Davis
Technologies). A software package (OpenEx; Tucker-
Davis Technologies) was used to generate acoustic stim-
uli, monitor cortical response properties on-line, and store
data for off-line analysis. The evoked spikes of a single
neuron or a small cluster of neurons were collected at
each site. Frequency-intensity receptive fields were reconstructed
by presenting pure tones of 63 frequencies (1–48 kHz;
0.1-octave increments; 25-ms duration; 5-ms ramps) at 8
sound intensities (0–70 dB SPL in 10-dB increments) to
the contralateral ear at a rate of one stimulus per second. Ten-minute-long trains of 50-ms tone pips were pre-
sented at 3 pulses per second at a sound intensity of 70
dB SPL. Each train had a commonly occurring frequency
(standard) with a probability of occurrence of 80% and 5 eNeuro.org July/August 2018, 5(4) e0051-18.2018 New Research
3 of 15 Table 1. Statistical table. Such an
exposure resulted in a significant overrepresentation of
the exposure tone in A1 of immature rats (average %
difference in the proportion of recording sites tuned within
octave of exposure tone, relative to control: 9.77
1.54% increase, p 0.001a, with Tukey–Kramer correc-
tion) but not in the young adult group (F(11,72) 4.02,
p 0.001; 3.84 1.3% increase, p 0.87b, with Tukey–
Kramer correction; Fig. 1B). Passive tone exposure, how-
ever, resulted in a significant overrepresentation of the the animals. PV cells were classified into four subclasses
as follows: low-PV, 0–0.8 105; intermediate low-PV, 8–1.6
105; intermediate high-PV, 1.6–2.4 105; high-PV, 2.4
105. PNNs were classified into four subclasses as follows:
low PV, 0–1 104, intermediate low-PV, 1–2 105; inter-
mediate high-PV, 2–3 105; high-PV, 3 105. Statistical analysis For normally distributed data, statistical significance was
assessed using unpaired two-tailed t tests or two-way anal-
ysis of variance with Tukey post hoc correction for multiple
comparisons. Wilcoxon rank-sum test or Kruskal–Wallis test
with Tukey post hoc correction for multiple comparisons
were used for nonparametric data analysis. Data are pre-
sented as mean SEM or median median absolute
deviation (MAD). Superscript letters listed with p-values cor-
respond to the statistical tests shown in Table 1. Table 1. Statistical table. Data structure
Type of test
Statistic and p value
a
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,168) 14.84, p 0.001; p 0.001
b
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 4.02, p 0.001; p 0.87
c
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 10.77, p 0.001; p 0.001
d
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 13.13, p 0.001; p 0.001, p 0.35
e
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 2.69, p 0.005; p 1, p 0.96
f
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 7.23, p 0.001; p 1, p 0.001
g
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,132) 14.62, p 0; p 0.001, p 0.15
h
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,120) 12.58, p 0; p 0.001, p 0.1
i
Nonnormal distribution
Wilcoxon rank-sum test
z –4.099, p 4.1 10–5
j
Nonnormal distribution
Wilcoxon rank-sum test
z –3.187, p 0.0014
K
Normal distribution
t test
t(579) 5.64, p 0.001
l
Normal distribution
t test
t(395) 3.35, p 9 10–4
m
Normal distribution
t test
t(750) 0.75, p 0.45
n
Normal distribution
t test
t(408) 0.64, p 0.52
o
Normal distribution
t test
t(383) 2.55, p 0.011
p
Nonnormal distribution
Wilcoxon rank-sum test
z –4.4, p 1.1 10–5
q
Nonnormal distribution
Wilcoxon rank-sum test
z 2.46, p 0.013
r
Normal distribution
t test
t(720) 5.29, p 0.001
s
Normal distribution
t test
t(345) 2.1, p 0.03
t
Normal distribution
t test
t(690) 0.86, p 0.39
u
Normal distribution
t test
t(308) 0.08, p 0.94
v
Normal distribution
t test
t(18) 2.32, p 0.032
w
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 13.42, p 0.001; p 0.018
x
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 6.57, p 0.001; p 0.004, p 0.41
y
Normal distribution
t test
t(6) 5.02, p 0.002
z
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 6.68, p 0.001; p 0.01
ab
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 1.41, p 0.18
ac
Normal distribution
2-way ANOVA; Tukey–Kramer test
F(11,72) 5.42, p 0.001; p 0.022
ad
Normal distribution
t test
t(6) 2.53, p 0.04
ae
Normal distribution
t test
t(6) 3.66, p 0.01
af
Nonnormal distribution
Kruskal–Wallis test; Tukey–Kramer post hoc test
H(4) 14.52, p 0.0058; p 0.52, p 0.011, p 0.96, p 0.97
ag
Nonnormal distribution
Kruskal–Wallis test; Tukey–Kramer post hoc test
H(4) 83.97, p 0.0001; p 0.0001, p 0.001, p 0.96, p 0.003
ah
Nonnormal distribution
Kruskal–Wallis test; Tukey–Kramer post hoc test
H(4) 13, p 0.011; p 0.82, p 0.005, p 0.99, p 0.99
ai
Nonnormal distribution
Kruskal–Wallis test; Tukey–Kramer post hoc test
H(4) 17.24, p 0.0017; p 0.48, p 0.04, p 0.004, p 0.8, p 0.99
aj
Nonnormal distribution
Kruskal–Wallis test; Tukey–Kramer post hoc test
H(4) 22.06, p 0.001; p 0.004, p 0.039, p 0.99, p 0.85 ley et al., 2012; Ouellet and de Villers-Sidani, 2014; Steb-
bings et al., 2016). Training
B h
i Behavior was shaped in three phases. During the first
phase, rats were trained to make a nose poke response to
obtain a food reward. During the second phase, rats were
trained to make a nose poke only after presentation of an
auditory stimulus. During the third phase, the actual training
program, rats were trained to make a nose poke only for the
target stimulus (a 5-kHz pure tone) and not for a foil nontar-
get stimulus (10-kHz pure tone). The tones were presented
at 60 dB SPL, stimulus presentation was randomized, and
the probability of a target stimulus presentation was set at
20%. Training was performed in an acoustically transparent
operant training chamber (60 45 35 cm, length width
height) contained within a sound-attenuated chamber. Sound presentation and response recording were per-
formed using OpenEx software and RZ6 auditory process-
ing hardware from Tucker-Davis Technology and delivered
in a free field manner through a calibrated loudspeaker. The intertrial interval was selected at random from a
range of 4–6 s. A rat’s behavioral state at any point in time eNeuro.org July/August 2018, 5(4) e0051-18.2018 eNeuro.org New Research
4 of 15 Table 1. Statistical table. This raises the possibility that the old
brain has in fact a higher plastic potential than its young
adult counterpart. To test this hypothesis, we examined
the effect of pure-tone exposure on spectral tuning in the
aged A1. We exposed old adult rats (OA, 22–23 months
old, n 4) to 5 kHz tone pips for 1 week. For comparison,
the same exposure was used in young adult (YA, 6–8
months old, n 4) and immature rats in their CP window
(I, P10–P17, n 8; Fig. 1A). We then compared the
proportion of A1 neurons whose characteristic frequency
was close to the exposure frequency. As expected, there
was a clear effect of 5-kHz tone exposure on the CF of
immature rats (two-way ANOVA, exposure group fre-
quency bin, F(11,168) 14.84, p 0.001a). Such an
exposure resulted in a significant overrepresentation of
the exposure tone in A1 of immature rats (average %
difference in the proportion of recording sites tuned within
octave of exposure tone, relative to control: 9.77
1.54% increase, p 0.001a, with Tukey–Kramer correc-
tion) but not in the young adult group (F(11,72) 4.02,
p 0.001; 3.84 1.3% increase, p 0.87b, with Tukey–
Kramer correction; Fig. 1B). Passive tone exposure, how-
ever, resulted in a significant overrepresentation of the ley et al., 2012; Ouellet and de Villers-Sidani, 2014; Steb-
bings et al., 2016). This raises the possibility that the old
brain has in fact a higher plastic potential than its young
adult counterpart. To test this hypothesis, we examined
the effect of pure-tone exposure on spectral tuning in the
aged A1. We exposed old adult rats (OA, 22–23 months
old, n 4) to 5 kHz tone pips for 1 week. For comparison,
the same exposure was used in young adult (YA, 6–8
months old, n 4) and immature rats in their CP window
(I, P10–P17, n 8; Fig. 1A). We then compared the
proportion of A1 neurons whose characteristic frequency
was close to the exposure frequency. As expected, there
was a clear effect of 5-kHz tone exposure on the CF of
immature rats (two-way ANOVA, exposure group fre-
quency bin, F(11,168) 14.84, p 0.001a). Table 1. Statistical table. Table 1. Statistical table. Passive tone exposure induces significant shifts in
A1 tuning Aging is characterized by a progressive reduction in
cortical inhibition to levels akin to those observed during
developmental critical periods (Caspary et al., 2008; Stan- July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org B
A
Figure 1. Passive sound exposure alters frequency tuning in the aged A1. A, Representative A1 CF maps from naïve rats (top) and
from rats exposed to 5-kHz pure tones during 1 week (bottom). D, dorsal; C, caudal; R, rostral; V, ventral. B, Difference in frequency
tuning between naïve and exposed rats expressed as A1 percentage area and separated by CF for immature, young adult, and old
adult groups. Immature group: n 8, recorded sites 389; YA: n 8, recorded sites 403; OA: n 8, recorded sites 382;
immature-exposed: n 8, recorded sites 362; YA-exposed: n 4, recorded sites 177; OA-exposed: n 4, recorded sites
168. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. New Research
5 of 15 New Research
5 of 15 A A B
Figure 1. Passive sound exposure alters frequency tuning in the aged A1. A, Representative A1 CF maps from naïve rats (top) and
from rats exposed to 5-kHz pure tones during 1 week (bottom). D, dorsal; C, caudal; R, rostral; V, ventral. B, Difference in frequency
tuning between naïve and exposed rats expressed as A1 percentage area and separated by CF for immature, young adult, and old
adult groups. Immature group: n 8, recorded sites 389; YA: n 8, recorded sites 403; OA: n 8, recorded sites 382;
immature-exposed: n 8, recorded sites 362; YA-exposed: n 4, recorded sites 177; OA-exposed: n 4, recorded sites
168. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. B B Figure 1. Passive sound exposure alters frequency tuning in the aged A1. A, Representative A1 CF maps from naïve rats (top) and
from rats exposed to 5-kHz pure tones during 1 week (bottom). D, dorsal; C, caudal; R, rostral; V, ventral. B, Difference in frequency
tuning between naïve and exposed rats expressed as A1 percentage area and separated by CF for immature, young adult, and old
adult groups. Passive tone exposure induces significant shifts in
A1 tuning Immature group: n 8, recorded sites 389; YA: n 8, recorded sites 403; OA: n 8, recorded sites 382;
immature-exposed: n 8, recorded sites 362; YA-exposed: n 4, recorded sites 177; OA-exposed: n 4, recorded sites
168. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. Enhancing cortical inhibition stabilizes frequency
representation in the aged A1 exposure tone in the aged A1 group (F(11,72) 10.77,
p 0.001, two-way ANOVA; 8.05 1.14% increase, p
0.001c, with Tukey–Kramer correction). Enhancing cortical inhibition stabilizes frequency
representation in the aged A1 Having documented the existence of age-related tuning
instability in A1, and considering the reduction of intra-
cortical inhibition in sensory cortices associated with ad-
vanced age (Lehmann et al., 2012; Wang and Fawcett,
2012), we hypothesized that increasing GABAergic tone
would restore the excitatory/inhibitory (E/I) balance and
prevent further plastic changes elicited by passive tone
exposure. To determine the effect of enhancing inhibition
on frequency tuning stability in aged rats, we systemically
administered the GABAA agonist diazepam (1 mg/kg i.p.,
twice a day; n 4) during two consecutive pure-tone
exposures as described above (10-kHz pure tones for 1
week followed by 5-kHz pure tones for 1 week; Fig. 2C). We found that diazepam administration resulted in an
overrepresentation of the first (10-kHz) rather than the
second (5-kHz) exposure tone (F(11,72) 7.23, p To further document the extent of this tuning instability
in older rats, we examined the effect of two consecutive
pure-tone exposures over a 2-week period. Young (n 4)
and old (n 4) adult rats were exposed to 10-kHz tone
pips during the first week and to 5-kHz tone pips during
the second week (Fig. 2A). This passive exposure proto-
col resulted in an overrepresentation of the second (5-
kHz) exposure tone in A1 of aged rats (F(11,72) 13.13,
p 0.001, two-way ANOVA; 5 kHz: 8.81 1.7% in-
crease, p 0.001; 10 kHz: 5.18 1.3% decrease, p
0.35d, with Tukey–Kramer correction) but did not alter the
frequency tuning map of young adults (F(11,72) 2.69,
p 0.005, two-way ANOVA; 5 kHz: 2.1 0.56% de-
crease, p 1; 10 kHz: 3.4 0.57% decrease, p 0.96e,
with Tukey–Kramer correction; Fig. 2B). eNeuro.org eNeuro.org eNeuro.org July/August 2018, 5(4) e0051-18.2018 New Research
6 of 15 D
C
B
A
Figure 2. Restoration of inhibition stabilizes frequency representation in the aged A1. Young and old adult rats were exposed to
10-kHz pure tones for 1 week, followed immediately by exposure to 5-kHz pure tones for 1 week. A, Representative A1 CF maps from
young (left) and old (right) adult rats that received sham (saline) intraperitoneal injections during the 2-week passive exposure period. Enhancing cortical inhibition stabilizes frequency
representation in the aged A1 B, Difference in frequency tuning between naïve and saline-treated rats expressed as A1 percentage area and separated by CF. C,
Representative A1 CF map from an old adult rat that received diazepam (DZP) intraperitoneal injections during the 2-week passive
exposure period. D, Difference in frequency tuning between naïve and DZP-treated rats. To investigate whether sequential exposure
to pure tones would have a similar effect in immature rats, 2-week exposures were conducted starting on P10 as described in Fig. 2-1. YA-saline group: n 4, recorded sites 230; OA-saline: n 4, recorded sites 203; OA-diazepam: n 4; recorded sites
218. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. Conventions as in Fig. 1. C
A C C A D D D
B B D Figure 2. Restoration of inhibition stabilizes frequency representation in the aged A1. Young and old adult rats were exposed to
10-kHz pure tones for 1 week, followed immediately by exposure to 5-kHz pure tones for 1 week. A, Representative A1 CF maps from
young (left) and old (right) adult rats that received sham (saline) intraperitoneal injections during the 2-week passive exposure period. B, Difference in frequency tuning between naïve and saline-treated rats expressed as A1 percentage area and separated by CF. C,
Representative A1 CF map from an old adult rat that received diazepam (DZP) intraperitoneal injections during the 2-week passive
exposure period. D, Difference in frequency tuning between naïve and DZP-treated rats. To investigate whether sequential exposure
to pure tones would have a similar effect in immature rats, 2-week exposures were conducted starting on P10 as described in Fig. 2-1. YA-saline group: n 4, recorded sites 230; OA-saline: n 4, recorded sites 203; OA-diazepam: n 4; recorded sites
218. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. Conventions as in Fig. 1. 0.001, two-way ANOVA; 5 kHz: 2.23 1.45% increase,
p 1; 10 kHz: 13.8 5.7% increase, p 0.001f, cor-
rected with Tukey–Kramer test; Fig. 2D). (Hensch et al., 1998; Fagiolini and Hensch, 2000). July/August 2018, 5(4) e0051-18.2018 Enhancing cortical inhibition stabilizes frequency
representation in the aged A1 In line
with these observations, sequential tone exposure in im-
mature rats treated with diazepam (n 4) resulted in a
significant expansion of the tone presented during the
span of the CP; i.e., the first exposure tone (F(11,120)
12.58, p 0.001, two-way ANOVA; 5 kHz: 11.93 3.6%
increase, p 0.018; 10 kHz: 6.11 1.1% decrease, p
0.1h, corrected with Tukey–Kramer test; Fig. 2-1A, B,
right). To investigate whether sequential exposure to pure
tones would have a similar effect in immature animals as
in old adult animals, we used a sequential 2-week expo-
sure paradigm starting at P10 (5 kHz pure tones for 1
week, followed by 10 kHz pure tones for 1 week, n 5). Previous experiments have shown that passive tone ex-
posure outside the CP for frequency tuning (P10–P14)
does not alter the A1 tonotopic map (de Villers-Sidani
et al., 2007). For this reason, we predicted that such an
exposure would result in an overrepresentation of the
tone presented during the CP—the first exposure tone—
regardless of any subsequent tone presentation. As ex-
pected, and in contrast to the results observed in the OA
group, we observed plasticity in response to the first exposure
tone (F(11,132) 14.62, p 0, two-way ANOVA; 5 kHz: 13.27
3.4% increase, p 0.001; 10 kHz: 5.72 1.6% decrease, p
0.15g, corrected with Tukey–Kramer test; Fig. 2-1A, left) in
the vehicle (saline) condition. Reversal of adaptation in the immature and aged A1
Auditory neurons continuously monitor the environ-
ment, suppressing their response to repetitive sounds
and making novel stimuli more salient (Ulanovsky et al.,
2003; Malmierca et al., 2014). In the adult A1, such
stimulus-specific adaptation prevents the overrepresen-
tation of repetitive stimuli that drive plasticity during early
development (Norena et al., 2006) and is also involved in
the selection of A1 representations that should be selec-
tively suppressed in the context of training (Froemke
et al., 2013). With aging, however, receptive fields be-
come less reliable across successive repetitions of the
same set of stimuli (Turner et al., 2005). Enhancing cortical inhibition stabilizes frequency
representation in the aged A1 Immature group:
n 8, recorded sites 376; YA: n 4, recorded sites 205; OA: n 4, recorded sites 192; I-MDZ: n 8, recorded sites 346;
OA-MDZ: n 4, recorded sites 155. Figure 3. Improved adaptation in the immature and aged A1 following administration of the GABAA agonist midazolam. A, Stimulation
paradigm. Left, a standard (high-probability) tone was presented 80% of times. Five oddball (low-probability) tones distributed around
the standard frequency (middle) were interspersed in the repetitive tone presentation (right). B, Representative normalized responses
of individual A1 neurons to a standard tone (5 or 12 kHz at a repetition rate of 3 Hz) as function of tone position in the stimulus
sequence. Red horizontal lines represent the average normalized firing rate in response to the standard tone during two different
intervals in the stimulus sequence: early (T1, event 100–300; dashed line), and late (T2, event 900–1100; solid line). Note that
adaptation is reduced in both immature (I) and old adult rats. C, Probability distribution plot of the slope of firing rate trace in response
to the standard tone (interval from event no. 150–1200). Red dots denote the location of the median value for each group. Fig. 3-1
provides a summary of data related to adaptation in response to repetitive tones for all five groups. D, Frequency tuning of
representative A1 neurons during T1 (dashed line) and T2 (solid line). The normalized spike rate is plotted for the standard tone (arrow)
and each of the five deviant tones. Note the acute change in tuning after standard-oddball presentation in I and OA rats. E,
Representative A1 activity maps depicting the change in firing rate at T2 relative to T1 (T2/T1 ratio of normalized firing rate). Warmer
colors (white, yellow) denote neurons with reduced adaptation, notably in the I and OA groups. Same conventions apply for panels
F–I, which show that midazolam improved adaptation and prevented changes in tuning in the immature and aged A1. Immature group:
n 8, recorded sites 376; YA: n 4, recorded sites 205; OA: n 4, recorded sites 192; I-MDZ: n 8, recorded sites 346;
OA-MDZ: n 4, recorded sites 155. 376; OA, 0.11 0.02 10 4, p 0.0014, z –3.187j,
number of recorded cortical sites 192; Wilcoxon rank-
sum test; Fig. 3B, C). Enhancing cortical inhibition stabilizes frequency
representation in the aged A1 Immature group:
n 8, recorded sites 376; YA: n 4, recorded sites 205; OA: n 4, recorded sites 192; I-MDZ: n 8, recorded sites 346;
OA-MDZ: n 4 recorded sites 155 A D B E C D E C B H F H G H I I F G I n in the immature and aged A1 following administration of the GABAA agonist midazolam. A, Stimulation e 3. Improved adaptation in the immature and aged A1 following administration of the GABAA agonist mid Figure 3. Improved adaptation in the immature and aged A1 following administration of the GABAA agonist midazolam. A, Stimulation
paradigm. Left, a standard (high-probability) tone was presented 80% of times. Five oddball (low-probability) tones distributed around
the standard frequency (middle) were interspersed in the repetitive tone presentation (right). B, Representative normalized responses
of individual A1 neurons to a standard tone (5 or 12 kHz at a repetition rate of 3 Hz) as function of tone position in the stimulus
sequence. Red horizontal lines represent the average normalized firing rate in response to the standard tone during two different
intervals in the stimulus sequence: early (T1, event 100–300; dashed line), and late (T2, event 900–1100; solid line). Note that
adaptation is reduced in both immature (I) and old adult rats. C, Probability distribution plot of the slope of firing rate trace in response
to the standard tone (interval from event no. 150–1200). Red dots denote the location of the median value for each group. Fig. 3-1
provides a summary of data related to adaptation in response to repetitive tones for all five groups. D, Frequency tuning of
representative A1 neurons during T1 (dashed line) and T2 (solid line). The normalized spike rate is plotted for the standard tone (arrow)
and each of the five deviant tones. Note the acute change in tuning after standard-oddball presentation in I and OA rats. E,
Representative A1 activity maps depicting the change in firing rate at T2 relative to T1 (T2/T1 ratio of normalized firing rate). Warmer
colors (white, yellow) denote neurons with reduced adaptation, notably in the I and OA groups. Same conventions apply for panels
F–I, which show that midazolam improved adaptation and prevented changes in tuning in the immature and aged A1. Enhancing cortical inhibition stabilizes frequency
representation in the aged A1 To examine the Although treatment with diazepam accelerates the clos-
ing of the CP (Iwai et al., 2003), it does not prevent
experience-dependent
plasticity
from
taking
place July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org eNeuro.org New Research
7 of 15 E
I
H
G
F
D
C
B
A
Figure 3. Improved adaptation in the immature and aged A1 following administration of the GABAA agonist midazolam. A, Stimulation
paradigm. Left, a standard (high-probability) tone was presented 80% of times. Five oddball (low-probability) tones distributed around
the standard frequency (middle) were interspersed in the repetitive tone presentation (right). B, Representative normalized responses
of individual A1 neurons to a standard tone (5 or 12 kHz at a repetition rate of 3 Hz) as function of tone position in the stimulus
sequence. Red horizontal lines represent the average normalized firing rate in response to the standard tone during two different
intervals in the stimulus sequence: early (T1, event 100–300; dashed line), and late (T2, event 900–1100; solid line). Note that
adaptation is reduced in both immature (I) and old adult rats. C, Probability distribution plot of the slope of firing rate trace in response
to the standard tone (interval from event no. 150–1200). Red dots denote the location of the median value for each group. Fig. 3-1
provides a summary of data related to adaptation in response to repetitive tones for all five groups. D, Frequency tuning of
representative A1 neurons during T1 (dashed line) and T2 (solid line). The normalized spike rate is plotted for the standard tone (arrow)
and each of the five deviant tones. Note the acute change in tuning after standard-oddball presentation in I and OA rats. E,
Representative A1 activity maps depicting the change in firing rate at T2 relative to T1 (T2/T1 ratio of normalized firing rate). Warmer
colors (white, yellow) denote neurons with reduced adaptation, notably in the I and OA groups. Same conventions apply for panels
F–I, which show that midazolam improved adaptation and prevented changes in tuning in the immature and aged A1. Direct application of midazolam (1 g/µl
at a rate of 0.5 l/min) to the cortex resulted on average in
the progressive suppression of A1 responses to repetitive
tones in the immature and older groups (median slope of
normalized response rate: I, –0.13 0.02 10 4, p 1.1
10 5, z –4.4p, number of recorded cortical sites
346; OA, –0.01 0.04 10 4, p 0.013, z –2.46q,
number of recorded cortical sites 155; Wilcoxon rank-
sum test; Fig. 3F, G and Fig. 3-1A). It also resulted in a
significant decrease in response to the high-probability
tone in these groups (change in normalized firing rate in
response to the standard tone, T2 minus T1; I: –0.12
0.04, p 0.001, t(720) 5.29r; OA: –0.09 0.06, p
0.03, t(345) 2.1s; t test). The overall response to the
standard-oddball stimulus remained constant from T1 to
T2 for both groups (difference in mean area under the
curve between T1 and T2: I, 6.08 4.55, p 0.39, t(690)
0.86t; OA, 1.63 5.52, p 0.94, t(308) 0.08u; t test;
Fig. 3H, I). A summary of A1 responses to repetitive tones
and oddballs is provided in Fig. 3-1B. To determine the retention of learning and persistence
of training-related A1 retuning, we characterized trained
younger (YA-Tdelay, n 4) and older (OA-Tdelay, n 4) rats
after a 4-week delay period following completion of train-
ing (Fig. 4D, top). On average, younger rats maintained a
significantly better performance than older when resum-
ing training (YA-Tdelay: d= 2.8 0.12; OA-Tdelay: d=
0.96 0.48, p 0.002 t(6) 5.02y; Fig. 4D, bottom). A1
CF maps were reconstructed in another group of younger
and older rats after the delay period (Fig. 4E). In these we
found that the target tone representation in A1 had per-
sisted in the younger but not older group (YA-Tdelay:
F(11,72) 6.68, p 0.001, two-way ANOVA; 5 kHz:
10.37 2.3% increase, p 0.01z, corrected with Tukey–
Kramer test; OA-Tdelay: F(11,72) 1.41, p 0.18ab, two-
way ANOVA; 5 kHz: 4.72 2.1% increase; Fig. 4F). Interestingly,
the sum of responses to high and low probability tones
remained constant in the immature and young adult
groups, while it increased for the old adult group (differ-
ence in mean area under the curve between T1 and T2: I,
6.2 3.3, p 0.45, t(750) 0.75m; YA, 4.78 5, p
0.52, t(408) 0.64n; OA, 13.83 2.71, p 0.011, t(383)
2.55o; paired t test; Fig. 3D, E). neurons in the immature and old adult groups exhibited a
significant increase in response to the high-probability
tone from T1 to T2, while the opposite was seen in the
young adult group (change in normalized firing rate, T2
minus T1: YA, –0.19 0.05; I, 0.18 0.04, p 0.001,
t(579) 5.64k, relative to YA; OA, 0.15 0.09 p 9
10 4, t(395) 3.35l, relative to YA; t test). Interestingly,
the sum of responses to high and low probability tones
remained constant in the immature and young adult
groups, while it increased for the old adult group (differ-
ence in mean area under the curve between T1 and T2: I,
6.2 3.3, p 0.45, t(750) 0.75m; YA, 4.78 5, p
0.52, t(408) 0.64n; OA, 13.83 2.71, p 0.011, t(383)
2.55o; paired t test; Fig. 3D, E). In immature rats, short periods of auditory stimulation
readily modify frequency tuning in A1, likely because of a
disrupted E/I balance following the onset of hearing (Dorrn
et al., 2010). Additionally, considering that GABAA-
mediated inhibition regulates SSA (Duque et al., 2014), we
hypothesized that transiently increasing inhibitory tone
would improve adaptation in both the immature and aged
A1. To test this possibility, we administered the short-
acting GABAA agonist midazolam during the presentation
of the same repetitive stimulus. Given the different time
scales between our adaptation (10 min) and passive ex-
posure (1–2 weeks) experiments, we decided to use
midazolam as opposed to the long-acting GABAA agonist
diazepam. Finally, to test whether pharmacologically increasing
GABA inhibition would improve the retention of training-
induced plastic changes, we treated a subgroup (n 4) of
older rats with diazepam (1 mg/kg i.p., twice a day) during
the delay period post-training. A1 mapping in this group
revealed a persistent target tone overrepresentation not
significantly different from what had been observed im-
mediately following training (F(11,72) 5.42, p 0.001,
two-way ANOVA; 5 kHz: 7.64 2.8% increase, p
0.022ac, corrected with Tukey–Kramer test; Fig. 4F). 8 of 15 et al., 2008; Lustig et al., 2009). To examine the impact of
age on the retention of training-related plastic changes in
A1, we compared the performance of young (n 8) and
older (n 12) adult rats on an auditory discrimination task
and then measured training-induced A1 changes at the
end of training and after a 4-week delay. Both groups
were trained on a two-tone discrimination task (target
tone: 5 kHz, non-target tone: 10 kHz). Training ended
once the rats’ discrimination reached a sustained value of
D-prime (d=) 1 for two consecutive days; Fig. 4A, top). Older rats required on average more training sessions to
reach criterion than younger adults (YA: 8.4 0.8 ses-
sions; OA: 11.9 1.1, p 0.032, t(18) 2.32v; t test; Fig. 4A, bottom). At the end of training, A1 CF maps were
obtained from a subgroup of young (YA-T, n 4) and a
subgroup of old adult rats (OA-T, n 4; Fig. 4B). Two-way
analysis of variance revealed a significant effect of training
frequency bin for both YA-T and OA-T groups (F(11,72)
13.42, p 0.001w; F(11,72) 6.57, p 0.001x; re-
spectively). Compared to age-matched controls, both
groups exhibited an increase in the number of neurons
tuned to the target tone by the end of the training period
(average % difference in the proportion of recording sites
tuned within octave of exposure tone, relative to control:
YA-T: 12.25 1.5% increase, p 0.029w; OA-T: 8.06
2.25% increase, p 0.004x, corrected with Tukey–
Kramer test; Fig. 4C). We also found, as previously re-
ported (Voss et al., 2016), that the nontarget frequency
was underrepresented in the trained YA but not in the OA
group (YA-T: 11.54 3.5% decrease, p 0.018w; OA-T:
6.7 2.2% decrease, p 0.41x, corrected with Tukey–
Kramer test; Fig. 4C). neurons in the immature and old adult groups exhibited a
significant increase in response to the high-probability
tone from T1 to T2, while the opposite was seen in the
young adult group (change in normalized firing rate, T2
minus T1: YA, –0.19 0.05; I, 0.18 0.04, p 0.001,
t(579) 5.64k, relative to YA; OA, 0.15 0.09 p 9
10 4, t(395) 3.35l, relative to YA; t test). Enhancing cortical inhibition stabilizes frequency
representation in the aged A1 extent to which aging A1 neurons exhibit SSA, we used
10-min-long trains of pure tones (Fig. 3A). As expected, we found a progressive decrease in A1
neuron responses to repetitive tones in younger adults
(median slope of normalized response rate: YA, –0.14
0.03 10 4, number of recorded cortical sites 205) but
an increase in responses to repetitive tones in the imma-
ture and old adult groups relative to YA (median slope of
normalized response rate: I, 0.09 0.03 10 4, p 4.1
10 5, z –4.099i, number of recorded cortical sites Tuning stability in the same A1 neurons was examined
by interspersing five oddball (low-probability) tones cov-
ering the hearing range during the repetitive (high-
probability) tone presentation (see Methods). Using this
method, coarse tuning curves could be constructed over
two time intervals during the tone train exposure (T1, from
60 to 120 s; T2, from 400 to 460 s). On average, A1 July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org New Research
8 of 15 New Research July/August 2018, 5(4) e0051-18.2018 Impact of aging and dysregulated plasticity on
auditory learning Our results using passive sound exposure over different
time scales suggest that age-related loss of inhibition
could return the cortex into a state of instability where
sensory representations are continuously distorted by
nonspecific passive experience. If the deleterious effects
of age-related loss of inhibition observed on passive ex-
perience extend to goal-oriented behavior, it is conceiv-
able that reduced inhibition might contribute to make
learning slower, harder, and more susceptible to decay,
as has been clinically observed in older patients (Boyke July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org New Research
9 of 15 F
E
D
C
B
A
Figure 4. Aging and decay of training-induced A1 plasticity. Young and old adult rats were trained on a two-tone discrimination task
(target tone: 10 kHz, nontarget: 5 kHz). A, Top: Experimental protocol. Bottom: Older adult rats needed on average more training
sessions to reach criterion than young adult rats (D-prime 1; YA no. of sessions 8.4 1.1; OA 11.9 1.4, p 0.03). B,
Representative A1 characteristic frequency (CF) maps from trained young (left) and old (right) adult rats. Bolded polygons have a CF
at the target tone 0.3 octaves. Hatched polygons have a CF at the nontarget tone 0.3 octaves. C, Difference in frequency tuning
between naïve and exposed rats expressed as A1 percentage area and separated by CF. The full arrows point to the target frequency;
the hatched arrows points to the nontarget frequency. D, Top: To determine the persistence of learning and training-induced A1 map
plasticity, a subgroup of YA-T and two subgroups of OA-T rats were subjected to a 4-week delay after reaching criterion, followed
by behavioral re-assessment and A1 mapping. Bottom: From the first session of the reassessment onwards, young adult rats
performed above criterion, while old adult rats performed above criterion from the second session onwards. E, Representative A1
characteristic frequency (CF) maps from trained rats that received daily sham (saline) or diazepam (DZP) injections during the delay
period. F, Difference in A1 area tuned to various frequencies between each experimental group and untrained age-matched controls. YA-T group: n 4, recorded sites 212; OA-T: n 4, recorded sites 209; YA-Tdelay: n 4; recorded sites 192; OA-Tdelay: n
4; recorded sites 203; OA-Tdelay(DZP): n 4; recorded sites 189. Tonic GABAergic inhibition is reduced in the aged
A1 Tonic GABAergic inhibition is reduced in the aged
A1 Tonic GABAergic inhibition is reduced in the aged
A1 To study the anatomic correlates of frequency tuning
instability and impaired training performance, we sampled
GABA concentration using microdialysis and quantified
PV/PNN expression in A1 through immunohistochemistry. As documented in previous research (Morrison and Bax-
ter, 2012; Rozycka and Liguz-Lecznar, 2017), we found
that GABA concentration in A1 interstitial fluid was 25%
lower in older adult rats (OA, 24 months old, n 4) than
in young adult controls (YA, 6 months old, n 4) when
measured in silence (YA, 100 7.9%; OA, 75.2 5.8%
relative to YA; p 0.04, t(6) 2.53ad, t test; Fig. 5-1A). This difference was more pronounced during continuous
sound presentation (see Methods). In the latter experi-
mental condition, a relative reduction close to 40% was
noted (YA-stim, 124 7.7%; OA-stim, 88.2 6.0%
relative to YA-stim; p 0.01, t(6) 3.66ae, t test; Fig. 5-1B). ;
y
;
g
g
)
Further examination revealed that staining intensity of
individual PV cells could be divided into four subgroups:
low, intermediate low, intermediate high, and high inten-
sity (Donato et al., 2013). We found a smaller proportion of
high-intensity PV cells in older rats compared to young
adults (H(4) 13, p 0.011aj, Kruskal–Wallis test; fraction
of PV cells with low staining intensity and p-value relative
to YA, per group: Ilow 16 7.1%, p 0.82; YAlow 14
3.2%; OAlow 2.9 0.4%, p 0.005; IDlow 12.1
1.7%, p 0.99; OADlow 14.2 3.2%, p 0.99ah;
Tukey–Kramer test; Fig. 5C and Fig. 5-4B). A similar anal-
ysis was performed on PNNs, which could also be divided
into four staining intensity groups. Tonic GABAergic inhibition is reduced in the aged
A1 We found on average a
higher proportion of low-intensity PNNs in aged rats com-
pared to young adults (H(4) 17.24, p 0.0017, Kruskal–
Wallis test; fraction of low-intensity PNNs and p-value
relative to YA, per group: Ilow 55 8.1%, p 0.48;
YAlow 34 2.2%; OAlow 55 1.7%, p 0.04ai,
Tukey–Kramer test) and a decrease in the high-intensity
PNN subgroup in immature and aged rats compared to
young adults (H(4) 22.06, p 0.001, Kruskal–Wallis
test; fraction of high-intensity PNNs and p-value relative
to YA, per group: Ihigh 3.5 1.7%, p 0.004; YAhigh
26 1.9%; OAhigh 9.3 2.7%, p 0.039aj; Tukey–
Kramer test). Notably, following diazepam treatment, the
proportion of low-intensity PNNs in older rats decreased,
whereas the proportion of high-intensity PNNs in both
immature and older rats increased, resulting in an inten-
sity staining distribution that resembled that of the control
(YA) group (fraction of PNN as a function of staining
intensity and p-value relative to YA, per group: IDlow
31.1 1.9%, p 0.8; OADlow 47 3.1%, p 0.99ai;
IDhigh 27.2 0.5%, p 0.99; OADhigh 21.2 3.5%,
p 0.85aj; Tukey–Kramer test; Fig. 5E and Fig. 5-4D). Impact of age on perineuronal nets and PV neurons
in A1 PV- and SST-positive cells constitute the two largest
interneuron subpopulations throughout the cortex. In par-
ticular, PV neurons and associated PNNs are important
regulators of experience-dependent plasticity throughout
life (Caroni et al., 2012; Wang and Fawcett, 2012). Re-
duced cortical staining of PV and PNN are both associ-
ated with cortical immaturity and increased instability of
cortical representations (Pizzorusso et al., 2002; McRae
et al., 2007; Wang and Fawcett, 2012; Donato et al.,
2013). To assess whether age-related representational insta-
bility would be paralleled by a reduction in these
plasticity-regulating structural elements, we first charac-
terized the expression of the main interneuron subpopu-
lations in the context of total cell counts for the three age
groups—immature, young adult, and older adult—in-
cluded in the present study (see Fig. 5-2 and Fig. 5-3 for
cell counts and representative micrographs of interneu-
rons, respectively). This analysis confirmed previous re-
search showing a decrease in PV and SST cell counts
associated with aging (Ouda et al., 2008; Ouellet and de
Villers-Sidani, 2014). We then examined PV and PNN
staining intensity in our different experimental groups (I, n
6; YA, n 6; OA, n 6; ID, n 3; OAD, n 3; Fig. 5A). In line with previous reports (Hilbig et al., 2002; Ouda
et al., 2008), we found decreased PV staining intensity
with aging, which was recovered with 2-week-long diaz-
epam treatment [median staining intensity MAD per
PV cell, arbitrary confocal units (au) 105; H(4) 14.52,
p 0.0058, Kruskal–Wallis test; I: 1.17 0.85, p 0.52,
relative to YA; YA: 1.19 0.69; OA: 1 0.53, p 0.011,
relative to YA; ID: 1.3 0.66, p 0.96, relative to YA;
OAD: 1.1 0.76, p 0.97af, relative to YA; Tukey–Kramer
test; Fig. 5B and Fig. 5-4A]. PNN staining intensity, in
contrast, showed a more contrasting lifetime trajectory,
increasing from immature to young adult age and then
reversing course with aging (Fig. 5D). Like our findings on
PV cells, diazepam treatment resulted in recovery of New Research
10 of 15 PNN intensity staining for immature and older adult rats
(median staining intensity per PNN, au 105; H(4)
83.97, p 0.0001, Kruskal–Wallis test; I: 0.7 0.79, p
0.0001, relative to YA; YA: 1.64 1.37; OA: 0.76 1.04,
p 0.001, relative to YA; ID: 1.79 1.39, p 0.96,
relative to YA; OAD: 1.11 1.33, p 0.003ag, relative to
YA; Tukey–Kramer test; Fig. 5D and Fig. 5-4C). Impact of aging and dysregulated plasticity on
auditory learning Values shown are mean SEM, t test, two-way ANOVA with A C
B B A A B C C D F
E E D E F Figure 4. Aging and decay of training-induced A1 plasticity. Young and old adult rats were trained on a two-tone discrimination task
(target tone: 10 kHz, nontarget: 5 kHz). A, Top: Experimental protocol. Bottom: Older adult rats needed on average more training
sessions to reach criterion than young adult rats (D-prime 1; YA no. of sessions 8.4 1.1; OA 11.9 1.4, p 0.03). B,
Representative A1 characteristic frequency (CF) maps from trained young (left) and old (right) adult rats. Bolded polygons have a CF
at the target tone 0.3 octaves. Hatched polygons have a CF at the nontarget tone 0.3 octaves. C, Difference in frequency tuning
between naïve and exposed rats expressed as A1 percentage area and separated by CF. The full arrows point to the target frequency;
the hatched arrows points to the nontarget frequency. D, Top: To determine the persistence of learning and training-induced A1 map
plasticity, a subgroup of YA-T and two subgroups of OA-T rats were subjected to a 4-week delay after reaching criterion, followed
by behavioral re-assessment and A1 mapping. Bottom: From the first session of the reassessment onwards, young adult rats
performed above criterion, while old adult rats performed above criterion from the second session onwards. E, Representative A1
characteristic frequency (CF) maps from trained rats that received daily sham (saline) or diazepam (DZP) injections during the delay
period. F, Difference in A1 area tuned to various frequencies between each experimental group and untrained age-matched controls. YA-T group: n 4, recorded sites 212; OA-T: n 4, recorded sites 209; YA-Tdelay: n 4; recorded sites 192; OA-Tdelay: n
4; recorded sites 203; OA-Tdelay(DZP): n 4; recorded sites 189. Values shown are mean SEM, t test, two-way ANOVA with
Tukey–Kramer correction. July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org Discussion Our findings indicate that experience-dependent plas-
ticity increases with aging following a natural reduction in
cortical inhibition. Such increased plasticity may facilitate
changes elicited by experience but also impair the brain’s
capacity to crystallize such changes. Brain aging is characterized by a down-regulation of
cortical inhibition, which contributes to a range of func-
tional deficits such as reduced selectivity of receptive
fields, degraded temporal processing, heightened re-
sponses to noise, and reduced adaptation to repetitive
stimuli (Turner et al., 2005; Hua et al., 2006; Caspary et al.,
2008; Liguz-Lecznar et al., 2014; Schreiner and Polley,
2014). What are the mechanisms of age-related reduction in
inhibition? Recent findings suggest that reduced inhibi-
tion might not be a result of aging itself (Gourevitch et al., July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org New Research
11 of 15 B
C
A
D
E
Figure 5. Impact of age on structural inhibitory elements in the auditory cortex. A, High-power microphotographs of representative
sections immunolabeled for perineuronal nets (PNN) and parvalbumin (PV) from immature (I), young adult (YA), old adult, immature
diazepam treatment (IA), and old adult diazepam treatment (OAD) rats. B, D, Group fluorescence optical density for (B) PV and
(D) PNN staining for each age group (all cortical layers; green boxes represent median values). C, E, Distribution of (C) PV cell and
(E) PNN intensity staining for each age group. Fig. 5-1 compares A1 GABA concentration between YA and OA rats. Cell count per
field for different neuronal types and age groups are detailed in Fig. 5-2. Fig. 5-3 shows representative micrographs of PV- and
SST-positive cells. A summary of the cumulative distribution of staining intensity and interindividual variability for all groups is
provided in Fig. 5-4. Number of hemispheres examined: I 12, YA 12, OA 12, ID 6, OAD 6; total cell count per group: I
418, YA 343, OA 236, ID 156, OAD 231. Values shown are mean SEM. p 0.05 relative to YA; Kruskal–Wallis test,
corrected for multiple comparisons using Tukey–Kramer test. New Research
11 of 15 B B
C A C C A B E D D E Figure 5. Impact of age on structural inhibitory elements in the auditory cortex. Discussion A, High-power microphotographs of representative
sections immunolabeled for perineuronal nets (PNN) and parvalbumin (PV) from immature (I), young adult (YA), old adult, immature
diazepam treatment (IA), and old adult diazepam treatment (OAD) rats. B, D, Group fluorescence optical density for (B) PV and
(D) PNN staining for each age group (all cortical layers; green boxes represent median values). C, E, Distribution of (C) PV cell and
(E) PNN intensity staining for each age group. Fig. 5-1 compares A1 GABA concentration between YA and OA rats. Cell count per
field for different neuronal types and age groups are detailed in Fig. 5-2. Fig. 5-3 shows representative micrographs of PV- and
SST-positive cells. A summary of the cumulative distribution of staining intensity and interindividual variability for all groups is
provided in Fig. 5-4. Number of hemispheres examined: I 12, YA 12, OA 12, ID 6, OAD 6; total cell count per group: I
418, YA 343, OA 236, ID 156, OAD 231. Values shown are mean SEM. p 0.05 relative to YA; Kruskal–Wallis test,
corrected for multiple comparisons using Tukey–Kramer test. 2014). Young rats housed in a noisy auditory environment
exhibit auditory perceptual deficits that mirror those ob-
served in aging (Kamal et al., 2013; Gourevitch et al.,
2014), alongside reduced GABA and interneuron expres-
sion (Zhou et al., 2011; Zhou and Merzenich, 2012). These
impairments, however, are observed exclusively in rats
exposed to continuous nonmodulated noise, but not after
amplitude-modulated noise exposure (Thomas et al.,
2018), suggesting that it is the lack of structured in-
puts—as opposed to noise per se—that drives maladap-
tive plasticity in the auditory cortex (Voss et al., 2017). It is
therefore possible that age-related maladaptive plastic
changes are a consequence of continuous, nonstructured
“noisy” inputs, whether originating from the environment
or resulting from conductive, sensorineural, or strial hear-
ing loss (Jayakody et al., 2018). Prolonged exposure to
distorted inputs might destabilize the activity of local
neural circuits (Gourevitch et al., 2014) and trigger com-
pensatory homeostatic changes (Burrone and Murthy,
2003; Dean et al., 2005; Turrigiano, 2011) that ultimately amplify excitatory inputs and reduce inhibition (Rothman
et al., 2009; Tyagarajan et al., 2011). 2014). Discussion In the present
study, this deficit was evident on a 10-min-long exposure
to repetitive tones (Fig. 3B–E). We found impaired adap-
tation and tuning instability in the aged A1, whereas in-
creasing inhibition with a short-acting GABAA agonist
improved adaptation and reversed the tendency of aged
A1 neurons to increase their tuning to the repetitive tone
(Fig. 3F–I). Although there might be differences in the
physiologic response to anesthesia between aged and
adult animals, it should be noted that SSA is a property
found in A1 and subcortical auditory nuclei that is mini-
mally affected by anesthesia (Richardson et al., 2013;
Duque and Malmierca, 2015). Tuning instability was further confirmed by the fact that
a short 1-week pip tone exposure sufficed to produce an
overrepresentation of the exposure tone in older rats, as
previously seen in immature rats (Fig. 1). However, this
increased plasticity in the aged auditory cortex does not
seem to be limited to a short time window, as is the case
with the CP. In the present study, immature rats exposed
successively to two different pure tones exhibited plastic-
ity in response to the first tone, most likely because only
the first tone exposure overlapped with the CP (Fig. 2A). Whereas a rapid and sustained increase in inhibition (Fa-
giolini and Hensch, 2000; Iwai et al., 2003; Hensch, 2005)
ends the CP and prevents additional alterations due to
passive sound exposure, a subsequent 1-week exposure
to a different tone resulted in the overrepresentation of the
latter tone in aged rats. Interestingly, boosting GABA
inhibition consolidated frequency tuning representation
and made the aging A1 again resistant to further altera-
tions, thus “closing” this period of maladaptive increased
plasticity (Fig. 2C). Follow-up studies may want to rule out
the possibility, although unlikely, that diazepam selec-
tively affects the processing of frequency tones in the
10-kHz range by presenting a lower frequency tone (e.g. 5
kHz) before the 10-kHz tone during diazepam treatment. Taken together, these findings suggest that the aging A1
appears to be in a permanent state of heightened plas-
ticity to levels akin to those observed during early devel-
opment. Discussion Proposed model of the impact of age on A1 plasticity. During periods of life characterized by a low inhibitory tone, passive
exposure alters the A1 CF map. Plastic changes to the immature A1 are long lasting: as inhibition increases, the CP ends and sensory
representations become stable. In contrast, plastic changes to the aged A1 are short-lived, as these cannot be consolidated due to
a persistent low inhibitory tone. New Research
12 of 15 New Research
12 of 15 Figure 6. Proposed model of the impact of age on A1 plasticity. During periods of life characterized by a low inhibitory tone, passive
exposure alters the A1 CF map. Plastic changes to the immature A1 are long lasting: as inhibition increases, the CP ends and sensory
representations become stable. In contrast, plastic changes to the aged A1 are short-lived, as these cannot be consolidated due to
a persistent low inhibitory tone. The slower rate of learning in aged rats supports
previous findings showing that age-related cortical pro-
cessing deficits contribute to degraded behavioral perfor-
mance (Barnes et al., 1997; Gazzaley et al., 2005; Samson
and Barnes, 2013; Fig. 4A–C). According to the map
expansion-renormalization model, initial sensory map ex-
pansion is necessary for discrimination learning (Taka-
hashi et al., 2010; Reed et al., 2011). However, once
subjects become experts at a task and reach a plateau in
performance, their maps return to their previous state
(Reed et al., 2011). In the present study, training was
suspended before rats reached this plateau, and both
groups exhibited typical training-induced map changes
(Blake et al., 2006; Polley et al., 2006; Zhou et al., 2010). Learning becomes more susceptible to decay with aging
(Lustig et al., 2009), which was evident after a 1-month
delay period (Fig. 4D-F). Interestingly, training-induced
map changes were preserved in the old rats treated with
diazepam during the delay period between end of training
and cortical mapping. Although map expansion was still
present after this relatively short delay period, we did not
measure the behavioral implications or the extent of this
persistence beyond 1-month follow-up. Further studies
will be necessary to fully understand the behavioral rele-
vance of sustained map plasticity for learning. Functional deficits in the aged A1 include slowed and
incomplete suppression of background distractors, which
further impairs the detection of novel stimuli (de Villers-
Sidani et al., 2010; Mishra et al., 2014). July/August 2018, 5(4) e0051-18.2018 Discussion Young rats housed in a noisy auditory environment
exhibit auditory perceptual deficits that mirror those ob-
served in aging (Kamal et al., 2013; Gourevitch et al.,
2014), alongside reduced GABA and interneuron expres-
sion (Zhou et al., 2011; Zhou and Merzenich, 2012). These
impairments, however, are observed exclusively in rats
exposed to continuous nonmodulated noise, but not after
amplitude-modulated noise exposure (Thomas et al.,
2018), suggesting that it is the lack of structured in-
puts—as opposed to noise per se—that drives maladap-
tive plasticity in the auditory cortex (Voss et al., 2017). It is
therefore possible that age-related maladaptive plastic
changes are a consequence of continuous, nonstructured
“noisy” inputs, whether originating from the environment
or resulting from conductive, sensorineural, or strial hear-
ing loss (Jayakody et al., 2018). Prolonged exposure to
distorted inputs might destabilize the activity of local
neural circuits (Gourevitch et al., 2014) and trigger com-
pensatory homeostatic changes (Burrone and Murthy,
2003; Dean et al., 2005; Turrigiano, 2011) that ultimately The aforementioned studies strongly suggest that age-
related anatomic and functional deficits can be modeled
in noise-exposed young adult rats. Furthermore, rats ex-
posed to nonstructured noise recover normal function
when returned to their normal environment (Zhou and
Merzenich, 2012; Kamal et al., 2013). Taken together,
these observations suggest that perceptual deficits ob-
served in the aged cortex have a significant activity-
dependent component, rather than being purely age-
related, and are thus at least partially reversible (Hilbig
et al., 2002; Zhou and Merzenich, 2012; Liguz-Lecznar
et al., 2014). For instance, GABA agonists increase selec-
tivity of receptive fields in the primary visual cortex (Lev-
enthal et al., 2003; Hua et al., 2006), classic conditioning
enhances the expression of GABAergic markers in the
barrel cortex (Liguz-Lecznar et al., 2014), and operant
conditioning results in increased PV expression in A1 (de
Villers-Sidani et al., 2010). July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org Figure 6. Proposed model of the impact of age on A1 plasticity. During periods of life characterized by a low inhibitory tone, passive
exposure alters the A1 CF map. Plastic changes to the immature A1 are long lasting: as inhibition increases, the CP ends and sensory
representations become stable. In contrast, plastic changes to the aged A1 are short-lived, as these cannot be consolidated due to
a persistent low inhibitory tone. New Research
12 of 15 Figure 6. eNeuro.org New Research
13 of 15 needed. Similarly, interventions that delay cortical matu-
ration during early development (Chang and Merzenich,
2003; de Villers-Sidani et al., 2008) and those that impair
auditory processing during adulthood (Martin del Campo
et al., 2012; Zhou and Merzenich, 2012) result in de-
creased PV staining and increased plasticity. In line with
these observations, we found a moderate increase in the
low-PV fraction in the immature and aged A1, the age
groups that showed increased experience-dependent
plasticity. Moreover, the high-PV fraction was significantly
diminished in the aged (Fig. 5B, C), which could account
for the inadequate consolidation of newly formed sensory
representations (Caroni et al., 2012; Donato et al., 2013). PNNs are extracellular matrix deposits produced jointly
by neurons and astrocytes, particularly around PV cells
(McRae et al., 2007; Nakamura et al., 2009), forming both
a structural and functional barrier that limits plasticity
(Pizzorusso et al., 2002; Berardi et al., 2004; Wang and
Fawcett, 2012). We found age-related changes in PNNs
that mirrored those documented for PV cells; namely, a
lower average staining density of PNNs in the extremes of
life, characterized by an increase in the low-PNN fraction
and a decrease in the high-PNN fraction. Interestingly,
while age-related PNN intensity differences were more
striking than those observed for PV cells, diazepam
treatment in both cases resulted in a redistribution of the
low- and high-intensity subgroups in immature and older
adult rats toward values that resembled those of the
young adult group (Fig. 5D, E). The disparity in histology
results between PV cells and associated PNNs in imma-
ture rats supports the idea that PV cell development
predates PNN assembly (Baker et al., 2017), suggesting
that adequate PV cell functioning is required for PNN
formation (Yamada et al., 2015; Quattromani et al., 2017). The present study contributes to the understanding of
how plasticity is regulated in the aged brain. Whereas
previous studies have shown that GABAergic inhibition
declines with age (Leventhal et al., 2003; Caspary et al.,
2008; Liguz-Lecznar et al., 2014) and that passive sound
exposure can alter cortical response properties in adult-
hood (Norena et al., 2006; Pienkowski et al., 2011), our
study is the first one to show that A1 experience-de-
pendent plasticity increases with aging. Further targeted In the human research domain, our findings may be
particularly relevant to studies that are currently underway
and that have potential clinical applications. Interestingly,
while age-related PNN intensity differences were more
striking than those observed for PV cells, diazepam
treatment in both cases resulted in a redistribution of the
low- and high-intensity subgroups in immature and older
adult rats toward values that resembled those of the
young adult group (Fig. 5D, E). The disparity in histology
results between PV cells and associated PNNs in imma-
ture rats supports the idea that PV cell development
predates PNN assembly (Baker et al., 2017), suggesting
that adequate PV cell functioning is required for PNN
formation (Yamada et al., 2015; Quattromani et al., 2017). Traditionally, aging has been regarded as a period of
limited plasticity. However, our experiments suggest that
this idea is unlikely to be correct in detail, as the aged
brain is in some ways more plastic than the young adult
brain. We propose that the inhibitory regulation of plas-
ticity, rather than plasticity per se, is reduced in the aged
brain (Fig. 6). Researchers and clinicians may build on this
knowledge to develop rehabilitation strategies with at
least two complementary objectives in mind: first, taking
advantage of increased plasticity to enhance seniors’
functional recovery after neurologic injury, and second,
regulating plasticity to preserve the benefits of rehabilita-
tion and promote long-lasting recovery. The present study contributes to the understanding of
how plasticity is regulated in the aged brain. Whereas
previous studies have shown that GABAergic inhibition
declines with age (Leventhal et al., 2003; Caspary et al.,
2008; Liguz-Lecznar et al., 2014) and that passive sound
exposure can alter cortical response properties in adult-
hood (Norena et al., 2006; Pienkowski et al., 2011), our
study is the first one to show that A1 experience-de-
pendent plasticity increases with aging. Further targeted
manipulations of GABAergic function will be necessary to
pinpoint the exact mechanisms underlying this age-related
dysregulation of plasticity and to understand whether altered
excitatory neurotransmission during aging (Benali et al.,
2008) also plays a role. Discussion g
Our findings of reduced PV and SST expression sup-
port numerous reports of reduced interneuron cell counts
associated
with
aging
(Rozycka
and
Liguz-Lecznar,
2017), suggesting that inhibitory deficits may be related to
the dysfunction of specific interneuron cell subtypes (Cha
et al., 1997; Ouda et al., 2008; Fish et al., 2013). Recent
research, however, has focused on PV expression as a
proxy for cellular function and has shown that cortical PV
staining intensity is tightly correlated with the degree of
experience-dependent plasticity (Zhou et al., 2011; Ca-
roni, 2015). As a case in point, recent studies by Donato
et al. (2013, 2015) demonstrate the impact of reduced PV
staining on cell function. High-intensity PV cells are
found on completion of learning and immediately after
fear conditioning, situations in which stable, long-lasting
sensory representations are warranted (Donato et al.,
2013). Conversely, low-intensity PV cells are abundant
during learning and following environmental enrichment,
situations in which a more flexible cortical network is July/August 2018, 5(4) e0051-18.2018 eNeuro.org In the ab-
sence of region-selective drugs to modulate GABAergic
neurotransmission, studies using noninvasive brain stim-
ulation (NIBS) are exploring the effects of manipulating
cortical E/I balance on learning in the elderly (Opie and
Cirillo, 2017). For instance, Opie et al. (2017) used two
modalities of transcranial magnetic stimulation to alter
cortical excitability before a motor learning task but found
no benefit in healthy aged volunteers. In contrast, a sub-
sequent study using transcranial direct current stimulation
found that increasing inhibition before testing, followed by
decreasing inhibition during testing, resulted in greater
skill improvement in older adults (Fujiyama et al., 2017). We posit that a follow-up experiment using NIBS could be
used to test our hypotheses of the role of inhibition in the
acquisition and retention of learning—specifically, to test
whether reducing inhibition early during training increases
plasticity and facilitates learning, and whether increasing
inhibition after learning facilitates the crystallization of
newly acquired skills. needed. Similarly, interventions that delay cortical matu-
ration during early development (Chang and Merzenich,
2003; de Villers-Sidani et al., 2008) and those that impair
auditory processing during adulthood (Martin del Campo
et al., 2012; Zhou and Merzenich, 2012) result in de-
creased PV staining and increased plasticity. In line with
these observations, we found a moderate increase in the
low-PV fraction in the immature and aged A1, the age
groups that showed increased experience-dependent
plasticity. Moreover, the high-PV fraction was significantly
diminished in the aged (Fig. 5B, C), which could account
for the inadequate consolidation of newly formed sensory
representations (Caroni et al., 2012; Donato et al., 2013). representations (Caroni et al., 2012; Donato et al., 2013). PNNs are extracellular matrix deposits produced jointly
by neurons and astrocytes, particularly around PV cells
(McRae et al., 2007; Nakamura et al., 2009), forming both
a structural and functional barrier that limits plasticity
(Pizzorusso et al., 2002; Berardi et al., 2004; Wang and
Fawcett, 2012). We found age-related changes in PNNs
that mirrored those documented for PV cells; namely, a
lower average staining density of PNNs in the extremes of
life, characterized by an increase in the low-PNN fraction
and a decrease in the high-PNN fraction. CrossRef de Villers-Sidani E, Alzghoul L, Zhou X, Simpson KL, Lin RC, Mer-
zenich MM (2010) Recovery of functional and structural age-
related changes in the rat primary auditory cortex with operant
training. Proc Natl Acad Sci U S A 107:13900–13905. CrossRef Kamal B, Holman C, DE Villers-Sidani E (2013) Shaping the aging
brain: role of auditory input patterns in the emergence of auditory
cortical impairments. Front Syst Neurosci 7:52. CrossRef Knoflach M, Matosevic B, Rucker M, Furtner M, Mair A, Wille G, Knoflach M, Matosevic B, Rucker M, Furtner M, Mair A, Wille G,
Zangerle A, Werner P, Ferrari J, Schmidauer C, Seyfang L, Kiechl
S, Willeit J (2012) Functional recovery after ischemic stroke—a
matter of age: data from the Austrian Stroke Unit Registry. Neu-
rology 78:279–285. CrossRef g
Dean I, Harper NS, Mcalpine D (2005) Neural population coding of
sound level adapts to stimulus statistics. Nat Neurosci 8:1684–
1689. CrossRef Medline matter of age: data from the Austrian Stroke Unit Registry. Neu-
rology 78:279–285. CrossRef Donato F, Rompani SB, Caroni P (2013) Parvalbumin-expressing
basket-cell network plasticity induced by experience regulates
adult learning. Nature 504:272–276. CrossRef Kuchibhotla KV, Gill JV, Lindsay GW, Papadoyannis ES, Field RE,
Sten TA, Miller KD, Froemke RC (2017) Parallel processing by
cortical inhibition enables context-dependent behavior. Nat Neu-
rosci 20:62–71. CrossRef Donato F, Chowdhury A, Lahr M, Caroni P (2015) Early- and late-
born parvalbumin basket cell subpopulations exhibiting distinct
regulation and roles in learning. Neuron 85:770–786. CrossRef Kuhlman SJ, Olivas ND, Tring E, Ikrar T, Xu X, Trachtenberg JT (2013)
A disinhibitory microcircuit initiates critical-period plasticity in the
visual cortex. Nature 501:543–546. CrossRef Dorrn AL, Yuan K, Barker AJ, Schreiner CE, Froemke RC (2010)
Developmental sensory experience balances cortical excitation
and inhibition. Nature 465:932–936. CrossRef Lehmann K, Steinecke A, Bolz J (2012) GABA through the ages:
regulation of cortical function and plasticity by inhibitory interneu-
rons. Neural Plast 2012:892784. CrossRef Medline Duque D, Malmierca MS, Caspary DM (2014) Modulation of
stimulus-specific adaptation by GABA(A) receptor activation or
blockade in the medial geniculate body of the anaesthetized rat. J
Physiol 592:729–743. CrossRef Medline Leventhal AG, Wang Y, PU, M, Zhou Y, MA, Y (2003) GABA and its
agonists improved visual cortical function in senescent monkeys. Science 300:812–815. CrossRef Duque D, Malmierca MS (2015) Stimulus-specific adaptation in the
inferior colliculus of the mouse: anesthesia and spontaneous ac-
tivity effects. Brain Struct Funct 220:3385–3398. New Research
14 of 15 New Research adult auditory system. Nat Rev Neurosci 15:483–491. CrossRef
Medline Caroni P (2015) Regulation of Parvalbumin Basket cell plasticity in
rule learning. Biochem Biophys Res Commun 460:100–103. CrossRef Medline Hensch TK, Fagiolini M, Mataga N, Stryker MP, Baekkeskov S, Kash
SF (1998) Local GABA circuit control of experience-dependent
plasticity in developing visual cortex. Science 282:1504–1508. CrossRef Carulli D, Pizzorusso T, Kwok JC, Putignano E, Poli A, Forostyak S,
Andrews MR, Deepa SS, Glant TT, Fawcett JW (2010) Animals
lacking link protein have attenuated perineuronal nets and persis-
tent plasticity. Brain 133:2331–2347. CrossRef Hensch TK (2005) Critical period plasticity in local cortical circuits. Nat Rev Neurosci 6:877–888. CrossRef Medline Caspary DM, Ling L, Turner JG, Hughes LF (2008) Inhibitory neu-
rotransmission, plasticity and aging in the mammalian central
auditory system. J Exp Biol 211:1781–1791. CrossRef Hilbig H, Bidmon HJ, Steingruber S, Reinke H, Dinse HR (2002)
Enriched environmental conditions reverse age-dependent gliosis
and losses of neurofilaments and extracellular matrix components
but do not alter lipofuscin accumulation in the hindlimb area of the
aging rat brain. J Chem Neuroanat 23:199–209. CrossRef Cha CI, Lee YI, Lee EY, Park KH, Baik SH (1997) Age-related
changes of VIP, NPY and somatostatin-immunoreactive neurons
in the cerebral cortex of aged rats. Brain Res 753:235–44. Cross-
Ref ng rat brain. J Chem Neuroanat 23:199–209. CrossRef Hua T, Li X, He L, Zhou Y, Wang Y, Leventhal AG (2006) Functional
degradation of visual cortical cells in old cats. Neurobiol Aging
27:155–162. CrossRef Chang EF, Merzenich MM (2003) Environmental noise retards audi-
tory cortical development. Science 300:498–502. CrossRef de Villers-Sidani E, Chang EF, Bao S, Merzenich MM (2007) Critical
period window for spectral tuning defined in the primary auditory
cortex (A1) in the rat. J Neurosci 27:180–189. CrossRef Iwai Y, Fagiolini M, Obata K, Hensch TK (2003) Rapid critical period
induction by tonic inhibition in visual cortex. J Neurosci 23:6695–
6702. Medline de Villers-Sidani E, Simpson KL, Lu YF, Lin RC, Merzenich MM
(2008) Manipulating critical period closure across different sectors
of the primary auditory cortex. Nat Neurosci 11:957–965. CrossRef Jayakody DMP, Friedland PL, Martins RN, Sohrabi HR (2018) Impact
of aging on the auditory system and related cognitive functions: a
narrative review. Front Neurosci 12:125. CrossRef narrative review. Front Neurosci 12:125. CrossRef Liguz-Lecznar M, Lehner M, Kaliszewska A, Zakrzewska R, Sobo-
lewska A, Kossut M (2014) Altered glutamate/GABA equilibrium in
aged mice cortex influences cortical plasticity. Brain Struct Funct
220:1681–1693. y
Fagiolini M, Hensch TK (2000) Inhibitory threshold for critical-period
activation in primary visual cortex. Nature 404:183–186. CrossRef
Medline Lustig C, Shah P, Seidler R, Reuter-Lorenz PA (2009) Aging, training,
and the brain: a review and future directions. Neuropsychol Rev
19:504–522. CrossRef Medline Fish KN, Hoftman GD, Sheikh W, Kitchens M, Lewis DA (2013)
Parvalbumin-containing chandelier and basket cell boutons have
distinctive modes of maturation in monkey prefrontal cortex. J
Neurosci 33:8352–8358. CrossRef Maffei A, Turrigiano G (2008) The age of plasticity: developmental
regulation of synaptic plasticity in neocortical microcircuits. Prog
Brain Res 169:211–223. Fritschy JM, Panzanelli P (2014) GABAA receptors and plasticity of
inhibitory neurotransmission in the central nervous system. Eur J
Neurosci 39:1845–1865. CrossRef Malmierca MS, Sanchez-Vives MV, Escera C, Bendixen A (2014)
Neuronal adaptation, novelty detection and regularity encoding in Malmierca MS, Sanchez-Vives MV, Escera C, Bendixen A (2014)
Neuronal adaptation, novelty detection and regularity encoding in
audition. Front Syst Neurosci 8:111. CrossRef Froemke RC, Carcea I, Barker AJ, Yuan K, Seybold BA, Martins AR,
Zaika N, Bernstein H, Wachs M, Levis PA, Polley DB, Merzenich
MM, Schreiner CE (2013) Long-term modification of cortical syn-
apses improves sensory perception. Nat Neurosci 16:79–88. CrossRef audition. Front Syst Neurosci 8:111. CrossRef Martin DEL Campo HN, Measor KR, Razak KA (2012) Parvalbumin
immunoreactivity in the auditory cortex of a mouse model of
presbycusis. Hear Res 294:31–39. CrossRef Medline Mcrae PA, Rocco MM, Kelly G, Brumberg JC, Matthews RT (2007)
Sensory deprivation alters aggrecan and perineuronal net expres-
sion in the mouse barrel cortex. J Neurosci 27:5405–5413. Cross-
Ref Fujiyama H, Hinder MR, Barzideh A, VAN DE Vijver C, Badache AC,
Manrique CM, Reissig P, Zhang X, Levin O, Summers JJ, Swinnen
SP (2017) Preconditioning tDCS facilitates subsequent tDCS effect
on skill acquisition in older adults. Neurobiol Aging 51:31–42. CrossRef Mishra J, DE, Villers-Sidani E, Merzenich M, Gazzaley A (2014)
Adaptive training diminishes distractibility in aging across species. Neuron 84:1091–1103. CrossRef Gazzaley A, Cooney JW, Rissman J, D’Esposito M (2005) Top-down
suppression deficit underlies working memory impairment in nor-
mal aging. Nat Neurosci 8:1298–1300. CrossRef Morrison JH, Baxter MG (2012, Mar 7) The aging cortical synapse:
hallmarks and implications for cognitive decline. Nat Rev Neurosci
13(4):240–250. References Baker KD, Gray AR, Richardson R (2017) The development of
perineuronal nets around parvalbumin gabaergic neurons in the
medial prefrontal cortex and basolateral amygdala of rats. Behav
Neurosci 131:289–303. CrossRef Barnes CA, Suster MS, Shen J, Mcnaughton BL (1997) Multistability
of cognitive maps in the hippocampus of old rats. Nature 388:272–
275. CrossRef Benali A, Weiler E, Benali Y, Dinse HR, Eysel UT (2008) Excitation and
inhibition jointly regulate cortical reorganization in adult rats. J
Neurosci 28:12284–12293. CrossRef Medline Berardi N, Pizzorusso T, Maffei L (2004) Extracellular matrix and
visual cortical plasticity: freeing the synapse. Neuron 44:905–908. CrossRef Our findings have the potential to inform future research
in animal models and humans. Recent studies have
shown that cortical interneurons gate critical period plas-
ticity locally (Takesian et al., 2018) and are necessary for
sustained behavioral performance in trained animals
(Kuchibhotla et al., 2017), but long-term outcomes of
manipulating inhibitory neurotransmission remain un-
known. Although we used a systemic GABA agonist, a
logical next step in animal research would be to modulate
inhibitory neurotransmission locally during passive expo-
sure or learning using optogenetics or DREADDs for acute
or chronic interventions, respectively. Blake
DT,
Heiser
MA,
Caywood
M,
Merzenich
MM
(2006)
Experience-dependent adult cortical plasticity requires cognitive
association between sensation and reward. Neuron 52:371–381. CrossRef Boyke J, Driemeyer J, Gaser C, Buchel C, May A (2008) Training-
induced brain structure changes in the elderly. J Neurosci 28:
7031–7035. CrossRef Burrone J, Murthy VN (2003) Synaptic gain control and homeostasis. Curr Opin Neurobiol 13:560–567. Medline Caroni P, Donato F, Muller D (2012) Structural plasticity upon learn-
ing: regulation and functions. Nat Rev Neurosci 13:478–490. CrossRef Medline July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org 14 of 15 New Research
15 of 15 New Research
15 of 15 Schreiner CE, Polley DB (2014) Auditory map plasticity: diversity in
causes and consequences. Curr Opin Neurobiol 24:143–156. CrossRef Medline Nakamura M, Nakano K, Morita S, Nakashima T, Oohira A, Miyata S
(2009) Expression of chondroitin sulfate proteoglycans in barrel
field of mouse and rat somatosensory cortex. Brain Res 1252:117–
129. CrossRef Stanley EM, Fadel JR, Mott DD (2012) Interneuron loss reduces
dendritic inhibition and GABA release in hippocampus of aged Stanley EM, Fadel JR, Mott DD (2012) Interneuron loss reduces
dendritic inhibition and GABA release in hippocampus of aged
rats. Neurobiol Aging 33:431.e1–e13. CrossRef Norena AJ, Gourevitch B, Aizawa N, Eggermont JJ (2006) Spectrally
enhanced acoustic environment disrupts frequency representation
in cat auditory cortex. Nat Neurosci 9:932–939. CrossRef rats. Neurobiol Aging 33:431.e1–e13. CrossRef Stebbings KA, Choi HW, Ravindra A, Caspary DM, Turner JG, Llano
DA (2016) Ageing-related changes in GABAergic inhibition in
mouse auditory cortex, measured using in vitro flavoprotein auto-
fluorescence imaging. J Physiol 594:207–221. CrossRef y
Opie GM, Cirillo J (2017) Commentary: Preconditioning tDCS facili-
tates subsequent tDCS effect on skill acquisition in older adults. Front Aging Neurosci 9:84. CrossRef g g
Opie GM, Vosnakis E, Ridding MC, Ziemann U, Semmler JG (2017)
Priming theta burst stimulation enhances motor cortex plasticity in
young but not old adults. Brain Stimul 10:298–304. Takahashi H, Funamizu A, Mitsumori Y, Kose H, Kanzaki R (2010)
Progressive plasticity of auditory cortex during appetitive operant
conditioning. Biosystems 101:37–41. CrossRef Ouda L, Druga R, Syka J (2008) Changes in parvalbumin immuno-
reactivity with aging in the central auditory system of the rat. Exp
Gerontol 43:782–789. CrossRef Medline Takesian AE, Bogart LJ, Lichtman JW, Hensch TK (2018) Inhibitory
circuit gating of auditory critical-period plasticity. Nat Neurosci
21:218–227. CrossRef Ouellet L, DE Villers-Sidani E (2014) Trajectory of the main GABAe-
rgic interneuron populations from early development to old age in
the rat primary auditory cortex. Front Neuroanat 8:40. CrossRef Thomas ME, Friedman NHM, Cisneros-Franco JM, Ouellet L, DE,
Villers-Sidani E (2018) The prolonged masking of temporal acous-
tic inputs with noise drives plasticity in the adult rat auditory
cortex. Cereb Cortex Paxinos G, Watson C, 2007. The rat brain in stereotaxic coordinates. Amsterdam; Boston: Academic Press/Elsevier. Turner JG, Hughes LF, Caspary DM (2005) Affects of aging on
receptive fields in rat primary auditory cortex layer V neurons. J
Neurophysiol 94:2738–2747. CrossRef Medline Gourevitch B, Edeline JM, Occelli F, Eggermont JJ (2014) Is the din
really harmless? Long-term effects of non-traumatic noise on the July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org CrossRef Medline Pienkowski M, Munguia R, Eggermont JJ (2011) Passive exposure of
adult cats to bandlimited tone pip ensembles or noise leads to
long-term response suppression in auditory cortex. Hear Res 277:
117–126. CrossRef Medline Turrigiano G (2011) Too many cooks? Intrinsic and synaptic homeo-
static mechanisms in cortical circuit refinement. Annu Rev Neuro-
sci 34:89–103. CrossRef Pizzorusso T, Medini P, Berardi N, Chierzi S, Fawcett JW, Maffei L
(2002) Reactivation of ocular dominance plasticity in the adult
visual cortex. Science 298:1248–1251. CrossRef Medline Tyagarajan SK, Ghosh H, Yevenes GE, Nikonenko I, Ebeling C,
Schwerdel C, Sidler C, Zeilhofer HU, Gerrits B, Muller D, Fritschy
JM (2011) Regulation of GABAergic synapse formation and plas-
ticity by GSK3beta-dependent phosphorylation of gephyrin. Proc
Natl Acad Sci U S A 108:379–384. CrossRef Polley DB, Steinberg EE, Merzenich MM (2006) Perceptual learning
directs auditory cortical map reorganization through top-down
influences. J Neurosci 26:4970–4982. CrossRef Ulanovsky N, LAS L, Nelken I (2003) Processing of low-probability
sounds by cortical neurons. Nat Neurosci 6:391–398. CrossRef
Medline Quattromani MJ, Pruvost M, Guerreiro C, Backlund F, Englund E,
Aspberg A, Jaworski T, Hakon J, Ruscher K, Kaczmarek L, Vivien
D, Wieloch T (2017) Extracellular matrix modulation is driven by
experience-dependent plasticity during stroke recovery. Mol Neu-
robiol 55:2196–2213. Voss P, Thomas M, Chou YC, Cisneros-Franco JM, Ouellet L, DE
Villers-Sidani E (2016) Pairing cholinergic enhancement with per-
ceptual training promotes recovery of age-related changes in rat
primary auditory cortex. Neural Plast 2016:1801979. CrossRef Reed A, Riley J, Carraway R, Carrasco A, Perez C, Jakkamsetti V,
Kilgard MP (2011) Cortical map plasticity improves learning but is
not necessary for improved performance. Neuron 70:121–131. CrossRef p
g p
y
g
g
primary auditory cortex. Neural Plast 2016:1801979. CrossRef Voss P, Thomas ME, Cisneros-Franco JM, DE Villers-Sidani E (2017)
Dynamic brains and the changing rules of neuroplasticity: implica-
tions for learning and recovery. Front Psychol 8:1657. CrossRef Reinhoud NJ, Brouwer HJ, VAN Heerwaarden LM, Korte-Bouws GA
(2013) Analysis of glutamate, GABA, noradrenaline, dopamine,
serotonin, and metabolites using microbore UHPLC with electro-
chemical detection. ACS Chem Neurosci 4:888–894. CrossRef Wang D, Fawcett J (2012) The perineuronal net and the control of
CNS plasticity. Cell Tissue Res 349:147–160. CrossRef Medline
Yamada J
Ohgomori T
Jinno S (2015) Perineuronal nets affect Wang D, Fawcett J (2012) The perineuronal net and the control of
CNS plasticity. Cell Tissue Res 349:147–160. Zhou X, Merzenich MM (2012) Environmental noise exposure de-
grades normal listening processes. Nat Commun 3:843. CrossRef CrossRef Medline
Yamada J, Ohgomori T, Jinno S (2015) Perineuronal nets affect
parvalbumin expression in GABAergic neurons of the mouse hip-
pocampus. Eur J Neurosci 41:368–378. CrossRef Yamada J, Ohgomori T, Jinno S (2015) Perineuronal nets affect
parvalbumin expression in GABAergic neurons of the mouse hip-
pocampus. Eur J Neurosci 41:368–378. CrossRef Richardson BD, Hancock KE, Caspary DM (2013) Stimulus-specific
adaptation in auditory thalamus of young and aged awake rats. J
Neurophysiol 110:1892–1902. CrossRef Medline p
p
Zhou X, DE Villers-Sidani E, Panizzutti R, Merzenich MM (2010)
Successive-signal biasing for a learned sound sequence. Proc
Natl Acad Sci U S A 107:14839–14844. CrossRef Medline Rothman JS, Cathala L, Steuber V, Silver RA (2009) Synaptic de-
pression enables neuronal gain control. Nature 457:1015–1018. CrossRef Medline Zhou X, Panizzutti R, DE Villers-Sidani E, Madeira C, Merzenich MM
(2011) Natural restoration of critical period plasticity in the juvenile
and adult primary auditory cortex. J Neurosci 31:5625–5634. CrossRef Rozycka A, Liguz-Lecznar M (2017) The space where aging acts:
focus on the GABAergic synapse. Aging Cell 16:634–643. Cross-
Ref Medline Samson RD, Barnes CA (2013) Impact of aging brain circuits on
cognition. Eur J Neurosci 37:1903–1915. CrossRef Medline Zhou X, Merzenich MM (2012) Environmental noise exposure de-
grades normal listening processes. Nat Commun 3:843. CrossRef July/August 2018, 5(4) e0051-18.2018 eNeuro.org
|
https://openalex.org/W4282970872
|
https://www.frontiersin.org/articles/10.3389/fphy.2022.872691/pdf
|
English
| null |
Multi Gigabit Wireless Data Transfer in Detectors at Future Colliders
|
Frontiers in physics
| 2,022
|
cc-by
| 9,462
|
REVIEW REVIEW
published: 16 June 2022
doi: 10.3389/fphy.2022.872691 Multi Gigabit Wireless Data Transfer in
Detectors at Future Colliders
R. Brenner 1*, C. Dehos 2 and E. Locci 3
1Uppsala University, Uppsala, Sweden, 2CEA, Leti, Université Grenoble-Alpes, Grenoble, France, 3Gangneung-Wonju National
University, Gangneung, South Korea The WADAPT (Wireless Allowing Data And Power Transmission) consortium has been
formed to identify the specific needs of different projects that might benefit from wireless
communication technologies with the objective of providing a common platform for
research and development in order to optimize effectiveness and cost. Wireless
technologies have developed extremely fast over the last decade and are now mature
enough to be a promising alternative to cables and optical links, with a possibility of
revolutionizing detector design. Although wireless readout has the qualities and properties
to be used in many collider detectors, this article focuses on the transmission of large
amount of data from vertex detectors at high rate, low power budget and in potential high
radiation environment. For vertex detectors, the 60 GHz band has proven to be adequate
and commercial products are already available, providing 6 Gbps data links. This
technology allows efficient partitioning of detectors in topological regions of interest,
with the possibility of adding intelligence on the detector to perform four-dimensional
reconstruction of the tracks and vertices online, in order to attach the tracks to their vertex
with great efficiency even in difficult experimental conditions, and conveniently substitutes
a mass of materials (cables and connectors). Early transceiver module products have been
successfully tested for signal confinement, crosstalk, electromagnetic immunity and
resistance to radiation. In the long run, emerging 140 GHz bands could also be used
for higher data rates (>100 Gbps) at future high energy and luminosity hadron colliders. INTRODUCTION The WADAPT consortium [1] chose to firstly investigate the relevance of wireless techniques for
data transfer within vertex detectors, where commercially-available products in the 60 GHz band [2]
would be adequate. The present ATLAS [3] and CMS [4] experiments have been designed for
nominal operation at luminosity of 2 × 1034 cm−2s−1 and 60 interactions per beam crossing. Pileup
lead to a number of mismeasured or misidentified tracks, and add extra energy to calorimeter
measurements. Pileup confuses the trigger and also the offline reconstruction and interpretation of
events. It also increases the execution time for the reconstruction of events in the High Level Trigger
and the offline analysis. Specialty section:
This article was submitted to
Radiation Detectors and Imaging,
a section of the journal
Frontiers in Physics Specialty section:
This article was submitted to
Radiation Detectors and Imaging,
a section of the journal
Frontiers in Physics Received: 09 February 2022
Accepted: 21 April 2022
Published: 16 June 2022 *Correspondence:
R. Brenner *Correspondence:
R. Brenner
Richard.Brenner@cern.ch Keywords: wireless, data transfer, WADAPT, vertex detector, collider Edited by:
Petra Merkel,
Fermi National Accelerator Laboratory
(DOE), United States Reviewed by:
David Christian,
Fermi National Accelerator Laboratory
(DOE), United States
Jingbo Ye, Reviewed by:
David Christian,
Fermi National Accelerator Laboratory
(DOE), United States
Jingbo Ye, Southern Methodist University,
United States Keywords: wireless, data transfer, WADAPT, vertex detector, collider Citation: The High Luminosity LHC (HL-LHC) is potentially able to deliver a luminosity up to 7.5 ×
1034cm−2s−1, increasing the interaction rate and collision pileup beyond existing or envisioned data
readout technologies. The detector systems in the experiment will currently need a trigger to sustain a
pileup up to 200 interactions per 25 ns beam crossing. The first event selection and data reduction is
typically done by a fast trigger decision within 3–6 microseconds after a collision where 40 million Brenner R, Dehos C and Locci E (2022)
Multi Gigabit Wireless Data Transfer in
Detectors at Future Colliders. Front. Phys. 10:872691. doi: 10.3389/fphy.2022.872691 June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 1 Multi Gigabit Data Transfer Brenner et al. events per second are currently reduced to about 100 kHz and at
HL-LHC this will be increased by an order of magnitude. In
present experiments this decision is based on information from
all detector systems except the tracker. For HL-LHC the CMS
experiment has developed a data reduction method with pT
filtering in the tracker which opens for the use of tracking
data in the trigger [5]. installation and repair, and reductions in detector dead material. These two last aspects are especially important in tracking
detectors and they may become particularly important in case
of limited access or/and hostile environment. For a full exploitation of the advantages of integrating a wireless
point-to-point readout, new architectures will be necessary. The tracker is the most granular detector system in the
experiment that is used to associate charged particles with the
correct interaction vertices. The tracking detector would ideally
read out all information for every single bunch crossing, perform
reconstruction in real time, and then apply trigger criteria to filter
events or if possible directly process the data in an event filter
farm. The challenge is however to read out the very granular
detector in time for the fast trigger decision or before data in the
pipelined front-end electronics gets overwritten. The data rate
needed to read out all hit clusters of 1-2 pixels in the next
generation pixel detectors is between 50 and 100 Tbps1. Data
from tracking detectors at the two big LHC experiments are today
transferred with optical links. The main benefit with optical links
compared to wire links is that they are electrically decoupled and
free from crosstalk. Citation: The weakness of optical links is the size of the
connectors, their alignment constrains, and the sensitivity to
mechanical damage. Wire/copper links suffer from bandwidth
limitation at higher data rates. Furthermore, the tracker is built in
a modular way that does not follow the topology of the physics
event. The readout is bound to the modularity of the tracker,
which is not optimal for a fast trigger decision based on event
topology. The advantage of wireless technology is that it is not
constrained to the mechanical modularity of the tracker. The
technology offers already today data rate comparable with present
optical links and no connectors are needed. The next generation
of hadron colliders, which might be the envisioned, FCC, would
even be more challenging with a peak luminosity of 30 ×
1035 cm−2s−1, leading to a pileup up to 1,000 interactions per
25 ns beam crossing, and more granular detectors. Although the
current electron-positron colliders do not introduce stringent
requirements on the trigger capabilities, the experiments would
certainly benefit from the wireless technology. For both types of
collider experiments, minimizing the amount of material in the
region of the tracking detectors will reduce multiple scattering
and nuclear interactions that degrade the precision on the
measurement of track momentum and interaction vertices,
and in addition will reduce the number of fake hits arising
from secondaries. Both CMS and ATLAS upgrades aim at
reducing passive material by embedding serial powering [7] or
by using DC-DC converters with reduced mass [8]. 2Here the signal to noise ratio is defined as the average received signal over the
bandwidth, and the noise is defined as the average noise or interference power over
the bandwidth. 1The latest description of the pixel detector layout, including the number of staves
per barrel and endcap layer, the number of sensors per stave and the estimated data
rates per chip can be found in [6]. MILLIMETER WAVE WIRELESS
TECHNOLOGY Data Rates and Frequency Band
According to the Shannon-Hartley theorem, the physical data rate at
which information can be transmitted over a communication
channel is limited by the channel bandwidth and the signal-to-
noise ratio2. The fast development of the wireless technologies is
linked to the improvements made in the electronics, especially the
semiconductor devices and the new simulation capacity [9–15]. This
technological evolution is expected to continue in the coming years. Some of the main strategies to improve the performance of radio
communication systems are the following: Over the last decade the spectral efficiency, meaning the data rate
of the physical layer that could be transmitted in a given radio
frequency bandwidth, has been increased by a factor 100. This
efficiency is obtained by the use of higher order modulation
coding scheme and multiple data streams (MIMO). The use of
these advanced techniques requires intensive digital signal
processing, increasing the complexity of the chipset design, the
size, as well as the power consumption. The recent progress in
terms of computing capability and energy per operation brought
by the advanced FinFET and FDSOI technologies comes along
with this increase in signal processing complexity, containing the
power consumption, heat dissipation and manufacturing cost. According to the Shannon-Hartley theorem, another strategy to
increase the throughput is to increase the spectrum bandwidth. Since the radio frequency frontend and antenna have a bandwidth
limited in a proportion of the carrier frequency (typically a
maximum of 15–20%), then larger signal bandwidths require
transmission at higher frequency, which became feasible, once
again, with the progresses made on the electronics. Over the last decade the spectral efficiency, meaning the data rate
of the physical layer that could be transmitted in a given radio
frequency bandwidth, has been increased by a factor 100. This
efficiency is obtained by the use of higher order modulation
coding scheme and multiple data streams (MIMO). The use of
these advanced techniques requires intensive digital signal
processing, increasing the complexity of the chipset design, the
size, as well as the power consumption. The recent progress in
terms of computing capability and energy per operation brought
by the advanced FinFET and FDSOI technologies comes along
with this increase in signal processing complexity, containing the
power consumption, heat dissipation and manufacturing cost. According to the Shannon-Hartley theorem, another strategy to
increase the throughput is to increase the spectrum bandwidth. MILLIMETER WAVE WIRELESS
TECHNOLOGY Since the radio frequency frontend and antenna have a bandwidth
limited in a proportion of the carrier frequency (typically a
maximum of 15–20%), then larger signal bandwidths require
transmission at higher frequency, which became feasible, once
again, with the progresses made on the electronics. According to the Free Space Path Loss equation, the attenuation of
a 60 GHz transmission at 1 m is about 68 dB, which is 21.6 dB
higher than a 5 GHz transmission. Consequently at constant
transmit power and using a given modulation scheme, the
communication range will be 12 times shorter. This shorter
signal range has the benefit that it will mitigate co-channel
interference making a high-density channel-reuse design possible. The higher frequencies lead to smaller sizes of the RF passive
components,
including
antennae,
which
can
be
easily
integrated into electronic systems. The application-related
antenna must be carefully chosen according to many
parameters
such
as
directivity/gain,
angle
aperture, Well-chosen detector technology and geometry, combined
with wireless techniques might help in reducing the amount of
cables and optimizing their path, and thus minimizing the
geometrical inefficiency. The total or even partial removal of
cables and connectors will result in cost reductions, simplified 2Here the signal to noise ratio is defined as the average received signal over the
bandwidth, and the noise is defined as the average noise or interference power over
the bandwidth. 1The latest description of the pixel detector layout, including the number of staves
per barrel and endcap layer, the number of sensors per stave and the estimated data
rates per chip can be found in [6]. June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 2 Brenner et al. Multi Gigabit Data Transfer FIGURE 1 | Coherent (A) and non-coherent (B) RF architecture schematics. FIGURE 1 | Coherent (A) and non-coherent (B) RF architecture schematics. (mmw) band. Non- coherent architecture brings high data rate
(up to 10 Gbps at 60 GHz) and low power (<10 pJ/bit) for short-
range applications [17]. Recent advance in antenna and packaging
design allows the integration of the mmw antenna on chip [17] or in
package [18] with good efficiency. Commercial products are now
available for mass market applications with 3 main competitors
(Lattice
(SiBeam),
Molex
(Keyssa)
and
STMicroelectronics
(Figure 2), proposing different integration schemes function of
the application. Transceiver Architectures Two main transceiver architectures may be considered at mmw
frequencies (Figure 1). Coherent architecture requires precise frequency synthesis
(using
Phase
Locked
Loop),
and
time
and
frequency
synchronization mechanism achieved by digital base-band
circuit [16]. This architecture allows complex amplitude and
phase modulations, achieving high spectral efficiency, but leads
to high power consumption. Research is progressing [20] towards very high data rate wireless
communication systems, using channel aggregation or channel
bonding
in
W
or
D-band
(110–170 GHz),
where
huge
bandwidths (35 GHz aggregated) are available for short range
communications. Channel bonding is particularly relevant for the
aggregation of data from multiple detectors. A total of 16 channels of
7 Gbps each can be aggregated in a D-band transceiver, reaching
100 Gbps. The data can be sent over a few tens of meter range using
directive planar antennas, such as transmit arrays [21], or over light
plastic waveguide material [22]. On the contrary non-coherent architecture allows amplitude
modulation only (On Off Keying, Amplitude Shift Keying or
Pulse Amplitude Modulation). The receiver can implement a
simple envelope detector, a comparator and digital interface,
without any frequency reference or digital base band processing. The quadratic envelope detector provides negative gain, so that the
overall receiver noise figure increases and affects the receiver
sensitivity. For this reason, this architecture is more dedicated to
short range and low power communication. MILLIMETER WAVE WIRELESS
TECHNOLOGY Strong efforts have also been put on the
compatibility with high/low speed digital protocols (USB3, PCIe,
Gig Ethernet, UART) for a seamless cable replacement. In parallel a
HEP dedicated 60 GHz Integrated Chip was under development in
Heidelberg, using 130 nm SiGe BICMOS technology [19] in order to
assess the feasibility and performance of the wireless link and
establish solid foundation for designing the final reading system. The first prototype was designed to handle a data rate of 4.5 Gbps
over a link distance of 1 m. Estimated power consumption for a first
full prototype readout is about 150 mW. bandwidth, etc. A wide range of antenna topologies can be
produced on chip, in package or on advanced printed circuits
boards. The use of RF lenses to increase the gain and the
directivity of the antenna is also a possibility at this frequency. Improvements lie in carefully selecting the communication
protocol. For a radio communication channel to work, a large
amount of the transmission time is devoted to transmitter and
receiver synchronisation, medium access, medium sensing,
legacy standard-protection mechanism or transmission error
compensation. The distribution of a system clock in particle
physics
detectors
will
facilitate
the
transmitter-receiver
synchronisation. Frontiers in Physics | www.frontiersin.org TOWARDS WIRELESS INTEGRATION IN A
DETECTOR The results of these
studies are reported in Sections 3.1–3.4. More recently, tests
have been conducted using non-coherent transceiver prototypes
from STMicroelectronics [28], especially for latency, connectivity
and radiation hardness. These features, the high path loss, high material penetration
loss,
narrow
beam-width,
Line-Of-Sight
(LOS)
mode
of
propagation, and operation in a controlled environment,
makes the 60 GHz band optimal for short range operation as
in the considered detector, where the signal propagates over a
10 cm distance between layers. In addition, the use of the high
carrier frequency translates into small form factor for passives
(antenna), which will reduce the material budget. This provides
an extremely desirable frequency re-use that can handle a large
number of transceivers in a small area as in the HEP detectors and
other detector systems. Signal is routed through each layer from
the bottom receiver to the transmitter at top side. This multi-hop
concept requires that the wave front stay confined between the
two considered layers, and does not crosstalks with neighbours. FIGURE 3 | Proposal of a radial readout for the tracking detector of the
ATLAS experiment. Feasibility studies regarding the integration of the 60 GHz
wireless technologies in silicon tracking detector were performed
[26], based on a commercial coherent transceiver from Hittite
[27]. Several aspects relevant for the implementation of 60 GHz
links were studied: transmission losses, interference effects,
absorbing materials and the influence of the antenna design
and directivity, power consumption. The results of these
studies are reported in Sections 3.1–3.4. More recently, tests
have been conducted using non-coherent transceiver prototypes
from STMicroelectronics [28], especially for latency, connectivity
and radiation hardness. experiments and low energy experiments at the intensity frontier for a
large range of particle physics detectors. The first step taken by the
WADAPT consortium is to bring the proof of concept in the context
of data transmission through a typical vertex detector. g
yp
Present and future collider experiments require more and
more bandwidth for the handling of ever increasing data rates. It
is especially true for highly granular tracking detectors operated
at high beam luminosities. The performance is currently limited
because of insufficient readout bandwidth. An example is the
ATLAS Phase II New Inner Tracker Pixel Detector with five-
barrel layers, four end-cap rings and a silicon strip detector with
four layers and six end-cap disks, in 1 m radius. TOWARDS WIRELESS INTEGRATION IN A
DETECTOR The readout
should operate at up to 4 MHz (25 µs) L0 rate. At downlink a
broadcast trigger and control signal will be sent at 160 Mbps while Frontiers in Physics | www.frontiersin.org TOWARDS WIRELESS INTEGRATION IN A
DETECTOR In the last decade there has been tremendous advances
in silicon technologies that have made it possible to build high
performance RF transceivers operating in the millimeter-wave Possible wireless applications encompass HEP experiments at high-
energy colliders, neutrino physics experiments, astroparticle-physics June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 3 Brenner et al. Multi Gigabit Data Transfer FIGURE 2 | ST Microelecronics ST60 contactless connectivity transceiver in BGA. FIGURE 2 | ST Microelecronics ST60 contactless connectivity transceiver in BGA. FIGURE 3 | Proposal of a radial readout for the tracking detector of the
ATLAS experiment. 10k up-links will transmit data at a rate of 5 Gbps. The data
readout problematic, based on wired transmission strategy, is
addressed in [23]. Different cabling schemes are evaluated with
the goal of 5 Gbps data transmission per cable, while reducing as
much as possible the material within the small detector volume. The proposed alternative for future colliders is to replace the
innermost dense wired network by a multi-hop point-to-point
wireless network, streaming the data radially from the centre to
outer enclosure (Figure 3) [24]. The worldwide license-free 60 GHz band (57–66 GHz) [25] is
very attractive in order to achieve high data rate transfer. y
g
These features, the high path loss, high material penetration
loss,
narrow
beam-width,
Line-Of-Sight
(LOS)
mode
of
propagation, and operation in a controlled environment,
makes the 60 GHz band optimal for short range operation as
in the considered detector, where the signal propagates over a
10 cm distance between layers. In addition, the use of the high
carrier frequency translates into small form factor for passives
(antenna), which will reduce the material budget. This provides
an extremely desirable frequency re-use that can handle a large
number of transceivers in a small area as in the HEP detectors and
other detector systems. Signal is routed through each layer from
the bottom receiver to the transmitter at top side. This multi-hop
concept requires that the wave front stay confined between the
two considered layers, and does not crosstalks with neighbours. Feasibility studies regarding the integration of the 60 GHz
wireless technologies in silicon tracking detector were performed
[26], based on a commercial coherent transceiver from Hittite
[27]. Several aspects relevant for the implementation of 60 GHz
links were studied: transmission losses, interference effects,
absorbing materials and the influence of the antenna design
and directivity, power consumption. Transmission and Reflection Tests The data throughput of a wireless read-out system, as depicted in
Figure 3, is maximized when links with maximum bandwidth are June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 4 Multi Gigabit Data Transfer Brenner et al. FIGURE 4 | (A) The ATLAS SCT barrel module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the
black arrow. (B) Transmission loss of the barrel module averaged over the frequency band for a position scan (along the arrow in panel 4A) and the noise limited sensitivity
of the spectrum analyzer. The uncertainties represent the RMS of the average measurements [26]. FIGURE 5 | (A) The ATLAS SCT endcap module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the
black arrow. (B) Transmission loss of the endcap module averaged over the frequency band for a position scan (along the arrow in panel 5A) [26]. FIGURE 4 | (A) The ATLAS SCT barrel module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the
black arrow. (B) Transmission loss of the barrel module averaged over the frequency band for a position scan (along the arrow in panel 4A) and the noise limited sensitivity
of the spectrum analyzer. The uncertainties represent the RMS of the average measurements [26]. FIGURE 4 | (A) The ATLAS SCT barrel module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the
black arrow. (B) Transmission loss of the barrel module averaged over the frequency band for a position scan (along the arrow in panel 4A) and the noise limited sensitivity
of the spectrum analyzer. The uncertainties represent the RMS of the average measurements [26]. FIGURE 5 | (A) The ATLAS SCT endcap module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the
black arrow. (B) Transmission loss of the endcap module averaged over the frequency band for a position scan (along the arrow in panel 5A) [26]. FIGURE 5 | (A) The ATLAS SCT endcap module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the
black arrow. Transmission and Reflection Tests (B) Transmission loss of the endcap module averaged over the frequency band for a position scan (along the arrow in panel 5A) [26]. densely packed. The main challenge is to avoid crosstalk between
parallel and subsequent chained links. transmission loss as function of the position on the module
(Figure 5B) is −20 dB to −40 dB in the electronics region due
to the assembly hole and the gap between hybrid and flex print. As expected the silicon strip region is opaque for the
millimeter waves. Transmission and reflection tests have been performed with a
spare silicon strip detector module from the ATLAS barrel detector
(Figure 4A). The module is mounted on a 2D movable stage and
placed in line of sight of two horn antennas for transmission and
reception. The module is irradiated with linearly polarized waves in
the range from 57.3 to 61.3 GHz. A spectrum analyzer measures the
power transmitted through the module in the radio frequency band
without down conversion. The transmitted power is normalized to
the power in the absence of module in-between. Figure 4B shows the
transmission loss averaged over the chosen frequency band for a few
positions along the module. Most of the signal is absorbed by the silicon material, and
small reflections may occur due to metallization of the chip and
PCB. In some configurations these reflections might induce
crosstalk. Absorbing materials (e.g., graphite foam) may be
used to attenuate reflections [26]. Link Density Studies with Al-Kapton® horn antennas installed on both sides, links can
be placed as close as 2 cm next to each other without significant
interference effects. Without using any directive antennas
crosstalk can be reduced just by absorber shields. This has
been tested by equipping all transmitters and receivers with
1 cm long, hollow graphite foam cylinders on top of the
waveguide apertures to shield lateral radiation. Then shielded
links can be placed as close as 4 cm next to each other. The different methods for reducing crosstalk discussed in the
previous section have been experimentally studied by measuring
how close two parallel 60 GHz links can be placed without interfering
(Figure 6). The parameter S/N is defined as the ratio of the signals
from transmitter #1 (useful signal) over transmitter #2 (interfering
signal) measured with the spectrum analyzer at the antenna of the
receiver #1. The link quality is considered to be acceptable when S/N
is higher than 20 dB, which corresponds to a theoretical bit error rate
(BER) of 10–12, for high order modulation scheme decoding and
forward error correction. For OOK the required S/N is in the range
30–35 dB function of the total jitter requirement. p
The Bit Error Rate (BER) measures the performance of a data
transmission device. With the setup described above the BER is
measured for a data rate of 1.76 Gbps using Minimum Shift Keying
(MSK) as modulation scheme. Both links use the same polarization
state and the same carrier frequency. Figure 8 shows the BER
measured as function of the pitch in different configurations. With horn antennas bit error rates smaller than 10–12 are
achieved for all considered pitches. The distance between transmitters and receivers is set at 10 cm
(expected distance between layers) and both links have identical
polarization. S/N is measured as a function of the antenna spacing for
different setups (Figure 7). For reference non-directive waveguide
apertures are used, for which S/N increases linearly as a function of
the pitch. In a real tracking detector 60 GHz radiation can be partially
reflected between the silicon detector layers, generating
multipath and crosstalk. The silicon detector environment
can be simulated by enclosing the volume with aluminium
plates (Figure 6). The distance between the links is set to 5, 10
and 15 cm. Reduction of Crosstalk All wireless links in a tracking detector are installed in stationary
positions. Therefore, wireless readout systems can be designed
and optimized in order to minimize the interference effects The measurement is repeated with a spare ATLAS SCT
endcap
module
(Figure
5A). The
frequency
averaged June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 5 Brenner et al. Multi Gigabit Data Transfer FIGURE 6 | Sketch of the setup to measure crosstalk with two links between highly reflective aluminium layers. LOS crosstalk is indicated as purple wave [26]. FIGURE 6 | Sketch of the setup to measure crosstalk with two links between highly reflective aluminium layers. LOS crosstalk is indicated as purple wave [26]. FIGURE 7 | S/N in the radio frequency spectrum with LOS induced
crosstalk as function of the antenna pitch for different setups [26]. between different links. Nevertheless crosstalk may be an issue for
extremely high link densities. However different actions can be
combined to reduce crosstalk, if necessary. One of them is acting on the antenna pattern, using directive
antennas with high gain, small beam width and low secondary
lobes. By increasing the gain of the antenna, the transmitted
power can be decreased while keeping the signal over noise ratio
(S/N) in the receiver constant. In addition the antenna linear or circular polarization
direction can be exploited. Crosstalk between adjacent links
can be significantly reduced by using orthogonal polarization
states. Furthermore low mass absorbing material can be used to
attenuate
the
spurious
reflections
without
increasing
the
material budget. Finally a tunable voltage controlled oscillator (VCO) with
sharp filters or low bandwidth antennas may be used to divide
the frequency band in different channels. Spreading (CDMA)
is also an option with the drawback of reducing the data
rate [26]. FIGURE 7 | S/N in the radio frequency spectrum with LOS induced
crosstalk as function of the antenna pitch for different setups [26]. Frontiers in Physics | www.frontiersin.org Link Density Studies FIGURE 9 | S/N for two parallel links operated between two fully
reflective aluminium layers at a distance of 10 cm. Results are shown for
parallel polarization states (top, white background) and orthogonal
polarization states (bottom, grey background) [26]. Link Density Studies FIGURE 9 | S/N for two parallel links operated between two fully
reflective aluminium layers at a distance of 10 cm. Results are shown for
parallel polarization states (top, white background) and orthogonal
polarization states (bottom, grey background) [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of
2.6 cm as function of the carrier frequency offset. The links are operated with
MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB
bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line,
twice the bandwidth as a blue line [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of
2.6 cm as function of the carrier frequency offset. The links are operated with
MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB
bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line,
twice the bandwidth as a blue line [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of
2.6 cm as function of the carrier frequency offset. The links are operated with
MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB
bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line,
twice the bandwidth as a blue line [26]. FIGURE 8 | Influence of LOS crosstalk on the BER of a wireless data
transmission, shown as function of the pitch between two parallel links. Distance between transmitter and receiver is set to 10 cm. Both links are
operated at the same carrier frequency [26]. FIGURE 8 | Influence of LOS crosstalk on the BER of a wireless data
transmission, shown as function of the pitch between two parallel links. Distance between transmitter and receiver is set to 10 cm. Both links are
operated at the same carrier frequency [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of
2.6 cm as function of the carrier frequency offset. The links are operated with
MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB
bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line,
twice the bandwidth as a blue line [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of
2.6 cm as function of the carrier frequency offset. Link Density Studies The measurements relative to all antenna setups In the absence of any mitigation a minimum pitch of about
8 cm is necessary to achieve a S/N of 20 dB. With one highly
directive (17 dBi) Al-Kapton® horn antenna on the transmitting
or receiving side, the minimum pitch is reduced to 4 cm, while June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 6 Multi Gigabit Data Transfer Brenner et al. 5 cm
is
possible
for
all
studied
configurations. For
orthogonal polarization of neighbouring links, a good S/N is
obtained for all tested setups even without directive antennas
and a distance smaller than 5 cm seems to be possible. The
combination of directive antennas and absorbing foam can
increase the S/N ratio further. Thus using directive antennas,
polarization, absorber materials, alone or in combination
allows
the
operation
of
60 GHz
links
between
highly
reflective materials even at a small pitch. A transmitter chip with tunable carrier frequency allows the
use of frequency channeling. The BER has been measured as a
function of the carrier offset when two parallel links are
positioned at a pitch of 2.6 cm using the same polarization
state. Foam cylinders on top of the waveguide apertures
provide a minimum shielding. The carrier frequency offset is
varied in steps of 500 MHz. Figure 10 shows that with this setup,
using 3 frequency channels in parallel within the full 60 GHz
band seems possible. Drawing full benefit from channeling
necessitates filters with very sharp cutoff frequencies. An estimate on the possible link density can be derived from
above results. Assuming a tracking detector environment with
distances of 10 cm between layers and a minimum pitch of 3.5 cm
between links., OOK as modulation scheme with a spectral
efficiency of ρOOK ≈0.5 bps/Hz, and using the full 9 GHz
bandwidth per channel yields a data rate of 4.5 Gbps per link,
the resulting data rate area density is about 3.7 Tbps/m2. This is a
theoretical
limit,
which
cannot
be
realistically
reached
experimentally. The estimated experimental data rate density
is rather around 1.2 Tbps/m2 [26]. FIGURE 8 | Influence of LOS crosstalk on the BER of a wireless data
transmission, shown as function of the pitch between two parallel links. Distance between transmitter and receiver is set to 10 cm. Both links are
operated at the same carrier frequency [26]. Link Density Studies The links are operated with
MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB
bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line,
twice the bandwidth as a blue line [26]. FIGURE 9 | S/N for two parallel links operated between two fully
reflective aluminium layers at a distance of 10 cm. Results are shown for
parallel polarization states (top, white background) and orthogonal
polarization states (bottom, grey background) [26]. 5 cm
is
possible
for
all
studied
configurations. For
orthogonal polarization of neighbouring links, a good S/N is
obtained for all tested setups even without directive antennas
and a distance smaller than 5 cm seems to be possible. The
combination of directive antennas and absorbing foam can
increase the S/N ratio further. Thus using directive antennas,
polarization, absorber materials, alone or in combination
allows
the
operation
of
60 GHz
links
between
highly
reflective materials even at a small pitch. A transmitter chip with tunable carrier frequency allows the
use of frequency channeling. The BER has been measured as a
function of the carrier offset when two parallel links are
positioned at a pitch of 2.6 cm using the same polarization
state. Foam cylinders on top of the waveguide apertures
provide a minimum shielding. The carrier frequency offset is
varied in steps of 500 MHz. Figure 10 shows that with this setup,
using 3 frequency channels in parallel within the full 60 GHz
band seems possible. Drawing full benefit from channeling
necessitates filters with very sharp cutoff frequencies. An estimate on the possible link density can be derived from
above results. Assuming a tracking detector environment with
distances of 10 cm between layers and a minimum pitch of 3.5 cm
between links., OOK as modulation scheme with a spectral
efficiency of ρOOK ≈0.5 bps/Hz, and using the full 9 GHz
bandwidth per channel yields a data rate of 4.5 Gbps per link,
the resulting data rate area density is about 3.7 Tbps/m2. This is a
theoretical
limit,
which
cannot
be
realistically
reached
experimentally. The estimated experimental data rate density
is rather around 1.2 Tbps/m2 [26]. FIGURE 9 | S/N for two parallel links operated between two fully
reflective aluminium layers at a distance of 10 cm. Results are shown for
parallel polarization states (top, white background) and orthogonal
polarization states (bottom, grey background) [26]. Connectivity A non-coherent transceiver was interfaced with Minimum Ionizing
MOnolithic Active pixel Sensors (MIMOSA) from IPHC Strasbourg
(Figure 14), which use the epitaxial layer of standard CMOS
(TowerJazz High Resistivity 180 nm technology [29]) processes as
detecting sensitive volume. The pixel detector board provides 5 μs
refreshment rate and generates up to 3 Gbps data rate. Signal integrity
tests were carried out with the detector feeding a wireless link. No
error was reported at oscilloscope. Different materials were then
introduced between the antennas. Signals well passed through the
non-metallized area of the thin flex Kapton PCB that embeds chips,
but not through low-density carbon foam that holds the detector. These results validate the proposed readout architecture, whose
principle is to isolate every detector layer and export data through
multiple hops between layers. At longer term, the RF transceiver may
be integrated within the detector chip. The antenna could also be part
of the chip with good efficiency, assuming the high resistivity
substrate of the CMOS backend material. Pixel detectors still need
to receive a clock or trigger reference from the network. It could then
be worth modifying the 60 GHz transceiver, so that the clock is also
transmitted wirelessly from chip to chip on the carrier by harmonic
injection locking. FIGURE 11 | Block diagram of the setup used for the irradiation test at
Freiburg. A, B, C and D indicate different antenna positions used in the test. The 12 readout chips are illustrated as brown boxes on the orange readout
hybrid [26]. as cut-off frequencies of sensors and readout chips for silicon
detectors are typically below a few GHz, no interference between
the 60 GHz links and tracking detector modules is expected. To
demonstrate this, 60 GHz irradiation tests are performed for different
silicon strip and pixel detectors. Two ATLAS Binary Chip-Next (ABCN) endcap electronics
hybrid prototypes for the Phase-2 upgrade of the silicon
tracking-detector for the ATLAS experiment are tested using the
setup shown on Figure 11. One is a bare electronics hybrid, while
the other one is connected to short silicon strip sensors with a strip
length of 2.4 cm. Each prototype includes 12 fully functional ABCN
readout chips. Noise is measured for each channel of the readout
ASICs under wireless irradiation. The hybrid module is irradiated
using a 20 dBi horn antenna from an distance of 1 cm resulting in a
irradiated power of about −1 dBm. Radiation Hardness A first irradiation experiment with protons was performed at Åbo
Akademi University, Turku, Finland [30]. Figure 15 shows a scheme
and a picture of the setup. The radiation hardness of the V-band TRX
chip in 65 nm CMOS, acting both in TX and RX modes, was FIGURE 12 | Noise distribution of all channels of the 12 ABCN readout
chips without strip sensors under irradiation. The reference measurement was
performed without 60 GHz irradiation. Mean μ and width σ of the Gaussian fits
are given. No significant difference is observed [26]. These results indicate that there should not be any obstacle to
wireless data transmission in the 60 GHz band with respect to the
operation and performance of current silicon tracking detector
sensors [26]. FIGURE 12 | Noise distribution of all channels of the 12 ABCN readout
chips without strip sensors under irradiation. The reference measurement was
performed without 60 GHz irradiation. Mean μ and width σ of the Gaussian fits
are given. No significant difference is observed [26]. FIGURE 12 | Noise distribution of all channels of the 12 ABCN readout
chips without strip sensors under irradiation. The reference measurement was
performed without 60 GHz irradiation. Mean μ and width σ of the Gaussian fits
are given. No significant difference is observed [26]. Connectivity Four different components are
irradiated (Figure 11) with carrier frequencies of 57, 60 and
63 GHz: (A) the power converter, (B) and (C) the readout chips,
and (D) the bonding wires. The noise level distribution of a
reference
measurement
and
a
measurement
with
60 GHz
irradiation are compared in Figure 12 for the electronics hybrid
without silicon strips and no significant differences are found in the
mean and width of the noise distributions. Similarly no significant
noise increase for the second prototype connected to silicon strips is
observed. As expected, no influence of the wireless signal on the
noise level is found at any carrier frequency. Noise Pickup with
both polarization
states (parallel
and
orthogonal)
between the two links are displayed in Figure 9. With
directive antennas, stable data transmission at a pitch of The pickup of noise from 60 GHz communications is a potential
worry for the operation of wireless links inside the detector. However, June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 7 Multi Gigabit Data Transfer Brenner et al. FIGURE 11 | Block diagram of the setup used for the irradiation test at
Freiburg. A, B, C and D indicate different antenna positions used in the test. The 12 readout chips are illustrated as brown boxes on the orange readout
hybrid [26]. low directivity antenna (Figure 13). The transmitter was fed by a
SLVS 8b/10b encoded signal from pseudo random binary sequence at
5 Gbps. At the receiver output the binary signal showed less than 75
ps total jitter, less than 35 ps 20–80% rising/falling time and less than
1 ns latency (without the cables). A range of 10 cm can be obtained
using 10 dB gain antenna. Signal Integrity The performance of non-coherent chips described in [2] was
measured at 1–5 cm range between transmitter and receiver using June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 8 FIGURE 13 | Emitted waveform (left) and received eye diagramm (right) for 5 Gbps wireless link. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 15 | irradiation tests at Turku Cyclotron. Brenner et al. Multi Gigabit Data Transfer Multi Gigabit Data Transfer Brenner et al. FIGURE 13 | Emitted waveform (left) and received eye diagramm (right) for 5 Gbps wireless link. FIGURE 13 | Emitted waveform (left) and received eye diagramm (right) for 5 Gbps wireless link. FIGURE 13 | Emitted waveform (left) and received eye diagramm (right) for 5 Gbps wireless link. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 15 | irradiation tests at Turku Cyclotron. FIGURE 15 | irradiation tests at Turku Cyclotron. experiment presents a first investigation of radiation hardness
that gives encouraging results despite the fact that the devices
were not specifically radiation hardened by either design or process. A second campaign of irradiation with electrons was carried out at
the CLEAR (CERN Linear Electron Accelerator for Research) facility
at CERN [31]. The TX and RX were exposed to a TID of 3.14 and
2.70 MGy respectively. The pre- and post-irradiation characterization
of the chips revealed a 80 MHz upshift in the centre frequency. An
overall link budget degradation of 10 dB was observed, which is a sum
of 4 dB reduced TX output power and 6 dB degraded receiver
sensitivity. Besides,
circuit
bandgap
(voltage
reference)
were
degraded, which affected the transceivers internal biasings and so investigated after 17 MeV proton irradiation. TID and fluence used
during the experiment were 74 and 42 kGy and 1.4 × 10 14Neq/cm2
and 0.8 × 1014Neq/cm2 for the RX and the TX, respectively. Transmission performance was measured before, during and after
irradiation. The RX experienced higher loss of sensitivity than the TX
power loss, accordingly to the respective TID and fluence. However,
both the RX and the TX were found operational through over-the-air
measurements at 5 Gbps after irradiation. Signal Integrity If some transmission errors
were observed during the irradiation, the chip recovered error free
transmission after irradiation with small gain degradation. experiment presents a first investigation of radiation hardness
that gives encouraging results despite the fact that the devices
were not specifically radiation hardened by either design or process. A second campaign of irradiation with electrons was carried out at
the CLEAR (CERN Linear Electron Accelerator for Research) facility
at CERN [31]. The TX and RX were exposed to a TID of 3.14 and
2.70 MGy respectively. The pre- and post-irradiation characterization
of the chips revealed a 80 MHz upshift in the centre frequency. An
overall link budget degradation of 10 dB was observed, which is a sum
of 4 dB reduced TX output power and 6 dB degraded receiver
sensitivity. Besides,
circuit
bandgap
(voltage
reference)
were
degraded, which affected the transceivers internal biasings and so Although the radiation levels expected in the real experiment at
HL-LHC or future hadron colliders are much higher, this June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 9 Multi Gigabit Data Transfer Brenner et al. antennas are particularly relevant for the considered innermost
part of the readout network, based on multi-hop transmission. Early feasibility tests with prototypes and commercial products
have demonstrated that crosstalk is not an issue for high density
of links and that no pickup noise is to be expected. The projected
theoretical limit with current technology is 3.7 Tbps/m2 and <10 pJ/
bit. Although the commercial products were not designed nor
manufactured as radiation hard components, they showed good
behaviour under irradiation with protons and electrons. They
could be easily hardened to be able to sustain radiation levels
expected at future hadron colliders. There is no show-stopper to
the early deployment and proof of concept using hardened RFICs and
associated electronics in HEP experiments. The mmw technological
roadmap shows soaring data rates using higher frequency bands
above 100 GHz, challenging optical links for data aggregation and
routing at short to medium range. the transmitter and receiver gains. Despite the mentioned degradation,
the
chips
were
found
operational
in
the
post-irradiation
characterization. Moreover, margins have been taken in chip
design in order to guarantee performance through P,V,T variations
and production yield, so that calibration means can restore part of the
chip performance. 4R. Brenner, D. Dancila, C. Dehos, P. De Lurgio, Z. Djurcic, G. Drake, J.L. Gonzalez
Jiménez, L. Gustafsson, D.W. Kim, E. Locci, U. Pfeiffer, D. Röhrich, D. Rydberg, A.
Schöning, A. Siligaris, H.K. Soltveit, K. Ullaland, P. Vincent, P.R. Vasquez, D.
Wiedner, S. Yang.
5J. Baudot, G. Claus, M. Goffe. Future Developments and Test At long term, the integration of wireless technologies in tracking
detector would certainly require the design of a dedicated
radiation hardened mmw transceiver IP, to be integrated
either as a companion chip or within silicon trackers. For this
purpose the ST C65SPACE radiation hardened ASIC technology
or 45 nm Partially Depleted SOI technologies seem good
candidates. The latter would allow the integration of antenna
directly on the High Resistivity substrate of its back-end. For a
better and versatile interfacing, the transceiver IP could also
contain serializer/deserializer. External antennas or focusing
lenses should be envisaged with the objectives of extending the
range and ease crosstalk management. The crosstalk can be
further improved by alternating antennas radiating in vertical
and horizontal polarization for better isolation. The antenna
should radiate a vertical beam (normal to the PCB plane) in
order to fit easily in the detector. Well-chosen detector technology and geometry, combined
with flexible wireless techniques might help in minimizing
dead
material
by
reducing
the
amount
of
cables
and
connectors. The absence of constrain to mechanical structures
allows radial readout following the event topology that would be
optimal for a fast trigger decision and would enhance on-detector
intelligence, which could also open up new possibilities of
communication between chips. Technologies should be mature enough to be envisaged as a
part of the readout network of future detectors at future colliders. ACKNOWLEDGMENTS The present document is based on the work of the whole WADAPT
consortium4, which has been partly presented at the 40th
International Conference on High Energy physics—ICHEP2020
[2]. The authors are grateful to their colleagues of the Heidelberg
University, Sebastian Dittmeier, André Schöning, Hans Kristian
Soltveit, Dirk Wiedner, for giving them the permission to use in
extenso large parts of their publication [26] for the sake of the
completeness of this review. Special thanks are due to Sebastian
Dittmeier for the tests of the Hittite transceiver, to Imran Aziz for
the irradiation tests, to Frederic Lagrange from STMicroelectronics
for providing equipment and support, to our colleagues5 of the
Institut Pluridisciplinaire Hubert Curien, Strasbourg, France for the
tests of connectivity to MIMOSA sensors as well as to Åbo Akademi
University, Finland for use of their irradiation facility. Warm thanks
go to Hans Kristian Soltveit for the careful reading of this document. AUTHOR CONTRIBUTIONS All authors listed have made a substantial, direct, and intellectual
contribution to the work and approved it for publication. At shorter term is envisaged the integration of the available non
coherent mmw transceivers BGA with external antennas, as
System In Package or System On Board. The antenna shall
provide a narrow beam broadside for dense wireless links. As a
proof of concept, a three (or four) layer silicon detector will be
build3, as shown on Figure 3. This mock-up of a central tracker will
be equipped with the transceiver chip in BGA package. This will
allow to study the added noise and data transmission quality
(impact on eye diagram, Jitter, Bit Error Rate) over the different
layers and get the antenna specifications: gain, polarization,
bandwidth and radiation robustness. Then we will integrate the
detectors to the setup to check the readout capabilities while using
multi-hop wireless link. Eventually a multilink scenario will be
considered to check if the isolation between channels is sufficient
for the considered application. This would bring us closer to the full
scale implementation and would help specify and integrate the
future wireless systems in detectors at future colliders. Signal Integrity Indeed TX power can be increased by 3dB by
changing the settings, while LNA gain can be boosted also to restore
the sensitivity. Radiation hardening shall however be considered on
C65SPACE (which includes libraries with hardened cells, tested up to
0.3 Mrad dose but could handle higher radiations) or more advanced
SOI technology for the highest radiation levels expected at future
colliders such as HL-LHC or FCC-hh. 3This project is supported by AIDAinnova. REFERENCES High Energy Physics — PoS(EPS-HEP2017); October 2017 (2017). doi:10. 22323/1.314.0520 High Energy Physics — PoS(EPS-HEP2017); October 2017 (2017). doi:10. 22323/1.314.0520 20. Gonzalez-Jimenez JL, Dehos C, Cassiau N, Siligaris A, Clemente A, D’Errico R,
et al. Channel-bonding CMOS Transceiver for 100 Gbps Wireless point-to-
point Links. EURASIP J Wireless Commun Networking, 2020 (2020). p. 117. doi:10.1186/s13638-020-01741-1 1. Brenner R, Ceuterickx S, Dehos C, De Lurgio P, Djurcic Z, Drake G, et al. Development of Wireless Techniques in Data and Power Transmission
Application for Particle-Physics Detectors. (2017) CERN-LHCC-2017-002;
LHCC-I-028 Available from: https://cds.cern.ch/record/2243480?ln=fr. 21. Manzillo FF, Luis Gonzalez-Jimenez J, Clemente A, Siligaris A, Blampey B,
Dehos C. Low-cost, High-Gain Antenna Module Integrating a CMOS
Frequency Multiplier Driver for Communications at D-Band. In: Proceedings
of The 2019 IEEE Radio Frequency Integrated Circuits Symposium (RFIC);
June 2019; Boston, MA, USA. IEEE (2019). p. 19–22. doi:10.1109/RFIC.2019. 8701772 2. Dehos C, Locci E, Brenner R, Dancila D, de Lurgio P, Djurcic Z, et al. Wireless Allowing
Data and Power Transfer. In: Proceesing of the 40th International Conference on High
Energy physics - ICHEP (2020) ; Jul 2020; Prague, Czech Republic. p. 832. 3. The ATLAS Collaboration. The ATLAS experiment at the CERN Large Hadron
Collider. J Instrum (2008) 3:S08003. doi:10.1088/1748-0221/3/08/S08003 4. The CMS Collaboration. The CMS experiment at the CERN Large Hadron
Collider. J Instrum (2008) 3:S08004. doi:10.1088/1748-0221/3/08/S08004 22. Voineau F, Dehos C, Martineau B, Sie M, Perchicot M, Nguyen NH, et al. A 12
Gb/s 64QAM and OFDM Compatible Millimeter-Wave Communication Link
Using a Novel Plastic Waveguide Design. In: Proceedings of The 2018 IEEE
Radio and Wireless Symposium (RWS); Jan 2018; Anaheim, CA. IEEE (2018). p. 250–2. doi:10.1109/RWS.2018.8305001 5. Béjar Alonso I, Brüning O, Fessia P, Lamont M, Rossi L, Tavian L, et al. High-
Luminosity Large Hadron Collider (HL-LHC): Technical Design Report. In:
CERN Yellow Reports: Monographs (2020). p. 378. CERN-2020-010. doi:10. 23731/CYRM-2020-0010 23. Muñoz Sánchez F. Module and Electronics Developments for the ATLAS ITk
Pixel System. In: Proceedings of The 19th iWoRiD; Krakow, Poland (2017). 6. ATLAS PUB Note. Expected Size and Read-Out Rate of the Data of the ATLAS
ITk Pixel Detector (2022). Available from: https://cds.cern.ch/record/2800852/
files/ATL-ITK-PUB-2022-001.pdf. 24. Brenner R, Cheng S. Multigigabit Wireless Transfer of Trigger Data through
Millimetre Wave Technology. J Instrumentation (2010) 5:c07002. doi:10.1088/
1748-0221/5/07/c07002 7. Sguazzoni G. The CMS Pixel Detector for the High Luminosity LHC. Nucl.Instrum.Meth.A (2019) 958:162089. doi:10.1016/j.nima.2019.04.043 25. REFERENCES Dehos C, González JL, De Domenico A, Kténas D, Dussopt L. Millimeter-wave
Access and Backhauling: the Solution to the Exponential Data Traffic Increase
in 5G mobile Communications Systems? IEEE Commun Mag (2014) 52(9):
88–95. doi:10.1109/MCOM.2014.6894457 8. Affolder A, Allongue B, Blanchot G, Faccio F, Fuentes C, Greenall A, et al. DC-DC Converters with Reduced Mass for Trackers at the HL-LHC. J Inst
(2011) 6:C11035. doi:10.1088/1748-0221/6/11/c11035 9. Rappaport TS, Murdock JN, Gutierrez F. State of the Art in 60-GHz Integrated
Circuits and Systems for Wireless Communications. Proc IEEE (2011) 99(No. 8):1390–436. doi:10.1109/jproc.2011.2143650 26. Dittmeier S, Schöning A, Soltveit HK, Wiedner D. Feasibility Studies for a
Wireless 60 GHz Tracking Detector Readout. Nucl.Instrum.Meth. (2016)
A830:417–26. doi:10.1016/j.nima.2016.06.016 27. Analog Devices. Millimeterwave Transmitter 57 - 64 GHz. Available from: https://
1224 www.analog.com/media/en/technical-documentation/data-sheets/hmc6000. pdf (Accessed 2012). 10. Siligaris A, Hamada Y, Mounet C, Raynaud C, Martineau B, Deparis N, et al. A
60 GHz Power Amplifier with 14.5 dBm Saturation Power and 25% Peak PAE
in CMOS 65 Nm SOI. IEEE J Solid-State Circuits (Jssc) (2010) 45(7):1286–94. doi:10.1109/jssc.2010.2049456 28. Wireless-Connectivity. Wireless-Connectivity. Available from: https://www.st. com/en/wireless-connectivity/st60a2g0.html (Accessed 2022). 11. Siligaris A, Richard O, Martineau B, Mounet C, Chaix F, Ferragut R, et al. A 65
Nm CMOS Fully Integrated Transceiver Module for 60 GHz Wireless HD
Applications. In: Proceeding of the International Solid-State Circuits
Conference (ISSCC); San Francisco (2011). p. 20–4. 29. Pernegger H. Monolithic Pixel Development in TowerJazz 180 Nm CMOS for
the Outer Pixel Layers in the ATLAS experiment. Nucl Instr Methods Phys Res
Section A: Acc Spectrometers, Detectors Associated Equipment (2018) 924:92–8. doi:10.1016/j.nima.2018.07.043 12. Siligaris A, Richard O, Martineau B, Mounet C, Chaix F, Ferragut R, et al. A 65-nm
CMOS Fully Integrated Transceiver Module for 60-GHz Wireless HD Applications. IEEE J Solid-State Circuits, 46 (2011). p. 3005–17. doi:10.1109/jssc.2011.2166662 30. Aziz I, Dancila D, Dittmeier S, Siligaris A, Dehos C, De Lurgio PM, et al. Effects
of Proton Irradiation on 60 GHz CMOS Transceiver Chip for Multi-Gbps
Communication in High-Energy Physics Experiments. J Eng (2019) 8:5391. doi:10.1049/joe.2018.5402 13. Kaouach H, Dussopt L, Lanteri J, Koleck T, Sauleau R. Wideband Low-Loss
Linear and Circular Polarization Transmit-Arrays in V-Band. IEEE Trans
Antennae Propagation (2011) 59:2513–23. doi:10.1109/tap.2011.2152331 31. Aziz I. Ultra-wideband Millimeter-waveAntenna Arrays and Front-End
SystemsFor High Data Rate 5G and High Energy Physics. PhD Thesis
Digital Compr Summ Uppsala Dissertations Fac Sci Tech (2021)
2005:68. 14. Pfeiffer UR, Goren D. CONCLUSION The recent advances in mmw technologies allows low latencies, high
data rates and low power wireless data transmission at short range. The association of non-coherent RF architecture and directive June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 10 Multi Gigabit Data Transfer Brenner et al. REFERENCES A 20 dBm Fully-Integrated 60 GHz SiGe Power
Amplifier with Automatic Level Control. IEEE J Solid-state Circuits (2007)
42(7):1455–63. doi:10.1109/jssc.2007.899116 15. Reynolds SK, Floyd BA, Pfeiffer UR, Beukema T, Grzyb J, Haymes C, et al. A Silicon
60-GHz Receiver and Transmitter Chipset for Broadband Communications. IEEE J Solid-state Circuits (2006) 41:2820–31. doi:10.1109/jssc.2006.884820 Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. 16. Diet
A,
Villegas
M,
Baudoin
G,
Robert
F. Radio-communications
Architectures. In: A Bazzi, editor. Radio Communications. Sciyo: Intech
(2010). p. 1–35. ffhal-00553229f. Publisher’s Note: All claims expressed in this article are solely those of the authors
and do not necessarily represent those of their affiliated organizations, or those of
the publisher, the editors and the reviewers. Any product that may be evaluated in
this article, or claim that may be made by its manufacturer, is not guaranteed or
endorsed by the publisher. 17. Siligaris A, Deparis N, Pilard R, Gloria D, Loyez C, Rolland N, et al. A 60 GHz
UWB Impulse Radio Transmitter with Integrated Antenna in CMOS65nm
SOI Technology. In: Proceeding of the 2011 IEEE 11th Topical Meeting on
Silicon Monolithic Integrated Circuits in RF Systems; Jan. 2011; Phoenix, AZ. IEEE (2011). p. 153–6. doi:10.1109/SIRF.2011.5719303 Copyright © 2022 Brenner, Dehos and Locci. This is an open-access article
distributed under the terms of the Creative Commons Attribution License
(CC BY). The use, distribution or reproduction in other forums is permitted,
provided the original author(s) and the copyright owner(s) are credited and
that the original publication in this journal is cited, in accordance with
accepted academic practice. No use, distribution or reproduction is
permitted which does not comply with these terms. 18. Dussopt L, Lamy Y, Joblot S, Lanteri J, Salti H, Bar P, et al. Silicon Interposer
with
Integrated
Antenna
Array
for
Millimeter-Wave
Short-Range
Communications. In: Proceeding of the 2012 IEEE/MTT-S International
Microwave Symposium Digest; June 2012; Montreal QC. IEEE (2012). p. 1–3. doi:10.1109/MWSYM.2012.6259424 19. Soltveit HK. Multi-Gigabit Wireless Data Transfer for High EnergyPhysics
Applications. In: Proceedings of The European Physical Society Conference on June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 11
|
https://openalex.org/W4223486921
|
https://www.repository.cam.ac.uk/bitstream/1810/339755/2/11102_2022_Article_1229.pdf
|
English
| null |
11C-methionine PET aids localization of microprolactinomas in patients with intolerance or resistance to dopamine agonist therapy
|
Research Square (Research Square)
| 2,022
|
cc-by
| 9,518
|
1
Cambridge Endocrine Molecular Imaging Group,
Metabolic Research Laboratories, Wellcome–MRC Institute
of Metabolic Science, University of Cambridge and National
Institute for Health Research Cambridge Biomedical
Research Centre, Addenbrooke’s Hospital, Cambridge
Biomedical Campus, Cambridge, UK * M. Gurnell
mg299@medschl.cam.ac.uk 11C‑methionine PET aids localization of microprolactinomas
in patients with intolerance or resistance to dopamine agonist therapy W. A. Bashari1 · M. van der Meulen1 · J. MacFarlane1 · D. Gillett1,2 · R. Senanayake1 · L. Serban1 · A. S. Powlson1 ·
A. M. Brooke3 · D. J. Scoffings4 · J. Jones4 · D. G. O’Donovan5 · J. Tysome6 · T. Santarius7 · N. Donnelly6 · I. Boros8 ·
F. Aigbirhio8 · S. Jefferies9 · H. K. Cheow1,2,4 · I. A. Mendichovszky1,2,4 · A. G. Kolias7 · R. Mannion7 · O. Koulouri1 ·
M. Gurnell1 W. A. Bashari1 · M. van der Meulen1 · J. MacFarlane1 · D. Gillett1,2 · R. Senanayake1 · L. Serban1 · A. S. Powlson1 ·
A. M. Brooke3 · D. J. Scoffings4 · J. Jones4 · D. G. O’Donovan5 · J. Tysome6 · T. Santarius7 · N. Donnelly6 · I. Boros8 ·
F. Aigbirhio8 · S. Jefferies9 · H. K. Cheow1,2,4 · I. A. Mendichovszky1,2,4 · A. G. Kolias7 · R. Mannion7 · O. Koulouri1 ·
M. Gurnell1 Accepted: 3 May 2022 / Published online: 24 May 2022
© The Author(s) 2022 Accepted: 3 May 2022 / Published online: 24 May 2022
© The Author(s) 2022 2
Department of Nuclear Medicine, University of Cambridge
and National Institute for Health Research Cambridge
Biomedical Research Centre, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK 3
Macleod Diabetes and Endocrine Centre, Royal Devon
and Exeter Hospital, Exeter, UK Abstract Purpose To assess the potential for 11C-methionine PET (Met-PET) coregistered with volumetric magnetic resonance imag-
ing (Met-PET/MRCR) to inform clinical decision making in patients with poorly visualized or occult microprolactinomas
and dopamine agonist intolerance or resistance. Patients and methods Thirteen patients with pituitary microprolactinomas, and who were intolerant (n = 11) or resistant
(n = 2) to dopamine agonist therapy, were referred to our specialist pituitary centre for Met-PET/MRCR between 2016 and
2020. All patients had persistent hyperprolactinemia and were being considered for surgical intervention, but standard clini-
cal MRI had shown either no visible adenoma or equivocal appearances. Results In all 13 patients Met-PET/MRCR demonstrated a single focus of avid tracer uptake. This was localized either to the
right or left side of the sella in 12 subjects. In one patient, who had previously undergone surgery for a left-sided adenoma,
recurrent tumor was unexpectedly identified in the left cavernous sinus. Five patients underwent endoscopic transsphenoidal
selective adenomectomy, with subsequent complete remission of hyperprolactinaemia and normalization of other pituitary
function; three patients are awaiting surgery. In the patient with inoperable cavernous sinus disease PET-guided stereotactic
radiosurgery (SRS) was performed with subsequent near-normalization of serum prolactin. Two patients elected for a further
trial of medical therapy, while two declined surgery or radiotherapy and chose to remain off medical treatment. C
l
i
I
ti
t
ith d
i
i t i t l
i t
d i d t
i
t
it it
MRI
l
l
(f f
Conclusions In patients with dopamine agonist intolerance or resistance, and indeterminate pituitary MRI, molecular (func-
tional) imaging with Met-PET/MRCR can allow precise localization of a microprolactinoma to facilitate selective surgical
adenomectomy or SRS. Keywords 11C-methionine PET · Microprolactinoma · Dopamine agonist intolerance/ resistance * M. Pituitary (2022) 25:573–586
https://doi.org/10.1007/s11102-022-01229-9 Pituitary (2022) 25:573–586
https://doi.org/10.1007/s11102-022-01229-9 Abstract Gurnell
mg299@medschl.cam.ac.uk
1
Cambridge Endocrine Molecular Imaging Group,
Metabolic Research Laboratories, Wellcome–MRC Institute
of Metabolic Science, University of Cambridge and National
Institute for Health Research Cambridge Biomedical
Research Centre, Addenbrooke’s Hospital, Cambridge
Biomedical Campus, Cambridge, UK
2
Department of Nuclear Medicine, University of Cambridge
and National Institute for Health Research Cambridge
Biomedical Research Centre, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK
3
Macleod Diabetes and Endocrine Centre, Royal Devon
and Exeter Hospital, Exeter, UK
4
Department of Radiology, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK
5
Department of Neuropathology, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK
6
Department of Otolaryngology, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK
7
Department of Neurosurgery, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK
8
Wolfson Brain Imaging Centre, University of Cambridge,
Addenbrooke’s Hospital, Cambridge Biomedical Campus,
Cambridge, UK
9
Department of Oncology, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK 7
Department of Neurosurgery, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK 8
Wolfson Brain Imaging Centre, University of Cambridge,
Addenbrooke’s Hospital, Cambridge Biomedical Campus,
Cambridge, UK 9
Department of Oncology, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK 9
Department of Oncology, Addenbrooke’s Hospital,
Cambridge Biomedical Campus, Cambridge, UK 3
Macleod Diabetes and Endocrine Centre, Royal Devon
and Exeter Hospital, Exeter, UK :(0123
1 3456789)
3 3456789)
3 574 Pituitary (2022) 25:573–586 adenomas and has been successfully used to facilitate
curative (including repeat) TSS in acromegaly and Cush-
ing Disease when MRI is indeterminate [32–34]. Several
PET radiotracers have been trialled for imaging prolactino-
mas, including 11C-raclopride and 11C-N-methylspiperone
(dopamine D2 receptor ligands) [35, 36], 18F-fluorodeox-
yglucose (metabolic activity as per the Warburg effect)
[37, 38], and 11C-methionine [taken up via the L-type
amino acid transporter 1 (LAT1) at sites of peptide syn-
thesis] [38–41]. 11C-methionine PET (Met-PET) has been
reported to have high sensitivity for the detection of func-
tioning pituitary adenomas, including prolactinomas [38,
42]. Moreover, compared to other pituitary adenoma sub-
types, prolactinomas show particularly avid 11C-methio-
nine uptake [41, 43]. We have therefore reviewed our
recent experience with Met-PET coregistered with volu-
metric MRI (Met-PET/MRCR) in patients with suspected
microprolactinomas who are being considered for pituitary
surgery due to intolerance or resistance to dopamine ago-
nist therapy, but in whom standard clinical MRI has not
conclusively identified a discrete lesion. Abstract Here, we show
that functional imaging can confirm or refute the suspected
site of a microprolactinoma queried on clinical MRI and
reveal the location of an adenoma when MRI is negative. Patients Thirteen patients with microprolactinomas were referred to
our tertiary center for consideration of surgery, because of
dopamine agonist intolerance (n = 11) or resistance (n = 2),
between April 2016 and March 2020. In all cases, the diag-
nosis of a prolactinoma was originally based on typical
symptoms (e.g. galactorrhea and/or gonadal dysfunction)
in the presence of confirmed raised serum prolactin levels
(females > 29 ng/ml, males > 18 ng/ml). Conventional pitui-
tary MRI (T1 spin echo with and without intravenous con-
trast and, where available, T2 fast spin echo) was deemed
equivocal (one or more possible abnormalities identified, but
low confidence to confirm site of the adenoma) or negative
(no abnormality seen). Each patient underwent Met-PET and
volumetric MRI with co-registration to yield hybrid images
(Met-PET/MRCR) as described in the following sections. The study received institutional approval (CUH QSIS 2020:
3039). Introduction Prolactinomas are the most common functioning pitui-
tary adenomas [1]. Microprolactinomas typically mani-
fest with galactorrhea and hypogonadism [2, 3], which can
have significant adverse effects on quality of life [4]. The
mainstay of treatment remains medical therapy with dopa-
mine agonists [5]. These are generally well tolerated [6],
but may cause side effects including postural dizziness,
daytime somnolence, gastro-intestinal upset and cardiac
valvular fibrosis [7–9], although risk of the latter when
using low dosages (as is typically required for prolacti-
nomas) is still debated [10]. In recent years, attention has
also focussed on potential psychological adverse effects,
including impulse control disorders (ICDs), which have
been reported in 8–24% of patients with prolactinomas
receiving treatment with dopamine agonists [11–15], and
which can have devastating consequences for patients and
their families [16].f When adverse effects prevent a successful treatment
trial (either with respect to drug dosage and/or duration
of therapy), patients are considered intolerant to dopa-
mine agonist therapy [3]. This should be distinguished
from dopamine agonist resistance, which is preferred
when there is failure to normalize serum prolactin and/or
achieve significant tumor shrinkage (in macroprolactino-
mas) despite good tolerance and concordance with stand-
ard clinical dosages [17, 18]. For patients with intolerance
or resistance to medical therapy, transsphenoidal surgery
(TSS) is an alternative treatment option [5], with several
recent reports suggesting a higher long-term remission
rate [19–24] and improved cost-effectiveness compared
with dopamine agonist therapy [25, 26]. As evidence for
the efficacy and safety of transsphenoidal surgery (TSS)
accrues, there is increasing discussion about the earlier
deployment of surgery for selected cases [27, 28]. How-
ever, even in experienced hands, TSS may be complicated
by cerebrospinal fluid leakage and new-onset hypopitui-
tarism (including diabetes insipidus) [19]. Careful preop-
erative appraisal must therefore balance the probability
of achieving surgical cure with these risks. High qual-
ity magnetic resonance imaging (MRI) of the sella and
parasellar regions is central to effective decision-making
and may provide important information regarding the
likelihood of achieving complete surgical resection [29]. Nonetheless, it is not always possible to reliably localize
the causative microadenoma, and MRI findings may be
considered equivocal or negative even prior to a trial of
medical therapy [30, 31]. Standard and 3D gradient echo MRI MR imaging was performed on clinical 1.5 T or 3 T sys-
tems (GE Healthcare, Waukesha, WI, USA) using a circu-
larly polarised head coil. Coronal T1 spin echo (SE) images
were obtained before and after intravenous injection of
0.1 mmol/kg gadobutrol. A fast spoiled gradient recalled
echo (FSPGR) acquisition sequence was performed to opti-
mise co-registration with the PET-CT dataset (Met-PET/
MRCR). In brief, sagittal T1-weighted FSPGR images [TR
(repetition time) 11.5 ms, TE (echo time) 4.2 ms, slice thick-
ness 1 mm, 0 mm gap, 256 × 256 matrix] of the whole head
were obtained following intravenous injection of 0.1 mmol/
kg gadobutrol. Image processing and analysis The PET tracer, L-[methyl-11C]-methionine, was synthe-
sised in compliance with good manufacturing practice
using a captive solvent in loop methylation method without
preparative HPLC, adapted from methods published pre-
viously [45–47]. Briefly, [11C]CO2 was produced using a
PETtrace cyclotron (GE Healthcare, Milwaukee, WI, USA)
via the 14 N(p,훼)11C reaction before conversion to [11C]MeI
in the MeI MicroLab (GE Healthcare). This was then trans-
ferred to the HPLC loop of a modified TracerLabFXC (GE
Healthcare) synthesiser containing an L-homocysteine pre-
cursor solution (0.5 M aqueous NaOH solution in ethanol). 11C-methionine was produced in yields averaging 376 MBq
with a radiochemical purity of > 96% and specific activity
between 263 and 452.5 MBq. Image processing was performed using open source soft-
ware 3D Slicer [48] (version 4.10.2, 05–2019). PET images
(GE SharpIR reconstruction) were prepared for visualiza-
tion by creating ratio PET (SUVr) images. SUVr images
were created by dividing each voxel in the image by the
mean value found in a region of interest (ROI) positioned in
the subject’s cerebellum. Each subject’s SUVr images were
displayed with identical colour scales (ColdToHotRainbow),
colour ranges (1.0–4.0), and threshold levels to remove low
level background uptake (< 1.0). SUVr images were regis-
tered with volumetric MRI images (FSPGR sequence) using
rigid registration with 6 degrees of freedom, a maximum
number of iterations of 1500 and a sample ratio of 0.01. Following registration, the SUVr images were overlaid on
the MRI images. Clinical care Molecular (functional) imaging using positron emis-
sion tomography-computed tomography (PET-CT) can
aid localization of de novo, residual or recurrent pituitary Patients were managed according to local approved pitui-
tary care pathways, which are consistent with international
clinical guidelines [5]. Pituitary function tests [including 3 3 Pituitary (2022) 25:573–586 575 prolactin, cortisol, free thyroxine (FT4), thyroid stimulat-
ing hormone (TSH), luteinizing hormone (LH), follicle
stimulating hormone (FSH), estrogen or testosterone, and
insulin-like growth factor 1 (IGF-1)] were performed on
serum samples collected between 8 and 9AM. All biochemi-
cal measurements (Siemens Medical Solutions Diagnostics
Ltd.) were performed in a Clinical Pathology Accreditation
Ltd. laboratory (CPA) with relevant internal and external
quality assurance as required by the CPA. Each patient pro-
vided informed consent for Met-PET. All patients remained
off dopamine agonist therapy for at least one month prior
to performing functional imaging to minimise the risk of
a false negative scan due to residual suppression of tumor
activity. Treatment decisions were made on a case-by-case
basis, considering patient preference, after discussion by
a specialist pituitary multidisciplinary team consisting of
pituitary neurosurgeons, endocrinologists, otolaryngolo-
gists, radiation oncologist, neuropathologist, and neurora-
diologists, who had full access to the Met-PET/MRCR scans
to inform clinical decision-making. Transsphenoidal pitui-
tary surgery or radiotherapy were performed as previously
described [34, 44]. 3D iterative reconstruction algorithms (three iterations, 24
subsets, 2 mm Gaussian post-filter) incorporating ToF and
resolution recovery software (VUE Point FX and Sharp IR)
to a 3.27 mm slice thickness. CT images were reconstructed
at 1.25 mm slice thickness. Met-PET studies were indepen-
dently reviewed by nuclear medicine physicians with exper-
tise in PET-CT on the Xeleris workstation (GE Healthcare,
Amersham, Buckinghamshire, UK). 11C‑methionine PET‑CT imaging Images were acquired on a GE Discovery 690 PET-CT scan-
ner (GE Healthcare). All patients fasted for 4 h before PET-
CT scanning. An intravenous injection of 264–423 MBq of
L-[methyl-11C]-methionine was given prior to each scan. The uptake time for PET-CT was standardized at 20 min. An attenuation correction (low dose) CT was performed
(140 kV, 220 mA, 0.5 s rotation, and 0.984 mm pitch)
followed by a single bed position PET acquisition of the
head. Time-of-flight (ToF) PET data were acquired for a
total acquisition time of twenty minutes. PET images were
reconstructed with CT attenuation correction using fully Results Thirteen patients, all of reproductive age, were included in
the study [twelve women, one man; mean age at time of
Met-PET scan 34 years (range 20–45)]. Eleven patients were
referred for Met-PET because of intolerance to DA therapy,
and two because of DA resistance (Table 1). All had expe-
rienced several years (in some instances > 10 years) of sub-
optimal disease control (Fig. 1). Results In seven subjects (Cases 2,
5, 7, 8, 11, 12, 13), findings on pituitary MRI at the time of 1 Pituitary (2022) 25:573–586 576 576
Pituitary (2022) 25:573 586
1 3
Table 1 Clinical, biochemical and radiological features at initial presentation, at the time of Met-PET, and following further treatment
Case
Sex
Baseline biochemistry
MRI findings
at diagnosis
Previous
treatment
DA side
effects or
resistance
MRI findings
following
previous
treatment
Met-PET/
MRCR find-
ings
PRL at time
of PET (ng/
ml) *
Further treat-
ment
Biochemistry following
further treatment
Latest
PRL (ng/
ml)*
PRL (ng/ml)*
Pituitary
deficits
PRL (ng/ml)* Pituitary
deficits
1
F
203
G
Infundibulum
central;
possible
right-sided
lesion
C, B, Q
Low mood
Infundibulum
central;
possible
bilateral
non-
enhancing
lesions
Focal high
tracer
uptake
adjacent to
left CS
107
TSS
10
None
24
2
F
67
G
Subtle left
infun-
dibular
deviation;
possible
bilateral
non-enhanc-
ing lesions
C
Low mood
Subtle left
infun-
dibular
deviation;
possible
bilateral
non-enhanc-
ing lesions
Focal high
tracer
uptake
within right
sella
74
TSS
5
None
5
3
F
172
G
Possible right
infun-
dibular
deviation;
no discrete
lesion
C, B, Q
Low mood,
headache
Right infun-
dibular
deviation;
no discrete
lesion
Focal high
tracer
uptake just
to left of
infun-
dibulum
inferiorly
73
TSS
15
None
8
4
F
48
G
Unavailable
C, Q
Low mood
Infundibulum
central;
possible
right sided
lesion with
subtle
depression
of sella
floor
Focal high
tracer
uptake
within right
sella
49
TSS
3
None
6
5
F
109
None
Infundibulum
central; no
discrete
lesion
C, A**
Low mood
Infundibulum
central; no
discrete
lesion
Focal high
tracer
uptake
within right
sella
100
Awaiting
TSS
NA
NA
100
6
M
191
G
Infundibulum
central;
possible
left-sided
lesion
C, B, Q
Aggression,
increased
libido
Infundibulum
central; no
discrete
lesion
Focal high
tracer
uptake
within left
sella
61
Nil
NA
G
46 Pituitary (2022) 25:573–586 577 )
Baseline biochemistry
MRI findings
at diagnosis
Previous
treatment
DA side
effects or
resistance
MRI findings
following
previous
treatment
Met-PET/
MRCR find-
ings
PRL at time
of PET (ng/
ml) *
Further treat-
ment
Biochemistry following
further treatment
Latest
PRL (ng/
ml)*
PRL (ng/ml)*
Pituitary
deficits
PRL (ng/ml)* Pituitary
deficits
52
None
Infundibulum
central;
minor
depression
of left sella
floor; no
discrete
lesion
C, B, Q
Low mood
Infundibulum
central;
minor
depression
of left sella
floor; no
discrete
lesion
Focal high
tracer
uptake
within sella
inferiorly to
the left of
midline
49
Awaiting
TSS
NA
N/A
49
56
G
Infundibulum
central;
minor
inferior
depression
of right
sella floor;
possible
right micro-
adenoma
C, Q
Nausea
Infundibulum
central;
minor
inferior
depression
of right
sella floor;
possible
right micro-
adenoma
Focal high
tracer
uptake
within
right sella
inferiorly
36
TSS
6
None
6
75
G
Infundibulum
central; no
discrete
lesion
C
Headache
Infundibulum
central;
possible
area of
reduced
enhance-
ment in left
side of sella
Focal high
tracer
uptake
within left
sella
46
C
29
None
35
470
G
Unavailable;
presumed
left-sided
adenoma
(site of
previous
TSS)
C, TSS
Raynaud
phenom-
enon
Post-
operative
changes;
no definite
residual/
recurrence
Focal high
tracer
uptake
within left
CS
82
SRS
86
None
40
65
G
Infundibulum
central;
possible
bilateral
non-
enhancing
lesions
C
Nausea,
increased
libido
Infundibulum
central;
possible
bilateral
non-
enhancing
lesions
Focal high
tracer
uptake
within right
sella
55
C
15
None
8 3 Pituitary (2022) 25:573–586 578 ole for a concomitant mental health condition
riptine, BP blood pressure, C cabergoline, CS cavernous sinus, DA dopamine agonist, F female, G hypogonadism, M male, NA not available, PRL prolactin, Q quina-
adiosurgery, TSS transsphenoidal surgery (endoscopic) 1 3
Case
Sex
Baseline biochemistry
MRI findings
at diagnosis
Previous
treatment
DA side
effects or
resistance
MRI findings
following
previous
treatment
Met-PET/
MRCR find-
ings
PRL at time
of PET (ng/
ml) *
Further treat-
ment
Biochemistry following
further treatment
Latest
PRL (ng/
ml)*
PRL (ng/ml)*
Pituitary
deficits
PRL (ng/ml)* Pituitary
deficits
12
F
120
G
Possible
subtle left
Infun-
dibular
deviation;
no discrete
lesion seen
C
Resistance
Possible
subtle left
Infun-
dibular
deviation;
no discrete
lesion seen
Focal high
tracer
uptake
within left
sella
111
Nil
NA
NA
35
13
F
84
G
Possible
subtle left
Infundibu-
lar devia-
tion with
right-sided
lesion in
superior
aspect of
gland
C
Resistance
Possible
subtle left
Infundibu-
lar devia-
tion with
right-sided
lesion in
superior
aspect of
gland
Focal high
tracer
uptake
within right
sella
39
Awaiting
TSS
NA
NA
37
*Prolactin references ranges: female (3–29 ng/ml), male (2–18 ng/ml)
**Treated with aripiprazole for a concomitant mental health condition
A aripiprazole, B bromocriptine, BP blood pressure, C cabergoline, CS cavernous sinus, DA dopamine agonist, F female, G hypogonadism, M male, NA not available, PRL prolactin, Q quina-
golide, SRS stereotactic radiosurgery, TSS transsphenoidal surgery (endoscopic) Pituitary (2022) 25:573–586 579 Fig. Results 1 Schematic representation of the clinical courses for each of the
thirteen patients prior to and following Met-PET. DA dopamine ago-
nist, Met-PET/MRCR 11C-methionine PET coregistered with volumet-
ric (FSPGR) MRI, PET Positron Emission Tomography, PRL prolac-
tin, SRS stereotactic radiosurgery, TSS transsphenoidal surgery, ULN
upper limit of normal Fig. 1 Schematic representation of the clinical courses for each of the
thirteen patients prior to and following Met-PET. DA dopamine ago-
nist, Met-PET/MRCR 11C-methionine PET coregistered with volumet- ric (FSPGR) MRI, PET Positron Emission Tomography, PRL prolac-
tin, SRS stereotactic radiosurgery, TSS transsphenoidal surgery, ULN
upper limit of normal effects, with one achieving a normal serum prolactin level,
while two patients have elected to remain off all treatment
with ongoing hyperprolactinemia (Fig. 1).i referral to our service were similar to those reported at initial
presentation (Table 1). In three patients initial MRI appear-
ances were either less informative regarding the suspected
site of the adenoma (Cases 3, 9) or incorrectly identified a
possible abnormality on the contralateral side to where the
adenoma was subsequently resected (Case 1) (Table 1). In
a single patient (Case 6), MRI at diagnosis identified a pos-
sible adenoma that was not readily visualized on repeat MRI
at the time of referral for Met-PET (Table 1). In two patients
(Cases 4, 10), initial imaging was unavailable for review. Met-PET identified a focus of increased tracer uptake in all
thirteen cases (Figs. 2–4 and Supplementary Fig. 1). Five
patients underwent uncomplicated PET-guided TSS with
intra-operative and, in four cases, histological confirmation
of PET findings. All had subsequent complete remission of
hyperprolactinemia, which has been maintained off medical
treatment, and all have normal pituitary function (Figs. 1–3). Three patients are awaiting surgery. One patient was deemed
to have unresectable lateral disease, and therefore received
stereotactic radiosurgery (SRS), with subsequent near nor-
malization of hyperprolactinemia (Table 1; Figs. 1 and 4). Four patients had a clear abnormal focus of tracer uptake
on Met-PET but chose not to undergo surgical intervention
after further consideration of the risks and benefits of sur-
gery (Table 1; Supplementary Fig. 1). Two of these patients
have returned to cabergoline therapy despite ongoing side referral to our service were similar to those reported at initial
presentation (Table 1). Results In three patients initial MRI appear-
ances were either less informative regarding the suspected
site of the adenoma (Cases 3, 9) or incorrectly identified a
possible abnormality on the contralateral side to where the
adenoma was subsequently resected (Case 1) (Table 1). In
a single patient (Case 6), MRI at diagnosis identified a pos-
sible adenoma that was not readily visualized on repeat MRI
at the time of referral for Met-PET (Table 1). In two patients
(Cases 4, 10), initial imaging was unavailable for review. Met-PET identified a focus of increased tracer uptake in all
thirteen cases (Figs. 2–4 and Supplementary Fig. 1). Five
patients underwent uncomplicated PET-guided TSS with
intra-operative and, in four cases, histological confirmation
of PET findings. All had subsequent complete remission of
hyperprolactinemia, which has been maintained off medical
treatment, and all have normal pituitary function (Figs. 1–3). Three patients are awaiting surgery. One patient was deemed
to have unresectable lateral disease, and therefore received
stereotactic radiosurgery (SRS), with subsequent near nor-
malization of hyperprolactinemia (Table 1; Figs. 1 and 4). Four patients had a clear abnormal focus of tracer uptake
on Met-PET but chose not to undergo surgical intervention
after further consideration of the risks and benefits of sur-
gery (Table 1; Supplementary Fig. 1). Two of these patients
have returned to cabergoline therapy despite ongoing side The five patients who underwent selective adenomectomy
and the single patient who underwent SRS, guided by the
findings on Met-PET, are presented in more detail below. Case 1 (Table 1 and Figs. 1–2) A young woman presented with secondary amenorrhea
and was found to have significant hyperprolactinemia
(serum prolactin 203 ng/ml). Initial and subsequent
MRI did not identify a clear adenoma, although a pos-
sible right-sided lesion was queried. Over the course of
15 years, several DAs were trialled, including bromocrip-
tine (maximum tolerated dosage 5 mg/day), cabergoline
(0.5 mg/week), and quinagolide (75 μg/day). Normopro-
lactinaemia was never achieved, and the patient experi-
enced recurrent episodes of low mood while on treat-
ment (Fig. 1). Repeat T1 SE MRI remained equivocal,
highlighting possible abnormalities on both sides of the
gland (Fig. 2). Met-PET identified a focus of intense
11C-methionine uptake in the left lateral sella (Fig. 2). The patient proceeded to endoscopic TSS, with selective
resection of a left-sided tumour which was histologically 1 3 580 Pituitary (2022) 25:573–586 Fig. 2 MRI and Met-PET findings with 3D reconstruction of the
sella and parasellar regions in case 1. A–B Pre- and post-contrast
coronal T1 SE MRI demonstrates equivocal appearances, with two
possible areas of reduced enhancement (arrows). C Met-PET/MRCR
reveals avid focal tracer uptake in the left side of the gland adjacent
to the cavernous sinus (arrow). D–I 3D reconstructed images, com-
bining PET, CT and FSPGR MRI datasets, allows appreciation of
the location of the tumor (yellow) with respect to the normal gland
(turquoise) and proximity of the tumor to key adjacent structures
including the intracavernous cartoid artery (red). At transsphenoi-
dal surgery, a microadenoma abutting the left cavernous sinus was
resected and confirmed histologically to be a prolactinoma. Postop-
eratively the patient remains normoprolactinemic and eupituitary. CT
computed tomography, FSPGR fast spoiled gradient recalled echo,
Gad gadolinium, MRI magnetic resonance imaging, Met-PET/MRCR
11C-methionine PET-CT coregistered with volumetric (FSPGR) MRI,
PET positron emission tomography, SE spin echo Fig. 2 MRI and Met-PET findings with 3D reconstruction of the
sella and parasellar regions in case 1. A–B Pre- and post-contrast
coronal T1 SE MRI demonstrates equivocal appearances, with two
possible areas of reduced enhancement (arrows). C Met-PET/MRCR
reveals avid focal tracer uptake in the left side of the gland adjacent
to the cavernous sinus (arrow). D–I 3D reconstructed images, com-
bining PET, CT and FSPGR MRI datasets, allows appreciation of
the location of the tumor (yellow) with respect to the normal gland
(turquoise) and proximity of the tumor to key adjacent structures including the intracavernous cartoid artery (red). Case 1 (Table 1 and Figs. 1–2) At transsphenoi-
dal surgery, a microadenoma abutting the left cavernous sinus was
resected and confirmed histologically to be a prolactinoma. Postop-
eratively the patient remains normoprolactinemic and eupituitary. CT
computed tomography, FSPGR fast spoiled gradient recalled echo,
Gad gadolinium, MRI magnetic resonance imaging, Met-PET/MRCR
11C-methionine PET-CT coregistered with volumetric (FSPGR) MRI,
PET positron emission tomography, SE spin echo Case 3 (Table 1 and Fig. 3) confirmed as a lactotroph pituitary adenoma. She remains
in remission off all treatment at 3 years follow-up, with
otherwise normal pituitary function. A young woman was found to have a raised serum prol-
actin level (172 ng/ml) during investigation for secondary
amenorrhea. A diagnosis of a presumed microprolacti-
noma was made, although T1 gadolinium-enhanced SE
MRI did not identify a discrete lesion. Trials of cabergo-
line (0.5 mg/week), bromocriptine (10 mg/day) and quina-
golide (150 µg/day) each allowed restoration of normopro-
lactinemia, but all resulted in intolerable side effects with
low mood and headaches. Repeat T1 gadolinium-enhanced
SE MRI showed subtle infundibular deviation to the right
but no discrete lesion (Fig. 3). Met-PET revealed a focus
of high tracer uptake inferiorly and just to the left of mid-
line (Fig. 3), which corresponded with a small area of
abnormal tissue at TSS. Although histology was unable
to confirm an adenoma (insufficient sample), immediately
following surgery the patient’s serum prolactin was nor-
mal, and she remains in remission 2 years after surgery
with no pituitary hormone deficits. 3 Case 2 (Table 1 and Fig. 3) A young woman developed secondary amenorrhea,
bilateral galactorrhea, and low libido. Serum prolac-
tin was raised at 67 ng/ml. T1 gadolinium-enhanced
SE and FSPGR MRI failed to demonstrate a convinc-
ing adenoma, although possible focal reduced contrast
enhancement was queried bilaterally (Fig. 3). Cabergo-
line therapy (maximum tolerated dosage 0.75 mg/week)
was associated with depressive symptoms and failure to
normalize serum prolactin (Fig. 1). Met-PET revealed a
focus of intense 11C-methionine uptake in the right side
of the pituitary gland. The patient underwent endoscopic
TSS with selective resection of a right-sided lactotroph
adenoma (with confirmatory histology). She remains in
remission 3 years later, with normal pituitary function. 3 581 Pituitary (2022) 25:573–586 Fig. 3 MRI and Met-PET
findings in cases 2, 3, 4 and
8. A–H Pre- and post-contrast
coronal T1 SE MRI show
equivocal appearances in four
patients, identifying either no
abnormality or possible single
or multiple lesions (arrows). I–L In contrast, in all four
subjects Met-PET/MRCR
demonstrates a single focus
of intense tracer uptake which
was subsequently confirmed at
transsphenoidal surgery to be
the site of a microprolactinoma. Postoperatively, all patients
remain normoprolactinemic
and eupituitary. FSPGR fast
spoiled gradient recalled echo,
Gad gadolinium, MRI magnetic
resonance imaging, Met-PET/
MRCR 11C-methionine PET-CT
coregistered with volumetric
(FSPGR) or SE MRI, PET
positron emission tomography,
SE spin echo Fig. 3 MRI and Met-PET
findings in cases 2, 3, 4 and
8. A–H Pre- and post-contrast
coronal T1 SE MRI show
equivocal appearances in four
patients, identifying either no
abnormality or possible single
or multiple lesions (arrows). I–L In contrast, in all four
subjects Met-PET/MRCR
demonstrates a single focus
of intense tracer uptake which
was subsequently confirmed at
transsphenoidal surgery to be
the site of a microprolactinoma. Postoperatively, all patients
remain normoprolactinemic
and eupituitary. FSPGR fast
spoiled gradient recalled echo,
Gad gadolinium, MRI magnetic
resonance imaging, Met-PET/
MRCR 11C-methionine PET-CT
coregistered with volumetric
(FSPGR) or SE MRI, PET
positron emission tomography,
SE spin echo Case 4 (Table 1 and Fig. 3) A–B Post-
contrast coronal T1 SE and FSPGR MRI demonstrate indeterminate
appearances in a patient who had previously undergone transsphenoi-
dal surgery for a left-sided microprolactinoma. C Axial FSPGR MRI
shows possible recurrent tumor in the left cavernous sinus (yellow
arrow). D–E Coronal and axial Met-PET/MRCR confirm avid tracer
uptake at the site of the suspected recurrence (yellow arrow); tracer Fig. 4 PET–guided stereotactic radiosurgery in case 10. A–B Post-
contrast coronal T1 SE and FSPGR MRI demonstrate indeterminate
appearances in a patient who had previously undergone transsphenoi-
dal surgery for a left-sided microprolactinoma. C Axial FSPGR MRI
shows possible recurrent tumor in the left cavernous sinus (yellow
arrow). D–E Coronal and axial Met-PET/MRCR confirm avid tracer
uptake at the site of the suspected recurrence (yellow arrow); tracer
uptake within the remaining normal gland is also seen (white arrow). F Treatment plan for PET-guided SRS. Three years later serum prol-
actin was near-normalized (1.4 × ULN). FSPGR fast spoiled gradient
recalled echo, Gad gadolinium, MRI magnetic resonance imaging,
Met-PET/MRCR 11C-methionine PET-CT coregistered with volumet-
ric (FSPGR) MRI, PET positron emission tomography, PTV Planning
Target Volume, SE spin echo, ULN upper limit of normal uptake within the remaining normal gland is also seen (white arrow). F Treatment plan for PET-guided SRS. Three years later serum prol-
actin was near-normalized (1.4 × ULN). FSPGR fast spoiled gradient
recalled echo, Gad gadolinium, MRI magnetic resonance imaging,
Met-PET/MRCR 11C-methionine PET-CT coregistered with volumet-
ric (FSPGR) MRI, PET positron emission tomography, PTV Planning
Target Volume, SE spin echo, ULN upper limit of normal Fig. 4 PET–guided stereotactic radiosurgery in case 10. A–B Post-
contrast coronal T1 SE and FSPGR MRI demonstrate indeterminate
appearances in a patient who had previously undergone transsphenoi-
dal surgery for a left-sided microprolactinoma. C Axial FSPGR MRI
shows possible recurrent tumor in the left cavernous sinus (yellow
arrow). D–E Coronal and axial Met-PET/MRCR confirm avid tracer
uptake at the site of the suspected recurrence (yellow arrow); tracer uptake within the remaining normal gland is also seen (white arrow). F Treatment plan for PET-guided SRS. Three years later serum prol-
actin was near-normalized (1.4 × ULN). FSPGR fast spoiled gradient
recalled echo, Gad gadolinium, MRI magnetic resonance imaging,
Met-PET/MRCR 11C-methionine PET-CT coregistered with volumet-
ric (FSPGR) MRI, PET positron emission tomography, PTV Planning
Target Volume, SE spin echo, ULN upper limit of normal Case 4 (Table 1 and Fig. 3) A young woman developed oligomenorrhea and bilateral
galactorrhea. Serum prolactin was raised at 56 ng/ml. Ini-
tial T1 gadolinium-enhanced SE MRI was considered sug-
gestive of a possible right-sided pituitary microadenoma,
with subtle depression of the sella floor. Cabergoline
(0.5 mg/week) was initiated; however, she developed sig-
nificant nausea, which did not improve despite changing
to quinagolide (75 μg/day). Her symptoms recurred on
subsequent rechallenging with dopamine agonist therapy
and surgery was therefore considered. Repeat T1 SE MRI
identified a suspected lesion in the right side of the pitui-
tary gland (Fig. 3). The possibility of proceeding direct to
surgery based on the MRI findings alone was considered
but, following discussion with the patient, Met-PET was
performed to confirm a functioning lesion at this loca-
tion. This demonstrated focal increased 11C-methionine
uptake in the anterior-inferior aspect of the pituitary fossa,
concordant with the site suspected on MRI (Fig. 3). The
patient underwent PET-guided TSS, with histological con-
firmation of a prolactinoma at this location. She remains in
remission postoperatively (at 12 months), with otherwise
normal pituitary function. A young woman with secondary amenorrhea was found
to have mild hyperprolactinemia (serum prolactin 48 ng/
ml). The findings from initial T1 gadolinium-enhanced SE
MRI were unavailable for review. The patient was com-
menced on cabergoline but was unable to tolerate even the
lowest dosage (0.25 mg/week) due to mood disturbance. Thereafter, quinagolide (75 µg/day) was tried but resulted
in return of depressive symptoms and the patient elected
to discontinue DA therapy. Several years later, she sought
further advice about possible surgical treatment of her
prolactinoma given her persistent symptoms and ongoing
hyperprolactinemia. Repeat T1 gadolinium-enhanced SE
MRI identified a possible right-sided pituitary microade-
noma (Fig. 3). Whilst surgery could have been undertaken
based on these MRI findings alone, after discussion with
the patient molecular imaging was performed to increase
confidence that the suspected lesion was indeed func-
tioning. Met-PET showed intense 11C-methionine tracer
uptake within the right side of the sella (Fig. 3). At TSS, a
right-sided adenoma was resected, with histological con-
firmation of a lactotroph adenoma. Thereafter, serum pro-
lactin levels have normalized, with restoration of regular
menses (and maintained for > 12 months). 1 3 Pituitary (2022) 25:573–586 582 Fig. 4 PET–guided stereotactic radiosurgery in case 10. Discussion A young woman was found to have hyperprolactinemia
(serum prolactin 470 ng/ml) while being investigated
for secondary amenorrhea. The findings of MRI at ini-
tial presentation were not available. She was treated with
cabergoline in increasing dosages (up to 4 mg/week), with
varying control of hyperprolactinemia. During this time,
the patient developed marked Raynaud phenomenon and
dopamine agonist therapy was discontinued. She then pro-
ceeded to TSS, and a left-sided lactotroph microadenoma
was resected (confirmed histologically). Following a short
period of normoprolactinemia, her symptoms returned,
and serum prolactin was again elevated (82 ng/ml). How-
ever, T1 gadolinium-enhanced SE MRI could not reliably
identify recurrent adenoma tissue (Fig. 4). Unexpectedly,
Met-PET revealed a small focus of avid 11C-methionine
uptake within the left cavernous sinus (Fig. 4). A small
hypointense abnormality could be appreciated at exactly
the same location on axial FSPGR MRI (Fig. 4). As the
recurrent tumour was considered inoperable, the patient
underwent SRS. Prolactin levels have decreased to 40 ng/
ml, at 3 years following SRS, with no new pituitary
deficits. We report our initial experience with Met-PET/MRCR in
13 patients with microprolactinomas and dopamine agonist
intolerance or resistance, in whom standard clinical MRI
was considered indeterminate or negative. In all 13 cases,
Met-PET demonstrated a focus of increased (often intense)
tracer uptake (Figs. 2–4 and Supplementary Fig. 1). In some
instances, this correlated with an area that had been identi-
fied on MRI as possibly in keeping with an adenoma, but in
other subjects Met-PET did not support MRI findings and/
or revealed a previously undisclosed abnormality (Table 1;
Figs. 1–4 and Supplementary Fig. 1). In all five patients
who proceeded to surgery, complete and sustained biochemi-
cal remission was achieved, often for the first time in many
years, with histology confirming a lactotroph adenoma in
four cases. In the fifth patient, an obvious abnormality was
found at surgery at the site identified on Met-PET, but his-
tology was not confirmatory of a prolactinoma; however,
this likely reflected a small tumor with total resection as
evidenced by restoration and maintenance of normal serum
prolactin following surgery—analogous to surgical/histolog-
ical findings in some corticotroph tumors. In the patient with
recurrent hyperprolactinemia following previous TSS (Case 1 3 3 Pituitary (2022) 25:573–586 583 10), in whom recurrent tumor was localized within the left
cavernous sinus, SRS was followed by a progressive fall in
serum prolactin to near normal levels (1.4 × ULN) (Table 1
and Figs. 1 and 4). Importantly, in all patients undergo-
ing surgery, normal pituitary function was maintained or
restored, and there were no other surgical complications. undergoing surgery because of resistance or intolerance to
dopamine agonists, or patient preference, and reported that
38% achieved sustained remission without further treatment
(66% of microprolactinomas, 22% of macroprolactinomas),
while 62% achieved remission with adjunctive dopamine
agonist therapy [64]. ,
g
p
Traditonally, dopamine agonist therapy has been consid-
ered the cornerstone of management of patients with prolac-
tinoma [5, 49]. In particular, cabergoline is recommended as
it has superior efficacy in achieving normoprolactinemia and
tumour shrinkage, when compared with bromocriptine and
quinagolide. However, two important factors merit consider-
ation before embarking on medical therapy: (1) the potential
need for long-term treatment and (2) possible adverse effects
of dopamine agonist therapy. With respect to treatment dura-
tion, two recent systematic reviews concluded that following
withdrawal of medical therapy, which is usually undertaken
after two years of treatment, only approximately one-third
of patients will achieve sustained remission [50, 51]. As a
result, many patients require long-term (even > 10 years)
treatment [16]. Although dopamine agonists are generally
considered safe, a longer duration of treatment means that
there is an extended exposure window in which the patient
may experience side effects, and which may have particular
relevance, for example, when considering the risk of car-
diac valvular fibrosis [8, 10]. In addition, in recent years,
concerns have surfaced regarding the possible adverse psy-
chological effects, and in particular the previously unrecog-
nized high prevalence of impulse control disorders (ICDs),
in those treated with dopamine agonists [11–15, 52], which
were not fully appreciated when earlier guidelines were pub-
lished [5]. Accordingly, recent guidelines acknowledge that
surgery can be considered as a first line treatment option
for microprolactinomas where complete resection is deemed
possible following specialist neurosurgical evaluation [53]. As the majority of prolactinomas are microadenomas
[49], selective and complete adenomectomy, which deliv-
ers long-term remission without causing additional pituitary
deficits (and where possible correcting exisiting deficits),
should be the goal of transsphenoidal surgery. 3 This is par-
ticularly important for young women considering repro-
duction, who are the group most commonly affected by
microprolactinomas. To facilitate selective adenomectomy,
accurate preoperative localisation of the adenoma is impor-
tant, to minimise the need for more extensive exploration of
the gland, and thereby potentially reducing the risk of new
pituitary deficiencies or other (e.g. neurovascular) complica-
tions. Nonetheless, even with advances in MR imaging, the
detection of microadenomas, especially < 3 mm in maximum
diameter, remains challenging [65]. Additionally, the find-
ing of an incidentaloma may confound management [66]. In
these situations, Met-PET may offer an additional route to
confirming/revealing the tumor, as exemplified by the cases
reported in our cohort, and also in other pituitary tumor sub-
types [32, 33]. In this way, Met-PET complements routine
clinical MRI to improve the accurate localization of small
functioning tumours, and thereby enable patients who might
otherwise not be considered suitable candidates for surgery
or radiotherapy to progress to TSS or SRS. Our findings are also consistent with previous reports that
indicate microprolactinomas are particularly 11C-methio-
nine-avid [41, 43]. Met-PET may therefore allow more
reliable distinction between true microprolactinomas and
coincidental small non-secretory adenomas, although for-
mal studies would be required to confirm this. It is also
likely that some patients with so-called “idiopathic hyper-
prolactinemia” harbor microadenomas that are beyond the
resolution of current standard clinical MRI, and these may
be identified by Met-PET. p
g p
g
In support of this, several groups have reported on the
effectiveness and safety of prolactinoma surgery [21–24,
29, 54–62]: after a follow-up of 13.5–102 months, overall
remission rates ranged from 26 to 92%, with most estimates
around 70%, although not all studies have provided clar-
ity on whether patients required ongoing dopamine agonist
therapy to achieve postoperative remission. Not surprisingly,
most studies have reported higher remission rates for micro-
prolactinomas compared to macroprolactinomas, and adeno-
mas that are enclosed within the gland may have a more
favourable outcome compared with adenomas located at the
lateral margins [29, 60]. These findings have been endorsed
in several systematic reviews and meta-analyses, which have
reported TSS to deliver superior clinical outcomes compared
to dopamine agonist therapy [19, 20, 63], with superior cost-
effectiveness, although the absence of any randomised trials
remains a major limitation [19]. Consent for publication All authors approved the final manuscript for
submission. Consent for publication All authors approved the final manuscript for
submission. Open Access This article is licensed under a Creative Commons Attri-
bution 4.0 International License, which permits use, sharing, adapta-
tion, distribution and reproduction in any medium or format, as long
as you give appropriate credit to the original author(s) and the source,
provide a link to the Creative Commons licence, and indicate if changes
were made. The images or other third party material in this article are
included in the article's Creative Commons licence, unless indicated
otherwise in a credit line to the material. If material is not included in
the article's Creative Commons licence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a
copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. In summary, when MRI appearances are indeterminate in
a patient with a microprolactinoma, it is logical for surgeons
and patients to be apprehensive about surgery, especially for
a condition where pharmacological therapy has traditionally
been considered as first line treatment. However, the find-
ings reported here indicate that Met-PET, a non-invasive
technique, can facilitate precise localization of microprol-
actinomas, including when MRI findings are inconclusive,
thereby enabling the surgeon to represent the benefits and
risks of surgery more accurately. Supplementary Information The online version contains supplemen-
tary material available at https://doi.org/10.1007/s11102-022-01229-9. Acknowledgements We are grateful to S Hader and L Li, from the
Radiopharmacy Unit of the Wolfson Brain Imaging Centre, University
of Cambridge, and V Warnes and H Mason from the PET-CT unit,
Addenbrooke’s Hospital, Cambridge for their support in performing
the 11C-methionine PET-CT scans. 5. Melmed S, Casanueva FF, Hoffman AR, Kleinberg DL, Montori
VM, Schlechte JA et al (2011) Diagnosis and treatment of hyper-
prolactinemia: an endocrine society clinical practice guideline. J
Clin Endocrinol Metab 96:273–288. https://doi.org/10.1210/jc.
2010-1692 6. Webster J, Piscitelli G, Polli A, Ferrari CI, Ismail I, Scanlon MF
(1995) A comparison of cabergoline and bromocriptine in the
treatment of hyperprolactinemic amenorrhea. ACOG Curr J Rev
8:24. https://doi.org/10.1056/nejm199410063311403 Author contributions All authors contributed to the article and
approved the submitted version. p
g
j
7. Schade R, Andersohn F, Suissa S, Haverkamp W, Garbe E (2007)
Dopamine agonists and the risk of cardiac-valve regurgitation. N
Engl J Med 356:29–38. https://doi.org/10.1056/nejmoa062222 Funding W Bashari, J MacFarlane, O Koulouri and M Gurnell are
supported by the NIHR Cambridge Biomedical Research Center
(BRC-1215–20014). 8. Stiles CE, Tetteh-Wayoe ET, Bestwick JP, Steeds RP, Drake WM
(2018) A meta-analysis of the prevalence of cardiac valvulopathy
in patients with hyperprolactinemia treated with cabergoline. J
Clin Endocrinol Metab 104:523–538. https://doi.org/10.1210/jc.
2018-01071 References 1. Karavitaki N (2012) Prevalence and incidence of pituitary adeno-
mas. Ann Endocrinol (Paris) 73:79–80. https://doi.org/10.1016/j.
ando.2012.03.039 2. Glezer A, Bronstein MD (2015) Prolactinomas. Endocrinol Metab
Clin North Am 44:71–78. https://doi.org/10.1016/j.ecl.2014.11.
003 3. Kars M, Dekkers OM, Pereira AM, Romijn JA (2010) Update in
prolactinomas. Neth J Med 68:104–112. https://doi.org/10.7599/
hmr.2012.32.4.192 4. Andela CD, Scharloo M, Pereira AM, Kaptein AA, Biermasz
NR (2015) Quality of life (QoL) impairments in patients with a
pituitary adenoma: a systematic review of QoL studies. Pituitary
18:752–776. https://doi.org/10.1007/s11102-015-0636-7f Supplementary Information The online version contains supplemen-
tary material available at https://doi.org/10.1007/s11102-022-01229-9. 3 Interestingly, one system-
atic review specifically investigated prolactinoma patients i
An important limitation of this study is the small sample
size. However, the cases reported here represent consecu-
tive patients referred to our tertiary center over a four-year
period and, importantly, all Met-PET scans demonstrated
unequivocal findings. Although outcomes following TSS
and SRS are only available for six patients, all demon-
strated clinical and biochemical responses that confirm the
accuracy of the PET. A further three patients are awaiting
surgery (delayed by the pandemic), and the remaining four
patients were all offered surgery. Accordingly, there was
no selection bias when referring for surgery, and it seems
unlikely that these patients would have fared less favora-
bly at surgery given the comparable Met-PET findings. 1 3 3 584 Pituitary (2022) 25:573–586 However, it will be important to reproduce our findings
in larger cohorts in a mutlicenter study. In addition, T2
MR sequences were not available in our patients, but may
have allowed the identification of some occult tumors as
previously reported [67, 68]. Accordingly, future studies
should also include a comparison of the performance of T2
MRI with Met-PET. Currently, the restricted availability
of 11C-methionine (with its short half-life of 20 min) is an
important limitation in making this technique more widely
available [32, 65], but several other centers in the UK and
Europe have recently established molecular imaging for
pituitary adenomas, including using related tracers [e.g. 18F-fluoroethyltyrosine (18F-FET)] and the establishment
of a small number of centers in each country that develop
appropriate expertise would be consistent with the broader
Pituitary Tumor Centre Of Excellence (PTCOE) model
[69]. Consent to participate All participants were appropriately consented
before any study procedures. Declarations Micko A, Vila G, Höftberger R, Knosp E, Wolfsberger S (2019)
Endoscopic transsphenoidal surgery of microprolactinomas: a
reappraisal of cure rate based on radiological criteria. Clin Neu-
rosurg 85:508–515. https://doi.org/10.1093/neuros/nyy385 14. Bancos I, Nannenga MR, Bostwick JM, Silber MH, Erickson D,
Nippoldt TB (2014) Impulse control disorders in patients with
dopamine agonist-treated prolactinomas and nonfunctioning
pituitary adenomas: a case-control study. Clin Endocrinol (Oxf)
80:863–868. https://doi.org/10.1111/cen.12375 g
p
g
yy
30. Bonneville J-F (2016) Magnetic resonance imaging of pituitary
tumors. Front Horm Res 45:97–120. https://doi.org/10.1159/
000442327 31. Bonneville J-F, Bonneville F, Cattin F (2005) Magnetic reso-
nance imaging of pituitary adenomas. Eur Radiol 15:543–8. https://doi.org/10.1007/s00330-004-2531-x 15. Martinkova J, Trejbalova L, Sasikova M, Benetin J, Valkovic P
(2011) Impulse control disorders associated with dopaminergic
medication in patients with pituitary adenomas. Clin Neurophar-
macol 34:179–181. https://doi.org/10.1097/WNF.0b013e3182
281b2f 32. Koulouri O, Kandasamy N, Hoole AC, Gillett D, Heard S, Powl-
son AS et al (2016) Successful treatment of residual pituitary
adenoma in persistent acromegaly following localisation by
11C-methionine PET co-registered with MRI. Eur J Endocrinol
175:485–498. https://doi.org/10.1530/EJE-16-0639 16. Noronha S, Stokes V, Karavitaki N, Grossman A (2016) Treat-
ing prolactinomas with dopamine agonists: always worth
the gamble? Endocrine 51:205–210. https://doi.org/10.1007/
s12020-015-0727-2 33. Koulouri O, Steuwe A, Gillett D, Hoole AC, Powlson AS, Don-
nelly NA et al (2015) A role for 11C-methionine PET imaging
in ACTH-dependent Cushing’s syndrome. Eur J Endocrinol
173:M107–M120. https://doi.org/10.1530/EJE-15-0616 17. Gillam MP, Molitch ME, Lombardi G, Colao A (2006) Advances
in the treatment of prolactinomas. Endocr Rev 27:485–534. https://doi.org/10.1210/er.2005-9998 34. Bashari WA, Senanayake R, Koulouri O, Gillett D, MacFarlane
J, Powlson AS et al (2020) PET-guided repeat transsphenoidal
surgery for previously deemed unresectable lateral disease in
acromegaly. Neurosurg Focus 48:E8. https://doi.org/10.3171/
2020.3.FOCUS2052 18. Maiter D (2019) Management of dopamine agonist-resistant pro-
lactinoma. Neuroendocrinology 109:42–50. https://doi.org/10.
1159/000495775 19. Zamanipoor Najafabadi AH, Zandbergen IM, De Vries F, Bro-
ersen LHA, Van Den Akker-Van Marle ME, Pereira AM et al
(2020) Surgery as a viable alternative first-line treatment for pro-
lactinoma patients. A systematic review and meta-analysis. J Clin
Endocrinol Metab 105:e32–e41. https://doi.org/10.1210/clinem/
dgz144 35. Muhr C, Bergström M, Lundberg PO, Bergström K, Lång-
ström B (1986) In vivo measurement of dopamine receptors in
pituitary adenomas using positron emission tomography. Acta
Radiol Suppl 369:406–408 36. Muhr C, Bergström M, Lundberg PO, Bergström K, Hartvig
P, Lundqvist H et al (1986) Dopamine receptors in pituitary
adenomas: PET visualization with 11C-N-methylspiperone. Declarations Competing interests The authors declare no competing interests. Competing interests The authors declare no competing interests. 9. Colao A, Di Sarno A, Guerra E, De Leo M, Mentone A, Lom-
bardi G (2006) Drug insight: cabergoline and bromocriptine in
the treatment of hyperprolactinemia in men and women. Nat Clin
Pract Endocrinol Metab 2:200–210. https://doi.org/10.1038/ncpen
dmet0160 Conflict of interest Authors have no competing interests, or other in-
terests that might be perceived to influence the results and/or discus-
sion reported in this paper. 10. Steeds R, Stiles C, Sharma V, Chambers J, Lloyd G, Drake W
(2019) Echocardiography and monitoring patients receiving dopa-
mine agonist therapy for hyperprolactinaemia: a joint position
statement of the British Society of Echocardiography, the Brit-
ish Heart Valve Society and the Society for Endocrinology. Clin
Endocrinol (Oxf) 90:662–669. https://doi.org/10.1111/cen.13940 Ethical approval The trial was conducted in accordance with Good
Clinical Practice and the principles in the Declaration of Helsinki. The study received institutional approval from Cambridge University
Hospitals NHS Foundation Trust (CUH QSIS 2020: 3039). 1 3 Pituitary (2022) 25:573–586 585 management of microprolactinoma in the United States. World
Neurosurg 87:65–76. https://doi.org/10.1016/j.wneu.2015.10.090 11. De Sousa SMC, Baranoff J, Rushworth RL, Butler J, Sorbello
J, Vorster J et al (2020) Impulse control disorders in dopamine
agonist-treated hyperprolactinemia: prevalence and risk factors. J Clin Endocrinol Metab 105:e108–e118. https://doi.org/10.1210/
clinem/dgz076 26. Zygourakis CC, Imber BS, Chen R, Han SJ, Blevins L, Molinaro
A et al (2017) Cost-effectiveness analysis of surgical versus medi-
cal treatment of prolactinomas. J Neurol Surgery, Part B Skull
Base 78:125–131. https://doi.org/10.1055/s-0036-1592193 g
12. Dogansen SC, Cikrikcili U, Oruk G, Kutbay NO, Tanrikulu S,
Hekimsoy Z et al (2019) Dopamine agonist-induced impulse con-
trol disorders in patients with prolactinoma: a cross-sectional mul-
ticenter study. J Clin Endocrinol Metab 104:2527–2534. https://
doi.org/10.1210/jc.2018-02202 27. Honegger J, Nasi-Kordhishti I, Aboutaha N, Giese S (2020)
Surgery for prolactinomas: a better choice? Pituitary 23:45–51. https://doi.org/10.1007/s11102-019-01016-z p
g
28. Donoho DA, Laws ER (2019) The role of surgery in the manage-
ment of prolactinomas. Neurosurg Clin N Am 30:509–514. https://
doi.org/10.1016/j.nec.2019.05.010 g
j
13. Celik E, Ozkaya HM, Poyraz BC, Saglam T, Kadioglu P (2018)
Impulse control disorders in patients with prolactinoma receiv-
ing dopamine agonist therapy: a prospective study with 1 year
follow-up. Endocrine 62:692–700. https://doi.org/10.1007/
s12020-018-1744-8 29. Declarations Wei L, Wei X (2021) Outcomes of transsphenoidal surgery
in dopamine agonist-resistant prolactinomas: a retrospective
study. Hormones (Athens) 20:745–752. https://doi.org/10.1007/
s42000-021-00309-yfi 57. Baussart B, Villa C, Jouinot A, Raffin-Sanson ML, Foubert L,
Cazabat L et al (2021) Pituitary surgery as alternative to dopamine
agonists treatment for microprolactinomas: a cohort study. Eur J
Endocrinol 185:783–791. https://doi.org/10.1530/EJE-21-0293 43. Bergstrom M, Muhr C, Lundberg PO, Langstrom B (1991) PET
as a tool in the clinical evaluation of pituitary adenomas. J Nucl
Med 32:610–615fi crinol 185:783–791. https://doi.org/10.1530/EJE-21-0293 44. Taku N, Koulouri O, Scoffings D, Gurnell M, Burnet N (2017)
The use of 11carbon methionine positron emission tomography
(PET) imaging to enhance radiotherapy planning in the treat-
ment of a giant, invasive pituitary adenoma. BJR Case Reports
3:20160098. https://doi.org/10.1259/bjrcr.20160098 58. Penn MC, Cardinal T, Zhang Y, Abt B, Bonney PA, Lorenzo P
et al (2021) Cure and hormonal control after prolactinoma resec-
tion: case series and systematic review. J Endocr Soc. https://doi.
org/10.1210/jendso/bvab074 59. Park K, Park KH, Park HR, Lee JM, Kim YH, Kim DY et al
(2021) Long-term outcome of microscopic transsphenoidal sur-
gery for prolactinomas as an alternative to dopamine agonists. J
Korean Med Sci 36:e97. https://doi.org/10.3346/jkms.2021.36.e97 p
g
j
45. Gómez V, Gispert JD, Amador V, Llop J (2008) New method for
routine production of L-[methyl-11C]methionine: in loop syn-
thesis. J Label Compd Radiopharm 51:83–86. https://doi.org/10.
1002/jlcr.1483 Med Sci 36:e97. https://doi.org/10.3346/jkms.2021.36.e97 60. Giese S, Nasi-Kordhishti I, Honegger J (2021) Outcomes of trans-
sphenoidal microsurgery for prolactinomas-a contemporary series
of 162 cases. Exp Clin Endocrinol Diabetes 129:163–171. https://
doi.org/10.1055/a-1247-4908 46. Pascali C, Bogni A, Iwata R, Decise D, Crippa F, Bombardieri E
(1999) High efficiency preparation of L-[S-methyl-11C]methio-
nine by on-column [11C]methylation on C18 Sep-Pak. J Label
Compd Radiopharm 42:715–724. https://doi.org/10.1002/(SICI)
1099-1344(199908)42:8%3c715::AID-JLCR224%3e3.0.CO;2-3 61. Zielinski G, Ozdarski M, Maksymowicz M, Szamotulska K,
Witek P (2020) Prolactinomas: prognostic factors of early remis-
sion after transsphenoidal surgery. Front Endocrinol (Lausanne)
11:439. https://doi.org/10.3389/fendo.2020.00439 47. Mitterhauser M, Wadsak W, Krcal A, Schmaljohann J, Eidherr H,
Schmid A et al (2005) New aspects on the preparation of [11C]
Methionine—a simple and fast online approach without pre-
parative HPLC. Appl Radiat Isot 62:441–445. https://doi.org/10.
1016/j.apradiso.2004.07.006 62. Han YL, Chen DM, Zhang C, Pan M, Yang XP, Wu YG (2018)
Retrospective analysis of 52 patients with prolactinomas follow-
ing endoscopic endonasal transsphenoidal surgery. Med (United
States) 97:e13198. https://doi.org/10.1097/MD.0000000000
013198 48. Declarations Fedorov A, Beichel R, Kalpathy-Cramer J, Finet J, Fillion-Robin
JC, Pujol S et al (2012) 3D Slicer as an image computing plat-
form for the quantitative imaging network. Magn Reson Imaging
30:1323–1341. https://doi.org/10.1016/j.mri.2012.05.001 63. Ma Q, Su J, Li Y, Wang J, Long W, Luo M et al (2018) The chance
of permanent cure for micro- And macroprolactinomas, medica-
tion or surgery? A systematic review and meta-analysis. Front
Endocrinol (Lausanne). https://doi.org/10.3389/fendo.2018.00636 49. Casanueva FF, Molitch ME, Schlechte JA, Abs R, Bonert V, Bron-
stein MD et al (2006) Guidelines of the pituitary society for the
diagnosis and management of prolactinomas. Clin Endocrinol
(Oxf) 65:265–273. https://doi.org/10.1111/j.1365-2265.2006.
02562.x 64. Yagnik KJ, Erickson D, Bancos I, Atkinson JLD, Choby G,
Peris-Celda M et al (2021) Surgical outcomes of medically failed
prolactinomas: a systematic review and meta-analysis. Pituitary
24:978–988. https://doi.org/10.1007/s11102-021-01188-7 50. Xia MY, Lou XH, Lin SJ, Wu ZB (2018) Optimal timing of dopa-
mine agonist withdrawal in patients with hyperprolactinemia: a
systematic review and meta-analysis. Endocrine 59:50–61. https://
doi.org/10.1007/s12020-017-1444-9 65. Bashari WA, Senanayake R, Fernández-Pombo A, Gillett D, Kou-
louri O, Powlson AS et al (2019) Modern imaging of pituitary
adenomas. Best Pract Res Clin Endocrinol Metab 33:101278. https://doi.org/10.1016/j.beem.2019.05.002 g
51. Hu J, Zheng X, Zhang W, Yang H (2015) Current drug withdrawal
strategy in prolactinoma patients treated with cabergoline: a sys-
tematic review and meta-analysis. Pituitary 18:745–751. https://
doi.org/10.1007/s11102-014-0617-2 66. Vasilev V, Rostomyan L, Daly AF, Potorac L, Zacharieva S, Bon-
neville JF et al (2016) Pituitary “incidentaloma”: neuroradio-
logical assessment and differential diagnosis. Eur J Endocrinol
175:R171–R184. https://doi.org/10.1530/EJE-15-1272 52. Ozkaya HM, Sahin S, Korkmaz OP, Durcan E, Sahin HR, Celik
E et al (2020) Patients with acromegaly might not be at higher
risk for dopamine agonist-induced impulse control disorders than
those with prolactinomas. Growth Horm IGF Res 55:101356. https://doi.org/10.1016/j.ghir.2020.101356 67. Bonneville J-F (2019) A plea for the T2W MR sequence for
pituitary imaging. Pituitary 22:195–197. https://doi.org/10.1007/
s11102-018-0928-9 68. Varlamov EV, Hinojosa-Amaya JM, Fleseriu M (2020) Mag-
netic resonance imaging in the management of prolactinomas;
a review of the evidence. Pituitary 23:16–26. https://doi.org/10.
1007/s11102-019-01001-6 53. Cozzi R, Ambrosio MR, Attanasio R, Battista C, Bozzao A,
Caputo M et al (2022) Italian Association of Clinical Endocri-
nologists (AME) and International Chapter of Clinical Endocri-
nology (ICCE). Position statement for clinical practice: prolactin-
secreting tumors. Eur J Endocrinol 186:P1-33. https://doi.org/10.
1530/eje-21-0977 69. Declarations J
Comput Assist Tomogr 10:175–180. https://doi.org/10.1097/
00004728-198603000-00001 20. Lu J, Cai L, Wu Z, Lin W, Xu J, Zhu Z et al (2021) Surgery and
medical treatment in microprolactinoma: a systematic review
and meta-analysis. Int J Endocrinol 2021:1–11. https://doi.org/
10.1155/2021/9930059 21. Park JY, Choi W, Hong AR, Yoon JH, Kim HK, Jang W-Y et al
(2021) Surgery is a safe, effective first-line treatment modality for
noninvasive prolactinomas. Pituitary 24:955–963. https://doi.org/
10.1007/s11102-021-01168-x 37. Daemen BGJ, Zwertbroek R, Elsinga PH, Paans AJM, Dooren-
bos H, Vaalburg W (1991) PET studies with l-[1-11C]tyrosine,
l-[methyl-11C]methionine and 18F-fluorodeoxyglucose in pro-
lactinomas in relation to bromocryptine treatment. Eur J Nucl
Med 18:453–460. https://doi.org/10.1007/BF00181283 22. Chen TY, Lee CH, Yang MY, Shen CC, Yang YP, Chien Y et al
(2021) Treatment of hyperprolactinemia: a single-institute expe-
rience. J Chinese Med Assoc 84:1019–1022. https://doi.org/10.
1097/JCMA.0000000000000584 38. Feng Z, He D, Mao Z, Wang Z, Zhu Y, Zhang X et al (2016)
Utility of 11C-methionine and 18F-FDG PET/CT in patients
with functioning pituitary adenomas. Clin Nucl Med 41:e130–
e134. https://doi.org/10.1097/RLU.0000000000001085 23. Andereggen L, Frey J, Andres RH, Luedi MM, Gralla J, Schubert
GA et al (2021) Impact of primary medical or surgical therapy
on prolactinoma patients’ BMI and metabolic profile over the
long-term. J Clin Transl Endocrinol 24:100258. https://doi.org/
10.1016/j.jcte.2021.100258 39. Bergström M, Muhr C, Lundberg PO, Bergström K, Lundqvist
H, Långström B (1986) Amino acid metabolism in pituitary
adenomas. Acta Radiol Suppl 369:412–414 40. Bergstrom M, Muhr C, Lundberg PO, Bergström K, Gee AD,
Fasth KJ et al (1987) Rapid decrease in amino acid metabolism
in prolactin-secreting pituitary adenomas after bromocriptine
treatment: a PET study. J Comput Assist Tomogr 11:815–819. https://doi.org/10.1097/00004728-198709000-00014 24. Mattogno PP, D’alessandris QG, Chiloiro S, Bianchi A, Giampi-
etro A, Pontecorvi A et al (2021) Reappraising the role of trans-
sphenoidal surgery in prolactin-secreting pituitary tumors. Can-
cers (Basel) 13:3252. https://doi.org/10.3390/cancers13133252 25. Jethwa PR, Patel TD, Hajart AF, Eloy JA, Couldwell WT, Liu
JK (2016) Cost-effectiveness analysis of microscopic and endo-
scopic transsphenoidal surgery versus medical therapy in the 41. Muhr C (2006) Positron emission tomography in acromegaly
and other pituitary adenoma patients. Neuroendocrinology
83:205–210. https://doi.org/10.1159/000095529 1 3 586 Pituitary (2022) 25:573–586 42. Bashari WA, Senanayake R, MacFarlane J, Gillett D, Powlson
AS, Kolias A et al (2021) Using molecular imaging to enhance
decision making in the management of pituitary adenomas. J
Nucl Med 62:57S-62S. https://doi.org/10.2967/jnumed.120.
251546 56. Declarations Casanueva FF, Barkan AL, Buchfelder M, Klibanski A, Laws
ER, Loeffler JS et al (2017) Criteria for the definition of Pitui-
tary Tumor Centers of Excellence (PTCOE): A Pituitary Soci-
ety Statement. Pituitary 20:489–498. https://doi.org/10.1007/
s11102-017-0838-2 j
54. Lasolle H, Teulade M, Lapras V, Vasiljevic A, Borson-Chazot F,
Jouanneau E et al (2022) Postoperative remission of non-invasive
lactotroph pituitary tumor: a single-center experience. Ann Endo-
crinol (Paris) 83:1–8. https://doi.org/10.1016/j.ando.2021.11.008 Publisher's Note Springer Nature remains neutral with regard to
jurisdictional claims in published maps and institutional affiliations. 55. Andereggen L, Frey J, Andres RH, Luedi MM, El-Koussy M,
Widmer HR et al (2021) First-line surgery in prolactinomas:
lessons from a long-term follow-up study in a tertiary referral
center. J Endocrinol Invest 44:2621–2633. https://doi.org/10.1007/
s40618-021-01569-6 1 3
|
https://openalex.org/W3014502522
|
https://pure.mpg.de/pubman/item/item_3222831_1/component/file_3222832/Pockrandt_2020.pdf
|
English
| null |
GenMap: ultra-fast computation of genome mappability
|
Bioinformatics
| 2,020
|
cc-by
| 7,230
|
Abstract Motivation: Computing the uniqueness of k-mers for each position of a genome while allowing for up to
e mismatches is computationally challenging. However, it is crucial for many biological applications such
as the design of guide RNA for CRISPR experiments. More formally, the uniqueness or (k, e)-mappability
can be described for every position as the reciprocal value of how often this k-mer occurs approximately
in the genome, i.e., with up to e mismatches. Results: We present a fast method GenMap to compute the (k, e)-mappability. We extend the mappability
algorithm, such that it can also be computed across multiple genomes where a k-mer occurrence is only
counted once per genome. This allows for the computation of marker sequences or finding candidates
for probe design by identifying approximate k-mers that are unique to a genome or that are present in all
genomes. GenMap supports different formats such as binary output, wig and bed files as well as csv files
to export the location of all approximate k-mers for each genomic position. Availability: GenMap can be installed via bioconda. Binaries and C++ source code are available on
https://github.com/cpockrandt/genmap. Contact: pockrandt@jhu.edu GenMap: Ultra-fast Computation of Genome
Mappability Christopher Pockrandt 1, 2, 3, *, Mai Alzamel 4, 5, Costas S. Iliopoulos 4 and
Knut Reinert 2, 3 1Center for Computational Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
2Department of Computer Science and Mathematics, Freie Universität Berlin, Berlin, Germany,
3Max Planck Institute for Molecular Genetics, Berlin, Germany,
4Department of Informatics, King’s College London, London, UK and
5Department of Computer Science, King Saud University, Riyadh, SA. ∗To whom correspondence should be addressed. Associate Editor: XXXXXXX
Received on XXXXX; revised on XXXXX; accepted on XXXXX Received on XXXXX; revised on XXXXX; accepted on XXXXX © The Author(s) 2020. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the
original work is properly cited. 2 Algorithm many applications. Sequencing errors and variations such as SNPs require
not only the k-mer to be unique or rare enough but also close matches of
this k-mer, i.e., all k-mers with a certain number of mismatches have to
be considered as well. Since the number of k-mers to be considered grows
exponentially in the number of mismatches, k-mer counters are infeasible
for this problem. many applications. Sequencing errors and variations such as SNPs require
not only the k-mer to be unique or rare enough but also close matches of
this k-mer, i.e., all k-mers with a certain number of mismatches have to
be considered as well. Since the number of k-mers to be considered grows
exponentially in the number of mismatches, k-mer counters are infeasible
for this problem. Before we present our algorithm, we give an overview of the approach of
Derrien et al. to compute the (k, e)-mappability. For reasons of clarity, we
consider computing its inverse, the (k, e)-frequency and neglect searching
the reverse strand throughout this paper. To consider the reverse strand,
each k-mer has simply to be searched by its reverse complement leading
to a doubling of the running time. Furthermore, we consider Hamming
distance, if not stated otherwise. It can be applied to other distance metrics
such as Edit distance as well. The suite GEM-Tools (Marco-Sola et al. (2012)) includes a program to
compute the mappability for arbitrary k-mers and number of mismatches. It is the most common and advanced algorithm to compute the mappability
of entire genomes. To improve its performance it offers a heuristic mode
leading only to an approximation of the mappability. Nevertheless, it is
not feasible to compute many instances of biological relevant k-mer sizes
and number of errors. To achieve a feasible running time Derrien et al. implemented a
heuristic. First, they initialize the frequency vector with 0s and perform a
linear scan over the text (see algorithm 1). Then each k-mer Ti is searched
with e errors in an FM index and the number of occurrences is stored in
F[i]. If the count value exceeds some user-defined threshold parameter t,
the locations of these occurrences are located. Let j be such a location. Since Ti has a high frequency, i.e., F[i] > t and D(Ti, Tj) ≤e, it is
likely that Ti and Tj share common approximate matches. Hence, F[j]
is assigned the frequency value F[i]. Definition ((k, e)-mappability and (k, e)-frequency). Definition ((k, e)-mappability and (k, e)-frequency). Given a string T of length n, the (k, e)-frequency counts occurrences of
every single k-mer in T with up to e errors. We denote the k-mer starting
at position i in T as Ti. The values are stored in a frequency vector F of
length n −k + 1 such that F[i] = |{j | D(Ti, Tj) ≤e, 1 ≤j ≤n −k + 1}| Algorithm1Inexactalgorithmtocomputethe(k, e)-frequencybyDerrien
et al. 1: procedure inexact_frequency(T, k, e, t)
2:
F[1..|T| −k + 1] ←{0}
3:
for i = 1, ..., |F| do
4:
if F[i] = 0 then
5:
P ←approximate matches with e errors
6:
F[i] ←|P|
7:
if |P| > t then
8:
for j ∈P do
9:
F[j] ←max(F[j], |P|)
10:
return F Algorithm1Inexactalgorithmtocomputethe(k, e)-frequencybyDerrien
et al. 1: procedure inexact_frequency(T, k, e, t)
2:
F[1..|T| −k + 1] ←{0}
3:
for i = 1, ..., |F| do
4:
if F[i] = 0 then
5:
P ←approximate matches with e errors
6:
F[i] ←|P|
7:
if |P| > t then
8:
for j ∈P do
9:
F[j] ←max(F[j], |P|)
10:
return F Algorithm1Inexactalgorithmtocomputethe(k, e)-frequencybyDerrien
et al. 1: procedure inexact_frequency(T, k, e, t)
2:
F[1..|T| −k + 1] ←{0}
3:
for i = 1, ..., |F| do
4:
if F[i] = 0 then
5:
P ←approximate matches with e errors
6:
F[i] ←|P|
7:
if |P| > t then
8:
for j ∈P do
9:
F[j] ←max(F[j], |P|)
10:
return F where D(Ti, Tj) denotes the distance of two k-mers given a metric
such as Hamming or Edit distance. Its elementwise multiplicative inverse
is called the (k, e)-mappability and stored in a mappability vector M with
M[i] = 1/F[i] for 1 ≤i ≤n −k + 1. A mappability value of 1 represents a unique k-mer, a mappability
value close to 0 indicates a k-mer occurring in repetitive regions. Figure 1
gives an example for the (4, 0) and (4, 1)-frequency of a given nucleotide
sequence considering Hamming distance. Since, for some applications, an exact computation of mappability is
favorable, we propose a new algorithm that is not only faster than previous
ones but also exact, i.e., does not rely on heuristics. Mappability can not
only be used straightforward to retrieve information on the repetitiveness
of the underlying data. 1 Introduction process (Fonseca et al. (2012)). Given a set of reads of some fixed length k
the process of re-sequencing depends heavily on how mappable a genome
is. Thus, for every substring of length k in the sequence, we want to count
how many times this substring appears in the sequence while allowing for
a small number e of errors. In other terms, mappability is a measure of
how unique or repetitive regions in the genome are and is closely related to
mapping. Theconceptofmappabilityforsequenceanalysiswasintroduced
by Koehler et al. (2010), taken up again and later formalized by Derrien
et al. (2012) (see also Antoniou et al. (2009)). Analyzing data derived from massively parallel sequencing experiments
often depends on the process of genome assembly via re-sequencing;
namely, assembly with the help of a reference sequence. In this process, a
large number of reads derived from a DNA donor during these experiments
must be mapped back to a reference sequence, comprising a few gigabases
to establish the section of the genome from which each read originates. An
extensive number of short-read alignment techniques and tools have been
introduced to address this challenge emphasizing different aspects of the While k-mer counting became extremely popular in the last years,
searching for k-mers with low occurrences does not meet the needs of 1 2 Pockrandt et al. 2 Algorithm To speed up the computation, k-
mers that already have frequency values assigned by this heuristic step are
skipped during the scan over the text. If a position j is located multiple
times as an approximate match of a repetitive k-mer, F[j] is assigned
the maximum frequency of all these k-mers to avoid underestimating the
frequency value F[j]. In the following paragraph, we give a formal definition of the problem,
present our algorithm in the next section and compare it to GEM. Our
algorithm does not rely on heuristics and outperforms GEM even in its
heuristic mode by far. Definition ((k, e)-mappability and (k, e)-frequency). In this paper, we will also illustrate that it can be
used to find marker sequences that allow distinguishing similar strains of
the same species, as well as separate strains by groups sharing common
k-mers. Theirexperimentsonchromosome19ofthehumangenomewitht = 7
show that almost 90 % of the 50-mers with a frequency of 3 are correct,
for 50-mers with frequency values between 8 and 12 only 75 % are correct
(similar errors for C. elegans with t = 6). This can be led back to an
overestimation of rather unique k-mers. We now present a fast and exact algorithm to compute the (k, e)-
frequency. Similar to the algorithm implemented in GEM we scan over
the text T while searching and counting the occurrences of each k-mer Ti
for 1 ≤i ≤n −k + 1 with up to e errors in an index on T. In contrast to
GEM we improve the running time by reducing redundant searches with
three major improvements which we introduce in the following. 2.2 Adjacent k-mers Adjacent k-mers in T are highly similar, since they have a large overlap. Hence, we do not search for every k-mer separately. Consider the adjacent
k-mers Tj, Tj+1, . . . , Tj+s−1 for some integer s ≤k −e + 1 which all
share the common sequence T[j + s −1..j + k −1] of length at least e. Since we already need to allow for up to e errors in their common sequence
when searching each k-mer, this infix should only be searched once. Thus,
we start searching this infix using optimum search schemes and extend
it afterwards to retrieve the occurrences for each k-mer separately using
backtracking, allowing for the remaining number of errors not spent in the
search of the infix. Since the extension is performed in both directions, a
bidirectional index is required. Figure 3a illustrates this approach. Optimum search schemes are based on a framework by Kucherov et
al. called search schemes that allows formalizing search strategies in a
bidirectional index (Kucherov et al. (2016)). The sequence to be searched
is split into p pieces and searched by certain combinations of the pieces in
the index while trying to reduce the number of search steps performed in
the index. Formally, a search is a triplet S = (π, L, U) of integer strings each
of length p. π is a permutation of the numbers {1, 2, ..., p} indicating the
order in which the pieces are searched. Starting from an arbitrary piece
π[0] the subsequent pieces need to be adjacent to the previously searched
pieces. L and U are non-decreasing integer strings indicating the lower
and upper bound of errors. After the piece π[i] is searched a total number
of errors from L[i] to U[i] must have been spent. A set of searches that
covers all possible error distributions with e errors and p pieces forms a
search scheme. As a result the number of errors allowed in the first pieces of
each search is reduced which speeds up approximate string matching. By
performing multiple searches starting with different pieces, it is guaranteed
that all possible error distributions among the pieces are covered. i
1
2
3
4
5
6
7
8
9
10 11 12 13 14 . . .
T[i] A G C C G T A C A
A
G
T
A
T
. . .
T1
A G C C G T A C A
A
G
T2
G C C G T A C A
A
G
T
T3
C C G T A C A
A
G
T
A
T4
C G T A C A
A
G
T
A
T C G
0 −0
T A
0 −0
C A
1 −2
A G
1 −2
(a)
Forward search
Sfwd = (1234, 0011, 0022)
C G
2 −2
T A
0 −2
C A
0 −1
A G
0 −0
(b)
Backward search
Sbwd = (4321, 0002, 0122)
1
2
C G
0 −1
T A
0 −1
C A
0 −0
A G
0 −2
(c)
Bidirectional search
Sbi = (3214, 0000, 0112) T[4, 11]
T[2, 11]
T1
A
T2
T
←−
G C
T[4, 13]
T3
C
T4
T
−→
T A
(b) The same strategy presented as a backtracking tree. It is traversed for
all occurrences reported by the search of the infix T[4, 11] using optimum
search schemes. Each edge also has to account for remaining errors, i.e.,
approximate string matching is performed using backtracking. T[4, 11]
T[2, 11]
T1
A
T2
T
←−
G C
T[4, 13]
T3
C
T4
T
−→
T A T3 2 (b) The same strategy presented as a backtracking tree. It is traversed for
all occurrences reported by the search of the infix T[4, 11] using optimum
search schemes. Each edge also has to account for remaining errors, i.e.,
approximate string matching is performed using backtracking. Fig. 3. Searching s overlapping k-mers using optimum search schemes for the infix and
extending it using backtracking. Illustrated for k = 11 and s = 4. Fig. 3. Searching s overlapping k-mers using optimum search schemes for the infix and
extending it using backtracking. Illustrated for k = 11 and s = 4. Fig. 2. The optimum search scheme for 2 mismatches consists of 3 searches with 4 pieces
each. The arrows indicate in which order the pieces are searched. The error bounds below
each part are cumulative bounds, i.e., the minimum number of errors that must respectively
the maximum number of errors that can be spent until searching the end of the corresponding
piece. Illustrated for searching the 8-mer CGTACAAG. The forward search covers the error
distributions 0010, 0011, 0020, the backward search covers 2000, 1100, 0200, 1010, 0110,
and the bidirectional search 0000, 0001, 0002, 1000, 1001, 0100, 0101. To further reduce the number of redundant computations, the set of
overlapping k-mers is recursively divided into two sets of k-mers of
roughly equal size that each share a larger common overlap among each
other. i
1
2
3
4
5
6
7
8
9
10 11 12 13 14 . . .
T[i] A G C C G T A C A
A
G
T
A
T
. . .
T1
A G C C G T A C A
A
G
T2
G C C G T A C A
A
G
T
T3
C C G T A C A
A
G
T
A
T4
C G T A C A
A
G
T
A
T Optimum search schemes are search schemes that are optimal under
certain constraints, i.e., the number of backtracking steps in an index
over all searches are minimized while still covering all error distributions. Figure 2 illustrates the optimum search scheme for e = 2 errors, p = e+2
pieces and up to 3 searches. (a) First, the common overlap (light gray) is searched using optimum
search schemes. Second, the search of T1 and T2 is continued recursively
by extending the previously identified approximate matches of the infix in
the index by GC to the left (allowing for the remaining number of errors;
medium gray). T1 and T2 are then retrieved separately by backtracking
in the index by one character to the left and one character to the right
(allowing for an error, if any left; dark gray). T3 and T4 are extended
analogously in a recursive manner. C G
0 −0
T A
0 −0
C A
1 −2
A G
1 −2
(a)
Forward search
Sfwd = (1234, 0011, 0022)
C G
2 −2
T A
0 −2
C A
0 −1
A G
0 −0
(b)
Backward search
Sbwd = (4321, 0002, 0122)
1
2
C G
0 −1
T A
0 −1
C A
0 −0
A G
0 −2
(c)
Bidirectional search
Sbi = (3214, 0000, 0112)
Fig. 2. The optimum search scheme for 2 mismatches consists of 3 searches with 4 pi
each. The arrows indicate in which order the pieces are searched. The error bounds be
each part are cumulative bounds, i.e., the minimum number of errors that must respecti
the maximum number of errors that can be spent until searching the end of the correspond
piece. Illustrated for searching the 8-mer CGTACAAG. The forward search covers the e
distributions 0010, 0011, 0020, the backward search covers 2000, 1100, 0200, 1010, 0
and the bidirectional search 0000, 0001, 0002, 1000, 1001, 0100, 0101. 2.1 Approximate String Matching using Optimum Search
Schemes When searching a k-mer in a string index, it is searched character by
character. Unidirectional indices only support extending characters into
one direction, either to the left or to the right, while bidirectional indices
support searching into both directions in any arbitrary order (Lam et al. (2009)). To search for every possible approximate match within the given
error bound, backtracking is performed. This leads to exponential running
time in the number of errors. Especially allowing for errors at the beginning
of the k-mer, i.e., branching at the topmost nodes in the backtracking tree is (b) (4, 1)-frequency Fig. 1. (k, e)-frequency vectors Fe for k = 4 and e ∈{0, 1} on the same sequence. A
frequency of 1 indicates that the k-mer starting at that position in the text is unique in the
entire sequence without errors respectively with up to one mismatch. GenMap: Ultra-fast Computation of Genome Mappability 3 expensive. Hence, we use optimum search schemes (Kianfar et al. (2018))
when searching each k-mer, a sophisticated search strategy that reduces
the number of search steps performed in the index while still searching for
all possible approximate matches. 2.2 Adjacent k-mers i
1
2
3
4
5
6
7
8
9
10 11 12 13 14 . . .
T[i] A G C C G T A C A
A
G
T
A
T
. . .
T1
A G C C G T A C A
A
G
T2
G C C G T A C A
A
G
T
T3
C C G T A C A
A
G
T
A
T4
C G T A C A
A
G
T
A
T This overlap is then searched using backtracking before the next
recursive partitioning of k-mers. The recursion ends when a single k-mer
is left and the number of occurrences can be reported and summed up, or
no hits are found. The recursive extension is shown in figure 3b. Note,
that there are two recursions involved: subdividing the set of k-mers and
backtracking in each recursion step. Hence, the same partitioning steps
and backtracking steps have to be performed for each set of preliminary
matches represented by suffix array ranges in the FM index. Abidirectionalindexisrequiredtoenabletostartasearchwithamiddle
piece as illustrated in figure 2c. To improve the overall running time of
the index-based search we use a fast implementation of bidirectional FM
indices based on EPR dictionaries (Pockrandt et al. (2017)). 4 Pockrandt et al. Tool
(36, 0)
(24, 1)
(36, 2)
(50, 2)
(75, 3)
GEM exact
5h 10m
N/A
N/A
N/A
N/A
GEM heuristic
23m
N/A
7h 11m 5h 50m 4h 26m
GenMap
3m
23m
1h 19m
42m
1h 27m
(a) Instances are taken from the experiments by Derrien et al. (2012). Tool
(101, 0) (101, 1) (101, 2) (101, 3) (101, 4)
GEM exact
44m
7h 28m
7h 34m
7h 45m
8h 8m
GEM heuristic
28m
2h 40m
3h 17m
3h 31m
3h 49m
GenMap
2m
7m
17m
46m
2h 42m
(b) Typical Illumina read length with growing number of mismatches. Table 1. Running times for computing the frequency of the human genome
(GRCh38) using 16 threads. Timeouts of 1 day are represented as N/A. Tool
(36, 0)
(24, 1)
(36, 2)
(50, 2)
(75, 3)
GEM exact
5h 10m
N/A
N/A
N/A
N/A
GEM heuristic
23m
N/A
7h 11m 5h 50m 4h 26m
GenMap
3m
23m
1h 19m
42m
1h 27m
(a) Instances are taken from the experiments by Derrien et al. (2012). The question remains on how to combine the improvements of sections
2.1 and 2.2, i.e., how to choose s, the number of adjacent k-mers that are
searched together starting with their common sequence using optimum
searchschemes. Onone hand, approximate stringmatching usingoptimum
search schemes is more efficient than simple backtracking; hence, a longer
common infix is favorable. On the other hand, a longer common infix
means fewer adjacent k-mers are searched at once which leads to more
redundant search steps due to the high similarity of overlapping k-mers. 3 Benchmarks At first, we compare the running times for computing the frequency on
the human genome for different lengths and errors based on Hamming
distance. We ran GEM in its exact mode as well as in its heuristic mode. Forthelatter, theauthorsrecommendt = 7. Table1acomparestherunning
times for shorter k that are of interest for applications such as identifying
marker sequences, presented in section 4. Table 1b shows typical instances
used for applications in read mapping based on a typical Illumina read
length. Even though longer Illumina read lengths are more common these
days, we choose a shorter read length, since the frequency is easier to
compute for longer k-mers. In conclusion, GenMap is a magnitude faster than GEM in its exact
mode, and still faster than GEM using its heuristic, while GenMap is
always exact. Even for up to 4 errors GenMap achieves a reasonable
running time. This is due to the three techniques described in the previous
section. Further improvements can be implemented which might speed
up the algorithm even further, such as in-text verification (Pockrandt
(2019)), i.e., locating partially searched k-mers and verifying whether
their locations in the text match the k-mer with respect to the error bound. A location and verification step in the text is often several times faster than
finishing an index-based approximate search. For all computed instances, GenMap is faster than GEM. Compared
to the approximate mode, we are almost a magnitude faster for a smaller
number of errors, but for 4 errors the heuristic of GEM pays off and is
almost as fast as our algorithm. Interestingly, the increase of the running
time of GEM in its exact mode gets smaller with more errors. For 101-
mers with 1 to 4 errors, the running time is always about 7 to 8 hours,
nonetheless GenMap is still faster by a factor from 3 of up to 64 (4 and 1
errors). Even when searching without errors where no backtracking has to
be performed, our tool is faster by a factor of 20 to 100 (for 101-mers and
36-mers). The most noticeable improvement is achieved for short k-mers. Derrien et al. point out that their algorithm is not suitable for small k and
completely unfeasible for k < 30 without its heuristic which is reflected
by our benchmarks, whereas GenMap can handle these instances easily. i
1
2
3
4
5
6
7
8
9
10 11 12 13 14 . . .
T[i] A G C C G T A C A
A
G
T
A
T
. . .
T1
A G C C G T A C A
A
G
T2
G C C G T A C A
A
G
T
T3
C C G T A C A
A
G
T
A
T4
C G T A C A
A
G
T
A
T GenMap chooses s according to the following equation derived from
optimal values that were determined experimentally on different genomes
such as the human and barley genome (see Pockrandt (2019) for details). clamp(v, l, r) returns v if it lies within the range, i.e., l ≤v ≤r, and
returns l or r if it is less or greater. Tool
(101, 0) (101, 1) (101, 2) (101, 3) (101, 4)
GEM exact
44m
7h 28m
7h 34m
7h 45m
8h 8m
GEM heuristic
28m
2h 40m
3h 17m
3h 31m
3h 49m
GenMap
2m
7m
17m
46m
2h 42m
(b) Typical Illumina read length with growing number of mismatches. Table 1. Running times for computing the frequency of the human genome
(GRCh38) using 16 threads. Timeouts of 1 day are represented as N/A. s =
⌊k · 0.7⌋
, e = 0
j
k ·
clamp
k
100 , 0.3, 1.0
· 0.7ek
, otherwise s =
⌊k · 0.7⌋
, e = 0
j
k ·
clamp
k
100 , 0.3, 1.0
· 0.7ek
, otherwise 2.3 Skipping redundant k-mers Finally, we avoid searching the same k-mer multiple times. Especially
k-mers from repeat regions may occur many times without errors in the
text. Since they all share the same frequency value, it should be avoided
to compute it more than once. Hence, after searching and counting the
occurrences of a k-mer, we locate the positions of the exact matches and
set all their frequency values in F accordingly. index with EPR dictionaries and a suffix array sampling rate of 10), while
GEM takes up 4.5 GB (using an unspecified FM index implementation
with a suffix array sampling rate of 32). GenMap is also suitable to compute the frequency of larger and more
repetitive genomes than the human genome. We computed the (50, 2)-
frequency of the barley genome (Mascher et al. (2017)) as it contains
large amounts of repetitive DNA (Ranjekar et al. (1976)). Barley has 4.8
billion base pairs while the human genome has 3.2 billion base pairs. As
expected the human genome has considerably more unique regions than
the barley genome. To be precise 75.4 % of the 50-mers are unique in
the human genome, and only 26.4 % in the barley genome. There are
12.0 % (54.4 %), 7.6 % (42.1 %) and 4.8 % (25.6 %) 50-mers in human
DNA (resp. barley DNA) with at least 10, 100 and 1,000 occurrences. Computing the (50, 2)-frequency of barley on 16 threads took less than
1h 15m with GenMap and nearly a day with GEM using its heuristic with
t = 6 (automatically chosen by GEM). We observed that this strategy leads to longer runs of frequency
values forwarded to positions with uncomputed frequency values. When
forwarded frequency values of previously counted k-mers are encountered
during the scan over the text, they are skipped. 3 Benchmarks GEM takes significantly longer, often does not even terminate within 24
hours on 16 threads. All tests were conducted on Debian GNU/Linux 7.1 with an Intel Xeon
E5-2667v2 CPU. To avoid dynamic overclocking effects in the benchmark
the CPU frequency was fixed to 3.3 GHz. The data was stored on a virtual
file system in the main memory to avoid loading it from disk during the
benchmark which might affect the results due to I/O operations. We used the only available version 1.759 beta of the GEM suite that
included the mappability algorithm. We did not reach the authors for other
versions including their method. Other available and newer versions do
not offer this feature anymore. The running times we measured for GEM
heuristic differ considerably from the running times for GRCh37 published
by the authors. Even when we ran it on a similar CPU with the same number
of cores we were 2 to 5 times slower than their published benchmarks. One reason might be that the only available version of GEM with the
mappability functionality was published as a beta version, however it
was a year after their paper. Nonetheless, GenMap is still faster than the
running times published by Derrien et al. For a fair comparison in our GenMap is also faster than GEM when computing the frequency of
small genomes like D. melanogaster. Since smaller genomes are generally
less challenging, we omit the benchmarks here. For the human genome, the
memory consumption of GenMap is about 9 GB (using a bidirectional FM GenMap: Ultra-fast Computation of Genome Mappability 5 benchmark we reduced the genomes to the dna4 alphabet, i.e., replaced Ns
by random bases. Based on tests we observed that GEM neither computes
the mappability of k-mers that have unknown bases, nor considers them
as mismatches in its default mode even when errors are allowed. benchmark we reduced the genomes to the dna4 alphabet, i.e., replaced Ns
by random bases. Based on tests we observed that GEM neither computes
the mappability of k-mers that have unknown bases, nor considers them
as mismatches in its default mode even when errors are allowed. We computed the (30, 2)-mappability on four different strains of group
B12. According to the study all strains within B1 share the anonymous
DNA fragment TspE4.C2 of 152 base pairs. 4 Experiments Although the main focus of this work lies on presenting a new and fast
algorithm for computing the mappability of a genome, we propose an
application to identify marker sequences illustrated by a small example on
E. coli strains. GenMap has an option to compute the mappability on multiple
genomes while at most one approximate occurrence for a k-mer is counted
for each genome. This allows us to quickly identify k-mers that are unique
to a genome (regardless of the overall number of approximate occurrences
in this genome) or k-mers that occur in every genome at least once. Additionally, GenMap not only outputs the mappability or frequency but
also outputs the locations where the approximate matches for each k-mer
occur into a csv file. This helps to find marker sequences or to select
candidates for probe design by identifying k-mers that are unique to a
genome or that are present in all genomes while allowing for errors. In table 3, we present the data of a second experiment, where we
select strains from more than one group (A and B1); see figure 4b for an
illustration. Again, we computed the (30, 2)-mappability, but this time
we counted k-mers that match all strains in one group but no strain in the
other group. Marker genes or marker sequences are short subsequences of genomes
whose presence or absence allows determining the organism, species or
even strain when sequencing an unknown sample or helping building
phylogenetic trees (Patwardhan et al. (2014)). Depending on the marker
length it can span up to dozens of reads. Instead of assembling the strain to
search for marker genes or applying experimental methods such as PCR-
based AFLP (amplified fragment length polymorphism, see Vos et al. (1995)), we propose using its mappability. all k-mers
non-adjacent k-mers
Group Strain
Unique
∅Dist. Unique
∅Dist. A
W3110 109,375 41 ± 731
2,398
1, 867 ± 4, 577
A
HS
111,179 39 ± 709
2,414
1, 796 ± 4, 471
B1
IAI1
125,042 37 ± 680
3,063
1, 485 ± 4, 091
B1
SE11
127,302 38 ± 690
3,123
1, 510 ± 4, 148
B1
11128
121,325 42 ± 766
3,275
1, 548 ± 4, 408
B1
11368
131,121 41 ± 814
3,473
1, 537 ± 4, 763
Table 3. (30, 2)-mappability on six strains of E. coli of the groups A and B1. 3 Benchmarks IAI1
171,942
4,992 27 ± 627
1,829
81 2,476 ± 5,560
SE11
305,439
10,365 15 ± 447
2,356
176 1,942 ± 4,708
11128 260,305
40,101 20 ± 953
2,494
685 2,049 ± 9,517
11368 434,033 108,968 13 ± 912
3,142
1,116 1,674 ± 10,592
Table 2. (30, 2)-mappability on four strains of E. coli assigned to the
phylogenetic group B1 based on the known marker genes by Clermont et al. We
computed the mean distance of the unique marker sequences and their standard
deviation. 3 Benchmarks We used GenMap to search
for both, unique k-mers among all strains as well as k-mers that occur in
each strain at least once, see figure 4a for an illustration. We observed that
TspE4.C2 is an exact match in all strains and the 30-mers in this region also
have a mappability value of exactly 0.25 when accounting for 2 errors. We
further found numerous 30-mers with a mappability of 1, thus allowing to
determine a strain among those four, while still accounting for sequencing
errors and mutations. Table 2 lists the number of k-mers identified. We
counted the number of k-mers matching only one strain, i.e., the strain the
k-mer originated from. We refer to this count as unique. Additionally, we
counted how many of these k-mers matched multiple times to the strain,
referred to as pseudo. GenMap allows to exclude these pseudo marker
sequences when computing the mappability on multiple sequence files,
i.e., it is only counted in how many sequence files a k-mer is present. To avoid counting highly overlapping k-mers in large unique regions, we
break down the numbers for non-adjacent k-mers as well, i.e., for a k-mer
to be considered it must have a preceding k-mer with a mappability value
smaller than 1. A more recent tool to compute the mappability is Umap (Karimzadeh
et al. (2018)). It is limited to computing the (k, 0)-mappability and
reporting only unique k-mers, i.e., regions with a mappability value of
1. It uses the read mapper Bowtie to search every single k-mer in the
genome and filter non-unique k-mers afterwards. Due to these constraints
we excluded it from our benchmarks. From the authors’ benchmarks, we
can conclude that GenMap still outperforms Umap as GenMap needs less
than one hour without parallelization to compute the (k, 0)-mappability
(see table 1), while Umap needs about 200 hours. To verify our tool we compared the results to an exhaustive search
with Bowtie1 (Langmead et al. (2009)) by mapping every k-mer to all
its possible locations. From the number of mappings of each k-mer the
mappability can be computed and written to a bed file. This approach
yields identical results. We tested it by computing the (20, 1)-mappability
on an E. coli genome1. Locating all mapping positions of each k-mer with
a read mapper would be too inefficient on eukaryotic genomes. all k-mers
non-adjacent k-mers
Strain
Unique
Pseudo
∅Dist. Unique Pseudo
∅Dist. 2 Strains:
IAI1
O8
(GCA_000026265.1),
SE11
O152:H28
(GCA_000010385.1),
11128 O111:H- (GCA_000010765.1),
11368
O26:H11 (GCA_000091005.1) 1 https://github.com/cpockrandt/genmap/blob/master/tests/bowtie-test.sh References Antoniou, P., Daykin, J. W., Iliopoulos, C. S., Kourie, D., Mouchard, L., and Pissis,
S. P. (2009). Mapping uniquely occurring short sequences derived from high
throughput technologies to a reference genome. In Information Technology and
Applications in Biomedicine, ITAB 2009, pages 1–4. IEEE. Clermont, O., Bonacorsi, S., and Bingen, E. (2000). Rapid and simple determination
of theescherichia coli phylogenetic group. Applied and environmental
microbiology, 66(10), 4555–4558. B1, Strain 6
B1, Strain 5
B1, Strain 4
B1, Strain 3
A, Strain 2
A, Strain 1
(b) Six sequences belonging to two different phylogenetic groups. Marker sequences are highlighted in light and dark gray. They only occur
in one of the groups and are present in all of its strains. Fig. 4. Illustration of the experiments performed on E. coli sequences in tables 2 and 3. Derrien, T., Estellé, J., Sola, S. M., Knowles, D. G., Raineri, E., Guigó, R., and
Ribeca, P. (2012). Fast computation and applications of genome mappability. PloS
one, 7(1), e30377. Fonseca, N. A., Rung, J., Brazma, A., and Marioni, J. C. (2012). Tools for mapping
high-throughput sequencing data. Bioinformatics, 28(24), 3169–3177. Karimzadeh, M., Hoffman, M. M., Ernst, C., and Kundaje, A. (2018). Umap and Karimzadeh, M., Hoffman, M. M., Ernst, C., and Kundaje, A. (2018). Umap and
Bismap: quantifyinggenomeandmethylomemappability. NucleicAcidsResearch,
46(20), e120–e120. Kianfar, K., Pockrandt, C., Torkamandi, B., Luo, H., and Reinert, K. (2018). Optimum search schemes for approximate string matching using bidirectional
fm-index. bioRxiv, page 301085. Koehler, R., Issac, H., Cloonan, N., and Grimmond, S. M. (2010). The uniqueome:
a mappability resource for short-tag sequencing. Bioinformatics, 27(2), 272–274. Kucherov, G., Salikhov, K., and Tsur, D. (2016). Approximate string matching using a bidirectional index. Theoretical Computer Science, 638, 145–158. (b) Six sequences belonging to two different phylogenetic groups. Marker sequences are highlighted in light and dark gray. They only occur
in one of the groups and are present in all of its strains. (b) Six sequences belonging to two different phylogenetic groups. Marker sequences are highlighted in light and dark gray. They only occur
in one of the groups and are present in all of its strains. Lam, T. W., Li, R., Tam, A., Wong, S., Wu, E., and Yiu, S.-M. (2009). High
throughput short read alignment via bi-directional bwt. In Bioinformatics and
Biomedicine, 2009. BIBM’09. IEEE International Conference on, pages 31–36. IEEE. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. L. (2009). References Ultrafast and
memory-efficient alignment of short dna sequences to the human genome. Genome
biology, 10(3), R25. Fig. 4. Illustration of the experiments performed on E. coli sequences in tables 2 and 3. Fig. 4. Illustration of the experiments performed on E. coli sequences in tables 2 and 3. Marco-Sola, S., Sammeth, M., Guigó, R., and Ribeca, P. (2012). The gem mapper:
fast, accurate and versatile alignment by filtration. Nature methods, 9(12), 1185. Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T.,
Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017). A chromosome Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T.,
Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017). A chromosome
conformation capture ordered sequence of the barley genome. Nature, 544(7651),
427. Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Acknowledgements The authors acknowledge the support of the de.NBI network for
bioinformatics infrastructure, the Intel SeqAn IPCC and the IMPRS
for Computational Biology and Scientific Computing. This work was
supported in part by US National Institutes of Health grant R35-
GM130151. This work has been supported also by the Royal Society,
UK under international exchange schema grant IE161405. (a) Four strains belonging to the same phylogenetic group. The sequence
in light gray is conserved within this group and a marker sequence. The
light gray k-mers belonging to this marker sequence are also all found
in the other strains. The k-mers in dark gray are unique among all four
strains and allow distinguishing each of the strains. 4 Experiments Only k-mers were counted that perfectly separated the strains in A from B1,
i.e., if and only if the k-mer matched all strains of A and no strain of B1 and
vice versa. When searching for marker sequences we consider two use cases: on
the one hand we want to identify k-mers that match a sequence uniquely
to determine the exact strain. On the other hand, we want to search for
k-mers shared by many or all strains in the same phylogenetic group. To test this approach we used a data set of E. coli strains. It was shown
that E. coli can be grouped into four major phylogenetic groups (A, B1,
B2, and D), see Clermont et al. (2000). The authors identified two marker
genes (chuA and yjaA) and an anonymous DNA fragment (TspE4.C2)
whose combination of presence or absence in the genome can determine
the phylogenetic group. This example shows that mappability on multiple species or strains
can be used to identify possible marker sequences. Short k-mers could be Pockrandt et al. 6 used to search a data set of reads instead of searching for marker genes
that span multiple reads. Since computing the (30, 2)-mappability on a
few E. coli strains even takes less than a minute on a consumer laptop, this
method is suitable to be run on large sets of similar E. coli strains to identify
new marker sequences, even with errors accounting for uncertainty arising
from sequencing and mutations such as SNPs. read mapping process itself instead of the post-processing phase. During
the index-based search of a read the possible locations of the eventually
completely mapped read can be examined beforehand to filter repetitive
regions without repeat masking. This allows for new mapping strategies
to improve the running time of state-of-the-art read mappers and reduce
post-processing overhead (Pockrandt (2019)). Strain 4
Strain 3
Strain 2
Strain 1
(a) Four strains belonging to the same phylogenetic group. The sequence
in light gray is conserved within this group and a marker sequence. The
light gray k-mers belonging to this marker sequence are also all found
in the other strains. The k-mers in dark gray are unique among all four
strains and allow distinguishing each of the strains. Strain 4
Strain 3
Strain 2
Strain 1 GenMap: Ultra-fast Computation of Genome Mappability Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T. v. d., Hornes, M., Friters,
A., Pot, J., Paleman, J., Kuiper, M., et al. (1995). Aflp: a new technique for dna fingerprinting. Nucleic acids research, 23(21), 4407–4414. 5 Discussion and Outlook We have presented GenMap, a fast and exact algorithm to compute the
mappability of genomes up to e errors, which is based on the C++ sequence
analysislibrarySeqAn(Reinertetal.(2017)). Itissignificantlyfaster, often
by a magnitude than the algorithm from the widely used GEM suite while
refraining from heuristics. Patwardhan, A., Ray, S., and Roy, A. (2014). Molecular markers in phylogenetic
studies-a review. Journal of Phylogenetics & Evolutionary Biology, 2014. Pockrandt, C. (2019). Approximate String Matching - Improving Data Structures
and Algorithms. Ph.D. thesis, Freie Universität Berlin. Pockrandt, C., Ehrhardt, M., and Reinert, K. (2017). Epr-dictionaries: A practical
and fast data structure for constant time searches in unidirectional and bidirectional
fm indices In International Conference on Research in Computational Molecular Pockrandt, C., Ehrhardt, M., and Reinert, K. (2017). Epr-dictionaries: A practical
and fast data structure for constant time searches in unidirectional and bidirectional
fm indices. In International Conference on Research in Computational Molecular
Biology, pages 190–206. Springer. Mappability has already been used for various purposes (Derrien et al. (2012)). In this paper, we proposed a new application, the computation of
mappability on a set of genomes to identify marker sequences for grouping
and distinguishing genomes by short k-mers and illustrated it with a small
example on closely related E. coli strains. It is also suitable for large scale
data as demonstrated by the benchmarks on human and barley genomes in
section 3. fm indices. In International Conference on Research in Computational Molecula
Biology, pages 190–206. Springer. Ranjekar, P., Pallotta, D., and Lafontaine, J. (1976). Analysis of the genome of
plants: Ii. characterization of repetitive dna in barley (hordeum vulgare) and wheat
(triticum aestivum). Biochimica et Biophysica Acta (BBA)-Nucleic Acids and
Protein Synthesis, 425(1), 30–40. Reinert, K., Dadi, T. H., Ehrhardt, M., Hauswedell, H., Mehringer, S., Rahn, R., Kim,
J., Pockrandt, C., Winkler, J., Siragusa, E., et al. (2017). The seqan c++ template
library for efficient sequence analysis: a resource for programmers. Journal of
biotechnology, 261, 157–168. The ability to compute the mappability efficiently opens up new
applications such as incorporating the mappability information into the 7 GenMap: Ultra-fast Computation of Genome Mappability fingerprinting. Nucleic acids research, 23(21), 4407–4414.
|
https://openalex.org/W4224884305
|
https://sciendo.com/pdf/10.2478/pomr-2022-0006
|
English
| null |
An Acoustic Sea Glider for Deep-Sea Noise Profiling Using an Acoustic Vector Sensor
|
Polish Maritime Research
| 2,022
|
cc-by
| 3,202
|
POLISH MARITIME RESEARCH 1 (113) 2022 Vol. 29; pp. 57-62
10.2478/pomr-2022-0006 Abstract An acoustic sea glider has been developed for ambient sea noise measurement and target detection through the
deployment of an acoustic vector sensor (AVS). The glider was designed with three cabins connected in sequence and
it can dive to depths exceeding 1200m. The AVS fixed on the glider measure acoustic pressure and particle velocities
related to undersea noise, and the inner attitude sensors can effectively eliminate the estimation deviation of the
direction of arrival. The inherent self-noises of the acoustic sea glider and AVS are presented respectively in respect to
the Knudsen spectra of sea noise. Sea trial results indicate that the AVS could work well for undersea noise measurement
when the glider is smooth sliding, and the target azimuth estimated by AVS after correction is remarkably consistent
with the values measured by the GPS, and direction-finding errors are less than 10 degrees. The research in this paper
shows that the acoustic sea glider is able to undertake tasks such as a wide range of underwater acoustic measurement
and detection. Keywords: acoustic sea glider; acoustic vector sensor; ambient sea noise; target detection Keywords: acoustic sea glider; acoustic vector sensor; ambient sea noise; target detection AN ACOUSTIC SEA GLIDER FOR DEEP-SEA NOISE PROFILING
USING AN ACOUSTIC VECTOR SENSOR Qindong Sun 1,2
Hongkun Zhou *3,4
1 Naval Submarine Academy, Qingdao , China
2 Pilot National Laboratory for Marine Science and Technology (Qingdao), China
3 China Ship Scientific Research Center, Wuxi, China
4 Taihu Laboratory of Deepsea Technology and Science, Wuxi, China
* C
di
h
h
hk 02 126
(H Zh
) Qindong Sun 1,2
Hongkun Zhou *3,4
1 Naval Submarine Academy, Qingdao , China
2 Pilot National Laboratory for Marine Science and Technology (Qingdao), China
3 China Ship Scientific Research Center, Wuxi, China
4 Taihu Laboratory of Deepsea Technology and Science, Wuxi, China * Corresponding author: zhouhk702@126.com (H. Zhou) INTRODUCTION data. Low-frequency acoustic signals produced by tsunamis,
undersea earthquakes, large mammals and artificial vessels are
of increasing concern in the area of natural disaster monitoring
and marine ecological protection [3],[4]. Moreover, the
detection and identification of surface and underwater objects
using acoustic sensors are another aspect of great concern
in ship navigation [5],[6]. In order to achieve high-efficiency
marine investigation and target detection, the integration of
acoustic sensors on underwater moving platforms such as
AUVs has become a new research hotspot [7],[8].h The sea glider is a long-range autonomous underwater
vehicle (AUV), utilising the buoyancy of sea water as the
driving force and converting vertical motion to horizontal in
conjunction with wings [1]. It can float upward and dive by
only adjusting the density with very low energy consumption. Consequently, the sea glider can be much quieter and more
energy-efficient compared to AUVs with propellers, since it
is gliding instead of propelling [2]. The acoustic sea glider, a kind of specially designed
glider with low self-noise from machinery and electricity,
is appropriate for acoustic sensors with their negligible
hydrodynamic noise induced by low-speed motion [9],[10]. As
a result, some acoustic sensors have been tentatively employed
on the sea glider in the area of natural disaster monitoring and
military surveillance [11]-[13]. Inherently, the temperature and salinity of sea water
along with depth are the basic parameters of the ocean, and
consequently conductivity, temperature and depth (CTD)
sensors are the most widely used sensors in surveys of ocean
physics. However, further intensive investigation for a better
understanding of the ocean needs to be performed and
more special sensors are being employed to collect various POLISH MARITIME RESEARCH, No 1/2022 57 Fig. 1. Exploded view of the acoustic sea glider Fig. 1. Exploded view of the acoustic sea glider The head cabin located at the front end of the glider is mainly
for installing sensors, including an acoustic module, CTD
sensors and buoyancy materials. The acoustic module includes
a composite AVS with an acoustic dome and the related signal
processor. The acoustic dome is made of polyurethane material
to ensure the penetrability of sound waves and alleviate the
influence of flow noise, and the AVS is flexibly suspended
inside the dome with metal springs. The dome connects the
head cabin through an aluminium alloy rod, to keep away from
the disturbed stream. INTRODUCTION The acoustic signal processor, situated in
the head cabin, is used to collect and store the output signals
derived from the AVS. The whole head cabin is exposed to the
water and all sensors and parts must be waterproof.h Compared to acoustic pressure sensors or hydrophones,
the acoustic glider based on acoustic vector sensors (AVS)
shows great superiority in underwater acoustic measurement
[14]. A single composite AVS measuring the acoustic pressure
and particle velocities (acceleration, displacement or pressure
gradient) synchronously can achieve a good signal-to-noise ratio
of low-frequency acoustic signals instead of the conventional
large-scale hydrophone array [15]. An AVS is insensitive to
isotropic noise due to natural cosine directivities and it can
be easily integrated on compact and lightweight underwater
vehicles [16]. In terms of target detection, the direction of
arrival of a target relative to the AVS can be estimated through
acoustic intensity processing, and then the absolute bearing
angle can be corrected using attitude information of the AVS
relative to the geographic coordinate system.h The middle cabin is divided into three separate pressurised
compartments. A set of batteries and a drive mechanism are
installed in the first compartment, constituting an attitude
adjustment module, and hence the desired pitch angle of the
glider can be achieved through the movement of batteries. In
the second compartment there is a navigation and controller
module, and another set of batteries is installed for providing
extra electric power. A buoyancy adjustment module is
located in the third compartment, and actually it works as
an underwater oil pump that changes the buoyancy through
filling in and pumping out the oil from the oilcan. A pair
of carbon-fibre wings is fixed on the two sides of the third
compartment for pitch attitude adjustment.h This paper presents an acoustic sea glider equipped with
an inertial-type AVS for deep-sea noise collection. The AVS
design integrates one omnidirectional hydrophone, a triaxial
accelerometer and the attitude sensors. The acoustic sensitivities
and self-noise of the AVS were obtained through laboratory
calibrations as well as the glider-radiated noise. Finally, the
direction of arrival (DOA) estimation using the AVS on the
acoustic sea glider was verified through a sea trial in the South
China Sea. SENSOR DESIGN used to achieve orientation correction during signal post-
processing. The attitude sensors, including a triaxial MEMS
gyroscope, a MEMS accelerometer and a MEMS magnetometer,
measure the angular velocity, gravitational acceleration and
magnetic flux density respectively. The attitude sensors
are located on the circuit board which is supported on the
piezoelectric accelerometer. The high-performance single-chip
microcomputer based on an ARM-Cortex core on the same
circuit board is used to achieve functions such as control,
attitude data acquisition and angle calculation.h The miniature and low-power CTD sensors (RBRlegato³) are
directly installed on the head of the sea glider with the probe
exposed to the seawater, as shown in Fig. 2. Conventionally,
the conductivity, temperature and depth data are recorded per
second respectively. The composite AVS flexibly suspended
inside the acoustic dome mainly consists of a hydrophone,
a triaxial piezoelectric accelerometer and attitude sensors. The
hydrophone and piezoelectric accelerometer sense the acoustic
pressure and particle velocity respectively. The dimensions of
the designed AVS are Ø66 × 78 mm with an average density
of 1.15 g/cm3. Test results indicate that the sensitivity of the
hydrophone is −191.5 dB (0 dB re 1 V/μPa), and the sensitivities
of the triaxial piezoelectric accelerometer are 2.85 V/g, with the
equivalent pressure sensitivities of −179 dB (0 dB re 1 V/μPa at
1 kHz). The working bandwidth of the AVS can extend from
10 Hz to 3 kHz.h The attitude sensors’ accuracies were tested at the First
Metrology and Test Center of National Defense Technology
Industry, China. Calibration frequencies were chosen as 0.1
Hz to 2 Hz since the motions induced by sea currents, tides
and surges are conventionally below 1 Hz. Test results indicate
that the measured heading and roll angle errors are less than
0.5° and the pitch angle error is less than 0.4° when the attitude
angles do not exceed 20°. The underwater sea current will change the orientation of an
AVS that is mounted on a moving platform, and consequently
it is necessary to measure the real-time azimuth and attitude
information of the AVS. Conventional countermeasures are
directly installed on an electronic compass and an attitude
sensor on the platform or vehicle. However, these methods
may be less accurate because of the flexible suspension of
the AVS and installation deviations of the attitude sensors. Therefore, attitude sensors are integrated into the AVS with
acoustic sensors, and then the extended Kalman filter is Fig. GLIDER DESIGN The tail cabin is immersed in the seawater just like the
head cabin. An oil bag installed in this cabin is part of the
buoyancy adjustment module. An iridium antenna for surface
communications and a configurable propeller for providing
short-term thrust are deployed outside the tail cabin. The acoustic sea glider is 3.2 m in length and 0.25 m in
diameter. It is designed for the maximum diving depth of
1200 m with an endurance of 60 days at the average speed of
one knot. The glider structure consists of three independent
cabins as presented in Fig. 1. POLISH MARITIME RESEARCH, No 1/2022 58 Fig. 2. CTD sensors and acoustic vector sensor Fig. 2. CTD sensors and acoustic vector sensor Fig. 2. CTD sensors and acoustic vector sensor POLISH MARITIME RESEARCH, No 1/2022 TARGET DETECTION EXPERIMENTS The DOA of a target can be estimated through acoustic
intensity processing. Acoustic intensity is generally a complex
quantity that describes the propagating power associated with
a sound wave in an acoustic medium, and it is mathematically
expressed as the cross spectrum between the pressure and
particle velocity in the frequency domain. Therefore the active
intensity component that describes the transport of acoustic
power can be used to determine the bearing of a sound source
without ambiguity. During target detection experiments
a scientific research ship, 42 m in length and 6 m in width,
served as the target. The glider dived twice in total to depths
of 579 m and 962 m respectively, and acquisition of the ship’s
radiated noise was executed by the AVS on the acoustic sea
glider during the first dive. The outputs of the attitude sensors
are presented in Fig. 5(a), and it can be observed that the
underwater glider adjusts the heading frequently between −10°
and 10°, making itself move forward as scheduled. Fig. 5(b)
shows the azimuths of the target ship estimated by AVS with
no attitude correction and veracious azimuths measured
by the GPS from the time of 15:16 to 16:17; obviously, the
glider’s movement caused serious deviations. Fig. 5(c) shows
the estimated azimuths after attitude correction (extended
Kalman filter), which are very close to the values measured by
the GPS, and the bearing accuracy achieved was better than 10°. SENSOR DESIGN 3(a) illustrates the self-noise characteristics of the AVS
from 20 Hz to 4 kHz, and the Knudsen ambient sea noise
levels at sea states 0 to 3 are also presented for comparison. The
results show that the self-noise of the hydrophone is 36 dB/√Hz
at 1 kHz, which is lower than Knudsen’s ambient noise of
zero order sea level, and the self-noises of the vector channels
gradually decrease and approach sea state 3 when the frequency
is increased to 100 Hz. In addition, the acoustically radiated noise from the acoustic
sea glider was tested from 20 Hz to 4 kHz in the anechoic tank Fig. 3. Self-noise of AVS (a) and radiated noise from the acoustic sea glider (b) d
i
f
h
i
lid
(b) Fig. 3. Self-noise of AVS (a) and radiated noise from the acoustic sea glider (b) POLISH MARITIME RESEARCH, No 1/2022 59 Fig. 4. CTD and ambient sea noise data collected through acoustic sea glider in the South China Sea Fig. 4. CTD and ambient sea noise data collected through acoustic sea glider in the South China Sea (pressure sensor), acoustic particle velocity sensors (triaxial
accelerometer) are more sensitive to high-frequency structure-
borne noise, and hence low-pass filters are essential in the
signal post-processing. under different working conditions and the result is provided
in Fig. 3(b). It is obvious that radiated noise from the glider
under battery sliding is lower than other conditions, although
it is almost 20 dB higher than the hydrophone’s self-noise from
400 Hz to 3 kHz. When the oil pump starts up, the radiated
noise increases as the noise peaks around 400 Hz and 1 kHz
respectively. The propeller, used for emergency manoeuvres,
has the most serious influence on the noise, and the peak
noise level exceeds 90 dB at 700 Hz when sailing at 3 knots. The measured noise level below 100 Hz may be less accurate
due to the size limitation of the anechoic tank. CONCLUSIONS measurements in the coastal zone”, Polish Maritime Research. 2020. Vol. 27(2), 168‒175, doi: 10.2478/pomr-2020-0038. Propeller-less propulsion and stable movement make the
sea glider the perfect underwater moving platform for various
acoustic measurements. A dedicated acoustic sea glider was
developed for underwater wide-range measurements of ambient
sea noise and vessel-radiated noise in this paper, through
incorporating an inertial-type acoustic vector sensor (AVS). The AVS located at the front end of the glider successfully
measured underwater noise relating to sound pressure and
particle velocity together with attitude angles. Test results
in the anechoic tank show that the AVS has comparatively
low self-noise, and the radiated noise is acceptable when the
acoustic sea glider is sliding. Sea trial results demonstrated that
the AVS worked well when the acoustic sea glider was diving
from the surface down to the deep sea. The bearing accuracy
of the target through the AVS on the sea glider is better than
10° after attitude correction. This research is of important
significance for the application of AVS on acoustic sea gliders,
and moreover underwater observation could be more effective
in both the military and civilian fields with the employment
of a sea glider cluster and various acoustic sensors. 6. Y. Ju, Z. Wei, L. Huangfu, et al., “A new low SNR underwater
acoustic signal classification method based on intrinsic
modal features maintaining dimensionality reduction”, Polish
Maritime Research. 2020. Vol. 27(2), 187‒198, doi: 10.2478/
pomr-2020-0040. 7. M.R. Benjamin, D. Battle, D. Eickstedt, et al., “Autonomous
control of an autonomous underwater vehicle towing a vector
sensor array”, Proceedings of IEEE International Conference
on Robotics and Automation, Rome, Italy, 2007. 4562‒4569,
doi: 10.1109/robot.2007.364182. 8. A. Mantouka, P. Felisberto, P. Santos, et al., “Development
and testing of a dual accelerometer vector sensor for AUV
acoustic surveys”, Sensors. 2017. Vol. 17(6), 1328, doi:
10.3390/s17061328. 9. L. Liu, L. Xiao, S. Lan, et al., “Using Petrel II glider to analyze
underwater noise spectrogram in the South China Sea”,
Acoustic Australia. 2018. Vol. 46(2), 1–8,10. doi: 10.1007/
s40857-018-0126-y. ACKNOWLEDGEMENTS 10. C. Jiang, J. Li, W. Xu, “The use of underwater gliders
as acoustic sensing platforms”, Applied Sciences. 2019. Vol. 9(22), 4839, doi: 10.3390/app9224839. This work was supported by the Programs for National
Key R&D Plan (Grant No. 2019YFC0311700), Natural Science
Foundation of Jiangsu Province (Grant No. BK20180171), and
Wenhai Plan (Grant No. 2017WHZZB0601) of Pilot National
Laboratory for Marine Science and Technology in Qingdao
of China. 11. S.E. Moore, B.M. Howe, K.M. Stafford, et al., “Including whale
call detection in standard ocean measurements: application
of acoustic sea gliders”, Marine Technology Society Journal. 2007. Vol. 41(4), 53–57, doi: 10.4031/002533207787442033. AMBIENT SEA NOISE GATHERING Underwater noise measurement experiments were
conducted based on the acoustic sea glider in the northern
part of the South China Sea in May 2020. During the sea
trial, the glider dived from the surface to a depth of 1000 m
and the deep-water noise was recorded simultaneously. The
conductivity and temperature at the depth from 700 m to 800 m
are presented with a 1 Hz sampling rate as shown in Fig. 4,
and hence the resulting sound velocity profile could be easily
achieved. Acoustic ambient sea noises were faithfully recorded
by the AVS under a 20 kHz sampling rate, benefiting from the
lower background noise of the acoustic sea glider. The collected
noise data related to the four sensors, i.e. the hydrophone and
the triaxial piezoelectric accelerometer. Unlike the hydrophone Fig. 5. Outputs of the attitude sensors when the glider is diving (a) and DOA estimation results before attitude correction (b) and after attitude correction (c) attitude sensors when the glider is diving (a) and DOA estimation results before attitude correction (b) and after attitude correction (c) Fig. 5. Outputs of the attitude sensors when the glider is diving (a) and DOA estimation results before attitude correction (b) and af POLISH MARITIME RESEARCH, No 1/2022 POLISH MARITIME RESEARCH, No 1/2022 60 POLISH MARITIME RESEARCH, No 1/2022 REFERENCES 12. H. Matsumoto, S.E. Stalin, R. W. Embley, et al., “Hydroacoustics
of a submarine eruption in the Northeast Lau Basin using an
acoustic glider”, Oceans 2010 MTS/IEEE Seattle. WA, USA,
2010. 1‒6, doi: 10.1109/oceans.2010.5664494. 1. X. Wu, P. Yu, G. Li, et al., “Numerical study of the effect
of wing position on the dynamic motion characteristics
of an underwater glider”, Polish Maritime Research. 2021. Vol. 28(2), 4‒17, doi: 10.2478/pomr-2021-0016. 13. L. Uffelen, E.H. Roth, B.M. Howe, et al., “A seaglider
integrated digital monitor for bioacoustic sensing”, IEEE
Journal of Oceanic Engineering. 2017. Vol. 42(4), 800–807,
doi: 10.1109/joe.2016.2637199. 2. R. Zimmerman, G.L. D’Spain and C.D. Chadwell,
“Decreasing the radiated acoustic and vibration noise of
a mid-size AUV”, IEEE Journal of Oceanic Engineering. 2005. Vol. 30(1), 179‒187, doi: 10.1109/joe.2004.836996. 14. P. Stinco, P. Guerrini, A. Tesei, et al., “Passive acoustic
signal processing at low frequency with a 3-D acoustic
vector sensor hosted on a buoyancy glider”, IEEE Journal of
Oceanic Engineering. 2021. Vol. 46(1), 283‒293, doi: 10.1109/
joe.2020.2968806. 3. K. Buszman, “Analysing the impact on underwater noise
of changes to the parameters of a ship’s machinery”, Polish
Maritime Research. 2020. Vol. 27(3), 176‒181, doi: 10.2478/
pomr-2020-0059. 4. X. Yan, H. Song, Z. Peng, et al., “Review of research results
concerning the modelling of shipping noise”, Polish
Maritime Research. 2021. Vol. 28(2), 102‒115, doi: 10.2478/
pomr-2021-0027. 15. K. Kim, T.B. Gabrielson and G.C. Lauchle, “Development
of an accelerometer-based underwater acoustic intensity
sensor”, Journal of the Acoustical Society of America. 2004. Vol. 116(6), 3384‒3392, doi: 10.1121/1.1804632. 5. K. Buszman and M. Gloza, “Detection of floating objects
based on hydroacoustic and hydrodynamic pressure 16. V.A. Gordienko, Vector-Phase Methods in Acoustics,
Fizmatlit (in Russian). 2007. POLISH MARITIME RESEARCH, No 1/2022 61 CONTACT WITH THE AUTHORS CONTACT WITH THE AUTHORS
Qindong Sun
e-mail: sqd2010@163.com
Naval Submarine Academy
No. 1, Jinshui Road, Licang District
266199 Qingdao
Pilot National Laboratory for Marine Science
and Technology (Qingdao)
No.168 Wenhai Zhong Lu, Jimo District
266237 Qingdao
China
Hongkun Zhou
e-mail: zhouhk702@126.com
China Ship Scientific Research Center
No. 222 Shanshui East Road Binhu District
214082 Wuxi
China
Taihu Laboratory of Deepsea Technology and Science
No. 222 Shanshui East Road Binhu District
214082 Wuxi
China POLISH MARITIME RESEARCH, No 1/2022 62
|
https://openalex.org/W4309713187
|
https://www.frontiersin.org/articles/10.3389/fped.2022.1052440/pdf
|
English
| null |
Ureteropelvic junction obstruction in infants: Open or minimally invasive surgery? A systematic review and meta-analysis
|
Frontiers in pediatrics
| 2,022
|
cc-by
| 7,019
|
TYPE Systematic Review
PUBLISHED 23 November 2022
DOI 10.3389/fped.2022.1052440 TYPE Systematic Review
PUBLISHED 23 November 2022
DOI 10.3389/fped.2022.1052440 Ureteropelvic junction
obstruction in infants: Open or
minimally invasive surgery?
A systematic review and
meta-analysis EDITED BY
Simone Sforza,
University of Florence, Italy
REVIEWED BY
Gilvydas Verkauskas,
Vilnius University, Lithuania
Peng Hong,
Peking University Third Hospital, China
*CORRESPONDENCE
Giuseppe Lauriti
giuseppe.lauriti@unich.it
SPECIALTY SECTION
This article was submitted to Pediatric Urology,
a section of the journal Frontiers in Pediatrics
RECEIVED 23 September 2022
ACCEPTED 31 October 2022
PUBLISHED 23 November 2022
CITATION
Cascini V, Lauriti G, Di Renzo D, Miscia M and
Lisi G (2022) Ureteropelvic junction obstruction
in infants: Open or minimally invasive surgery? A systematic review and meta-analysis. Front. Pediatr. 10:1052440. doi: 10.3389/fped.2022.1052440
COPYRIGHT
© 2022 Cascini, Lauriti, Di Renzo, Miscia and
Lisi. This is an open-access article distributed
under the terms of the Creative Commons
Attribution License (CC BY). The use,
distribution or reproduction in other forums is
permitted, provided the original author(s) and
the copyright owner(s) are credited and that the
original publication in this journal is cited, in
accordance with accepted academic practice. No use, distribution or reproduction is
permitted which does not comply with these
terms. EDITED BY
Simone Sforza,
University of Florence, Italy
REVIEWED BY
Gilvydas Verkauskas,
Vilnius University, Lithuania
Peng Hong,
Peking University Third Hospital, China
*CORRESPONDENCE
Giuseppe Lauriti
giuseppe.lauriti@unich.it
SPECIALTY SECTION
This article was submitted to Pediatric Urology,
a section of the journal Frontiers in Pediatrics
RECEIVED 23 September 2022
ACCEPTED 31 October 2022
PUBLISHED 23 November 2022
CITATION EDITED BY
Simone Sforza,
University of Florence, Italy
REVIEWED BY
Gilvydas Verkauskas,
Vilnius University, Lithuania
Peng Hong,
Peking University Third Hospital, China Valentina Cascini
1, Giuseppe Lauriti
2,3*, Dacia Di Renzo
1,
Maria Enrica Miscia
2,3 and Gabriele Lisi
2,3 1Pediatric Surgery Unit, “Spirito Santo” Hospital of Pescara, Pescara, Italy, 2Department of Medicine
and Aging Science, “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy, 3Pediatric Surgery Unit,
“Spirito Santo” Hospital of Pescara, Pescara, Italy Introduction: The historical gold standard treatment for ureteropelvic junction
obstruction (UPJO) was the open Anderson–Hynes dismembered pyeloplasty
(OP). Minimally invasive surgery (MIS) procedures, including laparoscopic
pyeloplasty (LP) and robot-assisted laparoscopic pyeloplasty (RALP), have been
reported to achieve better outcomes (i.e., decreased morbidity, reduced
postoperative pain, superior esthetic results, and shortened length of hospital
stay, LOS), with a success rate similar to OP. The main limitation of the MIS
approach is the age and weight of patients, limiting these procedures to
children >1 year. This study aims to evaluate the feasibility and benefits of MIS
pyeloplasty compared to OP to surgically treat UPJO in children <1 year of age. Materials and methods: A systematic review was independently performed by
two authors. Papers comparing both techniques (MIS pyeloplasty vs. OP) in
infants were included in the meta-analysis. Data (mean ± DS or percentage)
were analyzed using Rev.Man 5.4 A p < 0.05 was considered significant. CITATION Cascini V, Lauriti G, Di Renzo D, Miscia M and
Lisi G (2022) Ureteropelvic junction obstruction
in infants: Open or minimally invasive surgery? A systematic review and meta-analysis. Front. Pediatr. 10:1052440. doi: 10.3389/fped.2022.1052440 COPYRIGHT
© 2022 Cascini, Lauriti, Di Renzo, Miscia and
Lisi. This is an open-access article distributed
under the terms of the Creative Commons
Attribution License (CC BY). The use,
distribution or reproduction in other forums is
permitted, provided the original author(s) and
the copyright owner(s) are credited and that the
original publication in this journal is cited, in
accordance with accepted academic practice. No use, distribution or reproduction is
permitted which does not comply with these
terms. Results: Nine studies (eight retrospective and one prospective) meet the
inclusion criteria. A total of 3,145 pyeloplasties have been included, with 2,859
(90.9%) OP and 286 (9.1%) MIS. Age at operation was 4.9 ± 1.4 months in OP
vs. 5.8 ± 2.2 months in MIS, p = ns. Weight at surgery was 6.4 ± 1.4 kg in OP vs. 6.9 ± 1.4 kg in MIS, p = ns. Operative time was 129.4 ± 24.1 min for OP vs. 144.0 ± 32.3 min for MIS, p < 0.001. LOS was 3.2 ± 1.9 days for OP vs. 2.2 ± 0.9
days for MIS, p < 0.01. Postoperative complications were present in 10.0 ±
12.9% of OP vs. 10.9 ± 11.6% in MIS, p = ns. Failure of surgery was 5.2 ± 3.5% for
OP vs. 4.2 ± 3.3% for MIS, p = ns. Conclusion: The development of miniaturized instruments and technical
modifications has made MIS feasible and safe in infants and small children. MIS
presented a longer operative time than OP. However, MIS seemed effective for
treating UPJO in infants, showing shortened LOS compared to OP. No
differences have been reported with regard to the incidence of postoperative
complications and failure of pyeloplasty. Given the low quality of evidence of
the meta-analysis according to the GRADE methodology, we would suggest
limiting MIS procedures in infants to only those high-volume centers with
experienced surgeons. Frontiers in Pediatrics frontiersin.org 01 Cascini et al. 10.3389/fped.2022.1052440 KEYWORDS ureteropelvic
junction
obstruction,
Anderson–Hynes
dismembered
pyeloplasty,
minimally
invasive surgery, infants, systematic review, meta-analysis ureteropelvic
junction
obstruction,
Anderson–Hynes
dismembered
pyeloplasty,
minimally
invasive surgery, infants, systematic review, meta-analysis Introduction present study, we aimed to compare the outcomes of OP vs. MIS (both LAP and RALP) in infants affected by UPJO. The historical gold standard for the treatment of pediatric
ureteropelvic junction obstruction (UPJO) was the open
Anderson–Hynes
dismembered
pyeloplasty
(OP),
with
a
reported success rate of 90%–100% (1). Materials and methods Over the last decades, minimally invasive surgery (MIS)
procedures, i.e., conventional laparoscopic pyeloplasty (LAP)
and robot-assisted laparoscopic pyeloplasty (RALP), have
been reported to be a possible replacement for OP (2). Few
reports and a recent meta-analysis have confirmed that both
LAP and RALP seemed safe and effective (3–7). Moreover, a
multicenter study comparing both approaches in pediatrics
has confirmed how both procedures were safe and as
successful as OP, with an incidence of failure of <5% (2). Moreover, LAP and RALP have been reported to correlate
with
several
advantages,
such
as
decreased
morbidity,
reduced postoperative pain, superior esthetic results, and
shortened length of hospital stay (LOS). The main limit to
the MIS approach has been reported to depend on the age
and weight of the patients, limiting these procedures to
children >1 year (1, 8). Since the publication of Tan’s work
in 1999 (9), where LAP was not recommended in small
children, there has been a doubt about performing LAP in
small children. The main concerns were related to the
operative field offered by a pneumoperitoneum in infants,
the limited space for port placement, the small working
space, and the small ureteral diameter. However, following
studies have established that LAP was safe and feasible in
infants (10, 11). frontiersin.org Data sources and study selection The
present
study
was
registered
on
PROSPERO
(registration # CRD42022358981), an international database of
prospectively registered systematic reviews (National Institute
for Health Research) (14). The systematic review was drafted
according to the Preferred Reporting Items for Systematic
Reviews and Meta-Analyses (PRISMA) statement (15). Using a stated search strategy (Table 1), two investigators
(VC,
GLa)
individually
screened
the
main
databases
(PubMed/Medline, Scopus, Web of Science, and Cochrane)
with combined keywords. MeSH headings and terms used
were “Pyeloplasty” AND “Infants” (Supplementary material
S1). Studies published from 1984 to August 2022 in English
language were included. The list of references was screened as
well to detect possible pertinent cross references. Case reports,
opinion articles, and reviews were excluded. All comparative
studies reporting the outcomes of OP compared to those of
MIS (i.e., LAP and/or RALP) to treat UPJO in infants or
patients <15 kg were included. The full text of theoretically
suitable papers was retrieved and individually assessed for
eligibility by the same two authors. Any divergence over the
entitlement of papers was solved through a further debate
with a third author (GLi). fants (10, 11). More recently, RALP seemed to have advantages of
maneuverability, improved vision, comfort in suturing, and
improved ergonomics compared to LAP (4, 6). The main
issues in RALP are the absence of correct-sized trocars for
infants and the shortage of robots in most pediatric units
because of their cost (2, 8). It has been reported how MIS
pyeloplasty was extremely uncommon in infants, even if the
incidence of RALP procedures has boosted over the last
years
(12). Following
an
increased
knowledge
of
MIS
pyeloplasty, there have been few publications on LAP and
RALP in infants over the last few years. However, most of
them have reported outcomes in a reduced number of cases. RALP has been reported to simplify the MIS approach in
children,, with results comparable to OP (13). However, to the
best of our knowledge, only a few studies were focused on
infants. Those
comparing
the
results
of
the
different
approaches (OP vs. MIS) were extremely scarce. In the TABLE 1 Inclusion criteria of the systematic review. Publication
Language
English
Time period
January 1984–August 2022
Subject
Human studies
Study type
Retrospective
Prospective
Case–control
Cohort
Excluded
Case report
Case series (<10 patients)
Editorials
Letters
Gray literature
Keywords
Pyeloplasty
Infants
2
frontiersin.org TABLE 1 Inclusion criteria of the systematic review. Publication
Language
English
Time period
January 1984–August 2022
Subject
Human studies
Study type
Retrospective
Prospective
Case–control
Cohort
Excluded
Case report
Case series (<10 patients)
Editorials
Letters
Gray literature
Keywords
Pyeloplasty
Infants
frontiersin.org TABLE 1 Inclusion criteria of the systematic review. Publication
Language
English
Time period
January 1984–August 2022
Subject
Human studies
Study type
Retrospective
Prospective
Case–control
Cohort
Excluded
Case report
Case series (<10 patients)
Editorials
Letters
Gray literature
Keywords
Pyeloplasty
Infants TABLE 1 Inclusion criteria of the systematic review. Publication
Language
English
Time period
January 1984–August 2022
Subject
Human studies
Study type
Retrospective
Prospective
Case–control
Cohort
Excluded
Case report
Case series (<10 patients)
Editorials
Letters
Gray literature
Keywords
Pyeloplasty
Infants
frontiersin.org TABLE 1 Inclusion criteria of the systematic review. Frontiers in Pediatrics frontiersin.org 02 10.3389/fped.2022.1052440 Cascini et al. median and range were reported, mean ± SD were valued
(16). The studies comparing OP vs. MIS for the Anderson–Hynes
pyeloplasty in infants were included in the meta-analysis. The
exclusion criteria are as follows: The meta-analysis was managed with RevMan 5.4 (17). The
random effects model was selected. The risk ratio (RR) was
assessed for categorical variables. fants (10, 11). Differently, mean differences
(MD) were preferred in the case of continuous variables. Both
results were reported with 95% confidence intervals (CIs). Data were expressed as mean ± SD. I2 values were used to
judge homogeneity and quantify the dispersion of effect sizes. Biases among the papers included were evaluated with the
funnel
plot. Quantitative
and
demographic
data
were
compared using Fisher’s exact test and expressed as number,
percentage,
or
mean ± SD
using
the
RR
and
95%
CI. A p < 0.05 was considered significant. • treatment
other
than
Anderson–Hynes
pyeloplasty,
retroperitoneoscopy, OTAP, recurrent UPJO, secondary
UPJO, patients >1 year; and • studies without valid data about the comparison of these two
techniques. Systematic review The initial review retrieved 811 studies from databases using
keywords “Pyeloplasty” AND “Infants.” Thanks to the screening
of all these titles and abstracts, we selected 70 papers focusing
on infants or children <15 kg of weight with UPJO. Among
these, only 13 publications were comparative studies between
OP vs. MIS (1, 13, 22–32) (Figure 1). Six studies (1, 22, 24, 25, 27, 31) described OP vs. LAP, and
one was excluded (31) due to incomplete data. Three papers
treating OP vs. RALP (26, 30, 32) were included. Two studies
compared OP vs. LAP + RALP (13, 28); one was excluded
(28) due to incomplete information. Two papers (23, 29)
treating RALP vs. LAP were excluded. TABLE 2 Demographic data of papers included in the meta-analysis. TABLE 2 Demographic data of papers included in the meta-analysis. OP
MIS
p-Value
M (%)
2,092/2,859 (73.2)
209/286 (73.1)
ns*
F (%)
767/2,859 (26.8)
77/286 (26.9)
Left kidney (%)
162/279 (58.1)
101/183 (55.2)
ns*
Right kidney (%)
117/279 (41.9)
82/183 (44.8)
Age (months)
4.9 ± 1.4
5.8 ± 2.2
ns
Weight (kg)
6.4 ± 1.4
6.9 ± 1.4
ns
Follow-up (months)
21.5 ± 8.1
13.9 ± 4.7
ns
OP, open pyeloplasty; MIS, minimally invasive surgery. *Fisher’s exact test. Data analysis Categorical variable rates were compared with Pearson’s
χ2 test or two-tailed Fisher’s exact probability test. When FIGURE 1
Diagram of workflow in the systematic review and meta-analysis. Diagram of workflow in the systematic review and meta-analysis. frontiersin.org 03 Frontiers in Pediatrics Cascini et al. 10.3389/fped.2022.1052440 Quality assessment 75%–100%, respectively (20). If a score overlapped two
groups,
we
inserted
a
mixed
inconsistency
(e.g.,
low/
moderate) in our GRADE table. Finally, imprecision was
evaluated with optimal information size (OIS) based on 25%
relative risk reduction, 0.05 a-error, and 0.20 b-error (21). Two authors (DDR and MEM) assessed the risk of bias for
individual studies. This assessment was achieved with a
methodological index for nonrandomized studies (MINORS)
(18). Dissimilarities between the two authors (DDR and
MEM) were solved through a discussion with a third author
(GLi). The score for this index ranges between 0 and 24
points. The “gold standard” cutoff was 19.8 points. With
regard to the quality of each outcome, we graded the quality
of evidence, thanks to the Grading of Recommendations
Assessment,
Development
and
Evaluation
(GRADE)
methodology (19). The quality of evidence was graded as
high, moderate, low, and very low in all results. Observational
studies were assessed as low quality of evidence. The quality
of evidence was further reduced in the case of risk of bias,
inconsistency, indirectness imprecision, and publication bias. MINORS
was
adopted
to
judge
the
risk
of
bias
in
observational papers. Inconsistency was determined according
to
heterogeneity,
and
I2
value
was
used
to
evaluate
heterogeneity. As
established
in
Cochrane
guidelines,
heterogeneity was assessed as low, moderate, substantial, and
considerable when I2 values were 0–40, 30–60, 50–90, and Meta-analysis Nine articles were included in the meta-analysis, eight
retrospective
studies
(1,
22,
24–27,
30,
32)
and
one
prospective study (13). The total number of pyeloplasties performed in infants and
patients <15 kg of weight was 3,145, with 2,859 (90.9%) OP and
286 (9.1%) MIS, comprising 145 (50.7%) LAP and 141 (49.3%)
RALP. The M/F ratio was 3:1, with 2,301M (73.2%) and 844F
(26.8%). Of 2,859 OP patients, 2,092 were males (73.2%) and
767 were females (26.8%); of 286 in the MIS group, 209 were
males
(73.1%)
and
77
were
females
(26.9%),
with
no FIGURE 2
Forest plot comparison of age at procedure between OP and MIS in infants. Frontiers in Pediatrics frontiersin.org 04 frontiersin.org Cascini et al. 10.3389/fped.2022.1052440 differences between OP and MIS groups [p = ns, RR: 1.001, 95%
CI: (0.93–1.08), Table 2]. The side of the kidney affected by UPJO has been reported
in seven papers (1, 22, 24–26, 30, 32), with 462 patients (279
OP and 183 MIS). Of 279 OP patients, 162 had left kidneys
affected (58.1%) and 117 had right kidneys affected (41.9%). Of 183 in the MIS group, 101 had left kidneys affected
(55.2%) and 82 had right renal units affected (45%), with no
differences between the two groups [p = ns, RR: 1.052, 95%
CI (0.89–1.24), Table 2]. differences between OP and MIS groups [p = ns, RR: 1.001, 95%
CI: (0.93–1.08), Table 2]. The mean age at procedure has been reported in nine
papers (1, 13, 22, 24–27, 30, 32), with no difference between
OP infants (4.9 ± 1.4 months) and MIS patients [5.8 ± 2.2
months; p = ns, MD −0.9, 95% CI: (−2.21–0.22), Table 2 and
Figure 2]. The side of the kidney affected by UPJO has been reported
in seven papers (1, 22, 24–26, 30, 32), with 462 patients (279
OP and 183 MIS). Of 279 OP patients, 162 had left kidneys
affected (58.1%) and 117 had right kidneys affected (41.9%). Of 183 in the MIS group, 101 had left kidneys affected
(55.2%) and 82 had right renal units affected (45%), with no
differences between the two groups [p = ns, RR: 1.052, 95%
CI (0.89–1.24), Table 2]. The weight at surgery has been reported in six of the
included papers (1, 22, 24, 26, 30, 32). Weight was not
significantly different among the two groups: 6.4 ± 1.4 kg in
OP vs. Meta-analysis 6.9 ± 1.4 in MIS [p = ns, MD −0.71, 95% CI (−1.47–
0.06), Table 2 and Figure 3]. affected (58.1%) and 117 had right kidneys affected (41.9%). Of 183 in the MIS group, 101 had left kidneys affected
(55.2%) and 82 had right renal units affected (45%), with no
differences between the two groups [p = ns, RR: 1.052, 95%
CI (0.89–1.24), Table 2]. The weight at surgery has been reported in six of the
included papers (1, 22, 24, 26, 30, 32). Weight was not
significantly different among the two groups: 6.4 ± 1.4 kg in
OP vs. 6.9 ± 1.4 in MIS [p = ns, MD −0.71, 95% CI (−1.47–
0.06), Table 2 and Figure 3]. FIGURE 4
Forest plot comparison of operative time at procedure between OP and MIS in infants. FIGURE 5
Forest plot comparison of the length of hospital stay between OP and MIS in infants. FIGURE 3
Forest plot comparison of weight at procedure between OP and MIS in infants. FIGURE 3
Forest plot comparison of weight at procedure between OP and MIS in infants. FIGURE 4
Forest plot comparison of operative time at procedure between OP and MIS in infants. FIGURE 5
Forest plot comparison of the length of hospital stay between OP and MIS in infants. 05 05 Frontiers in Pediatrics frontiersin.org frontiersin.org Cascini et al. 10.3389/fped.2022.1052440 FIGURE 6
Forest plot comparison of the incidence of postoperative complications between OP and MIS in infants. FIGURE 6
Forest plot comparison of the incidence of postoperative complications between OP and MIS in infants. FIGURE 7
Forest plot comparison of the length of follow-up between OP and MIS in infants. FIGURE 8
Forest plot comparison of the incidence of failure between OP and MIS in infants. FIGURE 6
Forest plot comparison of the incidence of postoperative complications between OP and MIS in infants. FIGURE 7
Forest plot comparison of the length of follow-up between OP and MIS in infants. FIGURE 7
Forest plot comparison of the length of follow-up between OP and MIS in infants. FIGURE 8
Forest plot comparison of the incidence of failure between OP and MIS in infants. leakage, urinary infection, and bleeding. The incidence of
complications
was
comparable
between
the
two
groups:
10.0 ± 12.9% in OP (32/319 patients) vs. 10.9 ± 11.6% in MIS
procedures [27/248 patients; p = ns, RR: 0.95, 95% CI (0.45–
2.01), Figure 6]. Meta-analysis Operative time (OT) has been reported in seven studies
(1, 24, 26, 32, 25, 13, 32). OT was significantly lower in OP
than that in MIS [129.4 ± 24.1 vs. 144.0 ± 32.3 min, respectively;
p = 0.0004, MD: −18.19, 95% CI: (−28.35, −8.04), Figure 4]. Nine papers (1, 13, 22, 24–27, 30, 32) have shown an
increased LOS in OP compared to that in MIS [3.2 ± 1.9 vs. 2.2 ± 0.9 days, respectively; p = 0.01, MD: 0.76, 95% CI:
(0.16–1.36), Figure 5]. The length of postoperative follow-up has been reported in
five papers (13, 25, 26, 30, 32). OP presented a longer but not
significant follow-up than MIS [21.5 ± 8.1 months vs. 13.9 ±
4.7 months, respectively; p = ns; MD: 7.03, 95% CI: (−2.23–
16.29), Table 2 and Figure 7]. Eight
studies
have
been
reported
on
postoperative
complications (1, 13, 22, 24–26, 30, 32), such as urinary Frontiers in Pediatrics frontiersin.org 06 Cascini et al. 10.3389/fped.2022.1052440 TABLE 3 Risk of bias assessment for individual studies using the methodological index for nonrandomized studies (MINORS) (18). Item
Masieri
(1)
Andolfi
(13)
Neheman
(22)
Garcìa-
Aparicio
(24)
Tong
(25)
Bansal
(26)
Tanaka
(27)
Rague
(30)
Dangle
(11)
1. A clearly stated aim
2
2
2
2
2
2
2
2
2
2. Inclusion of
consecutive patients
2
2
2
2
2
2
2
2
2
3. Prospective collection
of data
0
2
0
0
0
0
0
0
0
4. Endpoints appropriate
to the aim of the study
2
2
2
2
2
2
2
2
2
5. Unbiased assessment of
the study endpoint
0
0
0
0
0
0
0
0
0
6. Follow-up period
appropriate to the aim
of the study
1
1
1
0
1
1
1
1
1
7. Loss to follow-up less
than 5%
0
0
0
0
2
0
0
0
0
8. Prospective calculation
of the study size
0
0
0
0
0
0
0
0
0
9. An adequate control
group
2
2
2
2
2
2
2
2
2
10. Contemporary groups
2
2
2
2
2
2
2
2
2
11. Baseline equivalence
of groups
1
1
2
2
2
1
2
1
1
12. Meta-analysis Adequate statistical
analyses
2
2
2
2
2
2
2
2
2
Total score
14
16
15
14
17
14
15
14
14
0 = not reported; 1 = reported but inadequate; 2 = reported and adequate. Validated “gold standard” cut-off: 19.8. 0 = not reported; 1 = reported but inadequate; 2 = reported and adequate. Validated “gold standard” cut-off: 19.8. hydronephrosis causing a mass effect, recurrent urinary tract
infection (UTI), worsening of hydronephrosis with thinning
of renal parenchyma, or UPJO in a solitary kidney (8, 30, 33). The gold standard procedure to treat UPJO is the
Anderson–Hynes
dismembered
pyeloplasty,
commonly
performed through an open miniflank approach in infants
(13, 33–36). MIS procedures have progressively been adopted
over the last years, although these procedures are technically
challenging with the need for a long learning curve, especially
for LAP. However, these procedures seemed safe and effective,
as an increasing number of studies have reported similar
outcomes compared to OP in pediatric patients. Several meta-
analyses comparing OP and MIS showed that children in the
MIS group were older than those in OP, with the same
success rate and complications for both techniques (3, 5, 6). MIS procedures have shown benefits in terms of shortened
LOS, decreased postoperative pain, and enhanced esthetic
outcomes
in
older
pediatric
cases,
gaining
increased
popularity as an alternative to OP (2, 37). The failure rate has been mentioned in seven papers (1, 13,
22, 24–26, 30). In most of the studies included, success has been
defined
as
resolutions
of
symptoms
and
improved
ultrasonographic or renographic parameters at the follow-up. The failure rate was not different in OP (5.2 ± 3.5%, 16/308
patients) and MIS [4.2 ± 3.3%, 10/238 patients; p = ns; RR:
1.28, 95% CI: (0.58–2.82), Figure 8]. hydronephrosis causing a mass effect, recurrent urinary tract
infection (UTI), worsening of hydronephrosis with thinning
of renal parenchyma, or UPJO in a solitary kidney (8, 30, 33). Only the paper by Andolfiet al. (13) further compared LAP
vs. RALP. No conversion was reported in both groups. Furthermore, the incidence of complications and the success
rates were similar for both procedures. We further screened these nine papers included in the meta-
analysis with regard to the outcomes between left surgery and
right surgery. Meta-analysis However, no data were reported on operative
time,
the
length
of
hospital
stay,
the
incidence
of
complications, and the failure rate regarding the side of the
procedure. Discussion A cohort study including a nationwide inpatient
sample data (time period 2008–2010) has reported that the
distribution of OP and MIS approaches for pyeloplasty in
infants was about 78% and 0.7%, respectively (28). The limits
of the utilization of MIS pyeloplasties in infants or smaller
children depend on the technical aspects unique to this
population. First, the increase of intra-abdominal pressure and
the
peritoneal
absorption
of
CO2
due
to
the
pneumoperitoneum
could
bring
physiological
and
time-
depending respiratory issues, such as displacement of the
diaphragm and acidosis (23, 41). A pressure of 10 mmHg or
greater
may cause
a
reduction
in venous return,
right
ventricular output, left cardiac output, and bradycardia due to
vagal
reflex. When
greater
than
8 mmHg,
the
pneumoperitoneum could cause renal issues because of the
stimulation of the renin–angiotensin–aldosterone system, with
consequent emission of the antidiuretic hormone, leading to
salt and water retention with oliguria (41). The further
concern in this population is the limited space for port
placement and the restricted working space, making the
procedure challenging (11, 42). The incidence of complications such as bleeding, UTI, or
urinary leakage was similar between OP (10.0%) and MIS
(10.9%). Looking specifically at MIS procedures, Bansal et al. (26) reported a higher complication rate in RALP (33.3%)
than OP (6.6%), whereas Chandrakhaseram et al. in their
meta-analysis
focusing
on
infants
(7)
reported
more
complications in RALP (16.2%) than LAP (9.3%). In a recent meta-analysis, the success of LAP and RALP in
infants was found to be similar, with RALP having more OT
duration and complications than LAP (21). Analyzing the
KID database, Liu et al. evidenced that the use of MIS in
children has gradually boosted from 0.3% in 2000 to 11.7% in
2009, with RALP representing 82% of these cases (40). Nevertheless, studies have reported outcomes on a small
number of infants (13). In fact, in the present systematic
review and meta-analysis, the included studies comparing OP
and MIS techniques were relatively scarce: all papers were
published between 2008 and 2022. Among 3,145 pyeloplasties,
only
9.1%
were
performed
with
MIS,
with
an
equal
distribution between LAP (50.7%) and RALP (49.3%). Finally, different from the previous report, where the follow-
up was longer for the traditional OP (25, 26, 32), this meta-
analysis
presented
no
statistically
significant
differences
between OP and MIS in terms of length of postoperative
follow-up. Discussion However, MIS was preferred in older children, with infants
still receiving OP (6, 38, 39). Liu et al. indicated in the Kid’s
Inpatient Database (KID) that age is the only characteristic
that augmented the odds of having MIS (40). In infants, the The indications to surgically treat UPJO in infants are
specific,
including
impaired
renal
function,
severe Frontiers in Pediatrics frontiersin.org 07 Cascini et al. 10.3389/fped.2022.1052440 TABLE 4 GRADE evidence profile (19) for the present meta-analysis. Quality assessment
No. of patients
Effect
Quality
No. of
studies
Study
design
Risk of
bias
Inconsistency
Indirectness
Imprecision
Other
considera-tions
Cases
Controls
Relative
(95% CI)
Absolute (95% CI)
Operative time between MIS and OP in infants
MIS
OP
7
OS
Moderatea
Substantial
Not serious
Seriousb
None
225
332
—
MD 18.19 lower (from 28.35
to 8.04 lower)
⊗OOO VERY
LOW
Length of hospital stay between MIS and OP in infants
MIS
OP
9
OS
Moderatea
Substantial
Not serious
Seriousb
None
286
2,898
—
MD 0.76 higher (from 0.16 to
1.36 higher)
⊗⊗OO LOW
Incidence of complications between MIS and OP in infants
MIS
OP
8
OS
Moderatea
Moderate
Not serious
Seriousb
None
27/248
(10.9%)
32/319
(10.0%)
RR 0.95 (0.45,
2.01)
9 more per 1,000 (from 99
less to 182 more)
⊗⊗OO LOW
Incidence of failure between MIS and OP in infants
MIS
OP
7
OS
Moderatea
Low
Not serious
Seriousb
None
10/238
(4.2%)
116/308
(5.2%)
RR 1.28 (0.58,
2.82)
10 fewer per 1,000 (from 15
fewer to 65 more)
⊗⊗OO LOW
MIS, minimally invasive surgery; OP, open pyeloplasty. GRADE Working Group grades of evidence. High quality: Further research is very unlikely to change our confidence in the estimate of effect. Moderate quality: Further research is likely to have an important impact on our confidence in the estimate of effect and may change the estimate. Low quality: Further research is very likely to have an important impact on our confidence in the estimate of effect and is likely to change the estimate. Very low quality: We are very uncertain about the estimate. aBias due to possible confounding. Frontiers in Pediatrics frontiersin.org 08 Cascini et al. 10.3389/fped.2022.1052440 miniflank lumbotomy is preferred for several reasons. First, it
avoids muscle splitting, thus decreasing postoperative pain
and allowing a fast recovery. Second, it allows for a direct
approach to the posterior side of both the renal pelvis and the
ureter (8). Discussion This result highlights that MIS has already been
used for a sufficient time to compare the outcome of both
techniques. While LAP showed a lengthier learning curve and known
technical
difficulties,
RALP
has
become
more
accepted
because of instruments with 7 degrees of motion, a 3D screen
with magnification, and hand-tremor reduction. Moreover, it
has been reported that the learning curve for RALP seemed to
be comparable to the one for OP (4, 8). The current
availability of miniaturized instruments has improved the use
of MIS. In LAP, a 5-mm camera and 3-mm instruments
enhance the ability to perform the anastomosis, reporting
similar results to OP (10, 24). Regarding RALP, the Si system
allowed an option for pediatric cases with an 8.5-mm camera
and 5-mm instruments, which decreased in comparison with
a 12-mm camera and 8-mm instruments of the standard
option (8). Moreover, it is necessary to consider that the
robot system is not available in all centers, and it presents
higher costs than OP. Limitation of the study There are several limitations of the present study. As
reported above, all but one studies were retrospective, which
may lead to select bias. None of the papers provided sample
size
calculations. As
expected,
a
blinded
evaluation
of
objective endpoints was not possible. Moreover, the outcomes
of MIS were strictly dependent on procedural volume. High-
volume centers presented perioperative outcomes that were
equivalent to or better than those of OP, different from low-
volume centers (28). Furthermore, none of the studies have
reported
with
regard
to
the
loss
of
follow-up. As
a
consequence,
in
our
meta-analysis,
none
of
the
studies
reached the gold standard cutoff on MINORS of 19.8 out of
24 (Table 3). From 2003 to 2015, the rate of RALP augmented by 29%
annually. However, most of these cases were children and
adolescents. RALP was 40% among these patients in 2015. Differently, 85% of infants were still treated with OP (8). Many authors still prefer to perform an OP in infants. In
these cases, the surgical procedure may be done by a mini-
incision, avoiding muscle splitting, with reduced postoperative
pain,
fast
patient
recovery,
and
good
aesthetic
result. Therefore, the role of MIS in infants is still controversial:
Tanaka et al. have reported that the benefits of LAP were
evident only in older children (27). Data availability statement The Supplementary Material for this article can be found
online
at:
https://www.frontiersin.org/articles/10.3389/fped. 2022.1052440/full#supplementary-material. The raw data supporting the conclusions of this article will
be made available by the authors without undue reservation. g
24 (Table 3). According to the GRADE methodology, the quality of
evidence of the meta-analysis was low regarding the length of
hospital stay, the incidence of postoperative complications,
and the failure of the surgical procedure (Table 4). Both the
reduced
number
of
MIS
infants
and
the
considerable
heterogeneity of the data could generate possible bias. However, when assessed in duplicate by two authors (DDR
and MEM) using A Measurement Tool to Assess Systematic Frontiers in Pediatrics frontiersin.org 09 Cascini et al. 10.3389/fped.2022.1052440 Publisher’s note However, more high-quality data from well-designed
randomized
control
trials
and
sufficient
adjustment
for
volume outcome are necessary to indicate the feasibility and
safety of MIS in infants compared with OP. Until then, in
our opinion, only experienced surgeons should perform MIS
procedures in infants, with appropriate counseling with the
family to evaluate the benefits and limitations of each
technique. All claims expressed in this article are solely those of the
authors and do not necessarily represent those of their
affiliated organizations, or those of the publisher, the editors
and the reviewers. Any product that may be evaluated in this
article, or claim that may be made by its manufacturer, is not
guaranteed or endorsed by the publisher. Conflict of interest The present systematic review and meta-analysis showed
that MIS seemed a safe and effective procedure for surgically
treating UPJO in infants. MIS procedures present similar
outcomes
in
terms
of
success
rate
and
postoperative
complications to OP, in front of a shortened length of
hospital stay. In the current practice, LAP and RALP may be
used as an alternative to the traditional open technique, but
their several limitations must be recognized. The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could
be construed as a potential conflict of interest. Reviews (AMSTAR) (43), the present study received an honest
score (Supplementary material S2). Reviews (AMSTAR) (43), the present study received an honest
score (Supplementary material S2). The PRISMA checklist was finally fulfilled (Supplementary
material S3). VC, GL, GL: conception/design, analysis and interpretation,
participated in drafting, and gave final approval. VC, GL: data
acquisition. GL, DDR, EM: quality assessment. DDR, MEM:
participated in revision. All authors contributed to the article
and approved the submitted version. References 7. Chandrasekharam VVS, Babu R. A systematic review and meta-analysis of
conventional
laparoscopic versus
robot-ssisted
laparoscopic pyeloplasty in
infants. J Pediatr Urol. (2021) 17(4):502–10. doi: 10.1016/j.jpurol.2021.03.009 1. Masieri L, Sforza S, Cini C, Escolino M, Grosso A, Esposito C, et al. Minilaparoscopic
versus
open
pyeloplasty
in
children
less
than
1
year. J Laparoendosc Adv Surg Tech A. (2019) 29(7):970–5. doi: 10.1089/lap.2018.0586 8. Passoni NM, Peters CA. Managing ureteropelvic junction obstruction in
the young infant. Front Pediatr. (2020) 242(8):1–11. doi: org/10.3389/fped.2020. 00242 2. Silay MS, Spinoit AF, Undre S, Fiala V, Tandogdu Z, Garmanova T, et al. Global minimally invasive pyeloplasty study in children: results from the
pediatric expert group of the European association of urology young academic
urologists working party. J Pediatr Urol. (2016) 12(4):229.e1–7. doi: 10.1016/j. jpurol.2016.04.007 9. Tan HL. Laparoscopic Anderson–Hynes dismembered pyeloplasty in
children. J Urol. (1999) 162(3 Pt 2):1045–7. doi: 10.1016/S0022-5347(01)68060-1 3. Mei H, Pu J, Yang C, Zhang H, Zheng L, Tong Q. Laparoscopic versus open
pyeloplasty for ureteropelvic junction obstruction in children: a systematic review
and meta-analysis. J Endourol. (2011) 25(5):727–36. doi: 10.1089/end.2010.0544 3. Mei H, Pu J, Yang C, Zhang H, Zheng L, Tong Q. Laparoscopic versus open
pyeloplasty for ureteropelvic junction obstruction in children: a systematic review
and meta-analysis. J Endourol. (2011) 25(5):727–36. doi: 10.1089/end.2010.0544 10. Kutikov A, Resnick M, Casale P. Laparoscopic pyeloplasty in the infant
younger than 6 months – is it technically possible? J Urol. (2006) 175
(4):1477–9. doi: 10.1016/S0022-5347(05)00673-7 4. Dothan D, Raisin G, Jaber J, Kocherov S, Chertin B. Learning curve of
robotic-assisted laparoscopic pyeloplasty (RALP) in children: how to reach a
level of excellence? J Robot Surg. (2021) 15(1):93–7. doi: 10.1007/s11701-020-
01082-7 4. Dothan D, Raisin G, Jaber J, Kocherov S, Chertin B. Learning curve of
robotic-assisted laparoscopic pyeloplasty (RALP) in children: how to reach a
level of excellence? J Robot Surg. (2021) 15(1):93–7. doi: 10.1007/s11701-020-
01082-7 11. Fuchs J, Luithle T, Warmann SW, Haber P, Blumenstock G, Szavay P. Laparoscopic surgery on upper urinary tract in children younger than 1 year:
technical aspects and functional outcome. J Urol. (2009) 182:1561–8. doi: 10. 1016/j.juro.2009.06.063 5. Huang Y, Wu Y, Shan W, Zeng L, Huang L. An updated meta-analysis of
laparoscopic versus open pyeloplasty for ureteropelvic junction obstruction in
children. Int J Clin Exp Med. (2015) 8(4):4922–31. 5. Huang Y, Wu Y, Shan W, Zeng L, Huang L. Author contributions Reviews (AMSTAR) (43), the present study received an honest
score (Supplementary material S2). 10. Kutikov A, Resnick M, Casale P. Laparoscopic pyeloplasty in the infant
younger than 6 months – is it technically possible? J Urol. (2006) 175
(4):1477–9. doi: 10.1016/S0022-5347(05)00673-7 References An updated meta-analysis of
laparoscopic versus open pyeloplasty for ureteropelvic junction obstruction in
children. Int J Clin Exp Med. (2015) 8(4):4922–31. 12. Varda BK, Johnson EK, Clark C, Chung BI, Nelson CP, Chang SL. National
trends of
perioperative outcomes and
costs for open,
laparoscopic and
robotic pediatric pyeloplasty. J Urol. (2014) 191(4):1090–5. doi: 10.1016/j.juro. 2013.10.077 6. Cundy TP, Harling L, Huges-Hallett A, Mayer EK, Najmaldin AS,
Athanasiou
T,
et
al. Meta-analysis
of
robot-assisted
vs
conventional
laparoscopic and open pyeloplasty in children. BJU Int. (2014) 114:582–94. doi: 10.1111/bjui.org 6. Cundy TP, Harling L, Huges-Hallett A, Mayer EK, Najmaldin AS,
Athanasiou
T,
et
al. Meta-analysis
of
robot-assisted
vs
conventional
laparoscopic and open pyeloplasty in children. BJU Int. (2014) 114:582–94. doi: 10.1111/bjui.org 13. AndolfiC, Lombardo AM, Aizen J, Recalab X, Walker JP, Barashi NS, et al. Laparoscopic and robotic pyeloplasty as minimally invasive alternatives to the
open approach for the treatment of uretero-pelvic junction obstruction in Frontiers in Pediatrics frontiersin.org 10 Cascini et al. 10.3389/fped.2022.1052440 infants: a multi-institutional comparison of outcomes and learning curves. World
J Urol. (2022) 40:1049–56. doi: .org/10.1007/s00345-022-03929-0 of procedure volume on operative outcomes. Urol. (2014) 84(1):180–4. doi: 10. 1016/j.urology.2014.02.002 14. PROSPERO international prospective register of systematic reviews. Available at: https://www.crd.york.ac.uk/prospero [on Sep 21, 2022]. 29. Wong YS, Pang KKY, Tam YH. Comparing robot-assisted laparoscopic
pyeloplasty vs laparoscopic pyeloplasty in infants aged 12 months or less. Front
Pediatr. (2021) 14(9):647139. doi: 10.3389/fped.2021.647139 15. Moher D, Liberati A, Tetzlaff J. Altman DG; PRISMA group. Preferred
reporting
items
for
systematic
review
and
meta-analyses:
the
PRISMA
statement. Int J Surg. (2010) 8(59):336–41. doi: 10.1016/j.ijsu.2010.02.007 30. Rague JT, Arora HC, Chu DI, Shannon R, Rosoklija I, Johnson EK, et al. Safety and efficacy of robot-assisted laparoscopic pyeloplasty compared to open
tepair in infants under 1 year of age. J Urol. (2022) 207(2):432–40. doi: 10. 1097/JU.0000000000002232 16. Hozo SP, Djulbegovic B, Hozo I. Estimating the mean and variance from
median, range, and the size of a sample. BMC Med Res Methodol. (2005)
20:5–13. doi: 10.1186/1471-2288-5-13 31. Piaggio LA, Franc-Guimond J, Noh PH, Wehry M, Figuerosa TE, Barthold J,
et al. Transperitoneal laparoscopic pyeloplasty for primary repair of ureteropelvic
junction obstruction in infants and children: comparison with open surgery. J Urol. (2007) 178:1579–83. doi: 10.1016/j,juro.2007.03.159 17. Review Manager (RevMan). The nordic cochrane centre. The Cochrane
Collaboration, Copenhagen. (2014). 18. Slim K, Nini E, Forestier D, Kwiatkowski F, Panis Y, Chipponi J. References Methodological index for nonrandomized studies (MINORS): development and
validation of a new instrument. ANZ J Surg. (2003) 73(9):712–6. doi: 10.1046/j. 1445-2197.2003.02748.x 32. Dangle PP, Kearns J, Anderson B, Gundeti MS. Outcomes of infants
undergoing robot-assisted laparoscopic pyeloplasty compared to open repair. J Urol. (2013) 190:2221–7. doi: 10.1016/j.juro.2013.07.063 33. Boysen WR, Gundeti MS. Robot-assisted laparoscopic pyeloplasty in the
pediatric population: a review of technique, outcomes, complications, and
special considerations in infants. Pediatr Surg Int. (2017) 33(9):925–35. doi: 10. 1007/s00383-017-4082-7 19. Guyatt GH, Oxman AD, Vist GE, Kunz R, Falck-Ytter Y, Alonso-Coello P,
et al. GRADE: an emerging consensus on rating quality of evidence and strength
of recommendations. Br Med J. (2008) 336(7650):924–6. doi: 10.1136/bmj.39489. 470347.AD 34. Gatti JM, Amstutz S, Bowling PR, Stephany HA, Murphy JP. Laparoscopic
versus open pyelolasty in children: results of a randomized, prospective controlled
trial. J Urol. (2017) 197(3Pt1):792–7. doi: 10.1016/j.juro.2016.10.056 20. Guyatt GH, Oxman AD, Kunz R, Woodcock J, Brozek J, Helfand M, et al. GRADE Guidelines: 7. Rating the quality of evidence – inconsistency. J Clin
Epidemiol. (2011) 64(12):1294–302. doi: 10.1016/j.jclinepi.2011.03.017 35. Kajbafzadeh AM, Tourchi A, Nezami BG, Khakpour M, Mousavian AA,
Talab SS. Miniature pyeloplasty as a minimally invasive surgery with less than 1
day admission infants. J Pediatr Urol. (2011) 7:283–8. doi: 10.11016/j.jpurol. 2011.02.030 21. Dupont WD, Plummer Jr WD. Power and sample size calculations. A review
and computer program. Control Clin Trials. (1990) 11(2):116–28. doi: 10.1016/
0197-2456(90)90005-m 22. Neheman A, Noh PH, Piaggio L, Gonzàlez R. The role of laparoscopic
surgery for urinary tract reconstruction in infants weighing less than 10 kg: a
comparison with open surgery. J Pediatr Urol. (2008) 4:192–6. doi: 10.1016/j. jpurol.2007.11.012 36. Singh V, Garg M, Sharma P, Sinha RJ, Kumar M. Mini incision open
pyeloplasty-improvement in patient outcome. Int Braz J Urol. (2015) 41
(5):927–34. doi: 10.1590/S1677-5538.IBJU.2014.0024 37. Lee RS, Retik AB, Borer JG, Peters CA. Pediatric robot assisted laparoscopic
dismembered pyeloplasty: comparison with a cohort of open surgery. J Urol. (2006) 175(2):683–7. doi: 10.1016/S0022-5347(05)00183-7 23. Neheman A, Kord E, Zisman A, Darawsha AE, Noh PH. Comparison of
robotic pyeloplasty and standard laparoscopic pyeloplasty in infants: a bi-
institutional study. J Laparoendosc Adv Surg Tech A. (2018) 28(4):467–70. doi: 10.1089/lap.2017.0262 38. Chacko JK, Koyle MA, Mingin GC, Furness III PD. Minimally invasive open
renal surgery. J Urol. (2007) 178:1575–8. doi: 10.1016/j.juro.2007.05.099 24. Garcìa-Aparicio L, Blazquez-Gomez E, Martin O, Manzanares A, Garcìa-
Smith N, Bejarano M, et al. 43. Shea BJ, Grimshaw JM, Wells GA, Boers M, Andersson N, Hamel C, et al.
Development of AMSTAR: a measurement tool to assess the methodological
quality of systematic reviews. BMC Med Res Methodol. (2007) 7:10. doi: https://
doi.org/10.1186/1471-2288-7-10 References Anderson-Hynes pyeloplasty in patients less than
12 months old. Is the laparoscopic approach safe and feasible? J Endourol. (2014) 28(8):906–8. doi: 1089/end.2013.0704 39. Vemulakonda VM, Cowan CA, Lendvay TS, Joyner BD, Grady RW. Surgical
management of congenital ureteropelvic junction obstruction: a pediatric health
information system database study. J Urol. (2008) 180:1689–92. doi: 10.1016.j. juro.2008.03.096 25. Tong Q, Zheng L, Tang S, Zeng F, Du Z, Mei H, et al. Comparison of
laparoscopic assisted versus open dismembered pyelolasty for uretropelvic
junction obstruction in infants: intermediate results. Urol. (2009) 74(4):889–93. doi: 10.10167j.urology.2009.03.053 40. Liu DB, Ellimoottil C, Flum AS, Casey JT, Gong EM. Contemporary national
comparison of open, laparoscopic, and robotic-assisted laparoscopic pediatric
pyeloplasty. J Pediatr Urol. (2014) 10:610–5. doi: 10.16/j.jpurol.2014.06.010 26. Bansal D, Cost NG, DeFoor Jr WR, Reddy PP, Minevich EA, Vanderbrink
BA, et al. Infant robotic pyeloplasty: comparison with an open cohort. J Pediatr
Urol. (2014) 10:380–5. doi: 10.1016/j.jpurol.2013.10.016 41. Kim SJ, Barlog JS, Akhavan A. Robotic-assisted urologic surgery in infants:
positioning, trocar placement, and physiological consideretinos. Front Pediatr. (2019) 7(6):411. doi: 10.3389/fped.2018.00411 27. Tanaka ST, Grantham JA, Thomas JC, Adams MC, Brock III JW, Pope JC. A
comparison of open vs laparoscopic pediatric pyelolsty using the pediatric health
information system database-do benefits of laparoscopic approach recede at
younger ages? J Urol. (2008) 180(4):1479–85. doi: 10.1016/j.juro.2008.06.044 42. Chandrasekharam VVS. Laparoscopic pyeloplasty in infants: single-surgeon
experience. J Pediatr Urol. (2015) 11(5):272. doi: 10.1016/j.jpurol.2015.05.013 43. Shea BJ, Grimshaw JM, Wells GA, Boers M, Andersson N, Hamel C, et al. Development of AMSTAR: a measurement tool to assess the methodological
quality of systematic reviews. BMC Med Res Methodol. (2007) 7:10. doi: https://
doi.org/10.1186/1471-2288-7-10 28. Sukumar S, Djhangirian O, Sood A, Sammon JD, Varda B, Janosek-Albright
K, et al. Minimally invasive vs open pyeloplasty in children: the differential effect Frontiers in Pediatrics frontiersin.org 11
|
https://openalex.org/W3091407527
|
https://www.aanda.org/articles/aa/pdf/2020/11/aa38892-20.pdf
|
English
| null |
Investigating the magnetospheric accretion process in the young pre-transitional disk system DoAr 44 (V2062~Oph). A multiwavelength interferometric, spectropolarimetric, and photometric observing campaign
|
arXiv (Cornell University)
| 2,020
|
cc-by
| 19,899
|
ABSTRACT Context. Young stars interact with their accretion disk through their strong magnetosphere. Context. Young stars interact with their accretion disk through their strong magnetosphere. Aims. We aim to investigate the magnetospheric accretion/ejection process in the young stellar system DoAr 44 (V2062 Oph). Methods. We monitored the system over several rotational cycles, combining high-resolution spectropolarimetry at both optical and
near-IR wavelengths with long-baseline near-IR inteferometry and multicolor photometry. Aims. We aim to investigate the magnetospheric accretion/ejection process in the young stellar system DoAr 44 (V2062 Oph). Methods We monitored the system over several rotational cycles combining high-resolution spectropolarimetry at both optical and Aims. We aim to investigate the magnetospheric accretion/ejection process in the young stellar system DoAr 44 (V2062 Oph). Methods. We monitored the system over several rotational cycles, combining high-resolution spectropolarimetry at both optical and
near IR wavelengths with long baseline near IR inteferometry and multicolor photometry Results. We derive a rotational period of 2.96 d from the system’s light curve, which is dominated by stellar spots. We fully char-
acterize the central star’s properties from the high signal-to-noise, high-resolution optical spectra we obtained during the campaign. DoAr 44 is a young 1.2 M⊙star, moderately accreting from its disk ( ˙Macc = 6.5 10−9 M⊙yr−1), and seen at a low inclination (i ≃30◦). Several optical and near-IR line profiles probing the accretion funnel flows (Hα, Hβ, HeI 1083 nm, Paβ) and the accretion shock
(HeI 587.6 nm) are modulated at the stellar rotation period. The most variable line profile is HeI 1083 nm, which exhibits modulated
redshifted wings that are a signature of accretion funnel flows, as well as deep blueshifted absorptions indicative of transient outflows. The Zeeman-Doppler analysis suggests the star hosts a mainly dipolar magnetic field, inclined by about 20◦onto the spin axis, with
an intensity reaching about 800 G at the photosphere, and up to 2 ± 0.8 kG close to the accretion shock. The magnetic field appears
strong enough to disrupt the inner disk close to the corotation radius, at a distance of about 4.6 R⋆(0.043 au), which is consistent with
the 5 R⋆(0.047 au) upper limit we derived for the size of the magnetosphere in our Paper I from long baseline interferometry. Conclusions. DoAr 44 is a pre-transitional disk system, exhibiting a 25–30 au gap in its circumstellar disk, with the inner and outer
disks being misaligned. J. Bouvier1, E. Alecian1, S. H. P. Alencar2, A. Sousa1, J.-F. Donati3, K. Perraut1, A. Bayo4,5, L. M. Rebull6,
C. Dougados1, G. Duvert1, J.-P. Berger1, M. Benisty1,7, K. Pouilly1, C. Folsom3,
C. Moutou3, and the SPIRou consortium 1 Univ. Grenoble Alpes, CNRS, IPAG, 38000 Grenoble, France
e-mail: jerome.bouvier@univ-grenoble-alpes.fr 2 Departamento de Fisica – ICEx – UFMG, Av. Antonio Carlos 6627, 30270-901 Belo Horizonte, MG, Brazil
3 Univ de Toulouse CNRS IRAP 14 avenue Belin 31400 Toulouse France 2 Departamento de Fisica – ICEx – UFMG, Av. Antonio Carlos 6627, 30270-901 B
3 3 Univ. de Toulouse, CNRS, IRAP, 14 avenue Belin, 31400 Toulouse, France ,
,
,
,
,
4 Instituto de Física y Astronomía, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
5
l
il
i d
i
l
i
i
id d d
l
l
hil 4 Instituto de Física y Astronomía, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
5 4 Instituto de Física y Astronomía, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso
5 Instituto de Física y Astronomía, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chi
5 Núcleo Milenio de Formación Planetaria – NPF, Universidad de Valparaíso, Valparaíso, Chile 5 Núcleo Milenio de Formación Planetaria – NPF, Universidad de Valparaíso, Valparaíso, Chile
6 p
p
6 Infrared Science Archive (IRSA), IPAC, 1200 E. California Blvd., California Institute of Tech
7 6 Infrared Science Archive (IRSA), IPAC, 1200 E. California Blvd., California Institute of Technology, Pasadena, Infrared Science Archive (IRSA), IPAC, 1200 E. California Blvd., California Institute of Technology, Pasadena, CA 91125, USA
7 Unidad Mixta Internacional Franco-Chilena de Astronomía (CNRS, UMI 3386), Departamento de Astronomía, Universidad de
Chile, Camino El Observatorio 1515, Las Condes, Santiago, Chile 7 Unidad Mixta Internacional Franco-Chilena de Astronomía (CNRS, UMI 3386), Departamento de Astronomía, Universidad de
Chile, Camino El Observatorio 1515, Las Condes, Santiago, Chile 7 Unidad Mixta Internacional Franco-Chilena de Astronomía (CNRS, UMI 3386), Departamento de Astronomía, Universidad de
Chile, Camino El Observatorio 1515, Las Condes, Santiago, Chile Received 10 July 2020 / Accepted 10 September 2020 Received 10 July 2020 / Accepted 10 September 2020 ABSTRACT On a scale of 0.1 au or less, our results indicate that the system is steadily accreting from its inner disk
through its tilted dipolar magnetosphere. We conclude that in spite of a highly structured disk on the large scale, perhaps the signature
of ongoing planetary formation, the magnetospheric accretion process proceeds unimpeded at the star-disk interaction level. pp
g
p
p
g
y
Conclusions. DoAr 44 is a pre-transitional disk system, exhibiting a 25–30 au gap in its circumstellar disk, with the inner and outer
disks being misaligned. On a scale of 0.1 au or less, our results indicate that the system is steadily accreting from its inner disk
through its tilted dipolar magnetosphere. We conclude that in spite of a highly structured disk on the large scale, perhaps the signature
of ongoing planetary formation, the magnetospheric accretion process proceeds unimpeded at the star-disk interaction level. Key words. stars: pre-main sequence – stars: variables: T Tauri, Herbig Ae/Be – stars: magnetic field – stars: formation –
accretion, accretion disks Open Access article, published by EDP Sciences, under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Astronomy
&
Astrophysics Astronomy
&
Astrophysics Astronomy
&
Astrophysics A&A 643, A99 (2020)
https://doi.org/10.1051/0004-6361/202038892
c⃝J. Bouvier et al. 2020 ⋆Full Table 1 is only available at the CDS via anonymous ftp
to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.
u-strasbg.fr/viz-bin/cat/J/A+A/643/A99 ⋆Full Table 1 is only available at the CDS via anonymous ftp
to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.
u-strasbg.fr/viz-bin/cat/J/A+A/643/A99
⋆⋆Based on observations obtained at the Canada-France-Hawaii
Telescope (CFHT), at the European Organisation for Astronomical
Research in the Southern Hemisphere under ESO programme 0103.C-
0097, and at the Las Cumbres Observatory global telescope network
(LCOGT). ey words. stars: pre-main sequence – stars: variables: T Tauri, Herbig Ae/Be – stars: magnetic field – stars: formatio
ccretion, accretion disks Investigating the magnetospheric accretion process in the young
pre-transitional disk system DoAr 44 (V2062 Oph)
A multiwavelength interferometric, spectropolarimetric, and photometric
observing campaign⋆,⋆⋆ J. Bouvier1, E. Alecian1, S. H. P. Alencar2, A. Sousa1, J.-F. Donati3, K. Perraut1, A. Bayo4,5, L. M. Rebull6,
C. Dougados1, G. Duvert1, J.-P. Berger1, M. Benisty1,7, K. Pouilly1, C. Folsom3,
C. Moutou3, and the SPIRou consortium J. Bouvier1, E. Alecian1, S. H. P. Alencar2, A. Sousa1, J.-F. Donati3, K. Perraut1, A. Bayo4,5, L. M. Rebull6,
C. Dougados1, G. Duvert1, J.-P. Berger1, M. Benisty1,7, K. Pouilly1, C. Folsom3,
C. Moutou3, and the SPIRou consortium 1. Introduction The rotational modulation over a timescale of weeks
of emission line profiles, veiling, and Zeeman signatures allows
one to draw magnetic maps of the stellar surface and to recon-
struct the structure of the magnetospheric accretion region and
investigate its dynamics. Previous monitoring campaigns have
been quite successful in interpreting the observed properties
and variability of young stellar objects in the framework of
the magnetospheric accretion model (e.g., Bouvier et al. 2007b;
Alencar et al. 2012, 2018; Donati et al. 2019). These provided
new insights into the physics of the interaction region between
the inner disk edge and the stellar surface, which impacts both
early stellar evolution, and, potentially, planet formation and/or
migration at the inner disk edge. addition, below we derive a photometric period of 2.96 d from
a publicly available ASAS-SN light curve (see Sect. 3.2), which
we ascribe to the stellar rotation period. These properties made
it a suitable target for a dedicated large-scale monitoring cam-
paign, with the additional interest of probing the magnetospheric
accretion process in a pre-transitional disk system. This sys-
tem featured a large dust-depleted cavity in its circumstellar
disk, extending up to a distance of 30 au from the central star
(Andrews et al. 2011). The goal of this campaign was to con-
strain the structure and dynamics of the magnetospheric accre-
tion region between the inner edge of the compact inner disk
and the central star by measuring the magnetic field strength at
the stellar surface, reconstructing the geometry of the magne-
tospheric funnel flows and accretion shocks from the analysis
of line profile variability and photometric variations, and, ulti-
mately, attempting to resolve the interaction region over scales
of a few stellar radii above the stellar surface using long-baseline
interferometry. The VLTI/GRAVITY interferometric results are
reported in an accompanying paper (Bouvier et al. 2020, here-
after Paper I). Section 2 describes the observations and data
reduction, Sect. 3 features our results, and Sect. 4 offers a con-
sistent interpretation of the observed variability of the system in
the framework of the magnetospheric accretion model. We present here the results of a new campaign target-
ing the young star DoAr 44 (also known as V2062 Oph,
Haro 1–16, ROXs 44, HBC 268) located at a distance of
146 ± 1 pc (Gaia Collaboration 2016, 2018) in the L1688 cloud
of the Rho Ophiuchi molecular complex. 1. Introduction material from their circumstellar disks, a remnant of the pro-
tostellar collapse and the birthplace of planetary systems. The
so-called classical T Tauri stars (cTTSs) have specific proper-
ties, such as a rich emission-line spectrum, large photometric
variability, and a strong continuum excess flux superimposed
onto a late-type photospheric spectrum (Herbig 1962). The
unique properties of this class of objects eventually vanish
as the disk dissipates on a timescale of a few million years,
and the young stellar object transitions to a weak-line T Tauri
star (wTTS, Ménard et al. 1999). Indeed, many of the spe-
cific properties of cTTSs are thought to derive from the accre-
tion process (Kenyon & Hartmann 1987; Bertout et al. 1988; T Tauri stars are low-mass pre-main sequence stars at an early
stage of their evolution. For a few million years, they accrete ⋆Full Table 1 is only available at the CDS via anonymous ftp
to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc. u-strasbg.fr/viz-bin/cat/J/A+A/643/A99 ⋆⋆Based on observations obtained at the Canada-France-Hawaii
Telescope (CFHT), at the European Organisation for Astronomical
Research in the Southern Hemisphere under ESO programme 0103.C-
0097, and at the Las Cumbres Observatory global telescope network
(LCOGT). A99, page 1 of 18 A99, page 1 of 18 A&A 643, A99 (2020) E
E
E
E
E
S
S
S
S
S
S
S
S G
G
8640
8645
8650
8655
8660
HJD-2,450,000.0
0.9
1.0
1.1
g' (mag)
June 2019
Fig. 1. Visual summary of observations obtained in June 2019, as
part of the DoAr 44 coordinated campaign. The differential g′-band
light curve (see Sect. 3.2) is shown as colored circles, with the color
scale reflecting the Julian Date, while the epochs of CFHT/ESPaDOnS,
CFHT/SPIRou, and ESO VLTI/Gravity observations are indicated by
triangles labeled with “E”, “S”, and “G”, respectively. Note that the
March 2019 ESPaDOnS run, which is part of the campaign reported
here, is not shown in this figure. The average g-band magnitude of the
system during the campaign was g = 13.35 according to the publicly
available Zwicky Transient Facility light curve (Masci et al. 2019). Basri & Bertout 1989) and, more specifically, to arise from the
interaction region between the inner disk and the star. 1. Introduction E
E
E
E
E
S
S
S
S
S
S
S
S G
G
8640
8645
8650
8655
8660
HJD-2,450,000.0
0.9
1.0
1.1
g' (mag)
June 2019 g
The currently accepted paradigm that describes this interac-
tion is the magnetospheric accretion scenario where the strong
stellar magnetic field controls, at least partly, the accretion flow
from the inner disk edge to the stellar surface (Camenzind
1990; Koenigl 1991, see reviews by Bouvier et al. 2007a;
Hartmann et al. 2016). With large-scale surface magnetic fields
of a few hundred to a few kG (e.g., Donati 2020; Sokal et al. 2020), the stellar magnetosphere truncates the inner gaseous
disk at a distance of a few stellar radii (typically 3–8 R⋆) above
the photosphere. From there, the accreted material is channeled
along magnetic funnel flows, and hits the stellar surface almost
at free-fall velocity to create a localized accretion shock where
the kinetic energy of the flow is dissipated. In this scenario, the
emission line spectrum of cTTSs is partly formed in the accre-
tion funnel flows (Hartmann et al. 1994), and the accretion shock
is responsible for the continuum excess flux from the X-ray
range to the optical wavelengths, which is referred to as veiling
(Calvet & Gullbring 1998). Fig. 1. Visual summary of observations obtained in June 2019, as
part of the DoAr 44 coordinated campaign. The differential g′-band
light curve (see Sect. 3.2) is shown as colored circles, with the color
scale reflecting the Julian Date, while the epochs of CFHT/ESPaDOnS,
CFHT/SPIRou, and ESO VLTI/Gravity observations are indicated by
triangles labeled with “E”, “S”, and “G”, respectively. Note that the
March 2019 ESPaDOnS run, which is part of the campaign reported
here, is not shown in this figure. The average g-band magnitude of the
system during the campaign was g = 13.35 according to the publicly
available Zwicky Transient Facility light curve (Masci et al. 2019). g
The magnetospheric process extends over a scale less than
0.1 au from the star, which corresponds to ≤1 mas angular sepa-
ration on the sky at the distance of nearby star forming regions. Therefore, most constraints on the physics of magnetospheric
accretion come from observational campaigns monitoring the
spectral variability of selected cTTSs over successive rotation
periods. 2. Observations In this section, we describe the acquisition and data-reduction
processes of photometric and spectropolarimetric datasets
obtained during the large-scale campaign performed on the cTTS
DoAr 44, which also included long-baseline near-IR interferom-
etry. A summary plot of the main part of the DoAr 44 observing
campaign is provided in Fig. 1. The dedicated monitoring campaign of this source we
present here combines, for the first time, high angular resolu-
tion (≃1 mas) long-baseline interferometry, optical and near-IR
high-resolution spectropolarimetry, and multicolor photometry. DoAr 44 was selected for this campaign based on its brightness
(V = 12.6, K = 7.6), which is amenable to both long-baseline
interferometry and spectropolarimetry; the presence of a Brγ line
in emission in its near-IR spectrum, with EW(Brγ) ≃4 Å mea-
sured on an archival ESO/XSHOOTER spectrum; and the recent
report of its high surface magnetic field (Lavail et al. 2017). In 1. Introduction This moderately
bright source of spectral type K3 exhibits strong Hα emis-
sion with EW(Hα) ≃50 Å (Bouvier & Appenzeller 1992) and
accretes at a substantial rate from its circumstellar disk,
˙Macc = 6.0–9.3 10−9 M⊙yr−1 (Espaillat et al. 2010; Manara et al. 2014). From the measurement of the Zeeman broadening of
near-IR FeI lines, Lavail et al. (2017) derived a mean surface
magnetic field strength amounting to 1.8 ± 0.4 kG, and possibly
up to 3.6 kG. These authors further derived a projected rotational
velocity of v sin i = 17.5 ± 1.0 km s−1, and estimated a mass of
1.25 M⊙for this source. A99, page 2 of 18 2.1. LCOGT photomery 2), the PSF photometry
includes the target DoAr 44, the nearby W Uma eclipsing binary
V2394 Oph, the T Tauri stars ROX 42B, ROX 43, ROX 47B, and
DoAr 43, as well as four potential comparison and check stars:
[JDH94]Oph 587, TYC 6795-600-1, TYC 6795-516-1, and an
anonymous star (RA, Dec: 247.8519d, −24.3306d), referred to
as C5 in the following. We verified that Oph 587 and C5, located
within 10 arcmin of DoAr 44, were stable at a few 0.01 mag level
in all filters. While the two TYC stars are brighter than Oph 587
and C5, and also appear to be photometrically stable at similar
levels, they are located in a corner of the image, and are therefore
more prone to systematics (e.g. flat-field correction). Table 2. Journal of ESPaDOnS observations of DoAr 44. Date
UT
HJD
Φrot
S/N
(2019)
(hh:mm:ss)
(2 450 000.+)
(731 nm)
Mar 15
14:31:32
8558.10852
0.48
137
Mar 16
15:32:19
8559.15082
0.83
141
Mar 18
15:11:40
8561.13665
1.50
133
Mar 19
14:47:48
8562.12015
1.83
124
Mar 20
14:13:53
8563.09667
2.16
131
Mar 21
14:50:36
8564.12225
2.51
132
Mar 22
13:32:39
8565.06818
2.83
143
Jun 08
09:16:27
8642.89230
29.12
139
Jun 09
09:21:13
8643.89558
29.46
135
Jun 10
09:19:12
8644.89415
29.80
135
Jun 11
10:15:19
8645.93308
30.15
134
Jun 12
10:07:45
8646.92779
30.48
130
Notes. All observations consist of sequences of four subexposures, each
lasting 950 s. Columns respectively list, for each observation, the UT
date, time, heliocentric Julian date (HJD), rotational phase, and signal-
to-noise ratio (S/N) at 731 nm (per 2.6 km s−1 velocity bin). Table 2. Journal of ESPaDOnS observations of DoAr 44. p
y
g
We therefore used Oph 587 as a reference star and C5 as
a check star to derive the differential light curves for DoAr 44. Stars Oph 587 and C5 are within one magnitude of difference
from the target’s brightness in all filters. The rms error of the
photometric measurement in each filter amounts to about 0.02
mag. DoAr 44 is found to be variable in all four filters: the rms
dispersion of the u′g′r′i′ differential light curves (DoAr 44 – Oph
587) is 0.17, 0.09, 0.07, and 0.09 mag, respectively, while the
corresponding values for the comparison and check stars (Oph
587 – C5) are 0.03, 0.03, 0.04, and 0.04 mag. 2.1. LCOGT photomery Photometric observations were obtained at the Las Cumbres
Observatory Global Network (LCOGT, Brown et al. 2013) with
the 1m Sinistro telescopes from June 4 to June 24, 2019. We
used SDSS/PanSTARRS u′g′r′i′ filters with exposure times of A99, page 2 of 18 J. Bouvier et al.: DoAr 44 Table 1. LCOGT u′g′r′i′ differential photometry (first 10 of 229 mea-
surements). Table 1. LCOGT u′g′r′i′ differential photometry (first 10 of 229 mea-
surements). Fig. 2. Field of view of LCOGT images, with the target, as well as
comparison and check stars identified. North is up, east is left. The FOV
is 27 arcmin on the side. Table 1. LCOGT u′g′r′i′ differential photometry (first 10 of 229 mea
surements). Julian date
Target Check Filt. Airmass
Moon
(2 450 000.+)
(mag) (mag)
dist. (◦)
8638.9847732
1.03
0.39
gp
1.14
163
8638.9858978
0.09
0.28
ip
1.13
163
8638.9867561
0.5
0.43
rp
1.13
163
8638.9876614
0.95
0.02
up
1.13
163
8639.7314887
0.99
0.43
gp
1.04
152
8639.7326015
0.09
0.3
ip
1.04
152
8639.7334362
0.46
0.43
rp
1.04
152
8639.7343175
0.97
0
up
1.04
152
8639.9927617
0.94
0.4
gp
1.1
149
8639.9939326
0.06
0.3
ip
1.1
149
. . . Notes. The columns list: Julian date, differential magnitude (see text)
between DoAr 44 and the comparison star, between the comparison
star and the check star, filter, airmass, and Moon distance from the tar-
get. We note that the results are given for different filters on each row. In any given filter, the comparison-check star values listed in the third
column are constant within errors (see text). The full table is available
electronically at CDS, Strasbourg. Fig. 2. Field of view of LCOGT images, with the target, as well as
comparison and check stars identified. North is up, east is left. The FOV
is 27 arcmin on the side. 60, 30, 10, and 5s, respectively. A total of 219 images centered
on DoAr 44 were obtained over 20 days with a cadence of nearly
three photometric sequences per 24 hours. Point-spread function
(PSF) photometry was performed using IRAF/DAOPHOT on the
pipe-line reduced images provided by LCOGT. Over the field
of view (FOV) of 27 arcmin (see Fig. 2.1. LCOGT photomery The nearby bright
Moon toward the middle of the photometric campaign (June 16,
2019; JD 2458650.5) strongly increased the sky background,
especially in the u′-band, leading to poorer quality photometry
around this date. DoAr 44’s differential photometry is provided
in Table 1. Notes. All observations consist of sequences of four subexposures, each
lasting 950 s. Columns respectively list, for each observation, the UT
date, time, heliocentric Julian date (HJD), rotational phase, and signal-
to-noise ratio (S/N) at 731 nm (per 2.6 km s−1 velocity bin). of 65 000 covering 370–1000 nm (Donati 2003). During the first
run, seven circularly polarized spectra were collected, and five
additional spectra were obtained during the second run. Raw
frames were reduced with the standard ESPaDOnS reduction
package, and a least-squares deconvolution (LSD, Donati et al. 1997) was applied to all spectra, using a line list appropriate to
DoAr 44. The journal of observations is presented in Table 2. Near-IR spectropolarimetric observations of DoAr 44 were com-
pleted from June 14 to 21, 2019 with the SPIRou spectropo-
larimeter at the CFHT, covering from 0.95 to 2.50 microns, at a
spectral resolution of 70 000 (Donati et al. 2020) at a rate of one
visit per night. Raw data were processed by the SPIRou pipe-
line at CFHT and the reduced data provided by the Canadian
Astronomy Data Center. The journal of observations is presented
in Table 3. 2.2. CFHT spectropolarimetry Optical spectropolarimetric observations of DoAr 44 were com-
pleted during two runs, from March 15 to 22 and from June
8 to 12, 2019, with the ESPaDOnS spectropolarimeter at the
Canada-France-Hawaii Telescope (CFHT), at a resolving power A99, page 3 of 18 A99, page 3 of 18 A&A 643, A99 (2020) Table 3. Journal of SPIRou observations of DoAr 44. (Gustafsson et al. 2008) and VALD line lists (Ryabchikova et al. 2015). Assuming log g = 4.0, we derived the following param-
eters: v sin i = 17.0 ± 1.1 km s−1, Vr = −5.70 ± 0.24 km s−1, Teff=
4600 ± 120 K, and Vmic = 0.27 ± 0.27 km s−1. The veiling, that is
to say, the ratio of the continuum excess flux to the stellar pho-
tospheric flux, is measured as constant over time and amounts to
r ≃0.18 ± 0.05 over the wavelength range 610–670 nm. Date
UT
HJD
Φrot
S/N
(2019)
(hh:mm:ss)
(2 450 000.+)
(2135 nm)
Jun 14
08:43:03
8648.8680960
31.14
223
Jun 15
08:54:21
8649.8759002
31.48
227
Jun 16
09:17:09
8650.8916925
31.82
227
Jun 17
09:39:18
8651.9070323
32.16
137
Jun 18
08:28:37
8652.8579025
32.49
216
Jun 19
09:27:16
8653.8985925
32.84
237
Jun 20
08:07:01
8654.8428144
33.16
237
Jun 21
10:17:10
8655.9331438
33.52
211
Notes. All observations consist of sequences of four subexposures, each
lasting 300 s. Columns respectively list, for each observation, the UT
date, time, HJD, and S/N at 2135 nm per 2.3 km s−1 velocity bin. g
g
Using the optical photometry of Bouvier et al. (1988)
and 2MASS J-band, and adopting a K2–K3 spectral type
with intrinsic colors listed in Pecaut & Mamajek (2013),
we derived color excesses in the (V−Ic) and (V–J) col-
ors that correspond to a visual extinction AV = 2.0 ± 0.2 mag. From the J-band magnitude, bolometric corrections from
Pecaut & Mamajek (2013) for K2–K3 young stars, and a dis-
tance of 146 ± 1 pc (Gaia Collaboration 2016, 2018), we thus
obtained L⋆= 1.6 ± 0.2 L⊙. Combined with Teff= 4600 K derived
above, this yields R⋆= 2.0 ± 0.15 R⊙. From its position in the
HR diagram, we derived M⋆= 1.23 ± 0.15 M⊙using the CESAM
evolutionary models (Marques et al. 3.2. Photometric variability Notes. The V-band and 2MASS J-band magnitudes, and the Gaia DR2
distance are taken from the literature (see text). All other values are
derived in this study. The LCOGT observations yielded 20 day-long differential light
curves for DoAr 44 in the u′g′r′i′ filters. We searched for a
periodicity in the photometric variations, excluding about five
measurements per filter taken when the bright moon was under
15 degrees away from the target. We used both the CLEAN
periodogram analysis (Roberts et al. 1987) and the string-length
method (Dworetsky 1983). The former yields a period of 3.09 d
in the r′ filter only, while the latter returns a most proba-
ble period in all filters in the range from 2.97 d to 3.07 d. In
order to confirm the period, we downloaded ASAS-SN pho-
tometry (Shappee et al. 2014), which contains 288 single fil-
ter measurements over a single season extending from MJD
57780 to MJD 58030 (February-September 2017). Using the
same period-search algorithms, we found a clear periodicity of
2.960 ± 0.018 d in this much richer dataset, with a peak-to-peak
amplitude of about 0.1 mag. The LCOGT g′r′i′ light curves
folded in phase with this period are shown in Fig. 3 and suggest a
low-level modulation by surface spots, of the order of a 0.08 mag
peak to peak in the g′r′i′ filters. While a period is found in the u′-
band light curve as well, the phased light curve exhibits a scat-
ter of the same order as the photometric amplitude. We there-
fore adopted the more accurate 2.960 d period derived from the
ASAS-SN dataset and ascribed it to the rotational period of the
star. We thus define an ephemeris such that the origin of phase
corresponds to the epoch of maximum brightness at the time of
our observations, so 2.3. ESO/VLTI interferometry DoAr 44 was observed on June 22 and 23, 2019 in the K-band
with the GRAVITY instrument (Gravity Collaboration 2017)
combining the four unit telescopes of the ESO/VLTI (ESO run
60.A-9256). At 2.2 µm, with a maximum baseline of 130 m,
we thus reach an angular resolution of λ/2Bmax = 1.7 mas,
corresponding to 0.25 au at 146 pc. We used the instru-
ment in its high spectral-resolution mode (R ∼4000), thus
partly resolving the Brγ line profile. The observations, data
reduction, and interferometric results are described in full in
Paper I. 2.2. CFHT spectropolarimetry 2013), and the star appears
to have a modest radiative core, with Mrad/M⋆= 0.22 ± 0.20 and
Rrad/R⋆= 0.35 ± 0.2, where Mrad and Rrad are the mass and radius
of the radiative core, respectively. We note, however, that the lat-
ter values are strongly model dependent, as, using Siess et al. (2000) models, we would derive M⋆= 1.4 M⊙, Mrad/M⋆= 0.73
and Rrad/R⋆= 0.50. Notes. All observations consist of sequences of four subexposures, each
lasting 300 s. Columns respectively list, for each observation, the UT
date, time, HJD, and S/N at 2135 nm per 2.3 km s−1 velocity bin. Table 4. Stellar properties of the DoAr 44 system. Table 4. Stellar properties of the DoAr 44 system. V, J
12.6, 9.1
SpT
K2–K3
AV
2.0 ± 0.2 mag
Teff
4600 ± 120 K
L⋆/L⊙
1.6 ± 0.2
R⋆/R⊙
2.0 ± 0.15
M⋆/M⊙
1.2 ± 0.15
EW(LiI)
430 mÅ
v sin i
17.0 ± 1.1 km s−1
Prot
2.960 ± 0.018 d
i
30 ± 5◦
˙Macc
7 ± 3 10−9 M⊙yr−1
d
146 ± 1 pc
rcor
0.043 au (4.63 R⋆)
rsub
0.044 au (4.74 R⋆)
Notes. The V-band and 2MASS J-band magnitudes, and the Gaia DR2
distance are taken from the literature (see text). All other values are
derived in this study. Finally, we used the above estimate of the stellar radius to
derive the inclination of the stellar rotational axis on the line
of sight (LoS). Using v sin i = 17 km s−1 and Prot = 2.96 d (see
below), and propagating the uncertainties, yields sin i = 0.50 ±
0.05, which translates to i = 30 ± 5◦, meaning the system is seen
at low inclination. Table 4 summarizes the properties of the stel-
lar system with their uncertainties. HJD(d) = 2, 458, 556.7 + 2.960 × E. 3.1. Stellar properties The g′r′i′ light curves (green,
blue, and red, respectively) are shown folded in phase with a period of
2.960 days derived from periodogram analysis (see text). A sine curve
was eye fit to the light curves and is shown for illustration with a peak-
to-peak amplitude of 0.08 mag in the g′r′i′ bands. qualitatively accounted for by dipolar magnetospheric accretion
models considering moderate to low inclinations, i ≃30−45◦
(Muzerolle et al. 1998, 2001). Both the Hα and Hβ profiles
exhibit significant variance in the blue and red wings up to
velocities of a few hundred km s−1, and comparatively less vari-
ability in the line center. As is often observed in T Tauri stars
(Beristain et al. 2001), the HeI line profile is composite, con-
sisting of a centrally peaked broad component, extending up to
velocities of ±200 km s−1, and a narrow component located close
to the line center with a FWHM of about 40 km s−1. The profile’s
variability seems to be predominantly associated with the narrow
component. According to Beristain et al. (2001), the properties
of this type of HeI profile suggest the narrow component arises
in the post-shock region close to the stellar surface, while the
broad component is formed in the main accretion column above
the accretion shock. Fig. 4. From left to right: mean (black) and variance (red) residual pro-
files for Hα, Hβ, and HeI 587.6 nm. Hα and Hβ appear on overlapping
spectral orders, which are both shown here. For HeI, the variance has
been multiplied by 10. The increased scatter over the blue wing of the
HeI line profile is due to spectral order overlap. Fig. 4. From left to right: mean (black) and variance (red) residual pro-
files for Hα, Hβ, and HeI 587.6 nm. Hα and Hβ appear on overlapping
spectral orders, which are both shown here. For HeI, the variance has
been multiplied by 10. The increased scatter over the blue wing of the
HeI line profile is due to spectral order overlap. Figure 5 shows the superimposed Hα and Hβ line profiles
recorded for DoAr 44 during the CFHT/ESPaDOnS runs of
March and June 2019. Figure 6 is another representation of the
same dataset, ordered by Julian date and by rotational phase. Similar plots are shown for the HeI 587.6 nm line in Fig. 7. 3.1. Stellar properties We derived estimates of the system’s properties based on the
newly acquired high-resolution spectra. We followed the same
procedure as we used in Pouilly et al. (2020) to which the reader is
referred for details. We selected 16 spectral windows between 600
and 800 nm where the mean ESPaDOnS spectrum of DoAr 44 is
fit with a synthetic spectrum generated from the ZEEMAN code
(Folsom et al. 2012) based on MARCS stellar atmosphere grids (1) HJD(d) = 2, 458, 556.7 + 2.960 × E. A99, page 4 of 18 J. Bouvier et al.: DoAr 44 Fig. 3. DoAr 44 photometric variations. The g′r′i′ light curves (green,
blue, and red, respectively) are shown folded in phase with a period of
2.960 days derived from periodogram analysis (see text). A sine curve
was eye fit to the light curves and is shown for illustration with a peak-
to-peak amplitude of 0.08 mag in the g′r′i′ bands. Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is
covered by two spectral orders and both are shown. qualitatively accounted for by dipolar magnetospheric accretion
models considering moderate to low inclinations, i ≃30−45◦
(Muzerolle et al. 1998, 2001). Both the Hα and Hβ profiles
exhibit significant variance in the blue and red wings up to
velocities of a few hundred km s−1, and comparatively less vari-
ability in the line center. As is often observed in T Tauri stars
(Beristain et al. 2001), the HeI line profile is composite, con- Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is
covered by two spectral orders and both are shown. Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is
covered by two spectral orders and both are shown. Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is
covered by two spectral orders and both are shown. Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is
covered by two spectral orders and both are shown. Fig. 3. DoAr 44 photometric variations. 3.1. Stellar properties We
note that the Balmer line profiles appear more symmetric in June
than in March, while the HeI line profile has remained the same,
and it exhibits a broad component and a narrow component at
both epochs. Remarkably, the Hα and Hβ profiles do no exhibit
high-velocity redshifted absorptions below the continuum at any
rotational phase, contrary to what is often seen in other accreting
sources as the funnel flow intercepts the LoS (e.g., Bouvier et al. 2007b; Alencar et al. 2012, 2018). The lack of inverse P Cygni
profile signatures provides further support for a low inclination
of the system (Muzerolle et al. 2001), as independently derived
for the stellar rotational axis and for the outer disk that both sug-
gest i ≃20−35◦(see above and Paper I). Finally, we note that the uncertainty on the derived period, δP =
0.018 d, could induce a phase shift between the March and June
ESPaDOnS runs up to δΦ = 0.16 rms. 3.3. Optical line profiles Deciphering the shape and variability of the emission line pro-
files seen in the spectra of cTTSs offers a window to the physical
processes occurring close to the star, particularly the structure
and dynamics of accretion and outflows (e.g., Alencar & Basri
2000; Edwards et al. 2006; Lima et al. 2010; Esau et al. 2014). In the optical range, DoAr 44’s spectrum shows line emission
primarily the HI Balmer and Paschen series, in the CaII H&K
doublet and near-IR triplet, as well as in the HeI 587.6 nm,
667.8 nm, and 706.6 nm, [OI] 630.0 nm, and OI 777.3 nm lines. Residual emission line profiles were computed by subtracting
the broadened photospheric spectrum of the Hyades cluster
member Melotte 25–151, a K2-type star with Vr = 37.98 km s−1,
v sin i = 4.83 km s−1, and Teff= 4920 K (Folsom et al. 2018), also
observed with ESPaDOnS. g
(
p
)
Equivalent width measurements for Hα, Hβ, and HeI emis-
sion lines are reported in Table 5. As the continuum is well
defined around these lines, the equivalent width measurement is
accurate to within a few percent. The median equivalent widths
over the two epochs amount to 44, 6.8, and 0.8 Å, for Hα, Hβ,
and HeI lines, respectively. The lines have slightly larger median
equivalent widths in June than in March. Their variation as a
function of rotational phase is shown in Fig. 8. There is a hint
of rotational modulation in the equivalent width variations of
the three line profiles during the June run, with minimum val-
ues close to a rotational phase of 0.5, while no such modula-
tion is seen in the March run. We estimate the mass accretion
rate onto the star from the flux measured in the Hα and Hβ
lines, using relationships between accretion and line luminosity
from Alcalá et al. (2014). From the Hα line we thus derive
Lacc/L⊙= 0.06–0.13, taking into account EW(Hα) variations, 3.3.1. Line profile variability The spectral series we obtained on DoAr 44 with CFHT/
ESPaDOnS allows us to investigate the spectral variability of
the source on timescales ranging from days to months. Figure 4
shows the mean and variance profile for the main emission
lines. The Balmer line profiles are double peaked with a slightly
depressed red peak, corresponding to the Type II(R) profiles in
the classification of Reipurth et al. (1996). This profile shape is A99, page 5 of 18 A&A 643, A99 (2020) 500
0
500
v (km/s)
phase
29.12
30.15
2.16
29.46
0.48
30.48
1.5
2.51
29.8
2.83
0.83
1.83 500
0
500
v (km/s)
phase
29.12
30.15
2.16
29.46
0.48
30.48
1.5
2.51
29.8
2.83
0.83
1.83
500
0
500
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07
8642.89
8643.9
8644.89
8645.93
8646.93
500
0
500
v (km/s)
phase
29.12
30.15
2.16
29.46
0.48
30.48
1.5
2.51
29.8
2.83
0.83
1.83
500
0
500
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07
8642.89
8643.9
8644.89
8645.93
8646.93
Fig. 6. Hα (top) and Hβ (bottom) residual line profile variability as
a function of date and phase. The color code corresponds to different
rotational cycles. We note that both profiles appear less asymmetric in
June than in March 2019, with a more depressed red wing at the earlier
epoch. 250
0
250
v (km/s)
phase
29.12
30.15
2.16
29.46
0.48
30.48
1.5
2.51
29.8
2.83
0.83
1.83
250
0
250
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07
8642.89
8643.9
8644.89
8645.93
8646.93
Fig. 7. Same as Fig. 6 for HeI 587.6 nm residual line profile. We note
the presence of a narrow component superimposed on a broad pedestal. Similar line profiles are observed in March and June 2019. Table 5. Photospheric radial velocity, Vr, and equivalent width, W, of
Hα, Hβ, and HeI emission lines from ESPaDOnS spectra. 3.3.1. Line profile variability HJD
Vr (†)
W(Hα)
W(Hβ)
W(HeI)
(−2 450 000)
km s−1
(Å)
(Å)
(Å)
8558.10852
−5.59
41.6
8.2
1.13
8559.15082
−5.78
38.2
5.8
0.62
8561.13665
−5.60
31.8
4.3
0.60
8562.12015
−5.80
48.1
7.7
0.85
8563.09667
−6.00
41.0
5.8
0.46
8564.12225
−5.63
44.1
6.8
0.76
8565.06818
−5.76
45.5
7.2
0.80
8642.89230
−6.10
60.5
12.5
1.06
8643.89558
−5.55
44.8
6.6
0.66
8644.89415
−5.66
53.3
10.0
1.04
8645.93308
−6.02
43.9
7.7
0.99
8646.92779
−5.58
39.6
6.1
0.77 500
0
500
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07
8642.89
8643.9
8644.89
8645.93
8646.93 250
0
250
v (km/s)
phase
29.12
30.15
2.16
29.46
0.48
30.48
1.5
2.51
29.8
2.83
0.83
1.83 250
0
250
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07
8642.89
8643.9
8644.89
8645.93
8646.93 500
0
500
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07
8642.89
8643.9
8644.89
8645.93
8646.93 500
0
500
v (km/s)
phase
29.12
30.15
2.16
29.46
0.48
30.48
1.5
2.51
29.8
2.83
0.83
1.83 v (km/s) v (km/s) Fig. 7. Same as Fig. 6 for HeI 587.6 nm residual line profile. We note
the presence of a narrow component superimposed on a broad pedestal. Similar line profiles are observed in March and June 2019. Table 5. Photospheric radial velocity, Vr, and equivalent width, W, of
Hα, Hβ, and HeI emission lines from ESPaDOnS spectra. HJD
Vr (†)
W(Hα)
W(Hβ)
W(HeI)
(−2 450 000)
km s−1
(Å)
(Å)
(Å)
8558.10852
−5.59
41.6
8.2
1.13
8559.15082
−5.78
38.2
5.8
0.62
8561.13665
−5.60
31.8
4.3
0.60
8562.12015
−5.80
48.1
7.7
0.85
8563.09667
−6.00
41.0
5.8
0.46
8564.12225
−5.63
44.1
6.8
0.76
8565.06818
−5.76
45.5
7.2
0.80
8642.89230
−6.10
60.5
12.5
1.06
8643.89558
−5.55
44.8
6.6
0.66
8644.89415
−5.66
53.3
10.0
1.04
8645.93308
−6.02
43.9
7.7
0.99
8646.92779
−5.58
39.6
6.1
0.77
Notes. (†)The rms uncertainty on Vr amounts to 0.05 km s−1. Fig. 6. Hα (top) and Hβ (bottom) residual line profile variability as
a function of date and phase. The color code corresponds to different
rotational cycles. We note that both profiles appear less asymmetric in
June than in March 2019, with a more depressed red wing at the earlier
epoch. Notes. (†)The rms uncertainty on Vr amounts to 0.05 km s−1. which yields ˙Macc = 4.0–8.5 10−9 M⊙yr−1 assuming a magneto-
spheric truncation radius of 5 R⋆. 3.3.1. Line profile variability Similarly, from the Hβ line, we
obtain Lacc/L⊙= 0.05–0.17 and ˙Macc = 3–10 10−9 M⊙yr−1. These
estimates are consistent with those reported by Manara et al. (2014), who obtained ˙Macc = 6.3 10−9 M⊙yr−1 from slab models
applied to XSHOOTER spectra. low number of spectra obtained during each run. Nevertheless,
the examination of the shape of the line profiles plotted as a func-
tion of rotational phase in Fig. A.1 tends to support rotational
modulation at both epochs, with a systematically depressed line
flux in the red part of the profile around phase 0.5 for Balmer
lines, as expected from accretion funnel flows as they cross the
LoS (e.g., Symington et al. 2005). low number of spectra obtained during each run. Nevertheless,
the examination of the shape of the line profiles plotted as a func-
tion of rotational phase in Fig. A.1 tends to support rotational
modulation at both epochs, with a systematically depressed line
flux in the red part of the profile around phase 0.5 for Balmer
lines, as expected from accretion funnel flows as they cross the
LoS (e.g., Symington et al. 2005). A periodogram analysis of the line profiles is detailed in
Appendix A. The analysis does not reveal any significant period-
icity in the intensity variations of the velocity channels across the
Hα, Hβ, and HeI line profiles when the full dataset is analyzed. This presumably results from the large temporal gap between the
March and June ESPaDOnS runs. As described in Appendix A,
when each run is analyzed independently, we do find some evi-
dence for the rotational modulation of the Hα and Hβ line pro-
files at the stellar rotation period. More specifically, the intensity
of the red wing (from about +50 to +150 km s−1) of the Hα and
Hβ profiles appears to be modulated at the stellar rotation period
during the March run. Since the veiling is nearly constant at these
dates, we ascribe these variations to changes in the intrinsic line
flux, as opposed to continuum variations. This result is of limited
significance, due to the poor rotational phase sampling and the 3.3.2. Line profile decomposition We further analyzed the line profiles attempting to reproduce
their shape as a combination of Gaussian components. Details
on the line profile decomposition are given in Appendix B, and
a few examples are illustrated in Fig. B.1. The Balmer line pro-
files are well fit with three Gaussian components, consisting of
a broad central emission peak and two absorption components,
one blueshifted, and the other redshifted, relative to the line
center. The HeI line profile can be reproduced using only two
emission components, a broad and a narrow one. The results are A99, page 6 of 18 J. Bouvier et al.: DoAr 44 Fig. 8. Equivalent width (Å) as a function of rotational phase. Left
panel: Hα (top) and Hβ (bottom); right panel: HeI. The color code cor-
responds to Julian date, mostly March (bright) and June (dark) 2019. broad components, and the fact that the radial velocities of both
components appear to be modulated but reach a maximum value
at different rotational phases (see Fig. 9), suggest the two com-
ponents probe different regions along the funnel flow. Considering the two absorption components in the Hα pro-
file, one being blueshifted, the other redshifted, we find that their
FWHMs are rotationally modulated and strongly anti-correlated
(see Table B.1). The equivalent width and peak absorption inten-
sity of the blueshifted component are the largest around phase 0,
while the equivalent width of the redshifted absorption compo-
nent is the largest around phase 0.5. As the former is probably
related to an outflow, while the latter probes accretion, this sug-
gests that both flows are physically related and occur at oppo-
site rotational phases. We also notice a hint of a correlation
between the radial velocity variations of these two absorption
components in the Hα line profile, as reported earlier for AA
Tau (Bouvier et al. 2003) and LkCa 15 (Alencar et al. 2018). Fig. 8. Equivalent width (Å) as a function of rotational phase. Left
panel: Hα (top) and Hβ (bottom); right panel: HeI. The color code cor-
responds to Julian date, mostly March (bright) and June (dark) 2019. Fig. 9. Radial velocity (left) and FWHM (right) variations of the narrow
(top) and broad (bottom) components of the HeI line profile in the stellar
rest frame as a function of rotational phase. The color code reflects the
Julian date for the March (bright) and June (dark) ESPaDOnS runs. 3.3.3. Correlation matrices The observed emission lines of DoAr 44 are highly variable,
with emission and absorption components superposed, as can be
seen in Fig 5. The different components may come from various
circumstellar regions, like the chromosphere, the accretion fun-
nel, and the wind, which can vary over different timescales. To
investigate how the variations across a line or between different
lines are related, we calculated correlation matrices consisting of
2D plots of the linear correlation coefficients of the line profile
intensity variations at different velocity bins. A good correlation
between two components indicates a common origin of the com-
ponents, for example. given in Table B.1, which lists the equivalent width, peak inten-
sity, radial velocity, and FWHM of each component. The narrow component of the HeI line profile shows signif-
icant radial velocity variations between +4.4 and +11.4 km s−1
in the stellar rest frame, while its FWHM varies over the range
38–47 km s−1. We find these variations to be modulated by stel-
lar rotation with a strong phase coherence between the March
and June ESPaDOnS runs (see Fig. 9). Assuming that the HeI
line narrow component arises from the accretion post-shock
(Beristain et al. 2001), as suggested by its slightly redshifted
velocity, and covers a small area on the stellar surface, one can
relate the radial velocity amplitude δVr to the hot spot latitude θ,
with δVr = 2 · v sin i · cos θ (Bouvier et al. 2007b). We deduce a
latitude of 78 ±2 ◦for the accretion shock at the stellar surface,
assuming an uncertainty of 0.5 km s−1 on δVr. The Hα and Hβ lines are similar, and their correlation matri-
ces also show the same characteristics (Fig. 10). There is little
correlation between the blue and red part of the profile, which
suggests different physical processes at the origin of their vari-
ability. The red wing of the profile varies coherently beyond
+200 km s−1 and is strongly anti-correlated with the red emis-
sion peak around 100 km s−1. This red emission peak is strongly
variable, as can be clearly seen in Figs. 5 and 6. As the velocity
channels corresponding to the peak appear to be modulated at
the stellar rotation period, we interpret its anti-correlation with
the profile’s far red wing as the signature of periodic redshifted
absorptions due to the funnel flow crossing the LoS. 3.3.2. Line profile decomposition As illustrated in Fig. B.1, the decomposition of the CaII
854.2 nm emission line reveals the presence of a highly red-
shifted absorption component during the March run, around
Vr ≃+120 km s−1. It is observed at phases 0.83 (JD 8559.15)
and 2.83 (JD 8565.07), but, surprisingly enough, not at phase
1.83 (JD 8562.12). Similar high-velocity redshifted absorptions
are also seen in the NaI D line profiles at the same phases. This
suggests transient accretion episodes onto the stellar surface or,
at least, mass accretion rate variations occur within the funnel
flow. No redshifted absorption components are seen in this line
profile during the June run. Fig. 9. Radial velocity (left) and FWHM (right) variations of the narrow
(top) and broad (bottom) components of the HeI line profile in the stellar
rest frame as a function of rotational phase. The color code reflects the
Julian date for the March (bright) and June (dark) ESPaDOnS runs. 3.3.3. Correlation matrices HJD
EW(HeI)
EW(Brγ)
EW(Paβ)
(−2 450 000)
(Å)
(Å)
(Å)
8648.86809
4.0
2.7
6.9
8649.87590
4.7
3.0
8.6
8650.89169
5.5
3.2
8.4
8651.90703
4.0
3.4
8.1
8652.85790
5.1
2.8
8.6
8653.89859
6.8
3.3
8.5
8654.84281
6.7
3.8
8.9
8655.93314
8.3
4.0
9.3
Notes. The uncertainty on EW is of the order of 0.1–0.2 Å depending
on the S/N. Notes. The uncertainty on EW is of the order of 0.1–0.2 Å depending
on the S/N. 2008) predict such a rotationally modulated intensity of the high
velocity redshifted wing of the Paβ profile, as funnel flows peri-
odically cross the LoS. A strong signal is also seen in the 2D
periodogram from the line center up to +100 km s−1 at frequen-
cies around 0.9 d−1, with its alias at 0.1 d−1. The former fre-
quency is close to the sampling rate, and the latter is beyond the
observation time span. The signal at these frequencies is there-
fore probably spurious, being induced by the observing window. Nevertheless, the variability seen in this part of the Paβ profile is
real, and is also seen in the Brγ line profile over the same veloc-
ity channels, where the line intensity seems to first increase then
decrease smoothly over the time span of the observations (see
Fig. 11). Fig. 10. Top: auto-correlation matrices of Hα (left) and Hβ (right) line
profile variation for ESPaDOnS March run. Bottom: auto-correlation
matrices of HeI (left) and cross-correlation matrices of HeI vs. Hα
(right). the HeI line profile becomes stronger, which is consistent with
both the redshifted Hα absorption and the HeI BC emission orig-
inating from an accretion funnel flow crossing the LoS. The 2D periodogram of the HeI line profile displays the
strongest signal at a frequency corresponding to the stellar rota-
tion period, extending over redshifted velocity channels from
+30 to +100 km s−1 (see Fig. 13). This periodic variability
of the red part of the line profile is most likely induced by
the rotational modulation of accretion funnel flow as the star
rotates (e.g., Fischer et al. 2008). The other parts of the HeI
profile are extremely variable, especially around the line cen-
ter and throughout the blueshifted wing down to velocities
of −350 km s−1. The blue wing exhibits a rapidly changing
blueshifted absorption component sometimes reaching below
the continuum. Yet, this outflow component shows no sign
of modulation. 3.3.3. Correlation matrices g
y
r
Interestingly, the radial velocity of the wide component of
the HeI line profile seems to be rotationally modulated as well,
albeit with increased scatter. If this component arises from a
hot wind close to the star, the modulation may result from
the geometric projection of the wind velocity pattern onto the
LoS. However, its slightly redshifted velocity relative to the star
instead suggests it arises from the accretion funnel flow, located
above the post-shock region probed by the narrow component
(Beristain et al. 2001). The FWHM of the narrow and wide com-
ponents appears to be rotationally modulated as well. They reach
a maximum at phase 0.5 of 259 km s−1 for the broad compo-
nent and 47 km s−1 for the narrow one, and both vary by about
15% along the rotational cycle. This variation could conceivably
be related to the projection on the LoS of the velocity gradi-
ents of the emitting regions responsible for the narrow and broad
HeI components. The vastly different FWHM of the narrow and The HeI line is composed of a broad and a narrow compo-
nent. The correlation matrix is shown in Fig. 10. It indicates that
the BC varies coherently and independently of the NC compo-
nent. The Hα vs. HeI cross correlation matrix reveals that the
HeI BC component is correlated with the high velocity wings of
the Balmer profile beyond 200 km s−1. The red wing of the HeI
BC is, however, strongly anti-correlated with the red emission
peak seen in the Hα profile around 100 km s−1. This suggests
that redshifted absorption in the Hα profile occurs as the BC of A99, page 7 of 18 A99, page 7 of 18 A&A 643, A99 (2020) Table 6. Equivalent width (EW) of HeI 1083.3 nm, Brγ, and Paβ emis-
sion lines from SPIRou spectra. Table 6. Equivalent width (EW) of HeI 1083.3 nm, Brγ, and Paβ emis-
sion lines from SPIRou spectra. Fig. 10. Top: auto-correlation matrices of Hα (left) and Hβ (right) line
profile variation for ESPaDOnS March run. Bottom: auto-correlation
matrices of HeI (left) and cross-correlation matrices of HeI vs. Hα
(right). 3.3.3. Correlation matrices Instead, we observe significant change in HeI
line profiles taken at the same rotational phase over succes-
sive cycles, for example, at φ = 31.14, 32.16, 33.16, and at
φ = 31.48, 32.49 (see Fig. 12), which suggests intrinsic varia-
tions of the outflow component over a timescale of days. The
velocity of the peak of the blueshifted absorption component
appears to be the most extreme at the beginning of the obser-
vations (vblue ≃−200 km s−1), shifting toward the line center up
to vblue ≃−60 km s−1 within three days, then returning to much
bluer channels (vblue ≃−130 km s−1) over the same timescale. Its width changes as well, the most blueshifted absorption hav-
ing the largest FWHM. 3.4. Infrared line profiles 500
0
500
v (km/s)
phase
31.14
33.16
32.16
31.48
32.49
33.52
31.82
32.84
500
0
500
v (km/s)
day
8648.87
8649.88
8650.89
8651.91
8652.86
8653.9
8654.84
8655.93 200
0
200
v (km/s)
phase
31.14
33.16
32.16
31.48
32.49
33.52
31.82
32.84 500
0
500
v (km/s)
phase
31.14
33.16
32.16
31.48
32.49
33.52
31.82
32.84
500
/s) 500
0
500
v (km/s)
phase
31.14
33.16
32.16
31.48
32.49
33.52
31.82
32.84 200
0
200
v (km/s)
phase
31.14
33.16
32.16
31.48
32.49
33.52
31.82
32.84 200
0
200
v (km/s)
day
8648.87
8649.88
8650.89
8651.91
8652.86
8653.9
8654.84
8655.93 200
0
200
v (km/s)
day
8648.87
8649.88
8650.89
8651.91
8652.86
8653.9
8654.84
8655.93 200
0
200
v (km/s) 200
0
200
v (km/s) 200
0
200
v (km/s) Fig. 12. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profile variability as a function of date and phase. The narrow, slightly
blueshifted absorption component close to the center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds
to different rotational cycles Fig. 12. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profile variability as a function of date and phase. The narrow, slightly
blueshifted absorption component close to the center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds
to different rotational cycles. 400
200
0
200
400
v (km/s)
0.2
0.4
0.6
0.8
1.0
Frequency (1/days)
hei profile 2D-periodogram
0.2
0.4
0.6
0.8
Power
300
200
100
0
100
200
300
v (km/s)
0.2
0.4
0.6
0.8
1.0
Frequency (1/days)
pab profile 2D-periodogram
0.2
0.4
0.6
0.8
Power
Fig. 13. 2D periodogram of the HeI 1083.3 nm (left) and Paβ (right)
line profiles computed from the eight SPIRou spectra obtained on con-
secutive nights. The color code represents the periodogram power, and
the superimposed white curve is the average line profile. We note the
symmetry of the periodogram around the frequency 0.5 d−1 due to the
one-day alias resulting from the night-to- night sampling. Fig. 14. Auto-correlation matrices for the HeI, Paβ, and Brγ line profiles
(left), and cross-correlation matrices for the three line profiles (right). 3.4. Infrared line profiles The wide spectral range covered by SPIRou includes a num-
ber of circumstellar diagnostics, such as HeI 1083.3 nm, Paβ
1282.2 nm, and Brγ 2166.1 nm. These lines are seen in emis-
sion in all the spectra acquired during the SPIRou observ-
ing run, and their equivalent widths are listed in Table 6. From the equivalent widths of the Paβ and Brγ line profiles
measured on the mean spectrum, EW(Paβ) = 8.75 ± 0.15 Å and
EW(Brγ) = 3.5 ± 0.2 Å, and using Alcalá et al. (2014) relation-
ship between line and accretion luminosities, we derived a mass
accretion rate ˙Macc = 6.5 ± 0.5 10−9 M⊙yr−1, which is consistent
with the estimate obtained above from the luminosity of the opti-
cal emission lines. Residual line profiles were computed following the same
procedure as described above for optical spectra, using the weak-
line T Tauri star V819 Tau (SpT K4) as a template, also observed
with SPIRou. Line profiles are shown in Fig. 11. The HeI
profile exhibits a strongly asymmetric shape, with significant
blueshifted absorption components reaching down to velocities
of −350 km −1 with a depth that varies on a timescale of days,
while the red wing appears in emission and also exhibits signif-
icant variability. In contrast, the Paβ and Brγ profiles are much
more symmetric, with only low-level variability in intensity over
the course of the observations. The profiles are plotted as a func-
tion of date and rotational phase in Fig. 12. Radiative transfer models assign the presence of moderately
blueshifted, narrow absorption components in the profile of the
HeI 1083.3 nm line to a disk wind (e.g., Kurosawa et al. 2011),
while broader absorptions extending to large blueshifted veloci-
ties are usually considered as the signature of accretion powered,
hot inner winds originating close to the star (e.g., Edwards et al. 2003, 2006). We are apparently witnessing here a mix of disk
and “stellar” winds, with a predominance of the former except We performed a 2D periodogram analysis across the line pro-
files. The 2D periodogram of the Paβ line profile is shown in
Fig. 13. A strong signal appears at the star’s rotational period in
the redshifted wing of the profile over a velocity range extending
from +100 to +200 km s−1. Radiative transfer models of magne-
tospheric accretion onto an inclined dipole (e.g., Kurosawa et al. 3.4. Infrared line profiles A99, page 8 of 18 J. Bouvier et al.: DoAr 44 J. Bouvier et al.: DoAr 44
400
200
0
200
400
v (km/s)
0.4
0.2
0.0
0.2
0.4
0.6
0.8
1.0
1.2
Residual flux
300
200
100
0
100
200
300
v (km/s)
0.2
0.0
0.2
0.4
0.6
0.8
1.0
1.2
Residual flux
300
200
100
0
100
200
300
v (km/s)
0.0
0.1
0.2
0.3
Residual flux
Fig. 11. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profiles. The narrow, slightly blueshifted absorption component close the
center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds to successive rotational cycles. 300
200
100
0
100
200
300
v (km/s)
0.2
0.0
0.2
0.4
0.6
0.8
1.0
1.2
Residual flux 300
200
100
0
100
200
300
v (km/s)
0.0
0.1
0.2
0.3
Residual flux 400
200
0
200
400
v (km/s)
0.4
0.2
0.0
0.2
0.4
0.6
0.8
1.0
1.2
Residual flux Fig. 11. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profiles. The narrow, slightly blueshifted absorption component close the
center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds to successive rotational cycles. 500
0
500
v (km/s)
phase
31.14
33.16
32.16
31.48
32.49
33.52
31.82
32.84
500
0
500
v (km/s)
day
8648.87
8649.88
8650.89
8651.91
8652.86
8653.9
8654.84
8655.93
200
0
200
v (km/s)
phase
31.14
33.16
32.16
31.48
32.49
33.52
31.82
32.84
200
0
200
v (km/s)
day
8648.87
8649.88
8650.89
8651.91
8652.86
8653.9
8654.84
8655.93
200
0
200
v (km/s)
phase
31.14
33.16
32.16
31.48
32.49
33.52
31.82
32.84
200
0
200
v (km/s)
day
8648.87
8649.88
8650.89
8651.91
8652.86
8653.9
8654.84
8655.93
Fig. 12. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profile variability as a function of date and phase. The narrow, slightly
blueshifted absorption component close to the center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds
to different rotational cycles. 3.4. Infrared line profiles Middle: Stokes I and Stokes V LSD profiles ordered as a
function of rotational phase. Right: Stokes I and Stokes V profiles of the HeI 587.6 nm line’s narrow component ordered as a function of rotational
phase. The broad component of the HeI line profile has been fitted by a Gaussian and subtracted. The color code corresponds to successive
rotational cycles. A&A 643, A99 (2020) A&A 643, A99 (2020) ,
(
) Fig. 15. Left: Stokes I and Stokes V LSD profiles ordered as a function of Julian date. Middle: Stokes I and Stokes V LSD profiles ordered as a
function of rotational phase. Right: Stokes I and Stokes V profiles of the HeI 587.6 nm line’s narrow component ordered as a function of rotational
phase. The broad component of the HeI line profile has been fitted by a Gaussian and subtracted. The color code corresponds to successive
rotational cycles. component of the large scale magnetic field, Bl, derived from the
Stokes I and V signatures (Donati et al. 1997; Wade et al. 2000),
are shown in Fig. 17. It varies between −14 and −136 Gauss
(see Table 5) and appears to be modulated by stellar rotation. Remarkably, the magnetic field intensity does not exhibit sig-
nificant change between the March and June runs, nor does the
phase of its modulation. This suggests a fairly stable magnetic
configuration between the two epochs. low-velocity and high-velocity redshifted channels, and the latter
also varies independently. The cross-correlation matrix between
Paβ and Brγ reveals the same three components: the blue
wing, the low-velocity red channels, and the high-velocity red
channels. While each of these components varies independently
of the other, they are well correlated between the Paβ and Brγ
line profiles. A more complex behavior is seen in the cross-correlation
matrices of HeI with Paβ and Brγ. The high-velocity blue wing
of the HeI line is clearly correlated with that of the hydrogen
lines. More surprisingly perhaps, there is a hint of a correlation,
albeit relatively weak, between the high-velocity redshifted wing
of HeI and the blueshifted wing of the Paβ profile. Another fea-
ture is the apparent anti-correlation between the low-velocity
redshifted HeI channels and the high-velocity redshifted hydro-
gen wings. This occurs over the interval of velocities where
both profiles are rotationally modulated, namely around 30–
100 km s−1 for HeI and beyond 100 km s−1 for Paβ. 3.4. Infrared line profiles 300
200
100
0
100
200
300
v (km/s)
0.2
0.4
0.6
0.8
1.0
Frequency (1/days)
pab profile 2D-periodogram
0.2
0.4
0.6
0.8
Power 400
200
0
200
400
v (km/s)
0.2
0.4
0.6
0.8
1.0
Frequency (1/days)
hei profile 2D-periodogram
0
0
0
0 Fig. 13. 2D periodogram of the HeI 1083.3 nm (left) and Paβ (right)
line profiles computed from the eight SPIRou spectra obtained on con-
secutive nights. The color code represents the periodogram power, and
the superimposed white curve is the average line profile. We note the
symmetry of the periodogram around the frequency 0.5 d−1 due to the
one-day alias resulting from the night-to- night sampling. for the first spectrum of the series, whose relative strength varies
on a timescale of days. Indeed, the gallery of emission line profiles gathered from
the quasi-simultaneous optical and near-IR high-resolution spec-
tra obtained for DoAr 44 during this campaign, including HeI
587.6 nm, HeI 1083.3 nm, Hα, Hβ, Paβ, and Brγ, bears strong
resemblance with synthetic line profiles derived from the com-
bined magnetospheric accretion and disk wind, low-inclination
(i = 20◦) model presented in Fig. 7 of Kurosawa et al. (2011). It is therefore likely that most of the emission seen in these
profiles comes from magnetospheric funnel flows controlled
by a misaligned dipole, with additional wind components best
seen in the HeI near-IR line profile. The qualitative agree-
ment between observations and models supports this interpre-
tation. The low inclination of the system is further supported
by the maximum edge velocity at which the blueshifted HeI
absorption component meets the continuum, which amounts to
−350 km s−1. According to the edge velocity versus the sys- Fig. 14. Auto-correlation matrices for the HeI, Paβ, and Brγ line profiles
(left), and cross-correlation matrices for the three line profiles (right). tem’s inclination relationship reported for this component by
Appenzeller & Bertout (2013), here the system’s inclination
should lie in the range 20–35◦. The auto-correlation matrices of the three profiles are shown
in Fig. 14 and share the same behavior: different parts of the
line profile vary independently of each other. In the Paβ line
for instance, the blue wing varies independently of both the A99, page 9 of 18 A&A 643, A99 (2020)
Fig. 15. Left: Stokes I and Stokes V LSD profiles ordered as a function of Julian date. 3.4. Infrared line profiles If real, this
anti-correlation is somewhat surprising as the redshifted absorp-
tions in both profiles, though appearing at different velocities,
are expected to occur simultaneously at the time the funnel flow
crosses the LoS. This feature is also present in the autocorre-
lation matrices of HeI and Paβ. In fact, the HeI vs. Paβ matrix
closely mimics the structures seen in the HeI auto-correlation
matrix. While these features are intriguing, the value of the cor-
relation coefficient remains of the order of 0.5 or less, and would
therefore have to be confirmed from a longer time series. A similar analysis has been performed in the CaII near-IR
triplet. The three lines of the CaII triplet exhibit consistent mag-
netic signatures in their Stokes V profiles as shown in Fig. 16. The longitudinal component of the magnetic field projected onto
the LoS is still modulated at the stellar rotation period (see
Fig. 17) and now reaches a maximum value of 800 G, which
is about four times larger than the intensity deduced from the
LSD profiles, as is often the case for young accreting stars (e.g.,
Donati et al. 2019). It is worth mentioning here that the inten-
sity of Bl, as well as its sign, are widely different when using
LSD (photospheric) profiles and the CaII IRT (chromospheric)
lines. Indeed, these spectral features probe different regions at
the stellar surface. The Stokes V signal in the optical HeI line
was also analyzed, as it provides the most direct estimate of the
magnetic field strength at the base of the funnel flow, close to
the accretion shock. Unfortunately, the Stokes V profile in the
narrow component of the line is weak (see Fig. 15), which trans-
lates into large uncertainties in the derivation of the longitudinal
field strength. Figure 17 shows the absence of modulation within
error bars, with an average field strength of 2 ± 0.8 kG. The lack
of significant modulation may result from the low inclination of
the system, where the high latitude accretion shock remains in
view during the whole rotational cycle. 3.5. Zeeman-Doppler analysis The polarimetric capabilities of CFHT/ESPaDOnS allow us to
investigate the large-scale structure of the magnetic field at the
surface of the star. Figure 15 shows the least-square deconvolu-
tion ((LSD) Donati et al. 1997) Stokes I and Stokes V profiles
over the two ESPaDOnS runs, computed using a mean Landé
factor of 1.2 and a central wavelength of 500 nm. We did not
use the spectrum obtained on JD 8559.15 (φ = 0.83) for the ZDI
analysis as the LSD profiles show contamination by the morn-
ing twilight. A clear and relatively stable magnetic signature is
present in all Stokes V profiles. The variation of the longitudinal We used the Doppler imaging (DI) and Zeeman-Doppler
imaging (ZDI) implementation of Folsom et al. (2018) to respec-
tively map the surface brightness and magnetic field of DoAr 44. A full description of the code can be found in Folsom et al. (2018). Briefly, the code uses a time series of Stokes I and V
LSD profiles to construct a surface brightness map and the large-
scale vector magnetic field. The local line models are calculated
using a Voigt profile, with a Gaussian width of 1.2 km s−1 and a
Lorentzian width of 1.9 km s−1. The local line models for Stokes A99, page 10 of 18 J. Bouvier et al.: DoAr 44
Fig. 16. Stokes I (left panels) and V (right panels) profiles ordered as a function of Julian date for the three emission components of the CaII IR
triplet: 849 nm (left), 854 nm (middle), 866 nm (right). The phase of the corresponding rotational cycles is indicated on the left of the profiles. The
color code corresponds to successive rotational cycles. J. Bouvier et al.: DoAr 44 Fig. 16. Stokes I (left panels) and V (right panels) profiles ordered as a function of Julian date for the three emission components of the CaII IR
triplet: 849 nm (left), 854 nm (middle), 866 nm (right). The phase of the corresponding rotational cycles is indicated on the left of the profiles. The
color code corresponds to successive rotational cycles. Table 7. Longitudinal magnetic field strength (Bl) expressed in Gauss and computed from photospheric Stokes LSD profiles, from each line of the
CaII IR triplet (CaII1,2,3), and from the HeI 587.6 nm line appearing on two successive spectral orders (HeI1,2). 3.5. Zeeman-Doppler analysis Longitudinal magnetic field strength Bl (G)
HJD
LSD
σ
CaII1
σ
CaII2
σ
CaII3
σ
HeI1
σ
HeI2
σ
8558.10852
−119
14
270
80
290
70
310
90
890
640
280
620
8559.15082
–
–
540
60
650
70
750
80
3020
470
4070
450
8561.13665
−122
14
310
60
300
70
370
90
2340
720
1210
630
8562.12015
−14
15
460
70
690
90
390
110
1780
880
420
910
8563.09667
−85
14
310
70
490
90
410
100
920
860
2700
770
8564.12225
−136
15
170
80
300
90
330
110
1380
640
2720
620
8565.06818
−50
14
480
60
550
60
520
70
2450
390
2480
370
8642.8923
−58
15
350
70
550
80
690
90
2110
380
1830
340
8643.89558
−123
14
60
70
140
90
140
110
400
520
2190
580
8644.89415
−43
14
490
70
790
80
730
90
2150
360
1860
350
8645.93308
−62
14
510
70
440
70
630
80
2280
470
1430
420
8646.92779
−116
14
340
80
310
80
320
120
1510
570
2500
610 V are calculated from the local I line profile, using the weak-field
approximation (Landi Degl’Innocenti & Landolfi2004), and the
LSD mean Landé factor and central wavelength. The magnetic
field is expressed as a combination of spherical harmonics as
in Donati et al. (2006). The integration over the surface of the
star is done using a linear limb-darkening coefficient of 0.8
(Claret & Bloemen 2011), adapted to the temperature and grav-
ity of DoAr 44. The fit to the data is performed by both minimiz-
ing χ2 and maximizing the entropy, using the maximum entropy
fitting routine of Skilling & Bryan (1984). We have adopted the
photometric ephemeris defined above, and fixed the inclination
of the rotation axis at 35◦, which is consistent with the inclina-
tion of the inner disk seen in interferometry on a scale of 0.14 au
(see Paper I). ZDI and reconstruct the magnetic map. We fixed the maximum
value of the Legendre polynomial degree l–15 in the spherical
harmonics decomposition. The resulting distribution of the mag-
netic vectors over the stellar surface is shown in Fig. 18. It indi-
cates a dominant dipolar component, encompassing 75% of the
total flux, while only 8% and 4% of the flux is contained in the
quadrupolar and octupolar components, respectively. 3.5. Zeeman-Doppler analysis The neg-
ative pole of the dipole is facing us at the phase 0.5, which is
consistent with the maximum absolute value of the longitudinal
field. It is located at the latitude of 70◦, and thus inclined by 20◦
onto the rotational axis. ZDI and reconstruct the magnetic map. We fixed the maximum
value of the Legendre polynomial degree l–15 in the spherical
harmonics decomposition. The resulting distribution of the mag-
netic vectors over the stellar surface is shown in Fig. 18. It indi-
cates a dominant dipolar component, encompassing 75% of the
total flux, while only 8% and 4% of the flux is contained in the
quadrupolar and octupolar components, respectively. The neg-
ative pole of the dipole is facing us at the phase 0.5, which is
consistent with the maximum absolute value of the longitudinal
field. It is located at the latitude of 70◦, and thus inclined by 20◦
onto the rotational axis. A99, page 11 of 18 4. Discussion 18. Top: brightness map derived from the variation of the LSD
Stokes I profiles. The color code is 1 for the photospheric temperature,
increases for hot spots, and decreases for cold ones. Bottom: the large-
scale total, radial, longitudinal, and latitudinal surface magnetic field
components, as derived from the variations of the LSD Stokes V pro-
files. The color code indicates the strength of the surface magnetic field
in Gauss. A&A 643, A99 (2020) A99 (2020) Fig. 17. Rotational modulation of the longitudinal component of the
large-scale magnetic field, derived from the LSD profiles (top), from
the CaII IR triplet (middle), and from the narrow component of the HeI
587.6 nm lines profile (bottom). The color code corresponds to succes-
sive rotational cycles. We emphasize the phase consistency between the
March and June datasets, as well as the apparently constant amplitude
of the field between the two epochs. In the top panel, the sine curve
has been fit with the period and origin of phase of the photometric
ephemeris. It shows that the maximum intensity of the photospheric
field occurs at phase 0.5, that is, at the time of minimum brightness (see
Fig. 3). In the middle panel, the three measurements at each phase are
obtained for each line of the CaII IR triplet. In the lower panel, there are
two measurements per spectrum, as the HeI line appears on successive
spectral orders. The three plots are not on the same scale. Fig. 17. Rotational modulation of the longitudinal component of the
large-scale magnetic field, derived from the LSD profiles (top), from
the CaII IR triplet (middle), and from the narrow component of the HeI
587.6 nm lines profile (bottom). The color code corresponds to succes-
sive rotational cycles. We emphasize the phase consistency between the
March and June datasets, as well as the apparently constant amplitude
of the field between the two epochs. In the top panel, the sine curve
has been fit with the period and origin of phase of the photometric
ephemeris. It shows that the maximum intensity of the photospheric
field occurs at phase 0.5, that is, at the time of minimum brightness (see
Fig. 3). In the middle panel, the three measurements at each phase are
obtained for each line of the CaII IR triplet. In the lower panel, there are
two measurements per spectrum, as the HeI line appears on successive
spectral orders. 4. Discussion The resulting brightness and magnetic maps are shown in
Fig. 18. One large cool spot is observed on the brightness
map, located close to the rotational axis and facing the observer
around phase 0.83. Two bright spots are present at lower lati-
tudes, facing the observer around phases 0.30 and 0.70. Due to
the low inclination of the system, little is known of the southern
hemisphere of the star. We used this brightness map to perform The variability analysis of the DoAr 44 system is complicated
by its nearly integer rotational period of 2.96 d. While we
observed the system over several rotational periods, the resulting
phase coverage remains limited, with essentially the same three
phases being sampled over the observations, at every third of the
rotational cycle. This prevents us from having a complete picture A99, page 11 of 18 A99, page 11 of 18 A&A 643, A99 (2020)
Fig. 17. Rotational modulation of the longitudinal component of the
large-scale magnetic field, derived from the LSD profiles (top), from
the CaII IR triplet (middle), and from the narrow component of the HeI
587.6 nm lines profile (bottom). The color code corresponds to succes-
sive rotational cycles. We emphasize the phase consistency between the
March and June datasets, as well as the apparently constant amplitude
of the field between the two epochs. In the top panel, the sine curve
has been fit with the period and origin of phase of the photometric
ephemeris. It shows that the maximum intensity of the photospheric
field occurs at phase 0.5, that is, at the time of minimum brightness (see
Fig. 3). In the middle panel, the three measurements at each phase are
obtained for each line of the CaII IR triplet. In the lower panel, there are
two measurements per spectrum, as the HeI line appears on successive
spectral orders. The three plots are not on the same scale. of the circumstellar environment of this young stellar object, and
Fig. 18. Top: brightness map derived from the variation of the LSD
Stokes I profiles. The color code is 1 for the photospheric temperature
increases for hot spots, and decreases for cold ones. Bottom: the large-
scale total, radial, longitudinal, and latitudinal surface magnetic field
components, as derived from the variations of the LSD Stokes V pro-
files. The color code indicates the strength of the surface magnetic field
in Gauss. A99 (2020)
Fig. 4. Discussion In Paper I, we measured the size of the Brγ line emitting
region, thought to reflect the extent of the magnetospheric cavity,
from long baseline near-IR interferometry, and we found it to be
less than 0.047 au, that is, 5 R⋆. All the results summarized above suggest that DoAr 44
was observed during a phase of stable magnetospheric accre-
tion with a magnetic topology that shares some similarities with
other young accreting systems that we previously studied, such
as V2129 Oph (Alencar et al. 2012). Some of these systems
exhibit dipper light curves at times, with deep periodic eclipses
of the central object being produced by circumstellar dust: for
example, AA Tau (Bouvier et al. 2003, 2007b) and LkCa 15
(Alencar et al. 2018), as well as periodic redshifted absorptions
reaching below the continuum appearing in the wings of emis-
sion lines formed in the funnel flow. These specific properties are
not shared by DoAr 44 in spite of a qualitatively similar magne-
tospheric structure. We estimate that the dust sublimation radius
lies at a distance of Rsub = 4.7 R⋆= 0.044 au, as derived from
Eq. (1) of Monnier & Millan-Gabet (2002) for Tsub = 1500 K
and Qr = 1. Dust might thus to be present at the disk trunca-
tion radius, even though the half-flux radius of the inner dusty
disk we report in Paper I is of the order of 0.14 au. While a pho-
tometric modulation is observed, the light curve is spot domi-
nated, with no evidence for significant dips. Similarly, while the
red wing of Balmer line profiles appear modulated at the stel-
lar rotation period, there is no sign of high-velocity redshifted
absorptions reaching below the continuum, even at phases where
the magnetic pole is facing the observer. Fig. 19. Photospheric radial velocity variations are plotted as a function
of rotational phase. The color code reflects the Julian date for the March
(bright) and June (dark) ESPaDOnS runs. the Doppler image, the high-latitude spot faces the observer at
phase 0.83, which yields symmetric LSD profiles (see Fig. 15). Indeed, the photospheric radial velocity lies midway from the
extrema of the Vr curve at this phase, as expected when the spot
is on the LoS (see Fig. 19). 4. Discussion The three plots are not on the same scale. Fig. 18. Top: brightness map derived from the variation of the LSD
Stokes I profiles. The color code is 1 for the photospheric temperature,
increases for hot spots, and decreases for cold ones. Bottom: the large-
scale total, radial, longitudinal, and latitudinal surface magnetic field
components, as derived from the variations of the LSD Stokes V pro-
files. The color code indicates the strength of the surface magnetic field
in Gauss. of the circumstellar environment of this young stellar object, and
also severely limits the longitudinal resolution we have on the
stellar surface for image reconstruction. With the data at hand
we are nevertheless able to derive the main physical and geo-
metrical properties of the system in the region where the stellar
magnetic field interacts with the inner disk. baseline near-IR interferometry. That the inner system seen at
low inclination is further supported by the lack of strong photo-
metric modulation. While we do recover a photometric period of
2.96 d, assigned to the stellar rotational period, the photometric
amplitude of ≤0.1 mag in the V-band is significantly lower than
that of most accreting T Tauri stars (e.g., Grankin et al. 2007). The photospheric radial velocity is modulated over the same
2.96 d period (see Fig. 19), which confirms the presence of a
long-lived, large, dark spot at the stellar surface. According to The combination of the rotational period derived above and
the v sin i we measure suggests that the star is seen at a low incli-
nation of 30 ± 5◦. In Paper I, we derived a similar inclination of
34 ± 2◦for the inner edge of the circumstellar disk from long A99, page 12 of 18 J. Bouvier et al.: DoAr 44 Fig. 19. Photospheric radial velocity variations are plotted as a function
of rotational phase. The color code reflects the Julian date for the March
(bright) and June (dark) ESPaDOnS runs. would derive a truncation radius that is about twice the coro-
tation radius. However, the large error bars associated with the
field strength and derived from the HeI NC component are not
inconsistent with the disk being truncated close to the corotation
radius. 4. Discussion These concordant results confirm
that the 2.96 d period is the rotational period of the star whose
surface, seen at a low inclination, is covered by a high-latitude,
large, cold spot. In contrast, the photometric minimum appears
to occur at phase 0.5, which suggests a more complex distri-
bution of bright and dark spots at the stellar surface drives the
photometric modulation. In spite of the low inclination, clear modulation signals are
also detected in several accretion diagnostics. This is the case of
the redshifted wings of emission lines formed in the funnel flow
(e.g., Hβ, Hα, Paβ, HeI 1083.3 nm) that smoothly vary along the
rotational cycle, even though they do not exhibit inverse P Cygni
components, that is, absorptions reaching below the continuum,
which are the hallmark of accretion funnel flow passing onto
the LoS in high-inclination systems. The radial velocity and the
intensity of the narrow component of the HeI 587.6 nm line pro-
file are also modulated at the stellar rotational period and indi-
cate a high-latitude hot spot at the stellar surface, presumably
the location of the accretion shock close to the magnetic pole. Indeed, the magnetic surface map reconstructed from the ZDI
analysis features a dominant dipolar field whose axis is moder-
ately inclined onto the rotational axis, thus producing an accre-
tion shock at high latitudes. These results suggest that the inner
disk is truncated at some distance above the stellar surface and
that the accretion onto the star proceeds along magnetospheric
funnel flows. Indeed, dipper characteristics and conspicuous inverse P
Cygni profiles are expected to occur primarily in systems
seen at a moderate to high inclination (e.g., McGinnis et al. 2015; Sousa et al. 2016; Fonseca et al. 2014). This is clearly
not the case in DoAr 44, and the low inclination of this sys-
tem accounts for the low-amplitude, smooth light curve; the
mildly varying red wings of the emission line profiles; and
more generally, the global shape of the emission line profiles
as suggested by radiative transfer models of magnetospheric
accretion onto a misaligned dipole. This clearly highlights the
importance of taking into account inclination when investi-
gating the variability of young stellar systems. Systems with
otherwise similar properties, notably regarding the magneto-
spheric accretion process, might exhibit quite different charac-
teristics depending on the viewing angle under which they are
seen. 4. Discussion If we assume that the disk’s truncation radius lies close to the
disk’s corotation radius, we get DoAr 44 is a pre-transitional disk system. On the large
scale, from mm observations, Andrews et al. (2009, 2011) and
van der Marel et al. (2016) reported the existence of a large cav-
ity extending from the central star up to 25–30 au in the circum-
stellar disk. They showed that cold dust emission arises from
an outer, relatively narrow ring (25 to 35 au wide), inclined by
20–35◦on the LoS. On much smaller scales, the existence of a
compact, inner disk close to the star is supported by the near-
infrared excess flux measured in the spectral energy distribution
of the system (Espaillat et al. 2010) and significant CO emis-
sion arising from the inner disk edge (Salyk et al. 2009, 2011). Furthermore, a misalignment between the inner and outer disk
was assumed to be responsible for shadows seen in the outer
dusty ring (Casassus et al. 2018). In Paper I, we reported the
direct detection of the inner disk from long baseline near-IR
interferometry. The half-flux radius is 0.14 au, and the compact rtr ≃rco = (GM⋆)1/3(Prot/2π)2/3 = 0.043 au = 9.2 R⊙= 4.6 R⋆,
and according to Bessolaz et al. (2008), the truncation radius
occurs at rtr ≃rco = (GM⋆)1/3(Prot/2π)2/3 = 0.043 au = 9.2 R⊙= 4.6 R⋆,
and according to Bessolaz et al. (2008), the truncation radius
occurs at rtr/R⋆= 2 · B4/7
⋆
˙M−2/7
acc M−1/7
⋆
R5/7
⋆, where the stellar field at the equator B⋆is normalized to 140 G,
the mass accretion rate ˙Macc to 10−8 M⊙yr−1, the stellar mass
M⋆to 0.8 M⊙, and the stellar radius R⋆to 2 R⊙. Thus, the condition rtr ≃rco requires a dipolar magnetic
field of the order of 537 G at the equator, which translates into
1.1 kG at the pole. The average value of the longitudinal com-
ponent of the magnetic field we measure in the narrow compo-
nent of the HeI 587.6 nm line amounts to 2 ± 0.8 kG. Assuming
this is the large scale component that interacts with the disk, we A99, page 13 of 18 A99, page 13 of 18 A&A 643, A99 (2020) disk is indeed found to be inclined relative to the outer ring, as
predicted by the Casassus et al. (2018) model to account for the
outer shadows. Acknowledgements.
We gratefully acknowledge the help from Tim Brown at
LCOGT for obtaining test images and from LCOGT support service for schedul-
ing and data reduction. We thank the very efficient QSO team at CFHT. This 4. Discussion This publication is based in part on data obtained under CNTAC
program CLN2019B-004. This publication is based in part on observations col-
lected at the European Organisation for Astronomical Research in the Southern
Hemisphere under ESO programme 0103.C-0097. This work has made use of
data from the European Space Agency (ESA) mission Gaia (https://www. cosmos.esa.int/gaia), processed by the Gaia Data Processing and Anal-
ysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/
consortium). Funding for the DPAC has been provided by national institu-
tions, in particular the institutions participating in the Gaia Multilateral Agree-
ment. SHPA acknowledges financial support from CNPq, CAPES, Fapemig, and
Cofecub. A. B. acknowledges support from FONDECYT Grant 1190748 and
from ICM (Iniciativa Científica Milenio) via the Núcleo Milenio de Formación
Planetaria grant. This project has received funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innova-
tion programme (grant agreement No 742095; SPIDI: Star-Planets-Inner Disk-
Interactions, http://www.spidi-eu.org, and Grant agreement No. 740651
NewWorlds). References Alcalá, J. M., Natta, A., Manara, C. F., et al. 2014, A&A, 561, A2 Alencar, S. H. P., & Basri, G. 2000, AJ, 119, 1881 Alencar, S. H. P., & Basri, G. 2000, AJ, 119, 1881 Alencar, S. H. P., Bouvier, J., Walter, F. M., et al. 2012, A&A, 541, A11 Alencar, S. H. P., Bouvier, J., Donati, J. F., et al. 2018, A&A, 620, A195 Andrews, S. M., Wilner, D. J., Hughes, A. M., Qi, C., & Dullemond, C. P. 2009,
ApJ, 700, 1502 Andrews, S. M., Wilner, D. J., Espaillat, C., et al. 2011, ApJ, 732, 42 Andrews, S. M., Wilner, D. J., Espaillat, C., et al. 201 Appenzeller, I., & Bertout, C. 2013, A&A, 558, A83 Basri, G., & Bertout, C. 1989, ApJ, 341, 340 p
y
In an attempt to link the outer scales, best studied with mid-
IR and radio interferometry, to the inner scales, we focused
here on the characterization of the DoAr 44 system at the star-
disk interaction level, meaning on a scale extending from the
stellar surface up to a few 0.1 au, combining photometric and
spectropolarimetric monitoring with long baseline interferome-
try. The accretion diagnostics studied here and the direct inter-
ferometric measurements we reported in Paper I (Bouvier et al. 2020) suggest the existence of an inner magnetospheric cavity
extending from a distance of about 4.6 stellar radii (0.043 au)
down to the stellar surface. A large-scale, mainly dipolar stellar
magnetic field of a few hundred Gauss over the photosphere, but
reaching up to 2 ± 0.8 kG close to the accretion shock, is suf-
ficient to disrupt the inner-disk region at the corotation radius
or beyond in this moderately accreting system. The reported line
profile variability is consistent with the expected behavior of fun-
nel flows rotating at the stellar period. Yet, due to the low incli-
nation of the inner system, of the order of 30◦, the modulation
signatures are not as pronounced as in other, more inclined sys-
tems. Importantly, the combination of contemporaneous optical
and near-IR high-resolution spectroscopic monitoring provides
us with a unique means to investigate diagnostics that simulta-
neously probe accretion funnel flows and stellar or disk winds. Beristain, G., Edwards, S., & Kwan, J. 2001, ApJ, 551, 1037 Bertout, C., Basri, G., & Bouvier, J. 1988, ApJ, 330, 350 Bessolaz, N., Zanni, C., Ferreira, J., Keppens, R., & Bouvier, J. 5. Conclusion We monitored the variability of the young stellar object, DoAr
44, over several rotational periods using several complementary
observational techniques to investigate the physics of accretion
onto the star in a pre-transitional disk system. The specific geom-
etry of pre-transitional disks, including large cavities and possi-
ble inner- or outer-disk misalignment, raises issues regarding the
accretion process in these systems. How does accretion proceed
from the outer disk to the inner scales through the gap? Is the
star-disk interaction process fed in the same way or differently
from what is observed in classical T Tauri stars with continu-
ous circumstellar disks? If the pre-transitional nature of disks is
the signature of ongoing planet formation in the disk, does this
process affect accretion on any scale? 4. Discussion The pre-transitional status of DoAr 44’s disk was
a strong motivation to include this specific target in our long-
term monitoring program of T Tauri stars. The goal here was to
investigate whether the highly structured disk, including a large
cavity and inner-outer disk misalignment, both possibly betray-
ing ongoing planetary formation, may impact the accretion pro-
cess on the central star. All the results obtained here suggest
that, at the star-disk interaction scale of less than 0.1 au, this pre-
transitional disk system is not qualitatively different from other
young stellar objects surrounded by smoother protoplanetary
disks. study is based in part on observations obtained at the Canada-France-Hawaii
Telescope (CFHT) which is operated by the National Research Council of
Canada, the Institut National des Sciences de l’Univers of the Centre National
de la Recherche Scientifique of France, and the University of Hawaii. The
observations at the Canada-France-Hawaii Telescope were performed with care
and respect from the summit of Maunakea, which is a significant cultural and
historic site. This publication is based in part on data obtained under CNTAC
program CLN2019B-004. This publication is based in part on observations col-
lected at the European Organisation for Astronomical Research in the Southern
Hemisphere under ESO programme 0103.C-0097. This work has made use of
data from the European Space Agency (ESA) mission Gaia (https://www. cosmos.esa.int/gaia), processed by the Gaia Data Processing and Anal-
ysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/
consortium). Funding for the DPAC has been provided by national institu-
tions, in particular the institutions participating in the Gaia Multilateral Agree-
ment. SHPA acknowledges financial support from CNPq, CAPES, Fapemig, and
Cofecub. A. B. acknowledges support from FONDECYT Grant 1190748 and
from ICM (Iniciativa Científica Milenio) via the Núcleo Milenio de Formación
Planetaria grant. This project has received funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innova-
tion programme (grant agreement No 742095; SPIDI: Star-Planets-Inner Disk-
Interactions, http://www.spidi-eu.org, and Grant agreement No. 740651
NewWorlds). study is based in part on observations obtained at the Canada-France-Hawaii
Telescope (CFHT) which is operated by the National Research Council of
Canada, the Institut National des Sciences de l’Univers of the Centre National
de la Recherche Scientifique of France, and the University of Hawaii. The
observations at the Canada-France-Hawaii Telescope were performed with care
and respect from the summit of Maunakea, which is a significant cultural and
historic site. References 2008, A&A, 478,
155 Bouvier, J., & Appenzeller, I. 1992, A&AS, 92, 481 Bouvier, J., Bertout, C., & Bouchet, P. 1988, A&AS, 75, 1 Bouvier, J., Grankin, K. N., Alencar, S. H. P., et al. 2003, A&A, 409, 169 Bouvier, J., Alencar, S. H. P., Boutelier, T., et al. 2007a, A&A, 463, 1017 Bouvier, J., Alencar, S. H. P., Harries, T. J., Johns-Krull, C. M., & Romanova, Bouvier, J., Alencar, S. H. P., Harries, T. J., Johns-Krull, C. M., & Romanova,
M. M. 2007b, in Protostars and Planets V, eds. B. Reipurth, D. Jewitt, & K. Bouvier, J., Alencar, S. H. P., Harries, T. J., Johns-Krull, C. M., & Romanova,
M. M. 2007b, in Protostars and Planets V, eds. B. Reipurth, D. Jewitt, & K. Keil, 479 Bouvier, J., Perraut, K., Le Bouquin, J. B., et al. 2020, A&A, 636, A108
Brown, T. M., Baliber, N., Bianco, F. B., et al. 2013, PASP, 125, 1031 Calvet, N., & Gullbring, E. 1998, ApJ, 509, 802 Camenzind, M. 1990, Rev. Mod, Astron., 3, 234 Casassus, S., Avenhaus, H., Pérez, S., et al. 2018, MNRAS, 477, 5104 Casassus, S., Avenhaus, H., Pérez, S., et al. 2018, Claret, A., & Bloemen, S. 2011, A&A, 529, A75 Donati, J. F. 2003, in Solar Polarization, eds. J. Trujillo-Bueno, & J. Sanchez
Almeida, ASP Conf. Ser., 307, 41 Almeida, ASP Conf. Ser., 307, 41 Donati, J. F. 2020, IAU General Assembly, 121 Donati, J. F., Semel, M., Carter, B. D., Rees, D. E., & Collier Cameron, A. 1997,
MNRAS, 291, 658 Donati, J. F., Howarth, I. D., Jardine, M. M., et al. 2006, MNRAS, 370, 629 J. F., Bouvier, J., Alencar, S. H., et al. 2019, MNRAS, 483, L1 Donati, J. F., Kouach, D., Moutou, C., et al. 2020, MNRAS, 498, 5684
Dworetsky, M. M. 1983, MNRAS, 203, 917 Donati, J. F., Kouach, D., Moutou, C., et al. 2020, MNRAS, 498, 5684
k Dworetsky, M. M. 1983, MNRAS, 203, 917 Edwards, S., Fischer, W., Kwan, J., Hillenbrand, L., & Dupree, A. K. 2003, ApJ,
599, L41 J. Bouvier et al.: DoAr 44 2020, ApJ, 888, 116 Sokal, K. R., Johns-Krull, C. M., Mace, G. N., et al. 20 Marques, J. P., Goupil, M. J., Lebreton, Y., et al. 2013, A&A, 549, A74 p
Sousa, A. P., Alencar, S. H. P., Bouvier, J., et al. 2016, A&A, 586, A47
Symington, N. H., Harries, T. J., & Kurosawa, R. 2005, MNRAS, 356, 1489
van der Marel, N., van Dishoeck, E. F., Bruderer, S., et al. 2016, A&A, 585,
A58 Masci, F. J., Laher, R. R., Rusholme, B., et al. 2019, PASP, 131, 018003 Sousa, A. P., Alencar, S. H. P., Bouvier, J., et al. 2016, A&A, 586, A47
Symington, N. H., Harries, T. J., & Kurosawa, R. 2005, MNRAS, 356, 1489 McGinnis, P. T., Alencar, S. H. P., Guimarães, M. M., et al. 2015, A&A, 577,
A11 599, L41 Overall, over our three-week observation period, DoAr 44
appeared to be in a state of stable magnetospheric accretion,
simultaneously driving outflows, in most aspects similar to what
we had previously witnessed in other systems we monitored in
the same way. This suggests that the physics of accretion from
the inner disk to the stellar surface is not significantly altered by
the complex large-scale structure of the circumstellar disk spe-
cific to pre-transitional systems. Edwards, S., Fischer, W., Hillenbrand, L., & Kwan, J. 2006, ApJ, 646, 319
Esau, C. F., Harries, T. J., & Bouvier, J. 2014, MNRAS, 443, 1022 Espaillat, C., D’Alessio, P., Hernández, J., et al. 2010, ApJ, 717, 441 Espaillat, C., D’Alessio, P., Hernández, J., et al. 2010, ApJ, 717, 441
Fischer, W., Kwan, J., Edwards, S., & Hillenbrand, L. 2008, ApJ, 687, 1117
F l
C P B
l
S W d
G A
t l 2012 MNRAS 422 2072 p
p
Fischer, W., Kwan, J., Edwards, S., & Hillenbrand, L. 2008, ApJ, 687, 1117 Folsom, C. P., Bagnulo, S., Wade, G. A., et al. 2012, MNRAS, 422, 2072 Folsom, C. P., Bouvier, J., Petit, P., et al. 2018, MNRAS, 474, 4956 Fonseca, N. N. J., Alencar, S. H. P., Bouvier, J., Favata, F., & Flaccomio, E. 20 Fonseca, N. N. J., Alencar, S. H. P., Bouvier, J., Favata, F., & Flaccomio, E. 2014,
A&A, 567, A39 Gaia Collaboration (Prusti, T., et al.) 2016, A&A, 595, A1
G i C ll b
ti
(B
A G A
t l ) 2018 A&A 61 Gaia Collaboration (Prusti, T., et al.) 2016, A&A, 595, A1
Gaia Collaboration (Brown A G A et al ) 2018 A&A 616 A1 Grankin, K. N., Melnikov, S. Y., Bouvier, J., Herbst, W., & Shevchenko, V. S. Grankin, K. N., Melnikov, S. Y., Bouvier, J., Herbst, W., & Shevchenko, V. S. 2007 A&A 461 183 ,
,
,
Gravity Collaboration (Abuter, R., et al.) 2017, A&A, 602, A94
Gustafsson, B., Edvardsson, B., Eriksson, K., et al. 2008, A&A, 486, 951 A99, page 14 of 18 y
Monnier, J. D., & Millan-Gabet, R. 2002, ApJ, 579, 694 J. Bouvier et al.: DoAr 44 T., Alencar, S. H. P., Guimarães, M. M., et al. 2015, A&A, 577,
A11
Ménard, F., & Bertout, C. 1999, in NATO Advanced Science Institutes (ASI)
Series C, eds. C. J. Lada, & N. D. Kylafis, NATO ASI Ser. C, 540, 341
Monnier, J. D., & Millan-Gabet, R. 2002, ApJ, 579, 694
Muzerolle, J., Calvet, N., & Hartmann, L. 1998, ApJ, 492, 743
Muzerolle, J., Calvet, N., & Hartmann, L. 2001, ApJ, 550, 944
Pecaut, M. J., & Mamajek, E. E. 2013, ApJS, 208, 9
Pouilly, K., Bouvier, J., Alecian, E., et al. 2020, A&A, 642, A99
Reipurth, B., Pedrosa, A., & Lago, M. T. V. T. 1996, A&AS, 120, 229
Roberts, D. H., Lehar, J., & Dreher, J. W. 1987, AJ, 93, 968
Ryabchikova, T., Piskunov, N., Kurucz, R. L., et al. 2015, Phys. Scr., 90, 054005
Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2009, ApJ, 699, 330
Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2011, ApJ, 743,
112
Shappee, B. J., Prieto, J. L., Grupe, D., et al. 2014, ApJ, 788, 48
Siess, L., Dufour, E., & Forestini, M. 2000, A&A, 358, 593
Skilling, J., & Bryan, R. K. 1984, MNRAS, 211, 111
Sokal, K. R., Johns-Krull, C. M., Mace, G. N., et al. 2020, ApJ, 888, 116
Sousa, A. P., Alencar, S. H. P., Bouvier, J., et al. 2016, A&A, 586, A47
Symington, N. H., Harries, T. J., & Kurosawa, R. 2005, MNRAS, 356, 1489
van der Marel, N., van Dishoeck, E. F., Bruderer, S., et al. 2016, A&A, 585,
A58
Wade, G. A., Donati, J. F., Landstreet, J. D., & Shorlin, S. L. S. 2000, MNRAS,
313, 851 Hartmann, L., Hewett, R., & Calvet, N. 1994, ApJ, 426, 669 Muzerolle, J., Calvet, N., & Hartmann, L. 1998, ApJ, 492, 74 ,
,
,
,
,
,
p ,
,
Hartmann, L., Herczeg, G., & Calvet, N. 2016, ARA&A, 54, 135 ,
,
,
,
,
,
p ,
,
Hartmann, L., Herczeg, G., & Calvet, N. 2016, ARA&A, 54, 135 Muzerolle, J., Calvet, N., & Hartmann, L. 2001, ApJ, 550, 944 g
Herbig, G. H. 1962, Adv. Astron. Astrophys., 1, 47 Pecaut, M. J., & Mamajek, E. E. 2013, ApJS, 208, 9 g
p y
Kenyon, S. J., & Hartmann, L. J. Bouvier et al.: DoAr 44 1987, ApJ, 323, 714 j
p
ouilly, K., Bouvier, J., Alecian, E., et al. 2020, A&A, 642, A99 y,
,
,
,
,
,
,
,
,
Reipurth, B., Pedrosa, A., & Lago, M. T. V. T. 1996, A&AS, 120, 229 y
p
Koenigl, A. 1991, ApJ, 370, L39 y
Koenigl, A. 1991, ApJ, 370, L39 g
p
Kurosawa, R., Romanova, M. M., & Harries, T. J. 2008, MNRAS, 385, 1931
Kurosawa R Romanova M M & Harries T J 2011 MNRAS 416 2623 g
p
Kurosawa, R., Romanova, M. M., & Harries, T. J. 2008, MNRAS, 385, 1931 Roberts, D. H., Lehar, J., & Dreher, J. W. 1987, AJ, 93, 968 Ryabchikova, T., Piskunov, N., Kurucz, R. L., et al. 2015, Phys. Scr., 90, 054005
Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2009, ApJ, 699, 330
Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2011, ApJ, 743, Ryabchikova, T., Piskunov, N., Kurucz, R. L., et al. 2015, Phys. Scr., 90, 054005
Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2009, ApJ, 699, 330 Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2009, ApJ, 699, 330
Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2011, ApJ, 743,
112 Landi Degl’Innocenti, E., & Landolfi, M. 2004, Polarization Spectral Lines,
307 Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2011, ApJ, 743,
112 ail, A., Kochukhov, O., Hussain, G. A. J., et al. 2017, A&A, 608, A Shappee, B. J., Prieto, J. L., Grupe, D., et al. 2014, ApJ, 788, 48 Shappee, B. J., Prieto, J. L., Grupe, D., et al. 2014, ApJ, 788, 48
Siess L Dufour E & Forestini M 2000 A&A 358 593 Lima, G. H. R. A., Alencar, S. H. P., Calvet, N., Hartmann, L., & Muzerolle, J. 2010, A&A, 522, A104 Shappee, B. J., Prieto, J. L., Grupe, D., et al. 2014, ApJ, 788, 48
Siess, L., Dufour, E., & Forestini, M. 2000, A&A, 358, 593 Siess, L., Dufour, E., & Forestini, M. 2000, A&A, 358, 593 Manara, C. F., Testi, L., Natta, A., et al. 2014, A&A, 568, A18 Skilling, J., & Bryan, R. K. 1984, MNRAS, 211, 111 g
y
Sokal, K. R., Johns-Krull, C. M., Mace, G. N., et al. J. Bouvier et al.: DoAr 44 J. Bouvier et al.: DoAr 44 Muzerolle, J., Calvet, N., & Hartmann, L. 1998, ApJ, 492, 743
Muzerolle, J., Calvet, N., & Hartmann, L. 2001, ApJ, 550, 944
Pecaut, M. J., & Mamajek, E. E. 2013, ApJS, 208, 9
Pouilly, K., Bouvier, J., Alecian, E., et al. 2020, A&A, 642, A99
Reipurth, B., Pedrosa, A., & Lago, M. T. V. T. 1996, A&AS, 120, 229
Roberts, D. H., Lehar, J., & Dreher, J. W. 1987, AJ, 93, 968
Ryabchikova, T., Piskunov, N., Kurucz, R. L., et al. 2015, Phys. Scr., 90, 054005
Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2009, ApJ, 699, 330
Salyk, C., Blake, G. A., Boogert, A. C. A., & Brown, J. M. 2011, ApJ, 743,
112
Shappee, B. J., Prieto, J. L., Grupe, D., et al. 2014, ApJ, 788, 48
Siess, L., Dufour, E., & Forestini, M. 2000, A&A, 358, 593
Skilling, J., & Bryan, R. K. 1984, MNRAS, 211, 111
Sokal, K. R., Johns-Krull, C. M., Mace, G. N., et al. 2020, ApJ, 888, 116
Sousa, A. P., Alencar, S. H. P., Bouvier, J., et al. 2016, A&A, 586, A47
Symington, N. H., Harries, T. J., & Kurosawa, R. 2005, MNRAS, 356, 1489
van der Marel, N., van Dishoeck, E. F., Bruderer, S., et al. 2016, A&A, 585,
A58
Wade, G. A., Donati, J. F., Landstreet, J. D., & Shorlin, S. L. S. 2000, MNRAS,
313 851 Hartmann, L., Hewett, R., & Calvet, N. 1994, ApJ, 426, 669
Hartmann, L., Herczeg, G., & Calvet, N. 2016, ARA&A, 54, 135
Herbig, G. H. 1962, Adv. Astron. Astrophys., 1, 47
Kenyon, S. J., & Hartmann, L. 1987, ApJ, 323, 714
Koenigl, A. 1991, ApJ, 370, L39
Kurosawa, R., Romanova, M. M., & Harries, T. J. 2008, MNRAS, 385, 1931
Kurosawa, R., Romanova, M. M., & Harries, T. J. 2011, MNRAS, 416, 2623
Landi Degl’Innocenti, E., & Landolfi, M. 2004, Polarization Spectral Lines,
307
Lavail, A., Kochukhov, O., Hussain, G. A. J., et al. 2017, A&A, 608, A77
Lima, G. H. R. A., Alencar, S. H. P., Calvet, N., Hartmann, L., & Muzerolle, J. 2010, A&A, 522, A104
Manara, C. F., Testi, L., Natta, A., et al. 2014, A&A, 568, A18
Marques, J. P., Goupil, M. J., Lebreton, Y., et al. 2013, A&A, 549, A74
Masci, F. J., Laher, R. R., Rusholme, B., et al. 2019, PASP, 131, 018003
McGinnis, P. Appendix A: Line profile variability 250
0
250
v (km/s)
phase
29.12
30.15
29.46
30.48
29.8 250
0
250
v (km/s)
phase
29.12
30.15
29.46
30.48
29.8
250
0
250
v (km/s)
day
8642.89
8643.9
8644.89
8645.93
8646.93 25
phase
29.12
30.15
29.46
30.48
29.8
250
0
250
v (km/s)
day
8642.89
8643.9
8644.89
8645.93
8646.93 250
0
250
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07 250
0
250
v (km/s)
day
8642.89
8643.9
8644.89
8645.93
8646.93 250
0
250
v (km/s)
phase
2.16
0.48
1.5
2.51
2.83
0.83
1.83 Fig. A.3. 2D periodogram of Hα, Hβ, and HeI line profiles from the five
spectra obtained during the ESPaDOnS June run. The color code repre-
sents the periodogram power, and the superimposed white curve is the
average line profile. We note the symmetry of the periodogram around
the frequency 0.5 d−1 due to the 1 d alias resulting from the night-to-
night sampling. Fig. A.1. Hα, Hβ, and HeI line profiles from the seven spectra obtained
during the ESPaDOnS March run (left panels) and the five spectra
obtained during the June run (right panels). In each panel, the profiles
are plotted in order of increasing date (left) and phase (right). Each color
corresponds to a specific rotational cycle. Since the shape of the emisson line profiles has varied between
the ESPaDOnS March and June 2019, runs, we present in
Fig. A.1 their variability over timescales of days, independently
for each run. The periodogram analysis of line profiles over the two
ESPaDOnS runs is inconclusive. We therefore proceed to ana-
lyzing the March and June 2019 runs independently. Figures A.2
and A.3 show the periodogram analysis of the Hα, Hβ, and HeI
line profiles for the two epochs, respectively. During the March
run, seven spectra were obtained over eight nights, while during
the June run, five spectra were obtained over five nights. More-
over, since the stellar period of 2.96 d is close to an integer,
the same rotational phase repeats every third night. The short
duration of each run combined with the poor phase sampling
makes the periodogram analysis fragile. Nevertheless, we find
marginal evidence for the rotational frequency of 0.34 d−1 in the
red wing of the Hα and Hβ line profiles around +100 km s−1
during the March run, and in the narrow central component
of the HeI line during the June run. Appendix A: Line profile variability 500
0
500
v (km/s)
phase
2.16
0.48
1.5
2.51
2.83
0.83
1.83
500
0
500
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07
500
0
500
v (km/s)
phase
29.12
30.15
29.46
30.48
29.8
500
0
500
v (km/s)
day
8642.89
8643.9
8644.89
8645.93
8646.93
500
0
500
v (km/s)
phase
2.16
0.48
1.5
2.51
2.83
0.83
1.83
500
0
500
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07
500
0
500
v (km/s)
phase
29.12
30.15
29.46
30.48
29.8
500
0
500
v (km/s)
day
8642.89
8643.9
8644.89
8645.93
8646.93
250
0
250
v (km/s)
phase
2.16
0.48
1.5
2.51
2.83
0.83
1.83
250
0
250
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07
250
0
250
v (km/s)
phase
29.12
30.15
29.46
30.48
29.8
250
0
250
v (km/s)
day
8642.89
8643.9
8644.89
8645.93
8646.93
Fig. A.1. Hα, Hβ, and HeI line profiles from the seven spectra obtained
during the ESPaDOnS March run (left panels) and the five spectra
obtained during the June run (right panels). In each panel, the profiles
are plotted in order of increasing date (left) and phase (right). Each color
corresponds to a specific rotational cycle. 500
0
500
v (km/s)
phase
2.16
0.48
1.5
2.51
2.83
0.83
1.83 500
0
500
v (km/s)
day
8642.89
8643.9
8644.89
8645.93
8646.93 500
0
500
v (km/s)
day
8642.89
8643.9
8644.89
8645.93
8646.93 500
0
500
v (km/s)
phase
29.12
30.15
29.46
30.48
29.8 500
0
500
v (km/s)
day
8558.11
8559.15
8561.14
8562.12
8563.1
8564.12
8565.07 500
0
500
v (km/s)
phase
2.16
0.48
1.5
2.51
2.83
0.83
1.83 Fig. A.2. 2D periodogram of Hα, Hβ, and HeI line profiles from the
seven spectra obtained during the ESPaDOnS March run. The color
code represents the periodogram power, and the superimposed white
curve is the average line profile. We note the symmetry of the peri-
odogram around the frequency 0.5 d−1 due to the 1 d alias resulting from
the night-to-night sampling. A11 van der Marel, N., van Dishoeck, E. F., Bruderer, S., et al. 2016, A&A, 585,
A58 Ménard, F., & Bertout, C. 1999, in NATO Advanced Science Institutes (ASI)
Series C, eds. C. J. Lada, & N. D. Kylafis, NATO ASI Ser. C, 540, 341 Wade, G. A., Donati, J. F., Landstreet, J. D., & Shorlin, S. L. S. 2000, MNRAS,
313, 851 ,
,
y
,
Monnier, J. D., & Millan-Gabet, R. 2002, ApJ, 579, 694 A99, page 15 of 18 A&A 643, A99 (2020) Fig. A.2. 2D periodogram of Hα, Hβ, and HeI line profiles from the
seven spectra obtained during the ESPaDOnS March run. The color
code represents the periodogram power, and the superimposed white
curve is the average line profile. We note the symmetry of the peri-
odogram around the frequency 0.5 d−1 due to the 1 d alias resulting from
the night-to-night sampling. Appendix A: Line profile variability Appendix A: Line profile variability Appendix B: Line profile decomposition absorption components are superimposed. The HeI line is well
fit by the combination of two Gaussian components in emis-
sion: a broad one and a narrow one, respectively. This is also
the case for the CaII line profile except for two occurrences,
on JD 8559.15 and JD 8565.07, where an additional redshifted
absorption component is required to reproduce the observed line
profile. Here, we illustrate examples of line profile decomposition by
multiple Gaussian fits for the Hα, Hβ, HeI, and CaII emission
line profiles observed on JD 8565.07 and JD8644.89. The Hα
and Hβ line profiles are well reproduced with a central Gaus-
sian emission peak onto which a blueshifted and a redshifted Table B.1. Gaussian components of optical emission line profiles. . Gaussian components of optical emission line profiles. Notes. The table lists the Julian date, the equivalent width, the peak intensity, radial velocity, and FWHM of the G Notes. The table lists the Julian date, the equivalent width, the peak intensity, radial velocity, and FWHM of the Gaussian fit for each component. Appendix A: Line profile variability While of limited signifi-
cance, the similar shapes exhibited by the various line profiles Fig. A.3. 2D periodogram of Hα, Hβ, and HeI line profiles from the five
spectra obtained during the ESPaDOnS June run. The color code repre-
sents the periodogram power, and the superimposed white curve is the
average line profile. We note the symmetry of the periodogram around
the frequency 0.5 d−1 due to the 1 d alias resulting from the night-to-
night sampling. at specific rotational phases (see Fig. A.1) lends credit to this
result. For instance, the Balmer line profiles appear much more
symmetric around phases 0.12–0.16 and 0.83–0.93 than around
phases 0.46–0.51, where the red wing is consistently depressed. This suggests additional redshifted absorption occurs at phases
around 0.5. A99, page 16 of 18 J. Bouvier et al.: DoAr 44 Appendix B: Line profile decomposition HJD
EW1
EW2
EW3
Int1
Vr1
FWHM1
Int2
Vr2
FWHM2
Int3
Vr3
FWHM3
(−2 450 000)
(Å)
(Å)
(Å)
km s−1
Å
km s−1
Å
km s−1
Å
Hα
8558.10852
59.7
−1
−16.4
10
13.1
255.7
−0.8
−39.7
53.1
−4.9
50.3
142.4
8559.15082
50.3
−5.8
−5.5
9
11.9
239.2
−2.7
−7.6
92.8
−3.4
47
67.7
8561.13665
46
−1.1
−12.2
8.7
6.9
226.3
−0.9
−42.8
51.7
−4.8
41.1
107.6
8562.12015
60.9
−8.7
−5.4
10.7
5
242.3
−3.1
−4.2
119.1
−2.7
50.4
84.1
8563.09667
52.2
−5.9
−3.8
9.5
−0.6
235.5
−2.9
−25.1
87.7
−2.3
41.3
69.3
8564.12225
61.2
−2.6
−14
10.5
8.5
249.8
−2
−41.9
55.9
−5.2
39.1
114.9
8565.06818
64
−4.1
−14.5
12.3
4.3
222.1
−2.7
−39.5
63.5
−6.5
29
94.7
8642.8923
86.3
−10.7
−13.8
15
4.9
246.5
−5.4
−34.5
85.1
−6.9
40.2
85.3
8643.89558
60.7
−1.4
−14.6
10.5
14.1
247.9
−1.1
−49.3
54.3
−5
30.6
125.3
8644.89415
69
−2.6
−12.1
11.3
6.5
261.6
−1.9
−41.2
59.2
−4.4
28.4
116.1
8645.93308
60.6
−7.1
−9.9
11.2
16.6
230.3
−3.5
−18.1
86.0
−5.1
49.8
83.4
8646.92779
58.2
−2.1
−16.7
11
12.7
226.5
−1.5
−33.7
57.3
−5.9
33.2
120.8
Hβ
8558.10852
13.9
−0.48
−4.4
3.3
18.9
241.3
−0.5
−41.8
55.2
−2.1
56.4
119.1
8559.15082
7.9
−0.27
−0.9
2
3.6
225.8
−0.31
−41
49.8
−0.8
45
58.3
8561.13665
7.9
−0.13
−1.6
2
1.5
223.3
−0.24
−37.5
31.0
−1.1
48.9
88.1
8562.12015
11.4
−0.33
−1.3
2.9
3.5
227.2
−0.41
−32.9
45.6
−1
41.2
69.6
8563.09667
8.9
−0.55
−0.6
2.4
−5
214.8
−0.59
−34.7
53.8
−0.5
42.5
66.3
8564.12225
15
−0.77
−5.5
3.9
15.5
222.3
−0.78
−39.4
57.3
−2.6
45.8
117.7
8565.06818
10.2
−0.26
−0.8
2.5
−3.9
229.4
−0.34
−32.8
43.5
−0.8
41.7
60.6
8642.8923
18.6
−1.94
−2.3
4.5
4.8
239.0
−1.68
−33.5
67.0
−1.8
39.9
74.0
8643.89558
13.4
−0.45
−4.2
3.3
19.1
231.9
−0.57
−43.7
45.4
−1.8
41.1
128.5
8644.89415
16.3
−1.06
−3
3.9
5.6
238.8
−0.98
−39.6
62.5
−1.5
39.9
113.7
8645.93308
12.9
−0.92
−2.1
3.2
14.5
232.2
−0.9
−34.7
58.8
−1.5
44.2
79.9
8646.92779
13.9
−0.5
−5.2
3.8
18.2
212.4
−0.62
−33.7
47.2
−2.4
39.5
122.2
HeI 587.6 nm
8558.10852
1.63
0.21
0.31
17.5
248.6
0.22
5.8
47.0
8559.15082
0.81
0.28
0.16
−4.1
238.8
0.31
7.1
43.0
8561.13665
0.99
0.17
0.18
11.1
259.0
0.2
5.6
41.4
8562.12015
1.12
0.19
0.25
−10.4
215.5
0.21
5.9
43.0
8563.09667
0.76
0.17
0.16
−8.5
229.1
0.21
10.9
38.5
8564.12225
1.15
0.23
0.21
5.3
256.6
0.24
5.6
46.8
8565.06818
1.02
0.31
0.21
−10.3
228.0
0.34
7
43.5
8642.8923
1.3
0.32
0.28
−0
221.6
0.4
11.4
38.8
8643.89558
1.1
0.20
0.2
14.1
264.1
0.23
6.1
41.8
8644.89415
1.27
0.33
0.27
0.4
222.8
0.38
4.4
40.9
8645.93308
1.3
0.28
0.27
4.7
228.9
0.35
11.2
38.3
8646.92779
1.12
0.24
0.22
12.7
236.4
0.25
6
46.3
CaII 854.2 nm
8558.10852
6.9
0.62
1.26
19.7
180.5
0.74
0.2
27.3
8559.15082
4.0
0.75
−0.25
0.87
16.7
149.9
0.83
2.1
29.6
−0.1
122.4
84.4
8561.13665
3.3
0.68
0.73
11.7
147.1
0.72
1
31.0
8562.12015
5.1
0.81
1.21
10.3
138.9
0.8
1.4
33.4
8563.09667
4.2
0.62
1
6.6
136.8
0.68
1.8
29.6
8564.12225
5.8
0.69
1.21
14.1
157.0
0.68
−0.2
33.6
8565.06818
4.6
0.92
−0.25
1.01
7.7
149.7
0.94
−0
32.2
−0.1
123.3
83.4
8642.8923
7.4
0.69
1.5
1.6
162.2
0.79
1.7
28.7
8643.89558
4.6
0.60
0.99
13.4
152.0
0.64
1.9
30.8
8644.89415
6.0
0.64
1.22
−6.3
161.2
0.69
−0.5
30.1
8645.93308
5.3
0.77
1.1
13.7
157.5
0.8
2.7
31.3
8646.92779
6.0
0.65
1.28
12.7
151.8
0.65
−0.7
32.9
e table lists the Julian date, the equivalent width, the peak intensity, radial velocity, and FWHM of the Gaussian fit for each com A99, page 17 of 18 A&A 643, A99 (2020) −600
−400
−200
0
200
400
600
−5
0
5
10
Hα − JD=8565.06
−600
−400
−200
0
200
400
600
v (km/s)
−5
0
5
10
normalized profile
−600
−400
−200
0
200
400
600
−2
0
2
4
6
8
10
12
Hα − JD=8644.89
−600
−400
−200
0
200
400
600
v (km/s)
−2
0
2
4
6
8
10
12
normalized profile
−600
−400
−200
0
200
400
600
0.5
1.0
1.5
2.0
2.5
3.0
3.5
Hβ − JD=8565.06
−600
−400
−200
0
200
400
600
v (km/s)
0.5
1.0
1.5
2.0
2.5
3.0
3.5
normalized profile
−600
−400
−200
0
200
400
600
0
1
2
3
4
Hβ − JD=8644.89
−600
−400
−200
0
200
400
600
v (km/s)
0
1
2
3
4
normalized profile
−400
−200
0
200
400
1.0
1.1
1.2
1.3
1.4
1.5
HeI − 5876A − JD=8565.06
−400
−200
0
200
400
v (km/s)
1.0
1.1
1.2
1.3
1.4
1.5
normalized profile
−400
−200
0
200
400
1.0
1.2
1.4
1.6
HeI − 5876A − JD=8644.89
−400
−200
0
200
400
v (km/s)
1.0
1.2
1.4
1.6
normalized profile
−400
−200
0
200
400
1.0
1.5
2.0
2.5
CaII − 8542A − JD=8565.06
−400
−200
0
200
400
v (km/s)
1.0
1.5
2.0
2.5
normalized profile
−400
−200
0
200
400
1.0
1.5
2.0
2.5
CaII − 8542A − JD=8644.89
−400
−200
0
200
400
v (km/s)
1.0
1.5
2.0
2.5
normalized profile
Fig. Appendix B: Line profile decomposition B.1. Line profile decomposition in Gaussian components. The Gaussian components are shown as blue curves, and the resulting modeled
profile in red, while the observed profile is in black. From top to bottom: Hα, Hβ, HeI, and Ca II 854.2 nm. −600
−400
−200
0
200
400
600
−2
0
2
4
6
8
10
12
Hα − JD=8644.89
−600
−400
−200
0
200
400
600
v (km/s)
−2
0
2
4
6
8
10
12
normalized profile −600
−400
−200
0
200
400
600
−5
0
5
10
Hα − JD=8565.06
−600
−400
−200
0
200
400
600
v (km/s)
−5
0
5
10
normalized profile −600
−400
−200
0
200
400
600
0
1
2
3
4
Hβ − JD=8644.89
−600
−400
−200
0
200
400
600
v (km/s)
0
1
2
3
4
normalized profile −600
−400
−200
0
200
400
600
0.5
1.0
1.5
2.0
2.5
3.0
3.5
Hβ − JD=8565.06
−600
−400
−200
0
200
400
600
v (km/s)
0.5
1.0
1.5
2.0
2.5
3.0
3.5
normalized profile −400
−200
0
200
400
1.0
1.1
1.2
1.3
1.4
1.5
HeI − 5876A − JD=8565.06
−400
−200
0
200
400
v (km/s)
1.0
1.1
1.2
1.3
1.4
1.5
normalized profile −400
−200
0
200
400
1.0
1.2
1.4
1.6
HeI − 5876A − JD=8644.89
−400
−200
0
200
400
v (km/s)
1.0
1.2
1.4
1.6
normalized profile −400
−200
0
200
400
1.0
1.5
2.0
2.5
CaII − 8542A − JD=8644.89
−400
−200
0
200
400
v (km/s)
1.0
1.5
2.0
2.5
normalized profile −400
−200
0
200
400
1.0
1.5
2.0
2.5
CaII − 8542A − JD=8565.06
−400
−200
0
200
400
v (km/s)
1.0
1.5
2.0
2.5
normalized profile Fig. B.1. Line profile decomposition in Gaussian components. The Gaussian components are shown as blue curves, and the resulting modeled
profile in red, while the observed profile is in black. From top to bottom: Hα, Hβ, HeI, and Ca II 854.2 nm. A99, page 18 of 18
|
https://openalex.org/W2131854463
|
https://zenodo.org/records/2211597/files/article.pdf
|
German
| null |
Zur elektrolytischen Bestimmung des Bleis
|
Justus Liebigs Annalen der Chemie
| 1,907
|
public-domain
| 2,886
|
283 283 1) Monatshefte f. Cheniie 13: 539 (1893). Zur elektrolytischen Bestimmung des Bleis;
von (2. Voytmann. (Eingelaufen beim Redactions-Cornit6 der Lieben-Festschrift
am 5. Juni 1906.) Die elektrolytische Abscheidung des Bleis als Superoxyd
gehort ohne Zweifel zu den fur die Laboratoriurnspraxis wich-
tigsten Methoden ; sie gestattet die FBllung in kurzester Zeit. auszufihren und das Blei von vielen anderen Metallen zu trennen. Die gunstigsten Fgllungsbedingungen sind durch die Arbeiten
von Luckow, v. Xlobukow, Classen, Neumann, Nissen-
son, Smith, Medicus u. A. zur Genuge festgestellt worden. Welchen Einfluss andere Karper auf die Filllung ausiiben, hat
namentlich Neumann ermittelt. Nach den bisher veroffent-
lichten Vorschriften mijchte man meinen, dass die Bleibestimmnng
durch Elektrolyse in den meisten Fallen gute Resultate g&be
und nur ausnahmsweise (hei Anwesenlieit von Arsen, Selen,
Mangan, Wisrnuth) nicht vortheilliaft auszufuhren wLre. Die
Bleibestiinmung durch Elektrolyse wird vielfach aur Analpse
des Bleiglanzes empfolilen (Classen, Nissenson), welclier zu-
ngchst durch Oxydation in Bleisulfat ubergefiihrt und dann
am salpetersaurer Losung als Bleisuperoxyd gefillt werden soll. Die in Folgendein veroffentlichten Versuche habe ich znm Die in Folgendein veroffentlichten Versuche habe ich znm
grossen Theil schon vor zeltn Jahren begonnen, doch war es
mir Mangels an Zeit nicht moglich dieselben zu Ende zu fuhren;
schon damals fand icli, dass die elektrolytische Bleibestimmnng Voi’tmanii, Zw elektrolytiscken Bestimmung des Bleis. 284 durcliaus niclit so gut ausfgllt als allgemein angenominen wurde,
und die inzwischen erschieneneii Arbeiten bestBtigen die von
iiiir gemachten Erfahrungen. Icli liabe meine Versuche in
letzter Zeit wieder aufgenommen und glaube eine liinllnglich
grosse Anzahl von Belegen zu liefern, aus welclien man erselien
kann, wann man sich mit Siclierheit auf das Resultat der
elekBrolytisclien Bleibestimmung verlassen kann. Ich scliicke zunaclist eine Zusammenstellung meiner ana-
lytischen Resultate voraus uud werde an der Hand derselben
die Bleibestiminung besprechen. Die Flllungen geschahen entweder in der mattirten Platin-
schale von Classen oder auf der mattirten uhrglasfdrmigen
Scheibe (Durchmesser = 7 cm)’); in den Tabellen bedeutet S
die Schale, U die Scheibe, w die Flllung in der Wlrme (60°),
k die FBllung in der Kllte; das Fliissigkeitsvolumen betrug
durchwegs 150 ccm. Beim Arbeiten mit der uhrglasfdrmigen
Elektrode wnrde die Analyse stets unter Auswechselung der
Elektrode fortgefiihrt, bis sich kein Superoxyd mehr abschied ;
bei Anwendung der Platinschale wurde nach Verlauf ent-
sprechender Zeit ein Tlieil der Flussigkeit auf Blei gepruft;
schliesslicli wurde die ganze Fliissigkeit mit Ammoniak und
Scliwefelammonium auf etwaigen Rleigehalt gepriift. Vortmnn 11, Zur elektrolytisdien Bestimmung des Bleis. Zur elektrolytischen Bestimmung des Bleis;
von (2. Voytmann. 285 I
I
1 I0,8473)
2 11 1,07391
3 'I 0,8166
5 1.0321
6 1 1,22721
7 1 1,0019
8 I
'
1,1751
!I 1 0,9537 I
4 11,0920i
I
1 __
- -_
._
__---
_-_______
I
I
I 0,6107 ' 0,6116 - 0,0009 I62,42 1 0,l
' 0,7747 0,7751 I - 0,0004 ,62,47 I 0,l
10,7866 0,7882 1 - 0,0016 I 62,38 I0,Of
' 0,7376 0,7377 I -
0,0001 162,49 1 0,2
0,8851 10,8858 1 - 0,0007 1 62,46 I 0,l
0,7232 0,72321 - I62,51~ 0,1
10,8482 0,84821 -
62,51 I 0,1
0,6885 0,6884 1 + 0,0001 1 62,52 i 0,2
0,7876 0,7884 I - 0,0006 16245
~ 0,l
j 0,8429,0,8426: + O,OOO.? 62,53 I 0,l
10,7583'0,7593' - 0,0010 162.43, 0,l
10,54191 - ,
- I62,41 j 0,s
0,D4P3( 0,9412 j + 0,0072 I62,98 0,l
I
j 0,5889 I 0,5894 - 0,0005 62,46 1 0,l
I ,
I
+ 0,0084 ! 63,08 0,l j w 1 S
i
l
l
+ 0,0038 ' 62,86 1 0,5 /
(
I
, \v U
-
-
%
g. a s
10
10
10
20
20
5
7,5
7,s
10
7,5
795
10
10
. -
._
LO
LO
.o
15
15
15 286
lio r t ma n n, Zur elektrolytischen Bestimmung des Bleis. 286 ,
c)
a
U
Nr. & &
~-
li
2311 0,688(
2411 0,795:
26 , 0,950:
25iI 0,545(
30 1,351~
31 1 0,807:
321 0,765(
I -
33 ' 0,806L
I
-
-
35 0,856:
-
Ange w
PbN,O,
36 1,0136
37 0,9424
38 0,7485
39 0,9305
40 1,0321
41 0,8282
42 0,5969
43, 0,8386
46 I 1,0308
d
! PbO,
C
fund. Zur elektrolytischen Bestimmung des Bleis;
von (2. Voytmann. 0,l g Se
0,104 Se
,5g Cr907(KH4&
0,14 g As,O,
0,28g As,O,
0,28 g As,O,
031 g As,O,
10 ccm
I/, n-SO,H,
),4010 g Sb,O,
0,303 g Sb,O,
-
0,6898 0 6878 + 0,0020 186.83
0,8126 0,7953 + 0,0173 188,4
0,5494 0,5448, + 0,0046 87,3
0.9578 I 0.9503 + 0,0075 ' 87,27
0,9508,0.9399 + 0,0109 187.58
0,8416 0,8411 - 0 0023 I 86,32
0,9539 I 0,9473 + 0,0066 87,18
1,3564 11.3511 + 0,0053 ' 86,92
0,8133 10.8077 1 + 0.0056 187,l8
I ' - +0,0327 19O,2
0,7981
I1
I
0,7656 0,7654
~ - 0,0002 8fi,61
- '+0,00751 -
0,8139 i
I
'I
0,80641 - 0,0003 I86,55
0,8061 I
1,2819
I I - i+0,0128/ -
+ 0,0036 -
'I
1,2691 - 0.0001 86.56
1,2690
I
I
'I
0,8563 -0,0021
1
1
1
-
),8598
1,6945 0,6802
1,6463 0,5403
1,0729 0,6716
1,7582 0,7594
1,5976 0,5978
1,4303 0,4308
1,6072 0,6053
1,7094 0,7110
1,4444 0,4453
1,7539 0,7440
1,7732
~ 0,7533! + 0,0199 I64,16
~
+ 0,0143 ,63,82
-0,5987
~ -
-
0,0012,62,41'
1
- 0,0002 : 62,49 1
- 0,0005 62,431 0:4
$0,0020 62,711 0,4
- 0,0016 62,351 0,4
1
-
0,0009 /62,34 0 3
+ 0,0009 63,34 1 013 1
W
W
W
W
W
W
W
k
W
W
W
W
W
W
1
W Vortninnn, Zur elektrolytischeia Bestiwmung des Bleis. 287 I
47 I0,5681
48 , 0,699
I
49 ' 0,am
I
I -
50 j 0,7621
52 /0,819! 51 I 0,899:
I
! '
'1 -
53 j 0,874;
! l
-
54
~ 0,8945
65 0,8942
56 ' 0,6469
57 0,7406
I'
1
-
58 0,8107
59 0,7266
60 0,8876
-
61 0,8739
62 0,3787
63 0,9144
64 1,0264
65 0,7987
66 0,7903
67 0,8429
68 0,9043
11
415 g Fe20,
; 0,5978
1
I1 :
-
10,6313 I
0,137 g AlzO, 10,6467 0,645:
0,137 g AJO,
10,6482; 0,6454
0,43 g CUO 10,4656 0,466:
0t40gZnO
10,5357. -
1
;
j
I1
1
I
I1 I
-
I 0.6397 j 0,6407
0,91 HgO
10,'8487 10,6308
0,32 AgNO,
0,2804 ~ 0,2734
iN,O, kryst. 1,0 0,7391 '0,7408
g NiN,O, kryst./O,6622 i 0,6600
- ;62,5
+ 0,0008 i62,51
+ 0,0028 /62,71
- 0,0013 ~ 62,3:
+ 0,0010 I ,62,6:
+ 0,0103 ,63,5
I
- 0,0003 ' 62,4! Zur elektrolytischen Bestimmung des Bleis;
von (2. Voytmann. I
- 0,0014 62,3(
0,0031 I 62,8t
I
- 0,0010 162,4:
-f- 0,0179 164,2E
+ 0,0070 j 64,2
f
0,0022 I 62,7E
- 0,0017 IG2,36
1,0 g CoCO,
/0,59O8'0,5761
I + 0,0147 64;06
1,0 g CaCO,
0,5761 0,5704 + 0,0047 63,02
1,0 g CaCO,
'0,6110 0,6084 + 0,0026 i62,77
3,0 g KNO,
- + 0,0013 162,63
1 1
I
-
45
-
41
15
10
-
12
-
14
20
20
12
20
20
20
20
15
15
15
5
20
!O
!O
!O
!O
5 Vortmaiin, Zur elektrolytiscken Bestimmztng des Bleis. 288 70
71
72
73
74
75
0,7346 2,O g PTaNO,
0,5384 '0,5302
0,9617 3,Og Nah'O,
0,6951 10,6942
0,8517 3,O g NH,NO,
0,6181 0,fi147
0,7929
3,0 g NH,NO,
0,3737,0,3723
10 ccm
10 ccm
I/, n - ~ ~ , ~ ,
0j8255
1
I,/. n-SO,H,
0SJ7*
0,7287 0,7199
I a,
D,
I
+0,0082
+0,ooO9
+ 0,0034
$0,0014
+ 0,0066
63,48
62,59
62,85
62,66
63,20
0,5
0,4
w s
k 1 s
-
-
3
g
R
-
- ._
15
15
16
24
20
20
20
20
20 Die Bestimmung des Bleis durcli Ftillung als Superoxyd
bietet im Falle nur Blei in salpetersaurer Losung vorhanden
ist keine Schwierigkeiten, wenn man die von den verschie-
denen Autoren angegebenen Vorschriften genau befolgt. Haupt-
bedingung ist, dass nicht zu wenig freie SalpetersLure zugegen
ist, da sich sonst metallisches Blei an der Kathode abscheidet. Als Grenze kann eiu Gehalt von 7 Volumprocenten Salpeter-
slure (D = 1,4) gelten. Im allgemeinen muss bei Flllung au8
kalter Losung mehr Slure vorhanden sein, a19 bei FlIlung aus
warmer Losung; die Stromsttirke bezw. Stromdichte kann inner-
halb weiter Grenzen schwanken. Ganz anders verhtilt es sicli aber, sowie nocli andere
Korper in der Fliissigkeit zugegen sind ; diese beeinflussen
fast stets die Bleisuperoxydabscheidung, indem sie dieselbe ent-
weder beeintrtichtigen oder sicli mit dem Superoxyd abscheiden,
wodurch zu hohe Resultate erzielt werden. Von besonderem
Einfluss ist die Anwesenheit von SchwefelsLure, da die elektro-
lytische Bleibestimmung von Classen zur Bestimmung des 289 Vor t m (in n , Zur eleh-trolytischen Bestimmung des Bleis. Bleis im Bleiglanz vorgeschlagen wurde; auch Nissenson
empfiehlt dieselbe fur kupfer- und antimonhaltigen Bleiglane,
wlhrend er sonst fur letzteren die Trockenprobe vorziebt. Es
ist merkwurdig, dass bis jetzt auf den schsdlichen Einflnss der
Schwefels%ure noch nicht anfmerksam gemacht wurde. 9, Nur in Lunge's ,,Untersuchungsmethoden" 11. Bd. Seite 256
Annden der Chemie 351. Ri1.
fiodet sich eine solche Angabe.
19 9, Nur in Lunge's ,,Untersuchungsmethoden" 11. Bd. Seite 256
fiodet sich eine solche Angabe. Zur elektrolytischen Bestimmung des Bleis;
von (2. Voytmann. Ihr
Einfluss macht sich dadnrch bemerkbar, dass zu hohe Resul-
tate erzielt werden und der Niederschlag schn efelshrebaltig
wirde). Ich habe eine grosse Anzahl von Versuclien gemacht
und stets zu hohe Zablen erhalten
(Versuche 14-35, 74, 75). Uebrigens beweisen zwei Beleganalysen Classen's bei der Ana-
lyse einer Mischung von Bleinitrat und Kupfersulfat, dass auch
er ein nm 0,0006 bezw. 0,0007 g zu hohes Resultat erhielt
(,,Quantitative Analyse durch Elektrolyse', 4. Aufl., Seite 227). In neuerer Zeit scheint George A. Guess (Cbemiker-Zeitung
Rep. 1906, 67) zu holie Resultate erhalten zu haben, denn
er empfiehlt als Umrechnungsfactor statt der theoretischen Zahl
0,866 die praktische Zalil 0,855. Die elektrolytische Abscbeidung des Bleisuperoxyds mochte
ich mir so vorstellen, dass durch den elektrisclien Strom das
Bleisalz an der Anode in ein Salz des vierwerthigen Bleis
(Plumbisalz)
ubergefiihrt
wird, w elches durch hydrolytische
Dissociation in Bleisuperoxyd bezw. dessen Hydrat und freie
Slure zerfallt, wie dies auch Lob in seineln ,,Leitfaden
der
praktischen ElektrochemieU Seite 74 angenommen hat. Bei
-4nwesenheit von Schwefelshre entsteht das Plunibisulfat, dessen
Dissociation nicbt so vollstgndig ist wie die des Nitrates. Die
Dissociation wird durcli Erwlrmen befdrdert, d'ther fallt die
Bleibestimmung uberhaiipt in der W b m e besser aus als in der
Kalte. Will man bei Anwesenbeit von Schwefelslure gute
Resultate erzielen, so verhhrt man am besten so, dass man
das gewogene Bleisuperoxyd in Salpeterstiure unter Zusatz von 19 V ortmann, Zur elektrolylischen Bestimtnung des Bleis. 290 wenig OxalsBure lost und die Flllung wiederholt (Versuche
20, 21, 22, 32, 33, 34, 35). Eine zweite weniger gute Methode ist die, dass man das
Blei zunachst aua einer mit Seignettesalz nnd Kalilauge her-
gestellten alkalischen Losung als Metallschwamm hllt, diesen
nach dem Waschen in Salpeterslure lost und nun als Super-
oxyd hut (Versueh 44). Die Methode von X e d i c u s (Versuche 28, 29) ist zu uin-
stindlieh und giebt leicht auch ein zu liohes Resultat, wahr-
scheinlich durCli Spuren von Chlor. Ebeiieo wie Sulfate bewirkt aucli Chromsaure eine Er-
hohnng des Resultates (Versuch 38); hier ist das Bleichromat
schon qnalitativ leicht erkeonbar, da in Oxalssure und Sal-
peterslue das Superoxyd sicli zuerst lost und das gelbe Chro-
mat hinterbleibt. Von Sanren wirken schadlich : die Selenslure, die Arsen-
und
die Pliosphorslnre. Neumann hat den Einflnss der
erst,eren beiden beobachtet und gefunden, dass beide auf die
Ansscheidusg des Superoxyds verzogernd wirken. Zur elektrolytischen Bestimmung des Bleis;
von (2. Voytmann. Nach meinen
Vereuchen wirkt die Selenslure wie die Schwefelsiiiure, also
erhohend auf das Resultat; zu dieseii Versuchen (Nr. 36, 37)
loste ich das Selen erst in Salpeterslure und gab diese Losung
zur Losung des Bleisalzes. Bei Arsens&ure dagegen fand ich ebenfalls eine Beein-
trlchtigung der Ftillung (Versuch 39). Um bei Anwesenheit
von Arsen das Blei elektrolytisch zu bestimmen, fallt man es
erst als Metal1 aus einer mit Seignettesalz versetzten alkalischen
Losung, lost den Ychwamm nach dem Waschen in Salpeterslure
und b l l t nnii als Superoxyd (Versuche 40, 42, 43). Man b l l t
am besten in einer Glasschale auf die untere Elektrode mit
einem Strom von 0,1--0,2
Ampere und weniger als 2 Volt
Spannnng (am besten 1 3 Volt) iiber Nacht, wlscht ohne Unter-
brechung des Stromes sorgdltig aus, lost den Schwamm in
20 ccm Salpeterslure (D = 1,4) und h l l t wie sonst. 1st der .Vortmann, Zur elektrolytischen Bestimmung des Bleis. 291 Bleischwamm nicht gut ausgewaschen, so kann durch Zuriick-
halten von Alkali die Bestimmung als Superoxyd zu hoch aus-
fallen und miisste letztere wiederholt werden. Bleischwamm nicht gut ausgewaschen, so kann durch Zuriick-
halten von Alkali die Bestimmung als Superoxyd zu hoch aus-
fallen und miisste letztere wiederholt werden. In derselben Weise wie von Arsen muss Rlei auch von
Antirnon getrennt werden; sowohl Arsen, wie Antimon miissen
als Pentoxyde zugegen sein. Die Trioxyde fuhrt man zu-
nBchst in saurer Losung durch Bromwasser in die Pent-
oxyde iiber und macht dann erst alkalisch (mit Kalilauge
oder Ammoniak). Schwieriger gestaltet sich die Bestimmung des Bleis neben
Pliosphorslure. Dieselbe beeintrlchtigt die Filllung desselben
als Superoxyd. Bei der Elektrolyse in der WLrme und Zusatz
von 2 0 ccm SalpetersBure auf 150 ccm Gesammtlosung haftet
der Niederschlag auch auf der mattirten Elektrode schlecht,
lost sich bald theilwpise ab und bleibt in der Fliissigkeit sus-
pendirt. Bei der Elektrolyse in der Kalte nnter Zusatz von
2 0 ccm Salpetersaure ist die Fallung unvollstLndig und trotz
des hohen SIuregehaltes sclieidet sich an der Kathode metalli-
sches BIei ab; bei Zusatz von 40-45
ccrn Salpetersbre
scheidet sich nur Superoxyd ab, jpdoch ist die Fgllung unvoll-
stllndig. Zur Bestimmung des Bleis neben Phosphorslure kann
man daber wie bei Anwesenheit von Arsen verfahren, d. h. das Blei zuerst ah Metal1 aus alkalischer, dann als Superoxyd
aus salpetersaurer Losung fLllen und eventuell die FBllung als
Superoxyd wiederholen (Versuche 49, 50). Zur elektrolytischen Bestimmung des Bleis;
von (2. Voytmann. 130, 1032) sol1 man sogar auf
0,3 g Bleisnlfat circa 5 g Ammonnitrat znsetzen. von C. M a r i e (Compt. rend. 130, 1032) sol1 man sogar auf
0,3 g Bleisnlfat circa 5 g Ammonnitrat znsetzen. 0,3 g Bleisnlfat circa 5 g Ammonnitrat znsetzen. Zur elektrolytischen Bestimmung des Bleis;
von (2. Voytmann. Bei Anwesenheit von Chlorid oder Jodid erhBlt man eben-
falls zu holie Resultate, was bereits bekannt ist (Versuche 51,
32 I). Im Versucli 32 wurde Bleiglanz durch Jodwasserstoff-
saure, das Bleijodid mit Salpetersaure zersetzt und
diese
Losung der Elektrolyse unterworfen. Aber nicht blos die Anfonen, sondern auch die Kationen
beeinflussen die Flllung des Bleisnperoxyds fast alle in nn-
giinstiger Weise, so dasb man zu hohe Resultate erhklt. Nur 19* 19* V o r t m a n n , Zur eleh-trolytischen Bestimmung des Bleis. 292 das Kupfer macht eine Ausnahme, indem aus salpetersanrer
Lbsung von Blei und Kupfer das Bleisuperoxyd rein heraus-
fidllt, wie dies bisher auch von anderen Autoren gefunden wurde. Dagegen scheinen alle anderen Elemente eine Erhiihung des
Resnltates zu verursachen. Ich habe die FLllung vorgenommen
in Gegenwart von Zink, Nickel, Kobalt, Quecksilber, Silber,
Eisen, Aluminium, Calcium, Kalium, Natrium, Ammonium und
stets zn hohe Zahlen erhalten; die zugesetzten Metalle liessen
sich im Superoxyd nachweisen. Die Trennung ist nur dann
verl&sslich, wenn man das zuerst gefallte Superoxyd in Sal-
petersanre und Oxalsaure lost und die FMlung wiederholt, so
dass man aus der Uebereinatimmung des Gewichtes auf die
Bichtigkeit der Bestimmung schliessen kann. Die Trennung
des Bleis von Kobalt ist in der Kalte schlecht vorzunehmen,
da der Niederschlag sich theilweise in Form eines feinen
Pulvers beim Waschen ablost. Das Verhalten des Silbers, Wismutlis und Mangans bei
der Bleibestimmung ist geniigend bekannt, so dass ich diese
Metalle nicht weiter beriicksichtigt habe. Im Versuch 62 wnrde
versucht, die Bildung des Silbersuperoxyds durch geringen
Alkoholzusatz zu verhindern. hlerkwiirdig ist es, dass die Bleibestimmung auch bei An-
wesenheit von Calcium, Kalium, Natrium und Ammonium zu
hoch aus8llt; das Superoxyd ist in solchen Fallen salpeter-
saurehaltig, denn nacli dem Erwarmen rnit Natriumcarbonat-
losung war in letzterer Salpeterszure nachweisbar. Diese Er-
scheinung wiirde die oben ausgesprochene Ansicht von der
Bildung eines Plnmbinitrats und dessen Dissociation besttitigen;
iudem die Neutralsalze die vollstandige Dissociation verhindern,
erhalt man zu hohe Resultate. Die Bleibestimmung im Blei-
snlfat, bezw. im Bleiglanz wird also ausser in Folge der An-
wesenlieit von Schwefrls&urc, auch durcli Ammoniumnitrat un-
richtig, da Classen das Bleisulfat erst mit Ammoniak bebandelt
snd dann in Salpetershre lost. Nach einer neneren Vorschrift Vortmann , ZUT elektrolytischeti Bestimmung des Bleis. 293 von C. M a r i e (Compt. rend. 130, 1032) sol1 man sogar auf von C. M a r i e (Compt. rend. Zusammenfassung der Resultate. 1) Die elektrolytische Bestimmnng des Bleis als Snper-
oxyd ist nur dann zuverUssig, wenn ausser Blei kein
anderes Element in der salpetersanren L b n n g ent-
halten ist; nnr das Kupfer bildet hier eine Ansnahme. 2) Bei Anwesenheit von Schwefelstinre, Selensgnre, Chrom-
sBure erhLlt man zu holie Resultate; bei zweimaliger
FBllung des Snperoxyds ist die Bestimmnng richtig. 3) Bei Anwesenheit von Arsen- nnd Phosphorsliure ist
die FLllung unvollstgndig; um eine Trennung zu er-
zielen muss inan das Blei zuerst als Yetall, sodann
als Superoxyd fillen, aber diese Trennnng ist umstgud-
lich und daher nicht empfehlenswerth. 4) Bei Anwesenheit aller iibrigen Metalle erhBlt man un-
sichere, znmeist zu holie Zahlen. Man kann sich auf
die Bestimmung nnr dann verlassen, wenn bei zwei-
nialiger FBllung das Gewicht des Superoxyds keine
wesentliclie Aendernng erleidet.
|
https://openalex.org/W2144431773
|
https://europepmc.org/articles/pmc1501059?pdf=render
|
English
| null |
Protease nexin-1 expression is altered in human breast cancer
|
Cancer cell international
| 2,006
|
cc-by
| 5,736
|
Published: 31 May 2006 Published: 31 May 2006 Cancer Cell International 2006, 6:16
doi:10.1186/1475-2867-6-16 This article is available from: http://www.cancerci.com/content/6/1/16 © 2006 Candia et al; licensee BioMed Central Ltd. ;
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Urokinase-type Plasminogen Activator (uPA), a serine protease, plays a pivotal role
in human breast cancer metastasis by mediating the degradation of extracellular matrix proteins
and promoting cell motility. In more advanced breast cancers, uPA activity is significantly up
regulated and serves as a prognostic indicator of poor patient outcome. Classically, regulation of
uPA activity, especially in breast cancers, is thought to be mediated by Type 1 Plasminogen
Activator Inhibitor (PAI-1). However, we have recently found that a lesser known natural inhibitor
of uPA, Protease Nexin 1 (PN-1), is expressed in normal human mammary tissue. Based on this
observation, we investigated if PN-1 is also expressed in human breast cancers where it may
contribute to the regulation of uPA and participate in the development of a metastatic phenotype. Results: Using quantitative real-time PCR analysis, we measured PN-1 mRNA expression in
tissues obtained from 26 human breast tumor biopsies and compared these values with those
obtained from 10 normal breast tissue samples. Since both PAI-1 and uPA expression levels are
known to be elevated in metastatic breast cancer, we also measured their levels in our 26 tumor
samples for direct comparison with PN-1 expression. We found that PN-1 expression was elevated
over that found in normal mammary tissue; an increase of 1.5- to 3.5-fold in 21 of 26 human breast
tumors examined. As anticipated, both PAI-1 and uPA mRNA levels were significantly higher in the
majority of breast tumors; 19 of 26 tumors for PAI-1 and 22 of 26 tumors for uPA. A quantile box
plot of these data demonstrates that the elevated PN-1 expression in breast tumor tissues directly
correlates with the increased expression levels found for PAI-1 and uPA. Conclusion: The fact that PN-1 expression is elevated in human breast cancer, and that its
increased expression is directly correlated with increases measured for PAI-1 and uPA, suggests
that PN-1 may contribute to the regulation of uPA-mediate tumor cell motility and metastatic
spread. cellular matrix (ECM). To achieve this elevated degrada-
tive capacity, tumor cells express a variety of proteases to
digest ECM proteins that typically encapsulate growing, Received: 13 February 2006
Accepted: 31 May 2006 Received: 13 February 2006
Accepted: 31 May 2006 Received: 13 February 2006
Accepted: 31 May 2006 Primary research Open Access Protease nexin-1 expression is altered in human breast cancer
Britny J Candia, William C Hines, Christopher M Heaphy, Jeffrey K Griffith
and Robert A Orlando* Address: Department of Biochemistry and Molecular Biology, University of NewMexico, School of Medicine, MSC08 4670, 1 University of New
Mexico, Albuquerque, New Mexico, 87131, USA ddress: Department of Biochemistry and Molecular Biology, University of NewMexico, School of Medicine, MSC08
exico, Albuquerque, New Mexico, 87131, USA Email: Britny J Candia - bcandia@unm.edu; William C Hines - Curthines@aol.com; Christopher M Heaphy - cheaphy@salud.unm.edu;
Jeffrey K Griffith - jkgriffith@salud.unm.edu; Robert A Orlando* - rorlando@salud.unm.edu * Corresponding author Background
i g
An important characteristic of highly invasive tumor cells
is an elevated capacity to degrade the surrounding extra- Page 1 of 7
(page number not for citation purposes) Page 1 of 7
(page number not for citation purposes) http://www.cancerci.com/content/6/1/16 Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 Preparation of tissue sections and RNA isolation p
Serial frozen sections of breast samples, 10 µm in width,
were mounted on Colorfrost slides (VWR, West Chester,
PA) and stored at -70°C. Specimens were stained with
hematoxylin/eosin and examined by a board-certified sur-
gical pathologist, who assigned a histopathologic grade to
the tumor and analyzed the normal tissue. Total RNA
from cultured cells and frozen tumor tissue was isolated
using silica-based spin-column extraction kits (RNeasy/
DNeasy mini kits, Qiagen, Valencia, CA) according to the
manufacturer's protocol. Total RNA was treated with
RNase-free DNase I (Ambion, Austin, TX) to eliminate
contaminating DNA. RNA integrity was evaluated by aga-
rose gel electrophoresis. Materials and methods
Breast tissue samples benign tumors [1,2]. It is now well established that pro-
teins of the plasminogen activation (PA) system are ele-
vated in breast cancer and serve as the primary functional
players in ECM degradation [3,4]. Expression of one
member of the PA system, the serine protease urokinase
(uPA), is significantly upregulated in tumor cells and cat-
alyzes the conversion of extracellular plasminogen to
plasmin [5]. Plasmin is a broad-spectrum protease that
cleaves many ECM proteins, as well as activates certain
matrix metalloproteinases [6]. This proteolytic cascade
enables highly migratory tumor cells to efficiently degrade
their surrounding matrices, exit the primary site of tumor
growth and colonize distant secondary sites [7]. In addi-
tion to its protease activity which augments breast tumor
cell motility, high expression levels of uPA is also a well-
established prognostic indicator of poor patient outcome
during the course of breast cancer [8,9]. benign tumors [1,2]. It is now well established that pro-
teins of the plasminogen activation (PA) system are ele-
vated in breast cancer and serve as the primary functional
players in ECM degradation [3,4]. Expression of one
member of the PA system, the serine protease urokinase
(uPA), is significantly upregulated in tumor cells and cat-
alyzes the conversion of extracellular plasminogen to
plasmin [5]. Plasmin is a broad-spectrum protease that
cleaves many ECM proteins, as well as activates certain
matrix metalloproteinases [6]. This proteolytic cascade
enables highly migratory tumor cells to efficiently degrade
their surrounding matrices, exit the primary site of tumor
growth and colonize distant secondary sites [7]. In addi-
tion to its protease activity which augments breast tumor
cell motility, high expression levels of uPA is also a well-
established prognostic indicator of poor patient outcome
during the course of breast cancer [8,9]. Frozen breast tumor specimens from anonymous patients
(n = 26) were obtained from the University of New Mex-
ico Cancer Research and Treatment Center Solid Tumor
Facility, Albuquerque, New Mexico. In 25 out of 26 cases,
tumor grade, tumor size, lymph node status, and the frac-
tion of cells in S phase (based on flow cytometry cell cycle
analysis) were included within the clinical history pro-
vided with each specimen. Anonymous normal breast
mRNA (n = 10) originating from female patients where
cause of death was unrelated to cancer, were purchased
from Ambion (Austin, TX). The normal, control samples
were supplied as two equal pools by the company. Cell culture MCF-7 human mammary epithelial cells, were provided
by Dr. Steven Abcouwer, Hershey Medical Center, Her-
shey, Pennsylvania. MDA-MB-231 metastatic human
mammary epithelial cells were obtained from American
Type Culture Collection (Rockland, MD). Both cell lines
were propagated in Dulbecco modified Eagle's medium
(DMEM, Life Technologies/Invitrogen, Carlsbad, CA)
supplemented with 10% fetal calf serum (Irvine Scientific,
Santa Ana, CA), 0.1 mM non-essential amino acids, 1 mM
sodium pyruvate, 0.01 mg/ml bovine insulin, and 100 U/
ml penicillin G. Cells were cultured at 37°C with 5% CO2
and passaged once a week. Regulation of extracellular uPA activity is known to occur
through the inhibitory properties of type I plasminogen
activator inhibitor (PAI-1), a serine protease inhibitor
(SERPIN) that is synthesized and secreted often by the
same cells that secrete uPA [10]. Because of the close func-
tional relationship between uPA proteolytic activity and
PAI-1 inhibitory function, it is thought that a well-con-
trolled balance of uPA and PAI-1 dictates the extent of cell
motility. Protease Nexin-1 (PN-1), another member of the
SERPIN family [11], is highly expressed by stromal cells
[12] and a potent inhibitor of uPA [10,13]. Interestingly,
although PN-1 activity has been extensively studied
within the context of neural development, few studies
have been reported examining its expression in cancerous
tissues and its potential role in cancer progression. PN-1 is
expressed by astrocytes and glial cells [14], as well as neu-
roblastoma cells [15] where it is thought to promote neu-
ronal cell survival [16] and modulate neurite outgrowth
[17]. In addition, PN-1 inhibits thrombin-stimulated cell
division [18], migration of cerebrellar granular cells [19],
and uPA-dependent ECM degradation [20]. Thus, based
on findings in other cell types, we hypothesize that PN-1
may contribute to tumor cell motility in advanced stage
breast cancer by playing a role in the regulation of uPA
activity. To address this hypothesis, we examined the
expression of PN-1 in advanced stage human breast can-
cer tissues to determine if its expression is altered when
compared to normal mammary tissue and to directly
compare its expression level to those of PAI-1 and uPA. To
accomplish this goal, we used quantitative real-time
reverse transcription-PCR (QRT-PCR) to measure PN-1,
PAI-1 and uPA expression levels within a set of breast
tumor and normal breast tissue samples. Quantitative real-time RT-PCR Q
cDNA was synthesized by random decamer-primed
reverse transcription of RNA (1 µg) using a TaqMan®
Reverse Transcription kit (Applied Biosystems, Foster
City, CA) according to the manufacturer's standard proto-
col. Negative controls contained RNase-free water substi-
tuted for reverse transcriptase. The mRNA levels of PN-1,
PAI-1, uPA and TATA-binding protein (TBP) were meas-
ured in breast specimens, the MCF-7 mammary epithelial
cell line, and the MDA-MB-231 metastatic mammary epi-
thelial cell line using the ABgene Absolute SYBR Green Page 2 of 7
(page number not for citation purposes) Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 QRT-PCR assay (Fisher Scientific, Hampton, NH). PN-1
primers were selected to amplify an 81 bp sequence span-
ning the intron located between exons 2 and 3. Primer
sequences used for PN-1 were 5'-GAAGCAGCTCGCCAT-
GGT-3' (forward), 5'-AGACGATGGCCTTGTTGATC-3'
(reverse). TBP primer sequences used were 5'-CACGAAC-
CACGGCACTGATT-3'
(forward),
5'-TTTTCTTGCT-
GCCAGTCTGGAC-3' (reverse). Primer sequences used for
PAI-1 were 5'-TGCTGGTGAATGCCCTCTACT-3' (for-
ward), 5'-CGG TCA TTC CCA GGT TCT CTA-3' (reverse). uPA primer sequences used were 5'-CAC GCA AGG GGA
GAT GAA-3' (forward), 5'-CA GCA TTT TGG TGG TGA
CTT-3' (reverse) [21]. Final concentration of PN-1, PAI-1
and uPA primers used for amplification was 600 nmol/L
forward, 600 nmol/L reverse; 600 nmol/L forward, 900
nmol/L reverse was used for TBP primers. Amplification
of PN-1, PAI-1, uPA and TBP cDNA was performed using
the MiniOpticon Real-Time PCR Detection System (Bio-
rad, Hercules, CA). The cycling parameters used were as
follows: 1 cycle, 95°C for 10 min; 50 cycles, 95°C for 15
sec and 60°C for 1 min; 1 cycle, 40°C for 3 min. The PN-
1, PAI-1 and uPA mRNA levels were normalized to TBP
mRNA levels using the Comparative CT method and are
reported in the figures as fold difference compared to lev-
els found in normal mammary tissue. Melting curve anal-
yses were performed for all amplifications to verify that
only single products were generated from the reactions. Amplicons were sequenced to verify authentic PN-1. The
cDNA for human PN-1 was obtained from the I.M.A.G.E. Consortium (ID: 4824856; Genbank: BC042628; Gen-
bank: BC042628). compared directly to quantitative PCR values obtained
using cDNA generated from normal human mammary tis-
sue. We found that PN-1 expression was elevated over that
found in normal mammary tissue; an increase of 1.5- to
3.5-fold in 21 of 26 human breast tumors examined (Fig. 1A). Quantitative real-time RT-PCR Since both PAI-1 [24-26] and uPA [24,26] expression
levels are known to be elevated in metastatic breast cancer,
we measured their levels in our 26 tumor samples for
direct comparison with PN-1 expression. As anticipated,
both PAI-1 (Fig. 1B) and uPA (Fig. 1C) mRNA levels were
significantly higher in the majority of breast tumors; 19 of
26 tumors for PAI-1 and 22 of 26 tumors for uPA. A quan-
tile box plot of the data shown in Figure 1 permits a direct
comparison of expression levels for PN-1, PAI-1 and uPA
(Fig. 2). These data clearly show that PN-1 expression is
elevated in the majority of human breast cancers exam-
ined and that this elevated expression directly correlates
with the expected higher expression levels found for PAI-
1 and uPA. Since the majority of our tumor samples rep-
resent advanced stage, grade 2 and 3 breast cancers, we are
unable to determine at this time if PN-1 expression levels
correlate with tumor grade, lymph node status or patient
reoccurrence. PN-1 expression in MCF-7 and MDA-MB-231 breast
cancer cells We plan to characterize the mechanism responsible for
increased expression of PN-1 in breast cancer and deter-
mine its functional role in breast cancer metastasis. To
accomplish this goal, we will require a cultured model sys-
tem for accurate, controlled assessment of PN-1 promoter
status, transcription factor requirements, and tumor cell
invasive capacity. MCF-7 and MDA-MB-231 cells are well
established cultured lines used extensively to study molec-
ular details of breast cancer progression [27]. Hormone-
responsive MCF-7 cells have a low invasive capacity and
represent earlier stages of breast cancer, while hormone-
independent MDA-MB-231 cells are highly invasive and
represent more advanced stage breast cancer. To deter-
mine if these cell models will be useful for examining PN-
1 function in breast cancer, we performed QRT-PCR anal-
ysis to identify if PN-1 expression is disregulated in a com-
parable manner to that seen in human breast cancer
tissues. We found that MDA-MB-231 cells express 3.5-fold
greater levels of PN-1 than MCF-7 cells (Fig. 3). Moreover,
increased expression of PAI-1 and uPA were also found in
MDA-MB-231 cells as compared to MCF-7. Results
Q
i Quantitation of PN-1 expression in human breast tumors
For QRT-PCR analysis, we designed primers to amplify an
81 bp sequence of PN-1 spanning the splice junction
between exons 2 and 3. Spanning a splice junction
ensures that amplified products are derived solely from
mRNA and not from genomic DNA that might remain in
our preparation. In order to test the specificity of these
novel primers, we amplified the 81 bp PN-I sequence by
straight RT-PCR using RNA purified from a normal
human fibroblast cell line (HuFb) and compared the
product to that obtained from amplification using the
human PN-1 cDNA. We chose to use human fibroblasts
since they synthesize and secrete active PN-1 at levels cor-
responding to ~1% of all secreted proteins [22,23]. As
anticipated, we found that our newly designed primers
amplified only the expected 81 bp sequence (data not
shown). Discussion Advanced stage breast cancer is accompanied by a dra-
matic increase in metastatic potential of epithelial-derived
tumor cells. The observed increase in tumor cell motility
is aided by increased expression and activity of uPA [4]. For effective tumor cell migration, the proteolytic activity
of uPA is thought to be balanced by the inhibitory activity To quantify PN-1 expression in human breast cancers, we
obtained 26 samples of breast tumor tissue, purified RNA
and generated cDNA from this material. The cDNA were
then analyzed by quantitative PCR and the results were Page 3 of 7
(page number not for citation purposes) Page 3 of 7
(page number not for citation purposes) Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 xpression in human breast tumor tissues and normal human m
NA expression in human breast tumor tissues and norm
ast tumors (T1–T26) and 10 normal breast samples. Normal sa
RNA levels for each gene were evaluated by QRT-PCR. Relative
ATA binding protein mRNA levels. Comparative CT method was
A (C) expression in breast tumor tissue as compared to levels m
oled normal samples was calculated and assigned a value of one
in the tumor samples. The standard deviation of the normal sam
f the mean values obtained from normal mammary tissues. PN-1, PAI-1 and uPA mRNA expression in human breast tumor tissues and normal human mammary tissue
Figure 1
PN-1, PAI-1 and uPA mRNA expression in human breast tumor tissues and normal human mammary tissue. RNA was isolated from 26 breast tumors (T1–T26) and 10 normal breast samples. Normal samples were pooled into two
equal groups (N1 and N2). mRNA levels for each gene were evaluated by QRT-PCR. Relative levels of PN-1, PAI-1 and uPA
mRNA were normalized to TATA binding protein mRNA levels. Comparative CT method was used to calculate fold difference
of PN-1 (A), PAI-1 (B) and uPA (C) expression in breast tumor tissue as compared to levels measured in normal breast tissue. The mean value of the two pooled normal samples was calculated and assigned a value of one in order to determine relative
fold change of expression within the tumor samples. The standard deviation of the normal samples was 0.263. The box repre-
sents one standard deviation of the mean values obtained from normal mammary tissues. Compariso
els in 26 br
Figure 2 Comparison of PN-1, PAI-1 and uPA mRNA expres-
sion levels in 26 breast tumor samples. The box for
each gene represents the interquartile range (25–75th per-
centile) and the line within this box is the median value. Bot-
tom and top bars of the whisker indicate the 10th and 90th
percentiles, respectively. Outlier values are indicated (closed
squares). QRT-PCR analysis of PN-1, PAI-1 and uPA mRNA expres-
sion in MCF-7 and MDA-MB-231 breast cancer cell lines
Figure 3
QRT-PCR analysis of PN-1, PAI-1 and uPA mRNA
expression in MCF-7 and MDA-MB-231 breast cancer
cell lines. PN-1, PAI-1 and uPA message levels were quanti-
tated in MCF-7 and MDA-MB-231 cells by QRT-PCR. Expression levels for PN-1, PAI-1 and uPA were normalized
to values obtained for TATA binding protein. CT values for
each gene obtained from MCF-7 cells were averaged and
assigned a value of one to assess relative fold increase in
expression in MDA-MB-231 cells. Although studies in the literature investigating a role for
PN-1 in cancer progression are limited, our results com-
plement and extend data presented in a recent report by
Buchholz and colleagues [31]. Their study demonstrated
that a highly metastatic pancreatic cancer line overex-
pressed PN-1, while a less metastatic subclone showed lit-
tle PN-1 expression. The authors also noted that stable
PN-1 overexpression in the less metastatic subclone
greatly enhanced its local invasiveness in in vivo studies. Our studies expand on these observations by demonstrat-
ing an increase in PN-1 expression in human breast cancer
tissues. Q
y
,
p
g
QRT-PCR analysis of PN-1, PAI-1 and uPA mRNA
expression in MCF-7 and MDA-MB-231 breast cancer
cell lines. PN-1, PAI-1 and uPA message levels were quanti-
tated in MCF-7 and MDA-MB-231 cells by QRT-PCR. Expression levels for PN-1, PAI-1 and uPA were normalized
to values obtained for TATA binding protein. CT values for
each gene obtained from MCF-7 cells were averaged and
assigned a value of one to assess relative fold increase in
expression in MDA-MB-231 cells. Q
y
,
p
g
QRT-PCR analysis of PN-1, PAI-1 and uPA mRNA
expression in MCF-7 and MDA-MB-231 breast cancer
cell lines. PN-1, PAI-1 and uPA message levels were quanti-
tated in MCF-7 and MDA-MB-231 cells by QRT-PCR. Expression levels for PN-1, PAI-1 and uPA were normalized
to values obtained for TATA binding protein. Discussion ,
a
u
e p ess o
u a b east tu o t ssues a
o
a
u a
a
a y t ssue
gu e
PN-1, PAI-1 and uPA mRNA expression in human breast tumor tissues and normal human mammary tissue. RNA was isolated from 26 breast tumors (T1–T26) and 10 normal breast samples. Normal samples were pooled into two
equal groups (N1 and N2). mRNA levels for each gene were evaluated by QRT-PCR. Relative levels of PN-1, PAI-1 and uPA
mRNA were normalized to TATA binding protein mRNA levels. Comparative CT method was used to calculate fold difference
of PN-1 (A), PAI-1 (B) and uPA (C) expression in breast tumor tissue as compared to levels measured in normal breast tissue. The mean value of the two pooled normal samples was calculated and assigned a value of one in order to determine relative
fold change of expression within the tumor samples. The standard deviation of the normal samples was 0.263. The box repre-
sents one standard deviation of the mean values obtained from normal mammary tissues. Page 4 of 7
(page number not for citation purposes) Page 4 of 7
(page number not for citation purposes) Page 5 of 7
(page number not for citation purposes) http://www.cancerci.com/content/6/1/16 Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 Comparison of PN-1, PAI-1 and uPA mRNA expression lev-
els in 26 breast tumor samples
Figure 2
Comparison of PN-1, PAI-1 and uPA mRNA expres-
sion levels in 26 breast tumor samples. The box for
each gene represents the interquartile range (25–75th per-
centile) and the line within this box is the median value. Bot-
tom and top bars of the whisker indicate the 10th and 90th
percentiles, respectively. Outlier values are indicated (closed
squares). of PAI-1 [28,29]. The cycling activities of proteolysis and
protease inhibition lead to sequential rounds of cell
detachment-reattachment, which in turn leads to an
increase in cell motility. Indeed, elevated expression levels
of both uPA and PAI-1 are characteristic of advanced stage
breast cancers [30]. Interestingly, although PN-1 is struc-
turally and functionally related to PAI-1, there have been
no studies to date investigating if PN-1 contributes to
breast cancer progression in a manner similar to that of
PAI-1. To address this gap in knowledge, we examined if
PN-1 expression is altered in human breast cancer by
quantitating levels of PN-1 expression in human tissue
samples obtained from tumor biopsies. In these same
samples, we also quantitated PAI-1 and uPA expression
levels for direct comparison to PN-1. Our findings indi-
cate that PN-1 expression is elevated in the majority of
human breast tumor tissues examined and that its expres-
sion levels are directly correlated with increases measured
for PAI-1 and uPA. We also found that the highly meta-
static, MDA-MB-231 breast cancer line expresses 3.5-fold
greater levels of PN-1 compared to the non-tumorgenic,
MCF-7 breast cancer cell line. This increase in PN-1 is also
correlated to increases seen for PAI-1 and uPA in MDA-
MB-231 cells. The elevated expression of all three genes is
consistent with our measurements in human breast tumor
samples. The significant differences in PN-1 expression
between non-tumorigenic MCF-7 cells and highly inva-
sive MDA-MB-231 cells should provide us with a good
basis for identifying the mechanism responsible for
altered PN-1 expression seen in breast tissues and allow us
to examine PN-1 function in the context of elevated PAI-1
and uPA levels. Taken together, these data indicate that
PN-1 expression is increased during breast cancer tumori-
genesis and may contribute, along with PAI-1, to uPA-
mediated tumor cell motility and a more advanced meta-
static phenotype. Authors' contributions BJC carried out the majority of studies and drafted the
manuscript. WCH and CMH provided confirmed breast
tumor and normal mammary samples. JKG assisted with
data interpretation. RAO provided the original conceptual
framework for the study, participated in the experimental
design and finalized the manuscript for submission. Authors read and approved the final version. Compariso
els in 26 br
Figure 2 CT values for
each gene obtained from MCF-7 cells were averaged and
assigned a value of one to assess relative fold increase in
expression in MDA-MB-231 cells. Quantitating expression of PAI-1 and uPA is of high prog-
nostic value for assessing breast cancer survival outcome
[24,25]. Numerous independent studies have shown that
patients with low levels of PAI-1 and uPA in their primary
tumor tissue have a significantly better survival rate than Page 5 of 7
(page number not for citation purposes) Page 5 of 7
(page number not for citation purposes) Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 http://www.cancerci.com/content/6/1/16 patients with high levels of either factor alone. Recently,
the prognostic value of PAI-1 and uPA has been verified
by a pooled analysis consisting of >8,000 breast cancer
patients [26]. In light of the overlapping protease specifi-
cities of PAI-1 and PN-1 [32], together with the estab-
lished role of PN-1 in neuronal cell regulation and
motility [33,34], we believe it is likely that PN-1 also plays
a role in breast cancer progression by contributing to
events necessary for increased tumor cell motility. Increased expression of PN-1 by tumor cells may serve to
modulate their adhesiveness or motility [35]. Alterna-
tively, tumor cell activity may be influenced by tumor-
stromal tissue crosstalk [36]. The breast neoplastic stroma
contains a heterogeneous cell population composed of
fibroblasts, myofibroblasts, and endothelial cells, which
are all known to synthesize and secrete significant
amounts of PN-1 [37]. Although it remains to be deter-
mined the precise mechanism by which PN-1 contributes
to breast cancer tumor progression, the results of the
present study establish a rationale for further investigation
of PN-1 as a modulator of uPA activity in breast tumor cell
motility. Future studies will be focused on identifying
transcriptional and/or translational mechanisms control-
ling PN-1 expression by cancer cells and determining if
PN-1 serves as an independent prognostic indicator of
breast cancer staging by using a more widely defined sam-
ple of tumor tissues, including earlier stage cancers as well
as late-stage carcinomas. In addition, the use of laser cap-
ture dissection technology will confine our QRT-PCR
measurements to tumor tissue and eliminate contribu-
tions from surrounding normal mammary tissue that are
likely to occur when using surgical specimens. Competing interests The author(s) declare that they have no competing inter-
ests. References 1. Price JT, Bonovich MT, Kohn EC: The biochemistry of cancer dis-
semination. Critical Reviews in Biochemistry & Molecular Biology 1997,
32(3):175-253. ( )
2. Dano K, Romer J, Nielsen BS, Bjorn S, Pyke C, Rygaard J, Lund LR:
Cancer invasion and tissue remodeling--cooperation of pro-
tease systems and cell types. APMIS 1999, 107(1):120-127. y
yp
,
( )
3. Carroll VA, Binder BR: The role of the plasminogen activation
system in cancer. Seminars in Thrombosis & Hemostasis 1999,
25(2):183-197. Abbreviations uPA, urokinase-type plasminogen activator; PAI-1, plas-
minogen activator inhibitor; ECM, extracellular matrix;
PA, plasminogen activation; SERPIN, serine protease
inhibitor; PN-1, protease nexin-1. Acknowledgements We thank Drs. Dorothy J. VanderJagt and Robert H. Glew (Department of
Biochemistry and Molecular Biology, University of New Mexico, School of
Medicine) for there valuable input and critical evaluation of this work. This
work was supported by the National Institutes of Health Grant #HL63291
(to R.A.O.), National Institutes of Health Initiative to Maximize Student
Diversity (IMSD) fellowship (to B.J.C.) and National Institutes of Health
Minority Access to Research Careers (MARC) fellowship (to B.J.C.). Conclusion We quantitated PN-1 expression in samples obtained
from biopsies of human breast tumors and from normal
mammary tissues by QRT-PCR analysis and compared
these results to those obtained for PAI-1 and uPA. Our
findings indicate that PN-1 expression is elevated in a
majority of human breast tumor tissues examined when
compared to normal human mammary tissue. In addi-
tion, the elevated PN-1 expression in tumor tissues
directly correlates with increased expression measured for
PAI-1 and uPA. We also found that the highly metastatic,
MDA-MB-231 breast cancer cell line expresses greater lev-
els of PN-1 compared to the non-tumorgenic, MCF-7
breast cancer cell line. Consistent with observations
obtained from tumor biopsies, PN-1 expression levels in
MDA-MB-231 directly correlate with increases found for
PAI-1 and uPA. These data indicate that PN-1 expression
is increased during breast cancer tumorigenesis and may
contribute, along with PAI-1, to uPA-mediated tumor cell
motility and a more advanced metastatic phenotype. ( )
4. Andreasen PA, Egelund R, Petersen HH: The plasminogen activa-
tion system in tumor growth, invasion, and metastasis. Cellu-
lar & Molecular Life Sciences 2000, 57(1):25-40. f
( )
5. Ellis V, Scully MF, Kakkar VV: Plasminogen activation initiated by
single-chain urokinase-type plasminogen activator. Potenti-
ation by U937 monocytes. Journal of Biological Chemistry 1989,
264(4):2185-2188. ( )
6. Pepper MS: Extracellular proteolysis and angiogenesis. Throm-
bosis & Haemostasis 2001, 86:346-355. 7. Liotta LA, Stetler-Stevenson WG: Tumor invasion and metasta-
sis: an imbalance of positive and negative regulation. Cancer
Research 1991, 51(18 Suppl):5054s-5059s. (
pp )
8. Knoop A, Andreasen PA, Andersen JA, Hansen S, Laenkholm AV,
Simonsen AC, Andersen J, Overgaard J, Rose C: Prognostic signif-
icance of urokinase-type plasminogen activator and plas-
minogen activator inhibitor-1 in primary breast cancer. British Journal of Cancer 1998, 77(6):932-940. t s Jo
of
ce
,
( )
9. Stephens RW, Brunner N, Janicke F, Schmitt M: The urokinase
plasminogen activator system as a target for prognostic
studies in breast cancer. Breast Cancer Research & Treatment 1998,
52(1-3):99-111. (
)
10. Collen D: The plasminogen (fibronolytic) system. Thrombosis &
Haemostasis 1999, 82:259-270. 11. Knauer DJ, Thompson JA, Cunningham DD: Protease nexins: cell-
secreted proteins that mediate the binding, internalization,
and degradation of regulatory serine proteases. J Cell Physiol
1983, 117(3):385-396. ( )
12. Conclusion Kim NK, Chio MJ, Chung HM, Sohn TJ, Hwang SG, Oh D, Lee HH,
Lee YH, Ko JJ: Increased expression and localization of a serine Page 6 of 7
(page number not for citation purposes) Page 6 of 7
(page number not for citation purposes) Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 http://www.cancerci.com/content/6/1/16 http://www.cancerci.com/content/6/1/16 protease inhibitor, protease nexin-1 (PN-1), in the ovary and
uterus during implantation in rat. Thrombosis Research 2001,
103 (2):135-142. protease inhibitor, protease nexin-1 (PN-1), in the ovary and
uterus during implantation in rat. Thrombosis Research 2001,
103 (2):135-142. 33. Cunningham DD: Regulation of neuronal cells and astrocytes
by protease nexin-1 and thrombin. Annals of the New York Acad-
emy of Sciences 1992:228-236. ( )
13. Kruithof EK: Plasminogen activator inhibitors--a review. Enzyme 1988, 40(2-3):113-121. y
34. Monard D: Cell-derived proteases and protease inhibitors as
regulators of neurite outgrowth. Trends in neurosciences 1988,
11(12):541-544. 14. Stone SR, Nick H, Hofsteenge J, Monard D: Glial-derived neurite-
promoting factor is a slow-binding inhibitor of trypsin,
thrombin, and urokinase. Archives of Biochemistry & Biophysics
1987, 252(1):237-244. (
)
35. Rossignol P, Ho-Tin-Noe B, Vranckx R, Bouton MC, Meilhac O,
Lijnen HR, Guillin MC, Michel JB, Angles-Cano E: Protease nexin-1
inhibits plasminogen activation-induced apoptosis of adher-
ent cells. J Biol Chem 2004, 279(11):10346-10356. ( )
15. Vaughan PJ, Cunningham DD: Regulation of protease nexin-1
synthesis and secretion in cultured brain cells by injury-
related
factors. Journal
of
Biological
Chemistry
1993,
268(5):3720-3727. J
(
)
36. Wiseman BS, Werb Z: Stromal effects on mammary gland
development
and
breast
cancer. Science
2002,
296(5570):1046-1049. ( )
16. Houenou LJ, Turner PL, Li L, Oppenheim RW, Festoff BW: A serine
protease inhibitor, protease nexin I, rescues motoneurons
from naturally occurring and axotomy-induced cell death. Proceedings of the National Academy of Sciences of the United States of
America 1995, 92(3):895-899. (
)
37. Baker JB, Low DA, Simmer RL, Cunningham DD: Protease-nexin:
a cellular component that links thrombin and plasminogen
activator and mediates their binding to cells. Cell 1980,
21(1):37-45. ( )
17. Zurn AD, Nick H, Monard D: A glia-derived nexin promotes
neurite outgrowth in cultured chick sympathetic neurons. Developmental Neuroscience 1988, 10(1):17-24. p
( )
18. Festoff BW, Smirnova IV, Ma J, Citron BA: Thrombin, its receptor
and protease nexin I, its potent serpin, in the nervous sys-
tem. Seminars in Thrombosis & Hemostasis 1996, 22(3):267-271. ( )
19. Conclusion Lindner J, Zinser G, Werz W, Goridis C, Bizzini B, Schachner M:
Experimental modification of postnatal cerebellar granule
cell migration in vitro. Brain Research 1986, 377(2):298-304. g
( )
20. Donovan FM, Vaughan PJ, Cunningham DD: Regulation of pro-
tease nexin-1 target protease specificity by collagen type IV. Journal of Biological Chemistry 1994, 269(25):17199-17205. J
g
y
(
)
21. Castello R, Estelles A, Vazquez C, Falco C, Espana F, Almenar SM, Fus-
ter C, Aznar J: Quantitative real-time reverse transcription-
PCR assay for urokinase activator, plasminogen activator
inhibitor type 1, and tissue metalloproteinase inhibitor type
1 gene expression in primary breast cancer. Clinical Chemistry
2002, 48(8):1288-1295. ( )
22. Howard EW, Knauer DJ: Biosynthesis of Protease Nexin 1. Jour-
nal of Biological Chemistry 1986:14184-14190. g
y
23. Scott RWBJB: Purification of human protease nexin. Journal of
Biological Chemistry 1983, 258:10439-10444. 24. Harbeck N, Alt U, Berger U, Kruger A, Thomssen C, Janicke F, Hofler
H, Kates RE, Schmitt M: Prognostic impact of proteolytic fac-
tors (urokinase-type plasminogen activator, plasminogen
activator inhibitor 1, and cathepsins B, D, and L) in primary
breast cancer reflects effects of adjuvant systemic therapy. Clinical Cancer Research 2001, 7(9):2757-2764. 25. Harbeck N, Kruger A, Sinz S, Kates RE, Thomssen C, Schmitt M, Jan-
icke F: Clinical relevance of the plasminogen activator inhibi-
tor type 1--a multifaceted proteolytic factor. Onkologie 2001,
24(3):238-244. ( )
26. Look MP: Pooled analysis of uPA and PAI-1 for prognosis in
primary breast cancer patients. EORTC Receptor and
Biomarker Study Group. International Journal of Biological Markers
2000, 15(1):70-72. ( )
27. Lacroix MLG: Relevance of breast cancer cell lines as models
for breast tumours: an update. In Breast Cancer Research and
Treatment Volume 83. Kluwer Academic Publishers; 2004:249-289. 28. Durand MK, Bodker JS, Christensen A, Dupont DM, Hansen M,
Jensen JK, Kjelgaard S, Mathiasen L, Pedersen KE, Skeldal S, Wind T,
Andreasen PA: Plasminogen activator inhibitor-I and tumour
growth, invasion, and metastasis. Thromb Haemost 2004,
91(3):438-449. Conclusion Publish with BioMed Central and every
scientist can read your work free of charge
"BioMed Central will be the most significant development for
disseminating the results of biomedical research in our lifetime."
Sir Paul Nurse, Cancer Research UK
Your research papers will be:
available free of charge to the entire biomedical community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central
yours — you keep the copyright
Submit your manuscript here:
http://www.biomedcentral.com/info/publishing_adv.asp
BioMedcentral
Page 7 of 7
(page number not for citation purposes) Publish with BioMed Central and every
scientist can read your work free of charge ( )
29. Stefansson S, McMahon GA, Petitclerc E, Lawrence DA: Plasmino-
gen activator inhibitor-1 in tumor growth, angiogenesis and
vascular remodeling. Curr Pharm Des 2003, 9(19):1545-1564. gen activator inhibitor-1 in tumor growth, angiogenesis and
vascular remodeling. Curr Pharm Des 2003, 9(19):1545-1564. 30. Duffy MJ: The urokinase plasminogen activator system: role in
malignancy. Current pharmaceutical design 2004, 10(1):39-49. g
,
(
)
30. Duffy MJ: The urokinase plasminogen activator system: role in
malignancy. Current pharmaceutical design 2004, 10(1):39-49. 31
B
hh l M B bl A N
b
A W
M I
T L d
G 31. Buchholz M, Biebl A, Neebetae A, Wagner M, Iwamura T, Leder G,
Adler G, Gress TM: SERPINE2 (protease nexin I) promotes
extracellular matrix production and local invasion of pancre-
atic tumors in vivo. Cancer Research 2003, 63(16):4945-4951. 32. Chorostowska-Wynimko J, Skrzypczak-Jankun E, Jankun J: Plas-
minogen activator inhibitor type-1: its structure, biological
activity and role in tumorigenesis (Review). International journal
of molecular medicine 2004, 13(6):759-766.
|
https://openalex.org/W2519347273
|
https://link.springer.com/content/pdf/10.1007%2Fs00436-016-5245-5.pdf
|
English
| null |
Cryptosporidium spp. and Enterocytozoon bieneusi in introduced raccoons (Procyon lotor)—first evidence from Poland and Germany
|
Parasitology research
| 2,016
|
cc-by
| 4,892
|
Parasitol Res (2016) 115:4535–4541
DOI 10.1007/s00436-016-5245-5 Parasitol Res (2016) 115:4535–4541
DOI 10.1007/s00436-016-5245-5 ORIGINAL PAPER ORIGINAL PAPER Cryptosporidium spp. and Enterocytozoon bieneusi in introduced
raccoons (Procyon lotor)—first evidence
from Poland and Germany Kinga Leśniańska1 & Agnieszka Perec-Matysiak1 & Joanna Hildebrand1 &
Katarzyna Buńkowska-Gawlik1 & Agnieszka Piróg2 & Marcin Popiołek1 Received: 3 August 2016 /Accepted: 2 September 2016 /Published online: 14 September 2016
# The Author(s) 2016. This article is published with open access at Springerlink.com Abstract The raccoon (Procyon lotor) carnivore native to
North America is a fast spreading, invasive species in the
Europe now. At the moment, the highest population occupies
areas near the German-Polish border. The data on the occur-
rence of Cryptosporidium spp. and microsporidia in raccoons
is limited to North America’s territory and is totally lacking in
the case of their introduction to Europe. Therefore, the objec-
tive of this study was to investigate the occurrence of
microparasites, i.e., Cryptosporidium spp. and microsporidia
in the introduced raccoons obtained from localities in Poland
and Germany. A PCR-based approach that permitted genetic
characterization via sequence analysis was applied to raccoon
fecal samples (n = 49), collected during 2012–2014. All fecal
samples were simultaneously tested with the use of genetic
markers, and DNA of microsporidia and Cryptosporidium
spp. was detected among the examined raccoons. The results
of our research confirmed the presence of Cryptosporidium
skunk genotype and Enterocytozoon bieneusi NCF2 genotype. The results suggest a possible role of raccoons in the contam-
ination of the environment, including urban areas, with
pathogens of zoonotic significance as well as their role in the
transmission and introduction of new genotypes of
microparasites in the areas where P. lotor has not been ob-
served yet. To our knowledge, there has been no literature data on the above genotypes detected previously in humans or an-
imals from the examined study sites so far. Keywords Raccoon .Cryptosporidiumspp. .Enterocytozoon
bieneusi . Genotyping Keywords Raccoon .Cryptosporidiumspp. .Enterocytozoon
bieneusi . Genotyping * Agnieszka Perec-Matysiak
agnieszka.perec-matysiak@uwr.edu.pl 2
Department of Invertebrates Systematic and Ecology, Institute of
Biology, Wrocław University of Environmental and Life Sciences,
Kożuchowska 5b, 51-631 Wrocław, Poland 1
Department of Parasitology, Institute of Genetics and Microbiology,
Wrocław University, Przybyszewskiego 63, 51-148 Wrocław, Poland 1
Department of Parasitology, Institute of Genetics and Microbiology,
Wrocław University, Przybyszewskiego 63, 51-148 Wrocław, Poland
2
Department of Invertebrates Systematic and Ecology, Institute of
Biology, Wrocław University of Environmental and Life Sciences,
Kożuchowska 5b, 51-631 Wrocław, Poland Study areas and collection of material This study was carried out on 49 raccoons, comprising 31
males and 18 females, collected from hunters and road-kills
from the area of Kostrzyn on the Oder and Warta Mouth
National Park, Poland (n = 32), and from localities near the
Müritz National Park, Mecklemburg-Vorpommern, Germany
(n = 17) (Fig. 1). A suburban environment of the city of
Kostrzyn is located in the surroundings of Warta Mouth
National Park (WMNP) (52 °34′ N, 14° 43′ E) which covers
about 80 km2 of the Warta River. Here, raccoons occupy
relatively small territories and live in high density (0.7–2.5
individuals per 1 km2)—their home ranges overlap with an
average of 80 %. This German-Polish border area is a zone of
high human activity associated with traffic at petrol stations,
restaurants, and hotels. WMNP is a part of Natura 2000
project, which makes it also attractive for tourists. Müritz
National Park (MNP) (53° 27′ N, 12° 49′ E) located in
Mecklenburg-Vorpommern contains a large amount of p
p
Enterocytozoon bieneusi and Encephalitozoon spp. are the
major microsporidians infecting humans and animals world-
wide (Santin and Fayer 2011). At present, over 240
E. bieneusi genotypes have been identified (Matos et al. 2012; Zhao et al. 2015). By internal transcribed spacer (ITS)
sequence analysis of E. bieneusi genotypes, eight different
groups of all genotypes were established (Karim et al. 2014). A large cluster named as group 1 contains more than 94 %
published genotypes of E. bieneusi (Henriques-Gil et al. 2010). The genotypes within this group are found both in
humans and animals. Even though some genotypes are genet-
ically similar to human pathogenic ones, they have been found
only in animals so far, suggesting their zoonotic potential
(Henriques-Gil et al. 2010). The remaining genogroups (2–8)
are found mostly in specific hosts and wastewater (Guo et al. 2014). Encephalitozoon spp., another microsporidia group, has
been generally studied among humans and domestic animals;
there is still insufficient information on the role of wild living
animals, including raccoons, which may be a potential source
of zoonotic contamination with this microsporidia species. Fig. 1 The map of Poland and Germany showing geographical origin
(black dots) of wild raccoons obtained for this study Sofar,30speciesandover100genotypesofCryptosporidium
have been described in various vertebrate hosts and environmen-
tal sources (Kváč et al. 2014). Introduction The knowledge on rac-
coon as reservoir hosts of the abovementioned group of para-
sites is rather limited and concerns Central and North
Americas’ territories (Feng et al. 2007; Guo et al. 2014; Perz
and Le Blancq 2001; Snyder 1988; Sulaiman et al. 2003; Zhou
et al. 2004). On the other hand, there is no data on these
microparasites in the case of invasive European raccoons. Therefore, the aim of this preliminary study was to investi-
gate the presence of intestinal microparasites occurring in the
raccoon population in newly colonized areas of Western
Poland and Germany. Molecular analyses were conducted to
identify and genotype Cryptosporidium spp. and microsporidia
species emphasizing their zoonotic potential in European
raccoons. Introduction The raccoon is a North American carnivore which was intro-
duced to Japan and Europe in the 20th century. In Europe, as a
result of escaped pets, releases, and escapes from fur farms,
raccoons are distributed almost across the whole mainland
(Beltrán-Beck et al. 2012). A rapid expansion of this species
has been observed in wild environment since the 1980s main-
ly on the German territory (Hohmann et al. 2001; Stubbe
1999). At present, the largest European stable population oc-
curs in Germany (over one million individuals) (Hohmann
et al. 2000; Michler and Michler 2012), but smaller popula-
tions inhabit also other European countries (Beltrán-Beck
et al. 2012; Schley et al. 2001; Stubbe 1999). In Poland, the
first individuals in wildlife were observed in the 1940s
(Bogdanowicz and Ruprecht 1987). In the 1980s and the
1990s, a wild population was reported in Western Poland,
and since that time, the abundance of the raccoons on the
Polish territory has grown rapidly (Bartoszewicz et al. 2008;
Bartoszewicz and Okarma 2007; Biedrzycka et al. 2014;
Popiołek et al. 2011). Raccoons, which become one of the fastest spreading wild
living population, are often found in forested areas as well in
urban space near human settlements, where they can find
alternative sources of food but also contribute to the transmis-
sion of many zoonotic groups of parasites to other wildlife and
humans (Kresta et al. 2009). Some studies have shown that
species introduced into a novel environment often lose their 2
Department of Invertebrates Systematic and Ecology, Institute of
Biology, Wrocław University of Environmental and Life Sciences,
Kożuchowska 5b, 51-631 Wrocław, Poland 4536 Parasitol Res (2016) 115:4535–4541 own parasites during the course of a new population establish-
ment (Torchin et al. 2003; Torchin and Mitchell 2004) but also
encounter and accumulate parasites that occur in newly colo-
nized areas. In addition, there may be a significant probability
of raccoons introducing some new parasite species, recorded
previously in individuals from North America, into European
ones. The raccoon as an alien and invasive species, both wild
living and potentially synanthropic, may serve as a susceptible
host for opportunistic intestinal parasites. The current epide-
miological data on Cryptosporidium spp. and microsporidia
has raised public health concerns about the zoonotic nature of
transmission of these microparasites. DNA extraction and PCR amplification NestedPCRdetectedE.bieneusiin2of49(4.1%)examinedfecal
samples of raccoons. Both positive samples, one obtained for a
female and the other one for a male raccoon, were recorded from
the area of Poland. The overall prevalence of Cryptosporidium
spp. was estimated in 34.7 % (17/49) with infection rates of
38.9 % (7/18) and 32.3 % (10/31) observed in female and male
raccoons, respectively. The prevalence of parasites according to
the study sites was determined in 43.8 % (14/32) and 17.6 %
(3/17) for Poland and Germany, respectively. No statistically sig-
nificant differences were found in the occurrence of
Cryptosporidiumspp.andE.bieneusibetweenthesamplingareas
and the sex of the examined raccoons. In our survey, we did not
detect any DNA of Encephalitozoon spp. in raccoons. DNA was isolated from all 49 fecal samples using
GeneMATRIX Stool DNA Purification Kit (EURx, Gdańsk,
Poland) according to the manufacturer’s instructions. Obtained DNA was stored at −20 °C until further use. PCR amplification was performed on a sets of nested
primers amplifying the ITS region of the ribosomal ribonucle-
ic acid (rRNA) gene, i.e., EBITS3, EBITS4 and EBITS1,
EBITS2.4 for E. bieneusi (Buckholt et al. 2002) and
INT580F, INT580R and Msp3, Msp4a for Encephalitozoon
spp. (Katzwinkel-Wladarsch et al. 1996). A fragment of
Cryptosporidium 18S rRNA and Cryptosporidium oocyst
wall protein (COWP) genes were amplified (Pedraza-Diaz
et al. 2001; Spano et al. 1997; Xiao et al. 1999). For the
amplification of actin genes, we used cycling parameters elab-
orated by Sulaiman et al. (2002). For all PCR reactions,
negative and positive controls were performed with sterile
water and reference DNA, respectively. Secondary PCR prod-
ucts were subjected to electrophoresis on a 1.0 % agarose gel
and stained with Midori Green (Nippon Genetics Europe
GmbH). Products of expected size were purified using
QIAquick PCR Purification Kit (Qiagen, Hilden, Germany)
and stored at 4 °C until sequencing. The analysis of the ITS region of E. bieneusi revealed the
existence of one known genotype in both positive samples,
namely NCF2. The phylogenetic analysis showed that the
genotype was identical to the ones previously reported in
fox (KT750163) and raccoon dog (KU847358) in China and
clustered into group 1 (Fig. 2). The isolates from Cryptosporidium positive samples ob-
tained from the amplification of 18S rRNA and/or COWP
genes were genotyped by the sequence analysis of the actin
gene. DNA extraction and PCR amplification The only Cryptosporidium genotype, namely skunk
genotype (identified from sequences of the actin gene), was
detected in 9 out of 14 actin positive raccoons. Although the
obtained sequences were not of the same length, they were
identical to the isolate obtained from Eastern fox squirrel
(KT027546) (Fig. 3). Isolates from the remaining actin posi-
tive raccoons yielded sequences of insufficient quality to
include in the analyses. Statistical analysis wetland habitats, especially bog and swamp districts. This
area demonstrates a very opportune habitat for raccoon—its
population density in the area is twice as much as that in the
middle part of Germany (6–8 individuals per 1 km2) (Fischer
et al. 2016; Hohmann 1998; Köhnemann and Michler 2008;
Muschik et al. 2011). Prevalence was expressed as a ratio of a number of PCR
positive samples for Cryptosporidium spp. 18S rRNA or/and
COWP genes and the total number of examined samples. Contingency tables were used to compare prevalence between
the sex of the raccoons and the different sampling areas using
the chi-square test; p < 0.05 was considered statistically sig-
nificant (STATISTICA®12). Frozen carcasses were delivered to the laboratory of
Department of Parasitology UWr and dissected. Collected fecal
samples were kept at −20 °C for further analysis. Each animal
was used for only one fecal specimen. Nucleotide sequencing Products were sequenced in both directions on Applied
Biosystems ABI PRISM 3100-Avant Sequencer (SEQme, the
Czech Republic). The nucleotide sequences obtained in this
study were edited using DNA Baser Sequence Assembly soft-
ware (Heracle BioSoft SRL Romania) then aligned with refer-
ence sequences of Cryptosporidium spp. and E. bieneusi avail-
able in GenBank. Phylogenetic analyses were performed using
MEGA6 software (Tamura et al. 2013). Trees were inferred by
neighbor joining (NJ) method based on the Kimura 2-
parameter distance model; bootstrapping was performed using
1000 replicates. Sequences from this study have been deposited
in GenBank database under the accession numbers KX639723
and KX621279. Study areas and collection of material Among them, Cryptosporidium
hominis and Cryptosporidium parvum are responsible for over
90 % of human cryptosporidiosis cases (Rossle and Latif 2013). Wildlivingmammals,includingcarnivores,havebeendescribed
as reservoirs of several Cryptosporidium species, especially
C. parvum and Cryptosporidium muris (Fayer et al. 2010; Ryan
and Hijjawi 2015) but also Cryptosporidium meleagridis,
Cryptosporidium ubiquitum, Cryptosporidium felis,
Cryptosporidium canis, Cryptosporidium cuniculus,
Cryptosporidiumskunkgenotype,chipmunkgenotype,andother
novel genotypes (Chalmers et al. 2009, 2011; Elwin et al. 2012; Li et al. 2014; Plutzer and Karanis 2009; Robinson
et al. 2008; Xiao 2010; Xiao et al. 1999). Fig. 1 The map of Poland and Germany showing geographical origin
(black dots) of wild raccoons obtained for this study Parasitol Res (2016) 115:4535–4541 4537 Discussion In this study, we have molecularly identified the presence of
E. bieneusi NCF2 genotype and Cryptosporidium skunk
genotype in the Polish-German population of introduced
raccoons. To our knowledge, this has been the first report on
these groups of parasites in raccoons colonizing Europe. By
now, literature data concerning this issue is based on the Parasitol Res (2016) 115:4535–4541 4538 Fig. 2 The phylogenetic
relationship of Enterocytozoon
bieneusi genotypes identified in
the present study (indicated by
solid circles) and others as
inferred by a neighbor-joining
analysis of ITS sequences. Bootstrapping was performed
using 1000 replicates, and the
values below 50 % are not shown. The E. bieneusi group
terminology is based on the works
of Guo et al. (2014), Zhao et al. (2015), and Xu et al. (2016) reports from the area of North America, where raccoon repre-
sents the native fauna. Also there are no available studies on
the parasites in the population of raccoons introduced to Japan,
but there are surveys on the raccoons introduced to Europe and
Japan that concern some other bacterial and viral pathogens as
well as parasites of protozoan and helminth species (Bauer
2013; Beltrán-Beck et al. 2012; Popiołek et al. 2011). molecular studies conducted by Sulaiman et al. (2003) and
Guo et al. (2014) revealed the presence of human pathogenic
genotypes i.e., Peru 11, EbpC, WL15, and D genotypes. Additionally, the following raccoon-adapted genotypes were
identified WL1-3, WL13, WL15-17, WL24, WL26, and
WW6 (Guo et al. 2014; Sulaiman et al. 2003). Cryptosporidium infection has been reported in raccoons
(Carlson and Nielsen 1982; Snyder 1988; Zhou et al. 2004;
Ziegler et al. 2007). Using indirect immunofluorescent assay,
Snyder (1988) found that 13 % of wild raccoons were infect-
ed. By using molecular tools, C. parvum infection was found
in 1 of 5 (20 %) raccoons from wildlife parks in New York
State (Perz and Le Blancq 2001), and 2 of 51 (3.9 %) raccoons
were Cryptosporidium skunk genotype positive in wetlands
adjacent to the Chesapeake Bay (Zhou et al. 2004). Cryptosporidium skunk genotype and C. ubiquitum were
identified in the raccoons and storm water from a New York Our survey has shown that 2 out of 49 fecal samples of
raccoons were E. bieneusi positive. During the phylogeny
analysis, the detected genotype NCF2, clustered with other
genotypes of group 1, suggesting its zoonotic potential. This
newly identified E. Fig. 2 The phylogenetic
relationship of Enterocytozoon
bieneusi genotypes identified in
the present study (indicated by
solid circles) and others as
inferred by a neighbor-joining
analysis of ITS sequences.
Bootstrapping was performed
using 1000 replicates, and the
values below 50 % are not shown.
The E. bieneusi group
terminology is based on the works
of Guo et al. (2014), Zhao et al.
(2015), and Xu et al. (2016) Parasitol Res (2016) 115:4535–4541 Parasitol Res (2016) 115:4535–4541 Fig. 3 The phylogenetic
relationship of Cryptosporidium
sp. skunk genotype identified in
present study (indicated by solid
circles) and others as inferred by a
neighbor-joining analysis of the
actin gene sequences. Bootstrapping was performed
using 1000 replicates, and the
values below 50 % are not shown Fig. 3 The phylogenetic
relationship of Cryptosporidium
sp. skunk genotype identified in
present study (indicated by solid
circles) and others as inferred by a
neighbor-joining analysis of the
actin gene sequences. Bootstrapping was performed
using 1000 replicates, and the
values below 50 % are not shown Fig. 3 The phylogenetic
relationship of Cryptosporidium
sp. skunk genotype identified in
present study (indicated by solid
circles) and others as inferred by a
neighbor-joining analysis of the
actin gene sequences. watershed area (Feng et al. 2007). The Cryptosporidium
skunk genotype was detected also in Eastern gray, American
red and fox squirrels, river otters, and striped skunks from the
area of the USA (Feng et al. 2007; Stenger et al. 2015; Ziegler
et al. 2007). The phylogenetic analysis showed that the
isolates obtained in the present study were organized in skunk
genotype clade containing isolates previously identified
among squirrels and skunk. Although uncommon, human
infections with skunk genotype have also been reported
(Davies et al. 2009; Elwin et al. 2012; Robinson et al. 2008). The wildlife origin of genotypes is increasingly recognized as
an important environmental source of Cryptosporidium infec-
tion in humans, and shifting boundaries between wildlife and
humans could result in the emergence of novel pathogens
(Stenger et al. 2015). Considering that more than 75 % of
human cases of cryptosporidiosis are determined to have the
zoonotic origin and are related to wildlife and domestic
animals, studies concerning a wide range of wild living hosts
seem to be reasonable. watershed area (Feng et al. 2007). The Cryptosporidium
skunk genotype was detected also in Eastern gray, American
red and fox squirrels, river otters, and striped skunks from the
area of the USA (Feng et al. 2007; Stenger et al. 2015; Ziegler
et al. 2007). The phylogenetic analysis showed that the
isolates obtained in the present study were organized in skunk
genotype clade containing isolates previously identified
among squirrels and skunk. Although uncommon, human
infections with skunk genotype have also been reported
(Davies et al. 2009; Elwin et al. 2012; Robinson et al. 2008). Parasitol Res (2016) 115:4535–4541 The wildlife origin of genotypes is increasingly recognized as
an important environmental source of Cryptosporidium infec-
tion in humans, and shifting boundaries between wildlife and
humans could result in the emergence of novel pathogens
(Stenger et al. 2015). Considering that more than 75 % of
human cases of cryptosporidiosis are determined to have the
zoonotic origin and are related to wildlife and domestic
animals, studies concerning a wide range of wild living hosts
seem to be reasonable. raccoon dog origin which is another species introduced from
the area of East Asia. Cryptosporidium skunk genotype has
been detected for the first time in the examined areas suggest-
ing a North American origin. Thus, our results have shown
that introduced raccoons could be considered as a potential
source of human pathogenic Cryptosporidium skunk geno-
type and potentially pathogenic E. bieneusi NCF2 genotype. Acknowledgments
We are grateful to Dr. M. Krappe (Kratzeburg,
Germany) and the staff of BWarta Mouth^ National Park for their help
in collecting raccoon samples. Fecal samples of raccoons used in the
study have been collected within the National Science Centre, Poland,
project no. 2014/15/B/NZ8/00261. Open Access This article is distributed under the terms of the Creative
Commons Attribution 4.0 International License (http://
creativecommons.org/licenses/by/4.0/), which permits unrestricted use,
distribution, and reproduction in any medium, provided you give appro-
priate credit to the original author(s) and the source, provide a link to the
Creative Commons license, and indicate if changes were made. Despite the fact that the raccoon as an alien species has
been present in Europe for 80 years, the knowledge about its
parasitofauna is still insufficient, especially concerning
microparasites. As our results have shown, raccoon as an
introduced species lost many of its originally detected
Cryptosporidium spp. and E. bieneusi genotypes. On the other
hand, it encountered the E. bieneusi genotype which has not
been identified either in Europe or in the North America. We
suppose that E. bieneusi NCF2 genotype might be of the Discussion bieneusi NCF2 genotype in European
raccoons has so far been present only in farmed foxes and
raccoon dogs from China (Xu et al. 2016; Zhang et al. 2016). The studies undertaken by Guo et al. (2014) showed
that the infection rate of E. bieneusi in raccoons from a New
York watershed area was as high as 82 % (18/22). The 4539 References Bartoszewicz M, Okarma H (2007) Szopy nad Wartą. Łowiec Polski
3:26–29 Bartoszewicz M, Okarma H, Zalewski A, Szczęsna J (2008) Ecology of
the raccoon (Procyon lotor) from western Poland. Ann Zool Fennici
45:291–298 Bauer C (2013) Baylisascariosis—infections of animals and humans with
‘unusual’ roundworms. Vet Parasitol 193:404–412 Bauer C (2013) Baylisascariosis—infections of animals and humans with
‘unusual’ roundworms. Vet Parasitol 193:404–412 Bauer C (2013) Baylisascariosis—infections of animals and humans with
‘unusual’ roundworms. Vet Parasitol 193:404–412 4540 Parasitol Res (2016) 115:4535–4541 Beltrán-Beck B, Garcia FJ, Gortázar C (2012) Raccoons in Europe:
disease hazards due to the establishment of an invasive species. Eur J Wildl Res 58:5–15 Katzwinkel-Wladarsch S, Lieb M, Heise W, Löscher T, Rinder H (1996)
Direct amplification and species determination of microsporidian
DNA from stool specimens. Trop Med Int Health 3:373–378 Köhnemann BA, Michler FU (2008) Der Waschbär in Mecklenburg-
Strelitz. Labus 27:50–58 Biedrzycka A, Zalewski A, Bartoszewicz M, Okarma H, Jędrzejewska E
(2014) The genetic structure of raccoon introduced in Central
Europe reflects multiple invasion pathways. Biol Invasions
16:1611–1625 Kresta AE, Henke SE, Pence DB (2009) Gastrointestinal helminths in
raccoons in Texas. J Wildl Dis 45:1–13 Bogdanowicz W, Ruprecht AL (1987) Przypadki stwierdzeń szopa
pracza, Procyon lotor (Linnaeus, 1758), w Polsce. Przegląd
Zoologiczny 31:375–383 Kváč M, McEvoy J, Stenger B, Clark M (2014) Cryptosporidiosis in other
vertebrates. In: Cacciò SM, Widmer G (eds) Cryptosporidium: para-
site and disease. Springer Vienna, Vienna, pp 237–323 Buckholt MA, Lee H, Tzipori S (2002) Prevalence of Enterocytozoon
bieneusi in swine: an 18-month survey at a slaughterhouse in
Massachusetts. Appl Environ Microbiol 68:2595–2599 Li N, Xiao L, Alderisio K, Elwin K, Cebelinski E, Chalmers R, Santin M,
Fayer R, Kvac M, Ryan U, Sak B, Stanko M, Guo Y, Wang L, Zhang
L, Cai J, Roellig D, Feng Y (2014) Subtyping Cryptosporidium
ubiquitum, a zoonotic pathogen emerging in humans. Emerg Infect
Dis 2:217–224 Carlson BL, Nielsen SW (1982) Cryptosporidiosis in a raccoon. J Am Vet
Med Assoc 181:1405–1406 Matos O, Lobo ML, Xiao L (2012) Epidemiology of Enterocytozoon
bieneusi infection in humans. J Parasitol Res 2012:981424
Ö Chalmers RM, Elwin K, Thomas AL, Guy EC, Mason B (2009) Long-
term Cryptosporidium typing reveals the etiology and species-
specific epidemiology of human cryptosporidiosis in England and
Wales, 2000 to 2003. Euro Surveill 14:19086 Michler FU, Michler BA (2012) Ökologische, ökonomische und
epidemiologische Bedeutung des Waschbären (Procyon lotor) in
Deutschland- eine aktuelle Übersicht. References Beiträge zur Jagd- und
Wildforschung 37:389–397 Chalmers RM, Smith R, Elwin K, Clifton-Hadley FA, Giles M (2011)
Epidemiology of anthroponotic and zoonotic human cryptospo-
ridiosis in England and Wales, 2004-2006. Epidemiol Infect
139:700–712 Muschik I, Köhnemann B, Michler FU (2011) Untersuchungen zur
Entwicklung des Raum- und Sozialverhaltens von Waschbär-
Mutterfamilien (Procyon lotor L.) und dessen jagdrechtliche
Relevanz. Beiträge zur Jagd- und Wildtierforschung 36:
573–585 Davies AP, Campbell B, Evans MR, Bone A, Roche A, Chalmers RM
(2009) Asymptomatic carriage of protozoan parasites in children
in day care centers in the United Kingdom. Pediatr Infect Dis J
28:838–840 Pedraza-Diaz S, Amar C, Nichols GL, McLauchlin J (2001) Nested po-
lymerase chain reaction for amplification of the Cryptosporidium
oocyst wall protein gene. Emerg Infect Dis 7:49–56 Elwin K, Hadfield SJ, Robinson G, Chalmers RM (2012) The epidemi-
ology of sporadic human infections with unusual cryptosporidia
detected during routine typing in England and Wales, 2000-2008. Epidemiol Infect 140:673–683 Perz JF, Le Blancq SM (2001) Cryptosporidium parvum infection involv-
ing novel genotypes in wildlife from lower New York State. Appl
Environ Microbiol 67:1154–1162 Fayer R, Santin M, Macarisin D (2010) Cryptosporidium ubiquitum n.sp. in animals and humans. Vet Parasitol 172:23–32 Plutzer J, Karanis P (2009) Genetic polymorphism in Cryptosporidium
species: an update. Vet Parasitol 165:187–199 Feng Y, Alderisio KA, Yang W, Blancero LA, Kuhne WG, Nadareski
CA, Reid M, Xiao L (2007) Cryptosporidium genotypes in wild-
life from a New York watershed. Appl Environ Microbiol 73:
6475–6483 Popiołek M, Szczęsna-Staśkiewicz J, Bartoszewicz M, Okarma H,
Smalec B, Zalewski A (2011) Helminth parasites of an introduced
invasive carnivore species, the raccoon (Procyon lotor L.), from the
Warta Mouth National Park (Poland). J Parasitol 97:357–360 Fischer ML, Sullivan MJP, Greiser G, Guerrero-Casado J, Heddergott M,
Hohmann U, Keuling O, Lang J, Martin I, Michler FU, Winter A,
Klein R (2016) Assessing and predicting the spread of non-native
raccoons in Germany using hunting bag data and dispersal weighted
models. Biol Invasions 18:57–71 Robinson G, Elwin K, Chalmers RM (2008) Unusual Cryptosporidium
genotypes in human cases of diarrhoea. Emerg Infect Dis 14:
1800–1802 Rossle NF, Latif B (2013) Cryptosporidiosis as threatening health prob-
lem: a review. Asian Pac J Trop Biomed 3:916–924 Guo Y, Alderisio KA, Yang W, Cama V, Feng Y, Xiao L (2014) Host
specificity and source of Enterocytozoon bieneusi genotypes in a
drinking source watershed. References Appl Environ Microbiol 80:218–225
Á Ryan U, Hijjawi N (2015) New developments in Cryptosporidium re-
search. Int J Parasitol 45:367–373 Santin M, Fayer R (2011) Microsporidiosis: Enterocytozoon bieneusi in
domesticated and wild animals. Res Vet Sci 90:363–371 Henriques-Gil N, Haro M, Izquierdo F, Fenoy S, del Águila C (2010)
Phylogenetic approach to the variability of the microsporidian
Enterocytozoon bieneusi and its implications for inter- and intrahost
transmission. Appl Environ Microbiol 76:3333–3342 Schley L, Schanck C, Schaul M, Sinner C (2001) Neubürger und
Heimkehrer unter den Wildtieren Luxemburgs. Beiträge zur Jagd-
und Wildforschung 26:141–154 Hohmann U (1998) Untersuchungen zur Raumnutzung des Waschbären
(Procyon lotor L. 1758) im Solling, Süd-Niedersachsen, unter
besonderer Berücksichtigung des Sozialverhaltens. Dissertation,
University of Götingen Snyder DE (1988) Indirect immunofluorescent detection of oocysts of
Cryptosporidium parvum in the feces of naturally infected raccoons
(Procyon lotor). J Parasitol 74:1050–1052 Hohmann U, Gerhard R, Kasper M (2000) Home range size of adult
raccoons (Procyon lotor) in Germany. Z Säugetierkunde 65:
124–127 Spano F, Putignani L, McLauchlin J, Casemore DP, Crisanti A (1997)
PCR-RFLP analysis of the Cryptosporidium oocyst wall protein
(COWP) gene discriminates between C. wrairi and C. parvum,
and between C. parvum isolates of human and animal origin. FEMS Microbiol Lett 150:207–217 Hohmann U, Voigt S, Andreas U (2001) Quo Vadis raccoon? New visi-
tors in our backyards—on the urbanization of an allochthone carni-
vore in Germany. In: Gottschalk E, Barkow A, Mühlenberg M,
Settele J (eds) Naturschutz und Verhalten, vol 2. UFZ-Berichte,
Lepzig, pp 143–148 Stenger BL, Clark ME, Kváč M, Khan E, Giddings CW, Prediger J,
McEvoy JM (2015) North American tree squirrels with overlapping
ranges host different Cryptosporidium species and genotypes. Infect
Genet Evol 36:287–293 Karim MR, Wang R, Dong H, Zhang L, Lib J, Zhanga S, Rumec FI, Qia
M, Jiana F, Sund M, Yange G, Zouf F, Ninga C, Xiao L (2014)
Genetic polymorphism and zoonotic potential of Enterocytozoon
bieneusi from nonhuman primates in China. Appl Environ
Microbiol 80:1893–1898 Stubbe M (1999) Procyon lotor (Linnaeus, 1758). In: Jones AJ, Amori G,
Bogdanowicz W, Krystufek B, Reijnders P, Spitzenberger F, Stubbe
M, Thissen JBM, Vohohralik V, Zima J (eds) The atlas of European
mammals. Mitchell Academic Press, London, pp 326–327 Parasitol Res (2016) 115:4535–4541 4541 Sulaiman IM, Lal AA, Xiao L (2002) Molecular phylogeny and evolu-
tionary relationships of Cryptosporidium parasites at the actin locus. References J Parasitol 88:388–394 Xu C, Ma X, Zhang H, Zhang XX, Zhao JP, Ba HX, Rui-Du XXM,
Wang QK, Zhao Q (2016) Prevalence, risk factors and molecular
characterization of Enterocytozoon bieneusi in raccoon dogs
(Nyctereutes procyonoides) in five provinces of Northern
China. Acta Trop 161:68–72 Sulaiman IM, Fayer R, Lal AA, Trout JM, Schaefer FW, Xiao L (2003)
Molecular characterization of microsporidia indicates that wild
mammals harbor host-adapted Enterocytozoon spp. as well as
human pathogenic Enterocytozoon bieneusi. Appl Environ
Microbiol 69:4495–4501 Zhang XX, Cong W, Lou ZL, Ma JG, Zheng WB, Yao QX, Zhao Q, Zhu
XQ (2016) Prevalence, risk factors and multilocus genotyping of
Enterocytozoon bieneusi in farmed foxes (Vulpes lagopus),
Northern China. Parasit Vectors 9:72 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6:
molecular evolutionary genetics analysis version 6.0. Mol Biol Evol
30:2725–2729 Zhao W, Zhang W, Yang F, Zhang L, Wang R, Cao J, Shen J, Liu A
(2015) Enterocytozoon bieneusi in dairy cattle in the Northeast of
China: genetic diversity of ITS gene and evaluation of zoonotic
transmission potential. J Eukaryot Microbiol 62:553–560 Torchin ME, Mitchell CE (2004) Parasites, pathogens and invasions by
plants and animals. Front Ecol Environ 2:183–190 Torchin ME, Lafferty KD, Dobson AP, McKenzie VJ, Kuris AM (2003)
Introduced species and their missing parasites. Nature 421:628–630 Zhou L, Fayer R, Trout JM, Ryan UM, Schaefer FW, Xiao L (2004)
Genotypes of Cryptosporidium species infecting fur-bearing mam-
mals differ from those of species infecting humans. Appl Environ
Microbiol 70:7574–7577 Torchin ME, Lafferty KD, Dobson AP, McKenzie VJ, Kuris AM (2003)
Introduced species and their missing parasites. Nature 421:628–630
Xiao L (2010) Molecular epidemiology of cryptosporidiosis: an update. Exp Parasitol 124:80–89 Xiao L (2010) Molecular epidemiology of cryptosporidiosis: an update. Exp Parasitol 124:80–89 Ziegler PE, Wade SE, Schaaf SL, Stern DA, Nadareski CA, Mohammed
HO (2007) Prevalence of Cryptosporidium species in wildlife pop-
ulations within a watershed landscape in southeastern New York
State. Vet Parasitol 43:586–596 Xiao L, Escalante L, Yang C, Sulaiman I, Escalante AA, Montali RJ,
Fayer R, Lal AA (1999) Phylogenetic analysis of Cryptosporidium
parasites based on the small-subunit rRNA gene locus. Appl
Environ Microbiol 65:1578–1583
|
https://openalex.org/W2984677339
|
https://europepmc.org/articles/pmc6853985?pdf=render
|
English
| null |
The unexpected importance of the fifth digit during stone tool production
|
Scientific reports
| 2,019
|
cc-by
| 7,259
|
OPEN Alastair J. M. Key1*, Christopher J. Dunmore1 & Mary W. Marzke2 Unique anatomical features of the human hand facilitate our ability to proficiently and forcefully
perform precision grips and in-hand manipulation of objects. Extensive research has been conducted
into the role of digits one to three during these manual behaviours, and the origin of the highly derived
first digit anatomy that facilitates these capabilities. Stone tool production has long been thought
a key influence in this regard. Despite previous research stressing the unique derived morphology
of the human fifth digit little work has investigated why humans alone display these features. Here
we examine the recruitment frequency, loading magnitude, and loading distribution of all digits on
the non-dominant hand of skilled flintknappers during four technologically distinct types of Lower
Palaeolithic stone tool production. Our data reveal the fifth digit to be heavily and frequently recruited
during all studied behaviours. It occasionally incurred pressures, and was used in frequencies, greater
or equal to those of the thumb, and frequently the same or greater than those of the index finger. The
fifth digit therefore appears key to >2 million years of stone tool production activities, a behaviour that
likely contributed to the derived anatomy observed in the modern human fifth ray. Forceful precision grips and proficient in-hand manipulation underpin many of the behaviours considered
unique to modern humans and our hominin ancestors1–4. While the ability of other primates to manipulate
objects with force and/or precision is increasingly being recognised5–9, available evidence still indicates that mod-
ern humans more frequently or easily generate greater forces and dexterity during these behaviours10,11. Due to
the human thumb’s robust skeletal morphology12,13, unique muscular anatomy14 and representation as a “defin-
ing” human feature15, it has been the focus of research into the evolution of hominin manual capabilities16–21. This
has often been to the exclusion of the other four digits, in particular the fourth and fifth, whose derived traits are
not as well explored and explained. p
p
Digits two and three have been investigated in multiple important works, partly due to their frequent employ-
ment in grips used to wield hammerstones and flaked stone tools2,22,23. www.nature.com/scientificreports www.nature.com/scientificreports Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w 1School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK. 2School of Human Evolution
and Social Change, Arizona State University, Tempe, AZ, USA. *email: a.j.m.key@kent.ac.uk OPEN Knappers five (A) and four (B) during their LAH reduction sequence. The video stills are taken prior
to flakes being removed with hard hammer and soft hammer percussors. Although not visible in the video stills,
note the fifth digit’s location beneath the point of impact (indicated with a star) (C) (see also: Supplementary
Information Video 1). ulno-palmar aspect of the fifth metacarpal shaft in human hands, suggesting frequent recruitment of this muscle,
likely during the opposition of the fifth finger to the thumb34. iti
Experimental research during the 1980s and 90s provided insight into the evolution of these uniquely human
traits. Marzke and Shackley22 highlighted that the fifth digit was frequently recruited to control stone cores during
flake removals and to adjust the flake platform’s angle relative to the hammerstone. Further, the fourth and fifth
digits were demonstrated to aid the stabilisation and securing of stone tools and antler billets during their use. More recent studies emphasised the variable, but at times vital, stabilising and manipulative role of the fifth digit
during stone tool production and use19,23,32. Other studies of stone tool related activities24 and carrying35 have
identified more limited roles for the fourth and fifth digits when compared to the radial digits. However, electro-
myographic studies of muscles serving the fifth digit (flexor and abductor digiti minimi muscles) during stone
tool production revealed their recruitment during hammerstone strikes32. These muscles were particularly heavily
recruited on the non-dominant, core holding hand, where the fifth digit was argued to play a critical role in stabi-
lizing the core against hammerstone impact forces32 (Fig. 1). Since the early studies by Marzke and colleagues22,32,
there has been little research specifically concerning the evolutionary history of the hominin fifth digit, its unique
anatomy36,37, or its role in gripping and in-hand manipulation during stone tool related behaviours38. In turn, our
understanding of the evolution of ulnar (digits 4–5) hand morphology in fossil hominins and modern humans is
highly limited, particularly when compared to the thumb.it g y
p
y
p
Here, we approach the question of why modern humans display derived fifth ray anatomy and increased
joint mobility from an experimental perspective. We examine the pressure levels experienced by nine expert
knappers across their non-dominant hand during four technologically distinct Lower Palaeolithic stone tool
production behaviours (Fig. 1). OPEN To date, analysis of digits four and five is
often, but not always24, limited to examining their length relative to the first digit17,25.hitl ti
The human fifth digit is relatively independent, unlike the fourth which during flexion and extension can also
unintentionally recruit the third and fifth26,27. This independence is in part due to the saddle- shaped articulation
for the fifth metacarpal base on the hamate, which allows the fifth metacarpal to flex and rotate at the same time,
and better oppose the thumb and the rest of the hand4,28. This morphology also provides for a greater range of
movement than in the other non-pollical metacarpals29,30. Movement of the fifth carpometacarpal (CMc) joint in
this manner allows for a greater degree of curvature in the transverse metacarpal arch of the human palm relative
to other apes29,31. In other great apes the fifth CMc joint is not sellar, and the hook of the hamate buttresses the
metacarpal, limiting abduction from the midline of the hand as well as axial rotation, movements that permit
opposition of the fifth digit with the first28. Combined with ulnar expansion of the palmar aspect of the fifth
metacarpal head the unique morphology of humans at this joint, allows for effective opposition of the fifth digit
to the thumb28.iti Opposition of the fifth finger to the rest of the hand, or a grasped object, is crucial to in-hand manipula-
tion, the forceful cradle precision grip required to produce and use flaked stone tools2,32, and to manipulating
cylindrical objects in a power grip33. The human fifth metacarpal is also unique in being second only to the first
metacarpal in robusticity33, reflecting its ability to sustain large loads. In addition, a site-specific concentration
of trabecular bone volume has been found beneath the opponens digiti minimi muscle insertion site, along the School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK. 2School of Human Evolution
nd Social Change, Arizona State University, Tempe, AZ, USA. *email: a.j.m.key@kent.ac.uk Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ www.nature.com/scientificreports/ www.nature.com/scientificreports
ificreports/
Figure 1. Knappers five (A) and four (B) during their LAH reduction sequence. The video stills are taken prior
to flakes being removed with hard hammer and soft hammer percussors. Although not visible in the video stills,
note the fifth digit’s location beneath the point of impact (indicated with a star) (C) (see also: Supplementary
Information Video 1). Figure 1. Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w OPEN Through analyses of pressure distribution, magnitude, and loading frequencies,
we investigate the role of the fifth digit during stone tool production, the biomechanical stress it experiences, and
how this relates to the type of stone tool being produced. Further, we compare these data directly with the other
non-pollical digits to explore the comparative evolutionary history of the radial and ulnar sides of the hominin
hand within a Lower Palaeolithic behavioural context. Results
P In comparison, the distal phalanx of digits three and four were not
heavily loaded during the reduction behaviours. Nor were the proximal phalanges of digits one, three, four or five. Pressure magnitude. Maximum recorded pressures are considerable, frequently ranging between 150–
250 kPa (Supplementary Information Table 1). Across all extracted peak values, however, pressures exceed-
ing 100 kPa were relatively rare (Supplementary Information Fig. 1; Supplementary Information Tables 6–9). Typically, 30–50% of pressure values for all sensors in all reductions ranged between 20–40 kPa (Supplementary
Tables 12–15.f Beyond these values there are differences between sensors and reduction types. Consistent with the pressure
distribution results, DP1, DP2, DP5, IP3, PP2, and PP3 returned pressure values of 40–60 kPa 20–30% of the
time, while DP3, DP4, IP2, PP1, PP4, and PP5 displayed these values < 20% of the time (often <10%). The sen-
sors that frequently (30–50%) returned values < 20 kPa were most often proximally located (PP1, PP3, PP4 and
PP5), but also include IP2 and DP3. Only DP1, DP2, and DP5 repeatedly returned >20% of their values as being
60 kPa or greater across all four reductions. g
Pressures above 100 kPa were rare. In total, there were 89, 112, 255 and 90 values > 100 kPa during the OF,
EAH, LAH and PP behaviours, respectively. Differences between reduction types were not, however, propor-
tionate to the number of mass removal events in each. Indeed, proportionately, PP behaviours more frequently
recorded values >100 kPa. Of these, the majority of values were recorded on DP1 during the OF, EAH and
PP behaviours, while DP1, DP2 and DP5 all displayed ~50 of these values during the LAH reduction. Mean
peak pressure values accord with the range data already described, with all sensors ranging between 25–65 kPa,
dependent on the type of reduction undertaken and the position of the sensor on the hand (Fig. 3). Recruitment frequency. Recruitment frequency data identify DP1, DP2, PP2, IP3, and DP5 as the five most
recurrently loaded sensors (Table 1). They experience loading during 60–90% of all analysed manual behaviours
in all tool production types. The remaining sensors display recruitment frequencies ranging between 13–63%,
with the proximal phalanges of digits one, three, four and five typically being the lowest. In three out of four
behaviours, DP5 is the most frequently loaded sensor. The only exception is the Oldowan reduction, where the
thumb is recruited most often. Results
P Pressure distribution. Post-hoc Dunn’s tests between the twelve sensors during the four reduction types are
presented in the accompanying Supplementary Information Tables 2–5. These statistical comparisons highlighted
significant differences in pressure between sensors distributed across the hand during all reduction behaviours
(Figs 1 and 2). On almost all occasions, the sensor on the distal phalanx of the thumb (DP1) experienced signif-
icantly greater relative pressure than all other sensors during the four tool production strategies (p = <0.0001). The only two exceptions were during the late Acheulean handaxe (LAH) sequence, where the sensors on the distal
phalanx of the second (DP2) and fifth (DP5) digit, recorded no significant pressure differences relative to DP1
(Supplementary Information Table 4). pp
y
DP2 and DP5 sensors are the next most heavily recruited across all four behaviours (Supplementary
Information Tables 2–5). For both sensors the LAH and platform preparation (PP) data returned the greatest
number of significant differences, each displaying substantially greater pressure than nine and seven other sen-
sors, respectively. The other two reductions (Oldowan flake [OF] and early Acheulean handaxe [EAH]) returned
six significant differences for these two sensors, thus still indicating their heavy recruitment. No significant differ-
ences were observed between DP2 and DP5 across all four comparisons, indicating their similar pressure levels. Results are less consistent across the four behaviours for the remaining sensors (Supplementary Information
Tables 2–5). Interestingly, sensors on the intermediate phalanges of digits two and three (IP2, IP3) and the prox-
imal phalanx of digit two (PP2) also experienced heavy loading, returning between three and six significantly www.nature.com/scientificreports/ Figure 2. Colour maps detailing the distribution of mean pressure data (top row) and frequency of recruitment
data (bottom row) during the four stone tool production behaviours. Figure 2. Colour maps detailing the distribution of mean pressure data (top row) and frequency of recruitment
data (bottom row) during the four stone tool production behaviours. greater results relative to the other sensors, in each of the four reduction types. Although relative to DP1, DP2
and DP5 these values were usually reduced. In comparison, the distal phalanx of digits three and four were not
heavily loaded during the reduction behaviours. Nor were the proximal phalanges of digits one, three, four or five. greater results relative to the other sensors, in each of the four reduction types. Although relative to DP1, DP2
and DP5 these values were usually reduced. Results
P It is notable that all sensors, bar DP1 and IP3, display increased recruitment fre-
quencies during the LAH and PP behaviours, relative to the Oldowan and EAH sequences. This is particularly
clear for DP2 and DP5, where recruitment frequencies are as high as 90% and 88% during the PP behaviours,
respectively (Table 1). Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w Discussion
h
d We have recorded the distribution, magnitude, and frequency of pressures acting on the non-dominant hand of
skilled flintknappers during multiple stone tool production procedures. Our results reveal a unique radio-ulnar
loading pattern observed in no other Plio-Pleistocene manual behaviours analysed to date. The uniqueness of this
pattern lies in the heavy recruitment of the fifth finger, alongside that of the thumb and index finger. These data
help explain derived manual anatomy in fossil hominins and modern humans.it Our data indicate substantial loading on distal aspects of the thumb, second and fifth digits, and although
more limited, also proximally on the second and third digits. Other phalanges returned lower loading levels. This distribution is consistent across records of mean and maximum pressure magnitude and loading frequency
(Fig. 2). Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ Figure 3. Boxplots displaying pressures experienced across the twelve sensors examined here. Data from
the Oldowan (A), Early Acheulean Handaxe (B), Late Acheulean Handaxe (C) and Platform Preparation (D)
reduction behaviours are depicted. Blue plots correspond to sensors on distal phalanges, while pink and red are
sensors on intermediate and proximal phalanges, respectively. ‘D’, ‘I’ and ‘P’ correspond to the distal phalanx,
intermediate phalanx and proximal phalanx sensors, respectively. Sensors numbers correspond to the respective
digit. Figure 3. Boxplots displaying pressures experienced across the twelve sensors examined here. Data from
the Oldowan (A), Early Acheulean Handaxe (B), Late Acheulean Handaxe (C) and Platform Preparation (D)
reduction behaviours are depicted. Blue plots correspond to sensors on distal phalanges, while pink and red are
sensors on intermediate and proximal phalanges, respectively. ‘D’, ‘I’ and ‘P’ correspond to the distal phalanx,
intermediate phalanx and proximal phalanx sensors, respectively. Sensors numbers correspond to the respective
digit. Discussion
h
d Sensor
PD1
PP1
PD2
IP2
PP2
PD3
IP3
PP3
PD4
PP4
PD5
PP5
OF (n = 523)
Instances
377
160
334
169
340
102
335
131
115
70
331
145
Frequency (%)
78
31
64
32
65
20
64
25
22
13
63
28
EAH (n = 789)
Instances
499
214
524
263
532
168
496
219
154
151
555
242
Frequency (%)
69
27
66
33
67
21
63
28
20
19
70
31
LAH
(n = 1251)
Instances
761
432
909
666
920
438
669
582
413
481
962
644
Frequency (%)
63
35
73
53
74
35
53
47
33
38
77
51
PP (n = 271)
Instances
194
155
242
171
229
137
162
130
104
121
238
140
Frequency (%)
75
57
90
63
85
51
60
48
39
45
88
52
Table 1. Digit recruitment frequencies expressed as a percentage relative to the total number of manual
behaviours recorded. Table 1. Digit recruitment frequencies expressed as a percentage relative to the total number of manual
behaviours recorded. Previous studies of manual loading during Plio-Pleistocene activities have either not investigated the fifth
digit18,19,39,40, or identified reduced loading relative to digits one-to-three24,35. Our results uniquely demonstrate
the fifth digit to be heavily and frequently loaded during stone tool production; being equal second in terms of
loading magnitude, and in three out of four reduction types, the most frequently recruited. It therefore appears
that the fifth digit could have experienced selective pressure in response to these high demands, subsequent to the
onset of habitual freehand stone tool production after ~2.6 Mya.hii t
The significantly greater pressures experienced by the thumb, relative to digits two-to-five, during the OF,
EAH and PP behavioural sequences is consistent with previous experimental research examining loading during
stone tool production in both the non-dominant and dominant hand19,24. Combined, these three studies support
the hypothesis that the production of flaked stone tools likely contributed to the robust first digit skeletal and
musculature anatomy observed in the hominin lineage3,4.it High loading on the fifth digit is not necessarily surprising given previous grip analyses and electromyo-
graphic studies of stone tool production19,22,32. Nevertheless, it is surprising that the magnitude and frequency of
this loading is greater or equal to that of the thumb in some instances and similar to that of the second digit. Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ www.nature.com/scientificreports/ the dominant arm41. As percussors strike a core supported in this way a proportion of the impact force propagates
through the stone and removes the flake. This force will disperse through all manual elements in contact with the
core proportionate to hammerstone strike direction, core morphology and manual element distribution across
the core’s surface. Understandably, the fifth digit experiences a high proportion of this force due to its positioning
in line with the point of impact (Fig. 1). High-speed videos (800 f/s) in Supplementary Information Video 1 high-
light the dispersion of force through the fifth digit. It is evident that during both hard hammer and soft hammer
flake detachments the fifth digit is directly beneath the point of impact, with reaction forces extending the digit
dorsally. To prevent hyperextension and the loss of the flake by not being supported, it is essential for the fifth digit
to resist these forces, in turn resulting in the high pressures recorded here. Additionally, the essential role of the
thumb in securing the core into to the hand can also be observed.it g
High loading on the distal fifth digit, particularly during platform preparation events and when securing the
core against the leg, may also result from its ability to oppose the thumb when creating a secure inclusive grip
around a core3. Certainly, as the most ulnarly located digit, when abducted it extends the reach of the hand and
can directly oppose the thumb across the midpoint of the palm. Increased pressure values on the fifth digit dur-
ing the production of late Acheulean handaxes (LAH, PP), in particular, can be attributed to their low thickness
to width ratios, smaller size, increased shaping, and greater requirement to remove long, elongated ‘thinning’
flakes38,42,43.h l
The magnitude of loads experienced by digits on the non-dominant hand have been demonstrated to be
considerable. Indeed, the pressure ranges recorded here are broadly equal to those observed on the dominant
hand of knappers18,24,39, a note of importance given recent statements to the contrary. The upper limits of 150–250
kPa detailed here are consistent with pressures recorded from the dominant hand of the same individuals39 and
non-skilled individuals24 during flake tool production.hf gl
p
There do, however, appear to be differences in the frequency with which high loads are experienced on indi-
vidual phalanges (sensors) between the non-dominant and dominant hand. www.nature.com/scientificreports/ Certainly, here pressures above ~100
kPa are infrequent and account for a low proportion of data values (Supplementary Information Tables 6–9). In
part, this may reflect differences in experimental design as all mass removal events, no matter how small, were
recorded in the present study. Additionally, previous dominant hand research has typically utilized stop-and-start
knapping sequences that are less typical of natural knapping behaviours18,24,39. We do, however, also consider this
to reflect important recruitment pattern differences between the dominant and non-dominant hand during stone
tool production. Certainly, in addition to their non-dominant hand knappers frequently support cores using their
leg and palm, consequently providing an additional surface to distribute forces. Moreover, cores typically have
larger surface areas that, as identified here, more frequently recruit ulnarly located digits and proximally located
phalanges during their manipulation. Dominant hand pressure distribution appears to focus solely on digits
one-to-three24. When compared at a whole hand level (i.e. cumulative peak pressures from 12 identically located
sensors), however, the non-dominant hand experiences cumulative loading magnitudes roughly four times as
large as the dominant hand24,38. g
Loading frequencies on the non-dominant hand broadly mirror the distribution of variation in pressure mag-
nitude, including the heavy recruitment of the fifth distal phalanx. It is, perhaps, not surprising that these metrics
of manual recruitment are related, however these metrics provide details essential for understanding the derived
traits observed in the human hand24. Our frequency data broadly corroborates previous findings that the first
digit on the non-dominant hand is recruited more often than the second or third during stone tool production19.hit gt
g
p
The data presented here underlines the important role played by the fifth digit during stone tool production
and helps explain the derived anatomy observed in the modern human fifth digit. It is interesting that many of
distinctively human features of the fifth ray are first seen among current hominin fossils in Homo naledi44, dated
to 236–325 ka45, and in Neandertals36. Its heavy and frequent recruitment, which is occasionally greater or equal
to the thumb, and the same or greater than the index finger, hints at the complex array of recruitment patterns
likely experienced by the hominin hand during the Plio-Pleistocene. To date, investigations into the derived anat-
omy of the modern human hand have, understandably, focused on lithic-related behaviours. www.nature.com/scientificreports/ However, numerous
manual activities likely undertaken by early hominins, and perhaps essential to their survival and reproductive
success, have not yet been examined (e.g. digging stick and spear use, manipulating food, grooming). While work
has started to address this deficit7,24,35,46, further studies investigating such behaviours are necessary if we are
to fully understand the evolutionary history of the hominin hand. Certainly, as highlighted here, the demands
placed on early hominin hands were likely far more diverse than current evidence indicates. Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w Discussion
h
d As
previously detailed19,22,32, the fifth digit is often located directly beneath or very close to the point of impact when
flakes are removed via freehand percussion (Fig. 1). This allows flakes to be supported during removals and their
platforms to be directed towards the knapper’s body and, importantly, their dominant hand; in turn, allowing per-
cussors to accurately and repeatedly strike flake platforms using free-flowing and comfortable arching motions by Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w Material and Methods Stone tool production procedures. Pressure values were recorded from the non-dominant hand of
participants using a wireless Novel Pliance® pressure system comprising of ten 17 × 17 mm sensors and two
10 × 10 mm sensors (Figs 1 and 3). Sensors were attached to the palmar side of the distal phalanges of digits one-
five, the intermediate phalanges of digits two and three, and the proximal phalanges of digits one-five. The two
10 × 10 mm sensors were secured to the distal and proximal phalanges of the fifth digit. Double-sided tape, Velcro
straps and finger cots secured each sensor. Sensors were ‘zeroed out’ prior to data collection and all pressure data
were recorded at a rate of 50 Hz.l Nine experienced flintknappers took part in the study (all were capable of consistently producing late Lower
Palaeolithic handaxes when required). Each was asked to undertake three stone tool production sequences;
Oldowan flake and core production, early Acheulean handaxe, and late Acheulean handaxe production. Hard
hammer percussion was used in all three sequences. Soft hammer percussion and platform preparation events
were only used during the LAH reduction. All tool production events were recorded using a HD video camera. Knappers were allowed to produce tools at their own pace and using their own hammerstones and billets. Ethical
approval was granted by the School of Anthropology and Conservation Ethics Committee (University of Kent; www.nature.com/scientificreports/ Ref. Ares 19065). All individuals gave informed consent and experiments were conducted in accordance with
industry (AAPA) guidelines. Ref. Ares 19065). All individuals gave informed consent and experiments were conducted in accordance with
industry (AAPA) guidelines. Pressure data. Sensors collected data throughout each reduction sequence, however, pressure data extracted
for analysis only refers to manual behaviours that removed mass from the core. Within Oldowan flake and EAH
reductions this only referred to attempted flake detachments, while the LAH sequence also included PP events
(see also38). Prior to starting a reduction knappers forcefully pinched between the thumb and index finger. This
created a point of known manual pressure that was easily identifiable in both the pressure data and the video
recording. Subsequently, behaviours observed in the video could be matched with their accompanying pressure
output and it was possible to identify individual mass removal events within the pressure data stream. y
Each sensor’s peak pressure during each mass removal event was extracted for analysis. Material and Methods During attempted
flake detachments, peak pressures were extracted from two second intervals (one second prior to and after the
point of impact). Platform preparation events were variable in duration and peak pressures were identified as the
highest values recorded from the start to end of these behaviours. Digits are intermittently recruited when secur-
ing stone cores19, and in turn, pressure values of 0 kPa were at times recorded by sensors during mass removal
events. To avoid examining loading as a combined function of peak pressures and the frequency of digit recruit-
ment, pressure records of zero were excluded from analyses (other than those examining loading frequency). In
turn, statistical comparisons of distribution and magnitude focus solely on peak pressure differences between
digits when they are actively recruited to manipulate a core. g
y
y
p
Data from all participants were combined for each of the statistical analyses performed. Participant seven’s
distal sensor on the first digit broke during data collection. All analyses for this sensor are, therefore, derived from
the remaining eight knappers and are adjusted accordingly. Supplementary Tables 1–15 reveal that mean, stand-
ard deviation, and range pressure values remain stable across the other 11 sensors with and without participant
seven; hence the continued inclusion of their data in the other sensors. Statistical analysis. Previous investigations of manual loading during stone tool related behaviours have
focused on pressure distribution18, magnitude38,39, magnitude and distribution28, force magnitude40 or force dis-
tribution and digit recruitment frequency19. Here, we conduct analyses of pressure distribution, magnitude and
frequency. Each is analysed independently for the Oldowan flake, EAH and LAH reduction sequences. The LAH
sequence was separated further into flake removals (LAH) and platform preparation events (PP), in turn creating
four stone tool behaviours. Pressure distribution. To examine how loading varies across the non-dominant hand peak pressure records
were compared between sensors. Shapiro-Wilk tests confirmed that all 48 sets of peak pressure data sets (twelve
sensors across four reduction types) were not normally distributed (p = < 0.05). In turn, Kruskal-Wallis and
post-hoc Dunn’s tests were used for these comparisons. Relative pressure measures were used to investigate load-
ing distribution throughout the hand; absolute pressures could have led to erroneous results if knappers with
particularly high or low values had individually favoured a particular finger. Relative data were calculated by
dividing each knapper’s pressures by their average per knapping behaviour. Material and Methods Participant seven was not included in
this analysis as the loss of one sensor would create non-comparable averages for the other sensors on this hand. Significance was assumed at p < 0.05 subsequent to a Bonferroni correction. Pressure magnitude. Beyond basic descriptive data for each sensor during each reduction type
(Supplementary Information Table 1), magnitude of peak pressure was examined between sensors relative to the
frequency that specific loading values were recruited. Specifically, the pressure range recorded during this exper-
iment (0–252.5 kPa) were divided into thirteen 20 kPa segments (e.g. 0–20, 20.1–40, 40.1–60) and the percentage
of peak pressure records for each sensor falling into these values were recorded. Recruitment frequency. Recruitment frequency was recorded as the percentage of times that a sensor
experienced a load during mass removal events relative to the total number of flake detachments and platform
preparation events that were undertaken during that reduction. For example, the total number of flake removals
attempted across the nine participant’s Oldowan core reductions was 523. Of these flake removal events, the distal
sensor on the thumb registered a load >0 kPa 377 times. In turn, this sensor had a recruitment frequency of 72%. This calculation was repeated for all twelve sensors in each of the four reduction behaviours. Data availabilityh y
The data supporting this article have been uploaded as electronic supplementary material. Received: 27 June 2019; Accepted: 31 October 2019;
Published: xx xx xxxx Received: 27 June 2019; Accepted: 31 October 2019;
Published: xx xx xxxx Received: 27 June 2019; Accepted: 31 October 2019; Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w 5. Pouydebat, E., Gorce, P., Coppens, Y. & Bels, V. Biomechanical study of grasping according to the volume of the object: human
versus non-human primates. J. of Biomech. 42(3), 266–272 (2009). g
p
gy
4. Kivell, T. L. Evidence in hand: recent discoveries and the early evolution of human manual manipulation. Phil. Trans. R. Soc. B. 370,
20140346 (2015). p
J
(
y
)
2. Marzke, M. W. Precision grips, hand morphology, and tools. Am. J. Phys. Anth. 102, 91–110 (1997). 3. Marzke, M. W. Tool making, hand morphology and fossil hominins. Phil. Trans. R. Soc. B. 368, 20120422 (2013). p
J
f
( ),
(
)
6. Pouydebat, E., Reghem, E., Borel, A. & Gorce, P. Diversity of grip in adults and young humans and chimpanzees (Pantroglodytes)
Behav. Brain. Res 218(1), 21–28 (2011). References Faisal, A., Stout, D., Apel, J. & Bradley, B. The manipulative complexity of Lower Palaeolithic stone toolmaking. PloS One 5, e13718
(2010).h 44. Kivell, T. L. et al. The hand of Homonaledi. NatComm. 6, 8431 (2015). h
45. Hawkes, J. et al. New fossil remains of Homonaledi from the Lasedi Chamber, South Africa. E-Life e24232 (2017). h
45. Hawkes, J. et al. New fossil remains of Homonaledi from the Lasedi Chamber, South Africa. E-Life e242 46. Marzke, M. W. & Marzke, R. F. Evolution of the human hand: approaches to acquiring, analysing and interpreting the anatomical
evidence. J. Anatomy. 197, 121–140 (2000). 46. Marzke, M. W. & Marzke, R. F. Evolution of the human hand: approaches to acquiring, analysing and interpreting the anatomical
evidence. J. Anatomy. 197, 121–140 (2000). 46. Marzke, M. W. & Marzke, R. F. Evolution of the human hand: approaches to acquiring, analysing and interpreting the anatomical
evidence. J. Anatomy. 197, 121–140 (2000). References Shrewsbury, M. M., Marzke, M. W., Linscheid, R. L. & Reece, S. P. Comparative morphology of the pollical distal phalanx. Am
Phys. Anth. 121(1), 30–47 (2003).h y
17. Almécija, S., Smaers, J. B. & Jungers, W. L. The evolution of human and ape hand proportions. Nat. Comms. 6, 7717 (2015). 18. Williams, E. M., Gordon, A. D. & Richmond, B. G. Hand pressure distribution during Oldowan stone tool production. J. Human. Evo. 62, 520–532 (2012).hl 19. Key, A. & Dunmore, C. J. The evolution of the hominin thumb and the influence exerted by the non-dominant hand during stone
tool production. J. Human. Evo. 78, 60–69 (2015).i p
20. Feix, T., Kivell, T. L., Pouydebat, E. & Dollar, A. M. Estimating thumb-index finger precision grip and manipulatio
extant and fossil primates Interface 12(106) 20150176 (2015) 0. Feix, T., Kivell, T. L., Pouydebat, E. & Dollar, A. M. Estimating thumb-index finger precision grip and manipulation potential in
extant and fossil primates. Interface 12(106), 20150176 (2015). 0. Feix, T., Kivell, T. L., Pouydebat, E. & Dollar, A. M. Estimating thumb-index finger precision grip and manipulation potential in
extant and fossil primates. Interface 12(106), 20150176 (2015). y
gi
g
p
g p
p
p
extant and fossil primates. Interface 12(106), 20150176 (2015). p
f
21. Skinner, M. M. et al. Human-like hand use in Australopithecus africanus. Science 347(6220), 395–399 (2015). M. et al. Human-like hand use in Australopithecus africanus. Scien 21. Skinner, M. M. et al. Human-like hand use in Australopithecus 2. Marzke, M. W. & Shackley, M. S. Hominid hand use in the Pliocene and Pleistocene: evidence from experimental archaeology and
comparative morphology. J. Human. Evo. 15, 439–460 (1986). p
p
gy
3. Key, A., Merritt, S. R. & Kivell, T. L. Hand grip diversity and frequency during Lower Palaeolithic stone-tool use. J. Human. Evo. 125
137–158 (2018).h 24. Williams-Hatala, E. M. et al. The manual pressures of stone tool behaviors and their implications for the evolution of the human
hand. J. Human. Evo. 119, 14–26 (2018).fi 5. Alba, D. M., Moyà-Solà, S. & Köhler, M. Morphological affinities of the Australopithecus afarensis hand on the basis of manua
proportions and relative thumb length. J. Human. Evo 44(2), 225–254 (2003).l p
p
g
6. Butler, T. J., Kilbreath, S. L., Gorman, R. B. & Gandevia, S. C. Selective recruitment of single motor units in human flexor digitorum
superficialis muscle during flexion of individual fingers. References J. Physiology 567(1), 301–309 (2005). ili
7. van Duinen, H., Yu, W. S. & Gandevia, S. C. Limited ability to extend the digits of the human hand independently with extensor
digitorum. J. Physiology 587(20), 799–4810 (2009). g
y
gy
28. Lewis, O. J. Joint remodelling and the evolution of the human hand. J. Anatomy 123(1), 157–201 (1977). bk
l
h l
f h h
d
f
( d
h ft
h 29. Koebke, J. Functional morphology of the human carpus in Hands of Primates (eds Preuschoft, H. & Chivers, D.) 235–244 (Spri
1993).h 29. Koebke, J. Functional morphology of the human carpus in Hands of Primates (eds Preuschoft, H. & Chivers, D.) 235–244 (Springer,
1993). 30 El Sh
M N k
K P
R M & Vi
S F Th
di
i
l ki
i
l
i
f h
d h
h fifth 30. El-Shennawy, M., Nakamura, K., Patterson, R. M. & Viegas, S. F. Three-dimensional kinematic analysis of the second through
carpometacarpal joints. J. Hand. Surgery 26(6), 1030–1035 (2001).it p
p
j
g y
( )
(
)
1. Reece, S. Getting a grip: functional morphology of the fifth ray in eight catarrhine species. (PhD thesis: Arizona State University, 2005) p
p
j
g y
31. Reece, S. Getting a grip: functional morphology of the fifth ray in eight catarrhine species. (PhD thesis: Arizona State University, 2005). 32. Marzke, M. W. et al. EMG study of hand muscle recruitment during hard hammer percussion manufacture of Oldowan tools. Am. J. Phys. Anth. 105, 315–332 (1998). 31. Reece, S. Getting a grip: functional morphology of the fifth ray in eight catarrhine species. (PhD thesis: Arizona State University, 2005). 32. Marzke, M. W. et al. EMG study of hand muscle recruitment during hard hammer percussion manufacture of Oldowan tools. Am. 2. Marzke, M. W. et al. EMG study of hand muscle recruitment during hard hammer percussion manufacture of Oldowan tools. Am
J. Phys. Anth. 105, 315–332 (1998). y
3. Marzke, M. W., Wullstein, K. L. & Viegas, S. F. Evolution of the power (“squeeze”) grip and its morphological correlates in hominids
Am. J. Phys. Anth. 89(3), 283–298 (1992). y
4. Stephens, N., Kivell, T., Pahr, D., Hublin, J. & Skinner, M. Trabecular bone patterning across the human hand. J. Human. Evo 123
1–23 (2018). 35. Key, A. Manual loading distribution during carrying behaviors: implications for the evolution of the hominin hand. References 1. Napier, J. Hands. (Princeton University Press, 1993). p
y
2. Marzke, M. W. Precision grips, hand morphology, and tools. Am. J. Phys. Anth. 102, 91–110 (1997) 2. Marzke, M. W. Precision grips, hand morphology, and g
p
gy
4. Kivell, T. L. Evidence in hand: recent discoveries and the early evolution of human manual manipulation. Phil. Trans. R. Soc. B. 370,
20140346 (2015). Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ 7. Marzke, M. W., Marchant, L. F., McGrew, W. C. & Reece, S. P. Grips and hand movements of chimpanzees during feeding in Mahale
Mountains National Park, Tanzania. Am. J. Phys. Anth. 156, 317–126 (2015). y
8. Bardo, A., Borel, A., Meunier, H., Guery, J.-P. & Pouydebat, E. Behavioural and functional strategies during tool use tasks in
bonobos. Am. J. Phys. Anth 161(1), 125–140 (2016). y
9. Neufuss, J., Robbins, M.M., Baeumer, J., Humle, T. & Kivell, T.L. Manual skills for food processing by maountain gorillas (Gorilla
beringei beringei) in Bwindi Impenetrable National Park, Uganda. Bio. J. Linnaean. Soc. bly071 (2018)t g
g
g
0. Christel, M. Grasping techniques and hand preferences in Hominoidea in Hand of Primates. (eds Preuschoft, H. & Chivers, D. J. 91–108 (Springer, 1993). p
g
11. Bardo, A., Cornette, R., Borel, A. & Pouydebat, E. Manual function and performance in humans, gorillas and orangutans during the
same tool use task. Am. J. Phys. Anth. 16(4), 21–836 (2017). y
2. Wong, A. L., Meals, C. G. & Ruff, C. B. Computed tomographic analysis of the internal structure of the metacarpals and its
implications for hand use. pathology, and surgical intervention. Anatom. Sci. Int 93(2), 231–237 (2018).hi p
gy
g
alletta, L., Stephens, N. B., Bardo, A., Kivell, T. L. & Marchi, D. Three-dimensional geometric morphometric analysis of the first
etacarpal distal articular surface in humans, great apes and fossil hominins. J. Human. Evo. 132, 119–136 (2019). 13. Galletta, L., Stephens, N. B., Bardo, A., Kivell, T. L. & Marchi, D. Three-dimensional geometric morphometric analysis of th
metacarpal distal articular surface in humans, great apes and fossil hominins. J. Human. Evo. 132, 119–136 (2019). 14. Diogo, R., Richmond, B. G. & Wood, B. Evolution and homologies of primate and modern human hand and forearm muscles, with
notes on thumb movements and tool use. J. Human. Evo. 63(1), 64–78 (2012). 15. Susman, R. L. Fossil evidence for early hominid tool use. Science 265(5178), 1570–1573 (1994). 16. References PloS One 11,
e0163801 (2016). (
)
36. Niewoehner, W. A. Neanderthal hands in their proper perspective in Neanderthals revisited: New Approaches and Perspectives (eds
Harvati, K. & Harrison, T.) 157–190 (Springer, 2006). g
37. Domalain, M., Bertin, A. & Daver, G. Was Australopithecus afarensis able to make the Lomekwian stone tools? Towards a realistic
biomechanical simulation of hand force capability in fossil hominins and new insights on the role of the fifth digit. Comptes. Rendus. Palevol 16(5–6), 572–584 (2017). (
)
(
)
38. Key, A. & Dunmore, C. J. Manual restrictions on Palaeolithic technological behaviours. Peer J. 6, e5399 (2018). y
g
39. Key, A., Dunmore, C. J., Hatala, K. G. & Williams-Hatala, E. M. Flake morphology as a record of manual pressure during stone tool
production. J. Arch. Sci. Rep. 12, 43–53 (2017). p
p
0. Rolian, C., Lieberman, D. E. & Zermeno, J. P. Hand biomechanics during simulated stone tool use. J. Human. Evo. 61, 26–41 (2011) 40. Rolian, C., Lieberman, D. E. & Zermeno, J. P. Hand biomechanics during simulated stone tool use. J. Human. Evo. 61, 26–41 (2011). 41. Williams, E. M., Gordon, A. D. & Richmond, B. G. Upper limb kinematics and the role of the wrist during stone tool production. Am. J. Phys. Anth. 143(1), 134–145 (2010). 40. Rolian, C., Lieberman, D. E. & Zermeno, J. P. Hand biomechanics during simulated stone tool use. J. Human. Evo. 61, 26–41 (2011). 41. Williams, E. M., Gordon, A. D. & Richmond, B. G. Upper limb kinematics and the role of the wrist during stone tool production. Am. J. Phys. Anth. 143(1), 134–145 (2010). g
(
)
41. Williams, E. M., Gordon, A. D. & Richmond, B. G. Upper limb kinematics and the role of the wrist during stone tool production. Am. J. Phys. Anth. 143(1), 134–145 (2010). y
42. Whittaker, J. C. Flinknapping: Making and Understanding Stone Tools. (University of Texas Press, 1994) 42. Whittaker, J. C. Flinknapping: Making and Un J
pp g
g
g
(
y
)
43. Faisal, A., Stout, D., Apel, J. & Bradley, B. The manipulative complexity of Lower Palaeolithic stone toolmaking. PloS One 5, e13718
(2010).h J
pp g
g
g
(
y
)
43. Faisal, A., Stout, D., Apel, J. & Bradley, B. The manipulative complexity of Lower Palaeolithic stone toolmaking. PloS One 5, e13718
(2010).h pp g
g
g
y
43. Author contributions A.K. and C.D. conceived the study following earlier work by M.M.; A.K. designed and organised data collection;
A.K. and C.D. collected the data; A.K. and C.D. analysed the data; all authors wrote the manuscript. Acknowledgements The authors would like to thank Tracy Kivell for loan of the Novel pressure sensor system and Erin Marie
Williams-Hatala for advice on its use. We are grateful to all knappers for their participation in the study. The
Supplementary Information videos were recorded with the kind assistance of Jesse Young and Metin Eren at Kent
State University using equipment from Northeast Ohio Medical University. We are grateful to three anonymous
reviewers who provided helpful suggestions to improve this article. A.K. was supported by a British Academy
Postdoctoral Fellowship (pf160022) during this research. C.D. is funded by E.R.C. Starting Grant #336301. Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ Author contributions
A.K. and C.D. conceived the study following earlier work by M.M.; A.K. designed and organised data collection;
A.K. and C.D. collected the data; A.K. and C.D. analysed the data; all authors wrote the manuscript. Competing interests
The authors declare no competing interests. Additional information
Supplementary information is available for this paper at https://doi.org/10.1038/s41598-019-53332-w. Correspondence and requests for materials should be addressed to A.J.M.K. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and
institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Cre-
ative Commons license, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons license and your intended use is not per-
mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the
copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2019 Additional information Supplementary information is available for this paper at https://doi.org/10.1038/s41598-019-53332-w. Correspondence and requests for materials should be addressed to A.J.M.K. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and
institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Cre-
ative Commons license, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons license and your intended use is not per-
mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the
copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2019 Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w
|
https://openalex.org/W2784249596
|
https://europepmc.org/articles/pmc5816768?pdf=render
|
English
| null |
Effect of immunonutrition on colorectal cancer patients undergoing surgery: a meta-analysis
|
International journal of colorectal disease
| 2,018
|
cc-by
| 6,547
|
Abstract Abstract
Purpose Immunonutrition has been used to prevent the complications after colorectal elective surgery. This systematic review
aimed to analyze and assess the effect of immunonutrition on colorectal cancer patients who received elective surgery. Purpose Immunonutrition has been used to prevent the complications after colorectal elective surgery. This systematic review
aimed to analyze and assess the effect of immunonutrition on colorectal cancer patients who received elective surgery. Methods Three electronic databases (Medline, Embase, Cochrane) were used to search the latent studies which investigated the
effects of enteral immunonutrition (EIN) compared with standard enteral nutrition (EN) or parenteral immunonutrition (PIN)
compared with standard parenteral nutrition (PN) on colorectal cancer patients who are undergoing surgery until 21st of April,
2017. Meta-analysis was conducted to calculate odd risk (OR), mean difference (MD), or standard mean difference (SMD) with
95% confidence interval (CI), and heterogeneity was tested by Q test. (
)
g
y
y Q
Results Nine publications were included. The meta-analysis results presented that EIN improved the length of hospital stay
(pooled MD, 2.53; 95% CI, 1.29–3.41), infectious complications (pooled OR, 0.33; 95% CI, 0.21–0.53) which contains the
Surgical Site Infections (pooled OR, 0.25; 95% CI, 0.22–0.58) and Superficial/Deep incisional infections (pooled OR, 0.27; 95%
CI, 0.12–0.64); meanwhile, PIN improved the length of hospital stay (pooled MD, 2.66; 95% CI, 0.62–4.76), IL-6 (pooled MD,
−6.09; 95% CI, −10.11 to −2.07), CD3 (pooled MD, 7.50; 95% CI, 3.57–11.43), CD4 (pooled MD, 5.47; 95% CI, 2.54–8.40),
and CD4/CD8 (pooled MD, 0.50; 95% CI, 0.22–0.78); the level of CD8 was lower (pooled MD, −4.32; 95% CI, −7.09 to −
1.55) in PIN. Conclusion Immunonutrition could be an effective approach to enhance the immune function of colorectal cancer patients
undergoing elective surgery and to improve the clinical and laboratory outcomes. Keywords Immunonutrition . Colorectal cancer . Meta-analysis . Surgery 1
School of Medicine and Life Sciences, Nanjing University of
Chinese Medicine, Box 21, 138 Xianlin Road, Nanjing 210023,
China Effect of immunonutrition on colorectal cancer patients undergoing
surgery: a meta-analysis ing Xu1 & Xian Sun1 & Qianqian Xin1 & Ying Cheng1 & Zhen Zhan1 & Junfeng Zhang1 & Juan Wu1 Accepted: 31 December 2017 /Published online: 15 January 2018
# The Author(s) 2018. This article is an open access publication International Journal of Colorectal Disease (2018) 33:273–283
https://doi.org/10.1007/s00384-017-2958-6 International Journal of Colorectal Disease (2018) 33:273–283
https://doi.org/10.1007/s00384-017-2958-6 ORIGINAL ARTICLE * Juan Wu
wujuan1213@hotmail.com * Junfeng Zhang
zhangjunfeng5_5@163.com Introduction homeostasis, defense mechanisms and inflammatory re-
sponse, which would increase the rate of postoperative com-
plications and prolong hospital stay [2, 3]. As nutritional sta-
tus being a key factor to influence the clinical outcomes, nu-
trition support has been widely used for elective colorectal
surgery patients. Recently, many researchers argued that
immunonutritional formulas supplemented with biologically
active nutrients were more effective than standard nutrition
intervention in improving inflammation, promoting the
wound healing and shortening the length of hospital stay
(LOS) after operation. Colorectal cancer is one of the most commonly diagnosed
cancers in the world [1]. Although early colorectal cancer
patients could be treated successfully by surgery, major oper-
ation itself possibly cause the dysfunction of the host Electronic supplementary material The online version of this article
(https://doi.org/10.1007/s00384-017-2958-6) contains supplementary
material, which is available to authorized users. The nutrients of immunonutrition formula usually include
arginine, omega-3 fatty acid, glutamine and RNA, etc. Omega-3 fatty acid could reduce the platelet-adhesive endo-
thelial interactions and the synthesis of proinflammatory ei-
cosanoids, while it could stimulate the produce of glutathione
which can decrease oxidative injury [4–6]. Arginine is the sole
substrate for nitric oxide (NO) synthesis, which is a crucial Int J Colorectal Dis (2018) 33:273–283 274 (Bglutamine^) OR (Bomega-3 fatty acid^) OR (BRNA^)
AND (Bparenteral nutrition^) OR (Benteral nutrition^) OR
(Bimmunonutrition^). Appropriate Medical Subject Heading
(MeSH) terms were combined in the search builder. The re-
sults were imported into the management software Endnote
X7 to extract data and delete duplicate references. element of innate antimicrobial immunity in the host’s first
line of defense [7]. It also plays an important role in maintain-
ing the physiological balance of gastrointestinal tract [8] and
regulating the metabolism of many kinds of lymphocyte [9]. Glutamine, as the major fuel source for macrophages, lym-
phocytes, and enterocytes, could increase the level of gut mu-
cosal glutathione, thereby reduce free radical availability, and
decrease inflammation [10, 11]. The protective effect of glu-
tamine on intestinal mucosa might be attributed to the induc-
tion of heat shock protein (HSP) synthesis. Enhanced expres-
sion of HSPs (in particular HSP70) has been shown to be
responsible for glutamine-mediated cellular protection after
inflammatory cytokine-induced cellular injury [12–14]. Deficiency of glutamine may lead to impaired immune func-
tion and dysfunction of intestinal epithelium [15]. Data extraction and quality assessment The information and data in all eligible studies were extracted:
basic characteristics of each study (first author, publication
year, country, sample size, age of the participants), study de-
sign (elements in immunonutrition formula, nutritional sup-
port duration, approach of the nutritional support), and out-
comes of interest (clinical outcomes, immune and biochemical
indices). To date, meta-analysis has focused on immunonutrition with
digestive system cancer and upper gastrointestinal surgery pa-
tients [21, 22], but pooled results about immunonutrition on
colorectal cancer patients are still lacking. This systematic re-
view and meta-analysis were done to evaluate whether
immunonutrition could be beneficial to colorectal cancer pa-
tients, and the conclusion will provide a higher level evidence
regarding usage of immunonutrition on colorectal cancer pa-
tients undergoing surgery. The quality of included investigations was assessed accord-
ing to the Cochrane Collaboration tool published in the
Cochrane Handbook for Systematic Reviews of Interventions
(Version 5.1.0). BRisk of bias^ consisting chiefly of six do-
mains: random sequence generation, allocation concealment,
blinding of participants and personnel, blinding of outcome
assessment, incomplete outcome data, selective reporting,
and other bias. Each domain was graded as Blow risk of bias,^
Bhigh risk of bias,^ or Brisk of bias unclear.^ Study selection The inclusion criteria for this study were as follows: (i) studies
designed as randomized controlled trials (RCTs), (ii) patients
with colorectal neoplasms who received surgery, (iii) interven-
tion of trials was EN vs EIN; PN vs PIN, (iv) both EIN and
PIN included at least one of the following nutrients: Arginine,
Glutamine, Omega-3 fatty acid. Although immunonutrition has been used in clinics for
more than 20 years, the findings have not been uniform in
all reports nor conclusive. For example, one literature ap-
proved to use immunonutrition to patients undergoing major
surgery regardless of their baseline nutritional status [16],
while two literatures suggested that immunomodulating diets
have no quantifiable efficacy in well-nourished patients [17,
18]. Senkal et al. [19] revealed a significant reduction of com-
plications receiving immunonutrition on day 3, while Lobo
et al. [20] revealed that enteral immunonutrition formula had
no advantage over traditional EN formula. Studies beyond the inclusion criteria or originally pub-
lished in language other than English or Chinese were
excluded. Study characteristics rate was used, we transferred it into events number by
sample size. If multiple intervention patterns were imple-
mented in one study, we took them as multiple indepen-
dent studies. Outcomes of continuous and dichotomous
data were measured using fixed-effect model or random-
effect model. The heterogeneity among eligible studies
was tested by Q test based on chi-square distribution
and I2 value. Fixed-effect model was used if no signifi-
cant heterogeneity (I2 < 50%) existed among studies; oth-
erwise, random-effect model was applied. We removed
one or two studies to explore the heterogeneity source
and recombined the remaining data to assess the sensitiv-
ity of the results. P value < 0.05 was considered statisti-
cally significant. rate was used, we transferred it into events number by
sample size. If multiple intervention patterns were imple-
mented in one study, we took them as multiple indepen-
dent studies. Outcomes of continuous and dichotomous
data were measured using fixed-effect model or random-
effect model. The heterogeneity among eligible studies
was tested by Q test based on chi-square distribution
and I2 value. Fixed-effect model was used if no signifi-
cant heterogeneity (I2 < 50%) existed among studies; oth-
erwise, random-effect model was applied. We removed
one or two studies to explore the heterogeneity source
and recombined the remaining data to assess the sensitiv-
ity of the results. P value < 0.05 was considered statisti-
cally significant. Characteristics of nine studies were outlined in Table 1. In
summary, perioperative (n = 4) [23–25, 28], preoperative
(n = 1) [26], and postoperative (n = 4) [27, 29–31] interven-
tions were included in this meta-analysis. Six studies taken
EN vs EIN [23–28] and three taken PN vs PIN [29–31]. Laboratory indicators including biochemical indices and im-
mune indices (e.g., T cell subsets, cytokines, and immuno-
globulin) were measured both before and after the surgery in
EN/EIN; in PN/PIN, they were measured 1 day and 1 week
after the surgery, respectively; the clinical outcomes including
LOS, readmission, and complications were measured within
30 days after surgery. Nine studies provided a total of 1004 participants diagnosed
with colorectal cancer, including 866 participants received the
EN/EIN nutrition support and 138 received the PN/PIN nutri-
tion support. In the EN/EIN group, the ratio of control group
and intervention group is 433:433; the ratio of control group
and intervention group in PN/PIN group is 69:69. Study characteristics More char-
acteristics of participants such as age, gender, weight, BMI, and
the situation of metastasis were listed in Table 2. Results Two thousand eight hundred seventy-four studies were
screened out through the initial search: 1531 from Medline
database, 1068 from Embase database, and 275 from
CENTRAL. After removal of duplicates and irrelevant arti-
cles, 38 full-text articles remained of which 26 studies were
excluded for not meeting the inclusion criteria. Three of the
remaining 12 studies were excluded with data unable to syn-
thesize. Eventually, nine studies [23–31] (six of the EN vs EIN
and three of the PN vs PIN) were included for this meta-
analysis (Fig. 1). Search strategy Statistical analysis was performed by Revman 5.3. For
continuous outcome, mean and standard deviation (SD)
of each study was extracted for calculating pool effect. One study conducted by Moya [23] described continuous
data by mean and standard error (SE); we transferred it
into SD through formula: SD = SE × √N (N = sample size). Mean difference (MD) was used as effect size when the
unit and order of magnitude adopted in all studies were
consistent; otherwise, standardized mean difference
(SMD) was used. Odds ratio (OR) and 95% confidence
interval (CI) were adopted as effect size for dichotomous
outcome; events number in intervention and control group
was extracted for calculating pooled effect. If effective The meta-analysis was performed in accordance with the
PRISMA guidelines. This systematic review was registered
with the International Prospective Register of Systematic
Review (PROSPERO), and the registration number is
CRD42016049748. Potential studies were searched on
Medline (via PubMed), Embase (via OVID), and Cochrane
Central Register of Controlled Trials (CENTRAL) from in-
ception to April 2017. The terms and keywords were as fol-
lows: (Bcolon/rectal/colorectal neoplasms^) OR (Bcolon/rec-
tal/colorectal cancer^) OR (Bcolon/rectal/colorectal
adenomas^) AND (Bnutritional support^) OR (Bnutrition^)
OR (Bnutritional sciences^) OR (Barginine^) OR Int J Colorectal Dis (2018) 33:273–283 275 Quality assessment Most studies had a clear description of their random sequence
generation. Three studies used a computer random number
generator [28–30], one used an envelope [25], two used the Full-text artical
analysis
n=38
Duplicates,irrelevant
records screened:
n=2836
Records identified through
Pubmed searching
n=1531
Records identified through
Embase searching
n=1068
Records identified through
Cochrane searching
n=275
Included studies
n=9
Full-text articals excluded n=29
Cannot find full text n=11
Included patients with other tumors
n=4
Outcomes not matching inclusion
criteria n=7
Systematic reviews n=2
Languages not in english or chinese
n=2
Data can not be merged n=3
Fig. 1 Flow diagram of the
literature search and studies
selection process Fig. 1 Flow diagram of the
literature search and studies
selection process Fig. Quality assessment 1 Flow diagram of the
literature search and studies
selection process Records identified through
Pubmed searching
n=1531 276 Int J Colorectal Dis (2018) 33:273–283 Table 1
Characteristics of the included studies
Author [Ref]
Year Country Duration of
supplementa-
tion
Lost to
follow up
(Con / IN)
Nutrients
Approaches
Outcomes
before sugery
1 day after
surgery
1 week after
surgery
0~30 days after surgery
Pedro Moya [24]
2016 Spain
7 days prior to
surgery and
5 days after
surgery
6/7
Arginine,RNA,n3FA
EN
Oral
Albumin,prealbumin,
transferrin
Albumin,prealbumin,
transferrin
Readmission,anastomotic
leak,ileus,Infectious
complications,Urinary tract
infections,Superficial/Deep incisional
infetious,Organ/Space
infectious,SSI,Respiratory infections
Pedro Moya [23]
2016 Spain
7 days prior to
surgery and
5 days after
surgery
0/0
Arginine,RNA,n3FA
EN
Oral
Readmission,wound infection,Anastomotic
leak,ileus,Infectious
complications,Respiratory infections
L.S.Sorensen [25]
2013 Denmark 2 days prior to
surgery and
7 days after
surgery
0/0
n3FA
EN
Oral
Readmission,wound infection,Anastomotic
leak,ileus,Urinary tract
infections,Respiratory infections
Hisanaga Horie [26] 2006 Japan
From 6 to 2 days
before surgery
NG
Arginine,RNA,n3FA
EN
Oral
albumin
Anastomotic leak,ileus,Urinary tract
infections,Superficial/Deep
incisional,Organ/Space,SSI,Respiratory
infections
Rong Chen [27]
2005 China
From 1 to 7 days
after surgery
NG
Glutamine,Arginine,n3FA EN
Nasointestinal tube
albumin,prealbumin,
Transferrin,CD4,CD8
albumin,prealbumin,
Transferrin
Marco Braga1 [28]
2002 Italy
5 days prior to
surgery
0/0
EN
Oral
LOS,Anastomotic leak,Infectious
complications
Marco Braga2 [28]
2002 Italy
5 days prior to
surgery and
4 days after
surgery
0/0
EN
Oral,jejunal infusion
LOS,Anastomotic leak,Infectious
complications
Mingwei Zhu [29]
2012 China
From 1 to 8 days
after surgery
0/0
n3FA
PN/peripherally-inserted
central catheter
CD4,CD8,CD4/CD8,
IL-6,TNFα
CD4,CD8,CD4/CD8,
IL-6,TNFα
Bin Liang [30]
2008 China
From 1 to 7 days
after surgery
0/1
n3FA
PN/central venous
catheter/Peripheral
catheter
CD4,CD8,CD3,
CD4/CD8,IL-6,
TNFα
CD4,CD8,CD3,
CD4/CD8,IL-6,
TNFα
Jingxiang Song [31] 2004 China
From 2 to 7 days
after surgery
NG
Glutmine
PN/Peripheral venous
catheter
CD4,CD8,CD3,
CD4/CD8
CD4,CD8,CD3,
CD4/CD8
Ref reference, Con control, IN immunonutrition, Marco Braga1 preoperative, Marco Braga2 peri-operative, NG not given, n3FA omega-3 fatty acids Int J Colorectal Dis (2018) 33:273–283 277 web-based randomization [23, 24], and three studies did not
give the sufficient information [26, 27, 31]. Among them,
three studies appropriately performed the allocation conceal-
ment [23–25]. Blinding of participants and personnel was
conducted in four studies [25, 28–30]. Blinding of participants
and personnel was conducted in five studies [25–28, 30, 31]. The remaining studies had no sufficient information about
blinding. Effect of enteral immunonutrition on laboratory index No pooled results of laboratory index were found significantly
different between EN and EIN in this meta-analysis
(Supplementary Table 2). Effect of enteral immunonutrition on clinical outcome
indicators after surgery The meta-analysis showed that EIN group had a shorter LOS
than EN group. Fixed-effect pooled MD was 2.35 (95% CI,
1.29–3.41) with null heterogeneity (I2 = 0%) (Fig. 2a). Infectious complications were reduced in EIN group for the
fixed-effect pooled OR 0.33(95% CI, 0.21–0.53); no hetero-
geneity was detected (I2 = 0%) (Fig. 2b). Surgical Site
Infections (SSI) and Superficial/Deep incisional infections
were reduced in EIN group; the fixed-effect pooled OR was
0.25 (95% CI, 0.11–0.58) in SSI and 0.27(95% CI, 0.12–0.64)
in Superficial/Deep incisional infections; no heterogeneity
was detected (I2 = 0%) (Fig. 2c, d). Other outcomes, such as
anastomotic leak, ileus, organ/space infections, urinary tract
infections, respiratory infections, and readmission, were not
significantly different between two groups (Supplementary
Table 1). Quality assessment Two studies reported the drop-out before conducting
the immunonutrition [24, 30]; therefore, corresponding do-
main was graded as Blow risk.^ All nine included studies
showed the pre-specified outcomes in the pre-specified way. The assessment of risk of bias outcome of each study is sum-
marized in Tables 3 and 4. Table 2
Patients characteristics of the included studies
Moya 2016 [24] Moya 2016 [23] Sorensen 2013 [25] Horie 2006 [26] Chen 2005 [27] Braga 20021 [28] Braga 20022 [28] Zhu 2012 [29] Liang 2008 [30] Song 2004 [31
Variables (control/intervention)
Sample size 128/129
61/61
74/74
34/33
36/36
50/50
50/50
28/29
21/21
20/20
Age*
68/70
68/69
71/69
63/69
58.1/57.9
61.8/63.0
61.8/60.5
70.8/69.8
59.19/55.80
56
Sex (male/female)
Control
69/53
27/34
36/38
18/16
18/18
31/19
31/19
11/17
15/6
26/14
Intervention
62/60
30/31
44/30
25/8
20/16
30/20
8/22
16/13
10/10
BMI
26.64/27.05
NG
26/26
22.8/22.8
NG
NG
NG
23.2/22.9
23.92/23.38
NG
Metastasis
13/15
NG
5/5
NG
NG
NG
NG
0/0
0/0
NG
Weight
NG
NG
76/77
58/59
59/62
NG
NG
NG
65.4/63.50
NG Effect of parenteral immunonutrition on clinical outcome
indicators after surgery PIN intervention could shorten the LOS compared to PN. Pooled MD was 2.66 (95% CI, 0.62–4.76), and the homoge-
neity was well (I2 = 0%) (Fig. 3). Effect of parenteral immunonutrition on laboratory index
CD8 and IL-6 were decreased in the PIN group than those in
PN group 1 week after the surgery. Effect of parenteral immunonutrition on laboratory index Braga 2002
Chen 2005
Horie 2006
Liang 2008
Moya 2016
Moya 2016
Song 2004
Sorensen 2013
Zhu 2012
Random sequence generation
(selection bias)
low risk
unknown risk
unknown risk
low risk
low risk
low risk
unknown risk
low risk
low risk
Allocation concealment
(selection bias)
unknown risk
unknown risk
unknown risk
high risk
low risk
low risk
unknown risk
low risk
unknown risk
Blinding of participants and
personnel (performance bias)
low risk
unknown risk
unknown risk
low risk
high risk
high risk
unknown risk
low risk
low risk
Blinding of outcome assessment
(detection bias)
low risk
low risk
unknown risk
low risk
high risk
high risk
low risk
low risk
unknown risk
Incomplete outcome data
(attrition bias)
low risk
low risk
low risk
low risk
low risk
low risk
low risk
low risk
low risk
Selective reporting
(reporting bias)
low risk
low risk
low risk
low risk
low risk
low risk
low risk
low risk
unknown risk
Other bias
low risk
high risk
low risk
low risk
low risk
low risk
low risk
low risk
low risk Effect of parenteral immunonutrition on laboratory index CD8 and IL-6 were decreased in the PIN group than those in
PN group 1 week after the surgery. CD8 and IL-6 were decreased in the PIN group than those in
PN group 1 week after the surgery. 278 Int J Colorectal Dis (2018) 33:273–283 Braga 2002
Chen 2005
Horie 2006
Liang 2008
Moya 2016
Moya 2016
Song 2004
Sorensen 2013
Zhu 2012
Random sequence generation
(selection bias)
low risk
unknown risk
unknown risk
low risk
low risk
low risk
unknown risk
low risk
low risk
Allocation concealment
(selection bias)
unknown risk
unknown risk
unknown risk
high risk
low risk
low risk
unknown risk
low risk
unknown risk
Blinding of participants and
personnel (performance bias)
low risk
unknown risk
unknown risk
low risk
high risk
high risk
unknown risk
low risk
low risk
Blinding of outcome assessment
(detection bias)
low risk
low risk
unknown risk
low risk
high risk
high risk
low risk
low risk
unknown risk
Incomplete outcome data
(attrition bias)
low risk
low risk
low risk
low risk
low risk
low risk
low risk
low risk
low risk
Selective reporting
(reporting bias)
low risk
low risk
low risk
low risk
low risk
low risk
low risk
low risk
unknown risk
Other bias
low risk
high risk
low risk
low risk
low risk
low risk
low risk
low risk
low risk Pooled MD for CD8 was −4.32 (95% CI, −7.09 to −1.55)
and −6.09 (95% CI, −10.11 to −2.07) for IL-6 (Fig. 4a, b). CD3, CD4/CD8, and CD4 increased in PIN group 1 week
after the surgery. Combined MD for CD3 was 7.50 (95% CI,
3.57–11.43), CD4/CD8 was 0.50 (95% CI, 0.22–0.78), and
CD4 was 5.47 (95% CI, 2.54–8.40) (Fig. 4c–e). In order to
find the source of relative high heterogeneity of CD4, a study
conducted by Zhu et al. [29] was removed and I2 reduced to
zero; meanwhile, pooled MD of CD4 level reached 7.59 (95%
CI, 3.97–11.22) (Fig. 4f). Discussion In the present meta-analysis, we evaluated the benefits of
immunonutrition in patients with colorectal cancer after sur-
gery. Overall, the pooled results supported the usage of EIN in
colorectal cancer patients, for the improvement of postopera-
tive complications and reduction of LOS, compared with EN. Meanwhile, PIN strategy also showed to be beneficial for
patients’ LOS and cellular immune function parameters. Regarding the proinflammatory factors, the PIN group had a
lower serum IL-6 level than that in the PN group, and the
increased CD4, CD4/CD8, and CD3 T lymphocytes in the
PIN group were reasonably observed, which reflect the en-
hancing immune function. Colorectal cancer is the third most commonly diagnosed
cancer in males and the second in females, and the mortality
rate ranked fourth in males and third in females. Statistics data
from IARC showed that the number of new cases of colorectal
cancer was 1.4 million and 693,900 cases died in 2012 in the
world [1]. Patients of colorectal cancer often suffer from mal-
nutrition, especially those undergoing tumorectomy, and the
worsening of nutritional status consequently deteriorated the
surgical outcomes. Thus, nutrition intervention has been the
focal point of postoperative recovery [32]. Despite the standard
nutrition support could reverse nitrogen imbalance and promote
patients’ nutritional status, it did little contribution in improving
the immune function. Thus, many researchers advocated the
usage of immunonutrition in colorectal cancer patients. A
growing body of studies suggests that the immunonutrition
could reduce the postoperative complications and shorten the
LOS in surgical patients, and it also lower toxic effect after the
chemoradiotherapy, such as nausea, vomiting, bloating, abdom-
inal pain, diarrhea, or constipation [33]. Immunonutrition for-
mula usually includes arginine, omega-3 fatty acid, glutamine
and RNA, etc. Andrade et al. [34] found dietary arginine could
preserve the intestinal mucosa and tend to decreased inflamma-
tion by histologic analysis. Glutamine supplementation in
enteral/parenteral nutrition was able to reduce septic complica-
tions, accelerate wound healing, and shorten LOS [35]. However, not all the studies showed the beneficial effects of
immunonutrition. For example, Giger-Pabst et al. Discussion [36] found Int J Colorectal Dis (2018) 33:273–283 279 Table 4
The percentage of each bias for all the included studies
Low risk (%)
High risk (%)
Unknown risk (%)
Random sequence generation (selection bias)
66.67
0
33.33
Allocation concealment (selection bias)
33.33
11.11
55.56
Blinding of participants and personnel (performance bias)
44.44
22.22
22.22
Blinding of outcome assessment (detection bias)
55.55
22.22
22.22
Incomplete outcome data (attrition bias)
100
0
0
Selective reporting (reporting bias)
88.89
0
11.11
Other bias
88.89
11.11
0 immunonutrition [39]. The above results indicated that the ef-
fects of immunonutrition would be different when the condi-
tions are different. Patient characteristics of demographic, sam-
ple size, control group selection, different administration dose,
and duration may be the sources of heterogeneity [40]. In this
meta-analysis, the present results confirmed that the that preoperative oral supplementation with an immune-
enriched diet for 3 days did not improve postoperative outcome
in patients with gastrointestinal cancer, and meanwhile, no pos-
itive effects of immunonutrition support were found in ICU
patients [37, 38]; furthermore, a study including 1223 critically
ill adults showed harmful effects of early administration of a
b
c
d
Fig. 2 Forest plot comparison between EN and EIN for clinical index. a LOS. b Infectious complications. c SSI. d Superficial/deep incisional infection
Braga 20021 preoperative group, Braga 20022 perioperative group b Fig. 2 Forest plot comparison between EN and EIN for clinical index. a LOS. b Infectious complications. c SSI. d Superficial/deep incisional infections,
Braga 20021 preoperative group, Braga 20022 perioperative group Fig. 2 Forest plot comparison between EN and EIN for clinical index. a LOS. b Infectious complications. c SSI. d Superficial/deep incisional infections,
Braga 20021 preoperative group, Braga 20022 perioperative group Int J Colorectal Dis (2018) 33:273–283 280 Fig. 3 Forest plot comparison between PN and PIN for LOS Fig. 3 Forest plot comparison between PN and PIN for LOS EN and PN were two different drug delivery routes. In
general, EN is prior to PN in clinical practice. PN is used immunonutrition support did work for the patients with colo-
rectal cancer. immunonutrition support did work for the patients with colo-
rectal cancer. a
b
c
d
e
f
ig. 4 Forest plot comparison between PN and PIN for laboratory index. a CD8. b IL-6. c CD3. d CD4/CD8. Conclusion only in patients with the following conditions: not feasible
or tolerated for EN, unable to receive and absorb adequate
amounts of oral/enteral feeding for at least 7 days due to
postoperative complications impairing gastrointestinal
function [41]. In this meta-analysis, we also found a dif-
ferent effect between EIN and PIN. EIN mainly improved
the clinical outcomes such as SSI and Superficial/Deep
incisional infection. However, PIN mainly increase the
immune function and reduce inflammation through sever-
al laboratory indices, such as raised level of CD4, CD4/
CD8, and CD3 T lymphocytes and decreased serum level
of IL-6. only in patients with the following conditions: not feasible
or tolerated for EN, unable to receive and absorb adequate
amounts of oral/enteral feeding for at least 7 days due to
postoperative complications impairing gastrointestinal
function [41]. In this meta-analysis, we also found a dif-
ferent effect between EIN and PIN. EIN mainly improved
the clinical outcomes such as SSI and Superficial/Deep
incisional infection. However, PIN mainly increase the
immune function and reduce inflammation through sever-
al laboratory indices, such as raised level of CD4, CD4/
CD8, and CD3 T lymphocytes and decreased serum level
of IL-6. Immunonutrition is beneficial for colorectal cancer pa-
tients undergoing surgery. It may decrease the rate of
postoperative complications, shorten LOS, and enhance
immune function. Immunonutrition could be encouraged
in the clinical treatment. More studies with specific tim-
ings (preoperative, perioperative, and postperative) are
needed for better understanding of immunonutrition in
clinical practice. Use of immunonutrition within an
ERAS may be more effective. Whether immunonutrition
has a long-time effect of patients also needs to be clarified
in future. Enhanced recovery after surgery (ERAS) protocols are de-
signed to accelerate recovery after surgery [42]. Several stud-
ies have demonstrated that ERAS protocols can reduce mor-
bidity and shorten the LOS following colorectal surgery
[43–48]. Two of the included studies evaluated benefits of
immunonutrition on colorectal cancer patients within an
ERAS [23, 24]. The wound infection decreased in both of
the two studies. However, reduction of infectious complica-
tions occurred only in patients undergoing laparoscopic sur-
gery. Those results indicated the potential effect difference of
immunonutrition in patients undergoing laparoscopic and
open surgery. Acknowledgements This work was supported by the National Natural
Science Foundation (81473458, 81473593) and the Jiangsu Qing Lan
Project (JSQL-2014). Conclusion This work was also supported partly by the
Priority Academic Program Development of Jiangsu Higher Education
Institutions (Integration of Chinese and Western Medicine) and the
Project of Clinical Scientific Research of Medicine State Administration
of TCM (JDZX2015089). Open Access This article is distributed under the terms of the Creative
Commons Attribution 4.0 International License (http://
creativecommons.org/licenses/by/4.0/), which permits unrestricted use,
distribution, and reproduction in any medium, provided you give
appropriate credit to the original author(s) and the source, provide a link
to the Creative Commons license, and indicate if changes were made. There are different opinions regarding the mechanisms
of immunonutrition on immune function and inflamma-
tion. Two reports found glutamine could raise secretion
of sIgA in the intestine and prevent the translocation of
intestinal microbiota [49, 50]. Costa et al. [51] found that
supplementation with arginine prevented the increases in
intestinal permeability and bacterial transfer caused by
exertional hyperthermia and indicated that dietary L-
arginine supplementation preserves the integrity of the
intestinal epithelium. Those may be the possible explana-
tion of the positive effect of immunonutrition in patients
with colorectal cancer in this meta-analysis. Discussion e CD4 a
b
c
d
e
f
4 Forest plot comparison between PN and PIN for laboratory index. a CD8. b IL-6. c CD3. d CD4/CD8. e CD4 Int J Colorectal Dis (2018) 33:273–283 281 References J Pharm Pract 24(1):70–77. https://doi.org/10.1177/
0897190010388142 28. Braga M, Gianotti L, Vignali A, Carlo VD (2002) Preoperative oral
arginine and n-3 fatty acid supplementation improves the
immunometabolic host response and outcome after colorectal re-
section for cancer. Surgery 132(5):805–814. https://doi.org/10. 1067/msy.2002.128350 16. Braga M (2012) Perioperative immunonutrition and gut function. Curr Opin Clin Nutr Metab Care 15(5):485–488. https://doi.org/10. 1097/MCO.0b013e3283567d8f 29. Zhu MW, Tang DN, Hou J, Wei JM, Hua B, Sun JH, Cui HY (2012)
Impact of fish oil enriched total parenteral nutrition on elderly pa-
tients after colorectal cancer surgery. Chin Med J 125(2):178–181 17. Klek S, Kulig J, Sierzega M, Szczepanek K, Szybinski P, Scislo L,
Walewska E, Kubisz A, Szczepanik AM (2008) Standard and
immunomodulating enteral nutrition in patients after extended gas-
trointestinal surgery—a prospective, randomized, controlled clini-
cal trial. Clin Nutr 27(4):504–512. https://doi.org/10.1016/j.clnu. 2008.04.010 30. Liang B, Wang S, Ye YJ, Yang XD, Wang YL, Qu J, Xie QW, Yin
MJ (2008) Impact of postoperative omega-3 fatty acid-supplemented
parenteral nutrition on clinical outcomes and immunomodulations in
colorectal cancer patients. World J Gastroenterol 14(15):2434–2439. https://doi.org/10.3748/wjg.14.2434 18. Klek S, Kulig J, Sierzega M, Szybinski P, Szczepanek K, Kubisz A,
Kowalczyk T, Gach T, Pach R, Szczepanik AM (2008) The impact
of immunostimulating nutrition on infectious complications after
upper gastrointestinal surgery: a prospective, randomized, clinical
trial. Ann Surg 248(2):212–220. https://doi.org/10.1097/SLA. 0b013e318180a3c1 31. Song JX, Tu XH, Wang L, Li CJ (2004) Glutamine dipeptide-
supplemented parenteral nutrition in patients with colorectal cancer. Clin Nutr Suppl 1(1):49–53. https://doi.org/10.1016/j.clnu.2004. 07.010 32. Klek S, Szybinski P, Szczepanek K (2014) Perioperative
immunonutrition in surgical cancer patients: a summary of a de-
cade of research. World J Surg 38(4):803–812. https://doi.org/10. 1007/s00268-013-2323-z 19. Senkal M, Zumtobel V, Bauer KH, Marpe B, Wolfram G, Frei A,
Eickhoff U, Kemen M (1999) Outcome and cost-effectiveness of
perioperative enteral immunonutrition in patients undergoing elec-
tive upper gastrointestinal tract surgery: a prospective randomized
study. Arch Surg 134(12):1309–1316. https://doi.org/10.1001/
archsurg.134.12.1309 33. Machon C, Thezenas S, Dupuy AM, Assenat E, Michel F, Mas E,
Senesse P, Cristol JP (2012) Immunonutrition before and during
radiochemotherapy: improvement of inflammatory parameters in
head and neck cancer patients. Supportive Care Cancer 20(12):
3129–3135. https://doi.org/10.1007/s00520-012-1444-5 20. References 1. Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A
(2015) Global cancer statistics, 2012. CA Cancer J Clin 65(2):87–
108. https://doi.org/10.3322/caac.21262 2. Chang HR, Bistrian B (1998) The role of cytokines in the catabolic
consequences of infection and injury. JPEN J Parenter Enteral Nutr
22(3):156–166. https://doi.org/10.1177/0148607198022003156 Several strengths and limitations in this meta-analysis
should be described. Both EN and PN effects on clinical
and laboratory indices were analyzed in this systematic re-
view and meta-analysis, and it could provide the compre-
hensive evaluation of immunonutrition in colorectal cancer
patients after surgery. Even though, there are aspects of this
study that can be improved in future. First, dose of nutrients
is an important factor for the effect of immunonutrition. Nutrient dose in immunonutrition formula was ranged from
3 to 15.8 g/d [25, 28] in EIN vs EN and from 0.2 to 0.4 g/kg/
d in PIN vs PN [30, 31]. In this meta-analysis, we did not
explore the dose-response relation, due to the small number
of included studies; second, population stratification (e.g.,
age, gender, and race) was not evaluated due to lacking of
enough included studies; third, studies in languages except
for English and Chinese were ineligible for inclusion
criteria. 3. Napolitano LM, Faist E, Wichmann MW, Coimbra R (1999)
Immune dysfunction in trauma. Surg Clin North Am 79(6):1385–
1416. https://doi.org/10.1016/S0039-6109(05)70084-0 4. Alexander JW (1998) Immunonutrition: the role of omega-3 fatty
acids. Nutrition 14(7–8):627–633. https://doi.org/10.1016/S0899-
9007(98)00004-5 5. Arends J, Bachmann P, Baracos V, Barthelemy N, Bertz H, Bozzetti
F, Fearon K, Hutterer E, Isenring E, Kaasa S, Krznaric Z, Laird B,
Larsson M, Laviano A, Muhlebach S, Muscaritoli M, Oldervoll L,
Ravasco P, Solheim T, Strasser F, de van der Schueren M, Preiser
JC (2017) ESPEN guidelines on nutrition in cancer patients. Clin
Nutr 36(1):11–48. https://doi.org/10.1016/j.clnu.2016.07.015 6. Glatzle J, Kasparek MS, Mueller MH, Binder F, Meile T, Kreis ME,
Konigsrainer A, Steurer W (2007) Enteral immunonutrition during
sepsis prevents pulmonary dysfunction in a rat model. J
Gastrointest Surg 11(6):719–724. https://doi.org/10.1007/s11605-
007-0144-9 7. Xiong L, Teng JL, Botelho MG, Lo RC, Lau SK, Woo PC (2016)
Arginine metabolism in bacterial pathogenesis and cancer therapy. Int J Mol Sci 17(3):363. https://doi.org/10.3390/ijms17030363 Int J Colorectal Dis (2018) 33:273–283 282 of randomized controlled trials. Surg Oncol 21(2):e87–e95. https://doi.org/10.1016/j.suronc.2012.01.002 8. Evoy D, Lieberman MD, Fahey TJ 3rd, Daly JM (1998)
Immunonutrition: the role of arginine. Nutrition 14(7–8):611–
617. https://doi.org/10.1016/S0899-9007(98)00005-7 23. References Moya P, Soriano-Irigaray L, Ramirez JM, Garcea A, Blasco O,
Blanco FJ, Brugiotti C, Miranda E, Arroyo A (2016)
Perioperative standard oral nutrition supplements versus
Immunonutrition in patients undergoing colorectal resection in an
enhanced recovery (ERAS) protocol: a multicenter randomized
clinical trial (SONVI study). Medicine 95(21):e3704. https://doi. org/10.1097/MD.0000000000003704 9. Klein D, Morris DR (1978) Increased arginase activity during lym-
phocyte mitogenesis. Biochem Biophys Res Commun 81(1):199–
204. https://doi.org/10.1016/0006-291X(78)91649-2 10. Avenell A (2009) Hot topics in parenteral nutrition. Current evi-
dence and ongoing trials on the use of glutamine in critically ill
patients and patients undergoing surgery. Proc Nutr Soc 68(3):
261–268. https://doi.org/10.1017/S0029665109001372 24. Moya P, Miranda E, Soriano-Irigaray L, Arroyo A, Aguilar MD,
Bellon M, Munoz JL, Candela F, Calpena R (2016) Perioperative
immunonutrition in normo-nourished patients undergoing laparo-
scopic colorectal resection. Surg Endosc 30(11):4946–4953. https://
doi.org/10.1007/s00464-016-4836-7 11. Kuhn KS, Muscaritoli M, Wischmeyer P, Stehle P (2010)
Glutamine as indispensable nutrient in oncology: experimental
and clinical evidence. Eur J Nutr 49(4):197–210. https://doi.org/
10.1007/s00394-009-0082-2 25. Sorensen LS, Thorlacius-Ussing O, Rasmussen HH, Lundbye-
Christensen S, Calder PC, Lindorff-Larsen K, Schmidt EB (2014)
Effects of perioperative supplementation with omega-3 fatty acids
on leukotriene B(4) and leukotriene B(5) production by stimulated
neutrophils in patients with colorectal cancer: a randomized,
placebo-controlled intervention trial. Nutrients 6(10):4043–4057. https://doi.org/10.3390/nu6104043 12. Peng ZY, Hamiel CR, Banerjee A, Wischmeyer PE, Friese RS,
Wischmeyer P (2006) Glutamine attenuation of cell death and in-
ducible nitric oxide synthase expression following inflammatory
cytokine-induced injury is dependent on heat shock factor-1 expres-
sion. J Parenter Enter Nutr 30(5):400–406. https://doi.org/10.1177/
0148607106030005400 13. Savarese DM, Savy G, Vahdat L, Wischmeyer PE, Corey B (2003)
Prevention of chemotherapy and radiation toxicity with glutamine. Cancer Treat Rev 29(6):501–513. https://doi.org/10.1016/S0305-
7372(03)00133-6 26. Horie H, Okada M, Kojima M, Nagai H (2006) Favorable effects of
preoperative enteral immunonutrition on a surgical site infection in
patients with colorectal cancer without malnutrition. Surg Today
36(12):1063–1068. https://doi.org/10.1007/s00595-006-3320-8 14. Singleton KD, Wischmeyer PE (2007) Glutamine’s protection
against sepsis and lung injury is dependent on heat shock protein
70 expression. Am J Physiol Regul Integr Comp Physiol 292(5):
R1839–R1845. https://doi.org/10.1152/ajpregu.00755.2006 27. Chen R, Cai JL, Zhou B, Jiang AF (2005) Effect of immune-
enhanced enteral diet on postoperative immunological function in
patients with colorectal cancer. Zhonghua wei chang wai ke za zhi =
Chin J Gastrointes Surg 8(4):328–330 (Chinese) 15. Gerlach AT, Murphy C (2011) An update on nutrition support in the
critically ill. References Lobo DN, Williams RN, Welch NT, Aloysius MM, Nunes QM,
Padmanabhan J, Crowe JR, Iftikhar SY, Parsons SL, Neal KR,
Allison SP, Rowlands BJ (2006) Early postoperative jejunostomy
feeding with an immune modulating diet in patients undergoing
resectional surgery for upper gastrointestinal cancer: a prospective,
randomized, controlled, double-blind study. Clin Nutr 25(5):716–
726. https://doi.org/10.1016/j.clnu.2006.04.007 34. Andrade ME, Santos RD, Soares AD, Costa KA, Fernandes SO, de
Souza CM, Cassali GD, de Souza AL, Faria AM, Cardoso VN
(2016) Pretreatment and treatment with L-arginine attenuate weight
loss and bacterial translocation in dextran sulfate sodium colitis. JPEN J Parenter Enteral Nutr 40(8):1131–1139. https://doi.org/10. 1177/0148607115581374 21. Wong CS, Aly EH (2016) The effects of enteral immunonutrition in
upper gastrointestinal surgery: a systematic review and meta-anal-
ysis. Int J Surg 29:137–150. https://doi.org/10.1016/j.ijsu.2016.03. 043 35. Lorenz KJ, Schallert R, Daniel V (2015) Immunonutrition—the
influence of early postoperative glutamine supplementation in
enteral/parenteral nutrition on immune response, wound healing
and length of hospital stay in multiple trauma patients and patients 22. Zhang Y, Gu Y, Guo T, Li Y, Cai H (2012) Perioperative
immunonutrition for gastrointestinal cancer: a systematic review Int J Colorectal Dis (2018) 33:273–283 283 after extensive surgery. Gms Interdiscip Plast Reconstr Surg
DGPW 4:Doc15. https://doi.org/10.3205/iprs000074 in colorectal surgery. Surgery 149(6):830–840. https://doi.org/10. 1016/j.surg.2010.11.003. 44. Spanjersberg WR, Reurings J, Keus F, van Laarhoven CJ (2011)
Fast track surgery versus conventional recovery strategies for colo-
rectal surgery. Cochrane Database Syst Rev 16(2):CD007635. https://doi.org/10.1002/14651858. 36. Giger-Pabst U, Lange J, Maurer C, Bucher C, Schreiber V,
Schlumpf R, Kocher T, Schweizer W, Krahenbuhl S, Krahenbuhl
L (2013) Short-term preoperative supplementation of an
immunoenriched diet does not improve clinical outcome in well-
nourished patients undergoing abdominal cancer surgery. Nutrition
29(5):724–729. https://doi.org/10.1016/j.nut.2012.10.007 45. Odermatt M, Miskovic D, Flashman K, Khan J, Senapati A,
O'Leary D, Thompson M, Parvaiz A (2015) Major postoperative
complications following elective resection for colorectal cancer de-
crease long-term survival but not the time to recurrence. Color Dis
17(2):141–149. https://doi.org/10.1111/codi.12757 37. Atkinson S, Sieffert E, Bihari D (1998) A prospective, randomized,
double-blind, controlled clinical trial of enteral immunonutrition in
the critically ill. Guy’s hospital intensive care group. Crit Care Med
26(7):1164–1172. https://doi.org/10.1097/00003246-199807000-
00013 46. Lv L, Shao YF, Zhou YB (2012) The enhanced recovery after
surgery (ERAS) pathway for patients undergoing colorectal sur-
gery: an update of meta-analysis of randomized controlled trials. Int J Color Dis 27(12):1549–1554. https://doi.org/10.1007/s00384-
012-1577-5 38. References Bower RH, Cerra FB, Bershadsky B, Licari JJ, Hoyt DB, Jensen
GL, Van Buren CT, Rothkopf MM, Daly JM, Adelsberg BR (1995)
Early enteral administration of a formula (impact) supplemented
with arginine, nucleotides, and fish oil in intensive care unit pa-
tients: results of a multicenter, prospective, randomized, clinical
trial. Crit Care Med 23(3):436–449. https://doi.org/10.1097/
00003246-199503000-00006 47. Lohsiriwat V (2014) Impact of an enhanced recovery program on
colorectal cancer surgery. Asian Pac J Cancer Prev 15(8):3825–
3828. https://doi.org/10.7314/APJCP.2014.15.8.3825 48. Ramírez JM, Blasco JA, Roig JV, Maeso-Martínez S, Casal JE,
Esteban F, Lic DC, Spanish working group on fast track (2011)
Surgery enhanced recovery in colorectal surgery: a multicentre
study. BMC Surg 11:9. https://doi.org/10.1186/1471-2482-11-9 39. Heyland D, Muscedere J, Wischmeyer PE, Cook D, Jones G, Albert
M, Elke G, Berger MM, Day AG, Canadian Critical Care Trials G
(2013) A randomized trial of glutamine and antioxidants in critical-
ly ill patients. N Engl J Med 368(16):1489–1497. https://doi.org/10. 1056/NEJMoa1212722 49. Ren W, Wang K, Yin J, Chen S, Liu G, Tan B, Wu G, Bazer FW,
Peng Y, Yin Y (2016) Glutamine-induced secretion of intestinal
secretory immunoglobulin a: a mechanistic perspective. Front
Immunol 7:503. https://doi.org/10.3389/fimmu.2016.00503 40. McCowen KC, Bistrian BR (2003) Immunonutrition: problematic
or problem solving? Am J Clin Nutr 77(4):764–770 50. Zou XP, Chen M, Wei W, Cao J, Chen L, Tian M (2010) Effects of
enteral immunonutrition on the maintenance of gut barrier function
and immune function in pigs with severe acute pancreatitis. JPEN J
Parenter Enteral Nutr 34(5):554–566. https://doi.org/10.1177/
0148607110362691 41. Weimann A, Braga M, Carli F, Higashiguchi T, Hübner M, Klek S,
Laviano A, Ljungqvist O, Lobo DN, Martindale R, Waitzberg DL,
Bischoff SC, Singer P (2017) ESPEN guideline: clinical nutrition in
surgery. Clin Nutr 36(3):623–650. https://doi.org/10.1016/j.clnu. 2017.02.013 51. Costa KA, Soares AD, Wanner SP, Santos R, Fernandes SO,
Martins Fdos S, Nicoli JR, Coimbra CC, Cardoso VN (2014) L-
arginine supplementation prevents increases in intestinal perme-
ability and bacterial translocation in male Swiss mice subjected to
physical exercise under environmental heat stress. J Nutr 144(2):
218–223. https://doi.org/10.3945/jn.113.183186 42. Wilmore DW, Kehlet H (2001) Management of patients in fast track
surgery. BMJ 322(7284):473–476. https://doi.org/10.1136/bmj. 322.7284.473 43. Adamina M, Kehlet H, Tomlinson GA, Senagore AJ, Delaney CP
(2011) Enhanced recovery pathways optimize health outcomes and
resource utilization: a metaanalysis of randomized controlled trials
|
https://openalex.org/W2559993133
|
https://uwe-repository.worktribe.com/preview/904991/AUA%20paper%20-%20final%20anon.pdf
|
English
| null |
Evaluating outreach activities: overcoming challenges through a realist ‘small steps’ approach
|
Perspectives
| 2,016
|
cc-by
| 5,511
|
Abstract: Practitioners are being placed under increasing pressure to evaluate the success of their outreach
activities, both by government and by their own universities. Based in a reductionist doctrine of
‘evidence-based practice’, there is a desire to demonstrate the effectiveness and value-for-money
across activities that now account for around £175 million per year across England. This article
examines some of the difficulties in evaluating the complex social world of outreach and suggests
a ‘small steps’ approach to overcome some of these. This uses the idea of a transformative
‘theory of change’ as a framework for understanding the particular contribution made by discrete
activities within a wider portfolio, providing a more reliable form of inference than attempts to
‘prove’ impact over longer timeframes. Introduction For some time, there has been concern about the effectiveness of outreach activities (e.g. summer
schools, university taster days and mentoring schemes) that are designed to encourage
disadvantaged individuals to apply to higher education. This is perhaps inevitable for any high-
profile and high-cost social policy, especially during a period of austerity; the latest figures show
outreach activities totalling nearly £175 million in England (Office for Fair Access [OFFA], 2016). The recent national strategy document lays out a clear expectation: ‘It is essential to understand which approaches and activities have the greatest impact, and
why. An improved evidence base, and a robust approach to evaluation, are critical in
helping the sector and partners to understand which of their activities are most effective
and have the greatest impact on access, student success and progression, so enabling
effort to be focused on these areas’ (Department of Business, Innovation and Skills [BIS],
2014, p.9). With slightly softer rhetoric, the recent OFFA strategic plan makes a similar point, signalling its
intent to use ‘…an evidence-based approach to more actively challenge and engage with universities and
colleges to make sustained and faster progress towards their targets across the student
lifecycle’ (OFFA, 2015, p.12). This fits within a wider doctrine of ‘evidence-based practice’ in education, sometimes colloquially
known as ‘what works’. The idea is simple: to focus resources on activities that have strong
evidence for effectiveness. The reality is significantly more problematic, as generating
unequivocal evidence in complex social fields is notoriously difficult (Donaldson, Christie and
Mark, 2009; Pawson, 2013; Lingenfelter, 2016). Outreach is clearly such a field, with its long
timescales, diverse settings and myriad influences. This complexity is exacerbated without a clear definition of ‘effectiveness’ in place. Current
government policy aims ‘to double the proportion of people from disadvantaged backgrounds
entering university in 2020 compared to 2009’ (BIS, 2016, p. 54), additionally focusing on increasing the proportion entering elite universities. Conversely, individual universities are duty
bound to direct their outreach activities towards meeting the requirements of the Access
Agreements that they negotiate with OFFA. These are generally couched in competitive terms of
meeting recruitment targets of disadvantaged students to that specific university (McCaig, 2015;
Rainford, in press). Senior university managers are inevitably keen to avoid censure (or worse)
from OFFA and ensure that their admissions remain buoyant, alongside wider social justice
motivations. Introduction The tension here is obvious: a university can meet its targets (and ostensibly be effective) for
recruiting disadvantaged students without impacting at all on the national targets if it is simply
capturing a greater share of the existing applicant pool; a ‘zero sum game’ where outreach is
conflated with recruitment and universities seek easy wins, leading to few additional students
being encouraged into higher education. This ‘confusion of successes’ is an added challenge to
practitioners: is it success against institutional or national targets that matters – effectiveness for
one university or for society in general? Outreach activities are often focused on changing attitudes to higher education by, for example,
making it appear desirable, achievable or ‘normal’. However, other changes may also occur in
terms of knowledge, behaviours or social relations. This article therefore focuses on evaluating
whether and how activities lead to change. This change could be the explicit intention to enter
higher education or, more likely, an intermediate state such as increased motivation at school,
having a clear career goal or developing more self-confidence. ‘Effectiveness’ is used hereafter in
an informal sense of judging the amount of change which can be ascribed to an activity. In other
words, it is an assessment of what did happen with respect to participants relative to what would
have happened otherwise – often described as the ‘counterfactual’ situation. Similarly, ‘causality’
is used informally to indicate the certainty that an activity is directly responsible for this change. These complexities underline the need for a considered and critical approach to evaluation that
generates credible claims to knowledge. This article is aimed at those expected to generate or
assess such claims, including researchers, practitioners, university managers and experienced
evaluators applying their expertise to outreach activities. It draws on the findings of the recent
Assessing Impact and Measuring Success project led by the authors (removed for review). Inter
alia, this study found that 32 percent of university outreach managers had concerns about the quality of evidence available to them, while 91 percent were seeking to improve their evaluation
processes. This article is methodologically agnostic, concerning itself instead with broad principles that can
usefully underpin all forms of evaluation. It might appropriately be positioned within the ‘realist’
tradition developed and advocated by Pawson (2006, 2013) which engages with the intricate
realities of how human choices are made within complex social fields. Introduction In particular, it looks at how
we might better understand the impact of outreach in terms of transformational changes that are
reflected in the choices made by young people who have been subject to deeply-ingrained
educational inequalities. It also obliquely questions whether an evaluative focus on institutionally-
driven ideas of success is actually a distraction from the wider issues of social justice that outreach
is intended to address. Five challenges for evaluating outreach This section briefly explores five key epistemological challenges that are inherent within
evaluations of outreach work and which any successful approach needs to consider, mitigate as far
as possible and preferably overcome. They are not intended to be exhaustive, but rather a
starting point for critiquing any proposed approach, including the tracking and trials approaches
outlined above; indeed, the former are likely to be susceptible to 1 and 3, while the latter are
more likely to be challenged by 2, 4 and 5. Dominant approaches to outreach evaluation At the time of writing, two approaches to evaluating outreach work are attaining a form of
dominance in the field, yet both have shortcomings: The ‘tracking’ approach. This has widespread support among current practitioner-
managers (removed for review) and is generally based on collecting data on individuals
over time with respect to (a) their involvement in activities, (b) their changing attitudes and
choices, and (c) school outcomes including qualifications. These data are then used to
explore the effectiveness of individual activities or a whole programme by identifying how
attitudes and behaviours shift in step with outreach activities. The ‘trials’ approach. This is emerging as a ‘borrowing’ from medicine and seeks to use
techniques like randomised controlled trials to isolate a direct causal effect of activities. This has historically strong support in the US, albeit that there are growing critical voices
about its claims (e.g. Bickman and Reich, 2009; Scriven, 2016; Lingenfelter, 2016). It is not
currently widely used in the UK, although some practitioners believe it offers something of
a ‘gold standard’ (removed for review). 1. Selection and self-selection biases A longstanding tenet of outreach is to target activities at individuals within identified
disadvantaged groups who are felt likely to benefit from them (e.g. Department for Education and
Employment, 2000; BIS, 2014). This is clearly appropriate in seeking to overcome structural
educational inequalities by providing more support to those most in need, but it is heightened
further where resources are constrained. From the evaluation perspective, this creates a strong
selection bias within any data collected. The participants are not representative of the school or
area from which they are drawn, but form a rarefied subgroup that have been selected for a
particular purpose – i.e. because they are deemed to be potentially ‘in the market’ for higher
education. This is further complicated where targeted young people, their families or their schools are able to
absent themselves from the activity, either through a choice to opt-out (e.g. a refusal to
participate) or a failure to opt-in – whether active (e.g. not completing a form) or passive (e.g. not
being aware of the activity). If an activity requires an opt-in or where there are significant
numbers of opt-outs, then self-selection bias is layered on top of the selection bias outlined above. Those families already positively predisposed towards education are likely to disproportionately
take up opportunities compared to those ‘hard-to-reach’ families who might benefit more but
who may be less likely to participate due to various forms of exclusion (Boag-Munroe and
Evangelou, 2012). Evaluations which seek to compare the (self-)selected group with an unselected group as a
counterfactual analysis are therefore likely to be fallacious and will usually over-estimate
effectiveness as the two groups are likely to have different demographic profiles and pre-activity
attitudes towards education. 2. Priming and social desirability effects The challenge with evaluating activities designed to shift attitudes is that young people very
quickly become attuned to the idea that there are a ‘correct’ collection of attitudes to express to
practitioners, teachers and parents. This is a form of social desirability bias; a well-attested
phenomenon in social research whereby the participant will reproduce what they understand to
be the required responses in order to please, impress or reassure the researcher. This potentially
compromises both the reliability and validity of the evaluation data collected from young people
about their educational experiences (Bowman and Seifert, 2011) Similarly, if a young person has been engaged in an activity that is designed to impart certain
knowledge about higher education, it is likely that they will reflect this back to evaluators and
others in the short term, especially if they are also asked about what they will do in the future. In
the context of outreach, a taster day is very likely to generate short-term results that suggest an
increased likelihood of attending university as this has been the purpose of the day and the events
are fresh in the young person’s mind. Unless it is effectively internalised or regularly reinforced,
this priming will fade over time as the information and experiences fall out of memory. As a
result, the effectiveness of activities are likely to appear greater the closer in time the data are
collected. 3. Deadweight and leakage The linked phenomena of leakage and deadweight are relevant to any social policy which is
predicated on targeting certain individuals, including participation in higher education (removed
for review). Leakage occurs when the targeting method fails and relatively advantaged individuals are
erroneously included within the target group. Aside from the wastage of resources, this is
challenge for evaluation as it will tend to cause an over-estimation of an activity’s effectiveness by
capturing individuals who were always likely to apply to university. This might occur, for example,
where relative advantaged children in a school serving a disadvantaged area are included in
general classroom-based activities. Deadweight is a more complex idea. It relates to the targeting of individuals who meet the
relevant criteria of disadvantage, but who would have followed the desired path without the
activity; in other words, a disadvantaged young person who is already on the pathway to higher
education without the need for outreach activities, even if they themselves are not aware of it at
the time. Clearly, this is very difficult to assess from the practitioner’s perspective, as it involves
engaging with future decisions yet to be made by a young person who cannot know at, say, the
age of 13 what their intentions will turn out to be at the age of 17. In this instance, changes in reported intention can be erroneously assigned to activities that
happen to coincide, without there being a causal relationship. In particular, this is a risk when
evaluating lengthy programmes of activities that occur over several years, which can appear very
effective simply by selecting high-achieving, but disadvantaged, young people who would almost
certainly have progressed anyway (Croll and Attwood, 2013). The inability to predict future
choices makes the construction of a viable comparison group problematic; indeed, improving this
prediction would be a useful goal for future research. 4. Complexity and bounded rationality Social fields like participation in higher education are inherently complex. It is, however, easy to
slip into a reductionist mindset of viewing outreach activities as quasi-scientific interventions,
where a specific stimulus leads inexorably to a measurable result (Doyle and Griffin, 2012;
Pawson, 2013). Within this mindset, the objective of the practitioner is to devise the ‘right’
portfolio of activities and the role of the evaluator is to confirm ‘what works’ by demonstrating
unequivocal causal changes. The reality is very different. The lives of all young people are ‘messy’ as they are buffeted by
myriad experiences and influences – some planned, but many accidental. The beliefs and
expectations of their families, schools and communities will shape their own attitudes and
ambitions. The intersection of their gender and ethnicity will also play a role, as will other social
factors like disability or sexuality. All of these elements are then mediated through the prism of
personality – itself mutable in the process of becoming an adult. Furthermore, Simon’s (e.g. 1979, 1997) seminal work on bounded rationality compelling asserts
the limits of human decision-making. This is not to say that young people are inherently irrational,
but that their decisions about higher education will be dictated by the information available to
them, their own subjective priorities, the time available and judgements about likelihoods and
risk. Humans also tend to make intuitive decisions that are grounded in emotions and a range of
unconscious heuristics (Kahneman, 2003). Given this complexity of environment and decision-making, the idea of an outreach activity having
a predictable causal outcome on a young person’s decisions appears thoroughly misguided. Activities will affect certain groups or individuals more than others – indeed, they may be actively
negative for some. Similarly, the impact may be positive from the perspective of the practitioner
in one element (e.g. raising motivation for schoolwork), but negative in another (e.g. making
apprenticeships seem more attractive than university). The same activity run twice with different
individuals or in different places may well have markedly different outcomes. This complexity means that effectiveness of activities will never be static or predictable. An
activity can only be judged to have been successful at one time and in one context – and probably
only with some of the participants (Pawson, 2013). This must limit the inferences that can be
drawn about effectiveness and the life expectancy of those inferences. 5. Confounding factors and non-linearity 4. Complexity and bounded rationality It also makes conclusions
about certain types of activity in the abstract particularly problematic – e.g. a claim that ‘summer
schools are effective’ – especially as every university will provide their own ‘flavour’ of the activity
with different staff and resources (Hoare and Mann, 2014). 5. Confounding factors and non-linearity From its inception, outreach has generally been conceived as a process rather than as a single
event in time. It is assumed, probably rightly, that shifting the knowledge, beliefs, attitudes and
behaviours of young people takes concerted effort over a series of encounters – especially where
there are ingrained expectations from their families, their schools or their communities acting to
prevent that change (Gorard et al., 2006). In its most extreme incarnations, it is a ten-year process
spanning mid primary through to late secondary schooling. In a related point to the previous one, one temptation may be to seek to evaluate changes in
young people over this time period as if the efforts of practitioners are the only influence when, in
reality, there are many confounding factors at work. In particular, the impact of the school and its
teachers, where young people spend far more time than in outreach activities, are very likely to
effect changes to knowledge about and attitudes towards higher education (Winterton and Irwin,
2012; Fuller, 2014). Within a long-term, but punctuated, programme of activities, there is a risk of
erroneously ascribing changes to those activities rather than what might occur in between: is it the
activities offered that are effective or the day-to-day influence of teachers? It may even be the
ongoing partnership between a university and a school which impacts on the knowledge,
expectations and ethos embodied in the latter, rather than any direct effect of activities. Within a structured and long-term series of activities with a young person, there is also the risk of
assuming that there is a linear and positive cumulative effect over time – i.e. that each activity
goes a little way further to tipping them towards higher education. This is likely to be fallacious. As noted earlier, some activities may have negative effects from the perspective of higher
education (e.g. by suggesting alternative routes) or may only have an effect months later when
reflected upon, perhaps in conjunction with other experiences. Alternatively, two activities might
only prove effective when offered several months apart, providing mutual reinforcement, with
neither being effective in isolation. This non-linearity makes conclusions about causality and
effectiveness problematic. Realist evaluation As a springboard, this article uses Pawson’s (2006, 2013) idea of ‘realist’ evaluation. This approach
places the individual’s choices at the heart of the evaluation, ‘recognising that the fate of social
policy lies in the real choices of choice makers and [evaluation’s] task is to explain the distribution
and consequences of those choices’ (Pawson, 2013, p. 71). Human choice is seen as the driving
force for changes in behaviour, so the purpose of an activity is to provide circumstances where
changes can take place. The idea of direct causality between activity and change is dismissed as
simplistic in a complex social field with multiple confounding influences. In particular, it rejects
‘medicalised’ approaches to evaluation that derive from a basic stimulus-effect model of human
behaviour. Pawson (2006, p.25) emphasises the ‘messiness’ of social fields and argues that the
only appropriate question is ‘What works for whom and in what circumstances?’, rather than
seeking authoritative statements about effectiveness that are decontextualized from people,
setting or time: ‘the ludicrous idea that evaluators and researchers are able to tell policy-makers
and practitioners exactly what works in the world of policy interventions’ (ibid, p.170). A key idea of realist evaluation is that a planned activity within a social field is the embodiment of
a ‘theory of change’ – it represents some conception of how an individual might be ‘moved’ from
one state to another. This might be a deliberate process, based in the expertise of the practitioner
or social theory, or a tacit one based on beliefs, prior experiences or borrowing from elsewhere. Pawson sees this transformational theory of change as being the focus of evaluation rather than
the outcomes of the activity, with the purpose of evaluation being to interrogate and hone this
theory. This approach embraces the inherent complexity of fields like outreach and the bounds on
human rationality, with a desire to understand the complex web of factors as work and how to
influence them, rather than seeking to ignore or eliminate them in pursuit of simplistic causal
relationships and dubious measures of effectiveness. Realist evaluation Realist evaluation rejects this as likely to
create misleading results with over-confident conclusions, while remaining silent on how to
improve practice: ‘There is […] no concealing the reality that the same intervention can trigger change in
myriad ways, and no way of camouflaging the truth that the different contexts in which
programmes are implemented are as wide as society is wide’ (Pawson, 2013, pp. 29-30). A ‘small steps’ approach This section outlines a potential alternative approach, broadly within the realist tradition, to both
conceiving and evaluating outreach activity based on ‘small steps’. This is intended to signal a
partial rejection both of long-term tracking (although this may have value for understanding key
junctures at which change occurs) and of unwieldy and over-engineered trials (although they may
have some value in evaluating short-term activities). It also denotes a conceptualisation of
participation in higher education as a process with many intermediate steps which young people
take and which evaluators must heed. It attempts to provide a means of addressing issues of effectiveness while overcoming some of the
challenges outlined above. It is methodologically neutral, in that it is compatible with a range of
data collection methods – both quantitative and qualitative – which need to be designed around
the intervention, the participant group and the practitioners involved. Rather, we suggest five
principles to guide how evaluation is conceived and undertaken, relating to theories of change,
measurement, causality, timescales and disadvantage: Articulation of a clear theory of change. Outreach activities are, at their heart, about
causing change within individuals. If practitioners expect to cause change, then they need
to have a clear articulation of the mechanisms by which they expect this to occur at the
individual level – a theory of change. As well as attending to outcomes, which is an
obvious concern of evaluation, the starting point of the individual needs to be recognised
alongside a deep engagement with psychological, sociological and psychosocial processes;
indeed, the first and last of these have been somewhat neglected within theorisations of
participation in general. For example, practitioners wanting to ‘raise aspirations’ need to
be clear what an aspiration is, how it is formed and how it is crystallised in reference to
others. This clarity then provides a framework for evaluation which focuses on individual
and group processes in sequence (i.e. a logic chain). The theory of change can then be
evaluated in terms of its effectiveness in describing processes and predicting outcomes, to
be further honed through reflective practice and empirical research. Criticality about causality. The complexity and non-linearity outlined above is problematic
for drawing strong conclusions about an activity and its causal effects on individuals. The trial approach attempts to resolve this by focusing on the outcomes of participants relative
to a (preferably randomised) group of non-participants. A ‘small steps’ approach If well-executed, this can provide
some evidence as to whether an intervention is effective (self-selection, priming and
confounding issues notwithstanding), but not the more important question of why it is
effective. This sort of evaluation risks reducing activities to a form of ‘magic box’ where
nothing is known about the processes within it. Indeed, it may fail to identify if the
effective element is incidental to the activity rather than integral to it – e.g. the personal
relationships developed alongside the activity. Instead, we advocate evaluating the
success of activities in terms of these intermediate processes – i.e. the logic chain within
the theory of change. In general, the research community knows surprisingly little about
the effects of interventions on educational disadvantage (Gorard and See, 2013). Instead,
much is assumed by practitioners and it is in these areas of small change that evaluations
focusing on causality might best be used. Criticality about measurability. While some of the measures used to understand widening
participation are broadly reliable and valid (e.g. examination results or the submission of a
university application), many are more subjective and readily contestable. In particular,
evaluations often rely on easily-collected self-reports of attitudes and future intentions
from young people (or teachers and parents) – measuring the measurable. Validity here is
very uncertain, especially given priming and social desirability effects. In order to ensure
evaluation through measures with strong reliability and internal validity, we suggest
eschewing attitudinal measures in favour of those based on knowledge or behaviours – e.g. asking about the number of university websites visited rather than a possible future
intention to apply. Future research may be able to reveal which of such measures are
strongly correlated with future behaviours and can therefore be used as a proxy. Greater
use of pre/post and quasi-experimental designs are also likely to support a more robust
approach to the identification of changes. Using appropriate timescales. There is a tension between evaluating individual activities
over a short time period and evaluating whole programmes over very long periods,
potentially measured in years. While the desire for the latter is understandable, we
suggest that it is probably unattainable due to complexity and the dominance of the
confounding factors in young people’s lives, as well as the difficulty in undertaking a counterfactual analysis. A ‘small steps’ approach Where there certainly is value is in tracking young people’s
attitudes at regular points in time, with appropriate distance from major activities to
mitigate social desirability and priming effects. Instead, we suggest that evaluative efforts
are focused on individual activities. If a robust theory of change for each activity is
evidenced and there is an overarching theory of change for the integrated programme,
then there is unlikely to be a need to evaluate the programme as a whole – and efforts to
do so are likely to be vexed for the reasons discussed above. It is more important to have
confidence in each intervention in its own terms, relative to its theory of change, especially
in universities which employ a ‘pick and mix’ approach where young people receive a
varying portfolio of activities built around their unique needs. A focus on educational disadvantage. Evidence is building that differences in participation
rates between socioeconomic groups results from the accumulated educational
disadvantages faced by some young people, rather than being an issue around aspirations
in the late-teenage years (e.g. Crawford, 2014; Whitty, Hayton and Tang, 2015). As such, it
is not only morally important that outreach should address itself more directly to these
structural inequalities, but it provides a useful distinction between effectiveness as
conceived as challenging disadvantage as opposed to success in recruitment for a specific
university; we suggest that evaluation also needs to recognise this distinction. Inequalities
in attainment are clearly key, but other areas that have been somewhat neglected include
challenging negative expectations from adults surrounding young people, broadening
career horizons and providing high-quality advice and guidance (removed for review). Conclusion This article does not seek to provide a toolkit for evaluation, but rather to identify challenges to be
mitigated and principles that are likely to underpin effective evaluation practice. We do not claim
that the ‘small steps’ approach we advocate provides a full solution to the vexed issues outlined in
the first half of the article. However, we do feel that it does provide a sounder basis than the
existing and emerging orthodoxies with their focus on excessive timeframes or certifying ‘the best’
interventions. Perhaps the most important element of this is the focus on the social and individual
theory of change embodied within an activity. In particular, our approach respects the role of practitioners as reflective professionals who, with help from evaluators, can refine their theories
of change and the resulting practices. We have contextualised our small steps approach within a period of policy that is marked by what
we have typified as a ‘confusion of successes’. On the one hand, the recent White Paper (BIS,
2016) commits to doubling participation rates for disadvantaged young people, however the main
policy levers used on individual universities instils a competitive market where targets can just as
easily be met by targeted recruitment activities as those designed to challenge educational
inequalities. We believe this risks distorting evaluation activity to focus on attempts to
demonstrate value-for-money against simplistic and inward-looking institutional recruitment
outcomes (removed for review). Our final point, then, is to encourage practitioners to refocus
their evaluative efforts back on effectiveness in addressing structural educational inequalities, in
particular through improving young people’s attainment, broadening the educational and
occupational opportunities available to them and offering guidance to help them realise their
ambitions. References References Bickman, L. and S. Reich. 2009. Randomized controlled trials: a gold standard with feet of clay? In
S. Donaldson, C. Christie and M. Mark (eds.) What counts as credible evidence in applied
research and evaluation practice? Thousand Oaks: Sage. Boag-Munroe, G. and M. Evangelou. 2012. From hard to reach to how to reach: A systematic
review of the literature on hard-to-reach families. Research Papers in Education 27(2): 209-
239. Bowman, N. and T. Seifert. 2011. Can college students accurately assess what affects their learning
and development? Journal of College Student Development 52(3): 270-290. Crawford, C. 2014. The link between secondary school characteristics and university participation
and outcomes. London: DFE. Croll, P. and Attwood, G. 2013. Participation in higher education: aspirations, attainment and
social background. British Journal of Educational Studies 61(2): 187-202. Department for Business, Innovation and Skills [BIS]. 2014. National strategy for access and
student success in higher education. London: BIS. Department for Business, Innovation and Skills [BIS]. 2014. National strategy for access and
student success in higher education. London: BIS. Department for Business, Innovation and Skills [BIS]. 2016. Success as a knowledge economy:
teaching excellence, social mobility and student choice. London: BIS. Department for Business, Innovation and Skills [BIS]. 2016. Success as a knowledge economy:
teaching excellence, social mobility and student choice. London: BIS. Department for Education and Employment. 2000. The Excellence Challenge. London: DFEE. Donaldson, S., Christie, C. and Mark, M. (eds.) 2009. What counts as credible evidence in applied
research and evaluation practice? Thousand Oaks: Sage. Doyle, M. and M. Griffin. 2012. Raised aspirations and attainment? A review of the impact of
Aimhigher (2004–2011) on widening participation in higher education in England. London
Review of Education 10(1): 75-88. Fuller, C. 2014. Social capital and the role of trust in aspirations for higher education. Educational
Review, 66(2): 131-147. Gorard, S., N. Adnett, H. May, K. Slack, E. Smith and L. Thomas. 2006. Overcoming the barriers to
higher education. Stoke-on-Trent: Trentham. Gorard, S. and B.H. See. 2013. Overcoming disadvantage in education. Abingdon: Routledge. Gorard, S. and B.H. See. 2013. Overcoming disadvantage in education. Abingdon: Routledge. Hoare, T. and R. Mann. 2012. The impact of the Sutton Trust’s Summer Schools on subsequent
higher education participation. London: Sutton Trust. Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American Hoare, T. and R. Mann. 2012. The impact of the Sutton Trust’s Summer Schools on subsequent
higher education participation. References London: Sutton Trust. Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American
Economic Review 93(5): 1449-1475. Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American
Economic Review 93(5): 1449-1475. Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American
Economic Review 93(5): 1449-1475. Lingenfelter, P. 2016. “Proof”, policy and practice: understanding the role of evidence in improving
education. Sterling: Stylus Publishing. Lingenfelter, P. 2016. “Proof”, policy and practice: understanding the role of evidence in improving
education. Sterling: Stylus Publishing. McCaig, C. 2015. Marketisation and widening participation in English higher education: a critical
discourse analysis of institutional access policy documents. Higher Education Review 48(1): 6- McCaig, C. 2015. Marketisation and widening participation in English higher education: a critical
discourse analysis of institutional access policy documents. Higher Education Review 48(1): 6-
24 24. Office for Fair Access [OFFA]. 2015. Strategic plan: 2015-2020. Bristol: OFFA. Office for Fair Access [OFFA]. 2016. Outcomes of access agreement monitoring for 2014-15. Bristol: OFFA. Pawson, R. 2006. Evidence-based policy: a realist perspective. London: Sage. P
R 2013 Th
i
f
l
ti
li t
if
t
L
d
S Pawson, R. 2006. Evidence-based policy: a realist perspective. London: Sage. Pawson, R. 2013. The science of evaluation: a realist manifesto. London: Sage. Pawson, R. 2013. The science of evaluation: a realist manifesto. London: Sage. Rainford, J. In press. Targeting of widening participation measures by elite institutions: widening
access or simply aiding recruitment? Awaiting publication in Perspectives: Policy and Practice
in Higher Education. DOI: 10.1080/13603108.2016.1148645 Scriven, M. 2016. Roadblocks to recognition and revelation. American Journal of Evaluation 37(1):
27-44. Simon, H. 1979. Rational decision-making in business organisations. American Economic Review
69(4): 493-513. Simon, H. 1979. Rational decision-making in business organisations. American Economic Review
69(4): 493-513. Simon, H. 1997. An empirically based microeconomics. Cambridge: Cambridge University Press. Simon, H. 1997. An empirically based microeconomics. Cambridge: Cambridge University Press. Winterton, M. and Irwin, S. 2012. Teenage expectations of going to university: the ebb and flow of
influences from 14 to 18. Journal of Youth Studies 15(7): 858-874. Winterton, M. and Irwin, S. 2012. Teenage expectations of going to university: the ebb and flow of
influences from 14 to 18. Journal of Youth Studies 15(7): 858-874. Whitty, G., A. Hayton and S. Tang. 2015. References Who you know, what you know and knowing the ropes: a
review of evidence about access to higher education institutions in England. Review of
Education 3 (1): 27-67. Whitty, G., A. Hayton and S. Tang. 2015. Who you know, what you know and knowing the ropes: a
review of evidence about access to higher education institutions in England. Review of
Education 3 (1): 27-67.
|
https://openalex.org/W2734390751
|
https://europepmc.org/articles/pmc5512781?pdf=render
|
English
| null |
Modelling infectious diseases with relapse: a case study of HSV-2
|
Theoretical biology and medical modelling
| 2,017
|
cc-by
| 13,590
|
*Correspondence:
toshikazu.kuniya@gmail.com
3Department of Applied
Mathematics, Graduate School of
System Informatics, Kobe University,
1-1 Rokkodai-cho, Nada-ku,
657-8501 Kobe, Japan
Full list of author information is
available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the
Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://
creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
DOI 10.1186/s12976-017-0059-4 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
DOI 10.1186/s12976-017-0059-4 Abstract Background: Herpes Simplex Virus Type 2 (HSV-2) is one of the most common
sexually transmitted diseases. Although there is still no licensed vaccine for HSV-2, a
theoretical investigation of the potential effects of a vaccine is considered important
and has recently been conducted by several researchers. Although compartmental
mathematical models were considered for each special case in the previous studies, as
yet there are few global stability results. Results: In this paper, we formulate a multi-group SVIRI epidemic model for HSV-2,
which enables us to consider the effects of vaccination, of waning vaccine immunity,
and of infection relapse. Since the number of groups is arbitrary, our model can be
applied to various structures such as risk, sex, and age group structures. For our model,
we define the basic reproduction number ℜ0 and prove that if ℜ0 ≤1, then the
disease-free equilibrium is globally asymptotically stable, whereas if ℜ0 > 1, then the
endemic equilibrium is so. Based on this global stability result, we estimate ℜ0 for
HSV-2 by applying our model to the risk group structure and using US data from 2001
to 2014. Through sensitivity analysis, we find that ℜ0 is approximately in the range of
2-3. Moreover, using the estimated parameters, we discuss the optimal vaccination
strategy for the eradication of HSV-2. Conclusions: Through discussion of the optimal vaccination strategy, we come to the
following conclusions. (1) Improving vaccine efficacy is more effective than increasing
the number of vaccines. (2) Although the transmission risk in female individuals is
higher than that in male individuals, distributing the available vaccines almost equally
between female and male individuals is more effective than concentrating them within
the female population. Keywords: Multi-group SVIRI epidemic model, Relapse, Basic reproduction number,
Global asymptotic stability, Herpes Simplex Virus Type 2, Vaccination Jinliang Wang1, Xiaoqing Yu1, Heidi L. Tessmer2, Toshikazu Kuniya3* and Ryosuke Omori2,4 Jinliang Wang1, Xiaoqing Yu1, Heidi L. Tessmer2, Toshikazu Kuniya3* and Ryosuke Omori2,4 Background Herpes Simplex Virus Type 2 (HSV-2) is one of the most common sexually trans-
mitted diseases, and has infected about 417 million people aged 15-49 worldwide [1]. Although there is still no licensed vaccine for HSV-2, a theoretical investigation of
the potential effects of a vaccine is considered important and has recently been con-
ducted by several researchers (see [2–4]). In [2, 3], compartmental epidemic models
with vaccination for HSV-2 were considered and the effectiveness of the vaccina-
tion was discussed in connection with the basic reproduction number ℜ0 (see [5]) Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 2 of 20 through numerical simulations. However, there was little discussion about the stability
of each equilibrium. As observed in several papers on epidemic models with vaccina-
tion (see, for instance, [6–8]), backward bifurcation can occur at ℜ0 = 1 for some
special models and ℜ0
< 1 does not necessarily imply the global asymptotic sta-
bility of the disease-free equilibrium, that is, the eradication of the disease. In that
case, the vaccination effort solely to make ℜ0
<
1 has less significance. There-
fore, a global stability analysis is critical for theoretically justifying the epidemiological
discussion. In [4], Lou et al. considered a compartmental epidemic model for HSV-2 with age
and risk group structures and discussed the effectiveness of the vaccination together
with the global stability analysis of each equilibrium. In their study, the vaccination
was limited to female individuals, who are known to be the high-risk group for HSV-
2, and it was concluded that such a vaccination strategy can reduce the total infections
in both females and males. However, to support their conclusion, we need to consider
a more general model in which male individuals can also benefit from the vaccina-
tion and show that the optimal distribution ratio of the vaccines is 1 to 0 for female
and male individuals. In this paper, we consider such a general model and investi-
gate the optimal distribution ratio of the vaccines. As opposed to their conclusion,
our result shows that distributing the vaccines almost equally to females and males is
more effective for the eradication of HSV-2 than concentrating them within the female
population. Background To consider the effect of vaccination with imperfect immunity, SVIR epidemic models
are often formulated, in which the total population is subdivided into the suscepti-
ble (S), vaccinated (V), infective (I) and recovered (R) populations (see, for instance,
[2, 6–10]). However, to take into account the relapse of HSV-2 (see [2, 11]), it is
necessary to also consider a direct transition from R to I. Thus, in this paper, we
formulate a multi-group SVIRI epidemic model for HSV-2, which enables us to con-
sider the effects of vaccination, of waning vaccine immunity, and of infection relapse. Since the number of groups is arbitrary, our model can be applied to various struc-
tures such as risk, sex, and age group structures. In the empirical portion of this
paper, we apply our model to the risk group structure and estimate the basic reproduc-
tion number ℜ0 for HSV-2 by using data from the US from 2001 to 2014. Since the
infective population of HSV-2 seems to be in endemic equilibrium, the estimation of
ℜ0 must be carried out under the global asymptotic stability of the endemic equilib-
rium. However, in general, the global asymptotic stability of the endemic equilibrium is
not trivial. Recently, multi-group epidemic models have been studied by many authors
[10, 12–24]. One of the most effective approaches for global stability analysis of multi-
group epidemic models is the graph-theoretic approach developed by Guo et al. [14]. Since our model has a quite complex form with the paths from V to S (the wan-
ing of vaccine-induced immunity), R to I (relapse) and distributed time delay, the
global asymptotic stability analysis is challenging. In this paper, by applying the graph-
theoretic approach as in [14] together with an approach of max function as in [10], we
prove that if ℜ0 > 1, then the endemic equilibrium is globally asymptotically stable,
whereas if ℜ0 ≤1, then the disease-free equilibrium is so. Based on this theoretical
result, we estimate ℜ0 for HSV-2 by using US data from 2001 to 2014. By using the Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 3 of 20 estimated parameters, we discuss the optimal vaccination strategy for the eradication
of HSV-2. The general multi-group SVIRI epidemic model (A6) The survival probability for recovered individuals in group i ∈N , who spent time t
in the recovered class, is Pi(t) := exp(−
t
0 δi(η)dη), where δi(η) denotes the relapse
risk for individuals who spent time η in the recovered class in group i. For each
i ∈N , δi ∈L1
loc,+(0, +∞) and
+∞
0
δi(η)dη = +∞. (A6) The survival probability for recovered individuals in group i ∈N , who spent time t
in the recovered class, is Pi(t) := exp(−
t
0 δi(η)dη), where δi(η) denotes the relapse
risk for individuals who spent time η in the recovered class in group i. For each
i ∈N , δi ∈L1
loc,+(0, +∞) and
+∞
0
δi(η)dη = +∞. (A6) The survival probability for recovered individuals in group i ∈N , who spent time t
in the recovered class, is Pi(t) := exp(−
t
0 δi(η)dη), where δi(η) denotes the relapse
risk for individuals who spent time η in the recovered class in group i. For each
i ∈N , δi ∈L1
loc,+(0, +∞) and
+∞
0
δi(η)dη = +∞. Under assumptions (A1)-(A2), we see that the time variation of Ni(t), i ∈N is governed
by the following differential equation: N′
i(t) = bi −μiNi(t), i ∈N . (1) N′
i(t) = bi −μiNi(t), i ∈N . (1) From the variation of constants formula, we easily see that limt→+∞Ni(t) = bi/μi =:
N∗
i , i ∈N . Hence, without loss of generality, we can assume that Ni(t) ≡N∗
i , i ∈N . Then, under assumptions (A1)-(A4), we obtain the differential equations for Si(t) and
Vi(t), i ∈N as follows: From the variation of constants formula, we easily see that limt→+∞Ni(t) = bi/μi =:
N∗
i , i ∈N . Hence, without loss of generality, we can assume that Ni(t) ≡N∗
i , i ∈N . Then, under assumptions (A1)-(A4), we obtain the differential equations for Si(t) and
Vi(t), i ∈N as follows: S′
i(t) =bi −Si(t)
n
j=1
βij
Ij(t)
N∗
j
−(μi + vi) Si(t) + ωiVi(t),
(2)
V ′
i (t) =viSi(t) −σiVi(t)
n
j=1
βij
Ij(t)
N∗
j
−(μi + ωi) Vi(t). The general multi-group SVIRI epidemic model The general multi-group SVIRI epidemic model Let n ∈N be the number of groups and let N
:= {1, 2, · · · , n}. Let Ni(t) be the
sexually active population in group i ∈N at time t. Let us divide Ni(t) into four sub-
populations: susceptible Si(t), vaccinated Vi(t), infective Ii(t), and recovered Ri(t). Thus,
Ni(t) = Si(t) + Vi(t) + Ii(t) + Ri(t) for all i ∈N . We make the following assumptions: (A1) The number of individuals becoming sexually active in group i ∈N per unit time
is bi > 0. (A1) The number of individuals becoming sexually active in group i ∈N per unit time
is bi > 0. (A2) The per capita rate of removal from the sexual activity in group i ∈N is μi > 0. (A3) The coefficient for disease transmission from infective individuals in group j ∈N
to uninfected (susceptible or vaccinated) individuals in group i ∈N is βij ≥0. The
matrix (βij)i,j∈N is irreducible. The vaccine efficacy in group i ∈N is σi ∈[0, 1]
and the force of infection to vaccinated individuals in group i ∈N is weakened by
multiplying σi. That is, (A3) The coefficient for disease transmission from infective individuals in group j ∈N
to uninfected (susceptible or vaccinated) individuals in group i ∈N is βij ≥0. The
matrix (βij)i,j∈N is irreducible. The vaccine efficacy in group i ∈N is σi ∈[0, 1]
and the force of infection to vaccinated individuals in group i ∈N is weakened by
multiplying σi. That is, λS
i (t) :=
n
j=1
βij
Ij(t)
Nj(t) and λV
i (t) :=σi
n
j=1
βij
Ij(t)
Nj(t),
i ∈N are the forces of infection to susceptible and vaccinated individuals in group i ∈N
at time t ≥0, respectively. Here we assume standard incidence. (A4) The per capita vaccination rate for susceptible individuals in group i ∈N is vi >
0. The per capita rate for the waning of vaccine-induced immunity for vaccinated
individuals in group i ∈N is ωi ≥0. (A5) The per capita recovery rate of infective individuals in group i ∈N is γi > 0. (A5) The per capita recovery rate of infective individuals in group i ∈N is γi > 0. The general multi-group SVIRI epidemic model (3) S′
i(t) =bi −Si(t)
n
j=1
βij
Ij(t)
N∗
j
−(μi + vi) Si(t) + ωiVi(t),
(2) (2) V ′
i (t) =viSi(t) −σiVi(t)
n
j=1
βij
Ij(t)
N∗
j
−(μi + ωi) Vi(t). (3) (3) Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
Page 4 of 20 Biology and Medical Modelling (2017) 14:13
Page 4 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
Page 4 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
Page 4 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 4 of 20 Under assumptions (A5)-(A6), the recovered population in group i ∈N at time t is given by Under assumptions (A5)-(A6), the recovered population in group i ∈N at time t is given by Ri(t) =
+∞
0
γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ
=
t
−∞
γiIi(ξ)e−μi(t−ξ)e−
t−ξ
0
δi(η)dηdξ,
i ∈N . (4) =
t
−∞
γiIi(ξ)e−μi(t−ξ)e−
t−ξ
0
δi(η)dηdξ,
i ∈N . (4) (4) By differentiating (4), we obtain the following integro-differential equation for Ri(t), i ∈N . R′
i(t) =γiIi(t) −μiRi(t) −
t
−∞
δi(t −ξ)γiIi(ξ)e−μi(t−ξ)e−
t−ξ
0
δi(η)dηdξ
=γiIi(t) −μiRi(t) −
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ. (5) (5) From (1)-(5) we obtain the integro-differential equation for Ii(t), i ∈N as follows. I′
i(t) = (Si(t) + σiVi(t))
n
j=1
βij
Ij(t)
N∗
j
−(μi + γi)Ii(t)
+
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ. Under this setting, we arrive at the following main model in this paper. ⎧
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩
S′
i(t) = bi −Si(t)
n
j=1
βij
Ij(t)
N∗
j
−(μi + vi)Si(t) + ωiVi(t),
V ′
i (t) = viSi(t) −σiVi(t)
n
j=1
βij
Ij(t)
N∗
j
−(μi + ωi) Vi(t),
I′
i(t) = (Si(t) + σiVi(t))
n
j=1
βij
Ij(t)
N∗
j
−(μi + γi)Ii(t)
+
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ,
i ∈N . (6) (6) +
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ,
i ∈N . Note that the differential equation of Ri(t), i ∈N can be omitted since it does not appear
in the above three equations. The equilibria of system (6) can be obtained as the solution of the following algebraic
equations. The general multi-group SVIRI epidemic model ⎧
⎪⎪⎪⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎪⎪⎪⎩
0 = bi −Si
n
j=1
βij
Ij
N∗
j −(μi + vi)Si + ωiVi,
0 = viSi −σiVi
n
j=1
βij
Ij
N∗
j −(μi + ωi) Vi,
0 = (Si + σiVi)
n
j=1
βij
Ij
N∗
j −(μi + γi −Qi)Ii,
i ∈N ,
(7) (7) where Qi :=
+∞
0
δi(ξ)γie−μiξe−
ξ
0 δi(η)dηdξ,
i ∈N . Note that Note that Qi <γi
+∞
0
δi(ξ)e−
ξ
0 δi(η)dηdξ = γi
−e−
ζ
0 δi(η)dη+∞
0
= γi,
i ∈N . Hence, we have μi + γi −Qi > 0 for all i ∈N . Hence, we have μi + γi −Qi > 0 for all i ∈N . Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 5 of 20 It is easy to see that the trivial solution of (7) such that Ii = 0 for all i ∈N always
exists. It is called the disease-free equilibrium of system (6) and we write it as E0 :=
S0
1, V 0
1 , 0, S0
2, V 0
2 , 0, · · · , S0
n, V 0
n, 0
∈R3n
+ , where S0
i := bi
μi
μi + ωi
μi + vi + ωi
,
V 0
i :=
vi
μi + ωi
S0
i = bi
μi
vi
μi + vi + ωi
,
i ∈N . Existence of the endemic equilibrium E∗:=
S∗
1, V ∗
1 , I∗
1, · · · , S∗
n, V ∗
n , I∗
n
∈R3n
+ such that
I∗
i > 0 for all i ∈N will be discussed in connection with the basic reproduction number
ℜ0, which is defined as the expected number of secondary cases produced by a typical
infected individual during its entire period of infectiousness at the initial invasion phase
into a fully susceptible population, and given by the spectral radius of the next generation
matrix (see [25]). Let F :=
⎛
⎜⎜⎝
S0
1 + σ1v0
1
β11
N∗
1 · · ·
S0
1 + σ1v0
1
β1n
N∗n
... ... ... S0
n + σnv0
n
βn1
N∗
1 · · ·
S0
n + σnv0
n
βnn
N∗n
⎞
⎟⎟⎠and V := diag
1≤i≤n
(μi + γi −Qi) . The general multi-group SVIRI epidemic model Then, according to [25], the next generation matrix is given by K := FV−1 =
⎛
⎜⎜⎜⎝
S0
1+σ1V 0
1
β11
(μ1+γ1−Q1)N∗
1 · · ·
S0
1+σ1V 0
1
β1n
(μn+γn−Qn)N∗n
... ... ... (S0
n+σnV 0
n)βn1
(μ1+γ1−Q1)N∗
1 · · · (S0
n+σnV 0
n)βnn
(μn+γn−Qn)N∗n
⎞
⎟⎟⎟⎠. K := FV−1 =
⎛
⎜⎜⎜⎝
S0
1+σ1V 0
1
β11
(μ1+γ1−Q1)N∗
1 · · ·
S0
1+σ1V 0
1
β1n
(μn+γn−Qn)N∗n
... ... ... (S0
n+σnV 0
n)βn1
(μ1+γ1−Q1)N∗
1 · · · (S0
n+σnV 0
n)βnn
(μn+γn−Qn)N∗n
⎞
⎟⎟⎟⎠. Hence, the basic reproduction number ℜ0 is defined by Hence, the basic reproduction number ℜ0 is defined by Hence, the basic reproduction number ℜ0 is defined by ℜ0 := ρ(K),
(8) (8) ℜ0 := ρ(K), where ρ(·) denotes the spectral radius of a matrix. We will obtain the global stability
results for (6) in connection with ℜ0 (see the “Results” section). The special multi-group SVIRI epidemic model for HSV-2 The general model (6) can be applied to analyze the field data of HSV-2 epidemics. Sim-
ilar to other sexually transmitted infections, the risk factor for HSV-2 infection is sexual
behavior. To describe the heterogeneity of HSV-2 infection risk between host individu-
als, we characterize the group as the combination of sex and their sexual behavior. We
consider the following levels of sexual activity: x = 0, 1, 2, · · · , 5 meaning the number of
sexual partners within the last 12 months, where x = 5 implies the number of sexual part-
ners is 5 or more. Let y ∈{1, 2} denote the sex, 1 denotes male and 2 denotes female. Then,
the risk group is characterized by i ∈{1, 2, · · · , 12} in the following way: i = 2xi + yi,
where (xi, yi) =
(m −1, 1) if i = 2m −1,
(m −1, 2) if i = 2m,
m = 1, 2, · · · , 6. For example, i = 2 corresponds to (xi, yi) = (0, 2) and implies the group of female indi-
viduals with no sexual partners and i = 11 corresponds to (xi, yi) = (5, 1) and implies
the group of male individuals with 5 or more sexual partners. Then, (6) can be written as
follows: Page 6 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 ⎧
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩
S′
i(t) = bi −Si(t)
12
j=1
βij
Ij(t)
N∗
j
−(μi + vi)Si(t) + ωiVi(t),
V ′
i (t) = viSi(t) −σiVi(t)
12
j=1
βij
Ij(t)
N∗
j
−(μi + ωi) Vi(t),
I′
i(t) = (Si(t) + σiVi(t))
12
j=1
βij
Ij(t)
N∗
j
−(μi + γi)Ii(t)
+
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ,
i ∈{1, 2, · · · , 12}. (9) (9) ⎪⎪⎪⎩i ∈{1, 2, · · · , 12}. Note that (9) is a special case of (6). In this section, we assume that δi(ξ) ≡δi > 0 for all
i ∈{1, 2, · · · , 12}. Note that the assumption (A6) is satisfied. In this case, we have: Note that (9) is a special case of (6). In this section, we assume that δi(ξ) ≡δi > 0 for all
i ∈{1, 2, · · · , 12}. Note that the assumption (A6) is satisfied. The special multi-group SVIRI epidemic model for HSV-2 In this case, we have: +∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ =δi
+∞
0
γiIi(t −ξ)e−μiξe−δiξdξ
=δiRi(t),
i ∈{1, 2, · · · , 12}. Hence, together with the Eq. 5 of Ri(t), (9) can be simplified to the following multi-group
SVIRI epidemic model. Hence, together with the Eq. 5 of Ri(t), (9) can be simplified to the following multi-group
SVIRI epidemic model. ⎧
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩
S′
i(t) = bi −Si(t)
12
j=1
βij
Ij(t)
N∗
j
−(μi + vi)Si(t) + ωiVi(t),
V ′
i (t) = viSi(t) −σiVi(t)
12
j=1
βij
Ij(t)
N∗
j
−(μi + ωi) Vi(t),
I′
i(t) = (Si(t) + σiVi(t))
12
j=1
βij
Ij(t)
N∗
j
−(μi + γi)Ii(t) + δiRi(t),
R′
i(t) = γiIi(t) −(μi + δi) Ri(t),
i ∈{1, 2, · · · , 12}. (10) (10) Vi(t))
12
j=1
βij
Ij(t)
N∗
j
−(μi + γi)Ii(t) + δiRi(t), No vaccine against HSV-2 infection is currently available, so we ignore the vaccinated
class Vi, i ∈{1, 2, · · · , 12} in the estimation of ℜ0. Then, (10) can be rewritten as follows. ⎧
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩
S′
i(t) = bi −Si(t)
12
j=1
βij
N∗
j
Ij(t) −μiSi(t),
I′
i(t) = Si(t)
12
j=1
βij
N∗
j
Ij(t) −(μi + γi)Ii(t) + δiRi(t),
R′
i(t) = γiIi(t) −(μi + δi) Ri(t),
i ∈{1, 2, · · · , 12}. (11) (11) The basic reproduction number ℜ0 for (11) is obtained as the spectral radius of the
following matrix. The basic reproduction number ℜ0 for (11) is obtained as the spectral radius of the
following matrix. ⎛
⎜⎜⎜⎝
S0
1
μ1+γ1−Q1
β1,1
N∗
1
· · ·
S0
1
μ12+γ12−Q12
β1,12
N∗
12
... ... ... S0
12
μ1+γ1−Q1
β12,1
N∗
1
· · ·
S0
12
μ12+γ12−Q12
β12,12
N∗
12
⎞
⎟⎟⎟⎠, Biology and Medical Modelling (2017) 14:13
P Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 7 of 20 where Qi = δiγi/(μi + δi) and we write βij as βi,j for improved readability. where Qi = δiγi/(μi + δi) and we write βij as βi,j for improved readability. where Qi = δiγi/(μi + δi) and we write βij as βi,j for improved readability. Transmission rates between the risk groups i and j, βij, depend on sexual behavior and
sex. We modeled βij as follows; βij = ρxiyiρxjyjRxixjSyiyj. The special multi-group SVIRI epidemic model for HSV-2 (12) (12) βij = ρxiyiρxjyjRxixjSyiyj. The meaning of each symbol for βij is as follows. The meaning of each symbol for βij is as follows. The meaning of each symbol for βij is as follows. • ρxiyi denotes the HSV-2 infection risk for the risk group i. The risk group is stratified
by sex and the number of partners within the last 12 months, the risk group i denotes
the individuals whose number of partners within the last 12 months is xi and sex is yi. ρxiyi is given by; ρxiyi = cyi(xi + 1)φ. ρxiyi = cyi(xi + 1)φ. Here, similar to previous modelling studies of sexually transmitted infections, we
modeled the relationship between infection risk and sexual behavior by a power law
function [26]. Here, similar to previous modelling studies of sexually transmitted infections, we
modeled the relationship between infection risk and sexual behavior by a power law
function [26]. • c denotes the sex specific HSV-2 transmission coefficient. • φ denotes the exponent parameter describing the heterogeneity of the infection risk
between different sexual behaviors. • R denotes the mixing matrix between the risk groups defined by sexual behavior, x; • R denotes the mixing matrix between the risk groups defined by sexual behavior, x; Rxixj = qδxixj + (1 −q)
y ρxyNxy
x
y ρxyNxy
. This is the classical one-parameter ‘preferred mixing’ formulation, proposed by [2 This is the classical one-parameter ‘preferred mixing’ formulation, proposed by [27]. • δ denotes Kronecker’s delta. • δ denotes Kronecker’s delta. • δ denotes Kronecker’s delta. • q denotes assortative coefficient. When q = 0, the mixing between risk groups
defined by sexual behavior is ‘proportionately mixing’, and the mixing is ‘fully
assortative mixing’ when q = 1. • q denotes assortative coefficient. When q = 0, the mixing between risk groups
defined by sexual behavior is ‘proportionately mixing’, and the mixing is ‘fully
assortative mixing’ when q = 1. • S denotes the mixing matrix between sexes; • S denotes the mixing matrix between sexes; • S denotes the mixing matrix between sexes; S =
a
1 −a
1 −a
a
. • a denotes the proportion of homosexual behavior. • a denotes the proportion of homosexual behavior. The special multi-group SVIRI epidemic model for HSV-2 We will use the special model (11) with transmission rate (12) to estimate the basic
reproduction number ℜ0 for HSV-2 (see the “Results” section), and (10) with (12) to
discuss the effectiveness of vaccination strategy (see the “Discussion” section). For the proofs of Proposition 1 and Theorem 1, see the Appendix. For the proofs of Proposition 1 and Theorem 1, see the Appendix. Theorem 1 still works for (10) since it is a special case of (6). In particular, although (10)
does not include the integrated time delay, to our knowledge, there is no previous study
on the global asymptotic stability of the endemic equilibrium of model (10). From this
viewpoint, our main theorem can be regarded as valuable for the empirical study in the
subsequent sections. The main theorem The main theorem of this paper is obtained for the general multi-group SVIRI epidemic
model (6). Since (6) has an infinite time delay, we define the fading memory space (see,
for instance, [28, 29]) as follows: C
:=
φ ∈C((−∞, 0] ; R+) : φ(s)e
s is uniformly continuous on(−∞, 0] ,
sup
s≤0
|φ(s)|e
s < +∞
,
(13) C
:=
φ ∈C((−∞, 0] ; R+) : φ(s)e
s is uniformly continuous on(−∞, 0] ,
sup
s≤0
|φ(s)|e
s < +∞
,
(13) (13) Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
Page 8 of 20 Biology and Medical Modelling (2017) 14:13
Page Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 8 of 20 where
is a positive constant such that 0 <
< mini∈N {μi}. Let us define the following
state space for system (6): where
is a positive constant such that 0 <
< mini∈N {μi}. Let us define the following
state space for system (6): :=
ψ1, ψ2, · · · , ψn, ˜ψ1, ˜ψ2, · · · , ˜ψn, φ1(·), φ2(·), · · · , φn(·)
∈R2n
+ × Cn
:
0 < ψi < S0
i , 0 < ˜ψi < V 0
i , φi(0) > 0,
0 < ψi + ˜ψi + φi(0) < bi
μi
, i ∈N
. (14) (14) The following proposition is proved: The following proposition is proved: The following proposition is proved: Proposition 1 is positively invariant for system (6). Proposition 1 is positively invariant for system (6). The main theorem of this paper is as follows. Theorem 1 Let ℜ0 and be defined by (8) and (14), respectively. Let ¯ denote the
closure of . (i)
If ℜ0 ≤1, then the disease-free equilibrium E0 ∈
¯ of system (6) is globally
asymptotically stable in and there exists no endemic equilibrium E∗in ¯. (ii)
If ℜ0 > 1, then the system (6) has the unique endemic equilibrium E∗in and it is
globally asymptotically stable in . Estimation of ℜ0 for HSV-2 Based on Theorem 1, we estimate the basic reproduction number ℜ0 for HSV-2
in the US from 2001 to 2014. For the estimation of ℜ0, we use the special model
(11) with transmission rate (12). Note that (11) corresponds to the case where vi =
σi
=
ωi
=
0 for all i
∈
{1, 2, · · · , 12}. Although the case where vi
=
0 for
all i
∈
{1, 2, · · · , 12} is excluded under assumption (A4), it is easy to check in a
completely similar way as in the Appendix that the global stability result similar to
Theorem 1 holds. Previous study derived the value of δi and γi from empirical data, δi and γi are param-
eterized based on [30], 1/δi = 78.5 days and 1/γi = 13 days for all i ∈{1, 2, · · · , 12}. Here note that we can regard μi as the removal rate from our system, which is given
by the sum of the sexual-inactivation rate and the mortality rate among those who
are sexually active. We assume that the sexual life span is 50 years (15-65 years old)
and parameterize the mortality rate by the national representative census data in the
US [31], μi = 0.0231 per year for all i ∈{1, 2, · · · , 12}. Based on the previous stud-
ies [32] and [33], we obtain the estimations q = 0.3 and a = 0.02, respectively
(see Table 1). Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 9 of 20 Table 1 The model parameters and related estimates
Parameter
Meaning
Value
Reference
δi (i = 1, 2, · · · , 12)
Relapse risk
1/78.5
[30]
γi (i = 1, 2, · · · , 12)
Recovery rate
1/13
[30]
μi (i = 1, 2, · · · , 12)
Rate of removal from sexual activity
0.0231
[31]
q
Assortative coefficient
0.3
[32]
a
Proportion of homosexual behavior
0.02
[33]
c1
Transmission coefficient for male
0.228
Estimated
c2
Transmission coefficient for female
1.78
Estimated
φ
Exponent parameter
0.700
Estimated
ℜ0
Basic reproduction number
2.07
Estimated Using the observed data of sero-prevalence of HSV-2 in the US from 2001 to 2014
reported by [34], sex specific transmission coefficient c and the exponent parameter φ
were estimated by maximum likelihood estimation. Estimation of ℜ0 for HSV-2 The estimated c are, transmission coefficient for male, c1 = 0.228 (95% CI 0.225
to 0.231), transmission coefficient for female, c2 = 1.78 (95% CI 1.75 to 1.81), exponent
parameter φ = 0.700 (95% CI 0.693 to 0.707) and estimated ℜ0 = 2.07 (95% CI 2.03 to 2.11). Sexual behavior shows wide variation between host individuals. To assess the sensitivity
of sexual behavior to ℜ0 of HSV-2, we conducted a sensitivity analysis of the parameters
describing sexual behavior, i.e., the proportion of homosexual partnership a and assorta-
tivity coefficient for the mixing between risk groups q. Fig. 2 shows the relation of a and q
to estimated ℜ0, ℜ0 increase if i) a increases, and ii) q decreases. The realistic variations
of a and q [36, 37] can induce the variation of ℜ0, which is approximately demonstrated
in the range of 2-3. Sexual behavior shows wide variation between host individuals. To assess the sensitivity
of sexual behavior to ℜ0 of HSV-2, we conducted a sensitivity analysis of the parameters
describing sexual behavior, i.e., the proportion of homosexual partnership a and assorta-
tivity coefficient for the mixing between risk groups q. Fig. 2 shows the relation of a and q
to estimated ℜ0, ℜ0 increase if i) a increases, and ii) q decreases. The realistic variations
of a and q [36, 37] can induce the variation of ℜ0, which is approximately demonstrated
in the range of 2-3. Estimation of ℜ0 for HSV-2 Since the antibody against HSV-2
infection (IgG) provides life-long immunity [35], we fitted I+R to the observed data of the
number of sero-positive cases for the estimation of c and φ. To estimate c and φ, endemic
equilibria of Ii and Ri were solved numerically with varied c1 and c2 and φ, and the set of
c1 and c2 maximizing the likelihood function was explored. The likelihood function for c1
and c2 is given by L(c1, c2, φ) =
T
i pmf
bin
Ndata
i,T , I∗
i (ci, c2, φ) + R∗
i (c1, c2, φ)
N∗
i
, Pdata
i,T
. Here pmf denotes the probability mass function, bin denotes a binomial distribution,
Ndata
i,T
denotes the observed data of the size of the risk group i in sampling year T, and Pdata
i,T
denotes the observed data of the number of HSV2-seropositive cases in the risk group i in
sampling year T, respectively. For the confidence interval (CI) of the estimated parameter,
profile likelihood-based confidence intervals were calculated. Using estimated c and φ the
basic reproduction number ℜ0 for HSV-2 in the US was calculated. Figure 1 shows the
comparison between the observed data of sero-prevalence of HSV-2 and the model esti-
mates. The estimated c are, transmission coefficient for male, c1 = 0.228 (95% CI 0.225
to 0.231), transmission coefficient for female, c2 = 1.78 (95% CI 1.75 to 1.81), exponent
parameter φ = 0.700 (95% CI 0.693 to 0.707) and estimated ℜ0 = 2.07 (95% CI 2.03 to 2.11). Here pmf denotes the probability mass function, bin denotes a binomial distribution,
Ndata
i,T
denotes the observed data of the size of the risk group i in sampling year T, and Pdata
i,T
denotes the observed data of the number of HSV2-seropositive cases in the risk group i in
sampling year T, respectively. For the confidence interval (CI) of the estimated parameter,
profile likelihood-based confidence intervals were calculated. Using estimated c and φ the
basic reproduction number ℜ0 for HSV-2 in the US was calculated. Figure 1 shows the
comparison between the observed data of sero-prevalence of HSV-2 and the model esti-
mates. Discussion Using the demographic and epidemiological parameters obtained above, we discuss the
effectiveness of each vaccination strategy. We investigate the sensitivity of the basic repro-
duction number ℜ0 to the vaccination parameters, that is, the vaccination rate among Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
Page 10 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 10 of 20 1.0
0.8
0.4
0.2
0.0
0.6
0
1
2
3
4
5+
The number of partner within 12 months
Sero-prevalence of HSV-2 among male
1.0
0.8
0.4
0.2
0.0
0.6
Sero-prevalence of HSV-2 among female
The number of partner within 12 months
0
1
2
3
4
5+
a
b
2001-2002
2003-2004
2005-2006
2007-2008
2009-2010
2011-2012
2013-2014
2001-2002
2003-2004
2005-2006
2007-2008
2009-2010
2011-2012
2013-2014
Year
Year
Estimate
Estimate
Fig. 1 Comparison between the observed data of sero-prevalence of HSV-2 and the model estimates 1.0
0.8
0.4
0.2
0.0
0.6
0
1
2
3
4
5+
Sero-prevalence of HSV-2 among male
a
2001-2002
2003-2004
2005-2006
2007-2008
2009-2010
2011-2012
2013-2014
Year
Estimate The number of partner within 12 months
1.0
0.8
0.4
0.2
0.0
0.6
Sero-prevalence of HSV-2 among female
The number of partner within 12 months
0
1
2
3
4
5+
b
2001-2002
2003-2004
2005-2006
2007-2008
2009-2010
2011-2012
2013-2014
Year
Estimate
Fig. 1 Comparison between the observed data of sero-prevalence of HSV-2 and the model estimates b The number of partner within 12 months Fig. 1 Comparison between the observed data of sero-prevalence of HSV-2 and the model estimates susceptible population v and the vaccination efficacy σ. Here we have assumed that vac-
cination is conducted with the same rate v for the susceptible population over time. For
simplicity, we assume that the efficacy of vaccine σ is the same for all risk groups. We first consider the case that vaccination rate v is the same between males and
females. In this case, the basic reproduction number ℜ0 with different σ when v varies
over (0, 1) is shown in Fig. 3. We see from Fig. 3 that, if σ is 0.3 or smaller, ℜ0 can
be less than 1. On the other hand, if σ is 0.4 or larger, ℜ0 cannot be less than 1
for any v ∈(0, 1). Discussion This implies that decreasing σ is more important than increasing 5
4
3
2
1
The basic reproduction number R0
The proportion of homo-sexual partnerships a
0.02
0.04
0.06
0.08
0.0
0.1
0.2
0.3
0.4
0.5
5
4
3
2
1
The basic reproduction number R0
Assortativity coefficient q
a
b
Fig. 2 Sensitivity analysis with respect to the parameters describing sexual behavior a and q 5
4
3
2
1
The basic reproduction number R0
The proportion of homo-sexual partnerships a
0.02
0.04
0.06
0.08
0.0
a 0.1
0.2
0.3
0.4
0.5
5
4
3
2
1
The basic reproduction number R0
Assortativity coefficient q
b b Fig. 2 Sensitivity analysis with respect to the parameters describing sexual behavior a and q Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 11 of 20 Fig. 3 The relation of v to estimated ℜ0 with different σ v to reduce the basic reproduction number ℜ0. That is, improving the vaccine effi-
cacy is more important for the eradication of HSV-2 than increasing the number of
vaccines. We next discuss the optimal sex ratio of the vaccinated population to control HSV-2. HSV-2 infection is observed among females more frequently than males, “opportunistic”
vaccination can induce higher vaccination coverage among females than males. To assess
the optimal sex ratio of the vaccination rate, we expand the vaccination rate v as follows; v1 = pv,
v2 = (1 −p)v,
v : total vaccination rate. Conclusion In this paper, we have formulated the multi-group SVIRI epidemic model (6), which
enables us to consider the effects of vaccination, the waning of vaccine-induced immunity,
and relapse. We have defined the basic reproduction number ℜ0 and proved Theorem 1,
which states that if ℜ0 ≤1, then the disease-free equilibrium E0 is globally asymp-
totically stable, whereas if ℜ0 > 1, then the endemic equilibrium E∗is so. Based on
Theorem 1, we have estimated the basic reproduction number ℜ0 for HSV-2 as 2.07
(95% CI 2.03 to 2.11) by using US HSV-2 data from 2001 to 2014. Through the sen-
sitivity analysis for uncertain parameters on sexual behavior, we have found that ℜ0
is approximately in the range of 2-3. Furthermore, using sensitivity analysis for vacci-
nation parameters, we have discussed the effectiveness of the vaccination. As a result,
we have come to the following conclusions. (1) Improving vaccine efficacy is more
effective than increasing the number of vaccines. (2) Although the transmission risk in
female individuals is higher than that in male individuals, distributing vaccines almost
equally to females and males is more effective than concentrating them within the female
population. v1 = pv,
v2 = (1 −p)v,
v : total vaccination rate. Here p denotes the sex ratio of vaccination. Figure 4 shows the relationship between p,
σ and ℜ0, we assumed v = 0.9 as the representative value. Interestingly, small or large p
increases ℜ0. This implies that vaccination biased to females (small p) or males (large p)
can result in persistence of the disease. In particular, it is noteworthy that the curves in
Fig. 4 are almost symmetric with respect to p and the minimum is attained near the center
p = 0.5. This implies that vaccination distributed equally to females and males is optimal
for the eradication of the disease even though the transmission coefficient for males is
lower than that for females. Fig. 4 The relation of p and σ to estimated ℜ0 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 12 of 20 We define the following matrix, which corresponds to the next generation matrix: We define the following matrix, which corresponds to the next generation matrix: M0 := V−1F =
⎛
⎜⎜⎜⎝
S0
1+σ1V 0
1
β11
(μ1+γ1−Q1)N∗
1 · · ·
S0
1+σ1V 0
1
β1n
(μ1+γ1−Q1)N∗n
... ... ... (S0
n+σnV 0
n)βn1
(μn+γn−Qn)N∗
1 · · · (S0
n+σnV 0
n)βnn
(μn+γn−Qn)N∗n
⎞
⎟⎟⎟⎠. (16) (16) In fact, it is easy to see that ρ(M0) = ρ(K) = ℜ0. In fact, it is easy to see that ρ(M0) = ρ(K) = ℜ0. In fact, it is easy to see that ρ(M0) = ρ(K) = ℜ0. First we show that system (6) has no endemic equilibrium E∗∈¯. Let us define the
following matrix-valued function on R2n, which is equal to M0 if (S1, V1, · · · , Sn, Vn) =
(S0
1, V 0
1 , · · · S0
n, V 0
n): M(S1, V1, · · · , Sn, Vn) :=
⎛
⎜⎜⎝
(S1+σ1V1)β11
(μ1+γ1−Q1)N∗
1 · · ·
(S1+σ1V1)β1n
(μ1+γ1−Q1)N∗n
... ... ... (Sn+σnVn)βn1
(μn+γn−Qn)N∗
1 · · ·
(Sn+σnVn)βnn
(μn+γn−Qn)N∗n
⎞
⎟⎟⎠. Suppose that (S1, · · · , Sn) ̸= (S0
1, · · · , S0
n). Then, from assumptions (A1)-(A6), we see
that 0 < M(S1, V1, · · · , Sn, Vn) < M0, where 0 denotes the zero matrix and the
inequality implies that it holds for each element and each of the two matrices are not
equal. Then, since it follows from assumptions (A1)-(A6) that matrices M0 and M0 +
M(S1, V1, · · · , Sn, Vn) are nonnegative and irreducible, we can apply the Perron-Frobenius
theorem (see [38, Corollary 2.1.5]) to obtain that ρ (M(S1, V1, · · · , Sn, Vn)) < ρ(M0) ≤1. This implies that the equation M(S1, V1, · · · , Sn, Vn) (I1, · · · In)T = (I1, · · · In)T has only
the trivial solution (I1, · · · , In)T = 0, where T denotes the transpose of a vector. This
implies that E∗does not exist in ¯. Next we show the global asymptotic stability of E0. It follows from the Perron-
Frobenius theorem (see [38, Theorem 2.1.4]) that M0 has a strictly positive left
eigenvector (ℓ1, · · · , ℓn), ℓi
> 0, i ∈N corresponding to the eigenvalue ρ(M0):
(ℓ1, · · · , ℓn) ρ(M0) = (ℓ1, · · · , ℓn) M0. Proof of Proposition 1 Theoretical Biology and Medical Modelling (2017) 14:13 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 13 of 20 The boundedness of the solution of system (6) immediately follows from the fact that
N′
i(t) = bi−μiNi(t), S′
i(t) ≤bi−(μi+vi)Si(t)+ωiVi(t) and V ′
i (t) ≤viSi(t)−(μi+ωi)Vi(t)
for all t > 0 and i ∈N . This completes the proof. Proof of Proposition 1 We first show the positivity of the solution of system (6). Suppose that there exist t1 > 0
and i∗∈N such that Si(t) > 0 and Vi(t) > 0 for all t ∈[ 0, t1) and i ∈N and
min (Si∗(t1), Vi∗(t1)) = 0. By the variation of constants formula, we have from the first
equation in the system (6) that Si∗(t1) =Si∗(0)e
−
t1
0
n
j=1 βi∗jIj(s)/N∗
j +μi∗+vi∗
ds
+
t1
0
(bi∗+ ωi∗Vi∗(s)) e
−
t1
s
n
j=1 βi∗jIj(u)/N∗
j +μi∗+vi∗
duds > 0. Hence, Vi∗(t1) = 0. However, by the variation of constants formula, we have from the
second equation in the system (6) that Hence, Vi∗(t1) = 0. However, by the variation of constants formula, we have from the
second equation in the system (6) that Vi∗(t) =Vi∗(0)e
−
t1
0
σi∗ n
j=1 βi∗jIj(s)/N∗
j +μi∗+ωi∗
ds
+
t1
0
vi∗Si∗(s)e
−
t1
s
σi∗ n
j=1 βi∗jIj(u)/N∗
j +μi∗+ωi∗
duds > 0, which is a contradiction. Hence, we see that Si(t) > 0 and Vi(t) > 0 for all t > 0 and
∈N . which is a contradiction. Hence, we see that Si(t) > 0 and Vi(t) > 0 for all t > 0 and
i ∈N . Suppose that there exist t2 > 0 and ˜i ∈N such that Ii(t) > 0 for all t ∈[ 0, t2) and i ∈N
and I˜i(t2) = 0. By the variation of constants formula, we have from the third equation in
the system (6) that Ii(t) =Ii(0)e−(μi+γi)t +
t
0
⎛
⎝(Si(s) + σiVi(s))
n
j=1
βij
Ij(s)
N∗
j
+ hi(s)
⎞
⎠e−(μi+γi)(t−s)ds, (15) where hi(t) :=
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ. We see that hi(t) ≥0 for all i ∈N
and t ∈[0, t1). Hence, from (15), we have I˜i(t2) > 0, which is a contradiction. Hence, we
see that Ii(t) > 0 for all t > 0 and i ∈N . where hi(t) :=
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ. We see that hi(t) ≥0 for all i ∈N
and t ∈[0, t1). Hence, from (15), we have I˜i(t2) > 0, which is a contradiction. Hence, we
see that Ii(t) > 0 for all t > 0 and i ∈N . Wang et al. We define the following matrix, which corresponds to the next generation matrix: Theoretical Biology and Medical Modelling (2017) 14:13 Hence, the derivative of LDFE gives Hence, the derivative of LDFE gives L′
DFE =
n
i=1
ci
⎛
⎝(Si + σiVi)
n
j=1
βij
Ij
N∗
j
−(μi + γi −Qi)Ii
⎞
⎠
=
n
i=1
ℓi
⎛
⎜⎜⎜⎝
(Si + σiVi)
n
j=1
βijIj
(μi + γi −Qi) N∗
j
−Ii
⎞
⎟⎟⎟⎠ L′
DFE =
n
i=1
ci
⎛
⎝(Si + σiVi)
n
j=1
βij
Ij
N∗
j
−(μi + γi −Qi)Ii
⎞
⎠
=
n
i=1
ℓi
⎛
⎜⎜⎜⎝
(Si + σiVi)
n
j=1
βijIj
(μi + γi −Qi) N∗
j
−Ii
⎞
⎟⎟⎟⎠ = (ℓ1, · · · , ℓn) · (M (S1, V1, · · · , Sn, Vn) −En) · (I1, · · · , In)T
≤(ℓ1, · · · , ℓn) ·
M
S0
1, V 0
1 , · · · , S0
n, V 0
n
−En
· (I1, · · · , In)T
=
ρ(M0) −1
(ℓ1, · · · , ℓn) · (I1, · · · , In)T ≤0,
(17) = (ℓ1, · · · , ℓn) · (M (S1, V1, · · · , Sn, Vn) −En) · (I1, · · · , In)T
≤(ℓ1, · · · , ℓn) ·
M
S0
1, V 0
1 , · · · , S0
n, V 0
n
−En
· (I1, · · · , In)T
(M0)
1
(ℓ
ℓ) (I
I )T
0 ≤(ℓ1,
, ℓn)
M
S1, V1 ,
, Sn, Vn
En
(I1,
, In)
=
ρ(M0) −1
(ℓ1, · · · , ℓn) · (I1, · · · , In)T ≤0,
(17) (17) where En denotes the n-dimensional unit matrix and · denotes the product of vectors. It
is easy to see that when ℜ0 < 1, L′
DFE = 0 holds if and only if Ii = 0 for all i ∈N , that is,
the solution is in the disease-free equilibrium E0. When ℜ0 = 1, from the third equality
in (17), we see that L′
DFE = 0 implies (ℓ1, · · · , ℓn) · M (S1, V1, · · · , Sn, Vn) · (I1, · · · , In)T
= (ℓ1, · · · , ℓn) · (I1, · · · , In)T. We define the following matrix, which corresponds to the next generation matrix: (18) (18) Suppose that (S1, V1, · · · , Sn, Vn)
̸=
S0
1, V 0
1 , · · · , S0
n, V 0
n
. Then (ℓ1, · · · , ℓn) ·
M (S1, V1, · · · , Sn, Vn) < (ℓ1, · · · , ℓn) · M0 = ρ(M0) (ℓ1, · · · , ℓn) = (ℓ1, · · · , ℓn). Hence,
(18) has only the trivial solution such that Ii = 0 for all i ∈N . This implies that L′
DFE = 0
holds only in the disease-free equilibrium E0 ∈
¯. Consequently, from the LaSalle’s
invariance principle (see [39]), we can conclude that the disease-free equilibrium E0 is
globally asymptotically stable. We define the following matrix, which corresponds to the next generation matrix: Let ci := ℓi/ (μi + γi −Qi) , i ∈N and Ji(t) :=
+∞
t
δi(ξ)γie−μiξe−
ξ
0 δi(η)dηdξ, i ∈N and consider the following Lyapunov function. LDFE (I1, · · · , In) :=
n
i=1
ci
Ii(t) +
+∞
0
Ji(ξ)Ii(t −ξ)dξ
. From assumption (A6), Ji(t) ≥0, i ∈N for all t ≥0 and hence, LDFE ≥0 and the equality
holds if and only if (I1, · · · , In) ≡0. Note that +∞
Ji(ξ)Ii(t −ξ)dξ
′
=
+∞
0
Ji(ξ) ∂
∂t Ii(t −ξ)dξ = −
+∞
0
Ji(ξ) ∂
∂ξ Ii(t −ξ)dξ +∞
0
Ji(ξ)Ii(t −ξ)dξ
′
=
+∞
0
Ji(ξ) ∂
∂t Ii(t −ξ)dξ = −
+∞
0
Ji(ξ) ∂
∂ξ Ii(t −ξ)dξ
= −[ Ji(ξ)Ii(t −ξ)]+∞
0
+
+∞
0
∂
∂ξ Ji(ξ)Ii(t −ξ)dξ
= QiIi(t) −
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ,
i ∈N . = −[ Ji(ξ)Ii(t −ξ)]+∞
0
+
+∞
0
∂
∂ξ Ji(ξ)Ii(t −ξ)dξ = QiIi(t) −
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ,
i ∈N . Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 14 of 20 Wang et al. Proof of (ii) of Theorem 1 components
S∗
1, V ∗
1 , I∗
1, · · · , S∗
n, V ∗
n , I∗
n
of E∗satisfy the following equations. mponents
S∗
1, V ∗
1 , I∗
1, · · · , S∗
n, V ∗
n , I∗
n
of E∗satisfy the following equations. bi = S∗
i
n
j=1
βij
I∗
j
N∗
j
+ (μi + vi)S∗
i −ωiV ∗
i ,
(19)
viS∗
i = σi
n
j=1
βij
I∗
j
N∗
j
+ (μi + ωi) V ∗
i ,
(20)
(μi + γi −Qi)I∗
i = (S∗
i + σiV ∗
i )
n
j=1
βij
I∗
j
N∗
j
,
i ∈N . (21) (19) (20) (21) As in [14], we define θij :=
S∗
i + σiV ∗
i
βijI∗
j /N∗
j , i, j ∈N and As in [14], we define θij :=
S∗
i + σiV ∗
i
βijI∗
j /N∗
j , i, j ∈N and As in [14], we define θij :=
S∗
i + σiV ∗
i
βijI∗
j /N∗
j , i, j ∈N and :=
⎛
⎜⎜⎜⎜⎜⎜⎜⎜⎝
j̸=1
θ1j −θ21 · · · −θn1
−θ12
j̸=2
θ2j · · · −θn2
... ... ... ... −θ1n
−θ2n · · ·
j̸=n
θnj
⎞
⎟⎟⎟⎟⎟⎟⎟⎟⎠
. Let ϕ := (ϕ1, · · · , ϕn)T be a basis of the solution space of linear system ϕ = 0. Then,
from [14, Lemma 2.1], we see that the dimension of the solution space is 1 and ϕi > 0,
i ∈N . In particular, from the form of matrix , the following equality holds. Let ϕ := (ϕ1, · · · , ϕn)T be a basis of the solution space of linear system ϕ = 0. Then,
from [14, Lemma 2.1], we see that the dimension of the solution space is 1 and ϕi > 0,
i ∈N . In particular, from the form of matrix , the following equality holds. n
j=1
θijϕi =
n
j=1
θjiϕj,
i ∈N . (22) n
j=1
θijϕi =
n
j=1
θjiϕj,
i ∈N . (22) Using this ϕ and H(x) := x −1 −ln x ≥H(1) = 0, we consider the following Lyapunov
functional to prove the global asymptotic stability of E∗. Proof of (ii) of Theorem 1 If ℜ0
>
1, then (ℓ1, · · · , ℓn) ·
M
S0
1, V 0
1 , · · · , S0
n, V 0
n
−En
· (I1, · · · , In)T
=
ρ(M0) −1
(ℓ1, · · · , ℓn) · (I1, · · · , In)T
> 0. Hence, we see from the third equality in
(17) that in a neighborhood of
S0
1, V 0
1 , · · · , S0
n, V 0
n
, L′
DFE > 0. This implies the instability
of the disease-free equilibrium E0. If ℜ0
>
1, then (ℓ1, · · · , ℓn) ·
M
S0
1, V 0
1 , · · · , S0
n, V 0
n
−En
· (I1, · · · , In)T
=
ρ(M0) −1
(ℓ1, · · · , ℓn) · (I1, · · · , In)T
> 0. Hence, we see from the third equality in
(17) that in a neighborhood of
S0
1, V 0
1 , · · · , S0
n, V 0
n
, L′
DFE > 0. This implies the instability
of the disease-free equilibrium E0. Since the disease-free equilibrium of E0 of system (6) is unstable if ℜ0 > 1, we see from
the uniform persistence result of [40] and an argument as in the proof of Proposition 3.3 of
[41] that system (6) is uniformly persistent. That is, there exists a positive constant c > 0
such that for any initial value, it holds that lim inft→+∞Si(t) ≥c, lim inft→+∞Vi(t) ≥c
and lim inft→+∞Ii(t) ≥c for all i ∈N . Since the uniform persistence together with
the uniform boundedness implies the existence of an interior equilibrium (see [42, 43]),
we see that system (6) has an endemic equilibrium E∗∈. From (7), we see that the Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
Page 15 of Biology and Medical Modelling (2017) 14:13
Page 15 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
Page 15 of 2 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13
Page 15 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 15 of 20 components
S∗
1, V ∗
1 , I∗
1, · · · , S∗
n, V ∗
n , I∗
n
of E∗satisfy the following equations. Proof of (ii) of Theorem 1 L′
EE =
n
i=1
ϕi
1 −S∗
i
Si
bi −Si
n
j=1
βij
Ij
N∗
j
−(μi + vi)Si + ωiVi
+
1 −V ∗
i
Vi
viSi −σiVi
n
j=1
βij
Ij
N∗
j
−(μi + ωi)Vi
+
1 −I∗
i
Ii
(Si + σiVi)
n
j=1
βij
Ij
N∗
j
−(μi + γi)Ii L′
EE =
n
i=1
ϕi
1 −S∗
i
Si
bi −Si
n
j=1
βij
Ij
N∗
j
−(μi + vi)Si + ωiVi
+
1 −V ∗
i
Vi
viSi −σiVi
n
j=1
βij
Ij
N∗
j
−(μi + ωi)Vi
+
1 −I∗
i
Ii
(Si + σiVi)
n
j=1
βij
Ij
N∗
j
−(μi + γi)Ii
+
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ
+
+∞
0
Ji(ξ)I∗
i
∂
∂t H
Ii(t −ξ)
I∗
i
dξ
=
n
i=1
ϕi
1 −S∗
i
Si
S∗
i
n
j=1
βij
I∗
j
N∗
j
+ (μi + vi)S∗
i −ωiV ∗
i −Si
n
j=1
βij
Ij
N∗
j
−(μi + vi)Si + ωiVi
+
1 −V ∗
i
Vi
Si
S∗
i
viS∗
i −σiVi
n
j=1
βij
Ij
N∗
j
−(μi + ωi)Vi
I∗
i
n
Ij +
1 −Vi
Vi
viSi −σiVi
j=1
βij
j
N∗
j
−(μi + ωi)Vi
+
1 −I∗
i
Ii
(Si + σiVi)
n
j=1
βij
Ij
N∗
j
−(μi + γi)Ii
+
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ
+
+∞
0
Ji(ξ)I∗
i
∂
∂t H
Ii(t −ξ)
I∗
i
dξ
=
n
i=1
ϕi
1 −S∗
i
Si
S∗
i
n
j=1
βij
I∗
j
N∗
j
+ (μi + vi)S∗
i −ωiV ∗
i −Si
n
j=1
βij
Ij
N∗
j
−(μi + vi)Si + ωiVi
+
1 −V ∗
i
Vi
Si
S∗
i
viS∗
i −σiVi
n
j=1
βij
Ij
N∗
j
−(μi + ωi)Vi
+
1 −I∗
i
Ii
(Si + σiVi)
n
j=1
βij
Ij
N∗
j
−(μi + γi)Ii
+
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ
−
+∞
0
Ji(ξ)I∗
i
∂
∂ξ H
Ii(t −ξ)
I∗
i
dξ
=
n
i=1
ϕi
μiS∗
i
2 −S∗
i
Si
−Si
S∗
i
+ viS∗
i
2 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
+ μiV ∗
i
1 −Vi
V ∗
i
+ ωiV ∗
i
−1 + S∗
i
Si
+ Vi
V ∗
i
−S∗
i Vi
SiV ∗
i
+ 1 −Vi
V ∗
i
+ S∗
i
n
j=1
βij
I∗
j
N∗
j
1 −S∗
i
Si
+
S∗
i + σiV ∗
i
n
j=1
βij
Ii
N∗
j
−(Si + σiVi)
n
j=1
βij
I∗
j
N∗
j
I∗
i Ij
IiI∗
j
+ (μi + γi)I∗
i
1 −Ii
I∗
i
+
1 −Ii
I∗
i
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ
−
+∞
0
Ji(ξ)I∗
i
∂
∂ξ H
Ii(t −ξ)
I∗
i
dξ
. Proof of (ii) of Theorem 1 LEE(S1, V1, I1, · · · , Sn, Vn, In) :=
n
i=1
ϕi
S∗
i H
Si
S∗
i
+ V ∗
i H
Vi
V ∗
i
+ I∗
i H
Ii
I∗
i
+
+∞
0
Ji(ξ)I∗
i H
Ii(t −ξ)
I∗
i
dξ
. In order to make this function well-defined, without loss of generality, we can restrict
our attention to the solution such that Ii(s) = ϕi(s), i ∈N on (−∞, 0], where ϕi(0) =
Ii(0) and 0 < mi < ϕi(s) < Mi < +∞, s ∈(−∞, 0] , i ∈N for positive constants mi
and Mi, i ∈N . Then, from the positive invariance of set and the uniform persistence
of system (6), we see that the Lyapunov functional LEE is well-defined. Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 16 of 20 Using (19), we can calculate the derivative of LEE as follows. Using (19), we can calculate the derivative of LEE as follows. Proof of (ii) of Theorem 1 j
+
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ
+
+∞
0
Ji(ξ)I∗
i
∂
∂t H
Ii(t −ξ)
I∗
i
dξ
=
n
i=1
ϕi
1 −S∗
i
Si
S∗
i
n
j=1
βij
I∗
j
N∗
j
+ (μi + vi)S∗
i −ωiV ∗
i −Si
n
j=1
βij
Ij
N∗
j
−(μi + vi)Si + ωiVi
+
1 −V ∗
i
Vi
Si
S∗
i
viS∗
i −σiVi
n
j=1
βij
Ij
N∗
j
−(μi + ωi)Vi +
Ii
( i +
i
i)
j=1
βij N∗
j
(μi + γi) i
+
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ
−
+∞
0
Ji(ξ)I∗
i
∂
∂ξ H
Ii(t −ξ)
I∗
i
dξ
=
n
i=1
ϕi
μiS∗
i
2 −S∗
i
Si
−Si
S∗
i
+ viS∗
i
2 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
+ μiV ∗
i
1 −Vi
V ∗
i
+ ωiV ∗
i
−1 + S∗
i
Si
+ Vi
V ∗
i
−S∗
i Vi
SiV ∗
i
+ 1 −Vi
V ∗
i
+ S∗
i
n
j=1
βij
I∗
j
N∗
j
1 −S∗
i
Si
+
S∗
i + σiV ∗
i
n
j=1
βij
Ii
N∗
j
−(Si + σiVi)
n
j=1
βij
I∗
j
N∗
j
I∗
i Ij
IiI∗
j
+ (μi + γi)I∗
i
1 −Ii
I∗
i
+
1 −Ii
I∗
i
+∞
0
δi(ξ)γiIi(t −ξ)e−μiξe−
ξ
0 δi(η)dηdξ
−
+∞
0
Ji(ξ)I∗
i
∂
∂ξ H
Ii(t −ξ)
I∗
i
dξ
. (23) (23) Now it follows from integration by parts that Now it follows from integration by parts that +∞
0
Ji(ξ)I∗
i
∂
∂ξ H
Ii(t −ξ)
I∗
i
dξ
= −Ji(0)I∗
i H
Ii
I∗
i
+
+∞
0
δi(ξ)γie−μiξe−
ξ
0 δi(η)dηI∗
i H
Ii(t −ξ)
I∗
i
dξ
= −Qi
Ii −I∗
i −I∗
i ln Ii(t)
I∗
i
+
+∞
0
δi(ξ)γie−μiξe−
ξ
0 δi(η)dη
Ii(t −ξ) −I∗
i −I∗
i ln Ii(t −ξ)
I∗
i
dξ. Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Wang et al. Proof of (ii) of Theorem 1 Theoretical Biology and Medical Modelling (2017) 14:13 Page 17 of 20 Hence, (23) can be calculated as follows: L′
EE
=
n
i=1
ϕi
μiS∗
i
2 −S∗
i
Si
−Si
S∗
i
+ viS∗
i
2 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
+ μiV ∗
i
1 −Vi
V ∗
i
+ ωiV ∗
i
S∗
i
Si
−S∗
i Vi
SiV ∗
i
+ S∗
i
n
j=1
βij
I∗
j
N∗
j
1 −S∗
i
Si
+
S∗
i + σiV ∗
i
n
j=1
βij
Ii
N∗
j
−(Si + σiVi)
n
j=1
βij
I∗
j
N∗
j
I∗
i Ij
IiI∗
j
+ (μi + γi −Qi)I∗
i
1 −Ii
I∗
i
−QiI∗
i ln Ii
I∗
i
−I∗
i
+∞
0
δi(ξ)γi
Ii(t −ξ)
Ii
−1 −ln Ii(t −ξ)
I∗
i
e−μiξe−
ξ
0 δi(η)dηdξ
. (24) (24) From (21) and (22), we have From (21) and (22), we have From (21) and (22), we have From (21) and (22), we have n
i=1
ϕi (μi + γi −Qi) Ii =
n
i=1
ϕi (μi + γi −Qi) I∗
i
Ii
I∗
i
=
n
i=1
ϕi
S∗
i + σiV ∗
i
n
j=1
βij
I∗
j
N∗
j
Ii
I∗
i
=
n
i=1
Ii
I∗
i
n
j=1
θijϕi =
n
i=1
Ii
I∗
i
n
j=1
θjiϕj =
n
i=1
n
j=1
θji
Ii
I∗
i
ϕj
=
n
i=1
n
j=1
θij
Ij
I∗
j
ϕi =
n
i=1
ϕi
n
j=1
θij
Ij
I∗
j
=
n
i=1
ϕi
S∗
i + σiV ∗
i
n
j=1
βij
Ij
N∗
j
. Proof of (ii) of Theorem 1 (25) (25) Hence, using (20), (21) and (25), we can calculate (24) as follows: Hence, using (20), (21) and (25), we can calculate (24) as follows: Hence, using (20), (21) and (25), we can calculate (24) as follows: L′
EE =
n
i=1
ϕi
μiS∗
i
2 −S∗
i
Si
−Si
S∗
i
+ μiV ∗
i
3 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
−Vi
V ∗
i
+ ωiV ∗
i
2 −SiV ∗
i
S∗
i Vi
−S∗
i Vi
SiV ∗
i
+ S∗
i
n
j=1
βij
I∗
j
N∗
j
2 −S∗
i
Si
−SiI∗
i Ij
S∗
i IiI∗
j
+ σiV ∗
i
n
j=1
βij
I∗
j
N∗
j
3 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
−ViI∗
i Ij
V ∗
i IiI∗
j
−QiI∗
i ln Ii
I∗
i
+ QiI∗
i ln Ii
I∗
i
−I∗
i
+∞
0
δi(ξ)γiH
Ii(t −ξ)
Ii
e−μiξe−
ξ
0 δi(η)dηdξ
. (26) (26) Using the inequality of arithmetic and geometric means, we see that the first three terms
in the right-hand side of (26) are non-positive and equal to zero if and only if (Si, Vi) =
S∗
i , V ∗
i
, i ∈N . From the positivity of the function H(x), we see that the last term in the Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 18 of 20 right-hand side of (26) is non-positive. Proof of (ii) of Theorem 1 Hence, taking the maximum as in [10] and using
the graph-theoretic approach as in [14], we can evaluate (26) as follows: L′
EE ≤
n
i=1
ϕi
n
j=1
S∗
i + σiV ∗
i
βij
I∗
j
N∗
j
× max
2 −S∗
i
Si
−SiI∗
i Ij
S∗
i IiI∗
j
, 3 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
−ViI∗
i Ij
V ∗
i IiI∗
j
=
n
i=1
ϕi
n
j=1
θij max
2 −S∗
i
Si
−SiI∗
i Ij
S∗
i IiI∗
j
, 3 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
−ViI∗
i Ij
V ∗
i IiI∗
j
=
G∈
w(G)
(i,j)∈A(CG)
max
2 −S∗
i
Si
−SiI∗
i Ij
S∗
i IiI∗
j
, 3 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
−ViI∗
i Ij
V ∗
i IiI∗
j
,
(27) =
G∈
w(G)
(i,j)∈A(CG)
max
2 −S∗
i
Si
−SiI∗
i Ij
S∗
i IiI∗
j
, 3 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
−ViI∗
i Ij
V ∗
i IiI∗
j
,
(27) (27) where denotes the set of all unicyclic graphs included in directed graphs with vertices
{1, 2, · · · , n}, G denotes the unicyclic graph included in , w(G) denotes the weight of
graph G, CG denotes the unicycle included in G and A(CG) denotes the set of all arcs
included in CG. Proof of (ii) of Theorem 1 For instance, for a unicycle CG : 1 →2 →1, we have A(CG) =
{(1, 2), (2, 1)} and thus,
(i,j)∈A(CG)
max
2 −S∗
i
Si
−SiI∗
i Ij
S∗
i IiI∗
j
, 3 −S∗
i
Si
−SiV ∗
i
S∗
i Vi
−ViI∗
i Ij
V ∗
i IiI∗
j
= max
2 −S∗
1
S1
−S1I∗
1I2
S∗
1I1I∗
2
, 3 −S∗
1
S1
−V ∗
1 S1
V1S∗
1
−V1I∗
1I2
V ∗
1 I1I∗
2
+ max
2 −S∗
2
S2
−S2I∗
2I1
S∗
2I2I∗
1
, 3 −S∗
2
S2
−V ∗
2 S2
V2S∗
2
−V2I∗
2I1
V ∗
2 I2I∗
1
= max
4 −S∗
1
S1
−S1I∗
1I2
S∗
1I1I∗
2
−S∗
2
S2
−S2I∗
2I1
S∗
2I2I∗
1
,
5 −S∗
1
S1
−S1I∗
1I2
S∗
1I1I∗
2
−S∗
2
S2
−V ∗
2 S2
V2S∗
2
−V2I∗
2I1
V ∗
2 I2I∗
1
,
5 −S∗
1
S1
−V ∗
1 S1
V1S∗
1
−V1I∗
1I2
V ∗
1 I1I∗
2
−S∗
2
S2
−S2I∗
2I1
S∗
2I2I∗
1
,
6 −S∗
1
S1
−V ∗
1 S1
V1S∗
1
−V1I∗
1I2
V ∗
1 I1I∗
2
−S∗
2
S2
−V ∗
2 S2
V2S∗
2
−V2I∗
2I1
V ∗
2 I2I∗
1
. We see that all elements in the max in the last expression of the above formula are non
positive because of the inequality of arithmetic and geometric means. Similarly, we can
easily check that for all unicycles CG with at most n vertices, the second sum in the
last expression of (27) are non-positive (see [10, Proof of Theorem 4.1]). Hence, L′
EE
is non-positive and it is easy to check that the equality L′
EE = 0 holds if and only if
(S1, V1, I1, · · · , Sn, Vn, In) =
S∗
1, V ∗
1 , I∗
1, · · · , S∗
n, V ∗
n , I∗
n
. This implies, from the LaSalle’s
invariance principle, that the endemic equilibrium E∗is globally asymptotically stable. g
JW was supported by National Natural Science Foundation of China (nos. 11401182, 11471089), Science and Technology
Innovation Team in Higher Education Institutions of Heilongjiang Province (No. 2014TD005). HT was supported by
Grant-in-Aid for JSPS Fellows from the Ministry of Education, Culture, Sports, Science, and Technology in Japan. TK was
supported by Grant-in-Aid for Young Scientists (B) of Japan Society for the Promotion of Science (No. 15K17585) and the
program of the Japan Initiative for Global Research Network on Infectious Diseases (J-GRID); from Japan Agency for Acknowledgements
ld l k
h
k We would like to thank the editor and anonymous reviewers for their helpful comments to the earlier version of this
paper. We would like to thank Dr. Akihiro Ishii for helpful discussions regarding the serological test for HSV-2. Competing interests Competing interests
The authors declare that they have no competing interests. Funding Page 19 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Medical Research and Development, AMED. RO was supported by Grant-in-Aid for Young Scientists (B) of Japan Society
for the Promotion of Science (No. 15K19217) and Precursory Research for Embryonic Science and Technology (PRESTO)
grant number JPMJPR15E1 from Japan Science and Technology Agency (JST). The authors were supported by JSPS
Bilateral Joint Research Project (Open Partnership). Availability of data and materials
h d
h
h f d
f The data that support the findings of this study are available in the National Health and Nutrition Examination Survey,
“http://www.cdc.gov/nchs/nhanes/”. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. References 1. World Health Organization. Media centre: Herpes simlex virus. 2017. Available from: http://www.who.int/. Accessed
25 Jan 2017. 2. Alsallaq RA, Schiffer JT, Longini IM, Wald A, Corey L, Abu-Raddad LJ. Population level impact of an imperfect
prophylactic HSV-2 vaccine. Sex Transm Dis. 2010;37:290–7. 3. Blower S. Modelling the genital herpes epidemic. Herpes. 2004;3:138A–146A. 3. Blower S. Modelling the genital herpes epidemic. Herpes. 2 4. Lou Y, Qesmi R, Wang Q, Steben M, Wu J, Hefferman JM. E 4. Lou Y, Qesmi R, Wang Q, Steben M, Wu J, Hefferman JM. Epidemiological impact of a genital he
f
f
l
P
S O vaccine for young females. PLoS ONE. 2012;7:e46027. y
g
5. Diekmann O, Heesterbeek JAP, Metz JAJ. On the definition and the computation of the basic reproduction ratio R y
g
5. Diekmann O, Heesterbeek JAP, Metz JAJ. On the definition and the computation of the basic
in models for infectious diseases in heterogeneous populations. J Math Biol. 1990;28:365–82. 5. Diekmann O, Heesterbeek JAP, Metz JAJ. On the definition and the computation of the basic reproduction ratio Ro
in models for infectious diseases in heterogeneous populations J Math Biol 1990;28:365–82 ,
,
p
in models for infectious diseases in heterogeneous populations. J Math Biol. 1990;28:365–82. 6. Kribs-Zaleta CM, Velasco-Hernández JX. A simple vaccination model with multiple endemic states. Math Biosci. 2000;164:183–201. 7. Arino J, McCluskey CC, van den Driessche P. Global results for an epidemic model with vaccination that exhbits
backward bifurcation. SIAM J Appl Math. 2003;64:260–76. backward bifurcation. SIAM J Appl Math. 2003;64:260–76. pp
8. Alexander ME, Bowman C, Moghadas SM, Summers R, Gumel AB, Sahai BM. A vaccination model for transmission 8. Alexander ME, Bowman C, Moghadas SM, Summers R, Gumel AB
dynamics of influenza. SIAM J Appl Dynam Syst. 2004;4:503–24. 8. Alexander ME, Bowman C, Moghadas SM, Summers R, Gumel AB, Sahai BM. A vaccination model for transmission
dynamics of influenza SIAM J Appl Dynam Syst 2004;4:503 24 8. Alexander ME, Bowman C, Moghadas SM, Summers R, Gu 8. Alexander ME, Bowman C, Moghadas SM, Summers R, Gumel AB, Sahai BM. A vaccination model for transmission
dynamics of influenza. SIAM J Appl Dynam Syst. 2004;4:503–24. 8. Alexander ME, Bowman C, Moghadas SM, Summers R, Gumel
dynamics of influenza. SIAM J Appl Dynam Syst. 2004;4:503–24. dynamics of influenza. SIAM J Appl Dynam Syst. 2004;4:503–24. y
y
y
9. Liu X, Takeuchi Y, Iwami S. Authors’ contributions
JW
d XY f
l
d h JW and XY formulated the model. HT improved the whole manuscript. TK carried out the theoretical analysis of the
model. RO carried out the epidemiological study including the estimation of ℜ0 for HSV-2. All authors read and approved
the final manuscript. Author details 1School of Mathematical Science, Heilongjiang University, 150080 Harbin, People’s Republic of China. 2Division of
Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, 001-0020 Hokkaido, Japan. 3Department of Applied Mathematics, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho,
Nada-ku, 657-8501 Kobe, Japan. 4JST, PRESTO, 4-1-8 Honcho, Kawaguchi, 332-0012 Saitama, Japan. Received: 9 April 2017 Accepted: 28 June 2017 Received: 9 April 2017 Accepted: 28 June 2017 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 References SVIR epidemic model with vaccination strategies. J Theoret Biol. 2008;253:1–11. . Liu X, Takeuchi Y, Iwami S. SVIR epidemic model with vaccinati p
g
10. Kuniya T. Global stability of a multi-group SVIR epidemic model. Nonlinear Anal RWA. 2013;14:1135–43. obal stability of a multi-group SVIR epidemic model. Nonlinear Anal 0. Kuniya T. Global stability of a multi-group SVIR epidemic model 11. van den Driessche P, Zou X. Modeling relapse in infectious diseases. Math Biosci. 2007;207:89–103. 12. Lajmanovich A, Yorke JA. A deterministic model for gonorrhea in a nonhomogeneous population. Math Biosci. 1976;28:221–36. 13. Feng Z, Huang W, Castillo-Chavez C. Global behavior of a multi-group SIS epidemic model with age structure. J Diff
Equat. 2005;218:292–324. q
;
14. Guo H, Li MY, Shuai Z. Global stability of the endemic equilibrium of multigroup SIR epidemic models. Canada Appl q
;
14. Guo H, Li MY, Shuai Z. Global stability of the endemic equilibrium of multigroup SIR epidemic models. Canada Appl
Math Quart. 2006;14:259–84. q
14. Guo H, Li MY, Shuai Z. Global
Math Quart. 2006;14:259–84. ;
15. Li MY, Shuai Z, Wang C. Global stability of multi-group epidemic models with distributed delays. J Math Anal Appl. 2010;361:38–47. 16. Ding D, Ding X. Global stability of multi-group vaccination epidemic models with delays. Nonlinear Anal RWA. 2011;12:1991–7. 17. Kuniya T. Global stability analysis with a discretization appraoch for an age-structured multigroup SIR epidemic
model. Nonlinear Anal RWA. 2011;12:2640–55. 18. Shu H, Fan D, Wei J. Global stability of multi-group S
transmission. Nonlinear Anal RWA. 2012;13:1581–92. 18. Shu H, Fan D, Wei J. Global stability of multi-group SE 18. Shu H, Fan D, Wei J. Global stability of multi-group SEIR epidemic models with distributed delays and nonlinear
transmission. Nonlinear Anal RWA. 2012;13:1581–92. transmission. Nonlinear Anal RWA. 2012;13:1581–92. ;
19. Yuan C, Jiang D, O’Regan D, Agarwal RP. Stochastically asymptotically stability of the multi-gro ;
19. Yuan C, Jiang D, O’Regan D, Agarwal RP. Stochastically asymptotically stability of the multi-group SE
models with random perturbation Commun Nonlinear Sci Numer Simulat 2012;17:2501–16 19. Yuan C, Jiang D, O’Regan D, Agarwal RP. Stochastica p
;
20. Muroya Y, Enatsu Y, Kuniya T. Global stability for a multi-group SIRS epidemic model with varying population sizes. Nonlinear Anal RWA. 2013;14:1693–704. Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 20 of 20 21. Wang Z, Fan X, Han Q. References Global stability of deterministic and stochastic multigroup SEIQR models in computer
network. Appl Math Model. 2013;37:8673–86. 21. Wang Z, Fan X, Han Q. Global stability of deterministic and stochastic multigroup SEIQR models in computer
network. Appl Math Model. 2013;37:8673–86. 22. Zhang L, Pang J, Wang J. Stability analysis of a multigroup epidemic model with general exposed distribution a
nonlinear incidence rates. Abstr Appl Math. 2013. 2013(Article ID .354287). 22. Zhang L, Pang J, Wang J. Stability analysis of a multigroup epidemic model w
nonlinear incidence rates. Abstr Appl Math. 2013. 2013(Article ID .354287). 22. Zhang L, Pang J, Wang J. Stability analysis of a multigroup epidemic model with general exposed distribution and
nonlinear incidence rates. Abstr Appl Math. 2013. 2013(Article ID .354287). 23. Wang J, Liu X, Pang J, Hou D. Global dynamics of a multi-group epidemic model with general exposed distrib
and relapse. Osaka J Math. 2015;52:117–38. 23. Wang J, Liu X, Pang J, Hou D. Global dynamics of a multi-group epidemic model with general exposed distribution
and relapse. Osaka J Math. 2015;52:117–38. 23. Wang J, Liu X, Pang J, Hou D. Global dynamics of a multi-gro 23. Wang J, Liu X, Pang J, Hou D. Global dynam
and relapse. Osaka J Math. 2015;52:117–38. and relapse. Osaka J Math. 2015;52:117–38. p
24. Wang J, Pang J, Liu X. Modelling diseases with relapse and nonlinear incidence of infection: a multi-group p
24. Wang J, Pang J, Liu X. Modelling diseases with relapse and nonlinear incidence of infection: a multi-group p
24. Wang J, Pang J, Liu X. Modelling diseases with relapse and nonlinear incidence of infection: a multi-group
epidemic model. J Biol Dynam. 2015;8:99–116. 24. Wang J, Pang J, Liu X. Modelling diseases with relapse and nonlinear incidence of infection: a multi-group
id
i
d l J Bi l D
2015 8 99 116 epidemic model. J Biol Dynam. 2015;8:99–116. p
y
25. van den Driessche P, Watmough J. Reproduction numbers and sub-threshold endemic equilibria for p
y
25. van den Driessche P, Watmough J. Reproduction numbers and sub-threshold endemic equilibria for
l
d l
f di
i i
M h Bi
i 2002 180 29 48 y
25. van den Driessche P, Watmough J. Reproduction numbers and sub-threshold endemic equilibria for
compartmental models of disease transmission. Math Biosci. 2002;180:29–48. 25. van den Driessche P, Watmough J. Reproduction numbers and sub-threshold
compartmental models of disease transmission. Math Biosci. 2002;180:29–48. References compartmental models of disease transmission. Math Biosci. 2002;180:29–48. compartmental models of disease transmission. Math Biosci. 2002;180:29–48. os F, Edling CR, Amaral LAN, Stanly HE, Aberg Y. The web of huma 26. Liljeros F, Edling CR, Amaral LAN, Stanly HE, Aberg Y. The w j
,
g
,
,
y
,
g
;
27. Jacquez JA, Simon CP, Koopman J, Sattenspiel L, Perry T. Modelling and analyzing HIV transmission: the effect of
contact patterns. Math Biosci. 1988;92:119–99. j
g
y
g
27. Jacquez JA, Simon CP, Koopman J, Sattenspiel L, Perry T. Modelling and analyzing HIV transmission: the effect of
contact patterns. Math Biosci. 1988;92:119–99. p
28. Hino Y, Murakami S, Naito T. Functional differential equations with infinite delay. vol. 1473 of Lecture Notes in
Mathematics. Berlin: Springer-Verlag Berlin Heidelberg; 1991. 28. Hino Y, Murakami S, Naito T. Functional differential equation
Mathematics. Berlin: Springer-Verlag Berlin Heidelberg; 1991. 29. Röst G, Wu J. SEIR epidemiological model with varying infectivity and infinite delay. Math Biosci Eng. 2008;5:389– 30. Abu-Raddad LJ, Schiffer JT, Ashley R, Mumtaz G, Alsallaw RA, Akala FA, et al. HSV-2 serology can be predictive of HIV
epidemic potential and hidden sexual risk behavior in the Middle East and North Africa. Epidemics. 2010;2:173–82. 31. Kochanek KD, Murphy SL, Xu J, Tejada-Vera B. Deaths: Final data for 2014. Natl Vital Stat Rep. 2016;65:1–122. 32. Abu-Raddad LJ, Jr IML. No HIV stage is dominant in driving the HIV epidemic in sub-Saharan Africa. AIDS. 2008;22:
1055–61. 33. Mumtaz G, Hilmi N, McFarland W, Kaplan RL, Akala FA, Semini I, et al. Are HIV epidemics among men who have
sex with men emerging in the Middle East and North Africa?: a systematic review and data synthesis. PLoS Med. 2011;8:e1000444. 34. The National Health and Nutrition Examination Survey (NHANES). 2016. Available from:http://www.cdc.gov/nchs/
nhanes/. Accessed 25 July 2016. 35. van Wagoner NJ, III EWH. Herpes diagnostic tests and their use. Curr Infect Dis Rep. 2012;14:175 ner NJ, III EWH. Herpes diagnostic tests and their use. Curr Infect D 36. Garnett GP, Anderson RM. Contact tracing and the estimation of sexual mixing patterns: the epidemiology of
gonococcal infections. Sex Trans Dis. 1993;20:181–91. 36. Garnett GP, Anderson RM. Contact tracing and the estimatio
gonococcal infections. Sex Trans Dis. 1993;20:181–91. 37. Sell RL, Wells JA, Wypij D. The prevalence of homosexual behavior and attraction in the United St
Kingdom and France: Results of national population-based samples. Arch Sex Behav. References 1995;24:235– 37. Sell RL, Wells JA, Wypij D. The prevalence of homosexual behavior and attraction in the United States, the U
Kingdom and France: Results of national population-based samples Arch Sex Behav 1995;24:235–48 37. Sell RL, Wells JA, Wypij D. The prevalence of homosexual behavior and attraction in the United States, the United
Kingdom and France: Results of national population-based samples. Arch Sex Behav. 1995;24:235–48. ,
,
yp j
p
,
Kingdom and France: Results of national population-based samples. Arch Sex Behav. 1995;24:235–48. 38. Berman A, Plemmons RJ. Nonnegative matrices in the mathematical sciences. New York: Ac 38. Be
a
,
e
o s J. o
egat e
at ces
t e
at e
at ca sc e ces. e
o :
cade
c
ess; 9 9. 39. LaSalle JP. The Stability of Dynamical Systems. Philadelphia: SIAM; 1976. 39. LaSalle JP. The Stability of Dynamical Systems. Philadelphia: SIAM; 1976. aSalle JP. The Stability of Dynamical Systems. Philadelphia: SIAM; 19 40. Freedman HI, Ruan S, Tang M. Uniform persistence and flows near a closed positively invariant set. J Dynam Diff
Equat. 1994;6:583–600. 41. Li MY, Graef JR, Wang L, Karsai J. Global dynamics of a SEIR model with varying total population size. Math Biosci. 1999;160:191–213. 42. Bhatia NP, Szego GP. Dynamical systems: stability theory and applications. Springer-Verlag; 1967. 43. Smith HL, Waltman P. The Theory of the Chemostat: Dynamics of Microbial Competition. Cambridge: Cambridge
University Press; 1995. • We accept pre-submission inquiries
• Our selector tool helps you to find the most relevant journal
• We provide round the clock customer support
• Convenient online submission
• Thorough peer review
• Inclusion in PubMed and all major indexing services
• Maximum visibility for your research
Submit your manuscript at
www.biomedcentral.com/submit
Submit your next manuscript to BioMed Central
and we will help you at every step: Submit your next manuscript to BioMed Central
and we will help you at every step: • We accept pre-submission inquiries
• Our selector tool helps you to find the most relevant journal
• We provide round the clock customer support
• Convenient online submission
• Thorough peer review
• Inclusion in PubMed and all major indexing services
• Maximum visibility for your research
Submit your manuscript at
www.biomedcentral.com/submit
y
p
and we will help you at every step:
|
https://openalex.org/W4221003540
|
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0265061&type=printable
|
English
| null |
Attitude of health professionals towards COVID-19 vaccination and associated factors among health professionals, Western Ethiopia: A cross-sectional survey
|
PloS one
| 2,022
|
cc-by
| 6,519
|
PLOS ONE PLOS ONE RESEARCH ARTICLE Tadesse TolossaID1*, Bizuneh Wakuma2, Ebisa Turi1, Diriba Mulisa2, Diriba Ayala3,
Getahun Fetensa2,4, Belayneh Mengist5, Gebeyehu Abera6, Emiru Merdassa Atomssa1,
Dejene Seyoum1, Tesfaye Shibiru7, Ayantu Getahun1 1 Department of Public Health, Institute of Health Science, Wollega University, Nekemte, Ethiopia,
2 Department of Nursing, Institute of Health Science, Wollega University, Nekemte, Ethiopia, 3 Department
of Midwifery, Institute of Health Science, Wollega University, Nekemte, Ethiopia, 4 Department of Health
Behavior and Society, Institute of Health, Jimma university, Jimma, Ethiopia, 5 Department of Public Health,
College of Health Science, Debre Markos University, Debre Markos, Ethiopia, 6 Nekemte Health Center,
Nekemte, Ethiopia, 7 School of Medicine, Institute of Health Sciences, Wollega University, Nekmete, Ethiopia Methods Received: June 30, 2021
Accepted: February 22, 2022
Published: March 9, 2022 An institution-based cross-sectional study was conducted among health care workers found
in Nekemte town from April 14–21, 2021. A total of 439 health professionals present on duty
during the study period was included in the study. The data were collected by using self-
administered questionnaire. Epidata version 3.2 was used for data entry, and STATA ver-
sion 14 was used for data analysis. The binary logistic regression model was employed to
determine factors associated with the attitude towards COVID-19 vaccination. Adjusted
Odds Ratio (AOR) with 95% confidence intervals was computed and statistical significance
was declared at a 5% level (p-value < 0.05). Peer Review History: PLOS recognizes the
benefits of transparency in the peer review
process; therefore, we enable the publication of
all of the content of peer review and author
responses alongside final, published articles. The
editorial history of this article is available here:
https://doi.org/10.1371/journal.pone.0265061 * yadanotolasa@gmail.com Introduction Citation: Tolossa T, Wakuma B, Turi E, Mulisa D,
Ayala D, Fetensa G, et al. (2022) Attitude of health
professionals towards COVID-19 vaccination and
associated factors among health professionals,
Western Ethiopia: A cross-sectional survey. PLoS
ONE 17(3): e0265061. https://doi.org/10.1371/
journal.pone.0265061 Even though people of the world were eagerly waiting for the hope of vaccine development,
vaccine hesitancy is becoming the top concern in both developed and developing countries. However, there is no adequate evidence regarding the attitude and perception of health pro-
fessionals towards the COVID 19 vaccine in resource-limited settings like Ethiopia. The aim
of this study was to assess health professionals’ attitudes and perceptions towards COVID
19 vaccine in Western Ethiopia. Editor: Syed Ghulam Sarwar Shah, Oxford
University Hospitals NHS Foundation Trust,
UNITED KINGDOM Editor: Syed Ghulam Sarwar Shah, Oxford
University Hospitals NHS Foundation Trust,
UNITED KINGDOM Editor: Syed Ghulam Sarwar Shah, Oxford
University Hospitals NHS Foundation Trust,
UNITED KINGDOM Attitude of health professionals towards
COVID-19 vaccination and associated factors
among health professionals, Western
Ethiopia: A cross-sectional survey Tadesse TolossaID1*, Bizuneh Wakuma2, Ebisa Turi1, Diriba Mulisa2, Diriba Ayala3,
Getahun Fetensa2,4, Belayneh Mengist5, Gebeyehu Abera6, Emiru Merdassa Atomssa1,
Dejene Seyoum1, Tesfaye Shibiru7, Ayantu Getahun1 Tadesse TolossaID1*, Bizuneh Wakuma2, Ebisa Turi1, Diriba Mulisa2, Diriba Ayala3,
Getahun Fetensa2,4, Belayneh Mengist5, Gebeyehu Abera6, Emiru Merdassa Atomssa1,
Dejene Seyoum1, Tesfaye Shibiru7, Ayantu Getahun1 PLOS ONE PLOS ONE Attitude of health professionals towards COVID-19 vaccination Data Availability Statement: All relevant data are
within the paper and its Supporting information
files. Funding: The author(s) received no specific
funding for this work. Competing interests: The authors have declared
that no competing interests exist. Abbreviations: AOR, Adjusted Odds Ratio; COR,
Crude Odds Ratio; HCW, Health Care Worker; MLS,
Medical Laboratory Science; WURH, Wollega
University Referral Hospital. Data Availability Statement: All relevant data are
within the paper and its Supporting information
files. associated with unfavorable attitude towards COVID-19 vaccine, whereas age less than
30 years (AOR = 2.14, 95%CI:1.25,3.67, P-value <0.001), working in a private clinic (AOR =
7.77, 95% CI: 2.19, 27.58, P-value <0.001) and health center (AOR = 2.45, 95%CI: 1.01,
5.92, P-value = 0.045) were positively associated with unfavorable attitude towards COVID-
19 vaccine. Funding: The author(s) received no specific
funding for this work. Conclusion and recommendation Abbreviations: AOR, Adjusted Odds Ratio; COR,
Crude Odds Ratio; HCW, Health Care Worker; MLS,
Medical Laboratory Science; WURH, Wollega
University Referral Hospital. In general, the attitude and perception of health care professionals toward the COVID-19
vaccine in the study area were unsatisfactory. Knowledge about the COVID-19 vaccine,
age of health care workers, and place of work are the factors which affects attitude towards
COVID-19 vaccine. Thus, we recommend the media outlets and concerned bodies to work
to develop trust among the public by disseminating accurate and consistent information
about the vaccine. Introduction Starting from the day it was declared a pandemic, COVID-19 remains the worst Global public
health challenge. According to the worldometer report, COVID-19 affects about 220 countries
and territories. More than 350 million cases, and 5.6 million deaths happened due to COVID-
19 as of January 24, 2022 [1,2]. The pandemic brought the double burden in developing coun-
tries already overwhelmed by the health care system challenges [3]. Given that sub-Saharan Africans are not the highest shareholder by cases and death during
the early phase [4], the direct effect of COVID-19 and the indirect effect of its mitigation, dis-
rupted the health care services [5]. The serious preventive measures (movement restriction,
physical distancing, lockdowns, hand washing and sanitizing) were practiced [6]. However,
the counter effect of some mitigation brought significant change in health care settings espe-
cially by task shifting and task sharing. Its effect on the economy is also evident. Though these
mitigation procedures played a paramount role in averting the burden of COVID19, the whole
world was hoping for vaccine development [7]. A few COVID-19 vaccines that are being used globally or locally [7]. As of June 10, 2021,
from 287 candidate vaccines, 102 are in the clinical phase, 185 are in the pre-clinical phase [8]. From these, WHO has listed the Pfizer/BioNTech, Astrazeneca-SK Bio, Serum Institute of
India, Janssen and Moderna vaccines for emergency use [6,7]. Believing Health Care Workers
(HCWs) are explicitly exposed to increased risk of infection through direct contact with
patients, they should be prioritized for vaccination [9]. The willingness of the general population to accept the vaccine ahead of COVID-19 vaccine
development was relatively promising compared to today’s reality [10–12]. Even though peo-
ple of the world were eagerly waiting for the vaccine development, vaccine hesitancy is becom-
ing the top concern in both developed and developing countries [11,13–17]. For instance, the
vaccine acceptance is 21% in Egypt [18], 54.6% in China[19], and 57.6% of the adult popula-
tion in the USA [20] intended to be vaccinated. Studies conducted in different regions of Ethi-
opia reported willingness to take COVID-19 vaccine were 46.1% in Southern Ethiopia
[21],39.7 in Addis Ababa [22], and 48.6% in Southwestern Ethiopia [23]. Result Copyright: © 2022 Tolossa et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited. A total of 431 health professionals participated in the study yielding a response rate of
98.1%. The results indicated that 51.28% (95%CI: 45.12%, 57.34%) of health professionals
had a favorable attitude towards COVID-19 vaccination. Having good knowledge about the
COVID-19 vaccine (AOR = 0.38, 95%CI: 0.22, 0.64, P-value <0.001) was negatively 1 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 Study design An Institutional based cross-sectional study design was employed. Study area and period This study was conducted in health institutions located in Nekemte town. Nekemte is the capi-
tal city of East Wollega Zone, and it is located 330 KM from Addis Ababa, the capital city of
Ethiopia. The study was conducted from April 15–21, 2021. Data from Nekemte Town Health
Office showed that the town has one teaching referral hospital owned by Wollega University,
one specialized hospital administered under Oromia Regional Health Bureau, two health cen-
ters (Nekemte and Cheleleki Health center), and more than fifteen medium and above private
clinics, and more than 800 health professionals are found in Nekemte town. Introduction The most common
reason mentioned for hesitancy were concerns about the safety of a vaccine and wide-ranging
lack of confidence, worries about the efficiency of the vaccine[17,18,24] 2 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Several studies indicate that healthcare professionals (HCPs) play a paramount role and can
significantly affect the general public’s decisions to receive the COVID- 19 vaccine [25,26]. In
Ethiopia, there have been 169,640 confirmed cases of COVID-19, with 9651 deaths till May 30,
2021 [1]. The Ethiopian government and the Ethiopian Ministry of health exert great efforts to
provide the COVID-19 vaccines and sort the vaccination as a priority for healthcare workers
(HCWs) and older people, especially people with chronic diseases history [27]. To overcome
the expected upcoming challenge of vaccination hesitancy, we have to measure and know the
exact reasons. However, there is no adequate evidence regarding the attitude and perception of
health professionals towards the COVID-19 vaccine in resource-limited settings like Ethiopia. Hence, this study aimed to assess health professionals’ attitudes and perceptions towards
COVID 19 vaccine in West Ethiopia. PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 Variables The attitude of health professionals towards the COVID-19 vaccine was the dependent variable
of this study. For attitude questions, the likert-scale method with a five points scale (strongly
agree, agree, neutral, disagree, strongly disagree) responses were used to allow the study partic-
ipants to express how much they agree or disagree with a particular question. Ten items were
used to assess the attitude of health professionals towards COVID-19 vaccine. Participants’
response was from 10 to 50. Higher scores denoted a “favorable attitude” towards COVID-19
vaccine. “Favorable attitude” was when the scoring was mean or 25 (50% and above) out of
50 items and < 25 (<50%) was rated as “unfavorable attitude”. Socio-demographic variables such as (age, sex, marital status, educational level, educational
background, religion), medical history (chronic medical disease and previously infected with
COVID-19), knowledge towards COVID-19 vaccine, and perception towards COVID-19 vac-
cine) were independent variables of this study. For knowledge related items, the questions contained the category of (“Yes”/“No”). A cor-
rect answer was assigned “1” point and an incorrect answer was assigned “0” points. The total
score ranged from 0 to 5. “Good knowledge” was when the scoring was 2.5 (50% and above)
out of 5 items and score below 2.5 indicated “poor knowledge” on COVID-19 vaccine. Finally, the perception of participants towards COVID-19 vaccine was assessed by using
five items with "Yes"/No" category. The total score ranged from 0 to 5. Respondents who
scored greater than or equal to the mean score ( 2.5 or 50%) were grouped to have "good
perception" and participants who scored less than the mean score (<2.5 or <50%) were
grouped to have "poor perception" towards COVID-19 vaccine (S3 File). Data collection techniques and data quality assurance A questionnaire was developed by reviewing previously published papers [28,29], and adapted
to local context. The tool was designed and distributed to respondents in English language
since the participants could read, write, and understand the language. The questionnaires
comprised socio-demographic data, medical history, knowledge, attitude, and perception
towards the COVID-19 vaccine. The data was collected by using self-administered question-
naires. The questionnaire was given to all health professionals on duty and returned to data
collectors after filling it. Cronbach’s alpha was used to assess the reliability of the tool, and the
value was 0.78 (value more than 0.7 to 0.95 is acceptable) [30]. To ensure its quality, the questionnaire was pre-tested on 5% of participants. Then possible
amendments were done based on the findings. The discussion was held between investigators
and data collectors, based on the pre-test result, and accordingly, some amendments were
made. The data collectors gave the one-day training about the tool and data collection proce-
dure. Data were checked daily for completeness, accuracy, clarity, and consistency by the
supervisors and principal investigator. Any error or ambiguity, and incompleteness were cor-
rected accordingly. Population, sample size and sampling techniques All health professionals working in private and public health institutions of Nekemte town
were a source population. Health professionals who were not on duty due to different reasons
were excluded from the study. All health professionals on duty during data collection and will-
ing to participate in the study were selected. The sample size was determined by single population proportion with the following
assumptions: Since this study was the first of its type in Ethiopia, p = 50% was taken, with a 5%
margin of error and a 95% confidence level. Accordingly, the calculated sample size was 384,
and after adding a 15% allowance for a non-response rate, the final sample size was 442 health
professionals. All health institutions found in Nekemte town were included in the study. There are two
public hospitals in Nekemte town, two health centers, and 15 medium clinics. Then the sample
size was proportionally allocated to hospitals, health centers and private clinics. Around 710
health professionals are working in two hospitals, 50 in two health centers and 60 health pro-
fessionals in all private clinics. For hospitals, we have used the identification number of the
health professionals, and the identification number was used as a sampling frame. Then com-
puter-generated simple random sampling technique was used to select the sample. Health pro-
fessionals who were not on duty during the study period were excluded from the sampling
frame. For health centers and private clinics, all health professionals who were available during
the study period were included in the study. Furthermore, health professionals working in
more than one health facility were considered only in a single health facility to prevent any dis-
tortion of information. 3 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Socio demographic characteristics of the health professionals Four hundred thirty-one health professionals were filled the questionnaire and yielded a
response rate of 98.1%. Two hundred sixty eight (62.28%) of participants were male. Regarding
the age of the health professionals, nearly two-thirds of them, 274 (63.57%), belong to less than
30 years old age group. More than half 253(58.07%) of the participants were protestant religion
followers. Greater than three fourth of the health professionals who participated in this study
were from hospital institutions 350 (81.21%) (Table 1). The attitude of the health professionals towards COVID-19 vaccine Almost half 210 (48.72%) of the participants have poor attitude toward COVID-19 vaccina-
tion. One-third of the participants strongly agreed that COVID-19 could not be controlled
without vaccination. Moreover, nearly one-third of participants agreed that mass vaccination
against COVID-19 helps overcome the pandemic (Table 2). Regarding the effectiveness of the
newly discovered COVID-19 vaccination, less than a quarter of the participants strongly dis-
agreed with 63 (14.62%) (Fig 1). Medical disorder related characteristics of the health professionals Thirty-three healthcare workers have a history of taking vaccination in their lives (7.66%). Nearly one fifth of the health care workers in this study had chronic medical diseases 19
(4.41%). Participants’ most commonly reported chronic disease was hypertension 6 (46.15%). Greater than half of the participants were vaccinated against coronavirus 240 (55.68%). Data management and analysis Epidata version 3.0 was used for data entry [31], and exported to STATA version 14.0 for fur-
ther analysis [32]. Descriptive statistics, like frequencies, percentages, mean and standard devi-
ation were computed. Before analysis, data were cleaned and edited by using simple
frequencies and cross-tabulation. Re-categorization of categorical variables and categorization
of continuous variables was done. The assumption of the logistic regression model was
checked before fitting to the model. The binary logistic regression model was fitted to deter-
mine factors associated with attitude towards COVID-19 vaccine. The multivariable logistic 4 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination regression analysis included factors associated with the outcome variable at 20% (p-value
0.20) significant level in the bivariable logistic regression analysis. Then crude and adjusted
odds ratio and their corresponding 95% confidence intervals were presented in the final multi-
variable logistic regression table. Finally, AOR with 95% confidence intervals was computed
and statistical significance was declared when it was significant at a 5% level (p-value < 0.05). Correlation matrices checked multicollinearity (association between explanatory variables),
and the model goodness of fit test was checked by Hosmer and Lemeshow test. Ethical considerations The study was approved, and ethical clearance letters were obtained from Wollega University,
Institute of Health Science Research Ethics review board (Min. No. 07/2021). After approval, a
permission letter was obtained from the administrative body of health facilities to respective
clinics. Verbal consent was obtained from study participants, and the purpose of this study
was stated to all participants. Everybody participated voluntarily in this study. PLOS ONE PLOS ONE Table 1. Socio demographic characteristics of the health professionals in Nekemte city, Western Ethiopia, 2021. Variables
Option
Frequency
Percent
Age
<30years old
274
63.57
> = 30years old
157
36.43
Sex
Male
268
62.18
Female
163
37.82
Marital status
Never married
176
40.84
Married
243
56.38
Separated
8
1.86
Others
4
0.93
Religion
Muslim
73
16.94
Protestant
253
58.70
Catholic
10
2.32
Orthodox
71
16.47
Others
24
5.57
Institution
Hospitals
350
81.21
Health center
34
7.89
Private
47
10.90
Education level
Diploma
38
8.82
First degree
362
83.99
Masters
24
5.57
Doctors
2
0.46
Specialty degree
5
1.16
Back ground
Nurses
186
43.16
Midwifery
56
12.99
Pharmacy
32
7.42
Medical practitioner
47
10.90
Public health
41
9.51
Anesthetists
19
4.41
MLS
36
8.35
Psychiatrics
6
1.39
others
8
1.86
https://doi org/10 1371/journal pone 0265061 t001 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 Health care workers perception towards COVID-19 vaccine The distributions of each perception item about the COVID-19 vaccine are presented in
Table 3. Concerning the question “Do you think the COVID-19 vaccine is effective”? Nearly
one-third of them thought the vaccine against COVID-19 was effective. More than half of the
participants responded unsure for the question “Do you think COVID-19 will be controlled
only by preventive measures without vaccination”? (Table 3). Almost half of the participants accept that the newly developed COVID-19 vaccine has side
effect 209 (48.49%) (Fig 2). 5 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 Attitude of health professionals towards COVID-19 vaccination PLOS ONE Table 2. Attitude of the health care workers towards COVID-19 vaccine in Nekemte health facilities, Western Ethiopia. Factors associated with attitude of health professionals towards COVID-19
vaccine In multivariable logistic regression, variables like age, sex, institution types, having chronic dis-
eases and allergic reaction to previous medication have shown significant association with the
outcome of interest. From those variables, two of them showed significant association with the
attitude of health professionals toward a vaccine against COVID-19. The odd of developing
poor attitude toward COVID-19 vaccine was 2.14 times higher among health professionals
aged < 30 years than their counterparts (AOR = 2.14, 95%CI: 1.25, 3.67). The likelihood of
having a poor attitude toward the COVID-19 vaccine was 2.45 times higher among health pro-
fessionals working at health centers than those working at hospitals AOR = 2.45(95%CI
1.01,5.92). Similarly, the odds of having a poor attitude towards the COVID-19 vaccine was
7.77 times higher among health professionals working at private clinics and hospitals
AOR = 7.77(95% CI 2.19,27.58). Moreover, the proportion of health professionals with unfa-
vorable attitudes was 62% lower among professionals who have good knowledge of COVID-19
vaccination than their counterparts AOR = 0.38(95%CI: 0.22, 0.64) (Table 4). 6 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 Attitude of health professionals towards COVID-19 vaccination PLOS ONE Variables
Option
Frequency
Percent
The vaccine that is currently given in Ethiopia is the actual one that those innovative countries are taking
Strongly disagree
114
26.45
Disagree
132
30.63
Neutral
81
18.79
Agree
79
18.33
Strongly agree
25
5.80
If one person takes COVID-19 vaccination, it has a great contribution for other people
Strongly disagree
65
15.08
Disagree
86
19.95
Neutral
53
12.30
Agree
155
35.96
Strongly agree
72
16.71
I will take the vaccine if I get it without hesitation
Strongly disagree
61
14.15
Disagree
183
42.46
Neutral
51
11.83
Agree
86
19.95
Strongly agree
50
11.60
I encourage my family and others to take the vaccination
Strongly disagree
58
13.46
Disagree
135
31.32
Neutral
61
14.15
Agree
127
29.47
Strongly agree
50
11.60
COVID-19 cannot be controlled without vaccination
Strongly disagree
85
19.72
Disagree
136
31.55
Neutral
65
15.08
Agree
111
25.75
Strongly agree
34
34
COVID-19 vaccine is fairly distributed for all
Strongly disagree
67
15.55
Disagree
122
28.31
Neutral
84
19.49
Agree
99
22.97
Strongly agree
59
13.69
Mass vaccination can overcome the epidemic attack of the COVID-19
Strongly disagree
53
12.30
Disagree
90
20.88
Neutral
77
17.87
Agree
138
32.02
Strongly agree
73
16.94
The best prevention method is to take vaccine against COVID-19
Strongly disagree
54
12.53
Disagree
91
21.11
Neutral
92
21.35
Agree
134
31.09
Strongly agree
60
13.92
The COVID-19 vaccine is not tested adequately for its effectiveness
Strongly disagree
28
6.50
Disagree
73
16.94
Neutral
67
15.55
Agree
129
29.93
Strongly agree
134
31.09
After vaccinated against COVID-19 other precaution can be avoided
Strongly disagree
89
20.65
Disagree
131
30.39
Neutral
62
14.39
Agree
66
15.31
Strongly agree
83
19.26
The overall attitude towards COVID-19 vaccine
Favorable
221
51.28
Unfavorable
210
48.72
https://doi.org/10.1371/journal.pone.0265061.t002 If one person takes COVID-19 vaccination, it has a great contribution for other people I will take the vaccine if I get it without hesitation I will take the vaccine if I get it without hesitation I encourage my family and others to take the vaccination COVID-19 cannot be controlled without vaccination COVID-19 vaccine is fairly distributed for all Mass vaccination can overcome the epidemic attack of the COVID-19 The best prevention method is to take vaccine against COVID-19 The COVID-19 vaccine is not tested adequately for its effectiveness After vaccinated against COVID-19 other precaution can be avoided The overall attitude towards COVID-19 vaccine https://doi.org/10.1371/journal.pone.0265061.t002 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 7 / 14 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Fig 1. PLOS ONE Attitude of the health professionals regarding effectiveness of the Corona virus vaccine, 2021. https://doi.org/10.1371/journal.pone.0265061.g001 Fig 1. Attitude of the health professionals regarding effectiveness of the Corona virus vaccine, 2021. https://doi.org/10.1371/journal.pone.0265061.g001 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 Discussion Though the vaccine development against COVID-19 was promising for the world population,
vaccine hesitancy has become a global challenge to the successful uptake of the vaccine [11,13–
17]. Literature shows that vaccine safety and efficacy are among the worries of the people and
the reasons for vaccine hesitancy [17,18,24]. Health care professionals are at a particular con-
cern to be vaccinated to influence the general population for vaccination positively. There was
a dearth of information about the attitude and perception of health professionals toward
COVID-19 vaccination and its associated factor in Ethiopia, particularly in the study area. Therefore, this study was intended to determine the attitude of health professionals toward
COVID-19 vaccination and its associated factors in Nekemte town. Accordingly, 31.55% of the study participants had agreed to take the vaccine without hesita-
tion if available in the present study. This is lower than the study findings from Southwestern
Ethiopia (48.4%) [23], Eastern Ethiopia (61.4%) [33], Bangladesh (58.6%) [34], Canada (72.40)
[35]. The possible explanation for this might be the variation in trust and reliability of the
source of information about COVID-19 vaccine. Moreover, 41.07% of the study subjects in the
present study have also agreed on encouraging families and others to take the vaccine while
65.5% of participants in Bangladesh agreed to do so. Furthermore, 59.75% of this study’s health
professionals agreed that COVID-19 would not be controlled without vaccination. This echoes
the finding from Bangladesh (63.4%) [34]. In addition, nearly half of the study participants in
the current study have agreed on mass vaccination to overcome the pandemic. This is also
congruent with study done in Libya [36]. Comparable to the study finding from Saudi Arabia
(37%) [37], only one-third of participants agreed on the vaccine’s effectiveness in the present
study. This depicts that there is still a need to provide reliable and accurate information about
the vaccine’s effectiveness against COVID-19 to health care professionals and the public. 8 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Table 3. Perception the health care professionals towards COVID-19 vaccine. Variables
Option
Frequency
Percent
Have you ever been infected with COVID-19
Yes
95
22.04
No
169
39.21
I don’t know
167
38.75
Do you think that the COVID-19 vaccine is effective? Discussion Yes
131
30.39
No
34
7.89
I don’t know
266
61.72
Do you think that COVID-19 vaccine is mandatory for health care workers? Yes
262
60.79
No
24
5.56
I don’t know
145
33.64
Do you think COVID-19 will be controlled only by preventive measures
without vaccination? Yes
85
19.72
No
102
23.67
I don’t know
244
56.61
Do you think that various COVID-19 vaccines have been discovered? Yes
142
32.95
No
46
10.67
I don’t know
243
56.38
Do you think that the COVID-19 vaccine will be affordable and accessible by
the common person! Yes
59
13.69
No
145
33.64
I don’t know
227
52.67
https://doi.org/10.1371/journal.pone.0265061.t003 PLOS ONE Table 4. Multivariable analysis of factors associated with attitude towards COVID-19 vaccine among health professionals in Nekemte city, Western Ethiopia. Characteristics
Attitude
COR(95%CI)
AOR(95%CI)
P-value
Poor
Good
Age
<30
149
125
1.87(1.25,2.79)
2.14(1.25,3.67)
<0.01
> = 30
61
96
Ref
Sex
Male
125
143
Ref
Female
85
78
0.80 (0.54,1.18)
0.93(0.54, 1.59)
0.795
Institution
Hospital
195
155
Ref
Health center
10
24
3.01(1.40, 6.50)
2.45(1.01,5.92)
0.045
Private clinic
5
42
10.56 (4.0,27.35)
7.77(2.19,27.58)
<0.01
Chronic diseases
Yes
9
10
Ref
No
201
211
0.94(0.37,2.37)
0.76(0.25,2.29)
0.630
History of allergic reaction to previous medication
Yes
21
20
Ref
No
189
201
1.11(0.58,2.12)
1.04(0.46,2.33)
0.914
Knowledge about COVID-19 vaccination
Poor knowledge
44
86
Ref
Good knowledge
139
163
0.30(0.18,0.49)
0.38(0.22,0.64)
<0.01
https://doi.org/10.1371/journal.pone.0265061.t004 of the general population had a favorable attitude toward COVID-19 vaccination [38]. The
possible reason for the observed discrepancy might be due to the relative information differ-
ence among the population of interest. Furthermore, it might be due to health care profession-
als being at higher risk of infection with the virus that might result in a favorable attitude
toward vaccination to minimize the risk of infection. This implies a need to assure the vac-
cine’s effectiveness, safety, and efficacy to enhance its uptake by health professionals and the
general public. Health professionals are the counselor and advocators of the general population
that their decision to receive the vaccine can greatly influence the uptake by the general
population. The factors affecting health care professionals’ attitude toward COVID-19 vaccination were
knowledge towards COVID-19 vaccination, age of respondents, and type of health facility. Accordingly, the proportion of health professionals who have unfavorable attitudes was 62%
lower among professionals with good knowledge of COVID-19 vaccination than their coun-
terparts. This might be because knowing the importance of the COVID-19 vaccine can posi-
tively influence someone to have a positive attitude toward it. Moreover, the odds of having
unfavorable attitudes were much higher among health professionals working in private clinics
and health centers than those in hospitals. This variation might be due to the relative number
of client flow to the health center and private clinic being much lower than the hospital and,
hence the professionals consider themselves at lower risk of exposure and infection to
COVID-19. In addition, almost all COVID-19 patients have been admitted to hospitals than
private clinics or health centers. https://doi.org/10.1371/journal.pone.0265061.t003 The current study revealed that half of the health care professionals who participated in this
study have a favorable attitude toward COVID-19 vaccination. This is lower than the study
done in Bangladesh reported that 78% of the general population had a favorable attitude [34]. However, it is higher than the online survey which was done in Ethiopia that reported 24.2% Fig 2. Perception the health care workers regarding Corona virus vaccine’s side effect, 2021. https://doi.org/10.1371/journal.pone.0265061.g002 Fig 2. Perception the health care workers regarding Corona virus vaccine’s side effect, 2021. https://doi.org/10.1371/journal.pone.0265061.g002 Fig 2. Perception the health care workers regarding Corona virus vaccine’s side effect, 2021. https://doi.org/10.1371/journal.pone.0265061.g002 Fig 2. Perception the health care workers regarding Corona virus vaccine’s side effect, 2021. PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 9 / 14 Attitude of health professionals towards COVID-19 vaccination PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 Limitation of the study The study did not provide qualitative perspectives on the attitude and perception of health
professionals towards the COVID-19 vaccine and its associated factors, which, if available,
could underpin the quantitative findings. Moreover, since it is a cross-sectional study, it did
not address the cause and effect relationship between the factors and the outcome variables. Supporting information S3 File. Tool. (DOCX) PLOS ONE Therefore, professionals working at health centers and private
clinics for known and obvious reasons consider themselves to have a lower risk of infection
with COVID-19. As a result, they might have an unfavorable attitude toward the COVID-19
vaccine than professionals working in the hospital setting. In this study, age of HCWs were significantly associated with attitude towards COVID-19
vaccine, in which health professionals aged less than 30 years had negative attitude towards the
vaccine. This is in line with study conducted in North Ethiopia which reported higher age pos-
itively associated with positive attitude towards COVID-19 vaccine [39]. This might be due to
the fact that, as age increase, the probability of developing comorbidity increase, and the
chance of infecting with COVID-19 also high. Thus the HCWs intention to receive the vaccine
would be high. 10 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Declaration Ethical approval and consent to participate. The study was approved, and ethical clearance
letters were obtained from Wollega University, Institute of Health Science Research Ethics
review board. After approval, a permission letter was obtained from the administrative body of
health facilities to respective clinics. Verbal consent was obtained from study participants, and
the purpose of this study was stated to all participants. Everybody participated voluntarily in
this study. Acknowledgments We want to thank all health facilities for their invaluable co-operation during data collection,
and our deep acknowledgment also goes to the data collectors for their interest and commit-
ment in carrying out the study. Conclusion In general, the attitude and perception of health care professionals toward the COVID-19 vac-
cine in the study area were unsatisfactory. Having poor knowledge about the COVID-19 vac-
cine, young age group, working in private clinics and health centers are the independent
determinants of unfavorable attitudes towards the COVID-19 vaccine. Therefore, there is still
a need to improve health professionals’ knowledge of the COVID-19 vaccine by providing reli-
able information regarding vaccine safety, efficacy, and effectiveness. Furthermore, the media
outlets need to work to develop trust among the public by disseminating accurate and consis-
tent information about the vaccine. In addition, future researchers should also explore more
about the attitude and perception of health care professionals toward the COVID-19 vaccine
and its determinants using qualitative data. Author Contributions Conceptualization: Tadesse Tolossa, Diriba Mulisa, Getahun Fetensa, Belayneh Mengist,
Gebeyehu Abera, Tesfaye Shibiru. Data curation: Diriba Ayala, Dejene Seyoum. Data curation: Diriba Ayala, Dejene Seyoum. 11 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Formal analysis: Tadesse Tolossa, Bizuneh Wakuma, Ebisa Turi, Diriba Mulisa, Getahun
Fetensa. Funding acquisition: Bizuneh Wakuma, Diriba Mulisa, Diriba Ayala, Gebeyehu Abera,
Emiru Merdassa Atomssa, Dejene Seyoum. Investigation: Ebisa Turi, Getahun Fetensa, Belayneh Mengist, Gebeyehu Abera, Tesfaye
Shibiru. Methodology: Tadesse Tolossa, Bizuneh Wakuma, Ebisa Turi, Diriba Ayala, Dejene Seyoum. Project administration: Getahun Fetensa, Belayneh Mengist, Gebeyehu Abera, Ayantu
Getahun. Resources: Tadesse Tolossa, Ebisa Turi, Diriba Mulisa, Emiru Merdassa Atomssa. Software: Tadesse Tolossa, Bizuneh Wakuma, Belayneh Mengist, Tesfaye Shibiru. Supervision: Bizuneh Wakuma, Diriba Ayala, Getahun Fetensa, Tesfaye Shibiru, Ayantu
Getahun. Validation: Diriba Mulisa, Getahun Fetensa, Belayneh Mengist, Gebeyehu Abera, Emiru Mer-
dassa Atomssa. Visualization: Tadesse Tolossa, Diriba Mulisa, Diriba Ayala, Gebeyehu Abera, Emiru Mer-
dassa Atomssa, Dejene Seyoum. Writing – original draft: Tadesse Tolossa, Bizuneh Wakuma, Ebisa Turi, Dejene Seyoum. Writing – review & editing: Tadesse Tolossa, Bizuneh Wakuma, Ebisa Turi, Diriba Mulisa,
Diriba Ayala, Getahun Fetensa, Emiru Merdassa Atomssa, Dejene Seyoum, Tesfaye Shibiru,
Ayantu Getahun. References 1. Worldometer, COVID-19 Coronavirus Pandemic. https://www.worldometers.info/coronavirus/? utmcampaign=homeAdvegas1? (accessed on May 30, 2021). 2021. 2. Du R.-H., et al., Predictors of mortality for patients with COVID-19 pneumonia caused by SARS-CoV-2:
a prospective cohort study. European Respiratory Journal, 2020. 55(5). 3. Wachamo D., et al., Sexual and Reproductive Health Services Utilization and Associated Factors
among College Students at West Arsi Zone in Oromia Region, Ethiopia. The Scientific World Journal,
2020. 2020. https://doi.org/10.1155/2020/3408789 PMID: 32908460 4. Mehtar S., et al., Limiting the spread of COVID-19 in Africa: one size mitigation strategies do not fit all
countries. The Lancet Global Health, 2020. 8(7): p. e881–e883. https://doi.org/10.1016/S2214-109X
(20)30212-6 PMID: 32530422 5. Muhaidat N., et al., Pregnancy During COVID-19 Outbreak: The Impact of Lockdown in a Middle-
Income Country on Antenatal Healthcare and Wellbeing. International Journal of Women’s Health
2020. 12: p. 1065–1073. https://doi.org/10.2147/IJWH.S280342 PMID: 33235516 6. Mosisa G., et al., Fertility desire and associated factors among people living with HIV in Ethiopia: a sys-
tematic review and meta-analysis. Archives of Public Health, 2020. 78(1): p. 1–16. https://doi.org/10. 1186/s13690-020-00504-0 PMID: 33292626 7. Jasim, S.K., Post Cesarean Section Surgical Site Infection; Incidence and Risk Factors. 8. World Health Organization COVID-19 vaccine tracker and landscape: https://www.who.int/publications/
m/item/draft-landscape-of-covid-19-candidate-vaccines. 2021. 9. Duch R., et al., Who should be first in line for the COVID-19 vaccine? Surveys in 13 countries of the pub-
lics preferences for prioritisation. medRxiv, 2021. 10. Belsti Y., et al., Willingness of Ethiopian Population to Receive COVID-19 Vaccine. Journal of Multidisci-
plinary Healthcare, 2021. 14: p. 1233. https://doi.org/10.2147/JMDH.S312637 PMID: 34093019 12 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination 11. Kaplan A.K., et al., The willingness to accept the COVID-19 vaccine and affecting factors among health-
care professionals: A cross-sectional study in Turkey. International Journal of Clinical Practice, 2021: p. e14226. https://doi.org/10.1111/ijcp.14226 PMID: 33864328 12. Dodd R.H., et al., Willingness to vaccinate against COVID-19 in Australia. The Lancet Infectious Dis-
eases, 2021. 21(3): p. 318–319. 13. Alabdulla M., et al., COVID-19 vaccine hesitancy and attitudes in Qatar: A national cross-sectional sur-
vey of a migrant-majority population. Influenza and other respiratory viruses, 2021. 15(3): p. 361–370. https://doi.org/10.1111/irv.12847 PMID: 33605010 14. Khubchandani J., et al., COVID-19 vaccination hesitancy in the United States: a rapid national assess-
ment. Journal of Community Health, 2021. 46(2): p. 270–277. https://doi.org/10.1007/s10900-020-
00958-x PMID: 33389421 15. References Lake E.A., et al., Knowledge, attitude and practice towards COVID-19 among health professionals in
Ethiopia: A systematic review and meta-analysis. PloS one, 2021. 16(2): p. e0247204. https://doi.org/
10.1371/journal.pone.0247204 PMID: 33606744 16. Latkin C.A., et al., Trust in a COVID-19 vaccine in the US: A social-ecological perspective. Social sci-
ence & medicine (1982), 2021. 270: p. 113684. 17. Troiano G. and Nardi A., Vaccine hesitancy in the era of COVID-19. Public Health, 2021. https://doi.org/
10.1016/j.puhe.2021.02.025 PMID: 33965796 18. Fares S., et al., COVID-19 Vaccination Perception and Attitude among Healthcare Workers in Egypt. Journal of Primary Care & Community Health, 2021. 12: p. 21501327211013303. https://doi.org/10. 1177/21501327211013303 PMID: 33913365 19. Lin Y., et al., Understanding COVID-19 vaccine demand and hesitancy: A nationwide online survey in
China. PLoS neglected tropical diseases, 2020. 14(12): p. e0008961. https://doi.org/10.1371/journal. pntd.0008961 PMID: 33332359 20. Fisher K.A., et al., Attitudes toward a potential SARS-CoV-2 vaccine: a survey of US adults. Annals of
internal medicine, 2020. 173(12): p. 964–973. https://doi.org/10.7326/M20-3569 PMID: 32886525 21. Zewude B. and Habtegiorgis T., Willingness to Take COVID-19 Vaccine Among People Most at Risk of
Exposure in Southern Ethiopia. Pragmat Obs Res, 2021. 12: p. 37–47. https://doi.org/10.2147/POR. S313991 PMID: 34079423 22. Mohammed R., et al., COVID-19 vaccine hesitancy among Ethiopian healthcare workers. PloS one,
2021. 16(12): p. e0261125. https://doi.org/10.1371/journal.pone.0261125 PMID: 34919597 23. Angelo A.T., Alemayehu D.S., and Dachew A.M., Health care workers intention to accept COVID-19
vaccine and associated factors in southwestern Ethiopia, 2021. PloS one, 2021. 16(9): p. e0257109. https://doi.org/10.1371/journal.pone.0257109 PMID: 34478470 24. Dereje N., et al., COVID-19 Vaccine hesitancy in Addis Ababa, Ethiopia: A mixed-methods study. medRxiv, 2021. 25. Griffin DS, M G., Griffin DO., Adolescents trust physicians for vaccine information more than their
parents or religious leaders. Heliyon, 2018. 4(12): p. e01006. https://doi.org/10.1016/j.heliyon.2018. e01006 PMID: 30619955 26. Karafillakis E, D I., Apfel F, et al., Vaccine hesitancy among healthcare workers in Europe: a qualitative
study. Vaccines, 2016. 34(41): p. 5013–5020. https://doi.org/10.1016/j.vaccine.2016.08.029 PMID:
27576074 27. Reliefweb, Accelerating broad and equitable access to the COVID-19 vaccine in Ethiopia: https://
reliefweb.int/report/ethiopia/accelerating-broad-and-equitable-access-covid-19-vaccine-ethiopia. 2021. 28. Kumar H., et al., Knowledge and Perception of Health Professionals towards COVID-19. Age (years),
2020. 25(090): p. 11.5. 29. Verger P., et al., Online study of health professionals about their vaccination attitudes and behavior in
the COVID-19 era: addressing participation bias. Human Vaccines & Immunotherapeutics, 2021: p. 1–
6. https://doi.org/10.1080/21645515.2021.1921523 PMID: 34047670 30. Tavakol M. and Dennick R., Making sense of Cronbach’s alpha. PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 39.
Alle Y.F. and Oumer K.E., Attitude and associated factors of COVID-19 vaccine acceptance among
health professionals in Debre Tabor Comprehensive Specialized Hospital, North Central Ethiopia;
2021: cross-sectional study. Virusdisease, 2021. 32(2): p. 272–278. https://doi.org/10.1007/s13337-
021-00708-0 PMID: 34222565 References International journal of medical educa-
tion, 2011. 2: p. 53. https://doi.org/10.5116/ijme.4dfb.8dfd PMID: 28029643 31. Lauritsen J.M. and Bruus M., EpiData entry. A comprehensive tool for validated entry and documenta-
tion of data. Odense Denmark: The EpiData Association, 2008. 32. Kohler U. and Kreuter F., Data analysis using Stata. 2005: Stata press. 33. Zewude B. and Belachew A., Intention to Receive the Second Round of COVID-19 Vaccine Among
Healthcare Workers in Eastern Ethiopia. Infect Drug Resist, 2021. 14: p. 3071–3082. https://doi.org/10. 2147/IDR.S326055 PMID: 34408451 13 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061
March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination 34. Islam M.S., et al., Knowledge, attitudes and perceptions towards COVID-19 vaccinations: a cross-sec-
tional community survey in Bangladesh. medRxiv, 2021. https://doi.org/10.1186/s12889-021-11880-9
PMID: 34645399 35. Verger P., et al., Attitudes of healthcare workers towards COVID-19 vaccination: a survey in France
and French-speaking parts of Belgium and Canada, 2020. Eurosurveillance, 2021. 26(3): p. 2002047. 36. Elhadi M., et al., Knowledge, attitude, and acceptance of healthcare workers and the public regarding
the COVID-19 vaccine: a cross-sectional study. BMC public health, 2021. 21(1): p. 1–21. https://doi. org/10.1186/s12889-020-10013-y PMID: 33388037 37. Ahmed N.J., et al., Public knowledge and attitudes toward COVID-19 Vaccination: A cross-sectional
study. Medical Science, 2021. 25(108): p. 279–284. 38. Mesesle M., Awareness and Attitude Towards COVID-19 Vaccination and Associated Factors in Ethio-
pia: Cross-Sectional Study. Infection and Drug Resistance, 2021. 14: p. 2193–2199. https://doi.org/10. 2147/IDR.S316461 PMID: 34163184 39. Alle Y.F. and Oumer K.E., Attitude and associated factors of COVID-19 vaccine acceptance among
health professionals in Debre Tabor Comprehensive Specialized Hospital, North Central Ethiopia;
2021: cross-sectional study. Virusdisease, 2021. 32(2): p. 272–278. https://doi.org/10.1007/s13337-
021-00708-0 PMID: 34222565 14 / 14
|
https://openalex.org/W2554955040
|
https://docusalut.com/bitstream/20.500.13003/10089/1/000387085500001.pdf
|
English
| null |
The evaluation of a remote support program on quality of life and evolution of disease in COPD patients with frequent exacerbations
|
BMC pulmonary medicine
| 2,016
|
cc-by
| 8,294
|
Alcazar et al. BMC Pulmonary Medicine (2016) 16:140
DOI 10.1186/s12890-016-0304-3 Alcazar et al. BMC Pulmonary Medicine (2016) 16:140
DOI 10.1186/s12890-016-0304-3 RESEARCH ARTICLE
Open Access
The evaluation of a remote support
program on quality of life and evolution of
disease in COPD patients with frequent
exacerbations
Bernardino Alcazar1*
, Pilar de Lucas2, Joan B. Soriano3, Alonso Fernández-Nistal4, Antonia Fuster5,
Jose Miguel Rodríguez González-Moro2, Aurelio Arnedillo6, Patricia García Sidro7
and María José Espinosa de los Monteros8 Abstract Background: Chronic obstructive pulmonary disease (COPD) patients often present considerable individual medical
burden in their symptoms, limitations, and well-being that complicate medical treatment. To improve their overall
health status, while reducing the number of exacerbations, a multidisciplinary approach including different elements of
care is needed. The aim of this study was to evaluate the effects of a remote support program on COPD patients at
high risk of experiencing worsening of their disease and other health-related outcomes. Methods: An observational, multicenter, prospective study aimed at evaluating the impact of a 7-month remote
support program on COPD patients in exacerbations control and changes in health status measured with the COPD
assessment test (CAT). Factors associated with a clinically relevant decrease in CAT were assessed using a logistic
regression analysis. Results: A total of 114 subjects started the program. The majority of the study population were males (81.6 %),
retired (70.2 %), without academic qualifications or with a low level of education (68.4 %), and ex-smokers (79.8 %). The
mean ± SD age was 69.6 ± 9.1 years and the BMI was 27.8 ± 5.5 Kg/m2. Overall, 41.9 % (95 % CI 31.9–52.0) patients,
significantly improved health status (CAT decrease ≥2 points). Univariate analysis showed that significant improvement
in CAT was associated with baseline CAT scores [high CAT score 19.2 (±7.5) vs. low CAT score 12.4 (±6.4); OR = 1.15,
95 % CI: 1.07–1.24; p < 0.001] and with being non-compliant [62.5 % (15/24) of non-compliant vs 34.7 % (24/69) of
compliant patients significantly improved CAT scores; OR = 3.13, 95 % CI: 1.19–8.19; p = 0.021). After controlling for the
effect of all variables in a multivariable logistic regression model, the only factor that remained significant was baseline
CAT score. The proportion of smokers in the total population remained constant during the study. There was a
significant reduction in the number of exacerbations after entering this remote support program with median -1
(IQR: -2, 0), (p < 0.001). The Morisky-Green questionnaire showed an increase of treatment compliance, namely at
baseline, 25.8 % (24/93) of patients were noncompliant while in the end 66.7 % (16/24) of them became compliant)
(p = 0.053). Conclusions: A remote support program for high-risk COPD patients results in an improvement of the patients’
health status, particularly in those with initially poor health status, and it helps to reduce COPD exacerbations. The evaluation of a remote support
program on quality of life and evolution of
disease in COPD patients with frequent
exacerbations Bernardino Alcazar1*
, Pilar de Lucas2, Joan B. Soriano3, Alonso Fernández-Nistal4, Antonia Fuster5,
Jose Miguel Rodríguez González-Moro2, Aurelio Arnedillo6, Patricia García Sidro7
and María José Espinosa de los Monteros8 © The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. * Correspondence: balcazarnavarrete@gmail.com
1Hospital de Alta Resolución de Loja, Agencia Sanitaria H. de Poniente, Avda
Tierno Galván s/n., CP 18300 Loja, Granada, Spain
Full list of author information is available at the end of the article Study population Patients of both genders, aged 40 years or older, fulfilling
the selection criteria who signed the informed consent
were recruited. The inclusion criteria were: a) COPD
confirmed by spirometry performed in stable state not
more than 12 months prior to recruitment in the study
with a post-bronchodilator ratio of FEV1/FVC < 0.7; b)
smoker or former smoker of at least 10 pack-years; c)
patients with 2 or more moderate/severe exacerbations
reported in the 12 months prior to study entry; d) pa-
tient clinically stable at the time of inclusion in the study
and who was willing to participate in the Horizonte pa-
tient support program. Disease-specific programs are an integral component
of collaborative self-management. This approach is recog-
nized to improve health outcomes in people with chronic
conditions [10] and has also successfully improved the
health related quality of life (HRQoL) of patients with
chronic respiratory disease, such as asthma [11]. These
programs provide information for patients to recognize
and therefore to prevent, and decrease the severity and/or
frequency of symptoms and to implement appropriate
treatment for the episodes [11]. The exclusion criteria in the study were: (i) patients who
had never smoked, (ii) those who suffered a moderate/
severe exacerbation in the previous 30 days (iii) other
chronic respiratory disease (e.g. bronchial asthma, allergic
rhinitis, severe bronchiectasis, cancer, restrictive lung
disease, etc.) or pulmonary surgery, (iv) or who, in the
opinion of the investigator, did not demonstrate sufficient
cognitive capacity; presented sensory or psychiatric dis-
ability or language barriers that might prevent or hinder
participation in the study, (v) and participation in another
study or clinical trial. A number of studies have evaluated the effect of differ-
ent education programs for COPD and have concluded
that participation in these programs was associated with
an increase in the knowledge of COPD, an improvement
in specific skills to manage the disease, an increased ad-
herence to inhaled therapy, and a decrease in emer-
gency room visits and hospital admissions due to COPD
exacerbations; among other positive outcomes [12–15]. However, the available evidence is still inconclusive due to
different study designs, different types of COPD patients
included, methodological limitations, and a wide variation
of reported outcome measures. An observation period of 12 months that included
7 months of allocation in the Horizonte remote support
program and a follow-up period of 5 months was estab-
lished. Abstract Keywords: Chronic obstructive pulmonary disease, Education, Management, Quality of life, Exacerbations Page 2 of 12 Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 2 of 12 Page 2 of 12 Background the disease (www.atlantishealthcare.com). It has been pre-
viously used in Spain under controlled conditions, to as-
sure its applicability in COPD patients, but has not been
incorporated in to common clinical practice until just
recently. Chronic obstructive pulmonary disease (COPD) is consid-
ered a preventable, treatable, disabling respiratory disease
characterized by an often progressive and mainly irre-
versible airflow obstruction [1, 2]. COPD is currently
the fourth leading cause of death worldwide, and is pro-
jected to be the third cause of death in developed coun-
tries by 2020 [3, 4]. Thus, the primary aim of the study was to assess the
outcomes of the Horizonte remote support program for
COPD patients at high risk, in terms of reduction in fre-
quency and severity of exacerbations, and improvement
in the patients’ health status measured with the COPD
assessment test (CAT) when used as a part of the usual
treatment. COPD is a paradigm of chronic disease, in which self-
management and support are essential for a proper con-
trol [5]. Primary medical management of COPD often
focuses on improving airflow using bronchodilators and
anti-inflammatory therapies; however, the airflow obstruc-
tion associated with COPD is not completely reversible
and often tends to progressively worsen over time [6]. Much of the deterioration and progression of the disease
is related to the number and severity of exacerbations ex-
perienced by patients [7] and, as the disease progresses,
the patients experience a worsening in their quality of
life [8]. Because complete recovery/cure from COPD is
impossible, health professionals should focus on the
improvement of patient-centered outcomes including
health status and quality of life; which are important
outcome measures for treatment and care in COPD pa-
tients [9]. Design of the study and data collection Design of the study and data collection
This was an observational, multicenter, prospective study
where 24 pulmonologists, distributed throughout the
Spanish national territory centres, recruited consecutive
patients between November 2013 and October 2014. Each
researcher aimed to recruit 9 consecutive patients. Sample size calculation For the sample size calculation, it was estimated that
171 completers were needed to detect a mean change in
CAT of at least 2.5 (±10.0) points, with 90 % power and
an alpha of 0.05. Assuming a dropout rate of 20 % from
the start of the study, the number of patients recruited
should total 214. Horizonte program “Moderate COPD exacerbations were defined as a sud-
den increase in respiratory symptoms that required am-
bulatory treatment with systemic corticosteroids and/or
antibiotics, and exacerbations were considered severe
when the patient required hospitalization”. The Horizonte program (developed by the company At-
lantis Healthcare) (15) is based on the sending of text
messages (SMS) and e-mails, in addition to calls made
by skilled nurses, to patients who have given their con-
sent. The program has been endorsed by the Spanish
Pulmonology and Thoracic Surgery Society (SEPAR) and
it is a support program for patients with COPD and was
designed to help them understand their disease and treat-
ment by changing their misconceptions, improving adher-
ence to prescribed treatments and healthy habits (eg. reducing smoking), and consequently their quality of life. The program is available for both newly diagnosed COPD
patients and those already diagnosed and treated. Initially,
the risk of non-adherence is assessed in each patient by
the completion of a questionnaire. According to these
results, segments and risk levels are set (high or low
risk of non-adherence), and different interventions are
established: Telephone calls from nurses, notebooks in
which the objectives are preset to guide the patient,
magazines (5 issues for high risk and 2 issues for low
risk), additional documentation focused on the specific
problems of each patient (max. 4 per patient), and SMS
and e-mails whose frequency varies depending on the
patient’s risk (see a complete description at the end of
the manuscript). Statistical analysis To describe the qualitative variables, absolute frequencies
and percentages were used. For quantitative variables,
those normally distributed used mean, standard deviation
(SD), minimum and maximum figures, while median,
interquartile range, minimum and maximum were used
when they were not normally distributed. Variables of interest were compared between study
groups using the Chi-squared or the Fisher’s exact test
for categorical variables, and the Student’s “t” test for
independent data (or the Mann-Whitney U test if the
assumption of normality was not met), to compare
quantitative variables. The Kolmogorov-Smirnov test or
Shapiro-Wilk test were used to assess if the quantitative
variables followed a normal distribution. Comparisons
of quantitative variables between more than two groups
were made using the Kruskal-Wallis test or analysis of
variance (ANOVA), depending on data distribution. The program’s objective is to improve patient educa-
tion with regard to the knowledge of their disease and to
achieve better adherence. Patient coordination is led by
the company Atlantis Healthcare and is funded by Takeda
Pharmaceutical Spain SA. A more detailed description of
the Horizonte program can be reviewed at Additional file 1. The pre and post-intervention comparisons of quantita-
tive variables were performed using the t Student test or
the Wilcoxon test, depending on the data distribution. The pre and post-intervention comparisons of qualitative
variables of two categories were performed using the
McNemar test. Study population An evaluation was carried out before and after a
2 and 5-month period posterior to the inclusion in the
study, in which the effectiveness of the measures imple-
mented in the support program were assessed. Each patient
conducted their own self-monitoring, comparing their
health status sequentially. For each patient included, We hypothesized that the implementation in a real
clinical practice setting of a disease-specific remote sup-
port program (Horizonte program) for COPD patients at
high risk, would positively influence these patients’ health
status. The Horizonte program basically consists of send-
ing text messages, e-mails, and conducting regular calls
by qualified nurses, to facilitate proper monitoring of Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 3 of 12 Page 3 of 12 from 0 to 5 (0 = no impairment). An overall score is calcu-
lated by adding the score from each item with total scores
ranging from 0 to 40; a higher score indicates a more se-
vere health status impairment or a poorer control of
COPD [17, 18]. The CAT’s minimal clinical important
difference (MCID) has not yet been established, and
has been estimated to be 2.0 or more points [19]. data was collected in an electronic data collection note-
book (e-CDR) designed for this purpose. The information
requested in this e-CDR conformed to usual clinical
practice, and referred to in the standard management
of patients with COPD. Subject characteristics The study flow-diagram and flow-chart are shown in
Figs. 1 and 2. A total of 148 subjects were initially recruited
in the study. Thirty-four were excluded because they did
not meet all the inclusion criteria (n = 114), then 100
completed the intervention program, and finally 93 com-
pleted all study procedures (62.8 %). Baseline demographic
characteristics of the patients are shown in Table 1. Most
participants were male (81.6 %) and were ex-smokers
(79.8). Mean age was 69.6 years ± 9.1 and mean BMI was
27.8 ± 5.5 Kg/m2. Clinical characteristics and pulmonary Study variables Recruiting physicians collected information regarding
demographic data, smoking, medical history, comorbidi-
ties, physical examination (weight, height, BMI, abdom-
inal circumference), pharmacological treatment, history
of exacerbations in the past 7 months, number of hospi-
talizations for COPD in the past 7 months, spirometry
(lung function), Morisky-Green and Levine Tests, Battle
test, exacerbations from baseline, and hospitalizations. The cardiovascular risk was assessed according to BMI,
gender, and waist circumference [16]. Incidence rates of exacerbations were described by annu-
alized incidence rates with their 95 % confidence interval
(95 % CI). Annualization of the rates and their correspond-
ing confidence intervals were performed by adjusting to a
Poisson model incorporating the time (expressed in years)
of each patient in the study as incidence rates with their
corresponding 95 % CI, and p-values. The analysis of a
clinically significant change in CAT was assessed by logistic
regression analysis, and expressed by the odds ratio (OR) Patients were asked to fill in the CAT questionnaire at
baseline (VB) and after 2 (V2), 7 (last Horizonte program
visit – V3) and 12 months (FV) in its validated Spanish
version. The CAT consists of 8 items with scores ranging Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 4 of 12 Fig. 1 Flow Diagram of the study with its 95 % confidence interval and p values. Changes in
CAT scores throughout the study were analyzed using a
generalized linear mixed model of repeated measures. Data
analysis was performed using the Statistical package SAS
version 9.4 and statistical significance was considered when
p < 0.05. function parameters of the sample at baseline are shown
in Tables 2 and 3, respectively. A total of 90 subjects
(78.9 %) had been vaccinated against influenza. Mean
FVC and FEV1 (%) at the baseline were 71.3 % (±19.4)
and 48.7 % (17.4 %) %, respectively. Regarding COPD
severity by spirometric GOLD stage, 5.3 % had mild
COPD, 36.8 % moderate, 43.9 % severe and 14.0 % very
severe COPD. At baseline, 98.2 % (112/114) of partici-
pating patients were receiving treatment/s for COPD
(Tables 1, 2 and 3) Changes in smoking status and pharmacological
treatment During the study, most participants (93.6 %) did not
change their smoking status. However, from baseline up
to 2 months prior to inclusion (V2), 4.3 % (4/93) of
participants changed their smoking status (2 gave up
smoking, one significantly decreased the number of
cigarettes/day, and another significantly increased the Fig. 2 Flow-chart of the study Alcazar et al. Chi-square test; FFisher’s exact test; UMann-Whitney U test COPD chronic obstructive pulmonary disease, S.D standard deviation, BMI body mass index
C
F
U are test; FFisher’s exact test; UMann-Whitney U test Changes in smoking status and pharmacological
treatment BMC Pulmonary Medicine (2016) 16:140 Page 5 of 12 Table 1 Socio-demographic characteristics of the study population
Overall
Treatment non-adherence based on Morisky-Green baseline score
High-Risk
Low-Risk
p-value
N = 114
27 (23.7)
87 (76.3)
Gender
Men
n(%)
93 (81.6)
18 (66.7)
75 (86.2)
0.043F
Women
n(%)
21 (18.4)
9 (33.3)
12 (13.8)
Missing
n
0
0
0
Age (years)
Mean (S.D.)
69.6 (9.1)
68.3 (10.0)
70.0 (8.8)
0.449U
≤65 years
n(%)
44 (38.6)
11 (40.7)
33 (37.9)
0.793C
> 65 years
n(%)
70 (61.4)
16 (59.3)
54 (62.1)
Missing
n
0
0
0
Level of education
No studies/Primary studies
n(%)
78 (68.4)
17 (63.0)
61 (70.1)
0.485C
Intermediate and higher education
n(%)
36 (31.6)
10 (37.0)
26 (29.9)
Missing
n
0
0
0
Employment situation
Retired
n(%)
80 (70.2)
16 (59.3)
64 (73.6)
0.156C
Other
n(%)
34 (29.8)
11 (40.7)
23 (26.4)
Missing
n
0
0
0
BMI (kg/m2)
Mean (S.D.)
27.8 (5.5)
27.8 (6.2)
27.8 (5.3)
0.931U
Underweight (<18.5)
n(%)
3 (2.6)
1 (3.7)
2 (2.3)
0.738F
Normal weight (18.5–24.9)
n(%)
36 (31.6)
10 (37.0)
26 (29.9)
Overweight (25.0–29.9)
n(%)
41 (36.0)
8 (29.6)
33 (37.9)
Obesity (≥30.0)
n(%)
34 (29.8)
8 (29.6)
26 (29.9)
Missing
n
0
0
0
Cardiovascular risk
None
n(%)
31 (27.2)
8 (29.6)
23 (26.4)
0.907C
Increased
n(%)
27 (23.7)
5 (18.5)
22 (25.3)
High
n(%)
29 (25.4)
7 (25.9)
22 (25.3)
Very/Extremely high
n(%)
27 (23.7)
7 (25.9)
20 (23.0)
Missing
n
0
0
0
Smoking status
Ex-smoker
n(%)
91 (79.8)
17 (63.0)
74 (86.1)
0.012C
Smoker
n(%)
23 (20.2)
10 (37.0)
13 (14.9)
Missing
n
0
0
0
COPD treatment (at baseline)
n(%)
112 (98.2)
27 (100.0)
85 (97.7)
1.000C
Long-acting B2 agonists
n(%)
101 (90.2)
23 (85.2)
78 (91.8)
0.456F
Long-acting anticholinergics
n(%)
99 (88.4)
24 (88.9)
75 (88.2)
1.000F
Phosphodiesterase-4 Inhibitors
n(%)
30 (26.8)
6 (22.2)
24 (28.2)
0.539C
Inhaled Corticosteroids
n(%)
88 (78.6)
17 (63.0)
71 (83.5)
0.023C
Oxygen therapy
n(%)
32 (28.6)
4 (14.8)
28 (32.9)
0.069C
non-invasive mechanical ventilation
n(%)
12 (10.7)
4 (14.8)
8 (9.4)
0.479F
Missing
n
0
0
0
COPD chronic obstructive pulmonary disease, S.D standard deviation, BMI body mass index
CChi-square test; FFisher’s exact test; UMann-Whitney U test Table 1 Socio-demographic characteristics of the study population Alcazar et al. Changes in smoking status and pharmacological
treatment BMC Pulmonary Medicine (2016) 16:140 Page 6 of 12 Table 2 Clinical characteristics
Overall
Treatment non-adherence based on Morisky-Green baseline score
High-Risk
Low-Risk
p-value
N = 114
27 (23.7)
87 (76.3)
Time of evolution of COPD (years)
Mean (S.D.)
8.8 (6.8)
7.7 (6.2)
9.2 (7.0)
0.314U
Missing
1
0
1
Number of moderate exacerbations in the last 12 months
Mean (S.D.)
1.6 (1.1)
1.5 (0.8)
1.6 (1.2)
0.967U
Missing
0
0
0
Number of severe exacerbations in the last 12 months
Mean (S.D.)
1.2 (1.6)
0.7 (1.0)
1.4 (1.8)
0.049U
Missing
0
0
0
Total number of exacerbations in the last 12 months
Mean (S.D.)
2.8 (1.4)
2.2 (0.5)
3.0 (1.5)
0.003U
2–3 exacerbations
n(%)
97 (85.1)
26 (96.3)
71 (81.6)
0.069F
4 or more exacerbations
n(%)
17 (14.9)
1 (3.7)
16 (18.4)
Missing
0
0
0
Comorbidities
Cardiac comorbidities
n(%)
41 (36.0)
8 (29.6)
33 (37.9)
0.432C
Coronary heart disease (CHD)
n(%)
22 (19.3)
4 (14.8)
18 (20.7)
0.499C
Peripheral vascular disease
n(%)
13 (11.4)
2 (7.4)
11 (12.6)
0.730F
Missing
n
0
0
0
COPD chronic obstructive pulmonary disease, S.D standard deviation
CChi-square test; FFisher’s exact test; UMann-Whitney U test COPD chronic obstructive pulmonary disease, S.D standard deviation
CChi-square test; FFisher’s exact test; UMann-Whitney U test mild stages respectively; p = 0.015), higher scores in the
mMRC (6.2 points more in those with mMRC > 2) and
BODEx (5.4 points more in BODEx >4; p < 0.001), and
being a current smoker (2.3 increase compared with
ex-smokers; p = 0.026); whereas a better health status
measured by CAT was associated with higher FEV1(%)
(0.09 decrease per % unit; p < 0.001), longer walking au-
tonomy (2.9 and 5.2 points less than <30 min walkers
among those walking 30–60 min and > 60 min respectively;
p < 0.001) and higher compliance measured by the
Morisky- Green questionnaire (2.6 points less in com-
pliant patients; p = 0.005). number of cigarettes/daily). Between V2 and V3, 4.3 %
(4/93) of patients changed their smoking status, (2
gave up smoking, one resumed smoking again, and one
significantly reduced the number of cigarettes/day). Fi-
nally, between the V3 and FV, 2.2 % (2/93) of patients
significantly reduced the number of cigarettes/day. During the baseline visit, COPD treatment was chan-
ged in 36.0 % (41/114) of patients. Changes in smoking status and pharmacological
treatment At the first follow-up
visit (V2), 99.1 % (111/112) of patients were receiving
treatment for COPD and during the visit; the treatment
was changed in 25.9 % (29/112) of them. At the last visit
of the program (V3) and at the end of the study (FV), all
patients were receiving treatment for COPD. Changes in
adherence are stated at the end of this section. Significant Improvements in CAT Significant Improvements in CAT
A total of 41.9 % (95 % CI 31.9–52.0) patients signifi-
cantly improved their reported health status (CAT de-
crease by 2 points or more). Univariate analysis showed
that significant improvement in CAT was associated with
baseline CAT scores [high CAT score 19.2 (±7.5) vs. low
CAT score 12.4 (±6.4); OR = 1.15, 95 % CI: 1.07–1.24;
p < 0.001] and being non-compliant as measured with
the Morisky-Green questionnaire [62.5 % (15/24) of
non-compliant vs 34.7 % (24/69) of compliant patients
significantly improved CAT scores; OR = 3.13, 95 % CI: Changes in CAT At baseline, patients had relatively high CAT scores:
[15.3 (SD = 7.6)]. Throughout the study period, CAT
scores improved an average of -0.4 (95 % CI: -1.6; 0.8)
points, although not statistically significant (p = 0.530,
paired t-Student) (Fig. 3). Worse health status measured
by CAT was associated with longer duration of COPD
(0.14 increase of CAT per year; p = 0.018), severe and
very severe GOLD stages (1.9 and 3.3 points more than Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 7 of 12 Table 3 Lung function at baseline 1.19–8.19; p = 0.021). After controlling for the effect of
all variables in a multivariable logistic regression model,
the only factor that remained associated with CAT change
(“significant improvement” vs. Changes in CAT “no improvement”) was the
baseline CAT score (Table 4)
Change in the number of exacerbations
The average duration of COPD in the sample was 8.8
6.8 years, while in the 12 months prior to the stud
85.1 % experienced 2 or 3 exacerbations and 14.9 % ex
perienced 4 or more D ring the Horizonte program
Table 3 Lung function at baseline
Overall
Treatment non-adherence based on Morisky-Green baseline score
High-Risk
Low-Risk
p-value
N = 114
27 (23.7)
87 (76.3)
Spirometry
No
n(%)
0 (0.0)
———
———
Yes, prior to the visit
n(%)
75 (65.8)
13 (48.2)
62 (71.3)
0.027C
Yes, during the visit
n(%)
39 (34.2)
14 (51.8)
25 (28.7)
Spirometry results
FVC (ml) - Mean (S.D.)
2485.4 (844.0)
2546.7 (788.7)
2466.4 (864)
0.668T
FVC (%) - Mean (S.D.)
71.3 (19.4)
75.7 (21.7)
69.9 (18.6)
0.142U
FEV1 (ml) - Mean (S.D.)
1239.7 (521.8)
1456.3 (544.9)
1172.5 (498.7)
0.013T
FEV1 (%) - Mean (S.D.)
48.7 (17.4)
56.7 (17.8)
46.2 (16.6)
0.007U
FEV1/FVC (%) - Mean (S.D.)
50.8 (13.2)
57.3 (10)
48.8 (13.5)
0.004U
Missing
n
0
0
0
GOLD stage
Stage I: Mild (80 ≤FEV1% ≤100)
n(%)
6 (5.3)
2 (7.4)
4 (4.6)
0.074F
Stage II: Moderate (50 ≤FEV1% ≤79)
n(%)
42 (36.8)
15 (55.6)
27 (31.0)
Stage III: Severe (30 ≤FEV1% ≤49)
n(%)
50 (43.9)
7 (25.9)
43 (49.4)
Stage IV: Very severe (FEV1% < 30)
n(%)
16 (14.0)
3 (11.1)
13 (14.9)
Missing
n
0
0
0
O2 saturation (%)
X (D.E.)
93.9 (3.0)
95.0 (2.7)
93.5 (3.0)
0.025U
O2 saturation >90 %
98 (86.0)
25 (92.6)
73 (83.9)
0.351F
Missing
n
0
0
0
Minutes of walking per day
< 30
n(%)
39 (34.2)
6 (22.2)
33 (37.9)
0.323C
30–60
n(%)
36 (31.6)
10 (37.0)
26 (29.9)
> 60
n(%)
39 (34.2)
11 (40.7)
28 (32.2)
Missing
n
0
0
0
Emphysema
No
n(%)
56 (49.1)
18 (66.7)
38 (43.7)
0.037C
Yes
n(%)
58 (50.9)
9 (33.3)
49 (56.3)
Missing
n
0
0
0
BODEx index
Quartile 1: 0–2 points
n(%)
28 (24.6)
12 (44.4)
16 (18.4)
0.011C
Quartile 2: 3–4 points
n(%)
44 (38.6)
11 (40.7)
33 (37.9)
Quartile 3: 5–6 points
n(%)
31 (27.2)
4 (14.8)
27 (31.0)
Quartile 4: 7–10 points
n(%)
11 (9.6)
0 (0.0)
11 (12.6)
Missing
n
0
0
0
S.D standard deviation
CChi-square test; FFisher’s exact test; TT-Test; UMann-Whitney U test Change in the number of exacerbations
The average duration of COPD in the sample was 8.8 ±
6.8 years, while in the 12 months prior to the study,
85.1 % experienced 2 or 3 exacerbations and 14.9 % ex-
perienced 4 or more. Discussion The objective of the present study was to examine the
impact of a remote support program on the health status
of moderate/severe COPD patients. Recommendations
for the use of specific support programs for patients with
COPD are based on experience with other chronic dis-
eases such as diabetes [20], coronary artery disease [21],
and asthma [22]. Studies investigating the utility of such
programs for COPD reported heterogeneous conclusions,
and meta-analyses have argued that more studies are
needed [23, 24]. Changes in COPD exacerbations frequency 12 months
before and after the study are presented in Fig. 4. During
the 12 months before the study, median total exacerba-
tions was 2 (IQR: 2-3), while during the study it decreased
to 1 (IQR: 0-3). Median change (post-pre study) in the
number of exacerbations was therefore -1 (IQR: -2, 0),
(p < 0.001). For moderate exacerbations, patients expe-
rienced a median of 2 (IQR 1-2) and, during the study,
1 (IQR 0-1). Median change (post-pre study) in the number
of moderate exacerbations is -1 (IQR: -2, 0), (p < 0.001). Fi-
nally for severe exacerbations, patients experienced a
median previous exacerbations of 1 (IQR 0-2) and, dur-
ing the study, 0 (IQR 0-1), with a median change (post-
pre study) in the number of severe exacerbations of 0
(IQR: -1, 0), (p = 0.017). Reducing the burden of disease by improving patients’
symptoms, functional status, and quality of life are import-
ant goals. There has been a substantial increase in the use
of newly developed tools that measure health status and it
is important for clinicians and researchers to assess
these instruments’ strengths and weaknesses in provid-
ing insight into a patient’s condition and experience. Relying only on mortality and physiological outcomes
could blind the clinician to the potential benefits that
patients may receive from a treatment. A growing body
of research utilizes end-points assessed directly by pa-
tients whose self-reported health status includes health-
related quality of life and their functional status [25]. Changes in adherence (VB-V3), 45.0 % of patients experienced exacerbations
[30.0 % moderate exacerbations, 24.0 % severe exacerba-
tions (8.0 % exacerbations that led to emergency room
visits, and 17.0 % hospitalization)]. The median number
of exacerbations was 2 for total exacerbations (IQR 1-3)
with a maximum of 8; 1 for moderate exacerbation
(IQR: 1-2) with up to 6; 1 for severe exacerbation (IQR:
1-1) with up to 8; and 1 emergency exacerbation (IQR:
1-1) with a maximum of 5. After program completion,
57.0 % of patients had suffered exacerbations [35.5 %
moderate exacerbations, 29.0 % severe exacerbations,
(15.1 % emergency exacerbations, and 22.6 % exacerba-
tions requiring hospitalization)). Changes in adherence were of borderline significance
(p = 0.053). According to the Morisky-Green question-
naire, at baseline 25.8 % (24/93) of patients were non-
compliant. Of these patients, at the end of the study,
66.7 % (16/24) became compliant. Of the 74.2 % (69/93)
of compliant patients at baseline, 91.3 % (63/69) did not
change their adherence and 8.7 % (6/69) became non-
compliant when the study finished. Changes in CAT During the Horizonte program Change in the number of exacerbations 1.19–8.19; p = 0.021). After controlling for the effect of
all variables in a multivariable logistic regression model,
the only factor that remained associated with CAT change
(“significant improvement” vs. “no improvement”) was the
baseline CAT score (Table 4). Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 8 of 12 Fig. 3 COPD assessment test (CAT) scores at baseline, at the first (V2) and second (V3) follow-up visits and at the end of the study (FV) Fig. 3 COPD assessment test (CAT) scores at baseline, at the first (V2) and second (V3) follow-up visits and at the end of ssment test (CAT) scores at baseline, at the first (V2) and second (V3) follow-up visits and at the end of the study (FV) Changes in pulmonary function No significant differences in pulmonary function were
observed from baseline. Initial mean FVE1 was 49.5 %
(16.9) and at the end of the study it was 49.0 % (18.2) not
statistically significant (0.0 (IQR: -5.0; 4.0), p = 0.822). Page 9 of 12 Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Table 4 Main objective analysis: Decrease in at least two points in CAT between the baseline and the final visit. Subgroup analysis:
univariate and multivariate models
Variable
Category
Univariate analysis
OR (CI 95 %)
Multivariate analysis
OR (CI 95 %)
Gender
Women
——————
Men
0.50 (0.17–1.48)
Age
0.97 (0.93–1.02)
Age
≤65 years
——————
>65 years
0.48 (0.20–1.11)
BMI
1.00 (0.92–1.08)
BMI classification
Normal (18.5–24.9)
——————
Overweight (25.0–29.9)
1.37 (0.49–3.82)
Obesity (≥30.0)
0.87 (0.31–2.49)
CAT
1.15 (1.07–1.24)
1.15 (1.07–1.24)
Time of evolution COPD (years)
0.96 (0.91–1.03)
Previous exacerbations
2–3
——————
≥4
0.42 (0.11–1.65)
FEV1(%) Postbronchodilation
1.01 (0.98–1.03)
GOLD stage
Mild-moderate
——————
Severe-very severe
0.96 (0.42–2.21)
Dyspnea
≤2
——————
>2
0.67 (0.27–1.63)
BODEx index
≤4
——————
>4
0.88 (0.38–2.07)
Minutes walking a day
<30
——————
30–60
1.48 (0.54–4.07)
>60
1.00 (0.36–2.78)
Morisky-Green questionnaire
Compliant
——————
Noncompliant
3.13 (1.19–8.19)
Significant cardiac comorbidity
No
——————
Yes
0.47 (0.17–1.36)
Cardiovascular risk
None
——————
Increased
0.92 (0.28–3.102)
High
0.89 (0.27–2.89)
Very/extremely high
1.05 (0.33–3.38)
Smoking status
Ex-smoker
——————
Smoker
1.98 (0.70–5.61)
COPD chronic obstructive pulmonary disease, BMI body mass index, CAT COPD Assessment Test Table 4 Main objective analysis: Decrease in at least two points in CAT between the baseline and the final visit. Subgroup analysis:
univariate and multivariate models COPD chronic obstructive pulmonary disease, BMI body mass index, CAT COPD Assessment Test need for effective care plans to optimize the use of lim-
ited resources. The main finding of this study is that high risk COPD
patients; who received a remote support program based
on disease-specific self-management principles showed an
improvement in their health status in nearly half of the pa-
tients analyzed assessed with the CAT questionnaire and a
significant reduction in the occurrence of exacerbations. Changes in pulmonary function Although we cannot identify which component of the
intervention had an effect, the results nevertheless re-
main important, considering the limitations of current
COPD treatments, the burden of the disease, and the To assess health status in COPD patients, the most
widely used short questionnaires are CAT [18], the Clin-
ical COPD Questionnaire (CCQ) [26], the Airways Ques-
tionnaire 20 (AQ20) [27], and the COPD severity score
(COPDSS) [28]. In particular, CAT, AQ20, and CCQ have
been assessed on their predictive value for exacerbations
and mortality [29, 30]. CAT covers a broad range of effects
of COPD on patients’ health including cough, phlegm, Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 10 of 12 Fig. 4 Difference in the number of exacerbation (12 months before starting the study and during the 12-months follow-up of the study) Fig. 4 Difference in the number of exacerbation (12 months before starting the study and during the 12-months follow reduction in lung function [39], and about one-half of
patients who seek treatment in an emergency depart-
ment report having had characteristic symptoms for at
least 4 days [40]. Early treatment of exacerbations has
been shown to reduce morbidity and effect on quality
of life [41] and the remote program implemented in the
study seems to be very effective at reducing exacerba-
tions, even in patients who are difficult to control and
with a long duration of COPD disease. Moreover, the
reduced number of exacerbation of the present study
confirms previous reports [42, 43] of improvements in
exacerbations with disease specific interventions. On the
contrary, in the study carried out by Van Wetering et al.,
no reductions in the number of exacerbations were ob-
tained [44]. This is probably associated with a less ad-
vanced COPD in the patients included in that study. chest tightness, breathlessness going up hills/stairs, ac-
tivity limitation at home, confidence leaving home,
sleep, and energy. CAT has demonstrated to be the best
predictive questionnaire for a series of outcomes (new
ambulatory or emergency exacerbations, hospitalization,
or death) in patients with moderate-to-severe COPD [31]. Some studies have shown that patients with severe
COPD improve less with specific health programs com-
pared with patients with less severe disease [32, 33]. Changes in pulmonary function Interestingly enough, our study suggests that non-
compliant patients and COPD patients with higher
CAT scores at baseline, which means a worse health
status, are the patients who have benefited the most
from this remote program. This could be explained, at
least partially, by differences in the severity of COPD
among these groups of patients which led to a better
health status and by the different interventions adapted to
each patient’s specific risk to non-adherence, with more
intense interventions for those patients at higher risk. Duration of intervention has been demonstrated to be an
important variable in a previous meta-analysis [14]. The
health-related quality of life scores, COPD-related ED
visits, and hospital admission rates were similar between
groups during the initial 3- to 6-month follow-up. How-
ever, all of these outcomes reached statistical significance
when the program outcomes were compared after a
12-month follow-up. The 7-month duration of the
Horizonte program could have limited the statistical
significance of some outcomes. Adherence to treatment was obtained in 100 % of the
sample at the end of the program and it was maintained
until the end of the study, which could suggest an im-
provement in the compliance of the patients. Moreover,
the results of the Morisky-Green questionnaire showed
a tendency to an increase in adherence. Regarding the impact of the program on smoking status,
significant heterogeneity has been observed in previous
studies assessing the impact of disease-specific education
programs. Only one out of three trials [45–47] reported
significant differences in the number of current smokers
between groups following the implementation of a
disease-specific education program, maybe due to the
fact that COPD patients lose their motivation after be-
ing discharged from the hospital, and supervised home-
based care could be more effective [48]. Exacerbations are important determinants of prognosis
in patients with COPD, and are associated with health
status [34, 35], lung function [36], mortality [37], and
economic costs [38]. Prodromal symptoms of an exacer-
bation commonly occur up to a week before a discernible This approach of care through a continuum sup-
port and favouring self-management does not require Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 11 of 12 Page 11 of 12 specialized resources and can be easily implemented. Conclusions 3. Eva OE, Birgitta K, Kjell L, Ehrenberg A, Fossum B. Communication and
self-management education at nurse-led COPD clinics in primary healthcare. Patient Educ Couns. 2009;77:209–17. The implementation of a remote support program for
high risk COPD patients results in improvements of
patients’ health status, particularly those with an ini-
tially poor health status, and it effectively reduces
exacerbations. 4. Carone M, Bertolotti G, Cerveri I, De Benedetto F, Fogliani V, Nardini S, et al. EDU-CARE, a randomised, multicentre, parallel group study on education
and quality of life in COPD. Monaldi Arch Chest Dis. 2002;57:25–9. 5. Bourbeau J, Van der Palen J. Promoting effective self-management
programmes to improve COPD. Eur Respir J. 2009;33:461–3. 6. Monninkhof E, van der Valk P, van der Palen J, van Herwaarden C, Zielhuis G. Effects of a comprehensive self-management programme in patients with
chronic obstructive pulmonary disease. Eur Respir J. 2003;22:815–20. 7. Wilkinson T, Wedzicha J, Strategies for improving outcomes of COPD
exacerbations. International journal of chronic obstructive pulmonary 4. Carone M, Bertolotti G, Cerveri I, De Benedetto F, Fogliani V, Nardini S, et al. EDU-CARE, a randomised, multicentre, parallel group study on education
and quality of life in COPD. Monaldi Arch Chest Dis. 2002;57:25–9. 5. Bourbeau J, Van der Palen J. Promoting effective self-management
programmes to improve COPD. Eur Respir J. 2009;33:461–3. 5. Bourbeau J, Van der Palen J. Promoting effective self-management
programmes to improve COPD. Eur Respir J. 2009;33:461–3. 6. Monninkhof E, van der Valk P, van der Palen J, van Herwaarden C, Zielhuis G. Effects of a comprehensive self-management programme in patients with
chronic obstructive pulmonary disease. Eur Respir J. 2003;22:815–20. References
b 1. Vestbo J, Hurd SS, Agusti AG, Jones PW, Vogelmeier C, Anzueto A, et al. Global strategy for the diagnosis, management, and prevention of chronic
obstructive pulmonary disease: GOLD executive summary. Am J Respir Crit
Care Med. 2013;187(4):347–65. 2. Chapman KR, Mannino DM, Soriano JB, Vermeire PA, Buist AS, Thun MJ, et
al. Epidemiology and costs of chronic obstructive pulmonary disease. Eur
Respir J. 2006;27(1):188–207. 2. Chapman KR, Mannino DM, Soriano JB, Vermeire PA, Buist AS, Thun MJ, et
al. Epidemiology and costs of chronic obstructive pulmonary disease. Eur
Respir J. 2006;27(1):188–207. Ethics approval and consent to participate The study was approved by the local ethics committees and the Agencia
Española del Medicamento y Productos Sanitarios (AEMPS) and all participants
provided a written informed consent. Additional file Additional file 1: Description and workflow of the Horizonte Program. (DOCX 92 kb) 7. Wilkinson T, Wedzicha J, Strategies for improving outcomes of COPD
exacerbations. International journal of chronic obstructive pulmonary
disease. Dove Med Press. 2006;1(3):335–42. 7. Wilkinson T, Wedzicha J, Strategies for improving outcomes of COPD
exacerbations. International journal of chronic obstructive pulmonary
disease. Dove Med Press. 2006;1(3):335–42. 8. Martín-Escudero JC. Quality of life and COPD Spanish Clinical Journal
2009; 209 (2):59–60 8. Martín-Escudero JC. Quality of life and COPD Spanish Clinical Journal
2009; 209 (2):59–60 Changes in pulmonary function The present study supports its use as an integral part
of the long-term care of patients with moderate to
advanced COPD, but further studies are needed to
confirm their effectiveness. Authors’ contributions BA, JBS, PL and AFN designed the study and directed the data analysis. MM
and AFN drafted the manuscript. AF, JRGM, AA, PGS, MEM participated in data
collection and critical revision of the data analysis. All authors read and
approved the final manuscript. 14. Hurst JR, Fitzgerald-Khan F, Goldring JJ, Quint JK, Dilworth JP, Mikelsons C,
et al. Use and utility of a 24-hour Telephone Support Service for “high risk”
With COPD patients. Prim Care RespirJ. 2010;19(3):260–5. Funding The ESOPO study was funded by Takeda Pharmaceutical Spain SA. 12. Moullec G, Lavoie KL, Rabhi K, Julien M, Favreau H. Effect of an Integrated
Care Programme on re-hospitalization of patients With chronic obstructive
pulmonary disease. Respirology. 2012;17(4):707–14. Availability of supporting data All supporting data is available in SPSS and Excel files from Oxon Epidemiology
(ignacio.mendez@oxonepi.com). 13. Roberts MM, Leeder SR Robinson TD. Nurse-led 24-hour hotline for patients
With chronic obstructive pulmonary disease you reduce hospital use and is
safe. Internal Medicine Journal [Internet]. Department of Respiratory Medicine,
Westmead Hospitals and Blacktown, New South Wales, Australia.;
2008; 38 (5): 334–40. Received: 28 March 2016 Accepted: 1 November 2016 Received: 28 March 2016 Accepted: 1 November 2016 Received: 28 March 2016 Accepted: 1 November 2016 Acknowledgements We would like to thank Belen San Jose, Ivan Alcolea, Esther Artime, Lorenzo
Dominguez, Ignacio Mendez, Ana Ortega and Ana Zabaljauregui who provided
support for the design, setup, coordination, monitoring, statistical analyses and
medical writing services on behalf of OXON Epidemiology which was sponsored
by Takeda Pharmaceutical Spain SA. 9. Voll-Aanerud M, Eagan TML, Wentzel-Larsen T, Gulsvik A, Bakke PS. Respiratory
symptoms, COPD severity, and health related quality of life in a general
population sample. Resp Med. 2008;102:399–406. 10. Bodenheimer T, Lorig K, Holman H, Grumbach K. Patient self management
of chronic disease in primary care. JAMA. 2002;288:2469–75. 9. Voll-Aanerud M, Eagan TML, Wentzel-Larsen T, Gulsvik A, Bakke PS. Respiratory
symptoms, COPD severity, and health related quality of life in a general
population sample. Resp Med. 2008;102:399–406. 10. Bodenheimer T, Lorig K, Holman H, Grumbach K. Patient self management
of chronic disease in primary care. JAMA. 2002;288:2469–75. 10. Bodenheimer T, Lorig K, Holman H, Grumbach K. Patient self management
of chronic disease in primary care. JAMA. 2002;288:2469–75. 11. Gibson PG, Powell H, Coughlan J, Wilson AJ, Abramson M, Haywood P, et al. Self-management education and regular practitioner review for adults with
asthma. Cochrane Database Syst Rev. 2003;1:CD001117. Author details
1 1Hospital de Alta Resolución de Loja, Agencia Sanitaria H. de Poniente, Avda
Tierno Galván s/n., CP 18300 Loja, Granada, Spain. 2Hospital Universitario
Gregorio Marañón, Madrid, Spain. 3Instituto de Investigación Hospital
Universitario de la Princesa (IISP), Universidad Autónoma de Madrid, Madrid,
Spain. 4Departamento médico Takeda Farmacéutica España S.A., Madrid,
Spain. 5Hospital Son Llàtzer, Mallorca, Spain. 6Hospital Universitario Puerta del
Mar, Cádiz, Spain. 7Hospital de la Plana, Castellón, Spain. 8Hospital
Universitario Virgen de la Salud, Toledo, Spain. Study limitations include lack of completion of the a
priori minimum sample size and those of any observa-
tional study, like neither randomization of the sample
nor reduced room for inferences. Additionally it would
have been desirable to have a control group to indetify
the effect of Horizonte program itself. Nevertheless, our
a priori defined recruitment procedure to minimize sam-
pling bias, systematic evaluation of consecutive COPD
patients from different centres, and evaluation of patients’
health status using a standardized assessment instrument
(CAT) strengthens our results. Our study characteristics
are very similar to those in COPD patients with frequent
exacerbations [14], so it is reasonable to assume that non-
included cases would have had similar characteristics. Competing interests 15. Tan JY, Chen JX, Liu XL, Zhang Q, Zhang M, Mei LJ. A goal -analysis on
the impact of disease-specific education programs on health outcomes
for patients With chronic obstructive pulmonary disease. Geriatr Nurs. 2012;33(4):280–96. Bernardino Alcázar reports personal fees from Novartis AG, Boehringer
Ingelheim, GSK, Almirall, AstraZeneca, Takeda and grants and personal fees
from Menarini. Alonso Fernández-Nistal is a full-time employee of Takeda
Farmaceútica España. The other authors report no conflicts of interest in this
work. 16. National Heart, Lung, and Blood Institute, National Institutes of Health. The
Practical Guide: Identification, Evaluation, and Treatment of Overweight and
Obesity in Adults (NIH Publication No. 00–4084) October 2000, Available
online: http://www.nhlbi.nih.gov/guidelines/obesity/prctgd_c.pdf. Accessed
21 June 2016. Consent for publication
Not applicable. Page 12 of 12 Page 12 of 12 17. Mackay AJ, Donaldson GC, Patel AR, Jones PW, Hurst JR, Wedzicha JA. Usefulness of the chronic obstructive pulmonary disease assessment test to
evaluate severity of COPD exacerbations. Am J Respir Crit Care Med. 2012;185:1218–24. 39. Seemungal TA, Donaldson GC, Bhowmik A, Jeffries DJ, Wedzicha JA. Time
course and recovery of exacerbations in patients with chronic obstructive
pulmonary disease. Am J Respir Crit Care Med. 2000;161(5):1608–13. 40. Camargo CA, Ginde AA, Clark S, Cartwright CP, Falsey AR, Niewoehner DE. Viral pathogens in acute exacerbations of chronic obstructive pulmonary
disease. Intern Emerg Med. 2008;3(4):355–9. 18. Jones PW, Harding G, Berry P, Wiklund I, Chen WH, Kline LN. Development and
first validation of the COPD Assessment Test. Eur Respir J. 2009;34(3):648–54. 41. Wilkinson TMA, Donaldson GC, Hurst JR, Seemungal TAR, Wedzicha JA. Early
therapy improves outcomes of exacerbations of chronic obstructive
pulmonary disease. Am J Respir Crit Care Med. 2004;169(12):1298–303. 19. Tsiligianni IG, van der Molen T, Moraitaki D, Lopez I, Kocks JW, Karagiannis K,
et al. Assessing health status in COPD. A head-to-head comparison between
the COPD assessment test (CAT) and the clinical COPD questionnaire (CCQ). BMC Pulm Med. 2012;12:20. 42. Rice KL, Dewan N, Bloomfield HE, Grill J, Schult TM, Nelson DB, et al. Disease
management program for chronic obstructive pulmonary disease: a
randomized controlled trial. Am J Respir Crit Care Med. 2010;182(7):890–6. 20. Stock S, Drabik A, Büscher G, Graf C, Ullrich W, Gerber A, et al. German
diabetes management programs improve quality of care and curb costs. Health Aff. 2010;29(12):2197–205. 43. Güell R, Resqueti V, Sangenis M, Morante F, Martorell B, Casan P, et al. Impact of pulmonary rehabilitation on psychosocial morbidity in patients
with severe COPD. Chest. 2006;129(4):899–904. 21. Rich MW, Beckhman V, Wittenberg C, Leven CL, Freedland KE, Carney RM. A
multidisciplinary intervention to prevent the readmission of elderly patients
with congestive heart failure. N Engl J Med. 1995;333:1190–5. 44. van Wetering CR, Hoogendoorn M, Mol SJ, Rutten-van Molken MP, Schols AM. Short- and long-term efficacy of a community-based COPD management
programme in less advanced COPD: a randomised controlled trial. Thorax. 2010;65(1):7–13. 22. Mehring M, Donnachie E, Mutschler R, Hofmann F, Keller M, Schneider A. Disease Management Programs for Patients with Asthma in Germany: A
Longitudinal Population based Study. Respir Care. 2013;58(7):1170–7. 45. Garcia-Aymerich J, Hernandez C, Alonso A, Casas A, Rodriguez-Roisin R,
Anto JM, et al. Consent for publication
Not applicable. Effects of an integrated care intervention on risk factors of
COPD readmission. Resp Med. 2007;101:1462–9. 23. Adams SG, Smith PK, Allan PF, Anzueto A, Pugh JA, Cornell JE. Systematic
review of the chronic care model in chronic obstructive pulmonary disease
prevention and management. Arch Intern Med. 2007;167(6):551–61. 46. Yang XM, Li WQ, Gao CH. Family nursing intervention to COPD patients
instable stage. J Nurs Sci. 2007;22:66–8. 24. Taylor SJC, Candy B, Bryar RM, Ramsay J, Vrijhoef HJM, Esmond G, et al. Effectiveness of innovations in nurse led chronic disease management for
patients with chronic obstructive pulmonary disease: systematic review of
evidence. BMJ. 2005;331(7515):485. 47. Hermiz O, Comino E, Marks G, Daffurn K, Wilson S, Harris M. Randomised controlled trial of home based care of patients with
chronicobstructivepulmonarydisease. BMJ. 2002;325:938. 25. Curtis JR, Patrick DL. The assessment of health status among patients with
COPD. Eur Respir J Suppl. 2003;41:36s–45s. 48. Karapolat H, Atasever A, Atamaz F, Kirazli Y, Elmas F, Erdinç E. Do the benefits
gained using a short-term pulmonary rehabilitation program remain in COPD
patients after participation? Lung. 2007;185:221–5. 26. van der Molen T, Willemse BW, Schokker S, ten Hacken NH, Postma DS,
Juniper EF. Development, validity and responsiveness of the Clinical COPD
Questionnaire. Health Qual Life Outcomes. 2003;1:13. 27. Hajiro T, Nishimura K, Jones PW, Tsukino M, Ikeda A, Koyama H, et al. A
novel, short, and simple questionnaire to measure health-related quality of
life in patients with chronic obstructive pulmonary disease. Am J Respir Crit
Care Med. 1999;159(6):1874–8. 28. Eisner MD, Trupin L, Katz PP, Yelin EH, Earnest G, Balmes J. Development and
validation of a survey-based COPD severity score. Chest. 2005;127(6):1890–7. 29. Lee SD, Huang MS, Kang J, Lin CH, Park MJ, Oh YM, et al. The COPD
assessment test (CAT) assists prediction of COPD exacerbations in high-risk
patients. Respir Med. 2014;108(4):600–8. 30. Blanco-Aparicio M, Vazquez I, Pita-Fernandez S, Pertega-Diaz S,
Verea-Hernando H. Utility of brief questionnaires of health-related quality
of life (Airways Questionnaire 20 and Clinical COPD Questionnaire) to
predict exacerbations in patients with asthma and COPD. Health Qual Life
Outcomes. 2013;11:85. 31. Miravitlles M, García-Sidro P, Fernández-Nistal A, Buendía MJ, Espinosa MJ,
Esquinas C, et al. The chronic obstructive pulmonary disease assessment
test improves the predictive value of previous exacerbations for poor
outcomes in COPD. Int J Chron Obstruct Pulmon Dis. 2015;10:2571–9. 32. Garrod R, Marshall J, Barley E, Jones PW. Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Consent for publication
Not applicable. Predictors of success and failure in
pulmonary rehabilitation. Eur Respir J. 2006;27:788–94. 33. Wedzicha JA, Bestall JC, Garrod R, Garnham R, Paul EA, Jones PW. Randomized
controlled trial of pulmonary rehabilitation in severe chronic obstructive
pulmonary disease patients, stratified with the MRC dyspnoea scale. Eur Respir J. 1998;12:363–9. 34. Seemungal TA, Donaldson GC, Paul EA, Bestall JC, Jeffries DJ, Wedzicha JA. Effect of exacerbation on quality of life in patients with chronic obstructive
pulmonary disease. Am J Respir Crit Care Med. 1998;157(5 Pt 1):1418–22. Submit your next manuscript to BioMed Central
and we will help you at every step: Submit your next manuscript to BioMed Central
and we will help you at every step: 35. Bourbeau J, Ford G, Zackon H, Pinsky N, Lee J, Ruberto G. Impact on patients’
health status following early identification of a COPD exacerbation. Eur Respir J. 2007;30(5):907–13. • We accept pre-submission inquiries
• Our selector tool helps you to find the most relevant journal
• We provide round the clock customer support
• Convenient online submission
• Thorough peer review
• Inclusion in PubMed and all major indexing services
• Maximum visibility for your research
Submit your manuscript at
www.biomedcentral.com/submit
and we will help you at every step: 36. Donaldson GC, Seemungal TAR, Bhowmik A, Wedzicha JA. Relationship
between exacerbation frequency and lung function decline in chronic
obstructive pulmonary disease. Thorax. 2002;57(10):847–52. 37. Soler-Cataluña JJ, Martínez-García MA, Román Sánchez P, Salcedo E, Navarro M,
Ochando R. Severe acute exacerbations and mortality in patients with chronic
obstructive pulmonary disease. Thorax. 2005;60(11):925–31. 38. Andersson F, Borg S, Jansson SA, Jonsson AC, Ericsson A, Prütz C, et al. The
costs of exacerbations in chronic obstructive pulmonary disease (COPD). Respir Med. 2002;96(9):700–8. 38. Andersson F, Borg S, Jansson SA, Jonsson AC, Ericsson A, Prütz C, et al. The
costs of exacerbations in chronic obstructive pulmonary disease (COPD). Respir Med. 2002;96(9):700–8.
|
https://openalex.org/W4362729385
|
https://zenodo.org/records/7810468/files/5-12.pdf
|
Kirghiz, Kyrgyz
| null |
NUMERICAL SOLUTION OF THE CAUCHY PROBLEM FOR IDEAL PLASTICITY EQUATIONS WITH YIELD CONDITION DEPENDING ON THE AVERAGE STRESS
|
Zenodo (CERN European Organization for Nuclear Research)
| 2,023
|
cc-by
| 2,815
|
NUMERICAL SOLUTION OF THE CAUCHY PROBLEM
FOR IDEAL PLASTICITY EQUATIONS WITH YIELD
CONDITION DEPENDING ON THE AVERAGE STRESS Nguyen Minh Hue, Pham Thi Thuy,
Faculty of Basic Science,
Ho Chi Minh City University of Transport,
Ho Chi Minh City, Vietnam Annotation: The Cauchy problem of the propagation of zones of a
plastic state in an unbounded medium from the boundary of a convex
surface, on which normal pressure, tangential forces, and given
displacement velocities act, is considered. In the case of complete plasticity
and linear dependence of the yield condition on the average stress, the
system of quasi-static ideal plasticity equations describing the stress-strain
state of the medium is hyperbolic. When solving this system numerically, a
different scheme is used for hyperbolic systems of conservation laws. Keywords: stress, deformation, full plasticity, yield strength, ideal
plasticity, hyperbolic system РАЗДЕЛ. ЕСТЕСТВЕННЫЕ НАУКИ https://doi.org/10.5281/zenodo.7810468
UDK 50 ЧИСЛЕННОЕ РЕШЕНИЕ ЗАДАЧИ КОШИ ДЛЯ УРАВНЕНИЙ
ИДЕАЛЬНОЙ ПЛАСТИЧНОСТИ С УСЛОВИЕМ ТЕКУЧЕСТИ
В ЗАВИСИМОСТИ ОТ СРЕДНЕГО НАПРЯЖЕНИЯ. Нгуен Минь Хюэ, Фам Тхи Туи,
Факультет фундаментальных наук,
Университет транспорта Хошимина,
Хошимин, Вьетнам Нгуен Минь Хюэ, Фам Тхи Туи,
Факультет фундаментальных наук,
Университет транспорта Хошимина,
Хошимин, Вьетнам Аннотация: Рассмотрена задача Коши о распространении зон
пластического состояния в неограниченной среде от границы INNOVATIVE SCIENTIFIC RESEARCH выпуклой поверхности, на которую действуют нормальное давление,
касательные силы и заданные скорости перемещений. В случае
полной пластичности и линейной зависимости условия текучести от
среднего напряжения система квазистатических уравнений идеальной
пластичности, описывающая напряженно-деформированное состояние
среды, является гиперболической. При численном решении этой
системы
для
гиперболических
систем
законов
сохранения
используется другая схема. у
ру
Ключевые
слова:
напряжение,
деформация,
полная
пластичность,
предел
текучести,
идеальная
пластичность,
гиперболическая система Quasi-static equations of ideal plasticity for determining stresses
and displacement rates in the case of complete plasticity have the form: (1)
(2) 𝜎,= 0, (1)
𝑚𝑎𝑥(|𝜎ଵ−𝜎ଶ|, |𝜎ଶ−𝜎ଷ|, |𝜎ଵ−𝜎ଷ|) = 2(𝑘௦−𝑚𝜎), (2)
𝜎< 𝑘௦/𝑚,
𝜎ଶ= 𝜎ଷ, (3)
𝑒ଵଵ+ 𝑒ଶଶ+ 𝑒ଷଷ= 0, (4)
𝑒ଵଵ
𝑒ଵଶ
𝑒ଵଷ
𝑒ଶଵ
𝑒ଶଶ
𝑒ଶଷ
𝑒ଷଵ
𝑒ଷଶ
𝑒ଷଷ
൩⋅
𝑛ଵ
𝑛ଶ
𝑛ଷ
൩= 𝜆
𝑛ଵ
𝑛ଶ
𝑛ଷ
൩, 2𝑒= 𝑢,+ 𝑢, (5) (2) (3)
(4) (3)
(4) (5) Here 𝜎 are the components of the symmetric stress tensor in the Cartesian coordinate system 𝑥ଵ, 𝑥ଶ, 𝑥ଷ; 𝜎=
(ఙభభାఙమమାఙయయ)
ଷ
is the mean stress;
𝜎ଵ, 𝜎ଶ, 𝜎ଷ are principal stresses; 𝑘௦> 0, 𝑚> 0 are constants; 𝑒 are the
strain rate tensor components; 𝑢 are the components of the displacement
velocity vector; 𝑛 are the components of the unit eigenvector of the stress
tensor corresponding to the non-multiple eigenvalue (principal stress) 𝜎ଵ. Equality (2) means a linear dependence of the maximum shear
stress on the average pressure [1] (such a dependence (Fig. 1) is typical for
some soils [2]). Equality (3) means the Haar–Karman completes plasticity
condition [3], equality (4) is the incompressibility condition [4], and
relation (5) is the isotropy condition [4]. ISSN 2713-0010
SCIENTIFIC NETWORK PUBLICATION
~ 6 ~ SCIENTIFIC NETWORK PUBLICATION ~ 6 ~ р Figure 1 – Physical and mechanical properties of sand under pressure System (1)–(3) is studied using D. D. Ivlev’s representation of the
stress tensor in the form [4]: 𝜎ଵଵ=
క
+
ೞ
+ 𝜉𝑛ଵ
ଶ, 𝜎ଵଶ= 𝜉𝑛ଵ𝑛ଶ,
𝜎ଶଶ=
క
+
ೞ
+ 𝜉𝑛ଶ
ଶ, 𝜎ଵଷ= 𝜉𝑛ଵ𝑛ଷ,
𝜎ଷଷ=
క
+
ೞ
+ 𝜉𝑛ଷ
ଶ, 𝜎ଶଷ= 𝜉𝑛ଶ𝑛ଷ,
𝜉= 2𝜀(𝑘௦−𝑚𝜎) = 2𝜀𝑒, 𝑎=
ି
ଷఌାଶ, 𝜀= ±1. . (6) (6) 𝜉= 2𝜀(𝑘௦−𝑚𝜎) = 2𝜀𝑒, 𝑎=
ି
ଷఌାଶ, 𝜀= ±1. ЧИСЛЕННОЕ РЕШЕНИЕ ЗАДАЧИ КОШИ ДЛЯ УРАВНЕНИЙ
ИДЕАЛЬНОЙ ПЛАСТИЧНОСТИ С УСЛОВИЕМ ТЕКУЧЕСТИ
В ЗАВИСИМОСТИ ОТ СРЕДНЕГО НАПРЯЖЕНИЯ. ଷఌାଶ
Substitution (6) identically satisfies relations (2), (3). In this case,
the principal stresses are equal
ସ
ଶ 𝜎ଵ=
ସ
ଷ𝜀(𝑘௦−𝑚𝜎) + 𝜎, 𝜎ଶ= 𝜎ଷ= −
ଶ
ଷ𝜀(𝑘௦−𝑚𝜎) + 𝜎. 𝜎ଵ=
ସ
ଷ𝜀(𝑘௦−𝑚𝜎) + 𝜎, 𝜎ଶ= 𝜎ଷ= −
ଶ
ଷ𝜀(𝑘௦−𝑚𝜎) + 𝜎. The functions 𝑝, 𝑛ଵ, 𝑛ଶ, 𝑛ଷ depending on 𝑥ଵ, 𝑥ଶ, 𝑥ଷ are determined
from the quasilinear system of first-order equations obtained from (1), (6),
and the finite relation 𝑛ଵ
ଶ+ 𝑛ଶ
ଶ+ 𝑛ଷ
ଶ= 1: 𝑝,+ 𝑛𝑛, + 𝑘𝑛𝑛௦, 𝑠= 0, 𝑖, 𝑗, 𝑠= 1,2,3; 𝑘=
(ଷఌାଶ)
(ଷఌିସ). (7 (7) The particle velocity vector for a known stress tensor is determined
from the conditions of incompressibility (4) and isotropy (5). p
y ( )
py ( )
At 𝑚= 0, the parameter 𝑘= 1 and system (7) formally coincide
with the system of equations of D. D. Ivlev [4] of the Tresca theory of
plasticity under the condition of complete plasticity. In this case, the
substitution that satisfies condition (2) and relation (3) for 𝑚= 0 differs
from substitution (6). ~ 7 ~ ISSUE № 3-1(27) March 2023 Analysis of the structure of solutions to system (7) for 𝑘= 1
applies to the system (7) and for 𝑘≠1. If for 𝑘= 1 the normals to the
characteristic surfaces form a cone with the half-angle 𝜑= 𝜋/4 and the
axis oriented along the unit eigenvector 𝐧= (𝑛ଵ, 𝑛ଶ, 𝑛ଷ) of the stress
tensor, then for 𝑘≠1 the half-angle 𝜑= arctg (1/√𝑘). The system for determining the velocity vector has a characteristic
cone with a half-angle 𝜑= 𝜋/4. Submodels for system (7) with 𝑘≠1 are considered in [5]. System (4), (5), and (7) is hyperbolic. For this system, the problem
of the propagation of plastic state zones in an unbounded medium from the
boundary of a convex cavity, which is subjected to normal pressure, shear
forces, and given displacement velocities, is considered. In [6, 7, 8], for
systems (4), (5), (7) with 𝑚= 0, a numerical method was proposed for
solving the Cauchy problem in an orthogonal curvilinear coordinate system
(𝛼, 𝜃, 𝛾) formed by rotation around the vertical 𝑧 axis of a smooth convex
curve 𝐿 with support function 𝐹(𝛾) (Fig. 2), where the coordinate surfaces
𝛼= const are equidistant. Taking into account (6), this method can be
applied to the solution of the Cauchy problem for systems (4), (5), and (7)
with 𝑚≠0. ИННОВАЦИОННЫЕ НАУЧНЫЕ ИССЛЕДОВАНИЯ ВЫПУСК №3-1(27) Март 2023 As an example, the problem of the propagation of zones of the
plastic state from the boundary of an ellipsoidal cavity formed by rotation
around the 𝑧 axis of a convex curve 𝐿 with the support function 𝐹(𝛾) =
ඥ𝑎ଶsinଶ 𝛾+ 𝑏ଶcosଶ 𝛾, where 𝑎, 𝑏 are the semiaxes of the ellipse, were
solved. The problem was solved in dimensionless variables. For 𝑚= 0, the
stresses have the form: 𝜎ఈఈ= 𝑝+ 𝑛ఈଶ,
𝜎ఈఏ= 𝑛ఈ𝑛ఏ,
𝜎ఈఊ= 𝑛ఈ𝑛ఊ,
𝜎ఏఏ= 𝑝+ 𝑛ఏ
ଶ,
𝜎ఊఊ= 𝑝+ 𝑛ఊଶ,
𝜎ఏఊ= 𝑛ఏ𝑛ఊ, 𝜎ఏఏ= 𝑝+ 𝑛ఏ
ଶ,
𝜎ఊఊ= 𝑝+ 𝑛ఊଶ,
𝜎ఏఊ= 𝑛ఏ𝑛ఊ,
where 𝜎ఈఈ, 𝜎ఈఏ, 𝜎ఈఊ, 𝜎ఏఏ, 𝜎ఊఊ, 𝜎ఏఊ are the stress components in the
coordinate
system
(𝛼, 𝜃, 𝛾)
divided
by
2𝑘௦𝜀; 𝑝= 𝜎/(2𝑘௦𝜀) −
1/3; 𝑛ఈ, 𝑛ఏ, 𝑛ఊ are the components of the unit eigenvector corresponding to
the principal stress 𝜎ଵ. At 𝑚≠0, the stresses were calculated by the
formula (6), in which 𝑛ଵ= 𝑛ఈ, 𝑛ଶ= 𝑛ఏ, 𝑛ଷ= 𝑛ఊ should be put. where 𝜎ఈఈ, 𝜎ఈఏ, 𝜎ఈఊ, 𝜎ఏఏ, 𝜎ఊఊ, 𝜎ఏఊ are the stress components in the
coordinate
system
(𝛼, 𝜃, 𝛾)
divided
by
2𝑘௦𝜀; 𝑝= 𝜎/(2𝑘௦𝜀) −
1/3; 𝑛ఈ, 𝑛ఏ, 𝑛ఊ are the components of the unit eigenvector corresponding to
the principal stress 𝜎ଵ. At 𝑚≠0, the stresses were calculated by the
formula (6), in which 𝑛ଵ= 𝑛ఈ, 𝑛ଶ= 𝑛ఏ, 𝑛ଷ= 𝑛ఊ should be put. ఊ
In the numerical solution, the semiaxis of the ellipsoid is 𝑎= 2,
and the semiaxis 𝑏= 1. At 𝑚= 0, the following initial conditions were set
on the surface of the cavity (𝛼= 0): 𝑝(0) = 1, 𝑛ఈ(0) = 1, 𝑛ఏ(0) =
𝑛ఊ(0) = 0. To compare the solutions obtained at 𝑚= 0 and 𝑚≠0, the
initial values for 𝜉(0) in formulas (6) were chosen so that the normal
stresses 𝜎ఈఈ at 𝛼= 0 coincided. Figure 3 shows the dependences of the stresses 𝜎ఈఈ on the
coordinate 𝛼 for the angles 𝛾= 0 and = 𝜋/2 at 𝑚= 0 and 𝑚= 0,5. ЧИСЛЕННОЕ РЕШЕНИЕ ЗАДАЧИ КОШИ ДЛЯ УРАВНЕНИЙ
ИДЕАЛЬНОЙ ПЛАСТИЧНОСТИ С УСЛОВИЕМ ТЕКУЧЕСТИ
В ЗАВИСИМОСТИ ОТ СРЕДНЕГО НАПРЯЖЕНИЯ. ISSN 2713-0010
SCIENTIFIC NETWORK PUBLICATION
~ 8 ~
Figure 2 – Orthogonal curvilinear coordinate system (𝛼, 𝜃, 𝛾): coordinate
surface 𝑆(𝛼= 0), basis vectors 𝑘ఈ, 𝑘ఏ, 𝑘ఊ and generatrix 𝐿 of the
coordinate surface 𝑆 Figure 2 – Orthogonal curvilinear coordinate system (𝛼, 𝜃, 𝛾): coordinate
surface 𝑆(𝛼= 0), basis vectors 𝑘ఈ, 𝑘ఏ, 𝑘ఊ and generatrix 𝐿 of the
coordinate surface 𝑆 ISSN 2713-0010 ~ 8 ~ ИННОВАЦИОННЫЕ НАУЧНЫЕ ИССЛЕДОВАНИЯ ВЫПУСК №3-1(27) Март 2023 ISSN 2713-0010
НАУЧНОЕ СЕТЕВОЕ ИЗДАНИЕ
Figure 3 – Distribution of stresses 𝜎ఈఈ near an elliptical cavity for angles
𝛾= 0 and 𝛾= 𝜋/2 depending on the coordinate 𝛼: dotted lines – m = 0,
solid lines – m = 0.5 Figure 3 – Distribution of stresses 𝜎ఈఈ near an elliptical cavity for angles
𝛾= 0 and 𝛾= 𝜋/2 depending on the coordinate 𝛼: dotted lines – m = 0,
solid lines – m = 0.5 Figure 3 – Distribution of stresses 𝜎ఈఈ near an elliptical cavity for angles
𝛾= 0 and 𝛾= 𝜋/2 depending on the coordinate 𝛼: dotted lines – m = 0,
solid lines – m = 0.5 Figure 3 – Distribution of stresses 𝜎ఈఈ near an elliptical cavity for angles
𝛾= 0 and 𝛾= 𝜋/2 depending on the coordinate 𝛼: dotted lines – m = 0,
solid lines – m = 0.5 ~ 9 ~ INNOVATIVE SCIENTIFIC RESEARCH ISSUE № 3-1(27) March 202
Figure 4 – Distribution of stresses 𝜎ఈఈ, 𝜎ఊఊ and 𝜎ఏఏ near the elliptical
cavity for the angle 𝛾=
గ
ସ depending on the coordinate 𝛼: dotted lines –
𝑚= 0, solid lines – 𝑚= 0,5 INNOVATIVE SCIENTIFIC RESEARCH ISSUE № 3-1(27) M Figure 4 – Distribution of stresses 𝜎ఈఈ, 𝜎ఊఊ and 𝜎ఏఏ near the elliptical
cavity for the angle 𝛾=
గ
ସ depending on the coordinate 𝛼: dotted lines –
𝑚= 0, solid lines – 𝑚= 0,5 Figure 4 – Distribution of stresses 𝜎ఈఈ, 𝜎ఊఊ and 𝜎ఏఏ near the elliptical
cavity for the angle 𝛾=
గ
ସ depending on the coordinate 𝛼: dotted lines –
𝑚= 0, solid lines – 𝑚= 0,5 Figure 4 shows the dependences of the stresses 𝜎ఈఈ, 𝜎ఏఏ, and 𝜎ఊఊ
on 𝛼 for 𝛾= 𝜋/4 at 𝑚= 0 and 𝑚= 0,5. Figure 4 shows the dependences of the stresses 𝜎ఈఈ, 𝜎ఏఏ, and 𝜎ఊఊ
on 𝛼 for 𝛾= 𝜋/4 at 𝑚= 0 and 𝑚= 0,5. Thus, under the linear dependence of the yield condition on the
average stress for the case of complete plasticity, the Cauchy problem of
the propagation of zones of the plastic state in an unbounded medium from
the boundary of a convex surface on which normal pressure acts is
numerically solved. ISSN 2713-0010 Bibliography Effect of hydrostatic pressure on the mechanical
properties of polymeric materials / S.B. Ainbinder, M.G. Laka, I.Yu. Majors // Polymer Mechanics. – 1965. No. 1. 65-75 p. [8] Pisarenko G.S. Deformation and strength of materials under
complex stress state / G.S. Pisarenko, A. A. Lebedev. – Kyiv, 1976. 416 p. [8] Pisarenko G.S. Deformation and strength of materials under
complex stress state / G.S. Pisarenko, A. A. Lebedev. – Kyiv, 1976. 416 p. Bibliography [1] Lode V. Influence of the average principal stress on the fluidity of
metals / V. Lode // Theory of Plasticity: Sat. Art. / ed. Yu. N. Rabotnova. –
M.: State. foreign publishing house lit., 1948. 168-205 p. [2] Kazachenko L.S. Physical and mechanical properties of sand under
pressure / L.S. Kazachenko, Yu. V. Kulinich // FTPRPI. – 1972. No. 1. 22-
30 p. [2] Kazachenko L.S. Physical and mechanical properties of sand under
pressure / L.S. Kazachenko, Yu. V. Kulinich // FTPRPI. – 1972. No. 1. 22-
30 p. [2] Kazachenko L.S. Physical and mechanical properties of sand under
pressure / L.S. Kazachenko, Yu. V. Kulinich // FTPRPI. – 1972. No. 1. 22-
30 p. [3] Haar A. On the Theory of Stressed States in Plastic and Loose
Media / A. Haar, T. Karman // Theory of Plasticity: Sat. Art. / ed. Yu. N. Rabotnova. – M.: State. foreign publishing house lit., 1948. 41-56 p. [3] Haar A. On the Theory of Stressed States in Plastic and Loose
Media / A. Haar, T. Karman // Theory of Plasticity: Sat. Art. / ed. Yu. N. Rabotnova. – M.: State. foreign publishing house lit., 1948. 41-56 p. [4] Ishlinsky A.Yu. Mathematical theory of plasticity / A.Yu. Ishlinsky, D.D. Ivlev. – M.: Fizmatlit, 2001. 704 p. [4] Ishlinsky A.Yu. Mathematical theory of plasticity / A.Yu. Ishlinsky, D.D. Ivlev. – M.: Fizmatlit, 2001. 704 p. SCIENTIFIC NETWORK PUBLICATION ~ 10 ~ [5] Annin B.D. On the equations of ideal plasticity with a yield
condition depending on the average stress / B.D. Annin // Advances in
continuum mechanics: on the occasion of the 70th anniversary of Acad. V. A. Levin: Sat. scientific tr. – Vladivostok: Dalnauka, 2009. 31–34 p. ,
p
[6] Annin B.D. Algorithm for the numerical solution of the Cauchy
problem for the Tresca plasticity equations / B.D. Annin, V. V. Alekhin, V. V. Ostapenko // Computational mechanics of continuous media. – 2008. V. 1. No. 1. 5-13 p. [6] Annin B.D. Algorithm for the numerical solution of the Cauchy
problem for the Tresca plasticity equations / B.D. Annin, V. V. Alekhin, V. V. Ostapenko // Computational mechanics of continuous media. – 2008. V. 1. No. 1. 5-13 p. [7] Ainbinder S.B. Effect of hydrostatic pressure on the mechanical
properties of polymeric materials / S.B. Ainbinder, M.G. Laka, I.Yu. Majors // Polymer Mechanics. – 1965. No. 1. 65-75 p. [7] Ainbinder S.B. Список литературы (перевод) [1] Лоде В. Влияние среднего главного напряжения на текучесть
металлов / В. Лоде // Теория пластичности: Сб. Искусство. / изд. Ю. Н. Работнова. – М.: Гос. иностранное изд-во лит., 1948. 168-205 с. [1] Лоде В. Влияние среднего главного напряжения на текучесть
металлов / В. Лоде // Теория пластичности: Сб. Искусство. / изд. Ю. Н. Работнова. – М.: Гос. иностранное изд-во лит., 1948. 168-205 с. [1] Лоде В. Влияние среднего главного напряжения на текучесть
металлов / В. Лоде // Теория пластичности: Сб. Искусство. / изд. Ю. Н. Работнова. – М.: Гос. иностранное изд-во лит., 1948. 168-205 с. р
,
[2] Казаченко Л.С. Физико-механические свойства песка под
давлением / Л.С. Казаченко, Ю. Кулинич В. // ФЦППИ. – 1972. № 1. 22-30 с. [2] Казаченко Л.С. Физико-механические свойства песка под
давлением / Л.С. Казаченко, Ю. Кулинич В. // ФЦППИ. – 1972. № 1. 22-30 с. [3] Хаар А. К теории напряженных состояний в пластичных и
рыхлых средах / А. Хаар, Т. Карман // Теория пластичности: Сб. Искусство. / изд. Ю. Н. Работнова. – М.: Гос. иностранное
издательство лит., 1948. 41-56 с. [3] Хаар А. К теории напряженных состояний в пластичных и
рыхлых средах / А. Хаар, Т. Карман // Теория пластичности: Сб. Искусство. / изд. Ю. Н. Работнова. – М.: Гос. иностранное
издательство лит., 1948. 41-56 с. [4] Ишлинский А.Ю. Математическая теория пластичности / А.Ю. Ишлинский, Д.Д. Ивлев. – М.: Физматлит, 2001. 704 с. [4] Ишлинский А.Ю. Математическая теория пластичности / А.Ю. Ишлинский, Д.Д. Ивлев. – М.: Физматлит, 2001. 704 с. [5] Аннин Б.Д. Об уравнениях идеальной пластичности с
условием текучести в зависимости от среднего напряжения / Б.Д. Аннин // Успехи механики сплошных сред: к 70-летию со дня
рождения акад. В. А. Левин: Сб. научный тр. – Владивосток:
Дальнаука, 2009. 31–34 с. [5] Аннин Б.Д. Об уравнениях идеальной пластичности с
условием текучести в зависимости от среднего напряжения / Б.Д. Аннин // Успехи механики сплошных сред: к 70-летию со дня
рождения акад. В. А. Левин: Сб. научный тр. – Владивосток:
Дальнаука, 2009. 31–34 с. Д
у
,
[6] Аннин Б.Д. Алгоритм численного решения задачи Коши для
уравнений пластичности Треска / Б.Д. Аннин, В. В. Алехин, В. В. Остапенко // Вычислительная механика сплошных сред. – 2008. Т. 1. № 1. 5-13 с. у
[6] Аннин Б.Д. Алгоритм численного решения задачи Коши для
уравнений пластичности Треска / Б.Д. Аннин, В. В. Алехин, В. В. Остапенко // Вычислительная механика сплошных сред. – 2008. Т. 1. № 1. Список литературы (перевод) 5-13 с. ISSN 2713-0010 ~ 11 ~ [7] Айнбиндер С.Б. Влияние гидростатического давления на
механические свойства полимерных материалов / С.Б. Айнбиндер,
М.Г. Лака, И.Ю. Направления // Механика полимеров. – 1965. № 1. 65-
75 с. [7] Айнбиндер С.Б. Влияние гидростатического давления на
механические свойства полимерных материалов / С.Б. Айнбиндер,
М.Г. Лака, И.Ю. Направления // Механика полимеров. – 1965. № 1. 65-
75 с. [8] Писаренко Г. С. Деформация и прочность материалов при
сложном напряженном состоянии / Г. С. Писаренко, А. А. Лебедев. –
Киев, 1976. 416 с. [8] Писаренко Г. С. Деформация и прочность материалов при
сложном напряженном состоянии / Г. С. Писаренко, А. А. Лебедев. –
Киев, 1976. 416 с. © Nguyen Minh Hue, Pham Thi Thuy, 2023
Поступила в редакцию 02.03.2023
Принята к публикации 16.03.2023 © Nguyen Minh Hue, Pham Thi Thuy, 2023
Поступила в редакцию 02.03.2023
Принята к публикации 16.03.2023 Для цитирования: Nguyen Minh Hue, Pham Thi Thuy Numerical solution of the cauchy
problem for ideal plasticity equations with yield condition depending on the
average stress // Инновационные научные исследования. 2023. № 3-
1(27). C. 5-12. URL: https://ip-journal.ru/ ISSN 2713-0010 ~ 12 ~
|
https://openalex.org/W3198947643
|
https://www.medrxiv.org/content/medrxiv/early/2021/09/16/2021.09.13.21263407.full.pdf
|
English
| null |
Episodic future thinking and compassion reduce public health guideline noncompliance urges: A randomised controlled trial
|
medRxiv (Cold Spring Harbor Laboratory)
| 2,021
|
cc-by
| 8,030
|
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
(which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021.
;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a 1
reprint reports new research that has not been certified by peer review and should not be used to guide clinical practice Background During the COVID-19 pandemic, public health departments have issued guidelines to limit viral
transmission. In this environment, people will feel urges to engage in activities that violate these
guidelines, but research on guideline adherence has been reliant on surveys asking people to self-
report their typical behaviour, which may fail to capture these urges as they unfold. Guideline
adherence could be improved through behaviour change interventions, but considering the wide range
of behaviours that COVID-19 guidelines prescribe, there are few methods that allow observing
changes of aggregate guideline adherence in the ‘wild’. Episodic future thinking and compassion
reduce public health guideline noncompliance
urges: A randomised controlled trial is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a Methods In order to administer interventions and to obtain contemporaneous data on a wide range of
behaviours, we use ecological momentary assessment. In this preregistered parallel randomised trial,
95 participants aged 18-65 from the UK were assigned to three conditions using blinded block
randomisation, and engage in episodic future thinking (n = 33), compassion exercises (n = 31), or a
sham procedure (n = 31) and report regularly on the intensity of their occurrent urges (min. 1, max. 10) and their ability to control them. We investigate whether state impulsivity and vaccine attitudes
predict guideline adherence, while assessing through which mechanism these predictors affect
behaviour. Findings We found that episodic future thinking (b = -1.60) and compassion exercises (b = -1.40) reduce the
intensity of urges. State impulsivity is associated with stronger urges, but we found no evidence that
vaccine hesitancy predicts lesser self-control. Introduction Enhancing adherence to national COVID-19 health guidelines is essential for saving lives and
preventing serious illness. However, studying predictors and methods for improving COVID-19
guideline adherence is challenging because this behaviour is not readily observed in laboratory
settings, nor easy to reveal with self-report cross sectional surveys. The focus of this study is, using
ecological momentary assessment rather than one-shot surveys, to find whether episodic future
thinking and compassion exercises could contribute to increasing adherence to public health
guidelines for preventing Covid-19 spread. We also investigate whether state impulsivity and vaccine
attitudes predict guideline adherence, while assessing through which mechanism these predictors
affect behaviour. A wealth of research has focused on best-practice for public health communication in order to achieve
optimal guideline adherence of the public (1). Adhering to guidelines such as staying home during a
lockdown can have immediate personal adverse impact on one’s financial situation (2), mental health
(3-5), and physical health (6, 7). In contrast, the effects of non-adherence are often less immediate:
when an individual contracts COVID-19 it may take time before symptoms and accompanying
negative consequences are experienced; and those consequences may often affect others, such as
infecting loved ones, or causing outbreaks in the community. Decisions on guideline adherence
therefore constitute a dilemma between choosing the long-term greater good, over the short-term
individual gain. Here, we therefore test if increasing people’s future-orientedness, and willingness to
make decisions for others’ benefit has potential for increasing adherence. Episodic future thinking (EFT) refers to imagining or simulating experiences that might occur in one's
personal future, and is known to decrease delay discounting (8, 9). The effects of EFT on delay
discounting imply that the valuation of immediate rewards is diminished relative to future rewards. This means that EFT likely affects the intensity of urges, but the effects of EFT in various domains
suggest that EFT might also impact self-control (10, 11). Accordingly, this study investigates whether
engaging in EFT exercises can change the intensity of urges and self-control. Adherence to guidelines is ultimately also prosocial, and prosocial behaviour can be enhanced by
stimulating compassion, the feeling that arises in witnessing another’s suffering and that motivates a
subsequent desire to help (12). Compassion training has a valuation element in addition to a
behavioural element, which means compassion training could affect both the intensity of urges and
self-control (13, 14); which this study will investigate. Interpretation We conclude that episodic future thinking exercises and compassion training may be used to stimulate
compliance of individuals who are a risk for the community, such as those in voluntary self-isolation. Keywords: impulsivity, episodic future thinking, compassion, inhibition, pandemic 2 2 is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a Introduction Vaccine hesitancy, attitudes on the effectiveness of these vaccines, and predictions about how soon
the pandemic will end could factor into people’s behaviour. These attitudes are usually linked to other
attitudes and behaviours relevant to pandemic behaviour such as lesser social distancing and mask
wearing (15, 16). We therefore also test how such predictors of guideline adherence influence
moment-to-moment behaviour. Impulsivity, the tendency to make rapid responses for short-term gratification and with insufficient
regard for negative consequences (17), is negatively correlated to public health guidelines adherence
(18, 19). The excessive future discounting characteristic of impulsivity can be influenced by
fluctuations in internal states (20). To understand how impulsivity affects moment-to-moment
behaviour, it is important to attain information on people’s mental state when behaviours occur (21,
22). Thus, we study these behaviours in an ecologically valid manner, where proximal information on
state impulsivity is obtained. This study seeks to avoid the distortions that often afflict self-report measures about typical behaviour
(23). In order to gain insights into moment-to-moment preventative behaviour in the ‘wild’ and real-
time changes following behaviour change interventions, we employ an ecological momentary 3 3 . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review)
The copyright holder for this
this version posted September 16, 2021. ;
0.1101/2021.09.13.21263407 . CC-BY 4.0 International license
It is made available under a assessment (EMA; or experience sampling) paradigm. Participants are asked on multiple occasions
each day about their urges pertaining to non-adherence of COVID-19 guidelines, and whether they
were able to control them. assessment (EMA; or experience sampling) paradigm. Participants are asked on multiple occasions
each day about their urges pertaining to non-adherence of COVID-19 guidelines, and whether they
were able to control them. Introduction In this experiment, the main variables of interest are the perceived intensity of urges, and the
probability of controlling urges, operationalised as self-control. In our preregistered analyses we
predicted that both the compassion intervention and the episodic future thinking intervention would
increase the likelihood of controlling urges, where we analyse their effect on self-control and on the
intensity of urges. Furthermore, we predicted that state impulsivity is associated with stronger urges
and fewer attempts to resist urges, and that vaccine hesitancy and shorter predicted back-to-normal
time frames are negatively correlated with the likelihood of controlling an urge through diminishing
self-control. In brief, we find that Compassion and EFT interventions reduce the intensity of urges,
but we find no evidence that self-control is affected. State impulsivity is significantly related to the
intensity of urges. Randomisation and Masking Randomisation and Masking Participants were randomly assigned a condition according to block randomisation (8 strata, 3
treatments, sequence obtained from sealedenvelope.com), see Figure A1 for the distribution of age
and sex per condition. Participants were unaware of their condition assignment, and were either
assigned to the EFT condition, the compassion condition, or the control condition. Participants The final sample contained 95 participants residing in the UK obtained through volunteer sampling
using the Prolific participant recruitment platform. Participants were required to be between 18-65
years of age, and within that age group we created a representative sample, based on sex and age
(2x4). Further details on the sample in Appendix A. In the final sample, there were 40 (42.1%) males, with a mean age of 41.4 (SD = 14.1), and 55
females (57.9%) with a mean age of 41.0 (SD = 12.5). 40 (42.1%) participants reported they had received a COVID-19 vaccine, and 5 reported that they had
been diagnosed with COVID-19 at some point, with one participant reporting they had experienced
both of these events. Even though the individual risk of COVID-19 is mitigated for vaccinated
individuals and those who previously contracted COVID-19, they were still required to comply with
public health guidelines. Therefore, vaccinated individuals were not excluded. To determine sample size, we estimated an effect size of a 5-percentage point increase in the
probability to control an urge in the EFT and Compassion treatments, and assumed that participants
would indicate they had an urge 3 times a day. We identified that 95% power could be achieved by
collecting data from 90 participants. Code is available here. Procedure Participants were asked whether they, or one of their family members, were part of a group that is
vulnerable to COVID-19. Participants also answered questions on their willingness to take a COVID-
19 vaccine and their beliefs about vaccine efficacy. We also elicited predictions of when people
would be able to resume on-site work (insofar as that will ultimately be the case), when people would
be able to go on holiday, and when life would go back to ‘normal’. These predictions and vaccination
attitudes were then combined into three scores, varying from 0 to 10. 4 . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
print
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review)
The copyright holder for this
this version posted September 16, 2021. ;
0.1101/2021.09.13.21263407 . CC-BY 4.0 International license
It is made available under a Each morning at 7.30am (expiry time 10am), participants would be asked to do either an EFT
exercise, a compassion (i.e., mentalising + affect-matching) exercise, or reflect on a recent news story
related to COVID-19 (respectively). All prompts are included in Table A1. After each condition-
dependent prompt, participants would be prompted with “Remember that your behaviour has an effect
on the COVID-19 situation”. Videos of the user interface can be accessed here. Throughout each day, participants would receive 5 surveys that were available for 1 hour. Procedure In
randomised order, they were asked whether since the last survey they had felt an urge to not wash
their hands, not cover their mouths when coughing or sneezing, not socially distance (e.g. to hug,
shake hands), not leave details for contact tracing, or whether they had felt an urge to leave their
house, touch their face, or avoid getting tested when it would have been better to do the opposite -
from a COVID-19 standpoint. Participants responded using a slider [0,10], where 0 indicated no urge,
1 indicated a very weak urge, and 10 indicated a very strong urge. We then administered the
Momentary Impulsivity Scale (24). The experiment took place from 29 March to 4 April 2021. The UK was in a state of lockdown at that
point in time, but most regions in the UK were in the early phase of reopening. Notably, the UK
government announced on 29 March that 6 people from 6 different households would be allowed to
meet outside. This, together with Easter weekend, produced a situation wherein people were likely to
have non-adherence urges. See Figure 1 for a visualisation of urge intensities per day during the
experiment. Figure 1. The perceived urge intensity (y-axis), partitioned by day (x-axis). The experiment was
partially conducted over a public holiday, at which time stronger urges of non-adherence would be
expected. 2 April (third line from the right) was Good Friday, and 4 April (the right-most line) was
Easter Sunday. The coloured points represent the estimated marginal means, and the error bars are
95% CIs. The grey data points each represent the aggregated data of one participant. Figure 1. The perceived urge intensity (y-axis), partitioned by day (x-axis). The experiment was
partially conducted over a public holiday, at which time stronger urges of non-adherence would be
expected. 2 April (third line from the right) was Good Friday, and 4 April (the right-most line) was
Easter Sunday. The coloured points represent the estimated marginal means, and the error bars are
95% CIs. The grey data points each represent the aggregated data of one participant. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a Analysis Our analyses were preregistered, and can be accessed here, data and code can be found here. The effects of impulsivity on the strength of an urge was analysed using a Linear Mixed Model
(LMM), with predictors: condition, the type of urge (and interaction between those), state impulsivity,
with the time of day and the day as control variables, and the participant as the random intercept. The
type of urge was not included as a predictor in the main preregistered model, but it was specified in
the exploratory analyses section and because the effects of the intervention might differ across
domains, we decided to include it in the main analyses. The analysis, conducted with the afex package
(25) used F-tests of fixed effects terms with Kenward-Roger approximation of degrees of freedom to
calculate p-values. We used a binomial generalised mixed model (GLMM) to conduct the self-control analysis. In
addition to the variables in the model above, vaccine hesitancy, vaccine effectiveness beliefs, back-to-
normal timeline predictions, and whether participants attempted to resist the urge were included. In
order to calculate p-values, likelihood ratio tests were used. In both analyses, we decided to deviate from the preregistration by including interaction terms with
the intervention because we deemed it likely that the intervention might affect some urges more than
others. The standard p<.05 criterion was used for determining whether the effects based on the Linear
Mixed Model (LMM), or on the Generalised Linear Mixed Model (GLMM) were significantly
different from those expected if the null hypothesis were correct. Reported effect sizes are model
coefficients for numerical variables, and post-hoc tests were conducted for factors with the emmeans
package, which calculates estimated marginal means of the outcome variable for factor levels. We
corrected for multiple comparisons using false discovery rate adjusted p-values in our post-hoc tests. Predictors for Urge Intensity Predictors for Urge Intensity Predictors for Urge Intensity Main Variables of Interest Results Different types of urges occurred at different rates, which matters for interpreting the results. Over the
one-week-long experiment, 83 out of the 95 participants reported the urge to leave the house at least
once, and did so 6.80 times on average (SD = 6.09), 79 reported the urge to touch their face (M =
7.91, SD = 8.14), while 60 reported the urge to not wash their hands (M = 5.03, SD = 6.11). Only 21
participants reported the urge to not leave their contact details (M = 3.86, SD = 7.18), and 17
participants reported the urge to avoid getting tested (M = 4.82, SD = 7.77). 73 Participants reported
the urge to disregard social distancing guidelines (M = 4.66, SD = 4.37), and 33 participants reported
the urge to not cover their mouth (M = 2.82, SD = 4.39). There was high variance in the number of urges people experienced, and the average number of urges
experienced was similar over the different conditions: in the EFT condition, people had 20.0 urges on
average (SD = 30.2) in the Compassion condition, people had 23.1 urges on average (SD = 16.3) and
in the Control condition 23.1 (SD = 26.7). Main Variables of Interest In accordance with our predictions, the condition factor (EFT, Compassion, Control) had a significant
effect on how strong they perceived urges to be, F(2, 110) = 7.59, p < .001. Post-hoc tests show that
participants experienced weaker urges in the EFT condition (estimated marginal mean (EMM) = 3.11,
95% CI [2.33, 3.89], t(111) = -3.571, p < .01), and in the Compassion condition (EMM = 3.30, 95%
CI [2.51, 4.09], t(105) = -3.113, p < .01), than in the Control condition (EMM = 4.71, 95% CI [3.94, 6 . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a 5.48]). Urge intensity was not significantly different in the EFT condition from the Compassion
condition (t(113) = .192, p = .67). See Figure 2. 5.48]). Urge intensity was not significantly different in the EFT condition from the Compassion
condition (t(113) = .192, p = .67). See Figure 2. Figure 2. The effects of the between-participants conditions: Episodic Future Thinking (EFT; left, in
purple) manipulation, the Compassion manipulation (middle, in blue), as compared to the Control
condition (right, in green), on the perceived intensity of urges (y-axis [1,10]). The points are
estimated marginal means, and the error bars are 95% CIs. The grey dots each represent the
aggregated data of a participant in one of the conditions. Figure 2. The effects of the between-participants conditions: Episodic Future Thinking (EFT; left, in
purple) manipulation, the Compassion manipulation (middle, in blue), as compared to the Control
condition (right, in green), on the perceived intensity of urges (y-axis [1,10]). The points are
estimated marginal means, and the error bars are 95% CIs. The grey dots each represent the
aggregated data of a participant in one of the conditions. The type of urge had a significant effect on the perceived strength of urges, F(6, 2000) = 27.60, p <
.001. Main Variables of Interest CC-BY 4.0 International license
It is made available under a State impulsivity had a significant effect on the perceived strength of urges, b = .429, 95% CI [0.262,
.597], F(1, 2030) = 25.25, p < .001. See Figure 3 for a depiction of the relationship between state
impulsivity and the intensity of urges. Figure 3. The relationship between state impulsivity as measured by the MIS (x-axis) and the intensity
of urges [1,10] (y-axis). The black lines at the bottom represent participants’ MIS scores per filled out
survey, and the blue band shows the 95% CI. Figure 3. The relationship between state impulsivity as measured by the MIS (x-axis) and the intensity
of urges [1,10] (y-axis). The black lines at the bottom represent participants’ MIS scores per filled out
survey, and the blue band shows the 95% CI. Figure 3. The relationship between state impulsivity as measured by the MIS (x-axis) and the intensity
of urges [1,10] (y-axis). The black lines at the bottom represent participants’ MIS scores per filled out
survey, and the blue band shows the 95% CI. Main Variables of Interest People reported the strongest urges for leaving the house (EMM = 4.80, 95% CI [4.42, 5.18]),
joint second strongest were urges to avoid getting tested (EMM = 3.94, 95% CI [3.34, 4.54]) and
urges to not socially distance (EMM = 3.94, 95% CI [3.54, 4.35]), fourth were urges to not leave
details for contact tracing (EMM = 3.78, 95% CI [3.15, 4.40]), fifth were urges to touch one’s face
(EMM = 3.62, 95% CI [3.24, 4.00]), sixth were urges to avoid washing hands (EMM = 3.12, 95% CI
[2.70, 3.55]), and the weakest urges pertained to covering mouth and nose when coughing/sneezing
(EMM = 2.74, 95% CI [2.19, 3.30]). The effect of the condition factor on urge intensity also significantly interacted with the type of urge
F(10, 1999) = 14.36, p < .001. Post-hoc tests revealed that urges to avoid leaving details for contact
tracing were weaker in the EFT condition (EMM = 1.85, 95% CI [.44, 3.26]; t(678) = 7.025, p < .001),
and in the Compassion condition (EMM = 2.47, 95% CI [1.00, 3.87]; t(644), = 6.161, p < .001), than
in the Control condition (EMM = 7.04, 95% CI [5.96, 8.12]), but were not significantly different from
each other, t(926) = .695, p = .49. Further, urges to avoid getting tested were also weaker in the EFT
condition (EMM = 1.77, 95% CI [.48, 3.06]; t(635) = 7.768, p < .001), and in the Compassion
condition (EMM = 2.68, 95% CI [1.33, 4.02]; t(618) = 7.768, p < .001), than in the Control condition
(EMM = 7.38, 95% CI [6.21, 8.55]), but were not different from each other, t(744) = 1.170, p = .24. 7 . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
reprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . Predictors for Self-Control Predictors for Self-Control The condition factor did not have a significant effect on self-control, χ2(2) = 4.56, p = .10. The type of urge had a significant effect on self-control, χ2(6) = 219.89, p < .001. The estimated
marginal means show that people were most likely to control an urge to not cover their mouths (EMM
(Probability) = .690, 95% CI [.498, .833]; they were second most likely to control to not wash their
hands (EMM = .637, 95% CI [.519, .741]); third were urges to not socially distance (EMM = .517,
95% CI [.407, .625]); fourth were urges to leave the house (EMM = .405, 95% CI [.318, .498]); fifth
were urges to touch one’s face (EMM = .154, 95% CI [.109, .213]), sixth were urges to not leave
contact details for contact tracing purposes (EMM = .086, 95% CI [.036, .193]); the most difficult
urges to control were those that pertain to not get tested (EMM = .009, 95% CI [.003, .031]). It is
important to note that these probabilities must be judged together with the relative frequencies of each
urge. For instance, the probability of controlling an urge that pertains to avoiding getting tested is
extremely low, but only 21 participants ever got one of these urges, for a total of 82 urges. See Figure
4 for a depiction of the probability to control various urges. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint is the author/funder, who has granted medRxiv a license to
(which was not certified by peer review)
preprint
this version posted September 16, 202
;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review)
The copyright holder for this
this version posted September 16, 2021. ;
0.1101/2021.09.13.21263407 . CC-BY 4.0 International license
It is made available under a Figure 4. The estimated marginal means for controlling various urges. Predictors for Self-Control Each point represents the
probability of controlling an urge pertaining to a certain type of behaviour, from left to right: the
probability of controlling an urge to not cover one’s mouth and nose when coughing or sneezing, to
not wash hands, to not socially distance, to not stay home, to avoid providing contact details when
entering an establishment, and to avoid getting tested. The error bars are 95% confidence intervals. The condition participants were assigned to significantly interacted with the type of urge in predicting Figure 4. The estimated marginal means for controlling various urges. Each point represents the
probability of controlling an urge pertaining to a certain type of behaviour, from left to right: the
probability of controlling an urge to not cover one’s mouth and nose when coughing or sneezing, to
not wash hands, to not socially distance, to not stay home, to avoid providing contact details when
entering an establishment, and to avoid getting tested. The error bars are 95% confidence intervals. The condition participants were assigned to significantly interacted with the type of urge in predicting
self-control, χ2(12) = 29.45, p < .01. State impulsivity did not have a significant effect on self-control, b = .054, 95% CI [-.224, .332], χ2(1)
= .16, p = .69. Furthermore, state impulsivity did not have a significant effect on the probability of
attempting to resist an urge b = -.108, 95% CI. Vaccine hesitancy did not have a significant effect on self-control, b = -.103, 95% CI [-.270, .063],
χ2(1) = 1.37, p < .24. Judgements about vaccine hesitancy did not have a significant effect on self-
control (b = .038, 95% CI [-.177, .253]; χ2(1) = .09, p = .77), and neither did predictions about when
life would go back to ‘normal’ after the pandemic (b = -.141, 95% CI [-.786, .505]; χ2(1) = .20, p =
.66). Discussion These mechanisms both likely promote the salience of the
potential negative consequences to people’s actions, which may be the reason for their effectiveness
in this context. Alternative explanations include that compassion exercises can lead to increased
positive affect and motivation (26), and can be helpful to deal with daily stressors (27), which may
also decrease the perceived intensity of urges. We found no evidence that vaccine attitudes or predictions of back-to-normal timelines were
associated with self-control. Other studies show that vaccine hesitancy is correlated with lesser social
distancing and mask wearing (16), but most studies reporting these relationships rely on judgements
about typical behaviour, or intentions to comply with guidelines. The lack of a significant relationship
between vaccine attitudes and guideline adherence in this study suggests that more research is needed
to understand how these attitudes affect moment-to-moment behaviour. We find that different urges occur at varying rates within and between participants, which is an
important consideration when assessing the relative impact of these urges. If an urge is relatively rare,
but difficult to control, then it may not be as relevant for policymakers and other key stakeholders to
see if the motivation to control this urge can be increased. Urges to avoid getting tested, or to not
leave contact details were relatively infrequent, but the fact that around 20% of the sample reported
one of these urges at least once is worrying given their importance to pandemic management (28). State impulsivity was related to stronger urges, but not to diminished self-control. This evidence
suggests that state fluctuations in impulsivity play an important, but poorly understood role in
determining public health guideline adherence during pandemics. A recent study has found this
‘bottom-up’ effect of state impulsivity for a different, more general domain of urges (29). It also
suggests that interventions targeting the internal state of the individual, and impulsivity in particular,
might be effective at ameliorating their guideline adherence. Future research could investigate
whether state impulsivity, as well as other internal states, can be targeted to improve public health
guideline adherence. The main limitations of this study were that the heterogeneity of the experience of certain types of
urges rendered the sample size too small to draw accurate inferences in some domains. Discussion Our findings show that episodic future thinking and compassion exercises reduced the intensity of
certain urges, but did not affect self-control. This finding broadly aligns with the evidence that EFT
can enhance future-oriented decision making in various contexts (10, 11). Given that urges usually
pertain to immediate rewards, this reduction in the strength of urges after an EFT exercise is most
likely because EFT reduces the relative value of immediate rewards compared to future rewards (8,
9). This finding suggests that an invitation to engage in EFT and compassion-inducing talking points
could be incorporated into press conferences and some public announcements to decrease urges of . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
rint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review)
The copyright holder for this
this version posted September 16, 2021. ;
0.1101/2021.09.13.21263407 . CC-BY 4.0 International license
It is made available under a noncompliance during public health crises. People who pose a specific risk to the community (e.g.,
those in voluntary self-isolation after travelling abroad) could be invited to periodically perform such
a task. noncompliance during public health crises. People who pose a specific risk to the community (e.g.,
those in voluntary self-isolation after travelling abroad) could be invited to periodically perform such
a task. The mechanisms through which EFT and compassion exercises affect behaviour differ: EFT is known
to enhance future-oriented decision making by decreasing delay discounting (8), whereas compassion
exercises can increase altruism (12). Discussion Only around
20 individuals reported having urges to avoid to getting tested or to avoid leaving details for contact
tracing at least once, and these 20 individuals were spread over the 3 conditions. This speaks to the
strengths and weaknesses of our ecological momentary assessment paradigm because, on the one
hand, it is a powerful paradigm for events that occur often and to a wide range of people (such as the
urge to abandon social distancing), and it can provide insight into behaviour ‘in the wild’. On the
other hand, for events that only happen for a narrow subset of people, or that happen infrequently,
ecological momentary assessment needs to be applied to that particular subset, or another approach
should be considered. The other limitation is that it is unclear to what extent the findings apply to
different populations. Future research could focus on the role of behavioural science interventions, including, but not limited
to, episodic future thinking and compassion-inducing exercises, in producing desired behaviour
during public health crises. We also deem it important that more research is devoted to uncovering the
factors predicting moment-to-moment decision making in people’s daily lives, where ecological
momentary assessment and GPS data (30) could play a critical role. These methods can provide a
more comprehensive understanding of the effects of behavioural interventions, shedding light on their 10 . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review)
The copyright holder for this
this version posted September 16, 2021. ;
0.1101/2021.09.13.21263407 . CC-BY 4.0 International license
It is made available under a . CC-BY 4.0 International license
It is made available under a longevity and externalities. For proper understanding of behavioural drivers during the pandemic,
there needs to be more emphasis on the proximal predictors to guideline compliance. Funding This research is supported by a Monash-Warwick Alliance Accelerator grant and by Martin and
Loreto Hosking’s Three Springs Foundation. The funding sources had no involvement in the research
conducted. Authors declare no competing interests. Authors declare no competing interests. Discussion longevity and externalities. For proper understanding of behavioural drivers during the pandemic,
there needs to be more emphasis on the proximal predictors to guideline compliance. Acknowledgements References 1. Bavel JJV, Baicker K, Boggio PS, Capraro V, Cichocka A, Cikara M, et al. Using social and
behavioural science to support COVID-19 pandemic response. Nature Human Behaviour. 2020;4(5):460 pp
p
p
2. Employment Situation Summary [press release]. U.S. Bureau of Labor Statistics, May 7 2021. p y
y [p
]
,
y
3. Barari S, Caria S, Davola A, Falco P, Fetzer T, Fiorin S, et al. Evaluating COVID-19 public health
messaging in Italy: Self-reported compliance and growing mental health concerns. MedRxiv. 2020. 4. Niedzwiedz CL, Green MJ, Benzeval M, Campbell D, Craig P, Demou E, et al. Mental health and
health behaviours before and during the initial phase of the COVID-19 lockdown: longitudinal analyses of the
UK Household Longitudinal Study. J Epidemiol Community Health. 2021;75(3):224-31. 4. Niedzwiedz CL, Green MJ, Benzeval M, Campbell D, Craig P, Demou E, et al. Mental health and
health behaviours before and during the initial phase of the COVID-19 lockdown: longitudinal analyses of the
UK Household Longitudinal Study. J Epidemiol Community Health. 2021;75(3):224-31. g
y
p
y
5. Pieh C, Budimir S, Delgadillo J, Barkham M, Fontaine JR, Probst T. Mental health during COVID-19
lockdown in the United Kingdom. Psychosomatic medicine. 2021;83(4):328-37. g
y
p
y
5. Pieh C, Budimir S, Delgadillo J, Barkham M, Fontaine JR, Probst T. Mental health during COVID-19
lockdown in the United Kingdom. Psychosomatic medicine. 2021;83(4):328-37. 6. Constandt B, Thibaut E, De Bosscher V, Scheerder J, Ricour M, Willem A. Exercising in times of
lockdown: an analysis of the impact of COVID-19 on levels and patterns of exercise among adults in Belgium. International journal of environmental research and public health. 2020;17(11):4144. 6. Constandt B, Thibaut E, De Bosscher V, Scheerder J, Ricour M, Willem A. Exercising in times of
lockdown: an analysis of the impact of COVID-19 on levels and patterns of exercise among adults in Belgium. International journal of environmental research and public health. 2020;17(11):4144. j
p
(
)
7. Robinson E, Boyland E, Chisholm A, Harrold J, Maloney NG, Marty L, et al. Obesity, eating behavior
and physical activity during COVID-19 lockdown: A study of UK adults. Appetite. 2021;156:104853. 8. Benoit RG, Gilbert SJ, Burgess PW. A neural mechanism mediating the impact of episodic prospection 7. Robinson E, Boyland E, Chisholm A, Harrold J, Maloney NG, Marty L, et al. Obesity, eating b
and physical activity during COVID-19 lockdown: A study of UK adults. Appetite. 2021;156:104853. Acknowledgements The authors would like to thank Dr. Peter Koval for the use of the SEMA3 platform. Availability of data and materials All data and analysis code are available, links are provided in the manuscript. We also provide videos
of the data collection procedure. References and physical activity during COVID-19 lockdown: A study of UK adults. Appetite. 2021;156:104853. 8. Benoit RG, Gilbert SJ, Burgess PW. A neural mechanism mediating the impact of episodic prospection
on farsighted decisions. Journal of Neuroscience. 2011;31(18):6771-9. 9
Peters J Büchel C Episodic future thinking reduces reward delay discounting through an enhancement p y
y
g
y
pp
;
8. Benoit RG, Gilbert SJ, Burgess PW. A neural mechanism mediating the impact of episodic prospection
on farsighted decisions. Journal of Neuroscience. 2011;31(18):6771-9. 9
P t
J Bü h l C E i
di f t
thi ki
d
d d l
di
ti
th
h
h
t Peters J, Büchel C. Episodic future thinking reduces reward delay discounting through an enhance
f prefrontal-mediotemporal interactions. Neuron. 2010;66(1):138-48. 10. Snider SE, LaConte SM, Bickel WK. Episodic future thinking: Expansion of the temporal window in
individuals with alcohol dependence. Alcoholism: clinical and experimental research. 2016;40(7):1558-66. 11. Stein JS, Wilson AG, Koffarnus MN, Daniel TO, Epstein LH, Bickel WK. Unstuck in time: episodic
future thinking reduces delay discounting and cigarette smoking. Psychopharmacology. 2016;233(21):3771-8. 12. Goetz JL, Keltner D, Simon-Thomas E. Compassion: an evolutionary analysis and empirical review. Psychological bulletin. 2010;136(3):351. 13. Omoto AM, Malsch AM, Barraza JA. Compassionate acts: Motivations for and correlates of
volunteerism among older adults. The science of compassionate love: Theory, research, and applications. 2009:257-82. 14. Weng HY, Fox AS, Shackman AJ, Stodola DE, Caldwell JZ, Olson MC, et al. Compassion training
alters altruism and neural responses to suffering. Psychological science. 2013;24(7):1171-80. 15. Romer D, Jamieson KH. Conspiracy theories as barriers to controlling the spread of COVID-19 in the
US. Social Science & Medicine. 2020;263:113356. 11 is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review)
The copyright holder for this
this version posted September 16, 2021. ;
0.1101/2021.09.13.21263407 . CC-BY 4.0 International license
It is made available under a 6. Latkin CA, Dayton L, Yi G, Colon B, Kong X. Mask usage, social distancing, racial, and gender
orrelates of COVID-19 vaccine intentions among adults in the US. PloS one. 2021;16(2):e0246970. 17. Moeller FG, Barratt ES, Dougherty DM, Schmitz JM, Swann AC. Psychiatric aspects of impulsivity. References ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a . CC-BY 4.0 International license
It is made available under a References American journal of psychiatry. 2001;158(11):1783-93. 18. Kooistra EB, van Rooij B. Pandemic Compliance: A systematic review of influences on social
distancing behaviour during the first wave of the COVID-19 outbreak. Available at SSRN 3738047. 2020. 19. Wismans A, Letina S, Wennberg K, Thurik R, Baptista R, Burke A, et al. The role of impulsivity and
delay discounting in student compliance with COVID-19 protective measures. Personality and Individual
Differences. 2021:110925. 20. Odum AL, Baumann AA. Delay discounting: State and trait variable. Impulsivity: The behavioral and
neurological science of discounting: American Psychological Association; 2010. p. 39-65. 21. Curran PJ, Bauer DJ. The disaggregation of within-person and between-person effects in longitudinal
models of change. Annual review of psychology. 2011;62:583-619. 1. Curran PJ, Bauer DJ. The disaggregation of within-person and between-person effects in longitudi
odels of change. Annual review of psychology. 2011;62:583-619. 22. Fisher AJ, Medaglia JD, Jeronimus BF. Lack of group-to-individual generalizability is a threat to
human subjects research. Proceedings of the National Academy of Sciences. 2018;115(27):E6106-E15. 23. Althubaiti A. Information bias in health research: definition, pitfalls, and adjustment methods. Journal
of multidisciplinary healthcare. 2016;9:211. p
y
Tomko RL, Solhan MB, Carpenter RW, Brown WC, Jahng S, Wood PK, et al. Measuring impulsivity
ily life: the momentary impulsivity scale. Psychological assessment. 2014;26(2):339. 25. Singmann H, Bolker B, Westfall J, Aust F, Ben-Shachar MS. afex: Analysis of factorial experiments. R
package version 013–145. 2015. 26. Dahl CJ, Lutz A, Davidson RJ. Cognitive processes are central in compassion meditation. Trends in
Cognitive Sciences. 2016;20(3):161-2. 27. Reddy SD, Negi LT, Dodson-Lavelle B, Ozawa-de Silva B, Pace TW, Cole SP, et al. Cognitive-based
compassion training: A promising prevention strategy for at-risk adolescents. Journal of Child and Family
Studies. 2013;22(2):219-30. 28. Stuart RM, Abeysuriya RG, Kerr CC, Mistry D, Klein DJ, Gray RT, et al. Role of masks, testing and
contact tracing in preventing COVID-19 resurgences: a case study from New South Wales, Australia. BMJ
open. 2021;11(4):e045941. p
29. van Baal S, Moskovsky N, Hohwy J, Verdejo-Garcia A. State impulsivity amplifies urges without
diminishing self-control. 2021. g
30. Gollwitzer A, Martel C, Marshall J, Höhs JM, Bargh JA. Connecting self-reported social distancing to
real-world behavior at the individual and us state level. 2020. 12 is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. Please imagine yourself after
lockdowns and restrictions are over.
You are doing your favourite activity
that became possible after lockdowns
lifted. Imagine how you feel, and
picture your surroundings (think about
smell and sound too). Please reflect on the fact that on 5
March, COVID-19 infections were
rising in Europe again. Please reflect on the reporting from 14
March that many people in
Lincolnshire are not turning up for
their vaccinations. Appendix A To become eligible for the study, participants (n = 293) completed an eligibility survey prior to the
experiment, which was used to create a representative sample. Participants were added to the EMA
software in two rounds in order to cope with varying drop-out across the eight groups, since there was
more dropout than anticipated during the EMA app download-phase. In total, 200 participants were
added to the EMA software, 112 of whom downloaded the app, and 97 of those completed more than
50% of the surveys. As indicated in our preregistration, participants who completed less than 50% of
surveys were excluded, the average survey completion rate for the rest was 83.7%. Finally, two
participants never reported having urges of non-adherence, and thus these were included from the
final sample, given that there was no variation in the data. Differing dropout across groups after the second round of participant entries led to an imbalance in
the female/male sample division. Given that this study is the first of its kind, we cannot assume that
these responses are missing at random. In order to address this issue, we analysed whether age and sex
influence urges and self-control. Figure A1. The age and sex distribution of the sample. Figure A1. The age and sex distribution of the sample. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021. ;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint . CC-BY 4.0 International license
It is made available under a . CC-BY 4.0 International license
It is made available under a Please imagine yourself as a
healthcare worker in the emergency
room. You have not been able to get
proper sleep and have had to keep
families separated because it was too
dangerous to see their loved ones. Try
to feel the emotions that might be
going through you. Table A1. The instructional prompts participants received each morning in their 7.30am survey. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
(which was not certified by peer review)
preprint
The copyright holder for this
this version posted September 16, 2021.
;
https://doi.org/10.1101/2021.09.13.21263407
doi:
medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
eer review)
The copyright holder for this
this version posted September 16, 2021.
;
0.1101/2021.09.13.21263407 Episodic future thinking Control Compassion Please reflect on the news that
shutdowns of the Ferguson shipyard
during the Covid pandemic have
added an extra £4.3m to the cost of
two over-budget and delayed CalMac
ferries. Please imagine yourself as a
vulnerable person. You have severe
asthma and will have significant
trouble breathing if you catch
COVID-19. Try to feel the emotions
that might be going through you. Please imagine yourself after
lockdowns and restrictions are over. You are on holiday, at your favourite
destination. Try to imagine how you
feel, and picture your surroundings
(think about smell and sounds too). Please imagine yourself as a family
member of a person in hospital due to
COVID-19. You want to be with
them, but you are not allowed to
because you might catch it yourself. Try to feel the emotions that might be
going through you. Please reflect on the news that the
COVID-19 restrictions in Scotland
were relaxed on 13 March. Up to four
people from two different households
can now gather outside. Please imagine yourself in the future
when lockdowns and restrictions are
over. You are travelling to a place you
always wanted to go. Imagine how
you feel and picture your surroundings
(think about smells and sound too). Please imagine yourself in the future
when lockdowns and restrictions are
over, and picture that you are doing
something you love. Imagine how you
feel and picture your surroundings
(think about smell and sound too). Please imagine yourself as a
vulnerable person. You are an elderly
person in a retirement home. You
have not been able to receive any
visitors for months, and your
interactions with the other residents
are restricted. Try to feel the emotions
that might be going through you. Please reflect on the reporting from 14
March that many people in
Lincolnshire are not turning up for
their vaccinations. Please reflect on the news that on 14
March people were fined 800 pounds
each for having a party in Gloucester. Please reflect on the news that 28% of
people in need of social care have
seen their health decline during
COVID-19. Table A1. The instructional prompts participants received each morning in their 7.30am survey. 14 14
|
https://openalex.org/W4225269822
|
https://epub.uni-regensburg.de/52243/1/Radeck2022_Article_RhegmatogenousRetinalDetachmen.pdf
|
English
| null |
Rhegmatogenous retinal detachment repair—does age, sex, and lens status make a difference?
|
Graefe's archive for clinical and experimental ophthalmology
| 2,022
|
cc-by
| 5,364
|
Key Messages In individuals operated for RRD over 40 years of age there were significantly more male patie In individuals operated for RRD over 40 years of age there were significantly more male patients. The male predominance in RRD was stronger in pseudophakic than in phakic eyes. The proportion of pseudophakic RRD has increased over the 15 years observation period. Graefe's Archive for Clinical and Experimental Ophthalmology
https://doi.org/10.1007/s00417-022-05674-x Graefe's Archive for Clinical and Experimental Ophthalmology
https://doi.org/10.1007/s00417-022-05674-x Graefe's Archive for Clinical and Experimental Ophthalmology
https://doi.org/10.1007/s00417-022-05674-x RETINAL DISORDERS Rhegmatogenous retinal detachment repair—does age, sex, and lens
status make a difference? Received: 21 October 2021 / Revised: 28 January 2022 / Accepted: 15 April 2022
© The Author(s) 2022 1
Department of Ophthalmology, University Hospital of
Regensburg, Franz‑Josef‑Strauss‑Allee 11, D‑93042
Regensburg, Germany * Viola Radeck
viola.radeck@ukr.de Abstract Purpose To analyze the correlation between lens status, age, and sex in the epidemiology and success rates of rhegmatog‑
enous retinal detachment (RRD) surgery.i Methods The files of all consecutive patients undergoing vitreoretinal surgery for uncomplicated RRD between Jan 2005
und Dec 2020 were retrospectively reviewed. Successful outcome was defined as no retinal redetachment occurring within
3 months after surgery. Results 5502 eyes with uncomplicated primary RRD were included. Mean age of the patients was 61.1 years (± 13.6 SD). In the age group over 40 years, a male predominance was found. The percentage of pseudophakic RRD increased from 25
to 40% during the 15 years observation period. In the age group 50 to 69 years, patients with pseudophakic detachments
were male in 786 out of 1079 cases (72.9%). In the same age group, 1285 of 2110 (60.9%) patients with phakic RRD were
male. Overall, primary success rate after one procedure was 91.2% (5018 of 5502). In the phakic eyes, the primary success
rate was higher in those eyes that underwent combined phacovitrectomy (93.0%), compared to those without simultaneous
cataract surgery (88.7%; p = 0.002). Conclusion The ratio of male and female patients with RRD varies between age groups. The proportion of pseudophakic
RRD has increased within 15 years. The male predominance in RRD is stronger in pseudophakic than in phakic eyes. In
phakic eyes with RRD, a combined phacovitrectomy yielded better anatomical results. Keywords Age · Cataract surgery · Sex · Pseudophakia · Retinal detachment surgery · Vitrectomy Keywords Age · Cataract surgery · Sex · Pseudophakia · Retinal detachment surgery · Vitrectomy
Key Messages
In individuals operated for RRD over 40 years of age there were significantly more male patients. The male predominance in RRD was stronger in pseudophakic than in phakic eyes. The proportion of pseudophakic RRD has increased over the 15 years observation period. Success rates of primary vitrectomy for phakic RD was higher if a combined phacovitrectomy was performed. Key Messages
In individuals operated for RRD over 40 years of age there were significantly more male patients. The male predominance in RRD was stronger in pseudophakic than in phakic eyes. The proportion of pseudophakic RRD has increased over the 15 years observation period. Success rates of primary vitrectomy for phakic RD was higher if a combined phacovitrectomy was performed Procedures A total of 810 (14.7%) eyes were treated with buckle sur‑
gery, 4692 (85.3%) with vitrectomy. In the vitrectomy cases,
95% received gas as a tamponade and 5% liquid silicone. The decision for buckle surgery or vitrectomy was left to
the respective surgeon. In young patients with attached
vitreous and atrophic holes or oral dialysis buckle surgery
was preferred, most pseudophakic eyes were vitrectomized. Preferences however changed over the observation period,
with an increasing proportion of eyes being treated with
vitrectomy [3]. Materials and methods The files of all patients undergoing primary RRD surgery
between January 2005 and December 2020 in our depart‑
ment were reviewed. Included were all eyes with uncom‑
plicated RRD undergoing buckle surgery or vitrectomy. Excluded were eyes with PVR grade C or more, eyes with a
history of penetrating injury to the posterior segment of the
eye, or a history of other vitreoretinal procedures in the past. Complicated cases such as malformations or retinopathy of
prematurity (ROP) were also excluded from the analysis. High myopic eyes (> 6 Dpt) were included, but pathological
myopia with RRD arising from macular holes in posterior
staphylomata was excluded.i From the 2614 phakic eyes treated with vitrectomy, 2163
(82.7%) were operated combined with phacoemulsification
and posterior chamber intraocular lens implantation. While
in the early years only a minority of the phakic eyes was
treated with combination surgery, at the end of the observa‑
tion period, about 90% were operated as phakovitrectomy
(Fig. 2). In 2008 to 2010, there was a paradigm shift to com‑
bining cataract surgery with vitrectomy. This was based on
reports of good results with combined surgery, sufficient
experience of the surgeons in both techniques, and the aim
to avoid a second (cataract) surgery for the patient. Failure was defined as diagnosis of redetachment docu‑
mented in the patient file within 3 months after primary sur‑
gery. In eyes with silicone oil tamponade, the silicone was
removed usually 3 to 6 months after primary surgery, which
may lead to an underestimation of redetachments since those
occurring after silicone removal were not included. Age distribution Overall, 5502 eyes with uncomplicated primary RRD had
VR surgery between January 2005 and December 2020
operated by 13 VR surgeons with different levels of surgical
experience. Mean age of the patients was 61.1 years (± 13.6
SD). The age distribution is shown in Fig. 1. The youngest
patient was 4, and the oldest was 98 years old. In the present study, we have analyzed the impact of lens
status, age, and sex on epidemiology and success rates of
RRD surgery. We investigated whether RRD occurring in
different age groups would also differ in other features such
as sex distribution and success rates. We have also analyzed
if the increasing number of cataract operations leads to a
distinct increase of pseudophakic RRD during the duration
of this study from 2005 to 2020 and how pseudophakia may
affect the sex distribution of RRD. Finally, we have com‑
pared success rates of combined phacovitrectomy with those
of vitrectomy alone. Introduction increasing number of cataract surgeries and refractive lens
exchanges, higher prevalence of myopia, and increasing life
expectancy [1].f Rhegmatogenous retinal detachment (RRD) is a common
surgical emergency in ophthalmology. Several factors con‑
tribute to an increasing occurrence of RRD, namely an RRD is not a homogenous entity. It can affect all age
groups, but with different clinical features. The most com‑
mon presentation is an RRD caused by retinal tears asso‑
ciated with a posterior vitreous detachment (PVD). Other
presentations include RRD with atrophic round holes in
individuals without PVD and vitreoretinal degeneration/
dystrophies. Most studies show a male predominance in (0121 3456789)
3 Graefe's Archive for Clinical and Experimental Ophthalmology already recorded in our own files, indicating that the overall
number of overlooked redetachments would not be signifi‑
cant [3, 4]. RRD patients, and the reason for the observed sex ratio is
however unclear. Another factor that characterizes different subgroups
of RRD is the lens status [2]. With the rising number
of cataract operations, an increasing proportion of pseu‑
dophakic RRD can be expected. In phakic RRD on the
other hand, vitrectomy is becoming increasingly common. Lens management during surgery is discussed controver‑
sially. Until today, there is no clear indication whether
vitrectomy should be performed primarily without lens
surgery or whether combined phacovitrectomy may be
the better strategy. The study was approved by the local ethic board (Ethik‑
kommission der Universität Regensburg) and adheres to the
principles of the declaration of Helsinki. 3 Graefe's Archive for Clinical and Experimental Ophthalmology Graefe's Archive for Clinical and Experimental Ophthalmology Graefe's Archive for Clinical and Experimental Ophthalmology
Fig. 1 Number of eyes of
patients with RRD in various
age groups
Fig. 2 Proportion of phakic
eyes with RRD treated with
vitrectomy alone or combined
phacovitrectomy umber of eyes of
with RRD in various
ps Fig. 2 Proportion of phakic
eyes with RRD treated with
vitrectomy alone or combined
phacovitrectomy Fig. 2 Proportion of phakic
eyes with RRD treated with
vitrectomy alone or combined
phacovitrectomy Sex distribution in different age groups Overall, 3360 of 5502 eyes (61.1%) with RRD occurred in
male patients. The proportion of male patients with RRD
in various age groups is shown in Fig. 3. In the age group
with RRD below 20 years, the proportion of boys was 56%. Between 20 and 39 years, 55% of the patients were female. Between 50 and 79 years, a majority of 64% was male. In
the oldest group over 80 years, no gender predominance was
observed (49.3% male). Our hospital is the only center for vitreoretinal emer‑
gencies in an area serving a population of about 2–3 mil‑
lion people. We assume that almost all redetachments were
referred to us. In order to investigate, if we had been missing
failures, in a subgroup of 1290 patients operated between
2007 and 2012, a more intense follow-up was conducted
by contacting patients and their ophthalmologists. No addi‑
tional redetachments were detected in addition to those 1 3 Graefe's Archive for Clinical and Experimental Ophthalmology Lens status and sex Overall, primary success rate after one surgery was
91.2% (5018 of 5502). Figure 4 shows the rate of rede‑
tachments in different age groups. The primary success
rate was lower for the youngest (age 0–19: success rate
84.4%; 38 out of 45) and oldest patients (age 80 + : success
rate 84.1%; 292 out of 347) compared to the middle-aged
group (age 20–79: success rate 91.7%; 4688 out of 5110). Primary failure rate of RDD surgery was 305/3360 (9.1%)
in male patients and 179/2142 (8.4%) in female patients,
which was not statistically significantly different (p = 0.4,
Pearson chi-square test). 3398 (61.7%) eyes were phakic, 27 (0.5%) aphakic, and 2077
(37.7%) had an artificial intraocular lens. The percentage
of pseudophakic RRD has increased over the observation
period from 25 to about 40%. The increase in pseudophakic
RRD occurred mainly between 2005 and 2014. Thereafter,
it remained relatively stable (Fig. 5). Of the pseudophakic RRDs, 67.3% occurred in male
patients, while the proportion of male patients was only
57.3% in the phakic RRDs. Since the sex ratio varied
between age groups (see Fig. 3), we separately analyzed
the age group 50–69 years of age. In this subset, the 1 Graefe's Archive for Clinical and Experimental Ophthalmology Graefe's Archive for Clinical and Experimental Ophthalmology
pseudophakic detachments were male in 786 out of 1079
cases (72.9%), while from the phakic eyes in the same age
group, 1285 out of 2110 (60.9%) were male. (n = 451; 88.7%). This difference was statistically significant
(p = 0.002; Pearson chi-square test). Fig. 3 Sex distribution of eyes
of patients with RRD in various
age groups. For the age group
40–49, the sex distribution was
significantly different from
equal with p = 0.01, for the
age groups 50–59, 60–69, and
70–79 with p < 0.0001. The
other age groups were not sig‑
nificantly different from equal
distribution. (Chi-square tests
for one-dimensional tables)
Fig. 4 Redetachment rates of
eyes of patients in various age
groups Fig. 4 Redetachment rates of
eyes of patients in various age
groups (n = 451; 88.7%). This difference was statistically significant
(p = 0.002; Pearson chi-square test). pseudophakic detachments were male in 786 out of 1079
cases (72.9%), while from the phakic eyes in the same age
group, 1285 out of 2110 (60.9%) were male. Fig. 3 Sex distribution of eyes
of patients with RRD in various
age groups. For the age group
40–49, the sex distribution was
significantly different from
equal with p = 0.01, for the
age groups 50–59, 60–69, and
70–79 with p < 0.0001. The
other age groups were not sig‑
nificantly different from equal
distribution. (Chi-square tests
for one-dimensional tables) Fig. 4 Redetachment rates of
eyes of patients in various age
groups 3 Lens status and success rates complicated RD cases were excluded, and some of them
(trauma, Coats disease) are more commonly found in boys,
the male predominance in children was less pronounced
compared to other publications [5]. RRD has been consistently shown to be more com‑
mon in male patients. This fact persisted after exclusion
of pseudophakia and trauma. It has been speculated that
males had a longer axial length and this could explain the
male predominance in RRD [9]. However, this would also
be a risk factor for atrophic round hole RRD with attached
posterior vitreous in young adults, but here females are
at higher risk. Males are more affected by PVD associ‑
ated RRD with tractional tears. Anatomical changes with
a more posteriorly located vitreous base in males have also
been described [10] and would provide a more convincing
explanatory approach. For young adults, most cases of RRD are due to atrophic
round holes with an attached vitreous. This type of RRD
is usually slowly evolving in myopic patients. Ung et al. showed that the mean age lies between 25 and 35 years and
scleral buckling procedures remained highly effective in this
selected group of patient [6]. Interestingly, this type of RRD
was found predominantly in females [6–8]. In the present
study, we also found a trend (not statistically significant) of
female predominance (55%) in the age group 20–39 years
of age. The majority of RRD occurs in the age group over 50 in
association with a PVD and traction-induced retinal tears. Between 50 and 79 years of age, 64% of the RRD patients
in our study were males. In the age group over 80, we
found both sexes were equally common affected, although
the proportion of males is only 38% in the general popu‑
lation in Germany according to the “Federal Office for
Stastistics.” Thus, if the sex distribution in the population
in this age group is taken into account, men over 80 years The number of cataract surgeries has increased in the
order of 10% per year over the last decades in industrialized
countries [11]. Increasingly, eyes with less advanced lens
opacities and better vision are operated. In particular, eyes
with high refractive errors undergo more commonly clear
lens extraction, with highly myopic eyes being at highest
risk for RRD. Lens status and success rates In this study, we provide data from a retrospective analysis of
over 5000 consecutive cases who underwent primary RRD
repair at a single university hospital. Mean age (61 years)
and male predominance (proportion of 61%) is in agreement
with other series in the literature [2]. However, a more dif‑
ferentiated analysis shows that there is no homogeneous sex
distribution over the whole age spectrum. Patients with pseudophakic RRD repair were on aver‑
age 67 ± 11 (mean ± SD, range) years old. The phakic
patients who had combined surgery were 63 ± 9 years old. Patients without cataract surgery during RRD repair were
49 ± 13 years of age. Mean age of the patients and rede‑
tachment rates for various subgroups are shown in Table 1. Notably, the primary success rate was higher in the phakic
eyes that underwent phacovitrectomy (n = 2163; 93.0%),
compared to those who were left phakic during vitrectomy For children, retinal detachment is found more often in
boys [5]. RRD in small children is commonly associated
with vitreoretinal degeneration/dysplasia. Since in our series 1 3 Graefe's Archive for Clinical and Experimental Ophthalmology Fig. 5 Proportion of pseudopha‑
kic lens status in eyes with RRD
between 2005 and 2020
Table 1 Age and redetachment
rates of various subgroups
depending on lens status and
surgical technique
Number of eyes
Redetachment
rate, %
Age, mean ± SD
Treated with buckle surgery
810
10.9
49.2 ± 16.5
Pseudophakic, treated with vitrectomy
2051
9.2
66.7 ± 11.4
Aphakic, treated with vitrectomy
27
18.5
49.2 ± 15.2
Phakic, treated with vitrectomy, no lens surgery
451
11.3
49.4 ± 12.9
Phakic, treated with combined phacovitrectomy
2163
7.0
62.8 ± 9.4 Number of eyes
Redetachment
rate, %
Age, mean ± SD
Treated with buckle surgery
810
10.9
49.2 ± 16.5
Pseudophakic, treated with vitrectomy
2051
9.2
66.7 ± 11.4
Aphakic, treated with vitrectomy
27
18.5
49.2 ± 15.2
Phakic, treated with vitrectomy, no lens surgery
451
11.3
49.4 ± 12.9
Phakic, treated with combined phacovitrectomy
2163
7.0
62.8 ± 9.4 Table 1 Age and redetachment
rates of various subgroups
depending on lens status and
surgical technique of age also have a higher individual risk for RRD than
women (p = 0.003, chi-square test). Table 1 Age and redetachment
rates of various subgroups
depending on lens status and
surgical technique Lens status and success rates Since cataract surgery is a major risk factor
for RRD, it is inevitably that the proportion of pseudophakic
RRD increases with time [1]. Here, we show an increase 1 Graefe's Archive for Clinical and Experimental Ophthalmology formation. Although not fully proven, it is assumed that
increased oxygen diffusion to the lens may play a role
[15]. Cataract formation after vitrectomy appears to
be age dependent, with older patients developing lens
opacifications earlier, often within a few months. Less
expected, after buckle surgery also a high frequency of
cataract surgery was observed [16]. Therefore, especially
in patients beyond the age of accommodation, RRD may
be operated primarily combined as phacovitrectomy. This saves the patient an additional surgery, is more
cost effective, and reduces time of reduced vision [17]. Especially in times of pandemic, it can reduce the risk
for nosocomial infection by avoiding additional hospital
visits [18]. from 25 to 40% pseudophakia in RRD eyes over the obser‑
vation period. Notably, in the age group 50–69, a proportion of 73% of
the patients with pseudophakic detachments was male, while
in phakic eyes in the same age group, only 61% were male,
although the majority (about 60%) of all cataract surgeries
is performed in females in Europe [12] and the USA [13]. A similar phenomenon was observed in Scotland, where
within the pseudophakic group, the overrepresentation of
men was even more marked (M:F, 2.3:1), despite a higher
rate of cataract surgery in women in the UK [14]. Although
the present study was not designed to evaluate this question,
a possible explanation for the data could be that males in this
age group have a higher risk for RRD than females, which
is further increased by cataract surgery. This effect appears
less pronounced for women. Cataract surgery is believed to
increase the RRD risk by accelerating vitreous degradation
and PVD. Therefore, it would be plausible that sex differ‑
ences in the vitreous base anatomy [10] might play a role for
the increased RRD risk for men. A major intraoperative advantage of combined sur‑
gery is uninhibited view and access to the most periph‑
eral retina and the vitreous base which allows a nearly
complete removal of vitreous traction and identification
of retinal tears. Lens status and success rates In a pseudophakic eye, the peripheral
secondary cataract will obscure the view, and in phakic
eyes, the complete release of traction to the vitreous base
is hardly possible without risking to touch the lens. This
may lead to better primary reattachment rates of phaco‑
vitrectomy. On the other hand, combined surgery requires
broader surgical skills and has a higher potential to create
intraocular inflammation which in turn may theoretically
increase the risk for PVR development. In our study, the overall primary anatomic success rate
was 91%, which is in accordance with other recently pub‑
lished studies for RRD surgery [2]. The high proportion of
vitreous surgery follows a general trend from buckle to vit‑
rectomy [3]. No difference was observed in success rates of
RD surgery between male and female patients. The redetachment rate in the very young and the very
old age group was somewhat higher. For children, lower
success rates have been previously observed [5]. This may
be due to more atypical findings and a delayed diagnosis in
children. In the very old, there is probably a higher rate of
ocular and general comorbidities, leading to later diagnosis
and more difficult ocular situations (e.g., PEX syndrome,
cloudy cornea, and narrow pupil). A reduced capacity of
the RPE to pump out subretinal fluid and reattach the retina
may also play a role. A recent analysis of BEAVRS data also
showed lower anatomical success rates in the age group over
80 with RRD [2]. Cataract surgery months or years after vitrectomy, when
the lens is opaque, may be more challenging due to miss‑
ing vitreous support of the lens and hard lens nucleus, both
leading to increased complications in cataract surgery. On
the other hand, disadvantages of phacovitrectomy may be a
reduced red light reflex due to vitreous hemorrhage or bul‑
lous detachment of the retina. Postoperative synechiae or
anterior dislocation of the IOL due to gas pushing forward
with iris capture may occur. In addition, calculation of the IOL may be more diffi‑
cult, especially if the macula is detached. Here the fellow
eye may be used for measuring axial length. The number
of eyes having undergone refractive surgery is increas‑
ing which also could complicate IOL calculation. Since
RRD often occurs in highly myopic eyes, the selection of
the intended refraction after lens surgery is difficult. References https://doi.org/10.1038/sj.
eye.6701618 7. Williams KM, Dogramaci M, Williamson TH (2012) Retrospec‑
tive study of rhegmatogenous retinal detachments secondary to
round retinal holes. Eur J Ophthalmol 22:635–640. https://doi.
org/10.5301/ejo.5000080f 7. Williams KM, Dogramaci M, Williamson TH (2012) Retrospec‑
tive study of rhegmatogenous retinal detachments secondary to
round retinal holes. Eur J Ophthalmol 22:635–640. https://doi.
org/10.5301/ejo.5000080f 8. Callaway NF, Vail D, Al-Moujahed A et al (2020) Sex differences
in the repair of retinal detachments in the United States. Am J
Ophthalmol 219:284–294. https://doi.org/10.1016/j.ajo.2020.06.
039 8. Callaway NF, Vail D, Al-Moujahed A et al (2020) Sex differences
in the repair of retinal detachments in the United States. Am J
Ophthalmol 219:284–294. https://doi.org/10.1016/j.ajo.2020.06.
039 9. Mitry D, Tuft S, McLeod D et al (2011) Laterality and gender
imbalances in retinal detachment. Graefes Arch Clin Exp Ophthal‑
mol 249:1109–1110. https://doi.org/10.1007/s00417-010-1529-0 10. Wang J, McLeod D, Henson DB et al (2003) Age-dependent
changes in the basal retinovitreous adhesion. Invest Ophthalmol
Vis Sci 44:1793–1800. https://doi.org/10.1167/iovs.02-0802 Funding Open Access funding enabled and organized by Projekt
DEAL. 11. Erie JC (2014) Rising cataract surgery rates: demand and supply. Ophthalmology 121:2–4. https://doi.org/10.1016/j.ophtha.2013.
10.002 Lens status and success rates Most studies however, including
a small randomized trial [25] and a recent meta-analysis
[26], found no difference in redetachment rates between
the two approaches [22, 27]. Open Access This article is licensed under a Creative Commons Attri‑
bution 4.0 International License, which permits use, sharing, adapta‑
tion, distribution and reproduction in any medium or format, as long
as you give appropriate credit to the original author(s) and the source,
provide a link to the Creative Commons licence, and indicate if changes
were made. The images or other third party material in this article are
included in the article’s Creative Commons licence, unless indicated
otherwise in a credit line to the material. If material is not included in
the article’s Creative Commons licence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a
copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. In the present study, we changed strategy in 2008 to
2010 and performed phacovitrectomy in most eyes over
50 years of age, even if the lens still was clear. When
comparing the redetachment rates, we found better results
in the group operated with combined surgery (7% vs 11%
redetachment rate). One has to keep in mind however that
the groups were not randomized and differed in several
aspects. The phacovitrectomy patients were generally
older and operated later in the observation period and the
absolute differences were small. Lens status and success rates An
intended emmetropia or low myopia will induce anisome‑
tropia, which necessitates contact lens correction or sub‑
sequent refractive lens surgery in the healthy fellow eye,
which in turn will expose this eye to an even higher risk
for RRD. Explaining this complex situation to a nervous
patient in an emergency situation can be challenging. The success rates also showed some correlation with the
lens status. In aphakic eyes, success rate was lower. In the
present series, aphakic eyes were not generally considered
to have complicated RRD and therefore were not excluded. They are only a small group of eyes, but may probably pre‑
sent with more confounding factors due to previous ante‑
rior segment trauma, narrow pupil, aphakia due to Marfan’s
syndrome, or a congenital cataract. This may explain the
higher redetachment rate. The small differences between
buckle surgery, and vitrectomy in phakic and pseudophakic
eyes are probably not relevant, considering that the groups
differ in their initial situations. The literature does not consistently recommend to per‑
form cataract and vitreous surgery in one or two steps. Some studies report a lower success rate of combined
surgery [19, 20]. In addition, combined surgery had less f
A controversial question is whether cataract surgery
should be performed simultaneously during vitreous sur‑
gery for RD. Vitrectomy leads to accelerated cataract 1 3 1 3 1 3 1 3 Graefe's Archive for Clinical and Experimental Ophthalmology favorable refractive outcome [20, 21] and there was a
higher complication rate for inexperienced surgeons [22]. In a scenario-related survey of BEAVRS, most vitreoreti‑
nal surgeons would avoid combined surgery in RDD cases
with a history of laser-assisted refractive surgery, even
when faced with a visually significant cataract [23]. Other
authors had better results with phacovitrectomy compared
to vitrectomy alone [24]. Most studies however, including
a small randomized trial [25] and a recent meta-analysis
[26], found no difference in redetachment rates between
the two approaches [22, 27]. Conflict of interest The authors declare no competing interests. favorable refractive outcome [20, 21] and there was a
higher complication rate for inexperienced surgeons [22]. In a scenario-related survey of BEAVRS, most vitreoreti‑
nal surgeons would avoid combined surgery in RDD cases
with a history of laser-assisted refractive surgery, even
when faced with a visually significant cataract [23]. Other
authors had better results with phacovitrectomy compared
to vitrectomy alone [24]. Funding Open Access funding enabled and organized by Projekt
DEAL. References 1. Nielsen BR, Alberti M, Bjerrum SS et al (2020) The incidence of
rhegmatogenous retinal detachment is increasing. Acta Ophthal‑
mol 98:603–606. https://doi.org/10.1111/aos.14380 2. Ferrara M, Mehta A, Qureshi H et al (2021) Phenotype and out‑
comes of phakic versus pseudophakic primary rhegmatogenous
retinal detachments: cataract or cataract surgery related? Am J
Ophthalmol 222:318–327. https://doi.org/10.1016/j.ajo.2020.09.
036 f
Limitations of our study are its retrospective design,
the lack of a stringent follow-up of the patients, the miss‑
ing information of preoperative PVD status, and missing
information about visual acuity and functional outcome. However, we present a large number of RRD cases over
a 15 years period from a single center and have focussed
on data that can be obtained reliably in retrospective from
the patients’ charts.l 3. Radeck V, Helbig H, Barth T et al (2021) Ablatiochirurgie: trends
über 15 Jahre (Retinal detachment surgery: trends over 15 years). Ophthalmologe. https://doi.org/10.1007/s00347-021-01430-4 4. Radeck V, Helbig H, Barth T et al (2021) The learning curve of
retinal detachment surgery. Graefes Arch Clin Exp Ophthalmol. https://doi.org/10.1007/s00417-021-05096-1 4. Radeck V, Helbig H, Barth T et al (2021) The learning curve of
retinal detachment surgery. Graefes Arch Clin Exp Ophthalmol. https://doi.org/10.1007/s00417-021-05096-1 5. Barth T, Zeman F, Helbig H et al (2017) Clinical features and
outcome of paediatric retinal detachment. Ophthalmologica
237:63–72. https://doi.org/10.1159/000455355 5. Barth T, Zeman F, Helbig H et al (2017) Clinical features and
outcome of paediatric retinal detachment. Ophthalmologica
237:63–72. https://doi.org/10.1159/000455355 In conclusion, our analysis of the influence of lens sta‑
tus, age, and sex in a large consecutive series of RD sur‑
gery revealed that the gender predominance in RD varies
within different age groups. While in children, more boys
were affected; in young adults, there were more females
with RD; and in patients over 50 years of age, a strong
male predominance was observed. The male predominance
in RRD is stronger in pseudophakic than in phakic eyes. The proportion of pseudophakic RD has increased during
the observation period from 25 to 40%. In phakic eyes with
RRD combined phacovitrectomy yielded better anatomical
results than vitectomy alone. 6. Ung T, Comer MB, Ang AJS et al (2005) Clinical features and
surgical management of retinal detachment secondary to round
retinal holes. Eye (Lond) 19:665–669. https://doi.org/10.1038/sj.
eye.6701618 6. Ung T, Comer MB, Ang AJS et al (2005) Clinical features and
surgical management of retinal detachment secondary to round
retinal holes. Eye (Lond) 19:665–669. Consent to participate Informed consent was waived because of the
retrospective design of the study. Declarations 12. Javaloy J, Druchkiv V, Beltrán J et al (2021) Retinal detach‑
ment after phacoemulsification in refractive surgery clinics: a
large series analysis with variable follow-up during 16 years. Graefes Arch Clin Exp Ophthalmol. https://doi.org/10.1007/
s00417-021-05160-w Ethics approval All procedures performed in studies involving human
participants were in accordance with the ethical standards of the ethical
committee of the University of Regensburg and with the 1964 Helsinki
declaration and its later amendments or comparable ethical standards. 13. Wu AM, Wu CM, Tseng VL et al (2018) Characteristics asso‑
ciated with receiving cataract surgery in the US Medicare and Consent to participate Informed consent was waived because of the
retrospective design of the study. 1 3 Graefe's Archive for Clinical and Experimental Ophthalmology Veterans Health Administration populations. JAMA Ophthalmol
136:738–745. https://doi.org/10.1001/jamaophthalmol.2018.1361 detachment. Can J Ophthalmol 50:360–366. https://doi.org/10.
1016/j.jcjo.2015.07.003 p
g
j
p
14. Mitry D, Charteris DG, Yorston D et al (2010) The epidemiology
and socioeconomic associations of retinal detachment in Scotland:
a two-year prospective population-based study. Invest Ophthalmol
Vis Sci 51:4963–4968. https://doi.org/10.1167/iovs.10-5400 22. Kim MS, Woo SJ, Park KH (2020) Phacovitrectomy versus lens-
sparing vitrectomy for rhegmatogenous retinal detachment repair
according to the surgical experience. Retina Publish Ahead of
Print. https://doi.org/10.1097/IAE.0000000000003090i p
g
15. Holekamp NM, Shui Y-B, Beebe DC (2005) Vitrectomy surgery
increases oxygen exposure to the lens: a possible mechanism
for nuclear cataract formation. Am J Ophthalmol 139:302–310. https://doi.org/10.1016/j.ajo.2004.09.046 23. Brent AJ, Bedi S, Wakefield M et al (2020) A comparative study
of lens management in the United Kingdom and India with regard
to rhegmatogenous retinal detachment surgery. Eur J Ophthalmol
30:1120–1126. https://doi.org/10.1177/1120672119855209f p
g
j j
16. Feng H, Adelman RA (2014) Cataract formation following vit‑
reoretinal procedures. Clin Ophthalmol 8:1957–1965. https://doi.
org/10.2147/OPTH.S68661 24. Caiado RR, Magalhães O, Badaró E et al (2015) Effect of lens
status in the surgical success of 23-gauge primary vitrectomy for
the management of rhegmatogenous retinal detachment: the Pan
American Collaborative Retina Study (PACORES) group results. Retina 35:326–333. https://doi.org/10.1097/IAE.0000000000
000307 g
17. Port AD, Nolan JG, Siegel NH et al (2021) Combined phaco-
vitrectomy provides lower costs and greater area under the curve
vision gains than sequential vitrectomy and phacoemulsification. Graefes Arch Clin Exp Ophthalmol 259:45–52. https://doi.org/10.
1007/s00417-020-04877-4 25. Mora P, Favilla S, Calzetti G et al (2021) Parsplana vitrectomy
alone versus parsplana vitrectomy combined with phacoemulsifi‑
cation for the treatment of rhegmatogenous retinal detachment: a
randomized study. BMC Ophthalmol 21:196. Declarations https://doi.org/10.
1186/s12886-021-01954-y 18. Antaki F, Milad D, Javidi S et al (2020) Vitreoretinal surgery in
the post-lockdown era: making the case for combined phacovit‑
rectomy. Clin Ophthalmol 14:2307–2309. https://doi.org/10.2147/
OPTH.S270934 26. Farahvash A, Popovic MM, Eshtiaghi A et al (2021) Combined
versus sequential phacoemulsification and pars plana vitrectomy:
a meta-analysis. Ophthalmol Retina. https://doi.org/10.1016/j.oret.
2021.01.004 19. Loukovaara S, Haukka J (2018) Repair of primary RRD—compar‑
ing pars plana vitrectomy procedure with combined phacovitrec‑
tomy with standard foldable intraocular lens implantation. Clin
Ophthalmol 12:1449–1457. https://doi.org/10.2147/OPTH.S1714
51 27. Guber J, Bentivoglio M, Sturm V et al (2019) Combined pars
plana vitrectomy with phacoemulsification for rhegmatogenous
retinal detachment repair. Clin Ophthalmol 13:1587–1591. https://
doi.org/10.2147/OPTH.S215352 20. Tan A, Bertrand-Boiché M, Angioi-Duprez K et al (2021) Out‑
comes of combined phacoemulsification and pars plana vitrec‑
tomy for rhegmatogenous retinal detachment: a comparative study. Retina 41:68–74. https://doi.org/10.1097/IAE.0000000000002803 Publisher's Note Springer Nature remains neutral with regard to
jurisdictional claims in published maps and institutional affiliations. p
g
21. Kim Y-K, Woo SJ, Hyon JY et al (2015) Refractive outcomes of
combined phacovitrectomy and delayed cataract surgery in retinal 1 3
|
https://openalex.org/W2897720154
|
https://europepmc.org/articles/pmc6209974?pdf=render
|
English
| null |
A Metagenomic Approach to Evaluating Surface Water Quality in Haiti
|
International journal of environmental research and public health/International journal of environmental research and public health
| 2,018
|
cc-by
| 9,420
|
Received: 8 August 2018; Accepted: 4 October 2018; Published: 10 October 2018 Abstract: The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over
9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have
declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to
accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap,
a metagenomic approach employing environmental samples was taken. In this study, surface water
samples were collected at two time points from several sites near the original epicenter of the cholera
outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and
subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists,
and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites
were analyzed by principle components analysis, and distinct genomic profiles were obtained for
each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages
at several sites. Members of the Acinetobacter family were frequently detected in samples, including
members implicated in waterborne diseases. These results indicate a metagenomic approach to
evaluating water samples can be useful for source tracking and the surveillance of pathogens such as
Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin. Keywords: cholera; metagenomic analysis; bioinformatics; whole genome sequencing; principle
components analysis; water quality; environmental sampling; Haiti International Journal of
Environmental Research
and Public Health A Metagenomic Approach to Evaluating Surface
Water Quality in Haiti Monika A. Roy 1,2, Jean M. Arnaud 1, Paul M. Jasmin 3, Steve Hamner 1, Nur A. Hasan 4,5,
Rita R. Colwell 4,5 and Timothy E. Ford 1,* 1
Department of Environmental Health Sciences, School of Public Health & Health Sciences,
University of Massachusetts Amherst, Amherst, MA 01003, USA; monikaroy@umass.edu (M.A.R.);
jarnaud@umass.edu (J.M.A.); shamner@montana.edu (S.H.) j
2
Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
3
Equipes mobiles d’intervention rapide (EMIRA) du Ministère de la Santé Publique et de la Population (MSPP),
Hinche HT 5111, Haiti; drpjasmin@gmail.com 2
Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
3
Equipes mobiles d’intervention rapide (EMIRA) du Ministère de la Santé Publique et de la Population (MSPP),
Hinche HT 5111, Haiti; drpjasmin@gmail.com pj
g
4
CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA; nur.hasan@cosmosid.com (N.A.H.);
rcolwell@umiacs.umd.edu (R.R.C.) 4
CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA; nur.hasan@cosmosid.com (N.A.H.);
rcolwell@umiacs.umd.edu (R.R.C.) 5
Center for Bioinformatics and Computational Biology, University of Maryland,
College Park, MD 20742, USA *
Correspondence: teford@umass.edu; Tel.: +1-413-545-3214 1. Introduction The emergence of cholera in Haiti, following the severe (7.0 Richter scale) earthquake south
of Port-au-Prince in 2010, resulted in 817,000 cases of illness and more than 9749 deaths through
2016, according to the Haitian Ministry of Public Health and Population (MSPP) [1]. As a result of
a coordinated response between the MSPP, the U.S. Centers for Disease Control and Prevention
(CDC), the United Nations Children’s Fund (UNICEF), the Pan American Health Organization
(PAHO), the World Health Organization (WHO), and other local and international health partners,
external financial resources were raised to strengthen Haiti’s disease surveillance and response Int. J. Environ. Res. Public Health 2018, 15, 2211; doi:10.3390/ijerph15102211 www.mdpi.com/journal/ijerph www.mdpi.com/journal/ijerph Int. J. Environ. Res. Public Health 2018, 15, 2211 2 of 16 systems. While these efforts made tremendous strides in the country, the lack of continual funding for
surveillance activities threatens progress towards eliminating diseases like cholera [2]. Cholera infection is caused by the bacterium Vibrio cholerae and is characterized by acute diarrhea
and vomiting; the illness can range from subtle to severe, leading to death [3]. Cholera is a waterborne
disease, with poor water and sanitation infrastructure a primary risk factor for transmission [4]. A significant correlation has also been found between rainfall and cholera incidence in Haiti, with a
4–7-day lag time [5]. Cholera has declined since its initial outbreak, with a total of 13,681 cases and
159 deaths in 2017 [1]. However, with declining surveillance funding, continued poor water quality,
failing infrastructure, and future hurricane risks, a need exists for reliable and low-cost diagnostics
for improving surveillance, prediction, and response to outbreaks using measurable environmental
parameters [6,7]. Diagnostics tools for environmental sampling are being tested to shorten the time and reduce the
number of expert personnel needed to determine cholera presence in a limited resource setting [8]. Several rapid diagnostic tests (RDTs) have been developed for cholera detection including the Crystal
VC Dipstick, Artron V. cholerae O1 and O139 Combo Test, and the SD Bioline Cholera Ag O1/O139
RDT. These tests have significant performance variation, suggesting that they may be useful for
initial surveillance in low resource settings, but that improvements are needed prior to their use in
clinical settings [9]. A relatively inexpensive membrane filtration plate count technique has also been
developed and tested that accurately quantifies V. 1. Introduction cholerae in a mixed-culture setting [10], however,
this method requires 24 hours of incubation time in specific laboratory settings. q
p
y
g
PCR methods have provided useful information for detecting cholera at specific locations
post-outbreak [11–13]. However, whole genome shotgun sequencing combined with advanced
bioinformatic analysis offers a method to examine the genetic diversity of environmental samples and
to characterize sites in terms of relative abundance of bacteria, fungi, protists, viruses, antimicrobial
resistance (AMR), and virulence associated genes [14]. Metagenomic approaches are now being used
to assess and characterize the microbiota and bacterial communities in diverse waters, ranging from
Amazonian rivers to water sources in urban environments [15–17]. This method provides a way to not
only identify factors related to cholera presence, but also provide characterization of factors related to
other waterborne diseases present in Haiti. To our knowledge, only limited environmental monitoring of surface waters is currently
conducted in Haiti. The University of Florida has established environmental monitoring sites in
the Gressier/Leogane region of Haiti, west of Port-au-Prince, but the focus of sampling is only on
monitoring environmental reservoirs of toxigenic V. cholerae 01 [11,13]. In the Artibonite region of the
Central Plateau, focus has also been on the isolation of V. cholerae, where basic water quality parameters
have been collected from the Artibonite River and tributaries. The results suggest high levels of E. coli,
with a geometric mean of 500 CFU/100 mL (this included some samples taken from rivers outside
the Artibonite region), with 74% of samples considered in the high risk category according to WHO
guidelines [18]. Continuous water quality monitoring is needed in Haiti for public health purposes in assessing
the epidemiology of waterborne diseases like cholera [19]. While still used on a point sampling basis,
the use of metagenomics provides a powerful tool that yields more profiling information beyond
V. cholerae presence, and has the potential to be used in a clinical setting. At present, hand-held
sequencing technologies, such as the Oxford Nanopore Technologies handheld MinION, are expensive,
at around $1000 per sample for reagents and a single flow cell. However, the potential for multiplexing
up to 12 samples could bring the cost down to approximately $80 per sample [20]. Advances in
barcoding chemistry [21], and the purchase of flow cells in bulk, also have the potential to further
reduce per sample costs. 1. Introduction Although bioinformatics technologies are improving, further optimization is necessary before
routine diagnostics for field use are possible. However, the advances made thus far make this
technology comparable to the cost of bench-top instruments, but in a handheld, mobile device. With the 3 of 16 Int. J. Environ. Res. Public Health 2018, 15, 2211 development of handheld DNA sequencing technologies that make such sample analysis in remote
locations and in as little as a few hours possible, this type of sample collection and metagenomic
analysis could soon be conducted on a local scale in Haiti [22]. This paper explores the utility of using a
metagenomic approach to evaluate surface water quality, and provides data on the relative abundance
of pathogens from several sites in Haiti. 2.1. Water Sampling and Shipping Triplicate water samples were collected between 5–6 January 2018 from five surface water sites
in the Central Plateau region of Haiti: Maïssade, Hinche, Thomonde, Mirebalais, and Lascahobas
(Figure 1, Table 1). Information on elevation, average temperature, and average rainfall for January and
July at largely populated communities close to these sampling sites is provided in Table 2. This reflects
the significant seasonal differences in rainfall between these sampling dates. These sites were chosen
based on ease of sampling, while at the same time targeting areas with the highest level of cholera
incidence as reported by the MSPP. These sites are close to river crossings on roads linking the major
towns in the Central Plateau region, including the Rivière La Thème in Mirebalais, close to the first
reported cholera cases in 2010. Due to their proximity to river crossings, these sites are heavily
used by communities for bathing, washing clothes and dishes, and other household activities where
water could be inadvertently consumed. This may be a particular risk for young children and infants. Samples had also been collected the previous summer, between 24–28 July 2017, but were not replicated
or collected from the exact same locations, though they were collected from the same region. They are
included to provide a seasonal comparison. Figure 1. Sampling sites in the Central Plateau of Haiti (Mapdata©2018 Google). A blue star denotes
the first cluster of cholera cases just south of Mirebalais [23]. Sites labelled 1 through 5a were sampled
in triplicate in January 2018. Single samples were taken from sites labelled 6 and 7 in July 2017. Sites 1,
4 and 5b were also sampled in July 2017. Figure 1. Sampling sites in the Central Plateau of Haiti (Mapdata©2018 Google). A blue star denotes
the first cluster of cholera cases just south of Mirebalais [23]. Sites labelled 1 through 5a were sampled
in triplicate in January 2018. Single samples were taken from sites labelled 6 and 7 in July 2017. Sites 1,
4 and 5b were also sampled in July 2017. 4 of 16 Int. J. Environ. Res. Public Health 2018, 15, 2211 Table 1. Location and description of sampling sites. Site (Approximate
Position on Map)
Coordinates
Description
January 2018
1. Rio Frio, Maïssade
19.1703 N
72.1353 W
Small tadpoles and fishes were visible in this water. Water depth was 2–3 feet
and the water was very turbid. 2. 2.1. Water Sampling and Shipping Rivière Guayamouc,
Hinche
19.1494 N
72.0092 W
Trash piles and foraging pigs were present on the river banks. The water was
extremely turbid. 3. Rivière de Thomonde,
Thomonde
19.0082 N
71.9520 W
Many people washed clothes and bathed at this site. The water was turbid
and sediment a unique silver gray color. 4. Rivière La Thème,
Mirebalais
18.8356 N
72.1071 W
The water was turbid and served as irrigation for the sweet potato field
nearby. Algae growth was present on the river banks. Trash bags and other
plastics were floating on the sides of the river. 5a. Rivière Lascahobas,
Lascahobas
18.8308 N
71.9451 W
The water was clear with a visible rocky bed. The sample was easily filtered. However, the river bank contained numerous plastic waste products. July 2017 (samples collected during this time were not replicated)
1. Rio Frio, Maïssade
19.1703 N
72.1353 W
People crossed their vehicles here, bathed, and washed clothes. 3. Rivière de Thomonde,
Thomonde
19.0082 N
71.9520 W
The water was clear and this site was upriver of considerable activity,
but was also used for bathing and washing clothes. 4. Rivière La Thème,
Mirebalais
18.8356 N
72.1071 W
This site contained the most contaminated water comparatively. There was
open defecation on the side of the river, trash piles, and many people
washing clothes. 5b. Tributary of Rivière
la Peigne, Lascahobas
18.8204 N
71.9464 W
Water from this site came from a groundwater spring through a water pipe
out of the side of a mountain. Many people were bathing near the pipe,
with clothes washing below the sampling point. 6. Rivière Artibonite,
below the Lac de Péligre
18.9026 N
72.0604 W
Water was collected about a mile below the dam where it was released at the
bottom of the reservoir. 7. Rivière Cabestor,
Cabestor
18.8689 N
72.0011 W
Water from the Rivière Cabestor mixed with water from a small creek near
the MFH birthing center. At this sampling point, vehicles crossed the river,
and people bathed and washed clothes. Table 1. Location and description of sampling sites. At each of the five sites for the January 2018 sampling, 250 mL water samples were collected and
filtered directly on-site in triplicate using SterivexTM filters (0.22 µm pore size, polyethersulfone sterile
membranes; Millipore® Sigma, St. Louis, MO, USA). These samples were collected approximately
10 m apart to minimize sediment disturbance. 2.2. Metagenomic Sequencing and Bioinformatics Analysis Metagenomic DNA was extracted from the filters using a DNeasy PowerWater Sterivex Kit
(QIAGEN) following the manufacturer’s guidelines. Concentrations of the metagenomic DNA were
measured using a Qubit Fluorometric Quantitation (Thermo Fisher Scientific, Waltham, MA, USA). Most samples yielded around 1–4 ng/µL genomic DNA (Table S1). Fragment libraries were constructed
from 100 ng DNA (except for one sample with low yield where 15 ng DNA was used) using the Thermo
Fisher IonXpress Plus Fragment Library kit (Thermo Fisher Scientific) according to the recommended
manufacturer instructions. Genomic DNA libraries were quantified by qPCR and then sequenced on an
Ion S5 XL Semiconductor Sequencer (Ion Torrent, Thermo Fisher Scientific) to generate 200 bp sequence
reads. Each sample was sequenced with an average of 17M sequence read depth. General Sequencing
Statistics of all samples, as well as Mean Sequence Quality distribution as measured by MultiQC [25]
are illustrated by Figures S1 and S2, and Table S1. As the mean quality value across each base position
in the read was always above quality score 17 for at least 80% of the read length (i.e., probability of
correct base call ~98%), reads were not subjected to quality trimming. Raw genomic sequences were
analyzed by CosmosID metagenomic software [26–31], including principle components analysis (PCA),
to reveal microbial community composition, antibiotic resistance markers, and virulence gene pools. y
p
g
p
Briefly, the CosmosID platform utilizes high performance data mining algorithms and highly
curated dynamic comparator databases (GenBook®) that rapidly disambiguate hundreds of millions
of short reads of a metagenomic sequence into the discrete microbial genomes and genes engendering
the identified sequences without the need for sequence assembly. Similarly, the community resistome
and virulome, and the collection of antibiotic resistance and virulence associated genes, respectively,
in the microbiome were also identified by querying the unassembled sequence reads against the
CosmosID curated antibiotic resistance and virulence associated gene database. The GeneBook
database is composed of over 150,000 microbial genomes and gene sequences representing bacterial,
viruses, protists, and fungi, as well as antibiotic resistant and virulence associated genes. The curated
databases provide extremely fine resolution in identification, discrimination of pathogens from
‘near neighbors’, and accurate measurement of relative abundance. Results are either reported
as “filtered”—which is based on internal statistical scores that indicate the organism or gene is
most likely present, or “unfiltered”—where further validation is recommended to confirm their
presence (CosmosID documentation https://app.cosmosid.com/docs). 2.2. Metagenomic Sequencing and Bioinformatics Analysis Data are deposited in the
NCBI Sequence Read Archive (SRA) database with accession number SRP158812. The resultant taxa
abundance tables were used to calculate observed species richness, alpha diversity indices, and beta
diversity distance matrices (data not shown for beta diversity). PCA was performed to cluster samples
based on abundance using the covariance matrix of normalized data as the measure of similarity. 3.1. Environmental Sampling Sampling sites were selected as previously described, and are depicted in Figure 1. Sampling
sites from January 2018 are labelled 1 through 5a, and sampling sites from the previous summer in
July 2017 are labelled 1, 3, 4, 5b, 6, and 7. The location and description of each site are described in
Table 1. Syringe cartridges were used to collect water samples to filter through Sterivex filters at all
sites during both time points. 2.1. Water Sampling and Shipping Samples were placed on ice and transported directly to
Port-au-Prince for shipping to the U.S. The shipping company, Deutsche Post DHL Group (DHL), required
a letter from a Haitian organization before shipping the samples. This caused extensive delays until a letter
was obtained from a local partner organization, Midwives for Haiti (MFH), based in Hinche, Haiti on
17 January 2018. The samples remained frozen during this waiting period. Regrettably, the samples were
unable to be shipped with ice blocks. They arrived at CosmosID in a thawed state six days later, when they
were immediately frozen prior to downstream processing and analysis. For samples collected the previous
summer in July 2017, several ~100 mL samples were collected at a selection of sites, and these samples
were transported over a 2-day period at room temperature to the U.S., whereby they were immediately
frozen prior to downstream processing and analysis. Table 2. Elevation, average temperature, and average rainfall for January and July at largely populated
communities close to the sampling sites [24]. Site Location
Elevation
(Meters)
Average Temperature (◦C)
Average Precipitation (mm)
January 2018
July 2017
January 2018
July 2017
Maïssade
270
22.4
25.8
30.8
151
Hinche
238
21.6
25
28.1
155.2
Thomonde
284
Monthly data not available for this site, ~10 miles from Hinche
Mirebalais
120
22.2
25.7
23.5
150.3
Lascahobas
219
20.3
23.7
29.5
136.3
Cabestor
300
Monthly data not available on this site, <10 miles from Lascahobas
Lac de Péligre
175
Monthly data not available for these sites (both for above and below the Lac de Péligre) Table 2. Elevation, average temperature, and average rainfall for January and July at largely populated
communities close to the sampling sites [24]. Int. J. Environ. Res. Public Health 2018, 15, 2211 5 of 16 2.2. Metagenomic Sequencing and Bioinformatics Analysis 3.2. Sequencing Analysis Sequence analysis of DNA extracted from the samples revealed a wide diversity of bacteria, with
over a thousand strains of sequences at each site. Figure 2 depicts a Krona [32] visualization of all
bacteria detected in January 2018 samples across the five sites. The predominant phylum of bacteria
was the gram-negative Proteobacteria at 84% of total bacterial diversity. This phylum includes a wide
variety of pathogens, and in this analysis Alphaproteobacteria comprised 41%, Betaproteobacteria Int. J. Environ. Res. Public Health 2018, 15, 2211 6 of 16 11%, and Gammaproteobacteria 44% of Proteobacteria. Within the Gammaproteobacteria class,
the Pseudomonadales order comprised 81% (30% of total bacterial diversity), of which 92% was
of the Acinetobacter genus (27% of total bacterial diversity). The Gammaproteobacteria class also
includes Vibrio cholerae in the Vibrionales order. Among the five sampling sites from the January 2018 time point, mean species diversity was
calculated to represent alpha diversity (Figure 3). All sites demonstrated similar levels of diversity,
however, replicates from the Lascahobas River site showed the most variability. Figure 2. Krona visualization. Total bacterial diversity, representing gamma diversity, among all
samples from the January 2018 time point. Figure 2. Krona visualization. Total bacterial diversity, representing gamma diversity, among all
samples from the January 2018 time point. Figure 3. Choa1 alpha diversity. All three replicates of each site are represented by a box plot. Raw data
used to generate the box plots are presented in Supplemental Table S2. Figure 3. Choa1 alpha diversity. All three replicates of each site are represented by a box plot. Raw data
used to generate the box plots are presented in Supplemental Table S2. 7 of 16 Int. J. Environ. Res. Public Health 2018, 15, 2211 Each site also contained a relatively unique bacterial composition, or fingerprint, demonstrated by
PCA performed on data gathered for all sites across the two sampling time points (Figure 4), and for
the January 2018 sites alone (Figure 5). Supplemental Figure S3 shows dominant bacteria identified for
all sites in the January 2018 sampling. Several Acinetobacter spp. appear in all sites, particularly the
Lascahobas site where they comprise 10 of the top 12 bacterial genera detected in terms of relative
abundance. In contrast, the other 4 sites had more bacterial diversity and Acinetobacter spp. comprised
about 5 of the top 11–13 bacteria detected. Figure 4. 3.2. Sequencing Analysis Principle components analysis (PCA) of relative abundance of bacteria at all sites, including
July 2017 samples, which were not replicated (* Site ~1 mile below Lac de Péligre dam). Figure 5. PCA of relative abundance of bacteria from replicate samples collected in January 2018. The relative abundance of the E. coli and V. cholerae bacteria, the V. cholerae Intl1 virule
ne, and the Stx2-converting phage was quantified across replicates for each of the five sites
J
2018
li
i d
d f
h it i
th J l
2017
li
i d Th
d Figure 4. Principle components analysis (PCA) of relative abundance of bacteria at all sites, including
July 2017 samples, which were not replicated (* Site ~1 mile below Lac de Péligre dam). Figure 4. Principle components analysis (PCA) of relative abundance of bacteria at all sites, including
July 2017 samples, which were not replicated (* Site ~1 mile below Lac de Péligre dam). Figure 5. PCA of relative abundance of bacteria from replicate samples collected in January 2018. Figure 5. PCA of relative abundance of bacteria from replicate samples collected in January 2018 The relative abundance of the E. coli and V. cholerae bacteria, the V. cholerae Intl1 virulence
gene, and the Stx2-converting phage was quantified across replicates for each of the five sites in
the January 2018 sampling period, and for each site in the July 2017 sampling period. These data
are presented in Table 3. For both January 2018 and July 2017 sampling, E. coli was present in all
replicates, although generally at low abundance. V. cholerae Intl1 was present in most replicates but
with a wider range of abundance; of note, the relative abundance of Intl1 in Maïssade samples in July
2017 was much higher at 17.65% than samples collected in January 2018, all below 5.0%. Replicates for
Mirebalais were all consistently higher for relative abundance of Intl1, above 7.0%, but one replicate The relative abundance of the E. coli and V. cholerae bacteria, the V. cholerae Intl1 virulence
gene, and the Stx2-converting phage was quantified across replicates for each of the five sites in
the January 2018 sampling period, and for each site in the July 2017 sampling period. These data
are presented in Table 3. For both January 2018 and July 2017 sampling, E. coli was present in all
replicates, although generally at low abundance. V. 3.2. Sequencing Analysis cholerae Intl1 was present in most replicates but
with a wider range of abundance; of note, the relative abundance of Intl1 in Maïssade samples in July
2017 was much higher at 17.65% than samples collected in January 2018, all below 5.0%. Replicates for
Mirebalais were all consistently higher for relative abundance of Intl1, above 7.0%, but one replicate Int. J. Environ. Res. Public Health 2018, 15, 2211 8 of 16 exhibited much higher abundance at 18.45%. V. cholerae was detected in some replicates across all
sites and sampling periods, but at very low relative abundance, with the highest detection level of
0.02%. Stx2-converting phage was also detected in some replicates across all sites, but ranging from
not detected to 9.82% relative abundance. Table 3. Relative abundance of sequences characterizing Escherichia coli, V. cholerae, V. cholerae Intl1
converting phage and Stx2 (Shiga toxin gene) converting phage. Site
Replicate
January 2018
E. coli
V. cholerae
V. cholerae Intl1
Stx2-converting phage
Maïssade
1
0.12
ND
1.61
ND
2
0.01
<0.01
4.91
8.45
3
<0.01
ND
ND
0.70
Hinche
1
0.04
ND
2.69
0.22
2
<0.01
<0.01
4.8
ND
3
<0.01
ND
0.11
ND
Thomonde
1
0.03
<0.01
6.93
ND
2
0.01
<0.01
6.05
0.52
3
0.03
0.02
3.52
7.11
Mirebalais
1
<0.01
ND
7.59
4.31
2
<0.01
ND
18.45
9.82
3
0.01
<0.01
7.55
7.62
Lascahobas
1
0.19
<0.01
2.13
1.78
2
0.06 *
ND
6.40
0.11
3
0.02
ND
ND
0.36
July 2017
Maïssade
1
1.11
<0.01 **
17.65
ND
Mirebalais
1
0.16
<0.01 ***
7.18
ND
Lascahobas
1
3.57
<0.01 ***
3.09
0.77
Below Péligre
1
0.14
ND
ND
ND
Cabestor
1
0.34
ND
ND
ND
Above
Péligre
1
0.08
<0.01 ***
3.31
ND
Notes: * E. coli O157:H7; ** V. cholerae RC385; *** V. cholerae HE-45; ND—not detected. All data are presented
as percentages. Table 3. Relative abundance of sequences characterizing Escherichia coli, V. cholerae, V. cholerae Intl1
converting phage and Stx2 (Shiga toxin gene) converting phage. Supplemental Figures S4–S6 provide filtered sequence data on viruses, virulence factors and
AMR genes for each site. Filtered data is used to allow these figures to be manageable. In the
case of viruses, filtered data only detected viruses at 9 of the 15 sample sites, so a relative view is
not possible (Figure S4). However, a large number of viruses were detected at lower confidence
in the unfiltered data. 3.2. Sequencing Analysis Dominant fungi
include Onygenales spp., Epichloe sylvatica, Puccinia arachidis, Clavaria fumosa, Lentinus polychrous, and at
two of the Lascahobas sites Candida parapsilosis (1.92% and 2.39% abundance), Enterocytozoon bieneusi at
one Hinche River site (2.52%) and two Lascahobas sites (1.98% and 2.85%), and Anncaliia algerae at two
Hinche River sites (4.58% and 2.78%), one Mirebalais site (2.76%), and two Lascahobas sites (4.48% and
4.67%). Unfiltered results also identify Candida albicans, Alspergillus fumigates, and Pneumocystis jirovecii. Protist sequences are dominated by Paramecium biaurelia and Pseudoperonospora cubensis. However,
Acanthamoeba polyphaga is present at one Hinche and one Mirebelais site (13.37 and 30.72%, respectively). Also present at almost all sites and highest at one Hinche River site (4.15%) is Plasmodium falciparum. Unfiltered data (not shown) also suggests sequence evidence for Entamoeba spp., Toxoplasma gondii,
and Trypanosome congolense. Supplemental Figures S7 and S8 present information on fungi and protists. Dominant fungi
include Onygenales spp., Epichloe sylvatica, Puccinia arachidis, Clavaria fumosa, Lentinus polychrous, and at
two of the Lascahobas sites Candida parapsilosis (1.92% and 2.39% abundance), Enterocytozoon bieneusi at
one Hinche River site (2.52%) and two Lascahobas sites (1.98% and 2.85%), and Anncaliia algerae at two
Hinche River sites (4.58% and 2.78%), one Mirebalais site (2.76%), and two Lascahobas sites (4.48% and
4.67%). Unfiltered results also identify Candida albicans, Alspergillus fumigates, and Pneumocystis jirovecii. Protist sequences are dominated by Paramecium biaurelia and Pseudoperonospora cubensis. However,
Acanthamoeba polyphaga is present at one Hinche and one Mirebelais site (13.37 and 30.72%, respectively). Also present at almost all sites and highest at one Hinche River site (4.15%) is Plasmodium falciparum. Unfiltered data (not shown) also suggests sequence evidence for Entamoeba spp., Toxoplasma gondii,
and Trypanosome congolense. 4. Discussion The data presented in this study provide relative abundances of bacteria, fungi, protists,
and viruses, as well as identify antibiotic resistance and virulence associated genes for several sites in
samples collected in Haiti over two time points, using a metagenomic approach. 3.2. Sequencing Analysis Viruses were dominated by phages and associated with a wide range of
potentially pathogenic bacteria. In the filtered sample set, Enterobacteria phages were dominant,
with specific Escherichia and Salmonella phages present. In unfiltered data, additional phages were
identified and associated with bacteria such as Aeromonas, Acetobacter, Arthrobacter, Bacillus, Bordatella,
Burkholdaria, Clostridium, Cronobacter, Haemophilus, Mycobacteria, Pseudomonas, Shigella, Staphylococcus,
Streptococcus, Vibrio, and Yersinia—all genera with important human pathogenic species. In addition,
human mastadenovirus was detected. Due to the number of virulence factors detected, only the
top factors representing 80% of total abundance are presented in Supplemental Figure S5. Virulence
factors are dominated by those associated with the important pathogens, Klebsiella pneumonia, Proteus
mirabilis, Pseudomonas aeruginosa, V. cholerae, and E. coli. Other pathogen-associated virulence factors
are also present. Antimicrobial resistance genes are dominated by those conveying aminoglycoside,
sulphonamide, beta-lactam, and in some cases tetracycline resistance (Figure S6). Int. J. Environ. Res. Public Health 2018, 15, 2211 9 of 16 Information on viruses, virulence factors, and AMR genes present in the most contaminated
replicate of samples collected from the Thomonde site are described in Table 4. Notable is detection of
Stx2-converting phage and Vibrio phage CTX. Table 4. Selection of some of the more dominant viruses and virulence factors detected in samples
collected at the Thomonde site, replicate #3 from January 2018 sampling (filtered data, * indicates
V. cholerae virulence factors from unfiltered data that require further confirmation). All classes of AMR
genes detected in filtered data from this sample are also reported. Viruses and Bacteriophages
Virulence Associated Genes
Classes of AMR Genes Detected
Enterobacteria phage HK630
Klebsiella pneumoniae: orf6, GI 42543951, tnpA
Aminoglycosides: aadA, aadA5, aadA7, aadA16,
aadA10, aac1, aac3 Ia, aph6 Id, aph, ant2” Ia
Siphoviridae_u_s
Enterobacter aerogenes: traM, tniB, ssb, korC
Sulphonamide sul2
Escherichia virus P1
V. cholerae: intI1, GI 42567126 *,
VCA0118 *, CARB-6 *
Trimethoprim: dfrC
Viruses_u_s
Serratia marcescens: orfA, intI3
Beta-lactam: blaOXA, blaAIM
Stx2-converting phage 1717
E. coli: qacEdelta1, aphA7
Macrolide: mphE, ermA
Human mastadenovirus C
Pseudomonas aeruginosa: intI1, accC1, aadA6
Phenicol: dha1
Enterobacteria phage BP-4795
Salmonella Infantis: tnpR
G7cvirus_u_s
Pseudomonas putida: qacEdelta1
Myoviridae_u_s
Proteus mirabilis: sul1
Vibrio phage CTX
Morganella morganii: oxa-2 Supplemental Figures S7 and S8 present information on fungi and protists. 4.3. Bacterial Diversity Of all replicates in the January 2018 sampling, the majority of bacteria detected originated
from either the Alphaproteobacteria and Gammaproteobacteria classes (Figure 2). From the
Gammaproteobacteria class, two bacterial genera of concern that were detected were Legionella and
Acinetobacter. The total relative abundance of the family Legionellaceae was a low 1%. In contrast,
the total relative abundance of Acinetobacter spp. was much higher, 27%, and Acinetobacter spp. were detected the most frequently in all five sites from the January 2018 samples, particularly from
the Lascahobas samples (Figure S3), though this site also showed the largest variability among
replicates (Figure 3). Acinetobacter spp. are nosocomial pathogens that survive for extended periods
in water, including in drinking water [36], and are associated with multiple antibiotic resistance
and a number of clinical outcomes, including pneumonia, wounds, and respiratory and GI tract
infections [37–39]. Additionally, the species Acinetobacter baumannii is implicated in ~80% of hospital
acquired Acinetobacter infections [40] and in this study comprised 5% of Acinetobacter species and 1% of
total relative abundance (Figure 2). Again, it should be noted that these relative abundances may have
been affected by the failure of the cold chain. In samples collected in July 2017, two non-toxigenic (environmental) strains of V. cholerae were
detected (Table 3); the Haitian strain, HE-45, was detected at the La Thème, Lascahobas site and at the
site above the Lac de Péligre, and the Chesapeake Bay environmental isolate, RC385, was detected
at the Maïssade site. When virulence genes were examined, the V. cholerae intI1 gene was identified
at these sites. The gene intI1 is included in a class of resistance integrons implicated in the spread of
antibiotic resistance via horizontal gene transfer [41]. In the July 2017 sampling sites, intI1 was not
detected in the absence of V. cholerae. In contrast, V. cholerae intl1 gene was detected in almost 90% of
samples collected in January 2018, although V. cholerae was detected in less than 50% of the samples,
and only at the species level. Although the focus of most prior studies has been on V. cholerae, one metagenomic study has been
conducted to the southwest of Hinche, primarily in the region of the Rivière Hinquitte, a tributary of
the Rivière Guayamouc [42]. This study examined bacterial diversity in source and point-of-use water. Consistent with our data, Acinetobacter was a dominant genus. 4.1. Limitations We are aware of the limitations of this study based on the failure of the cold chain due to
the unanticipated refusal of the shipping company in Haiti to ship ice packs. For future studies,
we are working with colleagues in Haiti for DNA extraction and preservation with DMSO-EDTA-salt
(DESS) [33] prior to shipping. However, in this study the possibility of both growth and inhibition of
select species call into question our measurements of relative abundance. In past work, members of the
research team have had no problems recovering and isolating specific pathogens, including V. cholerae
and enterohemorrhagic and enterotoxigenic E. coli (EHEC and EPEC) strains, from filters shipped wet
from India [34]. So, even though our current work may not be quantitative, we believe the qualitative
findings on specific pathogens are significant. Despite these limitations, several interesting trends are worth noting. The Mirebalais Rivière
La Thème site showed greatest consistency in replicates, as demonstrated by PCA (Figures 4 and 5). This site is located near the epicenter of the 2010 cholera outbreak [23]. Other sites showed greater
diversity among replicates, which may reflect the heterogeneity of the river samples collected at
multi-use sites. Overall, PCA analysis was able to distinguish the five sites sampled in January 2018, Int. J. Environ. Res. Public Health 2018, 15, 2211 10 of 16 and demonstrated that it was possible to characterize the sites in terms of bacterial community
structure. This finding is helpful for source tracking of groups of pathogens and determining potential
sources of contamination for future studies. 4.2. Seasonal Differences As shown in Figure 4, there is a clear difference between results obtained in July 2017 and in
January 2018, even though some samples were collected at the same sites. Samples collected in July 2017
demonstrated a different bacterial community composition compared to samples from any of the sites
sampled in January 2018. This may be due to seasonal differences between those two time points, with
a drier period occurring in January, compared to higher average temperatures and higher rainfall in
July [35]. Sites sampled in July 2017 are closely clustered except for the site below the Lac de Péligre
dam, which is an outlier. This was also the site with lowest diversity relative to other samples collected
in July 2017. Since water is released from the bottom of the reservoir, it could be expected that this site
would have a different microbial composition compared to the other sampling sites. 4.3. Bacterial Diversity Surprisingly, Klebsiella was the most
dominant genus found in their study, yet was only present at low relative abundance in our study
in unfiltered data (0.03%; 0.01% from the Rivière Guayamouc site). However, Klebsiella pneumoniae
virulence genes were dominant at most of our sites. The majority of other dominant bacterial genera
found in the two river water sources sampled in their study were also present at our sites, but also
at low relative abundance (<0.2%). These findings could reflect the proximity of water sources used
for drinking to the consumers, and hence to minimal sanitation, whereas our samples were taken
at larger river sites with potentially greater input from agricultural and other sources. For example, Int. J. Environ. Res. Public Health 2018, 15, 2211 11 of 16 dominance of Sphingobium yanoikuyae (Figure S3), often associated with PAH-contaminated soils [43],
at the Mirebalais Rivière La Thème site, as well as the presence of predatory Bacteriovorax spp. [44],
will change the bacterial community structure in our study compared to the pathogen-dominated
genera in the source and point-of-use study [42]. The finding of dominance of Klebsiella pneumoniae virulence genes in our samples, in the absence
of much evidence for the bacterium itself, speaks to the importance of a complete metagenomic
approach for potential health risk assessments from environmental samples. While there is evidence
for environmental reservoirs of virulence factors in the absence of clinically important pathogens [45],
the presence of these factors should not be ignored due to rapid dissemination through horizontal
gene transfer, and further studies in this area are warranted [46]. 4.4. Phage and Virulence Factor Diversity Almost all the bacterial pathogens reflected by the presence of phages were detected at low relative
abundance in the filtered data set with the exception of Cronobacter spp., Haemophilus spp. Shigella spp.,
and Vibrio spp. Cronobacter spp., Shigella spp., and Vibrio spp., were detected in the unfiltered dataset,
but Haemophilus spp. was not detected, which is surprising given that the Haemophilus phage, HP1 was
detected at almost all sites in unfiltered data, and as high as 9.1% relative abundance at one of the
Hinche River sites. Important human pathogens reflected by identified virulence factors were also
present in the filtered dataset, including Klebsiella pneumonia, Pseudomonas aeruginosa, and E. coli,
and in the unfiltered dataset, V. cholerae. However, Proteus mirabilis was not detected, although this
opportunistic pathogen is commonly found in soil and water [47]. 4.5. Fungal and Protozoan Diversity Fungi of greatest concern include Onygenales spp.,
which dominated most of the
samples and includes a number of emerging human pathogens [48], Candida parapsilosis [49],
Enterocytozoon bieneusi [50], and Anncaliia algerae [51]. Unfiltered results also suggest the presence of
Candida albicans, Alspergillus fumigates and Pneumocystis jirovecii (the causative organism of Pneumocystis
pneumonia). All of these pathogenic fungi are of concern, especially in Haiti where HIV infection rates
remain very high, and have been shown to be a risk factor in susceptibility to cholera in Haiti [52]. Some pathogenic protozoan sequences are also of concern, including sequences representative of
Acanthamoeba polyphaga at high relative abundance at two sites and the malaria parasite, Plasmodium
falciparum at almost all sites. Presence of potentially pathogenic Entamoeba spp., and Toxoplasma gondii
in unfiltered data is also of concern. Although not a human pathogen, the finding in unfiltered data
of Trypanosome congolense, a major cause of African animal trypanosomosis, has implications for a
subsistence agricultural economy [53]. 4.6. Cholera and EHEC Concerns The cholera toxin (CTX) converting phage is associated with cholera toxin production by
V. cholerae and was detected in one sample collected at the Thomonde site (Table 4). Detection of the
V. cholerae intI1 gene and the CTX converting phage are indicative of a potential risk for enhanced
cholera toxin production by these strains. While waters sampled in this study were not sources used for
drinking water, many of them are heavily used for bathing, washing clothes, and for other household
activities where water could be inadvertently consumed. Shiga toxin converting phages were detected at most of the sites (~70%) sampled in January 2018
(Table 3). These phages are important in Shiga toxin production by EHEC, a pathogen that can
cause disease with high mortality risk [54]. Although all sites were positive for E. coli at low relative
abundance during the January 2018 sampling, only one was definitively identified as EHEC from
the Lascahobas site at 0.06% relative abundance, where the Shiga toxin-producing EHEC serotype
0157:H7 was also detected. All sites sampled in July 2017 were positive for E. coli, at generally
higher relative abundance than January samples, with the highest relative abundance of 3.48% at Int. J. Environ. Res. Public Health 2018, 15, 2211 12 of 16 the Lascahobas site, most likely reflecting the relatively higher temperatures and surface runoff from
significant rainfall that had occurred over an extended period. Predictive models of disease events that combine both environmental parameters with
knowledge of the presence of putative pathogens and virulence or antibiotic resistance genes in
environmental samples, may be particularly useful in developing preventive strategies against a
cholera outbreak. Surveillance efforts, in combination with simple interventions such as bio-sand
filters [10] and development of an effective cholera vaccine [55–57] will aid in the elimination of
this disease. Once optimized, hand-held sequencing technologies could then potentially be used as
diagnostic tools and for source-tracking of pathogens. Overall, cholera surveillance requires multiple
methods to gather accurate data in a timely manner for decision-making purposes, but this preliminary
research provides an initial context for demonstrating the potential use of metagenomics to identify
sources of cholera, track cholera-related genes and bacteriophages, and identify bacterial community
fingerprints for different areas in Haiti. 5. Conclusions These preliminary results suggest that sequencing DNA from environmental water samples and
subsequently applying metagenomic analysis offers a useful approach to characterize environmental
samples collected from heavily used water bodies in Haiti. Toxigenic V. cholerae O1 and O139 strains
were not detected in this analysis, consistent with the recent decline in cholera cases, although
environmental V. cholerae strains and converting phages for both cholera and Shiga toxins were
detected, indicating that a potential disease risk remains for nearby populations. While further sample
collection and greater in-depth analysis are needed, the results of this preliminary study provide
insight and offer a potential monitoring tool for detecting the re-emergence of toxigenic V. cholerae and
other waterborne diseases in the aquatic environment in Haiti. Supplementary Materials: The following are available online at http://www.mdpi.com/1660-4601/15/10/2211/
s1, Figure S1. Mean Sequence Quality distribution representing the number of reads with average quality scores. Figure S2. Sequence Quality Histogram representing the mean quality value across each base position in the
read. Figure S3. Top 11–13 most abundant (relative) bacteria for each replicate at the (a) Maïssade, (b) Hinche,
(c) Thomonde, (d) Mirebalais, and (e) Lascahobas sites for January 2018 sampling. Figure S4. Filtered data for
Viruses. Figure S5. Filtered data for top 80% virulence factors. Figure S6. Filtered data for top 50% AMR. Figure S7. Filtered data for Fungi. Figure S8. Filtered data for Protists. Table S1. DNA concentrations and general sequencing
statistics of January 2018 samples measured by MultiQC. Table S2. Choa1 alpha diversity raw data used to
generate the box plots for Figure 3. Author Contributions: Conceptualization, T.E.F.; Methodology, N.A.H., R.R.C., and T.E.F.; Software, N.A.H. and R.R.C.; Validation, M.A.R., J.M.A., N.A.H., R.R.C., S.H., P.M.J., and T.E.F.; Formal Analysis, M.A.R., J.M.A.,
N.A.H., R.R.C., and T.E.F.; Investigation, M.A.R., J.M.A., and P.M.J.; Resources, T.E.F.; Data Curation, N.A.H. and R.R.C.; Writing-Original Draft Preparation, T.E.F. and M.A.R.; Writing-Review & Editing, M.A.R., N.A.H.,
R.R.C., S.H., and T.E.F.; Visualization, M.A.R., J.M.A., N.A.H., R.R.C., and T.E.F..; Supervision, T.E.F.; Project
Administration, T.E.F.; Funding Acquisition, T.E.F. Author Contributions: Conceptualization, T.E.F.; Methodology, N.A.H., R.R.C., and T.E.F.; Software, N.A.H. and R.R.C.; Validation, M.A.R., J.M.A., N.A.H., R.R.C., S.H., P.M.J., and T.E.F.; Formal Analysis, M.A.R., J.M.A.,
N.A.H., R.R.C., and T.E.F.; Investigation, M.A.R., J.M.A., and P.M.J.; Resources, T.E.F.; Data Curation, N.A.H. and R.R.C.; Writing-Original Draft Preparation, T.E.F. References 1. UN Office for the Coordination of Humanitarian Affairs. Haiti: Cholera figures, December 2017 (as of
29 January 2018). UN Office for the Coordination of Humanitarian Affairs: 2018. Available online: https:
//reliefweb.int/report/haiti/haiti-cholera-figures-december-2017-29-january-2018 (accessed on 6 May 2018). 1. UN Office for the Coordination of Humanitarian Affairs. Haiti: Cholera figures, December 2017 (as of
29 January 2018). UN Office for the Coordination of Humanitarian Affairs: 2018. Available online: https:
//reliefweb.int/report/haiti/haiti-cholera-figures-december-2017-29-january-2018 (accessed on 6 May 2018). 2. Juin, S.; Schaad, N.; Lafontant, D.; Joseph, G.A.; Barzilay, E.; Boncy, J.; Barrais, R.; Louis, F.J.; Jean Charles, N.L.;
Corvil, S.; et al. Strengthening National Disease Surveillance and Response—Haiti, 2010–2015. Am. J. Trop. Med. Hyg. 2017, 97, 12–20. [CrossRef] [PubMed] 2. Juin, S.; Schaad, N.; Lafontant, D.; Joseph, G.A.; Barzilay, E.; Boncy, J.; Barrais, R.; Louis, F.J.; Jean Charles, N.L.;
Corvil, S.; et al. Strengthening National Disease Surveillance and Response—Haiti, 2010–2015. Am. J. Trop. Med. Hyg. 2017, 97, 12–20. [CrossRef] [PubMed] . US Centers for Disease Control and Prevention. Cholera: Vibrio Cholerae Infection. Available on
https://www.cdc.gov/cholera/general/index.html (accessed on 6 May 2018). 3. US Centers for Disease Control and Prevention. Cholera: Vibrio Cholerae Infection. Available online:
https://www.cdc.gov/cholera/general/index.html (accessed on 6 May 2018). . Gazin, P.; Barrais, R.; Uwineza, F. Risk factors of cholera transmission in rural areas in Haiti. Med. Sante
2017, 27, 11–15. [CrossRef] [PubMed] 5. Eisenberg, M.C.; Kujbida, G.; Tuite, A.R.; Fisman, D.N.; Tien, J.H. Examining rainfall and cholera dynamics in
Haiti using statistical and dynamic modeling approaches. Epidemics 2013, 5, 197–207. [CrossRef] [PubMed] 5. Eisenberg, M.C.; Kujbida, G.; Tuite, A.R.; Fisman, D.N.; Tien, J.H. Examining rainfall and cholera dynamics in
Haiti using statistical and dynamic modeling approaches. Epidemics 2013, 5, 197–207. [CrossRef] [PubMed] 6. Ford, T.E.; Colwell, R.R.; Rose, J.B.; Morse, S.S.; Rogers, D.J.; Yates, T.L. Using satellite images of
environmental changes to predict infectious disease outbreaks. Emerg. Infect. Dis. 2009, 15, 1341–1346. [CrossRef] [PubMed] 7. Khan, R.; Anwar, R.; Akanda, S.; McDonald, M.D.; Huq, A.; Jutla, A.; Colwell, R. Assessment of Risk of
Cholera in Haiti following Hurricane Matthew. Am. J. Trop. Med. Hyg. 2017, 97, 896–903. [CrossRef]
[PubMed] 8. Briquaire, R.; Colwell, R.R.; Boncy, J.; Rossignol, E.; Dardy, A.; Pandini, I.; Villeval, F.; Machuron, J.L.;
Huq, A.; Rashed, S.; et al. Application of a paper based device containing a new culture medium to detect
Vibrio cholerae in water samples collected in Haiti. J. Microbiol. Methods 2017, 133, 23–31. [CrossRef] [PubMed] 9. 5. Conclusions and M.A.R.; Writing-Review & Editing, M.A.R., N.A.H.,
R.R.C., S.H., and T.E.F.; Visualization, M.A.R., J.M.A., N.A.H., R.R.C., and T.E.F..; Supervision, T.E.F.; Project
Administration, T.E.F.; Funding Acquisition, T.E.F. Funding: This research was funded by Uniting for Health Innovation, an “independent, nonprofit organization
that unites government, industry, and local communities in the Americas to advance innovation in public health.”
Funding was also provided to M.A.R. through a training fellowship at UMass Amherst as part of the Biotechnology
Training Program (National Research Service Award T32 GM108556). Acknowledgments: We would like to thank Midwives for Haiti (MFH) for providing housing and other in-country
support to M.A.R. and J.M.A. during the two sampling collections. We would also like to thank Shah Manzur
Rashed for his help in processing the water samples at Cosmos ID. Conflicts of Interest: The founding sponsor had no role in the design of the study; in the collection, analyses,
or interpretation of data; in the writing of the manuscript, and in the decision to publish the results. 13 of 16 13 of 16 Int. J. Environ. Res. Public Health 2018, 15, 2211 References [CrossRef] [PubMed] 14 of 16 Int. J. Environ. Res. Public Health 2018, 15, 2211 19. Widmer, J.M.; Weppelmann, T.A.; Alam, M.T.; Morrissey, B.D.; Redden, E.; Rashid, M.H.; Diamond, U.;
Ali, A.; De Rochars, M.B.; Blackburn, J.K.; et al. Water-related infrastructure in a region of post-earthquake
Haiti: High levels of fecal contamination and need for ongoing monitoring. Am. J. Trop. Med. Hyg. 2014,
91, 790–797. [CrossRef] [PubMed] 20. Pomerantz, A.; Penafiel, N.; Arteaga, A.; Bustamante, L.; Pichardo, F.; Coloma, L.A.; Barrio-Amoros, C.L.;
Salazar-Valenzuela, D.; Prost, S. Real-time DNA barcoding in a rainforest using nanopore sequencing:
Opportunities for rapid biodiversity assessments and local capacity building. Gigascience 2018, 7. [CrossRef]
[PubMed] 21. Srivathsan, A.; Baloglu, B.; Wang, W.; Tan, W.X.; Bertrand, D.; Ng, A.H.Q.; Boey, E.J.H.; Koh, J.J.Y.;
Nagarajan, N.;
Meier, R. A MinION-based pipeline for fast and cost-effective DNA barcoding. Mol. Ecol. Resour. 2018. [CrossRef] [PubMed] 22. Gardy, J.L.; Loman, N.J. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat. Rev. Genet. 2018, 19, 9–20. [CrossRef] [PubMed] 23. Piarroux, R.; Barrais, R.; Faucher, B.; Haus, R.; Piarroux, M.; Gaudart, J.; Magloire, R.; Raoult, D. Understanding the cholera epidemic, Haiti. Emerg. Infect. Dis. 2011, 17, 1161–1168. [CrossRef] [PubMed] 24. Weatherbase. Monthly-Weather Averages Summary. Available online: http://www.weatherbase.com/
(accessed on 28 April 2018). 25. Ewels, P.; Magnusson, M.; Lundin, S.; Kaller, M. MultiQC: Summarize analysis results for multiple tools and
samples in a single report. Bioinformatics 2016, 32, 3047–3048. [CrossRef] [PubMed] 26. Janes, V.A.; Matamoros, S.; Willemse, N.; Visser, C.E.; de Wever, B.; Jakobs, M.E.; Subramanian, P.;
Hasan, N.A.; Colwell, R.R.; de Jong, M.D.; et al. Metagenomic sequencing to replace semi-quantitative urine
culture for detection of urinary tract infections: A proof of concept. bioRxiv 2017. [CrossRef] 27. Junqueira, A.C.M.; Ratan, A.; Acerbi, E.; Drautz-Moses, D.I.; Premkrishnan, B.N.V.; Costea, P.I.; Linz, B.;
Purbojati, R.W.; Paulo, D.F.; Gaultier, N.E.; et al. The microbiomes of blowflies and houseflies as bacterial
transmission reservoirs. Sci. Rep. 2017, 7, 16324. [CrossRef] [PubMed] 28. Connelly, S.; Bristol, J.A.; Hubert, S.; Subramanian, P.; Hasan, N.A.; Colwell, R.R.; Kaleko, M. SYN-004
(ribaxamase), an oral beta-lactamase, mitigates antibiotic-mediated dysbiosis in a porcine gut microbiome
model. J. Appl. Microbiol. 2017. [CrossRef] [PubMed] 29. Ponnusamy, D.; Kozlova, E.V.; Sha, J.; Erova, T.E.; Azar, S.R.; Fitts, E.C.; Kirtley, M.L.; Tiner, B.L.;
Andersson, J.A.; Grim, C.J.; et al. Cross-talk among flesh-eating Aeromonas hydrophila strains in mixed
infection leading to necrotizing fasciitis. Proc. Natl. Acad. Sci. USA 2016, 113, 722–727. References Matias, W.R.; Julceus, F.E.; Abelard, C.; Mayo-Smith, L.M.; Franke, M.F.; Harris, J.B.; Ivers, L.C. Laboratory
evaluation of immunochromatographic rapid diagnostic tests for cholera in Haiti. PLoS ONE 2017,
12, e0186710. [CrossRef] [PubMed] 10. Thomson, A.A.; Gunsch, C.K. Evaluation of a field appropriate membrane filtration method for the
detection of Vibrio cholerae for the measurement of biosand filter performance in the Artibonite Valley,
Haiti. Environ. Monit. Assess. 2015, 187, 484. [CrossRef] [PubMed] 11. Alam, M.T.; Weppelmann, T.A.; Weber, C.D.; Johnson, J.A.; Rashid, M.H.; Birch, C.S.; Brumback, B.A.; Beau
de Rochars, V.E.; Morris, J.G., Jr.; Ali, A. Monitoring water sources for environmental reservoirs of toxigenic
Vibrio cholerae O1, Haiti. Emerg. Infect. Dis. 2014, 20, 356–363. [CrossRef] [PubMed] 12. Baron, S.; Lesne, J.; Moore, S.; Rossignol, E.; Rebaudet, S.; Gazin, P.; Barrais, R.; Magloire, R.; Boncy, J.;
Piarroux, R. No Evidence of Significant Levels of Toxigenic V. cholerae O1 in the Haitian Aquatic Environment
During the 2012 Rainy Season. PLoS Curr. 2013, 5. [CrossRef] [PubMed] 13. Alam, M.T.; Weppelmann, T.A.; Longini, I.; De Rochars, V.M.; Morris, J.G., Jr.; Ali, A. Increased isolation
frequency of toxigenic Vibrio cholerae O1 from environmental monitoring sites in Haiti. PLoS ONE 2015,
10, e0124098. [CrossRef] [PubMed] 14. McIntyre, A.B.R.; Ounit, R.; Afshinnekoo, E.; Prill, R.J.; Henaff, E.; Alexander, N.; Minot, S.S.; Danko, D.;
Foox, J.; Ahsanuddin, S.; et al. Comprehensive benchmarking and ensemble approaches for metagenomic
classifiers. Genome Biol. 2017, 18, 182. [CrossRef] [PubMed] 15. Ghai, R.; Rodriguez-Valera, F.; McMahon, K.D.; Toyama, D.; Rinke, R.; Cristina Souza de Oliveira, T.; Wagner
Garcia, J.; Pellon de Miranda, F.; Henrique-Silva, F. Metagenomics of the water column in the pristine upper
course of the Amazon river. PLoS ONE 2011, 6, e23785. [CrossRef] [PubMed] 16. Saleem, F.; Mustafa, A.; Kori, J.A.; Hussain, M.S.; Kamran Azim, M. Metagenomic Characterization of
Bacterial Communities in Drinking Water Supply System of a Mega City. Microb. Ecol. 2018. [CrossRef]
[PubMed] 17. Chu, B.T.T.; Petrovich, M.L.; Chaudhary, A.; Wright, D.; Murphy, B.; Wells, G.; Poretsky, R. Metagenomics
Reveals the Impact of Wastewater Treatment Plants on the Dispersal of Microorganisms and Genes in
Aquatic Sediments. Appl. Environ. Microbiol. 2018, 84. [CrossRef] [PubMed] 18. Kahler, A.M.; Haley, B.J.; Chen, A.; Mull, B.J.; Tarr, C.L.; Turnsek, M.; Katz, L.S.; Humphrys, M.S.; Derado, G.;
Freeman, N.; et al. Environmental surveillance for toxigenic Vibrio cholerae in surface waters of Haiti. Am. J. Trop. Med. Hyg. 2015, 92, 118–125. References [CrossRef] [PubMed] 30. Hasan, N.A.; Young, B.A.; Minard-Smith, A.T.; Saeed, K.; Li, H.; Heizer, E.M.; McMillan, N.J.; Isom, R.;
Abdullah, A.S.; Bornman, D.M.; et al. Microbial community profiling of human saliva using shotgun
metagenomic sequencing. PLoS ONE 2014, 9, e97699. [CrossRef] [PubMed] 31. Lax, S.; Smith, D.P.; Hampton-Marcell, J.; Owens, S.M.; Handley, K.M.; Scott, N.M.; Gibbons, S.M.; Larsen, P.;
Shogan, B.D.; Weiss, S.; et al. Longitudinal analysis of microbial interaction between humans and the indoor
environment. Science 2014, 345, 1048–1052. [CrossRef] [PubMed] 32. Ondov, B.D.; Bergman, N.H.; Phillippy, A.M. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 2011, 12, 385. [CrossRef] [PubMed] 33. Gray, M.A.; Pratte, Z.A.; Kellogg, C.A. Comparison of DNA preservation methods for environmental
bacterial community samples. FEMS Microbiol. Ecol. 2013, 83, 468–477. [CrossRef] [PubMed] 34. Hamner, S.; Broadaway, S.C.; Mishra, V.B.; Tripathi, A.; Mishra, R.K.; Pulcini, E.; Pyle, B.H.; Ford, T.E. Isolation of potentially pathogenic Escherichia coli O157:H7 from the Ganges River. Appl. Environ. Microbiol. 2007, 73, 2369–2372. [CrossRef] [PubMed] 35. Weatherbase. Hinche, Haiti. Available online: http://www.weatherbase.com/weather/weather.php3?s=
602189&cityname=Hinche-Centre-Haiti (accessed on 28 April 2018). 36. Pindi, P.K.; Yadav, P.R.; Shanker, A.S. Identification of opportunistic pathogenic bacteria in drinking water
samples of different rural health centers and their clinical impacts on humans. Biomed. Res. Int. 2013,
2013, 348250. [CrossRef] [PubMed] 37. Fournier, P.E.; Richet, H. The epidemiology and control of Acinetobacter baumannii in health care facilities. Clin. Infect. Dis. 2006, 42, 692–699. [CrossRef] [PubMed] 38. Hung, Y.T.; Lee, Y.T.; Huang, L.J.; Chen, T.L.; Yu, K.W.; Fung, C.P.; Cho, W.L.; Liu, C.Y. Clinical characteristics
of patients with Acinetobacter junii infection. J. Microbiol. Immunol. Infect. 2009, 42, 47–53. [PubMed] Int. J. Environ. Res. Public Health 2018, 15, 2211 15 of 16 15 of 16 39. Lolans, K.; Rice, T.W.; Munoz-Price, L.S.; Quinn, J.P. Multicity outbreak of carbapenem-resistant Acinetobacter
baumannii isolates producing the carbapenemase OXA-40. Antimicrob. Agents Chemother. 2006, 50, 2941–2945. [CrossRef] [PubMed] 40. Centers for Disease Control and Prevention. Healthcare-Associated Infections. Available online
//www.cdc.gov/hai/organisms/acinetobacter.html (accessed on 28 April 2018). 41. Deng, Y.; Bao, X.; Ji, L.; Chen, L.; Liu, J.; Miao, J.; Chen, D.; Bian, H.; Li, Y.; Yu, G. Resistance integrons:
Class 1, 2 and 3 integrons. Ann. Clin. Microbiol. Antimicrob. 2015, 14, 45. [CrossRef] [PubMed] 42. Mukherjee, N.; Bartelli, D.; Patra, C.; Chauhan, B.V.; Dowd, S.E.; Banerjee, P. Microbial Diversity of Source
and Point-of-Use Water in Rural Haiti—A Pyrosequencing-Based Metagenomic Survey. PLoS ONE 2016,
11, e0167353. References [CrossRef] [PubMed] 43. Cunliffe, M.; Kertesz, M.A. Effect of Sphingobium yanoikuyae B1 inoculation on bacterial community dynamics
and polycyclic aromatic hydrocarbon degradation in aged and freshly PAH-contaminated soils. Environ. Pollut. 2006, 144, 228–237. [CrossRef] [PubMed] 44. Chen, H.; Young, S.; Berhane, T.K.; Williams, H.N. Predatory Bacteriovorax communities ordered by various
prey species. PLoS ONE 2012, 7, e34174. [CrossRef] [PubMed] 45. Soborg, D.A.; Hendriksen, N.B.; Kilian, M.; Kroer, N. Widespread occurrence of bacterial human virulence
determinants in soil and freshwater environments. Appl. Environ. Microbiol. 2013, 79, 5488–5497. [CrossRef]
[PubMed] 46. Zhang, B.; Xia, Y.; Wen, X.; Wang, X.; Yang, Y.; Zhou, J.; Zhang, Y. The Composition and Spatial Patterns of
Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants. PLoS ONE
2016, 11, e0167422. [CrossRef] [PubMed] 47. Drzewiecka, D. Significance and Roles of Proteus spp. Bacteria in Natural Environments. Microb. Ecol. 2016,
72, 741–758. [CrossRef] [PubMed] 48. Dukik, K.; Munoz, J.F.; Jiang, Y.; Feng, P.; Sigler, L.; Stielow, J.B.; Freeke, J.; Jamalian, A.; Gerrits van den
Ende, B.; McEwen, J.G.; et al. Novel taxa of thermally dimorphic systemic pathogens in the Ajellomycetaceae
(Onygenales). Mycoses 2017, 60, 296–309. [CrossRef] [PubMed] 49. Trofa, D.; Gacser, A.; Nosanchuk, J.D. Candida parapsilosis, an emerging fungal pathogen. Clin. Microbiol. Rev. 2008, 21, 606–625. [CrossRef] [PubMed] 50. Matos, O.; Lobo, M.L.; Xiao, L. Epidemiology of Enterocytozoon bieneusi Infection in Humans. J. Parasitol. Res. 2012, 2012, 981424. [CrossRef] [PubMed] 51. Boileau, M.; Ferreira, J.; Ahmad, I.; Lavallee, C.; Qvarnstrom, Y.; Dufresne, S.F. Successful Treatment of
Disseminated Anncaliia algerae Microsporidial Infection With Combination Fumagillin and Albendazole. Open Forum Infect. Dis. 2016, 3. [CrossRef] [PubMed] 52. Richterman, A.; Cheung, H.C.; Meiselbach, M.K.; Jerome, G.; Ternier, R.; Ivers, L.C. Risk Factors for
Self-Reported Cholera within HIV-Affected Households in Rural Haiti. Open Forum Infect. Dis. 2018, 5. [CrossRef] [PubMed] 53. Faburay, B. The case for a ‘one health’ approach to combating vector-borne diseases. Infect. Ecol. Epidemiol. 2015, 5, 28132. [CrossRef] [PubMed] 54. Borriello, G.; Lucibelli, M.G.; De Carlo, E.; Auriemma, C.; Cozza, D.; Ascione, G.; Scognamiglio, F.;
Iovane, G.; Galiero, G. Characterization of enterotoxigenic E. coli (ETEC), Shiga-toxin producing E. coli
(STEC) and necrotoxigenic E. coli (NTEC) isolated from diarrhoeic Mediterranean water buffalo calves
(Bubalus bubalis). Res. Vet. Sci. 2012, 93, 18–22. [CrossRef] [PubMed] 55. Routh, J.A.; Sreenivasan, N.; Adhikari, B.B.; Andrecy, L.L.; Bernateau, M.; Abimbola, T.; Njau, J.; Jackson, E.;
Juin, S.; Francois, J.; et al. © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/). References Cost Evaluation of a Government-Conducted Oral Cholera Vaccination
Campaign-Haiti, 2013. Am. J. Trop. Med. Hyg. 2017, 97, 37–42. [CrossRef] [PubMed] Int. J. Environ. Res. Public Health 2018, 15, 2211 16 of 16 16 of 16 56. Ivers, L.C.; Hilaire, I.J.; Teng, J.E.; Almazor, C.P.; Jerome, J.G.; Ternier, R.; Boncy, J.; Buteau, J.; Murray, M.B.;
Harris, J.B.; et al. Effectiveness of reactive oral cholera vaccination in rural Haiti: A case-control study and
bias-indicator analysis. Lancet Glob. Health 2015, 3, e162–e168. [CrossRef] 56. Ivers, L.C.; Hilaire, I.J.; Teng, J.E.; Almazor, C.P.; Jerome, J.G.; Ternier, R.; Boncy, J.; Buteau, J.; Murray, M.B.;
Harris, J.B.; et al. Effectiveness of reactive oral cholera vaccination in rural Haiti: A case-control study and
bias-indicator analysis. Lancet Glob. Health 2015, 3, e162–e168. [CrossRef] 57. Franke, M.F.; Jerome, J.G.; Matias, W.R.; Ternier, R.; Hilaire, I.J.; Harris, J.B.; Ivers, L.C. Comparison of two
control groups for estimation of oral cholera vaccine effectiveness using a case-control study design. Vaccine
2017, 35, 5819–5827. [CrossRef] [PubMed] © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/). © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/).
|
https://openalex.org/W4362614627
|
https://aacr.figshare.com/articles/journal_contribution/Supplementary_Data_from_Implication_of_i_ZNF217_i_in_Accelerating_Tumor_Development_and_Therapeutically_Targeting_ZNF217-Induced_PI3K_AKT_Signaling_for_the_Treatment_of_Metastatic_Osteosarcoma/22521441/1/files/39984078.pdf
|
English
| null |
Supplementary Data from Implication of <i>ZNF217</i> in Accelerating Tumor Development and Therapeutically Targeting ZNF217-Induced PI3K–AKT Signaling for the Treatment of Metastatic Osteosarcoma
| null | 2,023
|
cc-by
| 655
|
Supplementary Figure 1 ZNF217 localization is additional TMA sections Supplementary Figure 1 ZNF217 localization is additional TMA sections Supplementary Figure 1 ZNF217 localization is additional TMA sections Additional images of positive TMA staining for ZNF217 in one representative site
per section; magnification 40X, scale bars 25 µm. Black arrows depict examples of
positive nuclear and cytoplasmic ZNF217 staining. Additional images of positive TMA staining for ZNF217 in one representative site
per section; magnification 40X, scale bars 25 µm. Black arrows depict examples of
positive nuclear and cytoplasmic ZNF217 staining. Supplementary Figure 2 Localization of ZNF217 in OSA cells
(a) Western blot staining of cytoplasmic extract (CYTO) and nuclear chromatin-
bound extract (NUC) using a ZNF217-specific antibody. (b) Confirmation of ZNF217
localization by immunofluorescence (IF) staining; magnification 40X, scale bars 100 µm. Red = ZNF217 staining and blue = DAPI counterstain. Supplementary Figure 2 Localization of ZNF217 in OSA cells (a) Western blot staining of cytoplasmic extract (CYTO) and nuclear chromatin-
bound extract (NUC) using a ZNF217-specific antibody. (b) Confirmation of ZNF217
localization by immunofluorescence (IF) staining; magnification 40X, scale bars 100 µm. Red = ZNF217 staining and blue = DAPI counterstain. (a) Western blot staining of cytoplasmic extract (CYTO) and nuclear chromatin-
bound extract (NUC) using a ZNF217-specific antibody. (b) Confirmation of ZNF217
localization by immunofluorescence (IF) staining; magnification 40X, scale bars 100 µm. Red = ZNF217 staining and blue = DAPI counterstain. Supplementary Figure 3 RNA-sequencing analysis of transient ZNF217 knockdown
SJSA-1 cells Supplementary Figure 3 RNA-sequencing analysis of transient ZNF217 knockdown
SJSA-1 cells (a) Heatmap of clustering in ZNF217 knockdown (KD) and control (CON) replicates
by normalized raw read counts. (b) Functional gene network comprised of 440 DEGs
identified using STRINGDB. (c) Functional GO analysis and (d) Reactome pathway
enrichment of highly significant biological processes following transient ZNF217
knockdown. Supplementary Figure 4 PI3K blockade in OSA cells
(a) PI3K inhibition with LY294002 reduces cell viability 48 hours post-treatment
and (b) induces modest apoptosis. All data shown as mean ± SEM. Panel (a) One-way
ANOVA with Bonferroni’s post hoc. Panel (b) Student’s T-test. **p < 0.01, ***p < 0.001,
****p < 0.0001. Supplementary Figure 4 PI3K blockade in OSA cells Supplementary Figure 4 PI3K blockade in OSA cells (a) PI3K inhibition with LY294002 reduces cell viability 48 hours post-treatment
and (b) induces modest apoptosis. All data shown as mean ± SEM. Panel (a) One-way
ANOVA with Bonferroni’s post hoc. Panel (b) Student’s T-test. Supplementary Figure 1 ZNF217 localization is additional TMA sections **p < 0.01, ***p < 0.001,
****p < 0.0001. Supplementary Figure 5 Flow plots of apoptosis in ZNF217 knockdown cells
Flow plots of Annexin V+ staining in ZNF217 knockdown cells (si-ZNF217)
compared to control (si-NS). entary Figure 5 Flow plots of apoptosis in ZNF217 knockdown cells plots of Annexin V+ staining in ZNF217 knockdown cells (si-ZNF217) Flow plots of Annexin V+ staining in ZNF217 knockdown cells (si-ZNF217)
compared to control (si-NS). Supplementary Figure 6 Flow plots of apoptosis following treatment with TCN
Flow plots of Annexin V+ staining in TCN-treated OSA cells (100 µM) compared to
DMSO control. mentary Figure 6 Flow plots of apoptosis following treatment with TCN Flow plots of Annexin V+ staining in TCN-treated OSA cells (100 µM) compared to
DMSO control plots of Annexin V+ staining in TCN-treated OSA cells (100 µM) compared to Flow plots of Annexin V+ staining in TCN-treated OSA cells (100 µM) compared to
DMSO control. Supplementary Figure 7 ZNF217 expression in tumors from TCN-treated animals
Representative IHC staining of ZNF217 in TCN- or control-treated animals;
magnification 40X, scale bars 100 µm. Supplementary Figure 7 ZNF217 expression in tumors from TCN-treated animals
Representative IHC staining of ZNF217 in TCN- or control-treated animals;
magnification 40X, scale bars 100 µm. Supplementary Figure 7 ZNF217 expression in tumors from TCN-treated animals Supplementary Figure 7 ZNF217 expression in tumors from TCN-treated animals
Representative IHC staining of ZNF217 in TCN- or control-treated animals;
magnification 40X, scale bars 100 µm.
|
https://openalex.org/W2997612579
|
https://digital.csic.es/bitstream/10261/206165/1/775719.pdf
|
English
| null |
STARD1 and NPC1 expression as pathological markers associated with astrogliosis in post-mortem brains from patients with Alzheimer's disease and Down syndrome
|
Aging
| 2,020
|
cc-by
| 10,329
|
Correspondence to: Jose C. Fernandez-Checa, Carmen Garcia-Ruiz; email: checa229@yahoo.com, cgrbam@iibb.csic.es
Keywords: cholesterol, NPC1, StARD1, mitochondria, lysosomes
Received: July 23, 2019
Accepted: December 23, 2019
Published: January 5, 2020 Correspondence to: Jose C. Fernandez-Checa, Carmen Garcia-Ruiz; email: checa229@yahoo.com, cgrbam@iibb.csic.es
Keywords: cholesterol, NPC1, StARD1, mitochondria, lysosomes
Received: July 23, 2019
Accepted: December 23, 2019
Published: January 5, 2020 Published: January 5, 2020 Copyright: Arenas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution
License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original
author and source are credited. ABSTRACT Alzheimer´s disease (AD) is a progressive neurodegenerative disorder of complex etiology, while Down
syndrome (DS) is considered a genetically determined form of AD. Alterations in cholesterol homeostasis have
been linked to AD although the role in this association is not well understood. Increased expression of STARD1
and NPC1, which are involved in intracellular cholesterol trafficking, has been reported in experimental AD
models but not in patients with AD. Here we analyzed endolysosomal/mitochondrial cholesterol homeostasis,
expression of NPC1 and STARD1 and correlation with pathological markers of AD in cortex and hippocampus
from post-mortem brains from patients with AD and DS. NPC1 expression was observed in hippocampus from
patients with AD and DS. Moreover, STARD1 expression increased in hippocampus and cortex from patients
with AD and DS, respectively, and its immunoreactivity discriminated controls from AD or DS with a better
accuracy than Aβ42. Hippocampal areas stained with the recombinant GST-PFO probe showed increased
mitochondrial cholesterol within astrocytes of brains from patients with AD and DS-brains compared to
controls. Lysosomal cholesterol accumulation within hippocampal astrocytes was higher in DS than in AD. These data revealed increased intracellular cholesterol loading in hippocampus from patient with AD and DS
and suggest that STARD1 could be a potential pre-clinical marker associated with early stages of AD pathology. AGING 2020, Vol. 12, Advance AGING 2020, Vol. 12, Advance www.aging-us.com Research Paper
STARD1 and NPC1 expression as pathological markers associated with
astrogliosis in post-mortem brains from patients with Alzheimer’s
d
d
d p
STARD1 and NPC1 expression as pathological markers associated with
astrogliosis in post-mortem brains from patients with Alzheimer’s
disease and Down syndrome Fabian Arenas1,2, Fernanda Castro1,2, Susana Nuñez1,2, Gemma Gay1, Carmen Garcia-Ruiz1,2,3,4,
Jose C. Fernandez-Checa1,2,3,4 Fabian Arenas1,2, Fernanda Castro1,2, Susana Nuñez1,2, Gemma Gay1, Carmen Garcia-Ruiz1,2,3,4,
Jose C. Fernandez-Checa1,2,3,4 1Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, Barcelona
Spain
2Liver Unit, Hospital Clinic I Provincial de Barcelona, Instituto de Investigaciones Biomédicas August Pi i Sunyer
(IDIBAPS), Barcelona, Spain
3Centro de Investigación Biomédica en Red (CIBEREHD), Barcelona, Spain
4Research Center for ALPD, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033,
USA 1Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, Barcelona,
Spain 2Liver Unit, Hospital Clinic I Provincial de Barcelona, Instituto de Investigaciones Biomédicas August Pi i Sunyer
(IDIBAPS), Barcelona, Spain
3 Intracellular cholesterol homeostasis in cortex from
patients with AD and DS As alterations in cortex occur late in AD and reflect
disease progression, we first examined the intracellular
cholesterol homeostasis in the cortex of sporadic AD
and DS using post-mortem cryopreserved cortex
samples from patients with AD and DS (Table 1). Transcripts
and
protein
expression
of
putative
cholesterol carriers involved in intracellular cholesterol
trafficking (NPC1, STARD3/MLN64, STARD4, and
STARD1), as well as sensors/regulators of de novo
cholesterol synthesis (INSIG-1 and SREBP2) were
examined [2] and summarized in Supplementary Table
1. While the expression at mRNA or protein levels of
STARD4, INSIG-1 and mature SREBP2 (mSREBP2)
seems to be similar between AD, DS and control
samples (Figure 1), cortex from patients with DS
exhibited a significant overexpression of transcripts for
the mitochondrial carrier STARD1 (Figure 1A), which
translated at the protein levels (Figure 1B). Moreover,
there was a trend for increased mRNA levels of NPC1
and STARD3/MLN64 in cortex from patients with DS
(Figure 1A). In addition, cortex from AD-brains
exhibited a small but significant increase in the NPC1
protein expression compared to control samples and a
trend for increased STARD1 protein levels (Figure 1B). These findings indicate that cortex from patients with
DS and AD exhibit increased expression of StARD1
and NPC1, respectively. Down syndrome (DS) is considered a genetically
determined form of AD and individuals with DS
invariably develop AD by their fourth decade [8]. Patients with DS exhibit cognitive markers of
preclinical and prodromal AD [9]. The progression of
AD pathology assessed by neuroimaging and/or
cerebrospinal fluid levels of Aβ and tau (total and
phosphorylated) revealed a similar pattern between
normal population and individuals with DS, although
these events in DS occur 10–20 years earlier than in
normal population [10, 11]. Aging, obesity and
ApoEε4-associated dyslipidaemia are important risk
factors for development of AD dementia in normal and
DS population [12]. Interestingly, hypercholesterolemic
subjects with DS treated with statins exhibit a lower risk
factor for AD development that correlates with slower
amyloidogenic burden [13]. Besides the overlap
between AD and DS, intracellular brain cholesterol
homeostasis in patients with DS has not been reported. We hypothesized that alterations in intracellular
cholesterol homeostasis in lysosomes and mitochondria
in the brain could contribute to the molecular events
involved in the AD continuum, emerging as a
pathological event that could contribute to disease
progression. Intracellular cholesterol homeostasis in cortex from
patients with AD and DS Investigating the intracellular cholesterol
homeostasis is critical to improve and expand the
therapeutic armamentarium for AD, especially at
preclinical stages, given that current clinical trials for
AD have been disappointing. In contrast to the
controversial role of changes in total brain cholesterol
levels in AD [2, 14], our findings on the expression of
putative intracellular cholesterol carriers (e.g. STARD1
and NPC1) in patients with AD and DS correlate with
disease markers, such as Aβ42, and suggest that
alterations in intracellular cholesterol homeostasis may
be an early molecular event that favours the progression
of the AD pathology. Moreover, the accuracy of
STARD1 to discriminate controls from AD in the INTRODUCTION genesis,
although
other
factors
such
as
tau
phosphorylation are also key for the progression of AD
[1]. While alterations in cholesterol homeostasis have
been linked to AD the role for this association is
controversial. For instance, there has been evidence
indicating that either increased or decreased total brain
cholesterol levels are associated with AD-pathogenesis
[2]. Whether intracellular cholesterol pools (e.g. Alzheimer’s disease (AD) is a progressive neuro-
degenerative disorder of complex etiology and the most
common form of dementia, which comprises early-onset
AD (EOAD, ~5% of patients) and late-onset AD (LOAD,
95% of patients). The generation of toxic beta amyloid
(Aβ) peptides is considered a central player in AD patho- AGING www.aging-us.com 1 endolysosomes and mitochondria) rather than total
cholesterol levels are more relevant for AD pathology
remains to be established. Indeed, hippocampus and
frontal cortex of patients with AD and AD-Tg mice have
been shown to exhibit increased expression of the
lysosomal cholesterol transporter NPC1 [3], while
increased
steroidogenic
acute
regulatory
protein
(STARD1) expression, which regulates the mitochondrial
cholesterol trafficking [4], has been reported in pyramidal
hippocampal neurons of patients with AD [5]. Moreover,
mitochondrial cholesterol accumulation in a hyper-
cholesterolemic AD-Tg mouse model has been shown to
impair mitochondrial antioxidant defense and stimulate
oxidative stress, which results in the acceleration of AD-
like neuropathology [6, 7]. However, the intracellular
cholesterol homeostasis in human AD has not been
explored. general population and in subjects with DS suggests that
StARD1 could be a potential novel marker associated
with early molecular events of AD pathology in both
populations. STARD1 and NPC1 immunoreactivity in
hippocampus from patients with AD and DS AD
pathology
is
characterized
by
atrophy
in
hippocampus, temporal lobes and parietotemporal
cortices where neuronal death correlates with amyloid
plaques (largely composed of Aβ42) and neurofibrillary
tangles (NFTs) [15]. Interestingly, an accelerated Aβ
burden with greater plaques deposition and NFT have
been described in the hippocampus of DS subjects
exhibiting AD pathology [8]. Therefore, we examined
the hippocampal expression of cholesterol carriers
involved in lysosomal (i.e. NPC1) and mitochondrial
(i.e. STARD1) trafficking and compared this outcome
with the pathological markers Aβ42 and p-tau,
summarized in Supplementary Table 1. Immuno-
histochemical analysis of paraffin-fixed hippocampal
sections
showed
increased
Aβ42
and
p-tau AGING 2 www.aging-us.com Table 1. Collected specimens from cases of AD, DS and controls. Subjects (males/females)
Group
Cryopreserved
Cortex
Paraffined
hippocampus
Cryopreserved
hippocampus
Total
subjects
Mean age ±
SEM
Anatomopatho-
logic diagnosis
Clinical
diagnosis
DS
5 (3/2)
7 (3/4)
4 (2/2)
7 (3/4)
56 ± 4.31
AD V-VI,
CERAD C
Dementia
AD
5 (2/3)
7 (4/3)
5 (2/3)
7 (4/3)
80.7 ± 3.00
AD V-VI,
CERAD B-C
Dementia
Control
6 (4/2)
7 (5/2)
5 (4/1)
7 (5/2)
69.7 ± 4.79
Without
neurological
lesions (5)
Cognitively
healthy
Frontotemporal
degeneration (1)
FTD
iLBD; incidental
Lewy body
disease (1)
Cognitively
healthy
Note: For immunohistochemical and immunofluorescence analysis, 5 µm thin paraffin sections of hippocampus were
available for all human brain samples, while 14 µm thin sections of frozen hippocampus were available for just 19 cases to
analyse the intracellular cholesterol levels by immunofluorescence. On the other hand, cryopreserved human cortex of just
16 donors were available to assess gene expression and western blotting analysis. FTD, frontotemporal dementia. Table 1. Collected specimens from cases of AD, DS and controls. Note: For immunohistochemical and immunofluorescence analysis, 5 µm thin paraffin sections of hippocampus were
available for all human brain samples, while 14 µm thin sections of frozen hippocampus were available for just 19 cases to
analyse the intracellular cholesterol levels by immunofluorescence. On the other hand, cryopreserved human cortex of just
16 donors were available to assess gene expression and western blotting analysis. FTD, frontotemporal dementia. immunoreactivity in patients with AD and DS
compared with control subjects (arrows in Figure 2A
and 2B). These differences were significant for Aβ42
staining in CA1, CA2 and CA3 hippocampal regions
from patients with DS, in agreement with the intrinsic
overproduction of Aβ in this population [8]. STARD1 and NPC1 immunoreactivity in
hippocampus from patients with AD and DS Moreover,
there was a trend for increased Aβ42 in CA1 region from
patients with AD. Interestingly, CA1, CA2 and CA3
hippocampal regions from patients with AD and DS
showed a significant higher NPC1 protein expression
than control samples (Figure 2A and 2B). In line with
previous findings [5], the expression of StARD1 in
hippocampal regions revealed a significant increase of
STARD1 immunoreactivity in CA1 and CA3 areas
from patients with AD compared with DS and controls
(Figure 2A and 2B). Moreover, when STARD1 and
Aβ42 immunoreactivity were compared among all
samples, the hippocampal region-specific pattern of
STARD1 expression significantly correlated with Aβ42
deposition in CA1 and CA3 (Figure 2C). Thus, although
AD and DS are two related diseases, each exhibit
specific
changes
regarding
the
expression
of
intracellular cholesterol carriers STARD1 and NPC1,
with STARD1 overexpression in hippocampus being
specific for AD while in cortex the increase seems to be
characteristic of DS. In contrast, the increase in
expression of NPC1 occurs in both diseases. In addition,
the differential turnover between proteins and their
corresponding mRNA likely contribute to the specific
pattern of expression of STARD1 and NPC1 at the
mRNA and protein levels in the cortex between AD and DS samples. Further research will be required to
understand the full impact of these changes in AD
pathology and its genetically related form DS. Discrimination capacity of NPC1 and STARD1
immunoreactivity in hippocampus from patients
with AD and DS In analogy with Aβ42, we searched for expression of both
NPC1 and STARD1 in the paraffin-fixed hippocampal
samples as potential discrimination factors between AD
and/or DS from normal controls. For each hippocampal
region we analyzed the relative area immunolabeled with
Aβ42, NPC1, and STARD1 and performed ROC curves
analysis between controls subjects and patients with AD,
DS, or the sum of both AD+DS groups (Figure 3). As
expected, Aβ42 deposition revealed a highly significant
AUC with a high accuracy not only to identify AD and/or
DS samples as positive (sensitivity), particularly in CA1
hippocampal areas, but also to identify the control
subjects (specificity) in all hippocampal regions from
DS-brains (Figure 3). Similarly, in hippocampal CA1 and
CA3
regions,
NPC1
immunolabeling
properly
discriminated AD individuals, but not DS subjects, from
controls (Figure 3). Unexpectedly, STARD1 dis-
criminated AD and/or DS samples from control
individuals in all hippocampal regions (Figure 3),
suggesting that STARD1 immunolabeling exhibits a
greater discrimination capacity than Aβ42. Moreover,
multivariate data analysis of the cohort by principal
components analysis (PCA) showed an efficient AGING 3 www.aging-us.com e 1. Cortical expression profile of intracellular cholesterol carriers and sensors/regulators. (A) Relative mRNA leve
StARD3, StARD4, and StARD1 in human cortex from AD (n=5), DS (n=5), and control (n=6) subjects. Transcripts levels were norma
espect to controls using β-actin. (*) p<0.05; (**) p<0.01. (B) Immunoblotting of NPC1, StARD1, StARD3/MLN64, mSREBP2 and INS
al protein extracts (90 µg/lane) from human cortex from AD (n=5), DS (n=5), and control (n=6) donors. (C) Protein levels quantifie
ometry and normalized using β−actin as housekeeping followed by normalization with control group. (*) p<0.05; (**) p<0.01. Figure 1. Cortical expression profile of intracellular cholesterol carriers and sensors/regulators. (A) Relative mRNA levels of
NPC1, StARD3, StARD4, and StARD1 in human cortex from AD (n=5), DS (n=5), and control (n=6) subjects. Transcripts levels were normalized
with respect to controls using β-actin. (*) p<0.05; (**) p<0.01. (B) Immunoblotting of NPC1, StARD1, StARD3/MLN64, mSREBP2 and INSIG-1
of total protein extracts (90 µg/lane) from human cortex from AD (n=5), DS (n=5), and control (n=6) donors. (C) Protein levels quantified by
densitometry and normalized using β−actin as housekeeping followed by normalization with control group. (*) p<0.05; (**) p<0.01. AGING 4 www.aging-us.com confocal immunofluorescence imaging to explore the
pattern distribution of the intracellular cholesterol
transporters NPC1 and STARD1 within the astrocytes
surrounding amyloid deposition in the different
hippocampal regions (Figure 4). Discrimination capacity of NPC1 and STARD1
immunoreactivity in hippocampus from patients
with AD and DS In agreement with
previous observations in post-mortem human AD
tissues as well as in animal models [16, 17], reactive
astrocytes surrounding Aβ42 deposition were observed
in hippocampus from patients with AD and DS (Figure
4A). Moreover, the colocalization analysis of ten
representative images per sample revealed that astro-
cytes
in
hippocampus
from
patients
with DS visualization of the data for CA1 and CA3, capturing
more than 97.6% and 85% of the markers variability,
respectively, with a clear separation between control
subjects from AD and DS patients (Supplementary
Figure 1). Amyloid-related hippocampal astrogliosis associated
with increased lysosomal and mitochondrial choles-
terol content in patients with AD and DS To investigate whether disruption of intracellular
cholesterol homeostasis correlate with AD, we used gure 2. Hippocampal expression of AD biomarkers and lysosomal/mitochondrial cholesterol carriers. (A) Representative
ages of immunohistochemistry of paraffin sections (5 µm) against Aβ42, p-tau, StARD1 and NPC1 for CA1, CA2 and CA3 hippocampa
gions from AD (n=7), DS (n=7), and control (n=7) subjects. Positive immunoreactivity is shown by black arrows. Scale bar: 100 µm. (B
antitation of IHC shown in A using Image J software as described in Supplementary methods. For each hippocampal region, the % of
munolabeled area was normalized to control group. (*) p<0.05; (**) p<0.01; (***) p<0.001. (C) Spearman’s correlation values between IHC
munolabeling for Aβ42 and StARD1 in each hippocampal region. Figure 2. Hippocampal expression of AD biomarkers and lysosomal/mitochondrial cholesterol carriers. (A) Representative
images of immunohistochemistry of paraffin sections (5 µm) against Aβ42, p-tau, StARD1 and NPC1 for CA1, CA2 and CA3 hippocampal
regions from AD (n=7), DS (n=7), and control (n=7) subjects. Positive immunoreactivity is shown by black arrows. Scale bar: 100 µm. (B)
Quantitation of IHC shown in A using Image J software as described in Supplementary methods. For each hippocampal region, the % of
immunolabeled area was normalized to control group. (*) p<0.05; (**) p<0.01; (***) p<0.001. (C) Spearman’s correlation values between IHC-
immunolabeling for Aβ42 and StARD1 in each hippocampal region. AGING 5 www.aging-us.com astrocytes
indicated
a
region-specific
significant
increase of STARD1/GFAP colocalization index in
CA1 and CA3 areas for patients with AD and DS,
respectively, compared to controls (Figure 4B). Moreover, pilot observations following the staining of exhibit higher NPC1 expression than in AD and control
samples, particularly in CA3 region (Figure 4B),
suggesting increased lysosomal cholesterol levels in
astrocytes from patients with DS. In addition, the
analysis of the STARD1 content in hippocampal sis of the STARD1 content in hippocampal
Moreover, pilot observations following the stainin
e 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. ROC curv
nolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison bet
ol and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that b
minate AD and/or DS condition from normal controls in each hippocampal region. (*) p<0.05; (**) p<0.01; (***) p<0.001. Figure 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. Amyloid-related hippocampal astrogliosis associated
with increased lysosomal and mitochondrial choles-
terol content in patients with AD and DS ROC curv
immunolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison bet
control and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that b Figure 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. ROC curves of
immunolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison between
control and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that better
discriminate AD and/or DS condition from normal controls in each hippocampal region. (*) p<0.05; (**) p<0.01; (***) p<0.001. Figure 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. ROC curves of
immunolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison between
control and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that better
discriminate AD and/or DS condition from normal controls in each hippocampal region. (*) p<0.05; (**) p<0.01; (***) p<0.001. Figure 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. ROC curves of
immunolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison between
control and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that better
discriminate AD and/or DS condition from normal controls in each hippocampal region. (*) p<0.05; (**) p<0.01; (***) p<0.001. AGING 6 www.aging-us.com strocytes-expressing lysosomal and mitochondrial cholesterol carriers in hippocampal regions. (A) Rep
ges of paraffined hippocampal regions (5 µm) from AD (n=7), DS (n=7), and control (n=7) subjects immunolabeled a
yellow), and NPC1 or StARD1 (both green). Nuclei are stained with Hoechst 33342 (blue). Lower panels show the co
en GFAP and NPC1 or StARD1 (white) highlighted in the squared areas. Scale bar: 10 µm. (B) Astrocyte colocalization
and StARD1 (mitochondrial) cholesterol carriers into hippocampal regions from AD, DS, and control subjects. 10
region and per sample were analysed with Image J to assess the index of astrocyte (GFAP+) colocalization with NPC1
**) p<0.01; (***) p<0.001. Figure 4. Astrocytes-expressing lysosomal and mitochondrial cholesterol carriers in hippocampal regions. Amyloid-related hippocampal astrogliosis associated
with increased lysosomal and mitochondrial choles-
terol content in patients with AD and DS (A) Representative
confocal images of paraffined hippocampal regions (5 µm) from AD (n=7), DS (n=7), and control (n=7) subjects immunolabeled against Aβ42
(red), GFAP (yellow), and NPC1 or StARD1 (both green). Nuclei are stained with Hoechst 33342 (blue). Lower panels show the colocalization
mask between GFAP and NPC1 or StARD1 (white) highlighted in the squared areas. Scale bar: 10 µm. (B) Astrocyte colocalization with NPC1
(lysosomal) and StARD1 (mitochondrial) cholesterol carriers into hippocampal regions from AD, DS, and control subjects. 10 images per
hippocampal region and per sample were analysed with Image J to assess the index of astrocyte (GFAP+) colocalization with NPC1 or StARD1. (*) p<0.05; (**) p<0.01; (***) p<0.001. AGING 7 7 www.aging-us.com astroglial
lysosomal
cholesterol
accumulation
(PFO/Lamp1 in GFAP+) significantly increased in
hippocampus from AD and DS patients compared to
controls (Figure 5B), an outcome that was more
pronounced in DS (14.41±1.322 fold) than in AD brains
(3.43±0.502 fold). Interestingly, these findings cor-
related with the increased Aβ42 accumulation in the
CA1, CA2 and CA3 hippocampal regions of DS-brains
(Figure 2B). Furthermore, PCA analysis revealed that
the levels of astroglial NPC1 and STARD1 content as
well as the intraorganelle-cholesterol levels are able to
separate each group (Supplementary Figure 2). paraffined hippocampal sections of brains from AD, DS
and control groups with NeuN and IBA1 antibodies as
neuronal and glial markers, respectively, indicated that
STARD1 and NPC1 expression increased in hippo-
campal neurons from AD and DA brains with respect to
control, without changes in glia (not shown). To assess the intracellular cholesterol distribution
within hippocampal astrocytes (i.e. GFAP+), cryo-
preserved hippocampal samples of patients with AD
and DS were analysed for the colocalization between
GST-PFO
probe,
which
detects
cholesterol
in
membranes, with Lamp1 or Tom20 immunoreactivity to
stain lysosome or mitochondria, respectively (Figure 5;
and Supplementary Table 2). In line with the
STARD1/GFAP colocalization, we found that the
mitochondrial cholesterol content into hippocampal
astroglia from patients with AD and DS was >2.5-fold
higher than control donors (Figure 5B). Moreover, DISCUSSION We
have
analyzed
the
intracellular
cholesterol
trafficking in post-mortem samples from patients with
DS and AD and assessed whether this event correlated
with AD markers. An intriguing finding was that Aβ42 Figure 5. Lysosomal and mitochondrial cholesterol homeostasis in hippocampal astrocytes. (A) Representative confocal
representative images of 4 µm thin-stacked cryopreserved hippocampus from AD (n=5), DS (n=4), and control (n=5) subjects immunolabeled
with GST-PFO (red), GFAP (yellow), and Tom20 or Lamp1 (both green). Nuclei are stained with Dapi (blue). Lower panels show colocalization
mask (white) between GST-PFO and Tom20 or Lamp1, respectively, highlighted in the squared areas. Scale bar: 10 µm. (B) Cholesterol (PFO+)
colocalization with mitochondria (Tom20+) or lysosome (Lamp1+) into hippocampal astrocytes (GFAP+) from AD, DS, and control donors. 10
images per sample were analysed with Image J to assess the index of astrocytic cholesterol colocalization with Tom20 or Lamp1. Values are
relativized with control to show differences as n-fold. (*) p<0.05; (**) p<0.01. Figure 5. Lysosomal and mitochondrial cholesterol homeostasis in hippocampal astrocytes. (A) Representative confocal
representative images of 4 µm thin-stacked cryopreserved hippocampus from AD (n=5), DS (n=4), and control (n=5) subjects immunolabeled
with GST-PFO (red), GFAP (yellow), and Tom20 or Lamp1 (both green). Nuclei are stained with Dapi (blue). Lower panels show colocalization
mask (white) between GST-PFO and Tom20 or Lamp1, respectively, highlighted in the squared areas. Scale bar: 10 µm. (B) Cholesterol (PFO+)
colocalization with mitochondria (Tom20+) or lysosome (Lamp1+) into hippocampal astrocytes (GFAP+) from AD, DS, and control donors. 10
images per sample were analysed with Image J to assess the index of astrocytic cholesterol colocalization with Tom20 or Lamp1. Values are
relativized with control to show differences as n-fold. (*) p<0.05; (**) p<0.01. AGING 8 www.aging-us.com but not p-tau immunoreactivity significantly increased
in CA1-3 hippocampal regions only in patients with DS,
with a trend for increased Aβ42 levels in CA1 from
patients with AD. These findings in DS are consistent
with the intrinsic Aβ overproduction in these subjects
[8]. Moreover, neuropathological analysis of amyloid
pathology in DS described the onset of mid-severity
changes in hippocampal CA1 region at 35 years of age,
in which Aβ42 deposition occurred in the absence of tau
pathology [18]. Conversely, tauopathies and the
presence of NFTs that commonly coexist with LOAD
can occur without amyloid pathology [19, 20]. DISCUSSION In
addition, it has been suggested that the earliest
appearance of tau pathology in AD occurs in the locus
caeruleus instead of hippocampus [21], which could
account for the lack of p-tau immnunoreactivity in
hippocampal samples from our cohort of patients with
AD. While the present work is the first to our
knowledge to address the expression of putative
intracellular cholesterol carriers (e.g. STARD1 and
NPC1) in AD and DS and their correlation with
pathological markers, the role of changes in total
cholesterol levels in AD is controversial [2, 14],
consistent with the unsettled impact of statins in the
prevention or treatment of the disease, which will
require further randomized controlled trials [22, 23]. (Figure 2), the NPC1 immunolabeling as a disease
marker of AD does not discriminate AD-pathology in
patients with DS from the controls (Figure 3), suggesting
that the AD continuum in the hippocampus of subjects
with DS differs from NPC disease. Cholesterol is known to promote the amyloidogenic
processing of APP, which occurs predominantly in lipid-
rafts where most components of the amyloidogenic
machinery, such as APP, Aβ, BACE1, presenilins
(PSEN1/2), and γ-secretase are present [26, 27]. Moreover, cholesterol is thought to interfere with the α-
secretase-dependent non-amyloidogenic APP processing
[28], and PSEN1/2 and γ-secretase have been localized at
the mitochondrial ER-associated membrane (MAM) [29,
30]. Interestingly, although mitochondrial membranes are
low in cholesterol, the pool of cholesterol of the
mitochondrial inner membrane (MIM) is crucial for the
synthesis of neurosteroids to maintain physiological
GABAergic responses that modulate memory function,
which is particularly affected in subjects with DS [31,
32]. The STARD1-dependent trafficking of cholesterol to
MIM is the rate-limiting step for steroidogenesis and
changes in mitochondrial cholesterol levels can impact
this process and affect mitochondrial antioxidant defense
[2, 5–7, 33]. However, the role of STARD1 in human
AD is poorly understood and has not been examined in
DS. We show for the first time that the hippocampal
overexpression of STARD1 correlates with amyloid
deposition suggesting a relationship between the
accumulation of mitochondrial cholesterol and the
development of AD-pathology (Figure 2). Unexpectedly,
our findings in hippocampal samples from patients with
DS and AD suggest that STARD1 immunolabeling can
act as a pathological mark of AD even better than Aβ42
deposition in post-morten samples (Figure 3), implying
that the hippocampal alterations in the expression of
STARD1 could occur in a temporal pattern parallel to the
pathogenic amyloidogenic burden. DISCUSSION Our
findings suggest that while altered hippocampal NPC1
expression could be a common feature of DS and AD AGING 9 www.aging-us.com Although not statistical significant, our findings do
suggest a trend for lower expression of STARD3/MLN64
in the cortex of AD samples (Figure 1B), whose impact in
regulating the mitochondrial pool of cholesterol remains
to be understood. In this regard, it is interesting to note
that increased expression of MLN64 has been reported in
the lysosomal storage disorder Niemann-Pick type C
disease, which correlated with increased mitochondrial
cholesterol accumulation [36]. However, it has also been
reported that targeted mutations of the MLN64 START
domain have been shown to cause minor alterations in
metabolism and intracellular distribution of cholesterol
[37]. Further investigation will be required to decipher the
impact of MLN64 in mitochondrial cholesterol regulation
and AD pathogenesis. implies accumulation of mitochondrial cholesterol in
activated astrocytes within CA1 independently of NPC1. Whether this outcome reflects that post-mortem samples
from patients with AD represent a late stage of the
disease masking the early intra-organelle cholesterol
mobilization remains to be further investigated. Finally, whether the increase in hippocampal Aβ42
deposits reflects an impaired Aβ clearance by increased
lysosomal cholesterol remains to be further confirmed
in human neurodegeneration. Although the astrocyte-
dependent lipidation of ApoE could contribute to the
ability of glia to clear Aβ burden, this event does not
seem to occur in ApoE4-carrying subjects [2], and
defects in Aβ clearance have been detected in
cerebrospinal fluid of >98% of LOAD cases [43], which
may reflect defects in the endolysosomal/autophagy
system in the early neuropathological stages of AD
[44]. In line with this possibility, we have recently
reported that elevated intracellular cholesterol levels in
a hypercholesterolemic mouse model increased Aβ-
induced autophagosome formation, but impaired the
fusion with lysosomal vesicles causing deficient
autophagy-dependent Aβ degradation [45]. Considering
that DS might serve as a model for early AD [12], the
observations of increased lysosomal cholesterol loading
support the notion that abnormal cholesterol distribution
in lysosomes can impact mitochondrial function through
sustained mitochondrial cholesterol accumulation and
Aβ clearance, emerging as an early event in AD
pathogenesis. Reactive astrogliosis has emerged as a relevant
pathological response in the early stages of AD [38],
which correlates with cognitive decline [16]. DISCUSSION Whether these
alterations in STARD1 occur before Aβ42 deposition in
human AD requires further investigation. However,
previous evidence in experimental models pointed that
enhanced mitochondrial cholesterol levels in AD mouse
models have been shown to sensitize neurons to Aβ-
induced inflammation and toxicity by depleting mGSH
by an ER stress-dependent mechanism [6, 7, 33]. Moreover, as Aβ-induced ER stress is considered an
indirect effector of the Aβ-neurotoxicity in early stages of
AD [34], our data suggest that STARD1 overexpression
in the hippocampus may be a potential early molecular
event associated with AD, as strengthened by the
increase seen in DS, an accelerated genetic form of AD. In this context, it is widely recognized that neuro-
inflammation in AD is an early pathological-associated
response, which is exacerbated with ageing and
contributes to disease progression [18, 35]. Although the groups studied were not age-matched given
the limited number of samples and the life-expectancy of
individuals with DS [8], we performed the comparisons
with AD and controls considering AD pathogenesis as a
function of age in DS, a population that exhibit a high
risk to develop AD-type dementia [12, 24]. Moreover, as
described previously [18], individuals with DS developed
signs of AD-pathology by 50-55 years of age, which
coincides with the age range of the subjects with DS
analyzed in our study (Table 1). In this context,
interestingly we found increased expression of NPC1 and
STARD1 in cortical samples from patients with AD and
DS, respectively, (Figure 1). A link between lysosomal
cholesterol and Aβ42 deposition in neurodegeneration has
been described in Niemann–Pick type C (NPC) disease,
a rare autosomal recessive disease associated mostly with
NPC1 mutations, characterized by lysosomal accumula-
tion of unesterified cholesterol [25]. While the etiology
and epidemiology of AD and NPC differ, these
neurodegenerative diseases share many disease-related
molecular pathways, including cholesterol accumulation,
lysosomal abnormalities, tau hyperphosphorylation, APP
processing and Aβ deposition [2, 25]. Moreover, while
increased mRNA and protein levels of NPC1 have been
described within the hippocampus of both patients with
AD and mice [3], the hippocampal expression pattern of
NPC1 in human DS-brains has not been reported. DISCUSSION Since
astrocytes are the most prevalent cell type in the brain
and form an intricate system of connections to control a
wide range of brain functions, including regulation of
blood-brain barrier, the astroglial atrophy could have far-
reaching consequences on synaptic transmission that
accounts for the spatio-temporal progression of AD-
neurodegeneration [17]. We confirm the presence of
reactive astrocytes surrounding amyloid plaque in the
hippocampus of AD and DS, and observed a hippo-
campal region-specific increased expression of STARD1
within astocytes (Figure 4) that correlates with the
accumulation of mitochondrial cholesterol in both groups
(Figure 5). Similarly, we also found astroglial NPC1
overexpression and astroglial accumulation of lysosomal
cholesterol in AD and DS (Figures 4 and 5). These
results are in line with findings reporting the activation of
rat astrocytes induced by cholesterol exposure in vitro,
resulting in enhanced APP/BACE-1 interaction within
lipid-rafts, increased APP content, and enhanced ROS
production [39]. Moreover, recent observations from a
single cell brain atlas of human AD indicated the
diversity of astrocytes in AD under the control of the
transcription factor EB, a master regulator of lysosomal
function, which initiated a regulatory cascade containing
multiple AD GWAS genes [40]. Taken in consideration
that subjects with DS display abnormal lipid metabolism
from the embryonic stages [41] and that SOD1, BACE-2,
S100β and APP genes are located at HSA21 [42], it is
conceivable that subjects with HSA21 trisomy could
have a basal cholesterol-mediated astrocyte activation. These findings along with the observed increased NPC1
expression in DS individuals (Figure 2) suggests that an
enhanced hippocampal lysosomal cholesterol trafficking
could result in increased mitochondrial cholesterol
loading in hippocampal areas, possibly coinciding with
signs of early AD-pathogenesis. Moreover, elevated
astrogial-STARD1 expression in individuals with AD In conclusion, this exploratory study in post-mortem
brains from patients with AD and DS revealed increased
mitochondrial and lysosomal cholesterol levels in
hippocampus from patients with AD and DS, which
correlate with higher expression of STARD1 and NPC1. Moreover, our findings indicate the ability of STARD1
expression to discriminate controls from AD in the
general population and in subjects with DS and suggest
that STARD1 could be a potential marker associated
with early molecular events of AD pathology. Further
studies with a higher number of human samples are
needed to validate these findings. In addition, future
research using mice with tissue-specific deletion of
STARD1 are warranted to define its role in AD
pathology. Immunofluorescence Paraffin sections (5 µm) of hippocampus were
dewaxed/rehydrated and treated for antigen retrieval as
was described above for immunohistochemical analysis. Sections were permeabilized with 0.2% Triton X-100 in
blocking buffer (5% goat serum + 1% BSA in PBS)
during 10 min, followed by washing ×3 with PBS and
incubation overnight at 4°C with primaries antibodies
(Supplementary Table 4) into a dark-humid chamber, as
described in detail in Supplementary Methods. Western blotting Human frozen cortex (350 mg) were homogenized on
ice
in
anti-proteases/anti-phosphatases
(Complete/
PhosSTOP, Roche) containing RIPA lysis buffer. Protein quantitation was assessed by BCA (Pierce) and
samples (90 µg/lane) were resolved by 4-12% SDS-
PAGE (Bio-Rad), electrotransferred to nitrocellulose
membranes (Trans-Blot Turbo, Bio-Rad), followed by
5% BSA-blocking and incubation with primary
antibodies (Supplementary Table 4) at 4°C overnight. After washing, membranes were incubated 1 hr at RT
with the corresponding horseradish peroxidase-coupled
secondary antibodies and visualized using the Pierce
ECL Western Blotting Substrate (Thermo Scientific). Immunoblots images were captured using LAS4000
(GE Healthcare) and quantitation of the bands was
performed by Image J free software (NIH). Immunohistochemistry Paraffin sections (5 µm) of hippocampus were processed
according to the avidin–biotin–peroxidase staining
method (Vectastain ABC kit; Vector Lab), as described
previously [7] and detailed in Supplementary Methods. Statistics Data are shown as mean ± S.E.M and statistical analysis
performed with the GraphPad Prism-5 software (San
Diego, CA). Due to the number of analysed samples (≤7
for each group), nonparametric tests were employed. Differences between AD, DS and control samples
were analysed with Kruskall-Wallis test followed by
Mann-Whitney U-test to analyze the differences
between two groups. The Spearman's rank-correlation
coefficient rs was also determined when pertinent. Two-
tailed p values <0.05 were considered statistically
significant. ROC curves were generated and the area
under ROC curves (AUC) was calculated to evaluate
sensitivity and specificity of immunolabeling within
hippocampal regions. ROC curves from control group
were compared to AD or DS or AD+DS groups. The
cut-off points on the ROC curves at which accuracy of
disease
detection
was
maximal
were
selected. Human brain samples Twenty-one cases from the Biobank of Hospital
Clinic/IDIBAPS of Barcelona were collected following
approval of the Clinical Research Ethics Committee of
the Hospital Clinic of Barcelona (HCB/2015/0595). AGING 10 www.aging-us.com Transferase (GST-PFO), as described [46]. In brain
tissues, PFO binds and detects cholesterol in membranes
when its levels exceed 30% mol, while the fusion with
GST allows PFO detection by immunofluorescence. The
sequence to design the plasmid was DNA M36704
(NCBI database) corresponding to the gen of PFO in the
Clostridium perfringens genome. Additionally, the signal
peptide was eliminated from the PFO gen to enable the
intracellular stance of the protein. The resulted sequence
was synthesized into the plasmid pGEX 4T-1 (GenScript)
between the BamHI and SmaI restriction sites. The
plasmid was engineered to make a fusion protein with the
GST tag. After bacterial production, protein extraction
and purification, the GST-PFO probe was dialyzed,
concentrated, quantified and stored at −80°C. Samples were scored by CERAD scale (A-C) and Braak
stage (0-VI) and categorized as AD, DS, and control
groups. For each group, demographic data as well as
clinical and anatomopathological diagnosis are detailed
in Table 1. Please find the BRISQ checklist in Sup-
plementary Methods detailing the biospecimen samples
collected from patients with AD and DS. Samples were scored by CERAD scale (A-C) and Braak
stage (0-VI) and categorized as AD, DS, and control
groups. For each group, demographic data as well as
clinical and anatomopathological diagnosis are detailed
in Table 1. Please find the BRISQ checklist in Sup-
plementary Methods detailing the biospecimen samples
collected from patients with AD and DS. mRNA isolation and RT-qPCR Total RNA was extracted from 150 mg of frozen cortex of
human brains, using TRIzol reagent (Invitrogen), cleaned
by RNeasy columns (Qiagen), and quantified through
Nanodrop spectrophotometer (Thermo-Fisher Scientific). Real-time qPCR was performed using the iScript™ One-
Step RT-PCR Kit with SYBR® Green (Bio-Rad)
following the manufacturer’s instructions. Briefly, 200 ng
of total RNA were mixed with 300 µmol/l of specific
primers for each gene assessed (Supplementary Table 3)
in 1× reaction buffer at final volume of 10.5 µl. RT-
qPCRs were performed in triplicate using a CFX380
Real-Time System (Bio-Rad) following the manufac-
turer’s instructions. Gene expression values were
normalized using actin as housekeeping gene. Image analysis Detection and quantitation of immunoreactivity for Aβ42,
p-tau, NPC1, and STARD1 was performed from high-
resolution scanned immunohistochemical images of
hippocampus using the Image J Software after Color
Deconvolution plug-in [47], as detailed in Supplementary
Methods. Recombinant GST-PFO probe To optimally assess the localization of cholesterol in
hippocampal tissues, we generated a recombinant
Perfringolysin O (PFO) fusioned with Glutathione-S- AGING 11 www.aging-us.com https://doi.org/10.1016/j.bbamem.2018.03.015 2. Arenas
F,
Garcia-Ruiz
C,
Fernandez-Checa
JC. Intracellular cholesterol trafficking and impact in
neurodegeneration. Front Mol Neurosci. 2017; 10:382. https://doi.org/10.3389/fnmol.2017.00382
PMID:29204109 3. Kågedal K, Kim WS, Appelqvist H, Chan S, Cheng D,
Agholme L, Barnham K, McCann H, Halliday G, Garner
B. Increased expression of the lysosomal cholesterol
transporter NPC1 in Alzheimer’s disease. Biochim
Biophys Acta. 2010; 1801:831–38. https://doi.org/10.1016/j.bbalip.2010.05.005
PMID:20497909 3. Kågedal K, Kim WS, Appelqvist H, Chan S, Cheng D,
Agholme L, Barnham K, McCann H, Halliday G, Garner
B. Increased expression of the lysosomal cholesterol
transporter NPC1 in Alzheimer’s disease. Biochim
Biophys Acta. 2010; 1801:831–38. REFERENCES 1. Bharadwaj P, Solomon T, Malajczuk CJ, Mancera RL,
Howard M, Arrigan DW, Newsholme P, Martins RN. Role of the cell membrane interface in modulating
production and uptake of Alzheimer’s beta amyloid
protein. Biochim Biophys Acta Biomembr. 2018. [Epub
ahead of print]. 1. Bharadwaj P, Solomon T, Malajczuk CJ, Mancera RL,
Howard M, Arrigan DW, Newsholme P, Martins RN. Role of the cell membrane interface in modulating
production and uptake of Alzheimer’s beta amyloid
protein. Biochim Biophys Acta Biomembr. 2018. [Epub
ahead of print]. CONFLICTS OF INTEREST Additional visualization of the association between
markers and subject status (i.e. control, AD, or DS) was
performed through multivariate data analysis by PCA
using JMP 9.0 software (SAS Institute Inc.). PCA show
the data variability as the covariance of samples for
each marker (descriptors) projected into a subspace
made of orthogonal linear axis, so-called principal
components. The authors declare there are no conflicts of interest. ACKNOWLEDGMENTS We want to thank Dr. María Carmona from the Hospital
de la Santa Creu y San Pau for critically reading the
manuscript and valuable suggestions. 5. Webber KM, Stocco DM, Casadesus G, Bowen RL,
Atwood CS, Previll LA, Harris PL, Zhu X, Perry G, Smith
MA. Steroidogenic acute regulatory protein (StAR):
evidence of gonadotropin-induced steroidogenesis in
Alzheimer disease. Mol Neurodegener. 2006; 1:14. Abbreviations AD: Alzheimer´s disease; Aβ42: beta amyloid peptide
42; DS: Down syndrome; EOAD: early-onset AD;
LOAD: late-onset AD; mGSH: mitochondrial GSH;
MAM: mitochondrial ER-associated membranes; MIM:
mitochondrial inner membrane; NFTs: neurofibrillary
tangles; NPC1: Niemann Pick type C1 protein; PCA:
principal component analysis; PFO: recombinant
perfringolysin; p-tau: phosphorylated tau; StARD1:
steroidogenic acute regulatory protein. AUTHOR CONTRIBUTIONS All authors read and approved the final manuscript. F.A. and S.N. performed gene expression, WB and
immunohistochemistry procedures. F.A., G.G. and
F.C. synthesized GST-PFO and performed immuno-
fluorescence. F.A., C.G-R and J.C. F-Ch analysed and
discussed data and wrote the manuscript. https://doi.org/10.1016/j.bbalip.2010.05.005
PMID:20497909 4. Elustondo P, Martin LA, Karten B. Mitochondrial
cholesterol import. Biochim Biophys Acta Mol Cell Biol
Lipids. 2017; 1862:90–101. 4. Elustondo P, Martin LA, Karten B. Mitochondrial
cholesterol import. Biochim Biophys Acta Mol Cell Biol
Lipids. 2017; 1862:90–101. https://doi.org/10.1016/j.bbalip.2016.08.012
PMID:27565112 8.
Wiseman FK, Al-Janabi T, Hardy J, Karmiloff-Smith A, 8.
Wiseman FK, Al-Janabi T, Hardy J, Karmiloff-Smith A, https://doi.org/10.3389/fneur.2019.01168 15. Braak H, Del Trecidi K. Neuroanatomy and pathology of
sporadic Alzheimer’s disease. Adv Anat Embryol Cell
Biol. 2015; 215:1–162. https://doi.org/10.1186/1750-1326-1-14
PMID:17018137 We acknowledge the support from grants SAF2014-
57674R, SAF-2015-69944R, and SAF2017-85877R
from Plan Nacional de I+D, by the CIBEREHD from
the Instituto de Salud Carlos III, by AGAUR of the
Generalitat de Catalunya SGR-2017-1112, and by the
“ER stress-mitochondrial cholesterol axis in obesity-
associated insulin resistance and comorbidities”-
Ayudas FUNDACION BBVA, Spain. We also
acknowledge
support
from
the
center
grant
P50AA011999 Southern California Research Center
for ALPD and Cirrhosis funded by NIAAA/NIH and
by the European Cooperation in Science and
Technology (COST) ACTION CA17112 Prospective
European Drug-Induced Liver Injury Network, and
Red Nacional 2018-102799-T de Enfermedades
Metabólicas y Cáncer. 6. Barbero-Camps E, Fernández A, Baulies A, Martinez L,
Fernández-Checa JC, Colell A. Endoplasmic reticulum
stress
mediates
amyloid
β
neurotoxicity
via
mitochondrial cholesterol trafficking. Am J Pathol. 2014; 184:2066–81. https://doi.org/10.1016/j.ajpath.2014.03.014
PMID:24815354 6. Barbero-Camps E, Fernández A, Baulies A, Martinez L,
Fernández-Checa JC, Colell A. Endoplasmic reticulum
stress
mediates
amyloid
β
neurotoxicity
via
mitochondrial cholesterol trafficking. Am J Pathol. 2014; 184:2066–81. 7. Barbero-Camps E, Fernández A, Martínez L, Fernández-
Checa JC, Colell A. APP/PS1 mice overexpressing
SREBP-2 exhibit combined Aβ accumulation and tau
pathology underlying Alzheimer’s disease. Hum Mol
Genet. 2013; 22:3460–76. https://doi.org/10.1093/hmg/ddt201 PMID:23648430 8. Wiseman FK, Al-Janabi T, Hardy J, Karmiloff-Smith A, 8. Wiseman FK, Al-Janabi T, Hardy J, Karmiloff-Smith A, AGING 12 www.aging-us.com Nizetic D, Tybulewicz VL, Fisher EM, Strydom A. A
genetic cause of Alzheimer disease: mechanistic
insights from Down syndrome. Nat Rev Neurosci. 2015;
16:564–74. https://doi.org/10.1038/nrn3983 PMID:26243569 production and Alzheimer’s disease. Open Biol. 2017; 7:7. 22. McGuinness B, Passmore P. Can statins prevent or help
treat Alzheimer’s disease? J Alzheimers Dis. 2010;
20:925–33.
https://doi.org/10.3233/JAD-2010-091570
PMID:20182019 22. McGuinness B, Passmore P. Can statins prevent or help
treat Alzheimer’s disease? J Alzheimers Dis. 2010;
20:925–33. https://doi.org/10.3233/JAD-2010-091570
PMID:20182019 13. Zigman WB, Schupf N, Jenkins EC, Urv TK, Tycko B,
Silverman W. Cholesterol level, statin use and
Alzheimer’s disease in adults with Down syndrome. Neurosci Lett. 2007; 416:279–84. https://doi.org/10.1016/j.neulet.2007.02.023
PMID:17353095 23. Schultz BG, Patten DK, Berlau DJ. The role of statins in
both cognitive impairment and protection against
dementia: a tale of two mechanisms. Transl
Neurodegener. 2018; 7:5. https://doi.org/10.1186/s40035-018-0110-3
PMID:29507718 14. Torres S, García-Ruiz CM, Fernandez-Checa JC. Mitochondrial cholesterol in Alzheimer’s disease and
Niemann Pick type C disease. Front Neurol. 2019;
10:1168. 24. Dubois B, Feldman HH, Jacova C, Hampel H, Molinuevo
JL, Blennow K, DeKosky ST, Gauthier S, Selkoe D,
Bateman R, Cappa S, Crutch S, Engelborghs S, et al. Advancing research diagnostic criteria for Alzheimer’s
disease: the IWG-2 criteria. Lancet Neurol. 2014;
13:614–29. https://doi.org/10.1016/S1474-4422(14)70090-0
PMID:24849862 https://doi.org/10.1098/rsob.170228 PMID:29237809 17. Heneka MT, Carson MJ, El Khoury J, Landreth GE,
Brosseron F, Feinstein DL, Jacobs AH, Wyss-Coray T,
Vitorica J, Ransohoff RM, Herrup K, Frautschy SA,
Finsen B, et al. Neuroinflammation in Alzheimer’s
disease. Lancet Neurol. 2015; 14:388–405. https://doi.org/10.1016/S1474-4422(15)70016-5
PMID:25792098 9. Startin CM, Hamburg S, Hithersay R, Al-Janabi T, Mok
KY, Hardy J, Strydom A, Strydom A, Fisher E, Nizetic D,
Hardy J, Tybulewicz V, Karmiloff-Smith A, et al, and
LonDownS
Consortium. Cognitive
markers
of
preclinical and prodromal Alzheimer’s disease in Down
syndrome. Alzheimers Dement. 2019; 15:245–57. https://doi.org/10.1016/j.jalz.2018.08.009
PMID:30503169 18. Davidson YS, Robinson A, Prasher VP, Mann DM. The
age of onset and evolution of Braak tangle stage and
Thal amyloid pathology of Alzheimer’s disease in
individuals with Down syndrome. Acta Neuropathol
Commun. 2018; 6:56. https://doi.org/10.1186/s40478-018-0559-4
PMID:29973279 10. Jack CR Jr, Knopman DS, Jagust WJ, Petersen RC,
Weiner MW, Aisen PS, Shaw LM, Vemuri P, Wiste
HJ, Weigand SD, Lesnick TG, Pankratz VS, Donohue
MC, Trojanowski JQ. Tracking pathophysiological
processes in Alzheimer’s disease: an updated
hypothetical model of dynamic biomarkers. Lancet
Neurol. 2013; 12:207–16. https://doi.org/10.1016/S1474-4422(12)70291-0
PMID:23332364 19. Lebouvier T, Pasquier F, Buée L. Update on
tauopathies. Curr Opin Neurol. 2017; 30:589–98. https://doi.org/10.1097/WCO.0000000000000502
PMID:28914736 https://doi.org/10.1016/S1474-4422(12)70291-0 20. Braak H, Thal DR, Ghebremedhin E, Del Tredici K. Stages of the pathologic process in Alzheimer disease:
age categories from 1 to 100 years. J Neuropathol Exp
Neurol. 2011; 70:960–69. https://doi.org/10.1097/NEN.0b013e318232a379
PMID:22002422 11. Portelius E, Soininen H, Andreasson U, Zetterberg H,
Persson R, Karlsson G, Blennow K, Herukka SK,
Mattsson N. Exploring Alzheimer molecular pathology
in
Down’s
syndrome
cerebrospinal
fluid. Neurodegener Dis. 2014; 14:98–106. https://doi.org/10.1159/000358800
PMID:24992945 21. Braak H, Del Tredici K. The pathological process
underlying Alzheimer’s disease in individuals under
thirty. Acta Neuropathol. 2011; 121:171–81. https://doi.org/10.1007/s00401-010-0789-4
PMID:21170538 12. Lott IT, Head E. Dementia in Down syndrome: unique
insights for Alzheimer disease research. Nat Rev
Neurol. 2019; 15:135–47. https://doi.org/10.1038/s41582-018-0132-6
PMID:30733618 12. Lott IT, Head E. Dementia in Down syndrome: unique
insights for Alzheimer disease research. Nat Rev
Neurol. 2019; 15:135–47. https://doi.org/10.1007/978-3-319-12679-1_1
PMID:25920101 https://doi.org/10.1007/978-3-319-12679-1_1
PMID:25920101 25. Malnar M, Hecimovic S, Mattsson N, Zetterberg H. 16. Frost GR, Li YM. The role of astrocytes in amyloid AGING 13 www.aging-us.com Bidirectional links between Alzheimer's disease and
Niemann-Pick type C disease. Neurobiol Dis. 2014;
72Pt A:37–47. https://doi.org/10.1016/j.nbd.2014.05.033
PMID:24907492 35. Rodríguez-Arellano JJ, Parpura V, Zorec R, Verkhratsky
A. Astrocytes in physiological aging and Alzheimer’s
disease. Neuroscience. 2016; 323:170–82.
https://doi.org/10.1016/j.neuroscience.2015.01.007
PMID:25595973 35. Rodríguez-Arellano JJ, Parpura V, Zorec R, Verkhratsky
A. Astrocytes in physiological aging and Alzheimer’s
disease. Neuroscience. 2016; 323:170–82. https://doi.org/10.1016/j.neuroscience.2015.01.007
PMID:25595973 26. Arbor SC, LaFontaine M, Cumbay M. Amyloid-beta
Alzheimer targets - protein processing, lipid rafts, and
amyloid-beta pores. Yale J Biol Med. 2016; 89:5–21. PMID:27505013 36. Balboa E, Castro J, Pinochet MJ, Cancino GI, Matías N,
Sáez PJ, Martínez A, Álvarez AR, Garcia-Ruiz C,
Fernandez-Checa JC, Zanlungo S. MLN64 induces
mitochondrial dysfunction associated with increased
mitochondrial cholesterol content. Redox Biol. 2017;
12:274–84. https://doi.org/10.1016/j.redox.2017.02.024
PMID:28282615 27. Colin J, Gregory-Pauron L, Lanhers MC, Claudepierre T,
Corbier C, Yen FT, Malaplate-Armand C, Oster T. Membrane raft domains and remodeling in aging
brain. Biochimie. 2016; 130:178–87. https://doi.org/10.1016/j.biochi.2016.08.014
PMID:27594339 37. Kishida T, Kostetskii I, Zhang Z, Martinez F, Liu P,
Walkley SU, Dwyer NK, Blanchette-Mackie EJ, Radice
GL, Strauss JF 3rd. Targeted mutation of the MLN64
START domain causes only modest alterations in
cellular sterol metabolism. J Biol Chem. 2004;
279:19276–85. 28. Barrett PJ, Song Y, Van Horn WD, Hustedt EJ, Schafer
JM, Hadziselimovic A, Beel AJ, Sanders CR. The amyloid
precursor protein has a flexible transmembrane domain
and binds cholesterol. Science. 2012; 336:1168–71. https://doi.org/10.1126/science.1219988
PMID:22654059 https://doi.org/10.1002/glia.22874 32. Stocco DM, Zhao AH, Tu LN, Morohaku K, Selvaraj V. A
brief history of the search for the protein(s) involved in
the acute regulation of steroidogenesis. Mol Cell
Endocrinol. 2017; 441:7–16. https://doi.org/10.1016/j.mce.2016.07.036
PMID:27484452 40. Grubman A, Chew G, Ouyang JF, Sun G, Choo XY,
McLean C, Simmons R, Buckberry S, Landin DV,
Pflueger J, Lister R, Rackham OJ, Petretto E, Polo JM. A
single cell brain atlas in human Alzheimer’s disease. bioRxiv. 2019. 33. Fernández A, Llacuna L, Fernández-Checa JC, Colell A. Mitochondrial cholesterol loading exacerbates amyloid
beta peptide-induced inflammation and neurotoxicity. J Neurosci. 2009; 29:6394–405. https://doi.org/10.1523/JNEUROSCI.4909-08.2009
PMID:19458211 https://doi.org/10.1093/brain/awv404 31. Rissman RA, Mobley WC. Implications for treatment:
GABAA receptors in aging, Down syndrome and
Alzheimer’s disease. J Neurochem. 2011; 117:613–22. https://doi.org/10.1111/j.1471-4159.2011.07237.x
PMID:21388375 39. Avila-Muñoz E, Arias C. Cholesterol-induced astrocyte
activation is associated with increased amyloid
precursor protein expression and processing. Glia. 2015; 63:2010–22. https://doi.org/10.1002/glia.22874
PMID:26096015 39. Avila-Muñoz E, Arias C. Cholesterol-induced astrocyte
activation is associated with increased amyloid
precursor protein expression and processing. Glia. 2015; 63:2010–22. 29. Area-Gomez E, Schon EA. Mitochondria-associated ER
membranes and Alzheimer disease. Curr Opin Genet
Dev. 2016; 38:90–96.
https://doi.org/10.1016/j.gde.2016.04.006
PMID:27235807 29. Area-Gomez E, Schon EA. Mitochondria-associated ER
membranes and Alzheimer disease. Curr Opin Genet
Dev. 2016; 38:90–96. https://doi.org/10.1016/j.gde.2016.04.006
PMID:27235807 38. Rodriguez-Vieitez E, Saint-Aubert L, Carter SF, Almkvist
O, Farid K, Schöll M, Chiotis K, Thordardottir S, Graff C,
Wall A, Långström B, Nordberg A. Diverging
longitudinal changes in astrocytosis and amyloid PET in
autosomal dominant Alzheimer’s disease. Brain. 2016;
139:922–36. https://doi.org/10.1093/brain/awv404
PMID:26813969 30. Area-Gomez E, Schon EA. On the pathogenesis of
Alzheimer’s disease: the MAM hypothesis. FASEB J. 2017; 31:864–67. https://doi.org/10.1096/fj.201601309 PMID:28246299 https://doi.org/10.1101/628347 41. Adelekan T, Magge S, Shults J, Stallings V, Stettler N. Lipid profiles of children with Down syndrome
compared with their siblings. Pediatrics. 2012;
129:e1382–87. https://doi.org/10.1542/peds.2011-1262
PMID:22585768 34. Hoozemans JJ, van Haastert ES, Nijholt DA,
Rozemuller AJ, Scheper W. Activation of the
unfolded protein response is an early event in
Alzheimer’s and Parkinson’s disease. Neurodegener
Dis. 2012; 10:212–15. 42. Zigman WB, Lott IT. Alzheimer’s disease in Down
syndrome: neurobiology and risk. Ment Retard Dev
Disabil Res Rev. 2007; 13:237–46. AGING 14 www.aging-us.com Immunohistochemistry analysis After paraffin sections were dewaxed and rehydrated,
the antigen retrieval of hippocampus sections was
performed using 99% formic acid (5 min at RT),
following by heating-incubation (120°C for 20 min)
with 10 mM Tris/1mM EDTA/0.05% Tween 20; pH
9.0. Endogenous peroxidase was blocked using 3%
H2O2/methanol for 45 min. In a dark-humid chamber,
blocking of sections was performed using Dako
antibody diluent background reducing components
(Dako) for 20 min, and treated with the Avidin/Biotin
blocking kit from Vector Lab according to the
manufacturer's instructions and incubated overnight
(4°C) with antibodies against human Aβ, pathological
phospho-tau (Ser202 and Thr205), NPC1, and
StARD1 (Supplementary Table 2). Sections were then
incubated (1 hr) with the corresponding biotinylated
secondary antibodies diluted 1:200, followed by ABC
staining for 30 min. The immunoreactivities were
visualized with diaminobenzidine (DAB enhanced
liquid substrate system, Sigma). Sections were
counterstained with hematoxylin (Dako) and mounted
with a coverslip. The final stained hippocampal
sections were then scanned in a 43X resolution using
Panoramic DESK digital slice scanner with Carl Zeiss
objectives (3DHISTECH) and images of entire hippo-
campus regions where capture using Panoramic
Viewer software (3DHISTECH). Images for all samples were taken with a Leica TCS
SP5 laser scanning confocal system with a 63X oil
immersion objective APO CS numerical aperture 1.4
equipped with a DMI6000 inverted microscope. Image analysis Briefly, after background subtraction and filtering
processes (median, radius 2.0), segmentation of
immunoreactivities was performed by the combination
of H-DAB vector matrix of Color Deconvolution plug-
in [14] – which separate channels corresponding to 3
determined colors of hematoxylin-DAB stain – with the
local standard threshold of the “Colour-2” (brown)
resulted images. Immunoreactivities were then sub-
jected to particle analysis for acquiring the percentage
of immunolabeled area relative with the total area of the
image. Confocal images of immunoreactivities for GFAP,
NPC1 and StARD1 from hippocampal paraffin sections
were analysed by Image J Software. In 10 different
images of each hippocampal region (CA1, CA2 or
CA3), percentage of total NPC1 or StARD1 mass
containing astrocytes (GFAP+) were analysed using the
Colocalization nBits n-images plug-in (Confocal
Microscopy Unit, Medicine Faculty, University of
Barcelona), which highlights the colocalized points of
two 32-bits images (Figure 4A). Two points are
considered as colocalized if their respective intensities
are strictly higher than the threshold of their channels
and if their ratio of intensity is strictly higher than the
ratio setting value, which have been defined at 50%. Colocalization index is calculated as the ratio of
colocalized points between total threshold-passed
intensity and relativized with control group. SUPPLEMENTARY MATERIALS with primaries antibodies (Supplementary Table 4). Secondary antibodies were diluted 1:200 in 1% Goat
Serum containing 0.05% Triton X-100 in PBS and
incubated for 90 min at RT with the mix of anti-rabbit
Alexa fluor-647 (for Tom20 or Lamp1), anti-mouse
Alexa fluor-532 (for GST) and anti-rat Alexa fluor-488
(for GFAP). After washing, slices were incubated 5 min
in Sudan black 0.1% in 70% ethanol to minimize
autofluorescence and mounted with prolong antifade
mountant with Dapi (Dako). https://doi.org/10.1002/mrdd.20163 PMID:17910085 43. Mawuenyega KG, Sigurdson W, Ovod V, Munsell L,
Kasten T, Morris JC, Yarasheski KE, Bateman RJ. Decreased
clearance
of
CNS
beta-amyloid
in
Alzheimer’s disease. Science. 2010; 330:1774. https://doi.org/10.1126/science.1197623
PMID:21148344 46. Kwiatkowska K, Marszałek-Sadowska E, Traczyk G,
Koprowski P, Musielak M, Lugowska A, Kulma M,
Grzelczyk A, Sobota A. Visualization of cholesterol
deposits in lysosomes of Niemann-Pick type C
fibroblasts
using
recombinant
perfringolysin
O. Orphanet J Rare Dis. 2014; 9:64. https://doi.org/10.1186/1750-1172-9-64
PMID:24775609 44. Cataldo AM, Peterhoff CM, Troncoso JC, Gomez-Isla T,
Hyman BT, Nixon RA. Endocytic pathway abnormalities
precede
amyloid
beta
deposition
in
sporadic
Alzheimer’s disease and Down syndrome: differential
effects of APOE genotype and presenilin mutations. Am J Pathol. 2000; 157:277–86. https://doi.org/10.1016/S0002-9440(10)64538-5
PMID:10880397 47. Ruifrok
AC,
Johnston
DA. Quantification
of
histochemical staining by color deconvolution. Anal
Quant Cytol Histol. 2001; 23:291–99. PMID:11531144 45. Barbero-Camps E, Roca-Agujetas V, Bartolessis I, de
Dios C, Fernández-Checa JC, Marí M, Morales A,
Hartmann T, Colell A. Cholesterol impairs autophagy-
mediated clearance of amyloid beta while promoting
its secretion. Autophagy. 2018; 14:1129–54. AGING 15 www.aging-us.com Immunofluorescence analysis Secondary antibodies (Thermofisher) were diluted 1:200
in 1% Goat Serum containing 0.05% Triton X-100 in
PBS and incubated (1 hr at RT) with the mix of anti-
rabbit Alexa fluor-532 (for StARD1 or NPC1), anti-
mouse Alexa fluor-635 (for Aβ42), and anti-rat Alexa
fluor-488 (for GFAP). Finally, sections were incubated
(10
min)
with
20
mM
Hoechst
33342
dye
(Thermofisher), washed and incubated (5 min) with 0.1
% sudan black dye (Sigma) in 70% ethanol to block
autofluorescence, followed by mounting using fluo-
rescent mounting medium (Dako). On the other hand, similar to as been described above to
paraffin sections, detection of cholesterol within lyso-
somes or mitochondria into astrocytes was performed in
cryopreserved hippocampal sections and analysed by
confocal imaging using Image J Software. Immuno-
fluorescence images were submitted to background
subtraction and filtering processes with Median filter set
at 2.0 of radius. Then, 0.4 µm spaced consecutive Human hippocampal cryopreserved 14 µm thin sections
were fixed in 4% paraformaldehyde for 20 min. In a
dark-humid chamber, the sections were permeabilized
with 0.2% Triton X-100 in blocking buffer (5% goat
serum + 1% BSA in PBS) for 2 hr. Then, slices were
incubated (3 hr at 4°C) with the probe GST-PFO
(20µg/ml) in 1% Goat Serum containing 0.05% Triton
X-100 in PBS, followed by incubation overnight (4°C) AGING 16 www.aging-us.com Intracellular cholesterol accumulation associated with
astrogliosis in postmortem brains from patients with AD
and DS collected from from Biobank of Hospital Clinic
(IDIBAPS) with the approval of the Clinical Research
Ethics Committee of the Hospital Clinic of Barcelona
(HCB/2015/0595). images were stacked at maximum intensity and
segmented by threshold to select the area of astrocytes
(GFAP+). All marks outside GFAP+ area were clean in
the
corresponding
images
for
GST+
and
Tom20+/Lamp1+. Resulted images were then analysed
using the Colocalization nBits n-images plug-in
(Confocal
Microscopy
Unit,
Medicine
Faculty,
University of Barcelona) as is described above. BRISQ checklist Based on Moore et al, Cancer Cytopathol 2011;
119(2):92–101. https://doi.org/10.1002/cncy.20147. Biospecimen type
Brain sections
Anatomical site
Cortex and Hippocampus
Disease status of patients
Alzheimer with or without Down Syndrome, Controls
without neurological disease
Clinical characteristics of patients
Patients with Dementia
Vital State of patients
Postmortem
Clinical diagnosis of patients
Alzheimer dementia
Pathology diagnosis
CERAD B-C and Braak V-VI; detailed in Methods and in
Table 1
Collection mechanism
Postmortem dissection
Type of stabilization
On ice
Type of long-term preservation
Formalin fixation, freezing
Constitution of preservative
10% neutral-buffered formalin
Storage temperature
−80 ºC, 20 to 25 ºC
Storage duration
5-10 years
Shipping temperature
−170 ºC to −190 ºC, 20 to 25 ºC
Composition assessment and selection
Brain sections used for anatomopathological diagnosis of
Alzheimer Brain sections AGING 17 www.aging-us.com www.aging-us.com Supplementary Figures ementary Figure 1. Principal Component Analysis (PCA) of Aβ42, p-tau, NPC1, and StARDl markers. For CA1,
ampus regions is show (left panel) the covariance between %area immunodetected by IHC of the corresponding marker
al plane (Component 1 + Component 2) represented on the first vectorial plan of the PCA. Histogram of Eigenvalue
on. (Right panel) Distribution of AD, DS, and control samples onto the two first axes of the PCA. Supplementary Figure 1. Principal Component Analysis (PCA) of Aβ42, p-tau, NPC1, and StARDl markers. For CA1, CA2, and CA3
hippocampus regions is show (left panel) the covariance between %area immunodetected by IHC of the corresponding marker, and the first
principal plane (Component 1 + Component 2) represented on the first vectorial plan of the PCA. Histogram of Eigenvalues explain the
variation. (Right panel) Distribution of AD, DS, and control samples onto the two first axes of the PCA. AGING 18 www.aging-us.com plementary Figure 2. Principal Component Analysis (PCA) of lysosomal and mitochondrial cholesterol conta
ers within hippocampal astrocytes. (Left panel) First vectorial plan of the PCA that describe the covariance between de
ent of both glial cholesterol carriers and lysosomal/mitochondrial cholesterol content) and the first principal plane (Compo
ponent 2). Histogram of Eigenvalues explain the variation. (Right panel) Distribution of AD, DS, and control samples onto the
of the PCA. Supplementary Figure 2. Principal Component Analysis (PCA) of lysosomal and mitochondrial cholesterol contain and
carriers within hippocampal astrocytes. BRISQ checklist (Left panel) First vectorial plan of the PCA that describe the covariance between descriptors
(content of both glial cholesterol carriers and lysosomal/mitochondrial cholesterol content) and the first principal plane (Component 1 +
Component 2). Histogram of Eigenvalues explain the variation. (Right panel) Distribution of AD, DS, and control samples onto the two first
axes of the PCA. AGING 19 www.aging-us.com Supplementary Tables pp
y
Supplementary Table 1. Overview of modulation of key proteins involved in intracellular cholesterol trafficking in the
brain (1). Control
Cortical levels (n-fold)
mean±SEM
Hippocampal levels (n-fold) mean±SEM
CA1
CA2
CA3
Marker
mRNA
Protein(a)
Proteln(b)
GFAP+
colocalization
Proteln(b)
GFAP+
colocalization Proteln(b)
GFAP+
colocalization
Aβ42
n.a. n.a. 1.00 ± 0.262
n.a. 1.00 ±0.471
n.a. 1.00 ±0,323
n.a
p-tau
n.a. n.a. 1.00 ±0.342
n.a. 1.00 ±0.368
n.a. 1.00 + 0.288
n.a. NPC1
1.00 ±0.019 1.00 ± 0.017 1.00 ±0.173
1.00 ±0.196
1.00 ±0.357
1.00 ±0.120 1.00 ± 0.331 1.00 ±0.192
StARDl
1.00 ±0.015 1.00 ± 0.044 1.00 ±0.321
1.00 ±0.271
1.00 ±0.458
1.00 ±0.331
1.00 ±0.396 1.00 ±0.178
StARD3/
MLN64
1.00 ±0.030 1.00 ± 0.237
n.a. n.a. n.a. n.a. n.a. n.a. StARD4 1.00 ±0.023
n.a. n.a. n.a. n.a. n.a. n.a. n.a. INSIG
n.a. 1.00 ± 0.053
n.a. n.a. n.a. n.a. n.a. n.a. SREBP2
n.a. 1.00 ± 0.028
n.a. n.a. n.a. n.a. n.a. n.a. Alzheimer´s disease
Cortical levels (n-fold)
mean±SEM
Hippocampal levels (n-fold) mean±SEM
CA1
CA2
CA3
Marker
mRNA
Protein(a)
Proteln(b)
GFAP+
colocalization
Proteln(b)
GFAP+
colocalization Proteln(b)
GFAP+
colocalization
Aβ42
n.a. n.a. 7.04 ± 2.106
n.a. 1.97 ±0.727
n.a. 1.91 ±0.556
n.a. p-tau
n.a. n.a,
2.42 ±0.736
n.a. 1.63 ±0.554
n.a. 1.67 ±0.621
n.a. NPC1
1.02 ±0.039 1.12 ±0.025
p1=0.0043
8.07 ± 1.834
p1=0.0006
0.92 ±0.194
3.77 ±0.800
p1=0.0111
1.25 ±0.238 8.06 ± 1.539
p1=0.0006
1.08 ± 0.087
p2=0.0023
StARDl
1.00 ±0.014 1.25 ±0.056
P1=0.0087
2.31 ±0.419
p1=0.0379
2.60 ±0.563
P1=0.0111
2.00 ±0.918
0.67 ± 0.232
5.92 ± 2.171
P1=0.0047;
p2=0.0130
1.19 ±0.249
StARD3/
MLN64 0.99 ± 0.062 0.64 ± 0.150
n.a. n.a. n.a. n.a. n.a. n.a. StARD4 1.00 ±0.020
n.a,
n.a. n.a. n.a. n.a. n.a. n.a. INSIG
n.a. 1.05 ± 0.160
n.a. n.a. n.a. n.a. n.a. n.a. SREBP2
n.a. 1.12 ±0.161
n.a. n.a. n.a. n.a. n.a. n.a. Down syndrome
Cortical levels (n-fold)
mean±SEM
Hippocampal levels (n-fold) mean±SEM
CA1
CA2
CA3
Marker
mRNA
Protein(a)
Proteln(b)
GFAP+
colocalization
Proteln(b)
GFAP+
colocalization Proteln(b)
GFAP+
colocalization
A(342
n.a. n.a. 11.30 ±3.423
Pi=0.0012
n.a. 4.27 ±1.275
Pi=0.0177
n.a. 3.99 ± 1.051
Pi=0.0221
n.a. BRISQ checklist p-tau
n.a. n.a. 2.59 ±0.783
n.a. 2.29 ±0.784
n.a. 2.88 ± 1.135
n.a. IMPCl
1.08 ±0.028 1.04 ±0.036 9.86 ±2.413
p1=0.0006
1.62 ±0.420
5.41 ±1.740
P1=0.0111
2.05 ± 0.577 8.79 ±1.822
P1=0.0006
1.08 ± 0.087
p1=0.0023
StARDl
1.08 ±0.013
P1=0,0087
1.35 ±0.044
P1=0.0043;
p2=0.0159
0.97 ±0.182
p2=0.0111
2.81 ± 0.755
0.56 ±0.212
0.80 ± 0.246 2.62 ±1.290
p2=0.0130
2.01 ±0.311
P1=0.0111
StARD3/
MLN64
1.13 ±0.053 1.47 ±0.277
n.a. n.a. n.a. n.a. n.a. n.a. Supplementary Table 1. Overview of modulation of key proteins involved in intracellular cholesterol trafficking in the
brain (1). AGING 20 www.aging-us.com StARD4 1.03 ± 0.008
n.a. n.a. n.a. n.a. n.a. n.a. n.a. INSIG
n.a. 1.14 ±0.043
n.a. n.a. n.a. n.a. n.a. SREBP2
n.a. 1.14 ±0.061
n.a. n.a. n.a. n.a. n.a. n.a. NOTE: P values are calculated by differences against control (pi) or differences between AD and DS (pz). Supplementary Table 2. Overview of modulation of key proteins involved in intracellular cholesterol trafficking in the
brain (1). Astrocyte (GFAP+) cholesterol (PFO+) colocalization (n-fold)
Organelle marker
Control
AD
DS
Tom20 (mitochondria)
1.00 ±0.257
2.55 ± 0.297; p1=0.0079
2.77 ± 0.203; p1=0.0159
Lampl (lysosome)
1.00 ±0.136
3.43 ± 0.502; p1=0.0079
14.41 ± 1.322; p1,2=0.0079
Supplementary Table 3. Oligonucleotides used for gene expression analysis by RT-qPCR. Gene
Sequence
StARD1
5′-GAGGAGGCCATGCAGAA
5′-GAACACCTTGCCCACATC
StARD3
5′-AGTGAGGAGCCCAGGGAG
5′-CCGTGGCTGACATGGAG
StARD4
5′-CGTTTTCTTAGCAACTCGCC
5′-CTTCCACGTCCTTGCTTCAC
NPC1
5′-CATCCTTTGGCAATGGTTTT
5′-CTGCTGCTACTGTGTCCAGC
β-Actin
5′-TTGCCGACAGGATGCAGAA
5′-GCCGATCCACACGGAGTACT Supplementary Table 2. Overview of modulation of key proteins involved in intracellular cholesterol trafficking in the
brain (1). Astrocyte (GFAP+) cholesterol (PFO+) colocalization (n-fold)
Organelle marker
Control
AD
DS
Tom20 (mitochondria)
1.00 ±0.257
2.55 ± 0.297; p1=0.0079
2.77 ± 0.203; p1=0.0159
Lampl (lysosome)
1.00 ±0.136
3.43 ± 0.502; p1=0.0079
14.41 ± 1.322; p1,2=0.0079 ementary Table 2. Overview of modulation of key proteins involved in intracellular choleste Overview of modulation of key proteins involved in intracellular cholesterol trafficking in t Supplementary Table 3. Oligonucleotides used for gene expression analysis by RT-qPCR. Gene
Sequence
StARD1
5′-GAGGAGGCCATGCAGAA
5′-GAACACCTTGCCCACATC
StARD3
5′-AGTGAGGAGCCCAGGGAG
5′-CCGTGGCTGACATGGAG
StARD4
5′-CGTTTTCTTAGCAACTCGCC
5′-CTTCCACGTCCTTGCTTCAC
NPC1
5′-CATCCTTTGGCAATGGTTTT
5′-CTGCTGCTACTGTGTCCAGC
β-Actin
5′-TTGCCGACAGGATGCAGAA
5′-GCCGATCCACACGGAGTACT Supplementary Table 3. Oligonucleotides used for gene expression analysis by RT-qPCR. AGING 21 www.aging-us.com Supplementary Table 4. Primary antibodies used in this study. BRISQ checklist Antibody
Source and type
Company
WB dilution
IHC/IF dilution
StARD1
Rabbit monoclonal
Abcam (ab133657)
1:1000
1:200
StARD3 (MLN64)
Rabbit polyclonal
Sant Cruz (sc-292868)
1:1000
SREBP2
Rabbit polyclonal
Abcam (ab28482)
1:500
INSIG-1
Rabbit polyclonal
Abcam (ab70784)
1:1000
NPC-1
Rabbit polyclonal
Abcam (ab36983)
1:500
1:200
Aβ human (6F/3D)
Mouse monoclonal
Dako (M0872)
1:2000
Lamp1
Rabbit polyclonal
Sant Cruz (sc-5570)
1:200
Tom20
Rabbit polyclonal
Sant Cruz (sc-11415)
1:200
GFAP
Rat monoclonal
Calbiochem (345860)
1:200
Glutathione-S-
Transferase
(GST)
Mouse monoclonal
Sant Cruz (sc-374171)
1:200
PHF-tau (AT8)
Mouse monoclonal
Thermofisher (MN1020)
1:200
β-Actin-HRP
Mouse monoclonal
Sigma (A3854)
1:20000
NeuN
Mouse monoclonal
Millipore (MAB377)
1:200
IBA1
Mouse monoclonal
Santa Cruz (sc-32725)
1:200 Supplementary Table 4. Primary antibodies used in this study. AGING 22 www.aging-us.com
|
https://openalex.org/W3163179083
|
https://publicacoes.epagri.sc.gov.br/RAC/article/download/932/1034
|
Portuguese
| null |
Produtividade de frutos e nutrição mineral de pepineiro para conserva submetido a soluções nutritivas em semi-hidroponia
|
Agropecuária Catarinense/Agropecuária catarinense
| 2,021
|
cc-by
| 4,899
|
ARTIGO CIENTÍFICO ARTIGO CIENTÍFICO Index terms: Cucumis sativus; fertigation; phenological phases. níveis múltiplos de uma dose padrão
de nutrientes sobre o acúmulo e a dis-
tribuição da matéria seca da planta de
pepino tipo conserva, híbrido Crispina,
cultivado em substrato sob abrigo. Estes
autores observaram efeito significativo
sobre o acúmulo de matéria seca dos
órgãos da parte aérea da planta. Entre-
tanto, relatam que o efeito das doses
sobre o crescimento da planta e dos fru-
tos mostrou tendência linear, sem indi-
car saturação, sugerindo a necessidade
de realização de novos experimentos
com níveis mais elevados de fertilizan-
tes para determinar o rendimento po-
tencial de frutos do híbrido testado. a campo em até 168,5%, dependendo
da época de cultivo (VIEIRA NETO et al.,
2018). Apesar deste benefício, é neces-
sário agregar outras práticas culturais
a fim de potencializar a rentabilidade
e reduzir custos de produção de pepi-
neiro cultivado sob abrigo. Dentre elas,
destaca-se a utilização de solução nutri-
tiva específica para a cultura cultivada
em substrato fertirrigado, levando-se
em consideração as diferentes fases fe-
nológicas, taxas de crescimento e absor-
ção de nutrientes. Recebido em 23/6/2020. Aceito para publicação em 23/12/2020.
¹ Engenheiro-agrônomo, Dr., Epagri/Estação Experimental de Ituporanga, C.P. 121, 88400-000 Ituporanga, SC, fone: (47) 3533-8844, e-mail: joaoneto@epagri.sc.gov.br.
² Engenheiro-agrônomo, Dr., Epagri/Estação Experimental de Itajaí, C.P. 277, 88301-970 Itajaí, SC, fone: (48) 3233-5244, e-mail: rafael.epagri@gmail.com.
³ Químico, MSc., Epagri/Estação Experimental de Ituporanga, C.P. 121, 88400-000 Ituporanga, SC, fone: (47) 3533-8844, e-mail: cmora@epagri.sc.gov.br. Termos de indexação: Cucumis sativus; fertirrigação; fases fenológicas. Termos de indexação: Cucumis sativus; fertirrigação; fases fenológicas. Fruit yield and mineral nutrition of pickling cucumber subjected to nutrient solutions in semi-hydroponics Abstract – The present work was carried out with the objective of evaluating concentrations of the nutrient solution on the
productivity and quality of pickling cucumber fruits under protected cultivation. Two experiments were conducted at Estação
Experimental de Ituporanga (Epagri/EEItu), SC, in 2019 and 2020 with the hybrid Kybria F1. The experimental design was a
randomized block with six replications, with treatments: 80, 90, 100, 110 and 120% of the fertilizer quantities recommended
by research, following the distribution table indicated by the industry for each stage of development. There was a significant
effect of the different concentrations of nutrient solutions evaluated on the yield of cucumber. The treatments that provided
the highest productive performance, using the management indicated by the industry, were 90% of the standard solution and
100% standard solution. Index terms: Cucumis sativus; fertigation; phenological phases. Produtividade de frutos e nutrição mineral de pepineiro para
conserva submetido a soluções nutritivas em semi-hidroponia João Vieira Neto¹, Rafael Gustavo Ferreira Morales² e Cristiano Mora³ Resumo – O presente trabalho foi realizado com objetivo de avaliar concentrações da solução nutritiva sobre a produtividade
e qualidade de frutos de pepineiro para conserva, sob ambiente protegido. Dois experimentos foram conduzidos na Estação
Experimental de Ituporanga (Epagri/EEItu), em SC, nos anos de 2019 e 2020, com o híbrido Kybria F1. O delineamento
experimental foi o de blocos casualizados com seis repetições, sendo os tratamentos: 80, 90, 100, 110 e 120% das quantidades
de fertilizantes recomendadas pela pesquisa, seguindo tabela de distribuição indicada pela indústria para cada estágio de
desenvolvimento. Houve efeito significativo das concentrações de soluções nutritivas avaliadas sobre a produtividade do
pepineiro. Os tratamentos que proporcionaram maior desempenho produtivo, utilizando o manejo indicado pela indústria,
foram 90% da solução padrão e solução padrão 100%. Material e métodos Durante o experimento foram medi-
dos semanalmente, por meio de peagâ-
metro e condutivímetro, o pH e a condu-
tividade elétrica das soluções nutritivas
de cada tratamento (solução aplicada
e drenada) para verificar a adequação
desses parâmetros em cada fase da cul-
tura. O volume de solução nutritiva foi
aplicado para possibilitar uma fração de
drenagem da ordem de 20 a 30%.i As mudas foram produzidas em ban-
dejas de isopor com 72 células e trans-
plantadas para os vasos nos dias 2 de
outubro de 2019 e 13 de janeiro 2020,
no estádio de duas folhas definitivas. Os vasos foram arranjados sobre plata-
forma de madeira com 2,5cm de espes-
sura, 25cm de largura a 15cm de altura
do chão, para evitar contato direto com
o chão do abrigo, no espaçamento de
0,4m x 1,0m. As plantas foram condu-
zidas verticalmente, com ajuda de fiti-
lhos plásticos. Foi utilizado o substrato
comercial (MaxFértil®) para a produção
de mudas e para o cultivo das plantas
nos vasos, nos dois anos de avaliação,
sendo utilizado substrato novo em cada
ensaio. Este substrato possui abundân-
cia na região de estudo, composto por Dois experimentos foram conduzi-
dos na Epagri, Estação Experimental de
Ituporanga, SC (27°38’ de LS e 49°60’ de
LO e altitude de 475m, clima tipo Cfa,
segundo a classificação de Köeppen) no
segundo semestre de 2019 e primeiro
de 2020. Os estudos foram instalados em es-
tufa com estrutura de aço galvanizado
com pé direito de 4,00m, teto em arco e
abertura zenital. O teto era coberto com
plástico agrícola difusor de luz ANTI-UV
de 150micras. As cortinas laterais so-
mente foram fechadas na ocorrência de
ventos fortes. Amostras foliares foram retiradas
das plantas no início do florescimento
para quantificar valores de nutrientes,
conforme preconizado pela Comissão
de Química e Fertilidade do Solo (CQFS-
RS/SC, 2004). As análises de tecido das
folhas foram realizadas conforme Te-
desco et al. (1995). O delineamento experimental utili-
zado foi o de blocos casualizados, com
cinco tratamentos e seis repetições,
sendo os tratamentos: 80, 90, 100, 110
e 120% das quantidades de fertilizan-
tes recomendadas por Andriolo & Peil
(2016) para pepineiros em substrato. Introdução Para aplicação dos tratamentos fo-
ram consideradas cinco fases fenoló-
gicas, adaptado de Yara (2018), bem
como as proporções de fertilizantes re-
comendadas para cada fase, conforme
descritos na Tabela 1. i As soluções, com as quantidades
de fertilizantes para cada tratamento,
foram aplicadas diariamente nos vasos
usando becker graduado nas quantida-
des: fase inicial (0,5L planta-1), fase ve-
getativa 1 (1,0L planta-1), fase vegetativa
2 (1,5L planta-1), fase vegetativa 3 (2,0L
planta-1), fase floração/produção (2,5L
planta-1). Todas as irrigações foram fei-
tas apenas com soluções nutritivas, uti-
lizando-se água coletada da chuva. Introdução O estado de Santa Catarina é o
maior produtor nacional de pepino para
conserva, produzindo anualmente 15
mil toneladas, equivalendo a cerca de
25% da produção nacional. Uma boa
parte da produção está concentrada na
região do Vale do Itajaí (FÓRUM BRASI-
LEIRO DE PRODUÇÃO DE PEPINO PARA
CONSERVA, 2019). i A produtividade dessa hortaliça
pode alcançar até 80t ha-1 em lavouras
cultivadas em campo aberto (MARTINS,
2004; REBELO et al., 2011). No entan-
to, quando cultivado em ambiente
protegido, tipo estufa, estima-se que a
produtividade obtida em abrigo tenha
potencial para superar a produtividade Andriolo & Peil (2016) apresentam
uma recomendação de solução nutriti-
va para cultivo de pepineiro em subs-
trato, mas não há uma especificação
quanto ao tipo de pepino, salada, japo-
nês ou conserva. No entanto, Espínola
et al. (2001) avaliaram o efeito de três O cultivo de pepineiro em substrato
vem crescendo na região do Alto Vale
do Itajaí, como alternativa ao cultivo
tradicional realizado no solo. Isso ocor- Este periódico está licenciado conforme Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021 48 vasos centrais considerados como par-
cela útil. uma mistura de casca de pínus compos-
tada e vermiculita. re devido à salinização e à incidência
de doenças no solo, em consequência
do manejo incorreto desse sistema de
produção, sem práticas de conservação
do solo e pelo uso incorreto dos ferti-
lizantes. Normalmente, os substratos
apresentam quantidades de nutrientes
insuficientes para o desenvolvimento
das plantas, sendo necessário o forne-
cimento de nutrientes via fertirrigação
para atender suas necessidades nutri-
cionais. O presente trabalho foi realiza-
do com objetivo de avaliar concentra-
ções da solução nutritiva sobre a pro-
dutividade e a qualidade de frutos de
pepineiro para conserva sob ambiente
protegido. Segundo análise feita pelo Labo-
ratório de Análise de Substratos para
Plantas da Faculdade de Agronomia do
Departamento de Horticultura e Silvi-
cultura da UFRGS, o substrato apresen-
ta as seguintes características químicas,
conforme extrato aquoso 1:5 (v/v): pH
(H2O) = 5,56; CE = 0,55mS cm-1; densida-
de seca = 337,5kg m-3; umidade atual =
43,7%; porosidade total = 79,6%; espa-
ço de aeração = 26,0%; água facilmente
disponível = 16,4%; água tamponante
= 2,8%; água remanescente = 34,2%; e
capacidades de retenção de água a 10
cm = 53,5%, 50cm = 37,1% e 100cm =
30,2%. Resultados e discussão Houve efeito significativo dos trata-
mentos sobre a massa fresca de frutos
comerciais por planta (MFFP) apenas
no experimento de 2019 (Tabela 2). Os
melhores resultados foram obtidos com
os tratamentos 90% e 100%, com mé-
dias de 2,69 e 2,87kg planta-1, respecti-
vamente. Em 2020, foram observados
valores inferiores aos obtidos em 2019
para a MFFP, com valores variando en-
tre 0,55 a 0,65kg planta-1. Os baixos va-
lores para MFFP observados em 2020
foram consequência de um ataque se-
vero de pulgões, associados a sintomas
de viroses. Este ataque reduziu o ciclo
de cultivo e o número de colheitas. Em
2019 foram realizadas 21 colheitas, en-
quanto que em 2020 apenas oito. Santa Maria, estado do Rio Grande do
Sul. ao observado para o mesmo período de
colheita em 2019. Neste mesmo perío-
do as médias de temperatura média e
umidade relativa do ar apresentaram
pouca variação entre os anos avalia-
dos, respectivamente, 2019 (20,11°C;
73,70%) e 2020 (21,82°C; 76,62%). O número de frutos comerciais por
planta (NFP) foi afetada pelos tratamen-
tos nos dois anos de avaliação (Tabela
2). Em 2019, observou-se maior núme-
ro de frutos comerciais por planta para
80% (154,4), 90% (161,6) e 100% (171,4)
e, em 2020, para 80% (34,0), 90% (32,7)
e 100% (33,7). Do mesmo modo que
ocorrido com MFFP em 2020, o NFP foi
afetado pela incidência de pulgões nas
plantas de pepineiro naquele ano. Estudo realizado por Vieira Neto et
al. (2019) em condição experimental
semelhante, na mesma localidade, al-
cançou rendimento de 1,83kg de MFFP
para o híbrido Kybria. Este resultado
equivale a 34,2% a menos na produção
em comparação à média resultante dos
dois melhores tratamentos do presente
trabalho, 90% e 100% (2,78kg planta-1). Por outro lado, Espínola et al. (2001)
obtiveram produtividade próxima a 31t
ha-1, equivalente a 1,55kg planta-1, para
pepino tipo conserva, híbrido Crispina,
cultivado em substrato sob abrigo em Quanto à massa fresca de frutos
comerciais (MFF), em 2019, não houve
diferença entre os diferentes tratamen-
tos, variando entre 16,7 a 17,2g (Tabela
2). Em 2020, houve efeito de tratamen-
tos, sendo que os maiores valores para
MFF foram de 19,4, 19,4, e 19,8g obti-
dos com os tratamentos 100%, 110% A radiação solar pode ter sido o
principal fator climático a ter contribu-
ído para a maior incidência de pulgões
nas plantas em 2020. Material e métodos Means of fresh weight of commercial fruits per plant (MFFP), number of commer-
cial fruits per plant (NFP), fresh weight of commercial fruits (MFF), percentage of commer-
cial fruits (% FC) and percentage of non-commercial fruits ( % FNC), for pickling cucumber
in the different treatments, obtained at the end of the experiments. Ituporanga, SC, Epagri,
2019 and 2020 Foram avaliadas as seguintes variá-
veis: o número de frutos comerciais por
planta, a porcentagem de frutos comer-
ciais e não comerciais (frutos com mais
de 9cm de comprimento, defeituosos e
danificados por pragas), a massa fres-
ca de frutos comerciais (g) e a massa
fresca de frutos comerciais por planta
(kg planta-1). Os dados dessas variáveis
acumulados até a última colheita foram
submetidos à análise de variância pelo
teste F e as médias comparadas pelo
teste de Scott-Knott, a 5% de probabili-
dade, utilizando-se o software livre “R”. Os valores médios de macro e micronu-
trientes foliares encontrados nas amos-
tras foram comparados aos valores de
nutrientes
considerados
adequados
para o pepineiro segundo a CQFS-RS/SC
(2004) pelo teste t de Student a 5% de
probabilidade. Ano/
2019
2020
2019
2020
2019
2020
Tratamentos
MFFP (kg planta-1)
NFP
MFF (g)
80%
2,59 b
0,61 NS
154,4 a
34,0 a
16,8 NS
17,9 b
90%
2,69 a
0,59
161,6 a
32,7 a
16,7
18,3 b
100%
2,87 a
0,65
171,4 a
33,7 a
16,7
19,4 a
110%
2,40 b
0,55
142,1 b
28,1 b
17,1
19,4 a
120%
2,40 b
0,55
139,4 b
27,9 b
17,2
19,8 a
CV%
10,62
14,52
10,39
16,06
8,15
5,67
Ano/
2019
2020
2019
2020
Tratamentos
%FC
%FNC
80%
97,7 NS
98,9 NS
2,3 NS
1,02NS
90%
98,0
99,7
2,0
0,26
100%
97,2
98,7
2,8
1,23
110%
98,1
96,8
1,9
3,13
120%
97,7
96,9
2,3
3,03
CV%
0,96
2,50
38,01
118,35
1 Médias não seguidas da mesma letra minúscula na vertical, dentro da mesma variável, diferem entre si
pelo teste de Scott-Knott a 5% de probabilidade NS: Não significativo pelo teste F a 5% 50
Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021 Material e métodos A solução padrão 100% (em g L-1) foi
composta das seguintes concentra-
ções de fertilizantes: nitrato de cálcio
(0,865), MKP (0,204), sulfato de magné-
sio (0,370), nitrato de potássio (0,425),
acrescido de ConMicros Standard®
(composição em %): B (1,82), Cu EDTA
(1,82), Fe EDTA (7,26), Mn EDTA (1,82),
Mo (0,36), Ni (0,335), Zn EDTA (0,73), na
dose de 0,03g L-1. ii Em 2019 a colheita de pepino teve
início no dia 13/11/2019 e estendeu- Tabela 1. Fase fenológica, intervalo de cada fase, porcentagem do total da mistura de fer-
tilizantes aplicada em cada fase (PMF) e quantidade de solução da mistura de fertilizantes
fornecida por planta a cada dia em cada tratamento por fase fenológica
Table 1. Phenological phase, interval of each phase, percentage of total fertilizer mixture
applied in each phase (PFM) and amount of fertilizer mixture solution supplied per plant
each day in each treatment per phenological phase Tabela 1. Fase fenológica, intervalo de cada fase, porcentagem do total da mistura de fer-
tilizantes aplicada em cada fase (PMF) e quantidade de solução da mistura de fertilizantes
fornecida por planta a cada dia em cada tratamento por fase fenológica
Table 1. Phenological phase, interval of each phase, percentage of total fertilizer mixture ii Mistura de fertilizantes (g L-1)
Fase fenológica
Intervalo
(Dias)
PMF
(%)
80%
90%
100%
110%
120%
Fase inicial
1 a 10
13
0,202
0,228
0,253
0,278
0,304
Vegetativa 1
11 a 20
27
0,405
0,456
0,507
0,557
0,608
Vegetativa 2
21 a 30
76
1,160
1,305
1,450
1,595
1,740
Vegetativa 3
31 a 40
80
1,216
1,369
1,521
1,673
1,825
Floração/
produção
> 41
100
1,525
1,715
1,906
2,097
2,287 Foram utilizados vasos de polieti-
leno com volume de 12 litros cada. As
parcelas experimentais foram compos-
tas por quatro plantas do híbrido Kybria
F1, uma planta por vaso, sendo os dois se até 06/01/2020, totalizando 21 co-
lheitas. Em 2020 foram realizadas oito
colheitas no período de 02/03/2020 a
18/03/2020. As colheitas foram realiza-
das em média a cada dois dias, quando
os frutos apresentavam entre 4 a 9cm
de comprimento, padrão exigido pelas
agroindústrias (REBELO et al., 2011). Table 2. 1 Médias não seguidas da mesma letra minúscula na vertical, dentro da mesma variável, diferem entre si
pelo teste de Scott-Knott a 5% de probabilidade. NS: Não significativo pelo teste F a 5%. Resultados e discussão (2019), com 98,3% dos frutos do cul-
tivar Kybria com padrão comercial. li 1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004). Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t
de Student a 5%. A boa qualidade dos frutos, refletida
na alta porcentagem de frutos comer-
ciais, sugere um bom equilíbrio entre os
nutrientes nas soluções nutritivas utili-
zadas, e que a quantidade de nutrientes
associada ao manejo nutricional ade-
quado são os fatores mais determinan-
tes nas elevações de produtividade do
pepineiro em substrato. i P, K, Ca e Mg das folhas de plantas do
híbrido de pepineiro Magnum F1, gru-
po caipira, cultivadas em substrato de
fibra de coco. Esses autores utilizaram
soluções nutritivas nas concentrações
de 12,5%, 17%, 25%, 50% e 100% da
solução nutritiva sugerida por Furlani et
al. (1999). Os níveis de pH oscilaram entre 5,70
a 6,45 e entre 5,60 a 6,50, respectiva-
mente, para a solução nutritiva aplicada
e drenada nos distintos tratamentos e
fases (Tabela 5). Os níveis observados
de pH, nos experimentos, estão den-
tro dos parâmetros considerados ideais
para solução nutritiva indicada por An- Na Tabela 3 é possível verificar que
os níveis de nutrientes foliares para
macronutrientes, de maneira geral,
não foram influenciados pelos trata-
mentos. Embora apenas P esteja den-
tro dos valores de referência definidos
pela Comissão de Química e Fertilidade
do Solo (CQFS-RS/SC, 2004), os demais
nutrientes, mesmo estando abaixo (N,
K, S) e acima (Ca, Mg), estão próximos
aos valores dos limites de intervalos de
normalidade para a cultura. Tabela 4. Valores médios de micronutrientes e semi-amplitude do intervalo de confiança
para a média, nas folhas de pepineiro em mg kg-1. Ituporanga, SC, Epagri, 2019 e 2020
Table 4. Means values of micronutrients and semi-amplitude of the confidence interval for
the mean, in cucumber leaves in mg/kg. Ituporanga, SC, Epagri, 2019 and 2020 Tratamento
B (mg kg-1)
Cu (mg kg-1) Fe (mg kg-1) Mn (mg kg-1) Zn (mg kg-1)
80%
66,5 NA
(7,4)
12,3 NA
(2,80)
408,1 NA
(116,04)
252,0 NA
(48,73)
143,6 Sup. (15,81)
90%
78,7 NA
(8,97)
12,3 NA
(2,53)
528,7 Sup. (42,54)
267,4 NA
(48,24)
129,4 Sup. (22,84)
100%
75,6 NA
(12,31)
11,8 NA
(2,58)
737,6 Sup. (216,68)
291,9 NA
(59,68)
116,0 NA
(27,87)
110%
70,0 NA
(12,22)
14,9 NA
(3,76)
710,0 Sup. (175,30)
337,4 Sup. Resultados e discussão Durante o período
de colheita de 2020, com duração de 16
dias, a soma de radiação média diária
foi de 3.724W/m2, valor 10,81% inferior 50 Tabela 3. Valores médios de macronutrientes e semiamplitude do intervalo de confiança
para a média, nas folhas de pepineiro em %. Ituporanga, SC, Epagri, 2019 e 2020
Table 3. Mean values of macronutrients and semiamplitude of the confidence interval for
the mean, in cucumber leaves in %. Ituporanga, SC, Epagri, 2019 and 2020
Tratamento
N%
P%
K%
Ca%
Mg%
S%
80%
3,2 Inf. (0,68)
0,9 NA
(0,16)
2,5 Inf. (0,46)
6,5 Sup. (1,35)
2,4 Sup. (0,33)
0,3 Inf. (0,03)
90%
3,0 Inf. (0,56)
0,9 NA
(0,14)
2,6 Inf. (0,43)
6,7 Sup. (0,31)
2,4 Sup. (0,29)
0,2 Inf. (0,06)
100%
2,3 Inf. (1,07)
0,9 NA
(0,22)
2,4 Inf. (0,37)
7,1 Sup. (1,28)
2,5 Sup. (0,50)
0,2 Inf. (0,03)
110%
3,7 Inf. (0,48)
1,0 NA
(0,17)
2,7 Inf. (0,75)
7,3 Sup. (0,96)
2,4 Sup. (0,22)
0,2 Inf. (0,08)
120%
3,6 Inf. (0,58)
0,9 NA
(0,13)
2,4 Inf. (0,49)
7,1 Sup. (0,83)
2,5 Sup. (0,32)
0,2 Inf. (0,06)
Referência 1
4,5-6,0
0,3-1,2
3,5-5,0
1,5-3,5
0,3-1,0
0,4-0,7
1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004). Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t
de Student a 5%. Tabela 3. Valores médios de macronutrientes e semiamplitude do intervalo de confiança
para a média, nas folhas de pepineiro em %. Ituporanga, SC, Epagri, 2019 e 2020
Table 3. Mean values of macronutrients and semiamplitude of the confidence interval for
the mean, in cucumber leaves in %. Ituporanga, SC, Epagri, 2019 and 2020 e 120%, respectivamente. Estes resul-
tados são compatíveis aos valores nor-
malmente encontrados em trabalhos
feitos com pepino tipo conserva, devido
à existência de um padrão de colheita
previamente estabelecido pela agroin-
dústria para frutos destinados ao en-
vasamento. Ou seja, os resultados en-
contrados por Vieira Neto et al. (2018)
e Vieira Neto et al. (2019) situam entre
18,53 a 21,52g. As porcentagens de frutos comer-
ciais e de frutos não comerciais não
foram influenciadas pelos tratamentos
nos dois anos de avaliação (Tabela 2). O rendimento médio de frutos comer-
cializáveis dos cinco tratamentos foi de
97,7% e 98,2% para 2019 e 2020, res-
pectivamente. Resultado bem próximo
a este foi encontrado por Vieira Neto et
al. 1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004).
Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t
de Student a 5%. Resultados e discussão (63,69)
133,9 Sup. (30,21)
120%
83,0 NA
(12,52)
14,4 NA
(3,68)
644,6 Sup. (138,31)
328,7 NA
(82,94)
116,2 NA
(21,03)
Referência 1
50-120
7-20
50-300
50-250
25-100
1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004). Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t
de Student a 5%. Tratamento
B (mg kg-1)
Cu (mg kg-1) Fe (mg kg-1) Mn (mg kg-1) Zn (mg kg-1) Tratamento
B (mg kg-1)
Cu (mg kg-1) Fe (mg kg-1) Mn (mg kg-1) Zn (mg kg-1) Quanto aos micronutrientes (Tabela
4), os níveis foliares amostrais apresen-
taram-se adequados para B e Cu, para
todos os tratamentos, e para Fe (80%),
para Mn ((80%, 90%, 100% e 120%) e Zn
(100% e 120%). Assim como observado
para macronutrientes, esse resultado
sugere uma falta de relação entre as
concentrações de nutrientes dos dife-
rentes tratamentos com os níveis dos
elementos nas folhas. No entanto, Diniz
et al. (2015) verificaram que a aplicação
de diferentes proporções de nutrientes
na solução nutritiva exerceu efeitos sig-
nificativos sobre os teores foliares de N, 1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004). Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t
de Student a 5%. 51
Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021 51 driolo & Peil, (2016), que é de 5,5 e 6,5. i co fases fenológicas proposta por Yara
(2018), pode ter contribuído para a ma-
nutenção dos valores de CE um pouco
mais próximos aos valores de referência
propostos pelo referido autor, para cada
fase de desenvolvimento das plantas de
pepineiro, a saber: fase 1 (0,33mS cm-1),
vegetativa 1 (0,64mS cm-1), vegetativa 2
(1,03mS cm-1), vegetativa 3 (0,88mS cm-
1) e floração/produção (0,88mS cm-1).i O manejo da solução nutritiva indi-
cado pela indústria, considerando cinco
fases fenológicas, bem como as propor-
ções de fertilizantes recomendadas para
cada fase, pode servir como referência
para produção de pepino para conserva
em cultivo semi-hidropônico. driolo & Peil, (2016), que é de 5,5 e 6,5. Quanto à condutividade elétrica (CE)
(Tabela 5), para os tratamentos 110% e
120%, com maiores concentrações e fer-
tilizantes na solução aplicada, os valores
oscilaram, respectivamente, entre 0,94
a 2,37mS cm-1 e 0,98 a 2,67mS cm-1 da
fase inicial à fase de produção/floração. Referências ANDRIOLO, J.L.; PEIL, R.M.N. Sistemas espe-
ciais de produção. In: Leandro Souza da Sil-
va; Luciano Colpo Gatiboni. (Org.). Manual
de Adubação e Calagem para os estados do
Rio Grande do Sul e Santa Catarina. 11ed. Porto Alegre: Comissão de Química e Ferti-
lidade do Solo- RS/SC, 2016, v., p. 287-293. ANDRIOLO, J.L.; PEIL, R.M.N. Sistemas espe-
ciais de produção. In: Leandro Souza da Sil-
va; Luciano Colpo Gatiboni. (Org.). Manual
de Adubação e Calagem para os estados do
Rio Grande do Sul e Santa Catarina. 11ed. Porto Alegre: Comissão de Química e Ferti-
lidade do Solo- RS/SC, 2016, v., p. 287-293. Agradecimentos Desta forma, as soluções nutritivas
representadas pelos tratamentos 90% e
100%, utilizando o manejo adotado no
presente trabalho para a elaboração das
soluções nutritivas ao longo do ciclo de
cultivo, são indicadas no manejo do pe-
pineiro fertirrigado por terem propor-
cionado maior produtividade. Aos colaboradores técnico agrícola
David Junior Rodrigues e assistente de
campo Marcelo Andrade, da Epagri, Es-
tação Experimental de Ituporanga, SC. Resultados e discussão Os maiores valores de CE, observados
principalmente na fase de produção/
floração, acima do parâmetro de refe-
rência indicado para solução nutritiva
em cultivo de pepineiro, ou seja, 1,8mS
cm-1 (ANDRIOLO & PEIL, 2016), podem
ter contribuído com o menor número
de frutos por planta, refletindo numa
menor produção. Pois, conforme obser-
vado por Diniz et al. (2015), o pepino
absorve e utiliza grande quantidade de
nutrientes, mas é muito sensível ao ex-
cesso de fertilizantes na solução do solo. Para os tratamentos 90% (1,95mS cm-1)
e 100% (2,12mS cm-1) os valores da CE
situaram-se mais próximos do valor de
referência, com ganhos de produção. Conclusões Porto Alegre,
RS: SBCS/Núcleo Regional Sul; Comissão de
Química e Fertilidade do Solo – RS/SC, 2004. 400p. TEDESCO, M.J.; GIANELLO, C.; BISSANI, C.A.;
BOHNEN, H. Análise de solo, plantas e ou-
tros materiais. 2.ed. Porto Alegre: UFRGS,
1995. (Boletim Técnico, 5). DINIZ, A. A.; DIAS, N. da S.; SOUZA, F. I. de
S.; SOUZA, A. C. M.; MESQUITA, F. de O.;
SOUZA, F. I. de. Efeito da solução nutritiva
sob o crescimento e composição mineral
em pepino cultivado em substrato de fibra
de coco. Semina: Ciências Agrárias (Onli-
ne), v. 36, p. 3043-3054, 2015. Disponível
em: https://www.researchgate.net/publica-
tion/283686114_Efeito_da_solucao_nutriti-
va_sob_o_crescimento_e_composicao_mi-
neral_em_pepino_cultivado_em_substra-
to_de_fibra_de_coco. Acesso em: 25 maio
2020. VIEIRA NETO, J.; GONÇALVES, P.A. de S.;
MENEZES JÚNIOR, F.O.G. de. Produtividade
de cultivares de pepino para conserva em
diferentes épocas de plantio sob ambiente
protegido. Revista Thema, v. 15, p. 93-101,
2018. Disponível em: http://periodicos.ifsul. edu.br/index.php/thema/article/view/809. Acesso em: 05 maio 2020. FURLANI, P. R.; BOLONHEZI, D.; SILVEIRA, L. C. P.; FAQUIN, V. Nutrição mineral de horta-
liças, preparo e manejo de soluções nutriti-
vas. Informe Agropecuário: Cultivo protegi-
do de hortaliças em solo e hidroponia, v. 20,
n. 200/201, p. 90-98, 1999. VIEIRA NETO, J.; MENEZES JÚNIOR, F.O.G. de; GONÇALVES, P.A. de S. Avaliação da pro-
dução de cultivares de pepino para conser-
va e de mini tomate com e sem aplicação
de fertilizante foliar. Revista Thema, v.16,
p.855-864, 2019. Disponível em: http://pe-
riodicos.ifsul.edu.br/index.php/thema/ar-
ticle/view/1473. Acesso em: 05 maio 2020. VIEIRA NETO, J.; MENEZES JÚNIOR, F.O.G. de; GONÇALVES, P.A. de S. Avaliação da pro-
dução de cultivares de pepino para conser-
va e de mini tomate com e sem aplicação
de fertilizante foliar. Revista Thema, v.16,
p.855-864, 2019. Disponível em: http://pe-
riodicos.ifsul.edu.br/index.php/thema/ar-
ticle/view/1473. Acesso em: 05 maio 2020. MARTINS, C.N. Pepino: produção triplicada. Revista Cultivar Hortaliças e Frutas, Pelotas,
2004. Disponível em: http://www.grupocul-
tivar.com.br/arquivos/hf24_producao.pdf. Acesso em: 19 abr. 2020. ESPÍNOLA, H.N.R.; ANDRIOLO, J.L.; BARTZ,
H.R. Acúmulo e repartição da matéria seca
da planta de pepino tipo conserva sob três
doses de nutrientes minerais. Ciência Ru-
ral, Santa Maria, RS, v. 31, n.3, p. 387-392,
2001. Disponível em: https://www.scielo.br/
pdf/cr/v31n3/a04v31n3.pdf. Acesso em: 11
maio 2020. ESPÍNOLA, H.N.R.; ANDRIOLO, J.L.; BARTZ,
H.R. Acúmulo e repartição da matéria seca
da planta de pepino tipo conserva sob três
doses de nutrientes minerais. Ciência Ru-
ral, Santa Maria, RS, v. 31, n.3, p. 387-392,
2001. Disponível em: https://www.scielo.br/
pdf/cr/v31n3/a04v31n3.pdf. Acesso em: 11
maio 2020. Conclusões O melhor desempenho de produção
de pepineiro para conserva, em semi-
hidroponia, foi obtido por soluções nu-
tritivas com 90% e 100% das quantida-
des de fertilizantes recomendadas pela
pesquisa. A estratégia de fornecer as soluções
nutritivas em diferentes concentrações
de fertilizantes, considerando as cin- CQFS-RS/SC. Manual de calagem e aduba-
ção para os estados do Rio Grande do Sul Tabela 5. Médias de duas safras 2019/20 do potencial hidrogeniônico (pH) e condutividade elétrica (CE, mS cm-1) da solução nutritiva apli-
cada e da solução drenada do substrato. Ituporanga, SC, Epagri, 2019 e 2020
Table 5. Means of two harvests 2019/20 of hydrogen potential (pH) and electrical conductivity (EC, mS cm-1) of the applied nutrient solu-
tion and the solution drained from the substrate. Ituporanga, SC, Epagri, 2019 and 2020 52
Tabela 5. Médias de duas safras 2019/20 do potencial hidrogeniônico (pH) e condutividade elétrica (CE, mS cm-1) da solução nutritiva apli-
cada e da solução drenada do substrato. Ituporanga, SC, Epagri, 2019 e 2020
Table 5. Means of two harvests 2019/20 of hydrogen potential (pH) and electrical conductivity (EC, mS cm-1) of the applied nutrient solu-
tion and the solution drained from the substrate. Ituporanga, SC, Epagri, 2019 and 2020
Solução aplicada
80%
90%
100%
110%
120%
Fase fenológica
pH
CE
pH
CE
pH
CE
pH
CE
pH
CE
Fase 1 (inicial)
6,40
0,64
6,43
0,74
6,37
0,80
6,33
0,94
6,20
0,98
Vegetativa 1
6,45
0,69
6,40
0,76
6,30
0,80
6,30
0,98
6,25
1,01
Vegetativa 2
6,28
0,73
6,43
0,78
6,35
0,83
6,25
1,03
6,20
1,03
Vegetativa 3
5,90
1,21
5,90
1,39
5,73
1,95
5,73
2,32
5,70
2,50
Floração/produção
6,08
1,21
5,95
1,95
5,96
2,12
5,85
2,37
5,81
2,67
Solução drenada
Fase fenológica
pH
CE
pH
CE
pH
CE
pH
CE
pH
CE
Fase 1 (inicial)
6,37
0,43
6,27
0,66
6,03
0,68
5,83
0,89
5,70
0,92
Vegetativa 1
6,50
0,47
5,90
0,68
5,95
0,70
5,75
0,92
5,60
0,95
Vegetativa 2
6,20
0,59
5,90
0,69
6,20
0,70
5,70
0,92
5,60
0,91
Vegetativa 3
6,10
0,66
6,10
0,84
5,77
1,50
5,80
2,07
5,63
2,23
Floração/produção
6,31
0,72
5,91
0,91
5,81
1,80
5,82
2,18
5,60
2,46
Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021 52 FÓRUM BRASILEIRO DE PRODUÇÃO DE PE-
PINO PARA CONSERVA, 2. 2019, Indaial. Pro-
dução sustentável com alta tecnologia. Dis-
ponível em: http://forumbrasilpepinocon-
serva.com.br/como-proteger-a-producao-
de-pepinos-de-pragas-ou-doencas/. Acesso
em: 21 maio 2020. e de Santa Catarina. 10.ed. Conclusões REBELO, J.A.; SCHALLENBERGER, E.; CANTÚ,
RR. Cultivo do pepineiro para picles no Vale
do Rio Itajaí e Litoral Catarinense. Florianó-
polis: Epagri, 2011. 55p. (Boletim Técnico,
154). YARA. Yara GranHorti: Programa nutricional
para pepino – fetirrigação. [2018]. 40p. 53
Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021
|
https://openalex.org/W4313397182
|
https://publishup.uni-potsdam.de/files/57863/pmnr1305.pdf
|
English
| null |
Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species
|
Scientific reports
| 2,022
|
cc-by
| 14,320
|
Katrin Kiemel | Marie Gurke | Sofia Paraskevopoulou | Katja Havenstein
| Guntram Weithoff | Ralph Tiedemann
Variation in heat shock protein 40 kDa
relates to divergence in thermotolerance
among cryptic rotifer species
Suggested citation referring to the original publication:
Scientific Reports 12 (2022), Art. 22626
DOI https://doi.org/10.1038/s41598-022-27137-3
ISSN 2045-2322
Journal article | Version of record
Secondary publication archived on the Publication Server of the University of Potsdam:
Zweitveröffentlichungen der Universität Potsdam :
Mathematisch-Naturwissenschaftliche Reihe 1305
ISSN: 1866-8372
https://nbn-resolving.org/urn:nbn:de:kobv:517-opus4-578635
DOI: https://doi.org/10.25932/publishup-57863
Terms of use:
This work is licensed under a Creative Commons License. This does not apply to quoted
content from other authors. To view a copy of this license visit
https://creativecommons.org/licenses/by/4.0/. Katrin Kiemel | Marie Gurke | Sofia Paraskevopoulou | Katja Havenstein
| Guntram Weithoff | Ralph Tiedemann Variation in heat shock protein 40 kDa
relates to divergence in thermotolerance
among cryptic rotifer species Suggested citation referring to the original publication:
Scientific Reports 12 (2022), Art. 22626
DOI https://doi.org/10.1038/s41598-022-27137-3
ISSN 2045-2322 Journal article | Version of record Secondary publication archived on the Publication Server of the University of Potsdam:
Zweitveröffentlichungen der Universität Potsdam :
Mathematisch-Naturwissenschaftliche Reihe 1305
ISSN: 1866-8372
https://nbn-resolving.org/urn:nbn:de:kobv:517-opus4-578635
DOI: https://doi.org/10.25932/publishup-57863 Secondary publication archived on the Publication Server of the University of Potsdam
Zweitveröffentlichungen der Universität Potsdam :
Mathematisch-Naturwissenschaftliche Reihe 1305
ISSN: 1866-8372
https://nbn-resolving.org/urn:nbn:de:kobv:517-opus4-578635
DOI: https://doi.org/10.25932/publishup-57863 Mathematisch-Naturwissenschaftliche Fakultät Mathematisch-Naturwissenschaftliche Fakultät OPEN K. Kiemel
1, M. Gurke
2,3, S. Paraskevopoulou
4, K. Havenstein 1, G. Weithoff
5 &
R. Tiedemann
1* K. Kiemel
1, M. Gurke
2,3, S. Paraskevopoulou
4, K. Havenstein 1, G. Weithoff
5 &
R. Tiedemann
1* Genetic divergence and the frequency of hybridization are central for defining species delimitations,
especially among cryptic species where morphological differences are merely absent. Rotifers are
known for their high cryptic diversity and therefore are ideal model organisms to investigate such
patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate
whether previously observed between species differences in thermotolerance and gene expression are
also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which
exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites,
alleles, and sites putatively under positive selection. These sites are located in protein binding regions
involved in chaperoning and may therefore reflect adaptive diversification. By comparing three
genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable
boundary between the cryptic species. According to the biological species concept1, a species is defined as a group that is reproductively isolated from
other species. Reproductive isolation can be maintained either by pre-zygotic isolation, post-zygotic isolation,
or a combination of both2. Pre-zygotic isolation occurs before a zygote is formed and involves physiological or
systemic barriers that prevent successful mating, such as differences in mating behaviour, habitat preferences
or isolation through ecological or geographical barriers3. Post-zygotic isolation mechanisms, such as increased
zygote mortality or hybrid sterility, occur after zygote formation3. Reproductive isolation mechanisms are how-
ever often imperfect, so that many closely related species such as cryptic species hybridize4–7, which counteracts
species divergence or may even erode species boundaries8. Cryptic species are species that require genetic markers to inform species delimitations9–11. Such genetically
identified species not only call for a revised taxonomy12–14, but also pose a major challenge to evolutionary and
ecological theories. Due to the lack of morphological and physiological differences, high similarity in ecologi-
cal traits and adaptations is expected15. When these species occur in sympatry16–19, the principle of competitive
exclusion20 is compromised, which further challenges the understanding of co-existence and the niche concept. Terms of use: This work is licensed under a Creative Commons License. This does not apply to quoted
content from other authors. To view a copy of this license visit
https://creativecommons.org/licenses/by/4.0/. https://creativecommons.org/licenses/by/4.0/. www.nature.com/scientificreports www.nature.com/scientificreports Scientific Reports | (2022) 12:22626 www.nature.com/scientificreports/ traits32, adaptation and the underlying regulatory mechanisms33–35, as well as on the robustness of species bounda-
ries through hybridisation experiments6,7. These studies are of great importance to understand not only how
these species have diverged, but also which of their adaptations are critical for the co-existence or exclusion of
certain species in a specific environment. p
pi
A previous lifetable experiment36 has demonstrated diverging temperature optima between Brachionus caly-
ciflorus s.s. (heat-tolerant) and Brachionus fernandoi (heat-sensitive). Comparison of transcriptome data from
the heat-tolerant B. calyciflorus s.s. and the heat-sensitive B. fernandoi revealed differential expression of Heat
Shock Protein (HSP) genes relative to temperature35. HSP gene expression levels correlated with life history
traits such that the upregulation of HSP gene expression consistently occurred when the population growth rate
was low. The two species were found to exhibit optimal growth at a different temperature (B. calyciflorus s.s. at
26 °C and B. fernandoi at 20/23 °C) and increased their HSP expression outside their optimal temperature range,
demonstrating a stress response of the organisms when optimal growth was not feasible35. The pronounced fit-
ness differences at different thermal conditions indicate underlying mechanisms of phenotypes’ responses to
environmental conditions that allow them to occur in sympatry, but in different seasons of the year31,35. y
p
yf
y
Temperature as an environmental variable is one of the most important drivers of evolution and
diversification37. Temperature adaptation is particularly interesting in aquatic invertebrates which as ecto-
therms are stronger influenced by temperature changes than homeotherms38. Increased temperature acceler-
ates ontogeny, shortens the time to maturation and the generation time35,39–41. The associated faster population
growth can foster competitive superiority and accelerate the underlying divergent selection that enforces niche
partitioning42–44. An organism’s adaptation to a particular environment or resource availability may occur at the
protein level through the regulation of gene expression45–48. This gene expression regulative mechanism can be
observed in situations of rapid environmental changes (i.e., length of growing seasons) in B. plicatilis s.s.49,50,
or in stress response via HSP upregulation35,51, which is a rapid and often the first response mechanism to
environmental perturbation. However, a differential regulatory response among genotypes/species to the same
environmental cue (genotype x environment (G x E) variation) has to be encoded somewhere in the genome,
typically upstream in gene regulatory elements (e.g., transcription factors, promoters52,53). www.nature.com/scientificreports/ In addition, a diver-
gent adaptation to different environmental conditions may also yield adaptive differences in protein structure,
i.e., altered amino acid sequences. Such changes stem from non-synonymous substitutions in the underlying
protein coding genes (as the HSP genes), such that signatures of selection can occur in specific genes or distrib-
uted over the whole genome54,55. Evolution of gene expression and protein structure do not necessarily occur
independently of each other56,57, and we often find their respective contribution correlating with the progress of
time, i.e., altered gene expression typically evolves more rapidly than altered protein structure53. Furthermore,
discovering signs of selection in gene sequences between different species allows us to understand the genetic
underpinning of the differentiation58,59. When put into perspective with the divergence time, the time frame of
the adaptation/speciation can be unravelled60. In this study, we investigated sequence/protein evolution and divergence in the HSP 40 kDa gene, which was
inferred by a candidate gene selection for temperature adaptation, both by its temperature-related differential
expression35 and by a transcriptome-wide SNP comparison among two species of the B. calyciflorus species
complex, i.e., the heat-tolerant species B. calyciflorus s.s. and the heat-sensitive B. fernandoi. To put HSP40kDa
gene evolution into perspective, this gene was further analysed in three Brachionus species outside of the species
complex. We hypothesise, (I) that the adaptation of B. calyciflorus s.s. and B. fernandoi to different environments
is driven by divergent selection on the structure of particular proteins (here, HSP 40 kDa) and (II) that the
selection for different temperatures can promote niche partitioning, and hence constitute a pre-zygotic isolation
mechanism. OPEN 21 p
g
g
p
Rotifers, with their approximately 2000 described species, belong to a very diverse phylum21, in which an
increasing number of nominal species have been declared cryptic species complexes in the last decades22. Among
them, the monogonont freshwater Brachionus calyciflorus species complex has recently been subdivided into
four species using genetics and morphometrics: Brachionus calyciflorus sensu stricto (s.s.), Brachionus dorcas,
Brachionus fernandoi, and Brachionus elevatus5,23. Prior to its delimitation into four species, the Brachionus caly-
ciflorus species complex had been studied with regard to molecular phylogeny23–25, co-existence26, life history
characteristics27, phylogeography28,29, and reproductive isolation28–30. More recent studies, which have taken
into account the new species classification, focus on ecological processes, e.g., niche differentiation31, life history 1Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of
Potsdam, Karl‑Liebknecht Straße 24‑25, 14476 Potsdam, Germany. 2Museum für Naturkunde – Leibniz Institute
for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany. 3Department of Biology,
Humboldt-University, Invalidenstraße 42, 10115 Berlin, Germany. 4Department of Biology, Lund University,
Microbiology Group, Sölvegatan 35, 223 62 Lund, Sweden. 5Unit of Ecology and Ecosystem Modelling, Institute
for Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany. *email:
tiedeman@uni-potsdam.de | https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 www.nature.com/scientificreports/ Results
C
did Candidate gene selection. To identify candidate genes within the B. calyciflorus species complex we
assembled 72,165 and 94,884 super-transcripts in B. calyciflorus s.s and B. fernandoi transcriptomes, respec-
tively. The reciprocal best blast hit identified 9655 putative orthologs which were reduced to 7976 after predicting
open reading frames, locally aligning, and translating into proteins. In the selection tests, out of 7976 orthologs,
649 were significant (< 0.05) in all four pairwise Likelihood Ratio Test (LRT) comparisons, hence inferred to be
putatively under positive selection. Comparing the orthologous genes under positive selection with the gene
expression data35, 155 genes were differentially expressed relative to temperature (control: 20 °C, mild heat: B. calyciflorus s.s. 26 °C, B. fernandoi 23 °C, high heat: B. calyciflorus s.s. 32 °C, B. fernandoi 26 °C) in at least one of
the two species (125 in B. calyciflorus s.s., 22 in B. fernandoi, and 8 in both species). Twenty-seven of these genes
were assigned to the GO term GO:0006950 (response to stress), of which one gene was annotated to “response
to heat” (GO:00009408). This gene (i.e., HSP 40 kDa) was differentially expressed in B. calyciflorus s.s. in cultures
grown after 4 h of heat exposure to different temperature (20 °C vs. 32 °C and 20 °C vs. 26 °C), while it did not
show a temperature-specific expression in B. fernandoi (Fig. 1). HSP 40 kDa sequence diversity. The sequence diversity of all five Brachionus species (B. calyciflorus
s.s., B. fernandoi, B. rubens, B. angularis, and B. diversicornis) was assessed by comparing HSP 40 kDa and
Cytochrome Oxidase Subunit I (COI) genes. We detected an overall higher nucleotide divergence in the mito-
chondrial COI compared to the HSP 40 kDa gene fragment (Fig. 2). For the HSP 40 kDa sequences, the lowest
nucleotide divergence was detected between B. angularis and B. diversicornis (0.103), followed by B. calyciflorus
s.s. and B. fernandoi (0.121). The highest nucleotide divergence was found between B. fernandoi and B. rubens
(0.198). For the COI fragment, the highest nucleotide divergence was detected between B. calyciflorus s.s. and B. diversicornis (0.243), while the lowest was between B. calyciflorus s.s. and B. fernandoi (0.154). Results
C
did The cross-species https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ response to heat
response to cold
response to topologically incorrect protein
response to starvation
regulation of response to stress
response to hypoxia
defense response
cellular response to stress
0
5
10
15
20
Number of genes assigned to GO terms
20°C vs. 32°C
20°C vs. 26°C
26°C vs. 32°C
20°C vs. 26°C
20°C vs. 23°C
23°C vs. 26°C
0.0
1.0
2.0
3.0
4.0
B. fernandoi
B. calyciflorus s.s. d
e
s
s
e
r
p
x
e
yllait
n
e
r
e
ffid
s
e
n
e
g
f
o
r
e
b
m
u
N
n
oit
pir
c
s
e
d
m
r
e
t
O
G
Figure 1. Annotation and differential expression of genes inferred to be under positive selection. Bar plot
shows the genes which were assigned to the term GO:0006950 (response to stress). Bars represent the number
genes assigned to one of the child terms of GO:0006950. More than one GO term can be assigned to the
same gene. The heatmap shows the number of genes differentially expressed in each GO term category in B. calyciflorus s.s. and B. fernandoi under different temperatures regimes35. response to heat
response to cold
response to topologically incorrect protein
response to starvation
regulation of response to stress
response to hypoxia
defense response
cellular response to stress
0
5
10
15
20
Number of genes assigned to GO terms
n
oit
pir
c
s
e
d
m
r
e
t
O
G Number of genes assigned to GO terms Figure 1. Annotation and differential expression of genes inferred to be under positive selection. Bar plot
shows the genes which were assigned to the term GO:0006950 (response to stress). Bars represent the number
genes assigned to one of the child terms of GO:0006950. More than one GO term can be assigned to the
same gene. The heatmap shows the number of genes differentially expressed in each GO term category in B. calyciflorus s.s. and B. fernandoi under different temperatures regimes35. Figure 2. Nucleotide divergence of nuclear and mitochondrial genes. Nucleotide divergence of the nuclear
HSP 40 kDa (orange) and the mitochondrial Cytochrome Oxidase Subunit I (COI) (grey) genes, based on
comparisons of B. calyciflorus s.s., B. fernandoi, B. rubens, B. angularis, and B. diversicornis. The colour intensity
indicates increasing nucleotide divergence between the compared sequences. Figure 2. Results
C
did Nucleotide divergence of nuclear and mitochondrial genes. Nucleotide divergence of the nuclear
HSP 40 kDa (orange) and the mitochondrial Cytochrome Oxidase Subunit I (COI) (grey) genes, based on
comparisons of B. calyciflorus s.s., B. fernandoi, B. rubens, B. angularis, and B. diversicornis. The colour intensity
indicates increasing nucleotide divergence between the compared sequences. comparison of non-synonymous (dN) vs. synonymous (dS) substitutions in the HSP 40 kDa gene yielded an
overall dN/dS: 0.049, with the the highest dN/dS ratio between B. angularis and B. diversicornis (0.085), while
the lowest one was found between B. calyciflorus s.s. and B. diversicornis, followed by B. calyciflorus s.s. and B. fernandoi (0.040 and 0.042, respectively) (Supplementary Fig. s4). Structural variation in HSP 40 kDA between B. calyciflorus s.s. and B. fernandoi. We produced
88 genomic HSP 40kDA gene sequences for our two focus species (B. calyciflorus s.s., n = 50; B. fernandoi, n = 38)
by polymerase chain reaction (PCR). The network approach based on all 88 phased sequences identified 32
unique HSP 40 kDa alleles (corresponding to 27 unique protein sequences) from which 13 alleles were exclu-
sively found in B. fernandoi specimens and 19 alleles were solely found in B. calyciflorus s.s. specimens (Fig. 3). https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ A1
A2
A3
A4
A5
A6
A7
A8
A9
A10
A11
A12
A13
A14
A15
A16
A17
A18
A19
A20
A21
A22
A23
A24
5
2
A
A26
A27
A28
A29
A30
A31
A32
B. fernandoi
Germany
B. calyciflorus s.s. Results
C
did Labels A1-A32 stand for the
identified alleles, red alleles are derived from B. calyciflorus s.s. and blue alleles from B. fernandoi. B. calyciflorus
s.s. alleles found in more than one location are coloured orange. Only one allele, which phylogenetically clustered to the B. calyciflorus s.s. HSP 40 kDa allele type 18 (A18) was
found in a B. fernandoi specimen (2484_4). The translated protein alignment (Supplementary Fig. s5) revealed
51 non-synonymous substitutions, among them the 14 found in the transcriptome data. The highest rate dN of
non-synonymous substitutions per non-synonymous site among the two species was detected in position 256,
followed by position 292 (Fig. 4). Only one allele, which phylogenetically clustered to the B. calyciflorus s.s. HSP 40 kDa allele type 18 (A18) was
found in a B. fernandoi specimen (2484_4). The translated protein alignment (Supplementary Fig. s5) revealed
51 non-synonymous substitutions, among them the 14 found in the transcriptome data. The highest rate dN of
non-synonymous substitutions per non-synonymous site among the two species was detected in position 256,
followed by position 292 (Fig. 4). Congruence among ITS1, HSP 40 kDa, and COI species affinity. The comparison of the nuclear
Internal Transcribed Spacer 1 (ITS1), HSP 40 kDa, and the mitochondrial COI sequences yielded congruent
species assignments for most analysed specimens. However, we identified four descendants of hybridization
events between B. calyciflorus s.s. and B. fernandoi (all originating from the same pond; 2484), all of which carry
the identical maternally inherited B. calyciflorus s.s. COI haplotype, but were assigned to B. fernandoi based on
ITS1 sequences (Fig. 5, Supplementary Figs. s6, s7). Three of these introgressed specimens carried B. fernan-
doi—specific HSP 40 kDa alleles (2484_1, 2484_9, 2484_10), while one individual (2484_4) carried a B. caly-
ciflorus s.s.—specific HSP 40 kDa allele, such that only its ITS1 sequence points towards a B. fernandoi affinity. Of the three introgressed specimens carrying B. fernandoi—specific HSP 40 kDa alleles, two were heterozygous
(2484_1: A11, A1; 2484_10: A12, A2), while one was homozygous for A1 allele (2484_9). The introgressed speci-
men which carried a B. calyciflorus s.s. specific allele was homozygous for A18. Inferences on selection and divergence. The conducted four LRT comparisons (M0 vs. M3, M1a vs. M2a, M7 vs. M8, M8a vs. M8) of the site substitution model in PAML significantly inferred positive selection
in the HSP 40 kDa gene among the five different Brachionus species (Table 1). Results
C
did Germany
Italy
Austria
USA
30%
5
40%
6
50%
7
60%
8
9
70%
10
80%
11
90%
12
100%
13
0
0%
1
20%
2
3
40%
4
60%
5
6
80%
7
100%
8
0
1
2
3
4
0
1
0
1
2
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
0%
1
10%
2
3
20%
4
5
30%
6
7
40%
8
9
10
50%
11
60%
12
13
70%
14
15
80%
16
17
90%
18
19
20
100%
0
0%
10%
1
20%
2
30%
3
40%
4
5
50%
60%
6
70%
7
80%
8
90%
9
10
100%
0
1
0
1
2
0
1
0
1
2
3
4
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0%
0
1
2
3
10%
4
5
6
7
20%
8
9
10
11
30%
12
13
14
15
40%
16
17
18
50%
19
20
21
22
60%
23
24
25
26
70%
27
28
29
30
80%
31
32
33
34
90%
35
36
37
100%
38
0
0%
1
2
10%
3
4
20%
5
6
30%
7
8
9
40%
10
11
50%
12
13
60%
14
15
16
70%
17
18
80%
19
20
90%
21
22
100%
23
0
0%
20%
1
40%
2
60%
3
80%
4
5
100%
0
0%
1
20%
2
3
40%
4
5
60%
6
7
80%
8
100%
9
0
0%
1
10%
2
20%
3
30%
4
40%
5
50%
6
7
60%
8
70%
9
80%
10
90%
11
100%
12
Figure 3. HSP 40 kDa allele identification. Circos plot of allele distribution among species B. calyciflorus s.s. and B. fernandoi and country of sample origin (Germany, Italy, Austria, USA). Labels A1-A32 stand for the
identified alleles, red alleles are derived from B. calyciflorus s.s. and blue alleles from B. fernandoi. B. calyciflorus
s.s. alleles found in more than one location are coloured orange. A21
A22
A23
A24
5
2
A
A26
A27
A28
A29
A30 Figure 3. HSP 40 kDa allele identification. Circos plot of allele distribution among species B. calyciflorus s.s. and B. fernandoi and country of sample origin (Germany, Italy, Austria, USA). Results
C
did The Bayes Empirical Bayes (BEB)
analysis detected six sites under selection (Table 1). Visual inspection of these positively selected sites in the
protein alignment (Supplementary Fig. s5) showed a species-specific protein variant pattern at one of these sites
(292), while variants were shared at the other sites, but differed in their relative frequencies among the species. The comparison of the positively selected sites with the functional domain description of the HSP 40kDa61
revealed that four out of the six sites are located in functional domains (J-domain and C-terminal domain; Sup-
plementary Fig. s5). The branch site model, which was conducted to identify selection and sites under selection https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ om/scientificreports/
50
100
150
200
250
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1.6
1.8
2.0
2.2
Site
dN
Figure 4. Number of non-synonymous substitutions per non-synonymous site among B. calyciflorus s.s. and B. fernandoi HSP 40 kDa for each amino acid alignment position of the 32 different HSP 40 kDa alleles. 50
100
150
200
250
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1.6
1.8
2.0
2.2
Site
dN
Figure 4. Number of non-synonymous substitutions per non-synonymous site among B. calyciflorus s.s. and B. fernandoi HSP 40 kDa for each amino acid alignment position of the 32 different HSP 40 kDa alleles. Figure 4. Number of non-synonymous substitutions per non-synonymous site among B. calyciflorus s.s. and B. fernandoi HSP 40 kDa for each amino acid alignment position of the 32 different HSP 40 kDa alleles. 5
Scientific Reports | (2022) 12:22626 |
https://doi.org/10.1038/s41598-022-27137-3
Figure 5. Relationship between HSP 40 kDa and COI. Tanglegram based on the nuclear HSP 40 kDa and the
mitochondrial COI of species (B. calyciflorus s.s., B. fernandoi, B. rubens, B. angularis, B. diversicornis) (n = 41). Black lines indicate connections of specimens outside of the Brachionus calyciflorus species complex, blue lines
indicate connections between specimens of B. fernandoi and red lines connect specimens of B. calyciflorus s.s. Yellow coloured connections indicate specimens originating from an introgression/hybridization event between
B. calyciflorus s.s. and B. fernandoi. They all occurred at the same location and all carried a B. fernandoi ITS
sequence. Figure 5. Relationship between HSP 40 kDa and COI. Tanglegram based on the nuclear HSP 40 kDa and the
mitochondrial COI of species (B. calyciflorus s.s., B. fernandoi, B. rubens, B. angularis, B. diversicornis) (n = 41). Results
C
did Likelihood ratio tests of seven different site models performed on 296 amino acids (888 bp) of the
HSP 40 kDa, including 29 of the 32 unique alleles (A11, A12 and A18 were excluded from the analysis, as they
only occurred in specimens affected by hybridization/introgression). Underlying phylogeny is based on the
ITS1 (532 bp) of B. calyciflorus s.s., B. fernandoi, B. angularis, B. diversicornis and B. rubens. For each likelihood
ratio test (LRT), we provide log likelihood (l) values of the compared tests (2∆l), degrees of freedom (df),
p-values, estimated average ratio of non-synonymous vs. synonymous substitutions (ω), and the sites inferred
to be under positive selection by Bayes Empirical Bayes (BEB) analysis, labeled with an * for a posterior
probability of > 95% and ** for > 99%. Table 1. Likelihood ratio tests of seven different site models performed on 296 amino acids (888 bp) of the
HSP 40 kDa, including 29 of the 32 unique alleles (A11, A12 and A18 were excluded from the analysis, as they
only occurred in specimens affected by hybridization/introgression). Underlying phylogeny is based on the
ITS1 (532 bp) of B. calyciflorus s.s., B. fernandoi, B. angularis, B. diversicornis and B. rubens. For each likelihood
ratio test (LRT), we provide log likelihood (l) values of the compared tests (2∆l), degrees of freedom (df),
p-values, estimated average ratio of non-synonymous vs. synonymous substitutions (ω), and the sites inferred
to be under positive selection by Bayes Empirical Bayes (BEB) analysis, labeled with an * for a posterior
probability of > 95% and ** for > 99%. Branch site model
Branch
2∆l
df
p-value
l
BEBs
Selection
CD
7.398576
1
0.0065
− 3477.294043
–
Neutral
− 3480.993331
Selection
C
0
1
1.0000
− 3480.993266
–
Neutral
− 3480.993266
Selection
D
3.859588
1
0.0495
− 3477.544980
–
Neutral
− 3479.474774 Table 2. Likelihood ratio test of branch site model performed on 296 amino acids (888 bp) of the HSP 40 kDa
including the 29 of the 32 unique alleles (A11, A12 and A18 hybrid alleles are excluded from the analysis) of
B. calyciflorus s.s. and B. fernandoi, B. angularis, B. diversicornis and B. rubens. Phylogeny is based on 532 bp
of the ITS1. For each branch selection test, we provide log likelihood (l) value of the compared tests (2∆l),
degrees of freedom (df), and the p-value. Results
C
did Black lines indicate connections of specimens outside of the Brachionus calyciflorus species complex, blue lines
indicate connections between specimens of B. fernandoi and red lines connect specimens of B. calyciflorus s.s. Yellow coloured connections indicate specimens originating from an introgression/hybridization event between
B. calyciflorus s.s. and B. fernandoi. They all occurred at the same location and all carried a B. fernandoi ITS
sequence. https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ Table 1. Likelihood ratio tests of seven different site models performed on 296 amino acids (888 bp) of the
HSP 40 kDa, including 29 of the 32 unique alleles (A11, A12 and A18 were excluded from the analysis, as they
only occurred in specimens affected by hybridization/introgression). Underlying phylogeny is based on the
ITS1 (532 bp) of B. calyciflorus s.s., B. fernandoi, B. angularis, B. diversicornis and B. rubens. For each likelihood
ratio test (LRT), we provide log likelihood (l) values of the compared tests (2∆l), degrees of freedom (df),
p-values, estimated average ratio of non-synonymous vs. synonymous substitutions (ω), and the sites inferred
to be under positive selection by Bayes Empirical Bayes (BEB) analysis, labeled with an * for a posterior
probability of > 95% and ** for > 99%. Site model
LRT
2∆l
df
p-value
l
ω
BEBs
M0 (one-ratio)
M0 vs. M3
262.398852
4
<< 0.001
− 3598.034542
0.0718
–
M3 (discrete)
− 3466.835116
0.1439
M1a (nearly Neutral)
M1a vs. M2a
11.558380
2
0.003
− 3480.993265
0.1328
–
M2a (positive selection)
− 3475.214075
0.1815
M7 (β)
M7 vs. M8
21.480488
2
<< 0.001
− 3477.904393
0.1108
–
M8 (β & ω)
− 3467.164149
0.1450
M8a (β & ω = 1)
M8a vs. M8
31.89007
1
<< 0.001
− 3483.109184
0.0769
10*; 38*; 249**; 256*; 286*; 292** Site model
LRT
2∆l
df
p-value
l
ω
BEBs
M0 (one-ratio)
M0 vs. M3
262.398852
4
<< 0.001
− 3598.034542
0.0718
–
M3 (discrete)
− 3466.835116
0.1439
M1a (nearly Neutral)
M1a vs. M2a
11.558380
2
0.003
− 3480.993265
0.1328
–
M2a (positive selection)
− 3475.214075
0.1815
M7 (β)
M7 vs. M8
21.480488
2
<< 0.001
− 3477.904393
0.1108
–
M8 (β & ω)
− 3467.164149
0.1450
M8a (β & ω = 1)
M8a vs. M8
31.89007
1
<< 0.001
− 3483.109184
0.0769
10*; 38*; 249**; 256*; 286*; 292** Table 1. Results
C
did No sites were inferred to be under positive selection by BEB in this
test framework. Branch site model
Branch
2∆l
df
p-value
l
BEBs
Selection
CD
7.398576
1
0.0065
− 3477.294043
–
Neutral
− 3480.993331
Selection
C
0
1
1.0000
− 3480.993266
–
Neutral
− 3480.993266
Selection
D
3.859588
1
0.0495
− 3477.544980
–
Neutral
− 3479.474774 Branch site model
Branch
2∆l
df
p-value
l
BEBs
Selection
CD
7.398576
1
0.0065
− 3477.294043
–
Neutral
− 3480.993331
Selection
C
0
1
1.0000
− 3480.993266
–
Neutral
− 3480.993266
Selection
D
3.859588
1
0.0495
− 3477.544980
–
Neutral
− 3479.474774 Table 2. Likelihood ratio test of branch site model performed on 296 amino acids (888 bp) of the HSP 40 kDa
including the 29 of the 32 unique alleles (A11, A12 and A18 hybrid alleles are excluded from the analysis) of
B. calyciflorus s.s. and B. fernandoi, B. angularis, B. diversicornis and B. rubens. Phylogeny is based on 532 bp
of the ITS1. For each branch selection test, we provide log likelihood (l) value of the compared tests (2∆l),
degrees of freedom (df), and the p-value. No sites were inferred to be under positive selection by BEB in this
test framework. Table 2. Likelihood ratio test of branch site model performed on 296 amino acids (888 bp) of the HSP 40 kDa
including the 29 of the 32 unique alleles (A11, A12 and A18 hybrid alleles are excluded from the analysis) of
B. calyciflorus s.s. and B. fernandoi, B. angularis, B. diversicornis and B. rubens. Phylogeny is based on 532 bp
of the ITS1. For each branch selection test, we provide log likelihood (l) value of the compared tests (2∆l),
degrees of freedom (df), and the p-value. No sites were inferred to be under positive selection by BEB in this
test framework. in specific species was able to identify selection on the CD (B. calyciflorus s.s. & B. fernandoi) and D branch (B. fernandoi), but did not detect any species-specific sites under selection (BEBs) (Table 2). The selection scenario
investigation by comparing only B. calyciflorus s.s. and B. fernandoi using a McDonald-Kreitman Test (MKT),
calculated a significant Neutrality Index of 12.06, p-value: ≤ 0.001 (i.e., indicative for balancing selection or
slightly deleterious mutations), while Tajima’s D (1.538) was not significant (p-value: ≥ 0.10).hiiil in specific species was able to identify selection on the CD (B. calyciflorus s.s. & B. Results
C
did fernandoi) and D branch (B. fernandoi), but did not detect any species-specific sites under selection (BEBs) (Table 2). The selection scenario
investigation by comparing only B. calyciflorus s.s. and B. fernandoi using a McDonald-Kreitman Test (MKT),
calculated a significant Neutrality Index of 12.06, p-value: ≤ 0.001 (i.e., indicative for balancing selection or
slightly deleterious mutations), while Tajima’s D (1.538) was not significant (p-value: ≥ 0.10).hiiil g
y
j
gi
p
The comparison of the fixed species-specific sites revealed 11 fixed sites between B. calyciflorus s.s. and B. fernandoi (Table 3). Out of these 11 fixed sites, 9 amino acid substitutions found in B. fernandoi are considered
benign in our Polyphen2 analysis, while two (site 63 and 66) may change protein function (inferred "possibly
damaging", Table 3). Additionally, among the six positively selected sites, two amino acid substitutions may
influence protein function (inferred "possibly damaging", Table 3). The inference of character polarity (ancestral
vs. derived) showed a prevalence of B. calyciflorus s.s. to retain the ancestral variant (10/17). For position 292,
the status ancestral or derived could not be identified with certainty (Table 3).l i
y (
)
We inferred a divergence time of 25–29 Million years (Myr) between B. calyciflorus s.s. and B. fernandoi,
based on mitochondrial cds, while the split between the freshwater and the marine species of Brachionus was
estimated to be in a range of 41–47 Myr (Supplementary Fig. s8). Discussion
C
did t (Bc), B. fernandoi (Bf), B. rubens (Br), B. angularis (Ba) and B. diversicornis (Bd). Ancestral amino acid
was inferred using the most parsimonious (i.e., fewest substitutions) scenario, taking the species’ phylogeny
into account. In case of multiple amino acids (aa) per species, compared aa are bold in the row Code. Asteriks
indicate sites under selection inferred by codeML. Note that Polyphen2 does not consider the possibility of a
positive effect of an aa substitution, such that it ranks any predicted change in protein function as "damaging". divergent evolution in the HSP 40 kDa. All but one allele, which originated from descendants of a hybrid, were
species-specific. The high number of alleles and expressed structural differences (27 unique protein sequences)
within and between the two species might be related to their cyclical parthenogenesis65. The dominant asexual
mode of reproduction via mitotic eggs from amictic females (i.e., clones) and a less frequent switch to sexual
reproduction together with a short generation time66 strongly reduces genomic recombination, making purify-
ing selection to eliminate slightly deleterious mutations less effective for those organisms, a phenomenon known
as Muller’s ratchet67–69.hil The comparison between all five analysed species revealed that the species from the B. calyciflorus species
complex are more similar (based on nucleotide divergence of the HSP 40 kDa and COI species-wise consensus
sequences) to one another than to representatives from outside that species complex (B. rubens, B. angularis
and B. diversicornis), with an overall higher nucleotide diversity in the COI. The higher diversity in the mito-
chondrial COI compared to nuclear HSP 40 kDa gene was expected as mitochondrial DNA in general exhibits
a higher mutation rate than nuclear genes70, a phenomenon observed as well in rotifers71. While HSP 40 kDa
gene divergence among Brachionus species generally resembled their phylogenetic affinity, the dN/dS ratio is the
smallest, when comparing the not directly related species B. diversicornis and B. calyciflorus s.s. This may have
arisen from similar environmental parameters that lead to similar selection pressures72. Indeed, a recent study
found the occurrence of B. diversicornis to be correlated with warmer water temperatures73, which could indicate
a higher thermotolerance—as observed in B. calyciflorus s.s.35,36—also in this species. Selection scenario of the HSP 40 kDa. Within the HSP 40KDa gene, six amino acid sites were inferred
to be under positive selection. Discussion
C
did t Candidate gene selection pipeline. The utilization of available transcriptomes and different expres-
sion patterns of B. calyciflorus s.s. and B. fernandoi allowed us to identify a candidate gene which likely plays a
role in the differences in temperature adaptation among the two Brachionus species. Indeed, HSPs have been
shown to be involved in the response to various environmental stressors such as thermal stress, toxins, oxida-
tive conditions62–64 and aging61. The importance of HSPs in the process of thermotolerance for invertebrates,
particularly HSP 40 kDa, HSP 60 kDa and HSP 70 kDa, was previously shown51 in the monogonont rotifer B. manjavacas. Genetic variation in the HSP 40 kDa gene among Brachionus species. The analysis of the success-
fully amplified HSP 40 kDa gene of the 44 specimens of the B. calyciflorus cryptic species complex (B. calyciflorus
s.s. and B. fernandoi) from 14 different locations (Europe, North America) revealed 32 unique alleles, indicating https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ Site (aa)
Code
Bc–Bf–Br–Ba–Bd
Ancestral
Score
Sensitivity
Specificity
Prediction
10*
H10V/I
H–V/I–H–R–-R
H
0.002
0.99
0.30
Benign
H10V/I
H–V/I–H–R–R
H
0.004
0.97
0.59
Benign
27
E27G
E–G–E–E–E
E
0.000
1.00
0.00
Benign
30
F30-
F–F–F–F
F
–
–
–
–
31
S31-
S–S–S–S
S
–
–
–
–
38*
E/K38E/K
E/K–E/K–E–E–E
E
0.231
0.91
0.88
Benign
63
L63M
L–M–L–M–L
L
0.953
0.97
0.93
Possibly damaging
66
T66S/F
T–F–T–F–T
T
0.143
0.92
0.86
Benign
T66S/F
T–F–T–F–T
T
0.997
0.41
0.98
Possibly damaging
127
T127A
T–A–T–T–T
T
0.019
0.95
0.80
Benign
175
F175V
F–V–V–F–V
V
0.001
0.99
0.15
Benign
177
Y177N
Y–N–Y–Y–Y
Y
0.000
1.00
0.00
Benign
226
R226K
R–K–R–K–R
R
0.000
1.00
0.00
Benign
242
H242L
H–L–I–H–H
H
0.000
1.00
0.00
Benign
249*
P/S249P
P/S–P–P–Q–Q
E
0.116
0.93
0.86
Benign
256*
L/F/N256L
L/F/N–L–L–L–L
L
0.024
0.95
0.81
Benign
L/F/N256L
L/F/N–L–L–L–L
L
0.094
0.93
0.85
Benign
285
D285E
D–E–D–E–D
E
0.000
1.00
0.00
Benign
286*
I/K286I
I/K–I–I–I–I
I
0.914
0.81
0.94
Possibly damaging
292*
T/I292R
T/I–R–A–S–V
? 0.001
0.99
0.15
Possibly damaging
T/I292R
T/I–R–A–S–V
? 0.000
1.00
0.00
Benign Table 3. Prediction of impact of non-synonymous (fixed or under selection cf. Table 1) amino acid
substitutions between B. calyciflorus s.s. and B. fernandoi in comparison to B. rubens, B. angularis and B. diversicornis. Predictions were made using Polyphen2. The code provides details on the amino acid substitution
and the position. Bc–Bf–Br–Ba–Bd provides the information of the respective amino acid of B. calyciflorus
s.s. Table 3. Prediction of impact of non-synonymous (fixed or under selection cf. Table 1) amino acid
b
b
l
fl
d
f
d
b
l
d www.nature.com/scientificreports/ calyciflorus s.s. and the
marine clade comprising B. plicatilis, B. manjavacas, B. rotundiformis and B. koreanus to about 41–47 Myr. This
latter estimate is considerably larger than an earlier estimate of divergence time between the freshwater species B. calyciflorus (species undefined) and the marine B. plicatilis, using COI and 18S as markers (~ 25 Myr85). This dis-
crepancy could be due to the increased number of Brachionus species used in our analysis and the different genes
and substitution rates used in the present study, relative to Tang et al. (2014)85. Tang et al. used a substitution rate
of 1.76% Myr−1 for COI and 0.02% Myr−1 for 18S85, while we used the standard mitochondrial substitution rate
for invertebrates (1.15% Myr−1)86. However, all these rates are derived from distant taxa and—to the best of our
knowledge—no rotifer-specific substitution rates are available so far. Hence, these analyses should be repeated
when substitution rate estimates for our target species (B. calyciflorus s.s. and B. fernandoi) become available. In any case, we note that estimated divergence times within the freshwater B. calyciflorus species complex are
in the same order of magnitude as in the marine B. plicatilis species complex (represented by B. plicatilis and B. manjavacas in our analysis; cf. Supplementary Fig. s8). Hybridization event. Our study revealed a natural hybridization event between B. fernandoi and B. caly-
ciflorus s.s. individuals originating at one sampling location (a single pond): Among the specimens collected
there, four exhibited B. fernandoi ITS1 alleles, but shared the same B. calyciflorus s.s COI haplotype.). This
comprises—to the best of our knowledge—the first reported in-situ hybridization among these two species. The
ability of the species within the B. calyciflorus species complex to hybridize has already been suggested by the
widespread occurrence of mitonuclear discordance23. However, only recent studies under laboratory conditions
observed hybridization between the most closely related species B. calyciflorus s.s. and B. elevatus6,7, but with a
significantly lower intraspecific fertilization (i.e., pre-zygotic isolation) and higher dormant propagule mortality
(i.e., post-zygotic isolation)6. Another study detected signs of hybridization between B. elevatus and B. dorcas87. The comparison of alleles/haplotypes (HSP, ITS1, COI) in our four hybrid specimens with other samples from
the same location revealed the hybrids to be F2 or a subsequent generation and that genes from B. calyciflorus
s.s. introgressed into the local B. fernandoi gene pool. www.nature.com/scientificreports/ downstream stress response, which is underlined by the predicted impact of amino acid substitutions on protein
function at two of the six sites. However, among the inferred sites under positive selection, only one (292, cf. Sup-
plementary Fig. s4) exhibited species-specific amino acids. One explanation could be that the large geographic
range of our study correlated with different local selection pressures, such that most substitutions were not fixed
among the entire distribution range of a species. Another explanation could be a low genomic recombination
rate (Muller’s ratchet), whereby clonal organisms easily accumulate slightly deleterious mutations that can gen-
erate noise in the selection analysis, hindering the identification of species-specific sites under selection82. The
latter is in line with the findings of the McDonald-Kreitman Test (MKT) where a high Neutrality Index of 12.05
was found between the unique alleles of B. calyciflorus s.s. and B. fernandoi. This indicates an overabundance of
replacement-site polymorphisms, which can arise from slightly deleterious polymorphic variants not eliminated
by purifying selection83, a phenomenon known from clonal organisms84. y p
y
g
p
g
Because of the potentially compromised power of selection analyses in clonal organisms82, we inspected all
further amino acid substitutions as well. Indeed, among them eleven fixed positions between our species were
identified, two of which (positions 63 and 66; cf. Table 3) with a potential impact on protein function. These sites
are not located in known functional domains of the HSP 40 kDa, yet they may have an impact on the structure
of the protein. The results of the branch site model test indicated positive (directional) selection in B. fernandoi,
but not in B. calyciflorus s.s. This is corroborated by character polarity, i.e., B. fernandoi predominantly exhibit-
ing derived substitutions, while B. calyciflorus s.s. mostly retaining the ancestral amino acids. This allows us to
draw the conclusion that B. fernandoi diverged from B. calyciflorus s.s. A divergent selection scenario for both
species is compatible with the positive Tajima’s D statistics (albeit not significant).hl p
p
p
j
(
gi
)
The substantial nucleotide divergence among the two formerly cryptic species B. fernandoi and B. calyciflorus
s.s. suggest these lineages to be evolutionary more ancient than one might expect for morphologically hardly
distinguishable sister species. We had inferred their divergence time as ~ 25–29 Myr. The same analysis dated the
split between the Brachionus freshwater clade comprising B. angularis, B. fernandoi and B. Discussion
C
did t A closer inspection of those sites revealed that four of them are in functional
domains of the gene. One site is located in the J-domain, a region known to be important in the chaperone activ-
ity of HSP 40 kDa and the HSP 70 kDa by interacting with the ATP domain of the HSP 70kDa74, which acceler-
ates ATP hydrolysis75,76 and thus, regulates the ATPase activity77. Three other sites are located in the C-terminal
domain of the HSP 40 kDa. Although the exact function of these sites is still undetermined, it is known that the
C-terminal domain of yeast Saccharomyces cerevisiae contains a peptide binding site78,79 and is therefore enabled
to interact with other proteins. Changes in amino acid composition at these sites can affect folding patterns and
thus binding with other proteins (e.g., HSP 70 kDa) through suboptimal structures or polarities80,81. These sub-
optimal structures can affect the strength of HSP 70 kDa ATPase regulation and potentially alter an organism’s https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ Materials and methods
Candidate gene selection. Candidate gene selection. To identify candidate genes with a sequence divergence pattern related to dif-
ferential temperature adaptation, previously published transcriptome data35 (GenBank accessions number SRA:
SRR10426055-76) was analysed using the following customized bioinformatic pipeline (Supplementary Fig. s1):
De novo transcriptome assemblies were used to generate a super transcript for each species using Trinity v. 2.11.0 gene splicer modeler89. This super transcript step was integrated to minimize redundancy in the data by
inferring original genes and alternative splice forms90. A reciprocal best blast hit process was performed, using
the blastn program of BLAST 2.9.0+91 to detect orthologous genes shared by B. calyciflorus s.s. and B. fernandoi. To determine the best blast hit, results were filtered using a combination of E-value, which is a size corrected
measure of statistical significance, and the bit score, which is a measure of matches and mismatches between
two sequences91. When E-values of the first two or more hits were the same, the best hit was chosen using the
bit score. For each search, a list was created that contained one best hit per query. Orthologous gene pairs were
extracted, and open reading frames were predicted using TransDecoder v 5.5.092. To calculate ratios of the rates
of non-synonymous and synonymous substitutions (dN/dS) from protein-coding regions, sequences were then
translated into amino acid sequences using Biopython93 and locally aligned within the Biopython integrated
package pairwise2 using a Smith-Waterman algorithm. Locally aligned coding sequences and the corresponding
unaligned DNA sequences were used to create codon alignments using pal2nal94. Selection tests were conducted
using all available seven (M0, M1a, M2, M3, M7, M8 and M8a) codeML models (Supplementary Table s1), as
implemented in PAML v. 4.995. These models where then compared in four (M0 vs. M3, M1a vs. M2, M7 vs. M8,
M8 vs. M8a) predefined likelihood-ratio tests (LRT) to decide whether the different null models (i.e., models
that do not allow for any codons ω > 1, corresponding to absence of positive selection) can be rejected95.i y
g
j
Orthologous genes that were significant (< 0.05) in all four LRT comparisons were annotated using Gene
Ontology (GO) terms96. These terms are hierarchically ordered descriptions of genes or proteins molecular func-
tions, biological processes, and cellular components. The GO term annotation was done on the online Server
Argot2.5 and its batch processing function97. Materials and methods
Candidate gene selection. To use this function, the longest available amino acid sequence of
each protein was used in a blast search against the Uniprot Swiss-Prot database98 and a hmmer search99,100 against
the Pfam-A database100. In addition, we compared the genes exhibiting positive selection in the selection tests
with those found to be differentially expressed relative to species and temperature (control: 20 °C; mild heat: B. calyciflorus s.s. 26 °C, B. fernandoi 23 °C; high heat: B. calyciflorus s.s. 32 °C, B. fernandoi 26 °C)35. Among those
genes functionally related to temperature tolerance (GO:00009408; “response to heat”; GO:00009409; “response
to cold”), only one orthologous gene, the HSP 40 kDa, exhibited signs of positive selection and was differentially
expressed in more than one temperature category, hence chosen for in-depth analysis. DNA extraction. To extract DNA, single rotifer specimens were collected from laboratory cultures, washed
in 96% EtOH and stored in a 1.5 mL reaction tube in10µL HPLC-H20. In total, 56 rotifer individuals (B. caly-
ciflorus s.s., n = 25; B. fernandoi, n = 19; B. rubens, n = 4; B. diversicornis, n = 3; B. angularis, n = 5), comprising
56 clonal cultures (WC medium at 20 °C under 16:8 light:dark photoperiod) which were established from one
individual isolated from the field, were collected from different locations in Germany. For B. calyciflorus s.s.,
additional samples from USA, Italy and Austria were available (Supplementary Fig. s2, Supplementary Table s2). To prevent that the DNA from single individuals is lost during the extraction process, 3 µL carrier RNA [1 µg/µL]
(QIAGEN, Germany) was added to the sample during the lysis. DNA was extracted using the NucleoSpin®Tissue
extraction kit (Macherey–Nagel, Germany) following the manufacturer’s protocol for animal tissue (page 12–14). Primer design HSP 40 kDa. To amplify the HSP 40 kDa from all five different Brachionus species, primers
were designed using the candidate gene sequences (B. calyciflorus s.s. and B. fernandoi) as well as the published
HSP 40 kDa sequence of B. calyciflorus (unknown species assignment regarding current taxonomy; Genbank:
KC176712.161). Sequences were aligned in Geneious v. 8.1.9101 using ClustalW102 and the implemented primer3
algorithm103 was used to design primer pairs. Amplification and sequencing of the ITS1, COI and HSP 40 kDa. To determine the species and
clonal diversity, both the nuclear internal transcribed spacer (ITS1) and the mitochondrial Cytochrome Oxidase
Subunit I (COI) were amplified, using universal invertebrate primers104,105. www.nature.com/scientificreports/ This is because all the introgressed specimens we detected
in this study were homozygous for B. fernandoi alleles at the ITS1 locus. Furthermore, three detected hybrids
carried B. fernandoi specific HSP 40 kDa alleles, while in one case a B. calyciflorus s.s. specific HSP 40 kDa
allele occurred. This different genetic makeup among the hybrids suggests that they either have emerged from
independent hybridization events or that the hybridization was sufficiently ancient to allow for repeated sexual
recombination after the hybridization event. In any case, our findings demonstrate that B. calyciflorus s.s. and B. fernandoi can naturally hybridize at sites where they occur in sympatry. It was found in the marine B. plicatilis
species complex that niche differentiation of very similar species (e.g., body size, biotic niches, competition abili-
ties) is facilitated by their response to changing physical environments in combination with life and diapause his-
tory traits16. In the B. calyciflorus species complex, a previous study reported strongest pronounced differences
in life history traits of B. fernandoi compared to B. calyciflorus s.s., B. elevatus and B. dorcas, such as prolonged
egg and juvenile development times and an overall lower egg production rate and mictic ratio32. The adaptation
to different temperature optima34, associated with differences in HSP 40 Da expression35 and protein structure
(this study), may lead to seasonal isolation of the two species. This illustrates the above example that the niche
of very similar species can be determined by their response to abiotic environmental conditions. The differential
niches (here preferred temperature) occupied by the respective species reflect divergent adaptation. This acts as
a pre-zygotic isolation mechanism by facilitating differences in timing of reproduction and population growth
based on distinct environmental cues (i.e., temperature, photoperiod) and thus maintaining the species bounda-
ries. Such pre-zygotic isolation by season has also been observed among Daphnia species (reviewed in88). This https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ mechanism may however be imperfect under certain environmental conditions, leading to occasional hybridiza-
tion, as observed in our study. mechanism may however be imperfect under certain environmental conditions, leading to occasional hybridiza-
tion, as observed in our study. Conclusion We used transcriptome and expression data to infer a suitable candidate, the HSP 40 kDa gene, which may play
a role in temperature adaptation in the Brachionus calyciflorus species complex. Species-specific alleles and fixed
amino acid substitutions sites as well as positively selected sites located in functional domains of the protein
were identified. The high number of detected alleles, the results of the branch site selection test, and the fixed
sites indicate a divergent adaptation process with B. calyciflorus s.s. retaining ancestral features, from which B. fernandoi derived by positive directional selection. Furthermore, the study revealed descendants of an in-situ
hybridization event between B. calyciflorus s.s. and B. fernandoi. This finding indicates that hybridization between
those species is possible. We hypothesize that the temporally isolated niches they populate serve as pre-zygotic
isolation mechanisms. This isolation may be imperfect under certain environmental conditions, yet hybridiza-
tions seem rare and seasonal niche separation generally prevents species boundaries from becoming blurred. Materials and methods
Candidate gene selection. calyciflorus s.s., n = 50; B. fernandoi, n = 38) were
translated using the published translation reading frame of the HSP 40 kDa gene of B. calyciflorus (Genbank:
KC176712.1). As we did not yield the complete sequence for all specimens, the alignment was truncated to
888 bp present in all sequences. Number of non-synonymous substitutions per non-synonymous site between
the two species were compared using SLAC analysis implemented in Datamonkey110,111. HSP 40 kDa allele identification. To identify different allele types within the B. calyciflorus species com-
plex, allele networks were generated from the resulting 88 phased sequences (B. calyciflorus s.s. n = 50 and B. fernandoi n = 38) using the program popART version 1.7112. Subsequently, a Circos plot113 was generated using
the web interface based on allele types identified by popART, species, and specimens’ origin. Sequence divergence in the HSP 40 kDa gene relative to established barcoding markers. Spe-
cies recognition within the B. calyciflorus complex relies on species-specific ITS1 sequences and clonal lineages
are further characterized by their mitochondrial COI haplotype. For 41 specimens (B. fernandoi n = 18, B. calyci-
florus s.s. n = 20, and consensus sequences of B. rubens, B. angularis, and B. diversicornis), sequences were avail-
able for both these marker genes and the HSP 40 kDa gene. For these specimens, congruence in genetic affinity
across genetic markers was assessed using a tanglegram approach. The respective phylogenies were calculated
using RaxML v.8114, performing 1000 bootstrap iterations. Dendrograms and the tanglegrams were generated in
R v.4.0.5 with the package dendextend v.1.15.1115. Selection tests and divergence time. To test whether the expressed genetic variation among the the
five different Brachionus species is under selection, a selection test was performed based on the 29 HSP 40 kDa
species-specific alleles using the Program PAML v.4.995. A specific focus was on the divergence of the two spe-
cies B. calyciflorus s.s. and B. fernandoi. This analysis needs a phylogeny as input which was based on the 532 bp
long ITS1 fragment and calculated using RaxML v.8, performing 1000 bootstrap iterations. The phylogeny was
viewed in FigTree version 1.4.4.116 and adapted using Inkscape version 1.0.1.117 (Supplementary Fig. s3). Materials and methods
Candidate gene selection. This
ITS1 phylogeny as well as the HSP 40 kDa unique alleles were used to infer sites under selection according to the
codeML site model implemented in PAML, testing all seven (M0, M1a, M2, M3, M7, M8 and M8a) different sub-
stitution models. The different models vary regarding substitution rates of synonymous and non-synonymous
sites (ω values; see Supplementary Table s1) with a subsequent site under selection inference via Bayes Empiri-
cal Bayes (BEBs) (for parameter setting see Supplementary Table s9). The models were compared in four (M0
vs. M3, M1a vs. M2, M7 vs. M8, M8a vs. M8) predefined Likelihood Ratio Tests (LRTs) to decide whether the
respective null models can be rejected. Significance of the M0 vs. M3 comparison indicates variation in ω, a pre-
requisite for further tests on positive selection. The null model M1a allows only negatively selected and neutral
sites (2 ω values), to which M2a adds a third ω for positively selected sites. M7 and M8 resemble M1a and M2a,
but allow for rate variation among negatively selected sites (10 ω values < 1 taken from a β distribution), without
consideration of neutral sites (ω = 1). The last comparison of M8a vs. M8 tests for positive selection against a null
model (M8a) resembling M7, but with an additional fixed ω = 1 (allowing for sites under selective neutrality);
this comparison has been found to increase robustness by yielding fewer false positive results118. An additional
branch site test was performed to identify patterns of selection on three different branches: (I) the shared branch
of B. calyciflorus s.s. and B. fernandoi, (II) B. calyciflorus s.s. only and (III) B. fernandoi only (Supplementary
Fig. s3). Subsequently, to further compare the two formerly cryptic species of B. calyciflorus s.s. and B. fernandoi,
a codon-based McDonald–Kreitman test (MKT) and Tajima’s D statistics (allele frequency based) were calcu-
lated based on the unique inferred alleles using DNAsp v. 6.iili q
g
p
Species-specific fixed amino acid substitutions within the B. calyciflorus species complex were identified (Sup-
plementary Fig. s5) and the ancestral amino acid was inferred under parsimony, using sequence information
from B. rubens, B. angularis and B. diversicornis and the ITS1 phylogeny (Supplementary Fig. s3). The functional
effects of the specific amino acid (aa) substitutions were predicted with Polyphen2119 using B. calyciflorus s.s. as
a reference. Materials and methods
Candidate gene selection. PCR conditions, primer sequences,
and used PCR chemicals mixes can be found in the Supplementary Tables s3, s4 and s5. The HSP 40 kDa gene of https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ all five Brachionus species was amplified using newly designed primer pairs (Supplementary Tables s3, s6 and s7). Successfully amplified HSP 40 kDa, COI and ITS1 products were purified using an enzymatic (ExoAP) proce-
dure and sequenced on a Sanger sequencing platform (Applied Biosystems™ 3500 Genetic Analyzer). Sequences
from all specimens used in this study (Supplementary Table s2) were visually inspected using Geneious v. 8.1.9 and heterozygous positions (for ITS1 and HSP 40 kDa) were encoded with the standard IUPAC code for
ambiguity106. To reconstruct both alleles of the diploid nuclear DNA, the PHASE algorithm version 2.1107,108 was
used, as implemented in DNAsp v. 6109. HSP 40 kDa sequence diversity. To compare sequence divergence in the HSP 40 kDa gene among the
five different species, consensus sequences per species were generated. In order to avoid any bias which may
arise from uneven geographic sampling across species, we only used specimens originating from the same region
“Uckermark” for this analysis: B. calyciflorus s.s. (n = 11), B. fernandoi (n = 8), B. rubens (n = 4), B. diversicornis
(n = 3) and B. angularis (n = 5). Sequence ambiguities in the consensus sequence were coded as N’s (see Supple-
mentary Table s8). Pairwise nucleotide diversities of the 1,025 bp long HSP 40 kDa gene sequence and the 435 bp
long COI sequences between the five species were calculated. For an 888 bp fragment of the HSP 40 kDa gene
(see below), non-synonymous resp. synonymous substitutions were identified using DNAsp v. 6. Expressed variation in the HSP 40 kDa gene between B. calyciflorus s.s. and B. fernan-
doi. Sequences originating from multiple individuals (B. calyciflorus s.s., n = 50; B. fernandoi, n = 38) were
translated using the published translation reading frame of the HSP 40 kDa gene of B. calyciflorus (Genbank:
KC176712.1). As we did not yield the complete sequence for all specimens, the alignment was truncated to
888 bp present in all sequences. Number of non-synonymous substitutions per non-synonymous site between
the two species were compared using SLAC analysis implemented in Datamonkey110,111. Expressed variation in the HSP 40 kDa gene between B. calyciflorus s.s. and B. fernan-
doi. Sequences originating from multiple individuals (B. www.nature.com/scientificreports/ such that it ranks any substitution without a predicted change in protein function as "benign" (i.e., no effect),
while any predicted change is ranked as "damaging" (i.e., predicted to impact protein function).ll To estimate the within B. calyciflorus species complex divergence time between B. calyciflorus s.s. and B. fer-
nandoi the program BEAST v.1.10.4120 was used. Whole mtGenome coding sequences (cds) of different rotifer
species were downloaded from NCBI: B. calyciflorus s.s.121, B. fernandoi121, B. angularis122, B. manjavacas123, B. plicatilis124, B. koreanus125, B. rotundiformis126, B. rubens127 and P. similis128 (for Genebank accession numbers cf. Supplementary figure s8). In absence of a published substitution rate for rotifers, the standard divergence rate
for invertebrates/insects (2.3% Myr−1) with a constant substitution rate of 0.0115 per million years per lineages86
was used to calibrate the phylogeny. Cds were aligned in Geneious v. 8.1.9 using ClustalW and the IQ-Tree
webserver129 was used to determine the best fitting substitution model. The BEAST run was conducted with 10
million MCMC iterations, with GTR + G4 + I chosen as the substitution model. Convergence was checked with
Tracer v.1.7.2130, using the first million MCMC iterations as the burn-in value and tree was visualized using
FigTree version 1.4.4. and adapted in Inkscape version 1.0.1. References 1. Mayr, E. Systematics and the Origin of Species, from the Viewpoint of a Zoologist (Harvard University Press, 1942). 2. Ostevik, K. L., Andrew, R. L., Otto, S. P. & Rieseberg, L. H. Multiple reproductive barriers separate recently diverged sunflowe
ecotypes. Evolution 70, 2322–2335 (2016). yp
3. Seehausen, O. et al. Genomics and the origin of species. Nat. Rev. Genet. 15, 176–192 (2014). y
3. Seehausen, O. et al. Genomics and the origin of species. Nat. Rev. Genet. 15, 176–192 (2014). g
p
(
)
4. Cheng, J. & Sha, Z.-L. Cryptic diversity in the Japanese mantis shrimp (Crustacea: Squillidae): Allopatric diversification, second-
ary contact and hybridization. Sci. Rep. 7, 1972 (2017).l 4. Cheng, J. & Sha, Z.-L. Cryptic diversity in the Japanese mantis shrimp (Crustacea: Squillidae): Allopatric diversification, second-
ary contact and hybridization. Sci. Rep. 7, 1972 (2017).l 5. Michaloudi, E. et al. Reverse taxonomy applied to the Brachionus calyciflorus cryptic species complex: Morphometric analysis
confirms species delimitations revealed by molecular phylogenetic analysis and allows the (re)description of four species. PLoS
ONE 13, e0203168 (2018). ,
(
)
6. Zhang, W. & Declerck, S. A. J. Intrinsic postzygotic barriers constrain cross-fertilisation between two hybridising sibling rotifer
species of the Brachionus calyciflorus species complex. Freshw. Biol. 67, 240–249 (2022). (
)
6. Zhang, W. & Declerck, S. A. J. Intrinsic postzygotic barriers constrain cross-fertilisation between two hybridising sibling rotifer
species of the Brachionus calyciflorus species complex. Freshw. Biol. 67, 240–249 (2022). p
y fl
p
p
7. Zhang, W. & Declerck, S. A. J. Reduced fertilization constitutes an important prezygotic reproductive barrier b
species of the hybridizing Brachionus calyciflorus species complex. Hydrobiologia 849, 1701–1711 (2022).i l
7. Zhang, W. & Declerck, S. A. J. Reduced fertilization constitutes an important prezygotic reproductive barrier between two sibling
species of the hybridizing Brachionus calyciflorus species complex Hydrobiologia 849 1701 1711 (2022) l
7. Zhang, W. & Declerck, S. A. J. Reduced fertilization constitutes an important prezygotic reproductive barrier between two si 7. Zhang, W. & Declerck, S. A. J. Reduced fertilization constitutes an important prezygotic reproductive barrier between two sibling
species of the hybridizing Brachionus calyciflorus species complex. Hydrobiologia 849, 1701–1711 (2022).i g
p
p
yg
p
species of the hybridizing Brachionus calyciflorus species complex. Hydrobiologia 849, 1701–1711 (2022).i l
8. Seehausen, O., van Alphen, J. J. M. & Witte, F. Materials and methods
Candidate gene selection. Note here that Polyphen2 does not consider the possibility of a positive effect of an aa substitution, https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ References Cichlid fish diversity threatened by eutrophication that curbs sexual sele
Science 277, 1808–1811 (1997). (
)
9. Bickford, D. et al. Cryptic species as a window on diversity and conservation. Trends Ecol. Evol. 22, 148–155 (2007). 10. Gill, B. A. et al. Cryptic species diversity reveals biogeographic support for the ’mountain passes are higher in the tr
hypothesis. Proc. R. Soc. B. 283, 20160553 (2016). y
11. Sáez, A. G. & Lozano, E. Body doubles. Nature 433, 111 (2005). 11. Sáez, A. G. & Lozano, E. Body doubles. Nature 433, 111 (2005 12. Fišer, C., Robinson, C. T. & Malard, F. Cryptic species as a window into the paradigm shift of the species concept. Mol. Ecol. 27
613–635 (2018).t 13. Mills, S. et al. Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through
DNA taxonomy. Hydrobiologia 796, 39–58 (2017). 13. Mills, S. et al. Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through
DNA taxonomy. Hydrobiologia 796, 39–58 (2017). y
y
g
(
)
14. Struck, T. H. et al. Finding evolutionary processes hidden in cryptic species. Trends Ecol. Evol. 33, 153–163 (2018). 15. Leibold, M. A. & McPeek, M. A. Coexistence of the niche and neutral perspectives in community ecology. Ecology 87, 1399–1410
(2006).f 16. Gabaldón, C., Fontaneto, D., Carmona, M. J., Montero-Pau, J. & Serra, M. Ecological differentiation in cryptic rotifer species:
What we can learn from the Brachionus plicatilis complex. Hydrobiologia 796, 7–18 (2017). y
g
17. Nicholls, B. & Racey, P. A. Contrasting home-range size and spatial partitioning in cryptic and sympatric pipistrelle bats. Behav
Ecol. Sociobiol. 61, 131–142 (2006). 18. Ortells, R., Gómez, A. & Serra, M. Coexistence of cryptic rotifer species: Ecological and genetic characterisation of Brachionus
plicatilis. Freshw. Biol. 48, 2194–2202 (2003). 19. Wellborn, G. A. & Cothran, R. D. Niche diversity in crustacean cryptic species: Complementarity in spatial distribution and
predation risk. Oecologia 154, 175–183 (2007).h p
g
20. Gause, G. F. The struggle for existence (Williams and Wilkins, 1934). p
g
20. Gause, G. F. The struggle for existence (Williams and Wilkins, 1934). h
21. Segers, H. Global diversity of rotifers (Rotifera) in freshwater. Hydrobiologia 595, 49–59 (2008). g
y
y
g
22. Fontaneto, D. Molecular phylogenies as a tool to understand diversity in rotifers. Int. Rev. Hydrobiol. 99, 178–187 (2014). D. Data availabilityh The genome sequence data (ITS1, COI and HSP 40 kDa) that supports the findings of this study are openly
available on Genbank of NCBI (http://www.ncbi.nlm.nih.gov/) under the Accession numbers: ITS1:
OP868747-OP868802, COI: OP861581-OP861626 and HSP 40 kDa: OP888060-OP888091. The associ-
ated BioProject, SRA, and Bio-Sample numbers are PRJNA544636, SRR10426055—SRR10426076 and
SAMN11845726—SAMN11845747. Received: 16 September 2022; Accepted: 26 December 2022 Received: 16 September 2022; Accepted: 26 December 2022 www.nature.com/scientificreports/ www.nature.com/scientificreports/ 30. Gilbert, J. J. & Walsh, E. J. Brachionus calyciflorus is a species complex: Mating behavior and genetic differentiation among four
geographically isolated strains. Hydrobiologia 546, 257–265 (2005).fl g
g
p
y
y
g
31. Zhang, Y. et al. Temporal patterns and processes of genetic differentiation of the Brachionus calyciflorus (Rotifera) complex in
a subtropical shallow lake. Hydrobiologia 807, 313–331 (2018).f f
a subtropical shallow lake. Hydrobiologia 807, 313–331 (2018). p
y
g
32. Zhang, W., Lemmen, K. D., Zhou, L., Papakostas, S. & Declerck, S. A. J. Patterns of differentiation in the life history and demog-
raphy of four recently described species of the Brachionus calyciflorus cryptic species complex. Freshw. Biol. 64, 1994–2005
(2019). (
)
33. Lemmen, K. D., Verhoeven, K. J. F. & Declerck, S. A. J. Experimental evidence of rapid heritable adaptation in the absence o
initial standing genetic variation. Funct. Ecol. 36, 226–238 (2022).f 34. Paraskevopoulou, S., Dennis, A. B., Weithoff, G., Hartmann, S. & Tiedemann, R. Within species expressed genetic variability and
gene expression response to different temperatures in the rotifer Brachionus calyciflorus sensu stricto. PLoS ONE 14, e0223134
(2019).f (
)
35. Paraskevopoulou, S., Dennis, A. B., Weithoff, G. & Tiedemann, R. Temperature-dependent life history and transcriptomic
responses in heat-tolerant versus heat-sensitive Brachionus rotifers. Sci. Rep. 10, 13281 (2020). k
l
d
h ff
ff
l
h
l
l
f (
)
35. Paraskevopoulou, S., Dennis, A. B., Weithoff, G. & Tiedemann, R. Temperature-dependent life h
responses in heat-tolerant versus heat-sensitive Brachionus rotifers. Sci. Rep. 10, 13281 (2020).ff 36. Paraskevopoulou, S., Tiedemann, R. & Weithoff, G. Differential response to heat stress among evolutionary lineages of an aquatic
invertebrate species complex. Biol. Lett. 14, 20180498 (2018).f ff
invertebrate species complex. Biol. Lett. 14, 20180498 (2018).f 37. Takemoto, K. & Akutsu, T. Origin of structural difference in metabolic networks with respect to temperature. BMC Syst. 2, 82 (2008).hh (
)
38. Angilletta, M. J. Thermal Adaptation: A Theoretical and Empirical Synthesis (Oxford University Press, 2009). M. J. Thermal Adaptation: A Theoretical and Empirical Synthesis (O hh
39. Atkinson, D. Temperature and organism size: A biological law for ectotherms?. Adv. Ecol. Res. 25, 1–58 (1994)
ll
l
h
ff
f
d
b 40. Gillooly, J. F., Brown, J. H., West, G. B., Savage, V. M. & Charnov, E. L. Effects of size and temperature on metabolic rate. Science
293, 2248–2251 (2001). 41. www.nature.com/scientificreports/ & Wilkins, A. S. The molecular elements that underlie developmental evolution. Nat. Rev. Genet. 6, 709–715 (2005). 52. Alonso, C. R. & Wilkins, A. S. The molecular elements that underlie developmental evolution. Nat. Rev. Genet. 6, 709–715 (2005). 53. Romero, I. G., Ruvinsky, I. & Gilad, Y. Comparative studies of gene expression and the evolution of gene regulation. Nat. Rev. G
t 13 505 516 (2012) 52. Alonso, C. R. & Wilkins, A. S. The molecular elements that underlie developmental evolution. Nat. Rev. Genet. 6, 709–715 (2005). 53
Romero I G R
insk
I & Gilad Y Comparati e st dies of gene e pression and the e ol tion of gene reg lation Nat Rev h
53. Romero, I. G., Ruvinsky, I. & Gilad, Y. Comparative studies of gene expression and the evolution of gene regulation. Nat. Rev
Genet. 13, 505–516 (2012). 54. Franch-Gras, L. et al. Genomic signatures of local adaptation to the degree of environmental predictability in rotifers. Sci. Rep
8, 16051 (2018). 55. Nowell, R. W. et al. Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species. PLoS Biol
16, e2004830 (2018). 56. Feugeas, J.-P. et al. Links between transcription, environmental adaptation and gene variability in Escherichia coli: Correlations
between gene expression and gene variability reflect growth efficiencies. Mol. Biol. Evol. 33, 2515–2529 (2016).h g
p
g
yl
gfi
57. Pai, A. A., Pritchard, J. K. & Gilad, Y. The genetic and mechanistic basis for variation in gene regulation. PLoS Genet. 11, e1004857
(2015).h 58. Gribble, K. E. & Mark Welch, D. B. The mate recognition protein gene mediates reproductive isolation and speciation in the
Brachionus plicatilis cryptic species complex. BMC Evol. Biol. 12, 134 (2012). p
yp
p
p
59. Via, S. Natural selection in action during speciation. Proc. Natl. Acad. Sci. USA. 106, 9939–9946 (2009). 60. Ho, S. Y. W. & Duchêne, S. Molecular-clock methods for estimating evolutionary rates and timescales. Mol. Ecol. 23, 5947–5965
(2014). 61. Yang, J., Mu, Y., Dong, S., Jiang, Q. & Yang, J. Changes in the expression of four heat shock proteins during the aging process in
Brachionus calyciflorus (Rotifera). Cell Stress Chaperones 19, 33–52 (2014). h
d
d
h
d
h d
ff
f
l
h
h
k y fl
p
62. Mahmood, K., Jadoon, S., Mahmood, Q., Irshad, M. & Hussain, J. Synergistic effects of toxic elements on heat shock proteins
Biomed. Res. Int. www.nature.com/scientificreports/ 2014, 564136 (2014).i (
)
Park, J. C. et al. Genome-wide identification and structural analysis of heat shock protein gene families in the marine rotifer
Brachionus spp : Potential application in molecular ecotoxicology Comp Biochem Physiol D 36 100749 (2020) 63. Park, J. C. et al. Genome-wide identification and structural analysis of heat shock protein gene families in the marine rotife
Brachionus spp.: Potential application in molecular ecotoxicology. Comp. Biochem. Physiol. D 36, 100749 (2020). 64. Santoro, M. Heat shock factors and the control of the stress response. Biochem. Pharmacol. 59, 55–63 (2000).h 64. Santoro, M. Heat shock factors and the control of the stress re 65. Birky, C. W. & Gilbert, J. J. Parthenogenesis in rotifers: The control of sexual and asexual reproduction. Am. Zool. 11, 245–266
(1971). (1971). 66. Snell, T. W. Rotifers as models for the biology of aging. Int. Rev. Hydrobiol. 99, 84–95 (2014). (
)
66. Snell, T. W. Rotifers as models for the biology of aging. Int. Rev. Hydrobiol. 99, 84–95 (2014).h 67. Felsenstein, J. The evolutionary advantage of recombination. Genetics 78, 737–756 (1974). enstein, J. The evolutionary advantage of recombination. Genetics h
68. Muller, H. J. Some genetic aspects of sex. Am. Nat. 66, 118–138 (1932).h h
68. Muller, H. J. Some genetic aspects of sex. Am. Nat. 66, 118–138 (1932).h g
p
69. Muller, H. J. The relation of recombination to mutational advance. Mut. Res. 1, 2–9 (1964).h ler, H. J. The relation of recombination to mutational advance. Mu h
70. Ballard, J. W. O. & Whitlock, M. C. The incomplete natural history of mitochondria. Mol. Ecol. 13, 729–744 (2004).fii h
p
y
71. Zhang, Y., Xu, S., Sun, C., Dumont, H. & Han, B.-P. A new set of highly efficient primers for COI amplification in rotifers. Mitochondrial DNA B 6, 636–640 (2021).f 72. Turner, C. B., Marshall, C. W. & Cooper, V. S. Parallel genetic adaptation across environments differing in mode of growth or
resource availability. Evol. Lett. 2, 355–367 (2018). y
Lan, B. et al. Tempo-spatial variations of zooplankton commu 73. Lan, B. et al. Tempo-spatial variations of zooplankton communities in relation to environmental factors and the ecological
implications: A case study in the hinterland of the Three Gorges Reservoir area. China. PLoS ONE 16, e0256313 (2021). 74. Pellecchia, M., Szyperski, T., Wall, D., Georgopoulos, C. & Wüthrich, K. References Molecular phylogenies as a tool to understand diversity in roti Fontaneto, D. Molecular phylogenies as a tool to understand diver 23. Papakostas, S. et al. Integrative taxonomy recognizes evolutionary units despite widespread mitonuclear discordance: Evid
from a rotifer cryptic species complex. Syst. Biol. 65, 508–524 (2016). y
y
24. García-Morales, A. E. & Elías-Gutiérrez, M. DNA barcoding of freshwater rotifera in Mexico: Evidence of cryptic speciation in
common rotifers. Mol. Ecol. Resour. 13, 1097–1107 (2013).fl 24. García-Morales, A. E. & Elías-Gutiérrez, M. DNA barcoding of
common rotifers. Mol. Ecol. Resour. 13, 1097–1107 (2013).f 24. García-Morales, A. E. & Elías-Gutiérrez, M. DNA barcodin common rotifers. Mol. Ecol. Resour. 13, 1097–1107 (2013). 25. Wang, X. L. et al. Differences in life history characteristics between two sibling species in Brachionus calyciflorus complex from
tropical shallow lakes. Ann. Limnol. Int. J. Lim. 50, 289–298 (2014).l 25. Wang, X. L. et al. Differences in life history characteristics be 26. Wen, X., Xi, Y., Zhang, G., Xue, Y. & Xiang, X. Coexistence of cryptic Brachionus calyciflorus (Rotifera) species: Roles of envi-
ronmental variables. J. Plankton Res. 38, 478–489 (2016). Wen, X., Xi, Y., Zhang, G., Xue, Y. & Xiang, X. Coexistence of cr ronmental variables. J. Plankton Res. 38, 478–489 (2016). (
)
27. Xiang, X.-L., Chen, Y.-Y., Han, Y., Wang, X.-L. & Xi, Y.-L. Comparative studies on the life history characteristics of two Brachionus
calyciflorus strains belonging to the same cryptic species. Biochem. Syst. Ecol. 69, 138–144 (2016).fl l
28. Xiang, X.-L. et al. Patterns and processes in the genetic differentiation of the Brachionus calyciflorus complex, a passively dispers-
ing freshwater zooplankton. Mol. Phylogenet. Evol. 59, 386–398 (2011).fl g
p
y g
29. Xiang, X.-L. et al. Genetic differentiation and phylogeographical structure of the Brachionus calyciflorus complex in eastern
China. Mol. Ecol. 20, 3027–3044 (2011). https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ Walczyńska, A., Franch-Gras, L. & Serra, M. Empirical evidence for fast temperature-dependent body size evolution in rotifers
Hydrobiologia 796, 191–200 (2017). y
g
42. Brown, W. L. & Wilson, E. O. Character displacement. Syst. Zool. 5, 49–64 (1956). 43. Marrone, F., Fontaneto, D. & Naselli-Flores, L. Cryptic diversity, niche displacement and our poor understanding of taxonomy
and ecology of aquatic microorganisms. Hydrobiologia https://doi.org/10.1007/s10750-022-04904-x (2022). 44. Pekkonen, M., Ketola, T. & Laakso, J. T. Resource availab
in a bacterial community. PLoS ONE 8, e76471 (2013).h 44. Pekkonen, M., Ketola, T. & Laakso, J. T. Resource availability and competition shape the evolution of survival and
in a bacterial community. PLoS ONE 8, e76471 (2013).h 44. Pekkonen, M., Ketola, T. & Laakso, J. T. Resource availability and competition shape the evolution of survival and growth ability
b
l
S O
(
) 44. Pekkonen, M., Ketola, T. & Laakso, J. T. Resource availability and competition shape the evolution of survival and growth ability
in a bacterial community. PLoS ONE 8, e76471 (2013).h y
45. Brawand, D. et al. The evolution of gene expression levels in mammalian organs. Nature 478, 343–348 (2011).h y
wand, D. et al. The evolution of gene expression levels in mammali 45. Brawand, D. et al. The evolution of gene expression levels in 46. Drummond, D. A. & Wilke, C. O. The evolutionary consequences of erroneous protein synthesis. Nat. Rev. Genet. 10, 715–724
(2009). 47. Fraser, H. B. Genome-wide approaches to the study of adaptive gene expression evolution: Systematic studies of evolutionary
adaptations involving gene expression will allow many fundamental questions in evolutionary biology to be addressed. BioEssays
33, 469–477 (2011). ,
(
)
48. Fraser, H. B. Gene expression drives local adaptation in humans. Genome Res. 23, 1089–1096 (2013). ene expression drives local adaptation in humans. Genome Res. 23 aser, H. B. Gene expression drives local adaptation in humans. Ge 49. Franch-Gras, L. et al. Rotifer adaptation to the unpredictability of the growing season. Hydrobiologia 844, 257–273 (2019). 50. Tarazona, E., Lucas-Lledó, J. I., Carmona, M. J. & García-Roger, E. M. Gene expression in diapausing rotifer eggs in response
to divergent environmental predictability regimes. Sci. Rep. 10, 21366 (2020).h g
y
g
51. Smith, H. A., Burns, A. R., Shearer, T. L. & Snell, T. W. Three heat shock proteins are essential for rotifer thermotolerance. J. Exp
Mar. Biol. Ecol. 413, 1–6 (2012).h (
)
Alonso, C. R. www.nature.com/scientificreports/ NMR structure of the J-domain and the Gly/Phe-rich
region of the Escherichia coli DnaJ chaperone. Mol. Biol. 260, 236–250 (1996). g
J
p
(
)
75. Greene, M. K., Maskos, K. & Landry, S. J. Role of the J-domain in the cooperation of Hsp40 with Hsp70. Proc. Natl. Acad. Sci
USA 95, 6108–6113 (1998). https://doi.org/10.1038/s41598-022-27137-3 https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ 76. Wittung-Stafshede, P., Guidry, J., Horne, B. E. & Landry, S. J. The J-domain of Hsp40 couples ATP hydrolysis to substrate capture
in Hsp70. Biochemistry 42, 4937–4944 (2003).ti p
y
77. Cintron, N. S. & Toft, D. Defining the requirements for Hsp40 and Hsp70 in the Hsp90 chaperone pathway. J. Biol. Chem. 281
26235–26244 (2006).h 78. Li, J., Qian, X. & Sha, B. The crystal structure of the yeast Hsp40 Ydj1 complexed with its peptide substrate. Structure 11
1475–1483 (2003).h 79. Sha, B., Lee, S. & Cyr, D. M. The crystal structure of the peptide-binding fragment from the yeast Hsp40 protein Sis1. Structure
8, 799–807 (2000).f 80. Brender, J. R. & Zhang, Y. Predicting the effect of mutations on protein-protein binding interactions through structure-based
interface profiles. PLoS Comput. Biol. 11, e1004494 (2015). pi
p
(
)
81. Shortle, D. One sequence plus one mutation equals two folds. Proc. Natl. Acad. Sci. USA 106, 21011–21012 (2009).hf q
p
q
82. Charlesworth, B. The effects of deleterious mutations on evolution at linked sites. Genetics 190, 5–22 (2012). hf
A. D. A Primer of Molecular Population Genetics (Oxford University hf
Cutter, A. D. A Primer of Molecular Population Genetics (Oxford f
p
y
84. Barraclough, T. G., Fontaneto, D., Ricci, C. & Herniou, E. A. Evidence for inefficient selection against deleterious mutations in
cytochrome oxidase I of asexual bdelloid rotifers. Mol. Biol. Evol. 24, 1952–1962 (2007). y
85. Tang, C. Q., Obertegger, U., Fontaneto, D. & Barraclough, T. G. Sexual species are separated by larger genetic gaps than asexua
species in rotifers. Evol. Int. J. Org. Evol. 68, 2901–2916 (2014).l p
g
86. Brower, A. V. Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from pat-
terns of mitochondrial DNA evolution. Proc. Natl. Acad. Sci. U.S.A. 91, 6491–6495 (1994).l 87. Yang, W., Deng, Z., Blair, D., Hu, W. & Yin, M. Phylogeography of the freshwater rotifer Brachionus calyciflorus species complex
in China. Hydrobiologia 849, 2813–2829 (2022). y
g
(
)
88. Chin, T. A. www.nature.com/scientificreports/ The polymerase chain reaction. Mol. Syst. 2, 205–247 (199 h
p y
y
105. Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c ox
subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994). Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase
subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994).i 105. Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c o
subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994).i 106. Cornish-Bowden, A. Nomenclature for incompletely specified bases in nucleic acid sequences: Recommendations. Nucleic Acids
Res. 39, 3021–3030 (1985). 107. Stephens, M., Smith, N. J. & Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978–989 (2001). 108. Stephens, M. & Donnelly, P. A Comparison of bayesian methods for haplotype reconstruction from population genotype
Am. J. Hum. Genet. 73, 1162–1169 (2003). 109. Rozas, J. et al. DnaSP 6: DNA sequence polymorphism a 110. Kosakovsky Pond, S. L. & Frost, S. D. W. Not so different after all: A comparison of methods for detecting amino acid sites u
selection. Mol. Biol. Evol. 22, 1208–1222 (2005). 111. Weaver, S. et al. Datamonkey 2.0: A modern web application for characterizing selective and other evolutionary processes. Mol
Biol. Evol. 35, 773–777 (2018).t 112. Leigh, J. W. & Bryant, D. popart: Full-feature software for haplotype network construction. Methods Ecol. Evol. 6, 1110–
(2015). (
)
113. Krzywinski, M. et al. Circos: An information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009). 114. Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30,
1312–1313 (2014). 115. Galili, T. dendextend: An R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics 31,
3718–3720 (2015).t 116. Andrew Rambaut Group. FigTree. (2022). http://tree.bio.ed.ac.uk/software/. 116. Andrew Rambaut Group. FigTree. (2022). http://tree.bio.ed 117. Inkscape Project. Inkscape. (2020). https://inkscape.org. p
j
p
p
p
g
Wong, W. S. W., Yang, Z., Goldman, N. & Nielsen, R. Accuracy and power of statistical methods for detecting adaptive evolution
in protein coding sequences and for identifying positively selected sites. Genetics 168, 1041–1051 (2004). 118. Wong, W. S. W., Yang, Z., Goldman, N. www.nature.com/scientificreports/ & Cristescu, M. E. Speciation in Daphnia. Mol. Ecol. 30, 1398–1418 (2021). 89. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29
644–652 (2011). 90. Davidson, N. M., Hawkins, A. D. K. & Oshlack, A. SuperTranscripts: A data driven reference for analysis and visualisation o
transcriptomes. Genome Biol. 18, 148 (2017). 91. Altschul, S. F., Gish, W. P., Miller, W., Myers, E. W. & Lipman, D. L. Basic local alignment search tool. Mol. Biol. 215, 403–410
(1990). 92. Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation
and analysis. Nat. Protoc. 8, 1494–1512 (2013). y
93. Cock, P. J. A. et al. Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinfor-
matics 25, 1422–1423 (2009). 94. Suyama, M., Torrents, D. & Bork, P. PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon
alignments. Nucleic Acids Res. 34, W609–W612 (2006). g
95. Yang, Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).ih 96. Ashburner, M. et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29
(2000). 97. Lavezzo, E., Falda, M., Fontana, P., Bianco, L. & Toppo, S. Enhancing protein function prediction with taxonomic constraints
The Argot2.5 web server. Methods 93, 15–23 (2016).hh h
g
98. The UniProt Consortium. UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Res. 49, D480–D489 (2021). hh
99. Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: Interactive sequence similarity searching. Nucleic Acids Re
W29-37 (2011). (
)
100. Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014).t 101. Kearse, M. et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analy
sequence data. Bioinformatics 28, 1647–1649 (2012).h q
f
102. Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence a
ment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–
(1994). ment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680
(1994). l
b l
d
f
l
d
(
) 103. Untergasser, A. et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 40, e115 (2012).h bi, S. R. Acknowledgementsh g
The authors would like to acknowledge Magdalena Litwin for providing rotifer specimens, Dr. Stefanie Hartmann
for her assistance in analysing the transcriptome data, Anja Ernst for her valuable help in the laboratory, and
Christina Schirmer, Sabine Donath and Claudia Wahl for their support in cultivating the rotifers. The authors would like to acknowledge Magdalena Litwin for providing rotifer specimens, Dr. Stefanie Hartmann
for her assistance in analysing the transcriptome data, Anja Ernst for her valuable help in the laboratory, and
Christina Schirmer, Sabine Donath and Claudia Wahl for their support in cultivating the rotifers. www.nature.com/scientificreports/ & Nielsen, R. Accuracy and power of statistical methods for detecting adaptive evolution
in protein coding sequences and for identifying positively selected sites. Genetics 168, 1041–1051 (2004). p
g
q
y
g p
y
119. Adzhubei, I. A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248–249 (2010) p
g
g
g
(
)
120. Suchard, M. A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, 016 (2018).f 121. Kiemel, K., de Cahsan, B., Paraskevopoulou, S., Weithoff, G. & Tiedemann, R. Mitochondrial genomes of the freshwater
monogonont rotifer Brachionus fernandoi and of two additional B. calyciflorus sensu stricto lineages from Germany and the
USA (Rotifera, Brachionidae). Mitochondrial DNA B 7, 646–648 (2022). USA (Rotifera, Brachionidae). Mitochondrial DNA B 7, 646 122. Kim, M.-S. et al. Complete mitochondrial genome of the freshwater monogonont rotifer Brachionus angularis (Rotifera,
chionidae). Mitochondrial DNA B. 5, 3754–3755 (2020). https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ 23. Kim, M.-S. et al. Complete mitochondrial genomes of two marine monogonont rotifer Brachionus manjavacas strains. Mito-
chondrial DNA B. 6, 1921–1923 (2021). 24. Suga, K., Mark Welch, D. B., Tanaka, Y., Sakakura, Y. & Hagiwara, A. Two circular chromosomes of unequal copy number make
up the mitochondrial genome of the rotifer Brachionus plicatilis. Mol. Biol. Evol. 25, 1129–1137 (2008). p
g
p
(
)
25. Hwang, D.-S. et al. Complete mitochondrial genome of the monogonont rotifer, Brachionus koreanus (Rotifera, Brachionidae)
Mitochondrial DNA B. 25, 29–30 (2014). 26. Kim, H.-S. et al. Complete mitochondrial genome of the monogonont rotifer Brachionus rotundiformis (Rotifera, Brachionidae)
Mitochondrial DNA B. 2, 39–40 (2017). 27. Choi, B.-S. et al. Complete mitochondrial genome of the freshwater monogonont rotifer Brachionus rubens (Rotifera, Brachio-
nidae). Mitochondrial DNA B. 5, 5–6 (2019). 28. Choi, B.-S. et al. Complete mitochondrial genome of the marine monogonont rotifer Proales similis (Rotifera, Proalidae)
Mitochondrial DNA B. 5, 1151–1152 (2020).i 29. Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A. & Minh, B. Q. W-IQ-TREE: A fast online phylogenetic tool for maximum
likelihood analysis. Nucleic Acids Res. 44, W232–W235 (2016). y
(
)
30. Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007). Author contributions K.K., R.T. and G.W. designed the research. K.K. and S.P. collected the samples. K.K. performed laboratory pro-
cessing of samples with support from K.H. K.K., M.G. and S.P. analysed the data with input from R.T. and G.W. K.K. produced the graphics and wrote the manuscript with the support of R.T. S.P., M.G. and G.W. All authors
approved the final version of the manuscript. © The Author(s) 2022 Funding g
Open Access funding enabled and organized by Projekt DEAL. This work was supported by Deutsche Forschun-
gsgemeinschaft (DFG) in the framework of the BioMove Research Training Group (DFG-GRK 2118). Additional information
Supplementary Information The online version contains supplementary material available at https://doi.org/
10.1038/s41598-022-27137-3. Additional information
Supplementary Information The online version contains supplementary material available at https://doi.org/
10.1038/s41598-022-27137-3. Correspondence and requests for materials should be addressed to R.T. Reprints and permissions information is available at www.nature.com/reprints. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and
nstitutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the
Creative Commons licence, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons licence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 |
|
https://openalex.org/W4206262157
|
https://www.frontiersin.org/articles/10.3389/fpls.2021.779834/pdf
|
English
| null |
Phenotyping and Quantitative Trait Locus Analysis for the Limited Transpiration Trait in an Upper-Mid South Soybean Recombinant Inbred Line Population (“Jackson” × “KS4895”): High Throughput Aquaporin Inhibitor Screening
|
Frontiers in plant science
| 2,022
|
cc-by
| 11,994
|
Phenotyping and Quantitative Trait
Locus Analysis for the Limited
Transpiration Trait in an Upper-Mid
South Soybean Recombinant Inbred
Line Population (“Jackson” ×
“KS4895”): High Throughput
Aquaporin Inhibitor Screening
Sayantan Sarkar1, Avat Shekoofa1*, Angela McClure1 and Jason D. Gillman2
1 Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States, 2 Plant Genetics Research Unit,
USDA-ARS University of Missouri Columbia MO United States 1 Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States, 2 Plant Genetics Research Unit,
USDA-ARS, University of Missouri, Columbia, MO, United States ORIGINAL RESEARCH
published: 20 January 2022
doi: 10.3389/fpls.2021.779834 Keywords: AgNO3, aquaporin inhibitor, genotyping, high throughput phenotyping, water conservation trait Edited by: Edited by:
Dejan Dodig,
Maize Research Institute Zemun Polje,
Serbia Edited by:
Dejan Dodig,
Maize Research Institute Zemun Polje,
Serbia Reviewed by:
Giriraj Kumawat,
ICAR-Indian Institute of Soybean
Research, India
Geng Bai,
University of Nebraska–Lincoln,
United States Reviewed by:
Giriraj Kumawat,
ICAR-Indian Institute of Soybean
Research, India
Geng Bai,
University of Nebraska–Lincoln,
United States *Correspondence:
Avat Shekoofa
ashekoof@utk.edu Specialty section:
This article was submitted to
Plant Abiotic Stress,
a section of the journal
Frontiers in Plant Science
Received: 19 September 2021
Accepted: 09 December 2021
Published: 20 January 2022 Soybean is most often grown under rainfed conditions and negatively impacted by
drought stress in the upper mid-south of the United States. Therefore, identification
of drought-tolerance traits and their corresponding genetic components are required to
minimize drought impacts on productivity. Limited transpiration (TRlim) under high vapor
pressure deficit (VPD) is one trait that can help conserve soybean water-use during late-
season drought. The main research objective was to evaluate a recombinant inbred line
(RIL) population, from crossing two mid-south soybean lines (“Jackson” × “KS4895”),
using a high-throughput technique with an aquaporin inhibitor, AgNO3, for the TRlim
trait. A secondary objective was to undertake a genetic marker/quantitative trait locus
(QTL) genetic analysis using the AgNO3 phenotyping results. A set of 122 soybean
genotypes (120-RILs and parents) were grown in controlled environments (32/25-d/n
◦C). The transpiration rate (TR) responses of derooted soybean shoots before and
after application of AgNO3 were measured under 37◦C and >3.0 kPa VPD. Then, the
decrease in transpiration rate (DTR) for each genotype was determined. Based on DTR
rate, a diverse group (slow, moderate, and high wilting) of 26 RILs were selected and
tested for the whole plant TRs under varying levels of VPD (0.0–4.0 kPa) at 32 and
37◦C. The phenotyping results showed that 88% of slow, 50% of moderate, and 11%
of high wilting genotypes expressed the TRlim trait at 32◦C and 43, 10, and 0% at 37◦C,
respectively. Genetic mapping with the phenotypic data we collected revealed three QTL
across two chromosomes, two associated with TRlim traits and one associated with leaf
temperature. Analysis of Gene Ontologies of genes within QTL regions identified several
intriguing candidate genes, including one gene that when overexpressed had previously
been shown to confer enhanced tolerance to abiotic stress. Collectively these results
will inform and guide ongoing efforts to understand how to deploy genetic tolerance for
drought stress. INTRODUCTION evaporative demand is higher. Under field conditions, drought-
tolerant peanut genotypes (with partial stomata closure trait)
displayed a downward LT slope with an increase in VPD during
midday (1100 to 1400 EST) (Balota and Sarkar, 2020). Bai and
Purcell (2018) observed an interaction between LT and slow and
fast-wilting soyabean genotypes, where slow-wilting genotypes
had a lower LT during water-deficit stress. Plant photosynthesis and transpirational rates are highly coupled
(Sinclair, 2017). Most of the water lost by plants under stress
is due to transpiration, which is linked to stomatal opening
to allow CO2 diffusion (Devi and Reddy, 2018a; Shekoofa
and Sinclair, 2020). Hence, water loss due to transpiration is
linked to plant biomass growth and yield (Tanner and Sinclair,
1983; Blum, 2009). Low water availability reduces assimilate
partitioning to reproductive sinks, and on a cellular level impairs
cell growth and division (Blum, 2011; Sarkar, 2020; Bennett
et al., 2021; Sarkar et al., 2021a). Water related stresses, such
as direct drought stress and associated factors including high
temperature and evaporative demand, reduce both transpiration
and photosynthesis, resulting in reduced crop yield (Sinclair,
2017; Balota et al., 2021). It is essential that any putative water saving trait should result
in monetarily relevant yield benefit and should have genetic
variability within the target crop species (Sadok and Sinclair,
2011). In fact, soybean genotype PI 416937 has been identified
as expressing the TRlim trait (i.e., slow-wilting) phenotype in the
field under high VPD (>2.5 kPa), and this has been traced to
low leaf hydraulic conductance (Sinclair et al., 2008). Sadok and
Sinclair (2012) suggested that the low leaf hydraulic conductance
in PI 416937 might be related to a unique population of
aquaporins (AQPs) in its leaves. Further studies have shown
that soybean genotypes expressing TRlim trait are insensitive to
aquaporin inhibitors, such as silver and zinc ions (Sadok and
Sinclair, 2010, 2012; Devi et al., 2016). However, it is suggested that under extreme drought or high
atmospheric vapor pressure deficit (VPD) conditions, restriction
of stomatal conductance might increase photosynthetic return
per unit of transpiration (Sinclair et al., 2005, 2010; Devi et al.,
2009; Gholipoor et al., 2010; Carpentieri-Pipolo et al., 2012;
Gaffney et al., 2015; Shekoofa et al., 2020). These traits result
in restricted TR under high vapor pressure conditions, such
that water is conserved in the soil and is available during
subsequent drought periods. INTRODUCTION Thus, plants resort to drought
avoidance mechanism such as limited transpiration (TRlim) and
minimizing stomatal conductance (Kooyers, 2015; Basu et al.,
2016; Devi et al., 2016). These studies also suggested that
reduced TR and stomatal conductance are controlled by gene
expression. Such mechanisms have been successfully studied in
crop species, including: maize (Zea Mays L.) (Fletcher et al., 2007;
Shekoofa et al., 2016), peanut (Arachis hypogaea L.) (Devi et al.,
2009; Shekoofa et al., 2013, 2017), cotton (Gossypium hirsutum
L.) (Devi and Reddy, 2018b; Shekoofa et al., 2020), sorghum
(Sorghum bicolor L.) (Gholipoor et al., 2010; Choudhary et al.,
2013), and soybean [Glycine max (L.) Merr.] (Bunce, 1981; Devi
et al., 2014; Sarkar et al., 2021b). Of particular interest, soybean
showed a decrease in stomatal conductance between VPD of 1.0
and 2.5 kPa, differing within genotypes (Bunce, 1981). In plants, AQPs occur in multiple isoforms in both
plasmalemma and tonoplast membranes resulting in regulation
of water flow in and out of cells. Physiological and molecular
studies have identified AQPs as playing key roles in regulating
hydraulic conductance in leaves and roots (Beaudette et al.,
2007; Shekoofa and Sinclair, 2018; Sung et al., 2021). Therefore,
the
high-throughput
phenotyping
of
structured
soybean
populations, along with molecular genotyping is needed for
marker development. This type of research is essential for
making the soybean genome sequence useful for breeding
purposes, in particular for screening drought-tolerant soybean
lines based on their sensitivity to aquaporin inhibitors. In this work, we used a two-tiered screening method to
identify soybean genotypes with the TRlim trait. Our method
is similar to the three-tiered approach by Sinclair et al. (2000). Direct measures of the transpiration response rate to increasing
VPD are low-throughput, tedious, and require specialized
equipment. Furthermore, the number of genotypes that can be
directly phenotyped for the TRlim trait is very limited. Thus, an
indirect measurement of TR that may be less accurate but can
allow characterization of a large number of genotypes would
be helpful in breeding for the TRlim trait (Choudhary and
Sinclair, 2014). Choudhary and Sinclair (2014) suggested that
one possibility is that the response in TR to feeding of chemical
inhibitors to leaves or roots of plants might allow discrimination
among genotypes under varying VPD levels. Appropriate parents
have to be chosen for crossing when it comes to screening for
drought tolerance traits. Abbreviations: TRlim, limited transpiration; VPD, vapor pressure deficit; RIL,
recombinant inbred line; QTL, quantitative trait locus; TR, transpiration rate;
DTR, decrease in transpiration rate; LT, leaf temperature; AQPs, aquaporins;
TRH2O, transpiration in water; TRAgNO3, transpiration rate following exposure
to silver nitrate; PCA, principle component analysis; H2, broad sense heritability;
DAP, days after planting; BP, breakpoint. Citation: Sarkar S, Shekoofa A, McClure A
and Gillman JD (2022) Phenotyping
and Quantitative Trait Locus Analysis
for the Limited Transpiration Trait in an
Upper-Mid South Soybean
Recombinant Inbred Line Population
(“Jackson” × “KS4895”): High
Throughput Aquaporin Inhibitor
Screening. January 2022 | Volume 12 | Article 779834 1 Frontiers in Plant Science | www.frontiersin.org Limited Transpiration in Soybean RILs Sarkar et al. INTRODUCTION Previous studies have reported that
soybean genotypes “KS4895” and “Jackson” differ in drought
tolerance traits such as delayed wilting, ureide, and nitrogen
concentration (Sinclair et al., 2007; Charlson et al., 2009; Hwang
et al., 2013, 2015a,b; King et al., 2014). Therefore, the objectives
of this study were to (a) evaluate 120 recombinant inbred lines
(RILs; F3 and F5 derived from “KS4895” × ”Jackson”) through
a high-throughput phenotyping technique while measuring
the RILs transpiration sensitivity rate to aquaporin inhibitor
(AgNO3) under high VPD condition (initial/indirect screening Decreases in transpiration rate and stomatal conductance are
affected by leaf temperature (LT) (Gates, 1964; Blum, 2011). Gates
(1964) argued convincingly that increase in LT can be lethal
for plants and that transpiration is required to cool the leaves. The study also argues that even a slow rate of transpiration can
dissipate enough heat from leaves to have a huge impact on
photosynthesis and growth of plants. This implies that plants
with slower rate of transpiration (with subsequently warmer
leaves than plants with higher rates of transpiration) could
be better drought-tolerant by conserving moisture during low
water stress, which would be available later in the season when January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 2 Limited Transpiration in Soybean RILs Sarkar et al. the derooted shoots were moved to a greenhouse in which both
temperature and VPD were high (Table 1). for TRlim) (b) directly measure the TR of 26 selected RILs from
objective “a” and categorize them for the TRlim trait under high
VPD and temperature (direct screening for TRlim), and finally (c)
undertake genetics/quantitative trait loci (QTLs) analysis for the
RIL population in objective “a” and associate the potential QTLs
with the drought tolerance trait, i.e., TRlim. Water-cooled lamps provided the photosynthetic photon flux
density, which was 600 µmol m−2 s−1 at plant level (Mullen and
Koller, 1988; Devi et al., 2016). The derooted shoots were allowed
to acclimatize for 60 min and then the flasks plus derooted shoots
were weighed (TR H2O initial). After another 60 min, the flasks
plus derooted shoots were reweighed (TR H2O final), and the
difference between the two weights divided by the time interval
was used to calculate the TR in water (TRH2O). INTRODUCTION Following the
second weighing of the derooted shoots in water, the individual
shoots were quickly transferred to dark-brown, 30-mL glass
bottles for exposure to the solution of 200 µM, AgNO3 aquaporin
inhibitor (Sadok and Sinclair, 2010). The AgNO3 solution was
freshly prepared on the day before each set of experiment. The
AgNO3 solution concentration of 200 µM was selected because
this concentration was the lowest concentration resulting in
maximum transpiration decrease (Sadok and Sinclair, 2010). The
derooted shoots were allowed to take up the AgNO3 solution
for 60 min by which time TR of the shoots had again reached a
constant value (Sadok and Sinclair, 2010). Leaf Temperature
h In each set, LT was measured for all tested derooted shoots using
a FLIR C3 Thermal Camera with WiFi (Teledyne FLIR LLC,
Wilsonville, OR, United States) between 1300 and 1500 CST. In
each set of experiment, the corresponding thermal images were
taken 1 m above the plant at a resolution of 0.9 cm per pixel
for three replications of derooted shoots. The temperature at the
central point of a fully expanded trifoliate leaf was obtained for
each of the three plants from a thermal image using the camera
software. The thermal data were collected after the last stage of
exposure to AgNO3 when the final weighing was done. These data
sets were used for calculating the average LT for each genotype. q
p
g
Five soybean seeds were planted in 3-L pots filled with soil
(commercially available Miracle-Gro potting mix) and inoculated
with Bradyrhizobium japonicum (Verdesian Life Sciences, Cary,
NC, United States). They were thinned to three plants per pot
after 1 week in three-pot replicates per genotype. Plants were
maintained in a well-watered condition, in 250 mL pots (i.e.,
pot capacity) during the initial growth pretreatment period. After
approximately 4 weeks, the plants were ready for AgNO3 test. For
the measurement of TR response to AQPs inhibitor, AgNO3, the
technique explained by Sadok and Sinclair (2010), Shekoofa et al. (2013), and Devi et al. (2016) was followed. Phenotyping and Phenotypic Traits
Experiment I Indirect Measurement of Transpiration Under High Vapor
Pressure Deficit: High Throughput Screening Using
Aquaporins Inhibitor, AgNO3 Frontiers in Plant Science | www.frontiersin.org Plant Materials and Study Site The experiments were conducted at the University of Tennessee
West Tennessee Research and Education Center (WTREC), in
Jackson, TN between 2018 and 2020. A group of 122 soybean
genotypes including 120 RILs and their parents “Jackson” and
“KS4895” that were tested during the study (Table 1) were
provided by Dr. Larry Purcell (Hwang et al., 2015a). Genotype
“KS4895” (PI 595081) is a maturity group (MG) IV developed in
Kansas (Schapaugh and Dille, 1998), and “Jackson” (PI 548657)
is an MG VII genotype developed by the USDA-ARS in North
Carolina (Johnson, 1958). Due to greenhouse space limitations,
and to increase the accuracy during data collection since a large
number of bottles were involved in each weighing process, only
a subset of genotypes was tested with the silver nitrate test. Thus,
the RILs were grown in six sets under controlled environments in
a greenhouse at 33–35◦C and 35–50% humidity during day, and
20–22◦C and 45–60% humidity during the night. Each set was
grown for 4 weeks and included both parents. After the 60 min period, all bottles were weighed to get
an initial weight for the transpiration measurement following
exposure to AgNO3 (TR AgNO3 initial). After 180 min, each
bottle was again weighed (TR AgNO3 final). Measurements of
TR for each shoot were generally completed in about 240 min
after AgNO3 treatment. The TR following exposure to silver
(TRAgNO3) was calculated based on the difference between these
two weights divided by the time interval. The difference between
TRH2O and TRAgNO3 were used to quantify decrease in TR using
various arithmetic combinations (Table 2). Statistical Analysis The evening before the application of AgNO3, three replicate
plants per soybean genotype were removed from the soil and
derooted by cutting the base of the plant stem underwater
using a sharp blade (Table 1). Then derooted soybean shoots
were immediately placed in 150-mL Erlenmeyer flasks filled with
deionized water. The shoots were kept in a dark laboratory room
overnight for about 14 to 15 h with temperature maintained
at 24◦C. The following morning, the derooted shoots were
transferred to another 150-mL Erlenmeyer flask containing fresh
deionized water and sealed with Parafilm-“M” (Pechiney Plastic
Packaging, Chicago, IL, United States) to avoid direct water
evaporation from the flask. Then, in each set of experiment, A mixed linear model was applied to TR response data using
the Fit Model function of JMP 14 (SAS Institute) using an input
of 120 RIL lines (and two parental lines), for which we had
both genotypic and phenotypic information. For mixed linear
models, three factors were included: (1) genotype; (2) experiment;
and (3) replication within each experiment. Only genotype
was considered fixed, whereas other factors were considered
random, and replication was nested within experiment. Principle
component analysis (PCA) was run to create a PCA biplot
of phenotypic measurements. Pearson’s correlation matrix was
used to measure correlation among phenotypes. Polynomial January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 3 “Jackson” and “KS4895” evaluated in this study. Statistical Analysis )
RIL
Date
Temp (◦C)
VPD (kPa)
RIL
Date
Temp (◦C)
VPD (kPa
Set 3
#90
07/31/2018
35.5–38
2.5–4
Set 6
#7
04/10/2019
37–38
2.5–4.2
#91
07/31/2018
35.5–38
2.5–4
#8
04/10/2019
37–38
2.5–4.2
#92
07/31/2018
35.5–38
2.5–4
#12
04/10/2019
37–38
2.5–4.2
#94
07/31/2018
35.5–38
2.5–4
#22
04/10/2019
37–38
2.5–4.2
#95
07/31/2018
35.5–38
2.5–4
#24
04/10/2019
37–38
2.5–4.2
#96
07/31/2018
35.5–38
2.5–4
#42
04/10/2019
37–38
2.5–4.2
#97
07/31/2018
35.5–38
2.5–4
#46
04/10/2019
37–38
2.5–4.2
#100
07/31/2018
35.5–38
2.5–4
#47
04/10/2019
37–38
2.5–4.2
#102
07/31/2018
35.5–38
2.5–4
#53
04/10/2019
37–38
2.5–4.2
#104
07/31/2018
35.5–38
2.5–4
#61
04/10/2019
37–38
2.5–4.2
#107
07/31/2018
35.5–38
2.5–4
#68
04/10/2019
37–38
2.5–4.2
#108
07/31/2018
35.5–38
2.5–4
#72
04/10/2019
37–38
2.5–4.2
#109
07/31/2018
35.5–38
2.5–4
#77
04/10/2019
37–38
2.5–4.2
Set 4
#113
08/07/2018
37–38
3–4.2
#78
04/10/2019
37–38
2.5–4.2
#115
08/07/2018
37–38
3–4.2
#80
04/10/2019
37–38
2.5–4.2
#117
08/07/2018
37–38
3–4.2
#86
04/10/2019
37–38
2.5–4.2
#120
08/07/2018
37–38
3–4.2
#88
04/10/2019
37–38
2.5–4.2
#121
08/07/2018
37–38
3–4.2
#93
04/10/2019
37–38
2.5–4.2
#125
08/07/2018
37–38
3–4.2
#98
04/10/2019
37–38
2.5–4.2
#127
08/07/2018
37–38
3–4.2
#106
04/10/2019
37–38
2.5–4.2
#129
08/07/2018
37–38
3–4.2
#124
04/10/2019
37–38
2.5–4.2
#131
08/07/2018
37–38
3–4.2
#128
04/10/2019
37–38
2.5–4.2
#133
08/07/2018
37–38
3–4.2
#130
04/10/2019
37–38
2.5–4.2
#134
08/07/2018
37–38
3–4.2
#135
04/10/2019
37–38
2.5–4.2
#136
08/07/2018
37–38
3–4.2
#138
04/10/2019
37–38
2.5–4.2
#137
08/07/2018
37–38
3–4.2
#143
04/10/2019
37–38
2.5–4.2
#139
08/07/2018
37–38
3–4.2
#144
04/10/2019
37–38
2.5–4.2
#140
08/07/2018
37–38
3–4.2
#147
04/10/2019
37–38
2.5–4.2
#141
08/07/2018
37–38
3–4.2
#151
04/10/2019
37–38
2.5–4.2
#142
08/07/2018
37–38
3–4.2
#152
04/10/2019
37–38
2.5–4.2
#149
08/07/2018
37–38
3–4.2
#153
08/07/2018
37–38
3–4.2
#154
08/07/2018
37–38
3–4.2
Set 5
#155
08/14/2018
37–38
3–4.3
#156
08/14/2018
37–38
3–4.3
(Continued Sarkar et al. Statistical Analysis Limited Transpiration in Soybean RILs RIL
Date
Temp (◦C)
VPD (kPa)
RIL
Date
Temp (◦C)
VPD (kPa)
RIL
Date
Temp (◦C)
VPD (kPa)
#34
07/05/2018
36–37
2.5–3.5
#157
08/14/2018
37–38
3–4.3
#35
07/05/2018
36–37
2.5–3.5
#160
08/14/2018
37–38
3–4.3
#36
07/05/2018
36–37
2.5–3.5
#161
08/14/2018
37–38
3–4.3
#71
07/05/2018
35.5–38
2.5–4
#162
08/14/2018
37–38
3–4.3
#73
07/05/2018
35.5–38
2.5–4
#164
08/14/2018
37–38
3–4.3
#74
07/05/2018
35.5–38
2.5–4
#165
08/14/2018
37–38
3–4.3
#79
07/05/2018
35.5–38
2.5–4
#166
08/14/2018
37–38
3–4.3
#81
07/05/2018
35.5–38
2.5–4
#168
08/14/2018
37–38
3–4.3
#87
07/05/2018
35.5–38
2.5–4
#169
08/14/2018
37–38
3–4.3
#89
07/05/2018
35.5–38
2.5–4
#170
08/14/2018
37–38
3–4.3
The plants were grown at 33–35◦C and 35–50% humidity during day, and 20–22◦C and 45–60% humidity during night. The date in this table presents the data collection date per each set for “experiment 1.” The
temperature (temp) and vapor pressure deficit (VPD) are the conditions that the plants were subjected to on the day of data collection. Along with the RILs both parents were tested in each set of data collection. regression was used to explain the variation of relative decrease
in TR due to LT. Broad Sense Heritability Broad sense heritability (H2) of all traits was calculated as the
ratio of genotypic variance (σ2
G) by phenotypic variance (σ2
P)
(Phansak et al., 2016). Variance was calculated as the ratio of total
sum of squares (TSS) to population size (n). The heritability data
have been included in Supplementary File 1. H2=
σ2
G
σ2
G+ σ2
Gσ2
E
E + σ2
E
ER
where
σ2
P
=
σ2
G+ σ2
Gσ2
E
E + σ2
E
ER;
o2
E, environmental variance; E, number of environments;
R, number of replications. H2=
σ2
G
σ2
G+ σ2
Gσ2
E
E + σ2
E
ER where
σ2
P
=
σ2
G+ σ2
Gσ2
E
E +
2 where o2
E, environmental variance; E, number of environments;
R, number of replications. o2
E, environmental variance; E, number of environments;
R, number of replications. Direct Measurement of Transpiration Under High Vapor
Pressure Deficit fi
Twenty-six soybean genotypes (24 RILs and both parents), based
on RDTRK and RNDTRK (from the indirect measurement of
transpiration, “Experiment I”), were selected to be tested for
the direct TR measurement under varying levels of VPD (0.5
to 4.0 kPa). Soybean genotypes that had RDTRK and RNDTRK
values from 0.00 to 0.50 were considered slow wilting, 0.51 to
1.00 were considered moderate wilting, and above 1.00 were
considered as fast wilting. The plants were grown in pots
constructed from polyvinyl chloride pipe (100-mm diameter
and 200-mm long). The bottom of each pot was fitted with
a flat end cap, in which a small hole was drilled to allow
drainage of excess water. A toilet flange was attached to the
top of the pot to allow easy attachment of a VPD chamber
during measurements (Fletcher et al., 2007; Shekoofa et al., 2013). The pots were filled with commercially available Miracle-Gro
potting mix. Five seeds per pot were sown and inoculated with
B. japonicum (Verdesian Life Sciences, Cary, NC, United States). After 1 week, the plants were thinned to one plant per pot. Plants
were fertilized with 200 mL of 0.075% V/V liquid fertilizer (0-
10-10, N-P2O5-K2O, GH Inc., Sebastopol, CA, United States) at
planting and again at 14 and 24 days after planting (DAP). Plants
were grown for 28 days under well-watered conditions, with
greenhouse temperatures regulated at 33◦C day/26◦C night. After
approximately 4 weeks, four replicate plants of each genotype
were selected and moved into a walk-in growth chamber and
enclosed in individual humidity-regulated chambers (21 L). As there were 12 individual chambers, this meant that the
genotypes had to be measured in batches that included three
genotypes in each batch. Measurements of transpiration response to VPD were carried
out at 32 and 37◦C. Each individual VPD chamber (21 L)
was fitted with a 12-V, 80-mm-diameter cooling fan (Masscool)
to continuously stir the air inside the chamber. Stirring of
the air helped to maintain plant temperature near ambient air
temperature within the VPD chamber. A humidity/temperature
data logger (Lascar Electronics) was mounted through the
sidewall of each container to monitor the environmental January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 5 Limited Transpiration in Soybean RILs Sarkar et al. Direct Measurement of Transpiration Under High Vapor
Pressure Deficit TABLE 2 | Various transpiration rate parameters and its derivatives used for evaluation of soybean genotypes, “experiment 1.”
Transpiration rate parameter
Full form
Formula
TRH2O
Transpiration rate in water
(TR H2O initial)−(TR H2O final)
Time interval
TRAgNO3
Transpiration rate following the aquaporin inhibitor (AgNO3) exposure
(TRAgNO3 initial)−(TRAgNO3 final)
Time interval
DTR
Decrease in transpiration rate
TRH2O−TRAgNO3
TRH2O
× 100
RTR
Ratio of transpiration rate
TRH2O
TRAgNO3
NDTR
Normalized decrease in transpiration rate
TRH2O−TRAgNO3
TRH2O+ TRAgNO3
RDTRJ
Relative decrease in transpiration rate by “Jackson”
DTR
DTR of Jackson
RDTRK
Relative decrease in transpiration rate by “KS4895”
DTR
DTR of“KS4895′′
RRTRJ
Relative ratio of transpiration rate by “Jackson”
RTR
RTR of“Jackson′′
RRTRK
Relative ratio of transpiration rate by “KS4895”
RTR
RTR of“KS4895′′
RNDTRJ
Relative normalized decrease in transpiration rate by “Jackson”
NDTR
NDTR of“Jackson′′
RNDTRK
Relative normalized decrease in transpiration rate by “KS4895”
NDTR
NDTR of“KS4895′′ BeadChip (Song et al., 2020), an Illumina Infinium
R⃝HD array. Genotypes were called using the iScan and Genome Studio
software (Illumina, San Diego, CA, United States) by Dr. Qijian
Song and Chuck Quigley of the USDA-ARS. Genotypic results
were imported into TASSEL 5 (Bradbury et al., 2007), where
nonsegregating markers were removed, missing genotypes were
imputed using LinkImpute (Money et al., 2015), functionality
incorporated into TASSEL 5 (settings = 30 High LD sites, 10
nearest, 10,000,000 maximum distance), and imputed genotypes
converted to ABH format (AA = “Jackson” allele homozygote,
AB = heterozygote, BB = “KS4895” allele homozygote) using
the ABH Genotype add-in. Data were then error-corrected
using the R package ABHGenotypeR (Reuscher and Furuta,
2016) with settings maxHapLength = 5 used throughout. This
resulted in 2,184 total genetic markers in the final genetic map. Genotypic data were then merged with phenotypic information
and imported in the QTL package in R (Broman and Sen,
2009). Distance between genetic markers was estimated using
the est.map function with settings typical of an F3 population
(error.prob = 0.01, overall genotypes ratios were AA = 33.0%,
AB = 33.8%, and BB = 33.3%). Markers which introduced large
gaps or increased genetic map length were identified using
the droponemarker1 command and manually removed if they
reduced the size of the overall genetic mapping significantly. conditions of the chamber. The plants were subjected to three
VPD levels: low (0–1.5 kPa), medium (1.5–2.5 kPa), and high
(2.5–4 kPa), on two consecutive days for each temperature (i.e.,
32 and 37◦C). Quantitative Trait Locus Analysis Genetic mapping was performed within the R/QTL program
(Broman and Sen, 2009) using two different QTL detection
methods: standard interval mapping (SIM) and composite
interval mapping (CIM) using the computer package R/QTL
(Broman and Sen, 2009). Lod thresholds were determined
from 1,000 permutation testing for each trait. Allelic effects
were estimated after using “sim.geno” function (16 draws and
an error probability of 0.01). QTL were used to build an
additive model, which was fitted, refined, and then refitted using 1https://github.com/kbroman/qtl/blob/master/R/droponemarker.R Direct Measurement of Transpiration Under High Vapor
Pressure Deficit The humidity in the VPD chambers was obtained
by adjusting the airflow rate through each chamber; in the case
of the highest VPD treatment (2.5–4 kPa), the air was also
initially flowed through a column of silica gel to dry the input
air (Fletcher et al., 2007). The observations of all plants for each genotype were
combined for a two-segment linear regression analysis (Prism 8.0,
GraphPad, Software Inc., San Diego, CA, United States) of TR
versus varying VPD at both levels 32 and 37◦C temperatures. If
VPD < BP, TR = Slope 1 (VPD) + Intercept 1. The slopes of the two linear regressions (Slopes 1 and 2)
were statistically compared to determine whether they differed
significantly (p < 0.05). If the slopes differed, the double-linear
regression was retained. When the slopes were not significantly
different, a simple linear regression was applied to all the data
(Devi et al., 2010; Shekoofa et al., 2020). Summary information on the genetic map is located
Supplementary File 2 and the complete R/QTL file containing
both genotypic and least square means (LSM) phenotypic data is
located in Supplementary File 3. Statistical Analysis The outputs of a successful regression fit to the two-segment
model were the coefficients defining two intersecting linear
regressions and the VPD value at the breakpoint (BP) between
the two linear segments: RESULTS FIGURE 1 | Box and whisker plots showing the differences in transpiration
rates of 122 soybean genotypes (A) in water, and (B) following the exposure
to an aquaporin inhibitor (AgNO3). the functions “makeqtl,” “refineqtl,” and “fitqtl.” Results were
extremely concordant between SIM and CIM; for brevity and
clarity only CIM results are presented in this study. 5%) and NDTR (0–0.02) whereas genotypes #52, #64, #17, #157,
#91, #23, #34, #136, #73, #45, and #57 had low DTR (5–10%)
and NDTR (0.03–0.05) (Supplementary Figure 1). However, the
LT had better correlation with RDTRK (r = 0.52, p < 0.0001)
and RNDTRK (r = 0.49, p < 0.0001) as compared with DTR
(r = 0.39, p < 0.0001) and NDTR (r = 0.38, p < 0.0001) (Table 4
and Figure 2). Furthermore, the analysis of data by a polynomial
regression showed that the variation in RDTRK and RNDTRK
could be explained by LT (R2 = 0.54 and 0.56) (Figure 3). Therefore, RDTRK and RNDTRK were used to select a diversity
of genotypes for further screening. Candidate Gene Analysis of Quantitative Trait Locus
Regions Genes present in QTL regions were examined to identify
potential candidate genes for the TRlim traits using the G. max
genome assembly version Glyma.Wm82.a2.1 (Schmutz et al.,
2010). Annotations were downloaded.2 We examined three detected QTL windows (Supplementary
Table 1) to investigate Gene Ontologies (GOs) terms for
biological process, cellular component, and molecular function. Genes were termed as candidates if they had biological process 2www.soybase.org, accessed November 11, 2021. Genetic Map Construction DNA was isolated from lyophilized leaf tissue for 118 out
of 120 RIL lines, as well as the parental lines “KS4895” and
“Jackson” using a Promega AS1600 kit (Promega, Madison, WI,
United States) using a Maxwell RSC instrument (Promega). Two genotypes did not germinate and the leaf tissue could
not be collected. Genotypes for genetic map creation and
QTL detection were obtained using the SoySNP6k iSelect January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 6 Limited Transpiration in Soybean RILs Sarkar et al. TABLE 3 | Summary of the phenotypic values distribution for greenhouse “experiment 1.”
Category
Least Sq mean LT
Least Sq mean TRAgNO3
Least Sq mean TRH2O
Mean
32.51
0.88
1.32
SD
1.25
0.38
0.60
SEM
0.11
0.03
0.05
Upper 95% mean
32.73
0.95
1.43
Lower 95% mean
32.28
0.81
1.21
N
122
122
122
Variance
1.56
0.14
0.36
Skewness
0.27
0.66
0.52
Kurtosis
0.57
−0.30
−0.14
CV
3.84
42.92
45.34
Jackson (RIL parent)
33.33 ± 0.86
0.94 ± 0.06
1.4 ± 0.1
KS4895 (RIL parent)
32.04 ± 0.86
0.8 ± 0.06
1.23 ± 0.1 TABLE 3 | Summary of the phenotypic values distribution for greenhouse “experiment 1.” FIGURE 1 | Box and whisker plots showing the differences in transpiration
rates of 122 soybean genotypes (A) in water, and (B) following the exposure
to an aquaporin inhibitor (AgNO3). GO terms associated with: abscisic acid, water transport, root
development, leaf senescence, jasmonic acid, heat acclimation,
stomata, and/or salicylic acid (Schulze, 1986; Jackson et al., 2000;
Schmutz et al., 2010; Khan et al., 2012; Jarzyniak and Jasinski,
2014; Sah et al., 2016). RESULTS Phenotyping and Phenotypic Traits
Indirect Measurement of Transpiration Under High
Vapor Pressure Deficit: High Throughput Screening
Using Aquaporins Inhibitor, AgNO3
Three primary traits (TRH2O, TRAgNO3, and LT) and nine
secondary traits (DTR, RTR, NDTR, RDTRJ, RDTRK, RRTRJ,
RRTRK, RNDTRJ, and RNDTRK) were phenotyped in the
experiment for all tested genotypes (Table 2). Phenotypic values
for the three primary traits followed a normal distribution for
LT and an approximately normal distribution for TRH2O and
TRAgNO3 (Table 3). Mean, upper 95% mean, and lower 95%
mean of TRH2O were higher than TRAgNO3 (1.32, 0.1.43, 1.21
for TRH2O compared with 0.88, 0.95, 0.81 for TRAgNO3) (Table 3
and Figure 1). Across RILs genotypes, #162, #89, #97, #74, #16,
#31, #161, #30, #168, #71, #26, and #137 had very low DTR (0–
5%)
d NDTR (0 0 02)
h
#52 #64 #17 #157 Phenotyping and Phenotypic Traits
Indirect Measurement of Transpiration Under High
Vapor Pressure Deficit: High Throughput Screening
Using Aquaporins Inhibitor, AgNO3
Three primary traits (TRH2O, TRAgNO3, and LT) and nine
secondary traits (DTR, RTR, NDTR, RDTRJ, RDTRK, RRTRJ,
RRTRK, RNDTRJ, and RNDTRK) were phenotyped in the
experiment for all tested genotypes (Table 2). Phenotypic values
for the three primary traits followed a normal distribution for
LT and an approximately normal distribution for TRH2O and
TRAgNO3 (Table 3). Mean, upper 95% mean, and lower 95%
mean of TRH2O were higher than TRAgNO3 (1.32, 0.1.43, 1.21
for TRH2O compared with 0.88, 0.95, 0.81 for TRAgNO3) (Table 3
and Figure 1). Across RILs genotypes, #162, #89, #97, #74, #16,
#31, #161, #30, #168, #71, #26, and #137 had very low DTR (0–
5%) and NDTR (0–0.02) whereas genotypes #52, #64, #17, #157,
#91, #23, #34, #136, #73, #45, and #57 had low DTR (5–10%)
and NDTR (0.03–0.05) (Supplementary Figure 1). However, the
LT had better correlation with RDTRK (r = 0.52, p < 0.0001)
and RNDTRK (r = 0.49, p < 0.0001) as compared with DTR
(r = 0.39, p < 0.0001) and NDTR (r = 0.38, p < 0.0001) (Table 4
and Figure 2). Furthermore, the analysis of data by a polynomial
regression showed that the variation in RDTRK and RNDTRK
could be explained by LT (R2 = 0.54 and 0.56) (Figure 3). Therefore, RDTRK and RNDTRK were used to select a diversity
of genotypes for further screening. Direct Measurement of Transpiration Under High
Vapor Pressure Deficit Based on RDTRK and RNDTRK values, 26 soybean genotypes
were divided into three levels. Values from 0.00 to 0.50 were January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 7 Sarkar et al. Limited Transpiration in Soybean RILs FIGURE 2 | Principle component biplot of various phenotypic traits of all 122 soybean genotypes evaluated in this work. Traits farther from the center have higher
variance, and higher the angle between traits lower the correlation. FIGURE 2 | Principle component biplot of various phenotypic traits of all 122 soybean genotypes evaluated in this work. Traits farther from the center have higher
variance, and higher the angle between traits lower the correlation. FIGURE 2 | Principle component biplot of various phenotypic traits of all 122 soybean genotypes evaluated in this work. Traits farther from the center have higher
variance, and higher the angle between traits lower the correlation. FIGURE 2 | Principle component biplot of various phenotypic traits of all 122 soybean genotypes evaluated in this work. Traits farther from the center have higher
variance and higher the angle between traits lower the correlation TABLE 4 | Pearson’s correlation matrix of all direct and traits measured in this study. Leaf temp (◦C)
TR H2O
TR AgNO3
DTR
RTR
NDTR
RDTRJ
RDTRK
RRTRJ
RRTRK
RNDTRJ
RNDTRK
Leaf temp (◦C)
1.00
***
***
***
***
***
***
***
**
***
**
***
TR H2O
0.47
1.00
***
***
***
***
***
***
***
***
***
***
TR AgNO3
0.32
0.79
1.00
ns
***
**
***
***
**
***
***
***
DTR
0.39
0.50
−0.06
1.00
***
**
***
***
***
***
***
***
RTR
0.34
0.44
−0.16
0.91
1.00
**
***
***
***
***
***
***
NDTR
0.38
0.49
−0.10
0.98
0.96
1.00
***
***
***
***
***
***
RDTRJ
0.14
0.57
0.20
0.79
0.59
0.71
1.00
***
***
***
***
***
RDTRK
0.52
0.53
0.38
0.32
0.18
0.28
0.36
1.00
***
***
***
***
RRTRJ
0.10
0.58
0.10
0.76
0.79
0.79
0.81
0.28
1.00
***
***
***
RRTRK
0.24
0.52
0.41
0.23
0.13
0.19
0.47
0.85
0.43
1.00
***
***
RNDTRJ
0.10
0.59
0.19
0.76
0.62
0.72
0.98
0.35
0.88
0.50
1.00
***
RNDTRK
0.49
0.52
0.37
0.30
0.18
0.26
0.33
1.00
0.28
0.85
0.33
1.00
Bottom left is the coefficient of correlation, top right half is significance level. Frontiers in Plant Science | www.frontiersin.org Direct Measurement of Transpiration Under High
Vapor Pressure Deficit Significance levels: ***P < 0.0001; **P < 0.01; ns, non-significant at P > 0.05. TABLE 4 | Pearson’s correlation matrix of all direct and traits measured in this study. considered as “slow wilting,” 0.51 to 1.00 as “moderate wilting,”
and above 1.00 “fast wilting.” Genotypes exhibited a decrease in
TR slope over increasing VPD, indicating the expression of the
TRlim trait, and those with constant linear slope exhibited no decrease in TR under high VPD, indicating the lack of the TRlim
trait. For example, between two parents “KS4895” expressed the
TRlim trait and “Jackson” did not (Figure 4). For those genotypes
that expressed the TRlim trait, the point on x-axis where the slope January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org Frontiers in Plant Science | www.frontiersin.org 8 Limited Transpiration in Soybean RILs Sarkar et al. FIGURE 3 | Regression curves of relative difference in transpiration rate response by “KS4895” (RDTRK) and relative normalized difference in transpiration rate by
“KS4895” (RNDTRK) over the leaf temperature for 122 soybean genotypes. FIGURE 3 | Regression curves of relative difference in transpiration rate response by “KS4895” (RDTRK) and relative normalized difference in transpiration rate by
“KS4895” (RNDTRK) over the leaf temperature for 122 soybean genotypes. FIGURE 4 | Transpiration rate response of two soybean genotypes (“Jackson”
and “KS4895”) over different levels of vapor pressure deficit at 32◦C. FIGURE 4 | Transpiration rate response of two soybean genotypes (“Jackson”
and “KS4895”) over different levels of vapor pressure deficit at 32◦C. Quantitative trait locus analysis was performed for four
drought-related traits using LSM calculated from phenotypic
measurements
taken
during
our
greenhouse
experiments
(Table 6). Three QTLs were identified in total (Tables 6, 7), two
QTLs for the TR traits (qTR_Gm10_1 and qTR_Gm12_1), and
one associated with LT (qLT_Gm12_1) (Figure 5). q
g
Furthermore, the effect of each QTL was estimated (Table 6). Alleles from “KS4895” for the qTR_Gm10_1 QTL were associated
with reduced transpiration relative to “Jackson” (−0.63 mg
H2O m2−1 s−1). In contrast, alleles from “Jackson” for the
qTR_Gm12_1 QTL were associated with reduced transpiration
relative to “KS4895” (−0.27 mg H2O m2−1s−1). The lowest TR
(and presumably most water saving) lines had a combination
of QTL from two different parents: qTR_Gm10_1 for “KS4895”
allele and qTR_Gm12_1 for the “Jackson” allele (Table 7). Identification of Candidate Genes From
Quantitative Trait Locus Regions changed was considered as the VPD breakpoint. Within slow
wilting genotypes, 6 out of 7 were found to express the TRlim trait
(i.e., VPD breakpoint) at high VPD under 32◦C (Table 5). Among
genotypes in moderate wilting category, 5 out of 10, and in high
wilting only 1 out of 9 expressed the TRlim trait at 32◦C. Whereas,
at 37◦C, the expression of TRlim trait was found to be limited only
to 3 out of 7 in slow wilting, 1 out of 10 in moderate wilting, and
none among fast wilting genotypes. g
For genes within three detected QTL windows in this work
(Table 6)
using
the
“Williams
82”
genome
assembly
2
(Glyma.W82.a2.1), we examined gene ontologies (biological
process, cellular component, and molecular function). Genes
were termed as candidate genes (Table 7 and Supplementary
Table 1) for the TRlim traits if they had biological process GO
terms associated with any of the following terms: abscisic acid,
water transport, root development, leaf senescence, jasmonic
acid, heat acclimation, stomata, and/or salicylic acid. It should be
noted that very few genes in soybean have direct experimental
or empirical evidence for gene function, and in large part
gene annotations are inferred from homologs identified by
BLAST searches using genomic assemblies from other species
(typically Arabidopsis). Direct Measurement of Transpiration Under High
Vapor Pressure Deficit Lines
which inherited alleles from “KS4895” for qLT_Gm12_1, which
was distinct from the TR QTL, had lower leaf temperatures
(0.84◦C lower on average). FIGURE 4 | Transpiration rate response of two soybean genotypes (“Jackson”
and “KS4895”) over different levels of vapor pressure deficit at 32◦C. Genotyping and Quantitative Trait Locus
Discovery A genetic map was created from genotypic data obtained using
the SoySNP6K Illumina array (Akond et al., 2013). The final
genetic map was composed of 2,181 genetic markers (average
109/chromosome) encompassing a total of 2,856.4 cm (each
chromosome was 142.8 cm on average) (Supplementary File 2). January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 9 Limited Transpiration in Soybean RILs Sarkar et al. TABLE 5 | Vapor pressure deficit (VPD) breakpoints of 26 soybean genotypes at 32 and 37◦C. Genotypes
RDTRK
RNDTRK
VPD breakpoint at
32◦C
37◦C
Slow wilting
Low-rate RDTRK and RNDTRK
#16
0.14
0.13
1.7
2.10
#91
0.24
0.22
2.7
Linear
#23
0.29
0.27
1.4
3.34
#73
0.30
0.27
2.9
1.96
#22
0.35
0.26
1.3
Linear
#79
0.43
0.40
2.8
Linear
#151
0.49
0.38
Linear
Linear
Moderate wilting
Mid-rate RDTRK and RNDTRK
#87
0.71
0.67
3.0
2.39
#102
0.72
0.68
Linear
Linear
#24
0.75
0.66
2.2
Linear
#168
0.78
0.78
Linear
Linear
#55
0.79
0.76
Linear
Linear
#93
0.79
0.71
2.1
Linear
#14
0.86
0.84
Linear
Linear
#56
0.92
0.91
Linear
Linear
#147
0.93
0.90
2.9
Linear
“KS4895”
1.00
1.00
2.0
Linear
Fast wilting
High-rate RDTRK and RNDTRK
#35
1.07
1.08
2.8
Linear
#152
1.08
1.12
Linear
Linear
#51
1.42
1.52
Linear
Linear
#108
1.51
1.64
Linear
Linear
#3
1.81
2.02
Linear
Linear
“Jackson”
3.05
3.61
Linear
Linear
#134
3.28
3.49
Linear
Linear
#142
6.24
7.25
Linear
Linear
#139
9.77
12.73
Linear
Linear
These genotypes have been selected based on “experiment 1” results. The wilting categories (slow, moderate, and fast) were determined based on the RDTRK and
RNDTRK values. Values from 0.0 to 0.50 were considered slow wilting, 0.51 to 1.0 were considered moderate wilting, and above 1.0 were considered as fast wilting. Both parents were included with the RILs. TABLE 5 | Vapor pressure deficit (VPD) breakpoints of 26 soybean genotypes at 32 and 37◦C. Fast wilting These genotypes have been selected based on “experiment 1” results. The wilting categories (slow, moderate, and fast) were determined based on the RDTRK and
RNDTRK values. Values from 0.0 to 0.50 were considered slow wilting, 0.51 to 1.0 were considered moderate wilting, and above 1.0 were considered as fast wilting. Both parents were included with the RILs. Within the qTR_Gm12_1 QTL region (Gm12:35946078-
36388059; Table 7 and Supplementary Table 1), we identified
eight candidate genes based on GO annotation (Supplementary
Table 1). Genotyping and Quantitative Trait Locus
Discovery Unfortunately, none of the candidate genes has any
direct evidence for gene function, with all annotations inferred
based on BLAST identification of presumably homologous
genes from other species. Four of the candidate genes in this
region are putative transcription factors (Glyma.12G199100,
Glyma.12G199200, Glyma.12G199600, and Glyma.12G203100)
whose annotations are associated with abiotic stress responses. Another interesting candidate gene is a homolog of a stomatal
patterning
gene
(Glyma.12G202700). The
qTR_Gm12_1
QTL displayed significant allelic differences for TR using
H2O
(Table
6),
but
no
significant
differences
between
parental alleles in the presence of the aquaporin inhibitor
(TRAgNO3). Although,
no
obvious
aquaporin
gene
is
present within the region identified in the “Williams 82”
reference genome, it remains possible that a nonobvious Within
the
qTR_Gm10_1
region
(Gm10:116991–
1903082;
Table
7),
we
identified
eight
candidate
genes
(Table
7
and
Supplementary
Table
1). These
included
three
ubiquitin
signaling
associated
genes
(Glyma.10G018800,
Glyma.10G019000,
Glyma.10G019500,
and Glyma.10G021500), a glycoside hydrolase/polygalacturonase
gene
(Glyma.10G016100),
an
abiotic
stress-associated
transcription factor (Glyma.10G016500) and two genes of
unknown function annotated as involved in root hair cell
differentiation
(Glyma.10G016600
and
Glyma.10G016700). One very intriguing candidate gene is Glyma.10G016600
(UniRef100_E0A235),
which
is
annotated
as
a
“drought
resistance
protein”
and
was
initially
identified
via
transcriptomic
studies
in
response
to
drought
stress,
and the researchers confirmed this gene’s role in abiotic
stress
tolerance
via
transgenic
overexpression,
which
conferred
increased
tolerance
for
several
abiotic
stresses
(Song et al., 2013). January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 10 Sarkar et al. Genotyping and Quantitative Trait Locus
Discovery Limited Transpiration in Soybean RILs Trait
QTL name
Coincident QTL
QTL peak
QTL interval
df
Type III SS
LOD
%var
P-value (Chi2)
P-value (F)
Allelic effect1
TR-H2O
qTR_Gm10_1
qSV_Gm102
Gm10@6.6 cM
2–14 cM
2
10.20
9.26
27.59
0
1.36E-09
−0.63 mg H2O m2−1 s−1
qTR_Gm12_1
qSV_Gm122
Gm12@138.0 cM
136–142 cM
2
5.29
5.21
14.29
0
1.03E-05
0.27 mg H2O m2−1 s−1
TR-AgNO3
q TR_10_1
qSV_Gm102
Gm10@6.6 cM
4–19 cM
2
2.57
7.57
25.58
2.69E-08
4.20E-08
−0.35 mg H2O m2−1 s−1
TR H2O – AgNO3
qTR_Gm10_1
qSV_Gm102
Gm10@6.6 cM
0–18 cM
2
2.48
4.45
13.75
0
5.43E-05
−0.28 mg H2O m2−1 s−1
qTR_Gm12_1
qSV_Gm122
Gm12@138.0 cM
136–142 cM
2
3.37
5.87
18.64
0
2.40E-06
0.25 mg H2O m2−1 s−1
LT (◦C)
qLT_Gm12_1
-
Gm12@91.0 cM
81–98 cM
2
30.09
4.80
17.10
1.57E-05
2.08E-05
−0.84◦C
1E ti
t d ll li
ff
t
f h
J
k
KS4895
ce | www.frontiersin.org aquaporin-encoding gene (but not identified as such either
due to problems with the assembly or diverged between
“Williams 82” and the parental lines) is present within
the qTR_Gm12_1 QTL region, which was affected by the
silver inhibitor and forms the underlying genetic basis for
qTR_Gm12_1 QTL. Within the qLT_Gm12_1 QTL region associated with
differential
LT
(Gm12:6971475.11867391,
Table
7
and
Supplementary Table 1), we identified a total of 312 genes,
of which 29 were termed candidate genes based on GO term
and KOG annotations. Only one gene was noted to have any
functional characterization; Glyma.12G104800 was identified
through RNA-Seq/RT-PCR analysis as associated with response
to salt stress (Sun et al., 2019). Other potential candidate
genes for the QTL include an aquaporin (Glyma.12G097800);
eight genes are involved in abscisic acid biosynthesis/signaling
(Glyma.12G087200,
Glyma.12G089200,
Glyma.12G094800,
Glyma.12G096100,
Glyma.12G098900,
Glyma.12G103100,
Glyma.12G106400, and Glyma.12G108900), and a there were
large
number
of
transcription
factors
with
annotations,
which
suggest
involvement
in
abiotic
stress
responses
(Glyma.12G087000,
Glyma.12G094500,
Glyma.12G094800,
Glyma.12G096100,
Glyma.12G098800,
Glyma.12G100100,
Glyma.12G100600,
Glyma.12G103100,
Glyma.12G104500,
Glyma.12G104600,
Glyma.12G104800,
Glyma.12G105400,
Glyma.12G105600, Glyma.12G106400, and Glyma.12G110400). Frontiers in Plant Science | www.frontiersin.org Phenotyping and Phenotypic Traits Treating the soybean plants with AgNO3, aquaporin inhibitor
reduced the TR responses (Table 3 and Figure 1). Silver
inhibition has been linked to the sulfhydryl group of cysteine
residue of AQPs resulting in blockage of the pore for water
passage (Niemietz and Tyerman, 2002). A couple of studies
using aquaporin inhibitor, silver nitrate on derooted, and intact
soybean plants indicated that most soybean genotypes were
quite sensitive to the treatment with silver nitrate (Sadok
and Sinclair, 2010; Devi et al., 2015). However, they reported
a varying range of DTRs across genotypes. In the current
research, the DTR amount varied across genotypes, ranging
from 0.46 to 74.6% (Supplementary Figure 1). Twelve RILs
had very low DTR (#162, #89, #97, #74, #16, #31, #161,
#30, #168, #71, #26, and #137) ranging from 0–5%, whereas
the other eleven genotypes had DTR ranging from 5–10%
(#52, #64, #17, #157, #91, #23, #34, #136, #73, #45, and
#57) (Supplementary Figure 1). These genotypes were almost
insensitive to AgNO3 exposure and can be categorized as slow
wilting (Sadok and Sinclair, 2010). The results also indicated that AgNO3 could be an effective
way for high-throughput screening of drought tolerant soybean
genotypes. Previous studies have suggested that silver nitrate
(AgNO3) may be an effective initial screen for the expression
of the TRlim trait in a multitier screening system (Sadok
and Sinclair, 2010; Choudhary and Sinclair, 2014; Shekoofa
and Sinclair, 2018). In this work, the second tier (first being January 2022 | Volume 12 | Article 779834 11 Limited Transpiration in Soybean RILs Sarkar et al. TABLE 7 | Candidate gene summary for three QTL regions. Trait
QTL
QTL interval
Physical QTL interval
(Gmax.W82.a2.1)
Total # genes
in region
Candidate genes in
region1
TR H2O; TRAgNO3; (TR H2O – TRAgNO3)
qTR_Gm10_1
4–19 cM
Gm10:116991–1903082
81
8
TR H2O; (TR H2O – TRAgNO3)
qTR_Gm12_1
136–142 cM
Gm12:35946078–36388059
55
8
LT (◦C)
qLT_Gm12_1
81–98 cM
Gm12:6971475–11867391
312
29
1Candidate genes were determined based on presence of GO terms associated with abscisic acid, water transport, root development, leaf senescence, jasmonic acid,
stomata, and/or salicylic acid. FIGURE 5 | Composite interval mapping results. (A) Transpiration rate response (mg H2O m−2 s−1) QTL mapping results. Black indicates TRH2O, blue indicates
TRAgNO3, and red indicates TRH2O – TRAgNO3. (B) Leaf temperature (LT) QTL mapping results, black indicates TRH2O results, and blue indicates LT results. Vertical
axis is logarithm of odds (LOD) score. Phenotyping and Phenotypic Traits Horizontal axis is markers along chromosomes 10 and 12, ascending in genetic position from left to right. TABLE 7 | Candidate gene summary for three QTL regions. Trait
QTL
QTL interval
Physical QTL interval
(Gmax.W82.a2.1)
Total # genes
in region
Candidate genes in
region1
TR H2O; TRAgNO3; (TR H2O – TRAgNO3)
qTR_Gm10_1
4–19 cM
Gm10:116991–1903082
81
8
TR H2O; (TR H2O – TRAgNO3)
qTR_Gm12_1
136–142 cM
Gm12:35946078–36388059
55
8
LT (◦C)
qLT_Gm12_1
81–98 cM
Gm12:6971475–11867391
312
29
1Candidate genes were determined based on presence of GO terms associated with abscisic acid, water transport, root development, leaf senescence, jasmonic acid,
stomata, and/or salicylic acid. FIGURE 5 | Composite interval mapping results. (A) Transpiration rate response (mg H2O m−2 s−1) QTL mapping results. Black indicates TRH2O, blue indicates
TRAgNO3, and red indicates TRH2O – TRAgNO3. (B) Leaf temperature (LT) QTL mapping results, black indicates TRH2O results, and blue indicates LT results. Vertical
axis is logarithm of odds (LOD) score. Horizontal axis is markers along chromosomes 10 and 12, ascending in genetic position from left to right. Of all primary and secondary traits, those subjected to
PCA, RDTRK, and RNDTRK had the best correlation with LT
(Figure 2). The regression curve of RDTRK and RNDTRK
with the LT shows that the slope is negligible for temperature
rates below 32◦C, but it drastically changes with increasing
the temperature above 32◦C (Figure 3). At optimum LT (24–
32◦C), the TR response was almost constant. These findings
were confirmed through the direct measurement of TR responses
under high VPD conditions at 32 and 37◦C (i.e., the second-tier
screening). Almost 88% of slow wilting genotypes (i.e., the
least sensitive genotypes to AgNO3 exposure), 50% of moderate
wilting genotypes, and 11% of high wilting genotypes (i.e., highly
sensitive genotypes to AgNO3 exposure) expressed the TRlim trait
at 32◦C. This was consistent with our hypothesis and previous
studies done on other legume crops (Devi et al., 2010; Shekoofa
et al., 2017). The genotypes with low sensitivity to aquaporin
inhibitor, AgNO3, had the TRlim trait with VPD breakpoint (BP)
at about 1.3–2.9 kPa (Table 5). The TRlim at lower VPD rates
(i.e., 1.3–2.9 kPa) allows those genotypes to conserve moisture
so that there would be more water available in the soil during
late-season drought to sustain soybeans physiological activities
and complete seed fill. Limitations of Our Study and Future
Directions about 43, 10, and 0% for slow, moderate, and high wilting
genotypes from Experiment I, respectively. This could be because
the rest of genotypes which expressed the TRlim (i.e., VPD
BP) at 32◦C started to increase TR under 37◦C to disperse
excess temperature and heat. Shekoofa et al. (2016) reported
that if very high temperatures are frequent, even to the point
of being high enough to threaten plants with heat stress, it
may be advantageous to consider corn hybrids that lose the
TRlim trait at 38◦C rather than at 32◦C or other temperatures
below 38◦C. However, soybean genotypes #16, #23, #73, and
#87 allowed full expression of the TRlim trait under both
temperatures (i.e., 32 and 37◦C) and displayed the maximum
water conservation, no matter what the temperature regime
was and performed better than both parents. Further evaluation
of these genotypes should be done in field by simulating
drought conditions. about 43, 10, and 0% for slow, moderate, and high wilting
genotypes from Experiment I, respectively. This could be because
the rest of genotypes which expressed the TRlim (i.e., VPD
BP) at 32◦C started to increase TR under 37◦C to disperse
excess temperature and heat. Shekoofa et al. (2016) reported
that if very high temperatures are frequent, even to the point
of being high enough to threaten plants with heat stress, it
may be advantageous to consider corn hybrids that lose the
TRlim trait at 38◦C rather than at 32◦C or other temperatures
below 38◦C. However, soybean genotypes #16, #23, #73, and
#87 allowed full expression of the TRlim trait under both
temperatures (i.e., 32 and 37◦C) and displayed the maximum
water conservation, no matter what the temperature regime
was and performed better than both parents. Further evaluation
of these genotypes should be done in field by simulating
drought conditions. Although one of the RIL parental lines (“Jackson”) has
resequencing data publicly available,3 the other parental line
(“KS4895”) to our knowledge has not been resequenced. Moreover, no resources for fine-level genetic mapping (e.g.,
near-isogenic lines) have previously been developed for detected
QTL regions identified for the TRlim traits. As such, fine-
mapping, identification of gene polymorphisms, correlation of
polymorphisms with water use efficiency, and TRlim traits, and
the ultimate cloning of causative polymorphisms from within
QTL regions remains to future work. Limitations of Our Study and Future
Directions Nevertheless, our results strongly suggest that advanced
mapping populations can reveal QTLs for drought-tolerance
traits under complicated genetic control to enhance the TRlim
trait (i.e., ability to tolerate late-season drought) in a RIL soybean
population from crossing “KS4895” × “Jackson.” Validation of
identified QTLs will be useful in molecular breeding of these
favorable and informative QTL alleles for a superior cultivar
with the ability to produce stable yield under water limiting
conditions. It will be an interesting approach to associate these
alleles with other agronomic traits, which are tightly linked to
desirable drought tolerance traits to increase soybean yield and
production under dryland conditions. Genotyping and Quantitative Trait Locus
Discovery Quantitative trait loci analysis for the RILs population was
done to associate the potential QTLs with the drought tolerance
traits. Two QTLs (qTR_Gm10_1 and qTR_Gm12_1; Table 6)
overlapped with two previously identified QTLs (qSV_Gm10 and
qSV_Gm12) associated with drought responses from PI 416937
(Carpentieri-Pipolo et al., 2012). QTL conditioning the sensitivity
of plants to silver nitrate were located in the same chromosomal
regions reported by Carpentieri-Pipolo et al. (2012). Although,
from investigations of pedigrees, it does not appear that the
population (“Jackson” × “KS4895”) studied in the current
research has any direct pedigree connection to the previously
studied PI416937, but these QTL may be evidence that variation
in the same underlying genes is causative. DATA AVAILABILITY STATEMENT The datasets presented in this study can be found in online
repositories. The
names
of
the
repository/repositories
and
accession
number(s)
can
be
found
in
the
article/
Supplementary Material. Furthermore, it has been hypothesized that insensitivity to
AgNO3 could be related to QTLs and the trait could be heritable
(Devi et al., 2016). Our study also found that all primary and
secondary traits had high broad sense heritability (H2 from 0.68
to 0.90) (Table 8). Therefore, these drought-tolerant traits can
be used for phenotypic selection of soybean genotypes in future
breeding efforts. 3https://soybase.org/projects/SoyBase.B2014.02.php, accessed November 17, 2021. AUTHOR CONTRIBUTIONS AS and SS: conceptualization and writing – original draft
preparation. AS, SS, and JG: methodology and data curation. AS:
investigation, resources, visualization, supervision, and funding
acquisition. AS, SS, JG, and AM: writing – review and editing. All authors have read and agreed to the published version
of the manuscript. The “KS4895” allele of the qTR_Gm10_1 QTL was associated
with lower TR (Table 6). This was true for the H2O treatment
(−0.63 mg H2O m2−1 s−1) and the AgNO3 treatment (−0.35 mg
H2O m2−1 s−1) as well as the differential trait (TR H2O –
AgNO3; −0.28 mg H2O m2−1 s−1). In contrast, the “KS4895”
allele of the qTR_Gm12_1 QTL had higher TR under the H2O
treatment (+0.27 mg H2O m2−1 s−1), and the differential trait
(+0.25 mg H2O m2−1 s−1), but not with the AgNO3 treatment
alone (Table 6). Phenotyping and Phenotypic Traits The plants with TRlim trait have also
shown to delay wilting under rainfed conditions (Devi et al., 2010;
Shekoofa et al., 2020). TABLE 8 | Broad sense heritability (H2) values of all direct and indirect traits
measured in this study. Trait
H2
TR H2O
0.86
TR AgNO3
0.90
DTR
0.78
NDTR
0.88
RTR
0.70
RDTRJ
0.77
RNDTRJ
0.74
RRTRJ
0.69
RDTRK
0.74
RNDTRK
0.87
RRTRK
0.68
LT (◦C)
0.90
H2 values range from 0 to 1; values closer to 1 have better heritability. alues range from 0 to 1; values closer to 1 have better heritability. AgNO3 treatment) would involve selection of fewer genotypes
for intensive and direct phenotyping for the TR response
under increasing VPD conditions. Therefore, it allowed for
considering not only the DTR trait, but also several other
secondary traits to represent the reduction in TR response. A simple but less accurate screen that allows a large number of
genotypes to be examined is a first-tier screen, followed by tiers of
more sophisticated screens of decreasing numbers of genotypes
(Sinclair, 2011). AgNO3 treatment) would involve selection of fewer genotypes
for intensive and direct phenotyping for the TR response
under increasing VPD conditions. Therefore, it allowed for
considering not only the DTR trait, but also several other
secondary traits to represent the reduction in TR response. A simple but less accurate screen that allows a large number of
genotypes to be examined is a first-tier screen, followed by tiers of
more sophisticated screens of decreasing numbers of genotypes
(Sinclair, 2011). Although the TR response results observed at 37◦C (i.e.,
Experiment II) show that observations of the TRlim trait at
32◦C do not necessarily predict expression of the trait at
higher temperatures, the expression of TRlim trait reduced to January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org Frontiers in Plant Science | www.frontiersin.org 12 Limited Transpiration in Soybean RILs Sarkar et al. REFERENCES doi: 10.2135/cropsci2009.04.0220 Bennett, R. S., Chamberlin, K., Morningweg, D., Wang, N., Sarkar, S., Balota, M.,
et al. (2021). “Response to drought stress in a subset of the U.S. peanut mini-
core evaluated in three states,” in Proceedings of the American Peanut Research
and Education Society Annual Meeting, Salt Lake City, UT. Fletcher, A. L., Sinclair, T. R., and Allen, L. H. (2007). Transpiration responses
to vapor pressure deficit in well watered ‘slow-wilting’ and commercial
soybean. Environ. Exp. Bot. 61, 145–151. doi: 10.1016/j.envexpbot.2007. 05.004 Blum, A. (2009). Effective use of water (EUW) and not water-use efficiency (WUE)
is the target of crop yield improvement under drought stress. Field Crops Res. 112, 119–123. doi: 10.1016/j.fcr.2009.03.009 Gaffney, J., Schussler, J., Löffler, C., Cai, W., Paszkiewicz, S., Messina, C., et al. (2015). Industry-scale evaluation of maize hybrids selected for increased yield
in drought-stress conditions of the US corn belt. Crop Sci. 55, 1608–1618. doi: 10.2135/cropsci2014.09.0654 Blum, A. (ed.). (2011). “Plant water relations, plant stress and plant production,”
in Plant Breeding for Water-Limited Environments (New York, NY: Springer),
11–52. Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y.,
and Buckler, E. S. (2007). TASSEL: software for association mapping of
complex traits in diverse samples. Bioinformatics 23, 2633–2635. doi: 10.1093/
bioinformatics/btm308 Gates, D. M. (1964). Leaf temperature and transpiration 1. Agron. J. 56, 273–277. doi: 10.2134/agronj1964.00021962005600030007x Gholipoor, M., Prasad, P. V. V., Mutava, R. N., and Sinclair, T. R. (2010). Genetic variability of transpiration response to vapor pressure deficit among
sorghum genotypes. Field Crops Res. 119, 85–90. doi: 10.1016/j.fcr.2010. 06.018 Broman, K. W., and Sen, S. (2009). A Guide to QTL Mapping With R/qtl. Dordrecht:
Springer. Hwang, S., King, C. A., Davies, M. K., Charlson, D. V., Ray, J. D., Cregan,
P. B., et al. (2015a). Registration of the KS4895× Jackson soybean mapping
population, AR93705. J. Plant Regist. 9, 266–271. doi: 10.3198/jpr2014.05.00
34crmp Bunce, J. A. (1981). Comparative responses of leaf conductance to humidity in
single attached leaves. J. Exp. Bot. 32, 629–634. doi: 10.1093/jxb/32.3.629 Carpentieri-Pipolo, V., Pipolo, A. E., Abdel-Haleem, H., Boerma, H. R., and
Sinclair, T. R. (2012). Identification of QTLs associated with limited leaf
hydraulic conductance in soybean. Euphytica 186, 679–686. doi: 10.1007/
s10681-011-0535-6 Hwang, S., King, C. A., Davies, M. K., Ray, J. D., Cregan, P. B., and Purcell, L. C. (2013). QTL analysis of shoot ureide and nitrogen concentrations in soybean
[Glycine max (L.) Merr.]. Crop Sci. REFERENCES Devi, J. M., Sinclair, T. R., Chen, P., and Carter, T. E. (2014). Evaluation of elite
southern maturity soybean breeding lines for drought-tolerant traits. Agron. J. 106, 1947–1954. doi: 10.2134/agronj14.0242 Akond, M., Liu, S., Schoener, L., Anderson, J. A., Kantartzi, S. K., Meksem, K.,
et al. (2013). A SNP-based genetic linkage map of soybean using the SoyS –
NP6K illumina infinium beadchip genotyping array. Plant Genet. Genomics
Biotechnol. 1, 80–89. doi: 10.5147/jpgs.2013.0090 Devi, J. M., Sinclair, T. R., Vadez, V., and Krishnamurthy, L. (2009). Peanut
genotypic variation in transpiration efficiency and decreased transpiration
during progressive soil drying. Field Crops Res. 114, 280–285. Bai, H., and Purcell, L. (2018). Aerial canopy temperature differences between
fast-and slow-wilting soya bean genotypes. J. Agron. Crop Sci. 204, 243–251. Devi, M. J., and Reddy, V. R. (2018a). Effect of temperature under different
evaporative demand conditions on maize leaf expansion. Environ. Exp. Bot. 155,
509–517. doi: 10.1093/jexbot/51.350.1505 Balota, M., and Sarkar, S. (2020). “Transpiration of peanut in the field under rainfed
production,” in Proceedings of the American Peanut Research and Education
Society Annual Meeting. Devi, M. J., and Reddy, V. R. (2018b). Transpiration response of cotton to vapor
pressure deficit and its relationship with stomatal traits. Front. Plant Sci. 9:1572. doi: 10.3389/fpls.2018.01572 Balota, M., Sarkar, S., Cazenave, A., and Kumar, N. (2021). “Plant characteristics
with significant contribution to peanut yield under extreme weather conditions
in virginia, USA,” in Proceedings of the ASA, CSSA, SSSA International Annual
Meeting 2021, Salt Lake City, UT. Devi, M. J., Sinclair, T. R., and Taliercio, E. (2015). Comparisons of the effects
of elevated vapor pressure deficit on gene expression in leaves among two
fast-wilting and a slow-wilting soybean. PLoS One 10:e0139134. doi: 10.1371/
journal.pone.0139134 Basu, S., Ramegowda, V., Kumar, A., and Pereira, A. (2016). Plant adaptation to
drought stress . F1000Research doi: 10.12688/f1000research.7678.1 Devi, M. J., Sinclair, T. R., and Taliercio, E. (2016). Silver and zinc inhibitors
influence transpiration rate and aquaporin transcript abundance in intact
soybean plants. Environ. Exp. Bot. 122, 168–175. doi: 10.1016/j.envexpbot.2015. 10.006 Beaudette, P. C., Chlup, M., Yee, J., and Emery, R. J. (2007). Relationships of
root conductivity and aquaporin gene expression in Pisum sativum: diurnal
patterns and the response to HgCl2 and ABA. J. Exp. Bot. 58, 1291–1300. doi: 10.1093/jxb/erl289 Devi, M. J., Sinclair, T. R., and Vadez, V. (2010). Genotypic variation in peanut
for transpiration response to vapor pressure deficit. Crop Sci. 50, 191–196. ACKNOWLEDGMENTS We would like to thank the United Soybean Board (USB) and
the University of Tennessee, Plant Sciences Department for
sponsoring this research. We would like to thank Qijian Song
and Chuck Quigley of the USDA-ARS for running SoySNP6K
arrays on their instrument, and recognize the superb technical
contribution of USDA-ARS technician Jeremy Mullis who was We identified a relatively small number of candidate genes
from within detected QTL regions (8, 8, and 29 for qTR_Gm10_1,
qTR_Gm12_1, and qLT_Gm12_1, respectively) based on GO
terms associated with abscisic acid, water transport, root
development, leaf senescence, jasmonic acid, stomata, and/or
salicylic acid. These candidate genes will be useful for future
efforts to determine the causative genetic basis for the three
QTLs we identified. January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 13 Limited Transpiration in Soybean RILs Sarkar et al. Supplementary Figure 1 | Variation of decrease in transpiration rate (DTR) and
normalized decrease in transpiration rate (NDTR) among 122 soybean genotypes. responsible for DNA isolation and quality control. Also, we thank
Larry Purcell and Andy King at the University of Arkansas for
providing the seeds for this research. We would furthermore like
to thank Kendall Sheldon and Sara Safikhan for their assistance
during data collection. Supplementary Figure 1 | Variation of decrease in transpiration rate (DTR) and
normalized decrease in transpiration rate (NDTR) among 122 soybean genotypes. Supplementary Figure 2 | Diagram of a two-tiered screening method to identify
soybean genotypes with the TRlim trait. Supplementary Table 1 | Candidate genes from GO term analysis from within
QTL regions identified in this study. Supplementary File 1 | Heritability analysis and values of all direct and
indirect traits. SUPPLEMENTARY MATERIAL Supplementary File 2 | Details on genetic map and marker distribution. The Supplementary Material for this article can be found
online at: https://www.frontiersin.org/articles/10.3389/fpls.2021. 779834/full#supplementary-material Supplementary File 3 | R/QTL package file containing genotypic and phenotypic
data used for genetic mapping. REFERENCES Transpiration response of ’slow-wilting’ and
commercial soybean (Glycine max (L.) Merr.) genotypes to three aquaporin
inhibitors. J. Exp. Bot. 61, 821–829. doi: 10.1093/jxb/erp350 Song, Q., Yan, L., Quigley, C., Fickus, E., Wei, H., Chen, L., et al. (2020). Soybean
BARCSoySNP6K: an assay for soybean genetics and breeding research. Plant J. 104, 800–811. doi: 10.1111/tpj.14960 Sadok, W., and Sinclair, T. R. (2011). Crops yield increase under water-limited
conditions: review of recent physiological advances for soybean genetic
improvement. Adv. Agron. 113, v–vii. Song, W. W., Duan, F. M., Li, W. B., Lin, Q., Zhou, H. X., Han, X., et al. (2013). GmPOI gene encoding a Pollen Ole_e_I conserved domain is involved in
response of soybean to various stresses. Biol. Plant 57, 85–90. doi: 10.1007/
s10535-012-0258-0 Sadok, W., and Sinclair, T. R. (2012). Zinc treatment results in transpiration rate
decreases that vary among soybean genotypes. J. Plant Nutr. 35, 1866–1877. doi: 10.1080/01904167.2012.706683 Sah, S. K., Reddy, K. R., and Li, J. (2016). Abscisic acid and abiotic stress tolerance
in crop plants. Front. Plant Sci. 7:571. doi: 10.3389/fpls.2016.00571 Sun, L., Song, G., Guo, W., Wang, W., Zhao, H., Gao, T., et al. (2019). Dynamic
changes in genome-wide histone3 lysine27 trimethylation and gene expression
of soybean roots in response to salt stress. Front. Plant Sci. 10:1031. doi: 10. 3389/fpls.2019.01031 Sarkar, S. (2020). Development of High-Throughput Phenotyping Methods and
Evaluation of Morphological and Physiological Characteristics of Peanut in a
Sub-Humid Environment. Ph.D. thesis. Blacksburg, VA: Virginia Polytechnic
Institute and State University. Sung, C., Balota, M., Sarkar, S., Bennett, R., Chamberlin, K., Wang, N., et al. (2021). “Genome-wide association study on peanut water deficit stress tolerance using
the u.s. minicore to develop improvement for breeding,” in Proceedings of the
American Peanut Research and Education Society Annual Meeting. Sarkar, S., Ramsey, A. F., Cazenave, A.-B., and Balota, M. (2021a). Peanut leaf
wilting estimation from RGB color indices and logistic models. Front. Plant Sci. 12:713. doi: 10.3389/fpls.2021.658621 Tanner, C., and Sinclair, T. (1983). “Efficient water use in crop production: research
or re-search?,” in Limitations to Efficient Water Use in Crop Production, eds
H. M. Taylor, W. A. Jordan, and T. R. Sinclair (Madison, WISC: American
Society of Agronomy). Sarkar, S., Shekoofa, A., Mcclure, A., and Gillman, J. D. (2021b). REFERENCES 53, 2421–2433. doi: 10.2135/cropsci2012.11. 0641 Charlson, D. V., Bhatnagar, S., King, C. A., Ray, J. D., Sneller, C. H., Carter, T. E. Jr.,
et al. (2009). Polygenic inheritance of canopy wilting in soybean [Glycine max
(L.) Merr.]. Theor. Appl. Genet. 119, 587–594. doi: 10.1007/s00122-009-1068-4 Hwang, S., King, C. A., Ray, J. D., Cregan, P. B., Chen, P., Carter, T. E. Jr.,
et al. (2015b). Confirmation of delayed canopy wilting QTLs from multiple
soybean mapping populations. Theor. Appl. Genet. 128, 2047–2065. doi: 10. 1007/s00122-015-2566-1 Choudhary, S., and Sinclair, T. R. (2014). Chemical screen for limited-
transpiration-rate trait among sorghum genotypes. J. Crop Improv.28, 377–389. doi: 10.1080/15427528.2014.893942 Jackson, R. B., Sperry, J. S., and Dawson, T. E. (2000). Root water uptake and
transport: using physiological processes in global predictions. Trends Plant Sci. 5, 482–488. doi: 10.1016/S1360-1385(00)01766-0 Choudhary, S., Sinclair, T. R., and Prasad, P. V. V. (2013). Hydraulic conductance
of intact plants of two contrasting sorghum lines, SC15 and SC1205. Funct. Plant Biol. 40, 730–738. doi: 10.1071/FP12338 Frontiers in Plant Science | www.frontiersin.org January 2022 | Volume 12 | Article 779834 14 Limited Transpiration in Soybean RILs Sarkar et al. Jarzyniak, K. M., and Jasinski, M. (2014). Membrane transporters and drought
resistance – a complex issue. Front. Plant Sci. 5:687. doi: 10.3389/fpls.2014. 00687 Shekoofa, A., Safikhan, S., Snider, J. L., Raper, T. B., and Bourland, F. M. (2020). Variation in stomatal conductance responses of cotton cultivars to high vapour
pressure deficit under controlled and rainfed environments. J. Agron. Crop Sci. 207, 332–343. doi: 10.1111/jac.12440 Johnson, H. W. (1958). Registration of soybean varieties, VI 1. Agron. J. 50,
690–691. doi: 10.2134/agronj1958.00021962005000110016x 207, 332–343. doi: 10.1111/jac.12440 Shekoofa, A., Sinclair, T. R., Messina, C. D., and Cooper, M. (2016). Variation
among maize hybrids in response to high vapor pressure deficit at high
temperatures. Crop Sci. 56, 392–396. Khan, N. A., Nazar, R., Iqbal, N., and Anjum, N. A. (2012). Phytohormones and
Abiotic Stress Tolerance in Plants. Dordrecht: Springer Science and Business
Media. doi: 10.1007/978-3-642-25829-9_3 Shekoofa, A., Sinclair, T., Aninbon, C., Holbrook, C., Isleib, T., Ozias-Akins, P.,
et al. (2017). Expression of the limited-transpiration trait under high vapour
pressure deficit in peanut populations: runner and virginia types. J. Agron. Crop
Sci. 203, 295–300. King, C. A., Purcell, L. C., Bolton, A., and Specht, J. E. (2014). A possible
relationship between shoot n concentration and the sensitivity of N2 fixation
to drought in soybean. Crop Sci. REFERENCES 54, 746–756. doi: 10.2135/cropsci2013.04.0271 Sinclair, T. R. (2011). Challenges in breeding for yield increase for drought. Trends
Plant Sci. 16, 289–293. doi: 10.1016/j.tplants.2011.02.008 Kooyers, N. J. (2015). The evolution of drought escape and avoidance in natural
herbaceous populations. Plant Sci. 234, 155–162. doi: 10.1016/j.plantsci.2015. 02.012 Sinclair, T. R. (2017). “Limited-transpiration rate under elevated atmospheric
vapor pressure deficit,” in Water-Conservation Traits to Increase Crop
Yields in Water-deficit Environments, ed. T. R. Sinclair (Cham: Springer),
11–16. Money, D., Gardner, K., Migicovsky, Z., Schwaninger, H., Zhong, G. Y., and Myles,
S. (2015). LinkImpute: fast and accurate genotype imputation for nonmodel
organisms. G3 (Bethesda) 5, 2383–2390. doi: 10.1534/g3.115.021667 Sinclair, T. R., Hammer, G. L., and Van Oosterom, E. J. (2005). Potential yield and
water-use efficiency benefits in sorghum from limited maximum transpiration
rate. Funct. Plant Biol. 32, 945–952. doi: 10.1071/FP05047 Mullen, J. A., and Koller, H. R. (1988). Daytime and nighttime carbon balance
and assimilate export in soybean leaves at different photon flux densities. Plant
Physiol. 86, 880–884. doi: 10.1104/pp.86.3.880 Niemietz, C. M., and Tyerman, S. D. (2002). New potent inhibitors of aquaporins:
silver and gold compounds inhibit aquaporins of plant and human origin. FEBS
Lett. 531, 443–447. doi: 10.1016/s0014-5793(02)03581-0 Sinclair, T. R., Messina, C. D., Beatty, A., and Samples, M. (2010). Assessment
across the United States of the benefits of altered soybean drought traits. Agron. J. 102, 475–482. doi: 10.2134/agronj2009.0195 Phansak, P., Soonsuwon, W., Hyten, D. L., Song, Q., Cregan, P. B., Graef, G. L.,
et al. (2016). Multi-population selective genotyping to identify soybean [Glycine
max (L.) Merr.] seed protein and oil QTLs. G3 (Bethesda) 6, 1635–1648. doi:
10.1534/g3.116.027656 Sinclair, T. R., Purcell, L. C., King, C. A., Sneller, C. H., Chen, P., and Vadez,
V. (2007). Drought tolerance and yield increase of soybean resulting from
improved symbiotic N2 fixation. Field Crops Res. 101, 68–71. Sinclair, T. R., Zwieniecki, M. A., and Holbrook, N. M. (2008). Low leaf hydraulic
conductance associated with drought tolerance in soybean. Physiol. Plant 132,
446–451. doi: 10.1111/j.1399-3054.2007.01028.x Reuscher, S., and Furuta, T. (2016). ABHgenotypeR: Easy Visualization of ABH
Genotypes. R Package Version 1. Available online at: http://github.com/
StefanReuscher/ABHgenotypeR 446–451. doi: 10.1111/j.1399-3054.2007.01028.x Sinclair, T., Purcell, L., Vadez, V., Serraj, R., King, C. A., and Nelson, R. (2000). Identification of soybean genotypes with N2 fixation tolerance to water deficits. Crop Sci. 40, 1803–1809. Sadok, W., and Sinclair, T. R. (2010). REFERENCES “Phenotyping and
QTLs analysis for the limited transpiration trait in soybean RILs population
‘Jackson’ X ‘KS4895’: high throughput screening,” in Proceedings of the ASA,
CSSA, SSSA International Annual Meeting 2021, Salt Lake City, UT. Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. Schapaugh, W., and Dille, R. (1998). Registration of ‘KS4895’soybean. Crop Sci. 38,
892–892. doi: 10.2135/cropsci1998.0011183x003800030065x Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature 463, 178–183. Publisher’s Note: All claims expressed in this article are solely those of the authors
and do not necessarily represent those of their affiliated organizations, or those of
the publisher, the editors and the reviewers. Any product that may be evaluated in
this article, or claim that may be made by its manufacturer, is not guaranteed or
endorsed by the publisher. Schulze, E. D. (1986). Carbon dioxide and water vapour exchange in response
to drought in the atmosphere and in the soil. Annu. Rev. Plant Physiol. 37,
247–274. Shekoofa, A., and Sinclair, T. R. (2018). Aquaporin activity to improve crop
drought tolerance. Cells 7:123. doi: 10.3390/cells7090123 Shekoofa, A., and Sinclair, T. R. (2020). Abscisic acid and sulfate offer a possible
explanation for differences in physiological drought response of two maize
near-isolines. Plants (Basel) 9:1713. doi: 10.3390/plants9121713 Copyright © 2022 Sarkar, Shekoofa, McClure and Gillman. This is an open-access
article distributed under the terms of the Creative Commons Attribution License
(CC BY). The use, distribution or reproduction in other forums is permitted, provided
the original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. No
use, distribution or reproduction is permitted which does not comply with these terms. Shekoofa, A., Devi, J. M., Sinclair, T. R., Holbrook, C. C., and Isleib, T. G. (2013). Divergence in drought-resistance traits among parents of recombinant
peanut inbred lines. Crop Sci. 53, 2569–2576. doi: 10.2135/cropsci2013.03. 0153 January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 15
|
https://openalex.org/W3122685436
|
https://fip.dp.ua/index.php/FIP/article/download/1041/1160
|
Ukrainian
| null |
ЛАТИНОАМЕРИКАНСЬКИЙ ВЕКТОР ЗОВНІШНЬОЇ ПОЛІТИКИ ІЗРАЇЛЮ: ТЕХНОЛОГІЧНИЙ ВИМІР
|
Fìlosofìâ ta polìtologìâ v kontekstì sučasnoï kulʹturi
| 2,020
|
cc-by
| 6,734
|
ЛАТИНОАМЕРИКАНСЬКИЙ ВЕКТОР ЗОВНІШНЬОЇ ПОЛІТИКИ
ІЗРАЇЛЮ: ТЕХНОЛОГІЧНИЙ ВИМІР Received 30 September 2020; revised 23 October 2020; аccepted 16 November 2020
DOI: 10.15421/352039
Анотація Аналізуються відносини між Ізраїлем та країнами Латинської Америки за останні десятиліття
(2000-2019 роки), і стверджується, що зміцнившийся імідж Ізраїлю як технологічного лідера, грає
ключову роль у цьому. Автори приділили особливу увагу з’ясуванню технологій зовнішньої політики
Ізраїлю на латиноамериканському напрямку, визначенню особливостей їх реалізації та результатів
застосування. Країни Латинської Америки стали розглядати Ізраїль як джерело технологій. Тенденція
спостерігається практично повсюдно і незалежно від політичної ситуації на Близькому Сході
та триваючого ізраїльсько-палестинського конфлікту. В останні роки, паралельно з політичними
кризами та зміною режиму у Латинській Америці, у країнах континенту відбулися значні поліпшення
у напрямку Ізраїлю. Перші дипломатичні візити прем’єр-міністра Ізраїлю Бен’яміна Нетан’яху до
латиноамериканських країн сприяли підписанню низки двосторонніх угод у різних сферах. Ключові слова: зовнішня політика, Ізраїль, Латинська Америка, вектор, дипломатія, ліві,
праві, технологічний підхід. МІЖНАРОДНІ ВІДНОСИНИ Влада Русланівна Нєгіна
Аспірантка кафедри міжнародних відносин,
Дніпровський національний університет
імені Олеся Гончара,
пр. Гагаріна 72, Дніпро, 49000, Україна
Е-mail: vnegina17@gmail.com,
Олександр Юрійович Висоцький
Доктор політичних наук, професор, професор
кафедри міжнародних відносин Дніпровського
національного університету імені Олеся Гончара,
пр. Гагаріна 72, Дніпро, 49000, Україна
Email: vysalek@gmail.com,
УДК 13 +122
ЛАТИНОАМЕРИКАНСЬКИЙ ВЕ
ІЗРАЇЛЮ: ТЕХНОЛ
Received 30 September 2020; revised 23 O Vlada Niehina
Ph.D. student of of the International Relations
Department,
Oles Honchar Dnipro National University,
72 Gagarin Ave., Dnipro, 49010, Ukraine
ORCID ID: https://orcid.org/0000-0002-2293-423X
Oleksandr Vysotskyi
D.Sc. (Political Science), PhD (History), Professor,
Professor of the International Relations Department,
Oles Honchar Dnipro National University,
72 Gagarin Ave., Dnipro, 49010, Ukraine
ORCID ID: https://orcid.org/0000-0003-0712-8499 Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Постановка проблеми. вільйон на Всесвітній виставці-2020 [Lazaroff
2019]. Усі ці події свідчать про позитивні змі
ни сприйняття Ізраїлю щодо до палестинсько
го питання, і це, безперечно, стосується також
країн Латинської Америки. В останні роки дипломатична діяльність
Ізраїлю в Латинській Америці активізувалася. У 2017 році прем’єр-міністр Ізраїлю Бен’ямін
Нетан’яху відвідав Аргентину, Колумбію,
Парагвай та Мексику. У 2018 році він відві
дав Колумбію, Гондурас, Чилі, Гватемалу та
Аргентину. Ближче до кінця цього року він
відлетів до Бразилії (ставши першим діючим
прем’єр-міністром Ізраїлю, який відвідав цю
країну), щоб відвідати церемонію інавгурації
президента Жаїра Болсонаро. Президент Бра
зилії здійснив взаємний візит до Єрусалиму
у 2019 році, повторивши свою підтримку ви
знання Єрусалима столицею Ізраїлю [Landau
2019; Oster 2019]. Дипломатичні зусилля, зда
ється, приносять свої результати. На додаток
до міцних та тривалих економічних відносин
між Латинською Америкою та Ізраїлем, по
літичні зв’язки були посилені. Пропалестин
ський запал ряду країн, зокрема деяких країн
Латинської Америки, зменшився за останнє
десятиліття внаслідок наполегливої зовніш
ньої політики Ізраїлю на глобальному та регі
ональному рівнях. На відміну від напружених
відносин між США та Ізраїлем за адміністра
ції колишнього президента Барака Обами,
зв’язки з Вашингтоном досягли нової куль
мінації з переїздом в Єрусалим посольства
США за часів президентства США Дональда
Трампа. Однак у деяких районах цей крок був
сприйнятий як загострення ізраїльсько-па
лестинського конфлікту, оскільки не було за
пропоновано жодного діючого механізму для
просування мирного процесу. Незважаючи на те, що існує значна кіль
кість літератури про детермінанти ізраїльської
зовнішньої політики, є дуже мало досліджень,
присвячених зростаючому впливу Ізраїлю у
Латинській Америці. Однією з причин цього
є своєрідна позиція Ізраїлю у своєму регіоні,
тобто більша частина грантів стосовно Ізраї
лю присвячена арабо-ізраїльському конфлік
ту, з особливим акцентом на ізраїльсько-па
лестинський мирний процес. Відповідно,
роботи із зовнішньої політики Ізраїлю в ос
новному досліджують динаміку регіональної
політики на Близькому Сході та у Північній
Африці. Окрім регіональних справ, іноземні
політики в Ізраїлі зробили важливі кроки у
напрямку розвитку відносин з країнами Ла
тинської Америки, Африки та Східної Азії. Тісні зв’язки Ізраїлю з Латинською Америкою
простежуються з часів створення єврейської
держави. Однак є кілька пояснень пожвав
лення цього явища. Необхідно вивчити як
системні, так і внутрішні фактори. Окрім по
гляду на Ізраїль, слід звернути увагу на остан
ні трансформації, що відбулися у Латинській
Америці. Ми прагнемо зробити це з позицій
технологічного підходу. Це означає, що зов
нішня політика Ізраїлю розглядається нами
як система технологій, спрямованих на реа
лізацію національних інтересів Ізраїльської
держави в латиноамериканському регіоні. Latin American Vector of Israel’s Foreign Policy:
Technological Dimension
Abstract This article analyzes relations between Latin American countries and Israel over the past decades (2000-
2019) and argues that Israel’s strengthened image as a technological leader. The authors paid special attention
to clarifying the technologies of Israel’s foreign policy in the Latin American direction, determining the specifics
of their implementation and the results of their application. Latin American countries to start viewing Israel
as a new and intriguing source for technology. This trend is almost across the board and irrespective of the
political situation in the Middle East and the ongoing Israeli-Palestinian conflict. In recent years, parallel to
the political crises and regime changes in Latin America, there has been a significant improvement in countries
on the continent towards Israel. The first diplomatic visits of Israeli Prime Minister Benjamin Netanyahu to
Latin American countries contributed to the signing of a number of bilateral agreements in various fields. The potential of economic growth in emerging markets such as Latin America makes it an attractive
destination for Israeli investors. The region is projected to expand in the next few years despite continued
economic uncertainty. The Israeli government is currently endorsing long-term investment channels in Latin
America to take advantage of these developments. © В.Р.Нєгіна, О.Ю.Висоцький, 2020. All rights reserved. 94 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Keywords: foreign policy, Israel, Latin America, vector, diplomacy, left-wing, right-wing, technological
approach Keywords: foreign policy, Israel, Latin America, vector, diplomacy, left-wing, right-wing, technological
approach. Постановка проблеми. Ми
розглядаємо дипломатичні обміни, політи
ку та торгівлю, а також культуру та оборону. Важливо також дослідити сектори, через які
розвиваються відносини, щоб запропонува
ти всеосяжну основу для розуміння останніх
подій у зовнішній політиці Ізраїлю. Нарешті,
досліджуємо останні події у відносинах між
Ізраїлем та країнами регіону. А
і
і
і
і
б і Регіональний розвиток також сприяв фор
муванню середовища в певних частинах сві
ту, яке є більш прихильним до Ізраїлю. Країни
Перської затоки утримуються від пропаганди
палестинських справ занадто голосно, щоб не
викликати протидії єврейській державі. Багато
хто вважав візит Бен’яміна Нетан’яху до Ома
ну у 2018 році переломним моментом, який
відкрив давні, неспокійні зв’язки та нову еру
у відносинах. Аналогічним чином, намагаю
чись нормалізувати відносини з Ізраїлем, Ду
бай погодився дозволити Ізраїлю відкрити па Аналіз останніх досліджень і публіка
цій. Грунтуючись на аналізі останніх публіка
цій по темі статті, варто відзначити, що остан 95 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Об’єднаних Націй для нещодавно створеної
держави. Однак підтримка Латинською Аме
рикою створення та визнання Ізраїлю була
здебільшого результатом тісних відносин цих
країн із США. нім часом з’явилася певна кількість цікавих
робіт з зовнішньої політики Ізраїлю у лати
ноамериканському регіоні. Ми хотіли б ви
ділити низку цікавих досліджень, серед яких
праці Д.Ваксмана [20], М.Діманта [3], А.М. Кацовіча [8], Я.Бар-Сіман-Тов [9], С.Р.Девіда
[2], А.Рана [14], Дж.А. Кахана [14], Г.Вермен
бола [21]. Ці роботи заклали міцну основу для
осмислення досліджуваної теми і дали нам
значний імпульс для розуміння зовнішньої
політики Ізраїлю в технологічному вимірі. Бразилія – найбільша країна Латинської
Америки, особливо голосно схвалила «План
розділу 1947 року на Генеральній Асамблеї
ООН». Хоча Бразилія була не єдиною краї
ною Латинської Америки, яка проголосувала
за, бразильський дипломат Озвалду Аран’я зі
грав ключову роль у процесі як тодішній гене
ральний секретар Генеральної Асамблеї ООН. Через його перенесення сесії, прихильники
плану мали додатковий час, щоб переконати
інші країни проголосувати на підтримку Їзраї
лю. Гватемала також була особливо важливою
учасницею дискусій як член Спеціального ко
мітету для Палестини (ЮНСКОП), де її пред
ставляв тодішній посол Хорхе Гарсія Грана
дос. Ізраїль згодом відзначив обидві країни та
їх відповідних представників. Взаємні дипло
матичні місії були створені в Ізраїлі та різних
країнах Латинської Америки, починаючи з
1949 року. Протягом наступних років двосто
ронні відносини швидко зміцнювались. Мета роботи - з’ясувати технології зов
нішньої політики Ізраїлю на латиноамерикан
ському напрямку, визначити особливості їх
реалізації та результати застосування. Постановка проблеми. Методологічною основою дослідження
став технологічний підхід, який дозволив нам
структурувати знання про зовнішню політику
Ізраїлю таким чином, щоб виділити її ефек
тивні практики, які можуть бути інтерпрето
вані як технології. Виклад основного матеріалу. Коротка історія ізраїльсько-латиноаме
риканських відносин Коротка історія ізраїльсько-латиноаме
риканських відносин гатьох країн регіону на прагматичну позицію,
яка диверсифікує їх економічних та диплома
тичних партнерів у всьому світі. Політичний клімат у Латинській Амери
ці під час «холодної війни» сприяв підтримці
Сполученими Штатами військових режимів,
які залежали від використання сили для сво
го виживання. Таким чином, ще одним фак
тором, який поставив відносини Ізраїлю з
країнами Латинської Америки у негативному
світлі, було озброєння таких правих урядів. Військові зв’язки між Ізраїлем та Латинською
Америкою можна простежити ще до 1970-х
років; зброя, що імпортується з Ізраїлю, ча
сто використовувалася для «придушення вну
трішнього інакомислення». Як вже зазначалося вище, арабо-ізраїль
ські війни 1967 та 1973 років породили нега
тивне ставлення до Ізраїлю у більшості країн,
що розвиваються. Протягом перших десяти
літь незалежності, відносини Ізраїлю з Радян
ським Союзом відзначалися підозрою і навіть
ворожістю, так що до 1970-х років Єрусалим
став пріоритетом налагодження міцних зв’яз
ків із США. Ізраїль також прагнув встановити
союзи з «периферійними» державами, таки
ми, як Туреччина, Ефіопія та з Іраном (до Іс
ламської революції 1979 року). Зовнішня по
літика Єрусалиму щодо латиноамериканських
держав також може вважатися продовженням
стратегії в обхід спроб ворогів Ізраїлю ізо
лювати його на міжнародній арені. З іншого
боку, більш ліберальна перспектива підкрес
лює демократичні повноваження Ізраїлю, що
робить його винятком у регіоні. Наприклад,
унікальні відносини між США та Ізраїлем
часто пояснюються тим, що обидві країни
віддані демократії, а також тим, що багато
хто вважає своїм спільним іудейсько-христи
янським надбанням недержавних суб’єктів у
формуванні зовнішньої політики. Прикладом
є те, що ізраїльська дипломатія спирається на
свої комерційні підприємства у всьому сві
ті та військово-промисловий комплекс, що
об’єднує уряд та приватні підприємства, віді
грає центральну роль у зміцненні відносин за
його межами. Крім того, пояснення «другого
образу», репрезентовані представником теорії
неореалізму Кеннетом Уолтцом [Waltz 2001],
дають корисну основу для аналізу зовнішньої
політики Ізраїлю. Як підкреслюють плюраліс
тичні теорії, процес прийняття рішень є про
дуктом множинних взаємодій між акторами
зовнішньої політики. Дійсно, безліч акторів
(починаючи від профспілок та закінчуючи по
літичними партіями), а також громадська дум
ка, мають значний вплив на процес прийняття Динаміка зовнішньої політики Ізраїлю
щодо Латинської Америки Коротка історія ізраїльсько-латиноаме
риканських відносин Єврейські громади у Латинській Амери
ці недостатньо великі, щоб чинити великий
вплив на політичні справи своїх країн. У той
же час існує триваюча життєздатність двосто
ронньої міграції, а також зусилля ізраїль
ського уряду та єврейських фондів в Ізраїлі та
Латинській Америці задля підтримки тісних
зв’язків між цими громадами та єврейською
державою, створили ситуацію, у якій латино
американська єврейська культура демонструє
сильну культурну свідомість. Ця близькість
ставиться під сумнів у суспільствах, в яких
вони живуть, де іноді вважають, що євреї ма
ють подвійну лояльність. Оскільки євреї на
стільки тісно ототожнюються з Ізраїлем або
так тісно ототожнюються з ним самі, а також
враховуючи яскравість ізраїльсько-палестин
ського конфлікту, латиноамериканські євреї
часто стикаються з критикою, спричиненою
діями Єрусалиму [Ran&Cahan 2012]. Існували два основні фактори, які ви
значали хід відносин у ті роки. Перший – це
сильний вплив Вашингтона на зовнішню по
літику латиноамериканських країн, а другий
– незначна роль, яку цей регіон відіграє у гло
бальних справах [Kacowicz 2017: 203]. Однак
особливі стосунки між США та Ізраїлем час
від часу перешкоджали зусиллям Ізраїлю роз
вивати відносини з Латинською Америкою –
особливо протягом 1960-х та 70-х років, коли
антиамериканські настрої були поширені, а
політичні реалії з домінуванням лівих урядів
Перу, Куби, Чилі та пероністської Аргентини. Зокрема, Шестиденна війна 1967 року запля
мувала імідж Ізраїлю, зробивши його схожим
на довірену особу Вашингтона та на верхів
ку західного імперіалізму на Близькому Схо
ді. Розриви у відносинах США та Латинської
Америки призвели до відповідного розриву
у відносинах цих країн з Ізраїлем. Нафто
ва криза 1973 року та одночасне небажання
Вашингтона надавати допомогу у розвитку,
прискорили перехід у зовнішній політиці ба Багато країн Латинської Америки пози
тивно сприйняли створення Ізраїлю у 1948
році: Ізраїль забезпечив підтримку «блоку
вісімнадцяти» латиноамериканських країн,
які проголосували за членство в Організації 96 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Університету Джона Гопкінса Стівен Р.Девід,
Ізраїль стикається з набором «екзистенційних
загроз», починаючи від внутрішніх демогра
фічних викликів та закінчуючи зовнішніми
бойовими діями [David 2008]. Численні ара
бо-ізраїльські війни змусили єврейську дер
жаву зберігати пильність перед постійними
загрозами з боку сусідів. гатьох країн регіону на прагматичну позицію,
яка диверсифікує їх економічних та диплома
тичних партнерів у всьому світі. Університету Джона Гопкінса Стівен Р.Девід,
Ізраїль стикається з набором «екзистенційних
загроз», починаючи від внутрішніх демогра
фічних викликів та закінчуючи зовнішніми
бойовими діями [David 2008]. Численні ара
бо-ізраїльські війни змусили єврейську дер
жаву зберігати пильність перед постійними
загрозами з боку сусідів. Динаміка зовнішньої політики Ізраїлю
щодо Латинської Америки У галузі досліджень зовнішньої політи
ки Ізраїлю існують суперечливі інтерпретації
факторів, що сприяють певному результату
зовнішньої політики. Наприклад, американ
ський професор Шиблі Телхамі стверджує,
що зовнішня політика Ізраїлю була розробле
на не лише з урахуванням абстрактної кон
цепції «національного інтересу», нав’язаної
структурними можливостями та обмеження
ми міжнародних систем як такої, але також на
ідеологічних платформах чинних політичних
партій та внутрішньому контексті. Професор
Каліфорнійського університету Дов Уоксмен
розширює думку, підкреслюючи, що зовніш
ню політику Ізраїлю неможливо повністю
пояснити без урахування його національної
ідентичності. Він підкреслює, що неореалізм з
його явними матеріалістичними рамками про
понує лише редукціоністську точку зору на це
питання. Отже, щоб надати цілісну перспек
тиву, ми повинні звернутися як до зовніш
нього, так і внутрішнього виміру латиноаме
риканської політики Ізраїлю. Незважаючи на
те, що для пояснення зовнішньої політики Із
раїлю виникло багато теорій, домінуюча пер
спектива, що базується на реальній політиці,
була і залишається повсюдною у літературі. З самого свого заснування Ізраїль, як держа
ва, оточена ворожими арабськими країнами,
стурбована своєю онтологічною безпекою. Як
наголосив професор з міжнародних відносин 97 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 ною промисловістю. Було очевидним у період
після холодної війни, і особливо в роки «Ро
жевої хвилі» у Латинській Америці (маючи на
увазі широкі зміни у лівому напрямку націо
нальних урядах). Угода між Ізраїлем та тор
говельно-економічним союзом МЕРКОСУР
(Аргентина, Бразилія, Парагвай, Уругвай) про
Вільну торгівлю 2007 року була підписана,
незважаючи на напруженість у двосторонніх
відносинах. рішень в Ізраїлі. Точно так же ці актори, осо
бливо оборонна промисловість, приймають
участь у формуванні зовнішньої політики Із
раїлю. У зв’язку з цим продаж зброї Ізраїлем
у Східній Азії, Південній Азії та Латинській
Америці призвели до розвитку двосторонніх
зв’язків. Відповідно, одним із найважливіших
елементів ізраїльсько-латиноамериканських
відносин є зростання обсягу торгівлі зброєю. ною промисловістю. Було очевидним у період
після холодної війни, і особливо в роки «Ро
жевої хвилі» у Латинській Америці (маючи на
увазі широкі зміни у лівому напрямку націо
нальних урядах). Угода між Ізраїлем та тор
говельно-економічним союзом МЕРКОСУР
(Аргентина, Бразилія, Парагвай, Уругвай) про
Вільну торгівлю 2007 року була підписана,
незважаючи на напруженість у двосторонніх
відносинах. рішень в Ізраїлі. Точно так же ці актори, осо
бливо оборонна промисловість, приймають
участь у формуванні зовнішньої політики Із
раїлю. У зв’язку з цим продаж зброї Ізраїлем
у Східній Азії, Південній Азії та Латинській
Америці призвели до розвитку двосторонніх
зв’язків. Відповідно, одним із найважливіших
елементів ізраїльсько-латиноамериканських
відносин є зростання обсягу торгівлі зброєю. Динаміка зовнішньої політики Ізраїлю
щодо Латинської Америки Немає сумнівів, що взаємодія Ізраїлю з
євреями у всьому світі є важливим аспектом
зовнішньої політики, і, звичайно, у Латин
ській Америці, а також стратегічний контекст,
в якому відбувається прийняття зовнішньопо
літичних рішень з урахуванням історії та про
блем євреїв. Як і в інших випадках, єврейська
діаспора у Латинській Америці є одним із фак
торів, що впливають на зовнішню політику Із
раїлю у регіоні. Існування давніх єврейських
громад, члени яких мігрували з різних частин
старого світу у різний час, зміцнює культурні
та економічні зв’язки з Ізраїлем та консолідує
м’яку силу Ізраїлю. Однак, незважаючи на ви
сокий рівень ототожнення латиноамерикан
ських євреїв з їхньою релігійною та етнічною
спадщиною (про що свідчить велика кількість
єврейських громадських організацій), немож
ливо говорити про латиноамериканську єв
рейську громаду як про однорідну, оскільки
її члени дотримуються різноманітних релігій
них, політичних та соціальних світоглядів. Однак політичний клімат у Латинській
Америці за останні кілька років, де спосте
рігається широка підтримка правих лідерів
та помітно посилений вплив євангельських
християн, здається, дав Ізраїлю можливість
зміцнити свої дипломатичні зв’язки у регіоні,
які погіршилися з 1990-х років. У ці роки на
пруженість з Аргентиною зросла після того,
як ця країна ефективно розслідувала вибухи
у посольстві Ізраїлю у Буенос-Айресі у 1992
році та у єврейському центрі «Аргентинської
єврейської асоціації взаємної допомоги» у
1994 році, які забрали життя понад 100 людей
і ще сотні постраждали. Протягом того ж де
сятиліття сходження венесуельського сильно
го представника Уго Чавеса, який налагодив
тісні стосунки з Іраном, змусило Каракас розі
рвати колись дружні стосунки з Єрусалимом. Однак ці події не стримували Ізраїль від но
вих зусиль покращення відносин з латиноаме
риканськими лідерами. Справді, з 2009 року
Ізраїль намагається поліпшити свої відносини
з країнами регіону за допомогою політики,
ініційованої тодішнім міністром закордонних
справ Авігдором Ліберманом. Зміни політичних умов Він порушив такі питання, як зростаюча
участь терористичної організації «Хезболла»
у торгівлі наркотиками у Латинській Америці
та серйозні наслідки, які можуть бути резуль
татом поглиблення зв’язків Ірану з Венесуе
лою та Болівією. І також повторив прохання
Ізраїлю до Аргентини щодо розслідування ви
бухів у Буенос-Айресі. Напруженість, спри
чинена цими проханнями та подальшою реак
цією уряду президента Крістіни Фернандес де
Кіршнер, не зменшилася відразу після візиту
Авігдора Лібермана. Однак ізраїльсько-ар
гентинські відносини набули нового оберту
у наступні роки та після виборів 2015 року
правоцентристського кандидата у президенти
Маурісіо Макрі (колишній мер Буенос-Айре
са). У січні 2020 року новообраний лівий пре
зидент Альберто Фернандес відвідав Ізраїль
з метою участі у церемонії в меморіальному
комплексі Голокосту «Яд-Вашем», в якій взя
ли участь багато світових лідерів, присвяченій
вшануванню пам’яті жертв Голокосту та 75-ї
річниці звільнення концентраційного табору
Аушвіц-Біркенау. Та зустрівся з прем’єр-мі
ністром Бен’яміном Нетан’яху, обговоривши
можливість поліпшення двосторонніх відно
син. тичній арені. р
У галузі економіки, окрім сировини, Ізра
їль в основному імпортує з Латинської Аме
рики такі продукти харчування, як м’ясо,
кава, цукор, зерно, кукурудза та какао, а також
експортує перероблену сільськогосподарську
та хімічну продукцію, електроніку, машини,
та програмне забезпечення. Окрім фінансово
го та будівельного секторів, ізраїльські фірми
також беруть активну участь у фазах перед
виробничої сільськогосподарської діяльності. Нещодавно уряд Ізраїлю поділився планами
щодо розробки конкретних схем фінансуван
ня у рамках Міжамериканського банку роз
витку з метою надання позик та допомоги
латиноамериканським компаніям. Основну
увагу планується зосередити на таких сферах,
як кібербезпека, водопостачання та сільське
господарство, що відображають конкуренто
спроможність ізраїльських технологій [Azran
2019]. Двосторонні інвестиційні договори
між Ізраїлем та країнами Латинської Аме
рики датуються 1990-ми роками. Такі угоди
були підписані з Аргентиною, Сальвадором,
Уругваєм та Гватемалою [IMF 2019]. Сьогодні
Ізраїль має угоди про Вільну торгівлю з Мек
сикою (з 2000 року) та блоком МЕРКОСУР (з
2007 року). Гватемала стала помітним торго
вим партнером Ізраїлю у Центральній Амери
ці. Під час візиту Бен’яміна Нетан’яху до цієї
країни у 2019 році, були підписані різні угоди
з метою покращення відносин. З 90-х років минулого століття іранська
загроза викликала головне занепокоєння. Од
нак події у 2000-х роках продемонстрували,
що ідеологічні розбіжності серед лівих лати
ноамериканських лідерів призвели до ряду
позицій щодо зміцнення зв’язків з Ісламською
Республікою. Більше того, бажання Південної
Америки нарощувати економічні зв’язки з
арабськими країнами зробили «палестинське
питання» набагато складнішим у відносинах
Ізраїлю та Латинської Америки. Зміни політичних умов Ізраїльсько-латиноамериканські відноси
ни, які дружно розпочались у 1940-х роках, з
того часу зазнали злетів та падінь – наслідків
ідеологічних розбіжностей та антиамерикан
ських чи проамериканських настроїв у регіо
ні. Загалом, економічні та військові відносини
велися в умовах, сприятливих для всіх сторін. Починаючи з 1960-х років, мовчазне порозу
міння поділяло відносини на два канали: ди
пломатичний та економічний. Здається, Ізра
їль фактично прийняв підтримку Латинської
Америки для палестинської справи (за винят
ком деяких невеликих держав Центральної
Америки), але не дозволив цій позиції пере
шкоджати взаємним зусиллям щодо поліп
шення економічних зв’язків, в основному за
снованих на торгівлі із ізраїльською оборон Етап
ізраїльсько-латиноамериканських
відносин після 2009 року набув сильного ан
тиіранського виміру, не лише завдяки свідчен
ням стовно вибухів у Буенос-Айресі у 1990-х
роках, ініційованих Тегераном та здійснені
терористичною організацією «Хезболла», але
і присутністю Ірану у регіоні. Для цього від
бувалися характерні дипломатичні візити на
високому рівні та підписували двосторонні
угоди про торгівлю та співробітництво, осо
бливо з країнами «Боліваріанського альянсу
для народів Америки», Болівією, Венесуелою
та Нікарагуа (Болівія покинула групу у 2019
році; Іран мав статус спостерігача в з перших 98 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 років союзу). У 2009 році під час свого візиту
Авігдор Ліберман, крім зміцнення існуючих
двосторонніх відносин у різних сферах, праг
нув пом’якшити все більшу присутність Іра
ну. Він порушив такі питання, як зростаюча
участь терористичної організації «Хезболла»
у торгівлі наркотиками у Латинській Америці
та серйозні наслідки, які можуть бути резуль
татом поглиблення зв’язків Ірану з Венесуе
лою та Болівією. І також повторив прохання
Ізраїлю до Аргентини щодо розслідування ви
бухів у Буенос-Айресі. Напруженість, спри
чинена цими проханнями та подальшою реак
цією уряду президента Крістіни Фернандес де
Кіршнер, не зменшилася відразу після візиту
Авігдора Лібермана. Однак ізраїльсько-ар
гентинські відносини набули нового оберту
у наступні роки та після виборів 2015 року
правоцентристського кандидата у президенти
Маурісіо Макрі (колишній мер Буенос-Айре
са). У січні 2020 року новообраний лівий пре
зидент Альберто Фернандес відвідав Ізраїль
з метою участі у церемонії в меморіальному
комплексі Голокосту «Яд-Вашем», в якій взя
ли участь багато світових лідерів, присвяченій
вшануванню пам’яті жертв Голокосту та 75-ї
річниці звільнення концентраційного табору
Аушвіц-Біркенау. Та зустрівся з прем’єр-мі
ністром Бен’яміном Нетан’яху, обговоривши
можливість поліпшення двосторонніх відно
син. років союзу). У 2009 році під час свого візиту
Авігдор Ліберман, крім зміцнення існуючих
двосторонніх відносин у різних сферах, праг
нув пом’якшити все більшу присутність Іра
ну. Зміни політичних умов Таким чином,
у 2000-х роках під час «Рожевої хвилі», незва
жаючи на вигідні економічні відносини Ізра
їлю з багатьма країнами регіону, ліві лідери,
такі як колишній президент Бразилії Луїс Іна
сіо Лула да Сілва та аргентинський президент
Нестор Карлос Кіршнер, демонстрували силь
ну солідарність з палестинцями на диплома Обидві сторони все ще працюють над
взаємовигідною угодою не лише щодо поліп
шення торгівлі та інвестицій, але і для надан
ня обмежених можливостей для тимчасового,
вільного обігу робочої сили. Ізраїль також
підписав двосторонні торгові угоди з Колум
бією (2013 рік) та Панамою (2018 рік), які ще
не діють [IMF 2018]. Проте, за останні два де
сятиліття, за винятком Колумбії, латиноаме
риканські країни визнали державу Палестина. Протягом останніх двох років, після «Рожевої
хвилі», унікальна комбінація факторів рап
тово створила політичний клімат, який, без
перечно, був сприятливим для спроб Ізраїлю
отримати латиноамериканську дипломатичну
підтримку на міжнародній арені. По-перше,
відверта підтримка з боку американського 99 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 уряду щодо ізраїльських територіальних пре
тензій, по-друге, поява правих президентів у
Латинській Америці, які прагнуть розвивати
тісні зв’язки з США. Цей клімат сприяв до
сягненню, хоча і з невеликим запізненням, ці
лей Ізраїлю, викладених у декларації від трав
ня 2014 року, в якій зазначено про прагнення
зміцнити економічні зв’язки з Латинською
Америкою протягом наступних трьох років,
особливо з Тихоокеанським союзом, в якому
було надано статус спостерігача у лютому
2014 року [IMFA 2014]. 2019 році був четвертим з 2007 року, три з них
відбулись між 2017-2019 роками. У контексті
того, що Ізраїль намагався скористатися ос
танніми подіями у континентальній політиці,
у деяких випадках досягалися цілі без прямих
запитів. Наприклад, переїзд американського
посольства з Тель-Авіва до Єрусалиму у 2018
році спонукав Гватемалу, Парагвай та Гонду
рас заявити, що їх посольства також змінять
адреси. Гватемала та Гондурас, крім Коста-Рі
ки з залежною від Сполучених Штатів еконо
мікою, також є основними імпортерами ізра
їльської зброї та складних систем оборони. У
2017 році Ізраїль уклав угоду з Гондурасом на
300 мільйонів доларів про надання йому зброї,
кораблів та послуг з кібербезпеки. Ще одним
яскравим прикладом є Бразилія. У 1990–2009
роках Ізраїль був сьомим за величиною екс
портером військової техніки до цієї країни. Під час президенства Луїса да Сілви, Ділми
Русефф та Мішеля Темера, після опубліку
вання Національної стратегії оборони у 2008
році, Бразилія розширила співпрацю з ізра
їльською оборонною промисловістю. Зміни політичних умов Євангелісти у Північній та Пів
денній Америці очікують визнання Єрусали
му як столиці Ізраїлю, згідно з пророцтвами
диспенсаціоналізму, тому не дивно, що вони
закликають своїх політичних лідерів офіцій
но оголосити її такою. Країни Латинської
Америки та Ізраїль зацікавлені у поглибленні
вже існуючої співпраці, що базується голов
ним чином на закупівлі високотехнологічних
оборонних виробів та зброї. Як підкреслюєть
ся у ізраїльській щоденній газеті «Гаарец»,
ізраїльський експорт зброї у 2017 році досяг
рекордного рівня - понад 9 мільярдів доларів. Згідно з аналізом «Стокгольмського міжна
родного інституту досліджень миру» (SIPRI),
про який повідомляє ізраїльське видавництво
«The Times of Israel», єврейська держава була
«8-м найбільшим експортером зброї у світі»
між 2014 та 2018 роками. Звичайно, за цим є
низка причин. Як правильно підкреслюють
бразильський професор міжнародних відно
син Рафаель Дуарте Вілла та Джуліана Віджа
но, «на південноамериканському ринку зброї
Сполучені Штати більше не домінують». Вій
ськова промисловість Ізраїлю багато в чому
перевершує свою конкуренцію завдяки своїм
інноваційним можливостям, передовим тех
нологіям та людському капіталу. Ця перевага, роках, а бразильська дочірня компанія «Ares»
ізраїльського оборонного підрядника «Elbit
Systems», отримала рамковий контракт вар
тістю приблизно 100 мільйонів доларів на
постачання дистанційного керування. Ізраїль
– другий за величиною постачальник зброї
до Колумбії (після США), включаючи зброю,
таку як протитанкові та ракети «земля-земля». Ізраїль також продавав шпигунське програмне
забезпечення Колумбії у 2015 році для вико
ристання у моніторингу діяльності «Револю
ційних збройних сил Колумбії», з яким уряд
Колумбії здійснював мирну угоду. Ізраїльська
оборонна промисловість також розвивала міц
ні стосунки з Мексикою у 2000-х роках. роках, а бразильська дочірня компанія «Ares»
ізраїльського оборонного підрядника «Elbit
Systems», отримала рамковий контракт вар
тістю приблизно 100 мільйонів доларів на
постачання дистанційного керування. Ізраїль – другий за величиною постачальник зброї
до Колумбії (після США), включаючи зброю,
таку як протитанкові та ракети «земля-земля». Ізраїль також продавав шпигунське програмне
забезпечення Колумбії у 2015 році для вико
ристання у моніторингу діяльності «Револю
ційних збройних сил Колумбії», з яким уряд
Колумбії здійснював мирну угоду. Ізраїльська
оборонна промисловість також розвивала міц
ні стосунки з Мексикою у 2000-х роках. – другий за величиною постачальник зброї
до Колумбії (після США), включаючи зброю,
таку як протитанкові та ракети «земля-земля». Ізраїль також продавав шпигунське програмне
забезпечення Колумбії у 2015 році для вико
ристання у моніторингу діяльності «Револю
ційних збройних сил Колумбії», з яким уряд
Колумбії здійснював мирну угоду. Ізраїльська
оборонна промисловість також розвивала міц
ні стосунки з Мексикою у 2000-х роках. Зміни політичних умов Голов
ною метою Бразилії було пожвавлення своїх
оборонних систем з особливим акцентом на
збільшення потенціалу досліджень та розро
бок як державного, так і приватного секторів,
що пропонують супутні товари. На дипломатичній арені Ізраїль прагне
переконати країни Латинської Америки вчи
нити певні дії, зокрема, проголосувати за про
позиції Ізраїлю у різних міжнародних органі
заціях, що включає: розрив зв’язків з Іраном,
терористичною організацією «Хезболла» та
Палестинською автономією; підтримку пере
несення посольств з Тель-Авіва до Єрусали
му. З іншого боку, Ізраїль не вимагає однако
вого рівня згоди від кожної країни, швидше,
воліє задовольнятися тим, що реалістично на
даний момент. Досяжність конкретних цілей
залежить від субрегіону країни-партнера Ла
тинської Америки, її економічного становища
та бажання підтримати Ізраїль у міжнародних
організаціях. Відносини Ізраїль–Уругвай мають свої
особливості. Ізраїльські дипломати в Уругваї,
країні-члені МЕРКОСУР, не пришвидшують
питання перенесення посольства, оскільки
це наразі нездійсненно, але все ж працюють,
щоб підтримувати добрі стосунки. Поточ
ні та попередні посли намагалися просувати
зв’язки між країнами-членами МЕРКОСУР
та Ізраїлем, внести зміни до угоди про Віль
ну торгівлю та прихильність до боротьби з
антисемітизмом. Вони також запропонували
співпрацю у галузі кібербезпеки, в якій ізра
їльські компанії мають високу конкуренто
спроможність, та підтримку у голосуваннях
міжнародних організацій, таких як Всесвітня
організація охорони здоров’я (ВООЗ), щоб не
допустити міжнародного визнання Палести
ни [Radio Uruguay 2019]. Бен’ямін Нетан’яху
намагався скористатись зростанням правих
урядів Латинської Америки, здійснивши кіль
ка візитів до регіону. Останній його візит у Деякі країни мають численні контакти з із
раїльським військовим сектором. Хоча даних
про продаж військових товарів з відкритим ко
дом небагато, «Стокгольмський міжнародний
інститут досліджень миру» (SIPRI) надає таку
інформацію. Згідно з даними, Бразилія та Ко
лумбія є одними з основних споживачів висо
котехнологічної ізраїльської зброї; авіаційних
радіолокаційних систем; систем повітря-по
вітря, повітря-земля та протитанкові ракетні
системи; та БПЛА (безпілотні літальні апара
ти), що продаються як основна зброя [SIPRI
2019]. Крім цих військових систем, Ізраїль
продає програмне забезпечення для спостере
ження багатьом країнам Латинської Америки. Поглиблюючи зв’язки цих країн із ізра
їльською індустрією безпеки, очевидно, що
Бразилія була одним з найважливіших торго
вих партнерів Ізраїлю. Бразилія стала голов
ним споживачем ізраїльської зброї у 2000-х 100 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 ньої та зовнішньої політики. Хоча наслідком
проізраїльської політики Дональда Трампа не
можна нехтувати, було б занадто спрощеним
пояснювати перебіг дій лише результатом
бажання наслідувати прикладу Сполучених
Штатів. Зміни політичних умов Дійсно, політична мета новообраних
правих урядів стерти те, що зробили попе
редні ліві лідери, включаючи встановлення
тісних зв’язків з деякими мусульманськими
країнами, відіграє важливу роль. Ці зв’язки не
тільки передбачали дипломатичну підтримку
палестинців, але також дозволили відкрити
Латинську Америку таким країнам, як Іран
та Сирія. Хоча зростання євангельського хри
стиянства у Латинській Америці не є новим
явищем, безумовно, це спонукає правих по
літиків наблизитися до США та підтримати
Ізраїль. Крім того, на рішення щодо зміцнен
ня відносин з Ізраїлем, особливо у Бразилії,
Гондурасі, Гватемалі та Болівії, впливає від
носна політична сила, яку мають євангельські
члени уряду . Євангелісти у Північній та Пів
денній Америці очікують визнання Єрусали
му як столиці Ізраїлю, згідно з пророцтвами
диспенсаціоналізму, тому не дивно, що вони
закликають своїх політичних лідерів офіцій
но оголосити її такою. Країни Латинської
Америки та Ізраїль зацікавлені у поглибленні
вже існуючої співпраці, що базується голов
ним чином на закупівлі високотехнологічних
оборонних виробів та зброї. Як підкреслюєть
ся у ізраїльській щоденній газеті «Гаарец»,
ізраїльський експорт зброї у 2017 році досяг
рекордного рівня - понад 9 мільярдів доларів. Згідно з аналізом «Стокгольмського міжна
родного інституту досліджень миру» (SIPRI),
про який повідомляє ізраїльське видавництво
«The Times of Israel», єврейська держава була
«8-м найбільшим експортером зброї у світі»
між 2014 та 2018 роками. Звичайно, за цим є
низка причин. Як правильно підкреслюють
бразильський професор міжнародних відно
син Рафаель Дуарте Вілла та Джуліана Віджа
но, «на південноамериканському ринку зброї
Сполучені Штати більше не домінують». Вій
ськова промисловість Ізраїлю багато в чому 101
ньої та зовнішньої політики. Хоча наслідком
проізраїльської політики Дональда Трампа не
можна нехтувати, було б занадто спрощеним
пояснювати перебіг дій лише результатом
бажання наслідувати прикладу Сполучених
Штатів. Дійсно, політична мета новообраних
правих урядів стерти те, що зробили попе
редні ліві лідери, включаючи встановлення
тісних зв’язків з деякими мусульманськими
країнами, відіграє важливу роль. Ці зв’язки не
тільки передбачали дипломатичну підтримку
палестинців, але також дозволили відкрити
Латинську Америку таким країнам, як Іран
та Сирія. Хоча зростання євангельського хри
стиянства у Латинській Америці не є новим
явищем, безумовно, це спонукає правих по
літиків наблизитися до США та підтримати
Ізраїль. Крім того, на рішення щодо зміцнен
ня відносин з Ізраїлем, особливо у Бразилії,
Гондурасі, Гватемалі та Болівії, впливає від
носна політична сила, яку мають євангельські
члени уряду . Зміни політичних умов Разом з цим, триваючий судовий процес над
Бен’яміном Нетан’яху може ще більше по
гіршити ситуацію та пригальмувати прогрес,
досягнутий за його перебування на посаді. Ці
внутрішні лінії розломів можуть попогірши
ти відносини. Довговічність чинних правих
урядів у Латинській Америці є ще одним фак
тором, що визначає майбутнє відносин з Ізра
їлем. Поглиблені політичні зміни в столицях
Латинської Америки можуть призвести до
негативної реакції, яка вимагатиме перезаван
таження дипломатичних відносин. Незважа
ючи на все це, нинішні ізраїльсько-латиноа
мериканські зв’язки заслуговують на увагу як
приклад успішної багатогранної дипломатії у
світовій політиці. «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 ків, посилена участь Єрусалиму в регіоні –
тема, яка не отримала належного наукового
висвітлення. Поява правих партій у Латин
ській Америці переорієнтувала дипломатію на
єврейську державу. Однак нещодавнє поліп
шення ізраїльської зовнішньої політики щодо
латиноамериканських держав не може бути
пояснене виключно політичною трансформа
цією континентальної політики. Для сприяння
ізраїльській дипломатичній діяльності у Ла
тинській Америці збіглися численні фактори. Сюди входять регіональна ізоляція єврейської
держави, підписання торгових договорів, ін
тереси зростаючої оборонної промисловості
Ізраїлю та культурні зв’язки з діаспорою. Із
раїльсько-латиноамериканські відносини до
сягли нової фази, яка характеризується спри
ятливим політичним, економічним та соціаль
ним середовищем як в Ізраїлі, так і у країнах
Латинської Америки. Крім того, не можна не
помітити вплив унікальних характеристик
американсько-ізраїльських відносин за ча
сів Дональда Трампа. На додаток до згаданої
вище динаміки, немає сумнівів, що зовнішня
політика Ізраїлю щодо латиноамериканських
держав втратила оберти після політичного
«глухого кута» внаслідок проведення трьох
раундів послідовних національних виборів у
2019–2020 роках. Нестабільність політичної
системи Ізраїлю негативно вплинула на про
цес прийняття зовнішньополітичних рішень. Разом з цим, триваючий судовий процес над
Бен’яміном Нетан’яху може ще більше по
гіршити ситуацію та пригальмувати прогрес,
досягнутий за його перебування на посаді. Ці
внутрішні лінії розломів можуть попогірши
ти відносини. Довговічність чинних правих
урядів у Латинській Америці є ще одним фак
тором, що визначає майбутнє відносин з Ізра
їлем. Поглиблені політичні зміни в столицях
Латинської Америки можуть призвести до
негативної реакції, яка вимагатиме перезаван
таження дипломатичних відносин Незважа безумовно, робить його більш конкуренто
спроможним на світових ринках, включаю
чи ринки Латинської Америки. Більше того,
певний час в Ізраїлі постійно підтримується
державна підтримка військових підрядників. Більше того, що стосується попиту, слід вра
ховувати геополітичну чутливість латиноаме
риканських держав. Зміни політичних умов Незважаючи на те, що у
наш час на континенті не було повномасштаб
ної війни, це не означає, що у регіоні не було
міждержавних мілітаризованих прикордон
них конфліктів . З першого десятиліття тися
чоліття з’явилася значна кількість літератури,
яка підкреслює триваючу гонку озброєнь у
Південній Америці, яка залежить від багатьох
факторів, включаючи, але не обмежуючись
цим, стратегічні розрахунки, рівень загрози та
обсяг бюджету. Крім того, з огляду на виник
нення громадянських заворушень, особливо,
як це спостерігається в сутичках між правими
та лівими фракціями, які були поширеними у
країнах Латинської Америки в останні роки
[ICBS 2010], багато правих урядів відчувають
потребу у збільшенні своїх можливостей вну
трішньої безпеки з великим арсеналом. безумовно, робить його більш конкуренто
спроможним на світових ринках, включаю
чи ринки Латинської Америки. Більше того,
певний час в Ізраїлі постійно підтримується
державна підтримка військових підрядників. Більше того, що стосується попиту, слід вра
ховувати геополітичну чутливість латиноаме
риканських держав. Незважаючи на те, що у
наш час на континенті не було повномасштаб
ної війни, це не означає, що у регіоні не було
міждержавних мілітаризованих прикордон
них конфліктів . З першого десятиліття тися
чоліття з’явилася значна кількість літератури,
яка підкреслює триваючу гонку озброєнь у
Південній Америці, яка залежить від багатьох
факторів, включаючи, але не обмежуючись
цим, стратегічні розрахунки, рівень загрози та
обсяг бюджету. Крім того, з огляду на виник
нення громадянських заворушень, особливо,
як це спостерігається в сутичках між правими
та лівими фракціями, які були поширеними у
країнах Латинської Америки в останні роки
[ICBS 2010], багато правих урядів відчувають
потребу у збільшенні своїх можливостей вну
трішньої безпеки з великим арсеналом. Зміни політичних умов У той час як Болівія за президента Ево
Моралеса розірвала свої дипломатичні зв’яз
ки з Ізраїлем у 2009 році, нові члени уряду Бо
лівії вирішили відновити відносини у грудні
2019 року після державного перевороту, який
змусив Ево Моралеса покинути країну. Од
нак найбільші зміни відбулися під час прези
дентської виборчої кампанії 2018 року у Бра
зилії, коли кандидат у президенти Жаїр Бол
сонару заявив, що ось-ось почнеться період
зближення з єврейською державою. Справді,
його прихід до влади, здавалося, активізував
відносини між Ізраїлем та Бразилією. На від
міну від попередніх керівників лівих урядів,
Жаїр Болсонару не висловлював застережень
щодо Ізраїлю і дуже прагнув розвивати зв’яз
ки у кількох напрямах – насамперед стосовно
економіки та безпеки. Бразилія навіть заяви
ла, що перенесе своє посольство з Тель-Аві
ва до Єрусалиму. Однак після вступу на по
саду Жаїр Болсонару відступив, мабуть, тому,
що не хотів розривати економічні відносини
з Лігою арабських держав, більшість з яких
закуповують бразильське м’ясо та інші хар
чові продукти. Щоб компенсувати невико
нану обіцянку, Жаїр Болсонару організував
швидкий дипломатичний візит до Ізраїлю у
третьому місяці свого президентства та від
крив комерційний офіс в Єрусалимі. На сьо
годнішній день лише Гватемала реалізувала
намір перенести посольство. Причини, що
лежать в основі загальної позитивної реак
ції Латинської Америки на спроби Ізраїлю
зблизитися, зумовлені поєднанням внутріш 101 культури», 2020, Т. 12, № 2
ків, посилена участь Єрусалиму в регіоні –
тема, яка не отримала належного наукового
висвітлення. Поява правих партій у Латин
ській Америці переорієнтувала дипломатію на
єврейську державу. Однак нещодавнє поліп
шення ізраїльської зовнішньої політики щодо
латиноамериканських держав не може бути
пояснене виключно політичною трансформа
цією континентальної політики. Для сприяння
ізраїльській дипломатичній діяльності у Ла
тинській Америці збіглися численні фактори. Сюди входять регіональна ізоляція єврейської
держави, підписання торгових договорів, ін
тереси зростаючої оборонної промисловості
Ізраїлю та культурні зв’язки з діаспорою. Із
раїльсько-латиноамериканські відносини до
сягли нової фази, яка характеризується спри
ятливим політичним, економічним та соціаль
ним середовищем як в Ізраїлі, так і у країнах
Латинської Америки. Крім того, не можна не
помітити вплив унікальних характеристик
американсько-ізраїльських відносин за ча
сів Дональда Трампа. На додаток до згаданої
вище динаміки, немає сумнівів, що зовнішня
політика Ізраїлю щодо латиноамериканських
держав втратила оберти після політичного
«глухого кута» внаслідок проведення трьох
раундів послідовних національних виборів у
2019–2020 роках. Нестабільність політичної
системи Ізраїлю негативно вплинула на про
цес прийняття зовнішньополітичних рішень. Бібліографічні посилання / References р ф
Azran, E. (2019). Israeli Government Fund to Direct Investment toward Latin America. Retrieved August
15, 2020 from https://www.haaretz.com/israel-news/business/israeli governmentfund-to-direct-
investment-toward-latin-america-1.6995588. David, S.R. (2008). Existential Threats to Israel, Contemporary Israel: Domestic Politics, Foreign Policy, and
Security Challenges, Robert O. Freedman (ed.)f Dimant, M. (2020). The“Mobileye Effect” in Latin America-Israel Relations, 2009-2019. Retrieved September
29, 2020 from https://strategicassessment.inss.org.il/en/articles/the-mobileye-effect-in-latin-america-
israel-relations-2009-2019/ Israeli Central Bureau of Statistics. (2010). Israel’s Foreign Trade: 2000–2010, Statistilite 115. Retrieved
August 15, 2020 from https://www.cbs.gov.il/en/Statistical/trade_115_e.pdf. Israeli Ministry of Finance. (2019). Bilateral Investment Treaties Retrieved August 15, 2020 from: https://mof. gov.il/en/InternationalAffairs/TradeAgreements/Pages/BIT.aspx. Israeli Ministry of Finance. (2018). Free Trade Area Agreements (FTAs). Retrieved August 15, 2020 from
https://mof.gov.il/en/InternationalAffairs/TradeAgreements/Pages/FreeTradeArea.aspx.f Israeli Ministry of Foreign Affairs (2014), Israel to strengthen economic ties with Latin America and
Pacific Alliance, Retrieved August 18, 2020 from https://mfa.gov.il/MFA/PressRoom/2014/Pages/
Government-approves-program-to-strengthen-economic-ties-with-Latin-American-countries.aspx. Kacowicz, A.M. (2017). Triangular Relations: Israel, Latin American Jewry, and Latin American Countries in
a Changing International Context, 1967-2017. The Israel Journal of Foreign Affairs, XI:2 (2017), 203.i Kacowicz, A. M., Bar-Siman-Tov, Y. (2000) Stable Peace Among Nations. Rowman & Littlefield Publishersm. Kacowicz, A. M., Bar-Siman-Tov, Y. (2000) Stable Peace Among Nations. Rowman & Littlefield Publishersm. Katz, Y. (2017). Why Israel has the most technologically advanced military on Earth, Retrieved August
17
2020
from
https://nypost com/2017/01/29/why israel has themost technologically advanced Kacowicz, A. M., Bar-Siman-Tov, Y. (2000) Stable Peace Among Nations. Rowman & Littlefield Publishersm. Katz, Y. (2017). Why Israel has the most technologically advanced military on Earth, Retrieved August
17, 2020 from https://nypost.com/2017/01/29/why-israel-has-themost-technologically-advanced-
military-on-earth. Landau, N. (2019). Netanyahu Welcomes Brazil’s Bolsonaro to Israel, Days Before Election, Retrieved August
15, 2020 from https://www.haaretz.com/israel-news/.premiumbrazil-s-bolsonaro-arrives-in-israel-
days-before-election-1.7067601.f Lazaroff, T. (2019). Israel to attend Expo 2020 Dubai, an Arab State with whom it has no Ties. Retrieved
August 31, 2020 from https://www.jpost.com/Arab-Israeli-Conflict/Israelis-permitted-to-come-to-
2020-World-Expo-in-UAE-607376. Oster, M. (2019). Brazilian President Jair Bolsonaro walks back embassy move promise, Retrieved from
https://www.jpost.com/Israel-News/Brazilian-President-Jair-Bolsonaro-walks-back-embassy-move-
promise-585160. p
Radio Uruguay. (2019). El embajador de Israel se entrevistó con Lacalle Pou, Retrieved August 22, 2020 from
https://radiouruguay.uy/embajador-de-israel-se-entrevisto-con-lacalle-pou/. Ran, A. & Cahan J.A. (2012). Introduction: Rethinking Jewish Identity in Latin America. Returning to Babel:
Jewish Latin American Experiences, Representations, and Identity (eds.), 6-7. SIPRI (2019). Arms Transfers Database. Retrieved from: http://armstrade.sipri.org/armstrade/page/trade_
register.php. The Times of Israel. (2019). Israel named world’s 8th largest arms exporter. Retrieved August 17, 2020 from
https://www.timesofisrael.com/israel-named-worlds-8th-largest-arms-exporter/i Vysotskyi, O.Y. (2017). Technologies of legitimation in international relations. Scientific and Theoretical
Almanac Grani, 20(10), 98-104. https://doi.org/10.15421/1717138. Waltz, K. (2001). Висновки. Отже, можна виокремити такі технології
[Vysotskyi 2017] зовнішньої політики Ізраїлю,
які він реалізовував на латиноамериканському
напрямі: укладання торгових угод, обіцянка
підтримки під час голосування у міжнарод
них організаціях, офіційні візити ізраїльских
високопосадовців до латиноамериканських
країн, укладання договорів з латиноамерикан
ськими державами, спрямованих на розвиток
науки, технологій та інновацій. У результаті ефективного застосування
зовнішньополітичних
технологій
Ізраїлем
були досягнуті такі цілі: зміцнення позицій у
регіоні, ослаблення впливу Ірану на латино
американські країни, виключення «палестин
ського питання» з порядку денного, зміна
розстановки сил щодо голосування в ООН
по відношенню до Ізраїлю, покращення еко
номічних зв’язків через експорт ізраїльської
продукції, програмного забезпечення та зброї. Хоча між Ізраїлем та державами Латин
ської Америки існують відносини багато ро 102 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Бібліографічні посилання / References Man, the State, and War: A Theoretical Analysis. New York, Columbia University Press,
80-123. Waxman, D (2003). Between Isolation and Integration: The Jewish Dimension in Israeli Foreign Policy, Israel
Studies Forum, XIX:1. Wermenbol, G. (2019). Israel’s Latin America Push. Retrieved August 25, 2020 from https://www. atlanticcouncil.org/blogs/new-atlanticist/israel-s-latin-america-push/ 103
|
https://openalex.org/W3039011798
|
https://cultureandvalues.org/index.php/JCV/article/download/43/50
|
English
| null |
Obstacles facing rural women development in the Palestinian society: Nablus Governorate as a Case Study
|
Journal of culture and values in education
| 2,020
|
cc-by
| 6,167
|
Abstract Women constitute 49 percent of the Palestinian population, but the participation of Palestinian
women in economic and social development in Palestinian society is low. The low participation
of women is due to many obstacles and constraints preventing them from contributing to the
economic and social development of Palestinian society. This study aims to address the most
important obstacles facing Palestinian women in achieving development, focusing on the
problems and constraints facing rural women in Nablus Governorate. The study used the
descriptive, analytical, inductive, and historical approach based on references, books,
periodicals, and field work. The data were collected through personal interviews and
questionnaires. One hundred questionnaires were distributed to obtain scientific results in an
objective manner. The study found that there are a number of factors preventing Palestinian
women from contributing to the development process, most importantly social, economic,
political, security, media, and personal factors. The study concluded with a number of
important recommendations and proposals necessary to increase the role of rural women as
well as the economic and social development of Palestinian society. Keywords: Development, Rural Women, Palestinian Women Keywords: Development, Rural Women, Palestinian Women Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 88 L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a
Case Study Case Study
Loai Mahmoud Aburaida*
An-Najah National University
*Corresponding Author: laburaida@najah.edu
Received : 2019-08-27
Rev. Req. : 2019-12-10
Accepted : 2020-02-05
How to cite this paper: Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a
Case Study. Journal of Culture and Values in Education, 4(1), 88-99, https://doi.org/10.46303/jcve.2020.1
This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International license
(https://creativecommons.org/licenses/by/4.0/)
10.46303/jcve.2020.1 Loai Mahmoud Aburaida*
An-Najah National University *Corresponding Author: laburaida@najah.edu How to cite this paper: Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a
Case Study. Journal of Culture and Values in Education, 4(1), 88-99, https://doi.org/10.46303/jcve.2020.1 This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International license
(https://creativecommons.org/licenses/by/4.0/) Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Introduction How can rural women be empowered to play an active role in the Palestinian society
and to increase their participation in overall development? The importance of this research stems from the fact that it studies an important segment of
the society. Future generations will depend on this segment to reach a comprehensive and
sustainable development in the countryside. In order to identify the obstacles preventing Palestinian rural women from development in
society, it was necessary to know the role of rural women in development. The researcher
considered conducting a field study that reflects this reality through a questionnaire designed
for this purpose. The questionnaire included questions related to study objectives and to
answer study questions from the following aspects: First: General information about rural women in Nablus Governorate. Second: Activities practiced by rural women in Nablus Governorate First: General information about rural women in Nablus Governorate. First: General information about rural women in Nablus Governorate. Second: Activities practiced by rural women in Nablus Governorate. Third: Obstacles and restrictions leading to non-participation in various development activities. Fourth: Recommendations and proposals to activate the role of rural women in real
development. Literature Review Introduction It is recognized that the participation of Palestinian women in social and economic life in the
West Bank is low. Moreover, rural women's activity is still ineffective in rural development
(Shteih, 2018). The Palestinian Central Bureau of Statistics shows that 85.4 percent of the
women in the West Bank are unemployed (PCBS, 2017a). According to the published report by 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 89 L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study
the Palestinian Central Bureau of Statistics, women constituted 49 percent of the Palestinian
population in 2019. Palestinian women’s participation in the labor force is 21 percent (Awad,
2018). In addition, there is a large gap between the rural and urban communities in Palestine. This leads to the absence of qualified cadres who can lead and develop rural communities. the Palestinian Central Bureau of Statistics, women constituted 49 percent of the Palestinian
population in 2019. Palestinian women’s participation in the labor force is 21 percent (Awad,
2018). In addition, there is a large gap between the rural and urban communities in Palestine. This leads to the absence of qualified cadres who can lead and develop rural communities. Based on secondary sources of books, periodicals, and related reports, the study followed the
analytical, inductive, historical, and descriptive method. In addition, the study depends on
primary sources represented by field data collected through personal interviews and
questionnaires. The questionnaires were distributed randomly in Nablus Governorate,
targeting 100 Palestinian women ages 15-65. This study aims at identifying the economic activities practiced by Palestinian rural women and
their community participation. It also aims at identifying the most important challenges and
constraints facing Palestinian rural women in achieving development. Finally, the study aims to
provide opinions, ideas, and proposals for activating Palestinian rural women’s roles and
performance in society through answering the following questions: 1. What are the social and educational characteristics of rural women? 1. What are the social and educational characteristics of rural women? 2. Is there a low participation in the development of Palestinian rural communities? Is this
decline due to the vulnerability of rural women? . What are the obstacles that prevent rural women from participating in th
development of Palestinian rural communities? 4. Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Literature Review 2021 Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 90 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Development is the exploitation of the available energies and possibilities to meet the required
needs of community and development in accordance with community, cultural, social, and
economic needs. It is a complex process encompassing all life aspects such as economic, social,
intellectual, political, and ideological life (Pinot, 1972). Over the past few years, many
definitions of development have emerged. One of these defines development as the
investment in the development of human resources and development through education and
training for members of society to participate positively in the community (Sarhan, 2014). Development is the exploitation of the available energies and possibilities to meet the required
needs of community and development in accordance with community, cultural, social, and
economic needs. It is a complex process encompassing all life aspects such as economic, social,
intellectual, political, and ideological life (Pinot, 1972). Over the past few years, many
definitions of development have emerged. One of these defines development as the
investment in the development of human resources and development through education and
training for members of society to participate positively in the community (Sarhan, 2014). There have been considerable efforts in rural development that have led to controversy about
the starting point in rural development. Is it through achieving awareness or through achieving
economic development? Should there be focus and attention on the community or the most
vulnerable economic and social sectors in society? What can be done toward patterns of
communal injustice? In this context, Gandhi’s ideas for rural development are the most
important of these ideas in terms of influence and continuity. He is recognized for his emphasis
on the fact that change does not come from violence but from persuasion (Hopkins, 1998). Women have a vital role in development. Their full participation is therefore necessary to
achieve sustainable development. Sustainable development is achieved through equality
between women and men in rights, opportunities, and responsibilities. Social justice is a
precondition in this process (Lohani & Aburaida, 2017). Rural women have a major role in the
development of the rural family. Figure 1: Participation in the labor force by women and men 15 years and older in Palestine,
2001-2018 Literature Review Women work in all social, economic, and political fields. Studies indicate that rural women contribute about four percent of the world's food. In fact,
this ratio may reach 80 percent in some developing countries (UNDP, 1990). Studies also show
that in many societies, such as in Africa and Asia, women work longer hours than men. Women’s weekly work increases by about 13 hours; on the other hand, women work in Eastern
European and Latin American countries about 6-7 hours more than men (Sayed, 1996). It is worth mentioning that international efforts to mainstream the role of women in
development have yielded positive results. Grassroots and non-governmental organizations
have played an active role in improving women's access to welfare and ease the restrictions
related to participation and control (Fonjong, 2001). However, overall rural development in
general and the role of Palestinian women in particular have been severely neglected. They
have been dismissed out of the economic and social development plans in the era of the Israeli
occupation, even after the establishment of the Palestinian Authority in 1994. Despite the high
participation of Palestinian women in the labor force during the past years, it is still very low
compared with men. Palestinian women’s participation rate in the Palestinian labor force was
21.7 percent in 2018, compared with 10.3 percent in 2001 (Figure 1). 2021 Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org 91 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study Source: Awad, 2018 Source: Awad, 2018 As the previous figure shows, women’s role in economic and social development is a vital one. Tim and Nadi (2010) studied the extent to which Palestinian women participate in development;
their findings show that women have an important role that can only be realized through justice
and equality between men and women in society. Najm (2013) studied Palestinian university youth trends toward women's issues in education
and work. The study concluded that youth attitudes are positive toward women’s education
and work. Hamayel (2003) examined the attitudes of Palestinian university students toward the
work of women. The researcher concluded that the society has a positive attitude toward
women. Literature Review It also emphasizes the role of women in economic development within the Palestinian
society. On the other hand, Jaber (2005) concluded, in research about obstacles facing
Palestinian women working in the public sector in the northern governorates of the West Bank,
that the most important obstacles are the Israeli security policies on the checkpoints between
the cities and villages of the West Bank. This prevents Palestinian women from reaching their
workplaces and delays their return home. The study by Mohamad (2011) found that there is
no correlation between the educational curricula and the needs of the society, which leads to
a lack of cultural awareness and high unemployment in Palestinian society. In addition, the
Palestinian-Israeli conflict and the lack of Palestinian unity have had a significant impact on the
limited funding, which is the core of economic activity. Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Methodology This study crosses both quantitative and qualitative research tools to collect original data,
which is analyzed in the framework of a case study methodological approach, studying the
development of rural women in Palestinian society and its main constraints under an
exploratory inductive approach. This study does not begin with a hypothesis, using instead
research questions to narrow the scope of the study. 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021
Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study
92 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 92 L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study The study of the obstacles facing rural women in Palestinian society benefits not only from
secondary data such as books, articles, periodicals, and related reports; it also uses original
primary data collected through questionnaires and interviews. The questionnaires were
designed to obtain scientific results objectively from 100 Palestinian women in Nablus
Governorate. The in-depth interviews were conducted with the heads of women's associations,
trade union organizations, women workers, and unemployed women. The study of the obstacles facing rural women in Palestinian society benefits not only from
secondary data such as books, articles, periodicals, and related reports; it also uses original
primary data collected through questionnaires and interviews. The questionnaires were
designed to obtain scientific results objectively from 100 Palestinian women in Nablus
Governorate. The in-depth interviews were conducted with the heads of women's associations,
trade union organizations, women workers, and unemployed women. Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Dataset Nablus Governorate is located in the north of the West Bank, 53 kilometers from Jerusalem. It
is located along 35.16 west and 32.13 north of the Equator (Figure 2). It covers an area of 605
square kilometers. Its population is 392,407. The governorate includes 52 rural communities in
addition to the city of Nablus (PCBS, 2017b), according to the administrative division approved
by the Palestinian Authority. Figure 2: Location of the study area Figure 2: Location of the study area
According to PCBS (2017b), Palestinian society is characterized by a young generation; 38.9
percent of the total population in Palestine is under 15 years of age, and 39.1 percent are male
and 38.7 percent are female. Youth ages 15-29 make up 29.7 percent of the total population,
distributed as 43.9 percent male and 56.1 percent female. Figure 2: Location of the study area Figure 2: Location of the study area According to PCBS (2017b), Palestinian society is characterized by a young generation; 38.9
percent of the total population in Palestine is under 15 years of age, and 39.1 percent are male
and 38.7 percent are female. Youth ages 15-29 make up 29.7 percent of the total population,
distributed as 43.9 percent male and 56.1 percent female. 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 93 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorat
Study The sample of this study consists of women in the rural areas in Nablus that contains 64 villages
and towns. The questionnaires were distributed randomly to the women in these areas. This
sample is characterized by the following characteristics, as shown in Figure 3. The sample of this study consists of women in the rural areas in Nablus that contains 64 villages
and towns. The questionnaires were distributed randomly to the women in these areas. This
sample is characterized by the following characteristics, as shown in Figure 3. Regarding the age of the sample, looking to Figure 3, it is clear that, on one hand, women aged
15-24 years constitute 40 percent of the population. This is a high percentage that can be relied
upon in all future development activities. Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Dataset On the other hand, women aged 25-34 constitute 26
percent, and women aged 35-44 years 13 percent. This is the age at which women can do all
developmental activities in society. As for those who are older than 45-65 years, they represent
21 percent; this segment is effective to raise awareness and educate the rural community since
they have life experiences. Figure 3: Age level of sample members
Source: Field Study 2018
Regarding the social status of the sample members, Figure 4 explains that the percentage of
single women is 58 percent of the total sample; undoubtedly this has a negative impact on rural
women’s performance and activity. Rural women’s psychological instability, fear of obsession,
and the society's attitude regarding spinsterhood are all reasons that expose them to
convergence and inability to interact with the surrounding community. It also prevents rural
women from carrying out any developmental role. Figure 4 explains also that the percentage
of married women is 39 percent. In spite of the fact that married women are more stable
psychologically, they are still inactive in performing their role in development. The inability of
women to reconcile their home chores and their work or their societal role idles their energies,
resulting in the absence of their developmental role. The presence of widows and divorced Figure 3: Age level of sample members
Source: Field Study 2018 Figure 3: Age level of sample members Source: Field Study 2018 Regarding the social status of the sample members, Figure 4 explains that the percentage of
single women is 58 percent of the total sample; undoubtedly this has a negative impact on rural
women’s performance and activity. Rural women’s psychological instability, fear of obsession,
and the society's attitude regarding spinsterhood are all reasons that expose them to
convergence and inability to interact with the surrounding community. It also prevents rural
women from carrying out any developmental role. Figure 4 explains also that the percentage
of married women is 39 percent. In spite of the fact that married women are more stable
psychologically, they are still inactive in performing their role in development. The inability of
women to reconcile their home chores and their work or their societal role idles their energies,
resulting in the absence of their developmental role. Dataset The presence of widows and divorced Regarding the social status of the sample members, Figure 4 explains that the percentage of
single women is 58 percent of the total sample; undoubtedly this has a negative impact on rural
women’s performance and activity. Rural women’s psychological instability, fear of obsession,
and the society's attitude regarding spinsterhood are all reasons that expose them to
convergence and inability to interact with the surrounding community. It also prevents rural
women from carrying out any developmental role. Figure 4 explains also that the percentage
of married women is 39 percent. In spite of the fact that married women are more stable
psychologically, they are still inactive in performing their role in development. The inability of
women to reconcile their home chores and their work or their societal role idles their energies,
resulting in the absence of their developmental role. The presence of widows and divorced 2021 94 L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case women in the sample of the study was very low: two percent widowed and one percent
divorced. Figure 4: Study sample social status
Source: Field Study 2018
Regarding the sample educational level, which is an important factor in the development
process: It affects all life aspects and social, economic, and political levels. The low level of
women’s education in many societies is considered the general factor of underdevelopment
and backwardness of society. This study shows that the educational level of rural women is one
of the most important pillars in developing the society. Through these educated rural women,
we can promote active participation in society. The percentage of those with a university
degree was 59 percent, with one percent of them holding a high degree. On the other hand,
women in the secondary school and those who attained this degree reached 39 percent. This
is a clear indicator of rural women’s interest in education, especially after they moved from this
stage to the university level; thus, their role contributes effectively in the future development. Figure 4: Study sample social status Figure 4: Study sample social status
Source: Field Study 2018 Source: Field Study 2018 Source: Field Study 2018 Regarding the sample educational level, which is an important factor in the development
process: It affects all life aspects and social, economic, and political levels. Dataset The low level of
women’s education in many societies is considered the general factor of underdevelopment
and backwardness of society. This study shows that the educational level of rural women is one
of the most important pillars in developing the society. Through these educated rural women,
we can promote active participation in society. The percentage of those with a university
degree was 59 percent, with one percent of them holding a high degree. On the other hand,
women in the secondary school and those who attained this degree reached 39 percent. This
is a clear indicator of rural women’s interest in education, especially after they moved from this
stage to the university level; thus, their role contributes effectively in the future development. Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Economic conditions The researcher found that the Palestinian-Israeli conflict and the lack of Palestinian unity had a
great impact on the limited funding, which is considered the mainstay of economic activity. Of
the respondents, 39 percent attribute the prevailing economic conditions not only to the study
area but to Palestinian women, which impedes the role of women in development, resulting
from the lack of funding for development projects and the spread of poverty in these rural
communities. Additionally, 35 percent of respondents said that there is a lack of services in
rural areas, which leads to women's reluctance to interact in development work. Findings Despite rural women’s high level of education, their participation in economic activities is still
very low. The percentage of female workers in the study sample was 6.3 percent, which is less
than the percentage of women working in Palestine, 9.7 percent (Shteih, 2018). The study finds
that the professions practiced by rural women in the countryside are still limited to traditional
occupations. About 29 percent are engaged in handicrafts such as sewing and embroidery,
while 26 percent work in agriculture; 23 percent work in education, and the rest work in 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 95 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case economic activities and social work such as literacy, charities, women's groups, rehabilitation
centers, trade unions, etc. The study showed that 12 percent of the respondents were active
in their societies, and this is a low percentage that hinders development. economic activities and social work such as literacy, charities, women's groups, rehabilitation
centers, trade unions, etc. The study showed that 12 percent of the respondents were active
in their societies, and this is a low percentage that hinders development. The study showed that there are many obstacles facing rural women in the Palestinian society
development process. This includes social, economic, and political aspects, in addition to the
lack of training and the institution and the women's collective form (Figure 5). Figure 5: The most important obstacles facing rural women in the development of the
Palestinian society Figure 5: The most important obstacles facing rural women in the development of the
Palestinian society Economic conditions Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org The structure of social systems and the cultural framework of society Economic life revolves around economic, social and political organizations in addition to the
cultural framework of society (values, barriers, traditions, beliefs, moral qualities, attitudes,
etc.). The existing framework indirectly affects women’s role in economic development. It also
affects the level of comprehensive development (Abdul-Rahman, 2003). The study explains that 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 96 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case reducing the role of women in development due to the contribution of the existing structure
of social systems and the cultural framework of society is 29 percent. It should be noted that
the dominant culture among women plays an important role in hindering their contribution to
the overall development. The study revealed that 27 percent of women direct their available
savings in many non-productive investments that do not benefit the beneficiary. Their saving is
directed toward agriculture, gold hoarding, and acquisition of ornaments. In addition, cultural
values and traditions result in spending on many consuming aspects, which do not contribute
positively to raising the level of material well-being of individuals and thus impede the role of
women in development. reducing the role of women in development due to the contribution of the existing structure
of social systems and the cultural framework of society is 29 percent. It should be noted that
the dominant culture among women plays an important role in hindering their contribution to
the overall development. The study revealed that 27 percent of women direct their available
savings in many non-productive investments that do not benefit the beneficiary. Their saving is
directed toward agriculture, gold hoarding, and acquisition of ornaments. In addition, cultural
values and traditions result in spending on many consuming aspects, which do not contribute
positively to raising the level of material well-being of individuals and thus impede the role of
women in development. The social systems, customs, and traditions prevailing in rural communities, lack of local council
confidence among rural women, and social oppression all lead to the reluctance of rural women
to participate in the various development activities. The structure of social systems and the cultural framework of society As a result, the study showed that 52
percent of the study sample believes that society does not give rural women the right of
decision-making. This leads to imbalance, mistrust, and a permanent conflict between society
and ambitions, and exposes rural women to the intransigence and inability to interact with the
surrounding society. Israeli actions at military checkpoints The Israeli measures at the military checkpoints are the most important obstacles that prevent
Palestinian women from taking part in their developmental role. These checkpoints, which are
described by Palestinians as death gates, were increased to hundreds after the intifada in 2000. They are spread throughout the West Bank. Israel military checkpoints are spread along the
entrances to cities and towns. Due to this abuse and humiliation, the lives of Palestinian citizens
are very difficult. They are subjected to barriers in addition to the killings and arrests that take
place at these checkpoints. Palestinians are no safer or freer when they pass a checkpoint. This
is directly reflected on Palestinian women, who are afraid of passing through these barriers. Moreover, they are always late at work or in returning home, resulting in staying at home and
waiting for a nearby job to avoid passing through these military barriers, which negatively
affects and limits their role in development. Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Absence of women's training center organizations In spite of the increased percentage of education in rural communities, 42 percent of the
respondent’s members indicated that the lack of training centers and lack of women's
organizations isolated rural women from their role in development; 11 percent mentioned that
the absence of training and rehabilitation associations for rural women and the lack of women's
societies in rural society is one of the important reasons that causes the absence of women
from development roles. In addition, undermining rural women in administrative structures
and local councils is one of the crucial aspects that led to rural women’s reluctance to interact
in the development work. 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 97 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Rural women are the main drivers of development, but limited access to credit, health care,
and education are among the many challenges women face. This crisis is compounded by the
global food and economic crisis and climate change. Therefore, empowerment is necessary,
not only for the well-being of individuals, families, and rural communities, but also for overall
economic productivity since the presence of women in the agricultural labor force is worldwide. Rural women are the main drivers of development, but limited access to credit, health care,
and education are among the many challenges women face. This crisis is compounded by the
global food and economic crisis and climate change. Therefore, empowerment is necessary,
not only for the well-being of individuals, families, and rural communities, but also for overall
economic productivity since the presence of women in the agricultural labor force is worldwide. Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Conclusions and Recommendations Rural women have a significant and effective impact on the real development of rural society. They also play a catalytic role in achieving the economic, environmental, and social
transformations that are necessary to achieve sustainable development. However, women in
these societies are still unable to play a real and active role due to their social conditions and
the clear discrimination against rural women. Lack of awareness, training, and rehabilitation,
lack of qualified communities for qualified personnel, the absence of women's institutions, the
weak role of government in rural areas, and the lack of service accessibility are all reasons for
underdevelopment, as well as the lack of economic potential of rural communities and rural
women where they do not have direct income, which prevents investment and makes them
non-productive and consuming. Empowerment of rural women is therefore critical, not only
for the welfare of individuals, families, and communities, but also for overall economic
productivity due to the presence of rural women in the workforce throughout the world. The researcher, through the field study on the obstacles facing rural women in achieving
development in Palestinian society, concluded with the following recommendations to activate
the role of rural women to achieve real development within its society: The researcher, through the field study on the obstacles facing rural women in achieving
development in Palestinian society, concluded with the following recommendations to activate
the role of rural women to achieve real development within its society: Promote the educational role of rural women to enable them to gain access to
education that ensures equality and parity with men. Promote the educational role of rural women to enable them to gain access to
education that ensures equality and parity with men. Work on improving and adjusting the image of rural women, combating
stereotypical and mental concepts prevailing in the Palestinian society that consider
women as housewives doing agricultural work only. All creative areas for rural
women must be highlighted. Conduct scientific studies on rural women in all aspects to identify needs and
develop plans and programs to improve the efficiency of rural women, and liberate
them from the economic and social controls imposed on them. It is also necessary
to establish a training center in rural areas to serve rural women and raise their
scientific and professional efficiency. E-ISSN: 2590-342X https://cultureandvalues.org Conclusions and Recommendations Establish civil associations to eliminate illiteracy and introduce women to their rights
in order to achieve their role in the development process. Establish civil associations to eliminate illiteracy and introduce women to their rights
in order to achieve their role in the development process. Work to improve the image of women in Palestinian society in the media. Also,
combat concepts and vulgar images that lead to discrimination against women. Support their work as a fundamental right to contribute to development. Work to improve the image of women in Palestinian society in the media. Also,
combat concepts and vulgar images that lead to discrimination against women. Support their work as a fundamental right to contribute to development. Activating the role of women within the family in the process of social upbringing has a great
impact on the comprehensive development of society. It also has an effective role in eliminating Activating the role of women within the family in the process of social upbringing has a great
impact on the comprehensive development of society. It also has an effective role in eliminating Journal of Culture and Values in Education 2021
E-ISSN: 2590-342X https://cultureandvalues.org 2021 Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 98 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study the negative social phenomena that limit the ability and contribution of women in development
such as education, early marriage, and frequent reproduction, etc., in addition to raising the
level of women's participation in public, political, and developmental life through their
participation in decision-making. The underdevelopment of societies is due to the backwardness of their cultures. Therefore, it
is necessary to create an effective and positive cultural balance. It is also important to liquidate
the negative residues, including the details of the daily lives of individuals in the society, so that
the continuous exchange between the individual's effective behavior and lifestyle achieves
individual autonomy and active participation in society. References Abdul-Rahman, A. (2003). Development management: Development management in the Arab
world and the new world order. Kingdom of Saudi Arabia: Center for Arab Unity Studies. Abdul-Rahman, A. (2003). Development management: Development management in the Arab
world and the new world order. Kingdom of Saudi Arabia: Center for Arab Unity Studies. Awad, P. (2018). The situation of Palestinian women. Ramallah: Palestinian Central Bureau of
Statistics. Fonjong, L. (2001). Fostering women’s participation in development through non‐
governmental efforts in Cameroon. Geographical Journal, 167(3), 223-234. Hamayel, S. (2003). Palestinian university students' attitudes towards the work of women. Nablus: An-Najah National University. Hopkins, N. (1998). Gandhi and the discourse of rural development in independent India. Journal of Comparative Poetics, 18, 205-236. Jaber, D. (2005). Difficulties facing Palestinian women working in the public sector in the
northern governorates of the West Bank. Nablus: An-Najah National University. Lohani, M., & Aburaida, L. (2017). Women empowerment: A key to sustainable
development. The Social ION, 6(2), 26-29. Mohamad, Y. (2011). The obstacles to development in Palestine. Khartoum: Sudan University of
Science and Technology, Institute of Family and Community Development. Najm, M. (2013). Palestinian university youth attitudes towards women's education and work. IUG Journal of Educational and Psychological Studies, 21(1), 567-617. PCBS. (2017a). Preliminary results of the general census of population, housing and
establishments. Ramallah: Palestinian Central Bureau of Statistics. Journal of Culture and Values in Education 2021
E-ISSN: 2590-342X https://cultureandvalues.org Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org 2021 Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org Journal of Culture and Values in Education
Volume 4 Issue 1, 2021 99 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case
Study y
PCBS. (2017b). Women and men in Palestine issues and statistics. Ramallah: Palestinian Central
Bureau of Statistics PCBS. (2017b). Women and men in Palestine issues and statistics. Ramallah: Palestinian Central
Bureau of Statistics Pinot, E. (1972). What is development? Beirut: Dar Alhaqiqa. Sarhan, H. (2014). Sustainable human development and building a knowledge society. Ahl al-
Bayt Journal, 1(16), 138-155. Sayed, P. (1996). Impact of the WTO agreement on agriculture on the role of women in rural
development. Yemen: Ministry of Agriculture. Shteih, A. (2018). Problems of women in the economic life and the labor market in the West
Bank, according to the data of the Palestinian labor force 2015. Nablus: An-Najah National
University, unpublished thesis. Journal of Culture and Values in Education
E-ISSN: 2590-342X https://cultureandvalues.org References Tim, H., & Anadi, E. (2010). The degree of Palestinian women's participation in development
from the perspective of graduate students at An-Najah National University in Nablus. Nablus:
An-Najah National University. UNDP. (1990). Rural women’s participation in development. New York, NY: UNDP. 2021
|
https://openalex.org/W4377693708
|
https://www.researchsquare.com/article/rs-2950961/latest.pdf
|
English
| null |
Ensuring leadership at the operational level of a health system in protracted crisis context. A cross-sectional qualitative study covering 8 health districts in Eastern Democratic Republic of Congo
|
Research Square (Research Square)
| 2,023
|
cc-by
| 10,993
|
Results The study has revealed deficiencies regarding Management and Organisation of the health zones, Internal
collaboration within their management teams as well as collaboration between these teams and the health
zone’s external partners. Communication and clinical and managerial capacities were identified as key
factors to be strengthened in improving leadership within the districts. The findings have also highlighted
the detrimental influence of vertical interventions from external partners and hierarchical supervisors in
health zones on planning, human resource management and decision-making autonomy of district
leaders, weakening their leadership. Research Article License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read
Full License Additional Declarations: No competing interests reported. Additional Declarations: No competing interests reported. Page 1/22 Version of Record: A version of this preprint was published at BMC Health Services Research on December
6th, 2023. See the published version at https://doi.org/10.1186/s12913-023-10336-7. Version of Record: A version of this preprint was published at BMC Health Services Research on December
6th, 2023. See the published version at https://doi.org/10.1186/s12913-023-10336-7. Page 2/22 Background This study examines how leadership is provided at the operational level of a health system in a protracted
crisis context. Despite advances in medical science and technology, health systems in low- and middle-
income countries struggle to deliver quality care to all their citizens. The role of leadership in fostering
resilience and positive transformation of a health system is established. However, there is little literature on
this issue in Democratic Republic of the Congo (DRC). This study describes leadership as experienced and
perceived by health managers in crisis affected health districts in Eastern DRC. Methods A qualitative cross-sectional study was conducted in eight rural health districts (corresponding to health
zones, in DRC’s health system organization), in 2021. Data were collected through in-depth interviews and
non-participatory observations. Participants were key health actors in each district. The study deductively
explored six themes related to leadership, using an adapted version of the Leadership Framework
conceptual approach to leadership from the United Kingdom National Health Service’s Leadership
Academy. From these themes, an inductive analysis extracted emerging subthemes. Conclusions Despite their decentralized basic operating structure, which has withstood decades of crisis and
insufficient government investment in healthcare, the districts still struggle to assert their leadership and
autonomy. The authors suggest greater support for personal and professional development of the health
workforce, coupled with increased government investment, to further strengthen health system capacities
in these settings. Background Page 3/22 Page 3/22 Advances in medical science and technology continue to expand the strategic opportunities for curative
and preventive interventions around the world to deliver better health for all and extend life (1). At the
country level, these interventions should be implemented through the health system, which the World
Health Organization (WHO) defines as a set of elements, structures, and individuals that interact in a
coordinated manner to ensure holistic and integrated care of the health of populations (2). The fit between
existing policy options and national health systems' capacity at delivering quality universal healthcare,
however, varies in practice. This is especially true for low- and middle-income countries, whose health
performance remains consistently subdued compared to that of high-income countries (3, 4). The 2020–2021 WHO Results Report (5) concludes that the Triple Billion Initiative has achieved relative
success in achieving the Sustainable Development Goals. However, 80% of these achievements have
occurred essentially in a handful of countries, leaving a rather worrisome health situation elsewhere,
particularly in sub-Saharan Africa. The Covid-19 pandemic has undoubtedly contributed to this
underperformance, as 90% of countries have acknowledged having experienced significant disruptions in
organizing and delivering essential health services (5, 6). Nevertheless, the pandemic has demonstrated
the importance of strong leadership, capable of ensuring multisectoral coordination in preparing the health
system to address health emergencies during international crisis (7, 8), at both national and sub-national
levels. Indeed, studies have reported the indirect effects of health emergencies and natural disasters on
health systems. Beyond the associated morbidity and mortality, these emergencies usually induce
disruptions in various health services across the health system’ six building blocks (6, 9, 10), including
leadership and governance. Most health policy experts consider managers with strong leadership to be a critical component for health
system development (1, 11), and a prerequisite for health system strengthening and overall progress (12). Several authors have demonstrated the key role of leadership in resilience and positive health system
change in various contexts (13–15). Factors such as good governance, political commitment, effective
management, and the ability to innovate and adapt to resource constraints or crises have been recognized
as characteristics of the best-performing health systems (16). Eastern Democratic Republic of Congo has been facing crisis for more than three decades. Settings and study period This study was conducted in the mountainous province of South Kivu in Eastern DRC. The health system
in the DRC is organized in three levels: (i) the Central level, where health policies, norms and strategies are
elaborated in the Ministry of Health ; (ii) the intermediate level represented by the 26 provinces which plays
a role of coordinating health interventions, planning and technical support (through the Provincial Health
Division – PHD) and of control, audit and inspection (through the Provincial Health Inspection (PHI); (iii)
and the operational level featuring 516 Health Zones (HZ – corresponding to health districts ) where health
policies and strategies are implemented (26, 27). The HZ is managed by an autonomous Health Zone
Management Team (HZMT) whose mission is to ensure the consistency of activities, including improving
health coverage and quality of care, streamlining the operation of integrated health structures, This study was conducted in the mountainous province of South Kivu in Eastern DRC. The health system
in the DRC is organized in three levels: (i) the Central level, where health policies, norms and strategies are
elaborated in the Ministry of Health ; (ii) the intermediate level represented by the 26 provinces which plays
a role of coordinating health interventions, planning and technical support (through the Provincial Health
Division – PHD) and of control, audit and inspection (through the Provincial Health Inspection (PHI); (iii)
and the operational level featuring 516 Health Zones (HZ – corresponding to health districts ) where health
policies and strategies are implemented (26, 27). The HZ is managed by an autonomous Health Zone
Management Team (HZMT) whose mission is to ensure the consistency of activities, including improving
health coverage and quality of care, streamlining the operation of integrated health structures,
management of human and financial resources, and organizing community participation. This team
therefore represents the foundation for the leadership that contributes to strengthening the health system
at the operational level (28, 29). This organization of the health system stems from the 1980s. it has been
inspired by the Alma Ata (1978) recommendations regarding Primary Health Care’s organization, renewed
through Astana Declaration (2018) (30, 31). Some authors consider it to be among the best designed and
most robust health system organizations in sub-Saharan Africa. It has proven its resilience by surviving an
environment of security, economic and governance crisis that has plagued the country throughout the 20
years following its independence in 1960. Settings and study period (32, 33). Private faith-based health care organizations play an
important role in health care delivery and are co-managers with the Congolese State of several integrated
health facilities. The health sector is poorly financed by the state. Therefore, it depends heavily on external
Technical and Financial Partners (TPF) support, and a large part of the operating funds for the facilities
and staff remuneration comes directly from households (34, 35). For the past three decades, the South-
Kivu province has evolved in a context of instability and protracted humanitarian crisis linked to the
recurrence of conflicts in the region (17, 36). The province is organized into a Provincial Health Division
(PHD), with 34 health zones. Our study takes place in eight rural health zones covering 1 812 123
inhabitants and considers data and events for the year 2021. g
q
y
,
g
p
g
,
management of human and financial resources, and organizing community participation. This team
therefore represents the foundation for the leadership that contributes to strengthening the health system
at the operational level (28, 29). This organization of the health system stems from the 1980s. it has been
inspired by the Alma Ata (1978) recommendations regarding Primary Health Care’s organization, renewed
through Astana Declaration (2018) (30, 31). Some authors consider it to be among the best designed and
most robust health system organizations in sub-Saharan Africa. It has proven its resilience by surviving an
environment of security, economic and governance crisis that has plagued the country throughout the 20
years following its independence in 1960. (32, 33). Private faith-based health care organizations play an
important role in health care delivery and are co-managers with the Congolese State of several integrated
health facilities. The health sector is poorly financed by the state. Therefore, it depends heavily on external
Technical and Financial Partners (TPF) support, and a large part of the operating funds for the facilities
and staff remuneration comes directly from households (34, 35). For the past three decades, the South-
Kivu province has evolved in a context of instability and protracted humanitarian crisis linked to the
recurrence of conflicts in the region (17, 36). The province is organized into a Provincial Health Division
(PHD), with 34 health zones. Our study takes place in eight rural health zones covering 1 812 123
inhabitants and considers data and events for the year 2021. Background This situation
has strongly contributed to the deterioration of the population's socio-economic conditions, and has
notably led to a weakened health system and a substantial lack of health care (17) for the vast majority of
the population. As a result, along with the combined burden of infectious diseases and malnutrition,
additional health problems directly related to crisis and armed conflict emerge, with major consequences
for the overall health of the local population (18, 19). The province of South Kivu in Eastern DRC is one of
the most affected provinces by these recurring conflicts (17, 20). Hence the need to promote the leadership
necessary to achieve greater resilience of the health system (16). Very often, academic training programs for health workers do not include modules on leadership (21, 22). It
is the same in DRC and little is known about leadership development in the Congolese health system (23). A few reports from the Ministry of Health mention a leadership training course focusing on the four
functions (scan, focus, align and inspire) organized for the chief medical officers of health districts and Page 4/22 some Ministry of Health executives by Management Science for Health (MSH) more than ten years ago,
without a clear follow-up program (24, 25). To date, there is no information on the proportion of managers
who have completed this training and whether they are still working. In this study, we analyze the state of
leadership at the health district level in South Kivu, Eastern DRC. some Ministry of Health executives by Management Science for Health (MSH) more than ten years ago,
without a clear follow-up program (24, 25). To date, there is no information on the proportion of managers
who have completed this training and whether they are still working. In this study, we analyze the state of
leadership at the health district level in South Kivu, Eastern DRC. Selection of health zones Eight health zones were selected based on geographical and security accessibility. We targeted health
zones benefiting from the support of a health system strengthening program funded by an international
non-governmental organization, thus ensuring that all eight zones have at least a minimum level of
functioning. International organizations are key partners in the survival of the Congolese health system in
this protracted crisis environment. They are intended to provide collaborative support to the system, Page 5/22 integrating their interventions within the country's contextual priorities (28). Our study’s HZs are spread
over five of the height territories that constitute the province, thus covering the province's different
geographical areas: (i) Minova HZ, on the northern axis of the province (Kalehe Territory), (ii) 3 HZs
(Kaziba, Mubumbano, Nyangezi) for the territory of Walungu located on the Central axis, (iii) Nyantede HZ
for the territory of Kabare which forms a belt around the city of Bukavu, (iv) Mwana HZ for the territory of
Mwenga located on the western axis of the province and (v) 2 HZs (Ruzizi and Uvira) for the territory of
Uvira located on the southern axis. Study type We performed a qualitative phenomenological study to describe the opinions, perceptions, and attitudes of
participants regarding leadership in their health zones. These participants were key leaders of the health
zones, gathered in the Health Zone Management Team (HZMT): managers at the Health Zone General
Referral Hospital and the Health Zone Central Office, and representatives of the local community involved
in the Health Development Committee of the zone. Conceptual Approach to Leadership Leadership is a concept that still varies greatly among experts. Thus, multiple theories have been
described, drawing on one or other of its underlying dimensions (37). For this study, we built our thematic
framework inspired from the Leadership Framework conceptual approach to leadership of the United
Kingdom’s National Health Service’s Leadership Academy (38, 39). We developed six themes, four of which
derive from the definition of the seven constitutive dimensions of the NHS’s Leadership Framework related
to the managerial functions recognized in a functional HZMT (Theme 1 to Theme 4) (Table 1): Page 6/22
Table 1
Leadership thematic framework deducted from the NHS’s Leadership Framework
NHS’s Leadership Framework’s
Leadership Dimensions
Study deducted themes
1) Demonstrating personal qualities
1) Perspective about Leadership
2) Working with others
3) Creating the vision
2) Internal collaboration within the HZMTs
3) Collaboration between the HZMTs and the Technical and
Financial Partners (TFPs)
4) Managing services
5) Improving services
6) Setting direction
7) Delivering the strategy
4) Management and organization of the HZs
5) Perception of the state of Leadership in the HZs
6) Leadership Strengthening Needs
Data Collection: Table 1 In-depth interviews and non-participatory observations were used to collect data (Table 2). The data were
collected by senior researchers from the Ecole Régionale de Santé Publique school of public health of the
Université Catholique de Bukavu, all of whom have extensive experience in qualitative data collection. As
the study took place while the barrier measures against the Covid-19 pandemic were still in effect, these
were respected throughout the data collection. Interviews were conducted in French and interviewers and
participants were all fluent in that language. The data collection tools were pre-tested on a small scale on a
population estimated similar to the one targeted by the study. An interview guide exploring all six themes guided the individual discussions. Respondents matching the
profiles were approached at their place of work, and the interview took place on the spot if the respondent
gave consent and was available. Data collectors conducted an initial debriefing after each interview. The
principle of saturation thus determined the number of interviews conducted in all eight HZs (Table 2). Structured non-participatory observations of activities that could provide an appreciation of leadership
practices and attitudes among managers were conducted whenever possible. Conceptual Approach to Leadership The observations were of two types: observation of the managers in their work environment (clinical room
rounds, team work sessions, supervisions) and observation of a routine work meeting of the members of
the HZMT. The observation themes of interest were the technical settings of organizing the targeted activities, and the
types of interactions during these activities. As attributes of the leadership dimensions "organization of
work" and "communication" (39), these themes contributed to exploring two of the six themes of our
thematic framework: Internal collaboration within the HZMT, and Management and organization of the HZ. The targeted activities were observed whenever they coincided with the interviewers' visit. The participants
were not prepared beforehand about the observations. Their informed consent was obtained just before
the onset of each observation. The average interview time was 45 minutes. The average length of a routine meeting observation was 1.5
hours, and that of observation of HZMT in their workplace was 8 hours. The average interview time was 45 minutes. The average length of a routine meeting observation was 1.5
hours, and that of observation of HZMT in their workplace was 8 hours. Page 7/22
Table 2
Summary of types of information collected. Collection
method
Profile
Total
Observations
Observation of a routine work
meeting of the HZMT
Observation of managers in their
work environment
05
06
11
Individual
interviews
CMO
MD-GRH
AM-HZCO
HDCM
MSC
SN
03
07
02
09
01
03
25 CMO: Chief Medical Officer of the HZ; MD-GRH: Medical Director of the General Referral Hospital; AM-
HZCO: Administrative Manager of the HZ Central Office; HDCM: member of Health Development Committee
of the HZ; MCS: Medical Staff Chief of the GRH; SN: Supervising Nurse of the HZ. D t A
l
i Data Analysis: Interviews were transcribed into Word documents. We performed a thematic analysis (40) with deductive
and inductive approaches. The six themes initially established allowed for initial coding of the data. Then,
within each theme, an inductive in vivo analysis identified various emerging sub-themes. A triangulation between the information from the interviews and that from the observations made it
possible to describe the state of leadership in the zones, as perceived and experienced by the HZMT. For
the sake of anonymity, and to avoid any possibility of linking the identity of a respondent to a health zone,
data were analyzed approaching all the height health zones as a whole. Ethical considerations: The research protocol was submitted to and validated by the ethics committee of the Université Catholique
de Bukavu under the reference UCB/CIES/NC/019/2021. Informed consent was obtained from each
participant prior to any interview or observation. Data were collected and analyzed in complete
confidentiality. All methods were carried out in accordance with relevant guidelines and regulations. In analyzing this theme, two sub-themes emerged: In analyzing this theme, two sub-themes emerged: Governance: Respondents consider a leader as someone capable of effectively organizing resources to
meet the community’ needs. This leader must furthermore have a good grasp of public health standards
and be able to hold his/her institution accountable to such standards. P-4: "A leader is a person who is trained in the health system and is able to organize or lead the health zone
to find solutions to identified problems with the least amount of cost..." P-10: "...In the health system, (leadership) is how to organize things as it should be, the need to meet the
expectations or needs of the community very well and needs of the health system." P-16: "...I think leadership is a team that mentors, that ensures that public health is really respected and
effective at the health zone level..." Vision/positive influence: Respondents also mentioned that a leader with a clear vision is one who able to
meet the expectations of the community. A leader inspires confidence in his collaborators and the local
community. He /she can positively influence his/her team and steer them towards the realization of this
common ideal of integral well-being. Page 8/22 P-12: "Leadership, a leader is someone who leads a team, who leads a team for a common ideal or vision." P-18: "When we talk about leadership, we mainly see someone who has a vision and who has the ability to
practically draw everyone towards him to bring them into that vision..." 2. Internal Collaboration within the HZMTs There is some variability in internal collaboration among the members of the HZMTs, with notable
differences between zones. Three sub-themes emerged from this theme: Positive collaboration: Some respondents appreciate the teamwork within their zones. The planning of
activities is good, tasks are clearly distributed, and work is decentralized in term of execution. Financial
management is transparent and honest, and personnel management is adequate. P-5: "...When we even do the planning of activities, we do it together to say that the health zone is
functional..." P-9: "I appreciate the way they work internally, because normally we work in a decentralized way, each one
does his job according to his attributions. I see that even in the absence of the zone's chief medical officer,
we organize the routine meetings of the management team; this already shows that there is delegation of
power at the HZ level..." Conflict and division: Other respondents reported that there is conflict and division in their zones. Particularly when
occasional activities generate dividends, some leaders step aside to share them without everyone's
participation. Some respondents report that these divisions have an impact on the governance of the zone,
leading to irregularities in the implementation of HZ activities. P-15: "... I see that apparently Chief Medical Officers of health zones do not collaborate well with the
subordinates. For the most part of the Chief Medical Officers of the zones that I have already met. Because
they are the ones who make decisions themselves, especially regarding collaboration with partners. Sometimes they don't give feedback on all the contacts they make with partners outside the team...". P-21: "... We do meetings together. We do all activities together. But when it comes to money, the
management team is divided: “oh no, these people are from the hospital, and us we are from the zone…”
and that sometimes causes problems. There are segregations when it comes to “war booty” ..." Communication: Our observations of meetings in some areas indicate poor communication. In some HZs,
observers noted meetings with an ambiance of a passive stillness where few people speak up, yet the
resolutions made in the meetings were not contested. However, in other zones, communication in the
meetings was smooth, with active participation of all, and collegiality in decision making. 3. Collaboration between the HZMTs and the Technical and
Financial Partners (TFPs) Page 9/22 By technical and financial partners (TFPs), we mean international non-governmental organizations and
other partner institutions from multilateral collaboration engaged with the national health sector. By technical and financial partners (TFPs), we mean international non-governmental organizations and
other partner institutions from multilateral collaboration engaged with the national health sector. In this theme too, two different positions are noted among respondents, through the following two sub-
themes: Communication and Planning: Some respondents are satisfied with the quality of communication between
the TFPs and their zones. Communication is two-way and planning of activities is collaborative. Elsewhere,
other respondents criticized the fact that the TFPs plan their activities without prior consultation with the
HZMT, which is the reason for the failure of these activities given their non-contextualization to the needs
of the zone. P-12: "The collaboration is good because in the team meetings we have reports (from partners) in relation
to everything and (feedback) on their different advocacies." P-12: "The collaboration is good because in the team meetings we have reports (from partners) in relation
to everything and (feedback) on their different advocacies." P-4: "As I told you we, i.e the management team, are in conflict with the partner (name of the partner) for
not working well together because of selfish interests. People don't collaborate; one hurts the other. Partnership is not respected." P-4: "As I told you we, i.e the management team, are in conflict with the partner (name of the partner) for
not working well together because of selfish interests. People don't collaborate; one hurts the other. Partnership is not respected." Financial management: Some respondents report a lack of transparency and traceability in the
management of funds that partners grant to zones but still decide how these funds shall be used,
sometimes resulting in situations of financial mismanagement for which the HZMT considers these
partners directly responsible. P-5: "I think the problem between the HZMT and the technical and financial partners is a planning problem. We have our operational action plan in the zone, which is where the TFPs should join. 3. Collaboration between the HZMTs and the Technical and
Financial Partners (TFPs) But the TFPs plan
activities outside this operational plan..." P-15: "...it's true that there are always small concerns among certain financial partners who are not clear in
their degree of collaboration with the zone, and therefore the transparency and traceability in relation to the
funds or in relation to the support they bring to the health zone are not always well traced. They are not
really very clear in the transparency, in the management..." 4. Management and Organization of the Health Zones Three sub-themes emerged from this theme: Health Zone management: The management is not optimal. The issue of lack of internal cohesion within
the teams and abuse of power by superiors is still noted in some HZ. This again takes the form of opaque
management of funds, especially bonuses from extraordinary activities such as vaccination campaigns
and large-scale campaigns of distribution of insecticide-treated bed nets. This mismanagement of the
zone is also reflected in the administrative management of human resources, and delays in the payment of
staffs’ salaries. Page 10/22 Page 10/22 P-4: "The management is not good, there is mismanagement of the HZ, the HZ Central Office is very badly
managed. The chief himself manages the money, he himself is the cashier, the administrative manager, the
accountant... So, everything is done in his office." P-18: "...there are several agents who do not receive (their remuneration), agents who are not matriculated,
there are also many agents whose files are not complete, there are agents who do not have proper
assignments and for whom regularization has not yet taken place..." Organization of the zone: A delay in carrying out the activities of the operational action plan of HZs is
reported at all levels (health center, referral hospital or HZ central office) and is mainly the result of
financial mismanagement or a failure to organize the work plan. This disorganization of the zone is also
found in the organization of different healthcare packages at the first and second lines of care: in some
HZs, there is no longer a clear demarcation between structures supposed to offer first- and second-line care
packages; some front-line facilities anarchically offer services that are exclusive to second-line facilities. The lack of communication is also translating into tensions between facilities’ co-managers over staff
assignment and other managerial decisions. P-3: "...In relation to the management of activities, I can say that there are times when the supervision
schedule is not followed, for example, at the referral hospital in (name of the zone) and at the level of the
primary structures, the health centers. Therefore, there is a lack of respect of the supervision schedule that
was established for the activities”. P-18: "... A health center that doesn't respect its minimum package of activities; it does what it wants. Imagine a health center that performs blood transfusions..." P-5: "Here we have a general referral hospital which has a private manager that always poses the problem
of co-management with the Ministry of Health... They can bring in someone who he is a teacher or an
agronomist, they appoint him as the hospital's administrative manager. There is really no collaboration in
the assignment of officers who manage the hospital..." Collaboration between the zones and the Provincial Health Division (PHD): Some respondents reported
close collaboration between the zones and the PHD. However, others found that the management of this
collaboration was not optimal. Page 10/22 In particular, they criticized the abuse of power by the PHD in the form of
interference in the management of HZ staff and the planning of HZ activities. In addition, the zone's
expectations in terms of capacity-building support from the PHD are not always met. P-2: "...PHD doesn't support the HZs like they used to when we had a lot of supervisions and that helped us. But now they're once or twice a year and if we got those supervisions once a quarter it would be fine..." P-18: "...there are still some irregularities when it comes to some activities that are practically the
responsibility of the HZ Chief Medical Officer or the management team but are carried out by PHD
managers... Examples of the opening of private health centers that do not meet any standards..." Page 11/22 Page 11/22 In addition to the results of the interviews, observations of the managers in their work environment reported
an overall respect for the start and end times of work. However, of the average 8 hours spent at work, less
than half (an average of 3 hours) is spent actually working, with time at work coexisting with untimely
comings and goings, unscheduled private visits, and frequent and sometimes long breaks outside of work
on the phone or in conversation with colleagues on site. Unlike meetings where the agenda is set in
advance, in none of the observations made was there any prior preparation of the daily work plan, nor were
there any specific time slots set aside for various tasks. 5. Perception of the state of Leadership in the Health Zones. The perception of the leadership of the HZMT varies among respondents. Some see effective leadership,
with initiatives to bring together different local leaders, while others point to difficulties in managing
unmotivated and resistant staff. In addition, issues of lack of cohesion within the HZMT, and the vertical
approach of Technical and Financial Partners in their support to zones, were raised as factors that weaken
the quality of leadership within the HZMT. P-1: "In the public health activities, leadership is conducted: the HZMT plans a meeting where it will call on
all local community leaders, as well as influential leaders, to take certain (measures) together in the
(management of) certain problems in society..." P-6: "It is not easy for (the zone leaders) to impose themselves on unmotivated staff. Often there is
resistance, and they often have difficulty managing staff. This problem has a negative impact on the
implementation of activities, but they do their best to keep us within the standards. P-18: "... And so instead of the different partners aligning themselves with the planning of the health zone,
we feel at times that it's the health zone that practically aligns itself with partners objectives and planning. And so, that's kind of the big constraint in practice.” P-18: "... And so instead of the different partners aligning themselves with the planning of the health zone,
we feel at times that it's the health zone that practically aligns itself with partners objectives and planning. And so, that's kind of the big constraint in practice.” Discussion Aiming to contribute to the strengthening of the DRC's health system through the integrated leadership of
the HZ (28, 29), this study describes the state of leadership as experienced by operational-level health
managers in rural areas in a context of crisis. The rural health zones in crisis in the DRC are similar in their
organization and in the challenges they face (17, 20, 27, 29, 41), we believe that the results from these
eight study areas will largely reflect the situation of all other areas in the same context. These results could
represent one of the worst cases of the state of the DRC health system, with the crisis context playing as
an aggravating factor (17, 41) on the rural context, which is even worse than the urban context (42–44). However, for this specific point, further studies are needed to confirm this assumption. 6. Leadership Strengthening Needs This theme explored respondents' views on the need for leadership development in the area. The following
three sub-themes emerged: Communication and planning: Respondents emphasized improving communication and collaboration
between the members of the HZMT, the PHD and technical and financial partners. This would restore
cohesion and promote planning adapted to the realities of the zone. P-5: "I would recommend that when there is an activity, that the team organizing at the provincial level take
into account the planning at the grassroots level." P-5: "I would recommend that when there is an activity, that the team organizing at the provincial level take
into account the planning at the grassroots level." Autonomy and decision-making power: Respondents expressed the need for more autonomy in
management and decision-making at the health zone level. Autonomy and decision-making power: Respondents expressed the need for more autonomy in
management and decision-making at the health zone level. Page 12/22 Page 12/22 P-18: "The first recommendation is to give more responsibility to the HZ Medical Officers. They know what
they have to do, but at times the PHD want to treat them like little children and that's something that
doesn't go down well..." Capacity building: Respondents expressed a need to strengthen the clinical and managerial capacities of
the various local actors to better manage the health zone, improve its performance and the health status of
the local community. Some respondents emphasized that better work planning and organization skills
would contribute to the achievement of the health zones' operational objectives. They felt that having a
daily work plan to help manage time on the job would help them perform better. P-9: "you know you can't punish someone for what they don't know, I can say that trainings are always
important because if you are trained in leadership and human resource management it can always build
capacity." P-20: "Yes, it's the training. Especially training in primary health care management could help the zone to
know how to apply or revitalize and sustain leadership in the health zone, but also the collaboration of
partners." Perspective of leadership Several key words in the definitions of leadership most found in the literature were used by most
respondents, suggesting that they had already been exposed to at least one update on the issue of
leadership. In fact, the Ministry of Health, as part of its capacity building for human resources, regularly
programs training for health zone managers that addresses, among other things, leadership and
management issues (28, 29). However, one might question the success of these trainings, considering that
most respondents seemed to equate leadership with simple respect for procedures, and to define it as the
exclusive prerogative of the most senior officials in the zone. In general, leadership remains a concept with
a rather changing definition, depending on the field and the understanding: It can be confused with
management, rigor, knowledge, the courage to undertake, or the charisma that one person can exert on one
or several others (37, 45). It can also be merged with governance, the two elements being presented by the
WHO as a single pillar of the health system (1). All these descriptions are scattered components of this Page 13/22 Page 13/22 concept, which is so dense that several authors have given it different definitions and theoretical
frameworks depending on their applications (37, 45, 46). By hypothesizing that a manager is more likely to apply a leadership style that is consistent with his
understanding of this concept (47), we perceive a leadership style that is more transactional than
transformational in these HZs. Transformational leadership aims to inspiring others to willingly follow, and
requires a high level of coordination, communication, and cooperation. Transactional leadership is
primarily based on processes and control and requires a strict management structure: rewards and
punishment are used as a motivating basis. This style is much more concerned with short-term planning
and execution than with the long-term vision of an institution and its innovation (48–51). Several authors
studying the perception of leadership in Sub-Saharan Africa have reported a preferential application of the
transformational style (52–54). According to some authors, in a turbulent and unstable environment, such
as the one in our study, the best adapted leadership style would be transformational, whereas a well-
established environment, where processes and practices are well established and the context is stable, can
thrive with a transactional leader (48, 49). Yet, we find that the HZs in our study tend to adopt a
transactional leadership style. Management, organization, and leadership in the HZ Government underfunding favors the development of a private informal sector (34, 55). Thus, in their search for alternative financing, facilities may be led to inflate their activities to increase their
income. This represents a potential danger for patients because, faced with difficult living conditions,
health workers may be more concerned with supplementing their income than providing quality care (59). Our observations revealed a poor level of organization and management of working time as a whole. Untimely visits, the use of cell phones for non-professional purposes, as well as the lack of a precise daily
work plan are all factors that have contributed to an effective working time that is far below the theoretical
working time. The use of cell phones and social networks in the workplace is becoming more and more
widespread, sometimes with negative effects on performance. It is in particular by increasing the mental
load by various cognitive solicitations, and by distracting the employees from their tasks, as it has been
described by some authors (60, 61). However, since new communication technologies have found a place
of choice in daily work, particularly by facilitating communication, some authors recommend that
employers supervise the use of social media at work rather than simply banning them (61, 62). They
suggest better human resource management, including drawing a well-defined daily work plan and
tracking its execution, as a way to avoid delays in deliverables related to time wasted on social media or
unplanned visits. Management, organization, and leadership in the HZ The issue of financial management of the HZ regularly came up as a point of contention among our
respondents. The DRC's health system is designed in such a way that the health zones have all the
management bodies necessary to ensure the ideally optimal management, operation and delivery of
primary health care with high decision-making autonomy (28). But, in the DRC, as in most low-income
countries (55), the government's contribution to health care spending remains insufficient, barely reaching
20%. In addition to increasing household expenditures, which account for up to 40% of current health
expenditures, this situation has an impact on human resources in the sector, which are poorly supported by
the State (34, 35). Thus, any opportunity to earn a salary bonus during extraordinary activities could prove
to be a godsend for these regularly underpaid agents. The tendency of leaders to manage these occasional
"windfalls" in a small circle, creating suspicion and frustration, affects the quality of collaboration among
members of the HZMT and undermines the cohesion of the group, as several of our respondents
complained. In such already divided communities, it is unlikely that the principles of good leadership can
be achieved, since from the outset it is no longer possible to unite the whole team behind a common vision,
which is the main essence of a good leader (12, 48). These frustrations, often downplayed, can have
devastating indirect consequences. This is the case in our health zones where weekly board meetings
become irregular and where we have observed meetings with such unbalanced power dynamics that the
session becomes more a formal briefing than a participative discussion. The literature provides
information on how interpersonal tensions between health care personnel have had negative impacts on
patient care and on the management of institutions (56, 57). Without these board meetings, which provide
the best frame for the realization of the zone's vision, all planning is doomed to failure in the short or long
term. Without dialogue, there is no leadership. An appropriate leadership can create an organizational
culture of good governance, and balance the power dynamics, which will result in improved system
performance and help achieve system goals (1, 58). Page 14/22 Our study found disorganization in the delivery of primary and secondary health care. Beyond the simple
observation of the disorganization of the health system, it is interesting to try to understand the underlying
reasons for it. Collaboration with TFPs Each health zone elaborates its Operational Action Plan yearly, in collaboration with the PHD and with the
support of the TFPs. TFPs are recognized as key contributors to the functioning of the DRC's health
system, given the context of low government funding. It is during this activity that the priority interventions
of the zones are planned, taking into account the context of each health zone. Our interviews revealed
interference between these plans and the interventions of the TFPs. The latter also appear to be the main
financiers of several activities, given the limited intervention of the State in covering the health expenses of
the zones (34). This dependence on external aid is often the Achilles heel of health systems in developing
countries (63–65). The prescriptive and unaligned nature of international partner interventions in low-
income country health programs contributes somewhat to the status quo in empowerment and leadership
development within health systems operating in these contexts (64, 65). This verticalization of aid has
been commented on by the DRC’s Ministry of Health, which noted that "The establishment of mid-level
structures by the Ministry of Health's partner institutions creates several problems for the already fragile
health sector. These problems include (i) increasing conflict with the structures they are supposed to
support, (ii) increasing verticalization of the system as a result of the intervention of these support
structures, including health centers and the community, and (iii) inefficiency, (iv) a gradual shift from the
support role that sector partners are supposed to play to that of providers.” (28) Respondents also felt that they lacked autonomy in their decisions, being stifled by interference from the
provincial level in operational level decision-making. This could indirectly indicate a non-delegative
leadership style on the part of provincial officials, which can lead to frustration and demotivation of HZMT Page 15/22 Page 15/22 members. Indeed, authors have shown a positive association between the degree of task delegation and
provider motivation (58, 66). Strengthening leadership We analyzed respondents' views on the need for leadership development in their areas across the 7
domains of the NHS’s Leadership Framework (39). Thus, across the three sub-themes identified by the
analysis of the results, respondents expressed needs for strengthening personal qualities (knowledge,
skills, and attitudes), teamwork, service management, direction setting, and strategy delivering. While admittedly the DRC's Ministry of Public Health, in collaboration with certain TFPs, regularly provides
capacity-building training to all health system agents, these trainings remain ad hoc unstructured briefings
that often do not reach all agents at the various levels of the health system in a systematic manner (24,
25). Further study is needed to document the real impact of these trainings on improving the performance
and functionality of the health zones. In several English-speaking countries in the same context, there is While admittedly the DRC's Ministry of Public Health, in collaboration with certain TFPs, regularly provides
capacity-building training to all health system agents, these trainings remain ad hoc unstructured briefings
that often do not reach all agents at the various levels of the health system in a systematic manner (24,
25). Further study is needed to document the real impact of these trainings on improving the performance
and functionality of the health zones. In several English-speaking countries in the same context, there is
evidence of structured and systematic capacity building programs at all levels of the health system (13, 14,
23). Researchers who have documented leadership development programs implemented in sub-Saharan
Africa have broadly identified several leadership development needs. These include conceptual leadership,
capacity building and theoretical knowledge from curricula and health policy; service, emergency planning
and management; communication and advocacy; as well as experiential learning through internships with
local mentors or Northern institutions (23, 67, 68). Conclusions Although leadership is recognized a key element in strengthening the health sector, we observe in our study
that some aspects of leadership are sorely lacking in the day-to-day work and management in the health
districts of eastern DRC. Management teams have a low level of cohesion, communication, and
organization of work. The heavy dependence on aid from external international partners and the vertical
nature of their interventions somewhat stifle the expression of leadership by local managers. Despite a
well-designed decentralized structure that manages to keep the local health system functioning in the
context of a protracted crisis and limited government investment in health care, this leadership deficit
further compounds the development challenges encountered by these health zones. There is a definite urge
to strengthen leadership. However, insufficient government contribution to health sector funding drastically
hinders empowerment efforts. Therefore, alongside supporting the personal development of its human
resources, the health sector should advocate for increased government investment in public health
spending. HZMT: Health Zone Management Team
NHS: National Health Service (of the United Kingdom)
PHD: Provincial Health Division
TFP: Technical and Financial Partners
WHO: World Health Organization HZMT: Health Zone Management Team
NHS: National Health Service (of the United Kingdom)
PHD: Provincial Health Division
TFP: Technical and Financial Partners
WHO: World Health Organization Competing interests Competing interests The authors declare that they have no financial and non-financial competing interests. Funding This research didn’t benefit from any funding. This research didn’t benefit from any funding. Declarations Ethics approval and consent to participate Availability of data and materials Availability of data and materials Availability of data and materials Data generated and analyzed during the current study are not publicly available due to confidentiality
restrictions, but anonymized transcripts and observation grids are available from the corresponding author
upon reasonable request. Consent for publication
Not applicable
Availability of data and materials Not applicable Abbreviations DRC: Democratic Republic of Congo DRC: Democratic Republic of Congo HZ: Health Zone Page 16/22 Ethics approval and consent to participate The research protocol was submitted to and validated by the ethics committee of the Université Catholique
de Bukavu under the reference UCB/CIES/NC/019/2021. Informed consent was obtained from each
participant prior to any interview or observation. Data were collected and analyzed in complete
confidentiality. All methods were carried out in accordance with relevant guidelines and regulations. Authors' contributions "R.B., G.B. and A.M. conceived the study design and data collection tools. M.M. supported design of
methods. R.B. led the data collection and analyzis. C.C. assisted in data analysis. P.S. and C.C. assisted
R.B. in manuscript preparation. G.B. and D.P. have substantively revised the manuscript. S.M., P.M., P.S.,
and M.M. provided critical feedback. All authors read and approved the final manuscript." Acknowledgements Page 17/22 References 1. World Health Organisation. Everybody’s business, Strengthening health system to improve health
outcomes, WHO’s framework for action. 2007; 2. World Health Organization. Key Components of a Well-Functioning Health System. World Health
Organization; 2010. 3. Organisation Mondiale de la Santé. Rapport mondial 2020 sur la capacité des pays à produire des
données sanitaires [Internet]. 2021. Available from:
https://apps.who.int/iris/bitstream/handle/10665/346556/9789240027190-fre.pdf 4. World Health Organization. World Health Statistics 2022 [Internet]. [cited 2023 Mar 11]. Available from:
https://www.who.int/data/gho/publications/world-health-statistics 5. World Health Organization. WHO Results Report 2020-2021 [Internet]. [cited 2023 Feb 3]. Available
from: https://www.who.int/about/accountability/results/who-results-report-2020-2021 6. Manus JM. Sars-CoV-2 perturbe l’exercice médical dans 9 pays sur 10. Rev Francoph Lab. 2020
Nov;2020(526):14. 7. Nicola M, Sohrabi C, Mathew G, Kerwan A, Al-Jabir A, Griffin M, et al. Health policy and leadership
models during the COVID-19 pandemic: A review. Int J Surg Lond Engl. 2020 Sep;81:122–9. 7. Nicola M, Sohrabi C, Mathew G, Kerwan A, Al-Jabir A, Griffin M, et al. Health policy and leadership
models during the COVID-19 pandemic: A review. Int J Surg Lond Engl. 2020 Sep;81:122–9. 8. Nonaillada J, Martin RA. Applying Situational Leadership to Redeployment Duties During COVID-19:
Lessons Learned. Qual Manag Health Care. 2022 Dec 1;31(4):274–7. 8. Nonaillada J, Martin RA. Applying Situational Leadership to Redeployment Duties During COVID-19:
Lessons Learned. Qual Manag Health Care. 2022 Dec 1;31(4):274–7. 9. Mulenga-Cilundika P, Ekofo J, Kabanga C, Criel B, Van Damme W, Chenge F. Indirect Effects of Ebola
Virus Disease Epidemics on Health Systems in the Democratic Republic of the Congo, Guinea, Sierra
Leone and Liberia: A Scoping Review Supplemented with Expert Interviews. Int J Environ Res Public
Health. 2022 Oct 12;19(20):13113. 9. Mulenga-Cilundika P, Ekofo J, Kabanga C, Criel B, Van Damme W, Chenge F. Indirect Effects of Ebola
Virus Disease Epidemics on Health Systems in the Democratic Republic of the Congo, Guinea, Sierra
Leone and Liberia: A Scoping Review Supplemented with Expert Interviews. Int J Environ Res Public
Health. 2022 Oct 12;19(20):13113. 10. Loewen S, Pinchoff J, Ngo TD, Hindin MJ. The impact of natural disasters and epidemics on sexual
and reproductive health in low- and middle-income countries: A narrative synthesis. Int J Gynaecol
Obstet Off Organ Int Fed Gynaecol Obstet. 2022 Apr;157(1):11–8. 10. Loewen S, Pinchoff J, Ngo TD, Hindin MJ. The impact of natural disasters and epidemics on sexual
and reproductive health in low- and middle-income countries: A narrative synthesis. Int J Gynaecol
Obstet Off Organ Int Fed Gynaecol Obstet. Page 17/22 Page 17/22 We thank all the participants who took part in this study and made it possible. We also acknowledge the
support of the research staff of the Ecole Regionale de Santé Publique of the Université Catholique de
Bukavu who helped with data collection. Bukavu who helped with data collection. References 2022 Apr;157(1):11–8. 11. World Health Organization. Systems Thinking for Health Systems Strengthening. World Health Organ
[Internet]. 2017 [cited 2022 Apr 1]; Available from: http://www.who.int/alliance-
hpsr/resources/9789241563895/en/ 11. World Health Organization. Systems Thinking for Health Systems Strengthening. World Health Organ
[Internet]. 2017 [cited 2022 Apr 1]; Available from: http://www.who.int/alliance-
hpsr/resources/9789241563895/en/ 12. Frenk J. The Global Health System: Strengthening National Health Systems as the Next Step for
Global Progress. PLOS Med. 2010 Jan;7(1):e1000089. 12. Frenk J. The Global Health System: Strengthening National Health Systems as the Next Step for
Global Progress. PLOS Med. 2010 Jan;7(1):e1000089. 13. Seims LRK, Alegre JC, Murei L, Bragar J, Thatte N, Kibunga P, et al. Strengthening management and
leadership practices to increase health-service delivery in Kenya: an evidence-based approach. Hum
Resour Health. 2012 Aug 29;10(1):1–7. 13. Seims LRK, Alegre JC, Murei L, Bragar J, Thatte N, Kibunga P, et al. Strengthening management and
leadership practices to increase health-service delivery in Kenya: an evidence-based approach. Hum
Resour Health. 2012 Aug 29;10(1):1–7. Page 18/22 Page 18/22 14. Chelagat T, Rice J, Onyango J, Kokwaro G. An Assessment of Impact of Leadership Training on Health
System Performance in Selected Counties in Kenya. Front Public Health. 2013;8:550796. 15. Samuels F, Amaya AB, Balabanova D. Drivers of health system strengthening: learning from
implementation of maternal and child health programmes in Mozambique, Nepal and Rwanda. Health
Policy Plan. 2017;32:1015–31. 16. Balabanova D, Mills A, Conteh L, Akkazieva B, Banteyerga H, Dash U, et al. Good Health at Low Cost 25
years on: lessons for the future of health systems strengthening. The Lancet. 2013 Jun
15;381(9883):2118–33. 17. Altare C, Malembaka EB, Tosha M, Hook C, Ba H, Bikoro SM, et al. Health services for women, children
and adolescents in conflict affected settings: experience from North and South Kivu, Democratic
Republic of Congo. Confl Health. 2020 May 27;14(1):31. 18. Mwene-Batu P, Bisimwa G, Ngaboyeka G, Dramaix M, Macq J, Hermans MP, et al. Severe acute
malnutrition in childhood, chronic diseases, and human capital in adulthood in the Democratic
Republic of Congo: the Lwiro Cohort Study. Am J Clin Nutr. 2021 Jul 1;114(1):70–9. 18. Mwene-Batu P, Bisimwa G, Ngaboyeka G, Dramaix M, Macq J, Hermans MP, et al. Severe acute
malnutrition in childhood, chronic diseases, and human capital in adulthood in the Democratic
Republic of Congo: the Lwiro Cohort Study. Am J Clin Nutr. 2021 Jul 1;114(1):70–9. 19. References Malembaka EB, Karemere H, Balaluka GB, Lambert AS, Muneza F, Deconinck H, et al. A new look at
population health through the lenses of cognitive, functional and social disability clustering in eastern
DR Congo: a community-based cross-sectional study. BMC Public Health. 2019 Jan 21;19(1):93. 20. Malembaka EB, Karemere H, Bisimwa Balaluka G, Altare C, Odikro MA, Lwamushi SM, et al. Are people
most in need utilising health facilities in post-conflict settings? A cross-sectional study from South
Kivu, eastern DR Congo. Glob Health Action. 2020;13(1):1740419. 21. Zimmerman-Oster K, Burkhardt JC. Leadership in the Making: A Comprehensive Examination of the
Impact of Leadership Development Programs on Students. J Leadersh Stud. 1999 Sep 1;6(3–4):50–
66. 22. Astin AW, Astin HS. Leadership Reconsidered: Engaging Higher Education in Social Change [Internet]. W; 2000 [cited 2023 Jan 23]. Available from: https://eric.ed.gov/?id=ED444437 23. Johnson O, Begg K, Kelly AH, Sevdalis N. Interventions to strengthen the leadership capabilities of
health professionals in Sub-Saharan Africa: a scoping review. Health Policy Plan. 2021;36:117–33. 24. Mpawa H, Mchacha I, Ngwalo C, Betha R, Birse S, Konings E. Malawi: District health system
strengthening and quality improvement for service delivery. Manag Sci Health. 2017; 25. Leadership Development Program Plus (LDP+) : Un guide pour les animateurs [Internet]. Management
Sciences for Health. [cited 2023 Mar 13]. Available from: https://msh.org/fr/resources/leadership-
development-program-plus-ldp-a-guide-for-facilitators/ 25. Leadership Development Program Plus (LDP+) : Un guide pour les animateurs [Internet]. Management
Sciences for Health. [cited 2023 Mar 13]. Available from: https://msh.org/fr/resources/leadership-
development-program-plus-ldp-a-guide-for-facilitators/ 26. Bisimwa G, Makali SL, Karemere H, Molima C, Nunga R, Iyeti A, et al. Contrat unique, une approche
innovante de financement du niveau intermédiaire du système de santé en République Démocratique
du Congo : processus et défis de mise en œuvre. Afr J Prim Health Care Fam Med. 2021 Dec
6;13(1):e1–9. 26. Bisimwa G, Makali SL, Karemere H, Molima C, Nunga R, Iyeti A, et al. Contrat unique, une approche
innovante de financement du niveau intermédiaire du système de santé en République Démocratique
du Congo : processus et défis de mise en œuvre. Afr J Prim Health Care Fam Med. 2021 Dec
6;13(1):e1–9. 27. Organisation Mondiale de la Santé. Rapport sur la santé dans le monde 2008 : les soins de santé
primaires - maintenant plus que jamais : introduction et résumé. [Internet]. 2008. Available from: 27. Organisation Mondiale de la Santé. References Rapport sur la santé dans le monde 2008 : les soins de santé
primaires - maintenant plus que jamais : introduction et résumé. [Internet]. 2008. Available from: 27. Organisation Mondiale de la Santé. Rapport sur la santé dans le monde 2008 : les soins de santé
primaires - maintenant plus que jamais : introduction et résumé. [Internet]. 2008. Available from: Page 19/22 Page 19/22 https://apps.who.int/iris/handle/10665/69862 28. Ministère de la Santé Publique, Secrétariat Général, Kinshasa. Stratégie de Renforcement du Système
de Santé, Deuxième édition. Ministère de la Santé Publique de la République Démocratique du Congo;
2010. 28. Ministère de la Santé Publique, Secrétariat Général, Kinshasa. Stratégie de Renforcement du Système
de Santé, Deuxième édition. Ministère de la Santé Publique de la République Démocratique du Congo;
2010. 29. Ministère de la Santé Publique de la République Démocratique du Congo. Plan National de
Développement Sanitaire recadré pour la période 2019-2022 : Vers la couverture sanitaire universelle
[Internet]. 2018. Available from:
https://www.globalfinancingfacility.org/sites/gff_new/files/documents/DRC_Investment_Case_FR.pdf https://www.globalfinancingfacility.org/sites/gff_new/files/documents/DRC_Investment_Case_FR.pdf
30. World Health Organization. Primary health care: report of the International Conference on primary
health care, Alma-Ata, USSR, 6-12 September 1978. World Health Organization; 1978. 30. World Health Organization. Primary health care: report of the International Conference on primary
health care, Alma-Ata, USSR, 6-12 September 1978. World Health Organization; 1978. 30. World Health Organization. Primary health care: report of the International Conference on primary
health care, Alma-Ata, USSR, 6-12 September 1978. World Health Organization; 1978. 31. World Health Organization. Report of the Global conference on primary health care: from Alma-Ata
towards universal health coverage and the Sustainable Development Goals. World Health
Organization; 2019. 31. World Health Organization. Report of the Global conference on primary health care: from Alma-Ata
towards universal health coverage and the Sustainable Development Goals. World Health
Organization; 2019. 32. Porignon D, Porignon D, Mugisho Soron‘Gane E, Elongo Lokombe T, Katulanya Isu D, and Van
Lerberghe W. How robust are district health systems? Coping with crisis and disasters in Rutshuru,
Democratic Republic of Congo. Trop Med Int Health. 1998;3(7):559–65. 32. Porignon D, Porignon D, Mugisho Soron‘Gane E, Elongo Lokombe T, Katulanya Isu D, and Van
Lerberghe W. How robust are district health systems? Coping with crisis and disasters in Rutshuru,
Democratic Republic of Congo. Trop Med Int Health. 1998;3(7):559–65. 33. Rajan D, Kalambay H, Mossoko M, Kwete D, Bulakali J, Lokonga JP, et al. References Health service planning
contributes to policy dialogue around strengthening district health systems: an example from DR
Congo 2008-2013. BMC Health Serv Res. 2014 Oct 31;14(1):522. 34. Ministère de la Santé Publique de la République Démocratique du Congo. Rapport sur les comptes de
la santé 2020. 2021. 35. World Health Organization. Improving health system efficiency: Democratic Republic of the Congo:
improving aid coordination in the health sector. World Health Organization; 2015. 36. Stearns J, Vogel C. The Landscape of Armed Groups in the Eastern Congo. Stearns Jason Vogel
Christoph 2015 Landsc Armed Groups East Congo N Y Congo Res Group N Y Univ CIC [Internet]. 2015
Dec [cited 2022 Apr 7]; Available from: http://congoresearchgroup.org/essay-the-landscape-of-armed-
groups-in-eastern-congo-2/ 37. Komives SR, Dugan JP, Owen JE, Slack C, Wagner W, Programs (NCLP) NC of L. The Handbook for
Student Leadership Development. John Wiley & Sons; 2011. 448 p. 37. Komives SR, Dugan JP, Owen JE, Slack C, Wagner W, Programs (NCLP) NC of L. The Handbook for
Student Leadership Development. John Wiley & Sons; 2011. 448 p. 38. Chapman ALN, Giri P. Learning to Lead: Tools for Self Assessment of Leadership Skills and Styles. In:
Godbole P, Burke D, Aylott J, editors. Why Hospitals Fail [Internet]. Cham: Springer International
Publishing; 2017 [cited 2022 Apr 8]. p. 137–48. Available from: http://link.springer.com/10.1007/978-
3-319-56224-7_14 38. Chapman ALN, Giri P. Learning to Lead: Tools for Self Assessment of Leadership Skills and Styles. In:
Godbole P, Burke D, Aylott J, editors. Why Hospitals Fail [Internet]. Cham: Springer International
Publishing; 2017 [cited 2022 Apr 8]. p. 137–48. Available from: http://link.springer.com/10.1007/978-
3-319-56224-7_14 39. NHS Institute for Innovation and Improvement. Leadership Framework [Internet]. NHS Institute for
Innovation and Improvement, Coventry House, University of Warwick Campus, Coventry, CV4 7AL.;
2011 [cited 2023 Apr 18]. Available from: https://www.leadershipacademy.nhs.uk/wp-
content/uploads/2012/11/NHSLeadership-Framework-LeadershipFramework.pdf 39. NHS Institute for Innovation and Improvement. Leadership Framework [Internet]. NHS Institute for
Innovation and Improvement, Coventry House, University of Warwick Campus, Coventry, CV4 7AL.;
2011 [cited 2023 Apr 18]. Available from: https://www.leadershipacademy.nhs.uk/wp-
content/uploads/2012/11/NHSLeadership-Framework-LeadershipFramework.pdf Page 20/22 40. Clarke V, Braun V, Hayfield N. Thematic analysis. Qual Psychol Pract Guide Res Methods. 2015;3:222–
48. 41. Malembaka EB, Altare C, Bigirinama RN, Bisimwa G, Banywesize R, Tabbal N, et al. The use of health
facility data to assess the effects of armed conflicts on maternal and child health: experience from the
Kivu, DR Congo. BMC Health Serv Res. 2021 Sep 13;21(1):195. 41. References Malembaka EB, Altare C, Bigirinama RN, Bisimwa G, Banywesize R, Tabbal N, et al. The use of health
facility data to assess the effects of armed conflicts on maternal and child health: experience from the
Kivu, DR Congo. BMC Health Serv Res. 2021 Sep 13;21(1):195. 42. Chenge F. De la nécessité d’adapter le modèle de district sanitaire au contexte urbain: exemple de la
ville de Lubumbashi en RD Congo. Antwerp: ITGPress; 2013. 132 p. ([SHSOP]). 42. Chenge F. De la nécessité d’adapter le modèle de district sanitaire au contexte urbain: exemple de la
ville de Lubumbashi en RD Congo. Antwerp: ITGPress; 2013. 132 p. ([SHSOP]). 43. Fraze TK, Lewis VA, Wood A, Newton H, Colla CH. Configuration and Delivery of Primary Care in Rural
and Urban Settings. J Gen Intern Med. 2022 Sep;37(12):3045–53. 43. Fraze TK, Lewis VA, Wood A, Newton H, Colla CH. Configuration and Delivery of Primary Care in Rural
and Urban Settings. J Gen Intern Med. 2022 Sep;37(12):3045–53. 44. Didier CK, Criel B. Investir dans les Equipes-cadres des Zones de Santé : une priorité conditionnelle
pour le renforcement du système de santé. CCSC [Internet]. 2020;(8). Available from:
https://www.ccsc-rdc.net/doc/ccsc_note_de_politique_08_web.pdf 45. Winston BE, Patterson K. An integrative definition of leadership. Int J Leadersh Stud. 2006 Jan 1;1:6–
66. 45. Winston BE, Patterson K. An integrative definition of leadership. Int J Leadersh Stud. 2006 Jan 1;1:6–
66. 46. Vecchio RP. Leadership: Understanding the Dynamics of Power and Influence in Organizations,
Second Edition. University of Notre Dame Pess; 2007. 565 p. 47. Aarons GA. Transformational and transactional leadership: Association with attitudes toward
evidence-based practice. Psychiatr Serv. 2006;57(8):1162–9. 48. Burns JM. Leadership. Open Road Media; 2012. 48. Burns JM. Leadership. Open Road Media; 2012. 49. McCall Jr. MW. Leadership and performance beyond expectations, by Bernard M. Bass. New York: The
Free Press, 1985, 191 pp. Hum Resour Manage. 1986;25(3):481–4. 50. Bass BM, Avolio BJ. Transformational leadership and organizational culture. Public Adm Q. 1993;112–21. 51. Odumeru JA, Ogbonna IG. Transformational vs. transactional leadership theories: Evidence in
literature. Int Rev Manag Bus Res. 2013;2(2):355. Page 21/22
athole T, Lembani M, Jackson D, Zarowsky C, Bijlmakers L, Sanders D. Leadership and the
unctioning of maternal health services in two rural district hospitals in South Africa. Health Policy
an. 2018 Jul 1;33(suppl_2):ii5–15. urry L, Taylor L, Chen PGC, Bradley E. Experiences of leadership in health care in sub-Saharan Africa. um Resour Health. 2012 Sep 13;10(1):33. References usinguzi C, Namale L, Rutebemberwa E, Dahal A, Nahirya-Ntege P, Kekitiinwa A. The relationship
etween leadership style and health worker motivation, job satisfaction and teamwork in Uganda. J
ealthc Leadersh. 2018 Dec 31;10:21–32. ills A. Health Care Systems in Low- and Middle-Income Countries. N Engl J Med. 2014 Feb
370(6):552–7. m S, Bochatay N, Relyea-Chew A, Buttrick E, Amdahl C, Kim L, et al. Individual, interpersonal, and
rganisational factors of healthcare conflict: A scoping review. J Interprof Care. 2017 May
31(3):282–90. 52. Mathole T, Lembani M, Jackson D, Zarowsky C, Bijlmakers L, Sanders D. Leadership and the
functioning of maternal health services in two rural district hospitals in South Africa. Health Policy
Plan. 2018 Jul 1;33(suppl_2):ii5–15. 53. Curry L, Taylor L, Chen PGC, Bradley E. Experiences of leadership in health care in sub-Saharan Africa. Hum Resour Health. 2012 Sep 13;10(1):33. 54. Musinguzi C, Namale L, Rutebemberwa E, Dahal A, Nahirya-Ntege P, Kekitiinwa A. The relationship
between leadership style and health worker motivation, job satisfaction and teamwork in Uganda. J
Healthc Leadersh. 2018 Dec 31;10:21–32. 55. Mills A. Health Care Systems in Low- and Middle-Income Countries. N Engl J Med. 2014 Feb
6;370(6):552–7. 56. Kim S, Bochatay N, Relyea-Chew A, Buttrick E, Amdahl C, Kim L, et al. Individual, interpersonal, and
organisational factors of healthcare conflict: A scoping review. J Interprof Care. 2017 May
4;31(3):282–90. Page 21/22 Page 21/22 57. Cullati S, Bochatay N, Maître F, Laroche T, Muller-Juge V, Blondon KS, et al. When Team Conflicts
Threaten Quality of Care: A Study of Health Care Professionals’ Experiences and Perceptions. Mayo
Clin Proc Innov Qual Outcomes. 2019 Mar 1;3(1):43–51. 57. Cullati S, Bochatay N, Maître F, Laroche T, Muller-Juge V, Blondon KS, et al. When Team Conflicts
Threaten Quality of Care: A Study of Health Care Professionals’ Experiences and Perceptions. Mayo
Clin Proc Innov Qual Outcomes. 2019 Mar 1;3(1):43–51. 58. Mosadeghrad AM, Ferdosi M. Leadership, Job Satisfaction and Organizational Commitment in
Healthcare Sector: Proposing and Testing a Model. Mater Socio-Medica. 2013;25(2):121–6. 58. Mosadeghrad AM, Ferdosi M. Leadership, Job Satisfaction and Organizational Commitment in
Healthcare Sector: Proposing and Testing a Model. Mater Socio-Medica. 2013;25(2):121–6. 59. Ferrinho P, Lerberghe W van. Providing health care under adverse conditions: health personnel
performance & individual coping strategies [Internet]. Antwerp: ITG Press; 2000. 247 p. (Studies in
health services organisation & policy). Available from:
https://www.hrhresourcecenter.org/node/1405.html 59. Ferrinho P, Lerberghe W van. References Providing health care under adverse conditions: health personnel
performance & individual coping strategies [Internet]. Antwerp: ITG Press; 2000. 247 p. (Studies in
health services organisation & policy). Available from:
https://www.hrhresourcecenter.org/node/1405.html 60. Zahmat Doost E, Zhang W. Mental workload variations during different cognitive office tasks with
social media interruptions. Ergonomics. 2022 Jul 20;0(0):1–17. 60. Zahmat Doost E, Zhang W. Mental workload variations during different cognitive office tasks with
social media interruptions. Ergonomics. 2022 Jul 20;0(0):1–17. 61. Wushe T, Shenje J. The relationship between social media usage in the workplace and employee
productivity in the public sector : case study of government departments in Harare. SA J Hum Resour
Manag. 2019 Jan;17(1):1–10. 61. Wushe T, Shenje J. The relationship between social media usage in the workplace and employee
productivity in the public sector : case study of government departments in Harare. SA J Hum Resour
Manag. 2019 Jan;17(1):1–10. 62. Tulu DT. Should online social Medias (OSMs) be banned at work? The impact of social Medias on
employee productivity in Ambo University, a case study. Res Int Bus Finance. 2017 Dec 1;42:1096–
102. 62. Tulu DT. Should online social Medias (OSMs) be banned at work? The impact of social Medias on
employee productivity in Ambo University, a case study. Res Int Bus Finance. 2017 Dec 1;42:1096–
102. 63. Ifeagwu SC, Yang JC, Parkes-Ratanshi R, Brayne C. Health financing for universal health coverage in
Sub-Saharan Africa: a systematic review. Glob Health Res Policy. 2021 Dec;6(1):8. 64. Moss TJ, Pettersson Gelander G, van de Walle N. An Aid-Institutions Paradox? A Review Essay on Aid
Dependency and State Building in Sub-Saharan Africa [Internet]. Rochester, NY; 2006 [cited 2023 Feb
23]. Available from: https://hdl.handle.net/1813/55015 65. Bräutigam D. Aid dependence and governance. Vol. 1. Almqvist & Wiksell International Stockholm;
2000. 66. Riisgaard H, Søndergaard J, Munch M, Le JV, Ledderer L, Pedersen LB, et al. Associations between
degrees of task delegation and job satisfaction of general practitioners and their staff: a cross-
sectional study. BMC Health Serv Res. 2017 Jan 17;17:44. 66. Riisgaard H, Søndergaard J, Munch M, Le JV, Ledderer L, Pedersen LB, et al. Associations between
degrees of task delegation and job satisfaction of general practitioners and their staff: a cross-
sectional study. BMC Health Serv Res. 2017 Jan 17;17:44. 67. Kimball AM, Harper D, Creamer K, Adeyemi A, Yates R, Lillywhite L, et al. Strengthening Public Health
Leadership in Africa: An Innovative Fellowship Program. References Acad Med. 2019 Aug;94(8):1146. 67. Kimball AM, Harper D, Creamer K, Adeyemi A, Yates R, Lillywhite L, et al. Strengthening Public Health
Leadership in Africa: An Innovative Fellowship Program. Acad Med. 2019 Aug;94(8):1146. 68. Evans D, Bolden R, Jarvis C, Mann R, Patterson M, Thompson E. How do you develop systems
leadership in public health? Insights from a scoping study. Public Health. 2021 Jul 1;196:24–8. 68. Evans D, Bolden R, Jarvis C, Mann R, Patterson M, Thompson E. How do you develop systems
leadership in public health? Insights from a scoping study. Public Health. 2021 Jul 1;196:24–8. Page 22/22
|
https://openalex.org/W2070682728
|
https://zenodo.org/records/1428738/files/article.pdf
|
English
| null |
Adaptation of the Mohr Volumetric Method to General Determinations of Chlorine.
|
The journal of industrial and engineering chemistry/Journal of industrial and engineering chemistry
| 1,919
|
public-domain
| 1,300
|
Aug., 1919
T H E J O U R N A L OF I N D U S T R I A L
ADAPTATION OF THE MOHR VOLUMETRIC METHOD
TO GENERAL DETERMlNATIONS OF CHLORINE
A N D ENGINEERING C H E M I S T R Y
Mohr titration must provide for the
bonates and phosphates, calcium acet Two ignitions with-
organic materials have not failed in our work to give
clear and colorless solutions. Fair examples of the
results obtained in the above procedure are reported
in the table. Votocek4 recently reported a method in which the
chlorides are titrated in about 2 5 0 cc. of slightly acid
solution with mercuric nitrate solution using 0.06 g. of sodizm nitroprusside crystals as the indicator. In
this method nitrites and sulfites interfere. The well-known method of Mohr in which alkaline
or alkaline-earth chlorides react with silver nitrate in
the presence of a few drops of potassium chromate
solution as indicator is as simple, direct. and fully as
accurate as the method of Votocek, provided the proper
conditions for the titration are as easily attained. The conditions necessary for an accurate titration
appear numerous and exacting because (I) the solu-
tion must be neutral, (2) no carbonates or phosphates
may be present since the silver salts of these acids
are less solable than the red silver chromate indicator
and would therefore be titrated as well as the chlo-
rides, and (3) the solution of the chlorides must have
&' proper concentration to produce the most definite
color change. Calculated
Weight
Weight
of
Error
of
Chlorine
or
Chlorine
Found
Difference
~ ~ ~ ~ * ~ / K ' ~ I H C 1
1 . . . . . . , . . . . . . 0.0472
0.0469
-0.0003
Feces No 19 2 g.. . . . . . . . . . . . . 0.0037
0.0035
-0.0002
0.0048
-0,0003
0.0049
* 0.0000
0.0022
+0.0002
0.0063
+0.0002
0,0015
-0.0003
Feces No: 23' 2 g.. . . . . . . . . . . . . . 0.0051
Alfalfa Hay No. 2, 3 g.. . . . . . . . . . 0.0061
0.0018
Feces No. 27' 2 g.. . . . . . . . . . . . . . 0.0049
Mixed Grain: No. 1 , 3 g.. . . . . . . . 0.0020
Mixed Grain No. 5, 3 g . , . , . . , . . . Aug., 1919
T H E J O U R N A L OF I N D U S T R I A L
ADAPTATION OF THE MOHR VOLUMETRIC METHOD
TO GENERAL DETERMlNATIONS OF CHLORINE
A N D ENGINEERING C H E M I S T R Y
Mohr titration must provide for the
bonates and phosphates, calcium acet Aug., 1919 755 Mohr titration must provide for the removal of car-
bonates and phosphates, calcium acetate solution was
substituted for the solution of sodium carbonate and
ferric acetate solution was subsequently added to the
ignited residue. Mohr titration must provide for the removal of car-
bonates and phosphates, calcium acetate solution was
substituted for the solution of sodium carbonate and
ferric acetate solution was subsequently added to the
ignited residue. By LESTER YODER
Received April 1 1 , 1919 By LESTER YODER
Received April 1 1 , 1919 By the proper preliminary preparation of
the
chloride solutions many determinations of
chlorine
as usually carried out may be simplified and shortened
by the use of
Mohr's volumetric method. Other
volumetric methods are less satisfactory as the fol-
lowing brief r&sum& will show: g
The following procedure gave the best results: To the sample is added 5 cc. of a 30 per cent solution of calcium
acetate with sufficient distilled water to thoroughly saturate the
material. The mixture is evaporated to dryness at 120' C. and ignited at a temperature not over 450° C. The cooled
residue is thoroughly moistened with a few cubic centimeters
of a IO per cent solution of ferric acetate, and again evaporated
to dryness and ignited below 450' C. The residue is triturated
with hot water, filtered, and washed until free from chlorides. The filtrate is evaporated to dryness or nearly to dryness and
taken up with just sufficient hot water to insure complete
solution of the chlorides, when cooled. After the addition of z
or 3 drops of potassium chromate, the solution is titrated with
0.05 N silver nitrate. The original Volhard method has been modified by
Drechsel,' Rothmund and Burgstaller,2 and Alefeld,3
to a short and accurate process. Excess of standard-
ized silver nitrate solution is added to the chloride
solution and the excess titrated with standardized
thiocyanate. The precipitate of silver chloride must
be rendered either more insoluble by flocculation with
heat or reagents or filtered from the excess of silver
nitrate for the titration with the thiocyanate. The calcium acetate fixes free chlorine and during
the extraction of the ignited residue precipitates car-
bonates and neutralizes the filtrate for the titration. The ferric acetate precipitates the phosphates and is
itself converted into the insoluble oxide and also re-
moved by the one filtration. 1 Z . anal. Chem., 16 (1877), 351.
2 2. anorg. Chem., 63 (1909), 330.
* Z . anal. Chem., 48 (1909), 79.
'
Chem.-Ztg., 4'2 (1918), 257-60. Since the modifications necessary for the use of the Aug., 1919
T H E J O U R N A L OF I N D U S T R I A L
ADAPTATION OF THE MOHR VOLUMETRIC METHOD
TO GENERAL DETERMlNATIONS OF CHLORINE
A N D ENGINEERING C H E M I S T R Y
Mohr titration must provide for the
bonates and phosphates, calcium acet The object of the work herein presented was to
develop and test modifications of procedure to meet
these conditions so that the Mohr method would be
applicable to rapid determinations of chlorine in various
materials and particularly in organic products con-
taining small amounts of the element. The modified method was applied to two solutions,
one containing known amounts of free hydrochloric acid
and its potassium salt, and another containing in
addition added soluble phosphate. These were evapo-
rated and ignited twice and subjected to a temper-
ature of 4joo C. in one of the ignitions. The results
show no loss of chlorine and only a negligible difference
from the calculated weight of chlorine in the samples. Determinations of chlorine were also made in different
kinds of cow feces and mixed grain and in alfalfa hay. The results differ only slightly from those of deter-
minations made gravimetrically and are well within the
limits of experimental error although the percentage
error in the weights of chlorine found is large by
reason of the low chlorine content of the materials. With the procedure outlined and from the results In the preparation of
a titratable solution of the
material in which chlorine is to be determined the
sample must be ignited (in the case of organic products,
at a low heat), and provision made for the fixation of
free chlorine. An excess of sodium carbonate is usually
added with the result that the sodium salts fuse and
thereby prevent even after repeated ignitions, the
complete oxidation of the carbonaceous matter which
will pass through the filter in the subsequent filtration. A large amount of carbonates will also be present in
the solution and the removal of any excess of phos-
phates IS not assured. With the procedure outlined and from the results
obtained by its use it seems that the Mohr direct
titration method could be used for determinations of
total chlorine in most instances. Since the modifications necessary for the use of the CHEMISTRY
SECTION
IOWA AGRICULTURAL
EXPERIMENT
STATION
AMES, IOWA
|
https://openalex.org/W3198847345
|
https://link.springer.com/content/pdf/10.1007%2F978-3-030-75645-1_8.pdf
|
English
| null |
Individual Parental Leave for Fathers: Promoting Gender Equality in Norway
|
Contributions to management science
| 2,021
|
cc-by
| 5,732
|
Individual Parental Leave for Fathers:
Promoting Gender Equality in Norway Elin Kvande E. Kvande (*)
Department of Sociology and Political Science, Norwegian University of Science and
Technology, Trondheim, Norway
e-mail: elin.kvande@ntnu.no © The Author(s) 2022
M. Grau Grau et al. (eds.), Engaged Fatherhood for Men, Families and Gender
Equality, Contributions to Management Science,
https://doi.org/10.1007/978-3-030-75645-1_8 1
Introduction How to increase fathers’ use of parental leave is a relevant question for countries that
want to promote men’s involvement in childrearing and gender equality more
broadly. As countries are searching for instruments that can effectively promote a
greater involvement of fathers in care work, the Nordic parental leave experiences
may be useful. The Nordic countries, Denmark, Finland, Iceland, Norway and
Sweden, have followed similar trajectories of development, not exactly following
the same timeline, but clearly inspired by each other. All of them have introduced
special incentives for fathers to use leave after having experienced that simply
offering shared parental leave was not enough to get fathers to use it. Norway was
the first country to introduce a fathers’ quota in 1993, followed by Sweden 2 years
later, Denmark in 1998 (until 2002 when it was discontinued) and Iceland in 2000. Finland had a bonus system providing fathers with 12 extra days if they used 12 days
of the shared parental leave. This was changed to an individual, non-transferable
right, a father’s quota in 2013. In comparative research on gender equality, the Nordic welfare states are
analysed as including regulations that support both working mothers and fathers
(Pascall 2012). Equality between men and women is encouraged through an indi-
vidual earner-carer regime (Sainsbury 1999). Important policy measures in this
regime include publicly funded parental leave schemes, universal, high quality
daycare, and access to reduced work hours. These are the same social arrangements 153 154 E. Kvande as Gornick and Meyers (2009) pinpoint as important in order to create a dual-earner/
dual-caregiver society. A comprehensive research literature on parental leave has evolved during the last
20 years. In fact, the study of parental leave is in the forefront of comparative social
policy research focusing on gender equality (Ray et al. 2010). This strong interest in
parental leave policies must be understood on the basis of these policies having the
potential to change women’s position in employment and engaging men in caregiv-
ing. Parental leave policy rights and designs vary substantially across countries
(Blum et al. 2018) and the effect of the different leave systems on gender equality
is also debated (Morgan 2008; Moss and Deven 1999; Moss et al. 2019). 1
Introduction In their analysis of what is needed to achieve “strong gender equality” in family
and working life, Brighouse and Wright (2008) distinguish between three types of
policies: (1) equality-impeding policies (e.g., unpaid caregiving leaves), (2) equality-
enabling policies (e.g., paid caregiving leaves given to families), and (3) equality-
promoting policies (e.g., paid caregiving leaves given to individuals rather than
families). According to them, shared parental leave granted to the family enables
parents to adopt egalitarian strategies, but do not represent strong incentives for
fathers to use the leave rights. Leave policies that promote equality are exemplified
by paid leave granted to individual parents, which lapses if it is not used. Brighouse
and Wright find that this type of leave is necessary for breaking down the cultural
barriers to gender equality in family and working life. Using this as a point of departure, this paper will describe the design elements of
the Norwegian parental leave system for fathers and examine how it works as a
regulatory measure to promote equality in care work. The paper will thus address the
request put forward by Ray et al. (2010), in which they point out that surprisingly
little research has been carried out that links the design of leave policies to their
outcomes. There are especially few empirical studies assessing which parental leave
schemes are gender egalitarian by design (Bartel et al. 2018; Dearing 2016), and this
has left a gap in cross-national literature on leave policies. 2
Designing Individualized Parental Leave for Fathers Research on social policy in European welfare states has increasingly focused on the
norm of individualization, thus indicating a social policy that treats women and men
as individual workers (Lewis 2015). Similarly Daly (2011) suggests applying the
concept of “individualization processes” in order to capture change in family
policies which implies a shift away from policy assumptions based on the male
breadwinner/female carer model and, instead, expecting all adults to be both bread-
winners and carers. Individualistic policy designs, however, do not necessarily
include gender equality (Ray et al. 2010). Therefore, how social policies relate to
this parameter dictates whether they are classified as supporting an individualistic or
familistic model according to Daly (2011). 155 Individual Parental Leave for Fathers: Promoting Gender Equality in Norway Research has documented that to give parental leave rights to individuals, rather
than to families, is more effective when it comes to getting fathers to take leave
(Duvander and Lammi-Taskula 2012; Haas and Rostgaard 2011; Eydal and Gíslason
2013). In their analyses of institutions that support gender equality in parenthood and
employment, Gornick and Meyers (2009) point to the importance of individualized
parental leave, as well as the principle of non-transferability, as in the fathers’ quota. They suggest a period of 6 months leave to each parent, which cannot be transferred
to the other parent. This is also what was suggested in a white paper produced by an
expert committee for the Norwegian government in 2017 (NOU 2017). The international literature on specific policy provisions for parental leave is
expanding (McKay and Doucet 2010), particularly concerning fathers. Within
research based on Nordic experiences, there is a consensus that parental leave rights
given to individuals, rather than to families, are most likely to get fathers to take
leave (Rostgaard 2002; Duvander and Lammi-Taskula 2012; Haas and Rostgaard
2011; Eydal et al. 2015). The father’s quota in Nordic countries has been successful
in involving fathers in taking care of their young babies (Haas and Rostgaard 2011;
Brandth and Kvande 1998, 2018). These results are also found internationally (Moss
and Kamerman 2009; Gornick and Meyers 2009; Miller 2013; Harvey and Tremblay
2019). Documented findings from a number of countries have shown that the shared
parental leave (and thus optional for fathers) is mostly used by mothers (O’Brien and
Wall 2017; Ray et al. 2010; Fougner 2012; Gíslason and Eydal 2013). 3
The Norwegian Parental Leave System for Fathers In 1978 the leave rights in Norway were changed so that most of the leave could be
shared between the parents, moving away from the idea of maternity leave as a
special right only for women. By granting fathers the right to shared leave, legisla-
tion signaled a new view of men’s responsibilities and participation in caregiving. In
the years to come, fathers, however, rarely used shared parental leave so the policy
did not promote more equal parenting. To advance that goal, an earmarked,
non-transferable leave of 4 weeks for fathers was introduced in 1993. At the same
time the total leave period was extended from 35 to 42 weeks with 100% wage
compensation. Proponents argued that a quota would give a strong signal to parents
as well as to employers that men as well as women are parents with obligations and
rights as caregivers. Children’s need for their fathers was also emphasized in the
debate. Since then the father’s quota has developed gradually, extended to 14 weeks
and then reduced to 10 weeks in 2014 following the politics of the parties in power. Both mothers and fathers have individual, non-transferable leave rights in addi-
tion to shared leave rights. Currently, mothers have an earmarked period of
13 weeks, of which 3 must be taken before the child’s birth. Beginning in 2014,
26 weeks are sharable between mothers and fathers. If the parents choose lower pay
(80% of wages), the leave is extended by 10 weeks. The fathers’ quota is now
10 weeks. In addition to parental leave, fathers have 2 weeks of paternity leave to be
taken after the birth of the child to assist the mother. There are no public records of
the usage of paternity leave, as wage compensation is based on collective agreements
and paid by employers. The fathers’ quota gives male employees the right and obligation to provide care
during the child’s early years of life. The principal aim of this leave is to break away
from the norm that men serve as breadwinners and women as caregivers even if they,
too, are employed outside the home. The system is based on the principle that parents
“earn” the right through participation in working life. To qualify for parental leave,
both mothers and fathers have to be in the workforce for 6 of the last 10 months prior
to the birth. 2
Designing Individualized Parental Leave for Fathers Fathers taking
leave challenge the traditional gender norm that mothers are the primary caregivers
of small children. This chapter explores fathers’ understandings and experiences with the father’s
quota (i.e., the leave programs), which, according to Brighouse and Wright (2008),
may promote equality. Studies of the Norwegian leave programme comparing the
father’s quota to the more optional schemes of shared parental leave and cash
allowances were conducted some years after the introduction of the father’s quota
(Brandth and Kvande 2009) This research documented that mandatory leave for
fathers made it easier for them to use the father’s quota to set boundaries against the
demands of work, thus reserving uninterrupted father-child time. It was also pointed
out that a statutory earmarking of the father’s quota lifts the decision of who should
take leave from the family up to the institutional level, where it would apply to “all”
fathers. The father’s quota became a pre-negotiated right for men also in terms of the
workplace, and it was supposed to eliminate the need to negotiate individually with
the employer over the use of the father’s quota. This chapter examines the impact of the expansion and maturation of the father’s
quota. Using Brighouse and Wright’s conceptual framework the chapter explores
how the Norwegian leave policies which are an individual right are experienced by
the fathers in our latest study. E. Kvande 156 3
The Norwegian Parental Leave System for Fathers 4
Data and Method The analysis is based on a qualitative study in which 22 fathers who had taken
parental leave were interviewed in 2012 and 2013. The interviews were carried out
during the second year after the child’s birth. Thus, the fathers in the sample had
rights to 10 or 12 weeks of individual leave and 27 or 26 weeks of shared leave if
they chose 100% compensation. If they chose the 80% compensation option, the
leave would have been prolonged accordingly. The fathers were recruited by contact
with various workplaces and then snowballing. The interviewees had to have
become fathers after the fathers’ quota was expanded to 10 weeks in 2009, as we
were interested in their experiences of relatively long leaves. The length of the leave
taken by the sample varied; most fathers had taken the father’s quota of 10 or
12 weeks, but 8 had also taken all or part of the shared parental leave. The research team endeavoured to find interviewees with varied social back-
grounds. Half had higher education (masters level), while the other half either had a
medium level education at the bachelor level (6) or no education beyond high school
(5). The fathers had a wide range of occupations, including engineers, artisans,
teachers, office workers, consultants, and administrative, healthcare, and technical
staff. They worked in organizations of various sizes and composition. As Norwegian leave rights are employment based (i.e., accrued by the participa-
tion of both parents in working life), all the fathers and most of their children’s
mothers (except for three) were in paid employment prior to the birth of their child
and had a right to parental leave. Half of the fathers were employed by private
companies, but only one was self-employed, and one, a student, was temporarily
employed. Except for this father, all worked full time. All the fathers lived together
with the mother and their child, and the child who triggered the interview could be
the father’s first, second, or third child. Most fathers were in their 30s, though they
ranged between 27 and 43. Eight of the fathers (36%) had taken shared parental
leave. Two of them had taken all the shared parental leave available, as the mothers
were not eligible due either to having returned to work or school. The interviews were semi-structured and lasted between 1 and 2 h. 3
The Norwegian Parental Leave System for Fathers If the mother is not eligible, the father loses his right to the fathers’ quota
but not to the shared leave if the mother returns to studies or takes on employment. This type of eligibility encourages both parents to combine work and family
obligations as it is built on a model in which both mothers and fathers are employed. Since its introduction, the fathers’ quota has been widely used, and more than 90% of
eligible fathers use all or part of this leave (Kitterød et al. 2017). Mothers take most
of the shared leave days, and, for most couples, mothers’ leave is considerably
longer than fathers’. 157 Individual Parental Leave for Fathers: Promoting Gender Equality in Norway 5.1
The Fathers’ Quota as a Norm The fathers’ quota enjoys a high degree of support among fathers in Norway (Hamre
2017), and studies on fathers’ quota usage have pointed out that it has become a
norm among men in Norway to take leave when they have become fathers (Halrynjo
and Kitterød 2016; Naz 2010). Our findings also support this claim. “There was no doubt that I should take the fathers’ quota,” said Steinar, an
engineer with two daughters. According to Ivar, “For fathers to have 12 weeks is
quite natural in a way.. . . It has become incorporated.” Their viewpoints illustrate
that the fathers’ quota is a matter of fact. Twenty-five years after it was introduced,
taking leave seems to be taken for granted among fathers in Norway. That it is based
in law, earmarked, and non-transferable identifies this leave with fathers and defines
it as their right and ‘property.’ It is also interpreted as an obligation and seen as a signal from the welfare state
that fathers are expected to engage in taking care of small children. “Society reacts if
you don’t take it, right,” Harold said. Lars, an engineer, claimed that the quota “feels
like something you ought to . . . that it’s something you should take, really.. . . It feels
like there’s pressure on you to take it. That . . . if you want to be a good parent, or a
good father, then you have to take the daddy leave.” Several fathers indicated that if
they had not taken the fathers’ quota, they would have to explain themselves to
others. Fathers’ leave-taking is supported by social norms of good fatherhood that these
fathers seem to have incorporated into their identities. As the next section shows,
fatherhood has also been incorporated into their practices as employees. 4
Data and Method The data was
collected by a research team, in which the author participated. To preserve anonym-
ity, the full name and contact details of the interviewees were not recorded, and
fictitious names have been used. The fathers were mostly interviewed in their homes. The fathers’ understandings were based on their own experiences and what they
observed with colleagues and friends. The recorded transcripts were examined to
identify each father’s stories about their experiences at their respective workplaces. We also asked hypothetical questions about what would have happened if there were
no father’s quota. The next stage was interpreting these themes in a dialogue with the
literature. The findings are illustrated by quotations. E. Kvande E. Kvande 158 5.2
Employers’ Support of Fathers’ Caregiving
Responsibilities Many of the fathers in the sample strongly felt that having a quota given to them as
employees was an unconditional strength in relation to work, and that it would have
been much more difficult to gain support from employers if it were not for their legal
right to the fathers’ leave. “It makes your position stronger when the quota is based
in law,” said Geir. Kristoffer and many others believed that if the father’s quota was
not retained as a father-specific right, they would fail in their negotiations over leave
with their employer. Since the fathers’ quota is statutory, employers have little
leeway to adopt discriminatory practices. The fathers’ sense of entitlement becomes explicit when Steinar reflects on how
he would have had to argue in his previous job as a consulting engineer with a small
company. “It was very intense with a call on us to work 80 h a week and perform all
we could with lots of pressure and bonuses. In this place, taking leave would have Individual Parental Leave for Fathers: Promoting Gender Equality in Norway 159 been frowned upon. But still, should you have to fight for your rights?” Moreover,
the fathers’ leave is paid by the state rather than the employer. Comparing his right to
the fathers’ quota with his right to paid holidays, Steiner said that if he did not take
his “3 months ‘holiday’ with pay,” he would lose it. Entitlements to paid time off are
acceptable in working life. To have to argue with his employer about his childcare
responsibilities would not work as well, Steinar claimed. None of the fathers in the study reported that they had experienced any serious
problems with their current employers when planning to use their entitlement
(Brandth and Kvande 2019a, b). Indeed, men seem to be expected to take the fathers’
leave by their employers and colleagues. Harold, a schoolteacher, said: “It was all
right, and it was expected! It would have been more of an issue if I hadn’t taken
it. Public workplaces have to play by the rules.” For fathers, it seems inevitable that
working life must adapt to the regulations of the welfare state. Christian, a senior
advisor in the municipal administration, pointed out that even though the fathers’
quota might sometimes represent challenges for workplaces, organizations do adapt
to this legislation. 5.2
Employers’ Support of Fathers’ Caregiving
Responsibilities The fathers’ quota has existed for a quarter century, which means that men who
have advanced to management positions in some organizations have taken fathers’
leave themselves. That experience influences what is considered fair and feasible. Tore, a doctor in a large hospital, described how his leave-taking was received by his
director, a 60-year-old chief physician: “He is up to date on the father’s quota.. . . He
has had young children himself. . . . And I am not the first father to be in this
situation.” Steinar, too, explained that his bosses are fathers: “They are 54 and
62, and both were home with their children at a time when it was much less common
than now. So, they pushed me, saying ‘Steinar, it is clear that you must stay home,’
and ‘Are you sure you won’t take a bit longer leave?’ They said so even if it was bad
for the job.” Likewise, Sivert described his boss as very positive: “He understood me
very well. I suppose he is 50 years, so he is very up to date.” His boss was eager to
help him find out about the regulations concerning the father’s quota and the rest of
the parental leave system. Sivert considered him a “modern” man who regarded
fathers’ involvement with children as important. Another father interviewed, Hans,
said: I think most employers today live in the modern world and understand that they must live up
to that. This is how it is. They need employees who are happy with their job and have a good
family life. Now, we see that both managers and middle managers in companies, 35 to
40 years old, experience the same tensions concerning career, childcare, parental leaves and
work hours. I have a mate who is manager of marketing, only a few years older than me in a
top job; he had four months daddy leave, so that says a lot. Fathers are more likely to take up family friendly working practices if they can
“compare themselves with other fathers and realize that it is feasible to do so” (Lewis
and Stumbitz 2017: 230). The fathers we interviewed reported that as leave takers
they did not stand out in any way. 5.3
Empowered as Caregivers The fathers communicated an identity as competent caregivers and attributed this to
their time on leave when they had gotten to know the child well. They thought that
children benefit from close contact with fathers, and that fathers are significant
caregivers for children. Erlend said: “It is quite unfair that only mothers are regarded as important for the children. Speaking as a
man I think this is a new situation for gender equality.. . . I have been able to prove that I can
be just as good a carer as the mother. I think it is super important! It increases men’s self-
confidence and society’s confidence in men as caregivers.” “It is quite unfair that only mothers are regarded as important for the children. Speaking as a
man I think this is a new situation for gender equality.. . . I have been able to prove that I can
be just as good a carer as the mother. I think it is super important! It increases men’s self-
confidence and society’s confidence in men as caregivers.” Regarding it as unfair that only mothers are given support as caregivers, these
men see the fathers’ quota as remedying this injustice. They justify their entitlement
to leave as based on their ability to care for their small children and think the fathers’
quota contributes to their being seen as needed and important caregiving parents. They feel entitled to both the joys and burdens of childcare, and they stress that the
fathers’ quota represents an opportunity to develop an autonomous relationship with
their children. “Being home on leave has in a way laid the foundation for the contact
we [father and child] have today. A lot will happen later in life, but this is the basis,”
Didrik said. The quota as a father-specific right simplifies negotiations with the mother. Sivert
realized that this was the point of earmarking it: “This is why they designed it like
that. If not, nothing would have come of it. Then the mother would have taken the
whole leave.” He thought that to many people it is still not obvious that the father
will choose to stay home with the child. 5.2
Employers’ Support of Fathers’ Caregiving
Responsibilities Hans, a communications advisor in a transport
company, told us that at his workplace “many of my male colleagues had a child at
about the same time as me, which was great! We were about three or four who had
kids within a 2- or 3-month span. In addition, many employees here have small 160 E. Kvande children.” The norms that are produced by these practices make it easy for fathers to
take leave and for organizations to plan for it. Dahl et al. (2014), who studied the
peer effect of father quota usage, found that fathers are even more likely to take the
quota if their colleagues did. The effect was greatest if a manager at a higher level in
the organization had taken the fathers’ leave. Many of the fathers confidently portrayed the quota as their leave. In so doing,
they conveyed a sense of entitlement and beliefs about what is right and fair. Hobson
and Morgan (2002: 14) hold that family friendly policies provide men with discur-
sive resources with which they can make claims upon their employers. For instance,
Ivar communicated that it was he who controlled how much and when he would
work, and he was not afraid to insist on his priorities. 5.3
Empowered as Caregivers To avoid making parental leave only
mothers’ leave, he said, it was important that things were not “made completely
flexible.” Employed fathers view the fathers’ quota as an entitlement, a support from the
welfare state for them to be active caregivers. There are strong moral obligations for
fathers to take the father’s quota and for employers to accept it. This finding seems
important in understanding the high use of the quota among fathers in Norway. 161 Individual Parental Leave for Fathers: Promoting Gender Equality in Norway 6
Practical Recommendations These findings illustrate that the design of the father’s quota as a statutory,
earmarked, and non-transferrable right for fathers promotes the fathers’ use of
leave and hence equality. The earmarking, and the fact that it cannot be transferred
to the mother, renders it unnecessary for fathers to negotiate with the mother about
this leave. The father’s quota is also an important bargaining chip in relation to the
job. Even if fathers have stories about situations where the employers do not want
the father to take leave, employers are most often described as positive towards the
father’s leave, and the interviews include few personally experienced stories about
employers impeding the fathers from taking leave. We interpret this as a sign that the
father’s quota as a legal earmarked right may have contributed to making visible and
promoting the fact that employed men are also fathers and “encumbered” with
caregiving responsibilities as much as employed mothers. Thus, in order to promote
gender equality, policy makers should choose paid parental leave given to individ-
uals rather than to families. These policies help the equality processes in work
organizations through normalizing that both female and male employees are parents. Much of the evidence indicates that if there were no earmarked and
non-transferrable leave for the father that was based in law, reluctant fathers would
not have taken any leave and mothers may have been unwilling to give up leave to
share with them. There are ambivalent and hesitant fathers who would then choose
differently. This also shows that leave for many fathers is not something that is fully
in place as an accepted and taken-for-granted practice. These findings thus support
other research on fathers’ use of leave which have shown that the design character-
istics of father’s quota represents a strong incentive for greater involvement on the
part of fathers. Considering these findings, it is interesting that the EU Commission in 2019
introduced a new package on work-life balance to ensure better leave provisions and
care facilities for working parents in all EU member states. The existing EU
Directives on maternity and parental leave are regarded as outdated as they have
largely failed to improve gender equality, neither expanding women’s participation
in the labour market, nor encouraging men to use leave provisions and take a greater
share of caring responsibilities. Blum S, Koslowski A, Macht A, Moss P (2018) 14th annual international review of leave policies
and research 2018. International network on leave policies & research. https://www.
leavenetwork.org/annual-review-reports/archive-reviews/
B
d h B K
d E (1998) M
li i
d hild
h
i
f f h i
S
i l R Bartel AP, Rossin-Slater M, Ruhm CJ, Stearns J, Waldfogel J (2018) Paid family leave, fathers’
leave-taking, and leave-sharing in dual-earner households. J Policy Anal Manage 37(1):10–37 Brandth B, Kvande E (1998) Masculinity and child care: the reconstruction of fathering. Sociol Rev
46(2):293–313 Bartel AP, Rossin-Slater M, Ruhm CJ, Stearns J, Waldfogel J (2018) Paid family leave, fathers’
leave-taking, and leave-sharing in dual-earner households. J Policy Anal Manage 37(1):10–37
Blum S, Koslowski A, Macht A, Moss P (2018) 14th annual international review of leave policies
and research 2018. International network on leave policies & research. https://www.
leavenetwork.org/annual-review-reports/archive-reviews/
Brandth B, Kvande E (1998) Masculinity and child care: the reconstruction of fathering. Sociol Rev
46(2):293–313 References Bartel AP, Rossin-Slater M, Ruhm CJ, Stearns J, Waldfogel J (2018) Paid family leave, fathers’
leave-taking, and leave-sharing in dual-earner households. J Policy Anal Manage 37(1):10–37 Blum S, Koslowski A, Macht A, Moss P (2018) 14th annual international review of leave policies
and research 2018. International network on leave policies & research. https://www. leavenetwork.org/annual-review-reports/archive-reviews/ Brandth B, Kvande E (1998) Masculinity and child care: the reconstruction of fathering. Sociol Rev
46(2):293–313 162 E. Kvande Brandth B, Kvande E (2009) Gendered or gender neutral care policies for fathers? Ann Am Acad
Polit Social Sci 624(1):177–189 Brandth B, Kvande E (2018) Masculinity and fathering alone. Men Masculinities 21(1):72–90 Brandth B, Kvande E (2019a) Fathers’ sense of entitlement to ear-marked and shared parental leave
Sociol Rev 67(5):1154–1169 Brandth B, Kvande E (2019b) Workplace support of fathers’ parental leave use in Norway
Community Work Fam 22:43–57 Brighouse H, Wright EO (2008) Strong gender egalitarianism. Polit Soc 36(3):360–372 Dahl GB, Løken KV, Mogstad M (2014) Peer effects in program participation. Am Econ Rev 104
(7):2049–2074 Daly M (2011) What adult worker model? A critical look at recent social policy reform in Europe
from a gender and family perspective. Soc Polit 18(19):1–24 Dearing H (2016) Gender equality in the division of work: how to assess European leave policies
regarding their compliance with an ideal leave model. J Eur Soc Policy 26(3):234–247 Dearing H (2016) Gender equality in the division of work: how to assess European leave policies
di
th i
li
ith
id
l l
d l J E
S
P li
26(3) 234 247 regarding their compliance with an ideal leave model. J Eur Soc Policy 26(3):234–247 Duvander A-Z, Lammi-Taskula J (2012) Parental leave. In: Gíslason IV, Eydal GB (eds) Parental
leave, childcare and gender equality in the Nordic countries. Nordic Council of Ministers,
Copenhagen, pp 31–64 Eydal GB, Gíslason IV (2013) Tredelt permisjon og lang fedrekvote: Erfaringer fra Island. In:
Brandth
B,
Kvande
E
(eds)
Fedrekvoten
og
den
farsvennlige
velferdsstaten. Universitetsforlaget, Oslo, pp 222–237 g
pp
Eydal GB, Gíslason IV, Rostgaard T, Brandth B, Duvander A-Z, Lammi-Taskula J (2015) Trends
in parental leave: has the forward march of gender equality halted? Community Work Fam 18
(2):161–181 Fougner E (2012) Fedre tar ut hele fedrekvoten - også etter at den ble utvidet til ti uker. [Fathers us
the whole father's quota – also after extension]. References Arbeid og velferd 2:71–77 Gíslason IV, Eydal GB (2013) Parental leave, childcare and gender equality in the Nordic countries
Nordic Council of Ministers, Copenhagen Gornick JC, Meyers MK (eds) (2009) Gender equality. Transforming family divisions of labor. Verso, London Haas L, Rostgaard T (2011) Fathers’ right to paid parental leave in the Nordic countries: conse-
quences for the gendered division of care. Community Work Fam 14(2):177–195 Halrynjo S, Kitterød RH (2016) Fedrekvoten – norm for fedres permisjonsbruk i Norge og Norden:
En litteraturstudie. Report 2016:06. ISF, Oslo. https://samfunnsforskning.brage.unit.no/
samfunnsforskning-xmlui/handle/11250/2442339 Hamre K (2017) Fedrekvoten – mer populær enn noen gang. Samfunnsspeilet, 1. Statistics Norway. https://www.ssb.no/befolkning/artikler-og-publikasjoner/fedrekvoten-mer-populaer-enn-noen-
gang Harvey V, Tremblay D-G (2019) The workplace: challenges for fathers and their use of leave. In:
Moss P, Duvander A-Z, Koslowski A (eds) Parental leave and beyond. Recent international
developments, current issues, future directions. Policy Press, Bristol, pp 223–240 Hobson B, Morgan DHJ (2002) Introduction. In: Hobson B (ed) Making men into fathers
Cambridge University Press, Cambridge, pp 1–23 Kitterød RH, Halrynjo S, Østbakken KM (2017) Pappaperm? Fedre som ikke tar fedrekvote – hvo
mange, hvem og hvorfor? Report 2017: 2. ISF, Oslo g
g
p
Lewis J (2015) The decline of the male breadwinner model. Soc Polit 8(2):152–169 Lewis S, Stumbitz B (2017) Research on work and family: some issues and challenges. In:
Liebig B, Oechsle M (eds) Fathers in work organizations. Barbara Budrich, Berlin, pp 227–244 McKay L, Doucet A (2010) “Without taking her leave”: a Canadian case study of couples’
decisions on fathers’ use of paid parental leave. Fathering 8(3):300–320 Miller T (2013) Shifting out of neutral on parental leave. Making fathers’ involvement explicit
Public Policy Res 19(4):258–262 Morgan KJ (2008) The political path to a dual earner/dual carer society: pitfalls and possibilities
Polit Soc 36(3):403–420 Individual Parental Leave for Fathers: Promoting Gender Equality in Norway 163 Moss P, Deven F (1999) Parental leave: progress or pitfall? Research and policy issues in Europe. Vlaamse Gemeenschap, Brussels Moss P, Kamerman SB (2009) Introduction. In: Kamerman S, Moss P (eds) The politics of parenta
leave policies. Policy Press, Bristol, pp 1–13 Moss P, Kamerman SB (2009) Introduction. In: Kamerman S, Moss P (eds) The politics of parental
leave policies. Policy Press, Bristol, pp 1–13
Moss P Duvander A Z Koslowski A (eds) (2019) Parental leave and beyond: recent developments leave policies. References Policy Press, Bristol, pp 1–13 Moss P, Duvander A-Z, Koslowski A (eds) (2019) Parental leave and beyond: recent developments
current issues, future directions. Policy Press, Bristol Naz G (2010) Usage of parental leave by fathers in Norway. Int J Sociol Soc Policy 30
(5/6):313–325 NOU (2017) NOU 2017:6 Offentlig støtte til barnefamiliene [Public support for families with
children]. Government of Norway. Ministry of Children and Equality, Oslo. https://www. regjeringen.no/no/dokumenter/nou-2017-6/id2540981/ O’Brien M, Wall K (eds) (2017) Comparative perspectives on work-life balance and gende
equality: fathers on leave alone. Springer, London Pascall G (2012) Gender equality in the welfare state? The Policy Press, Bristol Ray R, Gornick JC, Schmitt J (2010) Who cares? Assessing generosity and gender equality
parental leave policy designs in 21 countries. J Eur Soc Policy 20(3):196–216 Rostgaard T (2002) Setting time aside for the father: father’s leave in Scandinavia. Community
Work Fam 5(3):343–370 Sainsbury D (1999) Gender, policy regimes and politics. Chapter 8. In: Sainsbury D (ed) Gender
and welfare state regimes. Oxford University Press, New York Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing,
adaptation, distribution and reproduction in any medium or format, as long as you give appropriate
credit to the original author(s) and the source, provide a link to the Creative Commons license and
indicate if changes were made. g
The images or other third party material in this chapter are included in the chapter’s Creative
Commons license, unless indicated otherwise in a credit line to the material. If material is not
included in the chapter’s Creative Commons license and your intended use is not permitted by
statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder.
|
W2978071447.txt
|
https://www.degruyter.com/document/doi/10.1515/demo-2019-0016/pdf
|
en
|
On kernel-based estimation of conditional Kendall’s tau: finite-distance bounds and asymptotic behavior
|
Dependence Modeling
| 2,019
|
cc-by
| 18,449
|
Depend. Model. 2019; 7:292–321
Research Article
Open Access
Alexis Derumigny* and Jean-David Fermanian
On kernel-based estimation of conditional
Kendall’s tau: finite-distance bounds and
asymptotic behavior
https://doi.org/10.1515/demo-2019-0016
Received May 29, 2019; accepted August 31, 2019
Abstract: We study nonparametric estimators of conditional Kendall’s tau, a measure of concordance between
two random variables given some covariates. We prove non-asymptotic pointwise and uniform bounds, that
hold with high probabilities. We provide “direct proofs” of the consistency and the asymptotic law of conditional Kendall’s tau. A simulation study evaluates the numerical performance of such nonparametric estimators. An application to the dependence between energy consumption and temperature conditionally to
calendar days is finally provided.
Keywords: conditional dependence measures, kernel smoothing, conditional Kendall’s tau
MSC: 62H20, 62G05, 62G08, 62G20
1 Introduction
In the field of dependence modeling, it is common to work with dependence measures. Contrary to usual linear correlations, most of them have the advantage of being defined without any condition on moments, and of
being invariant to changes in the underlying marginal distributions. Such summaries of information are very
popular and can be explicitly written as functionals of the underlying copulas: Kendall’s tau, Spearman’s rho,
Blomqvist’s coefficient... See Nelsen [30] for an introduction. In particular, for more than a century (Spearman (1904), Kendall (1938)), Kendall’s tau has become a popular dependence measure in [−1, 1]. It quantifies
the positive or negative dependence between two random variables X1 and X2 . Denoting by C1,2 the unique
underlying copula of (X1 , X2 ) that is assumed to be continuous, their Kendall’s tau can be directly defined as
Z
τ1,2 := 4
C1,2 (u1 , u2 ) C1,2 (du1 , du2 ) − 1
(1)
[0,1]2
= IP (X1,1 − X2,1 )(X1,2 − X2,2 ) > 0 − IP (X1,1 − X2,1 )(X1,2 − X2,2 ) < 0 ,
where (X i,1 , X i,2 )i=1,2 are two independent versions of X := (X1 , X2 ). This measure is then interpreted as the
probability of observing a concordant pair minus the probability of observing a discordant pair. See [22] for
an historical perspective on Kendall’s tau. Its inference is discussed in many textbooks (see [18] or [24], e.g.).
Its links with copulas and other dependence measures can be found in [30] or [20].
Similar dependence measures can be introduced in a conditional setup, when a p-dimensional covariate
Z is available. When hundreds of papers refer to Kendall’s tau, only a few of them have considered conditional Kendall’s tau (as defined below) until now. The goal is now to model the dependence between the two
*Corresponding Author: Alexis Derumigny: CREST-ENSAE and University of Twente, 5 Drienerlolaan, 7522 NB Enschede,
Netherlands, E-mail: a.f.f.derumigny@utwente.nl.
Jean-David Fermanian: CREST-ENSAE, 5, avenue Henry Le Chatelier, 91764 Palaiseau cedex, France,
E-mail: jean-david.fermanian@ensae.fr.
Open Access.
© 2019 Alexis Derumigny and Jean-David Fermanian, published by De Gruyter. This work is licensed under the
Creative Commons Attribution alone 4.0 License.
On kernel-based estimation of conditional Kendall’s tau |
293
components X1 and X2 , given the vector of covariates Z. Logically, we can invoke the conditional copula¹
C1,2|Z=z of (X1 , X2 ) given Z = z for any point z ∈ Rp , and the corresponding conditional Kendall’s tau would
be simply defined as
Z
τ1,2|Z=z := 4
C1,2|Z=z (u1 , u2 ) C1,2|Z=z (du1 , du2 ) − 1
[0,1]2
= IP (X1,1 − X2,1 )(X1,2 − X2,2 ) > 0 Z1 = Z2 = z − IP (X1,1 − X2,1 )(X1,2 − X2,2 ) < 0 Z1 = Z2 = z ,
where (X i,1 , X i,2 , Zi )i=1,2 are two independent versions of (X1 , X2 , Z). As above, this is the probability of observing a concordant pair minus the probability of observing a discordant pair, conditionally on Z1 and Z2
being both equal to z. Note that, as conditional copulas themselves, conditional Kendall’s taus are invariant
w.r.t. increasing transformations of the conditional margins X1 and X2 , given Z. Of course, if Z is independent of (X1 , X2 ) then, for every z ∈ Rp , the conditional Kendall’s tau τ1,2|Z=z is equal to the (unconditional)
Kendall’s tau τ1,2 .
Conditional Kendall’s tau, and more generally conditional dependence measures, are of interest per se
because they allow to summarize the evolution of the dependence between X1 and X2 , when the covariate
Z is changing. Surprisingly, their nonparametric estimates have been introduced in the literature only a few
years ago ([15],[40],[13]) and their properties have not yet been fully studied in depth. Indeed, until now and
to the best of our knowledge, the theoretical properties of nonparametric conditional Kendall’s tau estimates
have been obtained “in passing” in the literature, as a sub-product of the weak-convergence of conditional
copula processes ([40]) or as intermediate quantities that will be “plugged-in” ([12]). Therefore, such properties have been stated under too demanding assumptions. In particular, some assumptions were related to
the estimation of conditional margins, while this is not required because Kendall’s tau are based on ranks.
In this paper, we directly study nonparametric estimates τ̂1,2|z without relying on the theory/inference of
copulas. Therefore, we will state their main usual statistical properties: exponential bounds in probability,
consistency, asymptotic normality.
Our τ1,2|Z=z has not to be confused with the so-called “conditional Kendall’s tau” in the case of truncated
data ([39], [28]), in the case of semi-competing risk models ([23], [19]), or for other partial information schemes
([6], [21], among others). Indeed, particularly in biostatistics or reliability, the inference of dependence models under truncation/censoring can be led by considering some types of conditional Kendall’s tau, given some
algebraic relationships among the underlying random variables. This would induce conditioning by subsets.
At the opposite, we will consider only pointwise conditioning events in this paper, under a nonparametric
point-of-view. Nonetheless, such pointwise events can be found in the literature, but in some parametric or
semi-parametric particular frameworks, as for the identifiability of frailty distributions in bivariate proportional models ([31], [27]). Other related papers are [3] or [25], that are dealing with extreme co-movements
(bivariate extreme-value theory). There, the tail conditioning events of Kendall’s tau have probabilities that
go to zero with the sample size.
In Section 2, different kernel-based estimators of the conditional Kendall’s tau are discussed. Moreover,
we propose a cross-validation criterion to select the associated bandwidth. In Section 3, numerous original
theoretical properties of the latter estimators are proved: at first, finite distance exponential bounds in probability (pointwise and uniformly w.r.t. z); then, under an asymptotic point-of-view, pointwise and uniform
consistency; and finally the asymptotic normality of conditional Kendall’s tau under unrestrictive assumptions (see below) and with an explicit limiting law. A short simulation study is provided in Section 4. Proofs
are postponed into the appendix.
1 The conditional copula of X1 and X2 given Z = z can be defined almost surely as the unique copula of the conditional c.d.f.
F X1 ,X2 |Z=z by Sklar’s theorem. It was introduced by Patton [33, 34].
294 | Alexis Derumigny and Jean-David Fermanian
2 Definition of several kernel-based estimators of τ1,2|z
Let (X i,1 , X i,2 , Zi ), i = 1, . . . , n be an i.i.d. sample distributed as (X1 , X2 , Z), and n ≥ 2. Assuming continuous
underlying distributions, there are several equivalent ways of defining the conditional Kendall’s tau:
τ1,2|Z=z = 4 IP X1,1 > X2,1 , X1,2 > X2,2 Z1 = Z2 = z − 1
= 1 − 4 IP X1,1 > X2,1 , X1,2 < X2,2 Z1 = Z2 = z
= IP (X1,1 − X2,1 )(X1,2 − X2,2 ) > 0 Z1 = Z2 = z − IP (X1,1 − X2,1 )(X1,2 − X2,2 ) < 0 Z1 = Z2 = z .
Motivated by each of the latter expressions, we introduce several kernel-based estimators of τ1,2|Z=z :
τ̂(1)
:= 4
1,2|Z=z
n X
n
X
w i,n (z)w j,n (z)1 X i,1 < X j,1 , X i,2 < X j,2 − 1,
i=1 j=1
τ̂(2)
:=
1,2|Z=z
n X
n
X
w i,n (z)w j,n (z) 1 (X i,1 − X j,1 )(X i,2 − X j,2 ) > 0 − 1 (X i,1 − X j,1 )(X i,2 − X j,2 ) < 0 ,
i=1 j=1
τ̂(3)
:= 1 − 4
1,2|Z=z
n X
n
X
w i,n (z)w j,n (z)1 X i,1 < X j,1 , X i,2 > X j,2 ,
i=1 j=1
where 1 denotes the indicator function, w i,n is a sequence of weights given by
K (Z − z)
,
w i,n (z) = Pn h i
j=1 K h (Zj − z)
(2)
with K h (·) := h−p K(·/h) for some kernel K on Rp , and h = h(n) denotes a usual bandwidth sequence that tends
to zero when n → ∞. In this paper, we have chosen usual Nadaraya-Watson weights. Obviously, there are
alternatives (local linear, Priestley-Chao, Gasser-Müller, etc., weight), that would lead to different theoretical
results.
, τ̂(2)
and τ̂(3)
look similar, but they are nevertheless different, as shown in
The estimators τ̂(1)
1,2|Z=z
1,2|Z=z
1,2|Z=z
Proposition 1. These differences are due to the fact that all the τ̂(k)
, k = 1, 2, 3 are affine transformations
1,2|Z=z
of a double-indexed sum, on every pair (i, j), including the diagonal terms where i = j. The treatment of these
P
diagonal terms is different for each of the three estimators defined above. Indeed, setting s n := ni=1 w2i,n (z),
takes values in the interval [−1 , 1 − 2s n ], τ̂(2)
in [−1 + s n , 1 − s n ], and
it can be easily proved that τ̂(1)
1,2|Z=z
1,2|Z=z
τ̂(3)
in [−1 + 2s n , 1]. Moreover, there exists a direct relationship between these estimators, given by the
1,2|Z=z
following proposition.
Proposition 1. Almost surely, τ̂(1)
+ s n = τ̂(2)
= τ̂(3)
− s n , where s n :=
1,2|Z=z
1,2|Z=z
1,2|Z=z
Pn
i=1
w2i,n (z).
This proposition is proved in A.2. As a consequence, we can easily rescale the previous estimators so that the
new estimator will take values in the whole interval [−1, 1]. This would yield
τ̃1,2|Z=z :=
τ̂(1)
1,2|Z=z
1 − sn
τ̂(2)
τ̂(3)
sn
sn
1,2|Z=z
1,2|Z=z
+
=
=
−
·
1 − sn
1 − sn
1 − sn
1 − sn
Note that none of the latter estimators depends on any estimation of conditional marginal distributions.
In other words, we only have to conveniently choose the weights w i,n to obtain an estimator of the conditional
Kendall’s tau. This is coherent with the fact that conditional Kendall’s taus are invariant with respect to conditional marginal distributions. Moreover, note that, in the definition of our estimators, the inequalities are
strict (there are no terms corresponding to the cases i = j). This is inline with the definition of (conditional)
Kendall’s tau itself through concordant/discordant pairs of observations.
On kernel-based estimation of conditional Kendall’s tau |
295
The definition of τ̂(1)
can be motivated as follows. For j = 1, 2, let F̂ j|Z (·|Z = z) be an estimator of the
1,2|Z=z
conditional cdf of X j given Z = z. Then, a usual estimator of the conditional copula of X1 and X2 given Z = z
is
n
X
Ĉ1,2|Z (u1 , u2 |Z = z) :=
w i,n (z)1 F̂1|Z (X i,1 |Z = z) ≤ u1 , F̂2|Z (X i,2 |Z = z) ≤ u2 .
i=1
See [40] or [13], e.g. The latter estimator of the conditional copula can be plugged into (1) to define an estimator
of the conditional Kendall’s tau itself:
Z
τ̂1,2|Z=z := 4 Ĉ1,2|Z (u1 , u2 |Z = z) Ĉ1,2|Z (du1 , du2 |Z = z) − 1
(3)
=4
n
X
w j,n (z)Ĉ1,2|Z F̂1|Z (X j,1 |Z = z), F̂2|Z (X j,2 |Z = z) Z = z − 1.
j=1
Since the functions F̂ j|Z (·|Z = z) are non-decreasing, this reduces to
τ̂1,2|Z=z = 4
n X
n
X
w i,n (z)w j,n (z)1 X i,1 ≤ X j,1 , X i,2 ≤ X j,2 − 1
i=1 j=1
=
4
n X
n
X
w i,n (z)w j,n (z)1 X i,1 < X j,1 , X i,2 < X j,2 − 1 + o P (1) = τ̂(1)
+ o P (1).
1,2|Z=z
i=1 j=1
Veraverbeke et al. [40], Subsection 3.2, introduced their estimator of τ1,2|Z=z by (3) for a univariate conditioning variable. Note that this estimator is the same as the one studied in [15, p.4], i.e. τ̂1,2|Z=z . By the functional
Delta-Method, they deduced its asymptotic normality as a sub-product of the weak convergence of the process
√
nh Ĉ1,2|Z (·, ·|z) − C1,2|Z (·, ·|z) when Z is univariate. In our case, we will obtain more and stronger theoreti-
cal properties of τ̂(1)
under weaker conditions by a more direct analysis based on ranks. In particular, we
1,2|Z=z
will not require any regularity condition on the conditional marginal distributions, contrary to [40]. Indeed,
in the latter paper, it is required that F j|Z (·|Z = z) has to be two times continuously differentiable (assumption
(R̃3)) and its inverse has to be continuous (assumption (R1)). This is not satisfied for some simple univariate
cdf as F j (t) = t1(t ∈ [0, 1])/2 + 1(t ∈ (1, 2])/2 + t1(t ∈ (2, 4])/4 + 1(t > 4), for instance. Note that we could
justify τ̂(3)
in a similar way by considering conditional survival copulas.
1,2|Z=z
Let us define g1 , g2 , g3 by
g1 (Xi , Xj ) := 41 X i,1 < X j,1 , X i,2 < X j,2 − 1,
g2 (Xi , Xj ) := 1 (X i,1 − X j,1 ) × (X i,2 − X j,2 ) > 0 − 1 (X i,1 − X j,1 ) × (X i,2 − X j,2 ) < 0 ,
g3 (Xi , Xj ) := 1 − 41 X i,1 < X j,1 , X i,2 > X j,2 ,
where, for i = 1, . . . , n, we set Xi := (X i,1 , X i,2 ). Clearly, τ̂(k)
is a smoothed estimator of E[g k (X1 , X2 )|Z1 =
1,2|z
Z2 = z], k = 1, 2, 3.
Note that such dependence measures are of interest for the purpose of estimating (conditional or unconditional) copula models too. Indeed, several popular parametric families of copulas have a simple one-to-one
mapping between their parameter and the associated Kendall’s tau (or Spearman’s rho): Gaussian, Student
with a fixed degree of freedom, Clayton, Gumbel and Frank copulas, etc. Then, assume for instance that the
conditional copula C1,2|Z=z is a Gaussian copula with a parameter ρ(z). Then, by estimating its conditional
Kendall’s tau τ1,2|Z=z , we get an estimate of the corresponding parameter ρ(z), and finally of the conditional
copula itself. See [36], e.g.
The choice of the bandwidth h could be done in a data-driven way, following the general conditional
U-statistics framework detailed in Dony and Mason [10, Section 2]. Indeed, for any k ∈ {1, 2, 3} and z ∈ Rp ,
k)
denote by τ̂(h,
the estimator τ̂(k)
that is made with the smoothing parameter h and our dataset,
1,2|Z=z
−(i,j), 1,2|Z=z
(h, k)
when the i-th and j-th observations have been removed. As a consequence, the random function τ̂−(i,j),
1,2|Z=·
296 | Alexis Derumigny and Jean-David Fermanian
is independent of (Xi , Zi ), (Xj , Zj ) . As usual with kernel methods, it would be tempting to propose h as the
minimizer of the cross-validation criterion
CV DM (h) :=
n
2
X
2
(h, k)
g k (Xi , Xj ) − τ̂−(i,j),
K h (Zi − Zj ),
1,2|Z=(Z
+Z
)/2
i
j
n(n − 1)
i,j=1
for k = 1, 2, 3 or for τ̃1,2|Z=· . The latter criterion would be a “naively localized” version of the usual crossvalidation method. Unfortunately, we observe that the function h 7→ CV DM (h) is most often decreasing in
the range of realistic bandwidth values. If we remove the weight K h (Zi − Zj ), then there is no reason why
g k (Xi , Xj ) should be equal to τ̂(k)
(on average), and we are not interested in the prediction of
−(i,j), 1,2|Z=(Z +Z )/2
i
j
concordance/discordance pairs for which the Z i and Z j are far apart. Therefore, a modification of this criteria
k)
is necessary. We propose to separate the choice of h for the terms g k (Xi , Xj ) − τ̂(h,
and the
−(i,j), 1,2|Z=(Z +Z )/2
selection of the “convenient pairs” of observations (i, j). This leads to the new criterion
CV h˜ (h) :=
n
2
X
2
(h, k)
g k (Xi , Xj ) − τ̂−(i,j),
K̃ h˜ (Zi − Zj ),
1,2|Z=(Z
+Z
)/2
i
j
n(n − 1)
i
j
(4)
i,j=1
˜ Even if more complex procedures
with a potentially different kernel K̃ and a new fixed tuning parameter h.
˜ so that only a fraction of the
are possible, we suggest to simply choose K̃(z) := 1{|z|∞ ≤ 1} and to calibrate h
˜ as the empirical quantile of {|Zi − Zj |∞ : 1 ≤ i < j ≠ n} of
pairs (i, j) has non-zero weights. In practice, set h
order 2N pairs /(n(n − 1)), where N pairs is the number of pairs we want to keep.
3 Theoretical results
3.1 Finite distance bounds
Hereafter, we will consider the behavior of conditional Kendall’s tau estimates given Z = z belongs to some
fixed open and bounded subset Z in Rp . For the moment, let us state an instrumental result that is of interest
P
per se. Let ˆfZ (z) := n−1 nj=1 K h (Zj − z) be the usual kernel estimator of the density fZ of the conditioning
variable Z. Note that the estimators τ̂(k)
, k = 1, . . . , 3 are well-behaved only whenever ˆfZ (z) > 0. Denote
1,2|Z=z
the joint density of (X, Z) by fX,Z . In our study, we need some usual conditions of regularity.
Assumption 3.1. (a) The kernel K is bounded, and set kK k∞ =: C K . (b) It is symmetrical in the sense that
R
R
R
K(u) = K(−u) for every u ∈ Rp and satisfies K = 1, |K | < ∞, K 2 < ∞. (c) This kernel is of order α for some
R
integer α > 1: for all j = 1, . . . , α − 1 and every indices i1 , . . . , i j in {1, . . . , p}, K(u)u i1 . . . u i j du = 0. (d)
R
Moreover, E[K h (Z − z)] > 0 for every z ∈ Z and h > 0. Set K̃(·) := K 2 (·)/ K 2 and kK̃ k∞ =: C K̃ .
Assumption 3.2. fZ is α-times continuously differentiable on Z ² and there exists a constant C K,α > 0 s.t., for
all z ∈ Z,
Z
p
X
∂ α fZ
(z + thu) du ≤ C K,α .
|u i1 . . . u i α | sup
|K |(u)
t∈[0,1] ∂z i1 . . . ∂z i α
i1 ,...,i α =1
Moreover, C K̃,2 denotes a similar constant replacing K by K̃ and α by two.
Assumption 3.3. There exist two positive constants fZ,min and fZ,max such that, for every z ∈ Z, fZ,min ≤ fZ (z) ≤
fZ,max .
2 This means that the partial derivatives ∂ k f Z (z)/∂z i1 · · · ∂z i k exist and are continuous for every z ∈ Z and every k-uplet
(i1 , . . . , i k ) of integers in {1, . . . , p}, k ≤ α.
On kernel-based estimation of conditional Kendall’s tau |
297
Since Z is bounded, Assumption 3.3 is most often satisfied with the commonly met continuous distribution.
Proposition 2. Under Assumptions 3.1-3.3 and if C K,α h α /α! < fZ,min , for any z ∈ Z, the estimator ˆfZ (z) is
strictly positive with a probability larger than
Z
2
1 − 2 exp − nh p fZ,min − C K,α h α /α! / 2fZ,max K 2 + (2/3)C K (fZ,min − C K,α h α /α!) .
The latter proposition is proved in A.3. It guarantees that our estimators τ̂(k)
, k = 1, . . . , 3, are well-behaved
1,2|z
with a probability close to one. The next regularity assumption is necessary to explicitly control the bias of
τ̂1,2|Z=z .
Assumption 3.4. For every x ∈ R2 , z 7→ fX,Z (x, z) is differentiable on Z almost everywhere up to the order α.
For every 0 ≤ k ≤ α and every 1 ≤ i1 , . . . , i α ≤ p, let
H k,~ι (u, v, x1 , x2 , z) := sup
t∈[0,1]
∂ α−k f
∂ k fX,Z
X,Z
x1 , z + thu
x2 , z + thv ,
∂z i1 . . . ∂z i k
∂z i k+1 . . . ∂z i α
denoting~ι = (i1 , . . . , i α ). Assume that H k,~ι (u, v, x1 , x2 , z) is integrable and there exists a finite constant CXZ,α >
0 such that, for every z ∈ Z and every h < 1,
!
Z
p
α
X
X
α
|K |(u)|K |(v)
H k,~ι (u, v, x1 , x2 , z)|u i1 . . . u i k v i k+1 . . . v i α | du dv dx1 dx2
k
k=0
i1 ,...,i α =1
is less than CXZ,α .
Assumptions 3.2 and 3.4 are satisfied when the density of Z is α-times continuously differentiable in a (strictly
larger) neighborhood of Z and K is compactly supported, for n sufficiently large. Indeed, the vectors thu and
thv will then be arbitrary small uniformly w.r.t. t ∈ [0, 1] and u (resp. v) in the support of K ³. If K is not
compactly supported, these assumptions are most often satisfied when the tails of fZ and its derivatives do
not exhibit pathological patterns. For instance, if fZ is a Gaussian density, this is the case because this density
and its derivatives are bounded on Rp .
The next three propositions state pointwise and uniform exponential inequalities for the estimators
τ̂(k)
, when k = 1, 2, 3. They are proved in Sections A.4, A.5 and A.6. We will denote c1 := c3 := 4 and
1,2|Z=z
c2 := 2.
Proposition 3 (Exponential bound with explicit constants). Under Assumptions 3.1-3.4, for every t > 0 such
that C K,α h α /α! + t ≤ fZ,min /2 and every t0 > 0, if C K̃,2 h2 < fz (z), we have
!
R
16fZ2 (z) C K,α h α
c k CXZ,α h α 3fz (z) K 2
0
(k)
+
+t × 1+ 3
+t
IP |τ̂1,2|Z=z − τ1,2|Z=z | > 2
α!
2nh p
α!
fz (z)
fZ,min
nh p t2
(n − 1)h2p t02
R
R
+ 2 exp − 2
≤ 2 exp −
2
2
2
2
0
2fZ,max K + (2/3)C K t
4fZ,max ( K ) + (8/3)C K t
p
2 2
nh (fz (z) − C K̃,2 h )
+ 2 exp −
,
R
8fZ,max K̃ 2 + 4C K̃ (fz (z) − C K̃,2 h2 )/3
for any z ∈ Z and every k = 1, 2, 3.
Alternatively, we can apply Theorem 1 in Major [26] instead of the Bernstein-type inequality that has been
used in the proof of Proposition 3.
3 Then, all the terms that involve fZ and its derivatives are uniformly bounded. And invoke the α-order property of K to check the
validity of such assumptions.
298 | Alexis Derumigny and Jean-David Fermanian
Proposition 4 (Alternative exponential bound without explicit constants). Under Assumptions 3.1-3.4, for
R
3
every t > 0 such that C K,α h α /α! + t ≤ fZ,min /2 and every t0 > 0 s.t. t0 ≤ 2h p ( K 2 )3 fZ,max
/C4K , there exist
some universal constants C2 and α2 s.t.
!
R
16fZ2 (z) C K,α h α
c k CXZ,α h α 3fz (z) K 2
(k)
0
IP |τ̂1,2|Z=z − τ1,2|Z=z | > 2
+
+t
+t × 1+ 3
α!
2nh p
α!
fz (z)
fZ,min
nh p (fz (z) − C K̃,2 h2 )2
nh p t2
R
+
2
exp
−
≤ 2 exp −
R
2fZ,max K 2 + (2/3)C K t
8fZ,max K̃ 2 + 4C K̃ (fz (z) − C K̃,2 h2 )/3
α2 nh p t0
nh p t2
R
R
R
R
+ C2 exp −
,
+ 2 exp
3
8fZ,max ( K 2 )
32 K 2 ( |K |)2 fZ,max
+ 8C K |K |fZ,max t/3
for any z ∈ Z and every k = 1, 2, 3, if C K̃,2 h2 < fZ (z) and 6h p
R
|K |
2
fz,max <
R
K2.
Remark 5. In Propositions 2, 3 and 4, when the support of K is included in [−c, c]p for some c > 0, fZ,max can be
replaced by a local bound supz̃∈V(z,ϵ) fZ (z̃), denoting by V(z, ϵ) a closed ball of center z and any radius ϵ > 0,
when h c < ϵ.
Propositions 3 and 4 look similar. Nonetheless, only the upper bound in the former case can be explicitly
calculated because this bound involves constants that can be numerically evaluated. But, on the other side,
Proposition 4 provides better rates of convergence. Indeed, by choosing t0 of the order h p , the latter result can
− τ1,2|Z=z | > ϵh p exp − Cnh2p ϵ , for some constants ϵ > 0 and C > 0. At the
be summarized as IP |τ̂(k)
1,2|Z=z
opposite, the bound obtained in Proposition 3 is of the type IP |τ̂(k)
− τ1,2|Z=z | > ϵ exp − C0 nh2p ϵ ,
1,2|Z=z
C0 > 0, what is clearly weaker.
As a corollary, the two latter results yield the weak consistency of τ̂(k)
for every z ∈ Z, when nh2p → ∞
1,2|Z=z
(choose the constants t and t0 ∼ h p sufficiently small, in Proposition 4, e.g.).
It is possible to obtain uniform bounds, by slightly strengthening our assumptions. Note that this next
result will be true if n is sufficiently large, when Proposition 4 was true for every n.
Assumption 3.5. The kernel K is Lipschitz on (Z, k · k∞ ), with a constant λ K and Z is a subset of an hypercube
in Rp whose volume is denoted by V. Moreover, K and K 2 are regular in the sense of [16] or [11].
Proposition 6 (Uniform exponential bound). Under the assumptions 3.1-3.5, there exist some constants L K
and C K (resp. L K̃ and C K̃ ) that depend only on the VC characteristics of K (resp. K̃), s.t., for every µ ∈ (0, 1) such
R
R
that µfz,min < CXZ,α h α /α! + b K K 2 fZ,max /C K , if fZ,max < C̃XZ,2 h2 /2 + b K̃ K̃ 2 fZ,max /C K̃ ,
R
!
CXZ,α h α 3fz,max K 2
ck
(k)
IP sup |τ̂1,2|Z=z − τ1,2|Z=z | > 2
+
+t
α!
2nh p
fz,min (1 − µ)2
z∈Z
C
h α 2
≤ L K exp − C f ,K nh p µfz,min − XZ,α
α!
p
α2 nth
p
2 2
R
+ C2 D exp −
+
L
exp
−
C
nh
f
−
C̃
h
/4
z,max
XZ,2
K̃
f , K̃
8fZ,max ( K 2 )
A2 nh p t2 C−4
A nh p t
+ 2 exp − 2 2 R 2 3 K R
+ 2 exp − 2 2
,
2
16C K A1
16 A1 K fz,max ( |K |)
R
3
for n sufficiently large, k = 1, 2, 3, and for every t > 0 s.t. t ≤ 2h p ( K 2 )3 fZ,max
/C4K ,
Z
Z
Z
Z
3
3
−16A1 C2K A g K 2 fz,max
( |K |)2 ln(h p K 2 fz,max
( |K |)2 ) < n1/2 h p/2 t, and
nh p t ≥
Z
K 2 fz,max M2 (p + β)3/2 log
4C2K
hp f
z,max
R
K2
, β = max 0,
log D
4C K λ K p
, D := dV
e,
log n
h
for some universal constants C2 , α2 , M2 , A1 , A2 and a constant A g that depends on K and fz,max .
On kernel-based estimation of conditional Kendall’s tau |
299
R
We have denoted C f ,K := log(1 + b K /(4L K ))/(L K b K fz,max K 2 ), for any arbitrarily chosen constant b K ≥ C K .
R
Similarly, C f , K̃ := log(1 + b K̃ /(4L K̃ ))/(L K̃ b K̃ fz,max K̃ 2 ), b K̃ ≥ C K̃ .
3.2 Asymptotic behavior
The previous exponential inequalities are not optimal to prove usual asymptotic results. Indeed, they directly
or indirectly rely on upper bounds of estimates, as in Hoeffding or Bernstein-type inequalities. In the case of
kernel estimates, this implies the necessary condition nh2p → ∞, at least. By a direct approach, it is possible
to state the consistency of τ̂(k)
, k = 1, 2, 3, and then of τ̃1,2|Z=z , under the weaker condition nh p → ∞.
1,2|Z=z
Proposition 7 (Consistency). Under Assumption 3.1, if nh pn → ∞, lim K(t)|t|p = 0 when |t| → ∞, fZ and
z 7→ τ1,2|Z=z are continuous on Z, then τ̂(k)
tends to τ1,2|Z=z in probability, when n → ∞ for any k = 1, 2, 3.
1,2|Z=z
This property is proved in A.7. Moreover, Proposition 6 does not allow to state the strong uniform consistency
of τ̂(k)
because the threshold t has to be of order h p at most. Here again, a direct approach is possible,
1,2|Z=z
nonetheless.
p
Proposition 8 (Uniform consistency). Under Assumption 3.1, assume that nh2p
n / log n → ∞, lim K(t)|t| = 0
when |t| → ∞, K is Lipschitz, fZ and z 7→ τ1,2|Z=z are continuous on a bounded set Z, and there exists a lower
− τ1,2|Z=z → 0 almost surely, when n → ∞
bound fZ,min s.t. fZ,min ≤ fZ (z) for any z ∈ Z. Then supz∈Z τ̂(k)
1,2|Z=z
for any k = 1, 2, 3.
This property is proved in A.8. To derive the asymptotic law of this estimator, we will assume:
Assumption 3.6. (i) nh pn → ∞ and nh p+2α
→ 0; (ii) K( · ) is compactly supported.
n
Proposition 9 (Joint asymptotic normality at different points). Let z01 , . . . , z0n0 be fixed points in a set Z ⊂ Rp .
Assume 3.1, 3.4, 3.6, that the z0i are distinct and that fZ and z 7→ fX,Z (x, z) are continuous on Z, for every x. Then,
as n → ∞,
D
(nh pn )1/2 τ̂1,2|Z=z0i − τ1,2|Z=z0i
−→ N(0, H(k) ), k = 1, 2, 3,
i=1,...,n0
,
τ̂(k)
1,2|Z=z
k = 1, 2, 3 or τ̃1,2|Z=z , and H is the n0 × n0 diagonal real
where τ̂1,2|Z=z denotes any of the estimators
matrix defined by
R
4 K 2 1{i=j}
(k)
E[g k (X1 , X)g k (X2 , X)|Z = Z1 = Z2 = z0i ] − τ21,2|Z=z0 ,
[H ]i,j =
i
fZ (z0i )
for every 1 ≤ i, j ≤ n0 , and (X, Z), (X1 , Z1 ), (X2 , Z2 ) are independent versions.
This proposition is proved in A.9.
Remark 10. The latter results will provide some simple tests of the constancy of the function z 7→ τ1,2|z , and
then of the constancy of the associated conditional copula itself. This would test the famous “simplifying assumption” (“H0 : C1,2|Z=z does not depend on the choice of z”), a key assumption for vine modeling in particular:
see [1] or [17] for a discussion, [8] for a review and a presentation of formal tests for this hypothesis.
4 Simulation study
In this simulation study, we draw i.i.d. random samples (X i,1 , X i,2 , Z i ), i = 1, . . . , n, with univariate explanatory variables (p = 1). We consider two settings, that correspond to bounded and/or unbounded explanatory
variables respectively:
300 | Alexis Derumigny and Jean-David Fermanian
1. Z =]0, 1[ and the law of Z is uniform on ]0, 1[. Conditionally on Z = z, X1 |Z = z and X2 |Z = z both follow
a Gaussian distribution N(z, 1). Their associated conditional copula is Gaussian and their conditional
Kendall’s tau is given by τ1,2|Z=z = 2z − 1.
2. Z =]−2, 2[ and the law of Z is N(0, 1). Conditionally on Z = z, X1 |Z = z and X2 |Z = z both follow a
Gaussian distribution N(Φ(z), 1), where Φ(·) is the cdf of the Z. Their associated conditional copula is
Gaussian and their conditional Kendall’s tau is given by τ1,2|Z=z = 2Φ(z) − 1.
These simple frameworks allow us to compare the numerical properties of our different estimators in
different parts of the space, in particular when Z is close to zero or one, i.e. when the conditional Kendall’s tau
is close to −1 or to 1. Note that these distributions are continuous, with infinitely differentiable densities. We
will use the Epanechnikov kernel. Therefore, they will satisfy Assumptions 3.1-3.6. We compute the different
estimators τ̂(k)
for k = 1, 2, 3, and the symmetrically rescaled version τ̃1,2|z . The bandwidth h is chosen
1,2|Z=z
as proportional to the usual “rule-of-thumb” for kernel density estimation, i.e. h = α h σ̂(Z)n−1/5 with α h ∈
{0.5, 0.75, 1, 1.5, 2} and n ∈ {100, 500, 1000, 2000}. For each setting, we consider three local measures
of goodness-of-fit: for a given z and for any Kendall’s tau estimate (say τ̂1,2|Z=z ), let
• the (local) bias: Bias(z) := E[τ̂1,2|Z=z ] − τ1,2|Z=z ,
h
2 i1/2
,
• the (local) standard deviation: Sd(z) := E τ̂1,2|Z=z − E[τ̂1,2|Z=z ]
h
2 i
• the (local) mean square-error: MSE(z) := E τ̂1,2|Z=z − τ1,2|Z=z .
We also consider their integrated version w.r.t the usual Lebesgue measure on the whole support of z, respectively denoted by IBias, ISd and IMSE. Some results concerning these integrated measures are given in
Table 1 (resp. Table 2) for Setting 1 (resp. Setting 2), and for different choices of α h and n. For the sake of effective calculations of these measures, all the theoretical previous expectations are replaced by their empirical
counterparts based on 500 simulations.
For every n, the best results seem to be obtained with α h = 1.5 and the fourth (rescaled) estimator,
particularly in terms of bias. This is not so surprising, because the estimators τ̂(k) , k = 1, 2, 3, do not have the
right support at a finite distance. Note that this comparative advantage of τ̃ in terms of bias decreases with
n, as expected. In terms of integrated variance, all the considered estimators behave more or less similarly,
particularly when n ≥ 500.
To illustrate our results for Setting 1 (resp. Setting 2), the functions z 7→ Bias(z), Sd(z) and MSE(z) have
been plotted on Figures 1-2 (resp. Figures 3-4), both with our empirically optimal choice α h = 1.5. We can note
that, considering the bias, the estimator τ̃ behaves similarly as τ̂(1) when the true τ is close to −1, and similarly
as τ̂(3) when the true Kendall’s tau is close to 1. But globally, the best pointwise estimator is clearly obtained
with the rescaled version τ̃1,2|Z=· , after a quick inspection of MSE levels, and even if the differences between
our four estimators weaken for large sample sizes. The comparative advantage of τ̃1,2|z more clearly appears
with Setting 2 than with Setting 1. Indeed, in the former case, the support of Z’s distribution is the whole
line. Then ˆfZ does not suffer any more from the boundary bias phenomenon, contrary to what happened with
Setting 1. As a consequence, the biases induced by the definitions of τ̂(k)
, k = 1, 3, appear more strikingly
1,2|z
in Figure 3, for instance: when z is close to (−1) (resp. 1), the biases of τ̂(1)
(resp. τ̂(3)
) and τ̃1,2|z are close,
1,2|z
1,2|z
when the bias τ̂(3)
(resp. τ̂(1)
) is a lot larger. Since the squared biases are here significantly larger than the
1,2|z
1,2|z
variances in the tails, τ̃1,2|z provides the best estimator globally considering “both sides” together. But even
in the center of Z’s distribution, the latter estimator behaves very well.
In Setting 2 where there is no boundary problem, we also try to estimate the conditional Kendall’s tau
using our cross-validation criterion (4), with N pairs = 1000. More precisely, denoting by h CV the minimizer of
the cross-validation criterion, we try different choices h = α h ×h CV with α h ∈ {0.5, 0.75, 1, 1.5, 2}. The results
in terms of integrated bias, standard deviation and MSE are given in Table 3. We do not find any substantial
improvements compared to the previous Table 2, where the bandwidth was chosen “roughly”. In Table 4,
On kernel-based estimation of conditional Kendall’s tau
| 301
we compare the average h CV with the previous choice of h. The expectation of h CV is always higher than
the “rule-of-thumb” h ref , but the difference between both decreases when the sample size n increases. The
standard deviation of h CV is quite high for low values of n, but decreases as a function of n. This may be seen
as quite surprising given the fact that the number of pairs N pairs used in the computation of the criterion
stays constant. Nevertheless, when the sample size increases, the selected pairs are better in the sense that
the differences |Z i − Z j | can become smaller as more replications of Z i are available.
Table 1: Results of the simulation in Setting 1. All values have been multiplied by 1000. Bold values indicate optimal choices
for the chosen measure of performance. These results are integrated measures of performance over the whole space Z; the
corresponding local measures of performance are displayed in Figures 1 and 2.
αh = 2
α h = 1.5
αh = 1
α h = 0.75
α h = 0.5
n = 100
n = 500
n = 1000
n = 2000
IBias
ISd
IMSE
IBias
ISd
IMSE
IBias
ISd
IMSE
IBias
ISd
IMSE
-133
197
66.5
-34.5
84.9
9.86
-18.2
61.6
4.85
-10.9
46
2.65
-12.9
187
43.7
-4.08
84.4
8.58
-0.9
61.5
4.49
-1.07
46
2.53
107
190
56.6
26.4
84.5
9.26
16.4
61.5
4.76
8.8
46
2.6
τ̃1,2|Z=·
-0.91
213
48.2
-1.18
86.9
8.55
0.733
62.4
4.46
-0.149
46.4
2.5
τ̂(1)
1,2|Z=·
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
-88
150
35.8
-26.3
68
6.32
-13.9
50.7
3.33
-7.98
37.6
1.8
-10.4
145
26.3
-5.97
67.9
5.6
-2.33
50.6
3.12
-1.39
37.5
1.74
67.2
146
30.6
14.3
67.9
5.75
9.2
50.6
3.19
5.2
37.5
1.76
τ̃1,2|Z=·
-2.06
157
26.7
-3.99
69.2
5.49
-1.21
51.2
3.05
-0.76
37.8
1.69
τ̂(1)
1,2|Z=·
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
-67.8
123
24.5
-19.2
58.7
4.8
-11
43.1
2.52
-6.34
33
1.44
-9.99
121
19
-3.95
58.6
4.39
-2.35
43.1
2.39
-1.39
33
1.4
47.8
122
20.9
11.3
58.7
4.47
6.34
43.1
2.41
3.57
33
1.41
τ̃1,2|Z=·
-3.48
128
18.1
-2.34
59.5
4.18
-1.46
43.4
2.29
-0.897
33.2
1.35
τ̂(1)
1,2|Z=·
-44.6
101
17.5
-15.9
50.4
4.12
-9.7
35.9
2.13
-5.52
27.6
1.28
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
-5.81
100
14.9
-5.68
50.3
3.84
-3.84
35.9
2.02
-2.18
27.6
1.24
33
101
15.5
4.58
50.3
3.77
2.01
35.9
1.99
1.15
27.6
1.23
τ̃1,2|Z=·
-1.09
104
13.4
-4.55
50.8
3.57
-3.19
36.1
1.9
-1.83
27.7
1.18
τ̂(1)
1,2|Z=·
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
-37.8
91.4
17.3
-11.8
43.8
4.14
-7.2
31.2
2.35
-5.97
23.7
1.43
-8.03
91.4
15.4
-3.93
43.8
3.94
-2.75
31.2
2.28
-3.44
23.7
1.39
21.7
91.7
15.4
3.91
43.8
3.87
1.7
31.2
2.24
-0.912
23.7
1.37
τ̃1,2|Z=·
-4.5
94.2
13.5
-3.01
44.1
3.62
-2.24
31.3
2.12
-3.16
23.8
1.32
τ̂(1)
1,2|Z=·
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
5 Application to real data
In this section, we present an application of this methodology to the dependence between electricity consumption and temperature. The first paper on this topic dates back to 1958 ([7]). Using UK data, they show
that a decrease in temperature increases the electricity demand. Moreover, they show that the marginal effect
of temperature levels on electricity consumption differs depending on the time of the day. Numerous other
302 | Alexis Derumigny and Jean-David Fermanian
Sd, alpha_h = 1.5 , n = 100
MSE, alpha_h = 1.5 , n = 100
0.06
MSE at point z
0.02
0.04
0.10
0.08
0.0
−0.3
−0.2
−0.1
Bias at point z
0.1
Standard deviation at point z
0.12
0.2
0.08
0.3
Bias, alpha_h = 1.5 , n = 100
0.0
0.2
0.4
0.6
0.8
1.0
0.0
0.2
0.4
z
0.6
0.8
1.0
0.0
0.2
0.4
z
0.6
0.8
1.0
z
Figure 1: Local bias, standard deviation and MSE for the estimators τ̂(1) (red) , τ̂(2) (blue), τ̂(3) (green), τ̃ (orange), with n = 100
and α h = 1.5 in Setting 1. The dotted line on the first figure is the reference at 0.
Sd, alpha_h = 1.5 , n = 500
−0.15
0.020
0.015
0.005
0.010
MSE at point z
0.05
0.02
−0.10
0.03
0.04
Standard deviation at point z
0.06
0.10
0.05
0.00
−0.05
Bias at point z
MSE, alpha_h = 1.5 , n = 500
0.07
0.15
Bias, alpha_h = 1.5 , n = 500
0.0
0.2
0.4
0.6
z
0.8
1.0
0.0
0.2
0.4
0.6
z
0.8
1.0
0.0
0.2
0.4
0.6
0.8
z
Figure 2: Local bias, standard deviation and MSE for the estimators τ̂(1) (red) , τ̂(2) (blue), τ̂(3) (green), τ̃ (orange), with n = 500
and α h = 1.5 in Setting 1. The dotted line on the first figure is the reference at 0.
1.0
On kernel-based estimation of conditional Kendall’s tau
Sd, alpha_h = 1.5 , n = 100
MSE, alpha_h = 1.5 , n = 100
MSE at point z
0.10
0.15
0.20
0.15
Standard deviation at point z
0.0
0.00
−0.4
0.10
0.05
−0.2
Bias at point z
0.2
0.20
0.4
0.25
Bias, alpha_h = 1.5 , n = 100
| 303
−2
−1
0
1
2
−2
−1
z
0
1
2
−2
−1
z
0
1
2
z
Figure 3: Local bias, standard deviation and MSE for the estimators τ̂(1) (red) , τ̂(2) (blue), τ̂(3) (green), τ̃ (orange), with n = 100
and α h = 1.5 in Setting 2. The dotted line on the first figure is the reference at 0.
0.012
0.055
MSE at point z
0.035
0.006
0.008
0.010
0.050
0.045
0.040
Standard deviation at point z
0.05
0.00
0.025
−0.10
0.002
0.030
0.004
−0.05
Bias at point z
MSE, alpha_h = 1.5 , n = 500
0.014
Sd, alpha_h = 1.5 , n = 500
0.10
Bias, alpha_h = 1.5 , n = 500
−2
−1
0
z
1
2
−2
−1
0
z
1
2
−2
−1
0
z
Figure 4: Local bias, standard deviation and MSE for the estimators τ̂(1) (red) , τ̂(2) (blue), τ̂(3) (green), τ̃ (orange), with n = 500
and α h = 1.5 in Setting 2. The dotted line on the first figure is the reference at 0.
1
2
304 | Alexis Derumigny and Jean-David Fermanian
Table 2: Results of the simulation in Setting 2. All values have been multiplied by 1000. Bold values indicate optimal choices
for the chosen measure of performance. These results are integrated measures of performance over the whole space Z; the
corresponding local measures of performance are displayed in Figures 3 and 4.
αh = 2
α h = 1.5
αh = 1
α h = 0.75
α h = 0.5
n = 100
n = 500
n = 1000
n = 2000
IBias
ISd
IMSE
IBias
ISd
IMSE
IBias
ISd
IMSE
IBias
ISd
IMSE
τ̂(1)
1,2|Z=·
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
-207
227
180
-54.1
83.9
16.9
-29.6
55.3
5.81
-16.9
38.9
2.49
1.15
207
97
0.845
80.5
10.8
0.557
54.4
4.35
0.145
38.6
2.04
210
228
181
55.7
83.2
16.4
30.7
55.4
5.9
17.2
38.9
2.5
τ̃1,2|Z=·
1.4
225
51.9
0.987
81.4
6.86
0.456
55
3.22
0.175
38.9
1.66
τ̂(1)
1,2|Z=·
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
-144
175
98.6
-33.3
60.6
7.5
-19.8
41.9
3.12
-10.6
30.5
1.42
-2.33
163
56.2
1.73
59.4
5.56
-0.0619
41.7
2.51
0.665
30.4
1.24
140
176
99.2
36.8
60.7
7.73
19.7
42.1
3.12
11.9
30.5
1.45
τ̃1,2|Z=·
-3.15
170
30.3
1.69
60.2
3.85
-0.093
42.1
1.95
0.645
30.5
1.05
τ̂(1)
1,2|Z=·
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
-99.8
143
57.7
-24.9
50.9
5.06
-13.5
36.6
2.28
-6.92
26.6
1.09
1.17
132
34.6
0.903
50.4
4.02
1.16
36.5
1.97
1.46
26.6
0.994
102
139
54.4
26.7
51
5.13
15.8
36.6
2.33
9.83
26.6
1.11
τ̃1,2|Z=·
2.51
138
20.1
0.897
50.9
2.89
1.16
36.7
1.56
1.48
26.7
0.847
τ̂(1)
1,2|Z=·
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
-59.1
104
28.1
-14.7
42.3
3.87
-7.56
29.7
1.86
-4.17
21.8
0.932
4.34
99.7
21.4
2.05
42.1
3.48
2.07
29.6
1.75
1.35
21.8
0.899
67.8
103
29.6
18.8
42.3
3.96
11.7
29.6
1.92
6.87
21.8
0.957
τ̃1,2|Z=·
3.34
103
13.4
2.08
42.5
2.6
2.08
29.7
1.39
1.35
21.8
0.755
τ̂(1)
1,2|Z=·
-37.2
88.2
23.9
-9.57
38.2
4.6
-3.75
26.2
2.34
-1.09
19.8
1.32
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
8.17
85.9
21.2
2.69
38
4.45
3.32
26.1
2.3
2.99
19.8
1.32
53.5
87.4
25.3
14.9
38.1
4.74
10.4
26.2
2.41
7.08
19.8
1.36
τ̃1,2|Z=·
8.47
88.5
15
2.69
38.4
3.59
3.33
26.3
1.93
3
19.9
1.15
articles have studied the dependence between these two variables, see for instance [4, 29, 32]. Generally,
in winter, electricity consumption increases when temperature decreases, because of the demand for heating. On the contrary, high temperatures in summer would cause an increased electricity demand for cooling
homes, offices and so on.
Formally, we study the dependence between the following two variables:
• Power t , the French electricity consumption⁴ in MW at time t;
• Temp t , the temperature in Celsius degree at the Orly Airport weather station (France)⁵.
These two variables are observed every 30 minutes from 01/01/1996 to 31/03/2019. The final dataset has got
n = 329, 756 rows. The unconditional Kendall’s tau between these two variables is −0.397, computed using
the fast Kendall’s tau algorithm [14]. In other words, on average, lower temperatures are associated to higher
electricity consumption.
4 downloaded from http://clients.rte-france.com/lang/an/visiteurs/vie/vie_stats_conso_inst.jsp
5 downloaded from https://gis.ncdc.noaa.gov/maps/ncei/cdo/hourly
On kernel-based estimation of conditional Kendall’s tau
| 305
Table 3: Results of the simulation in Setting 2 using h = α h × h CV where h CV has been chosen by cross-validation. All values
have been multiplied by 1000. Bold values indicate optimal choices for the chosen measure of performance.
α h = 1.5
αh = 1
α h = 0.75
α h = 0.5
n = 100
n = 500
n = 1000
n = 2000
IBias
ISd
IMSE
IBias
ISd
IMSE
IBias
ISd
IMSE
IBias
ISd
IMSE
-111
154
66.2
-36.9
66.8
9.01
-22.4
48.2
4.06
-12.9
36.1
2.04
0.0488
137
36.3
0.236
64.2
6.45
0.546
46.8
3.14
1.29
35.7
1.78
111
151
60.6
37.4
66.3
8.88
23.5
47.2
4.07
15.5
36.2
2.18
τ̃1,2|Z=·
1.38
132
18.3
0.27
64.5
4.49
0.61
46.8
2.36
1.29
35.6
1.49
τ̂(1)
1,2|Z=·
-67.4
117
35.7
-23.3
52.1
5.27
-13.9
37.8
2.4
-7.6
29
1.3
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
4.32
108
23.5
0.809
50.7
4.21
1.03
37.2
2.07
1.78
28.8
1.21
76.1
119
35.4
24.9
51.6
5.12
16
37.6
2.49
11.2
29.1
1.39
τ̃1,2|Z=·
4.98
106
13.3
0.86
51.6
3.13
1.03
37.5
1.63
1.81
28.9
1.02
τ̂(1)
1,2|Z=·
-43
101
28
-15.8
45.7
4.44
-9.51
33.1
2.04
-4.68
25.1
1.07
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
7.87
93.1
22.4
2.01
44.8
3.91
1.57
32.7
1.87
2.29
24.9
1.03
58.8
97.6
27.2
19.8
45.3
4.41
12.7
32.9
2.1
9.27
25.1
1.14
τ̃1,2|Z=·
8.51
98
15.7
2.05
46
3.01
1.57
33.1
1.5
2.33
25.1
0.871
τ̂(1)
1,2|Z=·
(2)
τ̂1,2|Z=·
τ̂(3)
1,2|Z=·
-16.1
95.6
41.7
-6.36
43
6.35
-4.04
30.6
2.87
-1.11
22.1
1.34
14.9
92.6
40.4
5.08
42.6
6.2
3.17
30.4
2.83
3.47
22
1.34
46
92.8
42.2
16.5
42.6
6.45
10.4
30.4
2.94
8.06
22.1
1.4
τ̃1,2|Z=·
15.6
100
35.2
5.11
44
5.31
3.17
31
2.45
3.5
22.4
1.17
τ̂(1)
1,2|Z=·
τ̂(2)
1,2|Z=·
τ̂(3)
1,2|Z=·
Table 4: Expectation and standard deviation of the bandwidth selected by cross-validation as a function of the sample size n,
and comparison with bandwidth h ref chosen by the rule-of-thumb.
n
E[h CV ]
Sd[h CV ]
ref
h = n−1/5
100
0.77
0.17
0.40
500
0.43
0.091
0.29
1000
0.34
0.060
0.25
2000
0.27
0.057
0.22
To have a more precise investigation about the dependence between these two variables, we decided to
use a usual “detrending method”: we fit a linear trend on both variables and consider only the dependence
between the two series of residuals. Formally, our model assumption is
Power t = a0, power + a1, power × t + ε1,t ,
(5)
Temp t = a0, temp + a1, temp × t + ε2,t ,
(6)
where t is the the number of half-hours since 01/01/1996, for some unknown coefficients a0, power , a1, power ,
a0, temp , a1, temp . And the couple of series (ε1,t , ε2,t ) is assumed to be stationary. We estimate these two linear regressions separately using ordinary least squares (OLS). The results are reported in Table 5. All the
coefficients are significant. Indeed, because of economic and technological growth, the electricity consumption increases on average by 0.0044 MW each hour. At the same time, temperature increases on average by
1.6 × 10−6 Celsius degree per hour, which corresponds to a Global Warming of 0.014 degree per year. Even
if this is a very simple model, with a linear growth, it correspond to the right order of magnitude commonly
found.
306 | Alexis Derumigny and Jean-David Fermanian
Table 5: Statistics for the OLS estimators of (5) and (6).
Std. Error
3.933e+01
2.066e-04
2.526e-02
1.327e-07
p-value
<2e-16
<2e-16
<2e-16
1.54e-09
0.2
0.1
0.0
Conditional Kendall’s tau
−0.3
−0.2
−0.1
0.2
0.1
0.0
−0.1
−0.3
−0.2
Conditional Kendall’s tau
t-value
1265.1
106.8
469.902
6.041
0.3
Estimate
4.976e+04
2.205e-02
1.187e+01
8.014e-07
0.3
a0, power
a1, power
a0, temp
a1, temp
Jan
Feb
Mar
Apr
May
June
Jul
Aug
Sep
Oct
Nov
Dec
Jan
Day of the year
Jan
Feb
Mar
Apr
May
June
Jul
Aug
Sep
Oct
Nov
Dec
Jan
Day of the year
Figure 5: Conditional Kendall’s tau between the detrended
electricity consumption ε̂1,t and the detrended temperature
ε̂2,t , given the day of the year and estimated using h CV = 5
days.
Figure 6: Conditional Kendall’s tau between the detrended
electricity consumption ε̂1,t and the detrended temperature
ε̂2,t , given the day of the year and estimated using h* = 12
days.
Our goal is to estimate whether the dependence between electricity consumption and temperature is
varying as a function of the day of the year (month, season...). The lack of stationarity on the original series
had an influence on the conditional Kendall’s tau. Indeed, a part of positive dependence between the original
variables is due to the fact that they both increase on average over time. We consider this as a spurious effect
caused by the non-stationarity. For this reason, we have studied the (conditional) dependence between the
estimated residuals ε̂1,t and ε̂2,t .
Concerning the bandwidth h choice, we followed the insights of our simulation in Section 4. Globally,
there exist two possibilities: choosing the bandwidth according to the usual rule-of-thumb h* = 1.5 × σ̂(Z) ×
n−1/5 , or using our cross-validation criterion, which yields h CV . Note that the computation time of this crossvalidation function is of order O(n2 ), by Equation (4). With our sample size n = 329 756, this criterion becomes computationally unfeasible in a reasonable time. To cope with this difficulty, we use a Monte-Carlo
approximation
CV N, h˜ (h) :=
N
2
1 X
˜
g k (Xi l , Xj l ) − τ̂−(i l ,j l ), 1,2|Z=(Zi +Zj )/2 1 d(Zi l , Zj l ) ≤ h
l
l
N
(7)
l=1
where, for every l = 1, . . . , N, we sample independently i l uniformly in [1, n] and j l |i l uniformly on the set
˜ }. In practice, we choose d(a, b) as the number of days between the two dates a
{j ∈ [1, n] : d(Z i l , Z j ) ≤ h
and b. For instance, the distance between January 1st and December 30th is 2 days. Similarly, (Z i l + Z j l )/2
corresponds to the mean day of the year between the days Z i l and Z j l , and is computed using the package
circular [2].
The estimated conditional Kendall’s tau with the bandwidth h CV or h* are displayed in Figures 5 and 6. We
observe that conditional Kendall’s tau is negative in winter, meaning that lower temperatures are associated
On kernel-based estimation of conditional Kendall’s tau
| 307
24
with higher electricity demands. This can be explained by the energy consumption for heating purpose. On
the contrary, in summer, higher temperatures are associated with higher energy demand, because of the energy consumption induced by cooling devices. It is interesting to note that the average conditional Kendall’s
tau in winter (−0.23) is slightly smaller in absolute value than in summer (0.30).
20
0.2
0.1
15
−0.1
−0.2
10
Hour of the day
0.0
5
−0.3
−0.4
0
−0.5
Jan
Feb
Mar
Apr
May
June
Jul
Aug
Sep
Oct
Nov
Dec
Jan
Day of the year
Figure 7: Conditional Kendall’s tau between electricity consumption and temperature given the day of the year (h*,1 = 12 days)
and the time of the day (in hours, h*,2 = 1 hour).
To complete this analysis, we decided to include a second variable, which is the hour of the day. The
choice of a bivariate bandwidth is not straightforward. To simplify, we decide to use a diagonal bandwidth
given by h*,1 = 1.5 × σ̂(Z1 ) × n−1/5 = 12 days and h*,2 = 1.5 × σ̂(Z2 ) × n−1/5 = 1 hour. The results are
displayed on Figure 7. On the x-axis, we globally find the same trend: negative dependence in winter and
positive dependence in summer, which is coherent. Moreover, in winter, the conditional Kendall’s tau is more
important (around −0.5) during nights (20:00-6:00) than in the daytime. This may be explained by the fact
that heating in households has a more important contribution to the total consumption than during daytime,
when many people live outside their homes.
Note that, during summers, the levels of Kendall’s tau given date and daytime are most often smaller
than Kendall’s tau given date only. This may appear as counterintuitive. But, as noticed in [9], the average of
the former quantity (over daytimes) is not equal to the latter quantity in general. In our particular case, we
can argue that, during summers, the levels of dependence between temperature and energy consumption is
rather weak once we control for daytime. This is the same phenomenon with usual factor models, where two
variables may be independent given a third one, but they may be strongly dependent (unconditionnally).
Acknowledgments
This work is supported by the Labex Ecodec under the grant ANR-11-LABEX-0047 from the French Agence
Nationale de la Recherche.
308 | Alexis Derumigny and Jean-David Fermanian
A Proofs
For convenience, we recall Berk’s (1970) inequality (see Theorem A in Serfling [37, p.201]). Note that, if m = 1,
this reduces to Bernstein’s inequality.
Lemma 11. Let m, n > 0, X1 , . . . , Xn i.i.d. random vectors with values in a measurable space X and g : Xm →
[a, b] be a symmetric real bounded function. Set θ := E[g(X1 , . . . , Xm )] and σ2 := Var[g(X1 , . . . , Xm )]. Then,
for any t > 0 and n ≥ m,
!−1
X
n
[n/m]t2
IP
g(Xi1 , . . . , Xi m ) − θ ≥ t ≤ exp −
,
m
2σ2 + (2/3)(b − θ)t
c
where
P
c
denotes summation over all subgroups of m distinct integers (i1 , . . . , i m ) of {1, . . . n}.
A.1 Notations
Let us define a few notations that will be used throughout the proofs. For every 1 ≤ i, j ≤ n and z ∈ Rp , let us
define
S i,j (z) := n−2 K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP X1 < X2 Z1 = Z2 = z ,
(8)
gz (Xi , Zi ), (Xj , Zj ) := K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP Xi < Xj Zi = Zj = z
,
(9)
− E K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP Xi < Xj Zi = Zj = z
g̃ i,j = gz (Xi , Zi ) , (Xj , Zj ) + gz (Xj , Zj ) , (Xi , Zi ) /2,
(10)
g i := E[g̃ i,j |Xi , Zi ],
(11)
ξz (Xi , Zi , Xj , Zj ) := ξ i,j := g̃ i,j − g i − g j ,
`z : (x1 , z1 , x2 , z2 ) 7→
(12)
2p
h
ξz (x1 , z1 ) , (x2 , z2 ) for a given h > 0,
4C2K
(13)
Note that ξ i,j is a degenerate (symmetrical) U-statistics because E[ξ i,j |Xi , Zi ] = E[ξ i,j |Xj , Zj ] = 0, when i ≠ j.
In the proofs, we will study the difference τ̂1,2|Z=z − τ1,2|Z=z using two quantities that can be bounded
P
separately: ˆf 2 (z) and
S i,j (z).
1≤i,j≤n
Z
τ̂1,2|Z=z − τ1,2|Z=z = 4
w i,n (z)w j,n (z)1 Xi < Xj − 4 IP X1 < X2 Z1 = Z2 = z
X
1≤i,j≤n
=
X
4
K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP X1 < X2 Z1 = Z2 = z
n2 ˆf 2 (z)
Z
=
1≤i,j≤n
4
S i,j (z),
ˆf 2 (z)
Z
1≤i,j≤n
X
(14)
This sum can be decomposed in the following way
X
X
S i,j (z) =
S i,j (z) − E[S i,j (z)] + n(n − 1)E[S1,2 (z)] − ∆ n (z).
1≤i,j≤n
(15)
1≤i≠j≤n
Pn
P
2
2
where the “diagonal term” ∆ n (z) := − ni=1 S i,i (z) = IP X1 < X2 Z1 = Z2 = z
i=1 K h (Zi −z)/n . The stochastic
component above can itself be rewritten as
X
1 X
1 X
S i,j (z) − E[S i,j (z)] = 2
gz (Xi , Zi ) , (Xj , Zj ) = 2
g̃ i,j
(16)
n
n
1≤i≠j≤n
1≤i≠j≤n
1≤i≠j≤n
On kernel-based estimation of conditional Kendall’s tau
=
| 309
n
1 X
2(n − 1) X
ξ
+
gi .
i,j
n2
n2
1≤i≠j≤n
(17)
i=1
A.2 Proof of Proposition 1
Since there are no ties a.s.,
1 + τ̂(1)
=4
1,2|Z=z
n X
n
X
w i,n (z)w j,n (z) 1 X i,1 < X j,1 − 1 X i,1 < X j,1 , X i,2 > X j,2
i=1 j=1
=4
n X
n
X
w i,n (z)w j,n (z)1 X i,1 < X j,1 + τ̂(3)
− 1.
1,2|Z=z
i=1 j=1
But
1=
n X
n
X
w i,n (z)w j,n (z) =
i=1 j=1
=2
n X
n
X
w i,n (z)w j,n (z) 1 X i,1 ≤ X j,1 + 1 X i,1 > X j,1
i=1 j=1
n X
n
X
n
X
w2i,n (z),
w i,n (z)w j,n (z)1 X i,1 < X j,1 +
i=1 j=1
i=1
= 2(1 − s n ) + τ̂(3)
− 1, and then τ̂(1)
= τ̂(3)
− 2s n . Moreover,
implying 1 + τ̂(1)
1,2|Z=z
1,2|Z=z
1,2|Z=z
1,2|Z=z
τ̂(2)
=
1,2|Z=z
n X
n
X
w i,n (z)w j,n (z) 1 X i,1 > X j,1 , X i,2 > X j,2 + 1 X i,1 < X j,1 , X i,2 < X j,2
i=1 j=1
− 1 X i,1 > X j,1 , X i,2 < X j,2 − 1 X i,1 < X j,1 , X i,2 > X j,2
=2
n X
n
X
w i,n (z)w j,n (z) 1 X i,1 > X j,1 , X i,2 > X j,2 − 1 X i,1 > X j,1 , X i,2 < X j,2
i=1 j=1
=
(1)
(3)
1 (3)
τ̂1,2|Z=z + τ̂1,2|Z=z
1 (1)
τ̂1,2|Z=z + 1 +
τ̂1,2|Z=z − 1 =
= τ̂(1)
+ s n = τ̂(3)
− sn .
1,2|Z=z
1,2|Z=z
2
2
2
A.3 Proof of Proposition 2
Lemma 12. Under Assumptions 3.1, 3.2 and 3.3, we have for any t > 0,
C hα
nh p t2
R
.
IP ˆfZ (z) − fZ (z) ≥ K,α + t ≤ 2 exp −
α!
2fZ,max K 2 + (2/3)C K t
This Lemma is proved below. If, for some ϵ > 0, we have C K,α h α /α! + t ≤ fZ,min − ϵ, then ˆf (z) ≥ ϵ > 0 with a
R
probability larger than 1 − 2 exp − nh p t2 /(2fZ,max K 2 + (2/3)C K t) . So, we should choose the largest t as
possible, which yields Proposition 2.
It remains to prove Lemma 12. Use the usual decomposition between a stochastic component and a bias:
ˆfZ (z) − fZ (z) = ˆfZ (z) − E[ˆfZ (z)] + E[ˆfZ (z)] − fZ (z) . We first bound the bias from above.
Z
ˆ
K(u) fZ z + hu − fZ (z) du.
E[fZ (z)] − fZ (z) =
Rp
310 | Alexis Derumigny and Jean-David Fermanian
Set ϕz,u (t) := fZ z + thu for t ∈ [0, 1]. This function has at least the same regularity as fZ , so it is αdifferentiable (by Assumption 3.2). By a Taylor-Lagrange expansion, we get
X
Z
α−1
1 (α)
1 (i)
ϕz,u (0) + ϕz,u
K(u) fZ z + hu − fZ (z) du =
(tz,u ) du,
K(u)
i!
α!
i=1
Rp
Rp
R
for some real number tz,u ∈ (0, 1). By Assumption 3.1(c) and for every i < α, Rp K(u)ϕ(i)
z,u (0) du = 0. Therefore,
Z
1 (α)
ˆ
E[fZ (z)] − fZ (z) =
(tz,u )du
K(u) ϕz,u
α!
p
R
Z
p
X
C
∂ α fZ
1
z + tz,u hu du ≤ K,α h α ,
K(u)
h α u i1 . . . u i α
=
α!
∂z i1 . . . ∂z i α
α!
i1 ,...,i α =1
Rp
Z
where the last inequality results from Assumption 3.2.
Second, the stochastic component may be written as
ˆfZ (z) − E[ˆfZ (z)] = n−1
n
X
n
n
h
i
X
X
K h (Zi − z) − E n−1
K h (Zi − z) = n−1
g(Zi ) − E[g(Zi )] ,
i=1
i=1
i=1
where g(Zi ) := K h (Zi − z). Apply Lemma 11 with m = 1 and the latter g(Zi ). Here, we have b = −a = h−p C K (by
R
Assumption 3.1(a)), θ = E g(Z1 ) ≥ 0 (by Assumption 3.1(d)), and Var g(Z1 ) ≤ h−p fZ,max K 2 (combining
Assumptions 3.1(b) and 3.3), so that we get
n
1X
K h (Zi − z) − E K h (Zi − z) ≥ t
n
IP
!
≤ 2 exp
i=1
−
2h−p fZ,max
R
nt2
.
K 2 + (2/3)h−p C K t
A.4 Proof of Proposition 3
We show the result for k = 1. The two other cases can be proven in the same way. Using the decomposition (14),
for any positive numbers x and λ(z), we have
X
1
1 + λ(z)
4(1 + λ(z))
> 2
S
(z)
>
x
+ IP
×
IP τ̂1,2|Z=z − τ1,2|Z=z > x ≤ IP
i,j
ˆf 2 (z)
fZ (z)
fZ2 (z)
Z
1≤i,j≤n
X
1
1
λ(z)
4(1 + λ(z))
≤ IP
− 2
> 2
+ IP
×
S
(z)
>
x
.
i,j
ˆf 2 (z) fZ (z)
fZ (z)
fZ2 (z)
1≤i,j≤n
Z
3
For any t s.t. C K,α h α /α! + t < fZ,min /2, set λ(z) = 16fz2 (z) C K,α h α /α! + t /fZ,min
. This yields
IP
τ̂1,2|Z=z − τ1,2|Z=z
1
16 C K,α h α
> x ≤ IP
−
> 3
+t
α!
ˆf 2 (z) fZ2 (z)
fZ,min
Z
X
fz2 (z)x
+ IP
S i,j (z) >
.
4(1 + λ(z))
1
1≤i,j≤n
By setting
x=
R
16fZ2 (z) C K,α h α
4 CXZ,α h α 3fz (z) K 2
0
+
+
t
1
+
+
t
,
3
α!
2nh p
α!
fz2 (z)
fZ,min
and applying the next two lemmas 13 and 14, we get the result.
On kernel-based estimation of conditional Kendall’s tau |
311
Lemma 13. Under Assumptions 3.1-3.3 and if C K,α h α /α! + t < fZ,min /2 for some t > 0,
IP
1
ˆf 2 (z)
Z
−
1
16 C K,α h α
nh p t2
R
>
+
t
≤
2
exp
−
,
3
α!
2fZ,max K 2 + (2/3)C K t
fZ2 (z)
fZ,min
and ˆfZ (z) is strictly positive on these events.
Proof : Applying the mean value inequality to the function x 7→ 1/x2 , we get the inequality 1/ˆfZ2 (z)−1/fZ2 (z) ≤
2 ˆfZ (z) − fZ (z) /fZ* 3 , where fZ* lies between ˆfZ (z) and fZ (z). Denote by E the event E := |ˆfZ (z) − fZ (z)| ≤
C K,α h α /α! + t . By Lemma 12, we obtain
IP(E) ≥ 1 − 2 exp −
2fZ,max
R
nh p t2
.
K 2 + (2/3)C K t
(18)
Therefore, on this event E, ˆfZ (z) − fZ (z) ≤ fZ,min /2. Moreover, we have fZ,min ≤ fZ (z) using Assumption 3.3
and then fZ,min /2 ≤ fZ* . Combining the previous inequalities, we finally get
1
ˆf 2 (z)
Z
−
1
16 ˆ
16 C K,α h α
f
(z)
−
f
(z)
+
t
,
≤
≤
Z
Z
3
3
α!
fZ2 (z)
fZ,min
fZ,min
on E. But since
IP
1
ˆf 2 (z)
Z
−
16 C K,α h α
1
> 3
+t
2
α!
fZ (z)
fZ,min
≤ IP(Ec ),
we deduce the result.
Lemma 14. Under Assumptions 3.1-3.4, if C K̃,2 h2 < fz (z), we have for any t > 0
IP
X
1≤i,j≤n
+
R
CXZ,α h α 3fz (z) K 2
(n − 1)h2p t2
R
+ t ≤ 2 exp − 2
+
S i,j (z) >
α!
2nh p
4fZ,max ( K 2 )2 + (8/3)C2K t
2 exp
−
nh p (fz (z) − C K̃,2 h2 )2
.
R
8fZ,max K̃ 2 + 4C K̃ (fz (z) − C K̃,2 h2 )/3
P
Proof : We will use the decomposition of 1≤i,j≤n S i,j (z) given in Equation (15) and bound separately each of
its three components with high probability.
R
We first bound the negligible diagonal term ∆ n . Note that K̃(·) := K 2 (·)/ K 2 is a two-order kernel, so that
˜fz (z) := Pn K̃ h (Zi − z)/n can be used as an estimator of fZ (z), where K̃ h (·) := h−p K̃(·/h). Therefore, applying
i=1
Lemma 12 to ˜f , we have for ε > 0 such that C K̃,2 h2 /2 + ε = fz (z)/2,
!
R
n
R K 2 C h2
K2 X
fZ (z) K 2
K̃,2
K̃ h (Zi − z) −
≥
+ε
nh p
nh p
2
n2 h p
i=1
C K̃,2 h2
˜
≤ IP fZ (z) − fZ (z) ≥
+ε
2
nh p ε2
.
≤ 2 exp −
R
2fZ,max K̃ 2 + (2/3)C K̃ ε
R
3fz (z) K 2
IP ∆ n ≥
≤ IP
2nh p
R
Second, let us deal with the bias term. Simple calculations provide, if i ≠ j,
−2
E[S i,j (z)] = n E K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP Xi < Xj Zi = Zj = z
(19)
312 | Alexis Derumigny and Jean-David Fermanian
= n−2
Z
K h (z1 − z)K h (z2 − z) 1 x1 < x2 − IP Xi < Xj Zi = Zj = z
R2p+2
= n−2
Z
× fX,Z (x1 , z1 ) fX,Z (x2 , z2 ) dx1 dz1 dx2 dz2
K(u)K(v) 1 x1 < x2 − IP Xi < Xj Zi = Zj = z
R2p+2
× fX,Z x1 , z + hu fX,Z x2 , z + hv − fX,Z (x1 , z) fX,Z (x2 , z) dx1 du dx2 dv,
because, for every z,
Z
1 x1 < x2 − IP X1 < X2 Z1 = Z2 = z fX,Z (x1 , z)fX,Z (x2 , z) dx1 dx2 .
0=
R4
Apply the Taylor-Lagrange formula to the function ϕx1 ,x2 ,u,v (t) := fX,Z x1 , z + thu fX,Z x2 , z + thv which is
differentiable by Assumption 3.4. This yields
Z
E[S i,j (z)] = n−2 K(u)K(v) 1 x1 < x2 − IP Xi < Xj Zi = Zj = z
1
1 (k)
ϕx1 ,x2 ,u,v (0) + ϕx(α)
(t
)
dx1 du dx2 dv
x ,x ,u,v
k!
α! 1 ,x2 ,u,v 1 2
k=1
Z
(α)
K(u)K(v)
=
1
x
<
x
−
IP
X
<
X
Z
=
Z
=
z
ϕx1 ,x2 ,u,v (tx1 ,x2 ,u,v )dx1 du dx2 dv.
1
2
i
j
i
j
n2 α!
×
X
α−1
Since ϕ(α)
x1 ,x2 ,u,v (t) is equal to
!
p
α
∂ α−k f
X
X
∂ k fX,Z
α
X,Z
x1 , z + thu
x2 , z + thv ,
h α u i1 . . . u i k v i k+1 . . . v i α
k
∂z i1 . . . ∂z i k
∂z i k+1 . . . ∂z i α
k=0
i1 ,...,i α =1
using Assumption 3.4, we get
E[S1,2 (z)] ≤ CXZ,α h α /(n2 α!).
(20)
Third, the stochastic component will be bounded from above. Indeed,
X
1 X
gz (Xi , Zi ) , (Xj , Zj ) ,
(S i,j (z) − E[S i,j (z)]) = 2
n
1≤i≠j≤n
1≤i≠j≤n
with the function gz defined in (9). We can now apply Lemma 11 to the sum of the g̃ i,j , which are symmetrized
versions of gz . With this notation, θ = E g̃ i,j = 0. Moreover,
Z
h
i
2
≤ K 2h (z1 − z)K 2h (z2 − z) 1 x1 < x2 − IP Xi < Xj Zi = Zj = z
Var gz (Xi , Zi ), (Xj , Zj )
× fX,Z (x1 , z1 )fX,Z (x2 , z2 ) dx1 dx2 dz1 dz2
2
2
K (t1 )K (t2 )
fX,Z (x1 , z − ht1 )fX,Z (x2 , z − ht2 ) dx1 dx2 dt1 dt2
h2p
Z
2
2
≤ h−2p fZ,max
K2 ,
≤
Z
where in the last line we used Assumptions 3.1(b) and 3.3. The same upper bound applies for g̃ i,j (invoke
Cauchy-Schwarz inequality). Here, we choose b = −a = 2C2K h−2p . Applying Lemma 11, for every t > 0, we
obtain
X
X
2
S i,j (z) − E[S i,j (z)] ≥ t ≤ IP
IP
g̃ i,j > t
n(n − 1)
1≤i≠j≤n
1≤i<j≤n
[n/2]t2
R
≤ 2 exp − −2p 2
.
(21)
2h fZ,max ( K 2 )2 + (4/3)C2K h−2p t
The latter inequality, (19) and (20) yield the result.
On kernel-based estimation of conditional Kendall’s tau |
313
A.5 Proof of Proposition 4
We will prove the following lemma, that straightforwardly implies the result.
Lemma 15. Under the assumptions and conditions of Proposition 4, we have
R
X
CXZ,α h α 3fz (z) K 2
IP
+
S i,j (z) >
+t
α!
2nh p
1≤i,j≤n
≤
+
nh p (fz (z) − C K̃,2 h2 )2
R
8fZ,max K̃ 2 + 4C K̃ (fz (z) − C K̃,2 h2 )/3
nh p t2
R
R
R
.
2 exp
3
32 K 2 ( |K |)2 fZ,max
+ 8C K |K |fZ,max t/3
C2 exp
−
α2 nh p t
R
8fZ,max ( K 2 )
+ 2 exp
−
P
Proof : As in the proof of Lemma 14, we will use the decomposition of 1≤i,j≤n S i,j (z) given in Equation (15)
and bound separately each of its three components with high probability. We keep the same bounds for the
diagonal term ∆ n from Equation (19) and for the bias term in Equation (20). The difference from Lemma 14
will come from the treatment of the stochastic term that is detailed below.
Now, we consider the function `z defined in Equation (13). Note that k`z k∞ ≤ 1. By usual changes of variables,
we get
Z
`2z (x1 , z1 , x2 , z2 ) fX,Z (x1 , z1 )fX,Z (x2 , z2 ) dx1 dx2 dz1 dz2
R 2
R
R
2
( K 2 fz,max )2
3p K f z,max ( | K | f z,max )
≤ 3h2p
+
6h
≤ σ2 , with
2
2
2
2
(4C K )
(4C K )
σ := h p C σ , C σ :=
Z
K 2 fz,max /(2C2K ),
(22)
R
R
R
because 6h p K 2 fz,max ( |K |fz,max )2 ≤ ( K 2 fz,max )2 and because of Assumptions 3.1(b) and 3.3. With the
notations of [26], this implies D = 1, m = 1 and L is arbitrarily small. Therefore, Theorem 2 in [26] yields
α x
1 X
,
(23)
IP
`z (Xi , Zi , Xj , Zj ) > x ≤ C2 exp − 2
2n
σ
i≠j
for some universal constants C2 and α2 when x ≤ nσ3 . By setting t/2 = 4C2K x/(nh2p ) and applying Lemma 11,
this provides
X
n
1
1 X
≤ IP 2
ξ ij ≥ t/2 + IP
IP
g i ≥ t/4
n
n
1≤i≠j≤n
1≤i≠j≤n
i=1
α2 nth p
nh p t2
R
R
R
R
≤ C2 exp −
,
+ 2 exp
3
8fZ,max ( K 2 )
32 K 2 ( |K |)2 fZ,max
+ 8/3C K |K |fZ,max t
X
S i,j (z) − E[S i,j (z)] ≥ t
R
3
when t ≤ 2h p ( K 2 )3 fZ,max
/C4K . Combining this inequality, (19) and (20) with the decomposition (15) conclude
the proof.
A.6 Proof of Proposition 6
For k
τ1,2|Z=z
=
1, we follow the path of the proof of Proposition 4 (of Section A.5). Since τ̂1,2|Z=z −
P
= 4 1≤i,j≤n S i,j (z)/ˆfZ2 (z) (by Equation 14), we prove the result if we bound from above 1/ˆfZ2 (z) and
314 | Alexis Derumigny and Jean-David Fermanian
1≤i,j≤n S i,j (z) uniformly w.r.t. z ∈ Z. To be specific, for any positive constant µ
−2
then 1/ˆfZ2 (z) ≤ fz,min
(1 − µ)−2 . We deduce
P
< 1, if |ˆfZ (z)−fZ (z)| ≤ µfz,min ,
4
sup
IP sup τ̂1,2|Z=z − τ1,2|Z=z > x ≤ IP kˆfZ − fZ k∞ > µfz,min + IP 2
f
(1
− µ)2 z∈Z
z∈Z
Z,min
X
S i,j (z) > x .
1≤i,j≤n
First invoke the uniform exponential inequality, as stated in [35], Proposition 9: for every ε <
R
b K K 2 fZ,max /C K ,
C
hα
IP kˆfZ − fZ k∞ > ε + XZ,α
≤ IP kˆfZ − E[ˆfZ ]k∞ > ε ≤ L K exp − C f ,K nh p ε2 ,
(24)
α!
for n sufficiently large. Then, apply Lemma 16, by setting (x, ε) so that
R
C
α
3fz,max K 2
C
hα
4
XZ,α h
+
= µfz,min .
x= 2
+ t and ε + XZ,α
p
2
α!
2nh
α!
fz,min (1 − µ)
Lemma 16. Under the assumptions and conditions of Proposition 6, we have
!
R
X
CXZ,α h α 3fz,max K 2
α2 nth p
R
+
t
+
≤
C
D
exp
−
IP sup
S i,j (z) >
2
α!
2nh p
8fZ,max ( K 2 )
z∈Z 1≤i,j≤n
C f , K̃ nh p (fz,max − C̃XZ,2 h2 )2
A2 nh p t2 C−4
A2 nh p t
+
2
exp
−
+ L K̃ exp −
+ 2 exp − 2 2 R 2 3 K R
.
4
16C2K A1
16 A1 K fz,max ( |K |)2
Proof : We will use the same arguments as in the proofs of Lemmas 14 and 15. We still invoke the decomposiR
P
tion (15). First let us find a uniform bound for the “diagonal term” ∆ n (z) = ni=1 S i,i (z) = K 2 ˜fz (z)/(nh p ). As
R
in (24), for every ε < b K̃ K̃ 2 fZ,max /C K̃ ,
C̃
h2
IP k˜fZ − fZ k∞ > ε + XZ,2
≤ L K̃ exp − C f , K̃ nh p ε2 ,
2
for n sufficiently large. This implies
R 2 n
R
R 2
!
K X
fZ (z) K 2
K
C̃XZ,2 h2
≥
ε+
≤ L K̃ exp − C f , K̃ nh p ε2 .
IP sup 2 p
K̃ h (Zi − z) −
p
p
nh
nh
2
n
h
z∈Z
i=1
Choose ε s.t. C̃XZ,2 h2 /2 + ε = fz,max /2 so that we have the bound
Z
IP sup |∆ n (z)| ≥ 3fz,max K 2 /(2nh p ) ≤ L K̃ exp − C f , K̃ nh p ε2 .
z∈Z
(25)
Second, it is easy to see that the bias term is uniformly bounded by
sup E[S1,2 (z)] ≤ CXZ,α h α /(n2 α!).
z∈Z
(26)
Third, we bound the two components of the stochastic
termogiven by (17). Now apply Theorem 1 in [26],
n
by recalling (13) and considering the family F := `z , z ∈ Z , for a fixed bandwidth h. The constant σ
has the same value as in (22). It is easy to check that the latter class of functions is L2 dense (see [26]). Set
ε ∈ (0, 1). Since K is λ K -Lipschitz by Assumption 3.5, every function `z ∈ F can be approximated in L2 by
R
a function `zj ∈ F, for some j ∈ {1, . . . , m} s.t. |`z − `zi |2 dν ≤ ε2 , for any probability measure ν. Indeed,
R
|`z − `zi |2 dν ≤ 64λ2K kz − zj k2∞ C2K h−2 that is less than ε2 , if we cover Z by a grid of m points (zj ) in Z s.t.
Qp
kz − zj k∞ ≤ εh/(8C K λ K ) := εδ. This can be done with m ≤ ε−p d k=1 (b k − a k )/δ e = ε−p dVδ−p e points. Then,
with the notations of [26], L = p and D = V(8C K λ K /h)p . As above, this yields
!
α nh p t Z
1 X
IP sup 2
ξZ (Xi , Zi , Xj , Zj ) > t ≤ C2 D exp − 2
K2 ,
(27)
8fZ,max
n
z∈Z
1≤i≠j≤n
On kernel-based estimation of conditional Kendall’s tau |
315
R
3
when t ≤ 2h p ( K 2 )3 fZ,max
/C4K .
It remains to bound IP(supz∈Z |n−1
Pn
i=1
g i | > t/4). Consider the family of functions
F := {(x1 , z1 ) ∈ R × Z 7→
hp
E[gz (x1 , z1 , X, Z)], z ∈ Z}.
4C2K
2
R
R
3
This family of functions is bounded by one and its variance is less than σ2 := h p K 2 fz,max
|K | . Therefore, using Assumption 3.5, we can apply Propositions 9 and 10 in [12] that are coming from [11]: for some
universal constants A1 and A2 , some constant A g that depends on K and fz,max (see Proposition 1 in [11]) and
for every x > 0,
!
n
hp X
A2 x2
1/2
IP sup 2
≤ 2 exp −
+ 2e−A2 x ,
E gz (Xi , Zi , X, Z) Xi , Zi > A1 x + A g n σ ln(1/σ)
nσ2
z∈Z 4C K i=1
that can be rewritten as
n
Ag σ
1 X
g i > 4A1 C2K x − 1/2 p ln(σ)
IP sup
n
n h
z∈Z
!
≤ 2 exp
−
i=1
A2 nh2p x2
σ2
+ 2 exp(−A2 nh p x).
For any positive t s.t. 4A1 C2K (n−1)A g σ ln(1/σ) < n3/2 h p t/8, note that we can find a real x > th p /(16C2K A1 ).
Then, we have
!
n
A2 nh p t2 C−4
t
(n − 1) X
A2 nh p t
KR
R
>
g
.
(28)
IP sup
≤
2
exp
−
+
2
exp
−
i
3
4
n2
16C2K A1
162 A21 K 2 fz,max
( |K |)2
z∈Z
i=1
The proof is completed by combining all the inequalities (25), (26), (27) and (28) with the decompositions (15) and (17).
A.7 Proof of Proposition 7
Note that τ1,2|Z=z = E g k (X1 , X2 ) Z1 = z, Z2 = z for every k = 1, 2, 3, and that our estimators with the
weights (2) can be written as τ̂(k)
:= U n (g k ) / {U n (1) + ϵ n }, where
1,2|Z=z
U n (g) :=
X
X
K h (z − Zi )K h (z − Zj )
1
1
=:
g(Xi , Xj )
g i,j ,
n(n − 1)
E[K h (z − Z)]2
n(n − 1)
1≤i≠j≤n
1≤i≠j≤n
Pn
2
for any measurable bounded function g, with the residual diagonal term ϵ n :=
i=1 K h (z − Zi )/ { n(n −
2
p −1
1)E[K h (z − Z)] }. By Bochner’s lemma (see Bosq and Lecoutre [5]), ϵ n is O P ((nh ) ), and it will be negligible compared to U n (1). Since the reasoning will be exactly the same for every estimator τ(k)
, i.e. for every
1,2|z
function g k , k = 1, 2, 3, we omit the sub-index k. Then, the functions g k will be simply denoted by g.
The expectation of our U-statistics is
E U n (g) := E g(X1 , X2 )K h (z − Z1 )K h (z − Z2 ) /E[K h (z − Z)]2
Z
=
g(x1 , x2 )K(t1 )K(t2 )fX,Z (x1 , z + ht1 )fX,Z (x2 , z + ht2 )dx1 dx2 dt1 dt2 /E[K h (z − Z)]2
Z
1
→
g(x1 , x2 )fX,Z (x1 , z)fX,Z (x2 , z)dx1 dx2 = E g(X1 , X2 ) Z1 = z, Z2 = z ,
fZ2 (z)
R
applying Bochner’s lemma to z 7→ g(x1 , x2 )fX|Z=z (x1 )fX|Z=z (x2 ) dx1 dx2 = τ1,2|Z=z , that is a continuous
function by assumption.
316 | Alexis Derumigny and Jean-David Fermanian
Set θ n := E[U n (g)], g * (x1 , x2 ) := (g(x1 , x2 ) + g(x2 , x1 ))/2 and g *i,j = (g i,j + g j,i )/2 for every (i, j),
i ≠ j. Note that U n (g) = U n (g * ). Since g * is symmetrical, the HÃąjek projection Û n (g * ) of U n (g * ) satisfies
P
*
Û n (g * ) := 2 nj=1 E[g0,j
|Xj , Zj ]/n − θ n . Note that E[Û n (g * )] = θ n = τ1,2|Z=z + o P (1). Since Var(Û n (g * ) =
*
4Var(E[g0,j
|Xj , Zj ])/n = O((nh p )−1 ), then Û n (g * ) = θ n + o P (1) = τ1,2|Z=z + o P (1).
Moreover, using the notation g i,j := g*i,j − E[g *i,j |Xj , Zj ] − E[g *i,j |Xi , Zi ] + θ n for 1 ≤ i ≠ j ≤ n, we have
P
U n (g* ) − Û n (g * ) = 1≤i≠j≤n g i,j /n(n − 1). By usual U-statistics calculations, it can be easily checked that
Var U n (g * ) − Û n (g * )
=
1
n2 (n − 1)2
X
X
E[g i1 ,j1 g i2 ,j2 ] = O
1≤i1 ≠j1 ≤n 1≤i2 ≠j2 ≤n
1
.
n2 h2p
Indeed, when all indices (i1 , i2 , j1 , j2 ) are different, or when there is a single identity among them,
E[g i1 ,j1 g i2 ,j2 ] is zero. The first nonzero terms arise when there are two identities among the indices, i.e. i1 = i2
and j1 = j2 (or i1 = j2 and j1 = i2 ). In the latter case, we get an upper bound as O((nh p )−2 ) when fZ is continuous at z, by usual changes of variable techniques and Bochner’s Lemma. Then, U n (g* ) = Û n (g * ) + o P (1) =
τ1,2|Z=z + o P (1). Note that U n (1) + ϵ n tends to one in probability (Bochner’s lemma). As a consequence,
τ̂1,2|Z=z = U n (g* ) / (U n (1) + ϵ n ) tends to τ1,2|Z=z /1 by the continuous mapping theorem.
A.8 Proof of Proposition 8
Let us note that
τ1,2|Z=z = E g k (X1 , X2 ) Z1 = z, Z2 = z =
Z
g k (x1 , x2 )fX|Z=z (x1 )fX|Z=z (x2 )dx1 dx2 =
ϕ k (z)
,
fZ2 (z)
R
ˆ k (z)/ˆf 2 (z), where ϕ
ˆ k (z) :=
= ϕ
where ϕ k (z) := g k (x1 , x2 )fX,Z (x1 , z)fX,Z (x2 , z)dx1 dx2 . Also write τ̂(k)
Z
1,2|Z=z
P
P
n−2 ni,j=1 K h (Zi − z)K h (Zj − z)g k (Xi , Xj ) and ˆfZ (z) := n−1 ni=1 K h (Zi − z). Therefore, we have
τ̂(k)
− τ1,2|Z=z =
1,2|Z=z
ˆ k (z) − ϕ k (z)
ˆf (z) − fZ (z)
ϕ
− τ1,2|Z=z Z
× ˆfZ (z) + fZ (z) .
ˆf 2 (z)
ˆf 2 (z)
Z
Z
By usual uniform consistency results (see for example Bosq and Lecoutre [5]), supz∈Z ˆfZ (z) − fZ (z) → 0
almost surely, as n → ∞. We deduce that
2
min ˆfZ2 (z) ≥ fZ,min
/2, and max |ˆfZ (z) + fZ (z)| ≤ 2 max fZ (z) a.s.
z∈Z
z∈Z
z∈Z
ˆ k on Z, to obtain that sup
This means it is sufficient to prove the uniform strong consistency of ϕ
τ̂(k)
−
z∈Z 1,2|Z=z
tends to zero a.s.
τ(k)
1,2|Z=z
ˆ k (z)] − ϕ k (z) → 0. Then, it remains to show that
Note that, by Bochner’s Lemma, supz∈Z E[ϕ
ˆ
ˆ
supz∈Z ϕ k (z) − E[ϕ k (z)] → 0 almost surely. Let ρ n > 0 be such that we cover Z by the union of l n open
balls B(tl , ρ n ), where t1 , . . . , tl n ∈ Rp and l n ∈ N* . Then
ˆ k (z) − E[ϕ
ˆ k (z)] ≤ sup
sup ϕ
z∈Z
ˆ k (tl ) − E[ϕ
ˆ k (tl )] + A n ,
ϕ
l=1,...l n
ˆ k (z) − ϕ
ˆ k (tl ) − (E[ϕ
ˆ k (z)] − E[ϕ
ˆ k (tl )]) . For any index l ∈ {1, . . . , l n } and
where A n := supl=1,...l n supz∈B(tl ,ρ n ) ϕ
any z ∈ B(tl , ρ n ), a first-order expansion yields
ˆ k (z) − ϕ
ˆ k (tl ) − (E[ϕ
ˆ k (z)] − E[ϕ
ˆ k (tl )])
ϕ
X
1
g k (Xi , Xj )K h (z − Zi )K h (z − Zj )
=
n(n − 1)
1≤i≠j≤n
On kernel-based estimation of conditional Kendall’s tau |
−
317
X
1
g k (Xi , Xj )K h (tl − Zi )K h (tl − Zj )
n(n − 1)
1≤i≠j≤n
− E g k (X1 , X2 )K h (z − Z1 )K h (z − Z2 ) − E g k (Xi , Xj )K h (tl − Zi )K h (tl − Zj )
X
C Lip,K
1
|g k (Xi , Xj )|
|z − tl | E |g k (X1 , X2 )| +
2p+1
h
n(n − 1)
1≤i≠j≤n
ρn
= O 2p+1 = o(1),
h
≤
for some constant C Lip,K and by choosing ρ n = o(h2p+1
). Actually, we can cover Z in such a way that l n =
n
−p(2p+1)
O(h n
). This is always possible because Z is a bounded set in Rp . The previous upper bound is uniform
w.r.t. l and z ∈ B(tl , ρ n ), proving A n = o(1) everywhere.
Now, for every l ≤ l n , apply Equation (21) for every z = tl . For any t > 0, this yields
h
C nh2p t2
X (l)
i
1
,
g (Xi , Zi ), (Xj , Zj ) − E g (l) (X1 , Z1 ), (X2 , Z2 )
IP
> t ≤ exp − 0 n
C1 + C2 t
n(n − 1)
i≠j
for some positive constants C0 , C1 , C2 , by setting
g (l) (Xi , Zi ), (Xj , Zj ) := g k (Xi , Xj )K h (tl − Zi )K h (tl − Zj ).
Therefore, we deduce
IP
ˆ k (tl ) − E[ϕ
ˆ k (tl )] ≥ t
ϕ
sup
l=1,...l n
!
C nh2p t2
≤ C4 h−p(2p+1)
exp − 0 n
,
n
C1 + C2 t
ˆ k (z) − E[ϕ
ˆ k (z)] tends to zero a.s.,
for some constant C4 . Finally, applying Borel-Cantelli lemma, supz∈Z ϕ
proving the result.
A.9 Proof of Proposition 9
By Markov’s inequality,
Pn
i=1
w2i,n (z) = O P ((nh p )−1 ) for any z, that tends to zero. Then, by Slutsky’s theorem,
, k = 1, 2, 3, and of their linearly
we get an asymptotic equivalence between the limiting laws of any τ̂(k)
1,2|z
transformed versions τ̃1,2|z . Thus, we will prove the asymptotic normality of τ̂(k)
for some index k = 1, 2, 3,
1,2|z
simply denoted by τ̂1,2|z .
Let g * (x1 , x2 ) := (g k (x1 , x2 ) + g k (x2 , x1 ))/2 for some index k = 1, 2, 3 (that will be implicit in the proof).
We now study the joint behavior of (τ̂1,2|Z=z0i − τ1,2|Z=z0i )i=1,...,n0 . We will extend Stute [38]’s approach, in the
case of multivariate conditioning variable z and studying the joint distribution of U-statistics at several conditioning points. As in the proof of Proposition 7, the estimator with the weights given by (2) can be rewritten
as τ̂1,2|Z=z0i := U n,i (g * ) / (U n,i (1) + ϵ n,i ), where
U n,i (g) :=
1
n(n − 1)E[K h (z0i − Z)]2
n
X
g(Xj1 , Xj2 )K h (z0i − Zj1 )K h (z0i − Zj2 ),
j1 ,j2 =1,j1 ≠j2
for any bounded measurable function g : R4 → R.
Now, we prove the joint asymptotic normality of U n,i (g) i=1,...,n0 . The HÃąjek projection Û n,i (g) of U n,i (g)
P
satisfies Û n,i (g) := 2 nj=1 g n,i Xj , Zj /n − θ n , where θ n := E U n,i (g) (see [37, Section 5.3.1]) and
g n,i (x, z) := K h (z0i − z)E g(X, x)K h (z0i − Z) / E[K h (z0i − Z)]2 .
318 | Alexis Derumigny and Jean-David Fermanian
Lemma 17. Under the assumptions of Proposition 9, for any measurable bounded function g,
D
−→ N(0, M∞ (g)), as n → ∞,
(nh p )1/2 Û n,i (g) − E U n,i (g)
i=1,...,n0
where, for 1 ≤ i, j ≤ n0 ,
[M∞ (g)]i,j :=
4
R
K 2 1{z0i =z0j } Z
fZ (z0i )
g x1 , x)g x2 , x)fX|Z=z0i (x)fX|Z=z0i (x1 )fX|Z=z0i (x2 )dx dx1 dx2 .
This lemma is proved in A.10. Similarly as in the proof of Lemma 2.2 in Stute [38], for every i = 1, . . . , n0 and
every bounded symmetrical measurable function g, we have (nh p )1/2 Var Û n,i (g) − U n,i (g) = o(1), which
implies
D
−→ N(0, M∞ (g)), as n → ∞.
(nh p )1/2 U n,i (g) − E U n,i (g)
i=1,...,n0
Considering two measurable bounded functions g1 and g2 , we have U n,i (c1 g1 + c2 g2 ) = c1 U n,i (g1 ) +
c2 U n,i (g2 ) for every numbers c1 , c2 . By the CramÃľr-Wold device, we check that
(nh p )1/2 U n,i (g1 ) − E U n,i (g1 )
, U n,i (g2 ) − E U n,i (g2 )
i=1,...,n0
i=1,...,n0
"
#!
M∞ (g1 )
M∞ (g1 , g2 )
D
−→ N 0,
,
M∞ (g1 , g2 )
M∞ (g2 )
as n → ∞, where
[M∞ (g1 , g2 )]i,j :=
4
R
K 2 1{z0i =z0j } Z
fZ (z0i )
g1 x1 , x)g2 x2 , x)fX|Z=z0i (x)fX|Z=z0i (x1 )fX|Z=z0i (x2 )dx dx1 dx2 .
Set τ̃1,2|Z=z0i := U n,i (g * ) / U n,i (1). Note that supi=1,...,n0 |ϵ n,i | = O P (n−1 h−p ). Since (nh pn )1/2 τ̂1,2|Z=z0i −
τ̃1,2|Z=z0i = O P (nh pn )1/2 ϵ n,i is o P (1) by Assumption 3.6(i), it is sufficient to establish the asymptotic law
of (nh pn )1/2 τ̃1,2|Z=z0i − τ1,2|Z=z0i . By a limited expansion of fX,Z w.r.t. its second argument, and under As
sumption 3.4, we easily check that E U n,i (g * ) = τ1,2|Z=z0i + r n,i , where |r n,i | ≤ C0 h αn /fZ2 (z0i ), for some constant
C0 that is independent of i. Since E[U n,i (1)] = 1 + o((nh p )−1/2 ) and E[U n,i (g * )] = τ1,2|Z=z0i + o((nh pn )−1/2 ) by
Assumption 3.6(i), we get
(nh p )1/2 U n,i (g * ) − τ1,2|Z=z0i
, U n,i (1) − 1
i=1,...,n0
i=1,...,n0
"
#!
M∞ (g * )
M∞ (g * , 1)
D
−→ N 0,
, as n → ∞.
M∞ (g * , 1)
M∞ (1)
Now apply the Delta-method with the function ρ(x, y) := x/y where x and y are real-valued vectors of size n0
and the division has to be understood component-wise. The Jacobian of ρ is given by the n0 × 2n0 matrix
h
i
−1
−2
−2
J ρ (x, y) = Diag y−1
,
1 , . . . y n0 , Diag − x 1 y 1 , · · · − x n0 y n0
where, for any vector v of size n0 ,Diag(v) is the diagonal
matrix whose diagonal elements are the v i , with
D
0
p 1/2
i = 1, . . . , n . We deduce (nh )
τ̃1,2|Z=z0i − τ1,2|Z=z0i
−→ N(0, H), as n → ∞, setting
i=1,...,n0
"
H := J ρ (~τ , e)
M∞ (g* )
M∞ (g * , 1)
#
M∞ (g * , 1)
J ρ (~τ , e)T ,
M∞ (1)
On kernel-based estimation of conditional Kendall’s tau |
319
where ~τ = τ1,2|Z=z0i
and e is the vector of size n0 whose all components are equal to 1. Thus, we have
i=1,...,n
h
i 0
J ρ (~τ , e) = Id n0 , −Diag(~τ) , denoting by Id n0 the identity matrix of size n0 and by Diag(~τ) the diagonal matrix
of size n0 whose diagonal elements are the τ1,2|z0i , for i = 1, . . . , n0 . To be specific, we get
H = M∞ (g * ) − Diag(~τ)M∞ (g * , 1) − M∞ (g * , 1)Diag(~τ) + Diag(~τ)M∞ (1)Diag(~τ).
For i, j in {1, . . . , n0 } and using the symmetry of the function g* , we obtain
Z
[M∞ (g * )]i,j = 4 K 2 1{z0i =z0j } E[g* (X1 , X)g * (X2 , X)|Z = Z1 = Z2 = z0i ]/fZ (z0i ),
Z
[Diag(~τ)M∞ (g * , 1)]i,j = 4τ1,2|Z=z0i
K 2 1{z0i =z0j } E[g * (X1 , X)|Z = Z1 = z0i ]/fZ (z0i )
Z
= 4 K 2 1{z0i =z0j } τ21,2|Z=z0 /fZ (z0i ) = [M∞ (g * , 1)Diag(~τ)]i,j = [Diag(~τ)M∞ (1)Diag(~τ)]i,j .
i
As a consequence, we obtain
R
4 K 2 1{z0i =z0j }
2
0
*
*
[H]i,j =
]
−
τ
E[g
(X
,
X)g
(X
,
X)
|
Z
=
Z
=
Z
=
z
0 .
1
2
1
2
i
1,2|Z=z
i
fZ (z0i )
A.10 Proof of Lemma 17
Let us first evaluate the variance-covariance matrix M n,n0
E g n,i (Xj , Zj ) = E Û n,i = E U n,i (g) , and that
(nh p )1/2 Û n,i − E[U n,i (g)]
i=1,...,n0
=
:=
[Cov(Û n,i , Û n,j )]1≤i,j≤n0 . Note that
n
2h p/2 X
g n,i (Xj , Zj ) − E[U n,i (g)] i=1,...,n0 ,
n1/2
j=1
that is a sum of independent vectors. Thus, Cov(Û n,i , Û n,j ) = 4n−1 Cov g n,i X, Z , g n,j X, Z , for every i, j
in {1, . . . , n0 }, and
E g n,i (X, Z)g n,j (X, Z)
Z
E g(X, x)K h (z0i − Z) E g(X, x)K h (z0j − Z)
0
0
=
K h (zi − z)K h (zj − z)
fX,Z (x, z)dx dz
E[K h (z0i − Z)]2 E[K h (z0j − Z)]2
Z
1
g x1 , x)g x2 , x)K h (z0i − z)K h (z0j − z)K h (z0i − w1 )K h (z0j − w2 )
∼
h p fZ2 (z0i )fZ2 (z0j )
×
fX,Z (x, z)fX,Z (x1 , w1 )fX,Z (x2 , w2 )dx dz dx1 dw1 dx2 dw2
Z
z0j − z0i
1
g
x
,
x)g
x
,
x)K(u
)K(u
)K(u)K(
+ u)fX,Z (x, z0i − hu)
1
2
1
2
2
0
2
0
h
h p fZ (zi )fZ (zj )
∼
fX,Z (x1 , z0i − hu1 )fX,Z (x2 , z0j − hu2 )dx du dx1 du1 dx2 du2 .
×
When i ≠ j and for n sufficiently large, the latter term is zero because K is compactly supported (Assumption 3.6(ii)). In this case, we have Cov(Û n,i , Û n,j ) = −4n−1 E[U n,i ]E[U n,j ] ∼ −4n−1 τ1,2|Z=z0i τ1,2|Z=z0j =
h
i
o (nh p )−1 . Otherwise, i = j and, as E g n,i X1 , Z1 = O(1), we have
Var
2
g n,i (X, Z)
∼
1
p
h fZ4 (z0i )
Z
g x1 , x)g x2 , x)K(u1 )K(u2 )K 2 (u)fX,Z (x, z0i − hu)
× fX,Z (x1 , z0i − hu1 )fX,Z (x2 , z0i − hu2 ) dx du dx1 du1 dx2 du2
320 | Alexis Derumigny and Jean-David Fermanian
K2
∼ p
h fZ (z0i )
R
Z
g x1 , x)g x2 , x)fX|Z=z0i (x)fX|Z=z0i (x1 )fX|Z=z0i (x2 ) dx dx1 dx2 ,
by Bochner’s lemma and 3.1. We have proved that, for every i, j ∈ {1, . . . , n0 },
R
4 K 2 1{z0i =z0j } Z
p
g x1 , x)g x2 , x)fX|Z=z0i (x)fX|Z=z0i (x1 )fX|Z=z0i (x2 ) dx dx1 dx2 ,
nh [M n,n0 ]i,j →
fZ (z0i )
as n → ∞. Therefore, nh p M n,n0 tends to M∞ .
We now verify Lyapunov’s condition with third-order moments, so that the usual multivariate central
limit theorem would apply. It is then sufficient to show that
n
h
h p/2 3 X
i
3
E g n,i (Xj , Zj ) − E[U n,i (g)]
= o(1).
1/2
n
(29)
j=1
For any j = 1, . . . , n, we have
h
i
3
E g n,i (Xj , Zj ) − E[U n,i (g)]
Z
Z
3
1
g(x1 , x)K h (z0i − z1 )K h (z0i − z)fX,Z (x1 , z1 )dx1 dz1 − E U n,i (g) fX,Z (x, z)dx dz.
∼
2
0
fZ (zi )
By the change of variable z1 = z0i − ht1 and z = z0i − ht, we get
Z
Z
h
i
1
3
E g n,i (Xj , Zj ) − E[U n,i (g)]
∼ h−2p
g(x1 , x)K(t1 )K(t)fX,Z (x1 , z0i − ht1 )dx1 dt1
fZ2 (z0i )
3
− h p E U n,i (g) fX,Z (x, z0i − ht)dx dt = O(h−2p ),
because of Bochner’s lemma and Assumptions 3.1 and 3.4. Therefore, we have obtained
n
h p/2 3 X
h
i
3
E
g
(X
,
Z
)
−
E[U
(g)]
= O(h3p/2 n−3/2 nh−2p ) = O((nh p )−1/2 ) = o(1),
n,i
j
j
n,i
n1/2
j=1
applying Assumption 3.6(i). Therefore, we have checked Lyapunov’s condition and the result follows.
References
[1]
[2]
[3]
Acar, E. F., C. Genest, and J. Nešlehová (2012). Beyond simplified pair-copula constructions. J. Multivariate Anal. 110, 74–90.
Agostinelli, C. and U. Lund (2017). circular: Circular Statistics. R package version 0.4-93. Available on CRAN.
Asimit, A. V., R. Gerrard, Y. Hou, and L. Peng (2016). Tail dependence measure for examining financial extreme co-movements.
J. Econometrics 194(2), 330–348.
[4] Bessec, M. and J. Fouquau (2008). The non-linear link between electricity consumption and temperature in Europe: A threshold panel approach. Energy Econ. 30(5), 2705–2721.
[5] Bosq, D. and J.-P. Lecoutre (1987). Théorie de l’Estimation Fonctionnelle. Economica, Paris.
[6] Chaieb, L. L., L.-P. Rivest, and B. Abdous (2006). Estimating survival under a dependent truncation. Biometrika 93(3), 655–
669.
[7] Davies, M. (1959). The relationship between weather and electricity demand. Proceedings of the IEE - Part C: Monographs 106(9), pp. 27–37.
[8] Derumigny, A. and J.-D. Fermanian (2017). About tests of the “simplifying” assumption for conditional copulas. Depend.
Model. 5, 154–197.
[9] Derumigny, A. and J.-D. Fermanian (2019). A classification point-of-view about conditional Kendall’s tau. Comput. Statist.
Data Anal. 135, 70–94.
[10] Dony, J. and D. M. Mason (2008). Uniform in bandwidth consistency of conditional U-statistics. Bernoulli 14(4), 1108–1133.
[11] Einmahl, U. and D. M. Mason (2005). Uniform in bandwidth consistency of kernel-type function estimators. Ann.
Statist. 33(3), 1380–1403.
On kernel-based estimation of conditional Kendall’s tau |
321
[12] Fermanian, J.-D. and O. Lopez (2018). Single-index copulas. J. Multivariate Anal. 165, 27–55.
[13] Fermanian, J.-D. and M. H. Wegkamp (2012). Time-dependent copulas. J. Multivariate Anal. 110, 19–29.
[14] Filzmoser, P., H. Fritz, and K. Kalcher (2018). pcaPP: Robust PCA by Projection Pursuit. R package version 1.9-73. Available
on CRAN.
[15] Gijbels, I., N. Veraverbeke, and M. Omelka (2011). Conditional copulas, association measures and their applications. Comput. Statist. Data Anal. 55(5), 1919–1932.
[16] Giné, E. and A. Guillou (2002). Rates of strong uniform consistency for multivariate kernel density estimators. Ann. Inst.
Henri Poincaré Probab. Stat. 38(6), 907–921.
[17] Hobæk Haff, I., K. Aas, and A. Frigessi (2010). On the simplified pair-copula construction – Simply useful or too simplistic?
J. Multivariate Anal. 101(5), 1296–1310.
[18] Hollander, M. and D. A. Wolfe (1973). Nonparametric Statistical Methods. John Wiley & Sons, New York.
[19] Hsieh, J.-J. and W.-C. Huang (2015). Nonparametric estimation and test of conditional Kendall’s tau under semi-competing
risks data and truncated data. J. Appl. Stat. 42(7), 1602–1616.
[20] Joe, H. (1997). Multivariate Models and Dependence Concepts. CRC Press, Boca Raton FL.
[21] Kim, Y.-J. (2015). Estimation of conditional KendallâĂŹs tau for bivariate interval censored data. Commun. Stat. Appl. Methods 22(6), 599–604.
[22] Kruskal, W. H. (1958). Ordinal measures of association. J. Amer. Statist. Assoc. 53(284), 814–861.
[23] Lakhal, L., L.-P. Rivest, and B. Abdous (2008). Estimating survival and association in a semicompeting risks model. Biometrics 64(1), 180–188.
[24] Lehmann, E. L. (1975). Nonparametrics: Statistical Methods Based on Ranks. Holden-Day, San Francisco.
[25] Liu, A., Y. Hou, and L. Peng (2015). Interval estimation for a measure of tail dependence. Insurance Math. Econom. 64,
294–305.
[26] Major, P. (2006). An estimate on the supremum of a nice class of stochastic integrals and U-statistics. Probab. Theory
Related Fields 134(3), 489–537.
[27] Manatunga, A. K. and D. Oakes (1996). A measure of association for bivariate frailty distributions. J. Multivariate Anal. 56(1),
60–74.
[28] Martin, E. C. and R. A. Betensky (2005). Testing quasi-independence of failure and truncation times via conditional Kendall’s
tau. J. Amer. Statist. Assoc. 100(470), 484–492.
[29] Moral-Carcedo, J. and J. Pérez-García (2019). Time of day effects of temperature and daylight on short term electricity load.
Energy 174, 169–183.
[30] Nelsen, R. B. (2006). An Introduction to Copulas. Second edition. Springer, New York.
[31] Oakes, D. (1989). Bivariate survival models induced by frailties. J. Amer. Statist. Assoc. 84(406), 487–493.
[32] Pardo, A., V. Meneu, and E. Valor (2002). Temperature and seasonality influences on Spanish electricity load. Energy
Econ. 24(1), 55–70.
[33] Patton, A. (2006a). Estimation of multivariate models for time series of possibly different lengths. J. Appl. Econometrics 21(2), 147–173.
[34] Patton, A. (2006b). Modelling asymmetric exchange rate dependence. Internat. Econom. Rev. 47(2), 527–556.
[35] Rinaldo, A. and L. Wasserman (2010). Generalized density clustering. Ann. Statist. 38(5), 2678–2722.
[36] Sabeti, A., M. Wei, and R. V. Craiu (2014). Additive models for conditional copulas. Stat 3(1), 300–312.
[37] Serfling, R. J. (1980). Approximation Theorems of Mathematical Statistics. John Wiley & Sons, New York.
[38] Stute, W. (1991). Conditional U-statistics. Ann. Probab. 19(2), 812–825.
[39] Tsai, W.-Y. (1990). Testing the assumption of independence of truncation time and failure time. Biometrika 77(1), 169–177.
[40] Veraverbeke, N., M. Omelka, and I. Gijbels (2011). Estimation of a conditional copula and association measures. Scand. J.
Stat. 38(4), 766–780.
|
|
https://openalex.org/W2075512617
|
http://www.scielo.cl/pdf/iusetp/v16n2/art14.pdf, https://www.redalyc.org/pdf/197/19715603014.pdf
|
es
|
PRISIÓN PREVENTIVA, TERREMOTO Y SAQUEOS: COMENTARIO A LAS SENTENCIAS DE LA CORTE SUPREMA
|
Ius et Praxis
| 2,010
|
cc-by
| 10,641
|
Revista Ius et Praxis, Año 16, Nº 2, 2010, pp. 393 - 414
ISSN 0717 - 2877
Universidad de Talca - Facultad de Ciencias Jurídicas y Sociales
“Prisión preventiva, terremoto y saqueos:
Comentario a las sentencias de la Corte Suprema”
Humberto Alarcón Corsi
Prisión preventiva, terremoto y saqueos:
comentario a las sentencias de la Corte Suprema*
Humberto Alarcón Corsi**
I. Contexto de las sentencias comentadas
Momentos después del terremoto y maremoto del 27 de febrero de 2010,
ocurrido en la zona centro sur del país, se produjeron sucesos consistentes en
ataques masivos a establecimientos de comercio, los cuales fueron calificados
de saqueos1. Dichos hechos ocurrieron especialmente en los principales centros
urbanos de la Provincia de Concepción, capital de la Región del Bío-Bío, los
que produjeron preocupación y temor en la ciudadanía2. La autoridad de la
época3, dados los sucesos descritos, decretó de conformidad con lo dispuesto
en el artículo 40 Nº 2 de la Constitución Política de la República (en adelante
CPR), el estado excepcional de emergencia constitucional, con la finalidad de:
1) Mantener, y garantizar el orden público en las regiones más afectadas por el
terremoto y maremoto; 2) Permitir que la ayuda estatal llegase a las víctimas,
* Colaboración recibida el 20 de octubre y aprobada el 29 de octubre de 2010.
** Abogado, Universidad de Talca; Mg. Derecho Penal. Profesor de Derecho Penal, Universidad de
Talca; Defensor Local Jefe de Concepción. Correo electrónico: halarcon@utalca.cl.
Dicha expresión no existe, al menos como una categoría típica en el texto de nuestro Código Penal, ni
en nuestra legislación. Sin embargo, fue utilizada masivamente por toda la comunidad a partir del 27 de
febrero de 2010. Así puede verse en los titulares de los periódicos de aquellos días, a modo ejemplar:
véase portada de los diarios: “La Tercera” del 1 de marzo de 2010. En: http://papeldigital.info/lt/index.
html?2010030101 [visitado el: 17/10/2010] y cuerpo de reportajes del diario “El Sur” de Concepción,
de fecha 21 de marzo de 2010. En: http://www.elsur.cl/diarioelsur/20100321/16/papeldigital.html [visitado 17/10/2010]. A diferencia de lo que ocurre en las ciencias jurídicas, en otras ciencias sociales, la
conceptualización de los saqueos ha tenido un mayor desarrollo, así Green, Stuar, “Looting, Law, and
Lawlessness”, 2006, p. 7, En: http://law.bepress.com/cgi/viewcontent.cgi?article=6879&context=expr
esso [visitado el 21/09/2010], conceptualiza los saqueos, “como entrar sin autorización a una casa o
negocio el cual no posee sistemas de seguridad en virtud de la vulnerabilidad producida por un desastre
natural o desórdenes colectivos, obteniendo así el control, y removiendo o dañando la propiedad de
otros sujetos” Indica, que el origen histórico de dicho concepto se vincula con la guerra.
1
Para una cabal comprensión de la situación, puede consultarse en la Web cualquier periódico de
circulación nacional o regional.
2
3
Con fecha 28 de febrero de 2010, la ex Presidenta de la República, Sra. Michelle Bachelet, decretó
el estado de excepción constitucional de emergencia.
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
393
Humberto Alarcón Corsi
Jurisprudencia
y 3) Finalmente, entre otras, permitir la iniciación de las labores de reposición
y/o reconstrucción de los servicios básicos que habían sido dañados por el
evento natural ya referido. Días más tarde, la policía bajo la dirección del
Ministerio Público realizó operativos policiales que condujeron a la detención
de un número importante de ciudadanos (los llamados saqueadores). La gran
mayoría de ellos, o casi su totalidad, eran quienes poseían, guardaban o tenían
a cualquier título, especies muebles que provenían de dichos actos; es decir,
autores del delito de receptación, tipificado y sancionado en el artículo 456 bis
A del Código Penal (en adelante CP). Todas estas personas fueron formalizadas
por este delito, y en su minoría por el delito de robo con fuerza en las cosas
que se encuentran en lugar no habitado, tipificado y sancionado en el artículo
442 del CP. En casi la totalidad de los casos4, se decretó la prisión preventiva
de los imputados formalizados, pues los magistrados que conocieron de dichos
causas, consideraron que la libertad de estas personas constituía un “peligro
para la seguridad de la sociedad”. Sin duda, que hasta aquí no hemos dicho
nada nuevo, pues dichas acciones –las detenciones y posteriores privaciones
de libertad– podrían ser consideradas como una consecuencia esperada, y por
algunos necesaria, ante los sucesos que hemos narrado; pero sin duda, ello
sólo puede ser pacífico, en tanto y en cuanto, dicho discurso sea analizado
desde una sola mirada: “La gravedad de los hechos ocurridos en una catástrofe
natural”. Más aún, puede ser la consecuencia de la actual configuración de
ciertos agentes sociales capaces de generar visiones y/o puntos de vista en el
actual esquema social, como son los medios de comunicación. Sin embargo,
dicho análisis pasa a ser cuestionable, cuando se comienza a revisar cada caso,
conforme con la regulación legal de la prisión preventiva y con la naturaleza
misma de dicha institución.
En este sentido, el presente comentario analiza dos resoluciones de la Excelentísima Corte Suprema, referentes a delitos de receptación ocurridos horas
después del terremoto y maremoto del 27 de febrero. Se revisará la procedencia
y finalidad de la prisión preventiva en un estado de excepción constitucional,
para terminar concluyendo que la imposición de esta medida cautelar, aun en un
Según información del Sistema Informático de Apoyo a la Gestión de Defensa Penal Pública (SIGDP),
al 17 de junio de 2010, en la Región del Bío-Bío, hubo 324 personas en prisión preventiva por
hechos vinculados a los sucesos post 27 de febrero de 2010. De esta cifra, 166 personas habían sido
formalizadas por el delito de receptación; otras 14, por el delito de hurto simple; 66 por el delito de
robo con fuerza de cosas que se encuentran en un lugar habitado o destinado a la habitación, y 78
personas formalizadas y sometidas a prisión preventiva por el delito de robo con fuerza en las cosas
que se encuentran en un lugar no habitado. Esta información fue proporcionada por el encargado de
la Oficina de Información, Reclamación y Sugerencias (OIRS) de la Defensoría Regional del Bío-Bío,
Sr. Pablo Carrasco Pérez, mediante correo electrónico de fecha 22 de septiembre de 2010. Como se ve,
no existió ninguna ponderación para decretar la prisión u otra medida cautelar, en uno u otro delito,
tal como se insistirá más adelante.
4
394
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
estado excepcional de garantías, como el vigente a la época de los hechos por
los cuales se impuso, no cumplió más que con fines puramente simbólicos.
II. Consideraciones y fundamentaciones de las Sentencias de la Excelentísima
Corte Suprema, Rol Nº 2218-2010 y Rol Nº 1975-2010
a) Dada la similitud de los hechos y las fundamentaciones de las resoluciones,
se describirán en forma conjunta las sentencias que serán objeto del presente
comentario. Así, en ambos casos se trata de imputados que fueron formalizados
por delitos de receptación5, esencialmente por guardar en su domicilio una
serie de alimentos no perecibles en un caso; y en el otro una lavadora. Ambos
imputados gozaban de irreprochable conducta anterior, no teniendo ni siquiera
antecedentes policiales previos, es decir, se trataba de su primer contacto con el
sistema criminal. Las resoluciones que decretaron la prisión preventiva tuvieron
por acreditado el presupuesto material, es decir, se acreditó la existencia del
delito y la participación, pese a que en uno de los casos al menos, ni siquiera
en los hechos formalizados se indicaba a quién pertenecía el artefacto electrodoméstico que se imputada haber tenido en su poder, simplemente, se indicaba
que provenía de bodegas comerciales de la ciudad, sin saber a cuál de todas las
casas comerciales que tienen bodegas en dicho lugar pertenecía ese objeto. Se
consideró, además, que la libertad de los imputados era peligrosa para la seguridad de la sociedad. Dicho peligro habría estado dado por lo siguiente: 1) El
Ministerio Público invocó las agravantes contenidas en: a) El artículo 12 Nº 10
del Código Penal, y b) la agravante contenida en el inciso 7º del artículo 5º, de
la Ley Nº 16.2826; 2) El estado de excepción que estaba vigente en la ciudad;
3) El carácter y ocurrencia del hecho punible y su impacto en la mantención
En la causa RUC 1010006270-K, los hechos que constan en el acta de formalización son: “El día 16
de marzo de 2010, siendo la 11:20 horas de la mañana aproximadamente, el imputado M.A.M.Z tenía
en su poder al interior de su domicilio ubicado en …, comuna de Concepción, distintas especies de
propiedad del supermercado Alvi, a saber, 3 cajas de cereal Nestum, 8 paquetes de corbatas marca
Aconcagua, un paquete de espirales marca Carozzi, 8 cajas de café marca Nescafé contenedoras de
100 sobres cada una, dos caja de café marca Gold contenedoras de 100 sobres cada una y 30 cajas
de Té Club etiqueta roja. Dichas especies habían sido robadas desde el supermercado Alvi, ubicado
en Avenida Los Carrera Nº 555 de la comuna de Concepción el día 28 de febrero de 2010 producto
de los saqueos que afectaron a distintos locales de Concepción en forma posterior al terremoto de
fecha 27 de febrero de 2010; el imputado sabía o no podía menos que saber el origen ilícito de dichas
especies”.
En la causa RUC 010005682-3, los hechos son: “El día 7 de marzo de 2010, alrededor de las 00:30
horas de la madrugada, el imputado Carlos Rubén J. S., mantenía en su poder una lavadora marca
Cónsul, la cual había sido sustraída desde el interior de las bodegas de tiendas comerciales ubicadas
en el sector Palomares de la comuna de Concepción. El imputado conocía, o no podía menos que
conocer el origen ilícito de las especies”.
5
6
El artículo 5º inciso 7º, dispone: En los delitos contra las personas o la propiedad será considerado
agravante el hecho de haber sido cometido el delito en la zona afectada.
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
395
Humberto Alarcón Corsi
Jurisprudencia
del orden público, alterado ostensiblemente por los desmanes, robos y hurtos
por saqueadores.
Frente a dichas resoluciones, los defensores penales públicos de los imputados, presentaron ante la Ilustrísima Corte de Apelaciones de esa misma ciudad
la acción constitucional de amparo, fundándola, esencialmente en: 1) La falta
del presupuesto material de la medida cautelar decretada y 2) La falta de proporcionalidad de la misma medida.
b) La Ilustrísima Corte de Apelaciones de Concepción7 rechazó las acciones
constitucionales de amparo, indicando esencialmente y escuetamente, tanto en
la resolución de fecha 12 de marzo de 2010, como la del 22 del mismo mes y
año, que la resoluciones del Juzgado de Garantía de Concepción, que habían
decretado la prisión preventiva en contra de los recurridos, fueron expedidas
conforme a derecho, observado el cumplimiento de los requisitos del artículo
140 del Código Procesal Penal (en adelante CPP). Es decir, la Ilustrísima Corte
de Apelaciones no se pronunció mayormente sobre la falta de presupuesto
material, ni sobre la falta de proporcionalidad de la medida cautelar.
c) La defensa de los amparados apeló las resoluciones antes indicadas. Así,
estos hechos fueron de conocimiento de la Excelentísima Corte Suprema, la cual,
en ambos casos, confirmó lo resuelto por la Ilustrísima Corte de Apelaciones de
Concepción, sin mayor fundamentación, con la única salvedad de que, en uno
de los casos –sentencia Rol 2218-210– fue confirmada, por mayoría, con un
voto en contra, el cual estuvo por acoger la acción constitucional de amparo,
en virtud del carácter de ultima ratio de la medida cautelar.
Conviene aclarar que las resoluciones que se analizarán tratan de casos en
que: 1) El delito imputado no es de aquellos cuya gravedad amerita, en todo
caso y en abstracto, la exclusión de beneficios alternativos al cumplimiento de la
pena en forma privativa de libertad, 2) Se trata de imputados con irreprochable
conducta anterior, lo que implica que en el peor de los casos, si éstos llegasen
a ser condenados, no cumplirían sus penas en forma efectiva, 3) En uno de los
casos, al menos, se trata de hechos que aisladamente considerados, pueden ser
calificados como insignificantes o de bagatela8 y 4) Se trata de resoluciones,
Nos referimos a las resoluciones de la Ilustrísima Corte de Apelaciones de 22 de marzo de 2010, Rol
6-2010. En: http://corte.poderjudicial.cl/SITCORTEPORWEB/?opc_menu=7 [visitado el 21/09/2010];
y resolución de la Iltma. Corte de Apelaciones de Concepción, que rechazó acción constitucional de
amparo, de fecha 12 de marzo de 2010, Rol 1-2010.
7
Al respecto, Silva Sánchez, Jesús María, “Delincuencia patrimonial leve: una observación del estado
de la cuestión”, Revista de Estudios Penales y Criminológicos Nº 25, Universidad de Santiago de
Compostela, 2005, pp. 333-334, para quien: “Los delitos patrimoniales leves muestran características
específicas en el conjunto de la criminalidad. Por un lado, aisladamente considerados, muestran una
lesividad muy limitada –se consideran, en general, hechos de bagatela–, de modo que la imposición
de sanciones penales convencionales podría parecer escasamente justificada desde la perspectiva del
8
396
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
que no cumplen la exigencia de fundamentación contenida en los artículos 36
y 143 del Código Procesal Penal.
III. Respecto a la medida cautelar de prisión preventiva
1. Consideraciones generales
La doctrina procesal penal tradicional atribuye a la prisión preventiva una
misión puramente cautelar o provisional, lo que se encuentra dado esencialmente, por cuanto a través de ella se pretende el aseguramiento de la realización de los actos del procedimiento, lo que implica el juzgamiento efectivo del
acusado y la ejecución de la sentencia del presunto responsable cuando sea
el caso9, lo que podría verse frustrado, por cuanto el imputado podría darse a
la fuga, lo que imposibilitaría la realización del juicios y la imposición de la
principio de proporcionalidad. Por otro lado, sin embargo, también es cierto que afectan a un derecho
individual que resulta esencial en la autocompresión de nuestra sociedad (la propiedad privada). En
tercer lugar, expresan una forma de comportamiento típica de la sociedad de masas, esto es, conforman
a su vez un fenómeno masivo. Ello determina que den lugar a daños materiales globales muy elevados,
que incidan de modo directo en la sensación social de inseguridad y que, a la vez, contribuyan de
modo decisivo a la sobrecarga de la administración de justicia penal pese a la elevada cifra oscura
existente también en este ámbito”.
Duce Julio, Mauricio; Riego R., Cristián, Proceso Penal, Editorial Jurídica de Chile, Santiago, 2007,
p. 250, para quienes la prisión preventiva, conforme la regulación del artículo 4° del Código Procesal Penal, que establece el principio de inocencia, “podría resultar justificable que para poder llevar
adelante el proceso, y para asegurar el cumplimiento de la decisión que se tome en la sentencia,
adoptar medidas de resguardo que signifiquen formas de coerción intensas sobre el imputado”, con lo
que reconocen el carácter cautelar de la prisión preventiva como medida cautelar personal. Carocca
Pérez, Álex, Manual El Nuevo Sistema Procesal Penal, Editorial LexisNexis, Santiago, 2005, p. 156,
para quien las medidas cautelares, entre ellas la prisión preventiva, sólo tienen como finalidad la
realización de los fines de procedimiento, y por ello su temporabilidad, es decir, duran mientras éstos
subsistan. En una opinión similar, pero con una variante importante se encuentran: Horvitz Lennon,
María Inés; López Masle, Julián, Derecho Procesal Penal Chileno, Tomo I, Editorial Jurídica de Chile,
Santiago, 2002, p. 344, para quienes si bien las medidas cautelares personales, entre las cuales está la
prisión preventiva, están llamadas a “asegurar la persona del imputado en el curso del procedimiento
penal” –naturaleza cautelar propiamente tal– reconocen estos autores que existen las denominadas
“medidas de coerción procesal” que “exceden la naturaleza cautelar que supone la tutela de fines
procesales”, citando a modo de ejemplo la prisión preventiva cuando es impuesta como medida de
peligrosidad social, para tal efecto, critican duramente la causal de peligro para la seguridad de la
sociedad, como una justificación de naturaleza cautelar para imponer una privación de libertad. En el
derecho comparado, Roxin, Claus, Derecho Procesal Penal, Traducción de Córdoba, Gabriela; Pastor,
Daniel, Revisada por Mayer, Julio, Editores del Puerto, Buenos Aires, 2000, p. 257. Para quien la prisión preventiva en el proceso penal es la privación de la libertad del imputado con el fin de asegurar
el proceso de conocimiento o la ejecución de la pena. Ella sirve a tres objetivos: 1. Pretende asegurar
la presencia del imputado en el procedimiento penal (§112, II, Nºs. 1 y 2). 2. Pretende garantizar
una investigación de los hechos, en debida forma, por los órganos de la persecución penal (§ 112, II,
Nº 3). 3. Pretende asegurar la ejecución penal (§ 457).
9
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
397
Humberto Alarcón Corsi
Jurisprudencia
condena; y/o la destrucción de las pruebas de cargo, lo que imposibilitaría a la
acusación probar la culpabilidad del acusado, con lo cual también se frustraría
la imposición de la pena.
En nuestra legislación, la prisión preventiva se encuentra regulada a nivel
constitucional, en el artículo 19 Nº 7 letra e) y en el artículo 5º inciso 2º, de la
CPR, que introduce a la legislación interna los tratados internacionales sobre
derechos fundamentales. Por otro lado, el propio CP, regula dentro de su Libro
I, Título V, las medidas cautelares personales, y en el párrafo 4º la prisión preventiva, regulación que en términos generales exige que ésta sea decretada por
resolución judicial fundada (artículo 143 del CPP), en una audiencia pública,
una vez que el Ministerio Público o el querellante, en su caso, puedan acreditar,
con antecedentes fundados, la existencia del delito. Además, se les exige que
esos mismos antecedentes permitan presumir fundadamente la participación
del imputado en dicho hecho típico y antijurídico (artículo 140 letras a) y b)
del CPP). Además de dicho presupuesto, al que comúnmente se le suele llamar
material10, se exige según lo entiende la doctrina y la jurisprudencia, el llamado
presupuesto cautelar. En este sentido, no es baladí que el legislador, al momento
de comenzar la regulación de esta medida, resalte dicho presupuesto, al indicar
en el artículo 139 del CPP, que: “La prisión preventiva procederá sólo cuando
las demás medidas cautelares personales fueren estimadas por el juez como
insuficientes para asegurar las finalidades del procedimiento, la seguridad del
ofendido o de la sociedad”. Así, el artículo 140 del CPP en su letra c), distingue cuatro causales alternativas, que configuran la necesidad de cautela, y que
justifican la prisión preventiva de una persona que se presume inocente. Estas
causales son señaladas por el legislador mediante cláusulas genéricas que, a su
vez, en algunos casos añaden cláusulas específicas pensadas para casos especiales como: reiteración o habitualidad en conductas delictivas. Estas causales son:
1) Peligro para la seguridad del ofendido, 2) Peligro para el éxito de diligencias
precisas y determinadas de la investigación, 3) Peligro para la seguridad de la
sociedad, y 4) Peligro de fuga11. Así entonces, la necesidad de cautela en nuestra
10
Entre otros, Duce; Riego, Proceso, cit., nota n. 9, p. 251.
Con la dictación de la Ley Nº 20.253 de 11/03/2008, se incorpora en forma explícita al artículo
140 del CPP, como causal de justificación cautelar: “el peligro de fuga”, como una causal alternativa
del “peligro para la seguridad de la sociedad”. Como se verá más adelante, la primera causal, era
considerada por la doctrina procesal penal nacional como equivalente a la segunda, o en otros términos, los esfuerzos interpretativos consideraban que la única interpretación posible, conforme al texto
constitucional y los tratados internacionales sobre derechos fundamentales incorporados al derecho
interno, conforme el artículo 5º inciso 2º de la CPR, era considerar que la letra c) del artículo 140 del
CPP, contenía en la cláusula genérica: “peligro para la seguridad de la sociedad”, una causal de riesgo
de fuga del imputado, y con ello frustrar los fines del proceso.
11
398
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
legislación viene dada por exigencias que se agrupan, al decir de la doctrina12,
en un “(…) mosaico y variopinto de presupuestos de difícil reconducción a un
denominador común (…)”, caracterizado por el “reino de la incertidumbre y
del arbitrio judicial, que puede llegar a ser «arbitrariedad» apenas limitada por
unos presupuestos en los que predomina la apreciación subjetiva del juez que
debe tomar la decisión”.
Se debe agregar que, además de los presupuestos indicados, la prisión preventiva tiene como límites en cuanto a su procedencia, ciertos principios, los
cuales se encuentran explicitados en el CPP, y ellos son: La subsidiariedad, es
decir, esta medida sólo puede operar cuando las restantes medidas cautelares
personales son insuficientes para lograr los fines procesales y del sistema penal,
principio consagrado en los artículos 112 y 139 inciso 2º del CPP. Además de
ello, la prisión preventiva deberá respetar el principio de proporcionalidad, lo
cual implica que ella no puede ser más gravosa que la sanción probable; y/o que
los costos que implica para el sistema la libertad del imputado, son mayores que
el costo que implica su afectación de libertad. La doctrina ve la consagración
de dicho principio en los artículos 122, 124; y, 141 del CPP.
Respecto de las causales relativas a la necesidad de cautela, aquella que
mayor problema plantea en su interpretación es la cláusula genérica denominada
por nuestra legislación: “Peligro para la seguridad de la sociedad”. Dicha problemática se acrecienta, luego de las reformas que se han ido introduciendo al
CPP, a poco tiempo de su entrada en vigencia. Dentro de estas modificaciones,
se encuentra la Ley Nº 20.253 conocida como “agenda corta antidelincuencia”,
que introdujo diversas modificaciones en materias tales como: Facultades policiales, Flagrancia, Reincidencia, y muy especialmente en la regulación de la
prisión preventiva, en donde las modificaciones más sustanciales y polémicas
dicen relación con el efecto del recurso de apelación interpuesto por el Ministerio Público en determinados delitos, y la inclusión del peligro de fuga como
una causal alternativa del peligro para la seguridad de la sociedad. Lo anterior,
acrecienta las dificultades para dilucidar el contenido de la cláusula “peligro
para la seguridad de la sociedad”, pues al hacer el legislador la distinción entre ésta y el peligro de fuga, podría llevar a pensar que esta polémica cláusula
implica necesariamente ser considerada de un modo diferente a la segunda13
12
Muñoz Conde, Francisco, “Cuestiones teóricas y problemas prácticos de la prisión provisional”, en
Prisión provisional, detención preventiva y derechos fundamentales, Ediciones de la Universidad de
Castilla - La Mancha (Estudios; 41), Cuenca - España, 1997, p. 223.
13
Lama Díaz, Rossy, “Agenda Corta Antidelincuencia. Modificaciones al Código Procesal Penal”, en
Gaceta Jurídica Nº 238, 2008, p. 17, para quien “su inclusión como elemento adicional plantea dos
cuestiones, la primera de ellas es que se permite decretar la prisión preventiva por la sola existencia
de esta circunstancia; y como elemento adicional ésta deberá tener una aplicación restringida, toda
vez que nos se establecieron los elementos que lo determinan, como las demás causales; por lo tanto,
se deberá aplicar en forma subsidiaria y fundarla según las circunstancias que cada caso lo ameri-
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
399
Humberto Alarcón Corsi
Jurisprudencia
y, por ende, considerar a la primera como un mecanismo dirigido a combatir a
los imputados reincidentes, es decir, se estará utilizando la “prisión preventiva”
como un medio de control social14.
Para efectos del análisis de los casos en comento, creemos necesario hacer
una somera descripción del estado de la cuestión, en específico, en lo que comúnmente se ha exigido por presupuesto material, proporcionalidad y peligro
para la seguridad de la sociedad, que son aquellos requisitos exigidos por la ley,
doctrina y jurisprudencia, como necesarios para decretar esta medida cautelar
y que, en la especie, entendemos no han sido respetados por las razones que
se indicarán.
2. Presupuesto material15
Dichos requisitos se encuentran establecidos en el artículo 140 del CPP16. Se
ha entendido por nuestra doctrina, que para poder decretar la prisión preventiva,
en un proceso seguido en contra de una persona que se presume inocente, se
requiere que el juez necesariamente haga una ponderación de los antecedentes
que presenta el Ministerio Público o el querellante en la audiencia respectiva,
y que los mismos lleven al juzgador, mediante un juicio de probabilidad acerca de la participación del imputado y la existencia del delito, a concluir que
existe un alto grado de probabilidad de que: 1) El caso será llevado a juicio,
o no se le dará termino a través de mecanismos alternativos a él, a excepción
de un procedimiento abreviado y 2) Que en ese juicio existirá, conforme a
esos antecedentes y los que razonablemente aparezcan durante el curso de la
investigación, una gran probabilidad de dictarse una sentencia condenatoria
en contra del imputado.
te”. Sin embargo, no concordamos con dicha interpretación que da la autora, toda vez que, como
se indicará, nuestra doctrina en su mayoría siempre entendió que una interpretación racionalmente
posible de la causal de peligro para la seguridad de la sociedad, debía ser el considerar el peligro de
fuga del imputado, pues entenderlo de otro modo era incompatible con el texto constitucional. En
este contexto, creemos que el intérprete dentro de las tantas opciones que tenga debe conducir su
labor por aquella que se ajuste a la Constitución, en ese orden de cosas, puede señalarse que lo que
el legislador quiere es reforzar este peligro de fuga, que impediría el cumplimiento de los fines de
proceso y del sistema penal.
14
Al respecto, pueden consultarse: Horvitz; López, Derecho, cit. nota n. 9. Duce; Riego, Proceso, cit.
nota n. 9.
Para un análisis detallado sobre el mismo, puede consultarse Duce; Riego, Proceso, cit. nota n. 9,
pp. 251 y ss., Horvitz; López, Derecho, cit. nota n. 9, p. 400 y siguientes; y, la obra más actual, que
incluye las últimas modificaciones legales: Maturana Miquel, Cristián; Montero López, Raúl, Derecho
Procesal Penal, Tomo I, Editorial AbeledoPerrot LegalPublishing, Santiago, 2010, pp. 491 y ss.
15
16
El artículo 140 del CPP, dispone en sus letras a y b, lo siguiente: a) Que existen antecedentes que
justificaren la existencia del delito que se investigare; b) Que existen antecedentes que permitieren
presumir fundadamente que el imputado ha tenido participación en el delito como autor, cómplice
o encubridor.
400
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
3. Peligro para la seguridad de la sociedad
Si bien, no pretendemos en este comentario hacer un análisis profundo
de la causal ni desentrañar el contenido de la misma, sí podemos indicar que
nuestra doctrina procesal ha hecho importantes esfuerzos por interpretar dicha
cláusula. Al respecto, se debe tener presente que, en una materia como ésta, por
ser limitativa de derechos y por así disponerlo el artículo 5º inciso 2º del CPP, la
interpretación de la misma debe ser restrictiva, proscribiéndose la analogía.
El legislador ha entregado algunos criterios respecto de cuándo la libertad
del imputado es peligrosa para la seguridad de la sociedad. Así el artículo 140
letra c) del CPP, dispone que: (…) Para estimar si la libertad del imputado resulta
o no peligrosa para la seguridad de la sociedad, el tribunal deberá considerar
especialmente alguna de las siguientes circunstancias: La gravedad de la pena
asignada al delito; el número de delitos que se le imputare y el carácter de los
mismos; la existencia de procesos pendientes, y el hecho de haber actuado en
grupo o pandilla.
Se entenderá, especialmente, que la libertad del imputado constituye un
peligro para la seguridad de la sociedad, cuando los delitos imputados tengan
asignada pena de crimen en la ley que los consagra; cuando el imputado hubiere
sido condenado con anterioridad por delito al que la ley señale igual o mayor
pena, sea que la hubiere cumplido efectivamente o no; cuando se encontrare
sujeto a alguna medida cautelar personal, en libertad condicional o gozando
de alguno de los beneficios alternativos a la ejecución de las penas privativas
o restrictivas de libertad contemplados en la ley (…)”.
La doctrina procesal penal nacional que ha interpretado esta causal, lo ha
hecho en forma previa a la modificación de la Ley Nº 20.253. Sin embargo,
conviene traer a colación sus argumentos, pues igualmente orientarán la interpretación de un asunto que no es de fácil despacho.
Si bien Marín González17 parte por reconocer la problemática que esta
causal conlleva, indica que el legislador en el artículo140 del CPP proporciona
ciertos elementos que permiten reconducir la interpretación de dicha norma
a los fines cautelares que la doctrina señala debe cumplir esta institución, “lo
que busca el legislador al explicitar en este inciso –el tercero– los motivos que
especialmente debe tener presente el juez al considerar si la libertad del imputado es peligrosa para la seguridad de la sociedad, no es otro que poner de
manifiesto el peligro de que en definitiva el imputado no comparezca al juicio
y, en su día, a la aplicación de la eventual pena”.
17
Marín González, Juan Carlos, “Las medidas cautelares personales en el nuevo Código Procesal Penal
Chileno”, Revista de Estudios de la Justicia Nº 1, 2002. En: http://web.derecho.uchile.cl/cej/ recej/recej1/
archivos/Medidas_Cautelares_personales%20(5).pdf [visitado el 21/09/2010].
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
401
Humberto Alarcón Corsi
Jurisprudencia
Por su parte, Horvitz y López18 plantean que, si bien existen interesantes
esfuerzos en ver en la causal en comento, un símil del peligro de fuga –citan en
su obra él ya aludido artículo de Marín19– dicha argumentación no les convence,
dada la fuerza cultural que en nuestro sistema tiene esta causal cautelar. Por
ello, para estos autores, la causal no es más que un “peligro de reincidencia”,
lo que puede observarse cuando el legislador alude a consideraciones como:
la existencia de procesos pendientes, el hecho de encontrarse sujeto a alguna
medida cautelar personal, en libertad condicional o gozando de algunos de los
beneficios alternativos a la ejecución de las penas privativas o restrictivas de
libertad, la existencia de condenas anteriores cuyo cumplimiento se encontrare
pendiente, entre otros. En definitiva, en concepto de estos autores, a través de
dicha cláusula se estarán legitimando fines de prevención especial negativos,
o mecanismos de control social, cuya ilegitimidad es patente y, por lo mismo,
comprometería el incumplimiento de las obligaciones del Estado de Chile
contraídas en los documentos internacionales que han sido suscritos sobre la
materia20.
Finalmente, para Duce y Riego21, la ambigüedad que ha existido sobre lo que
implica el peligro para la seguridad de la sociedad, es algo que se traspasó de
la antigua legislación22 al CPP. Así, para estos autores, los criterios informativos
que el artículo 140 letra c) señala, no serían más que criterios destinados a ser
ponderados por el arbitrio judicial. De este modo, el peligro para la seguridad
de la sociedad incluiría, según Duce y Riego, el peligro de fuga, la reiteración
delictiva y la alarma pública o legitimidad del sistema. Lo primero y segundo,
lo deducen de las consideraciones que la ley indica en el artículo 140 del CPP,
18
Horvitz; López, Derecho, cit. nota n. 9, pp. 415- 416. Así indican que: “El peligro para la seguridad de
la sociedad es, sin lugar a dudas, la justificación más problemática para la prisión preventiva, porque
resulta evidente que, en este caso, deja de ser una medida cautelar para convertirse en un instrumento
de control social, lo que claramente pone en crisis su legitimidad”.
Horvitz; López, Derecho, cit. nota n. 9, pp. 415- 416, “El mérito de este argumento es indudable, en
cuanto pretende solucionar, por vía interpretativa, una seria inconsistencia de nuestro ordenamiento
jurídico que, entendido de otro modo, autoriza la privación de libertad sobre la base de criterios de
defensa social que nos parecen inaceptables. Sin embargo, se trata de un esfuerzo interpretativo que no
resulta convincente, porque no logra desvirtuar toda la fuerza que, en nuestra cultura jurídica, tiene la
noción de ’peligro para la seguridad de la sociedad‘, como equivalente de ’peligro de reincidencia‘.
19
El artículo 9.3 del Pacto Internacional de los Derechos Civiles y Políticos, por su parte, sólo permite
subordinar la libertad a “garantías que aseguren la comparecencia del acusado en el acto del juicio,
o en cualquier otro momento de las diligencias procesales y, en su caso, para la ejecución del fallo”.
Por su parte, la Convención Americana de Derechos Humanos, en su artículo 7.5 sólo autoriza a condicionar la libertad del imputado “a garantías que aseguren su comparecencia en el juicio”.
20
21
Duce; Riego, Proceso, cit. nota n. 9, pp. 260 y ss.
Nos referimos a la regulación que existía en el antiguo 363 del Código de Procedimiento Penal de
1906, y que sufrió modificaciones mediante las Leyes Nºs. 19.503 de 1997 y 19.661 de 2000.
22
402
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
y para el tercer supuesto de peligro para la seguridad de la sociedad, lo extraen
que una negación de la misma puede provocar una grave afectación de la legitimidad del sistema, lo que podría originar una alarma social o deteriorar la
seguridad que el mismo sistema debe brindar a la población. Ciertamente, que
estos postulados son de compleja justificación, y muy cuestionables desde el
punto de vista constitucional, en un Estado respetuoso de los derechos humanos
y de la dignidad humana, pero con una visión bastante realista del modo como
esta medida cautelar es utilizada en la práctica.
En consecuencia, y tal como lo indicábamos en un comienzo, nos encontramos ante causales bastante indeterminadas, lo que, en palabras de Muñoz
Conde23, deja abierta la puerta a lo incierto, transformando el arbitrio del
juzgador en algo arbitrario, legitimándose mediante esta cláusula verdaderos
mecanismos de control social.
Pero no debemos perder de vista que, en la práctica, más allá del marco teórico y conceptual que hemos desarrollado, la aplicación de la prisión preventiva
es utilizada político criminalmente en la lucha contra un determinado grupo de
imputados: 1) Los reincidentes, 2) Los delitos contra la propiedad, esencialmente
el robo en cualquiera de sus formas y 3) La violencia intrafamiliar, en casos
de supuesta reiteración. Esto es cuestionable, ciertamente, en tanto implica
considerar que la prisión preventiva deja de ser una medida cautelar que tenga
por objeto el cumplimiento de los fines del proceso, lo cual sería más bien una
función de la pena y, por otro lado, al asignarle a la prisión preventiva fines
preventivos especiales, se vulneraría el principio de inocencia, pues se estaría
imponiendo una pena, no obstante, no ha existido juicio alguno en contra del
imputado, infringiéndose con ello garantías constitucionales. Pero, reiteramos,
que dichos fundamentos sin ser explícitamente señalados, son reiteradamente
ocupados en el día a día, y es lo que se indica como fundamentos apócrifos de
la prisión preventiva. Ratifica dicha situación, que el año 2006 fueron sometidos
a prisión preventiva en nuestro país 14.348 imputados, tres años más tarde, esta
cifra aumentó a 19.979 personas24.
Estas críticas son actualmente objeto de análisis, haciéndose esfuerzos por
superar las inconsistencias que presentaría la fundamentación cautelar de la
prisión preventiva. En este sentido, autores como Ragués25 consideran que la
23
Cit. nota n. 12.
24
MEMORIA ANUAL DE LA DEFENSORÍA PENAL PÚBLICA DE CHILE, 2009, p. 61.
Véase en: Ragués I Valles, Ramón, “Derecho Penal Sustantivo y Derecho Penal: Hacia una visión
integrada”, Anuario de Derecho Penal, Perú, 2004, pp. 129-163, y “Prisión Provisional y Prevención
de Delitos ¿Legítima protección de bienes jurídicos o derecho penal del enemigo?”, en Cancio Melia,
Manuel; Gómez-Jara Diez, Carlos (Coords.), Derecho Penal del Enemigo. El discurso penal de la exclusión, Editorial B de F, Buenos Aires-Argentina, 2006, pp. 713 - 734.
25
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
403
Humberto Alarcón Corsi
Jurisprudencia
tradicional separación que ha existido entre el Derecho Penal y Procesal Penal,
ha provocado que distintas instituciones como la prueba, la prescripción y la
prisión preventiva sean analizadas exclusivamente desde un prisma procesal. En
ese contexto, considera que “el proceso penal no es un fin en sí mismo susceptible de legitimación, sino sólo el cauce previsto para que pueda imponerse la
pena y ésta despliegue sus efectos preventivos. En otra palabras: la frustración
en un caso concreto del fin del proceso no es algo negativo per se, sino sólo
en la medida en que dicha frustración impide que la pena pueda desplegar
sus efectos preventivos y contribuir al fin último de pacificación social que
pretende la globalidad del sistema”26. En ese contexto, postula que la prisión
preventiva evita que puedan frustrarse los fines de la pena, contribuyendo con
ello a la función pacificadora del Derecho Penal, siempre que la misma –prisión
preventiva- cumpla los presupuestos de: proporcionalidad, subsidiariedad y
probabilidad27. Así, concluye que la prisión preventiva sólo será legítima como
medio en la prevención de delitos, en aquellos casos en los que, si el imputado
permaneciera en libertad, existiría un riesgo grave y concreto de la alteración de
la paz social o de lesión o puesta en peligro grave de los bienes jurídicos más
importantes, sin que para conjurar dicho peligro, exista ningún medio menos
lesivo que la privación de libertad del imputado.
4. Proporcionalidad
Como se indicó anteriormente, este principio se encuentra contemplado
en los artículos 122, 139 inciso 2º, y en el artículo 141 del Código Procesal
Penal. La doctrina procesal penal indica que el principio de proporcionalidad,
en las medidas cautelares personales que se adopten en el curso de un proceso penal, han de estar en relación con la finalidad del procedimiento que se
persigue cautelar y con la gravedad del hecho que se investiga28. Ahora bien,
la proporcionalidad en la prisión preventiva guarda directa relación con otros
principios limitadores de esta medida, como es su instrumentalidad (idoneidad
como proporcionalidad en sentido amplio), es decir, ellas son impuestas para
que el proceso logre sus fines (artículo 122 inciso 2º). Así se indica que una
interpretación en contrario, implicaría poner los medios por sobre los fines29.
26
Ragués, “Prisión”, cit. nota n. 25, p. 716.
Ragués, “Derecho”, cit. nota n. 25, este autor plantea que: para legitimar la prisión preventiva como
un instrumento que posibilite el cumplimiento de los fines de la pena, no frustrando los mismos, o afectándolos negativamente, los antecedentes que fundamentan la existencia del hecho y la participación
del imputado, deben llevar a una alta probabilidad de que en un juicio el imputado será condenado,
a fin de evitar encarcelamientos injustificados.
27
28
Horvitz; López, Derecho, cit. nota n. 9, p. 353.
29
Duce; Riego, Proceso, cit. nota n. 9, p. 266.
404
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
Por otro lado, también se vincula a este principio con la subsidiariedad de las
medidas cautelares, es decir, sólo se justifica una privación de libertad en el
proceso, si no existen otras medidas menos gravosas que permitan cumplir con
las finalidades del proceso (necesariedad como componente de la proporcionalidad), lo que se consagra en el artículo 139 inciso 2º del CPP. Finalmente,
también se le vincula con el principio de la temporalidad de las mismas, lo que
implica que la prisión preventiva sólo durará mientras subsistan los presupuestos que la hacían procedente, tal como se indica en el artículo 152 del CPP
(proporcionalidad en sentido estricto). Determinada la idoneidad, necesidad y
ponderación de las circunstancias que concurran en la especie, podemos realizar
el juicio de proporcionalidad en sentido estricto de la prisión preventiva. Así,
ésta será proporcional cuando “el sacrificio de los intereses individuales que
comporta la injerencia, guarda una relación razonable o proporcionada con la
importancia del interés estatal que se trata de salvaguardar30”. En consecuencia,
“si el sacrificio resulta excesivo, la medida deberá considerarse inadmisible,
aunque satisfaga el resto de presupuestos y requisitos derivados del principio
de proporcionalidad”31.
IV. Consideraciones sobre las sentencias en comento
a) Tanto en la resolución de la Ilustrísima Corte de Apelaciones de Concepción, que conoció las acciones constitucionales de amparo en contra de
las resoluciones de los Juzgados de Garantía de Concepción, como las resoluciones de la Excelentísima Corte Suprema, que conocieron de las apelaciones
de las acciones de amparo, se aprecia una ausencia de fundamentación. Lo
anterior, creemos que es una deficiencia de las resoluciones que comentamos,
pues se trata de resoluciones que recaen en asuntos sobre derechos y garantías
fundamentales. Así, por lo demás, el artículo 36 del CPP establece el deber de
fundamentar toda resolución judicial, norma que se ve reafirmada por lo que
dispone el artículo 143 del mismo Código, que es aplicable en específico a la
prisión preventiva. Podría observarse que la resolución del Juzgado de Garantía
que decretó la medida cautelar, fue debidamente motivada. Sin embargo, somos de opinión que, dada la trascendencia de los mismos –se trataba de casos
ocurridos en una situación de emergencia constitucional, producida por un
desastre natural–, la exigencia para resolver y mantener la privación de libertad
por razones de interés público o como se indica: “peligro para la seguridad de
la sociedad”, debe ser suficientemente fundada, lo que no ocurrió en la especie.
González-Cuéllar Serrano, Nicolás, Proporcionalidad y Derechos Fundamentales en el Derecho
Penal, Editorial COLEX, Madrid, España, 1990, p. 225.
30
31
González-Cuéllar, Proporcionalidad, cit. nota n. 30, p. 225.
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
405
Humberto Alarcón Corsi
Jurisprudencia
Esta será la única forma de evitar la arbitrariedad y posibilitar al mismo tiempo
el control32. Así, Ragués33es de la opinión que una prisión preventiva que pudiera ser considerada legítima por su contribución directa al aseguramiento de
la paz social, exigiría mucho más que la constatación de un riesgo abstracto de
perturbación del orden, siendo necesario que dicho riesgo fuera apreciado por
el juez de forma motivada en el momento de adoptar la medida sobre la base
de antecedentes inequívocos. En la especie, podemos apreciar que los fallos
se limitan a reproducir las resoluciones recurridas mediante la cláusula “vistos
se confirma”, y en el caso de las resoluciones de Cortes de Apelaciones, éstas
se limitan a la reproducción de lo argumentado por los recurrentes y las resoluciones recurridas, para en dos breves considerandos, desechar las acciones
constitucionales. Todo lo anterior, no es nada más contrario a lo que se espera
de las actuaciones de los órganos jurisdiccionales en un Estado Democrático
de Derecho, conforme a los artículos 1º, 4º y 5º inciso 2º de la CPR34. De este
modo, las resoluciones de los Tribunales de Garantía, que privaron de libertad
a personas sin antecedentes penales y por delitos de baja penalidad, haciendo
alusión en su fundamentación a la calamidad pública producida por el terremoto, y los posteriores ataques a la propiedad privada, denominados saqueos,
sin hacer referencia a cómo la libertad del imputado afectaría el orden público,
o cómo la privación de libertad contribuiría al restablecimiento del mismo, ya
sea en razón del peligro de reiteración criminal o, simplemente, por razones
del peligro que la libertad del imputado puede generar graves reacciones de
la comunidad y, con ello, la deslegitimación del sistema criminal. Por ello, la
simple utilización o alusión de frases sacramentales, resultan insuficientes para
justificar una privación de libertad.
En sentido, es un lugar común el planteamiento de que reunidos los supuestos señalados en el artículo 140 del CPP relativos a “peligro para la seguridad
de la sociedad”, se debe casi automáticamente decretar la prisión preventiva.
Nada de ello puede ser más contrario al tenor de la ley y la Constitución, en
tanto y en cuanto es el juez quien debe ponderar dichas circunstancias, éstas y
los antecedentes del caso concreto determinarán según su razonar si la prisión
preventiva es o no aplicable. Así nuestra Excelentísima Corte Suprema, lo ha
32
González-Cuéllar, Proporcionalidad, cit. nota n. 30, pp. 141 y ss.
33
Ragués, “Prisión”, cit. nota n. 25, p. 726.
En este sentido el Tribunal Europeo de Derechos Humanos en el caso “Letelier”, sentencia del año
1991, señaló que la prisión preventiva puede estar legitimada por ciertos motivos de orden público,
pero dichos motivos deben estar suficientemente motivados, y así también, el tribunal exige, como es
obvio, que para acordar la prisión por este motivo existan datos capaces de acreditar la existencia del
tal riesgo. Citado por Ragués, “Derecho”, cit. nota n. 25, p. 157.
34
406
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
reiterado en números fallos35. Ello implica que la resolución que decrete estas
medidas debe ser fundada, y no puede simplemente repetir estas causales, pues
aquello incumple los artículos 36 y 143 del CPP. En la especie, como decíamos,
y por haberse decretado esta medida en una situación excepcional y por fundamentos cuestionables, como es la alarma social, originada por la calamidad
pública producida por el terremoto del 27 de febrero de 2010, la fundamentación
debió ser mucho más detallada, y no simplemente hacer alusiones genéricas,
pues es aquello, precisamente, lo que la doctrina denuncia como el paso de la
razonabilidad judicial a lo irrazonable36.
b) Como se indicó, las citadas resoluciones omiten fundamentar lo resuelto y,
por lo mismo, reproducen las resoluciones recurridas de amparo, lo que resulta
criticable bajo todo punto de vista. Ahora bien, si se consideran como fundamentos aquellos esgrimidos por los respectivos jueces de garantía recurridos,
nos percatamos que como es tradicional, estas resoluciones se centran básicamente en fundar la prisión preventiva, haciendo referencia casi en su totalidad
a la necesidad de cautela. Ello, como se dijo en el punto anterior, mediante la
utilización de supuestos generales y abstractos indicados en el artículo 140 del
CPP, y además en estos casos, en la situación de excepción. Esto, nos lleva a
concluir que los requisitos materiales, como existencia del ilícito y participación, como es costumbre37 no son analizados con la rigurosidad que la materia
amerita, lo cual es inconsistente con la afectación de derechos y garantías, que
la resolución que se dicta importa.
De este modo, resulta curioso como en uno de los casos en análisis, los
hechos formalizados consistirían en que el imputado tendría en su poder una
lavadora que provendría de unas bodegas comerciales del sector Palomares de
Concepción, no indicándose en la comunicación fáctica a quién, previamente,
pertenecía dicho artefacto, ni menos se invoca si la receptación provendría de
otros delitos contra la propiedad, o de otra receptación, conforme el tipo del
artículo 456 bis A del CP. Se indica simplemente que dicha especie habría sido
“sustraída”. Es decir, la propia formalización de cargos no contendría todos
los supuestos fácticos que el tipo exige. Esto tiene relevancia, pues de acuerdo
35
Sentencias de la Excelentísima Corte Suprema: 1) Aquella que acoge recursos de apelación en contra
de la resolución de la Ilustrísima Corte de Apelaciones de San Miguel, que rechazó la acción de amparo
constitucional, 13 de enero de 2009, rol 192-2009, 2) Aquella que acoge recursos de apelación en
contra de la resolución de la Ilustrísima Corte de Apelaciones de San Miguel, que rechazó la acción
de amparo constitucional, 15 de julio de 2009, rol 4823-2009 y 3) Aquella que acoge recursos de
apelación, en contra de la resolución de la Ilustrísima Corte de Apelaciones de Santiago, que rechazó
la acción de amparo constitucional, 20 de julio de 2009, rol 4922-2009.
36
Muñoz, “Cuestiones”, cit. nota n. 9.
37
Al respecto, Ragués, “Derecho”, cit. nota n. 25.
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
407
Humberto Alarcón Corsi
Jurisprudencia
con lo dispuesto en el artículo 259 del CPP, la acusación debe referirse a los
mismos hechos que los contenidos en la formalización. Ahora bien, creemos
que dicha situación, y que se refiere a la descripción de la conducta que debe
encuadrarse en el tipo del artículo 456 bis A del CP, incide en los presupuestos de las letras a y b del artículo 140 del CPP, pues el tipo penal exige que
las especies hubieren sido hurtadas, o robadas, o producto de otra receptación, ello como mínimo para establecer que la conducta típica imputada es
constitutiva del delito imputado u otro. En la especie, la formalización no
cumple las exigencias del tipo penal de receptación y, en consecuencia, no
se podría haber tenido por acreditado el presupuesto material, toda vez que ni
siquiera la imputación cumplía las exigencias del tipo por el que se formalizó
investigación.
Lo denunciado, en ningún caso puede ser considerado irrelevante, puesto
que los mismos hechos que fueron comunicados a los amparados deberán
posteriormente ser objeto de acusación, y luego sentencia, acorde lo indica el
artículo 341 del CPP. La falta de dicha congruencia, acarrea la nulidad del juicio oral y la sentencia de acuerdo con el artículo 374 letra e) del CPP. Por otro
lado, cabe tener presente que la Ilustrísima Corte de Concepción, conociendo
recursos de nulidad en causas en juicios simplificados por delitos de receptación,
entiende que: si los hechos probados se limitan a indicar que las especies han
sido sustraídas, dichos hechos no son constitutivos del delito de receptación
del artículo 456 bis A del CP38. Dicha situación, ni siquiera aparece enunciada
en ninguno de los fallos en análisis.
Aunque no compartimos del todo que la prisión preventiva pueda ser esgrimida para fines preventivos generales, la doctrina entiende que “asumiendo tal
función, puede conseguirse una importante restricción de su empleo, exigiendo
que para su aplicación no baste con la mera constatación de la concurrencia de
meras sospechas o indicios de criminalidad, sino la necesidad de que consten en
lo instruido elementos indiciarios que, por su número e importancia, permitan
afirmar con un escaso margen de error que, en el caso de hacerse valer en el acto
del juicio por la acusación, permitirán considerar probada la culpabilidad del
imputado39”. De este modo, a las resoluciones en análisis, y por las especiales
circunstancias del caso, les era exigible una mayor motivación del presupuesto
material, dado que lo que se intentaba comunicar mediante ellas, era que la
privación de libertad de los imputados era algo necesario, debido a la alarma
38
Sentencia de la Iltma. Corte de Apelaciones de Concepción, acoge recurso de nulidad en contra
de la sentencia del Tribunal de Garantía de Cañete, presentado por la defensa, 25 de mayo 2010, Rol
155-2010.
39
Ragués, “Derecho”, cit. nota n. 25, p. 159.
408
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
social originada por los saqueos en los cuales, supuestamente, ellos habían
participado, guardando las especies provenientes de los mismos. Por tal motivo, y si se estima que la prisión preventiva puede operar con fines preventivos generales (negativos o positivos), lo cual como decíamos es discutible40,
debe exigirse una motivación suficiente del presupuesto material. Entender lo
contrario, implica y provoca un uso masivo del encarcelamiento preventivo
con lo cual se vulneraría la garantía jurisdiccional de la pena. Como se dijo,
nada de esto ocurrió en la especie, ni con el presupuesto material, ni con la
necesidad cautelar de peligro para la seguridad de la sociedad. Lo anterior,
creemos que lamentablemente ocurrió con la utilización masiva que se hizo
de esta medida cautelar en los hechos vinculados al 27 de febrero. Así, más
de 300 personas fueron detenidas y encarceladas preventivamente en la Región del Bío-Bío41, todas ellas, o en su mayoría, con el único fundamento de
privarlas de su libertad por la “alarma social” que su libertad, supuestamente,
contribuía a aumentar, y con presupuestos materiales muy precarios. Sin embargo, esta práctica parece no ser sólo aplicable en tiempos de excepción,
pues según cifras de la Defensoría Penal Pública, existe un creciente número
de personas de son privadas de libertad y luego absueltas. Así, según su Memoria Anual 200942, un 22,1% de los imputados absueltos fueron privados
de libertad. Seguramente en muchos de esos casos, las resoluciones que privaron de libertad a los imputados no tuvieron un adecuado fundamento del
presupuesto material43.
c) Si bien la prisión preventiva es una medida cautelar, no podemos negarnos
a la realidad que implica que es un instrumento, a través del cual el sistema
penal cumple su función más importante, como es la aplicación y ejecución
de la pena y sus efectos44. Por ello, no podemos dejar de analizar la prisión
preventiva como un instrumento que garantiza que la pena despliegue todas
Asencio Mellado, José María, La Prisión Provisional. Tesis Doctoral de la Universidad de Alicante,
España, 1987, p. 27. En: http://rua.ua.es/dspace/handle/10045/3483 [visitado el 29/09/2010].
40
41
Cifra entregada por OIRS Defensoría Regional del Bío-Bío, cit. n. 4.
42
Cit. nota n. 24.
Un caso paradigmático para el sistema de justicia nacional, lo constituye en esta materia el llamado
“Caso del Violador de Nuñoa”, quien fuera detenido y sometido a prisión preventiva por la Ilustrísima
Corte de Apelaciones de San Miguel, pese a que el Octavo Juzgado de Garantía de Santiago decretara
su libertad, por cuanto los antecedentes del proceso no eran suficientes para acreditar su participación.
Días más tarde, el propio Ministerio Público aceptaría la revocación de la medida, puesto que la prueba
científica (ADN) ratificaba su inocencia.
43
44
Sobre la materia, como se ha indicado, ver Ragués, en los artículos ya citados: “Prisión” y “Derecho”,
cit. nota n. 25.
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
409
Humberto Alarcón Corsi
Jurisprudencia
sus consecuencias, ello no obstante, estar convencidos del carácter cautelar y
procesal de la medida.
Ahora bien, queda meridianamente claro que en los casos en comento, la
naturaleza cautelar de la prisión preventiva no fue su sustento. Por lo mismo,
podríamos buscar su fundamentación, vinculándola con los fines de la pena,
conforme a una de las opciones que hemos revisado anteriormente. Sin embargo, creemos que ninguno de los aquellos fines –de la pena– podría haber
permitido que la prisión preventiva hubiere sido aplicada. Así, creemos que
aunque cabe descartar de antemano que ella hubiere sido aplicada para fines
preventivos especiales positivos, puesto que como indica Ragués45, parece poco
probable que se pueda considerar necesario privar de libertad a un sujeto para
evitar frustrar la eficacia de la pena, por un retraso en la resocialización (por
la demora de la práctica del juicio); en el evento que ello no fuera así, como
se indicaba más arriba, se trataba de imputados sin antecedentes penales, con
actividad laboral actual al momento de los hechos y con arraigo social. En
ese contexto, la prisión preventiva no puede ser el instrumento que permita
que el sistema penal cumpla sus funciones resocializadoras, ante la falta de
agilidad en la aplicación de la pena derivada de la demora en la realización del
juicio. Tampoco podríamos señalar que la prisión preventiva, en este caso, sirve
de instrumento para evitar una probable afectación de bienes jurídicos, pues,
dadas la características de los hechos y de los amparados, no existía riesgo de
reiteración. En este sentido, la doctrina46 manifiesta que la prisión preventiva
sólo podría justificar estos fines cuando, además de existir un riesgo de reincidencia, exista un peligro de afectación para bienes jurídicos de tal entidad,
que hagan que el costo de privar a una persona de su libertad sea inferior a
la lesión o ataque de bienes de tal envergadura, como puedan ser la vida,
la integridad de la persona o su seguridad la libertad sexual, entre otros. O
en el caso de bienes jurídicos supraindividuales, cuando a través de dicha
afectación se afecte de modo indirecto tales bienes –vida, salud, libertad
sexual, seguridad y libertad individual– como son los atentados contra el
medio ambiente o la salud pública. Por el contrario, una justificación en esa
línea, es decir, que hubiera existido tal peligro de reiteración de conductas
atentatorias contra la propiedad o que fomenten tales conductas –receptación,
por ejemplo–, debe igualmente ser rechazada, por cuanto colisiona con la
necesariedad de la prisión preventiva, como componente de la proporcionalidad en sentido amplio, pues, sí existían otras medidas menos restrictivas de
derecho que posibilitaban dichos fines, y que iban desde aplicar alguna de las
45
Ragués, “Prisión”, cit. nota n. 25, p. 723.
46
Ragués, “Prisión”, cit. nota n. 25, p. 724.
410
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
que contiene el catálogo del artículo 155 del CPP, hasta la responsabilidad
de los agentes del Estado en haber decretado en tiempo oportuno el estado
de excepción constitucional, y haberlo hecho efectivo en toda su magnitud,
es decir, mediante una prevención previa, a través de la presencia en terreno
de los efectivos militares y policiales. Dicha ausencia, impide legitimar una
medida como ésta.
Finalmente, si la prisión preventiva hubiera sido en esos casos considerada
como instrumento para evitar, no sólo la frustración de la pena, sino que además
para negar toda finalidad preventiva general de la misma, dicha fundamentación
tampoco creemos que en el caso en concreto pueda legitimar su aplicación
en las situaciones de los fallos que hemos venido comentando. Así, la prisión
preventiva, en estos casos, no podía ser un instrumento para fines preventivos
generales positivos ni negativos, pues resulta imposible determinar en qué
medida dichas privaciones de libertad –que se produjeron a semanas de la
catástrofe natural del 27 de febrero– podrían haber incidido en la intimidación
de potenciales delincuentes (prevención general negativa), o en la confianza
de los ciudadanos en la fidelidad al derecho (prevención general positiva). A
mayor abundamiento, debemos considerar que, comportamientos como los enjuiciados, es decir, acopio de especies luego de una catástrofe natural, o evento
revolucionario, son conductas que a pesar de la aplicación del sistema penal –la
pena– son reiterativas en el tiempo. Así, en nuestra historia, ya en la revolución
de 1891 y en el terremoto de Valparaíso de 190647 se registraron hechos como
los ocurridos luego del 27 de febrero de este año, pese a que tanto en la guerra
civil como luego en el puerto, los autores de aquellos hechos fueron sancionados severamente, no obstante, esas sanciones y estas conductas se repiten en
el tiempo. Ello no es más que una consecuencia de factores socio-estructurales,
psicológicos y del actuar colectivo en situaciones de catástrofe, en donde las
personas actúan pensando en el “aquí”, tiempo presente, olvidando lo pasado
y lo futuro, dando rienda suelta a sus impulsos48, y en donde se “despiertan y
47
Brevemente sobre sucesos como los ocurridos en forma posterior al 27 de febrero, pueden verse
En: http://latercera.com/contenido/1453_230311_9.shtml [visitado el 17/10/2010]. Aquí se relata la
participación del Almirante Luis Gómez Carreño, como el encargado de restaurar el orden en la ciudad
de Valparaíso luego del terremoto de 1906, suceso que provocó saqueos y disturbios en la ciudad. Al
respecto, cuenta la historia que algunos autores de tales actos fueron fusilados en el lugar por orden
de la autoridad de la Armada.
Sobre el particular, ver Green, “Looting”, cit. nota n. 1. Allí se hace un análisis histórico de las
situaciones que configuran lo que se califica como saqueo, y se ejemplifica con lo sucedido luego del
huracán Katrina, donde luego de la catástrofe las personas dieron rienda suelta a su desesperación,
haciéndose fácil presa de los medios de comunicación que informaban y juzgaban lo ocurrido, calificándolos de buenos y malos saqueadores. Los primeros, aquellos que acumulaban y recogían especies
para su alimentación (generalmente de raza blanca), y los segundos, los que acopiaban y sacaban de
48
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
411
Humberto Alarcón Corsi
Jurisprudencia
posicionan necesidades a resolverse individual o colectivamente, a raíz de la
ineficiencia de las autoridades”49 En consecuencia, y dado que sucesos como los
ocurridos el 27 de febrero de 2010, son eventos que gatillan conductas en las
personas que difícilmente pueden ser reconducidas a un respeto siempre irrestricto a las normas, dados los factores que hemos indicado, podemos concluir
que la prisión preventiva, incluso para efectos preventivos generales no cumple
finalidad alguna, pues no existirá intimidación penal que pueda garantizar, que
en 25 años más, de repetirse en Chile un evento como éste –lo que es altamente
probable, dada nuestra estadística histórica en la materia–, no vuelvan a ocurrir
eventos como los que hemos comentado.
En consecuencia, en estos casos la prisión preventiva está motivada por
fines claramente simbólicos, es decir, se trató de una intervención penal no
suficientemente legítima, que no se acomoda al fin político criminal que funda
la pena y, por lo mismo, el sistema penal50. La argumentación dada por las
resoluciones objeto de comentario, es decir, que la libertad de los imputados
constituía un peligro para la sociedad, son motivos que no satisfacen un juicio
de proporcionalidad.
e) Finalmente, consideramos que en ambos casos la prisión preventiva no sólo
resultaba desproporcionada, por no ser idónea ni necesaria, sino que también por
ser desproporcionada con la sanción probable. En la especie, en ambos casos
se trata de situaciones en que los imputados cumplirán sus penas en libertad,
gozando de los beneficios de la Ley Nº 18.216 sobre formas alternativas al cumplimiento de penas privativas de libertad. Es más, en ambos casos, sus causas
han terminado con penas cuyo cumplimiento no es privativo de libertad. Así, en
uno de los casos, causa RUC 1010006270-K, la pena fue de 41 días de prisión
en su grado medio, más la pena pecuniaria de 2 unidades tributarias mensuales.
Dicha sentencia fue recurrida por la defensa del imputado, fallo que se encuentra
pendiente a esta fecha, y que será objeto de nuevo comentario.
En conclusión, las resoluciones que se comentan no cumplieron las exigencias de una adecuada fundamentación, ni legitimación de la medida de
privación de derechos que estaban decretando, exigencias que en una situación
todo (generalmente de raza afroamericana). En uno y en otro caso, este autor indica que se trata de
situaciones límite en donde las personas no actúan pensando en lo que sucederá ni en los sucedido,
sino cómo y qué me puede ayudar a subsistir, lo que puede ser alimento, o también especies que
pueda luego reducir o cambiar.
Matus Acuña, Alejandra, “Nuestro Huracán Katrina”, Diario Electrónico El Mostrador, 1 de marzo
de 2010. En: http://www.elmostrador.cl/opinion/2010/03/01/nuestro-huracan-katrina/ [visitado el
17/10/2010].
49
50
Díez Ripollés, José Luis, “El Derecho Penal Simbólico y los Efectos de la Pena”, en Crítica y Justificación
del Derecho Penal en el cambio de siglo, Ediciones Universidad Castilla - La Mancha (Estudios; 91),
Cuenca 2003, pp. 147-172.
412
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema
de excepción son aún más exigibles, toda vez que la Constitución mantiene el
control del apego a la juridicidad en manos de los órganos judiciales. Por ello,
como indicaron al poco tiempo de sucedido el terremoto y maremoto, Hernández y Couso51: “las medidas excepcionales adoptadas en ese marco siguen
sometidas al derecho, uno que en nuestros días no se entiende sin referencia a
los derechos humanos (…) y que consecuentemente sólo legitima el ejercicio
de la fuerza estricta y racionalmente necesaria para la mantención del orden,
sin espacio para alardes ejemplificadores”, como al parecer, fue lo que sucedió
en la especie.
51
Hernández, Héctor; Couso, Jaime, “Derecho y los Tiempos de Excepción”, Diario la Tercera, Ideas y
Debates, 4 de marzo de 2010, Santiago de Chile, p. 4.
Revista Ius et Praxis, Año 16, Nº 2
2010, pp. 393 - 414
413
|
|
https://openalex.org/W1975854049
|
https://europepmc.org/articles/pmc2900240?pdf=render
|
English
| null |
The relationship between mosquito abundance and rice field density in the Republic of Korea
|
International journal of health geographics
| 2,010
|
cc-by
| 6,619
|
Abstract Background: Japanese encephalitis virus (JEV), the causative agent of Japanese encephalitis (JE), is endemic to the
Republic of Korea (ROK) where unvaccinated United States (U.S.) military Service members, civilians and family
members are stationed. The primary vector of the JEV in the ROK is Culex tritaeniorhynchus. The ecological relationship
between Culex spp. and rice fields has been studied extensively; rice fields have been shown to increase the prevalence
of Cx. tritaeniorhynchus. This research was conducted to determine if the quantification of rice field land cover
surrounding U.S. military installations in the ROK should be used as a parameter in a larger risk model that predicts the
abundance of Cx. tritaeniorhynchus populations. Mosquito data from the U.S. Forces Korea (USFK) mosquito surveillance program were used in this project. The average
number of female Cx. tritaeniorhynchus collected per trap night for the months of August and September, 2002-2008,
was calculated. Rice fields were manually digitized inside 1.5 km buffer zones surrounding U.S. military installations on
high-resolution satellite images, and the proportion of rice fields was calculated for each buffer zone. Results: Mosquito data collected from seventeen sample sites were analyzed for an association with the proportion of
rice field land cover. Results demonstrated that the linear relationship between the proportion of rice fields and
mosquito abundance was statistically significant (R2 = 0.62, r = .79, F = 22.72, p < 0.001). Conclusions: The analysis presented shows a statistically significant linear relationship between the two parameters,
proportion of rice field land cover and log10 of the average number of Cx. tritaeniorhynchus collected per trap night. The
findings confirm that agricultural land cover should be included in future studies to develop JE risk prediction models
for non-indigenous personnel living at military installations in the ROK. its primary vector Culex tritaeniorhynchus is plentiful in
many Asian countries. It has been shown that the number
of JEV vector mosquitoes collected in an area is highly
correlated with the number of JE patients in that area [3]. While a reliable JE vaccination exists, this disease still
affects many Southeast Asian countries [4,5]. Recent out-
breaks in the last five years (2005 through 2010) have
occurred in the indigenous population and unvaccinated
expatriates and travellers in India, Nepal, Taiwan, Malay-
sia, China, and Vietnam [6-12]. Recent maps showing the
geographical distribution of JE have been published in
several different papers [2,12,13]. © 2010 Richards et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited. Abstract The JE distribution map
in Figure 1 is based on the U.S. Centers for Disease Con-
trol and Prevention (CDC) 2009 version of the map cur-
rently distributed to international travellers [13]. Research
The relationship between mosquito abundance
and rice field density in the Republic of Korea Erin E Richards*1, Penny Masuoka1, David Brett-Major1,2, Matthew Smith3, Terry A Klein4, Heung Chul Kim5,
Assaf Anyamba3 and John Grieco1 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Background Japanese encephalitis virus has been identified by the U.S. National Center for Medical Intelligence as operationally
important to the U.S. military. Similarly, the pathogen is
important to unvaccinated personnel from other militar-
ies around the globe, expatriates, and travelers [1]. JE is a
potentially debilitating and deadly flavivirus that is
endemic in rural areas in east, south, and southwest Asia. Successful vaccination programs have diminished the
number of illnesses in many countries, causing many to
consider the disease to be rare and exotic [2]. However,
the JEV is maintained in populations of wading birds and * Correspondence: erin.e.richards@us.army.mil
1 Department of Preventive Medicine and Biometrics, Uniformed Services
University, Bethesda, Maryland, USA
Full list of author information is available at the end of the article Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Page 2 of 10 Figure 1 Geographical distribution of Japanese encephalitis. Geographical distribution of Japanese Encephalitis as published in CDC Health In-
formation for International Travel 2010 [13]. Guam and Saipan (not shown on this map) have also had cases of Japanese Encephalitis. Figure 1 Geographical distribution of Japanese encephalitis. Geographical distribution of Japanese Encephalitis as published in CDC Health In-
formation for International Travel 2010 [13]. Guam and Saipan (not shown on this map) have also had cases of Japanese Encephalitis. Culex tritaeniorhynchus is exophagic, prefers zoonotic
and domestic hosts, and tends to feed interspecifically
[18]. Primary vertebrate reservoirs for JEV are large water
birds of the family Ardeidae, while wild and domestic pigs
are amplifying hosts [17,19]. Cx. tritaeniorhynchus is
highly susceptible to viral infection; studies suggest that
over 30% become infected after feeding on a viremic pig
[20]. Mosquito populations are dependent on environ-
mental and seasonal factors for their propagation. In the
ROK, seasonal occurrence of Cx. tritaeniorhynchus are
reported between mid-June and early October, with adult
peak populations from late July through early September
[21-26]. JEV infections within vector populations peak in
late July and early August, with human disease rates
peaking in late August and September [15,27]. Culex tri-
taeniorhynchus breed in open sunlit temporary and per-
manent water habitats with vegetation, and have an
average flight range of 1.5 km [4,28]. The relative abun-
dance of Cx. Methods
Study Area The study area comprised seventeen U.S. military instal-
lations in the ROK and their immediate surrounding
areas. Military installations included in this study are a
convenience sample based on availability of high resolu-
tion images and mosquito data provided by the USFK
mosquito surveillance program. Installations included in
this study are Camp Humphreys, Camp Carroll, Gwangju
Air Base, Warrior Base, Camp Red Cloud, Camp Stanley,
Camp Jackson, Camp Essoyons, Camp Long, Camp
Eagle, Camp Casey, Camp Castle, Camp Nimble, Camp
Hovey, Osan Air Base, and Gunsan Air Base (Figure 2). Past studies on relative seasonal abundance and geo-
graphical distribution of Cx. tritaeniorhynchus in the
ROK have contributed to the success and development of
a JE disease surveillance systems for local populations
[34]. These surveillance systems have been based on
monitoring vector populations and seroprevalence in
swine from selected slaughterhouses; while such surveil-
lance systems have been effective, they have a negative
impact on the limited human resources and man-power
available to public health. For this reason, the Uniformed
Services University, the Armed Forces Health Surveil-
lance Center, Global Emerging Infections Surveillance
and Response System (AFHSC-GEIS), the National Aero-
nautics and Space Administration (NASA) Goddard
Space Flight Center (GSFC), and the 65th Medical Bri-
gade-Korea, began working together to develop a JEV risk
model in the ROK that incorporates remote sensing, land
cover, elevation, and historical climate data. y
g
Reorganization of the U.S. military in the ROK has led
to the realignment of existing military installations and
closure of others. Camp Humphreys, which has been
under construction since late 2007, is one of the largest
installations and has been augmented in order to accom-
modate an additional 20,000 relocated military, civilian,
and family members. Wetland rice fields adjacent to
Camp Humphreys were purchased for installation expan-
sion, with fill dirt used to elevate the low-lying rice pad-
dies for development, thus changing the local landscape. A portion of the secured rice paddies are programmed to
lay fallow, thereby contributing to a possible increase in
Cx. tritaeniorhynchus populations during the wet Mon-
soons (June-September). Two images of Camp Hum-
phreys were used in this project; one image is a 2006
QuickBird image and the other is a 2008 IKONOS image
of the same location. The rice field density statistics used
in analysis for Camp Humphreys is based on the 2006
image only. Background tritaeniorhynchus is closely related to local
rice agricultural practices, where wetland rice fields and
similar irrigation systems provide an optimal habitat for While JE clinical manifestations occur only in a small
number that become infected, the case fatality rate can be
as high as 40% for those demonstrating symptoms. Per-
manent neurologic sequelae are observed in 40 to 50% of
those who survive severe disease, resulting in minor to
severe complications and early death [14,15]. Further-
more, JE is often misdiagnosed and lacks effective treat-
ment beyond supportive care [16,17]. U.S. military personnel have been stationed in the ROK
since World War II. Currently, programmed extended
tour lengths have greatly increased the number of accom-
panying family, placing family members and young
unvaccinated children at risk of infection. While an estab-
lished Korean pediatric JEV vaccination program has
greatly reduced the number of cases occurring in the
Korean population, JEV continues to be of military public
health concern in the ROK because U.S. personnel are
not vaccinated for JE. Because of this disparity, human
disease rates in the indigenous population are unreliable
for estimating transmission and disease risks to U.S. mili-
tary, civilian, and family members stationed there. Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Page 3 of 10 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 larval development [18]. The ecological relationship
between mosquitoes and rice fields has been studied
extensively [29-31]; results show that these man-made
breeding sites result in a greater prevalence of Cx. tritae-
niorhynchus than natural breeding sites [32,33]. rate risk model based on remotely sensed land and cli-
mate data will allow for more efficient detection of
increased JE risk to U.S. military populations in the ROK. Additionally, the risk model would diminish reliance on
man-power intensive surveillance systems, and may pro-
vide rationale for the implementation of mandatory JEV
vaccination to USFK military, civilian, and family mem-
bers assigned to the ROK. Remote sensing and Geographical Information Systems
(GIS) are increasingly used in disease epidemiology to
map vector and disease distributions so that vector con-
trol efforts and disease intervention strategies are admin-
istered efficiently and effectively [29]. Past research has
demonstrated that remote sensing and GIS capabilities
can be used successfully to identify breeding habitats of
Cx. Background tritaeniorhynchus in Japan, the ROK, India, and Aus-
tralia [18]. Methods
Study Area The 2008 image shows the amount of rice
fields lost as a result of installation construction. The two
images were used in an exploratory fashion to help
describe how changes in local land cover effect the abun-
dance of Cx. tritaeniorhynchus. The goal of this project was to determine if quantifica-
tion of wetland rice field land cover via remote sensing
and GIS techniques could feasibly be used as a parameter
in a larger risk model to predict the abundance of Cx. tri-
taeniorhynchus at U.S. military installations in the ROK. While past studies have shown a correlation between Cx. tritaeniorhynchus collected at cow and pig sheds and sur-
rounding rice field acreage [35,36], this study examines
the number of Cx. tritaeniorhynchus collected on pri-
marily urban military bases and compares the number of
mosquitoes collected to the amount of rice field sur-
rounding those bases. Quantifying the relationship
between the amount of rice fields surrounding U.S. mili-
tary installations in the ROK and the abundance of Cx. tritaeniorhynchus captured at these sites will enhance the
U.S. military's capability to predict the risk of JEV trans-
mission to military, civilians, and family members
assigned to the ROK. This proposed risk model would be
used in conjunction with a predictive model for seasonal
JEV transmission using real-time data and would serve as
a disease risk monitoring system for U.S. military and
civilians living in the ROK. The development of an accu- Mosquito Data Retrospective mosquito data were provided by the USFK,
which conducts routine mosquito surveillance on U.S. military installations to monitor all mosquito species. Mosquitoes were collected weekly using un-baited New
Jersey (NJ) light traps in accordance with USFK preven-
tive medicine protocol from May through October, 2002
to 2008. One to eight traps were established at each mili- Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Page 4 of 10 Figure 2 Study area. The following military installations within South Korea are shown: Camp Humphreys, Camp Carroll, Gwangju Air Base (Kwangju)
Warrior Base, Camp Red Cloud, Camp Stanley, Camp Jackson, Camp Essoyons, Camp Long, Camp Eagle, Camp Casey, Camp Castle, Camp Nimble,
Camp Hovey, Osan Air Base, and Gunsan Air Base (Kunsan). Land cover obtained from MODIS Land Cover Group http://www-modis.bu.edu/landcover Figure 2 Study area. The following military installations within South Korea are shown: Camp Humphreys, Camp Carroll, Gwangju Air Base (Kwangju),
Warrior Base, Camp Red Cloud, Camp Stanley, Camp Jackson, Camp Essoyons, Camp Long, Camp Eagle, Camp Casey, Camp Castle, Camp Nimble,
Camp Hovey, Osan Air Base, and Gunsan Air Base (Kunsan). Land cover obtained from MODIS Land Cover Group http://www-modis.bu.edu/landcover. Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Page 5 of 10 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 tary installation. Collections were sent to the Entomology
Section, 5th Medical Detachment, for identification where
data on adult female mosquitoes (i.e. species, trap night,
month, and year) were prepared. A summary of the total
number of mosquitoes (males plus females) collected at
each location from 2002 to 2008 is listed in Table 1. Although NJ light traps are relatively inefficient for col-
lecting mosquitoes when compared to newer technolo-
gies, they are easy to operate and data can be compared
with collections made over more than 20 years of surveil-
lance in the ROK. comparison studies have demonstrated that land classifi-
cation outcomes are analogous for both image types [37]. Within each of the ten QuickBird images and one IKO-
NOS image, military installations were located using lati-
tude and longitude coordinates. Processing of image data
involved two steps: digitizing and area computation. Mosquito Data Rice fields were identified using photointerpretation
and manual digitization via ArcGIS® 9.3 software (Envi-
ronmental Systems Research Institute, Redlands, CA,
USA, http://www.esri.com). The border of each military
installation was digitized using publically available instal-
lation maps as aids. Buffers were used to designate the
study inclusion area. The buffer area surrounding each
military installation was based on the average flight range
of Cx. tritaeniorhynchus [4], and was set at 1.5 km from
the digitized military installation border. Rice fields
within the buffer area of each military installation were
then manually digitized as polygons. Manual digitization
was chosen because the majority of images available for
this project were acquired during the winter months
when rice fields were bare and spectrally similar to other
land cover, making automated classification difficult. Rice
field land cover was digitized as large polygons consisting
of many individual rice fields. Other non-rice features
such as irrigation ditches and small roads may have been
included in the rice field land cover. To minimize varia-
tion, all digitization was completed by one researcher in a
consistent manner. The final mosquito count at each military installation
used in the main analysis of this study is an average from
August to September from 2002 to 2008. August and Sep-
tember were selected for analysis to capture the peak Cx. tritaeniorhynchus breeding cycle [21]. To reduce the
effects of sampling variation between years and installa-
tions, data were standardized as the number of female
mosquitoes collected per trap night per month [mosqui-
toes per trap night = total female mosquitoes collected/
(number of traps * number of nights)]. The final mos-
quito capture rate for each military installation was calcu-
lated by adding the number of mosquitoes per trap night
for months August and September from 2002 to 2008,
then dividing by the number of nights mosquito sampling
was conducted during that time period. *Data are not adjusted for number of trap nights. The numbers in this table include both male and female mosquitoes and those trapped at
Gunsan, which was later dropped from the study. High Resolution Satellite Data A regression model was developed from the data to
predict mosquito abundance at Camp Humphreys after
environmental changes in 2007 altered the amount of rice
fields surrounding the installation. Rice field density in
the 2008 Camp Humphreys image was applied to the
regression model to determine a predicted mosquito
count and then compared to the observed 2008 number
of mosquitoes per trap night. This test was used to
explore the model's ability to predict the abundance of
female Cx. tritaeniorhynchus collected at an installation. High Resolution Satellite Data One IKONOS and ten QuickBird high resolution images,
encompassing visible and near infrared data, taken
between 2004 and 2008 were used for land cover classifi-
cation. QuickBird is a commercial earth observation sat-
ellite
operated
by
DigitalGlobe
http://
www.digitalglobe.com that records multispectral imagery
at 2.6 meter resolution at nadir. IKONOS is a similar
commercial earth observation satellite operated by Geo-
Eye http://www.geoeye.com that provides multispectral
images at four meter resolution. Although the QuickBird
images have a higher resolution than the IKONOS image, To obtain area measurements in kilometers, the digi-
tized military installations buffer area and rice field shape
files were reprojected from a Geographic Coordinate Sys-
tem (GCS) to a Universal Transverse Mercator (UTM)
map projection. The buffer area at each military installa-
tion was calculated and reported in square kilometers. The digitized rice field polygons within the buffer area of
each military installation was calculated and reported in
km2. To account for variation in installation size and thus
buffer area size, rice field densities were calculated as the
proportion of rice fields within the buffer area at each Table 1: Number of Culex tritaeniorhynchus mosquitoes collected in the ROK from 2002 to 2008 by month*
MAY
JUN
JUL
AUG
SEP
OCT
Total
2002
1
28
3724
27515
17995
524
49787
2003
0
7
315
1790
2282
38
4432
2004
0
12
650
32957
9446
1487
44552
2005
0
2
294
4264
2502
136
7198
2006
0
6
40
580
1046
6
1678
2007
1
12
986
2976
845
122
4942
2008
0
5
584
2421
1584
33
4627
*Data are not adjusted for number of trap nights. The numbers in this table include both male and female mosquitoes and those trapped at
Gunsan, which was later dropped from the study. Table 1: Number of Culex tritaeniorhynchus mosquitoes collected in the ROK from 2002 to 2008 by m *Data are not adjusted for number of trap nights. The numbers in this table include both male and female mosquitoes and those trapped at
Gunsan, which was later dropped from the study. Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Page 6 of 10 installation (rice fields proportion = rice field area/mili-
tary installation buffer area). An example of digitized rice
field data is presented in Figure 3. Discussion
Thi This research addresses the issues of mosquito abun-
dance and spatial patterns of agricultural land use. Emphasis has been put on determining the relationship
between average Cx. tritaeniorhynchus collected per trap
night and density of rice fields surrounding U.S. military
installations in the ROK; as well as assessing the value of
that relationship for inclusion in a larger disease risk
model. The future application of rice field density as a
parameter in models used to predict JEV disease risks can
be based on the strength of linear association, as it is pre-
sented here. A priori statistical power analysis stated that a sample
of sixteen sites carried 80% power to detect the propor-
tion of variability between mosquito abundance and rice
field density in the model with a coefficient of determina-
tion (R2) of 0.65. For our purposes, an R2 of 0.65 was
desired. The correlation coefficient (r) was also used in
this analysis to elucidate the relationship between mos-
quito abundance and the rice field density seen in the
data. Results revealed that 62% of the variation in the log10 of
Cx. tritaeniorhynchus collected per trap night on base
was accounted for by the density of rice fields in the area
surrounding the military base. The remaining 38% can be
explained by inherent variability or other variables, such
as species breeding cycle, proximity to blood source, or
regional climatic conditions [17,19-21,31]. Our data reaf-
firms past JE and Cx. tritaeniorhynchus research and sug-
gests that rice fields account for a large portion of the
mosquito's abundance but that populations cannot be
predicted by rice fields alone [29-31,35,36]. Rice Field Analysis The Mosquito Magnet is
the most effective trap for collecting Cx. tritaenio-
rhynchus; capturing up to 650 times as many mosquitoes
as the NJ light trap [23]. Primarily because trapping
methods were substantially different at Gunsan than
those at all other installations in the study sample, Gun-
san Air Base was excluded from the final analysis. all other years (Table 1). An observational retrospective
study of mosquito prevalence at U.S. military installations
in the ROK found that Cx. tritaeniorhynchus was the
most common mosquito species collected in 2002 [38]. In
2002, due to a high number of mosquitoes collected at
Gunsan Air Base, the overall average of Cx. tritaenio-
rhynchus populations in the ROK increased by 27.2%,
while populations of other mosquito species remained
relatively constant during the same time period [38]. The
increased number of Cx. tritaeniorhynchus caught at
Gunsan Air Base in 2002 and 2004 could be due to the
use of more efficient collection methods during these two
years. At Gunsan, NJ light traps were baited with dry ice
during collections in 2002 and the Mosquito Magnet® was
used for collections in 2004 [38]. The Mosquito Magnet is
the most effective trap for collecting Cx. tritaenio-
rhynchus; capturing up to 650 times as many mosquitoes
as the NJ light trap [23]. Primarily because trapping
methods were substantially different at Gunsan than
those at all other installations in the study sample, Gun-
san Air Base was excluded from the final analysis. In an exploratory analysis the regression model was
used to predict the abundance of Cx. tritaeniorhynchus at
Camp Humphreys in 2008. Despite major changes to the
Camp Humphreys area, the proportion of rice fields sur-
rounding the installation increased by only 1%. The num-
ber of predicted mosquitoes per trap night was 18.2 for
the 2008 Camp Humphreys image; the number of
observed mosquitoes per trap night was 22.2. Rice Field Analysis Simple linear regression analysis, using the SPSS® statisti-
cal program (SPSS Inc., Chicago, IL, USA) was conducted
on the data using two continuous variables, rice field den-
sity and log10 of the average number of Cx. tritaenio-
rhynchus per trap night from 2002-2008. The rice field
density statistic representing the proportion of rice fields
surrounding Camp Humphreys was based on the 2006
image only. Mosquito prevalence trend analysis showed extreme
variation over time. Years 2002 and 2004 had abnormally
high counts of Cx. tritaeniorhynchus when compared to Figure 3 Digitized rice field data example. The above is an image of a military installation located in the ROK taken in October. The base is shown
with a solid grey cover; the extent of the buffer zone area is depicted with a dark blue line; rice fields are shown with a solid yellow cover. The buffer
zone area extends 1.5 km from the military installation perimeter. Figure 3 Digitized rice field data example. The above is an image of a military installation located in the ROK taken in October. The base is shown
with a solid grey cover; the extent of the buffer zone area is depicted with a dark blue line; rice fields are shown with a solid yellow cover. The buffer
zone area extends 1.5 km from the military installation perimeter. Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Page 7 of 10 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 increase of female Cx. tritaeniorhynchus per trap night
can be expected. all other years (Table 1). An observational retrospective
study of mosquito prevalence at U.S. military installations
in the ROK found that Cx. tritaeniorhynchus was the
most common mosquito species collected in 2002 [38]. In
2002, due to a high number of mosquitoes collected at
Gunsan Air Base, the overall average of Cx. tritaenio-
rhynchus populations in the ROK increased by 27.2%,
while populations of other mosquito species remained
relatively constant during the same time period [38]. The
increased number of Cx. tritaeniorhynchus caught at
Gunsan Air Base in 2002 and 2004 could be due to the
use of more efficient collection methods during these two
years. At Gunsan, NJ light traps were baited with dry ice
during collections in 2002 and the Mosquito Magnet® was
used for collections in 2004 [38]. Results Average mosquito counts per trap night and the corre-
sponding rice field density statistics are presented for
each installation in Table 2. The area surrounding half of
the installations in this study were comprised of less than
10% rice fields. This is in sharp contrast to installations
that were surrounded by the most rice fields; coverage
ranged between 30-56% of the land surrounding five
installations. Mosquito data were log10 transformed prior
to regression analysis. Analysis conducted using log10
transformed mosquito data from 2002-2008 demon-
strated a statistically significant linear relationship
between rice field density and mosquito abundance (R2 =
0.62, r = .79, F = 22.72, p < 0.001). A scatter plot of the
data with the regression line is presented in Figure 4. A statistically significant linear association was demon-
strated between rice field density and mosquito popula-
tion. Given the strong relationship demonstrated
between rice field density and mosquito populations, this
variable should be considered when modelling Cx. tritae-
niorhynchus propagation or JEV transmission risks. Specific limitations to this study with regard to image
data include the inability to automatically extract rice
fields due to the lack of ground vegetation in many of the
images used. Due to cloud cover and other limiting fac-
tors, the remotely sensed imagery used in analysis were
not all acquired during the rice growing season, making
automated land cover extraction software unable to accu-
rately identify rice fields. While rice fields were extracted
manually, the potential for misclassification of land cover
remained. Field shape, image interpretation, and area
photographs guided rice field identification. This study
was also limited by the lack of images at each installation
for each year or month within the study period. Thus, the
authors were unable to explore variation in the correla- The resulting linear model [y = 2.71 × -0.28; where y
equals the log10 of the average mosquitoes per trap night,
and × equals the proportion of rice field land cover] was
used to predict the abundance of post-construction Cx. tritaeniorhynchus at Camp Humphreys using the 2008
image. The data reveals that for every 10% increase of rice
field land cover surrounding an installation, an 86% Richards et al. Results International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Page 8 of 10 Table 2: Rice field density and average number of mosquitoes collected per trap night, by installation**
Installation
Proportion of Rice
Fields in Buffer Area
Monthly Average Number Female
Mosquitoes
per Trap Night 2002-2008 (Aug-Sept)
Camp Jackson
0.00
0.62
Camp Casey
0.01
0.83
Camp Hovey
0.02
0.74
Camp Essoyons
0.02
0.73
Camp Nimble
0.02
0.44
Camp Mobile
0.02
1.23
Camp Red Cloud
0.03
0.82
Camp Castle
0.05
0.86
Camp Stanley
0.11
0.57
Camp Long
0.13
0.36
Camp Carroll
0.18
2.36
Camp Eagle
0.21
0.23
Gwangju Air Base
0.30
14.40
Warrior Base
0.38
14.81
Osan Air Base
0.44
3.64
Gunsan AB
0.53
222.42
Camp Humphreys
0.56
22.20
**Gunsan was dropped from subsequent analysis. 2: Rice field density and average number of mosquitoes collected per trap night, by installation** **Gunsan was dropped from subsequent analysis. This limitation restricts analysis and does not allow the
geographical variability among installations to be
explored. tion between rice field density and Cx. tritaeniorhynchus
throughout time. This study, and potentially all studies
conducted on military bases in the ROK, will be limited
by the number of installations and number of installa-
tions within the USFK mosquito surveillance program. Despite limitations, this study has a number of
strengths. It utilized USFK mosquito surveillance data
collected consistently for over 8 years in the ROK. This
data continues to be collected and can be similarly used
in the future. It also uses high resolution remotely sensed
imagery to determine rice field land cover. Using
remotely sensed data to map rice field land cover is less
time consuming than conventional ground survey meth-
ods used in the past to calculate agricultural land use. Figure 4 Fitted curve of model. The above is a scatter plot of the data
and the resulting regression line (y = 2.71 × -0.28). Each dot represents
data from one installation. mosquito per trap night
proportion of rice fields
log10 of the average m mosquito per trap night
proportion of rice fields
log10 of the average m Abbreviations
AFHSC A
d 9. Japanese encephalitis - Taiwan [http://www.promedmail.org]. Accession Number 20060909.2565 AFHSC: Armed Forces Health Surveillance Center; CDC: Centers for Disease
Control and Prevention; GCS: Geographic Coordinate System; GEIS: Depart-
ment of Defense Global Emerging Infections Surveillance and Response Sys-
tem; GIS: Geographical Information Systems; GSFC: Goddard Space Flight
Center; JE: Japanese encephalitis; JEV: Japanese encephalitis virus; NASA:
National Aeronautics and Space Administration; NJ: New Jersey; ROK: Republic
of Korea; USFK: United States Forces Korea; UTM: Universal Transverse Mercator. 10. Japanese encephalitis - Malaysia (Kelantan) [http://
www.promedmail.org]. Accession Number 20060130.0301 11. Japanese encephalitis & other - India (02): (AP) [http://
www.promedmail.org]. Accession Number 20100422.1309 12. van den Hurk AF, Ritchie SA, Mackenzie JS: Ecology and geographical
expansion of Japanese encephalitis virus. Annual Review of Entomology
2009, 54:17-35. expansion of Japanese encephalitis virus. Annual Review of Entomology
2009, 54:17-35. Competing interests
Th
h
d
l
h 13. Brunette GW, Kozarsky PE, Magill AJ, Shlim DR, Whatley AD: CDC Health
Information for International Travel 2010 (The Yellow Book) 2010 edition. CDC; 2009. p
g
The authors declare that they have no competing interests. The authors declare that they have no competing interests. Authors' contributions
l
d h 14. Thongcharoen P: Japanese encephalitis virus encephalitis: an overview. Southeast Asian Journal of Tropical Medicine and Public Health 1989,
20:559-573. 14. Thongcharoen P: Japanese encephalitis virus encephalitis: an overview. Southeast Asian Journal of Tropical Medicine and Public Health 1989,
20:559-573. ER implemented the mapping project, analysis of the data, drafting of the
manuscript, and contributed to the study design. PM conceived the study
design, acquired land cover data and contributed to the coordination of the
study, implementation of the mapping project, and revision of the manuscript. DB contributed to the study design and revision of the manuscript. MS partici-
pated in the creation of the mapping project and revision of the manuscript. AA contributed to the coordination of the study and advised on study design. HCK assisted with mosquito data collection, provided advice on mosquito data
analysis and provided coordination with USFK. TAK collected mosquito data,
provided advice on mosquito data analysis, provided coordination with USFK,
and assisted with manuscript revision. JG provided project resources, advised
on study design and analysis, and assisted in final editing. All authors have read
and approved the final manuscript. 15. Vaughn DW, Hoke CH Jr: The epidemiology of Japanese encephalitis:
prospects for prevention. Epidemiologic Reviews 1992, 14:197-221. 16. Kitchen LW, Vaughn DW: Role of U.S. military research programs in the
development of U.S.-licensed vaccines for naturally occurring
infectious diseases. Vaccine 2007, 25:7017-7030. 17. Sabin AB: Insect borne virus diseases of military importance. Military
Medicine 1955, 116:245-251. 18. Keiser J, Maltese MF, Erlanger TE, Bos R, Tanner M, Singer BH, Utzinger J:
Effect of irrigated rice agriculture on Japanese encephalitis, including
challenges and opportunities for integrated vector management. Acta
Tropica 2005, 95:40-57. 19. Buescher EL, Scherer WF: Ecologic studies of Japanese encephalitis virus
in Japan. IX. Epidemiologic correlations and conclusions. American
Journal of Tropical Medicine and Hygiene 1959, 8:719-722. Acknowledgements
h
k This work was supported through the partnership between the Uniformed
Services University, the AFHSC-GEIS, NASA GSFC, and the 65th Medical Brigade,
Korea. We thank Dr. Cara Olsen and Dr. Rodger Gibson from the Uniformed Ser-
vices University, who contributed to the analysis, methods and interpretation
of this project. We thank the Commander and Soldiers of the 5th Medical
Detachment, 168th Medical Battalion, 65th Medical Brigade, who performed the
collection and identification of mosquitoes used in this study. We are grateful
to the National Geospatial-Intelligence Agency (NGA) who provided imagery
for this project. 20. Maeda O, Takenokuma K, Karoji Y, Kuroda A, Sasaki O, Karaki T, Ishii T:
Epidemiological studies on Japanese encephalitis in Kyoto City area,
Japan. Japanese Journal of Medical Science & Biology 1978, 31:317-324. 21. Lee KW, Gupta RK, Wildie JA: The Collection of Adult Larval Mosquitoes
in U.S. Army Compounds in the Republic of Korea During 1979~1983. The Korean Journal of Parasitology 1984, 22:102-108. 22. Joo CY, Wada Y: Seasonal Prevalence of the Vector Mosquitoes of
Japanese Encephalitis Virus in Kyungpook Province, Korea. Korean
Journal of Parasitology 1985, 23:139-150. Conclusions Using the data presented here, an overall statistically sig-
nificant linear relationship between rice field density and
Cx. tritaeniorhynchus abundance was found. Use of the
regression model to predict mosquito abundance was
inconsistent. Future studies to develop JE risk prediction
models for non-indigenous personnel living at military
installations in the ROK should include agriculture land
use and irrigation patterns as variables. There are a number of implications in this study for
future research in JE risk prediction and Cx. tritaenio-
rhynchus population modelling in the vicinity of U.S. mil-
itary installations in the ROK. First, automated risk Figure 4 Fitted curve of model. The above is a scatter plot of the data
and the resulting regression line (y = 2.71 × -0.28). Each dot represents
data from one installation. Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 Page 9 of 10 Page 9 of 10 3. Solomon T, Dung NM, Kneen R, Gainsborough M, Vaughn DW, Khanh VT:
Japanese encephalitis. Journal of Neurology, Neurosurgery & Psychiatry
2000, 68:405-415. models must utilize land cover maps derived from
remotely sensed imagery acquired during the rice grow-
ing season. The use of images acquired with fallow rice
fields could hinder the accuracy of automated rice field
mapping, and could inhibit model efficiency. Second, if
possible, imagery should be acquired for each month or
year during the study period to facilitate the analysis of
rice field density and Cx. tritaeniorhynchus within and
among installations, and account for annual fluctuation
in average mosquito per trap night. 4. Bista MB, Shrestha JM: Epidemiological situation of Japanese
encephalitis in Nepal. Journal of Nepal Medical Association 2005,
44:51-56. 5. Kanojia PC: Ecological study on mosquito vectors of Japanese
encephalitis virus in Bellary district, Karnataka. Indian Journal of Medical
Research 2007, 126:152-157. 6. Japanese encephalitis - Belgium ex China: RFI [http://
www.promedmail.org]. Accession Number 20050413.1070 7. Japanese encephalitis - Viet Nam [http://www.promedmail.org]. Accession Number 20050626.1795 8. Japanese encephalitis - Nepal [http://www.promedmail.org]. Accession
Number 20060831.2475 2.
Solomon T: Control of Japanese encephalitis-within our grasp? New
England Journal of Medicine 2006, 355:869-871. Received: 5 April 2010 Accepted: 23 June 2010
Published: 23 June 2010
This article is available from: http://www.ij-healthgeographics.com/content/9/1/32
© 2010 Richards et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use
International Journal of Health Geographics 2010, 9:32 26. Kim HC, Lee KW, Robert LL, Sardelis MR, Chase FE: Seasonal prevalence of
mosquitoes collected from light traps in Korea (1991- 1992). Korean
Journal of Entomology 1995, 25:225-234. 27. Scherer WF, Buescher EL: Ecologic studies of Japanese encephalitis virus
in Japan. I. Introduction. American Journal of Tropical Medicine and
Hygiene 1959, 8:644-650. 1.
Japanese encephalitis [http://www.who.int/vaccine_research/diseases/
vector/en/index2.html] vector/en/index2.html] Author Details 23. Burkett DA, Lee WJ, Lee KW, Kim CH, Lee HI, Lee JS, Shin EH, Wirtz RA, Cho
HW, Claborn DM, Coleman RE, Kim WY, Klein TA: Late season commercial
mosquito trap and host seeking activity evaluation against
mosquitoes in a malarious area of the Republic of Korea. Korean
Journal of Parasitology 2002, 40:45-50. 1Department of Preventive Medicine and Biometrics, Uniformed Services
University, Bethesda, Maryland, USA, 2Military Tropical Medicine Course, Navy
Medicine Manpower Personnel Training and Education Command, Uniformed
Services University, Bethesda, Maryland, USA, 3Biospheric Sciences Branch,
Goddard Space Flight Center, National Aeronautics and Space Administration,
Greenbelt, Maryland, USA, 4Force Health Protection and Preventive Medicine,
65th Medical Brigade/MEDDAC-Korea, Seoul, Republic of Korea and 55th
Medical Detachment, 168th Medical Battalion, 65th Medical Brigade, Seoul,
Republic of Korea 24. Kim HC, Lee KW, Jones JW, Korch GW: Seasonal prevalence of
mosquitoes collected from light trap in Korea (1993-1994). Korean
Journal of Entomology 1997, 27:21-28. 25. Kim HC, Lee KW, Klein TA, Strickman DA: Seasonal prevalence of
mosquitoes collected from light traps in Korea (1995-1996). Korean
Journal of Entomology 1999, 29:181-187. Received: 5 April 2010 Accepted: 23 June 2010
Published: 23 June 2010
This article is available from: http://www.ij-healthgeographics.com/content/9/1/32
© 2010 Richards et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted u
International Journal of Health Geographics 2010, 9:32 References Page 10 of 10 Richards et al. International Journal of Health Geographics 2010, 9:32
http://www.ij-healthgeographics.com/content/9/1/32 28. Henrich TJ, Hutchaleelaha S, Jiwariyavej V, Barbazan P, Nitatpattana N,
Yoksan S, Gonzalez JP: Geographic dynamics of viral encephalitis in
Thailand. Microbes and Infection 2003, 5:603-611. 29. Beck LR, Lobitz BM, Wood BL: Remote Sensing and Human Health: New
Sensors and New Opportunities. Emerging Infectious Diseases 2000,
6:217-226. 30. Wood BL, Beck LR, Washino RK, Hibbard KA, Salute JS: Estimating high
mosquito-producing rice fields using spectral and spacial data. International Journal of Remote Sensing 1992, 13:2813-2826. International Journal of Remote Sensing 1992, 13:2813-2826. 31. Wood BL, Beck LR, Washino RK, Palchick SM, Sebesta PD: Spectral and
spatial characterization of rice field mosquito habitat. International
Journal of Remote Sensing 1991, 12:621-626. 32. Suzuki T: Bibliography on Culex tritaeniorhynchus in Japan 1945-1966. Book Bibliography on Culex tritaeniorhynchus in Japan 1945-1966 (Editor
ed.^eds.). City 1967. 33. Lacey L, Lacey C: The medical importance of rice-land mosquitoes and
their control using alternatives to chemical insecticides. Journal of the
American Mosquito Control Association 1990, 2:1-93. 34. Self LS, Shin HK, Kim KW, Lee CY, Chow CY, Hong HK: Ecological Studies
on Culex tritaeniorhynchus as a Vector of Japanese Encephalitis. Bulletin
of the WHO 1973, 49:41-47. 35. Matsuzaki S: Population dynamics of Culex tritaeniorhynchus in
relation to the epidemics of Japanese encephalitis in Kochi Prefecture,
Japan. Japanese Journal of Sanitary Zoology 1990, 41:247-255. 36. Ree HI, Lee SK: Studies on mosquito population dynamics in Chollabug-
do, Korea (1985-1990) II. Factors influencing population sizes of Culex
tritaeniorhynchus and Anopheles sinensis. Korean Journal of
Entomology 1993, 23:185-194. 37. Wang L, Sousa W, Gong P, Biging G: Comparison of IKONOS and
QuickBird images for mapping mangrove species on the Caribbean
coast of Panama. Remote Sensing of Environment 2004, 91:432-440. 38. Kim HC, Chong S, Collier BW, Lee HC, Klein TA: Seasonal Prevalence of
Mosquitoes Collected from Light Traps in the Republic of Korea, 2004. Entomological Research 2007:180-189. doi: 10.1186/1476-072X-9-32
Cite this article as: Richards et al., The relationship between mosquito abun-
dance and rice field density in the Republic of Korea International Journal of
Health Geographics 2010, 9:32
|
https://openalex.org/W4393055403
|
https://egusphere.copernicus.org/preprints/2024/egusphere-2023-2709/egusphere-2023-2709.pdf
|
English
| null |
Comment on egusphere-2023-2709
| null | 2,024
|
cc-by
| 13,451
|
Abstract. Global crude steel production is expected to continue to increase in the coming decades to meet the demands of the growing
world population. Currently, the dominant steelmaking technology worldwide is the conventional highly CO2-intensive Blast
Furnace–Basic Oxygen Furnace production route (also known as the Linz–Donawitz process) using iron ore as raw material
and coke as a reducing agent. As a result, large quantities of special gases that are rich in carbon monoxide (CO) are by-
5
products of the various stages of the steelmaking process. Given the challenges associated with satellite-based estimates of
carbon dioxide (CO2) emissions at the scale of emitting installations due to significant background levels, co-emitted CO may
serve as a valuable indicator of the carbon footprint of steel plants. We show that regional CO release from steel production sites can be monitored from space using 5 years of measurements
(2018-2022) from the TROPOspheric monitoring instrument (TROPOMI) on board the Sentinel-5 Precursor satellite benefiting
10
from its relatively high spatial resolution and daily global coverage. We analyse all German steel plants with blast furnaces
and basic oxygen furnaces and obtain associated CO emissions in the range of 50-400 kt yr−1 per site. A comparison with
the respective CO2 emissions on the level of emitting installations available from emissions trading data of the European
Union Emissions Trading System yields a linear relationship with a sector-specific CO/CO2 emission ratio for the analysed (2018-2022) from the TROPOspheric monitoring instrument (TROPOMI) on board the Sentinel-5 Precursor satellite benefiting
10
from its relatively high spatial resolution and daily global coverage. We analyse all German steel plants with blast furnaces
and basic oxygen furnaces and obtain associated CO emissions in the range of 50-400 kt yr−1 per site. A comparison with
the respective CO2 emissions on the level of emitting installations available from emissions trading data of the European
Union Emissions Trading System yields a linear relationship with a sector-specific CO/CO2 emission ratio for the analysed steelworks of 3.24%[2.73 −3.89; 1σ] suggesting the feasibility of using CO as a proxy for CO2 emissions from comparable
15
steel production sites. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Towards a sector-specific CO/CO2 emission ratio: Satellite-based
observation of CO release from steel production in Germany
Oliver Schneising, Michael Buchwitz, Maximilian Reuter, Michael Weimer, Heinrich Bovensmann,
John P. Burrows, and Hartmut Bösch
Institute of Environmental Physics (IUP), University of Bremen FB1, Bremen, Germany
Correspondence: O. Schneising (oliver.schneising@iup.physik.uni-bremen.de) Major sources of CO emissions include transportation, residential heating and cooking, biomass burning, industrial pro-
cesses, and natural sources like wildfires. In the broader category of industrial emissions, CO is generated as a byproduct
of incomplete combustion or chemical reactions. An important example is the steel producing industry with CO emissions mainly due to the formation and release of CO-rich gases in the widely used Linz–Donawitz process of integrated steel plants:
40
1) Sinter gas produced in a pre-treatment process step agglomerating iron ore fines into a porous, consistent high quality burden
suitable for direct use in the blast furnace, 2) blast furnace gas arising during iron ore reduction with carbon (primarily in the
form of coke), and 3) converter gas resulting from conversion of molten pig iron to steel by oxidation of carbon impurities to
harden the metal (Ishioka et al., 1992; Kim et al., 2016). These CO-rich by-product gases can be incinerated within the steel mainly due to the formation and release of CO-rich gases in the widely used Linz–Donawitz process of integrated steel plants:
40
1) Sinter gas produced in a pre-treatment process step agglomerating iron ore fines into a porous, consistent high quality burden
suitable for direct use in the blast furnace, 2) blast furnace gas arising during iron ore reduction with carbon (primarily in the
form of coke), and 3) converter gas resulting from conversion of molten pig iron to steel by oxidation of carbon impurities to
harden the metal (Ishioka et al., 1992; Kim et al., 2016). These CO-rich by-product gases can be incinerated within the steel production route for heat supply (Backes et al., 2021) or reused in the steelmaking process to replace some of the solid carbon
45
fuels to reduce CO2 emissions substantially (He and Wang, 2017; Kildahl et al., 2023). Understanding the CO loss processes
throughout the entire steelmaking workflow and their link to CO2 emissions is crucial for addressing the twin challenge of en-
vironmental pollution and climate change mitigation until the planned transformation to green steel is completed and the Blast
Furnace–Basic Oxygen Furnace route has been replaced by the Direct Reduction–Electric Arc Furnace route using pure hy- drogen (H2) obtained from renewable sources as the reducing agent avoiding direct emissions of non-condensable greenhouse
50
gases almost entirely (Graupner et al., 2023). 1
Introduction Carbon monoxide (CO) has a dual role as both an air pollutant and a crucial component of atmospheric chemistry. Its reactiv-
ity with the hydroxyl radical (OH) and other atmospheric constituents has a significant effect on the oxidising capacity of the
atmosphere, which subsequently influences the abundances of greenhouse gases, such as methane, and the formation of sec-
0
ondary pollutants, including tropospheric ozone (Holloway et al., 2000). It is therefore essential to gain accurate knowledge of
the sources of CO to ensure efficient air quality control, pollution management, and an improved understanding of atmospheric
composition and its impact on climate change. The atmospheric lifetime of CO is approximately 1-2 months, so that it is well
suited for tracing the transport of pollutants and can be used as a proxy for co-emitted CO2 (Wu et al., 2022; MacDonald et al., 20 1 1 https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. 2023), which is harder to observe from space than CO because CO2 is well-mixed in the atmosphere resulting in small signals
25
relative to large background levels. Satellite missions with global coverage significantly improve our ability to analyse atmospheric CO. Instruments using
measurements of shortwave infrared (SWIR) radiances to retrieve CO column abundances in the atmosphere are sensitive to
the planetary boundary layer and operate during daytime when there is sufficient sunlight to illuminate the Earth’s surface. 2023), which is harder to observe from space than CO because CO2 is well-mixed in the atmosphere resulting in small signals
25
relative to large background levels. Satellite missions with global coverage significantly improve our ability to analyse atmospheric CO. Instruments using
measurements of shortwave infrared (SWIR) radiances to retrieve CO column abundances in the atmosphere are sensitive to
the planetary boundary layer and operate during daytime when there is sufficient sunlight to illuminate the Earth’s surface. Prominent instruments measuring in this spectral range include the Measurement of Pollution in the Troposphere (MOPITT)
30
instrument (Drummond et al., 2010) on board NASA’s Terra satellite, the SCanning Imaging Absorption spectroMeter for
Atmospheric CHartographY (SCIAMACHY) (Burrows et al., 1995; Bovensmann et al., 1999) on board ESA’s ENVISAT, and
the Thermal And Near infrared Sensor for carbon Observations Fourier Transform Spectrometer 2 (TANSO-FTS-2) on board
GOSAT-2 (Suto et al., 2021). The application areas for satellite data were further extended with the TROPOspheric Moni- Prominent instruments measuring in this spectral range include the Measurement of Pollution in the Troposphere (MOPITT)
30
instrument (Drummond et al., 2010) on board NASA’s Terra satellite, the SCanning Imaging Absorption spectroMeter for
Atmospheric CHartographY (SCIAMACHY) (Burrows et al., 1995; Bovensmann et al., 1999) on board ESA’s ENVISAT, and
the Thermal And Near infrared Sensor for carbon Observations Fourier Transform Spectrometer 2 (TANSO-FTS-2) on board
GOSAT-2 (Suto et al., 2021). The application areas for satellite data were further extended with the TROPOspheric Moni-
toring Instrument (TROPOMI) (Veefkind et al 2012) which is considered a milestone for the determination of atmospheric
35 toring Instrument (TROPOMI) (Veefkind et al., 2012), which is considered a milestone for the determination of atmospheric
35
composition, including CO, from space by combining high spatio-temporal sampling and data quality. There are only a few studies on sector-specific CO emissions from steel production that were obtained by remote sensing. Atmospheric CO enhancements from steel production in Asia and Europe have been qualitatively analysed with TROPOMI
data before (Schneising et al., 2019, 2023). Tian et al. (2022) quantify CO emission rates for industrial parks in Asia using TROPOMI data without attributing them to a specific sector. There are also some other analyses that deal with urban emissions
65
(Park et al., 2021; Wu et al., 2022), but these are usually a mixture of emissions from different sectors, e.g. transport, heating,
and industry-related. Wu et al. (2022) derive CO/CO2 ratios for cities, including two in China that are explicitly highlighted
as industry- and energy-oriented with metal production sites such as aluminium or steel plants. In this manuscript, we use TROPOMI observations and their unique features to systematically quantify the CO emissions of all German steelworks applying the Linz–Donawitz process and to determine the corresponding sector-specific CO/CO2
70
emission ratio, which is as a first step towards the potential use of co-emitted CO as a proxy for CO2 emissions from the steel
industry. The locations of the analysed production sites are shown in Figure 1. of all German steelworks applying the Linz–Donawitz process and to determine the corresponding sector-specific CO/CO2
70
emission ratio, which is as a first step towards the potential use of co-emitted CO as a proxy for CO2 emissions from the steel
industry. The locations of the analysed production sites are shown in Figure 1. Given that the steel industry is highly energy-intensive and one of the leading industrial contributors to global anthropogenic
CO2 emissions, with a share of around 7%, the rapid and systematic decarbonisation of steel production is essential to meet
climate targets (International Energy Agency, 2020). With around 40 million tonnes of crude steel production, Germany is the largest steel producer in Europe and will likely exceed its sectoral CO2 budget for a 1.5◦C warming scenario in the 2030s at
55
the latest (Harpprecht et al., 2022). In both Germany and worldwide, the predominant method accounting for around 70% of
steel production is through primary production utilising the Blast Furnace–Basic Oxygen Furnace production route. There are several studies analysing the environmental impact of steel production sites using a bottom-up life cycle assessment
(Suer et al., 2022, and references therein), but most of them focus on CO2 emissions and do not quantify co-emitted CO There are several studies analysing the environmental impact of steel production sites using a bottom-up life cycle assessment
(Suer et al., 2022, and references therein), but most of them focus on CO2 emissions and do not quantify co-emitted CO 2 2 Figure 1. Locations of the analysed German steel production sites. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Figure 1. Locations of the analysed German steel production sites. Figure 1. Locations of the analysed German steel production sites. explicitly. One exception is the study by Burchart-Korol (2013), in which all inputs and outputs of the sub-processes involved
60
in steelmaking are explicitly broken down for an integrated steel plant in Poland and summarised in a corresponding inventory. There are only a few studies on sector-specific CO emissions from steel production that were obtained by remote sensing. Atmospheric CO enhancements from steel production in Asia and Europe have been qualitatively analysed with TROPOMI
data before (Schneising et al., 2019, 2023). Tian et al. (2022) quantify CO emission rates for industrial parks in Asia using explicitly. One exception is the study by Burchart-Korol (2013), in which all inputs and outputs of the sub-processes involved
60
in steelmaking are explicitly broken down for an integrated steel plant in Poland and summarised in a corresponding inventory. 2
Data and methods Sentinel-5 Precursor, launched in October 2017, operates in a sun-synchronous orbit with an Sentinel-5 Precursor, launched in October 2017, operates in a sun-synchronous orbit with an equator crossing time of 13:30 Sentinel-5 Precursor, launched in October 2017, operates in a sun-synchronous orbit with an equator crossing time of 13:30
local time. TROPOMI is a spaceborne nadir-viewing imaging spectrometer designed to measure solar radiation reflected by the
75
Earth in a push-broom configuration. With a swath width of 2600 km, it provides a rare combination of relatively high spatial
resolution and daily global coverage. The nadir measurements in the shortwave infrared (SWIR) offer a horizontal resolution of
5.5×7 km2 at nadir (7×7 km2 before 6 August 2019) and are sensitive to all altitude levels, including the planetary boundary
layer, making them well-suited for studying emissions from sources on the ground such as steelworks. local time. TROPOMI is a spaceborne nadir-viewing imaging spectrometer designed to measure solar radiation reflected by the
75
Earth in a push-broom configuration. With a swath width of 2600 km, it provides a rare combination of relatively high spatial
resolution and daily global coverage. The nadir measurements in the shortwave infrared (SWIR) offer a horizontal resolution of
5.5×7 km2 at nadir (7×7 km2 before 6 August 2019) and are sensitive to all altitude levels, including the planetary boundary
layer, making them well-suited for studying emissions from sources on the ground such as steelworks. 3 https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Figure 2. Example daily data for Duisburg to demonstrate the emission estimation process. The coordinate system has been rotated to the
wind direction. The background region is highlighted in cyan, the plume region in orange, and the hot spot region in magenta. The dimensions
and position of these regions remain constant for all days analysed within the rotated coordinate system. The hot spot region is only used to
establish selection criteria that ensure sufficient data coverage (see main text for details) and is not used directly in the emission estimation
process itself. The cross sections utilised for calculating the daily flux are indicated in red. Figure 2. Example daily data for Duisburg to demonstrate the emission estimation process. The coordinate system has been rotated to the
wind direction. The background region is highlighted in cyan, the plume region in orange, and the hot spot region in magenta. 2
Data and methods The dimensions
and position of these regions remain constant for all days analysed within the rotated coordinate system. The hot spot region is only used to
establish selection criteria that ensure sufficient data coverage (see main text for details) and is not used directly in the emission estimation
process itself. The cross sections utilised for calculating the daily flux are indicated in red. In this research, we use the latest version of the Weighting Function Modified DOAS (WFM-DOAS) algorithm, specifically
80
optimised for the simultaneous retrieval of methane and carbon monoxide from TROPOMI (Schneising et al., 2019, 2023). The involved column-averaged dry air mole fractions of carbon monoxide, denoted as XCO, retrieved with the scientific
TROPOMI/WFMD algorithm v1.8, are characterised by a random error (precision) of 5.1 ppb and a spatio-temporal systematic
error (relative accuracy) of 2.6 ppb after quality filtering (Schneising et al., 2023). In this research, we use the latest version of the Weighting Function Modified DOAS (WFM-DOAS) algorithm, specifically
80
optimised for the simultaneous retrieval of methane and carbon monoxide from TROPOMI (Schneising et al., 2019, 2023). The involved column-averaged dry air mole fractions of carbon monoxide, denoted as XCO, retrieved with the scientific
TROPOMI/WFMD algorithm v1.8, are characterised by a random error (precision) of 5.1 ppb and a spatio-temporal systematic
error (relative accuracy) of 2.6 ppb after quality filtering (Schneising et al., 2023). 80 The estimation of emissions presented here relies on the daily observations provided by TROPOMI and a Gaussian integral
85
method, also referred to as the cross-sectional flux method. To automatically process quality-filtered daily XCO retrievals
for a specific source region, the estimation method of Schneising et al. (2020b) is applied, which is briefly recapitulated
in the following. Initially, the data given as latitude and longitude are transformed to a coordinate system rotated to the wind
direction, in which the prime meridian and the equator are aligned with the centre of the analysed region and the zonal direction The estimation of emissions presented here relies on the daily observations provided by TROPOMI and a Gaussian integral
85
method, also referred to as the cross-sectional flux method. To automatically process quality-filtered daily XCO retrievals
for a specific source region, the estimation method of Schneising et al. (2020b) is applied, which is briefly recapitulated
in the following. 2
Data and methods Initially, the data given as latitude and longitude are transformed to a coordinate system rotated to the wind
direction, in which the prime meridian and the equator are aligned with the centre of the analysed region and the zonal direction The estimation of emissions presented here relies on the daily observations provided by TROPOMI and a Gaussian integral
85
method, also referred to as the cross-sectional flux method. To automatically process quality-filtered daily XCO retrievals
for a specific source region, the estimation method of Schneising et al. (2020b) is applied, which is briefly recapitulated
in the following. Initially, the data given as latitude and longitude are transformed to a coordinate system rotated to the wind
direction, in which the prime meridian and the equator are aligned with the centre of the analysed region and the zonal direction corresponds to the mean boundary layer wind direction (within the region of interest and within a time window of two hours
90
before the satellite overpass) obtained from the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA5
reanalysis product (Hersbach et al., 2018). Subsequently, the transformed daily data is gridded on a 0.05◦× 0.05◦grid, which
is comparable to the horizontal nadir resolution of TROPOMI, and a mean background upwind of the source is subtracted. An
example highlighting the position of the background and plume region is shown in Figure 2. corresponds to the mean boundary layer wind direction (within the region of interest and within a time window of two hours
90
before the satellite overpass) obtained from the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA5
reanalysis product (Hersbach et al., 2018). Subsequently, the transformed daily data is gridded on a 0.05◦× 0.05◦grid, which
is comparable to the horizontal nadir resolution of TROPOMI, and a mean background upwind of the source is subtracted. An
example highlighting the position of the background and plume region is shown in Figure 2. Let E represent the total column enhancement (in units of mass per area) and v the average wind speed within the boundary
95
layer. To assess the emission, we use the divergence theorem and compute the flux of the vector field Ev through cross Let E represent the total column enhancement (in units of mass per area) and v the average wind speed within the boundary
95
layer. The molar mass of carbon monoxide, MCO, is 28.01g mol−1, the Avogadro constant, NA, is 6.022·1023 molec mol−1
the O2 column (in units of molecules per area) depends on the actual mean surface pressure, and the dry air mole fraction of
oxygen, XO2, is 0.209. These values are used to convert between the enhancement in XCO and the total column enhancement
105
E. Additionally, ACO is the value of the lowest layer of the averaging kernel (which is approximately 0.95 for all analysed Here, ∆l represents the size of a grid cell and i corresponds to the meridional summation along the respective cross section
given by k. The molar mass of carbon monoxide, MCO, is 28.01g mol−1, the Avogadro constant, NA, is 6.022·1023 molec mol−1
the O2 column (in units of molecules per area) depends on the actual mean surface pressure, and the dry air mole fraction of oxygen, XO2, is 0.209. These values are used to convert between the enhancement in XCO and the total column enhancement
105
E. Additionally, ACO is the value of the lowest layer of the averaging kernel (which is approximately 0.95 for all analysed
source regions) characterising the boundary layer sensitivity of the retrieval method. oxygen, XO2, is 0.209. These values are used to convert between the enhancement in XCO and the total column enhancement
105
E. Additionally, ACO is the value of the lowest layer of the averaging kernel (which is approximately 0.95 for all analysed
source regions) characterising the boundary layer sensitivity of the retrieval method. Taking the average of all cross-sectional fluxes Φk results in the daily flux estimate, denoted as Φ, with the corresponding
uncertainty depending on the variability of the enhancements derived for the different cross sections, the variability of the Taking the average of all cross-sectional fluxes Φk results in the daily flux estimate, denoted as Φ, with the corresponding
uncertainty depending on the variability of the enhancements derived for the different cross sections, the variability of the absolute wind speed over the region, the wind history, and on the variability of the O2 column, which is determined by surface
110
pressure (Schneising et al., 2020b). In this daily averaging procedure, only those Φk are considered where at least 60% of
the maximum possible grid cells along the cross-section are validly filled with data. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. sections (red lines in Figure 2) perpendicular to wind direction, which is assumed to match the plume axis after rotation of the
coordinate system. Consequently, the fluxes through boundaries other than the cross sections under consideration are zero, as
the unit normals of the zonal boundaries are perpendicular to wind direction and there is no flux through any upwind meridional
boundary. Thus, the emission rate is equal to the flux through the kth cross section for all k and given by
100 100 Φk =
Z
V
(∇· Ev)dV =
I
∂V =S
Ev · dS =
X
i
Ek,i v∆li = v∆l
X
i
Ek,i = v · ∆l · MCO · O2
NA · ACO · XO2
X
i
(∆XCO)k,i
(1) Φk =
Z
V
(∇· Ev)dV =
I
∂V =S
Ev · dS =
X
i
Ek,i v∆li = v∆l
X
i
Ek,i = v · ∆l · MCO · O2
NA · ACO · XO2
X
i
(∆XCO)k,i
(1)
Here, ∆l represents the size of a grid cell and i corresponds to the meridional summation along the respective cross section
given by k. The molar mass of carbon monoxide, MCO, is 28.01g mol−1, the Avogadro constant, NA, is 6.022·1023 molec mol−1,
the O2 column (in units of molecules per area) depends on the actual mean surface pressure, and the dry air mole fraction of (1) Φk =
Z
V
(∇· Ev)dV =
I
∂V =S
Ev · dS =
X
i
Ek,i v∆li = v∆l
X
i
Ek,i = NA · ACO · XO2
X
i
(∆XCO)k,i
(1)
Here, ∆l represents the size of a grid cell and i corresponds to the meridional summation along the respective cross section
given by k. The molar mass of carbon monoxide, MCO, is 28.01g mol−1, the Avogadro constant, NA, is 6.022·1023 molec mol−1,
the O2 column (in units of molecules per area) depends on the actual mean surface pressure, and the dry air mole fraction of Here, ∆l represents the size of a grid cell and i corresponds to the meridional summation along the respective cross section
given by k. If there are less than five such Φk, this
particular day will not be used any further.i From the pool of available days, we select those that fulfill certain criteria (concerning data ground scatter, meridional asymmetry, and wind history), which are listed below, for calculating the averaged long-term emis-
115
sion rate ¯Φ of the respective source region (see Schneising et al. (2020b) for details). To better account for the quasi-point
source character of steelworks in contrast to the larger emission regions analysed in Schneising et al. (2020b), we use smaller
regions according to Figure 2 (e.g. cross sections of about 100 km length) and the following selection criteria optimised for
XCO: at least 50% of the plume, hot spot, and background regions have to be filled with data (additionally at least 20% each of the northern and southern half of the background region), v ∈(1.5m s−1,9m s−1), the coverage and background distri-
120
bution is required to be sufficiently uniform with respect to the equator (nN
p > 0.6 · nS
p , nS
p > 0.6 · nN
p , | ¯EN
b −¯ES
b | < 3ppb,
σ(Eb) < 4ppb), where ¯E is the mean enhancement of a region, n is the corresponding number of grid cells, and σ is the
standard deviation; ·N,S
b,p refers to the northern/southern half of the background/plume region. Additionally, days with wind di-
rection changes exceeding 30◦within the analysed wind history of 2 hours are also excluded. There is no criterion preventing negative meridional gradients ( ¯Ep < ¯Eb) and associated negative emissions to ensure an unbiased mean long-term emission
125
estimate ¯Φ. For small emissions, inversion noise can result in negative values, whose suppression would cause an overesti-
mation of the mean emission. The calculation method for the uncertainty of the averaged long-term emission rate ¯Φ from the
individual daily uncertainties by error propagation has been retained exactly as described in Schneising et al. (2020b). The European Union Emissions Trading System (EU ETS) regulates greenhouse gas emissions of energy-intensive indus-
tries and is based on the "cap and trade" principle. The cap limits the amount of greenhouse gases allowed to be emitted by an
130 The European Union Emissions Trading System (EU ETS) regulates greenhouse gas emissions of energy-intensive indus-
tries and is based on the "cap and trade" principle. 2
Data and methods To assess the emission, we use the divergence theorem and compute the flux of the vector field Ev through cross 4 3
Results and discussion The steel production sites in Germany that still utilise the conventional Blast Furnace–Basic Oxygen Furnace production route
are located in Duisburg, Dillingen/Saar, Salzgitter, Bremen, and Eisenhüttenstadt (ordered by pig iron and steel production
from high to low), which together account for approximately 70% of German steel production (Harpprecht et al., 2022). These
145
production sites have been analysed using the cross-sectional flux method to determine CO emissions during the time period
2018-2022. Theil-
Sen regression is a robust method, which is insensitive to outliers and influential points by using the median of the slopes of all
possible lines formed by pairs of points (Sen, 1968). The corresponding confidence interval is determined by bootstrapping,
140
fitting the Theil-Sen regressor to each resample, and analysing the resulting distribution of regression coefficients. possible lines formed by pairs of points (Sen, 1968). The corresponding confidence interval is determined by bootstrapping,
140
fitting the Theil-Sen regressor to each resample, and analysing the resulting distribution of regression coefficients. The cap limits the amount of greenhouse gases allowed to be emitted by an
130 5 5 3.1
Estimation of site-specific CO emissions The North Rhine-Westphalian city of Duisburg has a long history as a centre of the steel The North Rhine-Westphalian city of Duisburg has a long history as a centre of the steel industry as the region’s proximity The North Rhine-Westphalian city of Duisburg has a long history as a centre of the steel industry as the region s proximity
to coal and iron ore reserves made it an ideal location for steel production. The city is home to two of the most prolific steel
150
plants in Germany in service since more than a hundred years: Integriertes Hüttenwerk Duisburg with 4 blast furnaces and
Glocke Duisburg with 2 blast furnaces. The averaged multi-year CO enhancement distribution for Duisburg, which exhibits
a pronounced plume structure, and the daily emission estimates are displayed in Figure 3. The associated mean CO emission
estimate is determined by the daily estimates and amounts to 397 ± 58kt yr−1. The steel industry is one of the most important sectors of the economy in the German federal state of Saarland. Dillinger
155
Hütte is the most significant steel producing site in the region, with production of steel dating back to the 17th century. Today,
Dillingen is the only production site for pig iron in the Saarland, which is subsequently further refined into crude steel. Two
blast furnaces are operated on the site. Figure 4 illustrates both the average CO enhancement distribution and the daily emission
estimates for Dillingen. As in the case of Duisburg, there is a distinct plume shape visible in the long-term wind-rotated mean. The steel industry is one of the most important sectors of the economy in the German federal state of Saarland. Dillinger
155
Hütte is the most significant steel producing site in the region, with production of steel dating back to the 17th century. Today,
Dillingen is the only production site for pig iron in the Saarland, which is subsequently further refined into crude steel. Two
blast furnaces are operated on the site. Figure 4 illustrates both the average CO enhancement distribution and the daily emission
estimates for Dillingen. As in the case of Duisburg, there is a distinct plume shape visible in the long-term wind-rotated mean. The corresponding mean CO emission estimate based on the daily emissions is 157 ± 52kt yr−1. 160
Salzgitter steel works is a Blast Furnace–Basic Oxygen Furnace steel plant operating in Salzgitter, Lower Saxony. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. installation and is quantified in emission allowances, which can be traded with each other. For each year, the companies op-
erating the installations are obligated to surrender sufficient allowances to completely offset their actual emissions. Therefore,
industrial installions are required to have an approved monitoring plan for monitoring and reporting annual emissions. These
reported emissions data are verified annually by accredited independent verifiers (European Union, 2018). The corresponding
information is available on EUETS.INFO (https://www.euets.info/, last access: 14 November 2023) providing verified annual
135
CO2 emissions and surrendered allowances on the level of emitting installations and on country level. installation and is quantified in emission allowances, which can be traded with each other. For each year, the companies op-
erating the installations are obligated to surrender sufficient allowances to completely offset their actual emissions. Therefore,
industrial installions are required to have an approved monitoring plan for monitoring and reporting annual emissions. These
reported emissions data are verified annually by accredited independent verifiers (European Union, 2018). The correspondingi information is available on EUETS.INFO (https://www.euets.info/, last access: 14 November 2023) providing verified annual
135
CO2 emissions and surrendered allowances on the level of emitting installations and on country level. The CO/CO2 emission ratio is determined by Theil-Sen regression of the derived CO emissions for the different sites and
the respective verified CO2 emissions from the production of pig iron or steel available from the emission trading data. Theil-
Sen regression is a robust method, which is insensitive to outliers and influential points by using the median of the slopes of all The CO/CO2 emission ratio is determined by Theil-Sen regression of the derived CO emissions for the different sites and
the respective verified CO2 emissions from the production of pig iron or steel available from the emission trading data. Theil-
Sen regression is a robust method, which is insensitive to outliers and influential points by using the median of the slopes of all The CO/CO2 emission ratio is determined by Theil-Sen regression of the derived CO emissions for the different sites and
the respective verified CO2 emissions from the production of pig iron or steel available from the emission trading data. 3.1
Estimation of site-specific CO emissions The
history of the site can be traced back to the interwar period in the early 20th century. During that time, an initiative aiming The corresponding mean CO emission estimate based on the daily emissions is 157 ± 52kt yr−1. 160
Salzgitter steel works is a Blast Furnace–Basic Oxygen Furnace steel plant operating in Salzgitter, Lower Saxony. The
history of the site can be traced back to the interwar period in the early 20th century. During that time, an initiative aiming 6 Figure 3. Mean CO enhancement distribution and associated integrated enhancement along the cross sections (top) as well as daily emission
estimates Φ for the steel plants in Duisburg (bottom). The mean CO emission ¯Φ is calculated from the daily emissions. The original daily
wind directions, defined as the direction in which the wind blows, are visually represented in the wind rose overlaid in the upper left corner. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Figure 3. Mean CO enhancement distribution and associated integrated enhancement along the cross sections (top) as well as daily emission
estimates Φ for the steel plants in Duisburg (bottom). The mean CO emission ¯Φ is calculated from the daily emissions. The original daily
wind directions, defined as the direction in which the wind blows, are visually represented in the wind rose overlaid in the upper left corner. Figure 3. Mean CO enhancement distribution and associated integrated enhancement along the cross sections (top) as well as daily emission
estimates Φ for the steel plants in Duisburg (bottom). The mean CO emission ¯Φ is calculated from the daily emissions. The original daily
wind directions, defined as the direction in which the wind blows, are visually represented in the wind rose overlaid in the upper left corner. Figure 4. As Figure 3 but for Dillingen/Saar. Figure 4. As Figure 3 but for Dillingen/Saar. 7 Figure 5. As previous figures but for Salzgitter. at establishing a self-sufficient German steel industry included the construction of a massive steel plant in Salzgitter. After
shutdown and recommissioning, the site operates 3 blast furnaces today. The mean CO enhancement distribution is shown
https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Figure 5. As previous figures but for Salzgitter. Figure 5. As previous figures but for Salzgitter. 3.1
Estimation of site-specific CO emissions f
S l
i Figure 5. As previous figures but for Salzgitter. at establishing a self-sufficient German steel industry included the construction of a massive steel plant in Salzgitter. After
shutdown and recommissioning, the site operates 3 blast furnaces today. The mean CO enhancement distribution is shown
together with the daily emission estimates in Figure 5. The average CO emission is estimated to be 125 ± 48kt yr−1. 65 at establishing a self-sufficient German steel industry included the construction of a massive steel plant in Salzgitter. After
shutdown and recommissioning, the site operates 3 blast furnaces today. The mean CO enhancement distribution is shown together with the daily emission estimates in Figure 5. The average CO emission is estimated to be 125 ± 48kt yr−1. 165
The Bremen steel plant with 2 blast furnaces has its roots in a long history of steel production in the region. The reason
for establishing steelworks at this strategic location was the access to key transportation routes, including rivers and ports, that
facilitated the import of raw materials and the export of finished steel products. Over the years, the plant underwent several
redesigns, mergers and expansions to meet the changing needs of the steel industry. The averaged CO enhancement distribution together with the daily emission estimates in Figure 5. The average CO emission is estimated to be 125 ± 48kt yr−1. 165
The Bremen steel plant with 2 blast furnaces has its roots in a long history of steel production in the region. The reason
for establishing steelworks at this strategic location was the access to key transportation routes, including rivers and ports, that
facilitated the import of raw materials and the export of finished steel products. Over the years, the plant underwent several
redesigns, mergers and expansions to meet the changing needs of the steel industry. The averaged CO enhancement distribution and the daily emission estimates are displayed in Figure 6. The associated mean CO emission estimate is 92 ± 59kt yr−1. 170
The history of the Eisenhüttenstadt plant located in the German federal state of Brandenburg began in the 1950s as the
Eisenhüttenkombinat in East Germany producing pig iron with 6 blast furnaces. In the 1980s, a Linz–Donawitz steelworks
was installed. After German reunification a new blast furnace was built, which is the only one still in operation today. 3.1
Estimation of site-specific CO emissions Figure 7
illustrates both the average CO enhancement distribution and the daily emission estimates. The corresponding mean CO and the daily emission estimates are displayed in Figure 6. The associated mean CO emission estimate is 92 ± 59kt yr−1. 170
The history of the Eisenhüttenstadt plant located in the German federal state of Brandenburg began in the 1950s as the
Eisenhüttenkombinat in East Germany producing pig iron with 6 blast furnaces. In the 1980s, a Linz–Donawitz steelworks
was installed. After German reunification a new blast furnace was built, which is the only one still in operation today. Figure 7
illustrates both the average CO enhancement distribution and the daily emission estimates. The corresponding mean CO and the daily emission estimates are displayed in Figure 6. The associated mean CO emission estimate is 92 ± 59kt yr−1. 170
The history of the Eisenhüttenstadt plant located in the German federal state of Brandenburg began in the 1950s as the
Eisenhüttenkombinat in East Germany producing pig iron with 6 blast furnaces. In the 1980s, a Linz–Donawitz steelworks
was installed. After German reunification a new blast furnace was built, which is the only one still in operation today. Figure 7
illustrates both the average CO enhancement distribution and the daily emission estimates. The corresponding mean CO emission estimate is 48 ± 55kt yr−1. In contrast to the other analysed production sites, the emissions seem to be close to the
175
detection limit because only a rather weak plume is observable in the average CO distribution and there is hardly any variation
of the associated sums along the cross-sections. In accordance with this finding, the mean emission estimate is similar in
magnitude to the corresponding uncertainty indicating that the derived uncertainties are generally realistic. emission estimate is 48 ± 55kt yr−1. In contrast to the other analysed production sites, the emissions seem to be close to the
175
detection limit because only a rather weak plume is observable in the average CO distribution and there is hardly any variation
of the associated sums along the cross-sections. In accordance with this finding, the mean emission estimate is similar in
magnitude to the corresponding uncertainty indicating that the derived uncertainties are generally realistic. emission estimate is 48 ± 55kt yr−1. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. 3.2
Air quality assessment According to German air quality standards, the maximum allowed daily 8-hour mean of ambient CO is 10mg m−3 (Umwelt-
180
bundesamt, 2017). Typical background values in Germany are about 0.2mg m−3 (Umweltbundesamt, 2022). The largest local
daily enhancement anomalies occurring in the vicinity of German steelworks reach about 50ppb in very rare cases, which
translate to a total column enhancement E of roughly 0.5g m−2. It is assumed that the excess CO from the steel production
site is located in the well-mixed boundary layer and that the associated boundary layer concentration anomaly ∆ρbl (in units
of mass per volume) can be determined by division by the boundary layer height hbl (Schneising et al 2020a):
185 ∆ρbl = E
hbl
(2)
Assuming a boundary layer height of 500m, the boundary layer anomaly is about 1mg m−3, which is well below the air quality
standard of 10mg m−3 even after adding typical background concentrations. The figures in Section 3.1 show that the maximum annual averaged enhancements due to steelworks are of the order of ∆ρbl = E
hbl (2) Assuming a boundary layer height of 500m, the boundary layer anomaly is about 1mg m−3, which is well below the air quality
standard of 10mg m−3 even after adding typical background concentrations. The figures in Section 3.1 show that the maximum annual averaged enhancements due to steelworks are of the order of Assuming a boundary layer height of 500m, the boundary layer anomaly is about 1mg m−3, which is well below the air quality
standard of 10mg m−3 even after adding typical background concentrations. 10ppb locally, which corresponds to an annual mean boundary layer anomaly of about 0.2mg m−3 using the above assump-
190
tions. Adding a typical background value gives a maximum total annual mean concentration at TROPOMI resolution of about
0.4mg m−3 in the vicinity of steel production sites, which is in agreement with actually measured values, e.g. in Dillingen
(Umweltbundesamt, 2022). Consequently, the rough calculation has confirmed that the CO emissions from the analysed steel-
works are not an air quality issue. 3.1
Estimation of site-specific CO emissions In contrast to the other analysed production sites, the emissions seem to be close to the
175
detection limit because only a rather weak plume is observable in the average CO distribution and there is hardly any variation
of the associated sums along the cross-sections. In accordance with this finding, the mean emission estimate is similar in
magnitude to the corresponding uncertainty indicating that the derived uncertainties are generally realistic. 8 https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Figure 6. As previous figures but for Bremen. Figure 7. As previous figures but for Eisenhüttenstadt. 9 Figure 6. As previous figures but for Bremen. Figure 6. As previous figures but for Bremen. Figure 6. As previous figures but for Bremen. Figure 7. As previous figures but for Eisenhüttenstadt. Figure 7. As previous figures but for Eisenhüttenstadt. Figure 7. As previous figures but for Eisenhüttenstadt. 9 9 3.3
Sector-specific CO/CO2 emission ratio
195 3.3
Sector-specific CO/CO2 emission ratio
195
The European Union Emissions Trading System (EU ETS) provides verified annual CO2 emissions on the level of emitting
installations. The associated mean emissions of the steel production sites for the time period analysed here (2018-2022) are
summarised in Table 1. Figure 8 demonstrates that CO and CO2 emissions from the production of pig iron or steel are highly correlated. It is The European Union Emissions Trading System (EU ETS) provides verified annual CO2 emissions on the level of emitting
installations. The associated mean emissions of the steel production sites for the time period analysed here (2018-2022) are
summarised in Table 1. Figure 8 demonstrates that CO and CO2 emissions from the production of pig iron or steel are highly correlated. It is g
p
p g
g y
assumed that the temporal sampling of available daily CO emission estimates is representative for the actual variability of steel
200
production and associated reported CO2 emissions at the analysed sites. As the data point representing Duisburg is quite far
away from the main cluster of data points, it may be an influential point with large impact on the results when performing
an ordinary least-squares (OLS) regression, which potentially complicates the interpretation of the fitted coefficients and their
uncertainties. This potential issue can be mitigated by using the robust Theil-Sen regression (Sen, 1968), which calculates the assumed that the temporal sampling of available daily CO emission estimates is representative for the actual variability of steel
200
production and associated reported CO2 emissions at the analysed sites. As the data point representing Duisburg is quite far
away from the main cluster of data points, it may be an influential point with large impact on the results when performing
an ordinary least-squares (OLS) regression, which potentially complicates the interpretation of the fitted coefficients and their
uncertainties. This potential issue can be mitigated by using the robust Theil-Sen regression (Sen, 1968), which calculates the assumed that the temporal sampling of available daily CO emission estimates is representative for the actual variability of steel
200
production and associated reported CO2 emissions at the analysed sites. 3.3
Sector-specific CO/CO2 emission ratio
195 As the data point representing Duisburg is quite far
away from the main cluster of data points, it may be an influential point with large impact on the results when performing
an ordinary least-squares (OLS) regression, which potentially complicates the interpretation of the fitted coefficients and their
uncertainties. This potential issue can be mitigated by using the robust Theil-Sen regression (Sen, 1968), which calculates the slope by taking the median of all possible slopes between individual pairs of data points. To compute a confidence interval for
205
the Theil-Sen regression, we use bootstrapping (plus additional random perturbation of the data points in y-direction according
to the respective uncertainties of the individual CO emission estimates) to generate multiple resamples of the data and fit the
Theil-Sen Regressor to each resample. This results in a set of regression coefficients from which the final regression and the
associated 1σ-confidence interval are derived by determining the median of slopes and intercepts as well as the 16th and 84th slope by taking the median of all possible slopes between individual pairs of data points. To compute a confidence interval for
205
the Theil-Sen regression, we use bootstrapping (plus additional random perturbation of the data points in y-direction according
to the respective uncertainties of the individual CO emission estimates) to generate multiple resamples of the data and fit the
Theil-Sen Regressor to each resample. This results in a set of regression coefficients from which the final regression and the
associated 1σ-confidence interval are derived by determining the median of slopes and intercepts as well as the 16th and 84th
percentile of the distribution
210 10 https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Table 1. Mean emissions for the time period 2018-2022. The CO2 emissions from the production of pig iron or steel are obtained from the
European Union Emissions Trading System (EU ETS), the CO emissions are estimated in this study as well as extracted from the Thru.de
portal (providing key environmental data from industrial facilities in Germany) for comparison. EU ETS
This study
Thru.de
CO2 emissions
CO emissions
CO emissions
Site
ID
Operator
Blast furnaces
(Mt yr−1)
(kt yr−1)
(kt yr−1)
Duisburg
DU
Thyssenkrupp Steel Europe
4
7.75
397 ± 58
315
Hüttenwerke Krupp Mannesmann
2
4.61
Dillingen
DI
Dillinger Hüttenwerke
2
4.15
157 ± 52
90
Salzgitter
SZ
Salzgitter Flachstahl
3
3.92
125 ± 48
66
Bremen
HB
ArcelorMittal Bremen
2
2.30
92 ± 59
63
Eisenhüttenstadt
EH
ArcelorMittal Eisenhüttenstadt
1
1.48
48 ± 55
40
Figure 8. Theil-Sen regression of the derived CO emissions for the different sites and the respective CO2 emissions according to the
European Union Emissions Trading System (EU ETS) to determine the CO/CO2 emission ratio and the associated 1σ-confidence interval. The shaded region surrounding the regression line represents the prediction interval, which is determined by assessing the standard deviation
of Theil-Sen regressions from multiple bootstrap samples. R2 is the coefficient of determination of the prediction of the Theil-Sen regression. EU ETS
This study
Thru.de
CO2 emissions
CO emissions
CO emissions
Site
ID
Operator
Blast furnaces
(Mt yr−1)
(kt yr−1)
(kt yr−1)
Duisburg
DU
Thyssenkrupp Steel Europe
4
7.75
397 ± 58
315
Hüttenwerke Krupp Mannesmann
2
4.61
Dillingen
DI
Dillinger Hüttenwerke
2
4.15
157 ± 52
90
Salzgitter
SZ
Salzgitter Flachstahl
3
3.92
125 ± 48
66
Bremen
HB
ArcelorMittal Bremen
2
2.30
92 ± 59
63
Eisenhüttenstadt
EH
ArcelorMittal Eisenhüttenstadt
1
1.48
48 ± 55
40 Figure 8. Theil-Sen regression of the derived CO emissions for the different sites and the respective Figure 8. Theil-Sen regression of the derived CO emissions for the different sites and the respective CO2 emissions according to the
European Union Emissions Trading System (EU ETS) to determine the CO/CO2 emission ratio and the associated 1σ-confidence interval. The shaded region surrounding the regression line represents the prediction interval, which is determined by assessing the standard deviation
of Theil-Sen regressions from multiple bootstrap samples. R2 is the coefficient of determination of the prediction of the Theil-Sen regression. A facility is defined as
one or more installations at the same site that are run by one operator. For example, a facility in the steel industry (integrated CO/CO2 emission ratio is approximately 2.0%. However, this value cannot be directly compared with ours either, because
230
this activity also comprises other processes than conventional primary steel production. Deriving a sector-specific emission
ratio based on Thru.de data is also not straightforward because the reported releases are not provided on the level of emitting
installations (in contrast to the European Union Emissions Trading System), but on the facility level. A facility is defined as
one or more installations at the same site that are run by one operator. For example, a facility in the steel industry (integrated steelworks) may include a large number of different installations (e.g. coking plant, sintering plant, blast furnace, basic oxygen
235
furnace, rolling mill, power plant), whose combined emissions are then attributed to the so-called main activity of the facility,
which is usually the production of pig iron or steel. While the CO emissions are actually mainly attributable to the main activity,
the reported CO2 emissions typically also include significant contributions from other sectors such as the energy sector. As a
consequence, the facility-based Thru.de CO/CO2 emission ratio underestimates the actually targeted sector-specific emission ratio, just like the other potential comparison data sets discussed so far. However, the extent of underestimation is not even
240
consistent from site to site, but depends on which non-main activities are explicitly carried out additionally at a given facility. It is therefore not possible to obtain a representative CO/CO2 emission ratio from this data set by regressing the individual
CO and CO2 emissions of the respective facilities. Nevertheless, the reported Thru.de CO releases can be directly compared
with our emission estimates, because only the place of origin and not the exact breakdown by sector is relevant for this pur- ratio, just like the other potential comparison data sets discussed so far. However, the extent of underestimation is not even
240
consistent from site to site, but depends on which non-main activities are explicitly carried out additionally at a given facility. It is therefore not possible to obtain a representative CO/CO2 emission ratio from this data set by regressing the individual
CO and CO2 emissions of the respective facilities. regression of the derived CO emissions for the different sites and the respective CO2 emissions accordi Figure 8. Theil-Sen regression of the derived CO emissions for the different sites and the respective CO2 emissions according to the
European Union Emissions Trading System (EU ETS) to determine the CO/CO2 emission ratio and the associated 1σ-confidence interval. The shaded region surrounding the regression line represents the prediction interval, which is determined by assessing the standard deviation
of Theil-Sen regressions from multiple bootstrap samples. R2 is the coefficient of determination of the prediction of the Theil-Sen regression. The performed robust Theil-Sen regression of CO and CO2 emissions is illustrated in Figure 8. The shaded area around the
regression line visually represents the prediction interval, which is determined by the standard deviation of the regressions of
the multiple bootstrap samples and effectively reflects the predictive uncertainty of the model. The resulting CO/CO2 emission 11 https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. ratio for the analysed steelworks amounts to 3.24%[2.73−3.89; 1σ]; the corresponding 95%-confidence interval (obtained from
the 2.5th an 97.5th percentile of the slope distribution) is [1.90,5.50]. 5 ratio for the analysed steelworks amounts to 3.24%[2.73−3.89; 1σ]; the corresponding 95%-confidence interval (obtained from
h
h
7
h
il
f h
l
di
ib i
) i [
] the 2.5th an 97.5th percentile of the slope distribution) is [1.90,5.50]. 215
This sector-specific estimate can be hardly compared to global inventories such as the Emissions Database for Global Atmo-
spheric Research (EDGAR) (Crippa et al., 2020) because the underlying sector discrimination is typically not detailed enough. For example, iron and steel production is part of the EDGAR activity “Industrial combustion and processes” that also in-
cludes sectors with significantly less CO emissions than steelworks at comparable CO2 emissions. Consequently, the EDGAR This sector-specific estimate can be hardly compared to global inventories such as the Emissions Database for Global Atmo-
spheric Research (EDGAR) (Crippa et al., 2020) because the underlying sector discrimination is typically not detailed enough. For example, iron and steel production is part of the EDGAR activity “Industrial combustion and processes” that also in-
cludes sectors with significantly less CO emissions than steelworks at comparable CO2 emissions. Consequently, the EDGAR CO/CO2 emission ratio for the entirety of industrial processes is smaller than our sector-specific estimate for the steel industry
220
and amounts to about 0.5% for Germany. Similar representativeness issues arise when comparing to the estimated CO/CO2
ratios for cities of Wu et al. (2022): their estimate for the Chinese cities with metal production is about 1% (when transformed
to a mass ratio) but there are also other sectors, such as energy production, with significantly smaller CO/CO2 emission ratios
(significant CO2 emissions, but virtually no CO emissions) contributing to the derived city averages. CO/CO2 emission ratio for the entirety of industrial processes is smaller than our sector-specific estimate for the steel industry
220
and amounts to about 0.5% for Germany. Similar representativeness issues arise when comparing to the estimated CO/CO2
ratios for cities of Wu et al. (2022): their estimate for the Chinese cities with metal production is about 1% (when transformed
to a mass ratio) but there are also other sectors, such as energy production, with significantly smaller CO/CO2 emission ratios
(significant CO2 emissions, but virtually no CO emissions) contributing to the derived city averages. CO/CO2 emission ratio for the entirety of industrial processes is smaller than our sector-specific estimate for the steel industry
220
and amounts to about 0.5% for Germany. Similar representativeness issues arise when comparing to the estimated CO/CO2
ratios for cities of Wu et al. (2022): their estimate for the Chinese cities with metal production is about 1% (when transformed
to a mass ratio) but there are also other sectors, such as energy production, with significantly smaller CO/CO2 emission ratios
(significant CO2 emissions, but virtually no CO emissions) contributing to the derived city averages. Another register of emissions from industrial facilities in Germany is the Thru.de portal provided by the Umweltbundesamt
225
(https://thru.de/en/, last access: 14 November 2023) including annual loads of CO and CO2 based on measurements, calcula-
tions, or estimates of the operators. The reported values are reviewed for completeness and plausibility by authorities at federal
state level, but unlike the emissions trading data used to derive the CO/CO2 emission ratio, no independent verification is
required. Using the reported Thru.de mean releases from the German metal industry for the years 2018-2022, the associated Another register of emissions from industrial facilities in Germany is the Thru.de portal provided by the Umweltbundesamt
225
(https://thru.de/en/, last access: 14 November 2023) including annual loads of CO and CO2 based on measurements, calcula-
tions, or estimates of the operators. The reported values are reviewed for completeness and plausibility by authorities at federal
state level, but unlike the emissions trading data used to derive the CO/CO2 emission ratio, no independent verification is
required. Using the reported Thru.de mean releases from the German metal industry for the years 2018-2022, the associated CO/CO2 emission ratio is approximately 2.0%. However, this value cannot be directly compared with ours either, because
230
this activity also comprises other processes than conventional primary steel production. Deriving a sector-specific emission
ratio based on Thru.de data is also not straightforward because the reported releases are not provided on the level of emitting
installations (in contrast to the European Union Emissions Trading System), but on the facility level. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. The estimate that is conceptually closest to our estimate is obtained by using the outputs of the sintering plant, blast furnace,
and basic oxygen furnace of the comprehensive inventory of a Polish integrated steel plant (Burchart-Korol, 2013) resulting in
a CO/CO2 emission ratio of 2.60%. This value is considerably closer to our sector-specific estimate for steel production than
50
the other less representative estimates and within the associated 95%-confidence interval (even near the estimated 1σ-range). This consistency further corroborates the potential feasibility of using CO as a proxy for CO2 emissions from comparable steel
production sites The estimate that is conceptually closest to our estimate is obtained by using the outputs of the sintering plant, blast furnace,
and basic oxygen furnace of the comprehensive inventory of a Polish integrated steel plant (Burchart-Korol, 2013) resulting in a CO/CO2 emission ratio of 2.60%. This value is considerably closer to our sector-specific estimate for steel production than
250
the other less representative estimates and within the associated 95%-confidence interval (even near the estimated 1σ-range). This consistency further corroborates the potential feasibility of using CO as a proxy for CO2 emissions from comparable steel
production sites. a CO/CO2 emission ratio of 2.60%. This value is considerably closer to our sector-specific estimate for steel production than
250
the other less representative estimates and within the associated 95%-confidence interval (even near the estimated 1σ-range). This consistency further corroborates the potential feasibility of using CO as a proxy for CO2 emissions from comparable steel
production sites. Nevertheless, the reported Thru.de CO releases can be directly compared
with our emission estimates, because only the place of origin and not the exact breakdown by sector is relevant for this pur- pose. The corresponding values are also listed in Table 1. In general, the reported Thru.de CO releases are systematically
245
smaller than our estimates. If the respective uncertainties are taken into account, there is no significant deviation in Bremen
and Eisenhüttenstadt, but systematic residual underestimates of less than 20% in the Thru.de data at the other sites. pose. The corresponding values are also listed in Table 1. In general, the reported Thru.de CO releases are systematically
245
smaller than our estimates. If the respective uncertainties are taken into account, there is no significant deviation in Bremen
and Eisenhüttenstadt, but systematic residual underestimates of less than 20% in the Thru.de data at the other sites. 12 12 Data availability. The carbon monoxide data product presented in this publication is available at http://www.iup.uni-bremen.de/carbon_ghg/
275
products/tropomi_wfmd/. 4
Conclusions If locally observed CO emissions are very sector-specific, i.e. the vast majority of CO emissions can be attributed to a single
sector, as in the case of pig iron or steel production analysed here, the usage of realistic installation-based bottom-up CO2 the accurate reporting of CO2 emissions within the framework of emissions trading enables a good calibration of the CO/CO2
265
emission ratio, which is thus of significant value to use CO as proxy for CO2 emissions from the steel industry in particular
for comparable Linz–Donawitz steel plants, also in less regulated countries with less stringent reporting requirements. If locally observed CO emissions are very sector-specific, i.e. the vast majority of CO emissions can be attributed to a single
sector, as in the case of pig iron or steel production analysed here, the usage of realistic installation-based bottom-up CO2 the accurate reporting of CO2 emissions within the framework of emissions trading enables a good calibration of the CO/CO2
265
emission ratio, which is thus of significant value to use CO as proxy for CO2 emissions from the steel industry in particular
for comparable Linz–Donawitz steel plants, also in less regulated countries with less stringent reporting requirements. If locally observed CO emissions are very sector-specific, i.e. the vast majority of CO emissions can be attributed to a single
sector, as in the case of pig iron or steel production analysed here, the usage of realistic installation-based bottom-up CO2 emission data broken down by activity type simplifies obtaining sector-specific CO/CO2 emission ratios. In contrast, this is
270
difficult to achieve by means of space-based CO2 measurements, because emissions from the sector in question are potentially
entangled with atmospheric signals from nearby anthropogenic CO2 emissions associated with other sectors such as electricity
production, as well as natural sources and sinks. Future accurate CO2 satellite missions with very high spatial resolution could
help to better separate emissions from neighbouring anthropogenic sources belonging to different sectors from space. emission data broken down by activity type simplifies obtaining sector-specific CO/CO2 emission ratios. In contrast, this is
270
difficult to achieve by means of space-based CO2 measurements, because emissions from the sector in question are potentially
entangled with atmospheric signals from nearby anthropogenic CO2 emissions associated with other sectors such as electricity
production, as well as natural sources and sinks. 4
Conclusions We conducted an analysis of carbon monoxide enhancements originating from German steel plants using the conventional
255
highly CO2-intensive Blast Furnace–Basic Oxygen Furnace production route. This analysis utilised daily measurements in the
shortwave infrared spectral range of the TROPOMI instrument on board the Sentinel-5 Precursor satellite to estimate the CO
emissions for these steelworks during the 2018-2022 period benefiting from TROPOMI’s distinctive attributes, including its
high quality measurements and comprehensive spatio-temporal coverage. These qualities enable us to systematically detect
and quantify sufficiently large emission sources during a single satellite overpass
260 We conducted an analysis of carbon monoxide enhancements originating from German steel plants using the conventional
255
highly CO2-intensive Blast Furnace–Basic Oxygen Furnace production route. This analysis utilised daily measurements in the
shortwave infrared spectral range of the TROPOMI instrument on board the Sentinel-5 Precursor satellite to estimate the CO
emissions for these steelworks during the 2018-2022 period benefiting from TROPOMI’s distinctive attributes, including its
high quality measurements and comprehensive spatio-temporal coverage. These qualities enable us to systematically detect and quantify sufficiently large emission sources during a single satellite overpass. 260
Together with the comprehensive availability of verified site-specific CO2 emission data from the production of pig iron or
steel available from the European Union Emissions Trading System, an estimate for the associated sector-specific CO/CO2
emission ratio is derived. The high correlation of CO and CO2 emissions suggests that the raw material use and the involved
processes are comparable and reproducible for the steelworks studied. The focus on German steel plants has the advantage that and quantify sufficiently large emission sources during a single satellite overpass. 260
Together with the comprehensive availability of verified site-specific CO2 emission data from the production of pig iron or
steel available from the European Union Emissions Trading System, an estimate for the associated sector-specific CO/CO2
emission ratio is derived. The high correlation of CO and CO2 emissions suggests that the raw material use and the involved
processes are comparable and reproducible for the steelworks studied. The focus on German steel plants has the advantage that the accurate reporting of CO2 emissions within the framework of emissions trading enables a good calibration of the CO/CO2
265
emission ratio, which is thus of significant value to use CO as proxy for CO2 emissions from the steel industry in particular
for comparable Linz–Donawitz steel plants, also in less regulated countries with less stringent reporting requirements. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Author contributions. OS designed and operated the TROPOMI/WFMD satellite retrievals, performed the data analysis, interpreted the re-
sults, and wrote the paper. MB, MR, MW, HeB, JPB, HB made significant contributions to the conception of the analysis and the improvement
of the manuscript. All authors discussed the results and commented on the paper. Competing interests. The authors declare that they have no conflict of interest. 280 Competing interests. The authors declare that they have no conflict of interest. 280 280 Acknowledgements. This publication contains modified Copernicus Sentinel data (2018-2022). Sentinel-5 Precursor is an ESA mission
implemented on behalf of the European Commission. The TROPOMI payload is a joint development by ESA and the Netherlands Space
Office (NSO). The Sentinel-5 Precursor ground-segment development has been funded by ESA and with national contributions from The
Netherlands, Germany, and Belgium. We thank the European Centre for Medium-Range Weather Forecasts (ECMWF) for providing the
ERA5 reanalysis and acknowledge the use of carbon dioxide emission data from the European Union Emissions Trading System (EU ETS)
285
(https://www.euets.info/, last access: 14 November 2023). Acknowledgements. This publication contains modified Copernicus Sentinel data (2018-2022). Sentinel-5 Precursor is an ESA mission
implemented on behalf of the European Commission. The TROPOMI payload is a joint development by ESA and the Netherlands Space
Office (NSO). The Sentinel-5 Precursor ground-segment development has been funded by ESA and with national contributions from The
Netherlands, Germany, and Belgium. We thank the European Centre for Medium-Range Weather Forecasts (ECMWF) for providing the
ERA5 reanalysis and acknowledge the use of carbon dioxide emission data from the European Union Emissions Trading System (EU ETS)
285 ERA5 reanalysis and acknowledge the use of carbon dioxide emission data from the European Union Emissions Trading System (EU ETS)
285
(https://www.euets.info/, last access: 14 November 2023). ERA5 reanalysis and acknowledge the use of carbon dioxide emission data from the European Union Emissions Trading System (EU ETS)
285
(https://www.euets.info/, last access: 14 November 2023). Financial support. The research leading to the presented results received funding from the European Space Agency (ESA) via the projects
GHG-CCI+ and MethaneCAMP (ESA contract nos. 4000126450/19/I-NB and 4000137895/22/I-AG) and from the German ministry of
education and research (BMBF) within its project ITMS via grant 01 LK2103A. 4
Conclusions Future accurate CO2 satellite missions with very high spatial resolution could
help to better separate emissions from neighbouring anthropogenic sources belonging to different sectors from space. emission data broken down by activity type simplifies obtaining sector-specific CO/CO2 emission ratios. In contrast, this is
270
difficult to achieve by means of space-based CO2 measurements, because emissions from the sector in question are potentially
entangled with atmospheric signals from nearby anthropogenic CO2 emissions associated with other sectors such as electricity
production, as well as natural sources and sinks. Future accurate CO2 satellite missions with very high spatial resolution could
help to better separate emissions from neighbouring anthropogenic sources belonging to different sectors from space. 13 References Backes, J. G., Suer, J., Pauliks, N., Neugebauer, S., and Traverso, M.: Life Cycle Assessment of an Integrated Steel Mill Using Primary
Manufacturing Data: Actual Environmental Profile, Sustainability, 13, https://doi.org/10.3390/su13063443, 2021. i
Bovensmann, H., Burrows, J. P., Buchwitz, M., Frerick, J., Noël, S., Rozanov, V. V., Chance, K. V., and Goede, A. P. H.:
295
SCIAMACHY – Mission Objectives and Measurement Modes, J. Atmos. Sci., 56, 127–150, https://doi.org/10.1175/1520-
0469(1999)056<0127:SMOAMM>2.0.CO;2, 1999. Burchart-Korol, D.: Life cycle assessment of steel production in Poland: a case study, Journal of Cleaner Production, 54, 235–243,
https://doi.org/10.1016/j.jclepro.2013.04.031, 2013. Bovensmann, H., Burrows, J. P., Buchwitz, M., Frerick, J., Noël, S., Rozanov, V. V., Chance, K. V., and Goede, A. P. H.:
295
SCIAMACHY – Mission Objectives and Measurement Modes, J. Atmos. Sci., 56, 127–150, https://doi.org/10.1175/1520-
0469(1999)056<0127:SMOAMM>2.0.CO;2, 1999. h
l
if
l
f
l
d
i
i
l
d
d
l
f
l
d
i
5
5 Burchart-Korol, D.: Life cycle assessment of steel production in Poland: a case study, Journal of Cleaner Production, 54, 235–243,
https://doi.org/10.1016/j.jclepro.2013.04.031, 2013. Burrows, J. P., Hölzle, E., Goede, A. P. H., Visser, H., and Fricke, W.: SCIAMACHY – Scanning Imaging Absorption Spectrometer for
300
Atmospheric Chartography, Acta Astronautica, 35, 445–451, https://doi.org/10.1016/0094-5765(94)00278-T, 1995. Crippa, M., Solazzo, E., Huang, G., Guizzardi, D., Koffi, E., Muntean, M., Schieberle, C., Friedrich, R., and Janssens-Maenhout,
G.: High resolution temporal profiles in the Emissions Database for Global Atmospheric Research, Scientific Data, 7, 121,
https://doi.org/10.1038/s41597-020-0462-2, 2020. Burrows, J. P., Hölzle, E., Goede, A. P. H., Visser, H., and Fricke, W.: SCIAMACHY – Scanning Imaging Absorption Spectrometer for
300
Atmospheric Chartography, Acta Astronautica, 35, 445–451, https://doi.org/10.1016/0094-5765(94)00278-T, 1995. p
g p y
p
g
Crippa, M., Solazzo, E., Huang, G., Guizzardi, D., Koffi, E., Muntean, M., Schieberle, C., Friedrich, R., and Janssens-Maenhout,
G.: High resolution temporal profiles in the Emissions Database for Global Atmospheric Research, Scientific Data, 7, 121,
https://doi.org/10.1038/s41597-020-0462-2, 2020. Drummond, J. R., Zou, J., Nichitiu, F., Kar, J., Deschambaut, R., and Hackett, J.: A review of 9-year performance and operation of the
305
MOPITT instrument, Adv. Space Res., 45, 760–774, https://doi.org/10.1016/j.asr.2009.11.019, 2010. European Union: Commission Implementing Regulation (EU) 2018/2067 of 19 December 2018 on the verification of data and on the Drummond, J. R., Zou, J., Nichitiu, F., Kar, J., Deschambaut, R., and Hackett, J.: A review of 9-year performance and operation of the
305
MOPITT instrument, Adv. Space Res., 45, 760–774, https://doi.org/10.1016/j.asr.2009.11.019, 2010. Drummond, J. References R., Zou, J., Nichitiu, F., Kar, J., Deschambaut, R., and Hackett, J.: A review of 9-year performance and operation of the
305
MOPITT instrument, Adv. Space Res., 45, 760–774, https://doi.org/10.1016/j.asr.2009.11.019, 2010. European Union: Commission Implementing Regulation (EU) 2018/2067 of 19 December 2018 on the verification of data and on the
accreditation of verifiers pursuant to Directive 2003/87/EC of the European Parliament and of the Council, available at: http://data.europa. eu/eli/reg_impl/2018/2067/2021-01-01 (last access: 6 November 2023), 2018. European Union: Commission Implementing Regulation (EU) 2018/2067 of 19 December 2018 on the verification of data and on the
accreditation of verifiers pursuant to Directive 2003/87/EC of the European Parliament and of the Council, available at: http://data.europa. eu/eli/reg_impl/2018/2067/2021-01-01 (last access: 6 November 2023), 2018. Graupner, Y., Weckenborg, C., and Spengler, T. S.: Low-carbon primary steelmaking using direct reduction and electric arc furnaces: Prospec-
310
tive environmental impact assessment, Procedia CIRP, 116, 696–701, https://doi.org/10.1016/j.procir.2023.02.117, 30th CIRP Life Cycle
Engineering Conference, 2023. Graupner, Y., Weckenborg, C., and Spengler, T. S.: Low-carbon primary steelmaking using direct reduction and electric arc furnaces: Prospec-
310
tive environmental impact assessment, Procedia CIRP, 116, 696–701, https://doi.org/10.1016/j.procir.2023.02.117, 30th CIRP Life Cycle
Engineering Conference, 2023. Harpprecht, C., Naegler, T., Steubing, B., Tukker, A., and Simon, S.: Decarbonization scenarios for the iron and steel in-
dustry in context of a sectoral carbon budget: Germany as a case study
Journal of Cleaner Production
380
134 846 Engineering Conference, 2023. Harpprecht, C., Naegler, T., Steubing, B., Tukker, A., and Simon, S.: Decarbonization scenarios for the iron and steel in-
dustry in context of a sectoral carbon budget: Germany as a case study, Journal of Cleaner Production, 380, 134 846,
https://doi.org/10.1016/j.jclepro.2022.134846, 2022. 315 https://doi.org/10.1016/j.jclepro.2022.134846, 2022. 315
He, K. and Wang, L.: A review of energy use and energy-efficient technologies for the iron and steel industry, Renewable and Sustainable
Energy Reviews, 70, 1022–1039, https://doi.org/10.1016/j.rser.2016.12.007, 2017. Hersbach, H., de Rosnay, P., Bell, B., Schepers, D., Simmons, A., Soci, C., Abdalla, S., Alonso-Balmaseda, M., Balsamo, G., Bechtold, P.,
Berrisford, P., Bidlot, J.-R., de Boisséson, E., Bonavita, M., Browne, P., Buizza, R., Dahlgren, P., Dee, D., Dragani, R., Diamantakis, M., He, K. and Wang, L.: A review of energy use and energy-efficient technologies for the iron and steel industry, Renewable and Sustainable
Energy Reviews, 70, 1022–1039, https://doi.org/10.1016/j.rser.2016.12.007, 2017. Flemming, J., Forbes, R., Geer, A. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. The TROPOMI/WFMD retrievals presented here were
performed on HPC facilities of the IUP, University of Bremen, funded under DFG/FUGG grant nos. INST 144/379-1 and INST 144/493-1. 290
The article processing charges for this open-access publication were covered by the University of Bremen. 14 14 https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Kildahl, H., Wang, L., Tong, L., and Ding, Y.: Cost effective decarbonisation of blast furnace – basic oxygen furnace steel production through
thermochemical sector coupling, Journal of Cleaner Production, 389, 135 963, https://doi.org/10.1016/j.jclepro.2023.135963, 2023. Kildahl, H., Wang, L., Tong, L., and Ding, Y.: Cost effective decarbonisation of blast furnace – basic oxygen furnace steel production through Kildahl, H., Wang, L., Tong, L., and Ding, Y.: Cost effective decarbonisation of blast furnace – basic oxygen f rmochemical sector coupling, Journal of Cleaner Production, 389, 135 963, https://doi.org/10.1016/j.jclepro.20 330 Kim, T. W., Bae, S. S., Lee, J. W., Lee, S.-M., Lee, J.-H., Lee, H. S., and Kang, S. G.: A biological process effective for the conversion
of CO-containing industrial waste gas to acetate, Bioresource Technology, 211, 792–796, https://doi.org/10.1016/j.biortech.2016.04.038,
2016. MacDonald, C. G., Mastrogiacomo, J.-P., Laughner, J. L., Hedelius, J. K., Nassar, R., and Wunch, D.: Estimating enhancement ra-
tios of nitrogen dioxide, carbon monoxide and carbon dioxide using satellite observations, Atmos. Chem. Phys., 23, 3493–3516,
335
https://doi.org/10.5194/acp-23-3493-2023, 2023. P k
H
J
S
P k
H
L b
kii
L
D
d B
K
W
A
f
i i
h
i i
f N
h MacDonald, C. G., Mastrogiacomo, J.-P., Laughner, J. L., Hedelius, J. K., Nassar, R., and Wunch, D.: Estimating enhancement ra-
tios of nitrogen dioxide, carbon monoxide and carbon dioxide using satellite observations, Atmos. Chem. Phys., 23, 3493–3516,
335
https://doi.org/10.5194/acp-23-3493-2023, 2023. Park, H., Jeong, S., Park, H., Labzovskii, L. D., and Bowman, K. W.: An assessment of emission characteristics of North-
ern Hemisphere cities using spaceborne observations of CO2, CO, and NO2, Remote Sensing of Environment, 254, 112 246, 335 tios of nitrogen dioxide, carbon monoxide and carbon dioxide using satellite observations, Atmos. Chem. Phys., 23, 3493–3516,
335
https://doi.org/10.5194/acp-23-3493-2023, 2023. Park, H., Jeong, S., Park, H., Labzovskii, L. D., and Bowman, K. W.: An assessment of emission characteristics of North-
ern Hemisphere cities using spaceborne observations of CO2, CO, and NO2, Remote Sensing of Environment, 254, 112 246,
https://doi.org/10.1016/j.rse.2020.112246, 2021. Park, H., Jeong, S., Park, H., Labzovskii, L. D., and Bowman, K. W.: An assessment of emission characteristics of North-
ern Hemisphere cities using spaceborne observations of CO2, CO, and NO2, Remote Sensing of Environment, 254, 112 246,
https://doi.org/10.1016/j.rse.2020.112246, 2021. Schneising, O., Buchwitz, M., Reuter, M., Bovensmann, H., Burrows, J. P., Borsdorff, T., Deutscher, N. M., Feist, D. G., Griffith, D. W. T.,
340
Hase, F., Hermans, C., Iraci, L. T., Kivi, R., Landgraf, J., Morino, I., Notholt, J., Petri, C., Pollard, D. F., Roche, S., Shiomi, K., Strong,
K., Sussmann, R., Velazco, V. A., Warneke, T., and Wunch, D.: A scientific algorithm to simultaneously retrieve carbon monoxide and
methane from TROPOMI onboard Sentinel-5 Precursor, Atmos. Meas. Tech., 12, 6771–6802, https://doi.org/10.5194/amt-12-6771-2019,
2019. Schneising, O., Buchwitz, M., Reuter, M., Bovensmann, H., and Burrows, J. P.: Severe Californian wildfires in November 2018 observed
345
from space: the carbon monoxide perspective, Atmos. Chem. Phys., 20, 3317–3332, https://doi.org/10.5194/acp-20-3317-2020, 2020a. Schneising, O., Buchwitz, M., Reuter, M., Vanselow, S., Bovensmann, H., and Burrows, J. P.: Remote sensing of methane leakage from
natural gas and petroleum systems revisited, Atmos. Chem. Phys., 20, 9169–9182, https://doi.org/10.5194/acp-20-9169-2020, 2020b. Schneising, O., Buchwitz, M., Hachmeister, J., Vanselow, S., Reuter, M., Buschmann, M., Bovensmann, H., and Burrows, J. P.: Advances in Schneising, O., Buchwitz, M., Hachmeister, J., Vanselow, S., Reuter, M., Buschmann, M., Bovensmann, H., and Burrows, J. P.: Advances in
retrieving XCH4 and XCO from Sentinel-5 Precursor: improvements in the scientific TROPOMI/WFMD algorithm, Atmos. Meas. Tech.,
350
16, 669–694, https://doi.org/10.5194/amt-16-669-2023, 2023. retrieving XCH4 and XCO from Sentinel-5 Precursor: improvements in the scientific TROPOMI/WFMD algorithm, Atmos. Meas. Tech.,
350
16, 669–694, https://doi.org/10.5194/amt-16-669-2023, 2023. Sen, P. K.: Estimates of the Regression Coefficient Based on Kendall’s Tau, Journal of the American Statistical Association, 63, 1379–1389,
1968. retrieving XCH4 and XCO from Sentinel-5 Precursor: improvements in the scientific TROPOMI/WFMD algorithm, Atmos. Meas. Tech.,
350
16, 669–694, https://doi.org/10.5194/amt-16-669-2023, 2023. S
P K E ti
t
f th R
i
C
ffi i
t B
d
K
d ll’ T
J
l f th A
i
St ti ti
l A
i ti
63 1379 1389 16, 669–694, https://doi.org/10.5194/amt-16-669-2023, 2023. Sen, P. K.: Estimates of the Regression Coefficient Based on Kendall’s Tau, Journal of the American Statistical Association, 63, 1379–1389,
1968. Sen, P. K.: Estimates of the Regression Coefficient Based on Kendall’s Tau, Journal of the American Statistical Association, 63, 1379–1389,
1968. Suer, J., Traverso, M., and Jäger, N.: Review of Life Cycle Assessments for Steel and Environmental Analysis of Future Steel Production
Scenarios, Sustainability, 14, https://doi.org/10.3390/su142114131, 2022. 355 Scenarios, Sustainability, 14, https://doi.org/10.3390/su142114131, 2022. 355
Suto, H., Kataoka, F., Kikuchi, N., Knuteson, R. References J., Haiden, T., Hólm, E., Haimberger, L., Hogan, R., Horányi, A., Janiskova, M., Laloyaux, P., Lopez,
320
P., Munoz-Sabater, J., Peubey, C., Radu, R., Richardson, D., Thépaut, J.-N., Vitart, F., Yang, X., Zsótér, E., and Zuo, H.: Operational
global reanalysis: progress, future directions and synergies with NWP, ERA Report Series, https://doi.org/10.21957/tkic6g3wm, 2018. Holloway, T., Levy II, H., and Kasibhatla, P.: Global distribution of carbon monoxide, Journal of Geophysical Research: Atmospheres, 105,
12 123–12 147, https://doi.org/10.1029/1999JD901173, 2000. Flemming, J., Forbes, R., Geer, A. J., Haiden, T., Hólm, E., Haimberger, L., Hogan, R., Horányi, A., Janiskova, M., Laloyaux, P., Lopez,
320
P., Munoz-Sabater, J., Peubey, C., Radu, R., Richardson, D., Thépaut, J.-N., Vitart, F., Yang, X., Zsótér, E., and Zuo, H.: Operational
global reanalysis: progress, future directions and synergies with NWP, ERA Report Series, https://doi.org/10.21957/tkic6g3wm, 2018. global reanalysis: progress, future directions and synergies with NWP, ERA Report Series, https://doi.org/10.21957/tkic6g3wm, 2018. Holloway, T., Levy II, H., and Kasibhatla, P.: Global distribution of carbon monoxide, Journal of Geophysical Research: Atmospheres, 105,
12 123–12 147, https://doi.org/10.1029/1999JD901173, 2000. International Energy Agency: Iron and Steel Technology Roadmap: Towards more sustainable steelmaking, available at: https://www.iea. 325
org/reports/iron-and-steel-technology-roadmap (last access: 14 November 2023), 2020. International Energy Agency: Iron and Steel Technology Roadmap: Towards more sustainable steelmaking, available at: https://www.iea. 325
org/reports/iron-and-steel-technology-roadmap (last access: 14 November 2023), 2020. Ishioka, M., Okada, T., and Matsubara, K.: Formation and characteristics of vapor grown carbon fibers prepared in Linz-Donawitz converter
gas, Carbon, 30, 975–979, https://doi.org/10.1016/0008-6223(92)90124-F, 1992. Ishioka, M., Okada, T., and Matsubara, K.: Formation and characteristics of vapor grown carbon fibers prepared in Linz-Donawitz converter
gas, Carbon, 30, 975–979, https://doi.org/10.1016/0008-6223(92)90124-F, 1992. 15 O., Butz, A., Haun, M., Buijs, H., Shiomi, K., Imai, H., and Kuze, A.: Thermal and near-
infrared sensor for carbon observation Fourier transform spectrometer-2 (TANSO-FTS-2) on the Greenhouse gases Observing SATellite-2
(GOSAT-2) during its first year in orbit, Atmos. Meas. Tech., 14, 2013–2039, https://doi.org/10.5194/amt-14-2013-2021, 2021. Tian, Y., Sun, Y., Borsdorff, T., Liu, C., Liu, T., Zhu, Y., Yin, H., and Landgraf, J.: Quantifying CO emission rates of industrial point sources Suto, H., Kataoka, F., Kikuchi, N., Knuteson, R. O., Butz, A., Haun, M., Buijs, H., Shiomi, K., Imai, H., and Kuze, A.: Thermal and near-
infrared sensor for carbon observation Fourier transform spectrometer-2 (TANSO-FTS-2) on the Greenhouse gases Observing SATellite-2
(GOSAT-2) during its first year in orbit, Atmos. Meas. Tech., 14, 2013–2039, https://doi.org/10.5194/amt-14-2013-2021, 2021. Tian, Y., Sun, Y., Borsdorff, T., Liu, C., Liu, T., Zhu, Y., Yin, H., and Landgraf, J.: Quantifying CO emission rates of industrial point sources
from Tropospheric Monitoring Instrument observations, Environmental Research Letters, 17, 014057, https://doi.org/10.1088/1748-
360
9326/ac3b1a, 2022. from Tropospheric Monitoring Instrument observations, Environmental Research Letters, 17, 014057, https://doi.org/10.1088/1748-
360
9326/ac3b1a, 2022. 360 from Tropospheric Monitoring Instrument observations, Environmental Research Letters, 17, 014057, https://doi.org/10.1088/1748-
360
9326/ac3b1a, 2022. Umweltbundesamt: Informationen zum Luftschadstoff Kohlenmonoxid (CO), available at: https://www.umweltbundesamt.de/sites/default/
files/medien/370/dokumente/infoblatt_kohlenmonoxid_0.pdf (last access: 14 November 2023), 2017. Umweltbundesamt: Air data: Annual tabulation (CO), available at: https://www.umweltbundesamt.de/en/data/air/air-data/annual-tabulation/ Umweltbundesamt: Informationen zum Luftschadstoff Kohlenmonoxid (CO), available at: https://www.umweltbundesamt.de/sites/default/
files/medien/370/dokumente/infoblatt_kohlenmonoxid_0.pdf (last access: 14 November 2023), 2017. U
ltb
d
t Ai d t
A
l t b l ti
(CO)
il bl
t htt
//
ltb
d
t d /
/d t / i / i d t /
l t b l ti
/ Umweltbundesamt: Air data: Annual tabulation (CO), available at: https://www.umweltbundesamt.de/en/data/air/air-data/annual-tabulation/
eJxrWpScv9BoUWXqEiMDIyMAMLgFtA== (last access: 14 November 2023), 2022. 365 eJxrWpScv9BoUWXqEiMDIyMAMLgFtA== (last access: 14 November 2023), 2022. 365 eJxrWpScv9BoUWXqEiMDIyMAMLgFtA== (last access: 14 November 2023), 2022. 365 16 Veefkind, J. P., Aben, I., McMullan, K., Förster, H., de Vries, J., Otter, G., Claas, J., Eskes, H. J., de Haan, J. F., Kleipool, Q., van Weele,
M., Hasekamp, O., Hoogeveen, R., Landgraf, J., Snel, R., Tol, P., Ingmann, P., Voors, R., Kruizinga, B., Vink, R., Visser, H., and Levelt,
P. F.: TROPOMI on the ESA Sentinel-5 Precursor: A GMES mission for global observations of the atmospheric composition for climate,
air quality and ozone layer applications, Remote Sensing of Environment, 120, 70–83, https://doi.org/10.1016/j.rse.2011.09.027, 2012. Wu, D., Liu, J., Wennberg, P. O., Palmer, P. I., Nelson, R. R., Kiel, M., and Eldering, A.: Towards sector-based attribution using intra-city
370
variations in satellite-based emission ratios between CO2 and CO, Atmos. Chem. Phys., 22, 14 547–14 570, https://doi.org/10.5194/acp-
22-14547-2022, 2022. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709
Preprint. Discussion started: 8 February 2024
c⃝Author(s) 2024. CC BY 4.0 License. Wu, D., Liu, J., Wennberg, P. O., Palmer, P. I., Nelson, R. R., Kiel, M., and Eldering, A.: Towards sector-based attribution using intra-city
370
variations in satellite-based emission ratios between CO2 and CO, Atmos. Chem. Phys., 22, 14 547–14 570, https://doi.org/10.5194/acp-
22-14547-2022, 2022. Wu, D., Liu, J., Wennberg, P. O., Palmer, P. I., Nelson, R. R., Kiel, M., and Eldering, A.: Towards sector-based attribution using intra-city
370
variations in satellite-based emission ratios between CO2 and CO, Atmos. Chem. Phys., 22, 14 547–14 570, https://doi.org/10.5194/acp-
22-14547-2022, 2022. 17 17
|
https://openalex.org/W2964096549
|
https://www.researchsquare.com/article/rs-920/v3.pdf?c=1631840480000
|
English
| null |
Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies
|
BMC genomics
| 2,019
|
cc-by
| 9,467
|
Version of Record: A version of this preprint was published on July 19th, 2019. See the published version
at https://doi.org/10.1186/s12864-019-5967-8. Research article License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Page 1/28 Version of Record: A version of this preprint was published on July 19th, 2019. See the published version
at https://doi.org/10.1186/s12864-019-5967-8. Page 2/28 Abstract Background: Anti-CD3 immunotherapy was initially approved for clinical use for renal transplantation
rejection prevention. Subsequently, new generations of anti-CD3 antibodies have entered clinical trials for
a broader spectrum of therapeutic applications, including cancer and autoimmune diseases. Despite their
extensive use, little is known about the exact mechanism of these molecules, except that they are able to
activate T cells, inducing an overall immunoregulatory and tolerogenic behavior. To better understand the
effects of anti-CD3 antibodies on human T cells, PBMCs were stimulated, and then, we performed RNA-
seq assays of enriched T cells to assess changes in their gene expression profiles. In this study, three
different anti-CD3 antibodies were used for the stimulation: two recombinant antibody fragments,
namely, a humanized and a chimeric FvFc molecule, and the prototype mouse mAb OKT3. Results: Gene
Ontology categories and individual immunoregulatory markers were compared, suggesting a similarity in
modulated gene sets, mainly those for immunoregulatory and inflammatory terms. Upregulation of
interleukin receptors, such as IL2RA, IL1R, IL12RB2, IL18R1, IL21R and IL23R, and of inhibitory molecules,
such as FOXP3, CTLA4, TNFRSF18, LAG3 and PDCD1, were also observed, suggesting an inhibitory and
exhausted phenotype. Conclusions: In conclusion, we used a deep transcriptome sequencing method for
comparing three anti-CD3 antibodies in terms of Gene Ontology enrichment and immunological marker
expression. The present data showed that both recombinant antibodies induced a compatible expression
profile, suggesting that they might be candidates for a closer evaluation with respect to their therapeutic
value. Moreover, the proposed methodology is amenable to be more generally applied for molecular
comparison of cell receptor dependent antibody therapy. Background Immunosuppressive therapies based on monoclonal antibodies (mAbs) started in the 1980s, with the use
of Muromonab-CD3 (OKT3), an antihuman CD3 antibody, for attaining long-term graft survival after
organ transplantation1. After decades of use, this biopharmaceutical was withdrawn from clinics due to
its toxic side effects2. However, the emergence of a new generation of (re)engineered recombinant
antibodies has sparked hopes that anti-CD3 antibodies may again be used to induce peripheral
tolerance3, renewing the enthusiasm for CD3-targeted therapies. Hence, anti-CD3 therapy is now being
tested for several autoimmune and inflammatory diseases4,5. Furthermore, recent clinical data on the use
of Teplizumab in type I diabetes6 contribute to this optimism that new anti-CD3 therapies for
autoimmunity and transplantation will become available in a foreseeable time. The administration of
anti-CD3 antibodies induces the general activation of T cells, which may lead to a state of tolerance not
yet fully understood3,7. The proposed mechanism of a peripheral tolerance induction rests upon a
potential modulation of regulatory lineages of the CD4 phenotype8,9, even though CD8 regulatory cells
were also shown to be affected10,11. Peripherally induced regulatory cells control the activation of T cells,
promoting negative feedback in the inflammatory response. The induction of a more regulatory
environment by anti-CD3 antibodies could produce antigen-specific tolerance and alleviate the immune
response. More recent data on human clinical data suggest that other mechanisms such as T cell Page 3/28 Page 3/28 exhaustion11,12 or the induction of inhibitory receptors on T cells13,14 could also contribute to the
suppression of the immune response. The effect of anti-CD3 therapy has been addressed in different studies trying to elucidate its mechanism
by assessing the genetic profile of T cells induced by those antibodies. These studies have been
performed by microarray analysis15,16,17 or, more recently, by Next Generation Sequencing (NGS)18,19. Nevertheless, in the majority of the investigations, anti-CD3 is not the unique stimulus but is combined
with anti-CD28 antibody and/or interleukins, such as IL2. More importantly, these studies are often
performed using isolated T cells and thus are in a very different context from the PBMC environment. In
the present work, we compared two recombinant antibody fragments, a chimeric fragment and a
humanized fragment in an FvFc format, with their prototypic antibody OKT3. The treatment was
performed using healthy human donor PBMCs in vitro. The global changes in the transcriptome profile
were assessed using RNA-seq. Background Subsequently, their T cell differentiation markers and immunoregulatory
signatures were compared. Our data showed that, despite the antibody format, the three anti-CD3
antibodies induced a common pattern of gene expression strongly enriching regulatory genes as well as
genes involved in inhibitory signaling. We propose that these comparative analyses could be exploited as
a validation tool in designing new and more effective CD3-binding molecules. Global change in the gene expression profile in human T cells induced
by anti-CD3 treatments To compare the effects of each of the three anti-CD3 antibodies on human T cells, the gene expression
profiles were analyzed. T cells were obtained from 72-hour untreated or treated PBMCs with one of the
three anti-CD3 antibodies: OKT3, FvFc M (OKT3 scFv fused to human IgG1 Fc), and a humanized version
of this FvFc (FvFc R). Anti-CD3 was used as the sole stimulus. To avoid any further stimulation, T cells
were obtained by negative selection, using magnetic beads for cell surface markers. The purity of the T
cell population was assessed by flow cytometry and was above 96% (Supplementary Figure S1). The
transcriptomes of stimulated and unstimulated T cells from a single individual were obtained by
performing sequencing in two replicates. More than 55 million paired-end reads of 150 bp length were
obtained. The reads were mapped to the human reference genome (hg19); of the total reads, 84% to 94%
were mapped (Table 1). Subsequently, we assessed differentially expressed genes (DEGs) by comparing each anti-CD3 antibody-
treated sample with the control of unstimulated T cells. The gene sets found to be differentially
expressed in the different treatments are shown as a MA plot in Figure 1A and as a Venn diagram in
Figure 1B. OKT3 treatment resulted in a larger set of differentially expressed genes (7089) with a fold
change of less than –0.8 or above 0.8, followed by FvFc R treatment with 2425 DEG and FvFc M
treatment with 1406 DEG. We found 860 genes that were equally regulated among the treatments,
considering a padj ≤ 0.05. Except for FvFc R treatment, DEGs were mostly downregulated. FvFc R Page 4/28 Page 4/28 Page 4/28 induced the most unbalanced DEG dataset, with 58% (1,419) upregulated over 41% (1,006)
downregulated DEGs. The gene regulation profile promoted by FvFc R was more similar to OKT3 than
FvFc M, even though the cluster analysis suggested a similar DEG profile for each treatment (Figure 1C). Associations of DEGs with Gene Ontology categories Anti-CD3 stimulation was shown to affect different set of genes18,19. Therefore, functional
characterization of the differentially expressed genes was performed using GO term enrichment analysis. Anti-CD3 activated and repressed DEGs were separately classified for the GO category “biological
process”. Upregulated genes were dominated by terms associated with cell proliferation (Figure 2),
reflecting the anti-CD3 associated activation of T cells. To visualize changes in GO term enrichment and
coverage (completeness), immune-associated terms were selected among up- and downregulated DEGs
for each antibody treatment, focusing on those associated with the immune response and inflammation
typically associated with anti-CD3 therapy (Figure 3). All antibodies induced a similar profile of GO term enrichment, coverage and FDR adjusted p-value,
shown by radar plots (Figure 3). Among the upregulated genes, the predominance of OKT3-induced GO
term coverage was less obvious. Between selected terms, the most enriched GO term among the
upregulated genes was the Regulation of Regulatory T Cell Differentiation (GO:0045589), but terms for
the regulation of IFNγ (GO:0032729), IL–10 (GO:0032653) and IL–12 production (GO:0032655) were also
highlighted. The downregulated DEG set enriched terms reflected categories that fade after antibody treatment. It is
notable that, among the GO terms enriched by genes repressed after treatment, the term “regulation of
inflammatory response” (GO:0050727), was the most conspicuous. Furthermore, the terms “immune
response-regulating signaling pathway” (GO:0002433) and “activation of immune response”
(GO:0002253) were also evident (Figure 3). Regulation of cytokines and their receptors by anti-CD3 stimulation Anti-CD3 antibody therapy is strongly associated with an over secretion of cytokines, also known as a
“Cytokine Storm”4. The deleterious consequences of the cytokine production are assumed to be promoted
by the Fc part of the molecule, and novel humanized antibodies can circumvent these consequences by
inducing a nonmitogenic effect. Our data suggest that the in vitro administration of all three anti-CD3
antibodies induce the upregulation of several cytokine genes, including INFG, IL17A, IL17F, LIF and TNF
(Figure 4). However, when we analyzed the expression of IL17 in human donors by RT-qPCR, we noticed
that even though the IL17A gene expression was consistently expressed along all treatments in the NGS
panel, its induction was variable among antibody-treated donor T cells (Figure 5A). The FvFc R and OKT3
treatment also induced upregulation of IL6 and IL32. OKT3 treatment induced additional interleukins
such as IL1B, IL2, IL3, IL9, IL13, IL12B, IL21 and IL22 (Figure 4). Page 5/28 Page 5/28 Cytokine receptors were also induced after antibody treatment, including strong upregulation of the IL2
receptor subunit genes, IL2RA and IL2RB (Figure 4). IL2RA expression was also tested in the qPCR panel
of treated donor T cells, suggesting that any form of anti-CD3 induces the expression of the IL2 receptor
α-chain, also known as CD25 (Figure 5B). Moreover, all antibody treatments induced the expression of
IL1R2, IL12RB2, IL18R1, IL21R, IL23R (Figures 4 and 5C). However, as suggested by the NGS panel, anti-
CD3-treated T cells increased their sensitivity toward IL1, IL2, IL12, IL18, IL21 and IL23. Anti-CD3 antibody treatment induced the upregulation of several interleukin and interleukin receptors
genes, but only a few interleukins and receptors were downregulated due to antibody treatment. IL10 and
IL24 expression was significantly repressed after OKT3 and FvFc R treatment, while IL18BP was
repressed by OKT3 and FvFc M. In addition, OKT3 treatment also reduced the expression of IL18 (Figure
4). IL10 was further investigated by qPCR. Notwithstanding, the qPCR panel suggested that OKT3
treatment had a variable effect on IL10 expression among treated donor cells, and the FvFc-based
antibody had no significant effect (Figure 5D). Downregulation of interleukin receptors makes T cells less sensitive to their cognate cytokine. The NGS
panel suggested that OKT3 treatment might interfere with signaling of interleukins IL10, IL11 and IL13,
due to the downregulation of IL10RA, IL10RB, IL11RA and IL13RA1 (Figure 4). IL6R was downregulated
after treatment with OKT3 and FvFc R. Regulation of cytokines and their receptors by anti-CD3 stimulation The IL17RA codes for IL17A specific receptor and was found to be
downregulated after OKT3 treatment, with a barely significant q-value (0.0069); nevertheless, the qPCR
panel confirmed this tendency for downregulation after treatment with any of the antibodies (Figure 5E). The IL17RC gene, which codes for a receptor for both IL17A and IL17F, was found to be downregulated
after both OKT3 and FvFc M treatment. The receptor for IL7, IL7R, was shown to be downregulated with
both FvFc R and OKT3 treatment. The qPCR panel corroborated these results, suggesting that most donor
T cells respond to any anti-CD3 antibody format, reducing the IL7R expression levels (Figure 5F). Anti-CD3 stimulation regulates phenotypic marker genes Activation of resting T cells by anti-CD3 antibodies can induce cell differentiation, and indeed, several
phenotypic markers are modulated after antibody treatment. Resting T cells can differentiate in several
lineages of effector and regulatory phenotypes, and specific genetic markers can characterize these T cell
phenotypes. We compared several markers for CD4 and CD8 subpopulations depicted as panels to
visualize their possible differentiation (Figure 6). To confirm prototype marker expression levels found in
the NGS panel, qPCR analyses were performed using anti-CD3 treated T cells (Figure 7). Some expression
markers are key for charactering T cell subpopulations. The Th1 marker TBX21, which codes for the
TBET transcription factor, was shown to be significantly induced only with OKT3 treatment in the NGS
panel (Figure 4). The qPCR panel corroborated the NGS data (Figure 7A), suggesting a minimal effect of
FvFc antibodies on TBX21 expression. STAT4, another Th1 marker, was also only induced by OKT3 in the
NGS experiment, but qPCR data suggests that FvFc R could also affect the expression levels of STAT4 in
stimulated cells20,21 (Figures 4 and 7B). GATA3, a Th2 phenotypic marker, was not significantly induced Page 6/28 Page 6/28 in NGS or qPCR data (Figures 4 and 7C). However, other characteristic markers of this subtype were
induced21,22 (Figure 6). In addition, we also analyzed markers for the Th17 subpopulation23,24 (Figures 4, 5, 6 and 7). The gene
that codes for RORϒt, RORC was found to be slightly upregulated after treatment with both OKT3 and
FvFc M antibodies (Figure 4), but without significance (padj > 0.01). In the qPCR panel, RORC was shown
to be barely activated in all three treatments (Figure 7D). IL17A, known to be produced by Th17 cells, was
upregulated in the NGS panel, but these data were not supported by qPCR, which suggests a variable and
mild regulation of this gene (Figure 5A). The third marker, STAT3, was found to be induced by OKT3 in the
NGS data and was induced by OKT3 and FvFc R treatments, as measured by qPCR (Figure 7E). Interestingly, the FvFc M antibody induced a very contrasting effect on different donors. Half of the
donors showed an upregulated profile, while the other half showed a downregulated profile. Interestingly, the FvFc M antibody induced a very contrasting effect on different donors. Half of the
donors showed an upregulated profile, while the other half showed a downregulated profile. Anti-CD3 stimulation modulates genes that encode nuclear receptor
transcription factors VDR codes for the vitamin D3 receptor, and its overexpression was detected in all antibody
treatments by qPCR (Figure 7P). Among the downregulated DEGs, peroxisome proliferator-activated receptor gamma (PPARG), a gene
associated with the development of Tregs, was found to be 4- to 9-fold less expressed than that in the
unstimulated T cells (Figure 4). Moreover, the THRA gene that codes for thyroid hormone receptor alpha
was also repressed in all treatments. Anti-CD3 stimulation regulates phenotypic marker genes T cells can assume a regulatory phenotype, and many regulatory markers were found in this analysis25,26
(Figure 6). FOXP3, a major transcription factor that is associated with the human T regulatory phenotype,
was upregulated in the NGS data for all antibody treatments. These data were corroborated by qPCR
(Figure 7F). GITR (TNFRSF18) was strongly upregulated by all antibodies (approximately 16-fold, Figure
4), and this effect was also observed for all donors in qPCR (Figure 7G). CTLA4 and LAG3 were similarly
upregulated in the NGS (Figure 4), and qPCR data supported this finding (Figures 7H and I), but the effect
was less pronounced for FvFc antibodies compared to OKT3. The gene that codes for PD–1, namely,
PDCD1, was also consistently induced by all antibody treatments (approximately 5-fold, Figure 4), and
qPCR data confirmed this observation (Figure 7J). Modulations of CD8 T cell markers were also observed after anti-CD3 treatment, suggesting changes in
the CD8 T cell population27,28 (Figure 6). Among these markers, EOMES and KLRG1 were repressed after
all the anti-CD3 treatments, but GMZB was strongly induced by anti-CD3. These three markers were also
tested by qPCR, which confirmed the tendency of the NGS data (Figure 7K, L and M). Moreover, markers
of regulatory CD8 T cell29, such as IL2RA, were sharply induced by OKT3 and FvFc R but to a lesser extent
by FvFc M. CD274 (PD-L1) was only marginally induced in all treatments (Figure 6), and FOXP3 showed a
variable profile (Figure 7F). ICOS was weakly induced only by OKT3 and FvFc M (Figure 4). Phenotypic markers associated with T cell activation, cell death and apoptosis pathways were also
affected by anti-CD3 treatment. Figure 4 resumes the induction/repression of these markers after anti-
CD3 treatment. Overall, OKT3 induced most activation markers except EOMES and AIF1, while FvFc-
based antibodies had a milder profile. Among the activation molecules, IFGN, GZMB, IL2RA, TNFRSF4
and TNFRSF9 showed remarkable induction. Cell death was the fate of activated cells, and the
FAS/FASLG pathway was induced after T cell activation. The anti-CD3 effect on FAS induction was slight
(Figure 6) and variable among donors (Figure 7N), and FASLG was very consistent among donors with
the treatment of FvFc R (Figure 7O). GITR, along with PDCD1, was consistently induced by all the
treatments (Figures 4, 6, 7G and J). Page 7/28 Page 7/28 Effect of an exclusive anti-CD3 stimulation To compare the global gene expression profile under the effect of anti-CD3 antibodies with that of
activated T cells, we paralleled our results with those described by Zhao and colleagues (2014), who
probed DEGs of immortalized T cells cultured in the presence of anti-CD3 and anti-CD28 antibodies. Their
DEG dataset after 72 hours treatment was compared with NGS data generated in the present work
focusing on DEGs regulated after anti-CD3 treatment without the costimulatory anti-CD28 stimulus. Among the 12 most opposite DEG (Supplementary Table 3), three genes were selected for qPCR analysis:
AIF1, XCL1 and IDO1 (Figures 7Q, R and S). XCL1 and IDO1 were induced by all of the anti-CD3
treatments, as observed in the qPCR panel, while AIF1 was found to be repressed after anti-CD3
treatment. Anti-CD3 stimulation modulates genes that encode nuclear receptor
transcription factors Nuclear receptors integrate a family of transcription factors that respond to hormones and hydrophobic
molecules that have been associated with the control of the immune response30. Thus, the PFAM family
for Nuclear Receptor (PF00104), was used to probe antibody-induced DEGs. Anti-CD3 treatment induced
the expression of PF00104-associated genes. OKT3 induced 7 genes, while FvFc R induced 3 and FvFc M
induced 2 genes. The orphan nuclear receptor gene NR4A1 was activated in all treatments at a padj < 10–
5. Three other PF00104 annotated genes were found in two of three treatments: NR4A3, RORC, and VDR
(Figure 4). NR4A3 codes for a mitogen-associated nuclear receptor Nuclear receptors integrate a family of transcription factors that respond to hormones and hydrophobic
molecules that have been associated with the control of the immune response30. Thus, the PFAM family
for Nuclear Receptor (PF00104), was used to probe antibody-induced DEGs. Anti-CD3 treatment induced
the expression of PF00104-associated genes. OKT3 induced 7 genes, while FvFc R induced 3 and FvFc M
induced 2 genes. The orphan nuclear receptor gene NR4A1 was activated in all treatments at a padj < 10–
5. Three other PF00104 annotated genes were found in two of three treatments: NR4A3, RORC, and VDR
(Figure 4). NR4A3 codes for a mitogen-associated nuclear receptor
(http://www.uniprot.org/uniprot/Q92570). RORC is mentioned above as a marker for lymphocyte
lineages. VDR codes for the vitamin D3 receptor, and its overexpression was detected in all antibody
treatments by qPCR (Figure 7P). Nuclear receptors integrate a family of transcription factors that respond to hormones and hydrophobic
molecules that have been associated with the control of the immune response30. Thus, the PFAM family
for Nuclear Receptor (PF00104), was used to probe antibody-induced DEGs. Anti-CD3 treatment induced
the expression of PF00104-associated genes. OKT3 induced 7 genes, while FvFc R induced 3 and FvFc M
induced 2 genes. The orphan nuclear receptor gene NR4A1 was activated in all treatments at a padj < 10
5. Three other PF00104 annotated genes were found in two of three treatments: NR4A3, RORC, and VDR
(Figure 4). NR4A3 codes for a mitogen-associated nuclear receptor
(http://www.uniprot.org/uniprot/Q92570). RORC is mentioned above as a marker for lymphocyte
lineages. VDR codes for the vitamin D3 receptor, and its overexpression was detected in all antibody
treatments by qPCR (Figure 7P). (http://www.uniprot.org/uniprot/Q92570). RORC is mentioned above as a marker for lymphocyte
ineages. Discussion Anti-CD3 antibodies are known to induce immunosuppression and have been proposed for several
therapies, including those for different autoimmune diseases and acute transplanted organ rejection. For
approximately two decades, Muromonab-CD3 (OKT3) therapy was used as an adjuvant for acute
episodes of graft rejection, but its use was discontinued due to pronounced side effects2. However,
despite the prolonged clinical use, the mechanism of action of OKT3 is still uncertain. In this study,
human T cells were treated with anti-CD3 antibodies in vitro, within the complexity of the PBMC milieu, in
an attempt to simulate the natural ambiance that occurs in the intravenous administration of therapeutic Page 8/28 anti-CD3. This in vitro experimental model was used to compare the mouse mAb OKT3 with two
recombinant antibody fragments inspired by the mAb: a humanized and a chimeric human IgG1 in the
FvFc format (scFv-hinge-CH2-CH3). Currently, most antibody therapies rely on full-sized mAbs, derived from chimeric, humanized or fully
human sequences, but new molecular formats may represent technological and economical alternatives. The FvFc format used here represents a novel solution as a single-chained homodimeric molecule that
mimics heteromultimeric mAbs31,32,33,34,35,36. The DEG profiles induced by each antibody format were
i
il
j d
d f
h
i h
l
i
d
i
h l
DEG
i d
d b OKT3 Currently, most antibody therapies rely on full-sized mAbs, derived from chimeric, humanized or fully
human sequences, but new molecular formats may represent technological and economical alternatives. The FvFc format used here represents a novel solution as a single-chained homodimeric molecule that
mimics heteromultimeric mAbs31,32,33,34,35,36. The DEG profiles induced by each antibody format were
very similar as judged from the enrichment analysis, despite the larger DEG set induced by OKT3,
especially for the repressed DEG set. The ontology-based classification for up- and downregulated DEGs
suggests that all antibody formats induce a very similar profile, marked by a sharp mitotic response (with
a low p-value), and a higher, even significant, p-value for “Immune”-related GO. It is noteworthy that FvFc
compares positively for several terms, such as regulation of “regulatory T cell” and “interleukin–10
production” and “inflammatory response.” Overall, despite the larger set of OKT3 DEGs, FvFc molecules
could enrich GO terms at least similarly. The broader coverage of GO terms of OKT3 DEGs may reflect their greater mitogenic stimulus31, while the
humanized FvFc displayed a skewed DEG profile, yet preserving its function. Discussion Among those with the Th17 phenotype, IL17A, IL17F, and IL16 were
upregulated, and FOXP3, GITR, LAG3, and CTLA4 were characteristic of the regulatory phenotype. These
markers were all observed to some degree in each of treatments but commonly were weakly expressed
among donors stimulated with FvFc M. Several regulatory phenotypes have been proposed, along with genes usually associated with a
regulatory function44. For CD4 cells, regulatory cells are distinguished from effector cells that are
classified as Th1, Th2, and Th17. A TBET signature with high production of IFNγ characterizes Th1 cells,
but TBX21, which codes for TBET, is only weakly upregulated by OKT3, in line with previous
observations43. Th2 cells do not appear to be induced by anti-CD3 since no significant alteration in
GATA3 expression was observed. Beyond that, markers for Th17 and T regulatory cells are predominantly
found in anti-CD3-treated cells. Among those with the Th17 phenotype, IL17A, IL17F, and IL16 were
upregulated, and FOXP3, GITR, LAG3, and CTLA4 were characteristic of the regulatory phenotype. These
markers were all observed to some degree in each of treatments but commonly were weakly expressed
among donors stimulated with FvFc M. The anti-CD3 treatment seemed to bias toward a Th17/Treg polarity, as suggested before45,46. However,
FOXP3, an important marker of regulatory cells, was only weakly induced after PBMC stimulation. It is
possible that by analyzing gene expression after 72 h of anti-CD3 induction, we missed the transient
FOXP3 peak kinetics18,19. Moreover, the activation of IRF4, a late effect of FOXP3 activation, represses
FOXP3 and may negatively affect its expression47. IRF4 was upregulated in all the anti-CD3-treated cells. Interestingly, anti-CD3-treated cells showed an apparent decrease in the mRNA levels of CD127 (IL7R), the
IL–7 receptor, for which downregulation is considered to be a hallmark of a bona fide regulatory
phenotype in humans29,48,49. IL10 is a marker for regulatory CD8 and the CD4 (Tr1) phenotype50,51. We found no significant IL10
regulation except for a slight decline due to treatment with OKT3. However, we noted an enrichment of the
“regulation of Interleukin–10” GO term, suggesting that the machinery for IL10 production was activated
in anti-CD3-treated cells. FvFc R antibody was previously shown to induce a high IL10/IFNγ ratio
compared to OKT3 in anti-CD3-stimulated PBMCs31, although no significant induction of IL10 was
observed in the present study. Discussion Further analyses suggest
that the chimeric molecule FvFc R reproduces the OKT3 DEG profile more accurately than FvFc M, despite
the better binding proprieties of the latter molecule. Therefore, the humanization process seems to have
preserved the original OKT3 paratope in the recombinant molecules, suggesting them as alternative CD3
binders for clinical anti-CD3 therapy. The mitogenic activity of OKT3 and other anti-CD3 antibodies renders them especially investigated for
therapeutics37,38,39,40. The analysis of differentially expressed gene ontology classification suggests that
all three anti-CD3 antibodies modulate a distinct number of genes related to cell proliferation and mitosis. This supports a significant impact of anti-CD3 therapy on T cell proliferation as observed for the
proliferation marker MKI67 and the T-specific activation marker CD25 (IL2RA). The activation of T cells by
OKT3 and other anti-CD3 antibodies is usually associated with the clinical efficacy of this antibody39. However, upregulation of activation markers does not correlate with antibody mitogenic activity, since
non mitogenic anti-CD3 antibodies may also induce activation markers in vivo40. Therefore, these data
corroborate a previous characterization of the FvFc R antibody, shown to be less mitogenic than OKT331,
despite inducing several activation markers, as observed in the present study. Most models for anti-CD3 therapy rely on CD4 regulatory cells41,42,43, but the majority of data supporting
it came from mouse models. Recent data on humanized antibodies in clinical trials highlight the role of
CD8 cells in tolerance associated with anti-CD3 therapy, suggesting a two-phase model: a short-term
depletion of T cells followed by induction of regulatory mechanisms6. A burst of cell activation initially
induces mitotic mechanisms. Our data suggest that even after three days of anti-CD3 stimulation,
activated T cell DEGs are still dominated by a mitotic signature, as seen by GO term enrichment, but,
along with, barely detected emerging immunoregulatory mechanisms. Page 9/28 Several regulatory phenotypes have been proposed, along with genes usually associated with a
regulatory function44. For CD4 cells, regulatory cells are distinguished from effector cells that are
classified as Th1, Th2, and Th17. A TBET signature with high production of IFNγ characterizes Th1 cells
but TBX21, which codes for TBET, is only weakly upregulated by OKT3, in line with previous
observations43. Th2 cells do not appear to be induced by anti-CD3 since no significant alteration in
GATA3 expression was observed. Beyond that, markers for Th17 and T regulatory cells are predominant
found in anti-CD3-treated cells. Discussion Nevertheless, the increase in the IL10/IFNγ ratio observed by Silva and
colleagues could be explained in part by a more consistent induction of the IFNG gene in OKT3-treated T
cells, or likewise due to a non-lymphocytic origin of the produced IL10 probed in the whole PBMCs31. Clinical data on novel humanized antibodies suggest new mechanisms of anti-CD3 action in humans. In
mice, studies have suggested that anti-CD3 therapy induces immunosuppression dependent on CD4 T
cells, with stimulated helper cells developing a regulatory phenotype. However, in humans, the CD8
lineage also seems to contribute to the tolerogenic effect of anti-CD3, either by inducing differentiation
into CD8 regulatory cells15,29 or by leading CD8 T cells to exhaustion11,12. Data from Teplizumab clinical
trials suggested that the immunosuppressive effect of the humanized antibody is due to anergic and
exhausted CD8 cells12,52, along with CD8 and CD4 Tregs15. Nonetheless, inhibitory receptors were clearly
activated in our model system, including PDCD1, CTLA4, and LAG3, suggesting that inhibition of the
immune response and inflammation after 72 h of a proliferative stimulus might have led to an exhausted
phenotype14. Otherwise, inhibitory receptors may not indicate exhaustion, but a detuning of CD8 T
activation. It is possible that these inhibitory receptors signify the transition from a highly activated T cell Page 10/28 Page 10/28 state toward a differentiation/memory profile11,53. The high and consistent induction of the PDCD1 gene
(PD–1) observed here suggests a general detuning of anti-CD3-treated cells, that may underlie the basis
of anti-CD3 therapeutic effects. The detuning of T cell following PD–1 expression may contribute to the effect of anti-CD3, but other
molecular players may also contribute to immunosuppression. IDO1 is a tryptophan catabolic enzyme
known to induce regulatory T cells and immunosuppression54,55. Although usually produced by
monocytes, a CD4+IDO+ lymphocyte population had been characterized56. Anti-CD3 treatment induced
IDO1 upregulation in T cells, although not uniformly among donors. In this sense, a putative IDO-
producing T cell could trigger a profound regulatory effect by locally restricting available tryptophan. This
finding may represent an alternative mechanism of T-cell-induced immunosuppression that could be
therapeutically exploited. Donors Peripheral blood was collected from seven healthy individuals enrolled in this study (Supplementary
Table S1). For NGS a single donor was analyzed and for qPCR assays, seven healthy individuals were
enrolled. All human blood experiments were performed in accordance to the Ethics Committee of the
University of Brasilia guidelines, which approved the study protocol (CAAE: 32874614.4.0000.0030). A
written informed consent was obtained from all human donors. Conclusions Novel therapeutic anti-CD3 antibodies development could focus on regulatory associated GO term
enrichment and specific subpopulation markers. The in vitro assay proposed here, based on a simple and
economical procedure, seems to be efficient to compare novel antibody molecules before clinical
evaluation. Development of new antibodies or novel pharmaceutical association could benefit from this
in vitro methodology, allowing a novel discovery pipeline based on a System Biology approach. In conclusion, we used a deep transcriptome sequencing method for comparing three anti-CD3 antibodies
regarding Gene Ontology enrichment and immunological marker expression. The present data showed
that both recombinant antibodies induced a compatible expression profile, suggesting that they might be
candidates for closer evaluation concerning their therapeutic value. Moreover, the proposed methodology
is amenable to be more generally applied for molecular comparison purposes. Antibodies OKT3 was purchased from eBioscience (San Diego, CA, USA). The humanized antibody fragment FvFc R
is a single-chain FvFc molecule and was previously described (FvFc version R)31. The chimeric FvFc M Page 11/28 contains the original OKT3 VH and VL coding sequences fused to human IgG1 Fc and cloned in the
pMIRES expression vector. The FvFc antibody fragments were affinity purified from supernatants of CHO-
K1 transfected cells. PBMC stimulation and T cell preparation Fresh PBMCs were isolated using Ficoll-Paque density gradient centrifugation (GE Healthcare, Uppsala,
Sweden). PBMCs were cultured in RPMI media (Invitrogen, Carlsbad, CA, USA) supplemented with 4 mM
L-glutamine and 10% FBS in the presence or absence of soluble anti-CD3 antibodies. A total of 250 ng of
antibody was applied to 1 x 106 PBMC/mL. T cells were isolated after 72 hours of PBMC treatment, using
magnetic beads by negative selection (according to the manufacturer´s instructions). Briefly, PBMCs were
selectively depleted of CD16, CD19, CD20 cells and were discarded (Dynabeads® Untouched™ Human T
Cells Kit, Invitrogen, Carlsbad, CA, USA). The purity of T cell enrichment was checked using flow
cytometry (Supplementary Figure S1). RNA extraction Total RNA was extracted from T cells isolated after PBMC stimulation using the miRNeasy® Mini Kit
(Qiagen, Valencia, CA, USA) as described before46. RNA integrity and purity were evaluated using a
Bioanalyzer 2100 (Agilent Technologies Genomics, Santa Clara, CA, USA). All RNA samples used in this
work showed an RIN > 7. Sample sequencing and differential gene expression analysis RNA-seq was performed by Macrogen, Inc. (Seoul, Korea), using the Illumina HiSeq™ 2500 platform
(Illumina, San Diego, CA, USA) according to the manufacturer’s standard protocol. The total RNA, up to
1500 ng, was sent in a RNA-stable tube (Biomatrica, Inc., San Diego, CA) to preserve the integrity of the
RNA, and Illumina sequencing was performed in a 2 × 150 nt paired-end mode. All sequencing reads
produced by Illumina were analyzed for quality control using FASTQC57. The reads were aligned to the
human genome GRCh37/hg19 downloaded from the UCSC Genome Browser58 using open source
Segemehl, version 0.2.059 with the split read option -S. The aligned files were ordered and indexed using
Samtools60 followed by read counts using HTSeq-count61. For a differential gene expression analysis,
the reads of CD3 T cell treated and untreated samples uniquely aligned by Segemehl were used. To
identify differentially expressed genes (DEGs) for each treatment comparison (treated versus untreated),
two replicates per condition were analyzed using the Bioconductor package DESeq262 applying a
significance threshold for the adjusted p-values of 0.05. Gene expression analysis by qPCR assays Quantitative PCR was performed as previous described46. Briefly, total RNA isolated from T cells was
utilized for cDNA synthesis using an RT2 First Strand Kit (Qiagen, Valencia, CA, USA). The expression
genes were quantified using RT² qPCR SYBR Green/ROX MasterMix (Qiagen, Valencia, CA, USA) following
the manufacturer’s instructions. The housekeeping gene B2M was used as the endogenous control. qPCR
assays were performed using an ABI Step One Plus Real-Time PCR System (Applied Biosystems, Austin,
Texas, EUA) and the 2-ΔΔCt method was used to calculate mRNA transcript levels (fold change) using RT2
Profiler PCR Array Data Analysis software (SABiosciences, Frederick, MD, USA for analysis. Three
independent experiments were performed in triplicate. Analysis of gene functions The enrichment GO terms for biological processes of DEG were also assessed. For this purpose,
upregulated (log2FC >1.2) and downregulated (log2FC <1.2) gene set enrichment analyses were
performed using functional categories of the database Gene Ontology (GO). The Panther software63,64
was used to calculate enrichment, p-values and FDR adjusted p-values. The super category “biological
process” was used, and within this category, GO terms related to the immune system and inflammatory
process were further investigated. The enrichment GO terms for biological processes of DEG were also assessed. For this purpose,
upregulated (log2FC >1.2) and downregulated (log2FC <1.2) gene set enrichment analyses were
performed using functional categories of the database Gene Ontology (GO). The Panther software63,64
was used to calculate enrichment, p-values and FDR adjusted p-values. The super category “biological
process” was used, and within this category, GO terms related to the immune system and inflammatory
process were further investigated. Nuclear receptor analysis was performed exclusively for the Pfam family PF00104 of the Pfam database
(http://pfam.xfam.org/). Members of PF00104 were searched in the DEG set using regular expression
and analyzed individually. Statistical analysis All RNA-seq experiments statistical evaluations were performed using Bioconductor package DESeq262
based in Benjamini-Hochberg method for adjusted p-values. Gene function attribution was performed
using adjusted p-values calculated by the Binomial statistic and Mann-Whitney U Test (Wilcoxon Rank-
Sum Test) by Panther software63,64. Real Time qPCR p-values were calculated based on Student’s t-test
using RT2 Profiler PCR Array Data Analysis software. Funding Research work was supported by FAP-DF (grant number: 193.000.560/2009). This study was financed in
part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance
Code 001. Brazilian Council for Research (CNPq) contributes with fellowship. The funding agencies,
CAPES, CNPq and FAP-DF were not involved in the design of the study, collection, analysis, and
interpretation of data and in writing the manuscript. Consent for publication Not applicable. Availability of data and material RNA-Seq datasets are available at GEO (www.ncbi.nlm.nih.gov/geo) under the accession number
GSE112899. Supplementary informations are in Additional file.pdf Declarations
Ethics approval and consent to participate All human blood experiments were performed in accordance to the Ethics Committee of the University of
Brasilia guidelines, which approved the study protocol (CAAE: 32874614.4.0000.0030). A written
informed consent was obtained from all human donors. The authors declare that they have no competing interests. The authors declare that they have no competing interests. Abbreviations DEGs: Differentially Expressed Genes DEGs: Differentially Expressed Genes FvFc: antibody format - scFv fused to human IgG1 Fc
NGS: Next Generation Sequencing FvFc: antibody format - scFv fused to human IgG1 Fc Page 13/28 Page 13/28 Authors’ contributions I. G. S., K. C. R. S., M. M. B. and A. Q. M. designed the experiments. I. G. S., K. C. R. S. and M. A. G. B. processed the blood samples, performed cell culture for recombinant antibodies production and made
flow cytometry. I. G. S., K. C. R. S., G. D., T. R., M. M. B. and S. H. designed and performed all
bioinformatics analysis. I. G. S. and M. M. A. conducted qPCR experiments. I. G. S., M. M. A., A. Q. M. and
M. M. B. wrote the manuscript. A. Q. M., M. M. B., S. H. and P. S. contributed to the interpretation of the
results and corrected and improved the paper. All authors read and approved the final version of the
manuscript. Page 14/28 Page 14/28 Page 14/28 Acknowledgements We are thankful of CAPES and CNPq for scholarship funding and to FAPDF for financial support of this
project. We are thankful of CAPES and CNPq for scholarship funding and to FAPDF for financial support of this
project. References 1.Cosimi AB, Urton B, Colvin RB, Goldstein G, Laquaglia MP, N NT, et al. Treatment of acute renal allograft
rejection with OKT3 monoclonal antibody. Transplantation. 1981;32(6):535–9. 2.Reichert JM. Marketed therapeutic antibodies compendium. MAbs. 2012;4(3):413–5. 2.Reichert JM. Marketed therapeutic antibodies compendium. MAbs. 2012 3.Chatenoud L, Primo J, Bach JF. CD3 antibody-induced dominant self tolerance in overtly diabetic NOD
mice. J Immunol. 1997;158(6):2947–54. 4.Chatenoud L, Bluestone JA. CD3-specific antibodies: A portal to the treatment of autoimmunity. Nat Rev
Immunol. 2007;7(8):622–32. 5.Utset TO, Auger JA, Peace D, Zivin RA, Xu D, Jolliffe L, et al. Modified anti-CD3 therapy in psoriatic
arthritis: A Phase I/II clinical trial. J Rheumatol. 2002;29(9):1907–13. 6.Daifotis AG, Koenig S, Chatenoud L, Herold KC. Anti-CD3 clinical trials in type 1 diabetes mellitus. Clin
Immunol. 2013;149(3):268–78. 7.You S, Zuber J, Kuhn C, Baas M, Valette F, Sauvaget V, et al. Induction of Allograft Tolerance by
Monoclonal CD3 Antibodies : A Matter of Timing. Am J Transl Res. 2012;12(11):2909–19. 8.Belghith M, Bluestone JA, Barriot S, Mégret J, Bach JF, Chatenoud L. TGF-β-dependent mechanisms
mediate restoration of self-tolerance induced by antibodies to CD3 in overt autoimmune diabetes. Nat
Med. 2003;9(9):1202–8. 9.Gandhi R, Farez MF, Wang Y, Kozoriz D, Quintana FJ, Weiner HL. Cutting edge: human latency-
associated peptide+ T cells: a novel regulatory T cell subset. J Immunol. 2010;184(9):4620–4. 10.Bisikirska B, Colgan J, Luban J, Bluestone JA, Herold KC. TCR stimulation with modified anti-CD3 mAb
expands CD8+ T cell population and induces CD8+CD25+ Tregs. J Clin Invest. 2005;115(10):2904–13. 11.Legat A, Speiser DE, Pircher H, Zehn D, Fuertes Marraco SA. Inhibitory receptor expression depends
more dominantly on differentiation and activation than “exhaustion” of human CD8 T cells. Front
Immunol. 2013;4(DEC):1–15. 12.Long SA, Thorpe J, DeBerg HA, Gersuk V, Eddy JA, Harris KM, et al. Partial exhaustion of CD8 T cells
and clinical response to teplizumab in new-onset type 1 diabetes. Sci Immunol. 2016;1(5):7793–802. Page 15/28 Page 15/28 13.Horwitz DA, Pan S, Ou JN, Wang J, Chen M, Gray JD, et al. Therapeutic polyclonal human CD8+ CD25+
Fox3+ TNFR2+ PD-L1+ regulatory cells induced ex-vivo. Clin Immunol. 2013;149(PB):450–63. 14. Wallberg M, Recino A, Phillips J, Howie D, Vienne M, Paluch C, et al. Anti-CD3 treatment up-regulates
programmed cell death protein–1 expression on activated effector T cells and severely impairs their
inflammatory capacity. Immunology. 2017;151(2):248–60. 15.Ablamunits V, Bisikirska B, Herold KC. Acquisition of regulatory function by human CD8+ T cells
treated with anti-CD3 antibody requires TNF. References Eur J Immunol. 2010;40(10):2891–901. 16.Hamalainen H, Zhou H, Chou W, Hashizume H, Heller R, Lahesmaa R. Distinct gene expression profiles
of human type 1 and type 2 T helper cells. Genome Biol. 2001;2(7):RESEARCH0022. 17.Hess K, Yang Y, Golech S, Sharov A, Becker KG, Weng NP. Kinetic assessment of general gene
expression changes during human naive CD4+ T cell activation. Int Immunol. 2004;16(12):1711–21. 18.Birzele F, Fauti T, Stahl H, Lenter MC, Simon E, Knebel D, et al. Next-generation insights into regulatory
T cells: Expression profiling and FoxP3 occupancy in Human. Nucleic Acids Res. 2011;39(18):7946–60. 19.Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and microarray in
transcriptome profiling of activated T cells. PLoS One. 2014;9(1). 20.Weber C, Weber KSC, Klier C, Gu S, Wank R, Horuk R, et al. Specialized roles of the chemokine receptors
CCR1 and CCR5 in the recruitment of monocytes and T H 1-like / CD45RO + T cells Specialized roles of
the chemokine receptors CCR1 and CCR5 in the recruitment of monocytes and T H 1-like / CD45RO ϩ T
cells. Blood. 2011;97(4):1144–6. 21.Biedermann T, Rocken M, Carballido JM. TH1 and TH2 lymphocyte development and regulation of TH
cell-mediated immune responses of the skin. J Investig Dermatol Symp Proc. 2004;9(1):5–14. 22.Wurster AL, Rodgers VL, Satoskar AR, Whitters MJ, Young DA, Collins M, et al. Interleukin 21 Is a T
Helper (Th) Cell 2 Cytokine that Specifically Inhibits the Differentiation of Naive Th Cells into Interferon γ–
producing Th1 Cells. J Exp Med. 2002;196(7):969–77. 23. Maddur MS, Miossec P, Kaveri S V., Bayry J. Th17 cells: Biology, pathogenesis of autoimmune and
inflammatory diseases, and therapeutic strategies. Am J Pathol. 2012;181(1):8–18. 24.Schraml BU, Hildner K, Ise W, Lee W, Whitney A, Solomon B, et al. The AP–1 transcription factor Batf
controls TH 17 differentiation. Nature. 2009;460(7253):405–9. 25.Josefowicz SZ, Lu L-F, Rudensky AY. Regulatory T Cells: Mechanisms of Differentiation and Function. Annu Rev Immunol. 2012;30(1):531–64. Page 16/28 26. Xin Chen and Joost J. Oppenhein. Resolving the identity myth: key markers of functional
CD4+FOXP3+ regulatory T cells. Int Immunopharmacol. 2011;11(10):1489–96. 27.Mahnke YD, Brodie TM, Sallusto F, Roederer M, Lugli E. The who’s who of T-cell differentiation: Human
memory T-cell subsets. Eur J Immunol. 2013;43(11):2797–809. 28.Liu J, Chen D, Nie GD, Dai Z. CD8+CD122+ T-Cells: A Newly Emerging Regulator with Central Memory
Cell Phenotypes. Front Immunol. 2015;6(October):6–11. 29. References Churlaud G, Pitoiset F, Jebbawi F, Lorenzon R, Bellier B, Rosenzwajg M, et al. Human and Mouse
CD8+CD25+FOXP3+ Regulatory T Cells at Steady State and during Interleukin–2 Therapy. Front
Immunol. 2015;6(April):2–11. 30.Park B V., Pan F. The role of nuclear receptors in regulation of Th17/Treg biology and its implications
for diseases. Cell Mol Immunol. 2015;12(5):533–42. 31.Silva HM, Vieira PMMM, Costa PLN, Pimentel BMS, Moro AM, Kalil J, et al. Novel humanized anti-CD3
antibodies induce a predominantly immunoregulatory profile in human peripheral blood mononuclear
cells. Immunol Lett. 2009;125(2):129–36. 32.Shu L, Qi CF, Schlom J, Kashmiri S V. Secretion of a single-gene-encoded immunoglobulin from
myeloma cells. Proc Natl Acad Sci U S A. 1993;90(17):7995–9. 32.Shu L, Qi CF, Schlom J, Kashmiri S V. Secretion of a single-gene-encoded immunoglobulin from
myeloma cells. Proc Natl Acad Sci U S A. 1993;90(17):7995–9. 33. Vaz De Andrade E, Freitas SM, Ventura MM, Maranhão AQ, Brigido MM. Thermodynamic basis for
antibody binding to Z-DNA: Comparison of a monoclonal antibody and its recombinant derivatives. Biochim Biophys Acta - Gen Subj. 2005;1726(3):293–301. 33. Vaz De Andrade E, Freitas SM, Ventura MM, Maranhão AQ, Brigido MM. Thermodynamic basis for
antibody binding to Z-DNA: Comparison of a monoclonal antibody and its recombinant derivatives. Biochim Biophys Acta - Gen Subj. 2005;1726(3):293–301. 34.Secchiero P, Sblattero DI, Chiaruttinf C, Melloni E, Macor P, Zorzet S, et al. Selection and
characterization of a novel agonistic human recombinant anti-trail-r2 minibody with anti-leukemic activity
Department ofMorphology and Embryology, University ofFerrara, Ferrara ; 1 Department of Medical
Sciences, University Piemonte Orien. 2009;22(I):73–83. 35.Han T, Abdel-Motal UM, Chang D, Sui J, Muvaffak A, Campbell J, et al. Human Anti-CCR4 Minibody
Gene Transfer for the Treatment of Cutaneous T-Cell Lymphoma. PLoS One. 2012;7(9):e44455. 36.Abdel-Motal UM, Harbison C, Han T, Pudney J, Anderson DJ, Zhu Q, et al. Prolonged expression of an
anti-HIV–1 gp120 minibody to the female rhesus macaque lower genital tract by AAV gene transfer. Gene
Ther. 2014;21(9):802–10. 37.Van Wauwe JP, Goossens JG. The mitogenic activity of OKT3 and anti-Leu 4 monoclonal antibodies:
A comparative study. Cell Immunol. 1983;77(1):23–9. 38.Chatenoud LFCLC et al. In vivo cell activation following OKT3 administration.pdf. Transplantation. 1990;49(4):697–702. Page 17/28 Page 17/28 39.Malcolm SL, Smith EL, Bourne T, Shaw S. A humanised mouse model of cytokine release : Comparison
of CD3-speci fi c antibody fragments. J Immunol Methods. 2012;384(1–2):33–42. 40. Herold KC, Burton JB, Francois F, Poumian-Ruiz E, Glandt M, Bluestone JA. References Activation of human T
cells by FcR nonbinding anti-CD3 mAb, hOKT3??1(Ala-Ala). J Clin Invest. 2003;111(3):409–18. 41.Li Li, Nishio Junko MA van et al. Differential response of regulatory and conventional CD4+
lymphocytes to CD3 engagement: clues to a possible mechanism of anti-CD3 action? J Immunol. 2013;197(7):3694–704. 42.Chatenoud L. CD3-specific antibody-induced active tolerance: from bench to bedside. Nat Rev
Immunol. 2003;3(2):123–32. 43. Besançon A, Baas M, Goncalves T, Valette F, Waldmann H, Chatenoud L, et al. The induction and
maintenance of transplant tolerance engages both regulatory and anergic CD4+ T cells. Front Immunol. 2017;8(MAR):1–11. 44.Bluestone J, Mackay C, O’Shea J, Stockinger B. The functional plasticity of T cell subsets. Nat Rev
Immunol. 2009;9(11):811–6. 44.Bluestone J, Mackay C, O’Shea J, Stockinger B. The functional plasticity of T cell subsets. Nat Rev
Immunol. 2009;9(11):811–6. 45. Yang J, Fan H, Hao J, Ren Y, Chen L, Li G, et al. Amelioration of acute graft-versus-host disease by
adoptive transfer of ex vivo expanded human cord blood CD4+CD25+ forkhead box protein 3+ regulatory
T cells is associated with the polarization of Treg/Th17 balance in a mouse model. Transfusion. 2012;52(6):1333–47. 46.Sousa IG, do Almo MM, Simi KCR, Bezerra MAG, Andrade RV, Maranhão AQ, et al. MicroRNA
expression profiles in human CD3+ T cells following stimulation with anti-human CD3 antibodies. BMC
Res Notes. 2017;10(1):124. 47.Cretney E, Xin A, Shi W, Minnich M, Masson F, Miasari M, et al. The transcription factors Blimp–1 and
IRF4 jointly control the differentiation and function of effector regulatory T cells. Nat Publ Gr. 2011;12(4):304–11. 48.Liu W, Putnam AL, Xu-yu Z, Szot GL, Lee MR, Zhu S, et al. CD127 expression inversely correlates with
FoxP3 and suppressive function of human CD4 + T reg cells. J Exp Med. 2006;203(7):1701–11. 49.Shen LS, Wang J, Shen DF, Yuan XL, Dong P, Li MX, et al. CD4+CD25+CD127low/- regulatory T cells
express Foxp3 and suppress effector T cell proliferation and contribute to gastric cancers progression. Clin Immunol. 2009;131(1):109–18. 50.Saraiva M, Garra AO. The regulation of IL 10 production by immune cells. Nat Rev Immunol. 2010;10(3):170–81. Page 18/28 51.Dummer CD, Carpio VN, Felipe L, Gonçalves S, Manfro RC, Veronese FV. FOXP3 + regulatory T cells :
From suppression of rejection to induction of renal allograft tolerance ☆. Transpl Immunol. 2012;26(1):1–
10. 52.Long SA, Thorpe J, Herold KC, Ehlers M, Sanda S, Lim N, et al. Remodeling T cell compartments during
anti-CD3 immunotherapy of type 1 diabetes. Cell Immunol. 2017;319:3–9. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 58. University of California Santa Cruz. USCS Genome Browser. References 53.Speiser DE, Utzschneider DT, Oberle SG, Münz C, Romero P, Zehn D. T cell differentiation in chronic
infection and cancer: Functional adaptation or exhaustion?. Vol. 14, Nature Reviews Immunology. Nature
Publishing Group; 2014. p. 768–74. 54.Curran TA, Jalili RB, Farrokhi A, Ghahary A. IDO expressing fibroblasts promote the expansion of
antigen specific regulatory T cells. Immunobiology. 2014;219(1):17–24. 55.Curti A, Pandolfi S, Valzasina B, Aluigi M, Isidori A, Ferri E, et al. Modulation of tryptophan catabolism
by human leukemic cells results in the conversion of. Blood. 2006;109:2871–8. 56.Ratajczak P, Janin A, Peffault de Larour R, Koch L, Roche B, Munn D, et al. IDO in Human Gut Graft-
versus-Host Disease. Biol Blood Marrow Transplant. 2012;18(1):150–5. 57.Babraham Institute. Barbraham Bioinformatics, Cambridge. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ http://genome.ucsc.edu/cgi-bin/hgGateway?db = hg19 http://genome.ucsc.edu/cgi-bin/hgGateway?db = hg19 59.Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, et al. Fast mapping of short
sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol. 2009;5(9):1–10. 60.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format
and SAMtools. Bioinformatics. 2009;25(16):2078–9. 61.Anders S, Pyl PT, Huber W. HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9. 62.Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data
with DESeq2. Genome Biol. 2014;15(12):1–21. 63.Mi H, Muruganujan A, Thomas PD. PANTHER in 2013: Modeling the evolution of gene function, and
other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 2013;41(D1):377–86. Page 19/28 Page 19/28 64.Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. Enrichr : interactive and collaborative
HTML5 gene list enrichment analysis tool. 2013; 64.Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. Enrichr : interactive and collaborative
HTML5 gene list enrichment analysis tool. 2013; Tables Table 1. Read mapping rates and statistics for RNA-seq data. Replicate
All Reads
Mapped Reads
% Mapped Reads
Unstimulated (1)
59 623 760
54 990 450
92
Unstimulated (2)
61 444 968
58 149 032
94
FvFc R (1)
57 712 398
54 065 899
93
FvFc R (2)
54 633 094
51 012 088
93
FvFc M (1)
62 274 364
58 117 856
93
FvFc M (2)
65 142 278
60 452 698
92
OKT3 (1)
60 724 236
51 446 623
84
OKT3 (2)
59 435 924
50 336 034
84 Table 1. Read mapping rates and statistics for RNA-seq data. Replicate
All Reads
Mapped Reads
% Mapped Reads
Unstimulated (1)
59 623 760
54 990 450
92
Unstimulated (2)
61 444 968
58 149 032
94
FvFc R (1)
57 712 398
54 065 899
93
FvFc R (2)
54 633 094
51 012 088
93
FvFc M (1)
62 274 364
58 117 856
93
FvFc M (2)
65 142 278
60 452 698
92
OKT3 (1)
60 724 236
51 446 623
84
OKT3 (2)
59 435 924
50 336 034
84 Table 1. Read mapping rates and statistics for RNA-seq data. Figures Page 20/28 Page 20/28 Page 20/28 Page 20/28 Page 20/28 Figure 1 Global gene expression profiles in anti-CD3-treated human T cells by RNA-seq data. The transcriptome
was obtained in CD3 T cells collected from a healthy donor at two different moments, treated or
untreated with anti-CD3 antibodies. Only genes with padj ≤ 0.05 were considered differentially expressed. (A) MA-plot with the global gene expression profile; red dots indicate up- or downregulated genes. (B)
Venn diagrams showing an overlap of regulated expressed genes compared to the control, among
different anti-CD3 treatments. (C) Clustering analysis and heatmap of gene expression based on fold
change data. Cluster analysis was performed with 860 commonly regulated genes (shown in rows) for
each sample (columns). Gradient colors from purple to gold represent lower to higher expression (range
from −9.27 to 9.22). Global gene expression profiles in anti-CD3-treated human T cells by RNA-seq data. The transcriptome
was obtained in CD3 T cells collected from a healthy donor at two different moments, treated or
untreated with anti-CD3 antibodies. Only genes with padj ≤ 0.05 were considered differentially expressed. (A) MA-plot with the global gene expression profile; red dots indicate up- or downregulated genes. (B)
Venn diagrams showing an overlap of regulated expressed genes compared to the control, among
different anti-CD3 treatments. (C) Clustering analysis and heatmap of gene expression based on fold
change data. Cluster analysis was performed with 860 commonly regulated genes (shown in rows) for
each sample (columns). Gradient colors from purple to gold represent lower to higher expression (range
from −9.27 to 9.22). Page 21/28 Figure 2
Gene set enrichment analysis of differentially expressed genes. Gene ontologies associated with
upregulated genes in peripheral blood CD3 cells following anti-CD3 treatment. The top twelve enriche
biological process categories were calculated using Panther. GO terms associated with cell proliferat Figure 2 Gene set enrichment analysis of differentially expressed genes. Gene ontologies associated with
upregulated genes in peripheral blood CD3 cells following anti-CD3 treatment. The top twelve enriched
biological process categories were calculated using Panther. GO terms associated with cell proliferation
was found to be overrepresented. (A) FvFc M-treated, (B) FvFc R-treated, and (C) OKT3-treated T cells. Gene set enrichment analysis of differentially expressed genes. Gene ontologies associated with
upregulated genes in peripheral blood CD3 cells following anti-CD3 treatment. The top twelve enriched
biological process categories were calculated using Panther. GO terms associated with cell proliferation
was found to be overrepresented. (A) FvFc M-treated, (B) FvFc R-treated, and (C) OKT3-treated T cells. Page 22/28 Page 22/28 Page 22/28 Figure 3
Gene set enrichment analysis of differentially expressed genes associated with immune terms. Radar
Plot of the GO term profile enrichment, coverage (completeness) and FDR adjusted p-value of immune-
associated terms. The terms were selected among up- and downregulated DEGs for each antibody
treatment, accessing those associated with immune response and inflammation typically associated with
anti-CD3 therapy. The black line represents OKT3 treatment; the orange line, FvFc R treatment; and the
gray line, FvFc M treatment. Figure 3 Figure 3 Gene set enrichment analysis of differentially expressed genes associated with immune terms. Radar
Plot of the GO term profile enrichment, coverage (completeness) and FDR adjusted p-value of immune-
associated terms. The terms were selected among up- and downregulated DEGs for each antibody
treatment, accessing those associated with immune response and inflammation typically associated with
anti-CD3 therapy. The black line represents OKT3 treatment; the orange line, FvFc R treatment; and the
gray line, FvFc M treatment. Page 23/28 Page 23/28 Figure 4
Differentially expressed genes in treated T cells assessed by RNA-seq data. Individual anti
DEG fold changes were grouped according to their biological function. The results are pres
mean gene expression fold change from two RNA-seq experiments. The asterisk represent
OKT3 (black bars) FvFc R (orange bars) or FvFc M (gray bars) Figure 4
Differentially expressed genes in treated T cells assessed by RNA-seq data. Individual anti-C
DEG fold changes were grouped according to their biological function. The results are prese
mean gene expression fold change from two RNA-seq experiments. The asterisk represents
OKT3 (black bars), FvFc R (orange bars) or FvFc M (gray bars). Figure 4 Figure 4 Differentially expressed genes in treated T cells assessed by RNA-seq data. Individual anti-CD3-induced
DEG fold changes were grouped according to their biological function. The results are presented as the
mean gene expression fold change from two RNA-seq experiments. The asterisk represents padj < 0.05. OKT3 (black bars), FvFc R (orange bars) or FvFc M (gray bars). Page 24/28 Page 24/28 Figure 5
Cytokines and their receptor genes regulated by anti-CD3 stimulation. qPCR assays were performed with
total RNA extracted from T cells, 72 h post anti-CD3 stimulation. The results are expressed as the fold
change relative to unstimulated T cells (n = 7; p < 0,05). B2M was used as an internal control for data
normalization. (A) IL17A, (B) IL2RA, (C) IL23R, (D) IL10, (E) IL17RA, (F) IL7R, (G) TGFB1. Figure 5 Cytokines and their receptor genes regulated by anti-CD3 stimulation. qPCR assays were performed with
total RNA extracted from T cells, 72 h post anti-CD3 stimulation. The results are expressed as the fold
change relative to unstimulated T cells (n = 7; p < 0,05). B2M was used as an internal control for data
normalization. (A) IL17A, (B) IL2RA, (C) IL23R, (D) IL10, (E) IL17RA, (F) IL7R, (G) TGFB1. Page 25/28 Figure 6 T cell subpopulation signatures. Cluster analysis based on the fold change data of regulated genes
(shown in rows) for each sample (columns) and grouped into T cell populations. Only genes with padj ≤
0.05 were considered differentially expressed. Gradient colors from blue to dark brown represent lower to
higher expression (range from -2.69 to 9.22). T cell subpopulation signatures. Cluster analysis based on the fold change data of regulated genes
(shown in rows) for each sample (columns) and grouped into T cell populations. Only genes with padj ≤
0.05 were considered differentially expressed. Gradient colors from blue to dark brown represent lower to
higher expression (range from -2.69 to 9.22). Page 26/28 Page 26/28 Figure 7
Quantitative analysis of T cell marker expression in anti-CD3-treated T cells. qPCR assays were
performed with total RNA extracted from T cells, 72 h post anti-CD3 stimulation; the results are expr
as fold changes relative to levels in unstimulated T cells (n = 7; p < 0,05). B2M was used as an inter
control for data normalization. (A) TBX21, (B) STAT4, (C) GATA, (D) RORC, (E) STAT3, (F) FOXP3, (G Figure 7 Figure 7 Quantitative analysis of T cell marker expression in anti-CD3-treated T cells. qPCR assays were
performed with total RNA extracted from T cells, 72 h post anti-CD3 stimulation; the results are expressed
as fold changes relative to levels in unstimulated T cells (n = 7; p < 0,05). B2M was used as an internal
control for data normalization. (A) TBX21, (B) STAT4, (C) GATA, (D) RORC, (E) STAT3, (F) FOXP3, (G) Page 27/28 Page 27/28 TNFRSF18, (H) CTLA4, (I) LAG3, (J) PDCD1, (K) EOMES, (L) KLRG1, (M) GZMB, (N) FAS, (O) FASLG, (P)
VDR, (Q) AIF1, (R) XCL1, (S) IDO1, (T) CD38, (U) GZMM, (V) STAT5A. supplement1.pdf Supplementary Files This is a list of supplementary files associated with this preprint. Click to download. supplement1.pdf supplement1.pdf Page 28/28
|
https://openalex.org/W4312090937
|
https://zenodo.org/records/7472286/files/VCS_article_95767.pdf
|
English
| null |
Distribution of graminoids in open habitats in Tajikistan and Kyrgyzstan
|
Vegetation Classification and Survey
| 2,022
|
cc-by
| 10,346
|
Vegetation Classification and Survey 3: 273–286
doi: 10.3897/VCS.95767 Abstract Aims: Landscapes of Middle Asia are exposed to human influence due to long-lasting pastoral tradition, and now are
largely dominated by non-forest vegetation. Graminoids perform key ecosystem functions, and constitute an important
feed source for livestock. We studied the distribution patterns of graminoids cover under climatic and grazing pressure
gradients in different open vegetation types. Study area: Tajikistan, Kyrgyzstan. Methods: 1,525 vegetation plots repre
senting five open vegetation types (mires, salt marshes, tall-forb communities, pseudosteppes and steppes) were extract
ed from the Vegetation of Middle Asia Database. We assessed the relative cover of graminoid species in each vegetation
type. The importance of mean annual temperature, sum of annual precipitation, aridity and livestock density as drivers
of relative cover of graminoids contribution patterns in the five vegetation types were explored with use of polynomial
functions and commonality analysis. Results: Open ecosystems of Middle Asia are characterized by different graminoid
contributions. The highest relative cover of graminoids was found for steppes, pseudosteppes and mires. Comparison of
model fits for relationship between the graminoids cover, climatic parameters and livestock pressure indicated advantage
of polynomial models. The best-fitting models for pseudosteppes were for mean annual temperature, Aridity Index and
livestock density, for steppes mean annual temperature and Aridity Index, and for salt marshes mean annual temperature. For mires and tall-forb communities, the models showed a poor fit or no effect of the variables studied. Conclusions: Our
study shows that climate and livestock pressure have an impact on the contribution of graminoids in open vegetation
types, but a general pattern is difficult to describe. Ongoing climate change may influence the share of graminoids in salt
marshes, steppes and pseudosteppes. Grazing (with a common effect of climatic factors) is the most important factor
influencing graminoids contribution on pseudosteppes, confirming the secondary origin of this vegetation type. Taxonomic reference: The nomenclature of the vascular plants follows Plants of the World Online (POWO 2022) and
problematic taxonomic issues were based on The World Flora Online (WFO 2022). Nomenclature of Stipa spp. follows
Nobis et al. (2020). Distribution of graminoids in open habitats in
Tajikistan and Kyrgyzstan 5 Institute of Agroecology and Plant Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland Corresponding author: Sebastian Świerszcz (sebastian.swierszcz@ob.pan.pl) Academic editor: Idoia Biurrun ♦ Received 28 September 2022 ♦ Accepted 13 December 2022 ♦ Published 20 December 2022 aridity, climate, Cyperaceae, grassland, hot-spot, Juncaceae, Kyrgyzstan, Middle Asia, open habitat, Poaceae, steppe,
k International Association for Vegetation Science (IAVS) GRASSLANDS OF ASIA Introduction Graminoids are a major component of open habitats across
the world, particularly wetlands and grasslands (Gibbson
2009; Bragina et al. 2018; Nowak et al. 2020a). Graminoids
include vascular plants with a grass-like morphology from
three groups: grasses (Poaceae), sedges (Cyperaceae) and
rushes (Juncaceae). Poaceae, as one of the most species-rich
family worldwide, includes around 11,500–12,000 taxa
classified to about 770–780 genera (Christenhusz and
Byng 2016; Soreng et al. 2017). The second most abundant
family of graminoids, Cyperaceae, includes approx. 5,500
species within about 90 genera (Christenhusz and Byng
2016). The most common group are sedges, represented
mainly by the genus Carex, which are found in many types
of habitats, often as dominants or co-dominants (Spalink
et al. 2018). At high altitudes, e.g. the Pamir Plateau, the
Tibetan Plateau and the Himalayas, open vegetation is
dominated by cold-resistant sedge species such as Kobresia
spp. creating dense, low mats (Miehe et al. 2009; Vanselow
2011). Vegetation types dominated by species from Kobre
sia or Carex are used as winter pastures because they store
more nutrients in the cold season, and maintain the nu
tritional value for livestock longer than other graminoids,
e.g. grasses (Vanselow 2011). The third graminoid group,
Juncaceae, is less numerous and includes about 460 species
within eight genera (Christenhusz and Byng 2016). The
most species-rich genus is Juncus, with the majority of the
species growing sparsely in wetland habitats.f p
g
g p
y
Many grasses, sedges and rushes are effective colo
nisers, making them cosmopolitan (Spalink et al. 2016;
Linder et al. 2018; Martín-Bravo et al. 2019). Grass-dom
inated ecosystems cover 31–43% of the earth’s surface
(Gibbson 2009). Colonisation of new areas and habitats
is facilitated by dispersal and establishment ability, broad
environmental tolerance and ecological competitiveness
of the species (Scheiter et al. 2012; Linder et al. 2018). They
are often exposed to extreme environmental conditions
such as drought and high salinity and various disturbanc
es, e.g. intensive herbivory (Coughenour 1985; Gibbson
2009; Borer et al. 2019). Graminoids are intensively used
as forage for livestock (Linder et al. 2018). In the course
of evolution, graminoids have developed several features
that allow them to endure harsh conditions. For example,
traits allowing to tolerate drought, which are also useful
in adapting to grazing resistance, include basal meri
stems, rapid growth, high shoot density, nutrient storage
and rapid transpiration (Coughenour 1985). Keywords idity, climate, Cyperaceae, grassland, hot-spot, Juncaceae, Kyrgyzstan, Middle Asia, open habitat, Poaceae, steppe,
ajikistan aridity, climate, Cyperaceae, grassland, hot-spot, Juncaceae, Kyrgyzstan, Middle Asia, open habitat, Poaceae, steppe,
Tajikistan Copyright Sebastian Świerszcz et al. This is an open access article distributed under the terms of the Creative Commons Attribution
License (CC-BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and
source are credited. Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 274 of plants and vegetation types (Stanyukovich 1982). The
landscape of Middle Asia is dominated by open habi
tats with a high contribution of graminoids as a conse
quence of thousands of years of pastoralism. Steppes are
the most prominent biome in Middle Asia, divided into
three types: high altitude arid steppes (Nowak et al. 2018),
mountain steppes of semi-arid areas, and dry, thermophi
lous steppes of montane and subalpine belts (Nowak et al. 2016b, 2018, 2020a). The most abundant plant group of
the Middle Asian steppes is Poaceae. Examples of promi
nent grass genera in the steppe vegetation are Agropyron,
Avena, Bromus, Elymus, Elytrigia and Stipa (Nowak et al. 2020a) and the most diverse genus is Stipa with 76 species
and subspecies. Contrary to the steppes, pseudosteppes
are secondary grassland types that have replaced natural
thermophilous open woodlands and scrub vegetation, as
a result of clearing and subsequent grazing of the herb lay
er (Świerszcz et al. 2020; Nowak et al. 2022b). Mesophi
lous grasslands ranging from the lowlands to the alpine
belt form a distinct vegetation type, in which numerous
graminoid species occur. At high elevation in the alpine
belt, graminoid vegetation is often dominated by Kobresia
species (Nowak et al. 2020a). Graminoids are also core
species in fen and spring communities, as well as littoral
vegetation (Nowak et al. 2014, 2016a). A distinct vegeta
tion type are salt marshes, which develop on lake shores
at high altitudes but also in the colline and foothill belts
along rivers, springs and artificial leakages, under harsh
saline conditions (Nowak et al. 2020a). In areas of defor
estation of juniper woods, tall-forb communities domi
nated by dicotyledonous perennials with a variable pro
portion of graminoids develop (Nowak et al. 2020b). Introduction Saline and
wet habitats promote plants with lower requirements for
mechanical support characterized by long rhizomes and
short stature (Dolezal et al. 2019).l About 9,300 vascular plant species have been de
scribed from the Middle Asia region (Khassanov 2015). The vascular flora of Kyrgyzstan consists of ca. 4,000 spe
cies (Lazkov and Sultanova 2014), of which about 10%
are endemics (Lazkov and Umralina 2015). The families
Poaceae, Cyperaceae and Juncaceae account for a total of
430 species, and among them 120 species are endemics
or sub-endemics (21% of all graminoids; Lazkov and Sul
tanova 2014). The Tajik flora consists of ca. 4,300 species
(see Nowak et al. 2020c), where approx. 30% are known as
endemics (Nowak et al. 2011). In Tajikistan, 438 species
belong to the Poaceae, Cyperaceae and Juncaceae fami
lies, 70 of them are endemics or sub-endemics (16% of
all graminoids) and 133 are considered endangered at the
national level (Nowak et al. 2020c). These numbers show
how unique the flora of Middle Asia is, and how abundant
graminoids are. In terms of food and economic safety, Middle Asia is al
most entirely dependent on livestock production. This re
gion has a long tradition of pastoralism and since ancient
times a whole human population consider its welfare with
the quality of pasturelands and the number of livestock
herds. Besides typical grasslands, there are also other veg
etation types in Middle Asia such as tall-forb communities,
mires, and salt marshes used for grazing in which gram
inoids are likely key contributors to biomass and diversity. Due to its unique floristic richness, most of the terri
tory of Tajikistan and Kyrgyzstan is recognized by Con
servation International as a biodiversity hotspot – Moun
tains of Central Asia (Mittermeier et al. 2011). The diverse
landscape, extreme climate and varied habitat condi
tions shape the biogeography of Middle Asia (Nowak et
al. 2020a; Wagner et al. 2020), offering a high diversity 275 Vegetation Classification and Survey Thus, finding basic patterns of graminoid species abun
dance and distribution in different vegetation types in Mid
dle Asia is of high importance. In this paper, we addressed
three main questions: (1) How is graminoid species richness
shaped in the open vegetation types of Tajikistan and Kyr
gyzstan? (2) Is there a general pattern of graminoid occur
rence in different open vegetation types? (3) How do climate
and livestock density affect the proportion of graminoids? Introduction The region is characterized by a very long elevational
gradient ranging from 287 to 7,495 m a.s.l, which makes
this territory particularly diverse in terms of climate, land
relief and geomorphology. The geological profile is com
plex with a predominance of limestone, marble, dolomite,
dolomitic shale, clay shale, phyllitic schist, siltstone, and
argillaceous slates of Carboniferous, Cambrian, Siluri
an, and Early Cretaceous origin. However, the specific
geological conditions of this region are still under study
(Leven 1981; Budanov and Pashkov 1988; Lohr 2001).hfi Study area The study area is difficult to characterize in terms of
climatic conditions. The climate differs spatially in terms
of its continentality, topographic complexity, and orogra
phy. However, according to Latipova (1968), Narzikulov
and Stanyukovich (1968), and Safarov (2003), four main
climatic regions can be distinguished. The study area
is placed between two main biogeographic regions, Ira
no-Turanian and Central Asiatic, with climatic influences
from the Indo-Indochinese region in the south and the
Euro-Siberian region in the north. The specific conditions
of the regions are as follows (Figure 1):h The study was conducted within the administrative bor
ders of Tajikistan and Kyrgyzstan (Figure 1). The land
scape of the area is dominated by diverse open habitats,
which are shaped by the strongly varied environment,
landscape, and human activity, grazing of sheep, goats,
cattle and horses in particular. The study area is main
ly dominated by steppes and chasmophytic vegetation. However, hay meadows also contribute importantly to
the landscape at intermediate altitudes (ca. 2,000–3,000 m
a.s.l.). Alpine swards in subalpine and alpine belts are used
as summer pastures, and Kobresia mats at the highest al
titudes are used as winter pastures. Additionally, the wide
terraces of lowland river valleys and floodplains of the
alpine rivers offer suitable habitats for grassland develop
ment. Salt marshes develop under harsh saline conditions. The studied vegetation types differ considerably in terms
of topographic and edaphic conditions as well as altitude. The warm and continental Irano-Turanian region (Fer
gana Valley and south-western Tajikistan) is character
ized by low annual precipitation with the sum of ca. 200–
250 mm, and the peak in March (ca. 80 mm). During the
summer months (from June to August) the precipitation
is scarce, with the sum of 0–10 mm per month. Snow and
frost occur only in winter (from December to February). Temperatures strongly vary during the year; in the warmest Figure 1. Distribution of plots in the study area (n = 1,525). Figure 1. Distribution of plots in the study area (n = 1,525). 276 Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan The final data set consisted of 1,525 vegetation-plot re
cords of open habitats (Table 1). Plots were sampled from
2006 to 2019 in Tajikistan and Kyrgyzstan (Figure 1). Vegetation data preparation (
g
)
Based on the coordinates, we derived the mean annual
temperature and the sum of annual precipitation from the
CHELSA dataset, with a resolution of 0.00833 decimal de
grees (30 arc sec; Karger et al. 2017a, 2017b). Global Arid
ity Index (hereinafter referred to as Aridity Index) was
obtained from the Global-PET geospatial dataset available
on the CGIAR-CSI GeoPortal (Zomer et al. 2022). Arid
ity Index values are unitless and decrease with more arid
conditions (Zomer et al. 2022). Livestock density data were
obtained from the Gridded Livestock of the World database
at a spatial resolution of 0.083333 decimal degrees (approxi
mately 10 km at the equator) (GLW v3.1; Gilbert et al. 2018). For this study, we selected population densities (the average
number of animals per km2) of the most common and in
fluential livestock species: sheep, goats and cattle combined. The primary source of data was the Vegetation of Mid
dle Asia database (Nowak et al. 2017; GIVD ID: AS-00-
003) containing 4,649 vegetation plots (relevés) stored in
TURBOVEG (Hennekens and Schaminée 2001). Plots
that were previously classified as natural or semi-natural
vegetation of open habitats were extracted. We removed
plots with a shrub layer > 50% and also those that are
not typically used for grazing. At this stage, we obtained
a data set representing five types of vegetation (Table 1;
Figure 2). Because of the low number of records from
meadows in our database (26 vegetation plots), they
were excluded. The plant identification was based on the
ten-volume flora of Tajikistan (Ovchinnikov 1957, 1963,
1968, 1975, 1978, 1981; Chukavina 1984; Kochkareva
1986; Kinzikaeva 1988; Rasulova 1991) and the ten-vol
ume study of the flora of the former Soviet part of the
Middle Asia (Conspectus Florae Asiae Mediae; Kova
levskaya 1968–1993). B
temp
CHE
gree
ity I
obta
on t
ity I
cond
obta
at a s
mate
For
num
fluen
Sta
All s
(R C
noid
Junc
by w
‘ggri
W
annu
Inde
Table 1. Number of plots for each open vegetation type
(n = 1,525). Vegetation types
Number of plots Plot size range (m2)
Mires
489
2–30
Tall-forb communities
168
10
Pseudosteppes
150
10
Salt marshes
191
10–100
Steppes
527
10–30 The primary source of data was the Vegetation of Mid
dle Asia database (Nowak et al. 2017; GIVD ID: AS-00-
003) containing 4,649 vegetation plots (relevés) stored in
TURBOVEG (Hennekens and Schaminée 2001). Study area Each
plot contains a full list of vascular plant species recorded in
a plot, often also a list of bryophytes, and estimates of the
cover-abundance of species in each layer in the Braun-Blan
quet or percentage scale. For each plot, geographical co
ordinates were measured using a GPSMAP 60CSx device
with an accuracy of ± 5 m, and the WGS84 reference frame. In the case when the Braun-Blanquet scale was used, we
transformed to the percentage scale (r: 1%, +: 2%, 1: 3%,
2: 13%, 3: 38%, 4: 63%, 5: 88%). Then we calculated the rel
ative cover of each species within each plot. Relative cover
was calculated by dividing the cover of each species by the
total vegetation cover of all species in the plot. To deter
mine the relative cover of graminoids, we summed the rel
ative cover of each species in this group in the plot. months, they reach from 20°C (May) to 34°C (June, July,
August). In winter, the mean temperature is no lower than
-3°C with extreme values reaching -27°C in some years.h months, they reach from 20°C (May) to 34°C (June, July,
August). In winter, the mean temperature is no lower than
-3°C with extreme values reaching -27°C in some years. The warm, humid and continental region includes the
Tian Shan and Pamir-Alai ranges. The sum of annual pre
cipitation ranges from ca. 500 mm in northern slopes to
ca. 1000 mm in southern slopes. In June, the mean tem
perature in colline and montane belts reaches ca. 22°C
while in alpine belts, it reaches up to 10°C. The cold, semi-arid region includes the Issyk-Kul ba
sin, central and western parts of the Alai Valley, as well as
foothills and plateaus in the colline, montane and subal
pine belts. The area is characterized by low precipitation,
with the sum of ca. 200–400 mm per year. The precipita
tion reaches a peak of 70 mm per month in spring (from
May to July). The annual mean temperature is ca. 10°C, it
exceeds 20°C only in the summer months.h The cold and arid climate region includes the eastern
most sections of the Alai Valley and the eastern Pamirian
Plateau. The sum of annual precipitation is extremely low
and does not exceed 100 mm. Only in May and August
the monthly sum of precipitation is ca. 20 mm. Environmental variables We assessed the importance of mean annual temperature,
sum of annual precipitation, aridity, and livestock density
(surrogate of grazing intensity) as drivers of the relative
cover of graminoids. Mean annual temperature and sum
of annual precipitation are two key climate factors that de
termine plant distribution (Whittaker 1975). Aridity and
grazing are factors that promote species with grazing re
sistance traits (Coughenour 1985; Milchunas et al. 1988). Vegetation data preparation Plots
that were previously classified as natural or semi-natural
vegetation of open habitats were extracted. We removed
plots with a shrub layer > 50% and also those that are
not typically used for grazing. At this stage, we obtained
a data set representing five types of vegetation (Table 1;
Figure 2). Because of the low number of records from
meadows in our database (26 vegetation plots), they
were excluded. The plant identification was based on the
ten-volume flora of Tajikistan (Ovchinnikov 1957, 1963,
1968, 1975, 1978, 1981; Chukavina 1984; Kochkareva
1986; Kinzikaeva 1988; Rasulova 1991) and the ten-vol
ume study of the flora of the former Soviet part of the
Middle Asia (Conspectus Florae Asiae Mediae; Kova
levskaya 1968–1993). Study area The annual
mean temperature is slightly above 0°C, with a minimum
of ca. -30°C from January to February. Statistical analyses All statistical analyses were performed in R environment
(R Core Team 2022). The relative cover (%) of all grami
noids in the plots as well as of Poaceae, Cyperaceae and
Juncaceae was presented by density curves computed
by weighted kernel density smoothing functions using
‘ggridges’ package (Wilke 2021).f Table 1. Number of plots for each open vegetation type
(n = 1,525). Vegetation types
Number of plots Plot size range (m2)
Mires
489
2–30
Tall-forb communities
168
10
Pseudosteppes
150
10
Salt marshes
191
10–100
Steppes
527
10–30 We used linear models to explore the effects of the mean
annual temperature, sum of annual precipitation, Aridity
Index and livestock density for the patterns of graminoid 277 Vegetation Classification and Survey Figure 2. Photos of the open vegetation types: (a) steppe (Kosh-Dobo, Kyrgyzstan), (b) salt marsh (Zoogvand, Tajik
istan), (c) pseudosteppe (on the right site of the photo; Khoja Mumin Mt. near Vose, Tajikistan), (d) tall-forb commu
nity (near Rabot, Tajikistan), (e) mire near Jelondy (Tajikistan) and (f) overgrazing – one of the main human-driven
threats to grasslands in Middle Asia leading to land degradation. Figure 2. Photos of the open vegetation types: (a) steppe (Kosh-Dobo, Kyrgyzstan), (b) salt marsh (Zoogvand, Tajik
istan), (c) pseudosteppe (on the right site of the photo; Khoja Mumin Mt. near Vose, Tajikistan), (d) tall-forb commu
nity (near Rabot, Tajikistan), (e) mire near Jelondy (Tajikistan) and (f) overgrazing – one of the main human-driven
threats to grasslands in Middle Asia leading to land degradation. abundance in open habitats. We performed linear models
and evaluated the relevance of a quadratic term (polynomi
al) to account for potential curvilinear relationships. We built
models for each vegetation type and explanatory variable
separately. The best model among the linear and quadratic
ones was evaluated by their coefficient of determination (R2)
and root mean-squared error (RMSE) with the compare_per
formance function in the R package ‘performance’ version
0.8.0 (Lüdecke et al. 2021). Results of linear and polynomial
models performance are presented in Suppl. material 1.i of relative cover of graminoids. To do this, we decom
posed the variance of R2 into unique and common effects
of predictors. Unique effects indicate how much variance
is uniquely accounted for by a single predictor and com
mon effects indicate how much variance is common to
a predictor set (Ray-Mukherjee et al. 2014). Statistical analyses The sum of
unique and common effects (total) represents the total
contribution of a predictor to the dependent variable
irrespective of collinearity with other variables (Pru
nier et al. 2015). Commonality analysis was conducted
with commonalityCoefficients function in ‘yhat’ package
(Nimon et al. 2008). Additionally, we used commonality analysis to find
the most important factors influencing the contributions Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 278 munities. Mires and salt marshes had the lowest number
of shared graminoid species among all pair-wise compa
risions. The most common species were Calamagrostis
pseudophragmites and Poa bulbosa (Suppl. material 2).h Results In total, we recorded 255 graminoid species within all
vegetation types. Graminoid-richest vegetation types were
steppes (136 species – 53.3% of the total graminoid flora)
and pseudosteppes (94 species – 36.9% of the total grami
noid flora) (Table 2). Lower number of graminoid species
was recorded in mires (77), salt marshes (74) and tall-forb
communities (57). The observed number of shared spe
cies between vegetation types and the proportion of the
observed species varied between the pairs of vegetation
types (Table 2). The highest number of shared species was
found for steppes and pseudosteppes, steppes and tall-
forb communities, and pseudosteppes and tall-forb com The highest relative cover of graminoids was found
for steppes (median: 47.8%), mires (median: 43.06%)
and pseudosteppes (median: 39%). However, a particular
density peak cannot be distinguished because the relative
cover of graminoids is evenly distributed along the entire
range within these vegetation types (Figure 3a). The dis
tribution of the relative cover of Poaceae is similar to the
distribution of relative cover of all graminoids (Figure 3b)
indicating the apparent dominance of species from this
family. The only exception was mires, where Cyperaceae Figure 3. Density curves representing the distribution of relative cover (%) for all graminoids together (a) and split
by family (b, c, d) within open habitat types at plot level. The vertical red line shows the median value of relative
graminoid cover within each vegetation type. On the y-axis, the distributions are represented by relative values with
the maximum density of each group standardized to 1. Figure 3. Density curves representing the distribution of relative cover (%) for all graminoids together (a) and split Figure 3. Density curves representing the distribution of relative cover (%) for all graminoids together (a) and split
by family (b, c, d) within open habitat types at plot level. The vertical red line shows the median value of relative
graminoid cover within each vegetation type. On the y-axis, the distributions are represented by relative values with
the maximum density of each group standardized to 1. Vegetation Classification and Survey 279 hump-shaped with the highest values of graminoids be
tween ca. 0 and 10°C (Figure 4).h were dominating, with a median relative cover of 31%
(Figure 3c). The relative cover of Juncaceae was lowest in
all vegetation types (Figure 3d). Results The model showed that sum of annual precipitation
had statistically significant effect on all vegetation types,
although with a low model fit (R2 = 0.05–0.1; Table 3). The effect of this variable in pseudosteppes and tall-
forb communities was negative and in salt-marshes
and steppes was positive. The highest unique effect of
this factor was found in tall-forb communities (68.4%). No clear pattern was found for mires (Figure 4). The
models of Aridity Index and domestic animal pressure
measured by livestock density showed a statistically sig
nificant effect on the relative cover of graminoids in all
vegetation types except tall-forb communities (Table 3). Model comparison showed that polynomial models
provided a better fit for the relationship between gram
inoid relative cover and predictor variables (Table 3). The
model of mean annual temperature showed a significant
pattern of the relative cover of graminoids for salt marsh
es, pseudosteppes and steppes with the best fit and high
unique effect for salt marshes (R2 = 0.32 and 65.3% of the
regression effect; Table 3). The relative cover of gram
inoids increased in pseudosteppes, and decreased in salt
marshes with increasing mean annual temperature. The
effect of the mean annual temperature in steppes was Figure 4. The relationship between graminoids relative cover and mean annual temperature (MAT), sum of annual
precipitation (AP), Aridity Index and livestock density for open vegetation types in Tajikistan and Kyrgyzstan. Lines
are predictions of fitted polynomial models (for a comparison of linear and polynomial models see Suppl. material 1). Only significant models at p < 0.05 level are shown. Figure 4. The relationship between graminoids relative cover and mean annual temperature (MAT), sum of annual
precipitation (AP), Aridity Index and livestock density for open vegetation types in Tajikistan and Kyrgyzstan. Lines
are predictions of fitted polynomial models (for a comparison of linear and polynomial models see Suppl. material 1). Only significant models at p < 0.05 level are shown. Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 280 Table 2. Graminoid species cumulative number in each open vegetation type and the quantitative proportion of
graminoids in relation to the graminoid flora (255 species). Grey-shaded cells show the number and percentage val
ue (in brackets) of shared graminoid species between pairs of vegetation types. The darker the cell, the higher the
number of shared graminoid species between pairs of vegetation types. Results Total graminoid
species richness = 255
Mires
Tall-forb
communities
Pseudosteppes
Salt marshes
Steppes
Mires
77 (30.2)
10 (3.9)
24 (9.4)
22 (8.6)
13 (5.1)
Tall-forb
communities
57 (22.4)
41 (16.1)
15 (5.9)
40 (15.7)
Pseudosteppes
94 (36.9)
30 (11.8)
61 (23.9)
Salt marshes
74 (29)
26 (10.2)
Steppes
136 (53.3) Table 3. Results of the polynomial regression models and commonality analysis for the effect of mean annual tem
perature, sum of annual precipitation, Aridity Index and livestock density on graminoids relative cover for open veg
etation types. The significant values are shown in bold. Commonality analysis output represents a unique, common
and total contribution of each predictor variable to the regression effect. The proportion of variance explained by
the predictor is presented in parenthesis as a percentage of R2. Table 3. Results of the polynomial regression models and commonality analysis for the effect of mean annual tem
perature, sum of annual precipitation, Aridity Index and livestock density on graminoids relative cover for open veg
etation types. The significant values are shown in bold. Commonality analysis output represents a unique, common
and total contribution of each predictor variable to the regression effect. The proportion of variance explained by
the predictor is presented in parenthesis as a percentage of R2. The best-fitted models for Aridity Index were found for
pseudosteppes (R2 = 0.16) and steppes (R2 = 0.14). The
highest unique effect of Aridity Index was found for
mires (46.2%), however the highest common effect for
this factor was recorded for steppes (62.1%) and pseu
dosteppes (43 9%) In pseudosteppes and mires relative
However, the unique effect of livestock density is rela
tively low (7.4%), but the common effect with other fac
tors is the highest among all the open vegetation types
analysed (57.4%). The highest graminoids relative cover
values on pseudosteppes was found at a density of ca. Results 9,000 animals per km2 Similar hump-shape pattern
Explanatory variable
F
p-value
R2
Commonality analysis
Unique
Common
Total
Mires
Mean annual temperature
1.20
0.303
0.005
0.001 (0.8%)
0.004 (5.8%)
0.005 (6.6%)
Sum of annual precipitation
13.30
< 0.001
0.052
0.003 (4.6%)
0.016 (22.3%)
0.019 (27%)
Aridity Index
16.23
< 0.001
0.063
0.033 (46.2%)
0.028 (39.9%)
0.061 (86.1%)
Livestock density
12.25
< 0.001
0.048
0.003 (4.8%)
0.025 (35%)
0.028 (39.7%)
Tall-forb communities
Mean annual temperature
0.82
0.441
0.010
0.003 (5.4%)
0.005 (9.7%)
0.008 (15.2%)
Sum of annual precipitation
4.26
0.016
0.049
0.037 (68.4%)
0.003 (6%)
0.04 (74.3%)
Aridity Index
1.16
0.316
0.014
0.013 (25.1%)
-0.002 (-2.8%)
0.012 (22.3%)
Livestock density
0.88
0.417
0.011
0.004 (7.7%)
-0.004 (-7.3%)
0.0002 (0.4%)
Pseudosteppes
Mean annual temperature
13.31
< 0.001
0.153
0.029 (11.1%)
0.123 (46.4%)
0.152 (57.5%)
Sum of annual precipitation
8.55
< 0.001
0.104
0.004 (1.5%)
0.07 (26.6%)
0.074 (28.1%)
Aridity Index
14.40
< 0.001
0.164
0.045 (17%)
0.116 (43.9%)
0.161 (60.9%)
Livestock density
22.69
< 0.001
0.236
0.02 (7.4%)
0.152 (57.4%)
0.172 (64.9%)
Salt marshes
Mean annual temperature
43.51
< 0.001
0.316
0.239 (65.3%)
0.068 (18.6%)
0.307 (83.9%)
Sum of annual precipitation
7.56
< 0.001
0.074
0.001 (0.2%)
0.044 (11.9%)
0.044 (12.1%)
Aridity Index
10.91
< 0.001
0.104
0.004 (1.2%)
0.078 (21.2%)
0.082 (22.4%)
Livestock density
8.25
< 0.001
0.081
0.031 (8.4%)
-0.003 (-0.8%)
0.028 (7.6%)
Steppes
Mean annual temperature
43.02
< 0.001
0.141
0.0001 (0.1%)
0.001 (0.4%)
0.001 (0.5%)
Sum of annual precipitation
33.03
< 0.001
0.112
0.013 (9.6%)
0.085 (63.3%)
0.098 (73%)
Aridity Index
42.06
< 0.001
0.138
0.036 (26.6%)
0.083 (62.1%)
0.119 (88.6%)
Livestock density
25.31
< 0.001
0.088
0.001 (0.7%)
0.0002 (0.1%)
0.001 (0.8%) The best-fitted models for Aridity Index were found for
pseudosteppes (R2 = 0.16) and steppes (R2 = 0.14). The
highest unique effect of Aridity Index was found for
mires (46.2%), however the highest common effect for
this factor was recorded for steppes (62.1%) and pseu
dosteppes (43.9%). In pseudosteppes and mires relative
cover of graminoids decreased with increasing Aridity
Index (and therefore increasing moisture availability, see
the Methods), and in steppes and salt marshes, relative
cover of graminoids increased with increasing Aridi
ty Index (Figure 4). For livestock density, the best-fit
ted model was found for pseudosteppes (R2 = 0.24). Graminoids are not always the dominant group
in broadly-defined grasslands of Tajikistan and
Kyrgyzstan Grasslands are generally described as vegetation dominat
ed by graminoids, which typically have > 25% coverage
(Dengler et al. 2014). Referring to the definition of Allen
et al. (2011) the vegetation of grassland is broadly consid
ered because a variety of plant groups are present includ
ing grasses, legumes and other forbs, with no or scarce
occurrence of woody plants. The results of our research
showed that the analysed types of vegetation, which can be
broadly classified as grasslands (steppes, pseudosteppes,
mires, salt marshes and tall-forb vegetation), are charac
terized by different proportions of graminoids (Figure 2). It is not surprising that the highest proportion of grami
noids was recorded in steppes, mires and pseudosteppes. These are vegetation types that are shaped by the livestock
grazing. The area of Middle Asia is characterized by long
pastoral tradition, which for many years influenced the
formation of plant communities consisting of grazing
tolerant species (Wesche and Treiber 2012; Spengler et al. 2014). In grassland vegetation occurring in Tajikistan and
Kyrgyzstan, species from Poaceae dominate or constitute a
significant share. An important component of steppe veg
etation are species from the genus Stipa (Wesche and Trei
ber 2012); in this study 33 Stipa taxa (species and subspe
cies) were found within the study area. Pseudosteppes are
secondary grassland types developed in habitats primarily
dominated by shrublands. This vegetation type occurs in
lowlands (Figure 2c), in the southern regions of Middle
Asia characterized by relatively high annual precipitations
and high temperatures (Świerszcz et al. 2020). Similarly
to steppes, they are characterized by a constant and sig
nificant share of species from the Poaceae, including the
most frequently recorded Poa bulbosa. Also, some pseu
dosteppes are characterized by a higher frequency and
cover of annual species, e.g. Aegilops triuncialis, Avena
sterilis subsp. ludoviciana, Bromus lanceolatus, or Vulpia
persica (Suppl. material 2). Results However, the unique effect of livestock density is rela
tively low (7.4%), but the common effect with other fac
tors is the highest among all the open vegetation types
analysed (57.4%). The highest graminoids relative cover
values on pseudosteppes was found at a density of ca. 9,000 animals per km2. Similar hump-shape pattern
was found for steppes with the highest graminoids rel
ative cover values at a density of ca. 4,000 animals. On
the other hand, for salt marshes and mires we found a
U-shaped pattern with the lowest relative cover of gram
inoids at level of ca. 1,500 and 2,500 domestic animals
per km2 respectively (Figure 4). 281 Vegetation Classification and Survey spp. (Świerszcz et al. 2021) to vegetation with a negligi
ble share of graminoids, e.g. communities dominated by
stem succulent С3 chenopods of the genera Salicornia,
Halopeplis, and Suaeda (Akhani 2004). Our study showed
that the number of graminoid species is relatively low in
salt marshes of Middle Asia (74 taxa; Suppl. material 2);
however, they are used as pasture, mostly in the harsh
conditions of the Pamirs (Świerszcz et al. 2021). Tall-forb
communities are also characterized by a low graminoid
abundance. They are dominated by tall forbs, such as
species from the Apiaceae (e.g. Prangos pabularia, Feru
la kuhistanica, and Heracleum lehmannianii; Nowak et al. 2020b). Similar results were obtained by Wagner (2009) in
meadow-forb vegetation in the western Tian Shan, where
non-graminoid species dominate while only 19 graminoid
species were recorded. The low number and contribution
of graminoids in tall-forb vegetation can be explained by
their close relationship with juniper forests, xerophyt
ic shrubs, or screes in which graminoids occur with low
abundance (Nowak et al. 2020b, 2022a; Świerszcz et al. 2022). Moreover, tall-forb communities are used as pas
tures, but grazing animals use sward selectively because
the vegetation includes tasteless or even poisonous spe
cies (e.g. Prangos pabularia, species of the genus Ferula). This phenomenon causes a strong growth and dominance
of these plants and simultaneously inhibits the growth of
grasses and sedges (Figure 2d). Grazing-induced changes in graminoids abun
dance The vegetation cover of open habitats in Tajikistan and Kyr
gyzstan is strongly affected by livestock grazing, which re
sulted in changes in graminoid abundance. However, our
study shows that not all analysed vegetation types respond to
grazing in terms of graminoid contribution. We obtained the
best-fitted model for pseudosteppes, where the proportion
of graminoids increases with increasing livestock density to
the highest point of all vegetation types analysed. The results
confirm that pseudosteppes are a secondary vegetation type
created after the cutting of pistachio groves (Nowak et al. 2022b). Intensive grazing, mainly by sheep and goats, results
in the appearance of a high abundance of species resistant to
grazing (e.g. Poa bulbosa, Carex pachystylis, Cynodon dac
tylon) and characterized by animal-induced diaspore dis
persal (e.g. Aegilops triuncialis, Avena sterilis subsp. ludovi
ciana, Taeniatherum caput-medusae subsp. crinitum; Suppl. material 2). Many of them are ephemeral species (Toderich
et al. 2013) also resistant to aridity and high temperatures. Milchunas et al. (1988) showed that arid conditions pro
mote grazing resistance traits. It appears that semi-natural
pseudosteppes are associated with a long evolutionary his
tory of grazing, strongly linked to climatic conditions (e.g. seasonally dry soils; Guarino et al. 2020). Similar relation
ships have been confirmed in other parts of the world, e.g. the Patagonian steppes of southern Argentina (Adler et al. 2004; Guarino et al. 2020). On the other hand, in the steppes,
which are characterized by similar vegetation physiognomy
and land use type, according to our results, the variation in
relative graminoid cover is mainly related to climatic con
ditions. Grazing has a much smaller effect on their share of
patches in the vegetation; moreover, grazing intensification
may lead to a reduction in the proportion of graminoids at
the expense of other grazing-tolerant species, e.g. species of
the genus Astragalus (= Tragacantha, Astracantha). The contribution of graminoids in salt marshes also
varied along climatic gradients. The highest graminoid
cover was found on sites with a low mean annual tempera
ture, high precipitation and less arid conditions. Middle
Asian salt marshes vary according to geobotanical regions. In south-western Tajikistan and in the Ferghana Valley
salt vegetation inhabits e.g. shallow ponds and around riv
erbeds. The most common graminoid species is Aeluropus
littoralis, however, it does not make a significant contribu
tion to the vegetation. The high-elevation salt marshes in
the Eastern Pamir are different. Effects of climatic factors on the abundance of
graminoids Pseudo
steppes develop in zones with high average temperatures
with dry periods during the summer, when the entire
grasslands sesonally dry up (Guarino et al. 2020). High pre
cipitation in spring and autumn and dry summers promote
periodically drought-tolerant species that increase in abun
dance seasonally. Due to arid climatic conditions, high live
stock pressure, and soil erosion, the vegetation has a greater
contribution of graminoids, especially annual grasses, e.g. Avena sterilis subsp. ludoviciana, Bromus lanceolatus, and
Vulpia persica (Suppl. material 2; Świerszcz et al. 2020). This
secondary vegetation within the shrubland zone (Figure 2c)
is similar to the thermo-mesomediterranean grasslands oc
curring in the Mediterranean Region (San Miguel 2008;
Guarino et al. 2020; Świerszcz et al. 2020).h bioclimatic variables studied poorly explained patterns of
graminoids contribution. This may be explained by plant
species composition in tall-forb communities, which de
pends on specific microclimatic and soil conditions, not
examined in this study. For example, Central European tall-
forb communities with a high abundance of graminoids are
associated with acidic soils and/or excessive depositions of
atmospheric nitrogen (Świerkosz and Reczyńska 2022). Grazing-induced changes in graminoids abun
dance The vegetation is shaped
by extremely harsh conditions and is species poor. How
ever, a common feature of graminoid species found in salt
marshes, as in steppes, is their longevity and low resistance
to soil drought. Many vegetation patches are dominated
by graminoids adapted to the high salt content in the soil,
e.g. species of the genus Puccinellia (Nowak et al. 2020a). Although our results show some patterns in the propor
tions of graminoids with regard to precipitation and the
Aridity Index in mires, the models show a poor fit. The lack
of a clear climatic gradient may be due to the fact that sedges
are the main component of this type of vegetation (Spalink
et al. 2018; Martín-Bravo et al. 2019). Mires are hydrogenic
habitats, fed mainly by seeping groundwater (Nowak et al. 2016a), thus they buffer the surplus of water supplied by rain
fall. However, the highest share of graminoids in this type of
vegetation, mainly species from Cyperaceae, is recorded in
the driest areas (with low Aridity Index values). In the case
of Middle Asia, such conditions prevail mainly in high al
titudes of the Pamir Mountains, where long-rhizomatous
graminoids typical for high alpine vegetation are promoted
(Dolezal et al. 2019). Also, aridity facilitates the development
of other plant features, e.g. grazing‐resistance traits (Adler et
al. 2004). These features, combined with resistance to cold,
radiation, drought and strong wind are very important from
the point of view of livestock production, especially as winter
pastures (Göbel et al. 2019; Can et al. 2020). Effects of climatic factors on the abundance of
graminoids Grasslands in Middle Asia, despite having similar phys
iognomy, show high variation in species composition
(Wesche and Treiber 2012). Grasslands, similarly to other
vegetation types, change along environmental gradients in
relation to climatic variables such as precipitation, tem
perature, and aridity. The altitudinal gradient influenc
es the structure, phenology and species composition of
grasslands in this strongly mountainous region (Wagner
et al. 2020). Steppes are typical grassland vegetation and constitute
an important feature of the diverse landscape in Middle
Asia. Our study showed strong response of graminoids
relative cover to climatic gradients in these steppes. We
observed a sharp decrease of graminoids at low average
annual temperatures at altitudes above 3,000 m a.s.l. (own
observations). With the increasing altitude and harsh
er environmental conditions, graminoids are replaced by
resilient semi-desert taxa adapted to high elevations, e.g. Artemisia skorniakovii, Astragalus chomutowii or Braya
pamirica (Nowak et al. 2018; Świerszcz et al. 2020). Low
proportion of graminoids is also noted in the more ther
mophilic steppes in the colline and montane belts, where
the vegetation may consist mainly of dwarf shrubs (Nowak
et al. 2016b). A possible explanation for this may be that the
graminoids involved in the formation of the steppe vegeta
tion have a long life span and are less resistant to aridity and The vegetation type with the highest proportion of
graminoids are mires, which occur mostly in the moun
tainous areas of Middle Asia. Harsh environmental condi
tions at high elevational zones together with an intensive
grazing promote species from the Cyperaceae. An increas
ing abundance of Cyperaceae representatives with increas
ing altitude was also found in the Himalayas (Dolezal et
al. 2019). However, despite analogous relationships in the
proportion of graminoids in the altitudinal gradient our
results do not show any clear pattern in sedges-dominated
mires related to elevation (data not shown). Salt marshes and tall-forb vegetation had a low contri
bution of graminoids (median relative coverage < 25%,
Figure 3). Halophytic vegetation is quite diverse in terms
of dominant plant groups: from graminoid-dominat
ed communities with Aeluropus littoralis or Puccinellia Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 282 low annual precipitation. The opposite pattern was found
for pseudosteppes, where a higher contribution of gram
inoids was recorded in a more arid environment. Author contributions S.Ś. planned the research. S.Ś., G.S, and S.N. collected part
of the field data. S.Ś. prepared the final dataset, performed
statistical analyses and led the writing. G.S., M.R., and
S.N. critically revised and edited the manuscript. References Adler PB, Milchunas DG, Lauenroth WK, Sala OE, Burke IC (2004)
Functional traits of graminoids in semi-arid steppes: A test of graz
ing histories. Journal of Applied Ecology 41: 653–663. https://doi. org/10.1111/j.0021-8901.2004.00934.x Christenhusz MJM, Byng JW (2016) The number of known plants spe
cies in the world and its annual increase. Phytotaxa 261: 201–217. https://doi.org/10.11646/phytotaxa.261.3.1 Christenhusz MJM, Byng JW (2016) The number of known plants spe
cies in the world and its annual increase. Phytotaxa 261: 201–217. https://doi.org/10.11646/phytotaxa.261.3.1 Chukavina AP (1984) Flora Tadzhikskoi SSR. T. VII. Zontichnye – Ver
benovye [Flora of the Tajik SSR. T. VII. Umbelliferae – Verbenaceae]. Izdatelstvo Nauka, Leningrad, RU. [In Russian] Chukavina AP (1984) Flora Tadzhikskoi SSR. T. VII. Zontichnye – Ver
benovye [Flora of the Tajik SSR. T. VII. Umbelliferae – Verbenaceae]. Izdatelstvo Nauka, Leningrad, RU. [In Russian] Akhani H (2004) Halophytic vegetation of Iran: Towards a syntaxonomi
cal classification. Annali di Botanica 4: 65–82. https://rosa.uniroma1. it/rosa04/annali_di_botanica/article/view/9168/9093 Coughenour MB (1985) Graminoid responses to grazing by large herbivores:
adaptations, exaptations, and interacting processes. Annals of the Mis
souri Botanical Garden 72: 852–863. https://doi.org/10.2307/2399227 Allen VG, Batello C, Berretta EJ, Hodgson J, Kothmann M, Li X, McIvor
J, Milne J, Morris C, … Sanderson M (2011) An international ter
minology for grazing lands and grazing animals. Grass and Forage
Science 66: 2–28. https://doi.org/10.1111/j.1365-2494.2010.00780.x Dengler J, Janišová M, Török P, Wellstein C (2014) Biodiversity of Pa
laearctic grasslands: A synthesis. Agriculture, Ecosystems & Environ
ment 182: 1–14. https://doi.org/10.1016/j.agee.2013.12.015 Borer ET, Lind EM, Firn J, Seabloom EW, Anderson TM, Bakker ES, Bie
derman L, La Pierre KJ, MacDougall AS, … Stevens CJ (2019) More salt,
please: global patterns, responses and impacts of foliar sodium in grass
lands. Ecology Letters 22: 1136–1144. https://doi.org/10.1111/ele.13270 Dolezal J, Klimes A, Dvorsky M, Riha P, Klimesova J, Schweingruber
F
(2019)
Disentangling
evolutionary,
environmental
and
morphological drivers of plant anatomical adaptations to drought
and cold in Himalayan graminoids. Oikos 128: 1576–1587. https://
doi.org/10.1111/oik.06451 Bragina TM, Wagner V, Nowak A, Vanselow KA (2018) Grasslands of
Kazakhstan and Middle Asia: the ecology, conservation and use of
a vast and globally important area. In: Squires VR, Dengler J, Feng
H, Hua L (Eds) Grasslands of the world: diversity, management and
conservation. CRC Press Taylor & Francis Group, Boca Raton, Lon
don, New York, UK, US, 139–167. Gibbson DJ (2009) Grasses and Grassland Ecology. Oxford University Press,
Oxford, UK, 305 pp. Acknowledgements We are grateful to Idoia Biurrun, Arkadiusz Nowak, and
anonymous Reviewers for the valuable comments that
improved the quality of the manuscript. We also thank
Firuza Illarionova from the Dushanbe Nature Protection
Team for her assistance and help in organizing field ex
peditions. The project was partially supported by the Na
tional Science Centre, Poland, no. 2020/04/X/NZ8/00032. Data availability Primary data are stored in the Vegetation of Middle Asia
database (http://www.givd.info/ID/AS-00-003) (Nowak et
al. 2017). Conclusions Our study shows that the largest number of graminoid
species is associated with steppes, which are the most
common vegetation type in Middle Asia. However, there is
no universal pattern for graminoid distribution along the
climatic and grazing gradient, but such relationships were
found for particular vegetation types. Strong but not con
sistent relationships were found in steppes, pseudosteppes Tall-forb communities are not typical graminoid veg
etation. In most cases, graminoids do not dominate in
these communities, although there is great variability with
in this type of vegetation (Nowak et al. 2020b). However, Vegetation Classification and Survey 283 and salt marshes. These differences result mainly from bi
ogeographic features of the study area. But it is important
to bear in mind that current and upcoming climate change
may contribute to the potential extinction of some grami
noid species, including endemics (Vintsek et al. 2022). Grazing showed to be the strongest variable influencing
the proportion of graminoids in pseudosteppes, pointing
to their anthropogenic origin. The mountainous land
scape and the history of human activity, especially grazing
by sheep, cattle and horses, create favourable habitats for
various types of graminoid communities. It is worth not
ing that major changes in open ecosystems are related to
expanding human and livestock populations, resulting in
pastures that are often overgrazed, which can lead to more
serious problems related to soil erosion, among others
(Figure 2f). As Middle Asia is an area where the human
food and economic safety is largely depended on graz
ing animals, research on group of plants is necessary and
should be continued, also for vegetation types important
for grazing but not covered by our analyses (e.g. alpine
meadows, Kobresia mats). The knowledge about relative
cover patterns of graminoids and their underlying factors
increases our understanding of ecological patterns in the
open vegetation of Middle Asia. References https://doi.org/10.2989/10220111003703542 Gilbert M, Nicolas G, Cinardi G, Van Boeckel TP, Vanwambeke SO, Wint
GRW, Robinson TP (2018) Global distribution data for cattle, buffa
loes, horses, sheep, goats, pigs, chickens and ducks in 2010. Scientific
Data 5: e180227. https://doi.org/10.1038/sdata.2018.227 Budanov BI, Pashkov BR (1988) O masshtabakh rannekamennougol’ nogo
i permskogo vulkanizma v vostochnoy chasti Severnogo Pamira [On
the scale of early Carboniferous and Permian vulcanism in the eastern
part of the Northern Pamir]. Bulletin MOIP (of the Moscow Society for
the Investigation of Nature), Geological Section 63: 33–38. [In Russian] Göbel L, Coners H, Hertel D, Willinghöfer S, Leuschner C (2019) The
role of low soil temperature for photosynthesis and stomatal con
ductance of three graminoids from different elevations. Frontiers in
Plant Science 10: e330. https://doi.org/10.3389/fpls.2019.00330 Can M, Wei W, Zi H, Bai M, Liu Y, Gao D, Tu D, Bao Y, Wang L, … Qu
G (2020) Genome sequence of Kobresia littledalei, the first chromo
some-level genome in the family Cyperaceae. Scientific Data 7: 1–8. https://doi.org/10.1038/s41597-020-0518-3 Guarino R, Vrahnakis M, Rodriguez Rojo MP, Giuga L, Pasta S (2020)
Grasslands and shrublands of the Mediterranean region. In: Della
Sala DA, Goldstein MI (Eds) The Encyclopedia of the World’s Bi Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 284 Palaeoclimatology,
Palaeoecology
276:
130–147. https://doi. org/10.1016/j.palaeo.2009.03.005 omes. Elsevier, Oxford, UK, 638–655. https://doi.org/10.1016/B978-
0-12-409548-9.12119-0 omes. Elsevier, Oxford, UK, 638–655. https://doi.org/10.1016/B978-
0-12-409548-9.12119-0 Hennekens SM, Schaminée JHJ (2001) TURBOVEG, a comprehensive
data base management system for vegetation data. Journal of Vegeta
tion Science 12: 589–591. https://doi.org/10.2307/3237010 Milchunas DG, Sala OE, Lauenroth WK (1988) A generalized mod
el of the effects of grazing by large herbivores on grassland com
munity structure. American Naturalist 132: 87–106. https://doi. org/10.1086/284839 Karger DN, Conrad O, Böhner J, Kawohl T, Kreft H, Soria-Auza RW,
Zimmermann NE, Linder HP, Kessler M (2017a) Climatologies at
high resolution for the earth’s land surface areas. Scientific Data 4:
e170122. https://doi.org/10.1038/sdata.2017.122 Mittermeier RA, Turner WR, Larsen FW, Brooks TM, Gascon C (2011)
Global biodiversity conservation: the critical role of hotspots. In:
Zachos FE, Habel JC (Eds) Biodiversity Hotspots – Distribution and
Protection of Conservation Priority Areas. Springer-Verlag, Berlin,
DE, 3–22. https://doi.org/10.1007/978-3-642-20992-5_1 Protection of Conservation Priority Areas. Springer-Verlag, Berlin,
DE, 3–22. https://doi.org/10.1007/978-3-642-20992-5_1 Karger DN, Conrad O, Böhner J, Kawohl T, Kreft H, Soria-Auza RW,
Zimmermann NE, Linder HP, Kessler M (2017b) Data from: Clima
tologies at high resolution for the earth’s land surface areas. References https://
doi.org/10.1038/sdata.2017.122 [accessed 1 Sep 2022] Protection of Conservation Priority Areas. Springer-Verlag, Berlin, DE, 3–22. https://doi.org/10.1007/978-3-642-20992-5_1 Narzikulov IK, Stanyukovich KW (1968) Atlas Tajikskoi SSR [Atlas of
the Tajik SSR]. Akademia Nauk Tajikskoi SSR, Dushanbe, TJ. [In
Russian] doi.org/10.1038/sdata.2017.122 [accessed 1 Sep 2022] Khassanov OF (2015) Conspectus florae Asiae Mediae 11. Science Pub
lishers, Tashkent, UZ, 456 pp. Nimon K, Lewis M, Kane R, Haynes MH (2008) An R package to com
pute commonality coefficients in multiple regression case: an intro
duction to the package and a practical example. Behavior Research
Methods 40: 457–466. https://doi.org/10.3758/BRM.40.2.457 Kinzikaeva GK (1988) Flora Tadzhikskoi SSR. T. IX. Marenovye – Slozh
notsvetnye [Flora of the Tajik SSR. T. IX. Rubiaceae – Compositae]. Izdatelstvo Nauka, Leningrad, RU, 568 pp. [In Russian] Methods 40: 457–466. https://doi.org/10.3758/BRM.40.2.457 Nobis M, Gudkova PD, Nowak A, Sawicki J, Nobis A (2020) A Synop
sis of the Genus Stipa (Poaceae) in Middle Asia, including a Key to
Species Identification, an Annotated Checklist, and Phytogeograph
ic Analyses. Annals of the Missouri Botanical Garden 105: 1–63. https://doi.org/10.3417/2019378 Kochkareva TF (1986) Flora Tadzhikskoi SSR. T. VIII. Kermekovye –
Podorozhnikovye [Flora of the Tajik SSR. T. VIII. Limoniaceae – Plan
taginaceae]. Izdatelstvo Nauka, Leningrad, RU, 520 pp. [In Russian] Kovalevskaya SS (1968–1993) Opredelitel rastenii Srednej Azii [Deter
mination key to the flora of Middle Asia]. Vol. I–X. Akademia Nauk
USSR, Izdatelstvo “FAN” Uzbekskoi SSR, Tashkent, UZ. [In Russian] Nowak A, Nowak S, Nobis M (2011) Distribution patterns, ecological
characteristic and conservation status of endemic plants of Tadzhiki
stan - A global hotspot of diversity. Journal for Nature Conservation
19: 296–305. https://doi.org/10.1016/j.jnc.2011.05.003 Latipova WA (1968) Kolichestvo osadkov [Precipitation]. In: Narzikulov
IK, Stanyukovich KW (Eds) Atlas Tajikskoi SSR [Atlas of the Tajik
SSR]. Akademia Nauk Tajikskoi SSR, Dushanbe-Moskva, TJ, 68–69. [In Russian] 19: 296–305. https://doi.org/10.1016/j.jnc.2011.05.003 Nowak A, Nowak S, Nobis M (2014) Diversity and distribution of rush
communities from the Phragmito-Magno-Caricetea class in Pamir
Alai mountains (Middle Asia: Tajikistan). Pakistan Journal of Botany
46: 27–64. Lazkov GA, Sultanova B (2014) Checklist of vascular plants of Kyrgyz
stan. Natsenal‘naya Akademiya Nauk Kyrgyzskoi Respubliki, Bish
kek, KG, 166 pp. Nowak A, Nobis M, Nowak S, Plášek V (2016a) Fen and spring vegetation
in western Pamir-Alai Mountains in Tajikistan (Middle Asia). Phyto
coenologia 46: 201–220. https://doi.org/10.1127/phyto/2016/0106 Lazkov GA, Umralina AR (2015) Endemic and rare plant species of Kyr
gyzstan (Atlas). Food and Agriculture Organization of the United
Nations, Ankara, TR, 238 pp. References Leven EY (1981) Vozrast paleozoyskikh vulkanogennykh formatsiy
Severnogo Pamira [The age of Paleozoic volcanogenic formations
of the Northern Pamir]. Izv. Akad. Nauk SSSR, Ser. Geol. Izv. Akad. Nauk USSR, Ser. Geol. 9: 137–140. [In Russian] Nowak A, Nowak S, Nobis A, Nobis M (2016b) Vegetation of feather
grass steppes in the western Pamir Alai Mountains (Tajikistan, Mid
dle Asia). Phytocoenologia 46: 295–315. https://doi.org/10.1127/
phyto/2016/0145 Linder HP, Lehmann CER, Archibald S, Osborne CP, Richardson DM
(2018) Global grass (Poaceae) success underpinned by traits facilitat
ing colonization, persistence and habitat transformation. Biological
Reviews 93: 1125–1144. https://doi.org/10.1111/brv.12388 Nowak A, Nobis M, Nowak S, Nobis A, Swacha G, Kącki Z (2017) Vege
tation of Middle Asia - The project state of art after ten years of sur
vey and future perspectives. Phytocoenologia 47: 395–400. https://
doi.org/10.1127/phyto/2017/0208 Reviews 93: 1125–1144. https://doi.org/10.1111/brv.12388 Nowak A, Nobis A, Nowak S, Nobis M (2018) Classification of steppe
vegetation in the eastern Pamir Alai and southwestern Tian-Shan
Mountains (Tajikistan, Kyrgyzstan). Phytocoenologia 48: 369–391. https://doi.org/10.1127/phyto/2018/0237 Lohr T (2001) A short story about the geological history of the Pamir. University of Mining and Technology Freiberg, DE. http://www.geo. tu-freiberg.de/hydro/oberseminar/pdf/TinaLohr.pdf [accessed 15
Aug 2020] Nowak A, Nowak S, Nobis M (2020a) The Pamir-Alai Mountains (Mid
dle Asia: Tajikistan). In: Noroozi J (Ed.) Plant biogeography and veg
etation of high mountains of Central and South-West Asia [Plant and
Vegetation, vol 17]. Springer International Publishing, Cham, DE,
1–42. https://doi.org/10.1007/978-3-030-45212-4_1 Lüdecke D, Ben-Shachar MS, Patil I, Waggoner P, Makowski D (2021)
performance: An R package for assessment, comparison and test
ing of statistical models. Journal of Open Source Software 6: e3139. https://doi.org/10.21105/joss.03139 Martín-Bravo S, Jiménez-Mejías P, Villaverde T, Escudero M, Hahn
M, Spalink D, Roalson EH, Hipp AL, Benítez-Benítez C, … Starr J
(2019) A tale of worldwide success: Behind the scenes of Carex (Cy
peraceae) biogeography and diversification. Journal of Systematics
and Evolution 57: 695–718. https://doi.org/10.1111/jse.12549 Nowak A, Świerszcz S, Nowak S, Nobis M (2020b) Classification of tall-
forb vegetation in the Pamir-Alai and western Tian Shan Mountains
(Tajikistan and Kyrgyzstan, Middle Asia). Vegetation Classification
and Survey 1: 191–217. https://doi.org/10.3897/VCS/2020/60848 Miehe G, Miehe S, Kaiser K, Reudenbach C, Behrendes L, La Duo,
Schlütz F (2009) How old is pastoralism in Tibet? An ecological
approach to the making of a Tibetan landscape. References Palaeogeography, Nowak A, Świerszcz S, Nowak S, Hisorev H, Klichowska E, Wróbel A,
Nobis A, Nobis M (2020c) Red List of vascular plants of Tajikistan
– the core area of the Mountains of Central Asia global biodiversi Vegetation Classification and Survey 285 ty hotspot. Scientific Reports 10: e6235. https://doi.org/10.1038/
s41598-020-63333-9 C4 expansion in the late Miocene. New Phytologist 195: 653–666. https://doi.org/10.1111/j.1469-8137.2012.04202.x Nowak A, Nobis M, Nowak S, Kotowski M, Świerszcz S (2022a) Phyto
sociological survey of juniper wood vegetation in Tajikistan (Mid
dle Asia). Dendrobiology 88: 17–37. https://doi.org/10.12657/den
bio.088.002 Soreng RJ, Peterson PM, Romaschenko K, Davidse G, Teisher JK, Clark
LG, Barberá P, Gillespie LJ, Zuloaga FO (2017) A worldwide phylo
genetic classification of the Poaceae (Gramineae) II: An update and
a comparison of two 2015 classifications. Journal of Systematics and
Evolution 55: 259–290. https://doi.org/10.1111/jse.12262 Nowak A, Nobis M, Nowak S, Kotowski M, Klichowska E, Nobis M, Świ
erszcz S (2022b) Syntaxonomy and ecology of thermophilous decidu
ous open woodlands and scrub vegetation in Tajikistan (Middle Asia). Dendrobiology 87: 47-68. https://doi.org/10.12657/denbio.087.004 Spalink D, Drew BT, Pace MC, Zaborsky JG, Starr JR, Cameron KM,
Givnish TJ, Sytsma KJ (2016) Biogeography of the cosmopolitan
sedges (Cyperaceae) and the area-richness correlation in plants. Journal of Biogeography 43: 1893–1904. https://doi.org/10.1111/
jbi.12802 Ovchinnikov PN (1957) Flora Tadzhikskoi SSR. T. I, Paprotnikoobraz nye – Zlaki [Flora of the Tajik SSR. T. I. Polypodiophyta – Gramine
ae]. Izdatelstvo Akademii Nauk SSSR, Moskva-Leningrad, RU, 546
pp. [In Russian] Spalink D, Pender J, Escudero M, Hipp AL, Roalson EH, Starr JR, Wa
terway MJ, Bohs L, Sytsma KJ (2018) The spatial structure of phylo
genetic and functional diversity in the United States and Canada: An
example using the sedge family (Cyperaceae). Journal of Systematics
and Evolution 56: 449–465. https://doi.org/10.1111/jse.12423 Ovchinnikov PN (1963) Flora Tadzhikskoi SSR. T. II, Osokovye – Orkh
idnye [Flora of the Tajik SSR. T. II. Cyperaceae – Orchidaceae]. Iz
datelstvo Akademii Nauk SSSR, Moskva-Leningrad, RU, 456 pp. [In
Russian] Spengler R, Frachetti M, Doumani P, Rouse L, Cerasetti B, Bullion E,
Mar’yashev A (2014) Early agriculture and crop transmission among
Bronze Age mobile pastoralists of Central Eurasia. Proceedings
of the Royal Society B: Biological Sciences 281: 1–7. https://doi. org/10.1098/rspb.2013.3382 Ovchinnikov PN (1968) Flora Tadzhikskoi SSR. T. III, Opekhovye -
Gvozdichnye [Flora of the Tajik SSR. T. III. Juglandaceae – Caryo
phyllaceae]. Izdatelstvo Akademii Nauk SSSR, Moskva-Leningrad,
RU, 710 pp. References [In Russian] Ovchinnikov PN (1975) Flora Tadzhikskoi SSR. T. IV, Rogolistnikovye
– Rozotsvetnye [Flora of the Tajik SSR. T. IV. Ceratophyllaceae – Ro
saceae]. Izdatelstvo Akademii Nauk SSSR, Moskva-Leningrad, RU,
576 pp. [In Russian] Stanyukovich KW (1982) Rastitelnost [Vegetation]. In: Saidmuradow
CM, Stanyukovich KW (Eds) Tadzhikistan. Priroda i prirodnye re
sursy [Tajikistan. Nature and natural resources]. Izdatelstvo Donish,
Dushanbe, TJ, 358–435. [In Russian] Ovchinnikov PN (1978) Flora Tadzhikskoi SSR. T. V, Krestotsvetne Świerkosz K, Reczyńska K (2022) Diversity of Mulgedio-Aconitetea com
munities in the Sudetes Mts. (SW Poland) in the Central European
context. Vegetation Classification and Survey 3: 67–86. https://doi. org/10.3897/VCS.70200 – Bobovye [Flora of the Tajik SSR. T. V. Brassicaceae – Fabaceae]. Izdatelstvo Akademii Nauk SSSR, Moskva-Leningrad, RU, 678 pp. [In Russian] – Bobovye [Flora of the Tajik SSR. T. V. Brassicaceae – Fabaceae]. Izdatelstvo Akademii Nauk SSSR, Moskva-Leningrad, RU, 678 pp. [In Russian] Ovchinnikov PN (1981) Flora Tadzhikskoi SSR. T. VI, Bobovye (rod As
tragal) [Flora of the Tajik SSR. T. VI. Fabaceae (genus Astragalus)]. Izdatelstvo Nauka, Leningrad, 725 pp. [In Russian] Świerszcz S, Nobis M, Swacha G, Kącki Z, Dembicz I, Waindzoch K,
Nowak S, Nowak A (2020) Pseudosteppes and related grassland veg
etation in the Pamir-Alai and western Tian Shan Mts – the border
land of the Irano-Turanian and Euro-Siberian regions. Tuexenia 40:
147–173. https://doi.org/10.14471/2020.40.04 Ovchinnikov PN (1981) Flora Tadzhikskoi SSR. T. VI, Bobovye (rod As
tragal) [Flora of the Tajik SSR. T. VI. Fabaceae (genus Astragalus)]. Izdatelstvo Nauka, Leningrad, 725 pp. [In Russian] POWO (2022) Plants of the World Online. Facilitated by the Royal
Botanic Gardens, Kew. http://www.plantsoftheworldonline.org [ac
cessed 27 Apr 2022] POWO (2022) Plants of the World Online. Facilitated by the Royal
Botanic Gardens, Kew. http://www.plantsoftheworldonline.org [ac
cessed 27 Apr 2022] Świerszcz S, Nobis M, Wróbel A, Klichowska E, Nowak S, Nowak A
(2021) Halophytic vegetation and adjoining plant communities in
Middle Asia (Pamir-Alai and western Tian Shan). Tuexenia 41: 1–28. https://doi.org/10.14471/2021.41.003 Prunier JG, Colyn M, Legendre X, Nimon KF, Flamand MC (2015)
Multicollinearity in spatial genetics: separating the wheat from the
chaff using commonality analyses. Molecular Ecology 24: 263–283. https://doi.org/10.1111/mec.13029 Świerszcz S, Nobis M, Nowak S, Kotowski M, Klichowska E, Nobis A,
Nowak A (2022) Syntaxonomy and ecology of mesophilous scrub
vegetation in Tajikistan (Middle Asia). Phytocoenologia 51: 177–198. https://doi.org/10.1127/phyto/2022/0395 R Core Team (2022) R: A language and environment for statistical com
puting. [Available from:] https://www.r-project.org/ Rasulova MR (1991) Flora Tadzhikskoi SSR. References Journal of Vegetation Sci
ence 20: 199–208. https://doi.org/10.1111/j.1654-1103.2009.01032.x drecht, NL, 3–43. https://doi.org/10.1007/978-94-007-3886-7_1
WFO (2022) World Flora Online. Version 2022.07. http://www.worldflo
raonline.org [accessed 1 Sep 2022]
Whittaker R (1975) Communities and ecosystems. Macmillan, New
York, US, 385 pp. Wilke CO (2021) ggridges: Ridgeline Plots in ‘ggplot2’ R package version
0.5.3. https://wilkelab.org/ggridges/ [accessed 1 Sep 2022]
Zomer RJ, Xu J, Trabucco A (2022) Version 3 of the Global Aridity Index
and Potential Evapotranspiration Database. Scientific Data 9: 409. https://doi.org/10.1038/s41597-022-01493-1 drecht, NL, 3–43. https://doi.org/10.1007/978-94-007-3886-7_1
WFO (2022) World Flora Online. Version 2022.07. http://www.worldflo
raonline.org [accessed 1 Sep 2022]
Whittaker R (1975) Communities and ecosystems. Macmillan, New
York, US, 385 pp. Wilke CO (2021) ggridges: Ridgeline Plots in ‘ggplot2’ R package version
0.5.3. https://wilkelab.org/ggridges/ [accessed 1 Sep 2022]
Zomer RJ, Xu J, Trabucco A (2022) Version 3 of the Global Aridity Index
and Potential Evapotranspiration Database. Scientific Data 9: 409. https://doi.org/10.1038/s41597-022-01493-1 WFO (2022) World Flora Online. Version 2022.07. http://www.worldflo
raonline.org [accessed 1 Sep 2022] Wagner V, Bragina TM, Nowak A, Smelansky IE, Vanselow KA (2020)
Grasslands and Shrublands of Kazakhstan and Middle Asia. In:
Goldstein MI, DellaSala DA (Eds) Encyclopedia of the World’s Bi
omes 3. Elsevier, Oxford, UK, 750–758. https://doi.org/10.1016/
B978-0-12-409548-9.12043-3 Wesche K, Treiber J (2012) Abiotic and biotic determinants of steppe
productivity and performance – A view from Central Asia. In: References T. X, Slozhnotsvetnye [Flora
of the Tajik SSR. T. X. Compositae)]. Izdatelstvo Nauka, Leningrad,
620 pp. [In Russian] Rasulova MR (1991) Flora Tadzhikskoi SSR. T. X, Slozhnotsvetnye [Flora
of the Tajik SSR. T. X. Compositae)]. Izdatelstvo Nauka, Leningrad,
620 pp. [In Russian] Toderich KN, Shuyskaya EV, Rajabov TF, Ismail S, Shaumarov M, Yoshi
ko K, Li EV (2013) Uzbekistan: Rehabilitation of desert rangelands
affected by salinity, to improve food security, combat desertification
and maintain the natural resource base. In: Heshmati GA, Squires
VR (Eds) Combating Desertification in Asia, Africa and the Middle
East: Proven practices. Springer Netherlands, Dordrecht, NL, 249–
278. https://doi.org/10.1007/978-94-007-6652-5_13 Ray-Mukherjee J, Nimon K, Mukherjee S, Morris DW, Slotow R, Ham
er M (2014) Using commonality analysis in multiple regressions: a
tool to decompose regression effects in the face of multicollinear
ity. Methods in Ecology and Evolution 5: 320–328. https://doi. org/10.1111/2041-210X.12166 (Eds) Combating Desertification in Asia, Africa and the Middle Safarov N (2003) National strategy and action plan on conservation and
sustainable use of biodiversity. Governmental Working Group of the
Republic of Tajikistan, Dushanbe, TJ. Safarov N (2003) National strategy and action plan on conservation and
sustainable use of biodiversity. Governmental Working Group of the
Republic of Tajikistan, Dushanbe, TJ. Vanselow KA (2011) The high-mountain pastures of the Eastern Pamirs
(Tajikistan). An evaluation of the ecological basis and the pasture
potential. PhD dissertation, University of Erlangen–Nuremberg, Er
langen, Nuremberg, DE. San Miguel A (2008) Management of Natura 2000 habitats. 6220 *Pseu
do-steppe with grasses and annuals of the Thero-Brachypodietea. Eu
ropean Commission. Vintsek L, Klichowska E, Nowak A, Nobis M (2022) Genetic differ
entiation, demographic history and distribution models of high
alpine endemic vicariants outline the response of species to pre
dicted climate changes in a Central Asian biodiversity hotspot. Scheiter S, Higgins SI, Osborne CP, Bradshaw C, Lunt D, Ripley BS, Tay
lor LL, Beerling DJ (2012) Fire and fire-adapted vegetation promoted Scheiter S, Higgins SI, Osborne CP, Bradshaw C, Lunt D, Ripley BS, Tay
lor LL, Beerling DJ (2012) Fire and fire-adapted vegetation promoted Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 286 Ecological Indicators 144: e109419. https://doi.org/10.1016/j. ecolind.2022.109419 Werger MJA, Staalduinen MA van (Eds) Eurasian Steppes. Ecolog
ical Problems and Livelihoods in a Changing World. Springer, Dor
drecht, NL, 3–43. https://doi.org/10.1007/978-94-007-3886-7_1 Wagner V (2009) Eurosiberian meadows at their southern edge: Patterns
and phytogeography in the NW Tien Shan. E-mail and ORCID Sebastian Świerszcz (Corresponding author, sebastian.swierszcz@ob.pan.pl), ORCID: https://orcid.org/0000-0003-
2035-0035 Grzegorz Swacha (grzegorz.swacha@uwr.edu.pl), ORCID: https://orcid.org/0000-0002-6380-2954
Małgorzata W. Raduła (malgorzata.radula@upwr.edu.pl), ORCID: https://orcid.org/0000-0002-9578-6135
Sylwia Nowak (snowak@uni.opole.pl), ORCID: https://orcid.org/0000-0003-2867-9839 Supplementary material Supplementary material
Supplementary material 1
Comparison of models performance used in our study
Link: https://doi.org/10.3897/VCS.95767.suppl1
Supplementary material 2
A list of graminoid species recorded in the study area
Link: https://doi.org/10.3897/VCS.95767.suppl2
|
https://openalex.org/W2928652388
|
https://pure.rug.nl/ws/files/92802409/fimmu_10_00646.pdf
|
English
| null |
Cross-Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus Vaccines Are Determined by Adjuvants and Route of Immunization
|
Frontiers in immunology
| 2,019
|
cc-by
| 12,003
|
Citation for published version (APA):
Bhide, Y., Dong, W., Gribonika, I., Voshart, D., Meijerhof, T., de Vries-Idema, J., Norley, S., Guilfoyle, K.,
Skeldon, S., Engelhardt, O. G., Boon, L., Christensen, D., Lycke, N., & Huckriede, A. (2019). Cross-
Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus
Vaccines Are Determined by Adjuvants and Route of Immunization. Frontiers in Immunology, 10, Article
646. https://doi.org/10.3389/fimmu.2019.00646 University of Groningen University of Groningen Cross-Protective Potential and Protection-Relevant Immune Mechanisms of Whole
Inactivated Influenza Virus Vaccines Are Determined by Adjuvants and Route of
Immunization
Bhide, Yoshita; Dong, Wei; Gribonika, Inta; Voshart, Danielle; Meijerhof, Tjarko; de Vries-
Idema, Jacqueline; Norley, Stephen; Guilfoyle, Kate; Skeldon, Sarah; Engelhardt, Othmar G. Published in:
Frontiers in Immunology Bhide, Yoshita; Dong, Wei; Gribonika, Inta; Voshart, Danielle; Meijerhof, Tjarko; de Vries-
Idema, Jacqueline; Norley, Stephen; Guilfoyle, Kate; Skeldon, Sarah; Engelhardt, Othmar G. Published in:
Frontiers in Immunology DOI:
10.3389/fimmu.2019.00646 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from
it. Please check the document version below. IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from
it. Please check the document version below. IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from
it. Please check the document version below. Document Version
Publisher's PDF also known as Version of record Document Version
Publisher's PDF, also known as Version of record Publication date:
2019 Publication date:
2019 Publication date:
2019 Link to publication in University of Groningen/UMCG research database Download date: 24-10-2024 Edited by:
Cecil Czerkinsky,
Institut National de la Santé et de la
Recherche Médicale (INSERM),
France Yoshita Bhide 1, Wei Dong 1, Inta Gribonika 2, Daniëlle Voshart 1, Tjarko Meijerhof 1,
Jacqueline de Vries-Idema 1, Stephen Norley 3, Kate Guilfoyle 4†, Sarah Skeldon 4,
Othmar G. Engelhardt 4, Louis Boon 5, Dennis Christensen 6, Nils Lycke 2 and
Anke Huckriede 1* Reviewed by:
Baik Lin Seong,
Yonsei University, South Korea
Huan Huu Nguyen,
Arizona State University,
United States 1 Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of
Groningen, Groningen, Netherlands, 2 Department of Microbiology and Immunology, Institute of Biomedicine, Gothenburg
University, Gothenburg, Sweden, 3 Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany, 4 Division of
Virology, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory
Agency (MHRA), Potters Bar, United Kingdom, 5 Bioceros, Utrecht, Netherlands, 6 Adjuvant Research, Department of
Infectious Diseases Immunology, Statens Serum Institut (SSI), Copenhagen, Denmark *Correspondence:
Anke Huckriede
a.l.w.huckriede@umcg.nl Adjuvanted whole inactivated virus (WIV) influenza vaccines show promise as broadly
protective influenza vaccine candidates. Using WIV as basis we assessed the
relative efficacy of different adjuvants by carrying out a head-to-head comparison of
the liposome-based adjuvants CAF01 and CAF09 and the protein-based adjuvants
CTA1-DD and CTA1-3M2e-DD and evaluated whether one or more of the adjuvants
could induce broadly protective immunity. Mice were immunized with WIV prepared from
A/Puerto Rico/8/34 (H1N1) virus intramuscularly with or without CAF01 or intranasally
with or without CAF09, CTA1-DD, or CTA1-3M2e-DD, followed by challenge with
homologous, heterologous or heterosubtypic virus. In general, intranasal immunizations
were
significantly
more
effective
than
intramuscular
immunizations
in
inducing
virus-specific serum-IgG, mucosal-IgA, and splenic IFNγ-producing CD4 T cells. Intranasal immunizations with adjuvanted vaccines afforded strong cross-protection with
milder clinical symptoms and better control of virus load in lungs. Mechanistic studies
indicated that non-neutralizing IgG antibodies and CD4 T cells were responsible for the
improved cross-protection while IgA antibodies were dispensable. The role of CD4 T
cells was particularly pronounced for CTA1-3M2e-DD adjuvanted vaccine as evidenced
by CD4 T cell-dependent reduction of lung virus titers and clinical symptoms. Thus,
intranasally administered WIV in combination with effective mucosal adjuvants appears
to be a promising broadly protective influenza vaccine candidate. Link to publication in University of Groningen/UMCG research database Citation for published version (APA):
Bhide, Y., Dong, W., Gribonika, I., Voshart, D., Meijerhof, T., de Vries-Idema, J., Norley, S., Guilfoyle, K.,
Skeldon, S., Engelhardt, O. G., Boon, L., Christensen, D., Lycke, N., & Huckriede, A. (2019). Cross-
Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus
Vaccines Are Determined by Adjuvants and Route of Immunization. Frontiers in Immunology, 10, Article
646. https://doi.org/10.3389/fimmu.2019.00646 Citation for published version (APA):
Bhide, Y., Dong, W., Gribonika, I., Voshart, D., Meijerhof, T., de Vries-Idema, J., Norley, S., Guilfoyle, K.,
Skeldon, S., Engelhardt, O. G., Boon, L., Christensen, D., Lycke, N., & Huckriede, A. (2019). Cross-
Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus
Vaccines Are Determined by Adjuvants and Route of Immunization. Frontiers in Immunology, 10, Article
646. https://doi.org/10.3389/fimmu.2019.00646 Copyright
Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the
author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-
amendment. Take-down policy
If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately
and investigate your claim. Take-down policy
If you believe that this document breaches copyright please contact us providing details, and we will remove access to
and investigate your claim Take-down policy
If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately
and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the
number of authors shown on this cover page is limited to 10 maximum. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the
number of authors shown on this cover page is limited to 10 maximum. ORIGINAL RESEARCH
published: 29 March 2019
doi: 10.3389/fimmu.2019.00646 Keywords: whole inactivated virus (WIV) influenza vaccines, liposome-based adjuvants, protein-based adjuvants,
cross protection, non-neutralizing serum antibodies, CD4 T cells †Present Address:
Kate Guilfoyle,
Viroclinics Biosciences B.V,
Rotterdam, Netherlands Viroclinics Biosciences B.V,
Rotterdam, Netherlands Specialty section:
This article was submitted to
Mucosal Immunity,
a section of the journal
Frontiers in Immunology Received: 27 September 2018
Accepted: 11 March 2019
Published: 29 March 2019 INTRODUCTION Furthermore, CAF05, a predecessor adjuvant was successfully
administered via mucosal route (39). This motivated us to
administer CAF09 via intranasal route. CTA1-DD is a fusion
protein consisting of the enzymatically active A1 subunit of
cholera toxin and a dimer of an Ig binding element from
Staphylococcus aureus protein A. It targets cells of the innate
immune system which results in strongly enhanced humoral and
cellular immune responses (27–29). Contrary to whole cholera
toxin the mucosal CTA1-DD adjuvant is safe and non-toxic as
found in non-human primates and it does not accumulate in the
olfactory bulb and nerve following administration intranasally
(i.n.) and, hence, cannot cause Bell’s palsy (40). CTA1-3M2e-DD
harbors an insert of three copies of the exterior domain of the M2
protein of influenza virus, M2e (26, 30). Vaccination is the cornerstone for the prevention of influenza
(1). Current influenza vaccines predominantly mediate strain
specific protection by eliciting neutralizing antibody responses
to the globular head region of hemagglutinin (HA), one of the
surface glycoproteins of the virus. They do not provide protective
immunity against strains not included in the vaccine (1, 2). New virus strains regularly emerge through antigenic drift, the
phenomenon responsible for recurrent epidemics. Moreover,
zoonotic influenza virus subtypes pose a serious pandemic threat,
as exemplified by pandemic H1N1(2009) and the potentially
pandemic subtypes H5N1, H7N9, H10N8, or H5N6 (3–6). There
is therefore an urgent need for broadly protective influenza
vaccines which can prevent or at least mitigate infection by virus
strains not included in the vaccine. p
We
compared
these
adjuvants
head-to-head
to
assess
their relative potency in stimulating cross-reactive and cross-
protective anti-influenza immunity in mice. In order to mimick
the situation of antigenic drift and antigenic shift, mice
were immunized intramuscularly (i.m.) or i.n. with A/Puerto
Rico/8/34 (PR8) WIV with or without the different adjuvants and
2 weeks after the final immunization mice were challenged with
homologous PR8, heterologous (H1N1)pdm09 or heterosubtypic
X-31 (H3N2) virus to assess protection and several immune
parameters. We observed that WIV administered i.n. with the
mucosal adjuvants conferred much stronger cross-protection
than parenterally administered WIV with or without adjuvant. Studies into the significance of different immune mechanisms
for protection revealed that non-neutralizing serum antibodies
and CD4 T cells were important for cross-protection while
IgA, even when present in high levels, did not play a
critical role. Thus, WIV administered i.n. Citation: Citation:
Bhide Y, Dong W, Gribonika I,
Voshart D, Meijerhof T, de
Vries-Idema J, Norley S, Guilfoyle K,
Skeldon S, Engelhardt OG, Boon L,
Christensen D, Lycke N and
Huckriede A (2019) Cross-Protective
Potential and Protection-Relevant
Immune Mechanisms of Whole
Inactivated Influenza Virus Vaccines
Are Determined by Adjuvants and
Route of Immunization. Front. Immunol. 10:646. doi: 10.3389/fimmu.2019.00646 March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 1 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. INTRODUCTION in combination
with effective mucosal adjuvants provided the strongest cross-
protection against heterosubtypic influenza virus infections and
appears to be a promising candidate for a broadly protective
influenza vaccine. Whole inactivated virus (WIV) vaccines contain all the
structural viral proteins and retain the conformation of native
virus particles and as such make a promising basis for an
influenza vaccine. Moreover, WIV has an intrinsic ability to
activate innate immune responses, e.g., antigen presenting cells
via Toll-like receptor 7 (TLR7) signaling (7). Although WIV
was the first vaccine to be used, it was later replaced by split
and subunit vaccines that were considered safer (8), despite
WIV being superior at inducing immune responses in mice and
naïve human beings (7, 9–12). Interest has recently refocused on
WIV vaccines as studies have shown them capable of inducing a
certain degree of cross-protection upon parenteral and mucosal
vaccination (3, 13–16). However, a large amount of antigen was
required to achieve protection and/or virus challenge was only
performed shortly after immunization in these studies (16). One
approach to reduce the dose of WIV needed would be to use
adjuvants that might also improve the breadth of the immune
responses (17–19). p
There are various adjuvants under investigation for improving
the immunogenicity of influenza vaccines (20). In this study,
we compared the liposome-based adjuvants CAF01 and CAF09
and the protein-based adjuvants CTA1-DD and CTA1-3M2e-
DD. These adjuvants were chosen because they were previously
used successfully with several vaccine candidates, including
influenza vaccines and are ready for or currently evaluated
in clinical trials (21–38). The cationic adjuvant formulations,
CAF01 and CAF09, are liposomes consisting of N,N′-dimethyl-
N,N′-dioctadecylammonium (DDA) as delivery vehicle. For
CAF01, α,α′-trehalose 6,6′-dibeheneate (TDB) acts as an
immunomodulator and liposome-stabilizer, while CAF09 is
stabilized and adjuvanted with monomycoloyl glycerol (MMG)-
1 and contains the TLR3 ligand Poly(I:C) as an additional
immunomodulator (21, 24). CAF01 and CAF09 have been
shown to generate strong T cell and antibody responses, with
particularly high IgG2a responses for CAF01 (21, 22, 37). CAF09
is furthermore capable of inducing potent CD8+ T cell responses
against protein and peptide based antigens (24, 33, 37, 38). CAF01 can be administered parenterally while CAF09 is mainly
administered intraperitoneally (i.p.,). However, there has been a
number of studies which showed promising results when CAF09
was given mucosally (Christensen et al. unpublished data). Viruses and Vaccines Viruses and Vaccines
Live
influenza
viruses
PR8
(H1N1),
A/California/7/2009
(H1N1)pdm09, and X-31 (H3N2) (a reassortant strain carrying
the HA of A/Aichi/2/68 and the internal proteins of PR8) were
propagated in embryonated chicken eggs and were titrated
on MDCK cells and in CB6F1 mice. Whole inactivated virus
vaccines (WIV) were prepared from these viruses by inactivation
with beta-propiolactone. Beta-propiolactone was removed in
down-stream processing by concentration of the allantoic fluid
and purification using sucrose gradient centrifugation. The WIV
HA content (µg/ml) was determined by using Lowry protein
assay and SDS-PAGE (colloidal blue staining) to establish total
protein content and percentage HA, respectively, the HA content
was then calculated. Quality and quantity of HA were confirmed
by single radial immunodiffusion assay (41). Frontiers in Immunology | www.frontiersin.org CD4 T Cell Depletion Anti-CD4 antibody (200 µg/injection, clone GK 1.5 Bioceros,
Utrecht, The Netherlands) was used for in vivo CD4 depletion,
which was assessed by staining with FITC-labeled anti-CD4
(clone RM 4.4, Thermo Scientific). Female CB6F1 mice (aged
6–8 weeks) were immunized as described above (groups 1, 4, 5,
7 from Table 1) followed by a heterosubtypic challenge with X-
31 virus (105.5 TCID50/mouse). Mice were injected i.p. with the
anti-CD4 antibody 1 day before, 1 and 7 days after challenge. Six animals/group were sacrificed on day 3 post challenge for
assessment of lung virus titers while the remaining animals were
followed for 14 days for clinical symptoms using the scoring
system described above. Adjuvant Comparison Study j
p
y
Female CB6F1/OlaHsd (C57Bl/6 x BALB/c F1) mice aged 6–
8 weeks were purchased from Envigo (The Netherlands). The
mice were distributed randomly and housed in groups of six
within individually ventilated cages (IVC) at the animal facility,
receiving standard water and diet. Group sizes were determined
using Piface software aiming at a power of 80%. Mice were
vaccinated three times with 0.5 µg HA of PR8 (with or without
the adjuvants) on days 0, 10, and 20 as described in Table 1. Mice from groups 1–3 received 50 µl PBS or vaccine i.m., 25
µl per hindlimb. Mice from groups 4–7 received respective
vaccines i.n. in a volume of 40 µl, divided between the two
nostrils. Vaccination and virus challenge were carried out under
Isoflurane/O2 anesthesia. Three weeks after the 3rd vaccination
(day 41), six mice from each group (of 18) were sacrificed to
determine vaccine-induced immune responses. The remaining
mice were challenged with 104.4 TCID50/mouse of homologous
PR8 virus, 103.3 TCID50/mouse of heterologous (H1N1)pdm09
or 105.5 TCID50/mouse of heterosubtypic X-31 (titers were
chosen on the basis of titration experiments in CB6F1 mice). Six mice from each experimental group were sacrificed on day 3
post challenge to assess protection against virus replication in the
lungs. The remaining six mice were observed until day 10 post
challenge to assess clinical symptoms such as weight loss, ruffled
fur and activity. The humane endpoint was set to a loss of >20%
of the original weight from the day of challenge. Additionally,
for the mechanistic experiments, a score sheet was used to follow
the animals. Parameters such as weight loss, appearance (degree
of ruffled fur, hunched back) and behavior of the animals (slow
movements, difficulty in walking, circling, response to external
stimulus) were recorded. These parameters were given scores IgA Knockout Experiment IgA knock-out mice (IgA KO; BALB/c background, males and
females) were obtained from Margaret Conner, Baylor College of
Medicine, Houston, TX, US and bred at EBM in Gothenburg,
Sweden. The mice were immunized as described in Table 1,
groups 1, 4, 5, and 7 and challenged with X-31 virus on day
41. Female BALB/c mice were used as wild-type (wt) controls. Clinical symptoms were assessed for 14 days using the scoring
system described earlier. Adoptive Serum Transfer Serum samples were collected from mice mock-immunized
with PBS, or immunized with PR8 WIV i.n., WIV+ CAF09
or WIV+CTA1-3M2e-DD as described above. Two hundred
microliter of pooled sera were administered i.p. to naïve
mice. Mice were then challenged with 105.5 TCID50/mouse of
heterosubtypic X-31 virus 1 day post adoptive transfer. Mice
from positive control group received serum samples from mice
immunized with PR8 WIV and were challenged with PR8 live
virus. Animals were followed for 14 days and clinical symptoms
were assessed using the scoring system described above. Animal Experiments All animal experiments were approved by the Institutional
Animal Care and Use Committee of the University of Groningen
(IACUC-RUG, DEC 6923), or the Central Committee for Animal
Experiments CCD of the Netherlands (AVD105002016599),
the Animal Welfare and Ethics Review Body (AWERB) of
the National Institute for Biological Standards and Controls
(NIBSC), Potters Bar, UK (PPL 80/2537), or the IACUC of the
University of Gothenburg, Sweden. Adjuvants The liposomal adjuvants CAF01 and CAF09 were produced as
described previously (42). The dose for both adjuvants was 300 March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 2 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. µg per 50 µl for i.m. and 300 µg per 40 µl for i.n. administration. The protein adjuvants, CTA1-DD and CTA1-3M2e-DD, were
produced by MIVAC Development AB, Sweden. The latter
construct carried three copies of the extracellular domain of the
influenza virus M2 protein (SLLTEVETPIRNEWGSRSNDSSD). Briefly, the fusion proteins were expressed in E. coli DH5 cells,
transformed with the expression vector for the fusion protein,
and grown in 500 ml cultures overnight in SYPPG medium
with 100 ug/ml carbenicillin, at 37◦C, as previously described
(30). Endotoxin levels were below 100 EU/mg as verified by
use of the Endosafe R⃝testing system (Charles River). For both
protein adjuvants, the concentration was 5 µg per 40 µl WIV. Filtered Dulbecco’s phosphate buffered saline containing CaCl2
and MgCl2 (DPBS, GIBCO by Life TechnologiesTM) was used as
a diluent. from 1 to 4 for least to most severe. A cumulative score for a given
day of 10 was considered to be the humane endpoint. Sample Collection From Mice p
Before sacrifice, blood was drawn by cheek puncture for
determining IgG, IgA and neutralizing antibody titers. Nasal and
lung washes were taken using 1 ml PBS (pH 7.4) with Complete R⃝
protease inhibitor cocktail (Roche, Almere, The Netherlands) for
determining IgA titers. Lungs were collected in 1 ml complete
EPISERF medium (100 U/ml penicillin, 100 mg/ml streptomycin,
12.5 ml of 1 M HEPES, 5 ml of 7.5% sodium bicarbonate
for 500 ml medium, Thermo Fisher Scientific, Bleisweijk,
Netherlands) for determination of viral load. Spleens were
collected in 1 ml Iscove’s Modified Dulbecco’s Medium (IMDM)
(Thermo Fisher Scientific, Bleisweijk, Netherlands) containing
10% v/v FBS (Lonza, Basel, Switzerland), 100 U/ml penicillin, 100
mg/ml streptomycin and 50 µM 2-mercaptoethanol (Invitrogen,
Breda, The Netherlands) to assess cellular immune responses. Frontiers in Immunology | www.frontiersin.org Assessment of Antibody Responses y
p
Titers of influenza-specific IgG, IgG1, IgG2a, IgA, anti-NP, anti-
M2e and neutralizing antibodies were determined in blood
serum samples taken on day 41, i.e., the day of challenge. IgA
was determined in mucosal samples immediately after sample
collection. ELISAs were performed as described previously
using WIV prepared from each of the challenge viruses,
subunit vaccine (SU) prepared from X-31, NP protein, or M2e
protein for coating (44). To determine whether the serum
antibodies were (cross-)neutralizing, microneutralization (MN)
assays were performed using infectious PR8, (H1N1)pdm09
or X-31 virus as described previously (45). LoD for IgG
was determined by calculating the log10 of the 1st dilution
while LoD for MN titers was calculated using Log2 of the
1st dilution. Lung Virus Titration Limit of detection
(LoD) was determined by calculating the log10 of the 1st
dilution and the negative values were given half the value
of the LoD. Lung Virus Titration Virus titration was performed as described previously (43). Briefly,
the
lungs
were
homogenized
in
1 ml
EPISERF March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org Frontiers in Immunology | www.frontiersin.org 3 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. TABLE 1 | Vaccination and challenge scheme. Groups
Vaccine
(D 0, 10, 20)
Route
Vaccine dose
(µg HA)
adjuvant
dose (µg)
injection
volume (µl)
Challenge
D 41
1
PBS
i.m. –
–
50
2
WIV
i.m. 0.5
–
50
3
WIV+ CAF01
i.m. 0.5
300
50
4
WIV
i.n. 0.5
–
40
5
WIV+ CAF09
i.n. 0.5
300
40
A/PR/8/34
6
WIV+ CTA1-DD
i.n. 0.5
5
40
(H1N1)pdm09
7
WIV+ CTA1-3M2e-DD
i.n. 0.5
5
40
X-31 TABLE 1 | Vaccination and challenge scheme. ASNENMDAM for X-31 (University Medical Center Leiden,
The Netherlands) in the presence of co-stimulatory anti-
CD28 antibody for 16 h. For each mouse, non-stimulated
control cells were used to measure the baseline expression
of the cytokines. After 12 h of incubation, protein transport
inhibitor (Thermo Scientific, Netherlands) was added to
stop the transport of proteins out of the Golgi apparatus. Cell stimulation cocktail containing PMA-ionomycin (Thermo
Scientific, The Netherlands) was used as a positive control
stimulant. Next day, cells were washed once with FACS
buffer and stained for surface markers (anti-CD3-Alexa-fluor
700, anti-CD4-FITC, anti-CD8a PerCP-efluor720, all purchased
from Thermo Scientific, The Netherlands) for 45 min at 4◦C,
followed by rinsing with cold PBS and staining with the
fixable viability dye eFluor 780 for 30 min at 4◦C. After two
washes with FACS buffer, cells were fixed with fixation buffer
and then permeabilized with FACS permeabilization buffer
(Thermo Scientific). For intracellular cytokine staining (ICS),
antibodies (anti-IFNγ-PE-Cy7, anti-IL2-PE, anti-TNFα eFluor
450 and anti-IL4 APC, Thermo Scientific) were added to the
cells and incubated for 45 min. Ultracomp beads (Thermo
Scientific, The Netherlands) were used to prepare compensation
controls. Events were acquired on an LSRII flow cytometer
(BD Biosciences) and FlowJo software (Tree Star) was used
for analysis. medium
and
centrifuged
at
1,200
rpm
for
10 min
to
collect the supernatant. These supernatants were used to
infect MDCK cells with serial 2 fold dilutions of the lung
supernatants to determine lung virus titers as described before
(43). Viral titers are presented as log10 titer of 50% tissue
culture infectious dose per gram of lung. Immuno-Profiling Reveals Strong
Correlation Between Survival and Serum
Antibodies, Mucosal IgA and IFNγ+ CD4
T Cells To determine which immune mechanisms correlated with the
observed cross-protection and to what degree these mechanisms
would differ for the different adjuvanted vaccines, various
immunological assays were performed. Sera, nasal and lung
washes were collected 3 weeks after the 3rd immunization
for antibody titer assessments, while T cell responses against
heterologous (H1N1)pdm09 and heterosubtypic X-31 virus were
determined using spleens of vaccinated animals 3 days post
heterosubtypic challenge. The results of immunoprofiling for
the heterologous and heterosubtypic challenge experiments are
summarized as heatmaps (Figures 2A,B) to reveal patterns which
correlate with protection; the individual data can be found in the
Supplementary Information (Figures S1–S5). When infected with PR/8 virus, all mock immunized mice
reached the defined humane endpoint (>20% weight loss) and
were sacrificed by day 6 post challenge. In contrast, mice from
all groups immunized three times with WIV, with or without
adjuvants, were protected from weight loss post challenge with
homologous PR8 virus (Figures 1A,D). Furthermore, all but one
(with low titer) of the vaccinated mice were completely protected
from virus replication in the lungs (Figure 1G). Immunization
with
PR8
WIV
i.m. reliably
induced
neutralizing antibodies against the homologous virus, especially
when administered with adjuvant (Figure S1A). By contrast,
i.n. immunizations poorly stimulated neutralizing antibodies,
even in the presence of adjuvants. Importantly, we found no
neutralizing antibodies against heterologous (H1N1)pdm09 or
heterosubtypic X-31 virus irrespective of the immunization route
or adjuvant used (Figures 2A,B and Figures S1B,C). However,
all immunized mice developed serum IgG antibodies reactive
with homologous, as well as heterologous and heterosubtypic
virus and these titers were of identical magnitude for all three
virus strains (Figures 2A,B and Figures S1D–F). The addition
of adjuvants to i.m. and i.n WIV immunizations enhanced
cross-reactive serum IgG resulting in similar endpoint titers. CAF01 and CAF09 affected IgG titers most strongly and
enhanced both IgG1 and IgG2a. CTA1-DD and CTA1-3M2e-DD
were comparatively less effective in stimulating IgG and IgG1
and had only minor effects on IgG2a levels (Figures 2A,B
and Figures S2A,B). Challenge with heterologous (H1N1)pdm09 virus resulted
in gradual weight loss in mock immunized animals gradually
necessitating euthanasia on day 6 or 7 post infection. Animals
vaccinated with non-adjuvanted WIV i.m. showed some weight
loss but all survived until the end of the study. Surprisingly,
mice immunized i.m. with CAF01 adjuvanted vaccine lost more
weight and 2 out of 6 mice had to be sacrificed (Figures 1B,E). WIV Combined With Mucosal Adjuvants
Provides Best Cross-Protection WIV Combined With Mucosal Adjuvants
Provides Best Cross-Protection In order to determine the relative efficacy of WIV vaccines
combined with different adjuvants, mice were vaccinated three
times via the most suitable route of administration with
WIV derived from PR8 virus alone or mixed with CAF01,
CAF09, CTA1-DD or CTA1-3M2e-DD, followed by challenge
with homologous PR8, heterologous H1N1pdm09 (same virus
subtype as PR8 but different strain) or heterosubtypic X-31
(different virus subtype but same internal viral proteins). To
assess the protective efficacy of the tested vaccines, challenged
mice were observed for weight loss and clinical symptoms for a
period of 10 days or until they reached defined humane endpoint. Percent weight loss was calculated (Figures 1A–C) and survival
curves were plotted (Figures 1D–F). Furthermore, to assess
viral loads in the lungs, mock vaccinated and WIV vaccinated
animals were sacrificed 3 days after homologous, heterologous or
heterosubtypic virus challenge (Figures 1G–I). Statistics To assess the contribution of influenza-specific T cells in
protection, a multifunctional T cell assay was performed
which involved staining for intracellular cytokines IFNγ, TNFα,
IL2, and IL4 expressed by CD3+CD4+ and CD3+CD8+ T
lymphocytes. All reagents, buffers and antibodies were purchased
from eBioscience, The Netherlands. For statistical analysis of intracellular cytokine levels, the
numbers of cytokine positive and cytokine negative cells
in
the
stimulated
cell
populations
were
compared
with
paired
unstimulated
controls
using
MIMOSA
(Mixture
Models
for
Single-Cell
Assays)
for
IFNγ,
TNFα,
IL2
and IL4 (46). A false discovery rate of q ≤0.01 was
accepted. A Chi-Squared test was used to compare the
number of responders between groups. P ≤0.05 were
considered significant. Spleens collected in IMDM were immediately processed and
single cell suspensions were obtained using GentleMACS C
tubes and GentleMACS dissociator (Miltenyi Biotec, Leiden,
The Netherlands). Cell suspensions were then forced through
a cell strainer (BD Bioscience, Breda, The Netherlands) and
erythrocytes lysed using ACK lysis buffer (0.83% NH4Cl,
10 mM KHCO3, 0.1 mM EDTA). Cells were re-stimulated
with a final concentration of 10 µg/ml PR8, (H1N1)pdm09
or X-31 (H3N2) WIV plus 10 µg/ml of NP366 peptide,
ASNENMETM for PR8, ASNENVETM for (H1N1)pdm09 or The non-parametric Mann-Whitney U test was used to
test if the differences between two groups with respect to
different parameters were significant. A p < 0.05 was considered
significant. Significance is represented as ∗p < 0.05, ∗∗p <
0.01, ∗∗∗p < 0.0001. Statistical analyses were performed using
GraphPad Prism version 5 for Windows (GraphPad Sofware, La
Jolla, California, USA www.graphpad.com). March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 4 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. RESULTS i.n. immunization with CAF09, CTA1-DD or CTA1-3M2e-
DD adjuvanted WIV stimulated significantly broader protection
compared to systemic immunizations with WIV alone or WIV
plus i.m. CAF01 adjuvant. Frontiers in Immunology | www.frontiersin.org Immuno-Profiling Reveals Strong
Correlation Between Survival and Serum
Antibodies, Mucosal IgA and IFNγ+ CD4
T Cells Animals vaccinated with WIV i.n. exhibited little weight loss
except for one animal which reached the humane endpoint
on day 5 post challenge. Mice vaccinated with WIV plus
mucosal adjuvants presented the best cross-protection against
heterologous virus challenge: they showed little or no weight loss
and all animals survived to day 10 post challenge (Figures 1B,E). Although not significant, lung virus titers were somewhat
higher in well protected than in unprotected, mock-immunized
mice (Figure 1H). Furthermore, we wanted to identify the antigens targeted by
the cross-reactive IgG. Use of subunit vaccine for coating revealed
that vaccine-evoked, cross-reactive antibodies readily bound to
viral surface proteins. These antibodies were found in all mice
immunized i.m., but were present in mice immunized i.n. only
when adjuvanted vaccine was used (Figures 2A,B, Figure S2C). Anti-NP antibodies were detected only in mice vaccinated with
WIV plus CAF01 and one mouse from the WIV plus CAF09
group (Figures 2A,B and Figure S2D). Anti-M2e antibodies
were induced only by WIV adjuvanted with CTA1-3M2e-DD
(Figures 2A,B and Figure S2E). Vaccination, especially when
done with adjuvanted vaccines, therefore induced cross-reactive
antibodies which mainly targeted the viral surface proteins. The
levels of these antibodies correlated with protection from severe In the heterosubtypic X-31 challenge experiment, all animals,
whether vaccinated or not, initially showed a similar trend in
weight loss (Figure 1C). However, from day 3 onwards, all the
mice immunized mucosally with adjuvanted WIV recovered. In contrast, mock-immunized, parenterally immunized and
mice immunized i.n. with WIV alone continued to lose
weight and most animals had to be sacrificed, except for
4
out
of
6
mice
immunized
i.m. with
non-adjuvanted
WIV (Figure 1F). Only mice mucosally immunized with
adjuvanted WIV demonstrated significant reduction in lung
viral titers as compared to mock-immunized control mice. CTA1-DD and CTA1-3M2e-DD adjuvanted vaccines afforded
the largest reduction in lung viral titers (Figure 1I). Thus, March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 5 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 1 | Adjuvanted i.n. administered vaccine provides best protection. CB6F1 mice were vaccinated thrice 10 days apart with PBS, non-adjuvanted or
adjuvanted WIV vaccines. Three weeks after the last vaccination, 6 mice/group were challenged with homologous PR8 (H1N1) (A,D,G), heterologous
A/California/7/2009 (H1N1)pdm09 (B,E,H) or heterosubtypic X-31 (H3N2) viruses (C,F,I). Six animals/group were followed for 10 days for weight loss (A–C) and
survival (D–F). Immuno-Profiling Reveals Strong
Correlation Between Survival and Serum
Antibodies, Mucosal IgA and IFNγ+ CD4
T Cells Three days post challenge 6 mice/group were sacrificed for determining lung viral load (G–I). Groups are represented as in Table 1: 1: PBS, 2: WIV
i.m., 3: WIV+CAF01 i.m., 4: WIV i.n., 5: WIV+ CAF09 i.n., 6: WIV+ CTA1-DD i.n., 7: WIV+ CTA1-3Me-DD i.n. Dashed line indicates Limit of detection (LoD)
(G–I). Virus titers are represented as log10 titers/gram of lung tissue with level of significance as *p < 0.05 and **p < 0.01 calculated using Mann-Whitney U-test. FIGURE 1 | Adjuvanted i.n. administered vaccine provides best protection. CB6F1 mice were vaccinated thrice 10 days apart with PBS, non-adjuvanted or
adjuvanted WIV vaccines. Three weeks after the last vaccination, 6 mice/group were challenged with homologous PR8 (H1N1) (A,D,G), heterologous
A/California/7/2009 (H1N1)pdm09 (B,E,H) or heterosubtypic X-31 (H3N2) viruses (C,F,I). Six animals/group were followed for 10 days for weight loss (A–C) and
survival (D–F). Three days post challenge 6 mice/group were sacrificed for determining lung viral load (G–I). Groups are represented as in Table 1: 1: PBS, 2: WIV
i.m., 3: WIV+CAF01 i.m., 4: WIV i.n., 5: WIV+ CAF09 i.n., 6: WIV+ CTA1-DD i.n., 7: WIV+ CTA1-3Me-DD i.n. Dashed line indicates Limit of detection (LoD)
(G–I). Virus titers are represented as log10 titers/gram of lung tissue with level of significance as *p < 0.05 and **p < 0.01 calculated using Mann-Whitney U-test. disease, except in the group with CAF01-adjuvanted vaccine
delivered i.m. WIV demonstrated that mice immunized i.m and mice
immunized i.n. with non-adjuvanted WIV developed no or very
low levels of IFNγ-producing CD4 T cells. Mice immunized
i.n. with adjuvanted WIV demonstrated enhancement of IFNγ-
producing cells, with CTA1-3M2e-DD being most potent. In
addition to IFNγ, we also measured IL2 and TNFα responses
in CD4+ T cells, but although restimulation with WIV
and peptides increased the numbers of T cells producing
these cytokines, the percentages were low and no significant
differences between immunized and mock-immunized animals
were observed (results not shown). The large majority of vaccine-
specific CD4 T cells produced IFNγ, while very few cells were
multifunctional, also producing other cytokines (Figure S5). In
contrast to CD4+ T cells, CD8+ T cells were not induced
in significant numbers by any of the vaccines (Figures 2A,B
and Figures S4C,D). Frontiers in Immunology | www.frontiersin.org Immuno-Profiling Reveals Strong
Correlation Between Survival and Serum
Antibodies, Mucosal IgA and IFNγ+ CD4
T Cells In conclusion, IFNγ-producing CD4 T cells
were the only T cell population induced and their numbers Determination of influenza specific mucosal IgA revealed that
mice from the PBS control group as well as mice immunized i.m. with non-adjuvanted or CAF01-adjuvanted WIV developed no
or very low mucosal IgA responses (in nose and lungs) against
any of the viruses (Figures 2A,B and Figures S3A,B,C). In
contrast, all miceimmunized i.n. with adjuvanted WIV produced
significant levels of specific IgA antibodies in both nose and lungs
against all three virus strains, and these levels were significantly
higher than in mice immunized i.n. with non-adjuvanted WIV. Therefore, mucosal immunization in the presence of adjuvant
was required for successful induction of cross-reactive mucosal
IgA (Figures 2A,B and Figures S3A,B,C). IgA titers strongly
correlated with protection from weight loss (Figures 2A,B). We next assessed vaccine-induced T cell responses. In vitro re-
stimulation of splenocytes with heterologous or heterosubtypic March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 6 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 2 | Immunoprofiling against heterologous and heterosubtypic viruses. Animals were vaccinated 3 times with the vaccines indicated in Table 1. After 3
vaccinations, sera, nasal, and lung washes and spleens were collected to determine systemic, mucosal and cell mediated immune responses (n = 6). Some animals
were challenged with heterologous (A) and heterosubtypic (B) virus to determine protection, lung viral load (n = 6) and survival (n = 6). Generated data was used as
input and conditional formatting was performed in Ms Excel to plot heatmaps. Each column represents one animal. Survival is shown with different color scheme as
these are different animals compared to the rest. Dark blue indicates worst survival while light blue indicates best survival. For other parameters, heatmaps range from
red (lowest response) to green (best response). GURE 2 | Immunoprofiling against heterologous and heterosubtypic viruses. Animals were vaccinated 3 times with the vaccines indicated in Table 1. After 3
accinations, sera, nasal, and lung washes and spleens were collected to determine systemic, mucosal and cell mediated immune responses (n = 6). Some animals
ere challenged with heterologous (A) and heterosubtypic (B) virus to determine protection, lung viral load (n = 6) and survival (n = 6). Generated data was used as FIGURE 2 | Immunoprofiling against heterologous and heterosubtypic viruses. Immuno-Profiling Reveals Strong
Correlation Between Survival and Serum
Antibodies, Mucosal IgA and IFNγ+ CD4
T Cells Animals were vaccinated 3 times with the vaccines indicated in Table 1. After 3
vaccinations, sera, nasal, and lung washes and spleens were collected to determine systemic, mucosal and cell mediated immune responses (n = 6). Some animals
were challenged with heterologous (A) and heterosubtypic (B) virus to determine protection, lung viral load (n = 6) and survival (n = 6). Generated data was used as
input and conditional formatting was performed in Ms Excel to plot heatmaps. Each column represents one animal. Survival is shown with different color scheme as
these are different animals compared to the rest. Dark blue indicates worst survival while light blue indicates best survival. For other parameters, heatmaps range from
red (lowest response) to green (best response). serum followed by a homologous challenge with PR8 virus served
as positive control group. Mice were observed daily for clinical
symptoms using the score sheet described previously. We found
that PR8 immune serum completely protected mice against PR8
virus infection. Serum from mice immunized i.n. with PR8 WIV
without adjuvant did not provide protection against infection
with heterosubtypic X-31 virus and the mice transfused with
this serum exhibited high clinical scores and reduced survival
(Figures 3A,B). By contrast, serum from mice immunized with
WIV plus CAF09 or CTA1-3M2e-DD protected partially and
clinical scores were reduced by 50% compared to unimmunized
control mice. Thus, non-neutralizing serum IgG antibodies from
mice immunized i.n. with CAF09 or CTA1-3M2e-DD adjuvanted
WIV appeared to partially protect against heterosubtypic X-31
virus challenge. were enhanced significantly by adjuvanted WIV administered i.n. Protection from weight loss correlated well with the number of
IFNγ-producing CD4 T cells (Figures 2A,B and Figures S4A,B). Frontiers in Immunology | www.frontiersin.org Dissecting the Mechanisms of Protection The mice were followed for survival (A) and clinical symptoms (B) assessed using a score based on weight, appearance and behavior. the well immunized animals. Yet, CD4 T cell depletion had a
significant effect on lung virus titers in animals immunized
with WIV and CTA1-3M2e-DD while all other immunization
protocols showed comparable lung virus titers irrespective of
CD4 depletion (Figure 4I). Therefore, CD4 T cells appeared to
play a role in protection against heterobsubtypic challenge only
in the CTA1-3M2e-DD group. these would be vaccine-specific. The results indicate that i.n. administered WIV combined with a mucosal adjuvant provided
enhanced cross-protection compared to WIV administered i.m. with or without adjuvant and non-adjuvanted WIV administered
i.n.. We observed that non-neutralizing serum IgG, mucosal IgA
and IFNγ-producing CD4 T cells were significantly higher for
mice immunized i.n. with WIV plus adjuvant than for the other,
less well protected groups. While non-neutralizing serum IgG
antibodies and CD4 T cells were contributing to protection, our
experiments in IgA KO mice were less conclusive, but there
was a trend toward a protective effect of local IgA on the
clinical symptoms. Finally, we addressed whether cross-reactive local IgA
antibodies impacted on protection against infection in the
mice immunized i.n. by repeating the immunization/challenge
experiment in IgA KO mice. In line with reports in literature,
we found that mock-immunized IgA KO mice were more
susceptible to influenza infection than mock-immunized wt
BALB/c mice, demonstrated by higher clinical scores and survival
post challenge (47). Wild-type BALB/c mice immunized with
non-adjuvanted WIV demonstrated reduced clinical scores as
compared to non-immunized BALB/c mice but this was not the
case for IgA KO mice indicating a role for IgA in protection
(Figures 5A,E and Figures 5B,F). When immunized with WIV
and any of the mucosal adjuvants, wt and IgA KO mice
developed protective immunity and survived the challenge
infection (Figures 5C,D,G,H). Clinical scores of IgA KO mice
immunized with CAF09 adjuvanted vaccine were higher than
those of wt mice (Figure 5G). Mice immunized with CTA1-
3M2e-DD adjuvanted WIV developed the lowest clinical scores
with little difference between wt and IgA KO mice (Figure 5H). These results suggest that local IgA antibodies exerted some
protection from severe disease but were not critical for survival
in this model. Dissecting the Mechanisms of Protection Dissecting the Mechanisms of Protection
From the heat maps it can be deduced that animals which
were completely protected from heterosubtypic challenge had
high levels of serum IgG and mucosal IgA and high numbers
of IFNγ-producing CD4 T cells. We next performed a series
of experiments in order to determine whether any of these
factors was critical for protection from heterosubtypic virus
infection. For these experiments we focused on CAF09 and
CTA1-3M2e-DD as the most successful adjuvants from the
previous experiment and used PBS and non-adjuvanted WIV
as controls. Next, we studied the role of CD4+ T cells in protection. Depletion of CD4 T cells was achieved through anti-CD4 Mab-
treatment of mice and resulted in reduction of CD4 T cell
numbers in peripheral blood by >95% (data not shown). We
found that CD4 depletion did not affect survival (Figures 4A–D)
or clinical scores (Figures 4E–H) upon X-31 virus infection in To assess if serum antibodies can mediate cross-protection,
mice were passively immunized via the i.p. route with serum
collected from animals which had been mock-immunized with
PBS or immunized with WIV, WIV+CAF09 or WIV+CTA1-
3M2e-DD i.n. One day later they were challenged with
heterosubtypic X-31 virus. Animals which received PR8 immune March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 7 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 3 | Serum antibodies induced by mucosally adjuvanted WIV might induce cross-protection. Serum was collected from animals vaccinated thrice with PBS
i.n., non-adjuvanted WIV i.n., WIV+ CAF09 i.n., or WIV+ CTA1-3M2e-DD i.n. and was administered passively in naïve mice (n = 6) via the i.p. route. One day after
passive immunization animals were challenged with heterosubtypic X-31 virus. Animals from the positive control group received PR8 immune sera and were challenged
with homologous PR8 virus. The mice were followed for survival (A) and clinical symptoms (B) assessed using a score based on weight, appearance and behavior. FIGURE 3 | Serum antibodies induced by mucosally adjuvanted WIV might induce cross-protection. Serum was collected from animals vaccinated thrice with PBS
i.n., non-adjuvanted WIV i.n., WIV+ CAF09 i.n., or WIV+ CTA1-3M2e-DD i.n. and was administered passively in naïve mice (n = 6) via the i.p. route. One day after
passive immunization animals were challenged with heterosubtypic X-31 virus. Animals from the positive control group received PR8 immune sera and were challenged
with homologous PR8 virus. Dissecting the Mechanisms of Protection Mucosal immunization has been shown to be superior
to parenteral immunization for stimulating local immunity
and resident memory T cells in the lung (48–50) and to
provide cross-protection against heterosubtypic virus challenge
(14, 51). In agreement with these studies, we found that i.n. immunization with adjuvanted WIV afforded stronger cross-
protection than parenteral immunizations. This was the case even
though serum anti-viral IgG levels appeared quite comparable
for mice immunized i.m. or i.n. with adjuvanted vaccines. Upon heterologous infection with (H1N1)pdm09 virus, clinical
symptoms and survival correlated poorly with virus replication
in the lungs while for heterosubtypic infection with X-31 virus
we observed a clear correlation between clinical scores and lung
virus titers. We chose day 3 to assess the lung viral load because
we wanted to check if the vaccination has any impact on the
replicating virus at a stage where the replication is at peak which
in mice is on day 3 (52, 53). From experience we assume that in
successfully immunized mice virus titers resolved more quickly
than in mock immunized mice (45). Frontiers in Immunology | www.frontiersin.org DISCUSSION Mice (n = 12/group) were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV
(B,F), WIV+ CAF09 (C,G) or WIV+ CTA1-3M2e-DD (D,H) followed by heterosubtypic challenge. On day−1, 1 and 7 relative to the challenge, anti-CD4 antibody or
PBS was administered i.p.. Mice were followed for 14 days for survival (A–D) and clinical symptoms (E–H). Dotted lines in E-H indicate the humane endpoint. Six
animals/group were sacrificed on day 3 post challenge to determine lung virus titers (I). LoD is indicated by dashed line. Mock depletion is presented by filled symbols
with—and CD4 depletion is represented by open symbols with +. Virus titers are represented as log10 titers /gram of lung with level of significance as *p < 0.05
calculated using Mann-Whitney U-test. lungs and nose of mice. IgA has been shown to be more
cross-reactive than IgG (61, 62). Moreover, Maurer et al have
recently shown that IgA antibodies can also neutralize influenza
virus in an antigen-aspecific manner by providing sialic acid
in the glycosylated Fc part which serves as a decoy receptor
not only for influenza virus but also for other viruses using
sialic acid as a receptor (63). However, in our study adjuvanted
WIV administered i.n. completely protected IgA KO mice from
reaching the humane endpoint post heterosubtypic challenge,
similar to wt BALB/c mice, indicating that IgA was not crucial
for protection. Nevertheless, we cannot exclude that local IgA
antibodies exerted some protective function, as reflected in the
higher clinical scores in immunized and challenged IgA KO mice
compared to the wt mice. Whether local IgA plays a role in
cross-protection induced by adjuvanted WIV administered i.n. or not is controversial. For example, Zhang et al. (64) showed that
i.n. immunization with a CTB/CT-adjuvanted subunit vaccine in line with recent observations in humans that also indicate that
many influenza-specific antibodies, whether measured before or
after vaccination, are cross-reactive (54, 55). Although serum
antibodies induced by adjuvanted WIV were cross-reactive they
could not neutralize heterologous and heterosubtypic virus in
vitro, which was according to expectations (45, 56). Nevertheless,
when transferred to naïve animals these antibodies provided
partial protection against X-31 challenge. It has been shown that
anti-influenza antibodies can mediate cross-protection via non-
neutralizing mechanisms such as antibody dependent cellular
cytotoxicity (ADCC), antibody dependent cellular phagocytosis,
or complement mediated cytotoxicity (CDC) (57–60). DISCUSSION Adjuvanted WIV vaccines induced significantly higher
systemic immune responses compared to non-adjuvanted WIV. Interestingly, the levels of serum IgG antibodies reacting with
homologous, heterologous and heterosubtypic WIV in ELISA
assays were similar, suggesting that most of the IgG antibodies
induced by immunization with WIV were cross-reactive. This is In this study, we compared liposome and protein adjuvants
head-to-head to assess their relative efficacy in inducing cross-
reactive immunity in mice, when combined with i.m. and i.n. administered WIV. In addition, we dissected which immune
parameters contributed to protection and to what extent March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 8 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 4 | CD4 depletion does not affect protection but affects virus growth. Mice (n = 12/group) were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV
(B,F), WIV+ CAF09 (C,G) or WIV+ CTA1-3M2e-DD (D,H) followed by heterosubtypic challenge. On day−1, 1 and 7 relative to the challenge, anti-CD4 antibody or
PBS was administered i.p.. Mice were followed for 14 days for survival (A–D) and clinical symptoms (E–H). Dotted lines in E-H indicate the humane endpoint. Six
animals/group were sacrificed on day 3 post challenge to determine lung virus titers (I). LoD is indicated by dashed line. Mock depletion is presented by filled symbols
with—and CD4 depletion is represented by open symbols with +. Virus titers are represented as log10 titers /gram of lung with level of significance as *p < 0.05
calculated using Mann-Whitney U-test. FIGURE 4 | CD4 depletion does not affect protection but affects virus growth. Mice (n = 12/group) were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV
(B,F), WIV+ CAF09 (C,G) or WIV+ CTA1-3M2e-DD (D,H) followed by heterosubtypic challenge. On day−1, 1 and 7 relative to the challenge, anti-CD4 antibody or
PBS was administered i.p.. Mice were followed for 14 days for survival (A–D) and clinical symptoms (E–H). Dotted lines in E-H indicate the humane endpoint. Six
animals/group were sacrificed on day 3 post challenge to determine lung virus titers (I). LoD is indicated by dashed line. Mock depletion is presented by filled symbols
with—and CD4 depletion is represented by open symbols with +. Virus titers are represented as log10 titers /gram of lung with level of significance as *p < 0.05
calculated using Mann-Whitney U-test. FIGURE 4 | CD4 depletion does not affect protection but affects virus growth. Frontiers in Immunology | www.frontiersin.org DISCUSSION From
our observations, we think that mucosal IgA, though not being
crucial on its own, works in concert with other mechanisms to
provide the observed cross-protection. IFNγ-producing cross-reactive CD4 positive T cells increased
significantly upon mucosal vaccination, especially in mice
immunized with WIV plus CTA1-3M2e-DD. This could be due
to the fact that M2e contains an MHC class II restricted CD4
helper epitope (26). CD4 depletion shortly before and after
challenge did not affect survival, but impaired the control of lung
virus growth in animals vaccinated with WIV plus CTA1-3M2e-
DD, indicating a role of CD4 T cells in controlling virus growth
rather than controlling clinical symptoms and in turn survival. CAF09-adjuvanted WIV did not induce significant numbers of
CD4 T cells and accordingly, depletion of CD4 T cells during
infection did not affect clinical scores or lung virus titers. Although WIV plus CAF01 induced the highest levels of
cross-reactive antibodies, mice in the respective experimental
group showed severe clinical symptoms and reduced survival
post challenge. One thing which distinguished the CAF01
vaccinated mice group from the other groups was the induction
of anti-NP antibodies. In a pre-clinical study in pigs by Ricklin
et al. NP vaccination produced a strong immune response
but induced lung inflammation and immunized pigs were not
protected (68). In murine models the situation is not entirely
clear. Although it has been shown that anti-NP antibodies can
confer resistance to influenza virus infection (69–72) (contrary
to our results), a previous study from our group demonstrated
that mice vaccinated with NP adjuvanted with MPLA (which
developed NP-specific antibodies) showed more rapid weight
loss in the initial phase of infection than mock vaccinated mice
(73). Furthermore, animals receiving a virosomal vaccine without
NP showed fewer signs of illness compared to mice receiving a
virosomal vaccine with NP. We did not observe IFNγ-producing CD8 T cells induced
by vaccination. This was somewhat unexpected since at least
CAF01, CAF09, and CTA1-DD are known to support induction
of CD8 T cells (24, 33, 37, 66). Failure to detect CD8 T cells in
our experiments might be because they were indeed absent or
because we missed them due to the timing of the experiments. We assessed CD8 T cell responses on day 25 after the last
immunization, by which time the cells were already through the
retraction phase and the numbers might therefore have been
too low to detect. DISCUSSION Which of
these mechanisms, if any, is involved in protection afforded by
WIV adjuvanted with CAF09 or CTA1-3M2e-DD remains to
be elucidated. Vaccination with WIV plus mucosal adjuvants also led to
remarkably enhanced levels of cross-reactive local IgA in the March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 9 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 5 | IgA antibodies are not critical in cross-protection. IgA KO mice and BALB/c mice were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV
(B,F), WIV+CAF-09 (C,G) or WIV+CTA1-3M2e-DD (D, H) followed by heterosubtypic challenge. The mice were followed for survival (A–D) and development of
clinical symptoms (E–H) for a period of 14 days. IgA KO mice are represented by dashed lines with open symbols while BALB/c wt mice are represented by solid lines
with filled symbols. Dotted lines indicate humane endpoint. FIGURE 5 | IgA antibodies are not critical in cross-protection. IgA KO mice and BALB/c mice were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV
(B,F), WIV+CAF-09 (C,G) or WIV+CTA1-3M2e-DD (D, H) followed by heterosubtypic challenge. The mice were followed for survival (A–D) and development of
clinical symptoms (E–H) for a period of 14 days. IgA KO mice are represented by dashed lines with open symbols while BALB/c wt mice are represented by solid lines
with filled symbols. Dotted lines indicate humane endpoint. ELISPOT assay for the detection of CD8 T cells. Despite the fact
that we did not find them, we cannot categorically rule out that
CD8 T cells contributed to protection. It is known that lung tissue
resident memory (TRM) CD8 T cells have an important role in
protection from influenza infection (66, 67). These cells might
indeed have been induced in our experiments, but as parts of
the lungs had to be used for other purposes and the remaining
tissues were insufficient for isolating the required numbers of
lymphocytes, we were unable to investigate them. Follow up
studies will address this issue. stimulated equally efficient control of virus growth in wt and IgA
KO mice. Yet, using mice deficient in the poly Ig receptor and
thus unable to transport IgA across the respiratory epithelium,
Asahi et al demonstrated that mucosal IgA is critical, in particular
for protection from heterologous virus challenge (65). Frontiers in Immunology | www.frontiersin.org DISCUSSION Furthermore, we used intracellular cytokine
staining, a method which allows simultanous determination of
multiple cell populations and cytokines but is not as sensitive as One of the limitations of the study is the use of X-31
virus for heterosubtypic challeng. X-31 is a ressortant between
PR8 and A/HK/68 and thus contains internal genes derived
from PR8 virus. In future studies it would be ideal to March 2019 | Volume 10 | Article 646 10 Bhide et al. Cross-Protection by Mucosally Adjuvanted WIV use a wild type H3N2 virus for challenge and further
also performing challenge experiments with avian influenza
viruses to assess the breadth of protection afforded by
the adjuvanted vaccines. Another limitation is the fact that
heterologous virus challenge was performed 3 weeks after
the last immunization when adjuvant-induced innate immune
responses might still have been present. However, for CAF09
little induction of (systemic) innate immunity has been
observed (Christensen et al. unpublished observations) while for
CTA1-DD a low level of antigen-independent protection was
observed independent of the time period (2, 4, or 6 weeks)
between immunization and challenge (Lycke et al. unpublished
observations). Thus, while we cannot completely rule out an
effect of adjuvant-induced innate responses we consider it
unlikely that these are the major reason for the observed
cross-protection. Future experiments devoted to assessing the
durability of the induced immune responses by increasing the
period between immunization and challenge will clarify this
point definitely. by mucosal vaccination with adjuvanted WIV and optimal
protection thus requires a combination of different mechanisms. by mucosal vaccination with adjuvanted WIV and optimal
protection thus requires a combination of different mechanisms. SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found
online at: https://www.frontiersin.org/articles/10.3389/fimmu. 2019.00646/full#supplementary-material ACKNOWLEDGMENTS We would like to thank central animal facility of the UMCG
and Gothenburg university for animal caretaking and help with
vaccinations. Further, we would like to thank the European
Union Seventh Framework Program 19 (FP7/2007-2013) and
Universal Influenza Vaccines Secured (UNISEC) consortium
under grant agreement no. 602012 and also, Federation of
European Microbiological Societies (FEMS) research grant for
funding this research. We would like to dedicate this work to late
Dr. Stephen Norley whose help in the project was very valuable. The results of our head-to-head comparison of different
vaccines underline that mucosal immunization with adjuvanted
WIV is indeed a promising approach for developing a broadly
protective influenza vaccine. These vaccines induce a plethora
of immune responses including mucosal IgA, cross-reactive
(though not cross-neutralizing) systemic IgG, and CD4 Th
cells. Each of these seems to play a role in cross-protection
but neither appeared to be crucial. This indicates that, several
immune mechanisms contribute to the cross-protection induced AUTHOR CONTRIBUTIONS YB, AH, NL, and DC designed the study. YB, WD, IG, and
TM performed the animal experiments. YB, JdV-I, DV, and SN
performed assays and analysis of data. KG, SS, and OE produced
live and inactivated viruses and characterized them. LB provided
CD4 depletion antibody. YB and AH wrote the manuscript. YB, AH, NL, and DC designed the study. YB, WD, IG, and
TM performed the animal experiments. YB, JdV-I, DV, and SN
performed assays and analysis of data. KG, SS, and OE produced
live and inactivated viruses and characterized them. LB provided
CD4 depletion antibody. YB and AH wrote the manuscript. REFERENCES in
inducing
immune
responses
and
secretion
of
proinflammatory
cytokines
by
DCs. Influenza
Other
Respi
Viruses. (2008)
2:41–51. doi: 10.1111/j.1750-2659.2008.00038.x in
inducing
immune
responses
and
secretion
of
proinflammatory
cytokines
by
DCs. Influenza
Other
Respi
Viruses. (2008)
2:41–51. doi: 10.1111/j.1750-2659.2008.00038.x 1. Quiñones-Parra S, Loh L, Brown LE, Kedzierska K, Valkenburg SA. Universal
immunity to influenza must outwit immune evasion. Front Microbiol. (2014)
5:1–11. doi: 10.3389/fmicb.2014.00285 1. Quiñones-Parra S, Loh L, Brown LE, Kedzierska K, Valkenburg SA. Universal
immunity to influenza must outwit immune evasion. Front Microbiol. (2014)
5:1–11. doi: 10.3389/fmicb.2014.00285 10. Hovden AO, Cox RJ, Haaheim LR. Whole influenza virus vaccine is more
immunogenic than split influenza virus vaccine and induces primarily
an IgG2a response in BALB/c mice. Scand J Immunol. (2005) 62:36–44. doi: 10.1111/j.1365-3083.2005.01633.x 2. Keating R, Hertz T, Wehenkel M, Harris TL, Benjamin A, Mcclaren JL,
et al. Protective immunity to lethal influenza infections. (2014) 14:1266–76. doi: 10.1128/CVI.00251-13 2. Keating R, Hertz T, Wehenkel M, Harris TL, Benjamin A, Mcclaren JL,
et al. Protective immunity to lethal influenza infections. (2014) 14:1266–76. doi: 10.1128/CVI.00251-13 11. Bernstein DI, Cherry JD. Clinical reactions and antibody responses
to
influenza
vaccines. A
comparison
of
split
or
subunit
vaccines
in children and young adults. Am J Dis Child. (1983) 137:622–6. doi: 10.1001/archpedi.1983.02140330006003 3. Bodewes R, Kreijtz JHCM, Hillaire MLB, Geelhoed-Mieras MM, Fouchier
RAM, Osterhaus ADME, et al. Vaccination with whole inactivated virus
vaccine affects the induction of heterosubtypic immunity against influenza
virus A/H5N1 and immunodominance of virus-specific CD8+ T-cell
responses in mice. J Gen Virol. (2010) 91:1743–53. doi: 10.1099/vir.0.020784-0 12. Stephenson I, Nicholson KG, Gluck R, Mischler R. Safety and antigenicity of
whole virus and subunit influenza A/Hong Kong/1073/99 (H9N2) vaccine
in healthy adults: phase I randomised trial. Lancet. (2003) 362:1959–66. doi: 10.1016/S0140-6736(03)15014-3 4. Pan H, Zhang X, Hu J, Chen J, Pan Q, Teng Z, et al. A case report of avian
influenza H7N9 killing a young doctor in Shanghai, China. BMC Infect Dis. (2015) 15:1–8. doi: 10.1186/s12879-015-0970-4 4. Pan H, Zhang X, Hu J, Chen J, Pan Q, Teng Z, et al. A case report of avian
influenza H7N9 killing a young doctor in Shanghai, China. BMC Infect Dis. (2015) 15:1–8. doi: 10.1186/s12879-015-0970-4 13. Furuya Y. Return of inactivated whole-virus vaccine for superior efficacy. Immunol Cell Biol. (2012) 90:571–8. doi: 10.1038/icb.2011.70 5. Liu M, Li X, Yuan H, Zhou J, Wu J, Bo H, et al. REFERENCES doi: 10.1016/j.vaccine.2011.07.025 protective sites of pandemic avian H5N1 influenza virus. Sci Transl Med. (2010) 2:15ra5. doi: 10.1126/scitranslmed.3000624 protective sites of pandemic avian H5N1 influenza virus. Sci Transl Med. (2010) 2:15ra5. doi: 10.1126/scitranslmed.3000624 18. Khurana S, Verma N, Yewdell JW, Hilbert AK, Lattanzi M, Giudice G Del,
et al. MF59 adjuvant enhances diversity and affinity of antibody- mediated
immune response to pandemic influenza vaccines. Sci Transl Med. (2012)
3:85ra48. doi: 10.1126/scitranslmed.3002336 35. Dietrich J, Andreasen LV, Andersen P, Agger EM. Inducing dose sparing with
inactivated polio virus formulated in adjuvant CAF01. PLoS ONE. (2014)
9:1–12. doi: 10.1371/journal.pone.0100879 19. Chung KY, Coyle EM, Jani D, King LR, Bhardwaj R, Fries L, et al. ISCOMATRIXTM
adjuvant promotes epitope spreading and antibody
affinity maturation of influenza A H7N9 virus like particle vaccine that
correlate with virus neutralization in humans. Vaccine. (2015) 33:3953–62. doi: 10.1016/j.vaccine.2015.06.047 36. Billeskov R, Wang Y, Solaymani-Mohammadi S, Frey B, Kulkarni S, Andersen
P, et al. Low antigen dose in adjuvant-based vaccination selectively induces
CD4 T cells with enhanced functional avidity and protective efficacy. J
Immunol. (2017) 98:1600965. doi: 10.4049/jimmunol.1600965 37. Espinosa DA, Christensen D, Muñoz C, Singh S, Locke E, Andersen P, et al. Robust antibody and CD8+ T-cell responses induced by P. falciparum CSP
adsorbed to cationic liposomal adjuvant CAF09 confer sterilizing immunity
against experimental rodent malaria infection. NPJ Vaccines. (2017) 2:10. doi: 10.1038/s41541-017-0011-y 20. Tregoning JS, Russell RF, Kinnear E. Adjuvanted in fluenza vaccines. Hum
Vaccin Immunother. (2018) 14:550–64. doi: 10.1080/21645515.2017.1415684 21. Agger EM, Rosenkrands I, Hansen J, Brahimi K, Vandahl BS, Aagaard C,
et al. Cationic liposomes formulated with synthetic mycobacterial cordfactor
(CAF01): a versatile adjuvant for vaccines with different immunological
requirements. PLoS ONE. (2008) 3:e3116. doi: 10.1371/journal.pone.0003116 38. Overgaard NH, Frøsig TM, Jakobsen JT, Buus S, Andersen MH, Jungersen
G. Low antigen dose formulated in CAF09 adjuvant Favours a cytotoxic T-
cell response following intraperitoneal immunization in Göttingen minipigs. Vaccine. (2017) 35:5629–36. doi: 10.1016/j.vaccine.2017.08.057 22. Martel CJM, Agger EM, Poulsen JJ, Jensen TH, Andresen L, Christensen
D, et al. CAF01 potentiates immune responses and efficacy of an
inactivated influenza vaccine in ferrets. PLoS ONE. (2011) 6:e22891. doi: 10.1371/journal.pone.0022891 39. Lindenstrøm T, Aagaard C, Christensen D, Agger EM. High-frequency
vaccine-induced CD8 + T cells specific for an epitope naturally processed
during infection with Mycobacterium tuberculosis do not confer protection. Eur J Immunol. (2014) 44:1–11. doi: 10.1002/eji.201344358 23. REFERENCES Pal S, Tifrea DF, Follmann F, Andersen P, de la Maza LM. The
cationic liposomal adjuvants CAF01 and CAF09 formulated with the
major outer membrane protein elicit robust protection in mice against a
Chlamydia muridarum respiratory challenge. Vaccine. (2017) 35:1705–11. doi: 10.1016/j.vaccine.2017.02.020 40. Lycke
N,
Lebrero-Fernández
C. ADP-ribosylating
enterotoxins
as
vaccine
adjuvants. Curr
Opin
Pharmacol. (2018)
41:42–51. doi: 10.1016/j.coph.2018.03.015 41. Wood JM, Schild GC, Newman RW, Seagroatt V. An improved single-
radial-immunodiffusion technique for the assay of influenza haemagglutinin
antigen: application for potency determinations of inactivated whole virus and
subunit vaccines. J Biol Stand. (1977) 5:237–47. 24. Korsholm KS, Hansen J, Karlsen K, Filskov J, Mikkelsen M, Lindenstrøm
T, et al. Induction of CD8+ T-cell responses against subunit antigens by
the novel cationic liposomal CAF09 adjuvant. Vaccine. (2014) 32:3927–35. doi: 10.1016/j.vaccine.2014.05.050 25. Eriksson AM, Schön KM, Lycke NY. The cholera toxin-derived CTA1-DD
vaccine adjuvant administered intranasally does not cause inflammation or
accumulate in the nervous tissues. J Immunol. (2004) 173:3310–9. doi: 10. 4049/jimmunol.173.5.3310 42. Schmidt ST, Pedersen GK, Neustrup MA, Korsholm KS, Rades T, Andersen
P, et al. Induction of cytotoxic T-lymphocyte responses upon subcutaneous
administration of a subunit vaccine adjuvanted with an emulsion containing
the toll-like receptor 3 ligand poly(I: C). Front Immunol. (2018) 9:1–12. doi: 10.3389/fimmu.2018.00898 26. Eliasson
DG,
Omokanye
A,
Schön
K,
Wenzel
UA,
Bernasconi
V,
Bemark M, et al. M2e-tetramer-specific memory CD4 T cells are broadly
protective against influenza infection. Mucosal Immunol. (2017) 11:273–89. doi: 10.1038/mi.2017.14 43. Audouy SAL, van der Schaaf G, Hinrichs WLJ, Frijlink HW, Wilschut
J, Huckriede A. Development of a dried influenza whole inactivated
virus vaccine for pulmonary immunization. Vaccine. (2011) 29:4345–52. doi: 10.1016/j.vaccine.2011.04.029 27. Eliasson DG, Helgeby A, Schön K, Nygren C, El-Bakkouri K, Fiers W,
et al. A novel non-toxic combined CTA1-DD and ISCOMS adjuvant vector
for effective mucosal immunization against influenza virus. Vaccine. (2011)
29:3951–61. doi: 10.1016/j.vaccine.2011.03.090 44. Liu H, Patil HP, de Vries-Idema J, Wilschut J, Huckriede A. Enhancement of
the immunogenicity and protective efficacy of a mucosal influenza subunit
vaccine by the saponin adjuvant GPI-0100. PLoS ONE. (2012) 7:e52135. doi: 10.1371/journal.pone.0052135 28. Cunningham KA, Carey AJ, Lycke N, Timms P, Beagley KW. CTA1-
DD is an effective adjuvant for targeting anti-chlamydial immunity
to the murine genital mucosa. J Reprod Immunol. (2009) 81:34–8. doi: 10.1016/j.jri.2009.04.002 45. Budimir N, Huckriede A, Meijerhof T, Boon L, Gostick E, Price DA, et al. REFERENCES Induction of heterosubtypic cross-protection against influenza by a whole
inactivated virus vaccine: the role of viral membrane fusion activity. PLoS
ONE. (2012) 7:e30898. doi: 10.1371/journal.pone.0030898 29. Sundling C, Schön K, Mörner A, Forsell MNE, Wyatt RT, Thorstensson
R,
et
al. CTA1-DD
adjuvant
promotes
strong
immunity
against
human
immunodeficiency
virus
type
1
envelope
glycoproteins
following
mucosal
immunization. J
Gen
Virol. (2008)
89:2954–64. doi: 10.1099/vir.0.2008/005470-0 46. Finak G, Mcdavid A, Chattopadhyay P, Dominguez M, De Rosa S,
Roederer M, et al. Mixture models for single-cell assays with applications
to vaccine studies. Biostatistics. (2014) 15:87–101. doi: 10.1093/biostatistics/k
xt024 30. Eliasson DG, Bakkouri K El, Schön K, Ramne A, Festjens E, Löwenadler B,
et al. CTA1-M2e-DD: a novel mucosal adjuvant targeted influenza vaccine. Vaccine. (2008) 26:1243–52. doi: 10.1016/j.vaccine.2007.12.027 47. Arulanandam BP, Raeder RH, Nedrud JG, Bucher DJ, Le J, Metzger DW. IgA immunodeficiency leads to inadequate Th cell priming and increased
susceptibility to influenza virus infection. J Immunol. (2001) 166:226–31. doi: 10.4049/jimmunol.166.1.226 31. Rosenkrands I, Vingsbo-Lundberg C, Bundgaard TJ, Lindenstrøm T, Enouf V,
van der Werf S, et al. Enhanced humoral and cell-mediated immune responses
after immunization with trivalent influenza vaccine adjuvanted with cationic
liposomes. Vaccine. (2011) 29:6283–91. doi: 10.1016/j.vaccine.2011.06.040 48. Potter
CW,
Jennings
R. Intranasal
immunization
with
inactivated
influenza
vaccine. Pharm
Sci
Technolo
Today. (1999)
2:402–8. doi: 10.1016/S1461-5347(99)00194-7 49. Amorij J-P, Saluja V, Petersen AH, Hinrichs WLJ, Huckriede A, Frijlink HW. Pulmonary delivery of an inulin-stabilized influenza subunit vaccine prepared
by spray-freeze drying induces systemic, mucosal humoral as well as cell-
mediated immune responses in BALB/c mice. Vaccine. (2007) 25:8707–17. doi: 10.1016/j.vaccine.2007.10.035 32. Hansen J, Jensen KT, Follmann F, Agger EM, Theisen M, Andersen P. Liposome delivery of Chlamydia muridarum major outer membrane protein
primes a Th1 response that protects against genital chlamydial infection in a
mouse model1. J Infect Dis. (2008) 198:758–67. doi: 10.1086/590670 33. Gram GJ, Karlsson I, Agger EM, Andersen P, Fomsgaard A. A novel liposome-
based adjuvant CAF01 for induction of CD8+ cytotoxic T-lymphocytes (CTL)
to HIV-1 minimal CTL peptides in HLA-A∗0201 transgenic mice. PLoS ONE. (2009) 4:2–6. doi: 10.1371/journal.pone.0006950 50. Bhide Y, Tomar J, Dong W, de Vries-Idema J, Frijlink HW, Huckriede
A, et al. Pulmonary delivery of influenza vaccine formulations in cotton
rats: site of deposition plays a minor role in the protective efficacy
against clinical isolate of H1N1pdm virus. Drug Deliv. (2018) 25:533–45. doi: 10.1080/10717544.2018.1435748 34. REFERENCES Genetic diversity of avian
influenza A (H10N8) virus in live poultry markets and its association with
human infections in China. Sci Rep. (2015) 5:1–8. doi: 10.1038/srep07632 5. Liu M, Li X, Yuan H, Zhou J, Wu J, Bo H, et al. Genetic diversity of avian
influenza A (H10N8) virus in live poultry markets and its association with
human infections in China. Sci Rep. (2015) 5:1–8. doi: 10.1038/srep07632 14. Quan F-S, Compans RW, Nguyen HH, Kang S-M. Induction of heterosubtypic
immunity to influenza virus by intranasal immunization. J Virol. (2008)
82:1350–9. doi: 10.1128/JVI.01615-07 6. Pan M, Gao R, Lv Q, Huang S, Zhou Z, Yang L, et al. Human infection with
a novel, highly pathogenic avian influenza A (H5N6) virus: virological and
clinical findings. J Infect. (2016) 72:52–9. doi: 10.1016/j.jinf.2015.06.009 15. Budimir N, de Haan A, Meijerhof T, Waijer S, Boon L, Gostick E, et al. Critical role of TLR7 signaling in the priming of cross-protective cytotoxic
T lymphocyte responses by a whole inactivated influenza virus vaccine. PLoS
ONE. (2013) 8:e63163. doi: 10.1371/journal.pone.0063163 7. Geeraedts F, Goutagny N, Hornung V, Severa M, De Haan A, Pool J, et al. Superior immunogenicity of inactivated whole virus h5n1 influenza vaccine
is primarily controlled by toll-like receptor signalling. PLoS Pathog. (2008)
4:e1000138. doi: 10.1371/journal.ppat.1000138 16. Budimir N, de Haan A, Meijerhof T, Gostick E, Price DA, Huckriede A,
et al. Heterosubtypic cross-protection induced by whole inactivated influenza
virus vaccine in mice: influence of the route of vaccine administration. Influenza
Other
Respi
Viruses. (2013)
7:1202–9. doi:
10.1111/irv. 12142 8. Al-Mazrou A, Scheifele DW, Soong T, Bjornson G. Comparison of adverse
reactions to whole-virion and split-virion influenza vaccines in hospital
personnel. Cmaj. (1991) 145:213–8. 8. Al-Mazrou A, Scheifele DW, Soong T, Bjornson G. Comparison of adverse
reactions to whole-virion and split-virion influenza vaccines in hospital
personnel. Cmaj. (1991) 145:213–8. 9. Geeraedts F, Bungener L, Pool J, ter Veer W, Wilschut J, Huckriede A. Whole inactivated virus influenza vaccine is superior to subunit vaccine 17. Khurana S, Chearwae W, Castellino F, Manischewitz J, King LR, Honorkiewicz
A, et al. Vaccines with MF59 adjuvant expand the antibody repertoire to target Frontiers in Immunology | www.frontiersin.org March 2019 | Volume 10 | Article 646 11 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. HIV-1 vaccine based on 18 T-cell minimal epitope peptides applying
a
novel
cationic
adjuvant
CAF01. Vaccine. (2011)
29:7067–74. REFERENCES Fomsgaard A, Karlsson I, Gram G, Schou C, Tang S, Bang P, et al. Development and preclinical safety evaluation of a new therapeutic March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 12 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. 51. Ichinohe T, Tamura S, Kawaguchi A, Ninomiya A, Imai M, Itamura S,
et al. Cross-protection against H5N1 influenza virus infection is afforded by
intranasal inoculation with seasonal trivalent inactivated influenza vaccine. J
Infect Dis. (2007) 196:1313–20. doi: 10.1086/521304 65. Asahi Y, Yoshikawa T, Watanabe I, Iwasaki T, Hasegawa H, Sato Y, et al. Protection against influenza virus infection in polymeric Ig receptor knockout
mice immunized intranasally with adjuvant-combined vaccines. J Immunol. (2002) 168:2930–8. doi: 10.4049/jimmunol.168.6.2930 52. Czakó R, Vogel L, Lamirande EW, Bock KW, Moore IN, Ellebedy AH, et al. In vivo imaging of influenza virus infection in immunized mice. MBio. (2017)
8:1–13. doi: 10.1128/mBio.00714-17 66. Lycke N. The B-cell targeted CTA1-DD vaccine adjuvant is highly effective
at enhancing antibody as well as CTL responses. Curr Opin Mol Ther. (2001) 3:37–44. 53. Baz M, Paskel M, Matsuoka Y, Zengel J, Cheng X, Jin H, et al. Replication and
immunogenicity of swine, equine, and avian H3 subtype influenza viruses in
mice and ferrets. J Virol. (2013) 87:6901–10. doi: 10.1128/JVI.03520-12 67. Lapuente D, Storcksdieck genannt Bonsmann M, Maaske A, Stab V, Heinecke
V, Watzstedt K, et al. IL-1β as mucosal vaccine adjuvant: the specific
induction of tissue-resident memory T cells improves the heterosubtypic
immunity against influenza A viruses. Mucosal Immunol. (2018) 11:1265–78. doi: 10.1038/s41385-018-0017-4 54. Lee J, Boutz DR, Chromikova V, Joyce MG, Vollmers C, Leung K, et al. Molecular-level analysis of the serum antibody repertoire in young adults
before and after seasonal influenza vaccination. Nat Med. (2016) 22:1456–64. doi: 10.1038/nm.4224 68. Zens KD, Chen JK, Farber DL. Vaccine-generated lung tissue–resident
memory T cells provide heterosubtypic protection to influenza infection. JCI
Insight. (2016) 1:1–12. doi: 10.1172/jci.insight.85832 55. McCarthy KR, Watanabe A, Kuraoka M, Do KT, McGee CE, Sempowski GD,
et al. Memory B cells that cross-react with group 1 and group 2 influenza a
viruses are abundant in adult human repertoires. Immunity. (2018) 48:174–
84.e9. doi: 10.1016/j.immuni.2017.12.009 g
j
g
69. Ricklin ME, Python S, Vielle NJ, Brechbühl D, Zumkehr B, Posthaus H, et al. Virus replicon particle vaccines expressing nucleoprotein of influenza A virus
mediate enhanced inflammatory responses in pigs. Sci Rep. (2017) 7:16379. REFERENCES doi: 10.1038/s41598-017-16419-w j
56. Kim JH, Reber AJ, Kumar A, Ramos P, Sica G, Music N, et al. Non-neutralizing
antibodies induced by seasonal influenza vaccine prevent, not exacerbate
A(H1N1)pdm09 disease. Sci Rep. (2016) 6:1–13. doi: 10.1038/srep37341 70. Carragher DM, Kaminski DA, Moquin A, Hartson L, Randall TD. A novel role for non-neutralizing antibodies against nucleoprotein in
facilitating resistance to influenza virus. J Immunol. (2008) 181:4168–76. doi: 10.4049/jimmunol.181.6.4168 57. Henry Dunand CJ, Leon PE, Huang M, Choi A, Chromikova V, Ho IY,
et al. Both neutralizing and non-neutralizing human H7N9 influenza vaccine-
induced monoclonal antibodies confer protection. Cell Host Microbe. (2016)
19:800–13. doi: 10.1016/j.chom.2016.05.014 71. LaMere MW, Moquin A, Lee FE-H, Misra RS, Blair PJ, Haynes L,
et al. Regulation of antinucleoprotein IgG by systemic vaccination and
its
effect on
influenza
virus
clearance. J
Virol. (2011) 85:5027–35. doi: 10.1128/JVI.00150-11 58. Jegaskanda S, Vanderven HA, Wheatley AK, Stephen J. Fc or not Fc
; that is the question : antibody Fc-receptor interactions are key to
universal influenza vaccine design. Hum Vaccin Immunother. (2017) 13:1–9. doi: 10.1080/21645515.2017.1290018 72. Fujimoto Y, Tomioka Y, Takakuwa H, Uechi GI, Yabuta T, Ozaki K,
et al. Cross-protective potential of anti-nucleoprotein human monoclonal
antibodies against lethal influenza A virus infection. J Gen Virol. (2016)
97:2104–16. doi: 10.1099/jgv.0.000518 59. Leon PE, He W, Mullarkey CE, Bailey MJ, Miller MS, Krammer F, et al. Optimal activation of Fc-mediated effector functions by influenza virus
hemagglutinin antibodies requires two points of contact. Proc Natl Acad Sci
USA. (2016) 113:E5944–51. doi: 10.1073/pnas.1613225113 73. Dong W, Bhide Y, Marsman S, Holtrop M, Meijerhof T, de Vries-Idema J, et al. Monophosphoryl lipid a-adjuvanted virosomes with Ni-chelating lipids for
attachment of conserved viral proteins as cross-protective influenza vaccine. Biotechnol J. (2018) 1700645:1–9. doi: 10.1016/j.jbiotec.2018.08.022 60. Corti D, Cameroni E, Guarino B, Kallewaard NL, Zhu Q, Lanzavecchia A. Tackling influenza with broadly neutralizing antibodies. Curr Opin Virol. (2017) 24:60–9. doi: 10.1016/j.coviro.2017.03.002 Conflict of Interest Statement: LB is employed by Bioceros. Frontiers in Immunology | www.frontiersin.org Conflict of Interest Statement: LB is employed by Bioceros. 61. Tamura S. Studies on the usefulness of intranasal inactivated influenza
vaccines. Vaccine. (2010) 28:6393–7. doi: 10.1016/j.vaccine.2010.05.019 The remaining authors declare that the research was conducted in the absence of
any commercial or financial relationships that could be construed as a potential
conflict of interest. 62. Muramatsu M, Yoshida R, Yokoyama A, Miyamoto H, Kajihara M, Maruyama
J, et al. Comparison of antiviral activity between IgA and IgG specific to
influenza virus hemagglutinin: increased potential of IgA for heterosubtypic
immunity. PLoS ONE. (2014) 9:1–8. doi: 10.1371/journal.pone.0085582 63. Maurer MA, Meyer L, Bianchi M, Turner HL, Le NPL, Steck M, et al. Glycosylation of human IgA directly inhibits influenza A and other sialic-
acid-binding viruses. Cell Rep. (2018) 23:90–9. doi: 10.1016/j.celrep.2018. 03.027 Copyright © 2019 Bhide, Dong, Gribonika, Voshart, Meijerhof, de Vries-Idema,
Norley, Guilfoyle, Skeldon, Engelhardt, Boon, Christensen, Lycke and Huckriede. This is an open-access article distributed under the terms of the Creative Commons
Attribution License (CC BY). The use, distribution or reproduction in other forums
is permitted, provided the original author(s) and the copyright owner(s) are credited
and that the original publication in this journal is cited, in accordance with accepted
academic practice. No use, distribution or reproduction is permitted which does not
comply with these terms. 64. Zhang Y, Pacheco S, Acuna CL, Switzer KC, Wang Y, Gilmore X, et al. Immunoglobulin A-deficient mice exhibit altered T helper 1-type immune
responses but retain mucosal immunity to influenza virus. Immunology. (2002) 105:286–94. doi: 10.1046/j.0019-2805.2001.01368.x March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 13
|
https://openalex.org/W2768077201
|
https://figshare.com/ndownloader/files/9693859
|
English
| null |
Decreased plasma concentrations of BDNF and IGF-1 in abstinent patients with alcohol use disorders
|
PloS one
| 2,017
|
cc-by
| 458
|
S1 Table. Plasma concentrations of BDNF, IGF-1 and IGFBP-3 in the alcohol group according to psychiatric comorbidity
ANCOVA revealed no significant main effects or interaction using comorbidity and sex as factors and controlling for age
Data represented in the table are the estimated marginal means and 95%CI for levels of comorbidity.
(*) BDNF concentrations are the back-transformed means and 95% CI from logarithmic data.
Variable
Alcohol (N=91)
Psychiatric comorbidity
Comorbid substance use disorders
Comorbid mental disorders
No
(N=20)
Yes
(N=71)
No
(N=54)
Yes
(N=37)
No
(N=30)
Yes
(N=61)
BDNF (*)
[mean (95% CI)]
121.14
(72.70-201.86)
108.13
(78.00-149.89)
98.00
(68.71-137.21)
139.62
(91.25-213.63)
125.41
(78.86-199.44)
105.02
(74.63-147.78)
IGF-1
[mean (95% CI)]
103.61
(82.55-130.05)
113.00
(97.40-131.09)
103.05
(88.06-120.58)
123.38
(102.21-148.93)
109.62
(89.08-134.89)
110.94
(94.86-129.75)
IGFBP-3
[mean (95% CI)]
4.22
(3.48-4.97)
4.65
(4.16-5.14)
4.40
(3.87-4.92)
4.77
(4.13-5.39)
4.41
(3.73-5.10)
4.60
(4.09-5.12) S1 Table. Plasma concentrations of BDNF, IGF-1 and IGFBP-3 in the alcohol group according to psychiatric comorbidity
ANCOVA revealed no significant main effects or interaction using comorbidity and sex as factors and controlling for age
Data represented in the table are the estimated marginal means and 95%CI for levels of comorbidity. (*) BDNF concentrations are the back-transformed means and 95% CI from logarithmic data. Variable
Alcohol (N=91)
Psychiatric comorbidity
Comorbid substance use disorders
Comorbid mental disorders
No
(N=20)
Yes
(N=71)
No
(N=54)
Yes
(N=37)
No
(N=30)
Yes
(N=61)
BDNF (*)
[mean (95% CI)]
121.14
(72.70-201.86)
108.13
(78.00-149.89)
98.00
(68.71-137.21)
139.62
(91.25-213.63)
125.41
(78.86-199.44)
105.02
(74.63-147.78)
IGF-1
[mean (95% CI)]
103.61
(82.55-130.05)
113.00
(97.40-131.09)
103.05
(88.06-120.58)
123.38
(102.21-148.93)
109.62
(89.08-134.89)
110.94
(94.86-129.75)
IGFBP-3
[mean (95% CI)]
4.22
(3.48-4.97)
4.65
(4.16-5.14)
4.40
(3.87-4.92)
4.77
(4.13-5.39)
4.41
(3.73-5.10)
4.60
(4.09-5.12) S1 Table. Plasma concentrations of BDNF, IGF-1 and IGFBP-3 in the alcohol group according to psychiatric comorbidity
ANCOVA revealed no significant main effects or interaction using comorbidity and sex as factors and controlling for age
Data represented in the table are the estimated marginal means and 95%CI for levels of comorbidity. (*) BDNF concentrations are the back-transformed means and 95% CI from logarithmic data. Variable
Alcohol (N=91)
Psychiatric comorbidity
Comorbid substance use disorders
Comorbid mental disorders
No
(N=20)
Yes
(N=71)
No
(N=54)
Yes
(N=37)
No
(N=30)
Yes
(N=61)
BDNF (*)
[mean (95% CI)]
121.14
(72.70-201.86)
108.13
(78.00-149.89)
98.00
(68.71-137.21)
139.62
(91.25-213.63)
125.41
(78.86-199.44)
105.02
(74.63-147.78)
IGF-1
[mean (95% CI)]
103.61
(82.55-130.05)
113.00
(97.40-131.09)
103.05
(88.06-120.58)
123.38
(102.21-148.93)
109.62
(89.08-134.89)
110.94
(94.86-129.75)
IGFBP-3
[mean (95% CI)]
4.22
(3.48-4.97)
4.65
(4.16-5.14)
4.40
(3.87-4.92)
4.77
(4.13-5.39)
4.41
(3.73-5.10)
4.60
(4.09-5.12) ANCOVA revealed no significant main effects or interaction using comorbidity and sex as factors and controlling for age
Data represented in the table are the estimated marginal means and 95%CI for levels of comorbidity. (*) BDNF concentrations are the back-transformed means and 95% CI from logarithmic data.
|
https://openalex.org/W2922111079
|
https://www.jstage.jst.go.jp/article/jmsj/97/3/97_2019-038/_pdf
|
English
| null |
Frequency Change of Clear-Air Turbulence over the North Pacific under 2 K Global Warming – Ensemble Projections Using a 60-km Atmospheric General Circulation Model
|
Kisho shushi. Dai1shu/Kisho shushi. Dai2shu/Journal of the Meteorological Society of Japan
| 2,019
|
cc-by
| 6,319
|
Abstract Future changes in the climatological distribution of clear-air turbulence (CAT) and its seasonality over the
North Pacific are estimated on the basis of an ensemble of climate projections under warming for the globally
averaged surface air temperature of 2 K relative to preindustrial levels, which includes over 3000 years of ensem-
bles using a 60 km atmospheric general circulation model (AGCM). The AGCM outputs are interpolated to a 1.25°
horizontal resolution, and the climatological CAT frequency is computed. The CAT broadly decreases in the mid-
latitude central to western North Pacific along with the anticyclonic (south) side of its present-day high-frequency
band extending from Japan to the eastern North Pacific. Meanwhile, large relative increases are found outside
the band, implying an increased risk of CAT encounters. Uncertainty in future CAT changes due to uncertainties
in the spatial pattern of sea surface temperature (SST) change is addressed for the first time using six selected
Coupled Model Intercomparison Project Phase 5 (CMIP5) climate models. The uncertainty is greatest in the
boreal winter and spring over the central North Pacific and is associated with an uncertainty in future changes in
the jet stream and upper-level synoptic-scale disturbances. Keywords clear air turbulence; climate change; ensemble projection database Citation Watanabe, S., M. Fujita, S. Kawazoe, S. Sugimoto, Y. Okada, R. Mizuta, and M. Ishii, 2019: Frequency
change of clear-air turbulence over the North Pacific under 2 K Global Warming – Ensemble projections using a 60-
km atmospheric general circulation model. J. Meteor. Soc. Japan, 97, 757–771, doi:10.2151/jmsj.2019-038. Meteorological Research Institute of Japan Meteorological Agency, Tsukuba, Japan (Manuscript received 25 September 2018, in final form 9 Febuary 2019) (Manuscript received 25 September 2018, in final form 9 Febuary 2019) 757 757 S. WATANABE et al. une 2019
ournal of the Meteorological Society of Japan, 97(3), 757−771, 2019. doi:10.2151/jmsj.2019-038 Ryo MIZUTA and Masayoshi ISHII Ryo MIZUTA and Masayoshi ISHII rological Research Institute of Japan Meteorological Agency, Tsukuba, Japan Corresponding author: Shingo Watanabe, Japan Agency for
Marine-Earth Science and Technology, 3173-25, Showa-
machi, Kanazawa-ku, Yokohama, Kanagawa 236-0001, Japan
E-mail: wnabe@jamstec.go.jp
J-stage Advance Published Date: 13 March 2019 @j
g jp
J-stage Advance Published Date: 13 March 2019 Corresponding author: Shingo Watanabe, Japan Agency for
Marine-Earth Science and Technology, 3173-25, Showa-
machi, Kanazawa-ku, Yokohama, Kanagawa 236-0001, Japan
E-mail: wnabe@jamstec.go.jp 1. Introduction Clear-air turbulence (CAT) accompanies vertical
airflows greater than or equal to the size of an aircraft,
that is, tens to 2000 m. Aircraft often experience
CAT in the tropopause region near jet streams, where
environmental conditions frequently satisfy those re-
quired for Kelvin–Helmholtz instability. Since CAT is
not explicitly resolved by current numerical weather Corresponding author: Shingo Watanabe, Japan Agency for
Marine-Earth Science and Technology, 3173-25, Showa-
machi, Kanazawa-ku, Yokohama, Kanagawa 236-0001, Japan
E-mail: wnabe@jamstec.go.jp ©The Author(s) 2019. This is an open access article published by the Meteorological Society of Japan under
a Creative Commons Attribution 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0). Journal of the Meteorological Society of Japan 758 Vol. 97, No. 3 Vol. 97, No. 3 forecast models, several CAT indices have been devel-
oped to diagnose the potential for CAT to occur using
synoptic or mesoscale grid point parameters output
from forecast models (see Sharman et al. (2006) and
the references therein). In a recent paper by Kim et al. (2018), they described the latest development of the
Global Graphical Turbulence Guidance (G-GTG),
which considers CAT and mountain wave turbulence
diagnostics. ensemble projection data from 270 years of six-hourly
output for each of the six ΔSSTs. For the CAT indices,
we select four from the 20 presented by Storer et al. (2017), which showed a striking dissimilarity with
each other, to consider future changes in CAT patterns
over the North Pacific. The data and methodology are described in Section
2, followed by an analysis of the results in Section 3
and a summary and discussion in Section 4. From a climatological perspective, Jaeger and
Sprenger (2007) reported the climatological distri-
butions of CAT indices in the Northern Hemisphere
tropopause region derived from the ERA-40 reanal-
ysis dataset, which was interpolated from a 125 km
horizontal resolution to a 1° horizontal resolution, and
discussed their relevance to synoptic-scale dynamical
and thermal environments (e.g., jet streams and frontal
structures near the tropopause). They also discovered
an increasing trend in the CAT frequency in the North
Atlantic sector. Williams and Joshi (2013) were the
first to conduct a study using a coupled atmosphere–
ocean climate model to project future changes in
the CAT and reported an increase in the CAT in the
wintertime North Atlantic sector. Their atmospher-
ic model has a horizontal resolution of 2° × 2.5° in
latitude and longitude. Later, Storer et al. 2. Data and methodology In the present study, we use the database for Policy
Decision Making for Future Climate Change (d4PDF),
produced with a 60 km horizontal resolution AGCM,
MRI-AGCM3.2 (Mizuta et al. 2012, 2017). This
database includes an ensemble transient historical sim-
ulation of the recent past (PAST experiment) and an
ensemble time-slice 2 K warming simulation (referred
to as the +2 K experiment hereafter). Here, +2 K
denotes the 2 K warming of the globally averaged
surface air temperature relative to the preindustrial
level in the context of the Paris Agreement. See Mizu-
ta et al. (2017) and Fujita et al. (2019) for a detailed
experimental design. The ensembles are generated by
adding small perturbations to the observed (PAST) or
detrended (+2 K) SSTs. To capture the uncertainty in
future climate change projections arising from differ-
ences between models, the AGCM’s +2 K experiment
is forced with six different ΔSSTs obtained from se-
lected CMIP5 climate model results. These models are
abbreviated as CC (CCSM4: Community Climate Sys-
tem Model version 4), GF (GFDL-CM3: Geophysical
Fluid Dynamics Laboratory Climate Model version 3),
HA (HadGEM2-AO: Hadley Centre Global Environ-
mental Model version 2 AO), MI (MIROC5: Model
for Interdisciplinary Research on Climate version 5),
MP (MPI-ESM-MR: Mixed Resolution version of the
Max Planck Institute for Meteorology Earth System
Model), and MR (MRI-CGCM3: Meteorological Re-
search Institute Coupled Atmosphere–Ocean General
Circulation Model version 3). Following these earlier studies, in the present paper,
we report several new aspects of future changes in the
CAT frequency. We focus on the geographical patterns
of frequency changes in the North Pacific sector,
which have not been addressed in detail in previous
climate change studies. Unlike earlier studies that
compared climates under the preindustrial and double
the preindustrial concentrations of CO2 (Williams
and Joshi 2013) or the preindustrial and the late 21st
century in the RCP8.5 scenario (Storer et al. 2017),
we compare the present-day climate and the climate
under 2 K global warming with the preindustrial lev-
el. Unlike earlier studies where only a single climate
model was considered, we present future CAT changes
projected by an atmospheric general circulation model
(AGCM) forced with six different SST change pat-
terns (ΔSSTs) obtained from CMIP5 climate models. 1. Introduction (2017) ex-
tended this study to estimate the global change in the
CAT frequency for all four seasons, as diagnosed by
20 different CAT indices, which were projected using
a higher 1.25° × 1.875° horizontal resolution climate
model. More recently, Storer et al. (2018) presented a
detailed review on aviation turbulence, including its
response to climate change. 2. Data and methodology Averaging these
different projections of changes in CAT frequencies
diagnosed by different CAT indices may limit our
understanding of future changes in aviation risks. Therefore, the present paper focuses on the individual
CAT indices. As a first step, we limit the number of
CAT indices to the four mentioned above (i.e., TI1, Sv ,
DEF, and rNBE), which we selected from the 20 con-
sidered by Storer et al. (2017). Pacific is considered in detail. In Fig. 2 of Storer et al. (2017), the CAT index associated with the deforma-
tion of the horizontal flow (DEF), which potentially
leads to the spontaneous generation of gravity waves,
increases between 30°N and 50°N in the North Pacific. The magnitude of the residuals of the nonlinear bal-
ance equation (rNBE), which is a common diagnostic
method for the spontaneous generation of gravity
waves (e.g., Zhang et al. 2000; Plougonven and Zhang
2014), increases in the same latitude band as the DEF,
but its increase in the western Pacific sector is less
pronounced. In contrast, the vertical shear magnitude
of the horizontal wind (Sv), which is related to the
intensity of the CAT, generally decreases in the North
Pacific. Variant 1 of Ellrod’s turbulence index (TI1),
which is defined as the product of the DEF and Sv
and has been proven to be skillful in capturing pilot-
reported CAT (Ellrod and Knapp 1992), increases
between latitudes of 30 – 35°N around Japan and the
central to eastern North Pacific. Averaging these
different projections of changes in CAT frequencies
diagnosed by different CAT indices may limit our
understanding of future changes in aviation risks. Therefore, the present paper focuses on the individual
CAT indices. As a first step, we limit the number of
CAT indices to the four mentioned above (i.e., TI1, Sv ,
DEF, and rNBE), which we selected from the 20 con-
sidered by Storer et al. (2017). Table 1. 99.6th percentile values for CAT indices calculat-
ed in the North Pacific sector. Table 1. 99.6th percentile values for CAT indices calculat-
ed in the North Pacific sector. Table 1. 99.6th percentile values for CAT indices calculat-
ed in the North Pacific sector. CAT indices in the individual simulations are calcu-
lated using nine ensemble simulations with 30 years
of six-hourly data, which consists of about 10
5 time
steps per season at each grid point. 2. Data and methodology This is one or two
orders of magnitude greater than in previous studies. The larger time steps provide a smoother geographical
distribution of CAT frequency and a more reliable es-
timation of its future change. g
Following Williams (2017), the probability distri-
bution of the magnitude of the CAT indices sampled
over the target period and the grid points involved in
the target horizontal domain are calculated, and the
threshold values for the severity classes of the CAT
are obtained accordingly. As stated by Storer et al. (2017), moderate or greater (MOG) CAT is defined as
values exceeding the 99.6th percentile for each CAT
index over the entire 270 years of PAST experimental
ensembles, and the same threshold value is applied
to the +2 K experiment to diagnose the occurrence of
MOG CAT. Table 1 shows the threshold values for the
four CAT indices, which are larger than those in ear-
lier studies based on lower-resolution climate model
data (e.g., Williams 2017). These threshold values are
only valid for a particular model and spatial resolu-
tion. The present study focuses on the climatological
frequency of MOG CAT, which is represented as a
percentage, that is, 100 × (number of MOG CAT)/(total
time steps). These calculations are conducted at each
grid point for four seasons, that is, December–Febru-
ary (DJF), March–May (MAM), June–August (JJA),
and September–November (SON), each of which in-
cludes about 360 time steps per year. By definition, a
CAT frequency of around 0.28 % (1/360) corresponds
to a single occurrence of a MOG CAT event at the
200 hPa level in a season. We investigate the relative
change in the PAST and +2 K experimental data to
understand the response of the CAT frequency to cli-
mate change. By definition, Sv , DEF, and rNBE are independent
of each other, whereas TI1 is correlated with Sv and
DEF. These CAT indices are calculated for the
200 hPa level, using the last 30 years of PAST and
+2 K experimental results for d4PDF. 2. Data and methodology Unlike earlier studies where 20 years of daily means
or 30 years of six-hourly output were used, we use The present study uses six-hourly instantaneous
three-dimensional horizontal winds in the upper tro-
posphere–lower stratosphere levels, which are inter-
polated to a 1.25° horizontal resolution to reduce the
data volume. The target domain, the North Pacific
sector, is defined as 30 – 75°N and 120°E – 120°W and
covers the main North Pacific flight routes and some
of the domestic flight routes over Japan (Fig. 1). This
domain contains 37 × 97 = 3,589 grid points. Here, the disagreement among the changes in the
projected patterns of the CAT indices in the North 759 June 2019 June 2019 S. WATANABE et al. Fig. 1. Climatological distribution of CAT frequency at 200 hPa in the PAST experiment as diagnosed by TI1, Sv , DEF, and rNBE (from top to bottom) in DJF,
MAM, JJA, and SON (from left to right), respectively. Journal of the Meteorological Society of Japan 760 Vol. 97, No. 3 Vol. 97, No. 3 Table 1. 99.6th percentile values for CAT indices calculat-
ed in the North Pacific sector. CAT index
TI1
(10
−9 s
−2)
Sv
(10
−3 s
−1)
DEF
(10
−6 s
−1)
rNBE
(10
−12 s
−2)
99.6 percentile
833.3
10.7
116.7
8750 Pacific is considered in detail. In Fig. 2 of Storer et al. (2017), the CAT index associated with the deforma-
tion of the horizontal flow (DEF), which potentially
leads to the spontaneous generation of gravity waves,
increases between 30°N and 50°N in the North Pacific. The magnitude of the residuals of the nonlinear bal-
ance equation (rNBE), which is a common diagnostic
method for the spontaneous generation of gravity
waves (e.g., Zhang et al. 2000; Plougonven and Zhang
2014), increases in the same latitude band as the DEF,
but its increase in the western Pacific sector is less
pronounced. In contrast, the vertical shear magnitude
of the horizontal wind (Sv), which is related to the
intensity of the CAT, generally decreases in the North
Pacific. Variant 1 of Ellrod’s turbulence index (TI1),
which is defined as the product of the DEF and Sv
and has been proven to be skillful in capturing pilot-
reported CAT (Ellrod and Knapp 1992), increases
between latitudes of 30 – 35°N around Japan and the
central to eastern North Pacific. 3.2 Changes in +2 K climate 3.2 Changes in +2 K climate Figure 5 shows the horizontal distribution of the
percentage change of the CAT frequency diagnosed
by the TI1 in the +2 K experiment with the six CMIP5
ΔSSTs, relative to the PAST experiment, that is, 100
× (+2 K − PAST)/PAST. Figures 6, 7, and 8 show a
similar percentage change in the distributions of Sv ,
DEF, and rNBE, respectively. First, we overview
the characteristic morphology of the change in the
projected patterns. For TI1 and Sv , the most prominent
feature is a decrease of over 25 % in the midlatitude
central to western North Pacific along with the anticy-
clonic (south) side of the present-day maximum (Figs. 5, 6). In contrast, the DEF and rNBE show a broad
increase of 25 – 100 % in the eastern North Pacific,
which is outside the present-day high-frequency band
(Figs. 7, 8). Large relative increases are commonly
seen for all CAT indices surrounding the present-day
envelope of the CAT frequency maximum (e.g., sub-
tropical, coastal, and continental regions). To allow
a more practical evaluation of these large relative
increases, which may be exaggerated by the relatively
low frequency observed in the PAST experiment,
the light (dark) gray shading in Figs. 5 – 8 indicates
regions where the CAT frequency diagnosed by each
index is less than 0.1 % (0.01 %) in the +2 K experi-
ment, roughly corresponding to once every three (30)
years. The CAT frequency diagnosed by the four indices
shows a distinct seasonal variation; TI1 and Sv peak in
the boreal spring and autumn and have their minima
in the summer, whereas the DEF (rNBE) peaks in the
summer (winter). The seasonal variations in TI1 and
Sv in the PAST experiment seem to be associated with
variations in the activity of upper-level synoptic-scale
disturbances, which are diagnosed by the eddy kinetic
energy (EKE) due to the 2 – 8-day component at
the same 200 hPa level (Fig. 3). We define EKE as
0.5 (u¢
2 + v ¢
2), the 2 – 8-day eastward and northward
wind components are extracted using a temporal
filter following Inatsu and Hoskins (2004). Here, we
assume that EKE cascades into turbulence through a
wide variety of processes around the meandering jet-
front system. TI1 and Sv have broad peaks coinciding
with the cyclonic side of the EKE maximum, which
migrates northward from DJF to SON. 2. Data and methodology Sv is calculated
by combining the vertical finite differences among
the 150, 200, and 250 hPa horizontal winds as Sv
u
u
z
z
u
u
z
z
v
=
(
)
−
−
+
−
−
+
1
2
1
2
150
200
150
200
200
250
200
250
2
150−
−
+
−
−
(
)
v
z
z
v
v
z
z
200
150
200
200
250
200
250
2
,
where the subscripts denote the pressure levels and u,
v, and z denote the eastward wind component, the
northward wind component, and the log-pressure
height, respectively. The coarse vertical resolution
prohibits the exact estimation of Sv above and below
the jet axis, a common deficiency when using pressure
level outputs from AGCM and global reanalysis
products. Sv
u
u
z
z
u
u
z
z
v
=
(
)
−
−
+
−
−
+
1
2
1
2
150
200
150
200
200
250
200
250
2
150−
−
+
−
−
(
)
v
z
z
v
v
z
z
200
150
200
200
250
200
250
2
,
where the subscripts denote the pressure levels and u,
v, and z denote the eastward wind component, the
northward wind component, and the log-pressure
height, respectively. The coarse vertical resolution
prohibits the exact estimation of Sv above and below
the jet axis, a common deficiency when using pressure
level outputs from AGCM and global reanalysis
products. To reduce the uncertainty in the projections aris-
ing from natural climate variability, nine ensemble
members of the PAST experiment are used in the cal-
culation of the CAT indices. Similarly, nine ensemble
members from the +2 K experiment are used for each
of the six ΔSST patterns. Thus, the time series of the The climatological CAT frequency at each grid
point is derived from the PAST experimental ensem-
ble (270 years) and the +2 K experimental ensembles
forced by the six ΔSSTs (6 × 270 years), respectively. The horizontal distribution of the climatological CAT
frequency in the PAST experimental ensemble cal- S. WATANABE et al. 761 June 2019 synoptic-scale disturbances are reproduced by the
60 km resolution AGCM, which is an advantage of
using the d4PDF to study the CAT in this region. 2. Data and methodology The wintertime peak rNBE band extends from Japan
to the eastern North Pacific and migrates northward
from DJF to SON. rNBE is closely related to the
spontaneous generation of gravity waves in the jet-
front system (e.g., Zhang et al. 2000; Plougonven and
Zhang 2014), and its seasonal variation is strongly
associated with the strength and location of the
subtropical jet (Fig. 4). In addition, divergent flows
associated with large-scale mountain waves enlarge
the rNBE, generating hot spots over mountains. Be-
cause the accuracy of the resolved mountain waves
in the AGCM is limited because of its horizontal
resolution and the downsampling (i.e., 1.25° by 1.25°),
we avoid discussions on future changes in rNBE over
land. culated as above is validated against that calculated
using 30 years (from 1 December 1979 to 30 Novem-
ber 2009) of the Japanese 55-year Reanalysis (JRA-
55) data (Kobayashi et al. 2015; Harada et al. 2016). The AGCM used in JRA-55 has the same 60 km hori-
zontal resolution as that used in the present study, and
the outputs are interpolated to the same 1.25° horizon-
tal resolution (Japan Meteorological Agency 2013). culated as above is validated against that calculated
using 30 years (from 1 December 1979 to 30 Novem-
ber 2009) of the Japanese 55-year Reanalysis (JRA-
55) data (Kobayashi et al. 2015; Harada et al. 2016). The AGCM used in JRA-55 has the same 60 km hori-
zontal resolution as that used in the present study, and
the outputs are interpolated to the same 1.25° horizon-
tal resolution (Japan Meteorological Agency 2013). 3.1 Present-day climatology of CAT distributions Figures 1 and 2 compare the climatological seasonal
evolution of the CAT frequency at 200 hPa diagnosed
by the TI1, Sv , DEF, and rNBE derived from the PAST
experiment and JRA-55, respectively. The geograph-
ical distributions of the CAT frequency in the PAST
experiment generally agree with those in JRA-55 and
are smoother owing to the larger sample size. The TI1
distribution shown here qualitatively agrees with that
shown by Jaeger and Sprenger (2007), although some
differences are apparent since they analyzed a longer
period and included multiple altitudes near the tropo-
pause. 3. Results 3.1 Present-day climatology of CAT distributions 3.2 Changes in +2 K climate In particular,
Sv exhibits a maximum in the midlatitude central to
eastern North Pacific where synoptic-scale meander-
ing of the jet stream frequently occurs. In contrast, the
DEF peaks over the subtropical western North Pacific
and aligns with the cyclonic side of the subtropical
jet (Fig. 4). It is revealed from a six-hourly diagnosis
that the DEF shows a distinct peak in the summer
over Japan and further downstream in the jet stream,
because of the frequent passage of sub-synoptic-scale
disturbances associated with the Baiu front accompa-
nying large DEF and relatively small Sv. These sub- There are several interesting features in the season-
ality of the projected CAT change and its dependency
on the SST change. The most striking ΔSST depen-
dency can be found in DJF, when two or three of the
six ΔSST ensembles, depending on the index, project 762 Vol. 97, No. 3 Journal of the Meteorological Society of Japan Fig. 2. Same as Fig. 1 but for JRA-55 data. Fig. 2. Same as Fig. 1 but for JRA-55 data. 763 S. WATANABE et al. June 2019 Fig. 3. Top row: climatological distribution of EKE at 200 hPa (EKE200) at synoptic scales (2 – 8 days) in the PAST experiment for DJF, MAM, JJA, and SON
(from left to right), respectively. Second to seventh rows: future changes in EKE200 in +2 K ensembles forced by six different ΔSSTs (see Section 2). Contours al distribution of EKE at 200 hPa (EKE200) at synoptic scales (2 – 8 days) in the PAST experiment for DJF, MAM, JJA, and SON
vely. Second to seventh rows: future changes in EKE200 in +2 K ensembles forced by six different ΔSSTs (see Section 2). Contours
bl Fig. 3. Top row: climatological distribution of EKE at 200 hPa (EKE200) at synoptic scales (2 – 8 days) in the PAST experiment for DJF, MAM, JJA, and SON
(from left to right), respectively. Second to seventh rows: future changes in EKE200 in +2 K ensembles forced by six different ΔSSTs (see Section 2). Contours
show EKE200 in +2 K ensembles. Journal of the Meteorological Society of Japan 764 Vol. 97, No. 3 Fig. 4. Same as Fig. 3 but for 200 hPa horizontal wind speed. Fig. 4. Same as Fig. 3 but for 200 hPa horizontal wind speed. S. WATANABE et al. June 2019 765 . 5. 4. Summary and discussion The climatological distribution and future changes
of CAT over the North Pacific have been investigated
using the PAST and +2 K ensembles in the d4PDF. The present-day climatology of the CAT distribution
at 200 hPa and its seasonality derived from the PAST
experiment in d4PDF agree with those for the JRA-55
data. The CAT frequency in the +2 K experiment
decreases in the midlatitude central to western North
Pacific along with the anticyclonic side of its present-
day maximum, whereas it increases outside the
present-day high-frequency band. This decrease is one
of the key findings in the present study that has not
been uncovered in previous studies based on different
models and combinations of present and future sce-
narios, as well as the selection of CAT indices (Storer
et al. 2017). g p
The inter-ΔSST variation of the projected change
in the CAT frequency in MAM is smaller than that
in DJF, but larger than that in JJA and SON. Three
of the six ensemble members project a reduction
of over 25 % for TI1 and Sv near Japan, and two
of them project an increase in the frequency in the
central North Pacific. An increase in TI1 of more than
25 – 50 % over Japan is projected only in JJA, whereas
TI1 is projected to decrease (increase) in the northern
(southern) part of Japan and further downstream in
the jet stream in SON. Wider reductions (increases)
are commonly seen in the six ΔSSTs for Sv (DEF
and rNBE) in JJA and SON. Interestingly, despite
the small inter-ΔSST variation for all CAT indices
in these seasons, the future changes in the jet stream
(represented by the 200 hPa wind speed |V |) and the
activity of upper-level synoptic-scale disturbances
(represented by the 200 hPa EKE with 2 – 8-day com-
ponents) show a relatively large variation depending
on ΔSST (Figs. 3, 4). The reason for this is unclear
and is left for future studies. On the other hand, the
inter-ΔSST variation of |V | and EKE sometimes
coincides with that of the CAT indices. For example,
the largest changes in the CAT indices in DJF for one
ΔSST ensemble (+2 K_MI) might be attributable to
the largest poleward shift of the jet stream and associ-
ated enhancement of synoptic-scale disturbances over
the North Pacific. 3.2 Changes in +2 K climate In the eastern Pacific, DEF and rNBE show
a similar increase in DJF to that shown by Storer
et al. (2017), except that their DEF shows a wider
extension. Because the present result shows a large
inter-ΔSST variation in DJF, the differences between
the two studies may also be related to differences in
SST change patterns. a broad increase in the CAT frequency near the Aleu-
tian Low. Another interesting feature in DJF is that
Sv and DEF, whose future changes are not positively
correlated in the other three seasons, both decrease
near Japan and further downstream in the jet stream. Indeed, future changes in these two indices are not as
strongly correlated with each other in individual ΔSST
ensembles, whereas their product, TI1, shows a robust
reduction among all ΔSSTs. This future decrease in
the CAT frequency in TI1 near Japan is not consistent
with the results of Storer et al. (2017), which showed
increases in all four indices (i.e., TI1, Sv , DEF, and
rNBE). In the eastern Pacific, DEF and rNBE show
a similar increase in DJF to that shown by Storer
et al. (2017), except that their DEF shows a wider
extension. Because the present result shows a large
inter-ΔSST variation in DJF, the differences between
the two studies may also be related to differences in
SST change patterns. changes to changes in the climatological distribution
of the jet stream and activity of upper-level synoptic-
scale disturbances. 3.2 Changes in +2 K climate Top row: climatological distribution of CAT frequency at 200 hPa in the PAST experiment diagnosed by TI1 in DJF, MAM, JJA, and SON (from left to
right), respectively. Second to seventh rows: future changes in +2 K ensembles forced by six different ΔSSTs (see Section 2), displayed as relative changes in
percent: 100 × (+2 K − PAST)/PAST. The light- and dark-gray shading indicate regions where the CAT frequency in the 2 K ensembles is less than 0.1 % and
0.01 %, respectively. The black shading indicates grid boxes where no CAT is diagnosed throughout the analysis period (270 years) either in the PAST or in the
+2 K experiment. Fig. 5. Top row: climatological distribution of CAT frequency at 200 hPa in the PAST experiment diagnosed by TI1 in DJF, MAM, JJA, and SON (from left to
right), respectively. Second to seventh rows: future changes in +2 K ensembles forced by six different ΔSSTs (see Section 2), displayed as relative changes in
percent: 100 × (+2 K − PAST)/PAST. The light- and dark-gray shading indicate regions where the CAT frequency in the 2 K ensembles is less than 0.1 % and
0.01 %, respectively. The black shading indicates grid boxes where no CAT is diagnosed throughout the analysis period (270 years) either in the PAST or in the
+2 K experiment. Journal of the Meteorological Society of Japan 766 Vol. 97, No. 3 Fig. 6. Same as Fig. 5 but for Sv . 767 S. WATANABE et al. June 2019 Fig. 7. Same as Fig. 5 but for DEF. Journal of the Meteorological Society of Japan 768 Vol. 97, No. 3 Fig. 8. Same as Fig. 5 but for rNBE. S. WATANABE et al. June 2019 769 a broad increase in the CAT frequency near the Aleu-
tian Low. Another interesting feature in DJF is that
Sv and DEF, whose future changes are not positively
correlated in the other three seasons, both decrease
near Japan and further downstream in the jet stream. Indeed, future changes in these two indices are not as
strongly correlated with each other in individual ΔSST
ensembles, whereas their product, TI1, shows a robust
reduction among all ΔSSTs. This future decrease in
the CAT frequency in TI1 near Japan is not consistent
with the results of Storer et al. (2017), which showed
increases in all four indices (i.e., TI1, Sv , DEF, and
rNBE). 2017). models. Geophys. Res. Lett., 46, 435–442. models. Geophys. Res. Lett., 46, 435–442. )
The present study focused on the climatological
distribution of the CAT frequency and the projected
changes for four seasons over the North Pacific. Using
large ensembles of d4PDF, in future studies, it may
become possible to investigate more localized changes
(e.g., along flight routes) in the probability distri-
butions of the CAT intensity (e.g., Williams 2017). Furthermore, it would be informative to investigate
the interannual variability of CAT arising from natural
climate variability and its future changes (e.g., Kim
et al. 2016). The d4PDF also provides 20 km resolu-
tion ensemble projections over East Asia centered on
Japan, which have been produced by downscaling the
60 km AGCM ensembles using a nonhydrostatic re-
gional climate model, MRI-NHRCM20 (Sasaki et al. 2011; Murata et al. 2013). Using the high-resolution
ensembles and further turbulent indices, we will be
able to produce projections of aviation relevant turbu-
lence including those generated by other mechanisms
(e.g., mountain waves and convection) at multiple
flight levels. Haarsma, R. J., M. J. Roberts, P. L. Vidale, C. A. Senior, A. Bellucci, Q. Bao, P. Chang, S. Corti, N. S. Fučkar,
V. Guemas, J. von Hardenberg, W. Hazeleger, C. Kodama, T. Koenigk, L. R. Leung, J. Lu, J.-J. Luo,
J. Mao, M. S. Mizielinski, R. Mizuta, P. Nobre, M. Satoh, E. Scoccimarro, T. Semmler, J. Small, and J.-S. von Storch, 2016: High resolution model intercompar-
ison project (HighResMIP v1.0) for CMIP6. Geosci. Model Dev., 9, 4185–4208. Harada, Y., H. Kamahori, C. Kobayashi, H. Endo, S. Ko-
bayashi, Y. Ota, H. Onoda, K. Onogi, K. Miyaoka,
and K. Takahashi, 2016: The JRA-55 Reanalysis:
Representation of atmospheric circulation and climate
variability. J. Meteor. Soc. Japan, 94, 269–302. Inatsu, M., and B. J. Hoskins, 2004: The zonal asymmetry
of the Southern hemisphere winter storm track. J. Climate, 17, 4882–4892. Jaeger, E. B., and M. Sprenger, 2007: A Northern Hemi-
spheric climatology of indices for clear air turbulence
in the tropopause region derived from ERA40 reanal-
ysis data. J. Geophys. Res., 112, D20106, doi:10.1029/
2006JD008189. Japan Meteorological Agency, 2013: JRA-55 product users’
handbook: 1.25-degree latitude/longitude grid data. 22 pp. [Available at http://jra.kishou.go.jp/JRA-55/
index_en.html.] Acknowledgments The authors would like to thank two anonymous
reviewers and journal editors for providing helpful
comments and suggestions. The authors were support-
ed by the Social Implementation Program on Climate
Change Adaptation Technology (SI-CAT), MEXT,
Japan. This study utilized the database for Policy
Decision Making for Future Climate Change (d4PDF),
which was produced using the Earth Simulator of
JAMSTEC as a “Strategic Project with Special Sup-
port” and with support from the Program for Risk
Information on Climate Change (SOUSEI), the Social
Implementation Program on Climate Change Adap-
tation Technology (SI-CAT), the Integrated Research
Program for Advancing Climate Models (TOUGOU)
and the Data Integration and Analysis System (DIAS),
all of which were sponsored by the Ministry of
Education, Culture, Sports, Science and Technology
(MEXT), Japan. Kim, J.-H., W. N. Chan, B. Sridhar, R. D. Sharman, P. D. Williams, and M. Strahan, 2016: Impact of the North
Atlantic Oscillation on transatlantic flight routes and
clear-air turbulence. J. Appl. Meteor. Climatol., 55,
763–771. Kim, J.-H., R. Sharman, M. Strahan, J. W. Scheck, C. Bartholomew, J. C. H. Cheung, P. Buchanan, and N. Gait, 2018: Improvements in nonconvective aviation
turbulence prediction for the world area forecast
system. Bull. Amer. Meteor. Soc., 99, 2295–2311. Kobayashi, S., Y. Ota, Y. Harada, A. Ebita, M. Moriya, H. Onoda, K. Onogi, H. Kamahori, C. Kobayashi, H. Endo, K. Miyaoka, and K. Takahashi, 2015: The JRA-
55 Reanalysis: General specifications and basic char-
acteristics. J. Meteor. Soc. Japan, 93, 5–48. Mizuta, R., H. Yoshimura, H. Murakami, M. Matsueda, H. Endo, T. Ose, K. Kamiguchi, M. Hosaka, M. Sugi, S. Yukimoto, S. Kusunoki, and A. Kitoh, 2012: Climate
simulations using MRI-AGCM3.2 with 20-km grid. J. Meteor. Soc. Japan, 90A, 233–258. 4. Summary and discussion A similar example is found in MAM
for another ΔSST ensemble (+2 K_CC) that shows a
unique large reduction in the activity of synoptic-scale
disturbances, which leads to common reductions in all
CAT indices. These examples demonstrate the possi-
bilities and limitations in attributing CAT frequency The uncertainty in the projected CAT changes due
to the ΔSST patterns from six selected CMIP5 climate
models has been addressed for the first time. The un-
certainty is maximized in the boreal winter and spring
over the central North Pacific and is associated with
uncertainties in future changes in the jet stream and
the activity of upper-level synoptic-scale disturbances. Meanwhile, the inter-ΔSST variation of CAT changes
is minimized in SON, and a robust reduction of the
CAT frequency is projected in the midlatitude central
to western North Pacific. The relative increase of the CAT frequency outside
the present-day high-frequency envelope may also
have implications for aircraft operations, because air-
craft may experience CAT in different locations other
than the ones at present. Two of the CAT indices, DEF
and rNBE, show a remarkably broad increase over the
eastern North Pacific, which may imply more frequent
and spontaneous generation of small-scale gravity
waves. The increase in the CAT frequency over the
southern part of Japan and around the Bering Sea may
also affect future aircraft operations. Future studies
should investigate the model and scenario dependency
of the findings in the present study. The High Reso-
lution Model Intercomparison Project (HighResMIP)
would provide the first opportunity to estimate these
dependencies (Haarsma et al. 2016). The most serious
limitation of the present study is the number of CAT
indices considered, and these calculations should be
repeated in future work using all 20 indices used in
previous works (e.g. Williams 2017; Storer et al. Journal of the Meteorological Society of Japan Journal of the Meteorological Society of Japan 770 Vol. 97, No. 3 Vol. 97, No. 3 2017). References Mizuta, R., A. Murata, M. Ishii, H. Shiogama, K. Hibino, N. Mori, O. Arakawa, Y. Imada, K. Yoshida, T. Aoyagi,
H. Kawase, M. Mori, Y. Okada, T. Shimura, T. Naga
tomo, M. Ikeda, H. Endo, M. Nosaka, M. Arai, C. Takahashi, K. Tanaka, T. Takemi, Y. Tachikawa, K. Temur, Y. Kamae, M. Watanabe, H. Sasaki, A. Kitoh,
I. Takayabu, E. Nakakita, and M. Kimoto, 2017: Over
5,000 years of ensemble future climate simulations by
60-km global and 20-km regional atmospheric models. Ellrod, G. P., and D. I. Knapp, 1992: An objective clear-
air turbulence forecasting technique: Verification and
operational use. Wea. Forecasting, 7, 150–165. Fujita, M., R. Mizuta, M. Ishii, H. Endo, T. Sato, Y. Okada, S. Kawazoe, S. Sugimoto, K. Ishihara, and S. Watanabe,
2019: Precipitation changes in a climate with 2-K
surface warming from large ensemble simulations
by 60-km global and 20-km regional atmospheric S. WATANABE et al. 771 June 2019 June 2019 Storer, L. N., P. D. Williams, and M. M. Joshi, 2017: Global
response of clear-air turbulence to climate change. Geophys. Res. Lett., 44, 9976–9984. Bull. Amer. Meteor. Soc., 98, 1383–1398. Murata, A., H. Sasaki, M. Hanafusa, and K. Kurihara, 2013:
Estimation of urban heat island intensity using biases
in surface air temperature simulated by a nonhydro-
static regional climate model. Theor. Appl. Climatol.,
112, 351–361. Storer, L. N., P. D. Williams, and P. G. Gill, 2018: Aviation
turbulence: Dynamics, forecasting, and response to
climate change. Pure Appl. Geophys., doi:10.1007/
s00024-018-1822-0. Plougonven, R., and F. Zhang, 2014: Internal gravity waves
from atmospheric jets and fronts. Rev. Geophys., 52,
33–76. Williams, P. D., 2017: Increased light, moderate, and severe
clear-air turbulence in response to climate change. Adv. Atmos. Sci., 34, 576–586.i Sasaki, H., A. Murata, M. Hanafusa, M. Oh’izumi, and K. Kurihara, 2011: Reproducibility of present climate in a
non-hydrostatic regional climate model nested within
an atmosphere general circulation model. SOLA, 7,
173–176. Williams, P. D., and M. M. Joshi, 2013: Intensification of
winter transatlantic aviation turbulence in response to
climate change. Nat. Climate Change, 3, 644–648. Zhang, F., S. E. Koch, C. A. Davis, and M. L. Kaplan, 2000:
A survey of unbalanced flow diagnostics and their
applications. Adv. Atmos. Sci., 17, 165–183. Sharman, R., C. Tebaldi, G. Wiener, and J. Wolff, 2006: An
integrated approach to mid- and upper-level turbu-
lence forecasting. Wea. Forecasting, 21, 268–287.
|
https://openalex.org/W3120570605
|
https://europepmc.org/articles/pmc7847632?pdf=render
|
English
| null |
Microvascular Reactivity Measured by Dynamic Near-infrared Spectroscopy Following Induction of General Anesthesia in Healthy Patients: Observation of Age-related Change
|
International journal of medical sciences
| 2,021
|
cc-by
| 6,401
|
Abstract Background: The purpose of this study was to investigate the effect of general anesthesia on
microvascular reactivity and tissue oxygen saturation (StO2) using near-infrared spectroscopy in
conjunction with vascular occlusion tests (VOT). Age-related changes of microvascular reactivity, that is,
the capacity of capillary recruitment, were examined. Methods: This prospective observational study was performed on 60 patients without comorbidities
who underwent elective surgery under general anesthesia. Baseline StO2 on thenar eminence,
hemodynamics, and laboratory profile were monitored before (T0) and 30 min after general anesthesia
(T1). During VOT, occlusion slope representing oxygen consumption of muscle and recovery slope
representing microvascular reactivity were also collected at T0 and T1. Results: Baseline StO2 and minimum / maximum StO2 during VOT increased under general anesthesia. Occlusion slope decreased while the recovery slope increased under general anesthesia. To observe
aging effect, Receiver operating characteristic analysis was performed and age less than 65 years old
showed a fair performance in predicting the increase of microvascular reactivity after the induction of
anesthesia (AUC 0.733, 95% CI 0.594-0.845, P= 0.003). For age-related analyses, 27 patients of younger
group (< 65 years) and 26 patients of older group (≥ 65 years) were divided. Recovery slope significantly
increased under general anesthesia in younger group (2.44 [1.91-2.81] % ∙ sec-1 at T0 and 3.59 [2.58-3.51]
% ∙ sec-1 at T1, P <0.001), but not in older group (2.61 [2.21-3.20] % ∙ sec-1 at T0, 2.63 [1.90-3.60] % ∙ sec-1
at T1, P = 0.949). Conclusions: General anesthesia could improve StO2 through increase of microvascular reactivity and
decrease of tissue metabolism. However, microvascular reactivity to capillary recruitment under general
anesthesia significantly improves in younger patients, not in older patients. Key words: Aging; cardiovascular physiology; anesthesia, inhalation; microcirculation; spectroscopy,
near-infrared Microvascular Reactivity Measured by Dynamic
Near-infrared Spectroscopy Following Induction of
General Anesthesia in Healthy Patients: Observation of
Age-related Change Ah-Reum Cho1,2, Hyeon-Jeong Lee1,2, Hyae-Jin Kim1, Wangseok Do1, Soeun Jeon1, Seung-Hoon Baek1,2,
Eun-Soo Kim1,2, Jae-Young Kwon1,2, Hae-Kyu Kim1,2 1. Department of Anesthesia and Pain Medicine, Medical Research Institute, Pusan National University Hospital, Busan, Republic of Korea. 2. Department of Anesthesia and Pain Medicine, Pusan National University, School of Medicine, Yangsan, Republic of Korea Corresponding author: Hyeon-Jeong Lee, Department of Anesthesia and Pain Medicine and Medical Research Institute, Pusan National University Hospital,
Gudeok-ro 179, Seo-gu, Busan, 49241, Republic of Korea. Tel: 82-51-240-7399; Fax: 82-51-242-7466; E-Mail: lhjksk@pusan.ac.kr © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2020.08.26; Accepted: 2020.12.18; Published: 2021.01.01 Ivyspring
International Publisher Ivyspring
International Publisher International Journal of Medical Sciences
2021; 18(5): 1096-1103. doi: 10.7150/ijms.52433 1096 1096 Int. J. Med. Sci. 2021, Vol. 18 Ivyspring
International Publisher General anesthesia In the operating room, standard monitoring
including electrocardiography, non-invasive blood
pressure (NIBP) monitors, and pulse oximetry were
used. Skin temperature probes (400 series, GE
Healthcare, Helsinki, Finland) were placed on the
right palm. The operating room temperature was
maintained at 22-24°C. Skin temperature was
measured before and after induction of anesthesia. General anesthesia was induced with propofol 1.5 - 2
mg ∙ kg-1 and a continuous infusion of remifentanil 0.2
μg ∙ kg-1 ∙ min-1. After injection of rocuronium 0.8 mg ∙
kg-1,
tracheal
intubation
was
performed
and
mechanical ventilation was applied with an inspired
oxygen fraction of 0.5, a tidal volume of 8 ml ∙ kg-1,
and a respiratory rate adjusted to maintain end-tidal
CO2 of 30-35 mmHg. General anesthesia was
maintained with desflurane and remifentanil to
maintain a bispectral index (BIS; Bispectral Index™,
Aspect Medical System, Norwood, MA, USA) of 40-50
and hemodynamic parameters within 20% of the
baseline values. Hartman’s solution was infused
during the study period at the rate of 5 ml ∙ kg-1 ∙ h-1. Under general anesthesia, blood samples were
collected to measure the serum lactate level. Owing to near-infrared spectroscopy (NIRS)
technology,
the
detection
of
microcirculatory
dysfunction has become easier and non-invasive. Many studies have shown that the dynamic NIRS
parameters that can be measured with a brief ischemic
challenge are clinically more useful than static tissue
oxygen saturation (StO2) values [10,13-15]. A vascular
occlusion test (VOT) is a method of observing the
change in StO2 after applying a tourniquet with a
higher pressure than the patient’s systolic blood
pressure. The StO2 reduction rate (occlusion slope)
during the ischemic period reflects oxygen extraction. The rate of StO2 increase (recovery slope) during
reperfusion after the release of the vascular occlusion
reflects microvascular reactivity [10,13,14]. The purpose of this study was to investigate the
effect of anesthetics on microvascular reactivity and
StO2 using near-infrared spectroscopy in conjunction
with VOT. Age-related changes of microvascular
reactivity, which means the capacity of capillary
recruitment, were focused. Vascular occlusion test (VOT) VOT was performed twice for each patient,
before (T0) and 30 min after the induction of general
anesthesia (T1). Before induction, a NIRS sensor
(INVOSTM
5100C
Cerebral/Somatic
Oximeter;
Medtronic, Minneapolis, MN, USA) was placed on the
thenar eminence and an automated tourniquet
(A.T.S® 3000 Automatic Tourniquet System; Zimmer
Inc., Warsaw, IL, USA) was placed around the
ipsilateral upper arm. A NIBP was placed around the
contralateral upper arm and the baseline blood
pressure was measured. When the baseline StO2 was
stabilized, the automatic tourniquet was inflated to 50
mmHg over the patient’s baseline systolic blood
pressure and maintained for 5 min. After the 5 min
ischemic period, the tourniquet was rapidly deflated
to 0 mmHg. StO2 data were continuously recorded
during the VOT procedure. Baseline StO2, minimum
StO2 during the 5 min inflation of the tourniquet, time
to minimum StO2, maximum StO2 during deflation of Introduction should identify therapeutic targets for functional
microcirculatory restoration to prevent organ failure
[3]. Microcirculatory function is impaired in a number
of pathologies, including sepsis [4], diabetes mellitus Microcirculatory
dysfunction
and
impaired
tissue perfusion may persist even if systemic
hemodynamic variables are optimized and within the
therapeutic target [1,2]. This suggests that clinicians http://www.medsci.org 1097 Int. J. Med. Sci. 2021, Vol. 18 [5], shock [6,7], aging [8], and smoking [9]. However,
research
on
the
effects
of
anesthetics
on
microcirculatory function has begun only recently,
and the results are still inconsistent [10,11]. One study
reported that general anesthesia has a negative impact
on reperfusion reserve [10]. Another study showed
that general anesthesia increases the recovery slope,
suggesting improvement of tissue microvascular
reactivity and peripheral vasodilation [11]. As
patients with microcirculatory dysfunction due to
various underlying diseases were included in
previous studies, inconsistent outcomes may have
occurred. To accurately determine the effect of
anesthetic agents on microvascular reactivity, patients
without comorbidities must be studied. Moreover,
age could also be an important consideration in
studies on microcirculatory function, even in healthy
subjects [12]. classification > II, age < 18 or > 80 years, body mass
index > 30 kg m-2, disorders likely to influence
microcirculation
(uncontrolled
hypertension,
diabetes, peripheral vascular disease, or chronic
venous insufficiency), pregnancy, smoking, sleep
apnea, history of chronic obstructive and restrictive
pulmonary disease, contraindications for anesthetic
agents, or refusal to participate in the investigation. Results A total of 60 patients were enrolled in this study. Seven patients were excluded due to protocol
violation. Demographic
and
intraoperative
characteristics are summarized in Table 1. Statistical analysis Patient’s
characteristics
and
hemodynamic
variables of patients with and without the increase of
recovery slope under general anesthesia are shown in
Table 1. Patients whose recovery slope increased
under general anesthesia were significantly younger
than those whose recovery slope did not increase
(P=0.013). The area under the ROC curve for age to
predict the increase of recovery slope after the
induction of anesthesia was 0.733 (Fig. 1, P = 0.003;
95% CI 0.594 - 0.845). If age was lower than 65 years
old, the increase of recovery slope under general
anesthesia was predicted with a sensitivity of 85.7%
and a specificity of 61.1%. The primary outcome of this study was the
difference of the recovery slope of the VOT after the
induction of general anesthesia. According to our
pilot study performed prior to this investigation,
mean difference of recovery slope of 0.28 % ∙ sec-1 with
SD of 0.72 % ∙ sec-1 was obtained. A sample size of 54
patients was necessary to gain a power of 80%, by
using a Wilcoxon signed rank test with a two-sided
significance level of five. Considering a drop-out rate
of 10%, a total of 60 patients were required. Data are expressed as number (proportion),
median [IQR], or mean (SD). All continuous variables
were tested for normality assumption with a Q-Q plot
and Kolmogorov-Smirnov test. StO2 values during
VOT at T0 and T1 were compared with repeated
measures ANOVA with a Bonferroni post hoc test. A
paired t-test or Wilcoxon signed rank test was used to
analyze differences in the hemodynamic variables
and VOT-derived measurements between T0 and T1. Data collection Preoperative hemoglobin concentration was
obtained. Mean blood pressure (MBP), heart rate
(HR),
pulsed
oxygen
saturation
(SpO2),
skin
temperature,
and
VOT-derived
measurements,
including baseline StO2, occlusion slope, minimum
StO2, time to minimum StO2, recovery slope,
maximum StO2, and time to maximum StO2 were
recorded at T0 and T1. Serum lactate level was
measured at T1. Patients This study was approved by the Institutional
Review Board of Pusan National University Hospital
(IRB no. 1607-012-054, Busan, South Korea) and
written informed consent was obtained from all
subjects participating in the trial. The trial was
registered
prior
to
patient
enrolment
at
clinicaltrials.gov (NCT03060798, Hyeon-Jeong Lee:
February 19, 2017). This manuscript adheres to the
applicable STROBE statements. pp
Sixty adult patients who were referred for
elective surgery under general anesthesia participated
in this study. Exclusion criteria were an American
Society of Anesthesiologists (ASA) physical status http://www.medsci.org Int. J. Med. Sci. 2021, Vol. 18 1098 analyses, patients were divided at 65 years old; 27
patients of younger group (< 65 years) and 26 patients
of older group (≥ 65 years). An unpaired student t test
or Mann-Whitney U test was used to analyze
differences in the hemodynamic variables and
VOT-derived measurements between the age groups. A P-value < 0.05 was considered significant. All
statistical analyses were performed using PASW
Statistics for Windows, Version 18.0 (SPSS Inc.,
Chicago, IL, USA) and MedCalc for Windows, version
13.2 (MedCalc Software, Ostend, Belgium). analyses, patients were divided at 65 years old; 27
patients of younger group (< 65 years) and 26 patients
of older group (≥ 65 years). An unpaired student t test
or Mann-Whitney U test was used to analyze
differences in the hemodynamic variables and
VOT-derived measurements between the age groups. the tourniquet, and time to maximum StO2 were
obtained. The occlusion slope and recovery slope,
which are VOT-derived dynamic parameters related
to microcirculatory reactivity, were calculated based
on the measured StO2 data. The occlusion slope was
defined as the slope of StO2 descent to the lowest
value. The recovery slope was calculated from
deflation of the tourniquet until the recovery of StO2
to the highest value. A P-value < 0.05 was considered significant. All
statistical analyses were performed using PASW
Statistics for Windows, Version 18.0 (SPSS Inc.,
Chicago, IL, USA) and MedCalc for Windows, version
13.2 (MedCalc Software, Ostend, Belgium). Effects of general anesthesia on VOT-derived
parameters and hemodynamic variables If age was lower than 65 years old, the
increase of recovery slope under general anesthesia was predicted with a sensitivity of
85.7% and a specificity of 61.1%. Effects of general anesthesia on VOT-derived
parameters and hemodynamic variables Younger (< 65
years) (n = 27)
Older (≥ 65 years)
(n = 26)
P value
Endoscopic sinus
surgery
14 (51.9)
3 (11.5)
Lactate; mg.l-1
0.87 [0.78-1.18]
1.18 [0.78-1.58]
0.296
Hemoglobin; g.dl-1
13.9 (1.6)
13.0 (1.2)
0.031
Fluid administration; ml 176.4 (31.2)
165.4 (27.8)
0.278
Data are number (proportion), mean (SD) or median [IQR]. Younger (< 65
years) (n = 27)
Older (≥ 65 years)
(n = 26)
P value
Endoscopic sinus
surgery
14 (51.9)
3 (11.5)
Lactate; mg.l-1
0.87 [0.78-1.18]
1.18 [0.78-1.58]
0.296
Hemoglobin; g.dl-1
13.9 (1.6)
13.0 (1.2)
0.031
Fluid administration; ml 176.4 (31.2)
165.4 (27.8)
0.278
Data are number (proportion), mean (SD) or median [IQR]. [2.58-3.51] % ∙ sec-1 in the younger group and 2.63
[1.90-3.60] % ∙ sec-1 in the older group, P = 0.047). MBP
significantly increased and HR and skin temperature
significantly decreased under general anesthesia in
both groups. However, there were no differences in
MBP, HR, SpO2, and skin temperatures between two
age groups. surgery
Lactate; mg.l-1
0.87 [0.78-1.18]
1.18 [0.78-1.58]
0.296
Hemoglobin; g.dl-1
13.9 (1.6)
13.0 (1.2)
0.031
Fluid administration; ml 176.4 (31.2)
165.4 (27.8)
0.278
Data are number (proportion), mean (SD) or median [IQR]. Figure 1. Receiver operating characteristic curve for age to predict the increase of
recovery slope under general anesthesia. If age was lower than 65 years old, the
increase of recovery slope under general anesthesia was predicted with a sensitivity of
85.7% and a specificity of 61.1%. Table 1. Effects of general anesthesia on VOT-derived
parameters and hemodynamic variables Demographic and intraoperative characteristics
of two age groups divided by age of 65 years old are
shown in Table 2. The type of operation and
hemoglobin showed significantly different between
the groups. The changes in StO2 during VOT before
and after the induction of anesthesia in two age
groups are shown in Fig. 2. Repeated measures of
ANOVA revealed significantly different StO2 values
before and after the induction of anesthesia in both
groups (all p < 0.001); the Bonferroni post hoc test
revealed significant differences at all time points. The
changes in microcirculatory and hemodynamic
parameters during VOT at T0 and T1 depending on
the age are shown in Table 3. At T0, baseline StO2 was
significantly higher in the younger group compared
to the older group (P = 0.025). After the induction of
anesthesia, recovery slope were significantly higher in
the younger group compared to the older group (3.59 Patients were divided by an increase of recovery
slope under general anesthesia and an unpaired
student t test or Mann-Whitney U test was used to
analyze differences in the patient’s characteristics and
hemodynamic variables between the groups. The
significantly different variables were evaluated their
ability to predict the increase of recovery slope of
VOT under general anesthesia using a receiver
operating characteristics (ROC) curves analysis with
95% confidence interval (CI). The optimal cut-off was
selected to maximize the Youden index and age less
than 65 years old showed a fair performance in
predicting the increase of microvascular reactivity
after the induction of anesthesia. For age-related http://www.medsci.org Int. J. Med. Sci. 2021, Vol. 18 1099 up and 2.63
0.047). MBP
emperature
nesthesia in
fferences in
etween two
amic variables
ecovery slope
ith the
recovery
er
esthesia
P
value
0.013
0.145
0.803
0.906
0.713
0.065
0.301
Younger (< 65
years) (n = 27)
Older (≥ 65 years)
(n = 26)
P value
Endoscopic sinus
surgery
14 (51.9)
3 (11.5)
Lactate; mg.l-1
0.87 [0.78-1.18]
1.18 [0.78-1.58]
0.296
Hemoglobin; g.dl-1
13.9 (1.6)
13.0 (1.2)
0.031
Fluid administration; ml 176.4 (31.2)
165.4 (27.8)
0.278
Data are number (proportion), mean (SD) or median [IQR]. Figure 1. Receiver operating characteristic curve for age to predict the increase of
recovery slope under general anesthesia. If age was lower than 65 years old, the
increase of recovery slope under general anesthesia was predicted with a sensitivity of
85.7% and a specificity of 61.1%. Effects of general anesthesia on VOT-derived
parameters and hemodynamic variables Patient’s characteristics and hemodynamic variables
between patients with or without the increase of recovery slope
under general anesthesia
All
patients
(n=53)
Patients without the
increase of recovery
slope under
general anesthesia
(n=18)
Patients with the
increase of recovery
slope under
general anesthesia
(n=35)
P
value
Age; years
56.5 (14.5)
63.3 (14.4)
53.0 (13.5)
0.013
Sex
0.145
Male
24 (45.3)
10 (55.6)
14 (40.0)
Female
29 (54.7)
8 (44.4)
21 (60.0)
Body mass
index; kg.m-2
24.0 (3.2)
23.8 (3.4)
24.1 (3.1)
0.803
Weight; kg
63.1 (12.0)
62.8 (10.5)
63.2 (12.9)
0.906
Height; cm
161.6 (9.1)
162.3 (8.8)
161.3 (9.3)
0.713
ASA class
0.065
I
26 (49.1)
10 (55.6)
8 (44.4)15 (55.5)
17 (48.6)
II
27 (50.9)
8 (44.4)
18 (51.4)
Type of
operation
0.301
Laparoscopic
cholecystectomy
18 (34.0)
8 (44.4)
10 (28.6)
Thyroidectomy 18 (34.0)
5 (27.8)
13 (37.1)
Endoscopic
sinus surgery
17 (32.1)
5 (27.8)
12 (34.3)
Lactate; mg.l-1
0.99
[0.78-1.48]
0.79 [0.65-1.62]
1.02 [0.84-1.34]
0.296
Hemoglobin;
g.dl-1
13.5 (1.5)
13.6 (1.4)
13.5 (1.6)
0.837
Fluid
administration;
ml
170.7 (29.7) 163.3 (28.9)
174.6 (29.8)
0.194
Mean blood
pressure;
mmHg
96.0 [86.5-112.5]
95.0 [89.3-104.5]
0.954
SpO2; %
99.0
[97.0-100.0]
99.0 [97.0-100.0]
99.0 [96.0-100.0]
0.512
Heart rate;
beats.min-1
74.0
[64.0-86.0]
71.0 [60.0-76.0]
76.0 [66.0-88.0]
0.292
Skin
temperature; °C
32.3 (2.3)
31.7 (1.7)
32.9 (1.9)
0.245
Data are number (proportion), mean (SD) or median [IQR]. Table 2. Patients’ characteristics of the age groups
Younger (< 65
years) (n = 27)
Older (≥ 65 years)
(n = 26)
P value
Age; years
45.1 (10.7)
68.3 (5.8)
<0.001
Sex
0.502
Male
11 (40.7)
13 (50.0)
Female
16 (59.2)
13 (50.0)
Body mass index; kg.m-2 24.1 (3.3)
24.0 (3.1)
0.887
Weight; kg
64.2 (13.6)
62.0 (10.4)
0.521
Height; cm
162.7 (10.0)
160.5 (8.1)
0.389 Table 1. Patient’s characteristics and hemodynamic variables
between patients with or without the increase of recovery slope
under general anesthesia Table 1. Patient’s characteristics and hemodynamic variables
between patients with or without the increase of recovery slope
under general anesthesia Figure 1. Receiver operating characteristic curve for age to predict the increase of
recovery slope under general anesthesia. If age was lower than 65 years old, the
increase of recovery slope under general anesthesia was predicted with a sensitivity of
85.7% and a specificity of 61.1%. Figure 1. Receiver operating characteristic curve for age to predict the increase of
recovery slope under general anesthesia. Discussion Changes in tissue oxygen saturation (StO2) during vascular occlusion test (VOT) before and after induction of general anesthesia in the younger and the older groups. A repeated measures ANOVA revealed significantly different StO2 values between before and after the induction of anesthesia, with a significant Bonferroni post hoc test for the
differences at all the time points. Figure 2. Changes in tissue oxygen saturation (StO2) during vascular occlusion test (VOT) before and after induction of general anesthesia in the younger and the older groups. A repeated measures ANOVA revealed significantly different StO2 values between before and after the induction of anesthesia, with a significant Bonferroni post hoc test for the
differences at all the time points. en saturation (StO2) during vascular occlusion test (VOT) before and after induction of general anesthesia in the younger and the older groups
vealed significantly different StO2 values between before and after the induction of anesthesia, with a significant Bonferroni post hoc test for the Figure 2. Changes in tissue oxygen saturation (StO2) during vascular occlusion test (VOT) before and after induction of general anesthesia in the younger and the older groups. A repeated measures ANOVA revealed significantly different StO2 values between before and after the induction of anesthesia, with a significant Bonferroni post hoc test for the
differences at all the time points. Table 3. Microcirculatory and hemodynamic parameters of the age groups. Table 3. Microcirculatory and hemodynamic parameters of the age groups. Discussion Our study showed that general anesthesia
improves StO2 in healthy adult patients through an
increase of microvascular reactivity and reduced
metabolic demand. However, the important finding
of our study was that the recovery slope significantly
increased after the induction of general anesthesia
only in the younger patients. This result suggests that
general anesthesia may increase the microvascular
reactivity and capillary recruitment only in the young,
healthy patients [11,14]. Concordantly, age could
predict the increase of recovery slope after the
induction of anesthesia, showing an area under the
ROC curve of 0.733. Table 2. Patients’ characteristics of the age groups Table 2. Patients’ characteristics of the age groups
Younger (< 65
years) (n = 27)
Older (≥ 65 years)
(n = 26)
P value
Age; years
45.1 (10.7)
68.3 (5.8)
<0.001
Sex
0.502
Male
11 (40.7)
13 (50.0)
Female
16 (59.2)
13 (50.0)
Body mass index; kg.m-2 24.1 (3.3)
24.0 (3.1)
0.887
Weight; kg
64.2 (13.6)
62.0 (10.4)
0.521
Height; cm
162.7 (10.0)
160.5 (8.1)
0.389
ASA class
0.339
I
15 (55.5)
11 (42.3)
II
12 (44.4)
15 (57.7)
Type of operation
0.004
Laparoscopic
cholecystectomy
5 (18.5)
13 (50.0)
Thyroidectomy
8 (29.6)
10 (38.5) The recovery slope during VOT reflects the
capacity of microvascular reactivity to recruit the
capillary network [16]. At rest, only 30% of capillaries
are normally perfused, and 70% are not [17]. These
blood vessels are reserves that can be opened under
stress
conditions
through
relaxation
of
the
precapillary sphincter and arteriolar vasodilation [18]. Even in elderly patients without comorbidities in
daily life, the limit of physiologic reserve can be seen
during general anesthesia. This limited physiologic
reserve is one of the causes of microcirculation
changes during aging [19]. In aged organs, dynamic http://www.medsci.org 1100 Int. J. Med. Sci. 2021, Vol. 18 endothelial dysfunction, impaired vasodilatory and
vasoconstrictive
responses,
increased
vascular
stiffness, and decreased vascular density and
impaired vascular organization [8,22,23]. control of the precapillary sphincter to regulate blood
flow does not work well, and reserved vessels are
barely recruited [20,21]. A variety of mechanisms are
involved,
in
which aging is associated
with control of the precapillary sphincter to regulate blood
flow does not work well, and reserved vessels are
barely recruited [20,21]. A variety of mechanisms are
involved,
in
which aging is associated
with Figure 2. Int. J. Med. Sci. 2021, Vol. 18 First, VOT is not yet
standardized, and the duration of peripheral ischemia
is an area of strong debate. There are two methods to
advocate peripheral ischemia: time-targeted and
StO2-targeted VOT. We used 5-minute time-targeted
VOT because a smaller minimum StO2 value after
ischemia results in a more defined recovery slope
[40,41]. Second, it is difficult to confirm that older
participants are completely healthy as younger
patients. Because we enrolled only the patients
undergoing
minor
surgery,
more
advanced
hemodynamic
monitoring
or
tests
related
to
cardiovascular disease could not be performed. However, in clinical practice, completely healthy
elderly is rare and most of the elderly have the
compensated comorbidities in their daily life and
more severe microcirculatory dysfunction, which
more prominent results might be seen in real world. Finally, the effects of FiO2 on microcirculation are in
debate. Previous study showed that normobaric
hyperoxia reduced capillary perfusion and oxygen
consumption and increased heterogeneity of the
perfusion, while there was no change in recovery
slope of VOT in healthy subjects [42]. In the same line,
high FiO2 had only a relatively small increase in mean
(SD) StO2 of 5.3 (7.1) % and this effect reached a
plateau when FiO2 was between 30% and 40% [43]. When previous studies that investigated the effect of
anesthetics on StO2 in cardiac surgery, StO2 under
general anesthesia seems more likely affected by
anesthetic agents, rather than FiO2 [9,11,35]. In their
studies, despite of increasing FiO2 to 0.5-0.6 under
general anesthesia, only sevoflurane significantly
increased StO2 and propofol did not significantly
change StO2. Further research on the comparisons of y
VOT parameters after the induction of anesthesia
are not consistent among previous studies that
showed a reduced or an increased recovery slope after
the induction of anesthesia [10,11,35]. We assume that
the reason for these differences is that the previous
studies included patients with various comorbidities
who required cardiac surgery; our study included
only patients without comorbidities. Recent studies
showed that reactive hyperemia is significantly
decreased in elderly patients with heart failure with
preserved ejection fraction or hypertension compared
to
healthy
age-matched
controls,
indicating
endothelial dysfunction in these patient groups
[36,37]. Also, they demonstrated that vasodilation
under loading condition, such as exercise, was
blunted in these patients [36]. Considering these
results, patients who required cardiac surgery in the
previous
studies
would
have
significant
microvascular dysfunction and decreased capacity of
reactive vasodilation. Int. J. Med. Sci. 2021, Vol. 18 1101 Int. J. Med. Sci. 2021, Vol. 18 Int. J. Med. Sci. 2021, Vol. 18 Therefore, it is difficult to confirm that the
improvement of StO2 at T1 was solely due to general
anesthesia. However, other potential factors, such as
body temperature, stress hormone caused by
intubation, fluid administration, and decreased MBP
are estimated to have little influence on our results. Body temperature within normal range does not seem
to influence StO2 [38]. Previous study showed that
stress hormones increased slightly in response to
laryngoscopy and intubation, all returning to or
below baseline 5 min later in normotensive patients
[39]. Moreover, 161 ml of Hartman’s solution was
infused in our study, which is not the amount that
causes clinically significant hemodilution in people
with normal hemoglobin. MBP was significantly
decreased under general anesthesia where the lowest
value was 66 mmHg which might provide enough
perfusion
pressure
to
allow
peripheral
autoregulation. Vasodilation occurs in a complex way through
endothelium dependent vasodilation (EDV) mediated
by
endothelium
or
endothelium
independent
vasodilation (EIV) mediated by smooth muscle of the
vessel wall [12]. EDV is known to decrease with age
[12,24] and mechanisms include decreased NO
sensitivity and bioavailability, and an increased
oxidative stress [25,26]. On the contrary, EIV is
maintained even in aged vessel [27]. Recovery slope
of VOT has been known as a useful clinical tool for
evaluating EDV [28,29]. In our study, the baseline StO2
is much lower in elderly patients, however, other
VOT-derived parameters were not significantly
different at T0. Assuming EIV is age independent,
EDV may be also preserved during VOT in older
patients under non-stress condition. Inhalational
anesthetic agents inhibit EDV but promote EIV via
reduction of intracellular Ca2+ availability and
sensitivity to contractile proteins [30,31]. The net effect
of these 2 opposing effects is generally vasodilation. Propofol and opioids decreases systemic vascular
resistance in a predominantly EIV and partly
mediated by EDV [32-34]. Considering VOT at T1 was
performed 30 min after the injection of propofol and
remifentanil,
mainly
desflurane
affected
the
microcirculation. Our results showed opposite results
that desflurane promoted EDV in younger patients. The reason of the contradictory results is not
elucidative, but may not be consistent with the in vitro
results
because
numerous
factors
affect
the
microvascular system in vivo. g
There are some limitations to the interpretation
of the results of our study. Discussion All patients (n=53)
Younger (< 65 yrs) (n = 27)
Older (≥ 65 yrs) (n = 26)
T0
T1
P value
T0
T1
P value
T0
T1
P value
Baseline StO2; %
60.0
[56.0-68.0]
70.0
[63.0-78.0]
<0.001
66.0
[60.0-68.8]
71.0
[62.5-77.8]
0.002
58.0*
[53.0-65.0]
70.0
[63.0-78.0]
< 0.001
Occlusion slope; %.sec-1
0.19
[0.15-0.25]
0.15
[0.11-0.18]
<0.001
0.19
[0.16-0.25]
0.15
[0.12-0.18]
<0.001
0.21
[0.14-0.28]
0.12
[0.10-0.20]
< 0.001
Minimum StO2; %
15.0
[15.0-30.0]
29.0
[15.0-47.0]
<0.001
15.0
[15.0-31.5]
29.0
[15.0-46.0]
<0.001
15.0
[15.0-28.0]
27.5
[15.0-50.0]
<0.001
Time to minimum StO2; sec
271.0
[210.8-300.0]
300.0
[299.3-300.0]
<0.001
270.0
[214.3-300.0]
300.0
[297.8-300.0]
0.004
285.5
[210.0-300.0]
300.0
[300-300.0]
< 0.001
Recovery slope; %.sec-1
2.50
[1.99-2.97]
2.77
[2.24-3.98]
0.004
2.44
[1.91-2.81]
3.59
[2.58-3.51]
<0.001
2.61
[2.21-3.20]
2.63*
[1.90-3.60]
0.949
Maximum StO2; %
87.0
[80.8-95.0]
95.0
[89.8-95.0]
<0.001
90.0
[82.5-95.0]
95.0
[90.5-95.0]
0.008
86.5
[79.0-91.0]
93.5
[89.0-95.0]
<0.001
Time to maximum StO2; sec
27.0
[23.8-30.5]
22.0
[16.8-28.3]
0.202
26.0
[20.5-34.3]
24.0
[15.5-32.5]
0.559
28.0
[23.0-34.0]
22.0
[18.0-30.0]
0.264
Mean blood pressure; mmHg
95.5
[87.0-107.0]
89.0
[78.0-100.0]
<0.001
94.5
[87.0-104.0]
88.0
[77.0-99.0]
0.003
97.5
[88.0-108.5]
89.0
[78.5-103.0]
0.003
SpO2; %
99.0
[97.0-100.0]
100.0
[98.0-100.0]
0.004
99.0
[97.0-100.0]
99.5
[98.0-100.0]
0.469
99.0
[96.0-100.0]
100.0
[98.0-100.0]
0.001
Heart rate; beats.min-1
74.0
[64.0-86.0]
82.0
[75.3-93.0]
<0.001
78.0
[66.3-87.8]
85.5
[77.0-98.0]
0.029
72.0
[59.5-78.5]
82.0
[75.0-90.3]
0.013
Skin temperature; °C
32.3 (2.3)
33.5 (1.99)
<0.001
31.9 (1.8)
33.4 (2.1)
<0.001
32.3 (1.9)
33.6 (1.6)
0.041
Data are mean (SD) or median [IQR]. T0 = before the induction of anesthesia; T1 = after the induction of anesthesia; StO2 = tissue oxygen saturation. *p < 0.05 compared to the
younger group. http://www.medsci.org helped data analysis and revising paper. helped data analysis and revising paper. effects of different types of general anesthetics on
microcirculation of patients without underlying
disease is needed. Ethics approval y
gy
18. Levy BI, Schiffrin EL, Mourad JJ, Agostini D, Vicaut E, Safar ME,
Struijker-Boudier HA. Impaired tissue perfusion: a pathology common to
hypertension, obesity, and diabetes mellitus. Circulation 2008; 118: 968-76. This study was approved by the Institutional
Review Board of Pusan National University Hospital
(number
H-1607-012-054)
and
registered
at
www.clinicaltrials.gov (NCT03060798). 19. Montagna W, Carlisle K. Structural changes in ageing skin. The British Journal
of Dermatology 1990; 122 Suppl 35: 61-70. 20. Jackson DN, Moore AW, Segal SS. Blunting of rapid onset vasodilatation and
blood flow restriction in arterioles of exercising skeletal muscle with ageing in
male mice. The Journal of Physiology 2010; 588: 2269-82. References 1. De Backer D, Creteur J, Preiser JC, Dubois MJ, Vincent JL. Microvascular blood
flow is altered in patients with sepsis. American Journal of Respiratory and
Critical Care Medicine 2002; 166: 98-104. 2. Kara A, Akin S, Ince C. Monitoring microcirculation in critical illness. Current
Opinion in Critical Care 2016; 22: 444-52. 2. Kara A, Akin S, Ince C. Monitoring microcirculation in critical illness. Current
Opinion in Critical Care 2016; 22: 444-52. 3. Moore JP, Dyson A, Singer M, Fraser J. Microcirculatory dysfunction and
resuscitation: why, when, and how. British Journal of Anaesthesia 2015; 115:
366-75. 4. Lush CW, Kvietys PR. Microvascular dysfunction in sepsis. Microcirculation
(New York, N.Y.: 1994) 2000; 7: 83-101. 5. Muris DM, Houben AJ, Schram MT, Stehouwer CD. Microvascular
dysfunction is associated with a higher incidence of type 2 diabetes mellitus: a
systematic review and meta-analysis. Arteriosclerosis, Thrombosis, and
Vascular Biology 2012; 32: 3082-94. 5. Muris DM, Houben AJ, Schram MT, Stehouwer CD. Microvascular
dysfunction is associated with a higher incidence of type 2 diabetes mellitus: a 6. Fang X, Tang W, Sun S, Huang L, Chang YT, Castillo C, Weil MH. Comparison
of buccal microcirculation between septic and hemorrhagic shock. Critical
Care Medicine 2006; 34: S447-53. 7. Kirschenbaum LA, Astiz ME, Rackow EC, Saha DC, Lin R. Microvascular
response in patients with cardiogenic shock. Critical Care Medicine 2000; 28:
1290-4. Abbreviations 8. Bentov I, Reed MJ. The effect of aging on the cutaneous microvasculature. Microvascular Research 2015; 100: 25-31. ASA: American Society of Anesthesiologists; BIS:
Bispectral index; CI: Confidence interval; EDV:
Endothelium
dependent
vasodilation;
EIV:
Endothelium independent vasodilation; HR: Heart
rate; MBP: Mean blood pressure; NIRS: Near-infrared
spectroscopy; SpO2: Pulsed oxygen saturation; ROC:
Receiver operating characteristics; StO2: Tissue
oxygen saturation; VOT: Vascular occlusion test. 9. Rossi M, Pistelli F, Pesce M, Aquilini F, Franzoni F, Santoro G, Carrozzi L. Impact of long-term exposure to cigarette smoking on skin microvascular
function. Microvascular Research 2014; 93: 46-51. 10. Bernet C, Desebbe O, Bordon S et al. The impact of induction of general
anesthesia and a vascular occlusion test on tissue oxygen saturation derived
parameters in high-risk surgical patients. Journal of Clinical Monitoring and
Computing 2011; 25: 237-44. p
g
11. Kim TK, Cho YJ, Min JJ, Murkin JM, Bahk JH, Hong DM, Jeon Y. Tissue
microcirculation measured by vascular occlusion test during anesthesia
induction. Journal of Clinical Monitoring and Computing 2016; 30: 41-50. 12. Gerhard M, Roddy MA, Creager SJ, Creager MA. Aging progressively impairs
endothelium-dependent vasodilation in forearm resistance vessels of humans. Hypertension (Dallas, Tex.: 1979) 1996; 27: 849-53. Competing Interests General
anesthesia
is
known
to
reduce
cardiovascular function, which would ultimately
reduce organ perfusion. However, our study shows
that general anesthesia would compensate tissue
hypoperfusion by improving microvascular reactivity
representing the ability to recruit capillaries and
reducing metabolic demands. However, improved
microvascular reactivity by general anesthesia was
only apparent in the younger patients without
accompanying diseases, not in the older patients, even
those without comorbidities. These findings suggest
that general anesthesia could have different effects on
microvascular reactivity depending on the status of
the microvasculature. Additional studies on the
effects of general anesthesia on microvascular
reactivity in certain diseases are necessary. The authors have declared that no competing
interest exists. The authors have declared that no competing
interest exists. Funding 14. Futier E, Christophe S, Robin E et al. Use of near-infrared spectroscopy during
a vascular occlusion test to assess the microcirculatory response during fluid
challenge. Critical Care (London, England) 2011; 15: R214. This work was supported by the National
Research Foundation of Korea (NRF) grant funded by
the Korea government (MEST) (No. NRF-2018R1C1
B5040928) and clinical research grant in 2020 from
Pusan National University Hospital. challenge. Critical Care (London, England) 2011; 15: R214. 15. Shapiro NI, Arnold R, Sherwin R et al. The association of near-infrared
spectroscopy-derived
tissue
oxygenation
measurements
with
sepsis
syndromes, organ dysfunction and mortality in emergency department
patients with sepsis. Critical Care (London, England) 2011; 15: R223. p
p
(
g
)
16. Moens AL, Goovaerts I, Claeys MJ, Vrints CJ. Flow-mediated vasodilation: a
diagnostic instrument, or an experimental tool? Chest 2005; 127: 2254-63. 17. Chade AR. Renal vascular structure and rarefaction. Comprehensive
Physiology 2013; 3: 817-31. Acknowledgements yp
(
)
13. Butler E, Chin M, Aneman A. Peripheral Near-Infrared Spectroscopy:
Methodologic Aspects and a Systematic Review in Post-Cardiac Surgical
Patients. Journal of Cardiothoracic and Vascular Anesthesia. 2016. Int. J. Med. Sci. 2021, Vol. 18 And microvascular dysfunction
appears to be more severe in the cardiac patients than
in heathy elderly patients. There are numerous clinical variables that could
contribute to regulate microcirculation in human. http://www.medsci.org 1102 Int. J. Med. Sci. 2021, Vol. 18 Int. J. Med. Sci. 2021, Vol. 18 Int. J. Med. Sci. 2021, Vol. 18 Int. J. Med. Sci. 2021, Vol. 18 26. Taddei S, Virdis A, Ghiadoni L, Salvetti G, Bernini G, Magagna A, Salvetti A. Age-related reduction of NO availability and oxidative stress in humans. Hypertension (Dallas, Tex.: 1979) 2001; 38: 274-9. yp
(
)
27. Sinkler SY, Segal SS. Aging alters reactivity of microvascular resistance
networks in mouse gluteus maximus muscle. American Journal of
Physiology.Heart and Circulatory Physiology 2014; 307: H830-9. y
gy
y
y
gy
28. Patel S, Celermajer DS. Assessment of vascular disease using arterial flow
mediated dilatation. Pharmacological Reports : PR 2006; 58 Suppl: 3-7. 28. Patel S, Celermajer DS. Assessment of vascular disease using mediated dilatation. Pharmacological Reports : PR 2006; 58 Suppl: 29. Le Brocq M, Leslie SJ, Milliken P, Megson IL. Endothelial dysfunction: from
molecular mechanisms to measurement, clinical implications, and therapeutic
opportunities. Antioxidants & Redox Signaling 2008; 10: 1631-74. g
g
30. Akata T. General anesthetics and vascular smooth muscle: direct actions of
general anesthetics on cellular mechanisms regulating vascular tone. Anesthesiology 2007; 106: 365-91. gy
31. Villeneuve E, Blaise G, Sill JC, Guerard MJ, Buluran J, Girard D. Halothane 1.5
MAC, isoflurane 1.5 MAC, and the contractile responses of coronary arteries
obtained from human hearts. Anesthesia and Analgesia 1991; 72: 454-61. g
32. Robinson BJ, Ebert TJ, O'Brien TJ, Colinco MD, Muzi M. Mechanisms whereby
propofol mediates peripheral vasodilation in humans. Sympathoinhibition or
direct vascular relaxation? Anesthesiology 1997; 86: 64-72. 33. Duman A, Saide Sahin A, Esra Atalik K, oZtin ogun C, Basri Ulusoy H, Durgut
K, oKesli S. The in vitro effects of remifentanil and fentanyl on isolated human
right atria and saphenous veins. Journal of Cardiothoracic and Vascular
Anesthesia 2003; 17: 465-9. 34. Aguirre JA, Lucchinetti E, Clanachan AS, Plane F, Zaugg M. Unraveling
Interactions Between Anesthetics and the Endothelium: Update and Novel
Insights. Anesthesia and Analgesia 2016; 122: 330-48. g
g
35. Vandenbulcke L, Lapage KG, Vanderstraeten KV, De Somer FM, De Hert SG,
Moerman AT. Microvascular reactivity monitored with near-infrared
spectroscopy is impaired after induction of anaesthesia in cardiac surgery
patients: An observational study. European Journal of Anaesthesiology 2017;
34: 688-94. 36. Borlaug BA, Olson TP, Lam CS, Flood KS, Lerman A, Johnson BD, Redfield
MM. Global cardiovascular reserve dysfunction in heart failure with
preserved ejection fraction. Journal of the American College of Cardiology
2010; 56: 845-54. 37. Lee JF, Barrett-O'Keefe Z, Garten RS et al. Author Contributions y
gy
21. Scheeren TW. Journal of Clinical Monitoring and Computing 2015 end of year
summary: tissue oxygenation and microcirculation. Journal of Clinical
Monitoring and Computing 2016; 30: 141-6. AC
helped
study
design/planning,
study
conduct, data analysis, and writing and revising
paper. HL helped study design/planning, study
conduct, data analysis, and writing and revising
paper. HjK helped study design/planning and
revising paper. WD helped study conduct and
revising paper. SJ helped study conduct and revising
paper. SB helped study design/planning and revising
paper. EK helped study conduct and revising paper. JK helped data analysis and revising paper. HkK 22. Muller-Delp JM. Aging-induced adaptations of microvascular reactivity. Microcirculation (New York, N.Y.: 1994) 2006; 13: 301-14. (
)
23. Sweat RS, Sloas DC, Stewart SA et al. Aging is associated with impaired
angiogenesis, but normal microvascular network structure, in the rat
mesentery. American Journal of Physiology.Heart and Circulatory Physiology
2017; 312: H275-84. 24. DeSouza CA, Clevenger CM, Greiner JJ, Smith DT, Hoetzer GL, Shapiro LF,
Stauffer BL. Evidence for agonist-specific endothelial vasodilator dysfunction
with ageing in healthy humans. The Journal of Physiology 2002; 542: 255-62. g
g
y
y
gy
25. Muller-Delp JM, Spier SA, Ramsey MW, Delp MD. Aging impairs
endothelium-dependent vasodilation in rat skeletal muscle arterioles. American Journal of Physiology.Heart and Circulatory Physiology 2002; 283:
H1662-72. http://www.medsci.org 1103 Int. J. Med. Sci. 2021, Vol. 18 Evidence of microvascular
dysfunction in heart failure with preserved ejection fraction. Heart (British
Cardiac Society) 2016; 102: 278-84. y
38. Cho YJ, Lee SY, Kim TK, Hong DM, Jeon Y. Effect of Prewarming during
Induction of Anesthesia on Microvascular Reactivity in Patients Undergoing
Off-Pump Coronary Artery Bypass Surgery: A Randomized Clinical Trial. PloS One 2016; 11: e0159772. 39. Kayhan Z, Aldemir D, Mutlu H, Ogus E. Which is responsible for the
haemodynamic response due to laryngoscopy and endotracheal intubation? Catecholamines,
vasopressin
or
angiotensin? European
Journal
of
Anaesthesiology 2005; 22: 780-5. 40. Lipcsey M, Eastwood GM, Woinarski NC, Bellomo R. Near-infrared
spectroscopy of the thenar eminence: comparison of dynamic testing
protocols. Critical Care and Resuscitation : Journal of the Australasian
Academy of Critical Care Medicine 2012; 14: 142-7. 41. Iannetta D, Inglis EC, Soares RN, McLay KM, Pogliaghi S, Murias JM, CAPES
scholarship holder. Reliability of microvascular responsiveness measures
derived from near-infrared spectroscopy across a variety of ischemic periods
in young and older individuals. Microvascular Research 2019; 122: 117-24. y
g
42. Orbegozo Cortes D, Puflea F, Donadello K et al. Normobaric hyperoxia alters
the microcirculation in healthy volunteers. Microvascular Research 2015; 98:
23-8. 43. Kyle B, Litton E, Ho KM. Effect of hyperoxia and vascular occlusion on tissue
oxygenation measured by near infra-red spectroscopy (InSpectra): a volunteer
study. Anaesthesia 2012; 67: 1237-41. http://www.medsci.org
|
https://openalex.org/W2921893527
|
https://europepmc.org/articles/pmc6426782?pdf=render
|
English
| null |
Long Noncoding RNAs: Emerging Players in Medulloblastoma
|
Frontiers in pediatrics
| 2,019
|
cc-by
| 8,527
|
Long Noncoding RNAs: Emerging
Players in Medulloblastoma Pietro Laneve 1, Jessica Rea 2 and Elisa Caffarelli 1* 1 Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy, 2 Department of Biology and
Biotechnology, Sapienza University of Rome, Rome, Italy Central Nervous System tumors are the leading cause of cancer-related death in children,
and medulloblastoma has the highest incidence rate. The current therapies achieve a 5-
year survival rate of 50–80%, but often inflict severe secondary effects demanding the
urgent development of novel, effective, and less toxic therapeutic strategies. Historically
identified on a histopathological basis, medulloblastoma was later classified into four
major subgroups—namely WNT, SHH, Group 3, and Group 4—each characterized by
distinct transcriptional profiles, copy-number aberrations, somatic mutations, and clinical
outcomes. Additional complexity was recently provided by integrating gene- and non-
gene-based data, which indicates that each subclass can be further subdivided into
specific subtypes. These deeper classifications, while getting over the typical tumor
heterogeneity, indicate that different forms of medulloblastoma hold different molecular
drivers that can be successfully exploited for a greater diagnostic accuracy and for
the development of novel, targeted treatments. Long noncoding RNAs are transcripts
that lack coding potential and play relevant roles as regulators of gene expression in
mammalian differentiation and developmental processes. Their cell type- and tissue-
specificity, higher than mRNAs, make them more informative about cell- type identity than
protein-coding genes. Remarkably, about 40% of long noncoding RNAs are expressed
in the brain and their aberrant expression has been linked to neuro-oncological disorders. However, while their involvement in gliomas and neuroblastomas has been extensively
studied, their role in medulloblastoma is still poorly explored. Here, we present an
overview of current knowledge regarding the function played by long noncoding RNAs
in medulloblastoma biology. Edited by:
Andrea Carai,
Bambino Gesù Children Hospital
(IRCCS), Italy Reviewed by:
Anshu Malhotra,
Emory University, United States
Francesca Del Bufalo,
Bambino Gesù Children Hospital
(IRCCS), Italy *Correspondence:
Elisa Caffarelli
elisa.caffarelli@uniroma1.it Keywords: nervous system, pediatric tumor, medulloblastoma, long noncoding RNAs, oncogenes, tumor
suppressors, diagnostic biomarkers, therapeutic targets Specialty section:
This article was submitted to
Pediatric Oncology,
a section of the journal
Frontiers in Pediatrics MINI REVIEW MINI REVIEW
published: 14 March 2019
doi: 10.3389/fped.2019.00067 published: 14 March 2019
doi: 10.3389/fped.2019.00067 Keywords: nervous system, pediatric tumor, medulloblastoma, long noncoding RNAs, oncogenes, tumor
suppressors, diagnostic biomarkers, therapeutic targets INTRODUCTION Medulloblastoma (MB), with an estimated 5000–8000 cases/year worldwide (1, 2), is an
aggressive tumor arising in the cerebellum. It mainly affects children and is a major
cause of mortality in pediatric oncology (3). While the previous classification of MB
by the World Health Organization (WHO) was largely based on histological features
(4), the new classification in 2016 exploited molecular parameters to catalog the large
variety of tumors of the Central Nervous System (CNS) (5). Rational molecular-based
classification was supported by the advancement of sequencing technologies allowing extensive
genomic/transcriptomic studies. This classification benefits from the integration between
histological and molecular parameters and led to no longer considering MB as a unique pathology. Received: 08 June 2018
Accepted: 18 February 2019
Published: 14 March 2019 Group 4 G4, the most common subtype, accounts for 35% of all MBs. These tumors are often metastatic at diagnosis and have
intermediate prognosis. It is the most enigmatic subgroup,
characterized
by
a
neuronal
gene
expression
signature,
resembling
that
of
glutamatergic
neurons
(7). Common
alterations pertain to inactivating mutations in KDM6A gene,
duplication of SNCAIP gene, and amplification of MYCN
and CDK6 proto-oncogenes. G4 has been re-classified into
G4α,
characterized
by
MYCN
and
CDK6
amplifications,
G4β, strongly enriched for SNCAIP duplications and putative
PRDM6 overexpression, and G4γ enriched for focal CDK6
amplification (9). In this review, we highlight the link between MB tumors
and the emerging class of regulatory long noncoding RNAs
(lncRNAs), and their potential as promising cancer biomarkers
and novel therapeutic agents. Citation: Citation:
Laneve P, Rea J and Caffarelli E (2019)
Long Noncoding RNAs: Emerging
Players in Medulloblastoma. Front. Pediatr. 7:67. doi: 10.3389/fped.2019.00067 March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org Long Noncoding RNAs in Medulloblastoma Laneve et al. G3β with a more favorable prognosis compared to G3γ, which
frequently harbors increased MYC copy number (9). Several subclasses of MB have been unveiled, each displaying
dysregulated
genes—the
driver
genes—altered
by
single
nucleotide mutations, somatic copy-number aberrations, or by
defects in transcriptional or post-transcriptional gene regulation. Mechanisms of Action LncRNAs may be engaged in fine-scale modulation of gene
expression as well as in large-scale control of developmental
programs. They may act through a variety of mechanisms,
depending on their cellular localization. Some of them are
exclusively localized in the nucleus, others in the cytoplasm,
others
change
their
localization
during
development
or
differentiation,
and
still
others
show
both
localizations. In the latter case, a single lncRNA might have multiple
molecular functions. Medulloblastoma Recent genomic and transcriptomic analyses on a large cohort
of primary tumors assigned MBs to four molecularly distinct
subgroups (6, 7). They include the extensively characterized
WNT and SHH subgroups, and the Group 3 (G3) and
Group 4 (G4), whose pathogenesis and signaling pathways are
poorly defined. Group 3 G3 is the most aggressive subgroup accounting for about 25%
of all MBs, about half of them being metastatic at diagnosis
(10). These tumors display a MYC signature, being characterized
by amplification of the MYC proto-oncogene and exhibiting
aberrant MYC expression in almost all cases (7). G3 shows intra-
tumoral heterogeneity, including three further subtypes: G3α and SHH SHH MBs represent approximately 30% of all MB cases,
characterized by an intermediate prognosis, with survival rates
ranging from 60 to 80% (7). SHH tumors, mainly exhibiting
desmoplastic histology, display an aberrant activation of the
SHH signaling, due to mutations of negative regulators of
SHH pathway, such as PTCH1 and SUFU, and copy number
aberrations of SHH target genes, such as MYCN and GLI2 (7). TP53 mutations are found in about 30% of childhood SHH
MBs and are associated with extremely poor outcomes. Recent
analyses suggest that SHH subgroup consists of four distinct
subtypes. It includes SHHα, enriched for MYCN and GLI2
amplifications, with the worst prognosis; SHHβ, harboring PTEN
gene deletions and frequently metastatic; SHHγ displaying scarce
copy number aberrations and SHHδ, that is enriched for TERT
gene promoter mutations and has a favorable prognosis (9). LONG NONCODING RNAS Approximately 10% of all MB patients belong to this subgroup,
characterized by the most favorable prognosis with 95% of
survival (7, 8). WNT tumors, which exhibit classic histology,
are recognizable by a WNT gene expression signature. Nuclear
accumulation of β-catenin is considered a biomarker for
WNT signaling pathway activation. This subgroup often carries
heterozygous TP53 mutations, as well as mutations in the DEAD-
box helicase gene DDX3X and in chromatin modifiers genes,
such as SMARCA4 and CREBBP, indicating the implication of
altered epigenome in the development of this disease. Integration
of gene expression and DNA methylation profiles indicated that
WNT subgroup comprises at least two subtypes, WNTα, mainly
enriched for children and characterized by monosomy 6, and
WNTβ, including mainly adults without monosomy 6 (9). RNA is considered as the most “rediscovered” biological
macromolecule (11, 12) since, starting from the informational
role assigned to mRNAs in 1961 (13, 14), novel unexpected
functions have been attributed to RNA in the last three
decades. In the 1980s, its capacity to catalyze biochemical
reactions was associated with its ability to fold into complex
tridimensional structures (15). In the early 1990s, regulatory
functions were attributed to two long RNAs lacking protein-
coding capacity, H19 (16, 17), and XIST (18, 19). Since then,
a huge number of noncoding RNAs, both short and long in
size, was discovered in parallel with the finding that more than
half of the transcriptome encodes non-proteinogenic transcripts. Among them, the lncRNAs number in the tens of thousands and
include also circular RNAs, covalently closed RNA circles derived
from back-splicing of linear transcripts (20). LncRNAs are >200
nucleotides and represent very versatile molecules for their
unique ability to specifically recognize both nucleic acids and
protein partners via base-pairing and modular tridimensional
structures, respectively. They are flexibly involved in important
biological processes, such as development, cell differentiation
and growth, thanks to their main functions of gene expression
regulators and the genome structure architects. Frontiers in Pediatrics | www.frontiersin.org Nuclear lncRNAs Nuclear lncRNAs (Figure 1A) can be found in the nucleoplasm
or associated with chromatin (21). Typically, these latter are
supposed to control protein-coding gene expression at the March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 2 Long Noncoding RNAs in Medulloblastoma Laneve et al. FIGURE 1 | Mechanisms of action of lncRNAs. (A) In the nucleus, lncRNAs can regulate gene expression by guiding epigenetic (1) or transcription (2) factors to
specific loci, by acting as enhancers (3), by structuring the three-dimensional conformation of chromatin (4), or by recruiting splicing factors (5). (B) In the cytoplasm,
they act by modulating mRNA stability (6) or translation (7), by sequestering miRNAs (8), or by coding small peptides (9). FIGURE 1 | Mechanisms of action of lncRNAs. (A) In the nucleus, lncRNAs can regulate gene expression by guiding epigenetic (1) or transcription (2) factors to
specific loci, by acting as enhancers (3), by structuring the three-dimensional conformation of chromatin (4), or by recruiting splicing factors (5). (B) In the cytoplasm,
they act by modulating mRNA stability (6) or translation (7), by sequestering miRNAs (8), or by coding small peptides (9). positively as BACE1-AS (37) and TINCR (38), and negatively as
½-sbsRNAs (39), or translation, as lincRNA p21 (40). Another
role is that of decoys for microRNAs (miRNAs): in this case,
the lncRNA functions as a competing endogenous RNA (ceRNA)
that sequesters miRNAs from their mRNA targets, causing
translational de-repression. This activity is based on regulatory
crosstalk between multiple transcripts (41, 42). Notably, lncRNA-
mediated ceRNA networks in cancer are continuously emerging
(43, 44). However, only for a very limited number, such as Gas5
(45), linc-RoR (46, 47), NORAD (48), and linc-NeD125 (49),
this function has been characterized: their aberrant enrichment
or local increased concentration in pathological conditions
can culminate in tumorigenesis. Finally, some lncRNAs may
contain short open reading frames producing small, functional
peptides (50). epigenetic level by recruiting chromatin modifiers to specific
genomic loci. This is achieved through their scaffolding activity,
by which they interact simultaneously with distinct protein
complexes, and through their capability to act as “molecular
guides,” that ensure the specificity of target recognition (21). This
function can be carried out in cis or in trans. Nuclear lncRNAs The cis-acting RNAs
are typically low-abundant, and regulated genes are located in
the proximity of their transcription site; trans-acting RNAs are
more abundant and can modulate the expression of genes at
independent loci (21). Notably, perturbations of the epigenetic
regulation were recognized as causative of malignancies (22), and
some cancer-related lncRNAs, such as XIST (23), HOTAIR (24–
26), NBAT (27), and LINC-PINT (28), were reported to direct
epigenetic modifications (29). Nuclear lncRNAs can also act as regulators of transcriptional
programs, by recruiting transcription activators or repressors
to specific loci (30, 31), as enhancer RNAs that exert
enhancer-like functions (32, 33), as chromosome architects
and nuclear organizers that contribute to the formation of
specific sub-nuclear structures (21, 34, 35), or as regulators of
alternative splicing (36). THE ROLE OF LNCRNAS IN CNS The CNS of mammals is a very sophisticated system in which
neuronal and glial cells structurally and functionally interact
to guarantee the proper brain activity. Numerous evidence
correlates the evolutionary increase in human brain complexity
with the expanding number of lncRNAs (51, 52). Accordingly,
40% of human annotated lncRNAs are expressed in the brain,
where they display neuro-anatomical and/or cell-type specific
expression, and about 30% of lncRNAs appears to be primate-
specific (31, 53). Notably, compared to lncRNAs from other
tissues, the brain-specific lncRNAs are: (i) the most evolutionarily Frontiers in Pediatrics | www.frontiersin.org Cytoplasmic lncRNAs In vitro
studies revealed some lncRNAs, such as RMST (60), TUNA
(61), DALI (62), and PAUPAR (63), that control complex gene
expression programs underlying the neurogenic commitment
of pluripotent embryonic stem cells. This is mainly achieved
through their action of “guide” RNAs that convey transcriptional
and/or epigenetic factors on the promoters of neuronal genes. In vivo analyses identified other species such as GOMAFU
(56, 64, 65), EVF2 (66), PNKY (67), and linc-BRN1B (68) that,
through the recruitment of epigenetic, transcriptional, or splicing
factors, govern the balance between self-renewal and neuronal
differentiation. LncRNAs also contribute to synaptogenesis and
neuronal plasticity, which underlies learning, memory, and
cognition, by regulating crucial proteins that control neurite
elaboration (69), translation in synapses (70, 71), and ion channel
subunits (72). Neuroblastoma (NB) is a pediatric tumor of the sympathetic
NS, accounting for more than 7% of childhood malignancies
(85). The molecular link between deregulated lncRNA expression
and NB tumorigenic features is emerging (86), and several
deregulated lncRNAs during NB pathogenesis have been
uncovered (87–92). Our knowledge of lncRNA function in MB physiopathology
is still fragmentary. Genome-wide association studies may help
to understand how genetic polymorphisms in lncRNA loci
contribute to MB predisposition (93). Furthermore, in spite of the
numerous high-throughput expression studies carried out so far,
lncRNAs have been largely disregarded. However, re-annotation
of array-based data and integration of cancer phenotype
associations allowed prioritizing disease-related lncRNAs in
tumors, including MB (94), demonstrating the potential of data
re-analyses. In another study, a de-novo genome-wide inspection
of MB subgroup-specific chromosomal alterations identified the
first G3 MB gene fusions (6). They involve the 5′-end of PVT1, a
lncRNA hosting the putative MB oncogene miR-1024 (95, 96). In the PVT1-MYC fusion, the induction of miR-1024 and the
associated malignant phenotype may be explained through an
oncogenic positive feedback-loop, established by MYC on its
response elements on PVT1 promoter (6). Other studies focused on the role played in MB by previously
identified noncoding oncogenes. Among them, UCA1 (97)
and CRNDE (98, 99) are upregulated in MB samples. UCA1
knockdown in MB cells results in the arrest of cell cycle
progression, suppression of cell migration, and proliferation
(100). Similarly, in vitro downregulation of CRNDE blocked cell
cycle, inhibited proliferation and aggregation, while increasing
apoptosis. Tumor growth was also reduced in MB mouse models
silenced for CRNDE (101). Cytoplasmic lncRNAs Inversely, the lncRNA HOTAIR
(102) is downregulated in MB samples, whereas its target genes
HOXD8 and HOXD10 are upregulated (103). The misbalance of
these crucial developmental genes may partially account for the
embryonic origin and the pediatric onset of MB. However, their
mechanisms of action are presently unknown. Cytoplasmic lncRNAs Cytoplasmic lncRNAs (Figure 1B) regulate gene expression at
the post-transcriptional level, often exploiting their sequence
complementarity with transcripts deriving from the same
genomic locus or from independent loci. Upon specific target
recognition, they are able to modulate mRNA stability, both March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 3 Long Noncoding RNAs in Medulloblastoma Laneve et al. conserved species, (ii) predicted to retain conserved secondary
structures, and (iii) preferentially adjacent to protein-coding
genes involved in neuronal differentiation and function (54). Overall, these findings indicate that brain-specific lncRNAs likely
possess conserved functions and are crucially implicated in
higher-order cognitive abilities as well as in establishing neural
cell-type diversity and function. This hypothesis is sustained by
their spatiotemporal expression, which is exquisitely regulated
during NS development (55) and in response to neuronal
activity (56). So far, a growing body of literature shows that
lncRNAs influence every step of neurodevelopment, from early
stages of differentiation to synaptogenesis (57–59). In vitro
studies revealed some lncRNAs, such as RMST (60), TUNA
(61), DALI (62), and PAUPAR (63), that control complex gene
expression programs underlying the neurogenic commitment
of pluripotent embryonic stem cells. This is mainly achieved
through their action of “guide” RNAs that convey transcriptional
and/or epigenetic factors on the promoters of neuronal genes. In vivo analyses identified other species such as GOMAFU
(56, 64, 65), EVF2 (66), PNKY (67), and linc-BRN1B (68) that,
through the recruitment of epigenetic, transcriptional, or splicing
factors, govern the balance between self-renewal and neuronal
differentiation. LncRNAs also contribute to synaptogenesis and
neuronal plasticity, which underlies learning, memory, and
cognition, by regulating crucial proteins that control neurite
elaboration (69), translation in synapses (70, 71), and ion channel
subunits (72). conserved species, (ii) predicted to retain conserved secondary
structures, and (iii) preferentially adjacent to protein-coding
genes involved in neuronal differentiation and function (54). Overall, these findings indicate that brain-specific lncRNAs likely
possess conserved functions and are crucially implicated in
higher-order cognitive abilities as well as in establishing neural
cell-type diversity and function. This hypothesis is sustained by
their spatiotemporal expression, which is exquisitely regulated
during NS development (55) and in response to neuronal
activity (56). So far, a growing body of literature shows that
lncRNAs influence every step of neurodevelopment, from early
stages of differentiation to synaptogenesis (57–59). Frontiers in Pediatrics | www.frontiersin.org LNCRNAS IN
NEURO-ONCOLOGICAL DISORDERS Based on their crucial role in NS development and function,
lncRNA
qualitative
and/or
quantitative
alterations
may
profoundly
impact
on
different
neurological
pathologies,
including
neurodevelopmental,
neurodegenerative,
neuro-
immunological, and neuro-oncological disorders (73, 74). In
the latter settings, lncRNAs have drawn extensive attention
as molecules that may drive tumorigenesis. In addition, they
can serve as predictors of cancer sub-types as well as potential
therapeutic targets. Mechanistic insights into the role of lncRNAs in MB
biology have been carried out only for a very few species, as
discussed below. Mechanisms of Action of lncRNAs in Mb Mechanisms of Action of lncRNAs in Mb
The colon cancer upregulated transcript CCAT1 (104) is
a prototype of oncogenic lncRNA, associated with several
carcinomas, where it promotes cell proliferation, invasion,
migration, and chemoresistence (105–107). In MB, its expression
is upregulated in 20 unstratified tumor samples and also in at
least four MB cell lines (108). CCAT1 knockdown in MB cells
causes the decrease of cell proliferation rate, (depending on
CCNA and CDK2 gene repression), cell migration, and invasion. Its in vivo depletion reduces the volume of subcutaneous tumors
of xenotransplanted mice (108). CCAT1 has been proposed to
play its oncogenic role by altering the phosphorylated, active
status of components of the tumorigenic MAPK pathway. In combination with previous reports indicating CCAT1 as a
miRNA sponge (109–111), this study suggests that CCAT1 may
control tumorigenesis through multiple activities. It is widely understood that mutations, epigenetic alterations
or somatic copy number aberrations in the noncoding portion
of the genome underlie cancer pathology (75). Accordingly,
recent studies indicated that lncRNAs are highly deregulated
in cancer, where they participate as tumor-suppressors or
oncogenes in tumor initiation and progression. Notably, most
lncRNAs displaying aberrant expression are cancer-type unique
(76). However, despite the identification of a large number
of lncRNAs in neurological cancers, only for a few of them
mechanisms of action have been experimentally clarified. Extensive studies have been carried out in gliomas, the most
prevalent types of primary intracranial carcinoma (77). Several
lncRNAs associated with glioma stemness (78–80), proliferation,
and migration (81–84) have been identified, and most of them
function as miRNA decoys (81). March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 4 Long Noncoding RNAs in Medulloblastoma Laneve et al. FIGURE 2 | Linc-NeD125-based network in MB. (A) MiR-19a-3p, miR-19b-3p, and miR-106a-5p pleiotropically control KDM6A, MYCN, CDK6, SNCAIP gene
expression. (B) In G4 MB, linc-NeD125 is upregulated and, functioning as a decoy for the three miRNAs, causes translational derepression of the G4 MB driver genes
KDM6A, MYCN, CDK6, SNCAIP. FIGURE 2 | Linc-NeD125-based network in MB. (A) MiR-19a-3p, miR-19b-3p, and miR-106a-5p pleiotropically control KDM6A, MYCN, CDK6, SNCAIP gene
expression. (B) In G4 MB, linc-NeD125 is upregulated and, functioning as a decoy for the three miRNAs, causes translational derepression of the G4 MB driver genes
KDM6A, MYCN, CDK6, SNCAIP. Mechanisms of Action of lncRNAs in Mb Another lncRNA implicated in MB is ANRIL (112), which
plays a pivotal role in multiple cancers as an epigenetic
regulator
of
its
neighbor
tumor-suppressors
CDKN2A/B
(113, 114). ANRIL expression is upregulated in MB cells,
where its knockdown lowers cell viability and migration
while increasing apoptosis, by deranging the expression of
several apoptotic factors (115). ANRIL has been shown to
act as a decoy for miR-323, a miRNA identified in neurons
(116)
and
characterized
as
a
glioma
tumor-suppressor
(117,
118). Consistently,
miR-323
silencing
counteracted
the
abovementioned
ANRIL-dependent
cell
phenotypes. This regulative axis impinges on BRI3, a miR-323 target
gene (119) encoding for a brain-expressed transmembrane
factor (120). BRI3 activates MAPK, AKT and WNT signaling
cascades, already associated with MB progression (121–123),
through a double mechanism: BRI3 upregulation enhances
the phosphorylation of p38, MAPK, ERK, and AKT kinases
and stimulates the accumulation of Wnt3a, Wnt5a, and β-
catenin. The dysregulation of such pathways may partially
explain the apoptotic phenotypes observed upon imbalance of
ANRIL/miR-323/BRI3 module (115). Recently, the ceRNA mechanism has emerged as a crucial
pathogenic pathway in MB. Linc-NeD125 was the first ceRNA
identified in MB and, generally, in tumors of the CNS (49). It was identified in NB cells as the precursor of miR-125-b1
(126), a neuronal-enriched miRNA (127) involved in neural
cell differentiation (128), function (129) and NB and MB cell
proliferation, and apoptosis (130, 131). Notably, linc-Ned125 is
significantly and specifically upregulated in primary G4 MBs,
compared to the other subgroups. In this context, it functions
as a miRNA decoy. Linc-NeD125 interacts with miR-19a-3p,
miR-19b-3p, and miR-106a-5p that pleiotropically control the
expression of four G4 MB driver genes, namely KDM6A, MYCN,
CDK6, and SNCAIP (7) (Figure 2). Through this mechanism,
linc-NeD125 causes the driver gene translational de-repression,
contributing to G4 MB tumorigenesis and/or to the maintenance
of cancer cell identity. This study highlighted linc-NeD125 as a
novel potential G4 driver gene, as well as a specific biomarker and
a potential therapeutic target. Accordingly, its knockdown in G4-
derived cells caused a significant reduction of cell proliferation,
migration, and invasion (49). The second example of ceRNA in MB is the lncRNA Nkx2-
2as, that behaves as a tumor-suppressor in SHH MB subgroup. It is highly down-regulated in MB cells derived from a SHH
mouse model and it suppresses the malignant phenotype of MB
cells, functioning as a sponge for miR-103/107 and miR-548 m. Frontiers in Pediatrics | www.frontiersin.org REFERENCES 12. Ballarino M, Morlando M, Fatica A, Bozzoni I. Non-coding RNAs in muscle
differentiation and musculoskeletal disease. J Clin Invest. (2016) 126:2021–
30. doi: 10.1172/JCI84419 1. Ivanov DP, Coyle B, Walker DA, Grabowska AM. In vitro models of
medulloblastoma: choosing the right tool for the job. J Biotechnol. (2016)
236:10–25. doi: 10.1016/j.jbiotec.2016.07.028 13. Brenner S, Jacob F, Meselson M. An unstable intermediate carrying
information from genes to ribosomes for protein synthesis. Nature. (1961)
190:576–81. doi: 10.1038/190576a0 2. Ferlay J, Soerjomataram I, Ervik M, Dikshit R, Eser S, Mathers C, et al. GLOBOCAN 2012 v1.0, Cancer Incidence and Mortality Worldwide: IARC
CancerBase No. 11. Lyon (2013) 14. Jacob F, Monod J. Genetic regulatory mechanisms in the synthesis
of proteins. J Mol Biol. (1961) 3:318–56. doi: 10.1016/S0022-2836(61)
80072-7 3. Taylor MD, Northcott PA, Korshunov A, Remke M, Cho YJ, Clifford SC,
et al. Molecular subgroups of medulloblastoma: the current consensus. Acta
Neuropathol. (2012) 123:465–72. doi: 10.1007/s00401-011-0922-z 15. Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR. Self-splicing RNA: autoexcision and autocyclization of the ribosomal
RNA intervening sequence of Tetrahymena. Cell. (1982) 31:147–57. doi: 10.1016/0092-8674(82)90414-7 4. Louis DN, Ohgaki H, Wiestler OD, Cavenee WK. World Health Organization
Histological Classification of Tumours of the Central Nervous System. Lyon:
IARC (2007). 16. Brannan CI, Dees EC, Ingram RS, Tilghman, SM. The product of the
H19 gene may function as an RNA. Mol Cell Biol. (1990) 10:28–36. doi: 10.1128/MCB.10.1.28 5. Louis DN, Perry A, Reifenberger G, von Deimling A, Figarella-Branger D,
Cavenee WK, et al. The 2016 World Health Organization classification of
tumors of the central nervous system: a summary. Acta Neuropathol. (2016)
131:803–20. doi: 10.1007/s00401-016-1545-1 17. Gabory A, Jammes H, Dandolo L. The H19 locus: role of an im- printed
non-coding RNA in growth and development. Bioessays. (2010) 32:473–80. doi: 10.1002/bies.200900170 6. Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T,
et al. Subgroup-specific structural variation across 1,000 medulloblastoma
genomes. Nature. (2012) 488:49–56. doi: 10.1038/nature11327 18. Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R,
et al. A gene from the region of the human X inactivation centre is expressed
exclusively from the inactive X chromosome. Nature. (1991) 349:38–44. doi: 10.1038/349038a0 7. Northcott PA, Jones DT, Kool M, Robinson GW, Gilbertson RJ, Cho YJ,
et al. Medulloblastomics: the end of the beginning. Nat Rev Cancer. (2012)
12:818–34.doi: 10.1038/nrc3410 19. Pontier DB, Gribnau, J. Mechanisms of Action of lncRNAs in Mb This activity causes the depression of the tumor-suppressor genes
BTG2/Tis21/PC3 and LATS1/2, promoting tumor growth in vitro
and in vivo (132). More recently, the lncRNA LOXL1-AS1, the antisense
transcript to the LOXL1 genomic locus, whose variants are
strongly associated with the exfoliation syndrome (124), was
found to be overexpressed in MB tissues. In vitro and
in vivo experiments revealed that it controls cell viability,
proliferation, cell cycle, and metastasis by activating the PI3K-
AKT pathway (125). March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 5 Long Noncoding RNAs in Medulloblastoma Laneve et al. FUTURE DIRECTIONS and cerebrospinal fluids, making the tumor diagnosis less
invasive (75). Notably, lncRNAs are also considered new relevant
targets for cancer therapy as highly tissue-specific drivers of
cancer phenotypes. Finally, in this search for lncRNAs as novel
molecules that distinguish clinically relevant cancer subtypes and
predict tumor behavior, the circular RNAs are proving to be
effective cancer biomarkers for their abundance, stability, and
specificity (135). The main challenges in fighting cancer are the identification
of specific biomarkers, for timely diagnosis and prognosis,
and novel tumor-driver genes, which can be therapeutically
targeted for suppressing tumor growth. The former function
would help the choice of pre-operative treatments and facilitate
the tumor follow-up examinations. Unfortunately, very few
biomarkers are known for pediatric tumors (133) and in MB
<20 protein-coding genes have been characterized as promising
candidates. However, most of these biomarkers were identified
from single studies and from heterogeneous tumor types,
lacking tumor-specificity (133). The recent categorization of
MB into at least four subtypes, with distinct features, led
the scientists to consider them as distinct pathologies with
likely different responses to therapy. This new perspective
triggered the search for novel MB-subgroup specific biomarkers
and therapeutic targets. For both issues lncRNAs are very
challenging (75). Since many of them are uniquely expressed
in specific cancer types, they may function as powerful cancer
biomarkers (134). In addition, for their ability to fold into
complex tridimensional structures that increase their stability,
they can be easily detected into body fluids as urine, blood, FUNDING This work was partially supported by a grant from the Epigen-
Epigenomics Flagship Project to EC. This work was partially supported by a grant from the Epigen-
Epigenomics Flagship Project to EC. ACKNOWLEDGMENTS We apologize to colleagues whose work was not discussed or cited
in this review due to the space limitation. AUTHOR CONTRIBUTIONS PL and EC reviewed the literature and wrote the manuscript. JR
prepared the figures and contributed to the text discussion. REFERENCES Xist regulation and function explored. Hum Genet. (2011) 130:223–36. doi: 10.1007/s00439-011-1008-7 8. Wang J, Garancher A, Ramaswamy V, Wechsler-Reya RJ. Medulloblastoma:
from molecular subgroups to molecular targeted therapies. Annu Rev
Neurosci. (2018) 41:207–32. doi: 10.1146/annurev-neuro-070815-013838 20. Qu S, Yang X, Li X, Wang J, Gao Y, Shang R, et al. Circular
RNA: a new star of noncoding RNAs. Cancer Lett. (2015) 365:141–8. doi: 10.1016/j.canlet.2015.06.003 9. Cavalli FMG, Remke M, Rampasek L, Peacock J, Shih DJH, Luu B, et al. Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell. (2017) 31:737–54.e6. doi: 10.1016/j.ccell.2017.05.005 21. Engreit JM, Ollikainen N, Guttman M. Long non-coding RNAs: spatial
amplifiers that control nuclear structure and gene expression. Nat Rev Mol
Cell Biol. (2016) 17:756–70. doi: 10.1038/nrm.2016.126 10. Kool M, Korshunov A, Remke M, Jones DT, Schlanstein M, Northcott PA. Molecular subgroups of medulloblastoma: an international meta-analysis of
transcriptome, genetic aberrations, and clinical data of WNT, SHH, Group
3, and Group 4 medulloblastomas. Acta Neuropathol. (2012) 123:473–84. doi: 10.1007/s00401-012-0958-8 22. Shen
H,
Laird
PW. Interplay
between
the
cancer
genome
and
epigenome. Cell. (2013)
153:38–55. doi:
10.1016/j.cell.2013. 03.008 23. Lee
JT,
Bartolomei
MS. X-inactivation,
imprinting,
and
long
noncoding RNAs in health and disease. Cell. (2013) 152:1308–23. doi: 10.1016/j.cell.2013.02.016 11. Pyle
AM. Rediscovering
RNA. RNA. (2015)
21:714–5. doi: 10.1261/rna.050807.115 March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 6 Long Noncoding RNAs in Medulloblastoma Laneve et al. 24. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, et al. Long
noncoding RNA HOTAIR reprograms chromatin state to promote cancer
metastasis. Nature. (2010) 464:1071–6. doi: 10.1038/nature08975 of
miR-301a in
esophageal
cancer. Oncol
Res. (2018) 26:1285–94. doi: 10.3727/096504018X15166193231711 of
miR-301a in
esophageal
cancer. Oncol
Res. (2018) 26:1285–94. doi: 10.3727/096504018X15166193231711 46. Fu Z, Li G, Li Z, Wang Y, Zhao Y, Zheng S, et al. Endogenous miRNA
Sponge LincRNA-ROR promotes proliferation, invasion and stem cell-like
phenotype of pancreatic cancer cells. Cell Death Discov. (2017) 3:17004. doi: 10.1038/cddiscovery.2017.4 25. Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, et al. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin
modification and is associated with poor prognosis in colorectal cancers. Cancer Res. (2011) 71:6320–6. doi: 10.1158/0008-5472.CAN-11-1021 47. Wang L, Yu X, Zhang Z, Pang L, Xu J, Jiang J, et al. Linc-
ROR promotes esophageal squamous cell carcinoma progression through
the derepression of SOX9. J Exp Clin Cancer Res. (2017) 36:182. doi: 10.1186/s13046-017-0658-2 26. REFERENCES Zhang J, Zhang P, Wang L, Piao HL, Ma L. Long noncoding RNA HOTAIR
in carcinogenesis and metastasis. Acta Biochim Biophys Sin. (2014) 46:1–5. doi: 10.1093/abbs/gmt117 27. Hu P, Chu J, Wu Y, Sun L, Lv X, Zhu Y, et al. NBAT1 suppresses breast cancer
metastasis by regulating DKK1 via PRC2. Oncotarget. (2015) 6:32410–25. doi: 10.18632/oncotarget.5609 48. Li H, Wang X, Wen C, Huo Z, Wang W, Zhan Q, et al. Long
noncoding
RNA
NORAD,
a
novel
competing
endogenous
RNA,
enhances
the
hypoxia-induced
epithelial-mesenchymal
transition
to
promote metastasis in pancreatic cancer. Mol Cancer. (2017) 16:169. doi: 10.1186/s12943-017-0738-0 28. Marin-Bejar O, Mas AM, González J, Martinez D, Athie A, Morales
X, et al. The human lncRNA LINC-PINT inhibits tumor cell invasion
through a highly conserved sequence element. Genome Biol. (2017) 18:202. doi: 10.1186/s13059-017-1331-y 49. Laneve P, Po A, Favia A, Legnini I, Alfano V, Rea J, et al. The long
noncoding RNA linc-NeD125 controls the expression of medulloblastoma
driver genes by microRNA sponge activity. Oncotarget. (2017) 8:31003–15. doi: 10.18632/oncotarget.16049 29. Morlando M, Fatica A. Alteration of epigenetic regulation by long noncoding
RNAs in cancer. Int J Mol Sci. (2018) 19:pii: E570. doi: 10.3390/ijms19020570 50. Anderson DM, Anderson KM, Chang CL, Makarewich CA, Nelson
BR, McAnally JR, et al. A micropeptide encoded by a putative long
noncoding RNA regulates muscle performance. Cell. (2015) 160:595–606. doi: 10.1016/j.cell.2015.01.009 30. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into
functions. Nat Rev Genet. (2009) 10:155–9. doi: 10.1038/nrg2521 31. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, et al. The
GENCODE v7 catalog of human long noncoding RNAs: analysis of their
gene structure, evolution, and expression. Genome Res. (2012) 22:1775–89. doi: 10.1101/gr.132159.111 51. Clark
BS,
Blackshaw
S. Understanding
the
role
of
lncRNAs
in
nervous system development. Adv Exp Med Biol. (2017) 1008:253–82. doi: 10.1007/978-981-10-5203-3_9 32. Mousavi K, Zare H, Dell’orso
S, Grontved
L, Gutierrez-Cruz G,
Derfoul A, et al. eRNAs promote transcription by establishing chromatin
accessibility
at
defined
genomic
loci. Mol
Cell. (2013)
51:606–17. doi: 10.1016/j.molcel.2013.07.022 52. Qureshi IA, Mehler MF. Non-coding RNA networks underlying cognitive
disorders across the lifespan. Trends
Mol
Med. (2011) 17:337–46. doi: 10.1016/j.molmed.2011.02.002. j
33. Mousavi K, Zare H, Koulnis M, Sartorelli V. The emerging roles of
eRNAs in transcriptional regulatory networks. RNA Biol. (2014) 11:106–10. doi: 10.4161/rna.27950 j
53. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. REFERENCES Specific
expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci
USA. (2008) 105:716–21. doi: 10.1073/pnas.0706729105 54. Ponjavic
J,
Oliver
PL,
Lunter
G,
Ponting
CP. Genomic
and
transcriptional co-localization of protein-coding and long non-coding
RNA pairs in the developing brain. PLoS Genet. (2009) 5:e1000617. doi: 10.1371/journal.pgen.1000617 34. Hacisuleyman E, GoffLA, Trapnell C, Williams A, Henao-Mejia J, Sun L,
et al. Topological organization of multichromosomal regions by the long
intergenic noncoding RNA Firre. Nat Struct Mol Biol. (2014) 21:198–206. doi: 10.1038/nsmb.2764 35. Rinn J, Guttman M. RNA and dynamic nuclear organization. Long
noncoding RNAs may function as organizing factors that shape the cell
nucleus. Science. (2014) 12: 345:1240–1.doi: 10.1126/science.1252966 55. Luo H, Sun S, Li P, Bu D, Cao H, Zhao Y. Comprehensive characterization of
10,571 mouse large intergenic noncoding RNAs from whole transcriptome
sequencing. PLoS
ONE. (2013) 8:e70835. doi:
10.1371/journal.pone. 0070835 36. Romero-Barrios N, Legascue MF, Benhamed M, Ariel F, Crespi M. Splicing
regulation by long noncoding RNAs. Nucleic Acids Res. (2018) 46:2169–84. doi: 10.1093/nar/gky095 56. Barry G, Briggs JA, Vanichkina DP, Poth EM, Beveridge NJ, Ratnu, et al. The
long non- coding RNA Gomafu is acutely regulated in response to neuronal
activation and involved in schizophrenia-associated alternative splicing. Mol
Psychiatry. (2014) 19:486–94. doi: 10.1038/mp.2013.45. 37. Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE,
et al. Expression of a noncoding RNA is elevated in Alzheimer’s disease
and drives rapid feed-forward regulation of β-secretase. Nat Med. (2008)
14:723–30. doi: 10.1038/nm1784 57. Knauss J, Sun T. Regulatory mechanisms of long noncoding RNAs in
vertebrate central nervous system development and function. Neuroscience. (2013) 235:200–14. doi: 10.1016/j.neuroscience 38. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, et al. Control
of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. (2013) 493:231–5. doi: 10.1038/nature11661 58. Briggs JA, Wolvetang EJ, Mattick JS, Rinn JL, Barry G. Mechanisms of
long non-coding RNAs in mammalian nervous system development,
plasticity,
disease,
and
evolution. Neuron. (2015)
88:861–77. doi: 10.1016/j.neuron.2015.09.045 39. Gong C, Maquat LE. lncRNAs transactivate STAU1-mediated mRNA decay
by duplexing with 3
′ UTRs via Alu elements. Nature. (2011) 470:284–8. doi: 10.1038/nature09701 59. Quan Z, Zheng D, Qing H. Regulatory roles of long non-coding RNAs in the
central nervous system and associated neurodegenerative diseases. Front Cell
Neurosci. (2017) 11:175. doi: 10.3389/fncel.2017.00175 40. Yoon JH, Abdelmohsen K, Srikantan S, Yang X, Martindale JL, De S,
et al. REFERENCES In: Lanzkowsky P, Lipton J, Fish
J, editors. Manual of Pediatric Hematology and Oncology., 6th ed. Academic
Press (2016) p. 1054–8. 66. Bond AM, Vangompel MJ, Sametsky EA, Clark MF, Savage JC, Disterhoft
JF, et al. Balanced gene regulation by an embryonic brain ncRNA is critical
for adult hippocampal GABA circuitry. Nat Neurosci. (2009) 12:1020–7. doi: 10.1038/nn.2371 86. Pandey GK, Kanduri C. Long noncoding RNAs and neuroblastoma. Oncotarget. (2015) 6:18265–75. doi: 10.18632/oncotarget.4251 87. Pandey GK, Mitra S, Subhash S, Hertwig F, Kanduri M, Mishra K, et al. The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma
progression by regulating cell proliferation and neuronal differentiation. Cancer Cell. (2014) 26:722–37. doi: 10.1016/j.ccell.2014.09.014 67. Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz CC,
et al. The long noncoding RNA Pnky regulates neuronal differentiation of
embryonic and postnatal neural stem cells. Cell Stem Cell. (2015) 16:439–47. doi: 10.1016/j.stem.2015.02.007 88. Buechner J, Einvik C. N-myc and noncoding RNAs in neuroblastoma. Mol
Cancer Res. (2012) 10:1243–53. doi: 10.1158/1541-7786.MCR-12-0244 68. Sauvageau M, GoffLA, Lodato S, Bonev B, GroffAF, Gerhardinger C, et al. Multiple knockout mouse models reveal lincRNAs are required for life and
brain development. Elife. (2013) 2:e01749. doi: 10.7554/eLife.01749. 89. Castelnuovo M, Massone S, Tasso R, Fiorino G, Gatti M, Robello
M, et al. An Alu-like RNA promotes cell differentiation and reduces
malignancy of human neuroblastoma cells. FASEB J. (2010) 24:4033–46. doi: 10.1096/fj.10-157032 69. Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M,
Brothers SP, et al. Inhibition of natural antisense transcripts in vivo results in
gene-specific transcriptional upre- gulation. Nat Biotechnol. (2012) 30:453–9. doi: 10.1038/nbt.2158. 90. Liu PY, Erriquez D, Marshall GM, Tee AE, Polly P, Wong M, et al. Effects of a novel long noncoding RNA, lncUSMycN, on N-Myc expression
and neuroblastoma progression. J Natl Cancer Inst. (2014) 106:dju113. doi: 10.1093/jnci/dju113 70. Wang H, Iacoangeli A, Popp S, Muslimov IA, Imataka H, Sonenberg N, et al. Dendritic BC1 RNA: functional role in regulation of translation initiation. J
Neurosci. (2002) 22:10232–41. doi: 10.1523/JNEUROSCI.22-23-10232.2002 91. Atmadibrata B, Liu PY, Sokolowski N, Zhang L, Wong M, Tee
AE, et al. The novel long noncoding RNA linc00467 promotes cell
survival but is down-regulated by N-Myc. PLoS ONE. (2014) 9:e88112. doi: 10.1371/journal.pone.0088112 71. Zalfa F, Giorgi M, Primerano B, Moro A, Di Penta A, Reis S, et al. REFERENCES LincRNA-p21 suppresses target mRNA translation. Mol Cell. (2012)
47:648–55. doi: 10.1016/j.molcel.2012.06.027 60. Ng SY, Bogu GK, Soh BS, Stanton LW. The long noncod- ing RNA RMST
interacts with SOX2 to regulate neurogenesis. Mol Cell. (2013) 51:349–59. doi: 10.1016/j.molcel.2013.07.017 41. Jens M, Rajewsky N. Competition between target sites of regulators shapes
post-transcriptional gene regulation. Nat Rev Genet. (2015) 16:113–26. doi: 10.1038/nrg3853 61. Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, et al. An
evolutionarily
conserved
long
noncoding
RNA
TUNA
controls
pluripotency and neural lineage commitment. Mol Cell. (2014) 53:1005–19. doi: 10.1016/j.molcel.2014.01.021 g
42. Tay Y, Rinn J, PandolfiPP. The multilayered complexity of ceRNA crosstalk
and competition. Nature. (2014) 505:344–52. doi: 10.1038/nature12986 43. Yang C, Wu D, Gao L, Liu X, Jin Y, Wang D, et al. Competing endogenous
RNA networks in human cancer: hypothesis, validation, and perspectives. Oncotarget. (2016) 7:13479–90. doi: 10.18632/oncotarget.7266 62. Chalei V, Sansom SN, Kong L, Lee S, Montiel JF, Vance KW, et al. The long
non-coding RNA Dali is an epigenetic regulator of neural differentiation. Elife. (2014) 3:e04530. doi: 10.7554/eLife.04530 44. Chan JJ, Tay Y. Noncoding RNA: RNA regulatory networks in cancer. Int J
Mol Sci. (2018) 19:E1310. doi: 10.3390/ijms19051310 63. Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, et al. The long
non-coding RNA Paupar regulates the expression of both local and distal
genes. EMBO J. (2014) 33:296–311. doi: 10.1002/embj.201386225 45. Li W, Zhao W, Lu Z, Zhang W, Yang X. Long non-coding RNA
GAS5 promotes proliferation, migration and invasion by regulation March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 7 Long Noncoding RNAs in Medulloblastoma Laneve et al. 64. Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S. The mRNA-
like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset
of neurons. J Cell Sci. (2007) 120 (Pt 15):2498–506. doi: 10.1242/jcs.009357 RNA
ECONEXIN
on
gliomagenesis. Oncogene. (2017)
36:4629–40. doi: 10.1038/onc.2017.88. 84. Teng H, Wang P, Xue Y, Liu X, Ma J, Cai H, et al. Role of HCP5-miR-139-
RUNX1 feedback loop in regulating malignant behavior of glioma cells. Mol
Ther. (2016) 24:1806–22. doi: 10.1038/mt.2016.103 65. Tsuiji H, Yoshimoto R, Hasegawa Y, Furuno M, Yoshida M, Nakagawa
S. Competition between a noncoding exon and introns: gomafu contains
tandem UACUAAC repeats and associates with splicing factor-1. Genes Cells. (2011) 16:479–90. doi: 10.1111/j.1365-2443.2011.01502.x 85. Lanzkowsky P. Chapter 24: Neuroblastoma. REFERENCES The
fragile X syndrome protein FMRP associates with BC1 RNA and regulates
the translation of specific mRNAs at synapses. Cell. (2003) 112:317–27. doi: 10.1016/S0092-8674(03)00079-5 92. ScaruffiP, Stigliani S, Moretti S, Coco S, De Vecchi C, Valdora
F, et al. Transcribed-ultra conserved region expression is associated
with outcome in high-risk neuroblastoma. BMC Cancer. (2009) 9:441. doi: 10.1186/1471-2407-9-441 72. Zhao X, Tang Z, Zhang H, Atianjoh FE, Zhao JY, Liang L, et al. A long noncoding RNA contributes to neuropathic pain by silencing
Kcna2 in primary afferent neurons. Nat. Neurosci. (2013) 16:1024–31. doi: 10.1038/nn.3438 93. Chen YD, Zhang N, Qiu XG, Yuan J, Yang M. LncRNA CDKN2BAS
rs2157719 genetic variant contributes to medulloblastoma predisposition. J
Gene Med. (2018) 20:e300. doi: 10.1002/jgm.3000 73. Qureshi
IA,
Mattick
JS,
Mehler
MF. Long
non-coding
RNAs
in
nervous system function and disease. Brain Res. (2010) 1338:20–35. doi: 10.1016/j.brainres.2010.03.110 94. Xu C, Qi R, Ping Y, Li J, Zhao H, Wang L, et al. Systemically identifying
and prioritizing risk lncRNAs through integration of pan-cancer phenotype
associations. Oncotarget. (2017) 8:12041–51. doi: 10.18632/oncotarget.14510 74. Chen Y, Zhou J. LncRNAs: macromolecules with big roles in neurobiology
and
neurological
diseases. Metab
Brain
Dis. (2017)
32:281–91. doi: 10.1007/s11011-017-9965-8 95. Shtivelman E, Bishop JM. The PVT gene frequently amplifies with MYC in
tumor cells. Mol Cell Biol. (1989) 9:1148–54. doi: 10.1128/MCB.9.3.1148 75. Schmitt AM, Chang HY. Long noncoding RNAs in cancer pathways. Cancer
Cell. (2016) 29:452–463. doi: 10.1016/j.ccell.2016.03.010 96. Carramusa L, Contino F, Ferro A, Minafra L, Perconti G, Giallongo A,
et al. The PVT-1 oncogene is a Myc protein target that is overexpressed in
transformed cells. J Cell Physiol. (2007) 213:511–8. doi: 10.1002/jcp.21133 76. Yan X, Hu Z, Feng Y, Hu X, Yuan J, Zhao SD, et al. Comprehensive genomic
characterization of long non-coding RNAs across human cancers. Cancer
Cell. (2015) 28:529–40. doi: 10.1016/j.ccell.2015.09.006 97. Xiao C, Wu CH, Hu HZ. LncRNA UCA1 promotes epithelial-mesenchymal
transition (EMT) of breast cancer cells via enhancing Wnt/beta-catenin
signaling pathway. Eur Rev Med Pharmacol Sci. (2016) 20:2819–24. j
77. Peng Z, Liu C, Wu M. New insights into long noncoding RNAs and their
roles in glioma. Mol Cancer. (2018) 17:61. doi: 10.1186/s12943-018-0812-2 98. Graham LD, Pedersen SK, Brown GS, Ho T, Kassir Z, Moynhian AT, et al. Colorectal neoplasia differentially expressed (CRNDE), a novel gene with
elevated expression in colorectal adenomas and adenocarcinomas. Genes
Cancer. (2011) 2:829–40. doi: 10.1177/1947601911431081 78. REFERENCES doi: 10.1016/j.cancergen.2014.05.014 rhabdoid tumors and other pediatric brain tumors. Cancer Genet. (2014)
207:425–8. doi: 10.1016/j.cancergen.2014.05.014 104. Nissan A, Stojadinovic A, Mitrani-Rosenbaum S, Halle D, Grinbaum R,
Roistacher M, et al. Colon cancer associated transcript-1: a novel RNA
expressed in malignant and pre-malignant human tissues. Int J Cancer. (2012) 130:1598–606. doi: 10.1002/ijc.26170 121. Guldal CG, Ahmad A, Korshunov A, Squatrito M, Awan A, Mainwaring
LA, et al. An essential role for p38 MAPK in cerebellar granule
neuron precursor proliferation. Acta Neuropathol. (2012) 123:573–86. doi: 10.1007/s00401-012-0946-z 122. Włodarski P, Grajkowska W, Łojek M, Rainko K, Józwiak J. Activation of Akt
and Erk pathways in medulloblastoma. Folia Neuropathol. (2006) 44:214–20. 105. Chen J, Zhang K, Song H, Wang R, Chu X, Chen L. Long noncoding
RNA CCAT1 acts as an oncogene and promotes chemoresistance in
docetaxel-resistant lung adenocarcinoma cells. Oncotarget. (2016) 7:62474–
89. doi: 10.18632/oncotarget.11518 123. Snyder EY, Deitcher DL, Walsh C, Arnold-Aldea S, Hartwieg EA,
Cepko CL. Multipotent neural cell lines can engraft and participate
in
development
of
mouse
cerebellum. Cell. (1992)
68:33–51. doi: 10.1016/0092-8674(92)90204-P 106. Ma X, Sheng S, Wu J, Jiang Y, Gao X, Cen X, et al. LncRNAs as
an intermediate in HPV16 promoting myeloid-derived suppressor cell
recruitment of head and neck squamous cell carcinoma. Oncotarget. (2017)
8:42061–75. doi: 10.18632/oncotarget.14939 124. Hauser MA, Aboobakar IF, Liu Y, Miura S, Whigham BT, Challa P, et al. Genetic variants and cellular stressors associated with exfoliation syndrome
modulate promoter activity of a lncRNA within the LOXL1 locus. Hum Mol
Genet. (2015) 24:6552–63. doi: 10.1093/hmg/ddv347 107. Zhang E, Han L, Yin D, He X, Hong L, Si X, et al. H3K27 acetylation
activated-long non-coding RNA CCAT1 affects cell proliferation and
migration by regulating SPRY4 and HOXB13 expression in esophageal
squamous
cell
carcinoma. Nucleic
Acids
Res. (2017)
45:3086–101. doi: 10.1093/nar/gkw1247 125. Gao R, Zhang R, Zhang C, Liang W, Tang W. LncRNA LOXL1-
AS1 promotes the proliferation and metastasis of medulloblastoma by
activating the PI3K/AKT pathway. Anal Cell Pathol. (2018) 2018:9275685. doi: 10.1155/2018/9275685. 108. Gao R, Zhang R, Zhang C, Zhao L, Zhang Y. Long noncoding RNA CCAT1
promotes cell proliferation and metastasis in human medulloblastoma via
MAPK pathway. Tumori J. (2018) 104:43–50. doi: 10.5301/tj.5000662 126. Bevilacqua V, Gioia U, Di Carlo V, Tortorelli AF, Colombo T, Bozzoni I, et al. Identification of linc-NeD125, a novel long non coding RNA that hosts miR-
125b-1 and negatively controls proliferation of human neuroblastoma cells. RNA Biol. REFERENCES (2015) 12:1323–37. doi: 10.1080/15476286.2015.1096488 109. Chen L, Wang W, Cao L, Li Z, Wang X. Long non-coding RNA
CCAT1 acts as a competing endogenous RNA to regulate cell growth
and differentiation in acute myeloid leukemia. Mol Cells. (2016) 39:330–6. doi: 10.14348/molcells.2016.2308 127. Smirnova L, Gräfe A, Seiler A, Schumacher S, Nitsch R, Wulczyn FG. Regulation of miRNA expression during neural cell specification. Eur J
Neurosci. (2005) 21:1469–77. doi: 10.1111/j.1460-9568.2005.03978.x 110. Wang ZH, Guo XQ, Zhang QS, Zhang JL, Duan YL, Li GF, et al. Long non-coding RNA CCAT1 promotes glioma cell proliferation via
inhibiting microRNA-410. Biochem Biophys Res Commun. (2016) 480:715–
20. doi: 10.1016/j.bbrc.2016.10.047 128. Boissart C, Nissan X, Giraud-Triboult K, Peschanski M, Benchoua A. MiR-
125 potentiates early neural specification of human embryonic stem cells. Development. (2012) 139:1247–57. doi: 10.1242/dev.073627 129. Akerblom M, Petri R, Sachdeva R, Klussendorf T, Mattsson B, Gentner
B, et al. MicroRNA-125 distinguishes developmentally generated and
adult-born olfactory bulb interneurons. Development. (2014) 141:1580–8. doi: 10.1242/dev.101659 111. Zhou B, Wang Y, Jiang J, Jiang H, Song J, Han T, et al. The long noncoding
RNA colon cancer-associated transcript-1/miR-490 axis regulates gastric
cancer cell migration by targeting hnRNPA1. IUBMB Life. (2016) 68:201–10. doi: 10.1002/iub.1474 130. Laneve P, Di Marcotullio L, Gioia U, Fiori ME, Ferretti E, Gulino A, et al. The
interplay between microRNAs and the neurotrophin receptor tropomyosin-
related kinase C controls proliferation of human neuroblastoma cells. Proc Natl Acad Sci USA. (2007) 104:7957–62. doi: 10.1073/pnas.0700
071104 112. Pasmant E, Laurendeau I, Héron D, Vidaud M, Vidaud D, Bièche I. Characterization of a germ-line deletion, including the entire INK4/ARF
locus, in a melanoma-neural system tumor family: identification of ANRIL,
an antisense noncoding RNA whose expression coclusters with ARF. Cancer
Res. (2007) 67:3963–9. doi: 10.1158/0008-5472.CAN-06-2004 131. Ferretti E, De Smaele E, Po A, Di Marcotullio L, Tosi E, Espinola MS,
et al. MicroRNA profiling in human medulloblastoma. Int J Cancer. (2009)
124:568–77. doi: 10.1002/ijc.23948 113. Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, et al. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and
silencing of p15INK4B tumor suppressor gene. Oncogene. (2011) 30:1956–
62. doi: 10.1038/onc.2010.568 132. Zhang
Y,
Wang
T,
Wang
S,
Xiong
Y,
Zhang
R,
Zhang
X,
et
al. Nkx2-2as
suppression
contributes
to
the
pathogenesis
of
Sonic
hedgehog
medulloblastoma. Cancer
Res. (2018)
78:962–73. doi: 10.1158/0008-5472.CAN-17-1631. 114. REFERENCES Yap KL, Li S, Muñoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone
H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol
Cell. (2010) 38:662–74. doi: 10.1016/j.molcel.2010.03.021 133. Russell MD, Young AM, Karri SK. Biomarkers of pediatric brain tumors. Front Pediatr. (2013) 1:7. doi: 10.3389/fped.2013.00007 115. Zhang H, Wang X, Chen X. Potential role of long non-coding RNA
ANRIL in pediatric medulloblastoma through promotion on proliferation
and migration by targeting miR-323. J Cell Biochem. (2017) 118:4735–44. doi: 10.1002/jcb.26141 134. Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, et al. The
landscape of long noncoding RNAs in the human transcriptome. Nat Genet. (2015) 47:199–208. doi: 10.1038/ng.3192 116. Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, et al. Identification of many microRNAs that copurify with polyribosomes
in mammalian neurons. Proc Natl Acad Sci USA. (2004) 101:360–5. doi: 10.1073/pnas.2333854100 135. Kristensen LS, Hansen TB, Venø MT, Kjems J. Circular RNAs in cancer:
opportunities and challenges in the field. Oncogene. (2018) 37:555–65. doi: 10.1038/onc.2017.361 117. Lavon I, Zrihan D, Granit A, Einstein O, Fainstein N, Cohen MA,
et al. Gliomas display a microRNA expression profile reminiscent of
neural precursor cells. Neuro Oncol. (2010) 12:422–33. doi: 10.1093/neu
onc/nop061 Conflict of Interest Statement: The authors declare that the research was
conducted in the absence of any commercial or financial relationships that could
be construed as a potential conflict of interest. Conflict of Interest Statement: The authors declare that the research was
conducted in the absence of any commercial or financial relationships that could
be construed as a potential conflict of interest. The handling editor declared a past co-authorship with the authors PL and EC. 118. Qiu S, Lin S, Hu D, Feng Y, Tan Y, Peng Y. Interactions of miR-323/miR-
326/miR-329 and miR-130a/miR-155/miR-210 as prognostic indicators for
clinical outcome of glioblastoma patients. J Transl Med. (2013) 11:10. doi: 10.1186/1479-5876-11-10 Copyright © 2019 Laneve, Rea and Caffarelli. This is an open-access article
distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the
original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these
terms. 119. REFERENCES Katsushima K, Natsume A, Ohka F, Shinjo K, Hatanaka A, Ichimura N, et al. Targeting the notch-regulated non-coding RNA TUG1for glioma treatment. Nat Commun. (2016) 7:13616. doi: 10.1038/ncomms13616 79. Zhao
X,
Liu
Y,
Zheng
J,
Liu
X,
Chen
J,
Liu
L,
et
al. GAS5
suppresses malignancy of human glioma stem cells via a miR-196a-
5p/FOXO1 feedback loop. Biochim Biophys Acta. (2017) 1864:1605–17. doi: 10.1016/j.bbamcr.2017.06.020 99. Cabili MN, Trapnell C, GoffL, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals
global properties and specific subclasses. Genes Dev. (2011) 25:1915–27. doi: 10.1101/gad.17446611 80. Yao Y, Ma J, Xue Y, Wang P, Li Z, Liu J, et al. Knockdown of long
non-coding RNA XIST exerts tumor-suppressive functions in human
glioblastoma stem cells by up-regulating miR-152. Cancer Lett. (2015)
359:75–86. doi: 10.1016/j.canlet.2014. 100. Zhengyuan X, Hu X, Qiang W, Nanxiang L, Junbin C, Wangming Z. Silencing of urothelial carcinoma associated 1 inhibits the proliferation and
migration of medulloblastoma cells. Med Sci Monit. (2017) 23:4454–61. doi: 10.12659/MSM.904675 81. Chen Q, Cai J, Wang Q, Wang Y, Liu M, Yang J, et al. Long non-coding
RNA NEAT1, regulated by the EGFR pathway, contributes to glioblastoma
progression through the WNT/beta- catenin pathway by scaffolding EZH2. Clin Cancer Res. (2018) 24:684–95. doi: 10.1158/1078-0432.CCR-17-0605 101. Song H, Han LM, Gao Q, Sun Y. Long non-coding RNA CRNDE promotes
tumor growth in medulloblastoma. Eur Rev Med Pharmacol Sci. (2016)
20:2588–97. doi: 10.26355/eurrev_201712_13925 102. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA,
et al. Functional demarcation of active and silent chromatin domains
in human HOX loci by noncoding RNAs. Cell. (2007) 129:1311–23. doi: 10.1016/j.cell.2007.05.022 82. Zhang K, Sun X, Zhou X, Han L, Chen L, Shi Z, et al. Long non-
coding RNA HOTAIR promotes glioblastoma cell cycle progression
in
an
EZH2
dependent
manner. Oncotarget. (2015)
6:537–46. doi: 10.18632/oncotarget.2681 83. Deguchi S, Katsushima K, Hatanaka A, Shinjo K, Ohka F, Wakabayashi
T, et al. Oncogenic effects of evolutionarily
conserved noncoding 103. Chakravadhanula M, Ozols VV, Hampton CN, Zhou L, Catchpoole D,
Bhardwaj RD. Expression of the HOX genes and HOTAIR in atypical teratoid March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 8 Long Noncoding RNAs in Medulloblastoma Laneve et al. BRI3, a member of the BRI gene family. Gene. (2001) 266:95–102. doi: 10.1016/S0378-1119(01)00374-2 rhabdoid tumors and other pediatric brain tumors. Cancer Genet. (2014)
207:425–8. REFERENCES Yang L, Xiong Y, Hu XF, Du YH. MicroRNA-323 regulates ischemia/
reperfusion injury-induced neuronal cell death by targeting BRI3. Int J Clin
Exp Pathol. (2015) 8:10725–33. 120. Vidal
R,
Calero
M,
Révész
T,
Plant
G,
Ghiso
J,
Frangione
B. Sequence,
genomic
structure
and
tissue
expression
of
Human March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 9
|
https://openalex.org/W3117415196
|
https://djm.uodiyala.edu.iq/index.php/djm/article/download/646/513
|
English
| null |
Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis
|
Maǧallaẗ Diyālá al-ṭibbiyyaẗ/Maǧallaẗ diyālá al-ṭibbiyyaẗ
| 2,020
|
cc-by
| 2,508
|
Acute Lymphoblastic Leukemia, Classification, Clinical
features and Diagnosis Background: Leukemias are classified as lymphoid or myeloid, dependent on the type of
stem cell that is affected. In addition, leukemia is classified as chronic or acute. Acute
leukemia is a production of bone marrow-derived immature cells (blasts), include solid
organs or peripheral blood. The FAB Cooperative Group original classification scheme
proposed to divide1 ALL into three subtypes (L1 - L3). Currently, the world health
organization (WHO), modify FAB classification depending on immunophenotype. Symptoms presence of anemia, splenomegaly, and thrombocytopenia, and those are naturally
present at diagnosis, indicating the degree to which leukemic lymphoblasts have replaced the
bone marrow and the first mark to an ALL diagnosis is typically an abnormal complete blood
count result. Objective: To introduce causes of acute lymphocytic leukemia, recent classification
methods, diagnosis, and symptoms and diagnosis. Conclusion: Acute lymphocytic leukemia occurs due to a defect in the bone marrow and is
classified into several types. The most important classification by the World Health
Organization is depending on immunophenotype. The main symptoms are the increase in
white blood cells with anemia and thrombocytopenia. Fatimah Kadhim Ibrahim AL- Mahdawi Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical
features and Diagnosis Diyala Journal of Medicine Introduction ionizing radiation exposure, chromosomal
abnormalities (Down syndrome), chemical
compounds (benzene), or families with
leukemic history/ members constitute the risk
factors [2]. Abnormal production of blood cells in the
bone marrow and blood-forming organs leads
to a malignant disease usually referred to as
leukemia,
which
can
be
categorized
according to the rate progression [1]. Leukemia etiology is poorly described, with
most authors finding it to be multifactorial. Thus,
viral
infections
(Epstein
Barr), 1 Medical Lab Technologies Department, Bilad Al-Rafidain University College -Diyala- Iraq
2 Baqubah Teaching Hospital- Diyala Health Directorate-Diyala-Iraq Acute Leukemia Acute leukemia is a production of bone
marrow-derived immature cells (blasts),
include solid organs or peripheral blood. Lymphoid leukemia is derived from the
lymphoid stem cells, which normally give
rise to the lymphocytes (T-cells, B-cells,
dendric cells, natural killer cells, and plasma
cells) [5]. For several forms of leukemia, the
ratio of blast cells essential for acute
leukemia diagnosis is greater than twenty
percent, and don’t need any minimum
percentage of blast cell when certain
morphological and cytogenetic characteristics
are present [6]. Lymphoblastic Acute lymphoblastic leukemia. “Acute”
means leukemia will develop rapidly and will
be lethal within a few months if untreated. "Lymphoblastic" means that it develops from
early immature forms of lymphocytes, a type
of leukocytes [8]. Classification Leukemia
is
a
class
of
malignant
hematologic disorder with mesenchymal Vol.19.Issue 2,December 2020 59 Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis
Fatimah Kadhim Ibrahim AL- Mahdawi Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis (lymphoid or myeloid) origin arising from
the bone marrow, produces a high number of
abnormal hematopoietic cells in terms of
their proliferation, differentiation, and cell
death
programming
(apoptosis)
[3]. Leukemias are classified as lymphoid or
myeloid, dependent on the type of stem cell
that is affected. In addition, leukemia is
classified as chronic or acute [4]. Types of Acute Leukemia Acute leukemia is divided into two main
types acute lymphoblastic leukemia and acute
myeloid leukemia dependent on the origin of
whether the blasts are present to be
lymphoblasts or myeloblasts [7]. Vol.19.Issue 2,December 2020 Diyala Journal of Medicine Classification of ALL The classification of ALL by French-
American-British is based on morphology
and cytochemical staining of blasts [9] Figure
(1). The FAB Cooperative Group original
classification scheme proposed to divide1
ALL into three subtypes (L1 - L3) [10]. Table 1 explains the characteristics of three
subgroups of ALL as reported by Conter et
al., 2004 [11]. Table (1): Characteristics of Acute Lymphoblastic Leukemia
Subtypes of ALL
Characteristics
L1 lymphoblast
The small cells with a high nucleus-to-cytoplasm ratio.
Pale blue cytoplasm is rare, and confined to a tiny portion of the perimeter.
The cells have unclear nuclei and membranes of nuclei vary from round to
cleft. L2 lymphoblast
Larger cells with a lower nucleus-to-cytoplasm
ratio, particularly in a more heterogeneous population
Prominent nuclei (often with perinuclear chromatin condensation) and
membranes of nuclear may be irregular or reniform. L3 lymphoblast
Heterogeneous group of cells similar to Burkitt’s-like leukemia, with deep
basophilic cytoplasm and prominent cytoplasmic vacuolization Vol.19.Issue 2,December 2020 Diyala Journal of Medicine 60 c Leukemia, Classification, Clinical features and Diagnosis
Fatimah Kadhim Ibrahim AL- Mahdawi
A B
C
Figure (1): FAB morphological classification of lymphoblasts
A: L1, B:L2, and C: L3 lymphoblasts [12] Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis A B
C
Figure (1): FAB morphological classification of lymphoblasts
A: L1, B:L2, and C: L3 lymphoblasts [12] B A A B
C
Figure (1): FAB morphological classification of lymphoblasts
A: L1, B:L2, and C: L3 lymphoblasts [12] B A
C A A C Figure (1): FAB morphological classification of lymphoblasts
A: L1, B:L2, and C: L3 lymphoblasts [12] Currently, the World Health Organization
(WHO), modify FAB classification
depending on immunophenotype as follows:
[13]. of these advances, 2008 WHO classification
incorporated the category of B-lymphoblastic
leukemia/lymphoma with recurrent genetic
abnormalities into the classification of
precursor lymphoid neoplasms. Based on the
knowledge available at the time, genetic
lesions associated with distinct clinical
features, immunophenotype, prognosis, or
other unique biological characteristics were
included in this category [14]. • Acute Lymphoblastic Leukemia in B-cell • Acute Lymphoblastic Leukemia in B-cell • Early
pre-B
Acute
Lymphoblastic
Leukemia
(named
pro
B
Acute
Lymphoblastic Leukemia) - around 10% of
cases. • Common Acute Lymphoblastic Leukemia -
around 50% of cases. • Mature B-cell Acute
Lymphoblastic
Leukemia
(Burkitt's
leukemia) - around 4% of cases. Vol.19.Issue 2,December 2020 Diyala Journal of Medicine Diyala Journal of Medicine Classification of ALL Immunophenotyping
is
an
important
adjunct to diagnosis and is helpful in
confirming the diagnosis as well as lineage
allocation to leukemia. When interpreting the
immunophenotype data, one should keep in
mind that no single antigen is specific for any
neoplasm and that combining morphologic
features and a panel of antigenic markers is
necessary to obtain a correct diagnosis Table
(1). • Acute Lymphoblastic Leukemia in T-cell. • Pre-T Acute Lymphoblastic Leukemia -
around 5-10% of cases. • Mature-T
cell
Acute
Lymphoblastic
Leukemia - around 15-20% of cases. Recent
years
have
seen
tremendous
progress in uncovering genetic lesions that
influence the biology of ALL. In recognition Vol.19.Issue 2,December 2020 Diyala Journal of Medicine 61 Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis
Fatimah Kadhim Ibrahim AL- Mahdawi Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi In addition, the combinations of markers
expressed are to some extent reflective of the
normal B- and T-cell development and can be
used to determine the stage of development
at
which
the
leukemia
transformation
happened Table (2). In B-ALL this stage of
maturation frequently correlates with the
underlying cytogenetic abnormality. In T-
ALL, the stage of maturation has been shown
to correlate with survival in some studies. Finally, it must be pointed out that the
expression of myeloid antigens is see
frequently in B- and T-ALL and does no
preclude the diagnosis of ALL. Similarly, B
lineage antigens can be expressed in T-AL
and vice versa. The criteria for making th
diagnosis of acute leukemias of ambiguou
lineage have been extensively revised in th
2008 World Health Organization (WHO
classification. The requirements for assignin
more than 1 lineage to given leukemia ar
summarized in Table (3). In addition, the combinations of markers
expressed are to some extent reflective of the
normal B- and T-cell development and can be
used to determine the stage of development
at
which
the
leukemia
transformation
happened Table (2). In B-ALL this stage of
maturation frequently correlates with the
underlying cytogenetic abnormality. In T-
ALL, the stage of maturation has been shown
to correlate with survival in some studies. Finally, it must be pointed out that the expression of myeloid antigens is seen
frequently in B- and T-ALL and does not
preclude the diagnosis of ALL. Similarly, B-
lineage antigens can be expressed in T-ALL
and vice versa. Diyala Journal of Medicine Vol.19.Issue 2,December 2020 Classification of ALL The criteria for making the
diagnosis of acute leukemias of ambiguous
lineage have been extensively revised in the
2008 World Health Organization (WHO)
classification. The requirements for assigning
more than 1 lineage to given leukemia are
summarized in Table (3). ): Prevalence of migraine among obese versus non-obese individuals Table (2): Prevalence of migraine among obese versus non-obese individuals
Commonly positive
Variable expression
B-ALL CD19*
cCD22*
cCD79a*
PAX5†
CD10
sCD22
CD24
TdT
CD20
CD34
CD45
CD13
CD33
sIgM‡
T-ALL cCD3§
TdT
CD7
CD1a
CD2
sCD3
CD4¶
CD5
CD8¶
CD10
CD34
CD99
CD19
CD33
CD79a
CD117
CD56
Antigens are listed approximately in order of frequency. Abbreviations: c, cytoplasmic; s, surface. *Almost always positive. †Most specific for B lineage, but can be positive in t(8;21) AML. ‡Rarely present. §Only marker considered lineage specific. ¶ Maybe co-expressed. Diyala Journal of Medicine Vol.19.Issue 2,December 2020 Diyala Journal of Medicine 62 Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis
Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis
Fatimah Kadhim Ibrahim AL- Mahdawi Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi Table (3): Immunophenotype of B and T lymphocyte progenitors
B lineage
CD10
CD19
CD22
CD79a
Tdt
Ig
Early precursor (pro-B)
Intermediate (common)
Pre-B
-
+
±
+
+
+
+
+
+
+
+
+
+
+
+
-
-
C-mu
T lineage
CD1a
CD2
CD3
CD4
CD7
CD8
CD34
Pro-T
Pre-T
Cortical T
Medullary T
-
-
+
-
-
+
+
+
C
C
C
C,S
-
-
+
*
+
+
+
-
-
+
*
±
±
-
-
Abbreviations: C, cytoplasmic; S, surface. *Medullary T lymphocytes are positive for either CD4 or CD8, but not both. Table (4): Criteria for Ambiguous Lineage Assignment
Lineage
Markers
Myeloid
Myeloperoxidase staining or At least 2 markers of monocytic differentiation
● NSE
● CD11c
● CD14
● CD64
● Lysozyme
T lymphocyte
Cytoplasmic CD3 demonstrated by flow cytometry using antibody specific to the epsilon
chain
● Surface CD3
B lymphocyte
Strong CD19 with at least 1 additional marker or Weak CD19 with at least 2 additional
markers
● CD79a
● Cytoplasmic CD22
● CD10 Clinical features of ALL indicating the degree to which leukemic
lymphoblasts have replaced the bone marrow
[16]. The first mark to an ALL diagnosis is
typically an abnormal complete blood count
result. Conclusions Acute lymphocytic leukemia occurs due to
a defect in the bone marrow and is classified
into several types. The most important
classification
by
the
World
Health Classification of ALL A raised leukocyte (WBC count more
than 10.000/mm3) [12]. Peripheral blood
smears
show
blasts
cells. Present
thrombocytopenia (platelet count less than
100.000/mm3), and also anemia is present
(hemoglobin less than 10g/dL), which is
typically normocytic and normochromic with
decrease
reticulocytes
number[17]. Conclusions Symptoms and signs of acute leukemia are
caused by blasts cells infiltrating the bone
marrow or extramedullary [10]. The signs
are
anemia,
splenomegaly,
and
thrombocytopenia
[1]. Others
common
symptoms and signs include fever, fatigue,
weight loss, loss of appetite, malaise,
palpitations, shortness of breath, dizziness,
cold sensitivity, paleness, bleeding and easy
bruising, sore throat, problems in vision, pain
in joints, nausea, night sweats, heaabdominal
abdominal discomfort, Feeling of fullness in
the abdomen [15]. Diagnosis of ALL Abnormal
leukocyte,
thrombocytopenia
and anemia are naturally present at diagnosis, Vol.19.Issue 2,December 2020 Diyala Journal of Medicine Diyala Journal of Medicine 63 Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Organization
is
depending
on
immunophenotype. The main symptoms are
the increase in white blood cells with anemia
and thrombocytopenia. [9]N. L. Harris et al., “The World Health
Organization classification of hematological
malignancies report of the clinical advisory
committee meeting, Airlie House, Virginia,
November 1997,” Mod. Pathol., vol. 13, no. 2, p. 193, 2000. on Recommendations For classification of acute leukemia, it’s
better to involve many parameters including
morphology
and
immunophenotyping
markers. [10] P. Mittal and K. R. Meehan, “The acute
leukemias,” Hosp. Physician, vol. 5, pp. 37–
44, 2001. [11] V. Conter and C. Rizzari, “S Sala A,”
Chiesa R, Citterio M ala Biondi A Ab Acute
Lymphoblastic
Leuk. Orphanet
Encycl. Creat. date December, 2004. [11] V. Conter and C. Rizzari, “S Sala A,”
Chiesa R, Citterio M ala Biondi A Ab Acute
Lymphoblastic
Leuk. Orphanet
Encycl. Creat. date December, 2004. [12]J. Roganovic, “Acute lymphoblastic
leukemia
in
children,”
in
Leukemia,
IntechOpen, 2013. Vol.19.Issue 2,December 2020 Diyala Journal of Medicine References [1] M. Roy, A. Mukherjee, S. Mukherjee, and
J. Biswas, “Leukemia Causes, Symptoms &
Treatment. [1] M. Roy, A. Mukherjee, S. Mukherjee, and
J. Biswas, “Leukemia Causes, Symptoms &
Treatment. [12]J. Roganovic, “Acute lymphoblastic
leukemia
in
children,”
in
Leukemia,
IntechOpen, 2013. [2] P. Stana, G. Marina, and D. Anca, “Oral
Manifestations in Acute Leukemia as the
First Sign; The Interdisciplinary Approach of
Diagnosis and Treatment,” J Mind Med. Sci
2015; 2(2):186–192. [13]S. Mostert, M. N. Sitaresmi, C. M. Gundy, and A. J. P. Veerman, “Influence of
socioeconomic status on childhood acute
lymphoblastic
leukemia
treatment
in
Indonesia,” Pediatrics, vol. 118, no. 6, pp. e1600–e1606, 2006. [3]P. Chandran et al., “Mesenchymal stromal
cells from patients with acute myeloid
leukemia have altered capacity to expand
differentiated. hematopoietic progenitors,”
Leuk. Res., vol. 39, no. 4, pp. 486–493, 2015. [4] W. Lockwood, “Leukemia: AML, CML,
ALL and CLL.” 2015. [14]S. McGregor, J. McNeer, and S. Gurbuxani, “Beyond the 2008 World Health
Organization classification: the role of the
hematopathology laboratory in the diagnosis
and management of acute lymphoblastic
leukemia,”
in
Seminars
in
diagnostic
pathology, 2012, vol. 29, no. 1, pp. 2–11. [5]N. J. Goulden and C. G. Steward,
Pediatric
Hematology:
Methods
and
Protocols, vol. 91. Springer Science &
Business Media, 2004. [5]N. J. Goulden and C. G. Steward,
Pediatric
Hematology:
Methods
and
Protocols, vol. 91. Springer Science &
Business Media, 2004. [15] E. A. Shephard, R. D. Neal, P. W. Rose,
F. M. Walter, and W. Hamilton, “Symptoms
of adult chronic and acute leukaemia before
diagnosis: large primary care case-control
studies using electronic records,” Br J Gen
Pr., vol. 66, no. 644, pp. e182–e188, 2016. [16]G. Abdul-Hamid, “Classification of
Acute Leukemia,” in Acute Leukemia-The
Scientist’s
Perspective
and
Challenge,
IntechOpen, 2011. [6]M. Antica,
Acute
Leukemia:
The
Scientist’s Perspective and Challenge. BoD–
Books on Demand, 2011. [6]M. Antica,
Acute
Leukemia:
The
Scientist’s Perspective and Challenge. BoD–
Books on Demand, 2011. [7]A. V. Hoffbrand and D. P. Steensma,
Hoffbrand’s essential haematology. John
Wiley & Sons, 2019. [8]R. Hoffman, E. J. Benz Jr, L. E. Silberstein, H. Heslop, J. Anastasi, and J. Weitz, Hematology: basic principles and
practice. Elsevier Health Sciences, 2013. Vol.19.Issue 2,December 2020 Diyala Journal of Medicine 64 Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis [18]Stewart WF, Roy J, Lipton RB. Migraine
prevalence, socioeconomic status, and social
causation. Neurology. 2013;81(11):948-55. 65
|
https://openalex.org/W4220865662
|
http://ir.unimas.my/id/eprint/40578/3/Digital.pdf
|
English
| null |
Digital Socio-Technical Innovation and Indigenous Knowledge
|
IntechOpen eBooks
| 2,022
|
cc-by
| 6,800
|
Abstract Scientific research involving remote rural communities is often plagued by a lack
of understanding of what constitutes indigenous knowledge. That is, indigenous
perspectives, models of representation, and their ways of knowing. Through a
long-standing community-university partnership in working with remote and rural
communities in the Borneo Malaysian states of Sarawak and Sarawak and the Orang
Asli communities in Peninsular Malaysia, we address this concern in presenting
directions for shaping digital socio-technical innovation. We highlight the need to
adopt a balanced indigenous worldview based on two case studies from past inter-
actions with these indigenous communities to highlight how indigenous knowledge
can now become contextualized within contemporary problem-solving scenarios. Keywords: indigenous knowledge management, indigenous worldview,
sustainability oriented socio-technical innovation Poline Bala, Narayanan Kulathuramaiyer and Tan Chong Eng Poline Bala, Narayanan Kulathuramaiyer and Tan Chong En 1. Introduction Propelled by developments of industrial revolution 4.0, nations are gearing
towards a knowledge-intensive economy. Therefore, optimism towards scientific
knowledge and digital-based innovation to drive economic growth is on the rise. However, the roles of indigenous peoples’ place-based knowledge, skills, and
experiences have largely been overlooked in the expansion of the digital-based
framework of technological innovation. This is due to a lack of understanding
of what constitutes indigenous knowledge - indigenous perspectives, models of
representation, and their ways of knowing. In fact, because of the appearance of
incommensurables between the two types of knowledge, in their encounters with
each other, indigenous knowledge is often sidelined. This is despite for the untold
number of years indigenous knowledge has helped indigenous communities around
the globe to stay resilient in the face of complex challenges and diverse adversities. Drawing on two decades of community-university partnerships between Universiti
Malaysia Sarawak and five different rural indigenous communities in the Malaysian
states of Sarawak and Sabah on the island of Borneo and four remote Orang Asli
communities in Peninsular Malaysia, this paper highlights the need to adopt a bal-
anced indigenous worldview in order to ensure that traditional knowledge remains
intact in their encounters with other knowledge systems. This paper addresses this
concern through a socio-technical system framework, which is a balanced ecosys-
tem whereby technology is embedded and woven, rather than externally imposed,
into a social system for a balanced human-machine interaction and the integration
of scientific exploratory models in solving complex problems. This requires a 1 Recent Advances in Knowledge Management careful co-envisioned and co-designed framework in a participatory manner that
benefits the symbiosis between people, the ecosystem, and the environment. The next section of the chapter provides a brief overview of indigenous knowl-
edge; that is its characteristics and its increased importance in the development
agenda framework at different levels: international, national, and communities. It
then highlights an emerging barrier between indigenous knowledge and scientific
knowledge due to the appearance of incommensurables between the two types
of knowledge. The chapter then offers case studies to highlight what are the pos-
sibilities of the weaving of these two kinds of knowledge through a socio-technical
innovation system. This is followed by a discussion and conclusion to the chapter. 2. Literature review Over the last decade, there is increased awareness that the vast collection of
traditional knowledge of indigenous communities holds the key to solve many
complex problems. Built over generations through close interaction with natural
surroundings and a deep understanding of nature’s sociality, indigenous knowledge
has helped communities to be resilient, live sustainably, and face global challenges
such as climate change. Due to its significance as a tremendous resource, there have been attempts to
include indigenous knowledge to deal with global causes and concerns. A robust
example is an effort by James David Wolfensohn, who served as president of the
World Bank (1995–2005). In 1998, the World Bank acknowledges that indigenous
knowledge “represents an important component of global knowledge” (World
Bank, 1998, as cited by [1]). With that, there was a deliberate attempt to shift the
institution’s focus towards humanitarian efforts by drawing on indigenous knowl-
edge as a resource to enhance development processes. Over the years, considerable progress has been made in promoting indigenous
knowledge. In 2010, the World Bank’s [2] published its Indigenous knowledge for
development: a framework for action. The framework explains the need for indig-
enous knowledge to play strategic roles to expand the benefits of development assis-
tance through the organization’s development activities. Henceforth, the framework
for action to increase understanding on the significance of IK amongst its develop-
ment associates and to provide suggestions on how best it can be integrated into
development practices. What is obvious is indigenous knowledge is considered
essential for maintaining global cultural diversity and biological diversity. The UN special rapporteur on indigenous issues has pointed out that indigenous
communities around the world are the most effective custodians of millions of
hectares of forest, which act as the world’s lungs. It was suggested that localized
indigenous perceptions of ecosystems and natural habitats are able to provide solu-
tions to many of the world’s problems from climate change to biological diversity. Today, the role of indigenous knowledge are increasingly becoming part of the
development agenda; national initiatives and policies have emerged, with civil
society forming a broad base of support and the number of development projects
as well as programs integrating traditional and indigenous knowledge has doubled
up. This includes movement by indigenous peoples themselves to build a capac-
ity building to maintain and protect biodiversity while at the same time creating
alternative sources of economic income. 1. Introduction It
concludes that a socio-technical innovation model, which is a balanced ecosystem
where technology is embedded into a social system as an integral knowledge weav-
ing, provides a useful system framework to contextualize indigenous knowledge
within contemporary problem-solving scenarios. 2. Literature review A good example by the indigenous 2 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 communities themselves is the FORMADAT initiative. It was set up in 2015 as
The Alliance of the Indigenous Peoples of the Highlands in the Heart of Borneo. According to Bala, et al. [3] the initiative is “to build on the shared historical and
cultural bonds between the Lundayeh, Kelabit, Lun Bawang, and Sa’ban peoples
living in the highlands of the heart of Borneo. The group aims to integrate conserva-
tion and development at the landscape level and to generate benefits for local people
by preserving the rich natural and cultural diversity of the region, an area that
includes the largest surviving intact forested and traditionally farmed catchment
area on the island of Borneo.” 4. Taking indigenous knowledge seriously However, despite increased global recognition of indigenous communities’
knowledge to maintain global cultural diversity and biological diversity, arguably
indigenous knowledge is gradually disappearing. This is a result of worldwide rapid
development and landscape changes and also as a result of increased encounters
between the paradigms of indigenous knowledge and scientific knowledge. p
g
g
g
g
There is little doubt that UNESCO [10] has highlighted a recent shift in the rela-
tionship between science and other systems of knowledge, reflected in the explicit
recognition of indigenous knowledge in many global environmental governances
described above. Nonetheless, there are still conflicting ideas about what it means
to take indigenous knowledge seriously. There is still widespread assumption that
science is superior to other knowledge systems. This stems mainly from the incom-
mensurable between scientific and indigenous conceptual models, their ontologies,
and their systems [11–14], which continue to create barriers to meaningful collabo-
ration and the integration of indigenous and scientific knowledge. g
g
g
As aptly described by Simeone ([15], pg. 1–2). He says, “Unlike the western
custom of disseminating knowledge through publication, traditional knowledge
systems exist principally in the form of songs, proverbs, stories, folklore, com-
munity laws, common or collective property and inventions, practices, and
rituals. The knowledge is transmitted through specific cultural mechanisms such
as those just listed, and often through designated community knowledge hold-
ers, such as elders. The knowledge is considered collective to the community, not
private to one individual or small group.” He went to say that, “While Western
science tends to be written and compartmentalize, IK are more holistic and are
communicated orally. As orally based knowledge, IK are transmitted through
observations and experiences while scientific knowledge are passed on through
lectures and theories. Often times than not scientific knowledge are value-free
and theoretical, whilst indigenous knowledge is more spiritual and embedded in
social values.” The differences can be demonstrated by the following two diagrams, which
illustrate the framing of the two types of knowledge. Diagram 1(a) is an illustration
of indigenous knowledge, which was co-created with remote community leaders. Diagram 1(b) on the other hand represents the prescriptive modeling of knowledge
by researchers structuring and creation of scientific knowledge (Figure 1). y
g
g
g
Due to the differences, some observers express concern that western science
creates conflicts for indigenous knowledge and may even destroy it. • Context-embedded artifacts The characteristics listed above, highlights the knowledge gaps in current
literature, calling for a deepening of understanding of what indigenous knowledge
is, and how balance and fairness can be the basis for its assimilation. This paper
explores these defining characteristics through the case studies explored, to shed
some light towards a more balanced worldview. 3. Defining indigenous knowledge But what is indigenous knowledge? UNESCO provides a general portrayal to
local and indigenous knowledge as the understandings, skills, and philosophies
developed by societies with long histories of interaction with their natural sur-
roundings. For rural and indigenous peoples, local knowledge informs decision-
making about fundamental aspects of day-to-day life. g
p
y
y
Others are more descriptive in their definitions of indigenous knowledge. For
instance, Warren ([4], p. 127) argues, indigenous knowledge is a profound, detailed
and shared beliefs and rules with regards to the physical resource, social norms,
health, ecosystem, culture, livelihood of the people who interact with environment
both in rural and urban settings. It has been the basis for local level decision making
in agriculture, health care, food preparation, education, natural resource manage-
ment, and a host of other activities. Meanwhile, [5] highlights that “Indigenous people have had their own ways of
looking at and relating to the world, the universe, and to each other. Their tradi-
tional education processes were carefully constructed around observing natural
processes, adapting modes of survival, obtaining sustenance from the plant and
animal world, and using natural materials to make their tools and implements”
(as cited by [6], p. 10). y
p
Gorjestani [7] observed that “Indigenous knowledge (IK) is used at the local
level by communities as the basis for decisions pertaining to food security, human
and animal health, education, natural resources management, and other vital
activities. IK is a key element of the social capital of the poor and constitutes their
main asset in their efforts to gain control of their own lives.” Masango [8] defined indigenous knowledge as “The totality of all knowledge
and practices established on past experiences and observations that are held and
used by people”. Gope et al. [9] characterized “Indigenous knowledge” as community-centric by
nature, which reflects community practices and usually possesses a deep connection
with land, locale, and community. Indigenous knowledge is highly tactic and hence
it is quite difficult to codify and document Indigenous knowledge. Apart, indig-
enous knowledge is usually disseminating across generations through content and
by virtue of observing the various community practices. 3. Defining indigenous knowledge y
g
y
From the extensive definitions above, some common characteristics attribute to
indigenous knowledge include the following: • Multi-layered, multi-dimensional, based on a holistic worldview • Connections between all living things • Understanding for fair distribution of resource 3 Recent Advances in Knowledge Management • Integrated lifestyles (knowledge embedded in life) • Integrated lifestyles (knowledge embedded in life) • Modeled & exchanged implicitly • Context-embedded artifacts 4. Taking indigenous knowledge seriously This has led to
calls for a shift in understanding indigenous knowledge to dismantle the barriers
between indigenous traditional knowledge and scientific knowledge [16]. It is this
call which inspires this chapter for it encapsulates the experiences we have gained 4 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861
Figure 1. (a), (b): The framing of indigenous and scientific knowledge. Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Figure 1. (a), (b): The framing of indigenous and scientific knowledge. over two decades of research in rural digital inclusion efforts by introducing infor-
mation communication technologies (ICTs), especially the internet as new tools for
social and economic transformations amongst indigenous communities in Malaysia. This is within a challenging context: terrain with extreme variations in elevation,
long distances, and sparce populations located in widespread locations. Moreover,
with communities with diverse ethnic backgrounds and with different levels of
socioeconomic status, and at times zero digital literacy. g
y
The diverse and dispersed communities require a careful context-specific for the
deployment of the information communication technologies and their designs. Not
only the team encounter differences in terms of experiences and standard of living
but lifestyle, cultural practices, and worldviews, which are constitutive of their
indigenous knowledge. 5. Background context In 1999 an interdisciplinary team of researchers based at Universiti Malaysia
Sarawak (UNIMAS) has embarked on the e-Bario project in the Kelabit Highlands
of Sarawak [17]. This was to explore how indigenous communities in remote and
rural areas can be “integrated” in Malaysia’s race towards a Knowledge based-society
by 2010. The knowledge society framework was deemed to inculcate the values and
culture of life-long learning and the creation of knowledge-based products and
services amongst its population. Exploring the use of telephones, computers, Very
Small Aperture Terminals (VSATs), and the Internet, e-Bario was implemented as a
pilot project to explore the economic, social, and cultural potentials of ICTs through
community-based Telecentre model for rural development in Sarawak. This is
especially because ICTs are predicted to promote new social, economic, and cultural
opportunities in rural areas [18]. pp
Due to its success e-Bario became a catalyst to explore the roles that telecentre
can play in advancing community-based development amongst other indigenous
communities in Sarawak, Sabah, and Peninsular Malaysia. As a consequence, the
University has formed long-standing community-university partnerships with
diverse and dispersed indigenous communities who live in remote and rural areas in
Sarawak, Sabah, and Peninsular Malaysia. The out-of-the-way locations of these indigenous communities create immense
distance both in time and space and therefore exemplify the disconnected portion
of the digital divide in Malaysia. They are often are without network access, lack of 5 Recent Advances in Knowledge Management adjacent infrastructure (e.g., grid electricity), lack of digital and language literacy,
low income and affordability, lack of relevant content and services as well as lack
of cultural and social relevance and therefore acceptance [19]. See Table 1 for a
complete list of the indigenous communities involved. p
g
There is no doubt that because of the lack of digital and language literacy, it was
easy to assume that these indigenous communities are knowledge-poor and incom-
petent in a global world. This is in spite of their capacities to manage the fragility
of their own cultural heritage from human and non-human threats such as climate
change. Their inherent indigenous wisdom are orally based and more embedded,
therefore it was easy to overlook in the process of research and developmental
efforts. Moreover, digital innovation framework has been torn between a western-
scientific idea and a more indigenous, community-based concept. 5. Background context Little attention
is given to indigenous place-based knowledge, skills, and experiences within the No
Communities
(Ethnic
Group)
Location
Geographical
terrain
Economic
activities
Language
1
Kelabit
Bario,
Sarawak
Upland plateau
Wet Rice
farming,
hunting
Process Timber
Entrepreneurs
Kelabit
2. Penan
Long Lamai,
Sarawak
Mountain/riverine
Hill rice
farming,
hunting and
gathering
Penan
3
Lun Bawang
Ba Kelalan
Highland/Valley
Wet rice
farming,
border trading
Lun Bawang
4
Bajau
Pulau
Larapan,
Sabah
Island
Fishing
Bajau
5
Dusun
Kampung
Buayan,
Sabah
Mountain range
Farming,
hunting,
gathering
Dusun
6
Temiar
Pos Balar
Mountain/riverine
Farming,
hunting,
gathering
Temiar
7
Temiar
Pos Gob
Mountain/
headwaters
Farming,
hunting,
gathering
Temiar
8
Semai
Pos Lenjang
Mountain/riverine
Farming,
hunting,
gathering
Semai
9
Semai
Pos Sinderut
Mountain/
headwaters/valley
Farming,
hunting,
gathering,
rubber tapping
Semai
Table 1. List of diverse and dispersed indigenous communities and bridging digital divide initiative by the Universiti Table 1. List of diverse and dispersed indigenous communities and bridging digital divide initiative by the Universiti
Malaysia Sarawak (UNIMAS). 6 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 expanding digital-based framework for knowledge management. These unique
ways of knowing are important facets of the world’s cultural diversity and provide a
foundation for locally appropriate sustainable development. It is made up of a rich
understanding of the plant, crop, and tree species, medicines, animal breeds, and
local ecological and biological resources. This includes their useful and adaptive
techniques to respond to changes in the physical and social environment. Raise the question of whether is it possible to introduce and transfer academic
knowledge about the new digital technologies without displacing the position or
disintegrating the integrity of existing local indigenous knowledge. 7. Case study 1: community-led massive open online courses (MOOCs)
for life long learning The Massive Open Online Courses is an outcome of the emerging knowl-
edge society to empower everyone to contribute to knowledge exchange at the
global level; leading to making higher education accessible to everyone. (see for
instance Anant, [22]). Nonetheless, MOOCs model and framework is a challenge
to blend in with the indigenous rural community way of life to sustain lifelong
learning. Single mothers Association community members in Bario made the ill-
fitting very clear to us when we first mooted the idea at a focus group discussion
meeting. g
In response, the spokesperson said: “Thank you for introducing this new system
to us. We look at it and admire how it works for instance to provide means to receive
and learn new ideas and things. That is very admirable. However, I don’t think we
need any more ideas from outside to make us better farmers. In fact, over the years
we have developed our own farming system and we are very good at it. Ilah let ngen
tetepuh [knowledge from our ancestors]. And this is evident from the sufficient rice
and food we provide for our families and our community. We would like to ask, why
not use the platform for us to teach our skills and our languages to others especially
our grandchildren. Currently, most of us are far removed from our grandchildren
since most of them are living in town and are going to national schools where they
learn other languages such as Bahasa Malaysia and English. As a result, many do
not know to speak their mother tongue. We are not really able to communicate and
teach them at the moment because of the distance and language barrier. Can we
redesign your platform for us to teach them our way of life - for instance how to
prepare our own traditional food and to introduce our traditional adornment which
are important as markers of identity.” Another person went on to say, “With your platform [videos] you are able to
capture what we do and keep them to show them. For we teach our younger genera-
tion by showing them how it is done. They learn from observing and trying it out
for themselves. We don’t teach them by giving them instructions, because for us
when they try and do it for themselves after seeing us doing it, that knowledge will
last longer in their minds. 6.1 Socio-technical systems innovation and case studies Models of socio-technical technical innovation such as the telecentre as a driver
for socio-economic impact need to be carefully co-envisioned and co-designed in
a participatory manner. The context of the innovation has to adopt a knowledge-
based inquiry and as a value-creation activity that benefits the people, the ecosys-
tem, and the environment. The design of such an Indigenous Innovation model has to be aligned to cul-
tural protocols and norm and social practices to cultivate symbiotic relationships
with people, the environment and nature (see [20]). This process-oriented model
illustrated in Figure 2, will then drive balanced human-machine interactions and
integrate with scientific exploratory models in solving complex problems [21]. 6. Methodological framing The method and approach employed have been largely guided by principles of
participative, interdisciplinary, and transcultural interactions. First, it has been par-
ticipative whereby indigenous local communities have been engaged in the design,
planning, and implementation of the project. Second, the initiatives involved by an
interdisciplinary team of researchers from different academic fields: anthropology,
archaeology, geographer/geographic information system, computer science, and
knowledge engineering sciences. Thirdly, it was transcultural in nature. It involved
transcultural interactions between the scientists and community scholars, between
members of the indigenous communities, and members of the multidisciplinary
team. In short, it was a collaborative effort to ensure serious dialog and partnerships
between knowledge experts and the local communities as collaborators. The latter
are not merely recipients or objects of the technologies being introduced, but their
worldviews and knowledge systems are taken seriously. Raise questions in what ways can the team develop models, protocols, and
frameworks, which not only support the unique structure of indigenous knowledge
but also facilitate efforts to weave the two knowledge towards a better understand-
ing of indigenous knowledge systems. Is it possible to formulate knowledge portals
or protocols in order to assimilate two knowledge paradigms, for instance, to
digitally integrate the knowledge of the past through a digital based framework
to increase local awareness, interest, and understanding about the significance
and value of their world to others who matter to them. Two case studies of socio-
technical innovation below aim to answer these concerns. Figure 2. Socio-technical innovation model. g
Socio-technical innovation model. 7 7 Recent Advances in Knowledge Management 7. Case study 1: community-led massive open online courses (MOOCs)
for life long learning I want to teach my grandchildren how to make this orna-
ment using beads. There are many techniques that they should know, and they can
only learn from us. Nobody else knows how to do this; they cannot learn it on their
own. They have to learn from us.” y
Invited as collaborators, the single mothers’ community members reshaped
the current model of MOOC by fitting it into specific roles in the community. First, they have made it clear that they did not need any more information 8 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 to upgrade their standard of living as farmers. Second, they would like to
ensure that the knowledge – skills, expertise that they have accumulated over
the years, not only be documented but to be passed on to their descendants
(grandchildren). More importantly, by turning the project into a community-driven activity, the
single mothers are transformed into knowledge creators and co-designers and not
merely consumers of technological-based frameworks. They have redesigned the
MOOC channel into community sustainability channels. Their stories suggest that
for it to be fully appreciated, MOOCs has to deliver value as an integrated socio-
technical system to enable life-long learning for indigenous rural communities. 8. eToro: innovation ecosystem This research began in 2007 amongst the indigenous Penan community in
Long Lamai, Sarawak. Nomadic in the recent past, they still depend on the for-
est for their livelihood. Through a trans-disciplinary, participatory approach, a
long-standing partnership has evolved to closely mirror indigenous practices in
knowledge sharing [23–25]. g
g
The socio-technical model approach as a knowledge-sharing networks started
with the acknowledgment of the tremendous knowledge repository possessed by
the community elders and which are implicitly locked in traditional practices. In
order to understand their traditional knowledge system, the team adopted a visual
charting approach to map the close link between the community laws, nature, the
rainforest, social practices, language, culture and heritage, and customary practices
and rituals. The deep connection between the land, locale, and community began to unravel
through a family-based activity known as the Toro journey. As an intimate joint
activity of a Penan family, Toro is an activity-based knowledge sharing and men-
toring journey, which is usually undertaken within a period of a week solely for
hunting, to collect forest resources, and also to groom future guardians of the forest
(Figure 3). This is where plant knowledge related to social beliefs and for daily use
is shared and transmitted. This includes knowledge of medicinal plant use and the
meanings of different landscapes in their environment. As a forest-journey interac-
tions and knowledge exchanges, the Toro journey provided snapshots on models of
multidimensional layers of inherent indigenous wisdom. Figure 3. Penan elder: If you do not know your origin [Forest], you are not a Penan. Figure 3. Penan elder: If you do not know your origin [Forest], you are not a Penan. Figure 3. Figure 3. Penan elder: If you do not know your origin [Forest], you are not a Penan. 9 9 Recent Advances in Knowledge Management There is a concern that with the intervention of modern technology through the
telecentre, the knowledge related to this symbiotic relationship might erode. But,
the blended socio-technical model approach has enabled the rural community’s
‘knowledge-rich scholars’ to co-create technological solutions and involves the
community to decide on the design of the system thereby allowing a snaturalized
participation and involvement in collaboratively recording indigenous knowledge. A botanical indigenous knowledge base was thereby developed via a coordinated
co-creation method where the elders worked closely with rural youths in document-
ing local knowledge. 8. eToro: innovation ecosystem The knowledge elicitation activities benefitted fully from the
community’s integral knowledge management capability without over-looking
implicitly indigenous values. What is clear is that compared to a purely systemic approach in modeling
community sustainability, the approach has revealed directions for unlocking
intangible benefits by truly harnessing the previously untapped cultural heritage
and implicitly held knowledge resources. Moreover, through the approach a multi-
level decision-making process involving the community players in a variety of
roles such as knowledge extraction system and systems interface co-designers, a
co-constructed socio-technical innovation in an ecosystem of the equal partnership
was produced (Figure 2). The drive of the spirited community that believed in the
utmost need to conserve a symbiotic relationship with nature and the forest has
been the impetus in empowering a values-based socio-technical innovation. 9. Findings and discussion The cases above suggest that any scientific knowledge and technological innova-
tion as drivers either to promote knowledge-based products and services or to create
values and culture of life-long learning amongst indigenous communities require
careful co-envisioned and co-designed in a participatory manner. The context of
the innovation has to adopt a knowledge-based inquiry and a value-creation activity
that benefits the symbiosis between people, ecosystem, and environment. It is
imperative to ensure that the intervention of modern technology must not erode
knowledge processes related to this symbiotic relationship. This is important to bear in mind as indigenous communities are under increas-
ing pressure to adapt to global knowledge. In their encounter with scientific
knowledge, the values of their indigenous cultural knowledge are often in a disad-
vantageous position and being undermined. This is in spite of the increased global
recognition of indigenous communities’ knowledge not only to help indigenous
communities to be resilient, live sustainably in the face of challenges such as climate
change, but also to maintain global cultural diversity and biological diversity. g
g
y
g
y
For the interdiscplinarian team from UNIMAS, who values sound methodological
research, reframing the methodology towards participative, transcultural dialogs
provide a framework to adopt a balanced indigenous worldview leading to proto-
cols that inculcate the recognition of the coexistence of multiple worldviews and
knowledge systems. Compare to a purely systemic approach in modeling community
sustainability, the groundbreaking methodological model led to the development
of a socio-technical technical systems innovation. As illustrated in Figures 4 and 5
this can lead to the harnessing of indigenous knowledge and worldviews to design
indigenous innovation models. It involved the repurposing of technologies by align-
ing them to cultural protocols and norms and social practices to cultivate symbiotic
relationships with people, the environment, and nature. The process-oriented model
(Figure 2) allows for a balanced human-machine interaction and the integration of
scientific exploratory models in solving complex problems. 10 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861
Figure 4. eToro – Innovation ecosystem. Source: Adapted from [26, 27]. Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861
Harnessing their oral-based indigenous knowledge expressions, the indigenous
single mothers of the Kelabit community participated in producing MOOC modules
with the reshaped model. 9. Findings and discussion This is to enable life-long learning for the indigenous women
and their grandchildren through their community sustainability channels (Figure 5). Meanwhile, the e-Toro innovation system highlights indigenous place-based
structured knowledge. Through the Toro journey as an activity-based knowledge
sharing and mentoring journey, tacit indigenous knowledge is demonstrated and
observed through carefully selected oral stories in which instruction and values are
embedded In Figure 3 the designated community knowledge holder a Penan elder
Figure 4. eToro – Innovation ecosystem. Source: Adapted from [26, 27]. Figure 5. MOOCs for community sustainability channels. Figure 4. Figure 4. eToro – Innovation ecosystem. Source: Adapted from [26, 27]. Figure 5 Figure 5. MOOCs for community sustainability channels. Figure 5. MOOCs for community sustainability channels. Figure 5. MOOCs for community sustainability channels. Harnessing their oral-based indigenous knowledge expressions, the indigenous
single mothers of the Kelabit community participated in producing MOOC modules
with the reshaped model. This is to enable life-long learning for the indigenous women
and their grandchildren through their community sustainability channels (Figure 5). Meanwhile, the e-Toro innovation system highlights indigenous place-based
structured knowledge. Through the Toro journey as an activity-based knowledge
sharing and mentoring journey, tacit indigenous knowledge is demonstrated and
observed through carefully selected oral stories in which instruction and values are
embedded. In Figure 3, the designated community knowledge holder, a Penan elder
transmits the value of knowing the forest: If you do not know your origin [Forest],
you are not a Penan. Harnessing their oral-based indigenous knowledge expressions, the indigenous
single mothers of the Kelabit community participated in producing MOOC modules
with the reshaped model. This is to enable life-long learning for the indigenous women
and their grandchildren through their community sustainability channels (Figure 5). Meanwhile, the e-Toro innovation system highlights indigenous place-based
structured knowledge. Through the Toro journey as an activity-based knowledge
sharing and mentoring journey, tacit indigenous knowledge is demonstrated and
observed through carefully selected oral stories in which instruction and values are
embedded. In Figure 3, the designated community knowledge holder, a Penan elder
transmits the value of knowing the forest: If you do not know your origin [Forest],
you are not a Penan. Meanwhile, the e-Toro innovation system highlights indigenous place-based
structured knowledge. Through the Toro journey as an activity-based knowledge
sharing and mentoring journey, tacit indigenous knowledge is demonstrated and
observed through carefully selected oral stories in which instruction and values are
embedded. In Figure 3, the designated community knowledge holder, a Penan elder
transmits the value of knowing the forest: If you do not know your origin [Forest],
you are not a Penan. 11 Recent Advances in Knowledge Management As depicted in case studies, the inherent layers and dimensions of societal struc-
ture have to be preserved in the co-design efforts, to integrate within an encompass-
ing framework that stakeholders can relate to and contribute to in a meaningful
way. Figure 4. Connections between all living things relates to an over-arching principle of
“unity in diversity” that has captured (as in both case studies) in the simplistic
modeling terms through life-illustrations and analogical models of co-creation. 10. Conclusion Clearly, indigenous knowledge is integral to a cultural complex that also encom-
passes language, systems of classification, resource use practices, social interac-
tions, ritual, and spirituality. The recognition that local and indigenous people have
their own ecological understandings, conservation practices, and resource manage-
ment goals has important implications as indigenous people are now recognized as
essential partners in environmental management. p
g
The paper has revealed directions, protocols, and framework for collaborative
engagement between two different paradigms with regards to intangible benefits
of previously untapped cultural heritage and implicitly held knowledge resources
amongst indigenous communities. It has shed insights into how the socio-technical
innovation model, which is a balanced ecosystem where technology is embedded
into a social system as an integral knowledge weaving, provides a useful system
framework to contextualize indigenous knowledge within contemporary problem-
solving scenarios. As highlighted in this paper, the need to create a playground for the exchange of
implicitly held knowledge, in co-created models that preserve the local context and
scenario, and yet at the same time not separated from life-learning situations holds
the key to the symbiotic blending of knowledge. Author details
Poline Bala1*, Narayanan Kulathuramaiyer2 and Tan Chong Eng3
1 Institute of Borneo Studies, Universiti Malaysia Sarawak, Kuching, Malaysia
2 Institute of Social Informatics and Technological Innovation, Universiti Malaysia
Sarawak, Kuching, Malaysia
3 Faculty of Computer Science and Information Technology, Universiti Malaysia
Sarawak, Kuching, Malaysia
*Address all correspondence to: bpoline@unimas.my
© 2022 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms
of the Creative Commons Attribution License (http://creativecommons.org/licenses/
by/3.0), which permits unrestricted use, distribution, and reproduction in any medium,
provided the original work is properly cited. Author details 12 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 [12] Cruikshank J. Do glaciers Listen?
Local Knowledge, Colonial Encounters,
and Social Imagination. Vancouver,
British Columbia, Canada: University of
British Columbia Press; 2005 [6] Barnhardt R, Kawagley AO.
Indigenous knowledge systems and alaska
native ways of knowing. Anthropology &
Education Quarterly. 2005;36(1):8-23.
DOI: 10.1525/aeq.2005.36.1.008 References [8] Masango CA. Indigenous knowledge
protection: Prospects in South Africa’s
intellectual property framework. South
African Journal of Libraries and
Information Science. 2010;76(1):
74-80 [1] Adam L. Information and
communication technologies,
knowledge management and indigenous
knowledge: Implications to livelihood of
communities in Ethiopia. 2012. Available from: http://unpan1.un.org/
intradoc/groups/public/documents/
un-dpadm/unpan040822.pdf [Accessed
10 August 2021] [9] Gope L, Behera SK, Roy R. Identification of Indigenous Knowledge
Components for Sustainable
Development among the Santhal
Community. American Journal of
Educational Research. 2017;5(8):887-
893. DOI: 10.12691/education-5-8-8 [9] Gope L, Behera SK, Roy R. Identification of Indigenous Knowledge
Components for Sustainable
Development among the Santhal
Community. American Journal of
Educational Research. 2017;5(8):887-
893. DOI: 10.12691/education-5-8-8 [2] World Bank Group. Indigenous
Knowledge for Development: A
Framework for Action. Washington,
D.C: World Bank Group; 2010. Available
from: http://documents.worldbank.org/
curated/en/388381468741607213/
Indigenous-knowledge-for-
development-a-framework-for-action [10] UNESCO. Towards a UNESCO
Recommendation on Open Science
Online Consultation for Indigenous
Peoples on the UNESCO
Recommendation on Open Science 15
January 2021, United Nations
Educational, Scientific and Cultural
Organisation. 2021. Available from:
https://en.unesco.org/sites/default/files/
indigenous_people_report_unesco_
recommendation_os.pdf [Accessed: 21
August 2021] [3] Bala P, Narayanan KR, Harris RW. From the margins to the mainstream:
indigenised development in borneo with
information and communication
technologies and its contribution to
global sustainable development. Journal
of Borneo Kalimantan. 2020;6(2):19-35 [4] Warren DM. The Role of Indigenous
Knowledge in Facilitating the
Agricultural Extension Process. Bad
Boll, Germany: Paper presented at
International Workshop on Agricultural
Knowledge Systems and the Role of
Extension; 1991 May 21-24 [11] Atran S. The vanishing landscape of
the Petén Maya Lowlands: People,
plants, animals, places, words, and
spirits. In: Maffi L, editor. On
Biocultural Diversity: Linking
Language, Knowledge, and the
Environment. Washington, D.C., USA:
Smithsonian Institution Press; 2001. pp. 157-174 [5] Ascher M. Mathematics Elsewhere:
An Exploration of Ideas across Cultures. Princeton, NJ: Princeton University
Press; 2002 [12] Cruikshank J. Do glaciers Listen? Local Knowledge, Colonial Encounters,
and Social Imagination. Vancouver,
British Columbia, Canada: University of
British Columbia Press; 2005 [6] Barnhardt R, Kawagley AO. Indigenous knowledge systems and alaska
native ways of knowing. Anthropology &
Education Quarterly. 2005;36(1):8-23. DOI: 10.1525/aeq.2005.36.1.008 [6] Barnhardt R, Kawagley AO. Indigenous knowledge systems and alaska
native ways of knowing. Anthropology &
Education Quarterly. 2005;36(1):8-23. DOI: 10.1525/aeq.2005.36.1.008 [13] Pariyar A, Kulathuramaiyer N,
Bala P. Towards participatory MOOCs. In: Crompton H, Traxler J, editors. Critical Mobile Pedagogy: Cases of
Inclusion, Development, and
Empowerment. New York, London:
Routledge; 2020 [13] Pariyar A, Kulathuramaiyer N,
Bala P. References Towards participatory MOOCs. In: Crompton H, Traxler J, editors. Critical Mobile Pedagogy: Cases of
Inclusion, Development, and
Empowerment. New York, London:
Routledge; 2020 [13] Pariyar A, Kulathuramaiyer N,
Bala P. Towards participatory MOOCs. In: Crompton H, Traxler J, editors. Critical Mobile Pedagogy: Cases of
Inclusion, Development, and
Empowerment. New York, London:
Routledge; 2020 [7] Gorjestani N. Indigenous knowledge
for development: Opportunities and
Challenges. Geneva: United Nations
Conference on Trade and
Development; 2000 [7] Gorjestani N. Indigenous knowledge
for development: Opportunities and
Challenges. Geneva: United Nations
Conference on Trade and
Development; 2000 13 Recent Advances in Knowledge Management [14] Verran H. Science and an African
Logic. Chicago, Illinois, USA: Chicago
University Press; 2001 [14] Verran H. Science and an African
Logic. Chicago, Illinois, USA: Chicago
University Press; 2001 [21] Kulathuramaiyer N, Pariyar A,
Bala P, Meenatchisundaram JL,
Kee-Man C. Preserving cultural
knowledge through community-led
MOOCs. IPSI BgD Transactions on
Internet Research (TIR) 2020;16(1):
1-11. Web of Science Core
Collection:Emerging Sources
Citation Index [15] Simeone T. Indigneous Traditional
knowledge and Intellectual Property
Rights. Canada Government: Political
and Social Affairs Division, Library of
Parliament; 2004. Available from:
https://publications.gc.ca/collections/
Collection-R/LoPBdP/PRB-e/
PRB0338-e.pdf [Accessed: September
1, 2021] [22] Agarwal A. Why massive open
online courses (still) matter [Video file]. 2014. Available from: https://www.ted. com/talks/anant_agarwal_why_
massively_open_online_cours es_still_
ma tter?language=en. [Accessed:
September 30, 2019] [16] Agrawal A. Dismantling the divide
between indigenous and scientific
knowledge. Development and Change. 1995;26:413-439 [16] Agrawal A. Dismantling the divide
between indigenous and scientific
knowledge. Development and Change. 1995;26:413-439 [23] Zaman T, Kulathuramaiyer N,
Yeo AW, Falak H. Modelling indigenous
knowledge creation as a living system. International Journal of Knowledge
Management Studies. 2015;6(2):136-150 [17] Bala P, Songan P, Hamid KA,
Harris RW, Khoo EGL. Bridging the
digital divide: The eBario experience. Sarawak Development Journal. 2002;5(1):63-78 [17] Bala P, Songan P, Hamid KA,
Harris RW, Khoo EGL. Bridging the
digital divide: The eBario experience. Sarawak Development Journal. 2002;5(1):63-78 [24] Zaman T, Yeo AW,
Kulathuramaiyer N. Harnessing mobile
technology for penans indigenous
botanical knowledge management. In:
Hendriks DLEM, Grant S, editors. Indigenous Lives in the Mobile Age. Sydney: University of Technology; 2014 [18] Ernberg J. Empowering communities
in the information society: An
international perspective. In: The First
Mile of Connectivity. Rome, Italy: Food
and Agriculture Organisation of the
United Nations; 1998. Available from:
http://www.fao.org/WAICENT/
FAOINFO/SUSTDEV/ Cddirect/
Cdre0028.html [Accessed: April 28, 2000] [18] Ernberg J. Empowering communities
in the information society: An
international perspective. [27] Zaman T, Yeo AW,
Kulathuramaiyer N. In: Bidwell NJ, Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861
Winschiers-Theophilus H, editors.
Harnessing Community’s Creative
Expression and Indigenous Wisdom to
Create Value. Tacit-Implicit-Explicit
(TIE) Knowledge Creation Model.
Proceedings of IKTC2011: Embracing
Indigenous Knowledge Systems in a
New Technology Design Paradigm.
Windhoek, Namibia; 2011 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge
DOI: http://dx.doi.org/10.5772/intechopen.101861 Winschiers-Theophilus H, editors. Harnessing Community’s Creative
Expression and Indigenous Wisdom to
Create Value. Tacit-Implicit-Explicit
(TIE) Knowledge Creation Model. Proceedings of IKTC2011: Embracing
Indigenous Knowledge Systems in a
New Technology Design Paradigm. Windhoek, Namibia; 2011 References In: The First
Mile of Connectivity. Rome, Italy: Food
and Agriculture Organisation of the
United Nations; 1998. Available from:
http://www.fao.org/WAICENT/
FAOINFO/SUSTDEV/ Cddirect/
Cdre0028.html [Accessed: April 28, 2000] [18] Ernberg J. Empowering communities
in the information society: An
international perspective. In: The First
Mile of Connectivity. Rome, Italy: Food
and Agriculture Organisation of the
United Nations; 1998. Available from:
http://www.fao.org/WAICENT/
FAOINFO/SUSTDEV/ Cddirect/
Cdre0028.html [Accessed: April 28, 2000] [18] Ernberg J. Empowering communities
in the information society: An
international perspective. In: The First
Mile of Connectivity. Rome, Italy: Food
and Agriculture Organisation of the
United Nations; 1998. Available from:
http://www.fao.org/WAICENT/
FAOINFO/SUSTDEV/ Cddirect/
Cdre0028.html [Accessed: April 28, 2000] [25] Zaman T, Yeo AW,
Kulathuramaiyer N. Augmenting
indigenous knowledge management
with information and communication
technology. International Journal of
Services Technology and Management. 2013a;19:137-148 [19] Bala P, Tan CE. Digital inclusion of
the Orang Asli of Peninsular Malaysia:
Remote virtual mechanism for usability
of telecentres amongst indigenous
peoples. EJISDC. 2021;87(4). DOI:
10.1002/isd2.12171 [26] Zaman T, Yeo AW,
Kulathuramaiyer N. Indigenous
Knowledge Governance Framework: A
holistic model for indigenous knowledge
management. ELOKA Workshop: Data
Management and Local Knowledge:
Building a Network to Support
Community-Based Research and
Monitoring. Colorado, U.S.A.:
University of Colorado Boulder; 2011a [20] Bala P. Social shaping of technologies
for community development:
Redeployment of information
communication technologies among the
Kelabit in Bario of the Kelabit highlands. In: Martin J, Hawkins L, editors. Information communication
technologies for human services
education and delivery: Concepts and
cases. Hershey, NY: Information Science
Reference; 2010. pp. 201-214 [27] Zaman T, Yeo AW,
Kulathuramaiyer N. In: Bidwell NJ, 14 15
|
https://openalex.org/W4392036060
|
https://environmentalevidencejournal.biomedcentral.com/counter/pdf/10.1186/s13750-024-00326-5
|
English
| null |
Biochar improves the nutrient cycle in sandy-textured soils and increases crop yield: a systematic review
|
Environmental evidence
| 2,024
|
cc-by
| 23,566
|
Bekchanova et al. Environmental Evidence (2024) 13:3
https://doi.org/10.1186/s13750-024-00326-5 Bekchanova et al. Environmental Evidence (2024) 13:3
https://doi.org/10.1186/s13750-024-00326-5 Environmental Evidence Open Access Open Access © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Biochar improves the nutrient cycle
in sandy‑textured soils and increases crop yield:
a systematic review Madina Bekchanova1,2* , Luca Campion1, Stephan Bruns1, Tom Kuppens1,3, Johannes Lehmann4,
Marijke Jozefczak2, Ann Cuypers2 and Robert Malina1 Abstract Background Biochar is a relatively new development in sustainable agricultural management that can be applied
to ameliorate degraded and less fertile soils, especially sandy-textured ones, to improve their productivity with respect
to crop production through improved nutrient availability. However, as the literature has shown, the response
of sandy-textured soils to biochar varies in terms of effect size and direction. Therefore, the present study systemati-
cally reviewed the available evidence to synthesize the impact of biochar amendments on aspects of the nutrient
cycle of sandy-textured soils. Methods Both peer-reviewed and gray literature were searched in English in bibliographic databases, organizational
web pages, and Internet search engines. Articles underwent a two-stage screening (title and abstract, and full-text)
based on predefined criteria, with consistency checks. Validity assessments were conducted, utilizing specifically
designed tools for study validity. Data extraction involved categorizing the various properties of the nutrient cycle
into nine main Soil and Plant Properties (SPPs), each of which was studied independently. Nine meta-analyses were
performed using a total of 1609 observations derived from 92 articles. Comparing meta-averages with and without
correction for publication bias suggests that publication bias plays a minor role in the literature, while some indication
for publication bias is found when accounting for heterogeneity by means of meta-regressions. Review findings According to the results, soil total and available nitrogen [N], phosphorous [P] and potassium [K],
plant nutrient level, and potential cation exchange capacity (CEC) increased by 36% (CI [23%, 50%]), 34% (CI [15%,
57%]), 15% (CI [1%, 31%]), and 18% (CI [3%, 36%), respectively, and N2O emission and mineral nutrient leaching
decreased by 29% (CI [− 48%, − 3%]) and 38% (CI [− 56%, − 13%). On average, however, biochar had no effect on soil
mineral nitrogen and nutrient use efficiency. Publication bias was identified in the response of effective CEC. After
corrections for publication bias, the response shifted from 36% to a negative value of − 34% (CI [− 50%, − 14%]). Meta-
regression found that the effect modifiers experimental continent, biochar application rate, and soil pH, explain result
heterogeneity. Stronger responses came from the continent of South America, higher application rates, and higher
pH soils. Overall, biochar is found useful for many SPPs of nutrient cycling of sandy-textured soils, thereby contributing
to increased crop yields in such soils. Abstract Keywords Soil properties, Soil ecosystem services, Soil amendment, Soil fertility, Sustainable agriculture, Food crop
yield, Biomass production, Meta-analysis *Correspondence:
Madina Bekchanova
madina.bekchanova@uhasselt.be
Full list of author information is available at the end of the article *Correspondence:
Madina Bekchanova
madina.bekchanova@uhasselt.be
Full list of author information is available at the end of the article Background Sandy-textured soils are marginal soil types for crop pro-
duction [1] due to their poor fertility resulting from low
organic matter and nutrient contents [2, 3], poor aggre-
gate stability, and low water-holding capacity [4]. How-
ever, for certain crops, such as onions or asparagus, sandy
soils are considered fertile soils [5]. These soils cover 6%
of the Earth’s surface [2], and some are being intensively
cultivated in many countries to meet the high demand for
food [6]. Sandy soils rely heavily on external inputs such
as organic and inorganic fertilizers to restore soil produc-
tivity by increasing their nutrient level and consequently
engaging in agriculture [7]. However, the use of inorganic
fertilizer can cause environmental pollution by releasing
N2O into the atmosphere, increasing NH3 volatilization
and N leaching [8]. This situation increases the need for
environmentally sound technologies that can improve
soil nutrient management and fertility. The existing heterogeneity in results in the litera-
ture on the size and magnitude of biochar’s impact on
nutrient cycling in sandy-textured soils highlights the
need for a systematic review to synthesize and better
comprehend the underlying causes. Although three
previous studies [8, 38, 39] have investigated similar
aspects, our study brings forward new contributions
both in content and methodology, complementing
existing studies. For example, these reviews focused
on biochar’s impact on the soil nutrient cycle, provid-
ing state-of-the-art insights. In contrast, our research is
grounded in a systematic review, strictly following Col-
laboration for Environmental Evidence (CEE) guide-
lines at every stage [40]. The review study conducted
by Zhang, Jing [38] mainly addressed the biochar effect
on soil microbial activity and nutrient uptake in field
studies, while our study includes different experimen-
tal designs such as field, greenhouse, and laboratory. Studies conducted by Biederman and Harpole [39] and
Liu, Zhang [8] concentrated primarily on soil nutrient
cycling (in general) following biochar application, in
contrast, ours exclusively investigates changes in sandy-
textured soils, covering a broad spectrum of nutrient
cycling components in such soils. Methodologically,
we introduce an in-depth analysis of publication bias,
which is often overlooked in ecological reviews [41]. Since CEE guidelines recommend updates every 5 years
[40], our study could serve as a valuable update to
previously published two review studies [8, 39]. This
review helps to reduce uncertainty and enhances clarity
for policymakers about the effect of biochar on the soil
nutrient cycle. © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Page 2 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Introduction [31, 32], resulting in increased nutrient availability,
extractable P, microbial biomass N, and reduced NO3
−
leaching of sandy-textured soils [28, 33]. However,
some other studies have shown that the same biochar
types have no effect on nutrient availability [36, 41]. Review studies have highlighted that a higher biochar
application rate might increase soil NH3 volatilization
and the magnitude of soil N2O emissions [8, 30]. In
contrast, Shakoor, Shahzad [34] found that the biochar
application rate had no effect on N2O emissions. Varia-
tions in the effect of biochar on soil nutrients can also
be caused by pyrolysis temperature [35–37].h Stakeholder engagement measured by comparing the treatment (with biochar) to
the control (without biochar). To fully understand the
potential heterogeneity in the impact of biochar on SPPs,
we also examined potential effect modifiers as explained
in sub-section Potential Effect Modifiers and Reasons for
Heterogeneity. A systematic review of biochar’s effect on soil ecosys-
tem services was first brought forward in a meeting of
the BASTA project, funded by the Research Foundation
Flanders, in December 2019 (BASTA stands for “Bio-
char’s added value in sustainable land use with targeted
applications”) [42]. The main aim of that project was the
production of biochar from various residual biomasses
and their application in different agricultural settings
(composting, anaerobic digestion, manure storage, grow-
ing media, and open field). Stakeholders of the project
(academia, biochar producers, research institutes, agen-
cies, policymakers) are aware of the lack of synthesis on
biochar’s soil ecosystem services and they support the
systematic review. In this review, we defined sandy-textured soils as soils
consisting of at least 50 percent sand, using the soil tex-
ture categorization by the United States Department of
Agriculture (Table 1) [43]. Sandy-textured soils were
chosen as the BASTA project will conduct experiments
on this type of soil and fill the current research gap. Fur-
thermore, our analysis focused exclusively on biochar
experiments conducted on the topsoil layer (0–0.3 m soil
depth) to examine the impact on this uppermost layer of
soil. Hence, the scope of this study is limited to review-
ing the changes in the topsoil nutrient cycle following
biochar application. The results of this review clarify the
interaction between biochar and sandy-textured soils and
its effect on the nutrient cycle, which can be beneficial
for further analysis of soil nutrients. The advisory committee, which was set up during the
development of the protocol, was interested in various
soil ecosystem services such as the water cycle, the nutri-
ent cycle, climate regulation, and biomass/crop produc-
tion. The advisory committee also contributed to the
creation of search terms and search databases. Because
the search terms and databases were comprehensive, the
number of results retrieved became too vast to fit within
the applicable time and money constraints. Hence, in the
full-text screening phase, the advisory committee pro-
posed focusing only on the nutrient cycle. This choice
was based on its importance for the BASTA project. Background They can use the results of this review
as a roadmap to facilitate policy recommendations for
biochar applications as a soil amendment. The results
could be valuable to biochar producers, farmers, and
other stakeholders that are interested in improving soil
conditions through biochar application. Our review
also discerned research gaps in current studies and pro-
vides a roadmap for further research. Biochar, a recent development in agricultural manage-
ment [9], has attracted attention as an environmentally
sound and sustainable soil management method to reg-
ulate soil nutrient cycles, reduce nitrogen effluents [10],
and increase the fertility of agricultural land [11, 12]. Biochar is usually obtained by pyrolysis of various bio-
mass materials (such as wood and wood-related residues,
manure and litter, peat, organic waste, and agricultural
waste) [13] at different production conditions [14]. As a
soil amendment, biochar can mitigate soil N2O emissions
[15], reduce NH3 volatilization in soil [16], and increase
soil N retention by reducing the need for fertilizer [17–
19]. Furthermore, recent studies have revealed that bio-
char can enhance the uptake of N, P, and K by plants [20,
21]. However, other studies have also reported negative
effects of biochar associated with increased N leach-
ing due to soil structure deterioration [22, 23], acceler-
ated soil NH3 volatilization due to raised soil pH, and
increased soil N2O emissions through enhanced nitri-
fication [24]. These contradictory results show that the
effects of biochar are still ambiguous. f
Not all soil types can benefit from biochar appli-
cation to the same extent [25]. For example, sandy-
textured soils are more likely to benefit from biochar
amendments in the long run than other textured soils
[25–28]. Even for sandy-textured soils, the effects of
biochar addition can differ based on the interaction
between biochar characteristics and the properties of
sandy-textured soils [29]. Soil nutrient availability after
biochar application essentially depends on the biochar
characteristics and biochar application rate [30]. Some
primary studies reported higher levels of nutrients in
biochars obtained from manure and biosolids than
those derived from straw- and wood-based feedstocks Page 3 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Stakeholder engagement All
deviations from the protocol are explained explicitly in
each subsection where the deviations occurred. Methods Based on our prior protocol [44], the guidelines of the
Collaboration for Environmental Evidence [40], and the
ROSES reporting standards (Additional file 1) [45], we
used a systematic review, including meta-analyses, to
synthesize the existing evidence base on the effects of
biochar characteristics on sandy-textured soils’ nutri-
ent cycle. We also identify the factors that influence the
effect of biochar on the nutrient cycle of sandy-textured
soils (such as experimental design, geographic location,
climate type, duration of the experiment, soil type, soil
depth, and soil treatment before biochar). Review objectiveh The primary focus of this review was to systematically
review and synthesize studies of the effect of biochar on
the nutrient cycle of sandy-textured soils. To this end, we
formulated the following research question: What is the
direction and magnitude of biochar’s impact on nutrient
cycling provided by sandy-textured soils? The research
question components were structured based on the PICO
model: population, intervention, comparator, and out-
come. The population in this study consists of sandy-tex-
tured soil types. The intervention is the soil amendment
using biochar, where the control of no biochar amend-
ment serves as the comparator. Finally, the outcome is a
change in sandy-textured soils’ nutrient cycle, which was Bibliographic databasesh The following bibliographic databases were used to col-
lect publications: Deviation from protocol As mentioned in the Stakeholder Engagement section,
we focused only on one ecosystem service—that is, the
nutrient cycle—instead of four. Considering the large
number of articles (> 2,500) to be screened during the
full-text screening (Fig. 1), it was decided—after consul-
tation with the co-authors and advisory committee—to
reduce the number of papers by focusing only on the Table 1 Soil types chosen for the study
Common names of soils
Sand (%)
Silt (%)
Clay (%)
Textural class
Sandy soils (coarse-textured)
86–100
0–14
0–10
Sand
70–86
0–30
0–15
Loamy sand
Loamy soils (moderately coarse-textured)
50–70
0–50
0–20
Sandy loam
Loamy soils (moderately fine-textured)
45–80
0–28
20–35
Sandy clay loam Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 4 of 34 search strings as outlined in the previously published
protocol [44]. Search strings used in each source were
stored and are provided in Additional file 2. nutrient cycle instead of four ecosystem services. Text-
mining made this possible (see Screening for more infor-
mation). The research question was changed accordingly. Since these adjustments were made after the first phase
of the screening process, we did not make any changes
to the search strings. Instead, we restricted the second
screening stage to keywords related to the nutrient cycle
based on the relevant search strings. Deviations from
the protocol are explicitly elaborated under the specific
sections (see “Searching for Articles”, “Screening”, “Eligi-
bility”, “Study validity assessment”, and “Data Synthesis
and”). Searching for articles
Search string
T
i
h • Web of Science “Core collection”: https://www.webof
knowledge.com Topic searches were used that searched by title—
abstract—keywords (TITLE—ABS- KEY). Three of the
four PICO components (population, intervention, and
outcome) were combined to build search terms. Within
each component, search terms were combined using
‘OR’ operators. To combine the three PICO components,
‘AND’ operators were used. Truncation characters (* and
$) were used to make the search more expansive. To con-
struct the search string (Table 2), an initial scoping exer-
cise was carried out on the Web of Science (WoS) ‘Core
collection’ database, which was complemented with
related synonyms by the advisory committee. The insti-
tutional subscription of UHasselt was used to collect the
search results.h • Scopus: https://www.scopus.com/ • AGRICOLA: https://www.agricola.nal.usda.gov/ • AGRIS: https://www.agris.fao.org/ • ProQuest Environmental Sciences and Pollution
Management: https://search.proquest.com/advanced • EBSCO Open Dissertations: https://biblioboard.
com/opendissertations/h • Networked Digital Library of Theses and Disserta-
tions: http://www.ndltd.org/ • Open access theses and dissertations: https://oatd.
org/ The search terms were designed to retrieve all publi-
cations on biochar’s effect on the nutrient cycle, water
cycle, climate regulation, and crop/biomass yield of
sandy-textured and contaminated sandy soils. No
changes were made to the search terms, as the restric-
tion to the scope of the nutrient cycle occurred after
the first screening of the records retrieved using those
terms. Both peer-reviewed publications and gray lit-
erature (not submitted to peer-reviewed journals) were
retrieved to minimize publication bias [46]. The following
sources were searched: bibliographic databases (for peer-
reviewed publications), organizational/institutional web-
sites, and web-based searches (for gray literature, which
can include publications, organizational reports, theses,
etc.). The search terms displayed in Table 2 are mostly
applicable to bibliographic databases as they have more
advanced search functions. When the search terms were
applied to organizational websites and Internet-based
searches, the search formula and Boolean operators were
simplified because some had limited search interfaces. During the protocol development, the comprehensive-
ness of the search was tested against 15 benchmark arti-
cles, and the results demonstrated the adequacy of our Search languageh The search was conducted in English and search results
in other languages were not considered for this review. As English is the common language within the review
team, it provided dual consistency checking in screening,
full-text screening, quality appraisal, and data extraction. Organizational websitesh The following organizational websites were searched to
obtain potential additional studies that were not cov-
ered by the bibliographic databases. As mentioned
above, some organizational websites did not have a very
advanced search function. Thus, some manual searches
were executed using the search terms defined in Table 2. Furthermore, six of these organization websites returned
no results or no related results (Additional file 2). • International Biochar Initiative: https://biochar-inter
national.org/biochar/ • UK Biochar Research Center: https://www.biochar.
ac.uk/research.php?id=10&r=a • US Biochar Initiative: https://biochar-us.org/biochar-
introductioni • European Biochar Certificate: https://www.europ
ean-biochar.org/en/home • Sonoma Biochar Initiative: https://sonomabiocharin
itiative.org/ • Israel Biochar Research Network: https://sites.google.
com/site/ibrnisraelbiocharnetwork/home Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 5 of 34 Fig. 1 ROSES flow diagram [73], showing the search results, screening processes, critical appraisal, and the final number of articles included
in the systematic review. Blue indicates that articles have gone to the next stage; red dotted lines imply that articles/studies have been removed
at that stage Fig. 1 ROSES flow diagram [73], showing the search results, screening processes, critical appraisal, and the final number of articles included
in the systematic review. Blue indicates that articles have gone to the next stage; red dotted lines imply that articles/studies have been removed
at that stage Page 6 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Search record database • Research Institute for Agriculture, Fisheries and Food
(ILVO, Belgium, Flanders): https://www.ilvo.vlaan
deren.be/EN/Home Endnote X9 was used to import the search results. When
it was not possible to import a certain document into the
software, a record was generated manually. After final-
izing all searches, the reference files were merged and
checked for duplicates. Before removing any of the dupli-
cates, they were rechecked and compared with regard to
title, abstract, and year of publication. Once all duplicates
were removed, the final version was checked with End-
note’s deduplication tool. • Netherlands Organisation for Applied Scientific
Research (TNO, The Netherlands): https://www.tno.
nl/en/ • Wageningen University & Research (The Nether-
lands):
https://www.wur.nl/en/wageningen-unive
rsity.htm • Julius Kühn Institute—Federal Research Centre for
Cultivated Plants (Germany): https://www.julius-
kuehn.de/en/ Organizational websitesh Environmental Evidence Table 2 Search terms (formatted in Web of Science)
Intervention
Population
Outcome
(TS = (biochar* OR "biochar amendment$" OR agrichar OR "black
carbon$" OR "biochar-mediated" OR charcoal OR "biochar field
study"))
(TS = ("hydrological control*" OR "hydraulic properties*"
OR "hydrologic* cycle" OR “water retention” OR “clean water”
OR “hydrological control” OR “water leak*” OR “water leach*”
OR "water availabl*" OR "soil water availability" OR "readily
available water" OR evaporation OR "water runoff" OR "plant
available water" OR "WHC" OR "soil humidity" OR "field capac-
ity" OR "nutrient loss" OR "soil moisture" OR "water holding
capacity" OR "water content" OR "water infiltration" OR "water
cycle" OR "nutrient availabl*" OR "available nutrient$" OR nutri-
ent$ OR "nutrient cycle" OR "nitrogen availabil*" OR "nutrient
exchange capacit*" OR "available nitrogen" OR NPK OR "nutri-
ent leak*" OR "nutrient leach*" OR "soil nutrients" OR "available
phosphorus" OR "phosphorus availabil*" OR "available potas-
sium" OR "potassium availabil*" OR "climate regula*" OR "climate
mitigation" OR "climate change mitigation" OR "climate chang*"
OR "global warming" OR “carbon sequestration” OR "soil carbon
sequestration" OR “carbon capture and storage” OR "emission$"
OR "CCS" OR “ammonia emission$*” OR “methane emission$*”
OR "nitrate emission$" OR "nitrous-oxide emission$" OR " NH4 "
OR " NO3 " OR " CH4 " OR " N2O " OR " CO2 " OR "greenhouse gas
emission$" OR "crop growth" OR "crop yield" OR "crop produc-
tion" OR "biomass growth" OR "biomass yield" OR "biomass
production" OR "raw material" OR "plant growth" OR "field"
OR yield OR "increase" OR "improve*" OR "decrease" OR "mitiga*"
OR "growth" OR "alleviat*" OR "effect$" OR "impact"))
(TS = ("sand* soil$" OR "sandy soil" OR “sand* loamy soil$”
OR “loamy sandy soil” OR “contaminated* soil$” OR "heavy metal*
soil$" OR "sandy loam soil" OR "sandy loam" OR ultisol OR "agri-
cultural soil" OR "loamy sand" OR "sandy clay loam" OR "cropping
system" OR “sandy calcareous soil”))
Search formula = Intervention + Population + Outcome Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 7 of 34 • Biochar for sustainable soils: https://biochar.inter
national/ Subsequently, we chose 100 lowest-ranking results that
were randomly selected. Google Scholar returned many
results that were related and unrelated to the review
objective; therefore, following [46] and [47], we only
downloaded the first 1000 relevant results using Publish
or Perish software, as stated in the protocol. Organizational websitesh The software
assisted in retrieving relevant articles and adding them to
the reference list in Endnote. Citations or patents were
not considered in Google Scholar. Finally, we did not
include the reference lists of relevant articles for the addi-
tional searches due to the large number of hits retrieved
from all sources. • Ithaka Institute: http://www.ithaka-institut.org/en/
home • New Zealand Biochar Research Centre: https://www.
massey.ac.nz/massey/learning/colleges/college-of-
sciences/research/agriculture-environment-research/
biochar-research-centre/biochar-research-centre_
home.cfm • Environmental Protection Agency [18]: https://www.
epa.gov/ • Research Institute for Organic Agriculture: https://
knowledge4policy.ec.europa.eu/organisation/resea
rch-institute-organic-agriculture_en Article screening and study eligibility criteria
Screening processh • Mercator Research Institute on Global Commons
and Climate Change (Germany): https://www.mcc-
berlin.net/en/index.htmlh The screening processes involved two steps, both of
which were performed by two reviewers independently. In the first step, the results were filtered by title and
abstract. All titles and abstracts were double-screened. Before the actual screening began, both reviewers
screened 100 randomly selected articles from the search
results to ensure consistency. If a reviewer had any
doubts about excluding a paper, it was marked and later
discussed with the other reviewer to come to an agree-
ment. The involvement of an adjudicating reviewer was
not needed, since the reviewers could reach a consensus. The level of agreement with respect to consistency was
verified using the Kappa statistic [47]. All disagreements
were discussed in detail between reviewers prior to start-
ing the actual screening.h • Thünen Institute—Federal Research Institute for
Rural Areas, Forestry and Fisheries (Germany):
https://www.thuenen.de/en/about-us/the-institute/ • Agroscope (Switzerland): https://www.agroscope.
admin.ch/agroscope/en/home • James Hutton Institute (United Kingdom): https://
www.hutton.ac.uk/ • Rothamsted Research (United Kingdom): https://
www.rothamsted.ac.uk/ • UK Centre for Ecology & Hydrology (United King-
dom): https://www.ceh.ac.uk/ The second step involved a review of the full text
of the remaining articles. This is the stage at which
we deviated from the protocol, as the vast number of
results conflicted with our time and budget constraints. Instead of reviewing all results remaining after the first
stage, we only screened results that were related to the
nutrient cycle of sandy–textured soils. To implement
this, we employed a text-mining method with the key-
words related to the nutrient cycle (Additional file 3)
using tidyverse, magrittr, and pdftools packages of R ver-
sion 3.3.0 [48]. Before applying text-mining, we deter-
mined the cut-off level of eight counts of nutrient cycle Study validity assessment Eligibility criteria
The eligibility criteria were based on the PICO model and
are summarized in Table 3. All studies included after the full-text screening were
critically appraised to assess their internal and external
validity and to evaluate their suitability for the data syn-
thesis. Studies were appraised for the different types of
biases by being categorized as ‘low,’ ‘moderate,’ and ‘high’
risk of bias. Population To
establish
eligible
populations,
we
excluded studies that conducted experiments on soils not
classified as sandy-textured soils (Table 1) and studies that
did not focus on the topsoil layer (0–0.3 m). Contrary to
the protocol [44], if the soil type upon which an experi-
ment was performed was not defined, it was excluded
from this review. Due to the vast number of articles, we
were unable to contact every author when the soil type
was not specified. The criteria were created based on the critical appraisal
tool of v0.3 developed by CEE [51], and previously pub-
lished systematic review studies in the journal Environ-
mental Evidence [52] to assess the internal validity of the
studies and consider many possible biases: selection bias,
performance bias, attrition bias, and reporting bias. In
this study, we adapted these frameworks to the research
question of our review and deviated from the protocol
by making some minor changes to the criteria in Addi-
tional file 5: Table S5.1. For example, studies that lacked
randomized experiments were classified as a ’high’ risk
of bias. This classification was made because such stud-
ies have the potential to introduce confounding factors
into the analysis. This decision was taken after consulta-
tion with experts in the field. Studies were summarized
as a ‘moderate’ or ‘high’ risk of bias if they were evaluated
as ‘moderate’ or ‘high’ risk of bias for at least one of the
critical appraisal criteria. Our main reason for excluding
studies with a ‘moderate’ risk of bias from the data syn-
thesis was that they would increase the amount of miss-
ing data related to effect modifiers, and this might cause
sampling bias, limiting the generalizability of the results
[53]. Thus, contrary to the protocol, only studies with a
‘low’ risk of bias were used to extract the necessary data
for data synthesis [44]. All information related to the
critical appraisal (e.g., excluded studies) was recorded in
Excel and presented in Additional file 6. Web‑based searches In addition to the bibliographic database and organiza-
tional website searches, web-based searches were also
conducted. Contrary to what is stated in the protocol,
we only used Google Scholar, mainly because it yielded
very similar results to Google. We performed this test
by randomly selecting 100 results from each dataset and
comparing them against each other. To achieve this, we
initially exported the search results to an Excel sheet. We used the Excel randomization function, assigning
a 9-digit random number between 0 and 1 to each cell. Bekchanova et al. Environmental Evidence (2024) 13:3 Page 8 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence plots received the same amount of fertilizers, manure, or
compost. keywords by manually screening 150 randomly selected
papers that remained after the first stage of screening and
then comparing them to the text-mining results for con-
sistency. After the text-mining, papers that did not yield
eight counts of nutrient cycle keywords were excluded,
reducing the number of articles by 1014 (Fig. 1). The
manual full-text screening of the remaining articles was
based on the eligibility criteria provided in the following
section, which was slightly different from the previously
published protocol [44], as stated in detail in the sub-sec-
tion of Eligibility Criteria. Articles (co-)authored by one
of the reviewers were assigned to another reviewer so
that no reviewer had to assess their own work. As in the
first phase of screening, consistency checking was per-
formed before screening using 10 percent of the remain-
ing articles. All articles left out at the manual full-text
screening stage were recorded, together with an explana-
tion for their omission (Additional file 4). Outcomes The outcomes considered were: positive, neg-
ative, or no changes in different components of the nutri-
ent cycle of sandy-textured soils. Changes in major soil
nutrients were considered for this study, such as nitrogen
(N), phosphorus (P), potassium (K), and other soil min-
eral processes. Following discussion with the advisory
committee, it was decided that the various components of
the nutrient cycle should be referred to as soil and plant
properties (SPPs) relevant to the nutrient cycle. Study designs Experimental primary studies, especially
laboratory experiments, greenhouse experiments, and
field experiments using control and treatment groups,
were included in the review. Earlier review studies were
accounted for by screening their reference lists. Study validity assessment Intervention The eligible intervention was biochar,
produced from biomass and used in agriculture as a soil
amendment. Some studies have used terms such as char-
coal and black carbon as synonyms for biochar; however,
in production and application, black carbon and charcoal
can differ from biochar. For instance, black carbon can be
made by burning fossil fuels as well as biomass [49], while
charcoal is mainly produced to provide affordable energy
to rural areas [50]. However, we included the terms ‘black
carbon’ and ‘charcoal’ in the search terms and checked,
at the full-text screening stage, whether they were made
from organic feedstocks with the intended application as
a soil amendment. We also included the term Agrichar, as
it is used in some organizational websites and is closely
related to biochar. Comparator Control sites or plots without any interven-
tion—that is, no biochar added—were used as a compara-
tor. Control sites or plots that were treated with fertilizers,
manure, or compost were also included if the intervention Page 9 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Table 3 Overview of eligibility criteria
Screening stage I means screening of the title and abstract, Screening stage II means screening of the full text
Criterion
Included
Excluded
Screening
stage I
Screening
stage II
Justification
Population
Sandy-textured soils with 50% or more sand
in the soil composition
Other soil textures or soil types not given
X
X
Marginal soils, such as sandy-textured soils, are
widely used in agricultural processes and seem
to benefit from biochar. Data coding and extraction strategy Data were extracted from studies assessed as having a
‘low’ risk of bias. When each study reported estimates
for different SPPs or multiple estimates for the same
SPPs, all estimates were placed in individual rows with
the mean value of the given result. Essential data were
extracted based on the data coding table provided in the
protocol [44], which was complemented with further soil
and biochar data during the data extraction (for exam-
ple, soil and biochar bulk density, pH, and dry weight)
(Additional file 7: Table S7.1). This additional data was
necessary to conduct the meta-regression analysis and
subsequent calculations, including the conversion of
measurement units. Each study’s full text was read, and
data were manually extracted and entered into a spread-
sheet. If the data were only presented in tables or graphs,
they were extracted using WebPlotDigitizer (WPD) [54]. We excluded studies for which the data was impossible
to decipher using WPD. As mentioned in the protocol,
data extraction was managed by one reviewer (the first
author) instead of two. However, prior to conducting the
meta-analysis, a third co-author, an expert in the field,
rigorously reviewed the extracted data. To guarantee data
accuracy and reliability, five random articles were chosen
for detailed cross-checking. Study validity assessment The heterogeneity
in the results of primary studies is the reason why
this review focuses on these soils
Intervention
Biochar obtained by pyrolysis and/or gasification
of various biomass materials
Biochar made from materials other
than biomass or technologies other
than pyrolysis and/or gasification
X
X
In accordance with the definition of biochar
adopted for this review, the included biochar
samples were specifically derived from biomass
through pyrolysis and/or gasification processes
Comparator
Control sites or plots without biochar that corre-
spond to intervention sites or plots
Control sites or plots that do not corre-
spond to intervention sites or plots
X
To ensure comparability between comparator
and intervention
Outcome
Positive, negative, or no changes in different
soil ecosystem processes of the nutrient cycle
of sandy-textured soils
Other soil ecosystem processes of sandy-
textured soil
X
These soil ecosystem processes of the nutrient
cycle were identified as relevant by the advisory
committee of this review, being also the partners
in the project funding this review (BASTA, Research
Foundation – Flanders, grant S000119N)
Study design
Lab (incubation), greenhouse, and field experi-
ments
Review studies
X
Primary study designs provide observations
for qualitative and quantitative synthesis
Publication type
Research articles, research reports, dissertations,
etc
Review studies
X
X
In order to consistently account for primary data
only, review studies were excluded
Language
English
Other languages
X
X
English was the common language
within the review team, so it provided dual consist-
ency at all stages of the screening Page 10 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 Table 4 Potential effect modifiers
Existing modifiers
New modifiers
Experimental country
Soil pH
Experimental design (i.e., greenhouse,
lab, field)
Biochar pH
Experimental condition
Biochar application with manure
Climate type
Biochar with compost
Duration of experiment
Feedstock for biochar
Biochar carbon content
Pyrolysis temperature
Biochar application rate
Type of soil Table 4 Potential effect modifiers As with screening, consistency checking was also car-
ried out for the critical appraisal. Again, all studies were
independently evaluated by the same two appointed
reviewers. In case of disagreements regarding any of the
criteria, it was discussed between reviewers until a con-
sensus was reached. Data synthesis and presentation
Data preparation Since nutrient cycling in the soil is a complex system, we
tried to extract all related measurements and, after dis-
cussion with experts, grouped them into nine major SPPs
based on the data availability, as shown in Table 5. This
decision was taken at the data extraction stage after the
protocol was published. We believe that the combination
of these nine SPPs provides a reasonable representation
of nutrient cycling. However, before combining them,
we checked the divergence of the outcomes of different
measurement methods. For example, there are different
soil phosphorus measurement methods, such as Olsen P
and Mehlich 1, 3 extraction, which means that the results
can differ greatly, in which case the grouping would lead
to inaccurate results. Thus, we analyzed the statistical
difference among these methods (Additional file 8) and
found that the difference was not statistically significant. Potential effect modifiers and reasons for heterogeneity f
y
gi
Soil total NPK is the total content of NPK nutrients,
while soil NPK availability is the nutrients in the soil
that are readily available to plants. Soil mineral nitrogen
includes processes such as nitrification, ammonifica-
tion, as well as ammonium and nitrate, which are forms
of plant-available nitrogen if they are exchangeable or in
soil solution. The nutrients (NPK) absorbed by a plant
and the nutrient content in the roots and shoots of the
plant are considered as plant nutrient level. The differ-
ence between the two types of CEC is their measurement
methods. For example, effective CEC can be measured
at soil pH, whereas potential CEC is usually measured at
a pH of 7 by very different methods. Thus, it is not rec-
ommended to merge them into one CEC. NUE can be
defined as the crop yield or biomass per input unit (that
is, fertilizer or biochar), while mineral N leaching is the
leaching of ammonium or nitrate to groundwater.f Potential effect modifiers and reasons for heterogeneity
To better understand possible heterogeneity in the
effects found by different studies, possible effect modifi-
ers were retrieved and recorded in the spreadsheet. The
list of effect modifiers shown in Table 4 was compiled in
consultation with the advisory committee. These effect
modifiers were published in the peer-reviewed protocol
of this review [44]. We made minor updates on the effect
modifiers listed in the protocol with some new modera-
tors (Table 4). During the data extraction processes, we realized that
these new modifiers can have an effect on response varia-
tion, so we included them in the list of possible modifiers
as well. The effect of these effect modifiers on the varia-
tion in the outcome is investigated by means of the meta-
regression analysis. In addition, the results in different units were converted
to the same units for each SPP for analysis purposes. Bekchanova et al. Environmental Evidence (2024) 13:3 Page 11 of 34 Bekchanova et al. Potential effect modifiers and reasons for heterogeneity Environmental Evidence Table 5 Grouped major SPPs relevant to the nutrient cycle
Grouped (SPPs)
Soil and plant properties (SPPs)
Soil total NPK
K concentration, K content, N concentration, N content, P concentration, P content, total K, total N, total P
Soil mineral nitrogen
Ammonification rate, available ammonium, available nitrate nitrogen, exchangeable ammonium, extract-
able ammonium, N mineralization, nitrate nitrogen rate, nitrification, soil ammonium, soil ammonium
concentration, soil ammonium content, soil nitrate nitrogen, soil nitric nitrogen
Plant nutrient level
Shoot N, Shoot P, Shoot K, K uptake, P uptake, N uptake, plant N
N2O emission
Nitrous oxide emission
Soil NPK availability
Available N, available P, available K, dissolved K, dissolved P, exchangeable K, extractable K, extractable P
Potential CEC
Potential CEC
Effective CEC
Effective CEC
Nutrient use efficiency
Nutrient use efficiency
Mineral N leaching
Cumulative ammonium leaching, cumulative nitrate nitrogen leaching, leached ammonium, leached
nitrate nitrogen, nitrate leaching Table 5 Grouped major SPPs relevant to the nutrient cycle K concentration, K content, N concentration, N content, P concentration, P content, total K, total N, total P K concentration, K content, N concentration, N content, P concentration, P content, total K, total N, total P
Ammonification rate, available ammonium, available nitrate nitrogen, exchangeable ammonium, extract-
able ammonium, N mineralization, nitrate nitrogen rate, nitrification, soil ammonium, soil ammonium
concentration, soil ammonium content, soil nitrate nitrogen, soil nitric nitrogen where Xb is the mean value of the soil nutrient cycle with
the biochar treatment and Xnb is the mean value of the
soil nutrient cycle with the control of no biochar. We use
the natural logarithmic transformation, LnRR = ln(RR) ,
to normalize the data [57]. The biochar treatment is
considered to have no effect when the lnRR = 1 , a posi-
tive effect when lnRR > 1 , and a negative effect when
lnRR < 1 . The variance of LnRR was calculated as
follows: Furthermore, some studies have reported biochar appli-
cation rates in different measurement units (such as kg/
ha, kg/pot, or g/kg or in percentage). All were converted
into t/ha in order to standardize measurement units. The
data were cleaned up before analysis using the tidyverse
package of R version 3.3.0 [48]. Descriptive statistics and narrative synthesis Data from the ‘low’ risk of bias studies were also used
for the narrative synthesis and descriptive statistics of
evidence. We have made tables and figures to show the
number of publications per year and per experimen-
tal country, experimental designs, types of experiments
(control, treatment), and duration of experiments. (2)
v =
SD2
b
(nb ∗X2
b) +
SD2
nb
(nnb ∗X2
nb) (2) where SDb and SDnb are the standard deviations (SD) of
treatment and control, respectively, and nb is the sample
size of the treatment and nnb is the control sample size
[57]. Where it was not possible to extract SD, the stand-
ard error (SE) was used to calculate SD [41]. According
to Lajeunesse [58], Eqs. 1 and 2 are biased when deal-
ing with small to medium sample sizes. Consequently,
the following equations, grounded in the second-order
Taylor expansion, have been proposed to mitigate these
biases [59]. where SDb and SDnb are the standard deviations (SD) of
treatment and control, respectively, and nb is the sample
size of the treatment and nnb is the control sample size
[57]. Where it was not possible to extract SD, the stand-
ard error (SE) was used to calculate SD [41]. According
to Lajeunesse [58], Eqs. 1 and 2 are biased when deal-
ing with small to medium sample sizes. Consequently,
the following equations, grounded in the second-order
Taylor expansion, have been proposed to mitigate these
biases [59]. Effect size and its variance The square root of the inverse of the effective sample size
is given by (7)
yi = β0 + s(2)ij + u(3)j + ǫij (7) where β0 is the overall estimate (or meta-analytic mean),
yij is the effect size i nested in study j , s(2)ij accounts for
within-study heterogeneity (level 2), u(3)j accounts for
between-study heterogeneity on (level 3), and ǫij is the
corresponding sampling error (level 1). We compared
a three-level model with a two-level model using the
anova function in R, where the results showed that the
three-level model is a better fit for our data. The model
is estimated with multilevel model with random effects
(ML-REML), as it provides unbiased estimates of the var-
iance parameters [55]. We further account for depend-
ence due to multiple observations from the same study by
clustering standard errors at the level of primary studies
[64, 65]. We used inverse variance weighting to assign a
greater weight to more precisely estimated studies [57].f where β0 is the overall estimate (or meta-analytic mean),
yij is the effect size i nested in study j , s(2)ij accounts for
within-study heterogeneity (level 2), u(3)j accounts for
between-study heterogeneity on (level 3), and ǫij is the
corresponding sampling error (level 1). We compared
a three-level model with a two-level model using the
anova function in R, where the results showed that the
three-level model is a better fit for our data. The model
is estimated with multilevel model with random effects
(ML-REML), as it provides unbiased estimates of the var-
iance parameters [55]. We further account for depend-
ence due to multiple observations from the same study by
clustering standard errors at the level of primary studies
[64, 65]. We used inverse variance weighting to assign a
greater weight to more precisely estimated studies [57].f (9)
1/ni =
n1i+n2i/n1in2i (9) where n1i is the sample size of the control, while n2i is the
sample size of the treatment. When the true effect size
is zero [64], the PET method works best. PEESE is also
regressed in a similar way as PET. The difference is that,
instead of SE (in our case (
1/ni) ), the squared SE—
that is, the variance (in our case ( 1/ni ) [41])—is used as
the predictor [64]. If no evidence for publication bias is
found, a ML-REML model can be applied [64]. Effect size and its variance In addition to narrative synthesis, a quantitative synthe-
sis—that is, a meta-analysis—was performed to assess the
effects of biochar on the nutrient cycle of sandy-textured
soils. Studies with incomplete or missing information
that could not be retrieved were excluded from the meta-
analysis. For each SPP (Table 5), we studied the effect of
biochar (treatment) compared to no biochar (control). In
total, nine meta-analyses were performed. All calcula-
tions were carried out using the metafor package in R ver-
sion 3.3.0 [48, 55]. For each comparison between biochar
and no biochar, we calculated the response ratio (RR),
which is the favored method for calculating the effect size
in ecological studies [39, 56]: (3)
LnRR2 = ln
Xb
Xnb
+ 1
2(CV2
b
nb
−CV2
nb
nnb
)
(4)
v(LnRR)2 = CV2
b
nb
+ CV2
nb
nnb
+ CV4
b
2n2
b
+ CV4
nb
2n2
nb (3) (4) where CV (sd/m) is the coefficient of variation. If the
SDs were reported then we used Eq. 3 and 4 to calculate
effect sizes and variances. However, most studies did not
include data on SD and SE. To address this, we used a
method known as "missing cases," following the sugges-
tion of Nakagawa, Noble [60], and employed Eqs. 5 and (1)
RR = Xb
Xnb RR = Xb
Xnb (1) Bekchanova et al. Environmental Evidence (2024) 13:3 Page 12 of 34 6. In this approach, we imputed the pooled CV using data
from studies that did report SDs. presence of publication bias, the funnel plot would be
asymmetrical, with smaller studies showing large effect 6. In this approach, we imputed the pooled CV using data
from studies that did report SDs. presence of publication bias, the funnel plot would be
asymmetrical, with smaller studies showing large effect 6. In this approach, we imputed the pooled CV using data
from studies that did report SDs. 6. In this approach, we imputed the pooled CV using data
from studies that did report SDs. Effect size and its variance presence of publication bias, the funnel plot would be
asymmetrical, with smaller studies showing large effect (5)
LnRR3 = ln
Xb
Xnb
+ 1
2
k
i=1(nbiCV bi
/k
i=1nbi]
2
nb
−
k
i=1(nnbiCV nbi
/k
i=1nnbi]
2
nnb
(6)
v(LnRR3) =
k
i=1(nbiCV bi
/k
i=1nbi]
2
nb
+
k
i=1(nnbiCV nbi
/k
i=1nnbi]
2
nnb
+
k
i=1(nbiCV bi
/k
i=1nbi]
4
2n2
b
−
k
i=1(nnbiCV nbi
/k
i=1nnbi]
4
2n2
nb (5) (6) sizes being more likely to be published, while smaller
studies without significant or large effects may be miss-
ing [64]. Each study may report multiple effect sizes for the
same SPP [61], violating the traditional independency
assumption [62]. We applied a multilevel model using
the rma.mv function in the metafor R package to account
for the dependency of effect sizes Specifically, we use a
three-level model that accounts for the sampling variance
of individual effect sizes (level 1), the variance between
effect sizes from the same study (level 2), and the vari-
ance between studies (level 3) [63] using the following
formula: PET-PEESE deals with small study effects that are the
potential indicators of publication bias. The PET method
is based on a regression model where the SE of the study’s
effect size is used to correct for publication bias: (8)
yi = β0 + β1SEi + s(2)ij + u(3)j + ǫij (8) Unlike stated in the formula, we used the square root
of the inverse of effective sample size (
1/ni) instead of
SE because it is recommended for the studies where the
effect size is calculated based on response rate [41]. LnRR
includes both treatment and control means in its point
estimate, leading to a correlation between these estimates
and their sampling standard errors [41], which causes a
funnel asymmetry [68]. Therefore, when the effect size
is computed in the form of LnRR, it has been proposed
to use ‘effective sample size’ as a moderator instead of SE
[41] and it also accounts for unbalanced sampling [69]. Review findings
Review descriptive statistics
Literature searches and screening Searches were carried out in bibliographic databases in
April 2021, which returned 12,191 records.h The majority of records from bibliographic databases
resulted from the EBSCO Open Dissertations, Web of
Science core collection, Scopus, and AGRICOLA, with
4407, 2410, 2458, and 1612 results, respectively (Fig. 1). Other sources, such as organizational websites sug-
gested by the advisory committee and Google Scholar,
were searched in May 2021 and provided 300 and 2600
recordings, respectively (Additional file 2). We used
Endnote X9 to check for duplicates, which resulted in
3371 recordings. Afterward, we conducted a manual
duplicate check and found 2036 extra duplicates. After
all duplicates were removed, 9684 unique records
remained. Once the title and abstract screening had
been implemented, 2738 studies remained. Because
the amount for the full-text screening was very large,
we decided to focus on one ecosystem service, namely
the nutrient cycle, instead of four by applying text-min-
ing, as we described in the section ‘screening process.’
After the text-mining, we were able to reduce the num-
ber to 1724 articles, of which the full text was screened. Full-text screening reduced the number of articles by
1142 for the reasons listed in Fig. 1. Subsequently, 582
remaining articles were critically appraised, of which
109 articles were eligible for qualitative and quantita-
tive synthesis (see Additional file 6). Of these, 17 were
not suitable for the quantitative synthesis, which meant
that 92 studies were used for the data extraction and
meta-analysis. yif
We used funnel plots with 1/SE (precision) for lnRR as
measures of uncertainty to visualize outliers in the data-
set (Additional file 11), as suggested by Nakagawa, Lag-
isz [41]. Outliers that seemed to contribute to excessive
noise were further investigated. Subsequently, we used
a conventional boxplot method to remove these outli-
ers from the dataset. The removal process was guided by
the calculation of the first quartile, the third quartile, and
the interquartile range (IQR) of 1/SE. Data points falling
below the first quartile or above the third quartile by a
factor of 10 times the IQR were considered outliers and
removed from the analysis. A sensitivity analysis was
performed to assess the presence and absence of outliers
on the direction and magnitude of the effect sizes (Addi-
tional file 11). Effect size and its variance We used funnel plots and PET (the precision-effect
test) and PEESE (the precision-effect estimate with
standard error) tests to check for publication bias, as
this method is suggested for ecological studies [41, 66]. Publication bias happens when studies with non-signif-
icant or minimal effect sizes (small studies) are unpub-
lished, resulting in a non-normal distribution of LnRR
[41, 67]. In the absence of publication bias, all studies
would be symmetrically distributed around the pooled
effect size within the funnel plot [64]. However, in the We employed state-of-the-art model selection, namely
randomized LASSO (least absolute shrinkage and selec-
tion operator) to examine the impact of effect modifiers
on the overall effect. LASSO is a statistical technique Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 Page 13 of 34 Page 13 of 34 Page 13 of 34 Bekchanova et al. Environmental Evidence used for variable selection and regularization in regres-
sion analysis. It is specifically designed to handle high-
dimensional data where the number of predictors is
larger than the number of observations. By applying a
penalty to the regression coefficients, LASSO encour-
ages some coefficients to be shrunk to zero, effectively
identifying the most significant predictors [70]. This
method plays a crucial role in preventing overfitting and
enhancing the interpretability of the regression model. The randomized LASSO model solves the variable selec-
tion problems by resampling the data and computing a
LASSO on each resampling [70, 71]. We quantified vari-
able importance by running the LASSO model for five
different model sizes (1–5 regressors) per SPP (except
for NUE due to a limited number of unique papers) and
generating selection probabilities for each predictor
(effect modifiers). For the variables selected, we calcu-
lated the coefficient sign through ordinary least squares;
the results are visualized in Additional file 12. When
the selected variable had a higher probability, the model
variable was found to have a stronger explanation for
the biochar effect on SPPs, while the weaker effect was
seen when the probability sign had a lower percentage. Consistently high probabilities indicate that the underly-
ing variable is a robust predictor of the effect size for the
respective SPP. The variables with zero-percent probabil-
ity were read as unimportant predictors. We addressed
publication bias in LASSO models by incorporating the
square root of the effective sample size in the LASSO
model. Review findings
Review descriptive statistics
Lit
t
h
d Review findings
Review descriptive statistics
Literature searches and screening
Searches were carried out in bibliographic databases in
April 2021, which returned 12,191 records.h Effect size and its variance If the measure of precision is not a robust pre-
dictor, there is additional evidence that publication bias
might not be present, and vice versa if the precision is
robust. We implemented LASSO in glmnet package in R,
and it is only based on fixed effects models [72]. used for variable selection and regularization in regres-
sion analysis. It is specifically designed to handle high-
dimensional data where the number of predictors is
larger than the number of observations. By applying a
penalty to the regression coefficients, LASSO encour-
ages some coefficients to be shrunk to zero, effectively
identifying the most significant predictors [70]. This
method plays a crucial role in preventing overfitting and
enhancing the interpretability of the regression model. The randomized LASSO model solves the variable selec-
tion problems by resampling the data and computing a
LASSO on each resampling [70, 71]. We quantified vari-
able importance by running the LASSO model for five
different model sizes (1–5 regressors) per SPP (except
for NUE due to a limited number of unique papers) and
generating selection probabilities for each predictor
(effect modifiers). For the variables selected, we calcu-
lated the coefficient sign through ordinary least squares;
the results are visualized in Additional file 12. When
the selected variable had a higher probability, the model
variable was found to have a stronger explanation for
the biochar effect on SPPs, while the weaker effect was
seen when the probability sign had a lower percentage. Consistently high probabilities indicate that the underly-
ing variable is a robust predictor of the effect size for the
respective SPP. The variables with zero-percent probabil-
ity were read as unimportant predictors. We addressed
publication bias in LASSO models by incorporating the
square root of the effective sample size in the LASSO
model. If the measure of precision is not a robust pre-
dictor, there is additional evidence that publication bias
might not be present, and vice versa if the precision is
robust. We implemented LASSO in glmnet package in R,
and it is only based on fixed effects models [72]. Study validity assessment
f h
d Most of the studies were assigned low validity due to
a high risk of bias (303 articles; 52.1%). The second-
largest group of studies was given moderate validity
due to a moderate risk of bias (170 articles; 29.2%). The
remaining studies were of high validity with a low risk
of bias (109 articles; 18.7%). Of the studies that had a high risk of bias, most suf-
fered from performance bias (27.8%) with confounding
factors being present, or it was hard to judge whether
confounders exist (Fig. 2). Because the study design
was not based on proper experiments (that is, control
vs. treatment), a further 25% of the studies were at
high risk of bias. Another 21% of high risk of bias were
due to the fact that the sampling method of the stud-
ies was not appropriate to collect data on the popula-
tion in question. The remaining studies lacked clear
statistical analyses (5%), mismatch of intervention and Page 14 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence 2
9
17
19
20
28
28
29
128
153
167
375
15
77
20
36
84
49
7
11
1
0
Heterogeneity/ effect modifiers
Objecves & Hypothesis
External Validity
Intervenon
Adequate data availability
Selecon bias
Stascal analysis
Degree of replicaon
Sampling
Study design
Performance bias
Excluded (High risk of bias)
Excluded (Medium risk of bias)
Number of papers
Fig. 2 Excluded studies with high and moderate risk of bias (in percentage) and
isk
ge-
een
and
ula-
ils)
mal
ons
ar-
dity
sis,
20
28
28
29
128
153
167
36
84
49
7
11
1
0
vailability
Selecon bias
Stascal analysis
Degree of replicaon
Sampling
Study design
Performance bias
f bias)
Excluded (Medium risk of bias)
entage)
Fig. 3 Number of publications by years Excluded (High risk of bias)
Fig. 2 Excluded studies with high and moderate risk of bias (in percentage) Excluded (Medium risk of bias) Excluded (Medium risk of bias) Excluded (High risk of bias) Fig. 2 Excluded studies with high and moderate risk of bias (in percentage) Fig. 3 Number of publications by years Fig. 3 Number of publications by years comparator (5%), inadequate data availability (3%), and
intervention description (3%). Study location Included articles were published from 2008 to 2021. Over
time, the number of publications increased—that were
more than 10 times as many publications in recent years
as at the beginning of this decade (Fig. 3). Included studies were conducted across 28 coun-
tries. Asia is the continent where the highest number
of studies were conducted (37.6%; Additional file 10:
Table 10.1), most of which were in China (22 studies;
23.6%). A small number of contributions came from
other Asian countries (such as Iran and India, which
had three publications each). The second-most pub-
lications came from the European continent (20.4%),
where many countries made small contributions,
although Finland stands out with five studies (Fig. 4). Africa accounted for 17.2% of studies, 11 of which were
conducted in Nigeria. Furthermore, 9.7% of studies
were carried out in South America, all of which came
from Brazil (nine studies). Finally, 8.6% of studies were Study validity assessment
f h
d One hundred and seventy articles had a moderate risk
of bias, mainly due to a lack of consideration of heteroge-
neity/effect modifiers (55.6%), the discrepancy between
intervention and comparator (selection bias) (12.4%), and
a lack of external validity (for example, the study popula-
tion, in particular, cannot be generalized to sandy soils)
(11.4%). Insufficient data availability (5.3%) and minimal
description of statistical analysis (7.3%) were also reasons
for a moderate risk of bias (Fig. 2). As mentioned ear-
lier, only studies with a low risk of bias and high validity
were used for both qualitative and quantitative analysis,
thereby deviating from the protocol. Fig. 3 Number of publications by years Study design and population of interest Of the 92 articles retained after critical appraisal, 56
were based on field experiments (60.9%), making it the
most frequent study design, often performed in sandy
loam (32%) and sandy soil (16%). The remaining field
experiments were conducted in sandy clay loam (6.5%),
loamy sand (5.4%) and, to a lesser extent, in coarse sand
and loamy soil. Greenhouse experiments were the sec-
ond-most applied study design with 25 articles (27.2%),
mainly used for sandy loam (13.9%) followed by sandy
soil (10.8%). The remaining 11 articles (11.9%) were lab-
based studies, for which sandy loam (7.5%) and sandy soil
(3.2%) were the most studied. Given that the largest num-
ber of studies were carried out in sandy loam and sandy
soils, their proportion in each experimental design is
much higher than for other types of soils (Fig. 5). Outcome In total, there were 49 soil properties that were grouped
by their relevance into nine SPPs: mineral N leaching,
effective CEC, potential CEC, N2O emission, NUE, plant
nutrient level, soil mineral nitrogen, soil NPK availabil-
ity, and soil total NPK. Soil total NPK was studied most
(28.9%), followed by soil NPK availability (23.7%) and soil
mineral nitrogen (16.6%; Fig. 7). There were as many arti-
cles on plant nutrient level as on N2O emissions (7.1%),
while there were 13 articles on effective CEC and 12 on conducted in North America (mostly the USA) and
6.5% in Oceania. conducted in North America (mostly the USA) and
6.5% in Oceania. with no amendment means that the control site has not
been treated with any other treatments and biochar only
means that only biochar is applied to untreated soils
(Fig. 6). The second-most common type of comparator
and treatment was control with fertilizer (23.2%), treated
with fertilizer only and no biochar, and biochar with fer-
tilizer, followed by control with manure without biochar
and biochar with manure (8.5%). There were also experi-
mental studies (4.7%) where the control was treated with
compost and biochar with compost being its interven-
tion. The remaining studies (2.4%) applied control with
fertilizer and manure, and control with fertilizer and
compost, and their associated treatments. The effect of
these treatments varies across different SPPs. Narrative synthesish The narrative synthesis was based on 92 articles with a
low risk of bias. These included articles yielded 1609 data
observations. A database of these studies with qualitative
and quantitative data is available in Additional file 9. In
the narrative synthesis, we cover the following aspects:
study location, study design and population of interest,
intervention and comparator, outcome, potential effect
modifiers, and sources of heterogeneity. Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 15 of 34 Fig. 4 Number of publications by experimental country Fig. 4 Number of publications by experimental country Intervention and comparatorh There were six types of controls, with corresponding
treatments. Ninety-two unique articles yielded a total of
129 counts for types of controls and treatments. Controls
with no amendment and treatment alone were the most
applied comparator and treatment (61.2%). A control Bekchanova et al. Environmental Evidence (2024) 13:3 Page 16 of 34 Bekchanova et al. Environmental Evidence Fig. 5 Proportion of population of interest in different study designs
Fig. 6 Type of treatments with their corresponding controls Fig. 5 Proportion of population of interest in different study designs Fig. 5 Proportion of population of interest in different study designs Fig. 5 Proportion of population of interest in different study designs Fig. 6 Type of treatments with their corresponding controls Fig. 6 Type of treatments with their corresponding controls Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 17 of 34 Fig. 7 Number of articles for each SPP Fig. 7 Number of articles for each SPP (231), and Oceania (153). The fewest observations were
supplied from North America [86]. potential CEC. Less studied SPPs were NUE and mineral
N leaching (both representing 2.4% of articles). Various types of feedstocks were used for the produc-
tion of biochar, which were classified into three catego-
ries: agricultural residue, manure/digestate, and woody
biomass [74]. Among these, agricultural residues domi-
nated both in the number of articles [52] and in the num-
ber of data sets (844, after aggregation). Woody biomass
was also often studied, with 585 observations aggregated
from 42 articles (Table 6). On the contrary, only 14 arti-
cles considered manure/digestate, with 180 observations. Articles were also categorized with regard to pyrolysis
temperature: ‘low’ when the pyrolysis temperature is less
than or equal to 400 ℃, ‘medium’ when the temperature
is between 400 and 600 ℃, and ‘high’ when the tempera-
ture is equal to or greater than 600 ℃ [38]. In total, 52
articles were conducted on medium pyrolysis tempera-
ture, with 823 observations; low pyrolysis temperature
was studied in 30 articles, yielding 549 aggregated data
sets, and high pyrolysis temperature was not applied in
many experimental studies, with 173 data sets from 14
articles. There were four articles with 64 missing data
sets (Table 6). Altogether, this represents more than 92
unique articles, because several unique articles have not
studied just one type of pyrolysis temperature or type of
feedstock, but several. Effect modifiers and sources of heterogeneityf According to the data, some effect modifiers were
reported in almost every paper, such as geographic
location, experimental design, types of feedstock, and
pyrolysis temperature. Annual temperature and biochar
application rate were overlooked a few times. The least
reported effect modifiers were the type of climate and
annual precipitation. Soil pH, biochar pH, soil bulk den-
sity and soil dry weight were barely reported. Hence, to
provide consistency in the analysis, if there were more
than 50% missing values for any of the effect modifiers,
they were no longer considered effect modifiers in the
analysis (Additional file 9). Description of the data from primary studies included
in the meta‑analysis Most observations (1341) were retrieved from 83 peer-
reviewed while 268 observations from nine articles
were grey literature, comprised of five dissertations (120
observations), three master’s theses (132 observations),
and one university repository (16 observations). A sig-
nificant number of observations came from Asia (467
observations), followed by Africa (412). The remaining
observations came from Europe (259), South America For analysis purposes, the biochar application rate is
also divided into four groups based on data availability, Bekchanova et al. Environmental Evidence (2024) 13:3 Page 18 of 34 Bekchanova et al. Description of the data from primary studies included
in the meta‑analysis Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 19 of 34 changes from 38% (CI [6%, 78%]) to − 34% (CI [− 50%,
− 14%]). such as ‘ < 10’, ‘10–30’, ‘30–50’ and ‘ > 50’ t/ha. Biochar
application rates ‘ < 10’ and ‘10–30’ were the most com-
monly applied rates, the former being applied in 51 arti-
cles with 664 observations and the latter in 49 articles
with 536 aggregated observations. The remaining two
other categories, ‘30–50’ and ‘ > 50’, generated 194 obser-
vations from 17 articles and 215 observations from 19
articles, respectively (Table 6). Given that the duration of
the experiment varied in each study, we classified them
into five groups as follows: ‘ < 60,’ ‘60–160,’ ‘160–402,’
‘402–730,’ and ‘ > 730’ days. The most common experi-
ment duration was ‘60–160’ days, studied in 28 articles
(503 data sets). Subsequent experiments of ‘160–402’
and ‘402–730’ days were with data sets of 388 and 319,
respectively (Table 6). Observations 246 and 152 were
assigned to the shortest and longest experimental periods
of ‘ < 60’ and ‘ > 730’days, respectively. Other SPPs of sandy-textured soils had an effect after
biochar amendment before and after the publication bias
correction. When the CI of the effect size did not over-
lap with zero, it was deemed significantly different from
zero. For example, the soil total NPK of sandy-textured
soils increased by 36% (CI [23%, 50%]) after being treated
with biochar. Soil mineral nitrogen was also augmented
after biochar application by 5%; however, it was not sig-
nificantly different from a null (CI [− 8%, 19%]). This is
followed by plant nutrient levels, which had an increase
of 15% (CI [1%, 31%]) in sandy-textured soils induced
with biochar. N2O emissions were reduced significantly
by 29% (CI [− 48%, − 3%]) after biochar, resulting in
decreased emissions into the atmosphere. Soil NPK
availability was the second highest responded SPP of
sandy-textured soils following biochar application (34%,
CI [15%, 57%]), followed by potential CEC (18%, CI [3%,
36%]). Since no publication bias was detected in the
response of these SPPs, the responses with correction for
publication bias support the findings without correction
for publication bias (Figs. 8a and b). There were 42 articles with 556 observations that
applied irrigation before and after biochar application,
while 51 articles reported no irrigation application. The effect of biochar on SPPs related to nutrient cycleh The effect of biochar on SPPs related to nutrient cycle
The results of nine meta-analyses are shown in Fig. 8
(one meta-analysis for each of the nine SPPs). Of the total
observations used in the meta-analysis, 4% were detected
as outliers based on the criterion set in the method sec-
tion of “Effect Size and its Variance” (Additional file 11). When we removed outliers to analyze the sensitivity
of the results, the mean effect sizes did not vary from
positive to negative, from significant to non-significant,
or vice versa, for any of the SPPs reported here. There-
fore, we consider the results to be robust to the outlier
removal and we only provide the results without outliers. Figure 8 presents the estimated meta-averages for the
nine SPP without correction for publication bias (Fig. 8a)
and with correction for publication bias (Fig. 8b). Visual
inspection of funnel plots and the PET-PEESE models
suggest that publication bias is of minor importance in
the literature (Additional file 13). This is also consistent
with the observation that the estimated meta-average
and confidence intervals are similar for the models with
and without correction for publication bias (Fig. 8). An
exception applies for Effective CEC, where the estimate The effect of biochar on SPPs related to nutrient cycle
The results of nine meta-analyses are shown in Fig. 8
(one meta-analysis for each of the nine SPPs). Of the total
observations used in the meta-analysis, 4% were detected
as outliers based on the criterion set in the method sec-
tion of “Effect Size and its Variance” (Additional file 11). When we removed outliers to analyze the sensitivity
of the results, the mean effect sizes did not vary from
positive to negative, from significant to non-significant,
or vice versa, for any of the SPPs reported here. There-
fore, we consider the results to be robust to the outlier
removal and we only provide the results without outliers. In addition to SPPs, we also performed a supplemen-
tary analysis to assess the effect of biochar on food crop
yield and biomass production based on the observations
from the same papers. Description of the data from primary studies included
in the meta‑analysis Environmental Evidence Table 6 Description of the observations included in the meta-analysis
Variables
Categories
Subcategories
Unique papers (number
of observations)
Paper type
Peer-reviewed
Peer-reviewed
83 (1,341)
Gray literature
Dissertations
5 (120)
Master’s theses
3 (132)
University repository
1 (16)
Experimental design
Field experiment
Field
53 (893)
Controlled experiments
Greenhouse
19 (505)
Laboratory
11 (211)
Experimental continents
Africa
–
16 (412)
Asia
–
35 (468)
Europe
–
19 (254)
North America
–
8 (85)
Oceania
–
6 (149)
South America
–
9 (231)
Feedstock type
Agricultural residue
–
52 (844)
Manure/digestate
–
14 (180)
Wood-based
–
42 (585)
Pyrolysis group (°C)
≤ 400
Low
30 (549)
400 < ; > 600
Medium
52 (823)
≥ 600
High
14 (173)
Biochar application rate (t/ha)
< 10
–
51 (664)
10–30
–
49 (536)
30–50
–
17 (194)
50 <
–
19 (215)
Experiment duration (days)
< 60
–
14 (246)
60–160
–
28 (503)
160–402
–
23 (384)
402–730
–
20 (318)
730 <
–
9 (152)
Types of treatments
Biochar alone
–
79 (1,020)
Biochar with compost
–
6 (33)
Biochar with manure
–
11 (127)
Biochar with fertilizer
–
30 (401)
Biochar with fertilizer & compost
–
1 (6)
Biochar with fertilizer & manure
–
2 (12)
Tillage application
Not tilled
–
64 (1,047)
Tilled
–
29 (552)
Irrigation application
Not irrigated
–
51 (1,053)
Irrigated
–
42 (556)
Base fertilizer application before and after
biochar
Fertilizer applied
–
42 (589)
Fertilizer not applied
–
51 (1,010)
SPPs
Soil total NPK
–
61 (506)
Soil mineral nitrogen
–
35 (247)
Plant nutrient level
–
15 (106)
N2O emission
–
15 (53)
Soil NPK availability
–
50 (468)
Potential CEC
–
12 (37)
Effective CEC
–
13 (49) Table 6 Description of the observations included in the meta-analysis
Variables
Categories
Paper type
Peer-reviewed
Gray literature
Experimental design
Field experiment
Controlled experiments
Experimental continents
Africa
Asia
Europe
North America
Oceania
South America
Feedstock type
Agricultural residue
Manure/digestate
Wood-based
Pyrolysis group (°C)
≤ 400
400 < ; > 600
≥ 600
Biochar application rate (t/ha)
< 10
10–30
30–50
50 <
Experiment duration (days)
< 60
60–160
160–402
402–730
730 <
Types of treatments
Biochar alone
Biochar with compost
Biochar with manure
Biochar with fertilizer
Biochar with fertilizer & compost
Biochar with fertilizer & manure
Tillage application
Not tilled
Tilled
Irrigation application
Not irrigated
Irrigated
Base fertilizer application before and after
biochar
Fertilizer applied
Fertilizer not applied
SPPs
Soil total NPK
Soil mineral nitrogen
Plant nutrient level
N2O emission
Soil NPK availability
Potential CEC
Effective CEC
NUE
Mineral N leaching Table 6 Description of the observations included in the meta-analysis Subcategories
Unique pape
of observatio
Peer-reviewed
83 (1,341)
Dissertations
5 (120)
Master’s theses
3 (132)
University repository
1 (16)
Field
53 (893)
Greenhouse
19 (505)
Laboratory
11 (211)
–
16 (412)
–
35 (468)
–
19 (254)
–
8 (85)
–
6 (149)
–
9 (231)
–
52 (844)
–
14 (180)
–
42 (585)
Low
30 (549)
Medium
52 (823)
High
14 (173)
–
51 (664)
–
49 (536)
–
17 (194)
–
19 (215)
–
14 (246)
–
28 (503)
–
23 (384)
–
20 (318)
–
9 (152)
–
79 (1,020)
–
6 (33)
–
11 (127)
–
30 (401)
–
1 (6)
–
2 (12)
–
64 (1,047)
–
29 (552)
–
51 (1,053)
–
42 (556)
–
42 (589)
–
51 (1,010)
–
61 (506)
–
35 (247)
–
15 (106)
–
15 (53)
–
50 (468)
–
12 (37)
–
13 (49)
–
5 (23)
–
5 (44) Bekchanova et al. Description of the data from primary studies included
in the meta‑analysis Some
studies also mentioned the use of tillage, which was only
applied in field experiments, and 29 articles reported the
use of tillage during the experiment with 552 observa-
tions (Table 6). Several control soils were treated with
inorganic or organic fertilizer before being used in the
experiment. Specifically, 42 articles (589 observations)
indicated fertilizer as a base treatment. These effect mod-
ifiers, in turn, can affect the overall effect of biochar on
SPPs, which we discuss in the following sections. No significant difference was found between control
and biochar treatments for NUE (− 3%, CI [− 17%, 14%]). Finally, mineral N leaching from sandy-textured soils was
reduced by 38% (CI [− 56%, − 13%]), contributing to less
groundwater contamination. The results were practically
the same before and after correction for publication bias. It should be noted that meta-analyses of some SPPs—
such as NUE and mineral N leaching—are based only
on a few primary studies, so the corresponding results
should be read with caution. The effect of biochar on SPPs related to nutrient cycleh 8 The response of SPPs to biochar application, n means the number of observations: a estimated meta-averages without correction
for publication bias; b estimated meta-averages corrected for publication bias (PET & PEESE model). An effect is significant (P < 0.05) if its
95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1 , a positive effect
when lnRR > 1 , and a negative effect when lnRR < 1 . Confidence intervals are not symmetrical around the effect sizes because they were
back-transformed from the log response ratio Fig. 8 The response of SPPs to biochar application, n means the number of observations: a estimated meta-averages without correction
for publication bias; b estimated meta-averages corrected for publication bias (PET & PEESE model). An effect is significant (P < 0.05) if its
95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1 , a positive effect
when lnRR > 1 , and a negative effect when lnRR < 1 . Confidence intervals are not symmetrical around the effect sizes because they were
back-transformed from the log response ratio The effect of biochar on SPPs related to nutrient cycleh Food crop yields are annual food
crops such as cereals, maize, wheat, and rice, as well
as fruits and vegetables, while biomass production is
defined here as the shoot of a plant and all types of plants
that are produced as above-ground biomass and do not
include the harvested portion of food crops. As shown
in Fig. 9, food crop yield increased by 20% (CI [6%, 36%])
in sandy-textured soils treated with biochar, but biomass
production showed no effect (− 8%, CI [− 16%, 1%]). No
publication bias effect was detected. Figure 8 presents the estimated meta-averages for the
nine SPP without correction for publication bias (Fig. 8a)
and with correction for publication bias (Fig. 8b). Visual
inspection of funnel plots and the PET-PEESE models
suggest that publication bias is of minor importance in
the literature (Additional file 13). This is also consistent
with the observation that the estimated meta-average
and confidence intervals are similar for the models with
and without correction for publication bias (Fig. 8). An
exception applies for Effective CEC, where the estimate f
Provided that 60% of the included studies did not
report SD or SE to calculate the variations of the total
effect sizes, they were imputed with the pooled CV using
data from studies that did report SDs as described in the
methods section of ‘Effect size and its variation calcula-
tion.’ A sensitivity analysis was conducted by removing all
observations with variations determined based on pooled Page 20 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence ich changed some of the average treatment effects
Explaining heterogeneity: meta‑regression analysis o
The response of SPPs to biochar application, n means the number of observations: a estimated meta-averages without correction
ication bias; b estimated meta-averages corrected for publication bias (PET & PEESE model). An effect is significant (P < 0.05) if its
nfidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1 , a positive effect
RR > 1 , and a negative effect when lnRR < 1 . Confidence intervals are not symmetrical around the effect sizes because they were
nsformed from the log response ratio 8 The response of SPPs to biochar application, n means the number of observations: a estimated meta-averages without correction Fig. Explaining heterogeneity: meta‑regression analysis of each
SPP CV, which changed some of the average treatment effects
to non-significant (Additional file 11: Fig. S11.11). This is
because fewer observations result in less power, and the
loss of significance is not surprising. If the variations had
not been determined (based on the pooled CV) when SD
or SE was absent, huge amounts of important data would
have been missed in the analysis, and we would have been
limited to drawing a conclusion based on a few datasets. We analyzed the reasons for variations in the response
of each SPP to biochar application using the effect
modifiers mentioned in the sub Sect. "Potential Effect
Modifiers and Reasons for Heterogeneity". We pre-
sent the results of the LASSO analysis if the variables
selected in a minimum of one out of five LASSO mod-
els as explained in the sub-section of Effect Size and its Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 Page 21 of 34 Page 21 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Variance. The visualization of the full variable selection
is given in Additional file 12. Based on our analysis, the
following moderators were the main predictors explain-
ing the heterogeneity in the responses of SPPs to biochar
application: experimental continent, duration, biochar
application rate, fertilizer application rate, soil pH, and
publication year. In the sections below, we discuss the key
predictors for the response of each SPP based on Table 7,
and the results are visualized. LASSO analysis also underlined the significance of
medium-level fertilizer application with biochar as a
predictor, demonstrating its negative impact on the
response of soil total NPK (Fig. 10). This could be attrib-
uted to the relatively lower fertilizer application rate as
some studies have demonstrated significant benefit of
higher fertilizer application rates in combination with
biochar for soil NPK content [77, 78]. Publication year
was also highlighted as an influential predictor, indicat-
ing a positive trend in soil total NPK response to biochar
application over time. Soil total NPK According to the LASSO analysis, the
most important predictors affecting the response of
total soil NPK were biochar experimental continent,
biochar application rate, fertilizer application rate, and
publication year (Table 7). Specifically, the experimental
continent, such as South America, stood out as the most
important and key predictor, positively influencing the
response. Explaining heterogeneity: meta‑regression analysis of each
SPP In contrast, the response of soil total NPK was
negative in Oceania. This variation can be attributed to
the region’s specific climate and environmental factors,
notably rainfall patterns and temperature fluctuations. South America’s climate has appeared to enhance total
NPK in sandy-textured soils following biochar applica-
tion. Biochar application rate, particularly the highest
application rate, was the second important predictor for
the response of soil total NPK (Fig. 10), with a positive
impact on the response. Several studies showed that
higher biochar application rates led to an increase in
total NPK content in sandy-textured soils [8], contrib-
uting to their improved quality and fertility. A higher
application rate of biochar enriches soil nutrient con-
tent through mechanisms such as increased soil pH,
increased organic matter, and improved CEC [75, 76]. Soil mineral nitrogen The significant predictors of soil
mineral nitrogen response to biochar application were
soil pH, biochar application rate, soil texture, and experi-
mental duration (Table 7). A positive response in soil min-
eral nitrogen to biochar application was observed when
the soil pH ranged from 5.6 to 6.5. This finding aligns with
the results reported by [80, 81]. In sandy-textured soils,
higher pH levels contribute to reducing soil acidity, creat-
ing a favorable environment for processes like mineraliza-
tion and nitrification, ultimately leading to increased soil
mineral nitrogen. According to LASSO, a higher biochar
application rate increased soil mineral nitrogen, likely due
to enhanced microorganism activity promoting greater N
mineralization and biochar components with a high C:N
ratio stimulating N immobilization [80, 82]. Loamy sand had a negative impact on the response
(Fig. 11), which could be a result of limited improvement
in soil temperature, moisture, and aeration, which, in
turn, failed to stimulate soil mineral nitrogen with bio-
char application [83–85]. Furthermore, the influence of
biochar on soil mineral nitrogen appears to diminish over Fig. 9 The response of food crop yield and biomass production to biochar application, n means the number of observations. An effect is significant
(P < 0.05) if its 95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1, a positive
effect when lnRR > 1 , and a negative effect when lnRR < 1 . The reason why confidence intervals are not symmetrical around the effect sizes
is that they were transformed back from the log response ratio Fig. Page 22 of 34
Bekchanova et al. Environmental Evidence (2024) 13:3
Table 7 Coefficient signs following Randomized LASSO selection for each SPPs
Soil total NPK
Soil
mineral
nitrogen
Plant
nutrient
level
N2O emission
NPK
availability
Potential CEC
Effective CEC
NUE
Mineral
N
leaching
Study location and Climate
C
ti
t
±
± Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 Page 22 of 34 Table 7 Coefficient signs following Randomized LASSO selection for each SPPs
The direction of effect: “−” means that the effect of the predictor was negative in all selected models; “ + ” means the predictor was positive in all selected models. The
effect direction was consistent in the LASSO analysis; that is, the effect of the predictor was always positive or always negative. To determine the coefficient sign for
the selected variables, we employed ordinary least squares (79) regression. However, we could not perform LASSO analyses due to a scarcity of available papers on
NUE and mineral N leaching
Soil total NPK
Soil
mineral
nitrogen
Plant
nutrient
level
N2O emission
NPK
availability
Potential CEC
Effective CEC
NUE
Mineral
N
leaching
Study location and Climate
Continent
±
±
+
+
+
Annual temperature
Annual precipitation
Experimental condition
Experimental design
–
Experimental duration
–
±
+
Biochar application rate
+
+
+
-
±
+
–
Biochar with fertilizer
Fertilizer application
rate
–
–
±
Biochar with manure
Manure application rate
Biochar properties
Feedstock types
Pyrolysis temperature
+
–
Soil status
Soil texture
–
+
Soil pH
+
–
–
–
Soil minimum depth
Soil maximum depth
+
Fertilizer before biochar
Manure before biochar
Irrigation application
Tillage application
Publication status and bias
Publication year
+
–
+
-
Square root of effective
sample size
+
+
+
+
+
+ Table 7 Coefficient signs following Randomized LASSO selection for each SPPs The direction of effect: “−” means that the effect of the predictor was negative in all selected models; “ + ” means the predictor was positive in all selected models. The
effect direction was consistent in the LASSO analysis; that is, the effect of the predictor was always positive or always negative. To determine the coefficient sign for
the selected variables, we employed ordinary least squares (79) regression. However, we could not perform LASSO analyses due to a scarcity of available papers on
NUE and mineral N leaching an extended duration (Fig. 11). As explained by Singh
and Cowie [86], this diminishing effect can be attributed
to the depletion of labile soil organic carbon [87]. We
addressed publication bias with the square root of the
effective sample size in the LASSO model, and according
to the analysis, publication bias was also detected. Explaining heterogeneity: meta‑regression analysis of each
SPP 9 The response of food crop yield and biomass production to biochar application, n means the number of observations. An effect is significant
(P < 0.05) if its 95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1, a positive
effect when lnRR > 1 , and a negative effect when lnRR < 1 . The reason why confidence intervals are not symmetrical around the effect sizes
is that they were transformed back from the log response ratio Fig. 9 The response of food crop yield and biomass production to biochar application, n means the number of observations. An effect is significant
(P < 0.05) if its 95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1, a positive
effect when lnRR > 1 , and a negative effect when lnRR < 1 . The reason why confidence intervals are not symmetrical around the effect sizes
is that they were transformed back from the log response ratio Page 22 of 34
Bekchanova et al. Environmental Evidence (2024) 13:3
Table 7 Coefficient signs following Randomized LASSO selection for each SPPs
Soil total NPK
Soil
mineral
nitrogen
Plant
nutrient
level
N2O emission
NPK
availability
Potential CEC
Effective CEC
NUE
Mineral
N
leaching
Study location and Climate
C
ti
t
±
± ditions (Fig. 12). Biochar application rates, mainly higher
rates, had a positive effect on the response of plant nutri-
ent levels (Fig. 12). In contrast, some studies found that
higher application rates may significantly reduce nutri-
ent uptake [88, 89]. However, Liu, Zhang [90] highlighted
biochar’s ability to maximize N uptake in soils with poor
structure, such as sandy soils. The benefit of biochar
application to plant nutrient levels in sandy soils can be
explained by biochar’s ability to improve soil structure
and water-holding capacity [91]. LASSO analysis also
identified low pyrolysis temperature as having a positive
impact on the response (Fig. 12). Biochar produced at low
temperatures can lead to biochar with higher nutrient Plant nutrient level The key predictors influencing the
response of plant nutrient levels were the experimental
continent, biochar application rate, and pyrolysis tem-
perature (Table 7). The negative influence of biochar on
plant nutrient uptake in Oceania and its positive response
in Asia can be attributed to regional environmental con- Page 23 of 34 Page 23 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Fig. 10 The results of randomized LASSO on the key predictors in soil total NPK response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models Fig. 10 The results of randomized LASSO on the key predictors in soil total NPK response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models from the meta-analysis conducted by Liu, Zhang [90]. Biochar reduces N2O emissions in high-pH soils by pro-
moting nitrification, converting NH+
4 to NO−
3 , as elevated
pH levels improve aeration and microbial activity [94]. The results also indicated a slightly positive effect of pub-
lication bias on response (Fig. 13). content that can support nutrient release over time [92],
making it beneficial for plant nutrient uptake. The results
also indicate the presence of publication bias that is posi-
tively impacting on the response. N2O emission Experiment duration, biochar applica-
tion, and soil pH were selected as influential predictors
by LASSO (Table 7) for the N2O emission response. Page 22 of 34
Bekchanova et al. Environmental Evidence (2024) 13:3
Table 7 Coefficient signs following Randomized LASSO selection for each SPPs
Soil total NPK
Soil
mineral
nitrogen
Plant
nutrient
level
N2O emission
NPK
availability
Potential CEC
Effective CEC
NUE
Mineral
N
leaching
Study location and Climate
C
ti
t
±
± 11 The results of randomized LASSO on the key predictors in soil mineral nitrogen response. The importance of a variable is quantified
by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one
out of five LASSO models properties of the biochar, as they can vary in compo-
sition, surface area, and charge characteristics [100]. Some biochars may have a higher affinity for retaining
certain cations, while others may not be as effective. The
experimental continent, especially South America, was a
crucial predictor and positively influenced the response. As can be seen in Fig. 15, the response of potential CEC
was negative at lower soil pH “5.6–6.5” after biochar
application. This is mainly because soil pH is strongly
associated with soil CEC [100]. As soil pH decreases, it
becomes acidic, and the number of negative charges on
the colloids decreases [101], thereby decreasing poten-
tial CEC. LASSO also identified publication year as a
predictor with a negative impact on the response. tion, which may allow biochar to adsorb and hold more
nutrients [97], making them available in the soil. LASSO
analysis also identified a positive response of NPK avail-
ability to biochar application in South America (Fig. 14). Additionally, LASSO revealed the square root of the effec-
tive sample size as an influential predictor with a positive
effect, signifying the impact of publication bias on the
response. Potential CEC According to LASSO, fertilizer appli-
cation rate with biochar, experimental continent, bio-
char application rate, and soil pH were among the most
important and robust predictors for potential CEC
response (Table 7). Higher rates of fertilizer application
with biochar had an adverse impact on the response of
potential CEC (Fig. 15). A reduction in potential CEC
may result from declines in calcium ( Ca+
2 ) and magne-
sium ( Mg+
2 ) after higher fertilizer application rates [98],
or disruption in the balance of base cations in the sorp-
tion composite [99]. Additionally, a higher application
rate of fertilizer with biochar may cause a dilution effect
that may further diminish potential CEC [100]. On the
other hand, only biochar application at a higher rate was
favorable for the response of potential CEC in sandy-
textured soils (Fig. Page 22 of 34
Bekchanova et al. Environmental Evidence (2024) 13:3
Table 7 Coefficient signs following Randomized LASSO selection for each SPPs
Soil total NPK
Soil
mineral
nitrogen
Plant
nutrient
level
N2O emission
NPK
availability
Potential CEC
Effective CEC
NUE
Mineral
N
leaching
Study location and Climate
C
ti
t
±
± Bio-
char had a negative effect on the short-term response of
N2O emissions but showed a positive effect in the long
term (Fig. 13). This pattern could be related to the vola-
tile content of biochar, which could potentially explain the
short-term N2O emissions in sandy soils amended with
biochar [93]. The application of biochar at a medium rate
(30–50 t/ha) resulted in a decrease in the response of N2O
emissions (Fig. 13). This outcome can be explained by the
influence of biochar on various soil N transformation pro-
cesses in sandy soils, namely enhanced mineralization and
nitrification and a reduction in denitrification [94, 95]. The N2O emissions in soil occur mainly as a microbial
process, involving nitrifiers that oxidize NH+
4 under aer-
obic conditions and denitrifiers that reduce NO−
3 under
anaerobic conditions [90]. As it can be seen in Fig. 13, a
decrease in N2O emission following biochar is observed
in soils with higher pH (6.5–7.5), consistent with findings Soil NPK availability Soil texture, biochar applica-
tion rate, and the experimental continent were the most
influential and robust predictors of soil NPK availability
response (Table 7). Soil texture, namely coarse loamy,
was one of the most important predictors with a posi-
tive impact on the response of NPK availability following
biochar (Fig. 14). The porous nature of coarse loamy soils
may allow biochar to be integrated into the soil structure
effectively, promoting nutrient retention and reducing
nutrient leaching [89]. A low biochar application rate
negatively impacted the NPK availability response, while a
high application rate had a positive effect (Fig. 14). Sandy-
textured soils have lower nutrient retention capacity [96],
leading nutrients to leach more easily. High biochar appli-
cation rates may increase the nutrient-holding capacity of
sandy soils, preventing leaching and making them avail-
able to plants [89]. Furthermore, higher application rates
might provide a greater surface area for nutrient adsorp- Bekchanova et al. Environmental Evidence (2024) 13:3 Page 24 of 34 Page 24 of 34 Bekchanova et al. Environmental Evidence Fig. 11 The results of randomized LASSO on the key predictors in soil mineral nitrogen response. The importance of a variable is quantified
by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one
out of five LASSO models Fig. Page 22 of 34
Bekchanova et al. Environmental Evidence (2024) 13:3
Table 7 Coefficient signs following Randomized LASSO selection for each SPPs
Soil total NPK
Soil
mineral
nitrogen
Plant
nutrient
level
N2O emission
NPK
availability
Potential CEC
Effective CEC
NUE
Mineral
N
leaching
Study location and Climate
C
ti
t
±
± 15) This can be linked to different Effective CEC Randomized LASSO models selected
different predictors as important, such as experimen-
tal country, duration, soil pH, and publication year
(Table 7). The square root of effective sample size
emerged as the most influential, with a positive effect on
the response of effective CEC (Fig. 16), suggesting a like-
lihood of publication bias. The results show that effec-
tive CEC is positively affected at longer experimental
durations (Fig. 16). This can be attributed to the aging
processes that biochar undergoes over time, which Page 25 of 34 Page 25 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Fig. 12 The results of randomized LASSO on the key predictors in plant nutrient level response. The importance of a variable is quantified
by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one
out of five LASSO models Fig. 12 The results of randomized LASSO on the key predictors in plant nutrient level response. The importance of a variable is quantified
by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one
out of five LASSO models Fig. 12 The results of randomized LASSO on the key predictors in plant nutrient level response. The importance of a variable is quantified
by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one
out of five LASSO models may increase its ability to retain and exchange cations
[102]. Furthermore, microbial activity plays a crucial
role in altering the surface chemistry of biochar [103],
improving its ability to retain cations and consequently
increasing CEC. The response of effective CEC yielded
an intriguing result by showing a negative trend in soils
with higher pH levels (7.5–8.5). This outcome may be
attributed to variations in biochar properties and appli-
cation rates. In Africa, the effect of biochar on effective
CEC has yielded inconclusive results, with both positive
and negative outcomes. Further research is required to
clarify the impact of biochar on effective CEC in sandy
soils in this region. Furthermore, the selection of pub-
lication year as an important predictor with a positive
effect suggests a positive shift in the response over time. Page 22 of 34
Bekchanova et al. Environmental Evidence (2024) 13:3
Table 7 Coefficient signs following Randomized LASSO selection for each SPPs
Soil total NPK
Soil
mineral
nitrogen
Plant
nutrient
level
N2O emission
NPK
availability
Potential CEC
Effective CEC
NUE
Mineral
N
leaching
Study location and Climate
C
ti
t
±
± influence of higher fertilization rates on nutrient leaching
depends on the balance between nutrient uptake by plants
and nutrient losses due to leaching. At high fertilizer lev-
els, plants may not be able to utilize all of the nutrients
applied, resulting in a surplus that may leach into ground-
water. Our analysis indicated that low biochar applica-
tion rates reduced mineral N leaching (Fig. 17), although
other meta-analyses have demonstrated the benefits of
higher biochar application rates [89]. This discrepancy
may be attributed to the surface properties of biochar,
which enable it to adsorb ions in the soil solution [89]. The
electrostatic and capillary forces on the biochar surface
contribute to reducing nutrient leaching from soils. Soils
amended with biochar can adsorb NO−
3 through its anion
exchange sites, thus decreasing nitrogen losses. Addition-
ally, biochar may increase soil water-holding capacity due
to its large specific surface area and high porosity, reduc-
ing soil water percolation and the nitrogen contained in it
[104] [105]. As per the analysis, biochar produced at high
temperatures reduced the response to mineral N leaching,
which may be due to the ability of biochar at high temper-
atures to retain NO−
3-N effectively, preventing its leaching
into groundwater [30]. Nevertheless, our findings are in Mineral N leaching The key predictors contributing
to the heterogeneity in the overall response of mineral
N leaching to biochar application were found to be the
biochar application rate, pyrolysis temperature, fertilizer
application rate with biochar, and publication year. Higher
fertilizer rates with biochar increased mineral N leaching,
while lower rates had the opposite effect (Fig. 17). The Bekchanova et al. Environmental Evidence (2024) 13:3 Page 26 of 34 Bekchanova et al. Environmental Evidence Fig. 13 The results of randomized LASSO on the key predictors in N2O emission response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models Fig. 13 The results of randomized LASSO on the key predictors in N2O emission response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). Page 22 of 34
Bekchanova et al. Environmental Evidence (2024) 13:3
Table 7 Coefficient signs following Randomized LASSO selection for each SPPs
Soil total NPK
Soil
mineral
nitrogen
Plant
nutrient
level
N2O emission
NPK
availability
Potential CEC
Effective CEC
NUE
Mineral
N
leaching
Study location and Climate
C
ti
t
±
± This visualization shows the variables selected in a minimum of one out of five
LASSO models simplify the search string to "Biochar OR Charcoal OR
Agrichar" for most of them (Additional file 2: Table S8). However, compared to other systematic reviews, the
number of sources searched in this review was consid-
erable [8, 38, 39]. Therefore, we argue that the existence
of publication bias due to a lack of comprehensiveness
is negligible. Our review was limited to the English lan-
guage and, although most of the peer-reviewed journals
were in English, we discovered during the screening
process that some peer-reviewed and gray literature
was published in other languages. However, at the full-
text screening stage, only two articles (out of 1137) were
found to be ineligible due to language. This result indi-
cates that there is a very small chance of language bias. contrast to the results presented by Liu, Zhang [90], who
suggest the potential advantages of low-pyrolyzed biochar
for reducing N leaching. Our study specifically examines
biochar’s ability to mitigate N leaching in sandy-textured
soils, so direct comparisons with other studies may not be
appropriate. Publication year was another predictor iden-
tified in our analysis (Fig. 17), and it showed a decreasing
trend in response over the years. Limitations of the review methodsh Throughout the systematic review processes, we sought
to minimize potential biases regarding the review meth-
odology. The regular consultations with the advisory
committee and other experts facilitated the identification
of relevant and reliable studies and the reduction of likely
biases. We created comprehensive search strings with the
aim of applying them to diverse search sources. However,
the full search strings provided in Table 2 could only be
used in some bibliographic databases. When applied to
others, such as NDLTD (Networked Digital Library of
Theses and Dissertations) and OATD (Open access the-
ses and dissertations), simplified search strings had to be
used (Additional file 2; Table 7) and the same was true
for all organization websites. Hence, we were forced to During both screening stages (title and abstract and
full-text screening), all studies were independently
screened. In cases where there was uncertainty about
excluding studies, both reviewers worked together to
discuss and reach a consensus. The implementation
of the screening procedures independently aimed to
mitigate potential limitations linked to the screening
process, including the risk of biased decisions, and to
enhance the overall robustness of the screening. As mentioned in the section on deviations from the
protocol, we applied text-mining after the title and Page 27 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Fig. 14 The results of randomized LASSO on the key predictors in NPK availability response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models Fig. 14 The results of randomized LASSO on the key predictors in NPK availability response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models were not well matched, or when the sampling method
was not appropriate to collect data on the population
of interest, the studies struggled with the risk of selec-
tion bias or improper sampling. In this case, studies were
excluded from the review. One hundred and seventy pub-
lications were attributed a ‘moderate’ risk of bias, either
because most of the effect modifiers were missing (Fig. Limitations of the review methodsh 2)
or there was the risk of selection bias due to a mismatch
between treatment and control. Based on the review pro-
tocol, both studies with ‘low’ and ‘moderate’ risk of bias
were supposed to be used for the data extraction. How-
ever, only the former was included for data extraction and
in the analyses, while the latter was excluded after discus-
sion with the advisory committee. Due to the significant
number of ‘low’ risks of bias studies, our focus remained
on this category. The significant number of studies with
a ’moderate’ and a ’high’ risk of bias prevented us from
extracting data during the review, thus not allowing the
implementation of additional sensitivity analyses. It is
possible that some relevant studies were lost as a result
of this decision. Also, the outcome might have been dif-
ferent if the studies with a ‘moderate’ and ‘high’ risk of
bias had been included. However, studies with a ‘moder-
ate’ and ‘high’ risk of bias could have introduced bias and
caused missing data. Therefore, we believe such studies abstract screening to reduce the number of studies for
full-text screening. Although the text-mining followed
rigid procedures, setting cut-off thresholds to exclude
irrelevant papers may have led to the exclusion of some
relevant studies as well [106]. We tried to minimize this
bias by manually assessing 10% of the studies excluded
at text-mining (randomly selected), which suggests
there were few or no falsely excluded studies. It was also sometimes necessary to transform the
data when there were several potential interventions
or comparators in order to prevent duplicate extrac-
tions or dependent data. For example, we averaged data
when the data were provided for several years, months,
or days. However, the effects of biochar application to
the soil may have been different over time. Limitations of the evidence base Many articles (303) were excluded due to low validity or
high risk of bias, mainly because of performance, sam-
pling, and selection bias. Performance bias was the domi-
nant reason for attributing a high risk of bias, mainly
because studies were not based on randomization. Ran-
domization decreases the likelihood of confounding fac-
tors [107]. When the intervention and comparison sites Bekchanova et al. Environmental Evidence (2024) 13:3 Page 28 of 34 Bekchanova et al. Environmental Evidence Page 28 of 34 Fig. 15 The results of randomized LASSO on the key predictors in potential CEC response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models Fig. 15 The results of randomized LASSO on the key predictors in potential CEC response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models of articles and observations (5 articles and 44 observa-
tions). Nevertheless, prior review studies have found
that biochar addition to sandy-textured soils decreased
N leaching by 44% [8], so we deem our results regard-
ing the reduction of mineral N leaching to be reliable. Biochar had no influence on soil mineral nitrogen and
NUE of sandy-textured soils. However, the number of
observations for NUE in this review was relatively low. Therefore, it is possible that with a higher number of
observations, an effect may have been found. Although
NUE was not affected by biochar treatment in this
study, food crop yields showed a contrasting response
to biochar application. Again, this could be due to the
lack of studies for NUE in this review, which future
studies should address. However, for soil mineral nitro-
gen, the number of studies and observations was large
enough, so we can say with reasonable certainty that
biochar has no effect on it. would have been excluded from the quantitative synthe-
ses and, hence, we believe it is reasonable to assume the
overall effect of biochar on SPPs would not change and
results obtained without bias accurately reflect the true
effect of biochar on SPPs. Limitations in generalizing the results Of the 109 articles included in this review, 17 were
excluded at the data extraction stage and they were not
included in both qualitative and quantitative synthe-
sis largely due to data readability issues (the data were
not readable with webplotdigitizer). Other than stated
in the protocol [44], we only used the 92 ‘low’ risk of
bias articles for both quantitative and qualitative syn-
thesis, as we believed this could ensure consistency
and comparability in the analyses. The overall effect
of biochar on nine SPPs was computed in quantitative
synthesis (Fig. 8) and we observed that biochar had a
significant positive effect on soil total NPK, plant nutri-
ent level, NPK availability, N2O emission, potential
CEC, and mineral N leaching. However, the number of
articles and observations among these SPPs differed. For example, soil total NPK had the highest number of
articles and observations (61 articles and 505 observa-
tions), while mineral N leaching had a lower number f
The PET-PEESE method we used to correct for pub-
lication bias is one of the recommended techniques for
ecological review studies [41, 64]. However, PET-PEESE
may perform poorly when the number of included stud-
ies is small (< 20) and heterogeneity is very high. The
number of unique articles recorded for some of the
SPPs violated this rule, but the number of observations Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 29 of 34 Page 29 of 34 Fig. 16 The results of randomized LASSO on the key predictors in effective CEC response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models Fig. 16 The results of randomized LASSO on the key predictors in effective CEC response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models Fig. 16 The results of randomized LASSO on the key predictors in effective CEC response. The importance of a variable is quantified by running
the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five
LASSO models Fig. Implications for management and policy
l
d
b
h
h
h Estimating the variance based on the pooled CV when
SD or SE was not given may raise concerns about the
credibility of the results. A sensitivity analysis was per-
formed by removing all observations from these vari-
ances based on the pooled CV and the results differed
considerably, as almost two-thirds of the observations
were excluded from the analysis (Additional file 11). However, Nakagawa, Noble [60] proposed this method
as one of the approved methods when the variance could
not be calculated in a straightforward way. Furthermore,
using this method meant we could avoid losing valuable
studies for our review. Policy discussions on biochar have shown hesitancy, pri-
marily arising from the prevailing uncertainty regard-
ing biochar’s effects on ecosystem services [109]. Prior
investigations into biochar’s role in the soil nutrient
cycle highlighted the variability of relationships between
some key components (N2O emission, N leaching, plant
N uptake, and soil NH3 volatilization) due to diverse soil
and biochar characteristics [8, 38, 39]. However, these
studies did not specifically address the impact of biochar
on the nutrient cycle in sandy-textured soils. While some
of our findings align with previous reviews, our review
distinguishes itself through its systematic approach and
the provision of the most recent findings. According to
our review, biochar offers a suite of benefits for address-
ing the nutrient cycle problem. From enhancing nutrient
retention and soil fertility to reducing nutrient runoff and
greenhouse gas emissions, biochar can play an important
role in promoting sustainable nutrient management prac-
tices in future agriculture. In practice, the potential gen-
eralizability of our findings regarding biochar’s impact on
nutrient dynamics of sandy-textured soils functions as a
strategic guide for agricultural policymakers and farmers,
assisting their decision-making that addresses the com-
plexities of biochar, such as different biochar types, soil
management during and after biochar application, and
optimal biochar application rates.ii Limitations in generalizing the results 17 The results of randomized LASSO on the key predictors in mineral N leaching response. The importance of a variable is quantified
by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one
out of five LASSO models Fig. 17 The results of randomized LASSO on the key predictors in mineral N leaching response. The importance of a variable is quantified
by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one
out of five LASSO models Fig. 17 The results of randomized LASSO on the key predictors in mineral N leaching response. The importance of a variable is quantified
by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one
out of five LASSO models Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 30 of 34 exceeded 20 for all SPPs (Additional file 13). Therefore,
we assume that PET-PEESE is the right approach for our
case. After correction for publication bias, effective CEC
of sandy-textured soils did not appear to benefit from
biochar treatment. To further our understanding of the
potential benefits of biochar on effective CEC of sandy-
textured soils, future review studies should explore this
topic more, using a larger number of observations. addition, like tillage and irrigation, had minimal impact
on SPP responses. The key strength of our systematic
review, aiming to provide globally applicable outcomes,
faced a hurdle due to the uneven distribution of observa-
tions across different regions. Implications for future researchh Additional file 12. Meta-regression results. Contains the results of LASSO
analyses for each SPP. Additional file 12. Meta-regression results. Contains the results of LASSO
analyses for each SPP. Additional file 13. Correction for publication bias. Contains funnel plots
for each SPP and PET-PEESE results. Given the complexity of studying all components of
the soil nutrient cycle in one review study, it is likely that
the response of other nutrient cycle components besides
SPPs has not been specifically examined in this study. For
instance, the responses of the microbial activity or soil
mineralization to biochar application in sandy-textured
soils, which are important indicators of soil quality and
components of soil nutrient cycles [110, 111], are miss-
ing in this review. Besides, biochar characteristics such as
biochar porosity, its CEC, and its specific surface area can
significantly affect the nutrients of sandy-textured soils
[31, 112], which have not been investigated in this review. Furthermore, plant and/or crop ID was not included in
the analysis of this study. Thus, future review studies
could address these missing components of the soil nutri-
ent cycle and biochar features to complement this review. Additional file 14. Consistency check results for all screening stages (title
& abstract screening and full-text screening) and critical appraisal. Additional file 15. R code. Contains all codes used for meta-analysis,
meta-regression and correction for publication bias. Additional file 15. R code. Contains all codes used for meta-analysis,
meta-regression and correction for publication bias. Acknowledgements This review study was supported by the BASTA project and the authors would
like to thank all project stakeholders who contributed to the development of
the final review. Funding
h The review is implemented as part of Madina Bekchanova’s PhD, which is
funded through the BASTA project. Luca Campion also receives funding from
the BASTA project. Abbreviations
NUE
Nutrient use efficiency
CEC
Cation exchange capacity
SPPs
Soil and plant properties
NPK
Nitrogen-phosphorus-potassium
SD
Standard deviation
SE
Standard error Author contributions MB and LC jointly worked on the screening and critical appraisal stages. MB
extracted the data for the protocol. MB carried out narrative synthesis and
meta-analyses. SB consulted on the meta-analysis. MB and RM took the lead
in the preparation of the manuscript. All other authors contributed to the
manuscript with their critical comments. The final manuscript has been read
and approved by all authors. Conclusion According to our results, the nutrient cycle of sandy-tex-
tured soils is changed by biochar application by increas-
ing soil total NPK, plant nutrient level, NPK availability
and potential CEC. At the same time, biochar application
decreases N2O emissions and mineral N leaching. The
results are also in reasonable agreement with previously
performed meta-analyses [8, 38, 39]. However, we have
focused on the effects of biochar on the nutrient cycle of
sandy-textured soils, with the ability to compare different
SPPs. In addition to SPPs, an increase in food crop yields
is noted, while biomass production was not affected. The
limited number of articles and observations for certain
SPPs, such as N2O emissions, potential CEC, NUE, and
mineral N leaching, limits the ability to draw strong con-
clusions about their effects. More specifically, the findings of this review provide
policymakers with valuable insights into the potential of
integrating biochar into agricultural practices offering a
sustainable approach to mitigating the impacts of nitrate
pollution on both a local and global scale. Based on our
findings, biochar application diminishes N2O emissions,
particularly when employing a shortened experimental
duration alongside a moderate biochar application rate. Additionally, a lower rate of biochar application has dem-
onstrated a notable decrease in mineral N leaching from
sandy-textured soils. These abilities of biochar showcase
not only its potential to remedy environmental pollution
but also its promising offer to address groundwater pol-
lution in various countries [108]. This review highlights
biochar’s ability to stimulate NPK availability in coarse-
textured soils and intensify overall NPK content and
potential CEC in sandy-textured soils at higher applica-
tion rates. These findings not only show that biochar has f
The change in these SPPs after biochar application
depends on a number of factors. For example, in par-
ticular, experimental continent, biochar application rate,
soil pH, and publication year (Table 7) were the predic-
tors that explained the heterogeneity in the response of
many SPPs to biochar application. Unfortunately, rand-
omized LASSO was not feasible for analyzing NUE due
to insufficient observations, which could compromise
the reliability of the results. Some predictors were not
selected for SPP responses, likely due to missing values or
their limited impact. Variables like average precipitation,
annual temperature, and fertilizer application before or
after biochar lacked variability, making their effect on the
overall response uncertain. Conclusion LASSO results also showed
that soil management practices during and after biochar Page 31 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence potential to improve environmental sustainability but
also underscores biochar’s promising potential in con-
tributing to agricultural productivity. Implications for future researchh Additional file 2. Search strategy and results. Provides a description of
the search strategy and results of the literature searches. For each source,
we provided full details on the search date(s), search strings used, search
settings and restrictions, subscriptions (if applicable), and the number of
returns. Additional file 2. Search strategy and results. Provides a description of
the search strategy and results of the literature searches. For each source,
we provided full details on the search date(s), search strings used, search
settings and restrictions, subscriptions (if applicable), and the number of
returns. The geographical spread of the studies included in this
review revealed that more research is needed on the
effect of biochar on the nutrient cycling of sandy-tex-
tured soils. In general, the evidence is especially lacking
in continents such as North and South America and Oce-
ania (Additional file 10: Table S10.1). Relevant experi-
mental studies were lacking for mineral N leaching, NUE,
and potential and effective CEC of sandy-textured soils. Moreover, most experiments were carried out on either
sandy soil or sandy loam, while very few studies were
conducted on coarse loamy, coarse sand, and loamy soil. Unfortunately, some predictors such as climate type,
compost application with biochar, or before biochar
could not be included in the analyses due to the large
amount of missing data in all SPPs. Therefore, future
research should focus on filling these gaps. We encourage
future experimental studies to incorporate true replica-
tion and randomization methods to enhance the gener-
alizability of their findings. Finally, we recommend that
the research community presents the results in a readable
form of figures and tables to further facilitate the use of
data in meta-analyses. Additional file 3. Papers excluded after text-mining. Provided further
keywords used in text-mining. Additional file 3. Papers excluded after text-mining. Provided further
keywords used in text-mining. Additional file 4. The results of full-text screening included both
excluded and included articles. Separate lists of unobtainable articles and
duplicates in full-text screening. Additional file 8. Statistical analysis of variation in the results of different
measurement methods of SPPs. Additional file 9. Data-extraction sheet. Contains the coding of extracted
data for all articles included in both qualitative and quantitative synthesis. Additional file 10. Descriptive statistics. Contains further descriptions of
data for narrative synthesis. Additional file 11. Sensitivity analyses. The effect of outlier removal and
estimated SD from P value removal on the total outcome. The online version contains supplementary material available at https://doi.
org/10.1186/s13750-024-00326-5. The online version contains supplementary material available at https://doi.
org/10.1186/s13750-024-00326-5. The online version contains supplementary material available at https://doi.
org/10.1186/s13750-024-00326-5. Additional file 1. ROSES systematic review report. References 1. Jimin S, Zhongli D, Tungsheng L. Desert distributions during the glacial
maximum and climatic optimum: example of China. Epis J Int Geosci. 1998;21(1):28–31. 25. Ippolito JA, Laird DA, Busscher WJ. Environmental benefits of biochar. J
Environ Qual. 2012;41(4):967–72. 2. Yost JL, Hartemink AE. Soil organic carbon in sandy soils: a review. Adv
Agron. 2019;158:217–310. 26. Sohi SP, Krull E, Lopez-Capel E, Bol R. A review of biochar and its use and
function in soil. Adv Agron. 2010;105:47–82. 27. Hansen V, Müller-Stöver D, Munkholm LJ, Peltre C, Hauggaard-Nielsen
H, Jensen LS. The effect of straw and wood gasification biochar on
carbon sequestration, selected soil fertility indicators and functional
groups in soil: an incubation study. Geoderma. 2016;269:99–107. 3. Dwevedi A, Kumar P, Kumar P, Kumar Y, Sharma YK, Kayastha AM. Soil
sensors: detailed insight into research updates, significance, and future
prospects. In: New pesticides and soil sensors. Amsterdam: Elsevier;
2017. p. 561–94. 4. Van Asperen H, Bor A, Sonneveld M, Bruins H, Lazarovitch N. Properties
of anthropogenic soils in ancient run-off capturing agricultural terraces
in the Central Negev desert (Israel) and related effects of biochar and
ash on crop growth. Plant Soil. 2014;374(1):779–92. 28. Gao S, Hoffman-Krull K, Bidwell A, DeLuca T. Locally produced wood
biochar increases nutrient retention and availability in agricultural soils
of the San Juan Islands, USA. Agr Ecosyst Environ. 2016;233:43–54. ash on crop growth. Plant Soil. 2014;374(1):779–92. 29. Clough TJ, Condron LM, Kammann C, Müller C. A review of biochar and
soil nitrogen dynamics. Agronomy. 2013;3(2):275–93. 5. Shannon M, Grieve C. Tolerance of vegetable crops to salinity. Sci Hortic. 1998;78(1–4):5–38. 30. Hossain MZ, Bahar MM, Sarkar B, Donne SW, Ok YS, Palansooriya KN,
et al. Biochar and its importance on nutrient dynamics in soil and plant. Biochar. 2020;2(4):379–420. 6. Hartemink AE, Huting J. Land cover, extent, and properties of Arenosols
in Southern Africa. Arid Land Res Manag. 2008;22(2):134–47.l 7. Uzoma K, Inoue M, Andry H, Zahoor A, Nishihara E. Influence of biochar
application on sandy soil hydraulic properties and nutrient retention. J
Food, Agric Environ. 2011;9(3/4 part 2):1137–43. 31. El-Naggar A, Lee SS, Rinklebe J, Farooq M, Song H, Sarmah AK, et al. Biochar application to low fertility soils: a review of current status, and
future prospects. Geoderma. 2019;337:536–54. 8. Liu Q, Zhang Y, Liu B, Amonette JE, Lin Z, Liu G, et al. How does biochar
influence soil N cycle? A meta-analysis. Plant Soil. 2018;426(1):211–25. 32. Received: 24 July 2023 Accepted: 13 February 2024 22. Singh BP, Hatton BJ, Singh B, Cowie AL, Kathuria A. Influence of biochars
on nitrous oxide emission and nitrogen leaching from two contrasting
soils. J Environ Qual. 2010;39(4):1224–35. 3. Mukherjee A, Lal R. The biochar dilemma. Soil Res. 2014;52(3):21 24. Sánchez-García M, Roig A, Sánchez-Monedero MA, Cayuela ML. Biochar
increases soil N2O emissions produced by nitrification-mediated path-
ways. Front Environ Sci. 2014;2:25. Consent for publication 18. Güereña D, Lehmann J, Hanley K, Enders A, Hyland C, Riha S. Nitrogen
dynamics following field application of biochar in a temperate North
American maize-based production system. Plant Soil. 2013;365:239–54. Availability of data and materials All data analyzed during this study are included in this published article and
its Additional files. Page 32 of 34 Page 32 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence 16. Taghizadeh-Toosi A, Clough TJ, Sherlock RR, Condron LM. A wood based
low-temperature biochar captures NH3-N generated from ruminant
urine-N, retaining its bioavailability. Plant Soil. 2012;353(1):73–84. Declarations Ethics approval and consent to participate
Not applicable. Ethics approval and consent to participate
Not applicable. 17. Laird D, Fleming P, Wang B, Horton R, Karlen D. Biochar impact on
nutrient leaching from a Midwestern agricultural soil. Geoderma. 2010;158(3–4):436–42. 17. Laird D, Fleming P, Wang B, Horton R, Karlen D. Biochar impact on
nutrient leaching from a Midwestern agricultural soil. Geoderma. 2010;158(3–4):436–42. Author details 1 Centre for Environmental Sciences, Research Group Environmental Econom-
ics, UHasselt—Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek,
Belgium. 2 Centre for Environmental Sciences, Research Group Environmental
Biology, UHasselt—Hasselt University, Agoralaan Gebouw D, 3590 Diepen-
beek, Belgium. 3 Vrije Universiteit Brussel, Multidisciplinary Institute for Teacher
Education (MILO), Pleinlaan 9, 1050 Brussels, Belgium. 4 School of Integrative
Plant Science, College of Agriculture and Life Sciences, Cornell University,
Ithaca, NY, USA. 20. Kannan P, Paramasivan M, Marimuthu S, Swaminathan C, Bose J. Applying both biochar and phosphobacteria enhances Vigna mungo
L. growth and yield in acid soils by increasing soil pH, moisture
content, microbial growth and P availability. Agric, Ecosyst Environ. 2021;308:107258. 21. Azeem M, Hayat R, Hussain Q, Ahmed M, Pan G, Tahir MI, et al. Biochar
improves soil quality and N2-fixation and reduces net ecosystem CO2
exchange in a dryland legume-cereal cropping system. Soil Tillage Res. 2019;186:172–82. Received: 24 July 2023 Accepted: 13 February 2024 Received: 24 July 2023 Accepted: 13 February 2024 Competing interests 19. Sun H, Min J, Zhang H, Feng Y, Lu K, Shi W, et al. Biochar application
mode influences nitrogen leaching and NH3 volatilization losses in
a rice paddy soil irrigated with N-rich wastewater. Environ Technol. 2018;39(16):2090–6. Competing interests
The authors declare that they have no competing interests. References Purakayastha T, Bera T, Bhaduri D, Sarkar B, Mandal S, Wade P, et al. A
review on biochar modulated soil condition improvements and nutri-
ent dynamics concerning crop yields: pathways to climate change
mitigation and global food security. Chemosphere. 2019;227:345–65. 9. Lehmann J, Gaunt J, Rondon M. Bio-char sequestration in ter-
restrial ecosystems–a review. Mitig Adapt Strat Glob Change. 2006;11(2):403–27. 33. Uzoma KC, Inoue M, Andry H, Fujimaki H, Zahoor A, Nishihara E. Effect
of cow manure biochar on maize productivity under sandy soil condi-
tion. Soil Use Manag. 2011;27(2):205–12. 10. Sohi SP. Carbon storage with benefits. Science. 2012;338(6110):1034–5. 11. Zhang C, Zeng G, Huang D, Lai C, Chen M, Cheng M, et al. Biochar for
environmental management: mitigating greenhouse gas emissions,
contaminant treatment, and potential negative impacts. Chem Eng J. 2019;373:902–22.f 34. Shakoor A, Shahzad SM, Chatterjee N, Arif MS, Farooq TH, Altaf MM,
et al. Nitrous oxide emission from agricultural soils: application of
animal manure or biochar? A global meta-analysis. J Environ Manage. 2021;285:112170. 12. Agbede T, Odoja A, Bayode L, Omotehinse P, Adepehin I. Effects of
biochar and poultry manure on soil properties, growth, yield and qual-
ity of cocoyam (Xanthosoma sagittifolium Schott) grown in sandy soil. Commun Soil Sci Plant Anal. 2020;51(7):932–47. 35. Khadem A, Raiesi F, Besharati H, Khalaj MA. The effects of biochar on soil
nutrients status, microbial activity and carbon sequestration potential
in two calcareous soils. Biochar. 2021;3(1):105–16. 13. Panwar N, Pawar A, Salvi B. Comprehensive review on production and
utilization of biochar. SN Appl Sci. 2019;1(2):1–19. 36. Dennis J, Kou K. Evaluating the agronomic benefits of biochar
amended soils in an organic system: Results from a field study at the
UBC Farm, Vancouver. 2013. 14. Razzaghi F, Obour PB, Arthur E. Does biochar improve soil water
retention? A systematic review and meta-analysis. Geoderma. 2020;361:114055. 37. Tammeorg P, Simojoki A, Mäkelä P, Stoddard FL, Alakukku L, Helenius J. Short-term effects of biochar on soil properties and wheat yield forma-
tion with meat bone meal and inorganic fertiliser on a boreal loamy
sand. Agr Ecosyst Environ. 2014;191:108–16. 15. Cayuela ML, Sánchez-Monedero MA, Roig A, Hanley K, Enders A,
Lehmann J. Biochar and denitrification in soils: when, how much and
why does biochar reduce N2O emissions? Sci Rep. 2013;3(1):1–7. 38. Zhang L, Jing Y, Chen C, Xiang Y, Rezaei Rashti M, Li Y, et al. Effects
of biochar application on soil nitrogen transformation, microbial 38. References Zhang L, Jing Y, Chen C, Xiang Y, Rezaei Rashti M, Li Y, et al. Effects
of biochar application on soil nitrogen transformation, microbial Page 33 of 34 Page 33 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 functional genes, enzyme activity, and plant nitrogen uptake: a meta-
analysis of field studies. GCB Bioenerg. 2021;13(12):1859–73. functional genes, enzyme activity, and plant nitrogen uptake: a meta-
analysis of field studies. GCB Bioenerg. 2021;13(12):1859–73. functional genes, enzyme activity, and plant nitrogen uptake: a meta-
analysis of field studies. GCB Bioenerg. 2021;13(12):1859–73. 64. Harrer M, Cuijpers P, Furukawa TA, Ebert DD. Doing meta-analysis with R:
A hands-on guide. Boca Raton: Chapman and Hall/CRC; 2021. yi
g
39. Biederman LA, Harpole WS. Biochar and its effects on plant productivity
and nutrient cycling: a meta-analysis. GCB bioenergy. 2013;5(2):202–14. g
p
65. Pustejovsky JE, Tipton E. Meta-analysis with robust variance estimation:
expanding the range of working models. Prev Sci. 2022;23(3):425–38. 66. Stanley TD, Doucouliagos H. Meta-regression analysis in economics and
business. Abingdon: Routledge; 2012. 66. Stanley TD, Doucouliagos H. Meta-regression
business. Abingdon: Routledge; 2012. 40. Collaboration for Environmental Evidence. Guidelines and standards for
evidence synthesis in environmental management, Version 5.1 (Pullin
AS, Frampton GK, Livoreil B, Petrokofsky G, Eds). 2022. https://www.envir
onmentalevidence.org/information-for-authors. 67. Egger M, Smith GD, Schneider M, Minder C. Bias in meta-analysis
detected by a simple, graphical test. BMJ. 1997;315(7109):629–34. 41. Nakagawa S, Lagisz M, Jennions MD, Koricheva J, Noble DW, Parker TH,
et al. Methods for testing publication bias in ecological and evolution-
ary meta-analyses. Methods Ecol Evol. 2022;13(1):4–21. 68. Peters JL, Sutton AJ, Jones DR, Abrams KR, Rushton L. Comparison
of two methods to detect publication bias in meta-analysis. JAMA. 2006;295(6):676–80. y
y
42. BASTA. Biochar’s added value in sustainable land use with targeted
applications. 2019. https://biochar.solutions/?page_id=201&lang=en. 43. USDA. Textural classification of soils. https://www.nrcs.usda.gov/resou 69. Stanley TD. Beyond publication bias. J Econ Surv. 2005;19(3):309–45. 42. BASTA. Biochar’s added value in sustainable land use with targeted
applications. 2019. https://biochar.solutions/?page_id=201&lang=en.i 42. BASTA. Biochar’s added value in sustainable land use with targeted
l
h
//b
h
l
/? d
&l 70. Meinshausen N, Bühlmann P. Stability selection. J Royal Stat Soc: Series
B (Stat Methodol). 2010;72(4):417–73. 43. USDA. Textural classification of soils. https://www.nrcs.usda.gov/resou
rces/guides-and-instructions/soil-classification. 71. Wang S, Nan B, Rosset S, Zhu J. Random lasso. Ann Appl Stat. 2011;5(1):468. 44. References Effects of combined appli-
cation of chemical fertilizer and biochar on soil physio-biochemical
properties and maize yield. Agriculture. 2023;13(6):1200. 51. Konno K, Livoreil B, Pullin AS. Collaboration for Environmental Evidence
Critical Appraisal Tool, version 0.3. 2021. 79. Kang S, Post WM, Nichols JA, Wang D, West TO, Bandaru V, et al. Marginal
lands: concept, assessment and management. J Agric Sci. 2013;5(5):129. 52. Savilaakso S, Johansson A, Häkkilä M, Uusitalo A, Sandgren T, Mönk-
könen M, et al. What are the effects of even-aged and uneven-aged
forest management on boreal forest biodiversity in Fennoscandia and
European Russia? A systematic review. Environl Evid. 2021;10(1):1–38. 80. Nelissen V, Rütting T, Huygens D, Staelens J, Ruysschaert G, Boeckx P. Maize biochars accelerate short-term soil nitrogen dynamics in a loamy
sand soil. Soil Biol Biochem. 2012;55:20–7. 81. Qian X, Li Q, Chen H, Zhao L, Wang F, Zhang Y, et al. Enhancing soil
nitrogen retention capacity by biochar incorporation in the acidic soil
of pomelo orchards: the crucial role of pH. Agronomy. 2023;13(8):2110. 53. Bhandari. P. Missing Data | Types, Explanation, & Imputation. Scribbr. 2023. 54. Rohatgi A. Webplotdigitizer: Version 4.4. 2020. URL https://automeris.io/
WebPlotDigitizer/. 82. Deenik JL, McClellan T, Uehara G, Antal MJ, Campbell S. Charcoal
volatile matter content influences plant growth and soil nitrogen
transformations. Soil Sci Soc Am J. 2010;74(4):1259–70. 55. Viechtbauer W. Conducting meta-analyses in R with the metafor pack-
age. J Stat Softw. 2010;36(3):1–48. 83. Nguyen TTN, Xu C-Y, Tahmasbian I, Che R, Xu Z, Zhou X, et al. Effects of
biochar on soil available inorganic nitrogen: a review and meta-analysis. Geoderma. 2017;288:79–96. 56. Shackelford GE, Kelsey R, Dicks LV. Effects of cover crops on multiple
ecosystem services: ten meta-analyses of data from arable farmland in
California and the Mediterranean. Land Use Policy. 2019;88:104204. 57. Hedges LV, Gurevitch J, Curtis PS. The meta-analysis of response ratios
in experimental ecology. Ecology. 1999;80(4):1150–6. 84. Mukherjee A, Lal R. Biochar impacts on soil physical properties and
greenhouse gas emissions. Agronomy. 2013;3(2):313–39. 58. Lajeunesse MJ. Bias and correction for the log response ratio in ecologi-
cal meta-analysis. Ecology. 2015;96(8):2056–63. 85. Zhang X, Liu W, Schloter M, Zhang G, Chen Q, Huang J, et al. Response
of the abundance of key soil microbial nitrogen-cycling genes to multi-
factorial global changes. PLoS ONE. 2013;8(10): e76500. 59. Senior AM, Viechtbauer W, Nakagawa S. Revisiting and expanding the
meta-analysis of variation: the log coefficient of variation ratio. References Bekchanova M, Campion L, Bruns S, Kuppens T, Jozefczak M, Cuypers
A, et al. Biochar’s effect on the ecosystem services provided by sandy-
textured and contaminated sandy soils: a systematic review protocol. Environ Evid. 2021;10(1):1–12. 72. Trevor Hastie JQ, Kenneth Tay. An Introduction t
glmnet.stanford.edu/articles/glmnet.html 72. Trevor Hastie JQ, Kenneth Tay. An Introduction to glmnet. 2023. https://
glmnet.stanford.edu/articles/glmnet.html 73. Haddaway NR, Macura B, Whaley P, Pullin AS. ROSES RepOrting
standards for systematic evidence syntheses: pro forma, flow-diagram
and descriptive summary of the plan and conduct of environmental
systematic reviews and systematic maps. Environ Evid. 2018;7:1–8. 45. Haddaway NR, Macura B, Whaley P, and Pullin AS. 2017. ROSES for Sys-
tematic Review Protocols. Version 1.0. https://doi.org/10.6084/m9.figsh
are.5897269.v4 46. Hopewell S, McDonald S, Clarke MJ, Egger M. Grey literature in meta-
analyses of randomized trials of health care interventions. In: Cochrane
Database of Systematic Reviews. Chichester: John Wiley & Sons, Ltd;
2007. 74. Lataf A, Jozefzcak M, Vandecasteele B, Viaene J, Schreurs S, Carleer R,
et al. The Effect of Pyrolysis Temperature and Feedstock on Biochar
Agronomic Properties. SSRN 4111410. 75. Mendez A, Gomez A, Paz-Ferreiro J, Gasco G. Effects of sewage sludge
biochar on plant metal availability after application to a Mediterranean
soil. Chemosphere. 2012;89(11):1354–9. 47. Cohen J. Weighted kappa: nominal scale agreement provision for
scaled disagreement or partial credit. Psychol Bull. 1968;70(4):213. 76. Schofield HK, Pettitt TR, Tappin AD, Rollinson GK, Fitzsimons MF. Biochar
incorporation increased nitrogen and carbon retention in a waste-
derived soil. Sci Total Environ. 2019;690:1228–36. 48. Team C, Team RDC. R: A language and environment for statistical com-
puting. Vienna: R Foundation for Statistical Computing; 2012. 49. Liang B, Lehmann J, Solomon D, Kinyangi J, Grossman J, O’Neill B, et al. Black carbon increases cation exchange capacity in soils. Soil Sci Soc
Am J. 2006;70(5):1719–30. 77. Phares CA, Amoakwah E, Danquah A, Afrifa A, Beyaw LR, Frimpong KA. Biochar and NPK fertilizer co-applied with plant growth promoting
bacteria (PGPB) enhanced maize grain yield and nutrient use efficiency
of inorganic fertilizer. J Agric Food Res. 2022;10:100434. 50. Lisboa SN, Woollen E, Grundy IM, Ryan CM, Smith HE, Zorrilla-Miras P,
et al. Effect of charcoal production and woodland type on soil organic
carbon and total nitrogen in drylands of southern Mozambique. For
Ecol Manage. 2020;457:117692. 78. Wu J, Jin L, Wang N, Wei D, Pang M, Li D, et al. 90. Liu Q, Zhang Y, Liu B, Amonette JE, Lin Z, Liu G, et al. How does biochar
influence soil N cycle? A meta-analysis. Plant Soil. 2018;426:211–25. References Fertilizers and nitrate pollution of surface and ground water:
an increasingly pervasive global problem. SN Appl Sci. 2021;3(4):518. 109. Verde SF, Chiaramonti D. The biochar system in the EU: the pieces are
falling into place, but key policy questions remain. Fiesole: European
University Institute; 2021. 110. Chen G, Zhu H, Zhang Y. Soil microbial activities and carbon and nitro-
gen fixation. Res Microbiol. 2003;154(6):393–8. 111. Johnson C, Albrecht G, Ketterings Q, Beckman J, Stockin K. Nitrogen
basics–the nitrogen cycle. Agronomy Fact Sheet Series. 2005. 112. Yuan J-H, Xu R-K, Qian W, Wang R-H. Comparison of the ameliorating
effects on an acidic ultisol between four crop straws and their biochars. J Soils Sedim. 2011;11:741–50. References f
agricultural land: a laboratory experiment. Agronomy. 2022;12(8) 96. Matichenkov V, Bocharnikova E, Campbell J. Reduction in nutrient
leaching from sandy soils by Si-rich materials: laboratory, greenhouse
and filed studies. Soil Tillage Res. 2020;196:104450. i
97. Ding Y, Liu Y, Liu S, Li Z, Tan X, Huang X, et al. Biochar to improve soil
fertility. Rev Agron Sustain Dev. 2016;36:1–18. y
g
98. Barak P, Jobe BO, Krueger AR, Peterson LA, Laird DA. Effects of long-term
soil acidification due to nitrogen fertilizer inputs in Wisconsin. Plant Soil. 1997;197:61–9. 99. Bednik M, Medyńska-Juraszek A, Dudek M, Kloc S, Kręt A, Łabaz B, et al. Wheat straw biochar and NPK fertilization efficiency in sandy soil recla-
mation. Agronomy. 2020;10(4):496. 100. Domingues RR, Sánchez-Monedero MA, Spokas KA, Melo LCA, Trugilho
PF, Valenciano MN, et al. Enhancing cation exchange capacity of weath-
ered soils using biochar: feedstock, pyrolysis conditions and addition
rate. Agronomy. 2020;10(6):824. 101. Chowdhury S, Bolan N, Farrell M, Sarkar B, Sarker JR, Kirkham MB, et al. Role of cultural and nutrient management practices in carbon seques-
tration in agricultural soil. Adv Agron. 2021;166:131–96. 102. Rahim HU, Allevato E, Vaccari FP, Stazi SR. Biochar aged or combined
with humic substances: fabrication and implications for sustainable
agriculture and environment-a review. J Soils Sedim. 2023. https://doi.
org/10.1007/s11368-023-03644-2. 103. Bolan S, Hou D, Wang L, Hale L, Egamberdieva D, Tammeorg P, et al. The
potential of biochar as a microbial carrier for agricultural and environ-
mental applications. Sci Total Environ. 2023;886:163968. 104. Novak JM, Busscher WJ, Watts DW, Amonette JE, Ippolito JA, Lima IM,
et al. Biochars impact on soil-moisture storage in an ultisol and two
aridisols. Soil Sci. 2012;177(5):310–20. 105. Lehmann J, Pereira da Silva J, Steiner C, Nehls T, Zech W, Glaser B. Nutrient availability and leaching in an archaeological Anthrosol and a
Ferralsol of the Central Amazon basin: fertilizer, manure and charcoal
amendments. Plant Soil. 2003;249:343–57. 106. Talib R, Hanif MK, Ayesha S, Fatima F. Text mining: techniques, applica-
tions and issues. Int J Adv Comput Sci Appl. 2016. https://doi.org/10.
14569/IJACSA.2016.071153. 107. Fuller J. The confounding question of confounding causes in rand-
omized trials. Br J Philos Sci. 2019. https://doi.org/10.1093/bjps/axx015. omized trials. Br J Philos Sci. 2019. https://doi.org/10.1093/bjps/axx015. 108. Craswell E. Fertilizers and nitrate pollution of surface and ground water:
an increasingly pervasive global problem. SN Appl Sci. 2021;3(4):518. 108. Craswell E. References Res
Synth Methods. 2020;11(4):553–67. 86. Singh BP, Cowie AL. Long-term influence of biochar on native
organic carbon mineralisation in a low-carbon clayey soil. Sci Rep. 2014;4(1):3687. y
60. Nakagawa S, Noble DW, Lagisz M, Spake R, Viechtbauer W, Senior AM. A robust and readily implementable method for the meta-analysis of
response ratios with and without missing standard deviations. Ecol Lett. 2023;26(2):232–44. 87. (IFA) IFA. Public Summary Medium-Term Fertilizer Outlook 2021–2025. IFA report. 2021. 88. Karer J, Wimmer B, Zehetner F, Kloss S, Soja G. Biochar application to
temperate soils: effects on nutrient uptake and crop yield under field
conditions. Agric Food Sci. 2013;22(4):390–403. 61. Song C, Peacor SD, Osenberg CW, Bence JR. An assessment of statistical
methods for nonindependent data in ecological meta-analyses. Ecol-
ogy. 2020;101(12): e03184. 89. Hossain MZ, Bahar MM, Sarkar B, Donne SW, Ok YS, Palansooriya KN,
et al. Biochar and its importance on nutrient dynamics in soil and plant
Biochar. 2020;2:379–420. 62. Rosenthal R, Rubin DB. Meta-analytic procedures for combining studies
with multiple effect sizes. Psychol Bull. 1986;99(3):400. 90. Liu Q, Zhang Y, Liu B, Amonette JE, Lin Z, Liu G, et al. How does biochar
influence soil N cycle? A meta-analysis. Plant Soil. 2018;426:211–25. 63. Assink M, Wibbelink CJ. Fitting three-level meta-analytic models in R: a
step-by-step tutorial. Quant Methods Psychol. 2016;12(3):154–74. Page 34 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 91. Liu Q, Liu B, Zhang Y, Lin Z, Zhu T, Sun R, et al. Can biochar alleviate soil
compaction stress on wheat growth and mitigate soil N2O emissions? Soil Biol Biochem. 2017;104:8–17. 92. Gaskin J, Steiner C, Harris K, Das K, Bibens B. Effect of low-temperature
pyrolysis conditions on biochar for agricultural use. Trans ASABE. 2008;51(6):2061–9. 93. Ameloot N, De Neve S, Jegajeevagan K, Yildiz G, Buchan D, Funkuin YN,
et al. Short-term CO2 and N2O emissions and microbial properties of
biochar amended sandy loam soils. Soil Biol Biochem. 2013;57:401–10. 94. Case SD, McNamara NP, Reay DS, Stott AW, Grant HK, Whitaker J. Biochar
suppresses N2O emissions while maintaining N availability in a sandy
loam soil. Soil Biol Biochem. 2015;81:178–85. 95. Lee J-M, Park D-G, Kang S-S, Choi E-J, Gwon H-S, Lee H-S, et al. Short-
term effect of biochar on soil organic carbon improvement and nitrous
oxide emission reduction according to different soil characteristics in
agricultural land: a laboratory experiment. Agronomy. 2022;12(8):1879. Publisher’s Note
S Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations.
|
https://openalex.org/W4392462126
|
https://bmcophthalmol.biomedcentral.com/counter/pdf/10.1186/s12886-024-03369-x
|
English
| null |
Dislocation force of scleral flange-fixated intraocular lens haptics
|
BMC ophthalmology
| 2,024
|
cc-by
| 6,281
|
© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use,
sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and
the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included
in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The
Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available
in this article, unless otherwise stated in a credit line to the data. Spela Stunf Pukl1,2,3, Martin Kronschläger1*, Manuel Ruiss1, Stéphane Blouin4, Emre Rüştü Akcan1 and Oliver Findl1 Abstract
Purpose To measure the dislocation forces in relation to haptic material, flange size and needle used. Setting Hanusch Hospital, Vienna, Austria. Design Laboratory Investigation. Methods, main outcome measures 30 G (gauge) thin wall and 27 G standard needles were used for a
2 mm tangential scleral tunnel in combination with different PVDF (polyvinylidene fluoride) and PMMA
(polymethylmethacrylate haptics). Flanges were created by heating 1 mm of the haptic end, non-forceps assisted
in PVDF and forceps assisted in PMMA haptics. The dislocation force was measured in non-preserved cadaver sclera
using a tensiometer device. Results PVDF flanges achieved were of a mushroom-like shape and PMMA flanges were of a conic shape. For 30 G
needle tunnels the dislocation forces for PVDF and PMMA haptic flanges were 1.58 ± 0.68 N (n = 10) and 0.70 ± 0.14 N
(n = 9) (p = 0.003) respectively. For 27 G needle tunnels the dislocation forces for PVDF and PMMA haptic flanges were
0.31 ± 0.35 N (n = 3) and 0.0 N (n = 4), respectively. The flange size correlated with the occurring dislocation force in
experiments with 30 G needle tunnels (r = 0.92), when flanges were bigger than 384 micrometres. Conclusions The highest dislocation forces were found for PVDF haptic flanges and their characteristic mushroom-
like shape for 30 G thin wall needle scleral tunnels. Forceps assisted flange creation in PMMA haptics did not
compensate the disadvantage of PMMA haptics with their characteristic conic shape flange. Keywords Scleral fixation, Flange-fixated IOL, Yamane technique, Dislocation force Purpose To measure the dislocation forces in relation to haptic material, flange size and needle used. Setting Hanusch Hospital, Vienna, Austria. Design Laboratory Investigation. Methods, main outcome measures 30 G (gauge) thin wall and 27 G standard needles were used for a
2 mm tangential scleral tunnel in combination with different PVDF (polyvinylidene fluoride) and PMMA
(polymethylmethacrylate haptics). Flanges were created by heating 1 mm of the haptic end, non-forceps assisted
in PVDF and forceps assisted in PMMA haptics. The dislocation force was measured in non-preserved cadaver sclera
using a tensiometer device. Results PVDF flanges achieved were of a mushroom-like shape and PMMA flanges were of a conic shape. For 30 G
needle tunnels the dislocation forces for PVDF and PMMA haptic flanges were 1.58 ± 0.68 N (n = 10) and 0.70 ± 0.14 N
(n = 9) (p = 0.003) respectively. Spela Stunf Pukl1,2,3, Martin Kronschläger1*, Manuel Ruiss1, Stéphane Blouin4, Emre Rüştü Akcan1 and Oliver Findl1 For 27 G needle tunnels the dislocation forces for PVDF and PMMA haptic flanges were
0.31 ± 0.35 N (n = 3) and 0.0 N (n = 4), respectively. The flange size correlated with the occurring dislocation force in
experiments with 30 G needle tunnels (r = 0.92), when flanges were bigger than 384 micrometres. Conclusions The highest dislocation forces were found for PVDF haptic flanges and their characteristic mushroom-
like shape for 30 G thin wall needle scleral tunnels. Forceps assisted flange creation in PMMA haptics did not
compensate the disadvantage of PMMA haptics with their characteristic conic shape flange. Keywords Scleral fixation, Flange-fixated IOL, Yamane technique, Dislocation force Backgroundhl The flanged intra-scleral IOL (intraocular lens) fixation
technique includes formation of two scleral tunnels,
externalisation of the IOL haptics, and haptic end heating
to create a flange that seals the scleral tunnel [1]. *Correspondence:
Martin Kronschläger
martin.kronschlaeger@gmx.at
1Vienna Institute for Research in Ocular Surgery (VIROS), A Karl
Landsteiner Institute, Hanusch Hospital, Heinrich-Collin Str. 30,
AT-1140 Vienna, Austria
2Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
3Eye Hospital, University Clinical Centre Ljubljana, Ljubljana, Slovenia
4Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of
OEGK and AUVA Trauma Centre Meidling, Medical Department Hanusch
Hospital, Vienna, Austria l
When performed appropriately, this technique has
been shown to offer stable IOL positioning in eyes with
out capsular support, however the surgical steps are chal
lenged and are, along with the equipment and materials,
still a matter of several modifications [2, 3]. i
The most important risk after the surgery is erosion
of the flange out of the scleral tunnel and through the © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use,
sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and
the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included
in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The
Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available
in this article, unless otherwise stated in a credit line to the data. BMC Ophthalmology BMC Ophthalmology Stunf Pukl et al. BMC Ophthalmology (2024) 24:103
https://doi.org/10.1186/s12886-024-03369-x Open Access Dislocation force of scleral flange-fixated
intraocular lens haptics Spela Stunf Pukl1,2,3, Martin Kronschläger1*, Manuel Ruiss1, Stéphane Blouin4, Emre Rüştü Akcan1 and Oliver Findl1 Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 2 of 9 Page 2 of 9 Solutions Pack (MicroSurgical Technology, Redmond,
USA). Previously studied techniques for flanging were
used as follows: (i) for the IOL with PMMA, the hap
tic was grasped with forceps 1 mm from the tip during
flange formation; (ii) for the IOL with PVDF haptics a
non-grasping technique was used. The flange was wedged
into the outer ostia of the scleral tunnel. conjunctiva. On the contrary, during the surgery and
immediately postoperatively, the meticulous surgical
steps can be complicated by flange slippage trough the
scleral tunnel into the eye. The stability of the IOL during
the procedure and immediately after the surgery mostly
depends on fixing force of the flange - its resistance to
slip through the scleral tunnel. Experiments were carried on non-preserved human
scleral tissue provided by the Vienna Eye Bank. Sclera is the opaque, firm collagenous outermost layer
of the eye. Its stiffness and stress-stain properties differ
at various regions of the eye, and they do change signifi
cantly depending on the healing processes [4–7]. Scleral
tissue has a non-linear behaviour with low stiffness at
lower stress, and increasing stiffness at higher stress. Its
in-vivo resistance thus depends also on the IOP changes
[7]. i For measurement of the dislocation force of the
intra-scleral flange fixated IOL haptic a bench setup
was designed. An electronic force gauge instrument
(PCE-DFG-N20, PCE Instruments) was secured in the
horizontal plane. A straight clamp was attached to the
instrument. The clamp was applied on the sclera parallel
to the scleral tunnel. The haptic exiting the scleral tun
nel at its interior was pulled with forceps while measur
ing the applied force. The maximal force until the flange
slipped though was recorded. The thickness of the pulled-
out flange was then analysed with light microscopy and
measured (Fig. 1).l Before the onset of scleral tunnel healing and fibrosis,
and especially in cases of intra- or early post-operative
lover IOP, the fixing force of the flanges depends exclu
sively on the relationship of the scleral tunnel dimensions
versus the flange size and shape. l
Typically, the scleral tunnel in Yamane technique is
positioned 2 mm behind the limbus, is angled slightly
posteriorly, and is parallel to the limbus. For flange analysis and measurement, the haptics of
the IOLs with dislocated flanges were observed in reflec
tion mode by circular differential interference contrast
using an optical upright microscope (Axio Scope.A1,
Carl Zeiss Meditec AG, Jena, Germany) equipped with a
5x EC Epiplan Neofluar high-density differential interfer
ence contrast lens (Carl Zeiss Meditec AG). A compact
charge-coupled device monochrome camera (Lumenera
Corp.) recorded 1392 × 1040 pixels images with a resolu
tion of 1.3 mm/pixels. Microscopic images of each hap
tic and flange were taken. The diameter of the peripheral
end of each haptic and each flange were measured per
pendicularly to the long axis of the haptic with the aid of
the straight tool in ImageJ. Relationship between the diameter of the tunnel, which
is initially determined by the needle thickness, versus the
haptic and flange size, change after the surgery. However,
during and immediately after the surgery, a suitable size
relationship would add additional safety and stability of
the flanges and IOL. l
The present study was designed to measure the forces
needed to dislocate haptic flanges of known dimension
out of characteristic scleral tunnels in human autopsy eye
sclera in order to better understand the potential impact
of size matching of needle to haptic and flange dimen
sions for scleral fixation. For statistical analysis the SPSS software (IBM, USA)
was used, the groups were compared by the Mann-Whit
ney U test, the diameter of flanges as well as the material
of the haptics and size of the needle were correlated by
the ANOVA test to the dislocation force measured. For
correlation analysis the Pearson correlation coefficient
was used. Methodsf Four different 3-piece IOLs, that are often used for the
scleral fixation technique, were included in this experi
mental study. The haptics were of two different materi
als: Polyvinylidene fluoride– PVDF (n = 10): CT Lucia
202 (Carl Zeiss Meditec AG, Jena, Germany) and the
Avansee Preset (Kowa, Tokyo, Japan), and Polymeth
ylmethacrylate– PMMA (n = 9): Sensar AR40 IOL
(Johnson&Johnson, Santa Ana, USA) and Tecnis ZA9003
IOL (Johnson&Johnson, Santa Ana, USA). Resultsh The mean dislocation force for PVDF haptic flanges from
the 2 mm tangential scleral tunnel created with a 30 G
thin wall needle was 1.58 ± 0.68 N (n = 10) and the mean
dislocation force for PMMA haptic flanges under the
same settings was 0.70 ± 0.14 N (n = 9). The difference was
statistically significant, p = 0.003, Mann-Whitney U test
(Fig. 1). A typical tangential 2 mm long scleral tunnel was cre
ated with a 30 gauge (G) thin-wall needle with a length
of 13 mm (TSK Laboratory Europe, Oisterwijk, Nether
lands). For comparison of the fixing forces, a 27 gauge
(G) standard needle, with a length of 12 mm (Sterican B. Braun, Hessen, Germany) was used alternatively. When the 2 mm long tangential tunnel was for com
parison to the 30 G created with a 27 G standard needle,
the flange slippage occurred in experiments with PMMA Flanging of the introduced haptic was done with a low-
temperature cautery from the MST Scleral IOL Fixation Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 3 of 9 Fig. 1 Measurement of dislocation force: A: An electronic force gauge instrument was secured in the horizontal plane, B: scleral tissue fixated into a
straight clamp, C: 30 G thin wall needle used for a 2 mm scleral tunnel, D: 1 mm haptic flanging with no-grasp technique, E: the flange, F to H: pulling of
the haptic until dislocated Fig 1 Measurement of dislocation force: A: An electronic force gauge instrument was secured in the horizontal plane B: scleral tissue fixated An electronic force gauge instrument was secured in the horizontal plane, B: scleral tissue fixated into a Fig. 1 Measurement of dislocation force: A: An electronic force gauge instrument was secured in the horizontal plane, B: scleral tissue fixated into a
straight clamp, C: 30 G thin wall needle used for a 2 mm scleral tunnel, D: 1 mm haptic flanging with no-grasp technique, E: the flange, F to H: pulling of
the haptic until dislocated technique, as well as sizes and characteristic shapes of
flanges for different IOLs are in Table 1; Fig. 3a and b.l haptics. The dislocation forces could be measured only
in few experiments with the PVDF haptics (n = 3) and
were substantially and statistically significantly lower
compared to experiments with 30 G needles and PVDF
haptics (Fig. Resultsh 2a): PVDF group, 0.31 ± 0.35 N (p = 0.011,
Fig. 2b). lf
PVDF flanges were of mushroom like shape and
PMMA flanges were of conic like shape (Table 1; Fig. 3a). Flangesl Mean flange diameter of all analysed flanges (flanges
that slipped through the tunnel and those that produced Mean values of dislocation force and standard devia
tions when the tunnel was made with a thin wall 30 G Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 4 of 9 Page 4 of 9 Stunf Pukl et al. BMC Ophthalmology Fig. 2 (a) Dislocation forces measured in Newtons (N), 2 mm tangential scleral tunnel created with a 30 G thin wall needle or 27 G standard needle, mea
surements for flanges of PVDF haptics. * p < 0.05. (b) Dislocation forces measured in Newtons (N), 2 mm scleral tunnel, 30 G thin wall needle and 3-piece
IOLs with haptics of different materials: PVDF, PMMA. ** p < 0.01 Fig. 2 (a) Dislocation forces measured in Newtons (N), 2 mm tangential scleral tunnel created with a 30 G thin wall needle or 27 G standard needle, mea
surements for flanges of PVDF haptics. * p < 0.05. (b) Dislocation forces measured in Newtons (N), 2 mm scleral tunnel, 30 G thin wall needle and 3-piece
IOLs with haptics of different materials: PVDF, PMMA. ** p < 0.01 resistance) was 376 ± 27 μm for the Zeiss CT Lucia 202
IOLs (Figs. 4), 361 ± 14 μm for the in Kowa Avansee Pre
set IOLs, 356 ± 18 μm for the Johnson&Johnson Tecnis
ZA903 IOLs, and 409 ± 11 μm for the Johnson&Johnson
Sensar AR40 IOLs. All of the flanges from PVDF hap
tics were created without grasping the haptic, and result
in a mushroom-like shape (Fig. 3a). On the other hand, flanges from PMMA haptics were performed by flang
ing 1 mm from the haptic end and grasping the haptic
1 mm from the haptic tip. They were of a conic-like shape
(Table 1; Fig. 3a). In 30 G thin-wall needle tunnels, a higher disloca
tion force was measured in larger flanges in for most of
the performed experimental dislocations (Fig. 5a: A-D). Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 5 of 9 Fig. 3 (a) Microscopic images of flanges of different IOLs: A– Zeiss CT Lucia 202, B– Kowa Avansee Preset, C– Johnson&Johnson Tecnis ZA9003, D–
Johnson&Johnson Sensar AR40. Flangesl (b) Dislocation force in Newtons for different IOLs, 30 G thin wall needle tunnel (Zeiss CT Lucia 202: n = 6, Kowa Avansee
Preset: n = 5, Johnson&Johnson Tecnis ZA9003: n = 5, Johnson&Johnson Sensar AR40: n = 4) Fig. 3 (a) Microscopic images of flanges of different IOLs: A– Zeiss CT Lucia 202, B– Kowa Avansee Preset, C– Johnson&Johnson Tecnis ZA9003, D–
Johnson&Johnson Sensar AR40. (b) Dislocation force in Newtons for different IOLs, 30 G thin wall needle tunnel (Zeiss CT Lucia 202: n = 6, Kowa Avansee
Preset: n = 5, Johnson&Johnson Tecnis ZA9003: n = 5, Johnson&Johnson Sensar AR40: n = 4) Table 1 Dislocation force and flange size for different IOLs
IOL label
IOL company
Mean size of the flange,
micrometres (µm)
Dislocation
force, New
tons (N)
Mean
SD
Mean
SD
Zeiss CT Lucia 202
Carl Zeiss Meditec (Jena, Germany)
376.40
26.9
1.31
1.0
Kowa Avansee Preset
Kowa (Tokyo, Japan)
360.63
13.8
1.37
1.0
Johnson&Johnson Tecnis ZA9003
Johnson&Johnson, Abbott Medical Optics (Santa Ana, USA)
356.30
18.2
0.46
0.1
Johnson&Johnson Sensar AR40
Johnson&Johnson, Abbott Medical Optics (Santa Ana, USA)
409.05
10.4
0.99
0.5
* Scleral tunnel 2 mm, 30 G thin wall needle, heating 1 mm of haptic, non-forceps assisted in PVDF haptics and forceps assisted in PMMA haptics of haptic ends under and through the conjunctiva. The
numerous combinations of different haptic materials and
thicknesses of IOLs available, as well as the needles used
for externalisation, make standardisation challenging. With all the IOLs, the correlation of size to force is a flat
curve for all IOLs up to the flange size of 384 microme
tres (correlation coefficient– 0.04). For flanges larger than
385 microns, flange size correlated with dislocation force
(0.92) (Fig. 5b). According to the experimental study with cadaver
sclera, the flange is an effective way to stabilize the haptic
in the immediate post-implantation period [8]. Ma et al. further showed that the haptic material and flange to tun
nel size coefficient do influence the dislocation of flanged
haptic from cadaveric sclera [9]. In a 27 G needle tunnel no dislocation force could be
obtained with PMMA haptic flanges since they all slipped
through the tunnel and the mean dislocation force for
PVDF haptic flanges was 0.31 ± 0.347 N, n = 3 (Fig. 2a). Discussionhi Among the PVDF haptic
flanges, substantially higher dislocation forces were mea
sured when a 30 G thin wall needle was used for creation
of the 2 mm long tangential scleral tunnel as compared
to the 27 G needle tunnel. The findings are in accordance
with previously published results from Ma et al. However,
in their study the scleral tunnel was not tangential and
2 mm long as described in the original technique report
[1], and also the PMMA haptics were flanged without the
forceps holding technique, which was proved to results in
a broader flange [9]. We thus propose the scleral tunnel
in Yamane style scleral fixation to be performed as origi
nally described − 2 mm behind the limbus, angled slightly
posteriorly, parallel to the limbus - with a 30 G thin wall
needle, 2 mm tangentially trough the sclera in order to
achieve the optimal flange fixation force.ll cone-like shaped flange, which was proposed to provide
maximum hold in the scleral tunnel and minimum leak
to the sub-conjunctival space [10]. Not using the forceps
in PMMA haptics during heating, the flanges creates less
prominent conic flanges [10]. Forceps assisted flange cre
ation in PMMA haptics during the experiments reported
here however, did not compensate the disadvantage of
PMMA haptic characteristic conic shaped flange, result
ing in lower dislocation forces, which means less stabil
ity of the IOLs with PMMA haptics in the scleral tunnel. Appropriate type of IOL selection is thus also an impor
tant step. A PVDF haptic IOL represents a more secure
option for Yamane scleral fixation according to measure
ments in the present study. Ma et al. performed a no-grasp haptic heating tech
nique and reported flange sizes of 0.5–2.0 mm. They
found that heating the haptic beyond 1.0 mm did not
result in a larger or differently shaped flange [9]. Disloca
tion forces in their experiments correlated to the flange
to needle diameter ratio, speaking in favour of suffi
ciently large flanges. Discussionhi Incorporating the knowledge of how to obtain an
optimal flange [10], and imitating the surgical steps,
as described by Yamane concerning the scleral tunnel
preparation [1, 2], the present laboratory study was per
formed to measure dislocation forces immediately after
the haptic insertion and flanging.hl The scleral fixation technique with flanged intrascleral
haptic fixation, first described by Yamane, has been an
important addition to the techniques used for fixating
IOLs in eyes without capsular support [1]. Standardi
sation of the technique, however, may be needed for
increasing safety, such as avoiding either haptic disloca
tion or oversized flanges which may cause protrusion l
The dislocation forces for PVDF haptic flanges were
significantly higher, meaning more stable IOL, than Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 6 of 9 Fig. 4 Flange size in micrometres for all analysed flanges (Zeiss CT Lucia 202: n = 6, Kowa Avansee Preset: n = 9, Johnson&Johnson Tecnis ZA9003: n = 10,
Johnson&Johnson Sensar AR40: n
3) Fig. 4 Flange size in micrometres for all analysed flanges (Zeiss CT Lucia 202: n = 6, Kowa Avansee Preset: n = 9, Johnson&Johnson Tecnis ZA9003: n = 10,
Johnson&Johnson Sensar AR40: n = 3) Fig. 4 Flange size in micrometres for all analysed flanges (Zeiss CT Lucia 202: n = 6, Kowa Avansee Preset: n = 9, Johnson&Johnson Tecnis ZA9003: n = 10,
Johnson&Johnson Sensar AR40: n = 3) for the PMMA haptic flanges. Among the PVDF haptic
flanges, substantially higher dislocation forces were mea
sured when a 30 G thin wall needle was used for creation
of the 2 mm long tangential scleral tunnel as compared
to the 27 G needle tunnel. The findings are in accordance
with previously published results from Ma et al. However,
in their study the scleral tunnel was not tangential and
2 mm long as described in the original technique report
[1], and also the PMMA haptics were flanged without the
forceps holding technique, which was proved to results in
a broader flange [9]. We thus propose the scleral tunnel
in Yamane style scleral fixation to be performed as origi
nally described − 2 mm behind the limbus, angled slightly
posteriorly, parallel to the limbus - with a 30 G thin wall
needle, 2 mm tangentially trough the sclera in order to
achieve the optimal flange fixation force.ll for the PMMA haptic flanges. Discussionhi The optimal shape of a prominent
cone with PMMA haptics may be obtained with forceps-
assisted heating [10], which however in the contrary to
our expectations, did not prove higher dislocation forces li
As far as flanges, the flange shape depends on the hap
tic material and flanging technique [10, 11] and can, if not
consistent, result in instability of the flange in the scleral
tunnel, or on the other hand conjunctival erosions [12]. The flange shape of PVDF haptics appears to be inde
pendent of whether forceps are used for assistance while
heating. Conversely, with PMMA haptics, a forceps grip
ping is needed to attain mushroom-like or a prominent Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 7 of 9 Page 7 of 9 Fig. 5 (a) Flange size in micrometres (left of double y axis) and dislocation force in Newtons (right of double y axis) for A: PVDF1 (Zeiss CT Lucia 20
n = 4; B: PVDF2 (Kowa Avansee Preset) n = 5; C: PMMA1 (Johnson&Johnson Tecnis ZA9004) n = 5; and D: PMMA2 (Johnson&Johnson Sensar AR40) n =
(b) Flange size in micrometres (x axis) and dislocation force in Newtons (y axis) for all flanges, dislocated out for 30 G thin wall tunnels, which produce
resistance Fig. 5 (a) Flange size in micrometres (left of double y axis) and dislocation force in Newtons (right of double y axis) for A: PVDF1 (Zeiss CT Lucia 202)
n = 4; B: PVDF2 (Kowa Avansee Preset) n = 5; C: PMMA1 (Johnson&Johnson Tecnis ZA9004) n = 5; and D: PMMA2 (Johnson&Johnson Sensar AR40) n = 3. (b) Flange size in micrometres (x axis) and dislocation force in Newtons (y axis) for all flanges, dislocated out for 30 G thin wall tunnels, which produced
resistance Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 8 of 9 Page 8 of 9 Stunf Pukl et al. BMC Ophthalmology in PMMA haptic IOLs compared to the published data
[9]. in PMMA haptic IOLs compared to the published data
[9]. elasticity change, if used beyond the first two days after
retrieval, was noticed. This speaks for early processes of
tissue degradation and/or hydration. Tissue quality is of
course an important aspect when interpreting these labo
ratory results concerning dislocation forces. Conclusionsh The present experimental study was performed to imi
tate the intraoperative and early postoperative stability of
flanged intrascleral fixation of three-piece IOL haptics in
an aphakic eye. Using the model of non-preserved cadav
eric sclera, the 2 mm tangential tunnel provided highest
dislocation forces if created with a 30 G thin wall needle
and when a PVDF haptic flange was used, suggesting that
the scleral tunnel diameter, length, and direction, as well
as proper IOL type selection are essential for the fixa
tion force in Yamane scleral fixation. The post-dislocation
analysis of flanges proved that a larger flange diameter
resulted in higher dislocation forces independent to the
haptic material when larger than 384 microns. Forceps
assisted flange creation with PMMA haptics did not com
pensate for the disadvantage of the less stable PMMA
characteristic conic-shaped flange. However, flanging of
1 mm haptic end assures a sealing flange not smaller than
350 microns. fl
Heating 1 mm of the haptic end in theory results in
a flange diameter of approximately 350 μm [10]. The
flanges performed showed a slight variability in flange
size (Table 1). The largest diameters were measured for
the Sensar AR40 IOLs, which does, however, have the
thickest haptics compared to the other three IOLs used
[14]. The flange should thus be performed by heating at
least 1 mm of the haptic end in order not to be smaller
than 350 μm. Being of the same importance as the flange, a precise
sclera tunnel formation has several important impacts
during and after the procedure. When a 30 G thin wall
needle was used for the scleral tunnel, a larger flange size
when more than 380 micrometres in diameter positively
correlated to a higher dislocation force regardless of
the IOL type. This suggest that independent of the hap
tic material, a well-formed flange will provide enough
stability of the IOL in a 30 G thin wall needle tunnel
[10], which is long and deep in sclera enough. However,
beyond the stability of the IOL, safety after the surgery
in terms of postoperative leak and endophthalmitis risk
depends also on long enough scleral tunnel (at least
2 mm) and sufficient flange burial [12]. To large flange
diameter might not burry and seal and could represent
a risk for flange erosions, postoperative leakage, invasion
of microorganisms [12]. The length and orientation of
the scleral tunnel additionally stabilise the flanged hap
tic. Discussionhi Additionally,
the clinical and long-term stability of flanged intrascleral
fixation of three-piece IOL haptics also depend on the
elastic and healing/scarring properties of the sclera. Measurements of the dislocation forces in this cadaver
scleral model thus only applies to the specific aspect of
the procedure and long-term clinical follow-up studies
are needed. A mushroom-like shape of the PVDF haptics resulted
in a better stability in our study. Even though the flange
sizes were comparable to the flanges of the PMMA hap
tics (Table 1), the dislocation forces were larger for PVDF
haptics (Table 1). However, a grasp assisted prominent
conic shape of the PMMA haptic according to intuitive
thinking offers easier slip of the flange into the scleral
tunnel and a good seal immediately after burial of the
flange into the scleral tunnel. While mid-term flange sta
bility, reported in the literature [13], results also from the
fibrotic sclera response. Further studies are needed to
assess the sealing properties of differently shaped flanges. Heating 1 mm of the haptic end in theory results in
a flange diameter of approximately 350 μm [10]. The
flanges performed showed a slight variability in flange
size (Table 1). The largest diameters were measured for
the Sensar AR40 IOLs, which does, however, have the
thickest haptics compared to the other three IOLs used
[14]. The flange should thus be performed by heating at
least 1 mm of the haptic end in order not to be smaller
than 350 μm.l A mushroom-like shape of the PVDF haptics resulted
in a better stability in our study. Even though the flange
sizes were comparable to the flanges of the PMMA hap
tics (Table 1), the dislocation forces were larger for PVDF
haptics (Table 1). However, a grasp assisted prominent
conic shape of the PMMA haptic according to intuitive
thinking offers easier slip of the flange into the scleral
tunnel and a good seal immediately after burial of the
flange into the scleral tunnel. While mid-term flange sta
bility, reported in the literature [13], results also from the
fibrotic sclera response. Further studies are needed to
assess the sealing properties of differently shaped flanges. Abbreviations Abbreviations
G
Gauge
IOL
Intraocular lens
PMMA
Polymethylmethacrylate
PVDF
Polyvinylidene fluoride Abbreviations
G
Gauge
IOL
Intraocular lens
PMMA
Polymethylmethacrylate
PVDF
Polyvinylidene fluoride Conclusionsh The close-to-limbus tangential insertion [7], long
scleral tunnel (at least 2 mm), and appropriate burial of
the flange into the sclera covered with tenon’s capsule
and conjunctiva provide stability, and appear to also be
important to avoid flange erosions, act as an effective
barrier to invasion of microorganisms, which may other
wise result in postoperative endophthalmitis [12].h Competing interests 14. Stunf Pukl S, Kronschläger M, Ruiss M, Blouin S, Findl O. Size variability and
fitting of 30-gauge thin-wall needles and 3-piece intraocular lens haptics
for the flanged intrascleral fixation technique. J Cataract Refract Surg. 2023;49:874–8. p
g
Spela Stunf Pukl, Martin Kronschläger, Manuel Ruiss, Stephane Blouin, Emre
Rüştü Akcan: The authors have no compending interests, no financial or
proprietary interest in any material or method mentioned. Oliver Findl
is a scientific advisor to Alcon, BVI, Carl Zeiss Meditec AG, Croma and
Johnson&Johnson. Data availability 9. Ma KK, Yuan A, Sharifi S, Pineda R. A Biomechanical Study of Flanged Intra
scleral Haptic fixation of three-piece intraocular lenses. Am J Ophthalmol. 2021;227:45–52. 9. Ma KK, Yuan A, Sharifi S, Pineda R. A Biomechanical Study of Flanged Intra
scleral Haptic fixation of three-piece intraocular lenses. Am J Ophthalmol. 2021;227:45–52. The datasets analysed during the current study are available from the
corresponding author on reasonable request. 10. Kronschläger M, Blouin S, Roschger P, Varsits R, Findl O. Attaining the optimal
flange for intrascleral intraocular lens fixation. J Cataract Refract Surg. 2018;44:1303–5. Funding Funding
There was no financial support for the study. Declarations 11. Agrawal V, Raju B. Creating the flange in Yamane’s technique. Indian J Oph
thalmol. 2021;69:465. 11. Agrawal V, Raju B. Creating the flange in Yamane’s technique. Indian J Oph
thalmol. 2021;69:465. Ethics approval and consent to participate
Not applicable. Received: 13 December 2023 / Accepted: 25 February 2024 Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Consent for publication
Not applicable. 13. Canabrava S, Rodrigues G, Halabi NN, Rezende AC, Cardoso M. 18-month
results of double-flanged 5– 0 polypropylene suture transscleral bag fixation
in subluxated cataracts. Arq Bras Oftalmol. 2022;7:0004–27492022005004205. 13. Canabrava S, Rodrigues G, Halabi NN, Rezende AC, Cardoso M. 18-month
results of double-flanged 5– 0 polypropylene suture transscleral bag fixation
in subluxated cataracts. Arq Bras Oftalmol. 2022;7:0004–27492022005004205. Author contributions The three-dimensional organization of collagen fibrils in the
human cornea and sclera. Invest Ophthalmol Vis Sci. 1991;32:2244–58. 5. Kamma-Lorger CS, Boote C, Hayes S, et al. Collagen and mature elastic fibre
organisation as a function of depth in the human cornea and limbus. J Struct
Biol. 2010;169:424–30.i 6. Newton RH, Meek KM. Circumcorneal annulus of collagen fibrils in the
human limbus. Invest Ophthalmol Vis Sci. 1998;39:1125–34. 7. Elsheikh A, Geraghty B, Alhasso D, Knappett J, Campanelli M, Rama P. Regional variation in the biomechanical properties of the human sclera. Exp
Eye Res. 2010;90:624–33. 8. Stem MS, Wa CA, Todorich B, Woodward MA, Walsh MK, Wolfe JD. 27-gauge
sutureless intrascleral fixaiton of intraocular lens with haptic flanging:
short-term clinical outcomes and a Disinsertion Force Study. Retina. 2019;39:2149–54. 8. Stem MS, Wa CA, Todorich B, Woodward MA, Walsh MK, Wolfe JD. 27-gauge
sutureless intrascleral fixaiton of intraocular lens with haptic flanging:
short-term clinical outcomes and a Disinsertion Force Study. Retina. 2019;39:2149–54. Author contributions J Struct
Biol. 2010;169:424–30. 6. Newton RH, Meek KM. Circumcorneal annulus of collagen fibrils in the
human limbus. Invest Ophthalmol Vis Sci. 1998;39:1125–34. 7. Elsheikh A, Geraghty B, Alhasso D, Knappett J, Campanelli M, Rama P. Regional variation in the biomechanical properties of the human sclera. Exp
Eye Res. 2010;90:624–33. 8. Stem MS, Wa CA, Todorich B, Woodward MA, Walsh MK, Wolfe JD. 27-gauge
sutureless intrascleral fixaiton of intraocular lens with haptic flanging:
short-term clinical outcomes and a Disinsertion Force Study. Retina. 2019;39:2149–54. 9. Ma KK, Yuan A, Sharifi S, Pineda R. A Biomechanical Study of Flanged Intra
scleral Haptic fixation of three-piece intraocular lenses. Am J Ophthalmol. 2021;227:45–52. 10. Kronschläger M, Blouin S, Roschger P, Varsits R, Findl O. Attaining the optimal
flange for intrascleral intraocular lens fixation. J Cataract Refract Surg. 2018;44:1303–5. 11. Agrawal V, Raju B. Creating the flange in Yamane’s technique. Indian J Oph
thalmol. 2021;69:465. 12. Werner L. Flange erosion/exposure and the risk for endophthalmitis. J Cata
ract Refract Surg. 2021;47:1109–10. 13. Canabrava S, Rodrigues G, Halabi NN, Rezende AC, Cardoso M. 18-month
results of double-flanged 5– 0 polypropylene suture transscleral bag fixation
in subluxated cataracts. Arq Bras Oftalmol. 2022;7:0004–27492022005004205. 14. Stunf Pukl S, Kronschläger M, Ruiss M, Blouin S, Findl O. Size variability and
fitting of 30-gauge thin-wall needles and 3-piece intraocular lens haptics
for the flanged intrascleral fixation technique. J Cataract Refract Surg. 2023;49:874–8. 2. Yamane S, Ito A. Flanged fixation: Yamane technique and its application. Curr
Opin Ophthalmol. 2021;32:19–24. not personally involved, are appropriately investigated, resolved, and the
resolution documented in the literature.Emre Rüştü Akcan acquisition,
analysis of data; interpretation of data; AND approved the submitted version;
AND agreed both to be personally accountable for own contributions and
ensured that questions related to the accuracy or integrity of any part of
the work, even ones in which was not personally involved, are appropriately
investigated, resolved, and the resolution documented in the literature. Oliver
Find conception, design of the work; interpretation of data; substantively
revised the work AND approved the submitted version; AND agreed both to
be personally accountable for own contributions and ensured that questions
related to the accuracy or integrity of any part of the work, even ones in which
was not personally involved, are appropriately investigated, resolved, and the
resolution documented in the literature. ,
,
p
(
)
;
4. Komai Y, Ushiki T. Publisher’s Note Received: 13 December 2023 / Accepted: 25 February 2024 1.
Yamane S, Sato S, Maruyama-Inoue M, Kadonosono K. Flanged intrascleral
intraocular Lens fixation with Double-Needle Technique. Ophthalmology.
2017;124:1136–42. Author contributions Spela Stunf Pukl acquisition, analysis of data; interpretation of data; have
drafted the work AND approved the submitted version; AND agreed both to
be personally accountable for own contributions and ensured that questions
related to the accuracy or integrity of any part of the work, even ones in which
was not personally involved, are appropriately investigated, resolved, and the
resolution documented in the literature. Martin Kronschläger conception,
design of the work; interpretation of data; substantively revised the work
AND approved the submitted version;AND agreed both to be personally
accountable for own contributions and ensured that questions related to
the accuracy or integrity of any part of the work, even ones in which was
not personally involved, are appropriately investigated, resolved, and the
resolution documented in the literature. Manuel Ruiss acquisition, analysis of
data; interpretation of data; substantively revised the work AND approved the
submitted version; AND agreed both to be personally accountable for own
contributions and ensured that questions related to the accuracy or integrity
of any part of the work, even ones in which was not personally involved, are
appropriately investigated, resolved, and the resolution documented in the
literature. Stephane Blouin acquisition, analysis of data; interpretation of data;
AND approved the submitted version; AND agreed both to be personally
accountable for own contributions and ensured that questions related to
the accuracy or integrity of any part of the work, even ones in which was The scleral tunnel length may result in instability of
the IOL if too short resulting in slippage of the flange
through the sclera post-operatively resulting in sub
luxation of the IOL, or resulting in IOL decentration if
unpaired to the contralateral tunnel length, During the
experiments, the non-preserved cadaver sclera tissue Page 9 of 9 Page 9 of 9 Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Stunf Pukl et al. BMC Ophthalmology 2. Yamane S, Ito A. Flanged fixation: Yamane technique and its application. Curr
Opin Ophthalmol. 2021;32:19–24. 3. Jacob S, Intrascleral IOL, Fixation. Asia Pac J Ophthalmol (Phila). 2017;6:381–7. 4. Komai Y, Ushiki T. The three-dimensional organization of collagen fibrils in the
human cornea and sclera. Invest Ophthalmol Vis Sci. 1991;32:2244–58. 5. Kamma-Lorger CS, Boote C, Hayes S, et al. Collagen and mature elastic fibre
organisation as a function of depth in the human cornea and limbus. Ethics approval and consent to participate
Not applicable. 12. Werner L. Flange erosion/exposure and the risk for endophthalmitis. J Cata
ract Refract Surg. 2021;47:1109–10. 12. Werner L. Flange erosion/exposure and the risk for endophthalmitis. J Cata
ract Refract Surg. 2021;47:1109–10. Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. References 1. Yamane S, Sato S, Maruyama-Inoue M, Kadonosono K. Flanged intrascleral
intraocular Lens fixation with Double-Needle Technique. Ophthalmology. 2017;124:1136–42.
|
https://openalex.org/W2015705410
|
https://indieskriflig.org.za/index.php/skriflig/article/download/307/202
|
English
| null |
Barnabas: Early Church leader and model of encouragement
|
In die skriflig/In die Skriflig
| 2,007
|
cc-by
| 12,270
|
Barnabas: Early Church leader and
model of encouragement Robin Gallaher Branch
Research Associate, Joy Project
North-West University
POTCHEFSTROOM
E-mail: robinbranch@yahoo.com
rgbranch@crichton.edu Barnabas: Early Church leader and model of encouragement Barnabas: Early Church leader and model of encouragement Acts presents Barnabas, an early church leader, as a model of
integrity and character. It loads him with accolades. It calls him
a good man (Acts 11:24), a prophet and teacher (Acts 13:1), an
apostle (Acts 14:14), and one through whom God worked
miracles (Acts 15:12). It recounts the times he faced
persecution (Acts 13:45; 14:19) and risked his life for the name
of the Lord Jesus Christ (Acts 15:26). He believed Saul truly
had been converted (Acts 9:27) and saw the potential of John
Mark (Acts 12:25) and championed them both at different times
(Acts 11:25-26; 15:36-41). 1 Corinthians 9:6 affirms his charac-
ter by noting he worked while serving congregations in order
not to burden them. Acts introduces him as Joseph, a Levite
from Cyprus, and praises his generous spirit (Acts 4:36). Arguably, Acts portrays no one else – except the Lord Jesus –
in such glowing terms. The apostles nicknamed him Barnabas,
Son of Encouragement, probably because he earned it! Significantly, a passage relating the character attributes and big
heartedness of Barnabas note that the disciples were called
Christians first at Antioch (Acts 11:19-26). Because of its textual
context, it may well be that the character traits of Barnabas
defined the early use of the word Christian. Barnabas played a decisive role in the Early Church. Yet over
two millennia, he has slipped into unjustified obscurity behind
Paul, Peter, John, and James, the brother of Jesus. This article
examines selected stories about him that showcase his
contributions to the Early Church and establish his significant
leadership role. In die Skriflig 41(2) 2007:295-322 295 Barnabas: Early Church leader and model of encouragement bas: leier van Vroeë Kerk en rolmodel vir motivering Handelinge beskryf Barnabas as ʼn kerkleier, ʼn mens met ’n
sterk karakter en integriteit. Daar word ook na hom verwys as ʼn
goeie man (Hand. 11:24), ʼn profeet en onderwyser (Hand. 13:1), ʼn dissipel (Hand. 14:14), en ʼn persoon deur wie God
wonderwerke kon verrig (Hand. 15:12). Verder word ook verwys
na die kere wat hy vervolging in die gesig gestaar (Hand.13:45;
14:19), en sy lewe in gevaar gestel het ter wille van die Naam
van Jesus Christus (Hand. 15:26). Hy het waarlik geglo dat
Saulus bekeerd geraak het (Hand. 9:27), en hy het ook die
potensiaal in Johannes (Markus) raakgesien (Hand. 12:25), en
het hulle albei lof toegesing op verskillende kere (Hand. 11:25-
26 en Hand. 15:36-41). 1 Korintiërs 9:6 belig Barnabas se
karakter deur aan te toon dat terwyl hy sendingwerk by verskeie
kerke verrig het, hy ook gewerk het, sodat hy nie ʼn geldelike las
op hulle sou plaas nie. Handelinge stel hom voor as Josef, ’n
Leviet van Siprus, en erken sy vrygewige karakter (Hand. 4:36). Handelinge verwys slegs na een ander persoon met soveel lof
– Jesus Christus. Die apostels het hom die bynaam, Barnabas,
Seun van Vertroosting gegee. Hy het hierdie naam heel-
waarskynlik verdien! Handelinge verwys ook na Barnabas se karaktereienskappe en
groothartigheid en noem dat die apostels die eerste keer in
Antiochië Christene genoem is (Hand. 11:19-26). As gevolg van
die tekstuele konteks van die Skrif, was dit heel waarskynlik dat
Barnabas se karaktereienskappe die betekenis van die woord
Christen geïnspireer het. Barnabas het ʼn belangrike rol gespeel in die ontwikkeling van
die Vroeë Kerk. Hy is egter deur die eeue heen oorskadu in
belangrikheid deur Paulus, Petrus, Johannes en Jakobus, die
broer van Jesus. Hierdie artikel belig opnuut sy merkwaardige
karaktereienskappe en sy belangrike bydra tot die Vroeë Kerk. 1
The elements of a short story include the central idea, character, conflict, point
of view, setting, language, and tone (see Lostracco & Wilkerson, 1998). Literary 1. Introduction This article looks at the life of Barnabas as portrayed in Acts in
terms of the leadership his life exhibited in the Early Church. This
article employs a literary approach (Hill & Walton, 2000:575). Character development, setting, and conflict are among the literary
and structural elements considered.1 Interpretation of the texts 1
The elements of a short story include the central idea, character, conflict, point
of view, setting, language, and tone (see Lostracco & Wilkerson, 1998). Literary In die Skriflig 41(2) 2007:295-322 296 Robin Gallaher Branch about Barnabas from Acts comes from seeing the stories both
contextually and as part of the whole canon. This article also
employs a canonical approach because I favour allowing Scripture
to interpret Scripture.2 The Biblical text portrays character in terms
of actions and words. This article includes a brief survey of extra-
canonical literature about Barnabas. Stories about him in Acts
present workable models on how to use money, deal with the radical
and amazing inclusion of new converts, and pastor a large and
growing church. One story shows him and his fellow apostle Paul in
a less-than-favorable light as leaders who strongly disagree with
each other. Acts presents Barnabas and Peter, John, Paul and James, the
brother of Jesus, as the primary Early Church leaders. Yet during
the passing of two millennia, Barnabas and James have received
less scholarly attention than have Peter, John, and especially Paul. Kollmann (2004:vii) notes that Barnabas unfortunately now resides
in “undeserved obscurity” despite the fact that he “played a
substantial role in every stage of early Christianity and had a
decisive influence on the fate of the church in the first century”. Regarding James, Witherington (Shanks & Witherington, 2003:111)
acknowledges that “there has been so much neglect of a figure like
James, the brother of Jesus” and believes it is because Petrine
Christianity (derived from Peter) became dominant in the West. This
article seeks to retrieve Barnabas from “undeserved obscurity” and
take a fresh look at his contributions. 2
See the Westminster Confession of Faith, I:6: “The whole counsel of God … is
either expressly set down in Scripture or by good and necessary consequence
may be deduced from Scripture” (italics added). 2. Barnabas, Son of Encouragement in Acts Presented as a “lovable character” (Winn, 1960:51), Barnabas is
mentioned 24 times in Acts, in chapters 4, 9, 11, 12, 13, 14, and 15. Paul’s epistles mention him five times (1 Cor. 9:6; Gal. 2:1, 9, 13;
Col. 4:10). Barnabas is introduced as Joseph Barnabas, a Levite
and native of Cyprus; he sells a field and gives its proceeds to the
apostles (Acts 4:36-37). These details, though meagre, help define
him. elements also include the plot and structure of various stories, dramatic tension,
impact on the reader, and the ordering of events (Elwell & Yarbrough,
2005:174). 2
See the Westminster Confession of Faith, I:6: “The whole counsel of God … is
either expressly set down in Scripture or by good and necessary consequence
may be deduced from Scripture” (italics added). In die Skriflig 41(2) 2007:295-322 297 Barnabas: Early Church leader and model of encouragement Acts speaks very favourably of Barnabas. Significantly, Acts never
presents the older Barnabas as Saul/Paul’s subordinate or junior
partner, although as their working relationship develops, Paul
becomes the more talkative of the two (Acts 14:12). Barnabas is
called a prophet and teacher (Acts 13:1), an apostle (Acts 14:14)
and one through whom God worked miraculous signs and wonders
(Acts 15:12). Barnabas faced persecution (Acts 13:45; 14:19), and
risked his life for the name of the Lord Jesus Christ (Acts 15:26). Physical description and behavioral characteristics form part of
characterisation (Lostracco & Wilkerson, 1998:12). Acts 14 provides
clues to both for Barnabas. On a missionary journey with Paul to
Lystra, a miracle takes place – a lame man walks! – and the
astonished people call Barnabas Zeus and Paul Hermes, because
Paul was the chief speaker (Acts 14:11-13). Something about
Barnabas impressed the people to call him Zeus. Perhaps he was a
very handsome man – or at least a big man with an impressive
appearance. Typically, Zeus statues portray a man broad-chested
and fiercely bearded (Wangerin, 2000:796). Busts of Zeus, the
supreme ruler of Mount Olympus, depict a middle-aged but
physically powerful and muscular man who is both regal and
commanding. Perhaps because Barnabas is dubbed Zeus, he is the
more imposing figure of the two (Gardner, 1995:76). Tribal affiliation also defines Joseph Barnabas. Acts introduces him
as a Levite. 3
Mary, a home-owner, opened her house to believers for prayer despite the
possibility of persecution by authorities (Acts 12:12-13). She is among wealthy
and leading women mentioned by Luke (Joanna and Susanna: Luke 8:1-3; 2. Barnabas, Son of Encouragement in Acts As such, Barnabas performed routine tasks in the
temple; he was not of Aaronic or Zadokite lineage, evidently, and
therefore probably only served in a supportive role of slaughtering
sacrificial animals or guarding the Temple forecourt and singing in
the temple (Kollmann, 2004:7). Nevertheless, this lineage detail
shows Barnabas held a certain status in the Jewish communities of
the first century. Would Barnabas define himself as a Hebrew or a Hellenist? While
his thought patterns are impossible to ascertain, it seems he was a
man who, according to Acts, straddled both worlds. When intro-
duced in Acts he probably would call himself a Hebrew. A Hebrew
was a Diaspora Jew with strong ties to the motherland. Through
Mary, his sister or close relative, he had ties with Jerusalem. Both
were wealthy.3 John Mark was her son and Barnabas’ nephew (Acts 3 In die Skriflig 41(2) 2007:295-322 298 Robin Gallaher Branch 12:12; Col. 4:10). Probably over the years as Barnabas saw his
ministry developing more internationally with the Greek-speaking
Roman world, he arguably came to see himself as a Hellenist. A
working definition of Hellenists is that they were Greek-speaking
Jews in Jerusalem (Acts 6:1; 9:29).4 As a Hellenist, he likely
adopted a broader, more liberal attitude toward the law (Paget,
1994:4). Location also plays a part in characterisation. Barnabas hailed from
Cyprus, the third largest island in the Mediterranean. It had been
ruled by Cleopatra. Following the deaths of Anthony and Cleopatra
after the Battle of Actium, Octavian placed Cyprus under his direct
control in 30 BC and made the island in 22 BC a senatorial province
governed by a proconsul who was chosen annually (Kollmann,
2004:4). Cypriots worshipped Aphrodite, Zeus, Isis, and Apollo. In
addition to profitable agricultural lands, Cyprus had forestry and
copper and silver mining; many Roman ships were built from Cyprus
lumber (Kollmann, 2004:5). Dates and settings likewise contribute to character development for
they enhance the narrative’s meaning (Lostracco & Wilkerson,
1998:31). For example, c. AD 48 Barnabas, his cousin John Mark,
and Saul embark on an evangelisation tour of Asia Minor cities. Acts
(following Biblical narrative tradition) designates Barnabas as the
initial leader of what has come to be known as Paul’s first
missionary journey (Acts 13:1-3; Daniels, 1992:1:610). Prominence shifts back and forth, however, from here on in Acts. The order,
Paul and Barnabas, appears three times in Acts 13 (v. 42, 46, 50), and the
order, Barnabas and Paul, appears twice in Acts 15 (v. 12, 25). The tradition in
Biblical narrative is that the most important figure is named first. 4
Hellenists may have interpreted the Torah less rigidly than did Aramaic-
speaking Jewish believers in Jerusalem (Achtemeier, 1985:382). Hellenisation
shaped the social consciousness of the day throughout the Mediterranean
world. It fostered the spread of the Greek language, commerce, and the
founding of cities. Military expansion, slavery, taxation, and ghettos within the
cities were part of Hellenisation (see Elwell & Yarbrough, 2005:197-198.) 2. Barnabas, Son of Encouragement in Acts A third of the
way through the chapter, Saul/Paul becomes the more prominent
one.5 Significantly in terms of the later working relationship between
the two strong leaders Barnabas and Paul, John Mark leaves them
in Pamphylia and returns to Jerusalem (Acts 13:13). Mary: Acts 12:12-17; prominent women in Thessalonica and Berea: Acts 17:4,
12; Arlandson, 2004:155). 4
Hellenists may have interpreted the Torah less rigidly than did Aramaic-
speaking Jewish believers in Jerusalem (Achtemeier, 1985:382). Hellenisation
shaped the social consciousness of the day throughout the Mediterranean
world. It fostered the spread of the Greek language, commerce, and the
founding of cities. Military expansion, slavery, taxation, and ghettos within the
cities were part of Hellenisation (see Elwell & Yarbrough, 2005:197-198.) 4
Hellenists may have interpreted the Torah less rigidly than did Aramaic-
speaking Jewish believers in Jerusalem (Achtemeier, 1985:382). Hellenisation
shaped the social consciousness of the day throughout the Mediterranean
world. It fostered the spread of the Greek language, commerce, and the
founding of cities. Military expansion, slavery, taxation, and ghettos within the
cities were part of Hellenisation (see Elwell & Yarbrough, 2005:197-198.) 5
Prominence shifts back and forth, however, from here on in Acts. The order,
Paul and Barnabas, appears three times in Acts 13 (v. 42, 46, 50), and the
order, Barnabas and Paul, appears twice in Acts 15 (v. 12, 25). The tradition in
Biblical narrative is that the most important figure is named first. 5 In die Skriflig 41(2) 2007:295-322 299 Barnabas: Early Church leader and model of encouragement In c. AD 52, Paul asks Barnabas to accompany him on a visit to the
churches they had established during their earlier missionary
journey. Barnabas wants to take John Mark with them. Paul and
Barnabas quarrel strongly over John Mark and separate; Barnabas
and John Mark sail for Cyprus and Paul and Silas go overland to
Derbe on what became known as Paul’s second missionary journey
(Acts 15:39-40). From Acts 16 on, the text focuses on Paul, and
Barnabas drops out of Biblical record in Acts. In the Biblical text, names likewise play an important role in defining
character. Barnabas’ Biblical name is Joseph. He is a Levite, a
member of the priestly class, from Cyprus. Acts (4:36-37) introduces
him in the context of giving and sharing, and indeed that was his life. The multiple entries in Acts show his generosity and unselfishness. 7
The word describing Barnabas is kin to paraclete, a word describing the Holy
Spirit. It means “called to the side of” and carries the implication of one who is
called alongside to help in various ways including being a legal assistant or
advocate (Morris, 1986:263). 2. Barnabas, Son of Encouragement in Acts He was a “people person,” a natural minister and effective leader. His nickname, Barnabas Son of Encouragement (Acts 4:36),
presents scholars with interesting possibilities. The bar could come
from the Aramaic for son; the name could really mean son of
prophecy (bar nebuah) or could refer to a heathen deity, Nabu. Scholars agree that Son of Encouragement is an inaccurate etymo-
logy of Barnabas and should be seen rather as an endearment
speaking of his character (Kollmann, 2004:13; Barnabas, 1995:75). Although no explanation accompanies his nickname, the apostles
probably gave it to him because he earned it!6 Barnabas’ name also
encompasses the ideas of refreshment and prophecy, exhortation
and consolation (Bruce, 1954:109). 6
That the apostles changed Joseph’s name to Barnabas shows their authority as
well as the social conventions of the day in the church (Wall, 2002:97). 8
Based on the Codex Bezae, there is some discussion that Barnabas may have
been the Joseph who was proposed, along with Matthias, to replace Judas as
an apostle (Acts 1:23-26); perhaps the nominee’s name was really Joseph
Barnabas rather than Joseph Barsabbas (Read-Heimerdinger, 1998:41). Yet the
consensus of scholarly debate refutes this, primarily because Joseph Barnabas
was a Levite whose nickname was Son of Encouragement and Joseph
Barsabbas, while not distinguished by tribe is distinguished by his nickname,
Justus (Acts 1:23; Kollmann, 2004:13). 9
On the whole, scholars support the old view of Origen about Hebrews. Origen
reportedly said that “who wrote the epistle is known to God alone” (Kollmann,
2004:53-4). 2.1 A canonical definition of encouragement What is a canonical definition of encouragement? Proverbs offers
two verbal insights: “An anxious heart weighs a man down, but a
kind word cheers him up” (Prov. 12:25); and, “A word aptly spoken is
like apples of gold in settings of silver” (Prov. 25:11). The New
Testament broadens the definition by linking encouragement to a
trait and gift of the Holy Spirit. The word “encouragement”
(paraklesis) occurs 29 times in the New Testament.7 It means “one In die Skriflig 41(2) 2007:295-322 300 Robin Gallaher Branch who comes alongside,” and carries the connotations of comforter
and consoler. Acts 9:31 speaks of “the comfort of the Holy Spirit”
and Romans 12:8 lists it as a gift of the Holy Spirit. Barnabas’ words,
actions, and life combined human kindness and God’s blessings;
quite likely, his nickname reflected what God was doing in him and
through him. Since it was given to him by the apostles, it shows how
he consistently related to others. 10
Significantly, the Gospel of Barnabas is well known among Muslim polemicists
in Pakistan, India, Indonesia, and Egypt (Sox, 1994:1-2). 3. Extra-canonical traditions about Barnabas’ life Stories not included in the canon surround the lives of Barnabas and
other Biblical characters. One legend says Barnabas studied with
Gamaliel in Jerusalem and knew a younger student, Saul (Kollmann,
2004:6; Van Deun, 1993:188). According to early Christian tradition
recorded by Clement of Alexandria, Barnabas knew Jesus. He
became a follower of Jesus because he witnessed the healing of the
lame man (John 5:2-9) and other miracles. Barnabas was one of the
70 sent out by Jesus to evangelise (Luke 10:1-24; Jeffreys, 1995:26-
28; Eusebius, 1986:98). This probably means he was about the
same age as Jesus.8 Perhaps he numbered among the inter-
nationals who experienced Pentecost (Acts 2:1-11). Although
Tertullian names Barnabas as the writer of the epistle to the
Hebrews (Richardson, 2000:151), the argument is not strong (Long,
1997:1).9 According to Christian tradition, Barnabas was the first
bishop of Milan (Eusebius, 1986:98). His death, however, is
shrouded in mystery. One tradition maintains he was martyred in
Salamis in AD 55 and that John Mark brought news of his death to
Paul in Ephesus (Van Deun, 1993:533-55). Another tradition says
he was martyred in AD 61 in Syria; he was stoned to death and
burned (Jeffreys, 1995:26-28). His feast day is June 11. This extra-
canonical information helps to develop a portrait of Barnabas; it In die Skriflig 41(2) 2007:295-322 301 Barnabas: Early Church leader and model of encouragement complements the insights in the Biblical text that portray Barnabas
as a fine man and significant leader of the Early Church. 4. Barnabas in extra-canonical literature Five books bearing his name or about him confirm the significance
of Barnabas in Early Church tradition. The five are the Acts of
Barnabas by John Mark, the Acta Bartholomaei et Barnabae, the
Laudatio Barnabae by Alexander Monachus, the Gospel of Bar-
nabas, and the Epistle of Barnabas. The Acts of Barnabas were
composed under the fake authorship of John Mark probably toward
the end of the 5th century; this volume ends with Barnabas’ death
via martyrdom in Salamis; his ashes were buried with a copy of the
Gospel of Matthew (Schneemelcher, 1989:465). The Acta Bartho-
lomae et Barnabae are not apostolic works but instead are com-
bined traditions about Bartholomew and Barnabas (Schneemelcher,
1989:466-7). In the Laudatio Barnabae of Alexander Monachus, a sixth century
monk, details of Barnabas’ early life emerge. Taught by Gamaliel, he
became a follower of Jesus. Among his first converts is Mary, his
kinswoman and John Mark’s mother. Barnabas accompanies Jesus
during his travels in Galilee and Jesus chooses him as one of the
Seventy. Barnabas attempts to convert Saul, whom he knew be-
cause of their association under Gamaliel, but these attempts fail,
and Saul continues persecuting the church (Kollmann, 2004:58; Van
Deun, 1983:83-122). The Gospel of Barnabas may well become a very important docu-
ment in this century because of its Muslim influence and
implications. It attacks and denies Jesus’ death and resurrection,
ending with the view that Judas Iscariot was Jesus’ substitute on the
cross and that Paul was deceived when he preached that Jesus was
the Son of God (Sox, 1994:2, 20-21).10 The Epistle of Barnabas cannot be taken as written by Barnabas; it
stands alone in Early Church literature because of its “uncom-
promising antagonism of Judaism” and because its writer is
unconnected with the apostles (Lightfoot, 1981:503-504). The writer
of the Epistle of Barnabas takes passages from Daniel and ties them 10 In die Skriflig 41(2) 2007:295-322 302 Robin Gallaher Branch to the Roman emperors of his day but stops short of suggesting an
overthrow of the government. Two other books also mention this leading apostle, Barnabas. The
Acts of Peter, a non-canonical book dated to c. AD 260 also gives
credence to Barnabas’ status. 4. Barnabas in extra-canonical literature For example, the sorcerer Simon
came to Rome and caused confusion among the brethren because
of the absence of the church leaders: “Paul was not at Rome, nor
were Timothy and Barnabas, since they had been sent by Paul to
Macedonia” (Schneemelcher, 1989:290). The Clement Romance, one of the Pseudo Clementine documents,
presents evidence that Barnabas preached to a multitude in Rome
about the Son of God who had appeared in the land of Judaea and
“promises eternal life to everyone who will hear, provided that he
fashions his doings according to the will of God the Father, by whom
he has been sent” (Schneemelcher, 1989:505). Barnabas, a
Hebrew, was part of the circle of disciples of this Son of God,
according to the Clement Romance, and Barnabas spoke “without
circumlocution what he had heard from the Son of God or had seen
of him” (Schneemelcher, 1989:506). According to the story, when
Barnabas faced an angry mob, Clement defended him because he
sensed he was a sincere messenger of God. He and Barnabas
became friends almost immediately because they were men of like
character. Clement eventually sailed to Caesarea Stratonis, the
largest city in Palestine, and met Peter and Barnabas there
(Schneemelcher, 1989:506-8). Clement attested to the significance
Barnabas’ words had on his conversion. 11
By general agreement throughout the centuries, Luke is considered the writer of
the Gospel of Luke and the Acts of the Apostles (Matthews, 2000:15). This
article does not tackle questions of authorship and treats Luke as the author. 5. Barnabas and money (Acts 4:37) Acts provides more authoritative, consistent, and credible infor-
mation about Barnabas than do extra-canonical literature. Luke, the
writer of Acts,11 introduces Barnabas during a time of economic
stress and church growth. There were 3 000 new converts at Pente-
cost (Acts 2:41) and more later. If these 3 000-plus represent only
men, then quite possibly the Early Church faced the wonderful
problem of what to do with perhaps 14 000 new believers. Arguably,
Barnabas saw the church at its best – a whole body of believers
united in heart and soul (Packer, 1966:43). The text records no In die Skriflig 41(2) 2007:295-322 303 Barnabas: Early Church leader and model of encouragement selfishness, no want, no division. This church expected the Holy
Spirit to work in power within the community (Acts 3:1-10). The Early Church at this time lacked a formal, rigid ecclesiastical
structure. Acts says the apostles continued preaching with great
power; and outsiders looked on the new community with favor (Acts
2:40, 47). Significantly, this church had no needy persons (Acts
2:44; 4:34), for from time to time those who owned lands or houses
sold them and brought the money from the sales and put it at the
apostles’ feet (Acts 4:32-34). In this orderly, idyllic setting, Luke
signals out one man who shares with abandonment and abundance,
and yet with an attitude of humility: “Joseph, a Levite from Cyprus,
whom the apostles called Barnabas (which means Son of En-
couragement) sold a field he owned and brought the money and put
it at the apostles’ feet” (Acts 4:37). Calvin (1965:130) believes
Barnabas may have sold the only piece of land which he possessed,
and is therefore signaled out by Luke as surpassing all the others in
the Early Church for generosity.12 First impressions set the tone in a
reader’s mind. Luke introduces this future church expositor as one whose humble-
ness and generosity stand in sharp contrast to a subsequent
example: the conniving attitude of Ananias and Sapphira (Acts 5:1-
11; Blaiklock, 1961:68). The story’s dramatic tension highlights their
lie. The sin of Ananias and Sapphira was not in holding back part of
the money but in pretending they had handed over the whole
amount (Packer, 1966:43). In contrast, Barnabas’ gesture of
planned giving indicates not only his ethics regarding finances but
also the genuineness of his faith and character (Maclaren,
1944:175). 12
However, there is no way of knowing if this was his only field or if he had others.
It is not a renunciation of wealth for a lifetime. Indeed, other indications through-
out the epistles point to the fact that Barnabas enjoyed financial independence.
Luke emphasises instead the qualities of openness and humility that
accompany the gift. 5. Barnabas and money (Acts 4:37) Evidently the sale of the field and the donation of its proceeds put
Joseph Barnabas in an immediate leadership position, even though
he is not part of the original Twelve disciples nor a member of the
Seven Greek-speaking servants of the widows who dealt with the
daily distribution of food (Acts 6:1-2, 5). The Seven all bear Greek
names and Nicolas from Antioch was a convert to Judaism (Acts
6:5b). Quite likely cosmopolitan Barnabas, because of his big- In die Skriflig 41(2) 2007:295-322 304 Robin Gallaher Branch hearted temperament, felt camaraderie with these men who were
full of the spirit and wisdom (Acts 6:3). hearted temperament, felt camaraderie with these men who were
full of the spirit and wisdom (Acts 6:3). The text gives no indication that Barnabas’ gift was a response to a
call from church leadership for money. Unlike other New Testament
situations (1 Cor. 16:1, 3), there seems to have been no pressing
need for a financial contribution. Instead, Barnabas’ gesture
sparkles with spontaneity and joy. In a public presentation, Bar-
nabas gives the gift for the use of the community. Perhaps the gift
represented a conviction of sin, for Pentateuchal regulations
prohibited the Levites from holding property (Bruce, 1954:109). The
Levites were to be dedicated to the land and Israel’s well being
rather than to stewardship or cultivation of the land (Deut. 12:12;
Josh. 14:3-4; Wall, 2002:97). Additionally, the fact that Barnabas is a
Levite indicates how the new faith is creeping into the very heart of
the old system (Maclaren, 1944:175). Dramatic tension increases. It is possible that Barnabas’ gift represented a considerable amount. Perhaps his field came from the rich fruit-growing lands of Cyprus
(Neil, 1973:94); if so, his land probably was worth more than a stony
field in Palestine. Along with Mary (the mother of John Mark),
Joseph of Arimathea, and Nicodemus (John 12:1-5; 19:39-41),
Barnabas is quite possibly the first giver of financial standing in the
new church. Unlike Ananias and Sapphira, he gives without a
backward glance; he leaves himself no options. Although probably a
person of more financial standing than were the apostles, he puts
his money at their feet – a gesture showing he sees rank in the
kingdom as different from status in society. 13
The Biblical text frequently presents others who introduce those who sub-
sequently take a more prominent position in the Biblical text, at least in terms of
space. For example, the baby Moses was surrounded by three deliverers: his
sister, his mother, and a princess of Egypt (Exod. 2:1-0; Branch, 2006:258). 5. Barnabas and money (Acts 4:37) Arguably, he considered
the gift of the proceeds of the sale as a way to serve God in a
monetary fashion; his action of giving, as do other episodes about
him recorded in Acts, show his total commitment to Jesus Christ; his
action, here and elsewhere, is both positive and generous – and
marks him as a leader (Willimon, 1988:53). This single act of abandoned generosity unquestionably earned him
lifelong favor and standing in the community. It probably led to his
easy acceptance shortly thereafter (Acts 9:27) as a mediator
between Saul and the apostles of the Jerusalem church (Wall,
2002:97). Significantly by his action, he acknowledges the authority
of the apostles and submits to it. Barnabas leads by example. His action shows a disciple of Jesus at
his best (Packer, 1966:43). Barnabas’ generosity shows he believes
in the work of the kingdom. The setting is one in which believers
shared a keen sense of responsibility for the welfare of each other – 305 In die Skriflig 41(2) 2007:295-322 Barnabas: Early Church leader and model of encouragement even to the point of giving all they had (Barclay, 1976a:43). It also
shows a trust in God that Ananias and Sapphira lacked. Un-
expectedly because of his action and Luke’s treatment of it,
Barnabas becomes a Biblical model of good stewardship (see
Rodin, 2000:14). His decision to give obviously was influenced by
his relationship with God (see Hoge, 1994:205). Significantly,
Barnabas’ action did not represent looking for praise, yet Luke ends
up writing in such a way that he is praised. Evidently that’s what
happens to encouragers: they receive unexpected praise and walk
into positions of leadership. 6. Barnabas seeks out others One of the hallmarks of Barnabas, the Early Church leader and
constant encourager, is that he repeatedly seeks out and champions
others; often these others are believers in Jesus (both individuals
and groups) who for whatever reason are running a bit against the
current of mainstream thought and action. Instead of ostracising
individuals and groups, Barnabas not only seeks them out but also
listens to them and welcomes them warmly. He champions them
when others exclude them. Barnabas adds openness to his earlier
attribute of financial generosity by introducing the very suspect Saul
to the apostles, and presenting Saul as one with the credential of
boldness (Crowe, 1979:68). Barnabas believes in family loyalty, for
he seeks out John Mark and puts his professional reputation on line
by defending his ward against Paul’s strong denunciations. The references in Acts show Barnabas, a “people person,” believed
in people. He believed the Lord could work with very unlikely
candidates like a blood-thirsty persecutor and even with the un-
circumcised gentiles. Barnabas changes the course of history
because he befriends Saul. Twice he seeks out Saul. Another time
he journeys to Antioch in Syria to see what’s happening in a
gentile/Jewish congregation of believers. Each time Barnabas does
these things his actions serve as a model of leadership, personal
courage, and sound theology. Although a significant church leader,
he ends up seeming to take a lesser position of vocal importance –
and not seeming to mind it at all.13 Even in taking a second seat
(perhaps especially so), his sterling character shows. 13 In die Skriflig 41(2) 2007:295-322 306 Robin Gallaher Branch 15
Barnabas believed that Saul, the former hot-headed persecutor of the church,
had suddenly, amazingly, become its most eloquent advocate. Saul at this time
in his life could well be called a loose canon and a lone ranger. He certainly
acted independently. Later he kept a theological independence and even a
physical distance from the Jerusalem church (Gal. 1:1-18). Moses grew to become known as the great lawgiver and Israel’s greatest
prophet. Similarly, Andrew brought his brother Peter to Jesus (John 1:40-42),
and Peter ended up being the more prominent of the two. 14
Canonical examples include Solomon and Jeroboam (1 Kings 11:26-40); Elijah
and Elisha (1 Kings 19:16; 2 Kings 2:1-18); and Jesus’ calling his disciples
(John 1:35-50). 6.1 Barnabas seeks out Saul – the first time (Acts 9:27) An established leader spots those with leadership abilities coming
up in the ranks.14 Barnabas does this. He befriends Saul. Acts
(7:58; 8:1-3) introduces Saul as one who hates the church and
persecutes the new believers. He obtains letters from the high priest
in Jerusalem to officials of Damascus synagogues authorising him to
bind new believers and bring them to Jerusalem. On the way to
Damascus, he has a “blinding” experience with the risen Lord Jesus,
becomes a believer himself, and starts preaching that Jesus is the
Son of God in the Damascus synagogues (Acts 9:1-20)! Saul
preaches so boldly that the Jews in Damascus want to kill him, so
he leaves Damascus and comes to Jerusalem (Acts 9:21-26). The
disciples in Jerusalem face him fearfully, not believing he really is a
disciple (Acts 9:26). Luke writes: “But Barnabas took Saul and
brought him to the apostles. Barnabas told them how Saul on his
journey had seen the Lord and that the Lord had spoken to him and
how in Damascus he had preached fearlessly in the name of Jesus”
(Acts 9:27).15 This significant verse merits scrutiny. Barnabas goes to Saul; he
seeks him out. By this action, Barnabas puts himself and his
reputation among the believing community on the line. More than
that, Barnabas exhibits personal courage: he risks his life. Barnabas
listens to Saul. Barnabas believes Saul. Barnabas, here an en-
courager with a keen sense of ethics, backs up his encouragement
with action. Barnabas’ ethical attitude of listening, believing, testing
what he heard Saul say and then acting with words and deeds is
consistent in the texts about him. Barnabas gives Saul a favorable
introduction to the apostles (Daniels, 1992:1:610). Barnabas’
gesture expresses leadership in action. 14
Canonical examples include Solomon and Jeroboam (1 Kings 11:26-40); Elijah
and Elisha (1 Kings 19:16; 2 Kings 2:1-18); and Jesus’ calling his disciples
(John 1:35-50). 15
Barnabas believed that Saul, the former hot-headed persecutor of the church,
had suddenly, amazingly, become its most eloquent advocate. Saul at this time
in his life could well be called a loose canon and a lone ranger. He certainly
acted independently. Later he kept a theological independence and even a
physical distance from the Jerusalem church (Gal. 1:1-18). In die Skriflig 41(2) 2007:295-322 307 Barnabas: Early Church leader and model of encouragement Barnabas’ action is magnanimous (Longenecker, 1981:378). It
changed the course of history, too. 16
Canonical examples abound. God sent Moses, Aaron, and Miriam to lead his
people out of Egypt (Mic. 6:4). God promised Joshua that he would be with him
as he was with Moses (Josh. 1:5). In the time of the Judges, God sent deliverers
like Ehud and Gideon (Judg. 3:15; 6:14). Deborah, a prophetess who clearly
has the backing of the tribes, serves as a leader in Israel (Judg. 4-5). Matthew
presents Jesus as God’s choice of King of Israel (Branch, 2004:385-388). Paul
lists himself and Barnabas as leaders within the context of discussions with the
acknowledged leaders of the Jerusalem Council, James, Peter, and John (Gal.
2:9). Paul states so beautifully a truth about Jesus: “But when the time had fully
come, God sent his Son, born of a woman, born under law, to redeem those
under law, that we might receive the full rights of sons” (Gal. 4:4-5). 6.1 Barnabas seeks out Saul – the first time (Acts 9:27) Saul became a mighty apostle,
the one who fashioned the church as we know it for the last 2 000
years. The New Testament credits thirteen books to him. By going to
Saul, Barnabas acts like a modern-day coach who assists people to
get from where they are after conversion to a new phase of their life
in Christ, as Paul would come to say (Col. 1:14, 17, 19). Barnabas’
action shows he views the Holy Spirit’s work as big, creative, and
open to new ways of doing things in the world. For example, Isaiah
43:19 (“See, I am doing a new thing!”) clearly holds true in terms of
the life of Jesus, the work of the Holy Spirit at Pentecost (Acts 2),
and the work of the Holy Spirit in the life of Saul the persecutor (Acts
9) and in the lives of those born outside the covenant, the gentiles
(Acts 10). Leaders like Barnabas share a big vision about God’s big
plans for the gospel and God’s big plans for individual lives. 7. How to deal with new converts (Acts 11:22-23) Throughout the Biblical text, God’s choice of a leader is backed up
by recognition by people.16 The next story in Acts about Barnabas,
his being sent by the Jerusalem Council to Antioch, re-affirms this
Biblical principle. In this story, Acts shows that cosmopolitan
Barnabas’ open attitude and encouragement extend to all who are
new creatures in Christ Jesus, be they Jews or gentiles. In the first chapters of Acts, the church is confined to the Jews. Then
Philip the evangelist goes to Samaria and shares the messianic
news and meets an Ethiopian eunuch who requests water baptism
(Acts 8). Then the apostle Peter, who is in Joppa, receives a
revelation in a vision that the gentiles also can be cleansed (Acts
10:1-16). The Holy Spirit then falls on those gentiles listening to
Peter in the house of a Roman, Cornelius (Acts 10:17-47). Simul-
taneously, the Holy Spirit is working in Antioch, a city on the Orontes 16 In die Skriflig 41(2) 2007:295-322 308 Robin Gallaher Branch River in Cappadocia, a city known as luxurious and corrupt (Acts
10:19-21; Maclaren, 1944:324). The text says a great number of
Jews and Greeks believed and turned to the Lord (Acts 10:21). The Jerusalem Council sends Barnabas to Antioch to see what is
happening. The Council’s intent probably is not hostile; it is more
likely one of inquiry (Maclaren, 1944:324). Barnabas with this
assignment (possibly given because he is already an international
person and can fund his own trip) begins his career as a missionary
(Wagner, 2000:252). When Barnabas arrives in Antioch, he displays the same charac-
teristics he had exhibited in the money incident. He acts openly. He
listens to people. He makes ethical decisions. The text says he “saw
the evidence and grace of God and was glad” (Acts 10:23). Calvin
(1965:330) thinks Barnabas’ joy undisputedly shows his sincere
godliness. Typical of a man of honorable character, Barnabas’ mind
looks at the facts: these people – uncircumcised gentiles! – really
are new converts! Barnabas sees that they were in possession, like
himself and other Jewish converts to this radical new faith, of the
visible and audible effects of the Holy Spirit’s gifts (Maclaren,
1944:325). The text indicates he carried no pre-conceived agenda. Evidently he
widened his own theories about God’s actions to suit the new facts
and circumstances (Maclaren, 1944:324). 7. How to deal with new converts (Acts 11:22-23) Bruce (1954:240) puts it
this way: Barnabas’ “generous spirit was filled with joy at what he
found” in Antioch. Then, true to character, he responds ethically and
broadly and “encouraged them all to remain true to the Lord with all
their hearts” (Acts 10:23). Barnabas leads the Antioch disciples in
being steadfast in heart to the Lord. The text indicates Barnabas encourages the gentile believers in
Antioch in three ways. First, he recognises God’s grace in others’
lives. Barnabas, instead of criticising a new work, has the maturity
and discernment to recognise God’s good work and to encourage
that work instead of putting a damper on it by judging it. Second,
because Barnabas is focused, he helps others be focused. His
focus, as he tells the Antioch believers, is “to remain true to the
Lord” (Acts 11:23). Barnabas has a purpose of heart; in other words,
he knows God has sent him to Antioch. He helps them have
“purpose of heart,” too, and to focus on God’s will, God’s kingdom,
and God’s purposes for this congregation in Antioch. Third,
Barnabas is useable because he is available to God. Luke (11:24)
calls him a good man, full of the Holy Spirit and faith. Throughout 309 In die Skriflig 41(2) 2007:295-322 Barnabas: Early Church leader and model of encouragement Acts, God empowers people beyond their natural abilities. This
happens with Barnabas. The result of God’s empowerment is
blessing and increase. The text says, “And considerable numbers
were brought to the Lord” (Acts 11:24). Significantly, the name
Joseph carries with it the ideas of God’s increase. Then Luke gives a surprising editorial comment about this man we
can assume was his friend and brother in the Lord. Luke (Acts
11:24) writes that Barnabas “was a good man, full of the Holy Spirit
and faith”. This is a significant statement. The only other time Luke
uses “good” about a person other than Jesus is in connection with
Joseph of Arimathea (Luke 23:50; Barrett, 1994:553). “Full of the
Holy Spirit” can mean that the Lord worked miracles through
Barnabas; a later text bears this out (Acts 15:12). Barnabas quite
likely had what is called the gift of faith.17 Perhaps the character of Barnabas as the leader of the church
overflowed to the believers in Antioch. Perhaps this spurred the
Antioch community to nickname their neighbors Christians. 18
However, scholars speculate the new name also could be a derision, an
insulting nickname and designation (Longenecker, 1981:402). A canonical
precedent for a possible insulting appositive as an alien is “Ruth the Moabitess”
(Ruth 1:22; 2:6, 21; 4:5; Roop, 2002:39-40, 48, 270-271). “Troubler of Israel” is
an appositive Ahab and Elijah exchange (1 Kings 18:17-18). 7. How to deal with new converts (Acts 11:22-23) Luke
(Acts 11:26b) says, “The disciples were called Christians first at
Antioch”. However, given the context, it could very well be that the
name (or nickname) Christian came into being because of Bar-
nabas, this Christ-like man.18 Certainly it was his broad-mindedness
and generous nature that led to the strengthening of the believers
and a great extension of the work of the Holy Spirit (Erdman,
1929:94). 17
Paul writes that faith is one of the manifestations of the Spirit given to a person
for the common good; other manifestations are the message of wisdom, the
message of knowledge, and the gifts of healing, miraculous power, prophecy,
distinguishing between spirits, speaking in different kinds of tongues, and
interpretation of tongues (1 Cor. 12:7-10). 8. Barnabas seeks out Saul – the second time
(Acts 11:25-26) The Antioch church expands. The work is more than one leader,
Barnabas, can do. Barnabas seeks Saul yet a second time. Barnabas leaves Antioch, goes to Tarsus, and brings back Saul 17
Paul writes that faith is one of the manifestations of the Spirit given to a person
for the common good; other manifestations are the message of wisdom, the
message of knowledge, and the gifts of healing, miraculous power, prophecy,
distinguishing between spirits, speaking in different kinds of tongues, and
interpretation of tongues (1 Cor. 12:7-10). 18
However, scholars speculate the new name also could be a derision, an
insulting nickname and designation (Longenecker, 1981:402). A canonical
precedent for a possible insulting appositive as an alien is “Ruth the Moabitess”
(Ruth 1:22; 2:6, 21; 4:5; Roop, 2002:39-40, 48, 270-271). “Troubler of Israel” is
an appositive Ahab and Elijah exchange (1 Kings 18:17-18). 18 310 In die Skriflig 41(2) 2007:295-322 Robin Gallaher Branch (Acts 11:25-26). Barnabas’ action shows his humility and dis-
cernment. The text indicates Barnabas’ overriding concerns were
the needs of the people and the success of the gospel. Yet he must
have realised that Saul’s skill in debate and his incredible mind
might overshadow his own qualities. However, the possibility of
sinking into second place didn’t seem to matter to Barnabas
(Erdman, 1929:95). Barnabas offers the younger man a job: co-pastoring the dynamic
Antioch disciples. Saul accepts. The young church is growing – and
grows even more under their joint leadership. Barnabas and Saul
met with the church for a year and taught great numbers (Acts
11:26). It must have been a glorious and fruitful time for both
congregation and teachers. Quite likely, this time shaped much of
Saul/Paul’s theology, especially that in 1 Thessalonians (Kollmann,
2004:50-1).19 Barnabas’ action of seeking Saul and bringing him to Antioch
probably ties in with the Biblical concept of forgiveness. The church
in Antioch sprang up because the Jews were scattered (Acts 11:19). Who scattered them? The Biblical text points to Saul. The Biblical
text says he tried to destroy the young church and dragged off men
and women and put them in prison (Acts 7:54-8:3). Chrysostom
(1989:129) describes Saul as “terrible” when he is first presented in
Acts. Within Acts’ context, it is possible that those who fled Saul’s on-
slaught in Jerusalem settled far north in Antioch and discussed their
new faith with their new neighbors. 20
An abuser is one who invades, trespasses, and violates the freedom and
healthy boundaries of another (Wuellner, 2001:64). A root of violence is jealousy
(Ochs, 2004:6). 19
It is thought that 1 Thessalonians may well be Paul’s first letter (especially if a
later date for Galatians is allowed) (Arnold, 2002:405, 265). In die Skriflig 41(2) 2007:295-322 8. Barnabas seeks out Saul – the second time
(Acts 11:25-26) Perhaps Saul instigated the
confiscation of the properties of these early, spontaneous evan-
gelists; perhaps he ordered the deaths of some believers. Saul,
when he scattered the church, abused others; he admits this and
calls himself a violent man (1 Tim. 1:13).20 In seeking Saul, Barnabas leads the Antioch disciples in new ways. He realises several things and was putting into practice Jesus’ In die Skriflig 41(2) 2007:295-322 311 Barnabas: Early Church leader and model of encouragement teaching on forgiveness (Luke 11:4).21 First, Saul needed to ask
forgiveness and share his conversion experience; second, the new
believers needed to practice forgiveness by forgiving their former
oppressor. teaching on forgiveness (Luke 11:4).21 First, Saul needed to ask
forgiveness and share his conversion experience; second, the new
believers needed to practice forgiveness by forgiving their former
oppressor. It would seem the Antioch believers also made a choice to forgive
(Wuellner, 2001:63). Forgiveness can be an ethical adventure. It is
also enlightened self-interest, because forgiveness frees the one
wronged from the tyranny of being tied by unforgiveness to the guilty
party. The believers in Antioch must forgive Saul for the destruction
he caused in their lives years before. Evidently the adventure of
forgiveness for Saul and the Antioch disciples was successful, for
the text indicates growth and harmony prevailed (Acts 11:26). Furthermore, the text indicates a Christ-like spirit likewise domi-
nated, because the disciples of Jesus were first called Christians in
Antioch. Barnabas clearly gave both Saul and the new Antioch
converts room to grow. He gave them the freedom of second
chances. Leading in a big-hearted way, Barnabas consistently
encouraged others to remain true to the Lord with all their heart; one
way to do this was by forgiving mistakes. 22
Church growth is defined as a conscious effort to increase membership (Lim,
2004:125). It is hoped that people, once they are in church, will take advantage
of programs for their spiritual growth. 23
Studies indicate church growth seems to be the result of concentrated effort and
planning and takes place in an optimistic climate. Internal spiritual growth of the
members shows itself in external numerical growth (Cummings, 1983:323). 21
The essence of forgiveness is knowing you are forgiven yourself (Jeffress,
2003:7-9). 9. How to pastor a large and growing church
(Acts 11:25-30) Acts 11:25-30 offers a number of insights on leading a large,
diverse, and growing church. First, get another pastor. Barnabas
brought in a capable reinforcement, Saul. Together they organised a
heavy routine of teaching the faith. Together they got those new
converts rooted and grounded in sound doctrine. Together they and
the congregation welcomed, encouraged, and taught new mem-
bers.22 In other words, the new church of gentiles and Jews grew.23
Barnabas and Saul welcomed visiting prophets. Barnabas and Saul
believed and acted quickly upon the prophetic word Agabus
delivered. They decided to help their fellow believers in Jerusalem 21
The essence of forgiveness is knowing you are forgiven yourself (Jeffress,
2003:7-9). 22
Church growth is defined as a conscious effort to increase membership (Lim,
2004:125). It is hoped that people, once they are in church, will take advantage
of programs for their spiritual growth. In die Skriflig 41(2) 2007:295-322 312 Robin Gallaher Branch with a monetary gift to prepare for the upcoming famine. The
Antioch disciples immediately sent their gift to the elders in
Jerusalem by dispatching Barnabas and Saul (Acts 11:30). From the Acts sketch, Barnabas and Saul had what modern
missiologists call an educational model of a church (Hill, 2001:31).24
An educational model emphasises teaching. Barnabas and Saul
gave teaching on what it meant to be a disciple in the Roman world,
and what it meant to function as an individual in a church. Barnabas
and Saul taught the heritage of the new faith from existing
Scriptures.25 Barnabas and Saul as co-leaders pastored a large and growing
church by adapting to meet the local cultural needs (Nyberg,
1999:24); this congregation mixed Jewish and gentile converts. The
cosmopolitan Antioch congregation contained those of Cypriot and
Libyan background (Walls, 2004:4). They began talking about Jesus
in a new way – with little stress on the term Messiah. Jesus was
presented as Lord, Kyrios, in a way more Hellenistic than Jewish
(Walls, 2004:4). Ignatius (1989:63) sees this dynamic church as a
fulfillment of Isaiah 62:2 and 12, namely that this combination of
people is both righteous and holy. The text indicates Antioch was a lively, growing, excited church
whose members constantly sought each other out and wanted to
learn more. They talked about the Christ so much so that they were
named Christians in Antioch for the first time (Acts 11:26). 9. How to pastor a large and growing church
(Acts 11:25-30) The text
indicates that Barnabas and Saul taught the people in a way that
expected them to become leaders and to carry on the fellowship if
the lead pastors left. 25
A modern educational model would indicate the confessions and catechisms
were taught (Hill, 2001:31). 24
The other two models are informational and retreat (Hill, 2001:31). 24
The other two models are informational and retreat (Hill, 2001:31). 24
The other two models are informational and retreat (Hill, 2001:31).
25
A modern educational model would indicate the confessions and catechisms
(
2001 31) 24
The other two models are informational and retreat (Hill, 2001:31).
25
A modern educational model would indicate the confessions and catechisms
were taught (Hill, 2001:31). 10. The first missionary journey, the Council in Jerusalem
(Acts 13-15:35) When the Antioch church is in prayer and fasting, the Holy Spirit tells
the church to “set apart for me Barnabas and Saul for the work to
which I have called them” (Acts 13:2). This becomes what scholars
term Paul’s first missionary journey; Paul’s name is changed from
Saul midway through the journey’s account on Cyprus (Acts 13:9), In die Skriflig 41(2) 2007:295-322 313 Barnabas: Early Church leader and model of encouragement and Paul from here on in Acts becomes the more prominent or at
least more vocal one (Acts 13:13a). Probably the name change
reflects the emphasis of his life from here on: his outreach to the
Roman world. Significantly, John Mark leaves them in Perga and
goes back to Jerusalem (Acts 13:13b). Paul and Barnabas, now a
missionary duo with perhaps ancillary companions, continue on
preaching in Antioch – Pisida, Lystra, Iconium, and Derbe. In an
exciting journey, they meet both conversions and antagonisms (Acts
13:42-51; 14:1-7, 19-21). Significantly, they plant churches and
leave behind them an established system of elders for governing
(Acts 14:23). In Lystra, the crowd to whom Paul and Barnabas speak witnesses a
miracle and thinks that Paul and Barnabas (dubbed Hermes and
Zeus respectively) are gods incarnate from Mount Olympus. Paul
and Barnabas tear their clothes and rush into the crowd proclaiming
they are merely men, too (Acts 14:15). Perhaps because Barnabas
is called Zeus, he is the more imposing figure (Gardner, 1995:76). In
Pisidian Antioch, Paul and Barnabas speak in a synagogue and
receive abusive talk from hostile Jews (13:45). Luke (13:46) credits
both apostles as answering the jealous Jewish opposition by
promising they would now turn to the gentiles because the Jews had
rejected the word of God and did not consider themselves worthy of
eternal life. Paul and Barnabas then return to Antioch Syria. Men from Jeru-
salem (who are not named by Luke) come to Antioch and say that
the gentiles need to be circumcised in order to be saved (Acts 15:1-
2). Paul and Barnabas sharply dispute this and then are appointed
to take their view to the Council in Jerusalem. Barnabas and Paul
argue that the gentiles should be fully admitted into the new church
(Acts 15:1-5, 12). Their argument prevails, thereby changing the
course of history. 10. The first missionary journey, the Council in Jerusalem
(Acts 13-15:35) What seems to turn the Council’s feeling is the
description of the workings of the Holy Spirit among the gentiles that
Barnabas and Paul recount (Acts 15:12). James, the Council leader,
rules that life should not be made more difficult for their new gentile
brothers by requiring circumcision. Instead he sends Barnabas and
Paul back with a letter calling the two “dear friends” and containing
three directives and encouragements for the gentile believers:
abstain from food offered to idols; abstain from sexual immorality;
abstain from the meat of strangled animals and blood (Acts 15:25,
29). Barnabas and Paul return to Antioch, where the Council’s
decision is welcomed warmly (Acts 15:30-35). In die Skriflig 41(2) 2007:295-322 314 Robin Gallaher Branch 26
Canonical examples include Abram’s deception (Gen. 12:10-20); Moses’ anger
(Num. 20:1-12); David’s adultery and murder (2 Sam. 12:7-9); and Peter’s
cowardice (Matt. 26:69-75). 27
Calvin (1966:61) posits, on the one hand, that some great pride in Barnabas
caused him to forsake the great honor of being Paul’s companion and, on the
other hand, that Paul lacked kindliness in pardoning the mistake of a faithful
assistant. Calvin (1966:61) warns that this example teaches Christians to be on
the look-out for the chinks open to Satan. 11. Leadership disagreements (Acts 15:36-41) The Biblical text presents its heroes and heroines realistically. Biblical leaders have faults.26 Another story about Barnabas shows
how he and Paul quarreled. It seems that their disagreement grew
from their personality strengths. It also grew from their different
perspectives (based on their personalities) of an earlier incident:
John Mark’s action of leaving the first missionary journey in
Pamphylia and returning to Jerusalem (Acts 13:13). Acts already
had shown Barnabas’ loyalty to individuals and his big heartedness. Similarly, Paul’s boldness, fearlessness, tenacity under persecution,
devotion to the gospel’s purity, and ability to count all obstacles as a
loss for the joy of proclaiming Christ stand among his strong points
already seen in Acts. These leadership attributes in both men clash
head on. The issue, as Acts presents it, concerns their second missionary
journey. Arguably, Barnabas, the “people person,” advocates giving
John Mark another chance. The older Barnabas, seeing people as
preeminent, seeks to include his cousin, perhaps to mentor him. Arguably, the easily irritated, feisty, younger Paul, however, sees the
situation differently: the mission predominates. Research indicates
that as first century people, Paul, Barnabas, and John Mark were
sociocentric (group oriented) and not egocentric or individualistic in
identity (Augsburger, 1996:150). Consequently, John Mark as a
team member was there because he wanted to be; he was willing to
make a commitment to its fellowship (Griswold et al., 1993:204). He
chose not to exit – but Paul gave him the left foot of fellowship by
demanding he leave the team (Acts 15:38). Paul seemingly recalled
John Mark’s earlier desertion (Acts 13:13) and decided he could not
be entrusted with the work of evangelism on another journey. This story in Acts illustrates that conflict between believers – even
apostles – happens. Yet disagreement between Christians should
not be seen as fatal to the proclamation of the Gospel. Neither
should disagreement be seen in a win/lose mindset. However, the
text in Acts reads as if Barnabas and Paul decided to argue first and
talk later – something surely typical of church and denomination
squabbles today (Stafford, 1997:33). 26 In die Skriflig 41(2) 2007:295-322 315 Barnabas: Early Church leader and model of encouragement The text omits two factors many find crucial to avoiding or mini-
mising conflict. First, prayer: there is no evidence Barnabas and
Paul prayed – and Acts abounds with examples of prayer (see Acts
1:14; 2:42; 6:4; 9:11). 28
Separation is a Biblical principle that is often overlooked. Genesis abounds with
stories of friends and families who separate. Examples include Lot and
Abraham, Esau and Jacob, Joseph and his brothers (see Petersen, 2005:31). 29
The idea in Acts is that the Holy Spirit is alive, is present, and is active in the
lives of believers. Barnabas’ life as portrayed in Acts is one in which ministry to
others flowed as a source of blessing to others). Barnabas is a man like 11. Leadership disagreements (Acts 15:36-41) Second, a mediator, a peacemaker, is absent. The text offers no indication that Barnabas and Paul sought peace
or called in a peacemaker/mediator. This is ironic because they had
served as peacemakers/mediators shortly before in the Council in
Jerusalem (Acts 15:12-15). Peacemaking or mediation requires a
number of characteristics. For example, all parties must want a
constructive result. Selecting a neutral place is helpful. Parties must
avoid rushing to a solution. Feelings must be listened to and vented. If the goal is conciliation, the parties must choose not to repay wrong
with wrong (Stafford, 1997:32-34). Significantly, Luke indicates no direct benefit to either party re-
garding the dispute and assigns no right or wrong to the dispute.27
With the exception of choosing to write from here on about Paul,
Luke takes no sides. Reconciliation involves facing the tension that initially separates
people (see Lyon, 1999:290). Barnabas and Paul choose to
separate.28 They choose to part and to cool their tempers. The text
indicates that Paul and John Mark later experienced reconciliation
and a good working relationship (2 Tim. 4:11). There is no textual
indication either way about Paul and Barnabas. The fine character
traits of each man, however, lead readers to expect reconciliation. In
addition, Pauline references in Galatians 2, 1 Corinthians 9:6, and
Colossians 4:19 indicate the split probably was not final or terminal
(Paget, 1994:4). In Biblical thought, forgiveness is a relational pro-
cess between disputants. Indeed, years later Paul may have been
writing to himself when he described the different dimensions of
reconciliation, a word that occurs thirteen times in his writings. Augsburger (1996:151) outlines Paul’s three stages of reconciliation. First, a person must be reconciled to God; second, people are In die Skriflig 41(2) 2007:295-322 316 Robin Gallaher Branch reconciled to others from whom they were alienated, and third,
people are called to be reconcilers and do the work of conciliation
between those who are alienated and at enmity with each other (see
2 Cor. 5:18-19). 12. Conclusion The multiple New Testament entries about Barnabas portray a man
of sterling character. These qualities make Barnabas a successful
leader and one who merits the appositive of the Bible’s great
encourager. Barnabas clearly and consistently recognised God’s
grace in unlikely people – the murderer Saul, the uncircumcised
gentiles in Antioch, and his cousin John Mark who seemed a fearful,
spineless deserter, an early casualty on the mission field. He sought
them out. His nickname Son of Encouragement also is sometimes
translated Son of Consolation (Bruce, 1954:109). If consolation is
the meaning, then Barnabas was a skilled, compassionate com-
forter. The evidence given in Acts shows that Barnabas’ own life had a
purpose. He decided to remain true to the Lord Jesus. His money
backed up his commitment. From his own experience and purpose
of heart, he convinced the new believers in Antioch also “to remain
true to the Lord with all their hearts” (Acts 11:23). The focused,
purposeful life is very attractive. The fact that Barnabas was focused
meant he could lead others. Barnabas’ life with the new Antioch
disciples showed his perseverance as an apostle. A principle among
the apostles was this: follow me as I follow the Lord (John 10:27;
2 Thess. 3:9). Every instance in Acts presents Barnabas as one who whole-
heartedly follows the Lord Jesus, is available for kingdom purposes,
and readily gives himself to God’s service. The basis of Barnabas’ nickname, Son of Encouragement, needs to
be considered. Yes, the text shows it both as a natural inclination –
he was a “people person”, someone who genuinely liked people and
enjoyed being around them – and a gift from the Holy Spirit (Rom. 12:8). Any gift of the Holy Spirit needs constant replenishment via
prayer, study, and use.29 Barnabas could only give out what was 29 In die Skriflig 41(2) 2007:295-322 317 Barnabas: Early Church leader and model of encouragement given to him. Going on one’s own merit and energy makes a person
“Mr. Nice Guy” or a “Ms. Congeniality” (see Hoyt-Oliver, 2006:21);
there’s nothing wrong with these nicknames. But merely being nice
doesn’t last for eternity. Barnabas’ work lasted. How did it last? Why
does Luke cite it as an example again and again? Some clues stand
out. Barnabas gave encouragement because he received encourage-
ment. The text mentions he was a prophet, teacher, apostle, and
miracle worker. Stephen who is described as one full of the Holy Spirit. Spiritual fullness speaks
of God’s overflowing gift of the Holy Spirit. 12. Conclusion As a teacher he studied the Scrolls – the same way
Paul did (2 Tim. 4:13). In order to teach sound doctrine, he con-
stantly needed to study. He internalised, incorporated, and taught
the Word of God he studied. Seeing God’s work made him glad
(Acts 11:23) – it encouraged him. His glad countenance and big
attitude were contagious; others became glad and glimpsed the big
vision of God through him. From the Lord’s personal encouragement
to him, Barnabas gave encouragement and provided a model of
encouragement to others. Barnabas was equally at ease with the Hebrews and the Hellenists. He probably felt closer theologically to the Stephen group of inter-
nationals than to the Twelve disciples (Kollmann, 2004:62). Barnabas sponsored his younger colleague, Saul, and championed
him. For the majority of what came to be known as Paul’s first
missionary journey, Barnabas led. True, gradually, but only
gradually, Paul emerged from Barnabas’ shadow as the primary,
vocal advocate of a gospel that was gentile-friendly and did not
require circumcision. Despite the 29 New Testament entries about Barnabas attesting to
his stature and importance in the Early Church, he is not too well
known in modern Christian circles. His slide into obscurity was
apparent even in the Middle Ages. For example, commenting on
Acts 11:25-30, Gregory of Nazianzus said that “even though
Barnabas stood by Paul during conflicts, he was indebted to Paul for
choosing him and making him his partner” (italics added; Kollmann,
2004:61). According to the Biblical record, Gregory is incorrect. Barnabas chose Saul/Paul and championed him. They shared
leadership. Calvin (1966:61) likewise errs when he writes that Paul
bestowed “a great honor” on Barnabas when he suggested they “go
back and visit the brothers in all the towns where we preached the Stephen who is described as one full of the Holy Spirit. Spiritual fullness speaks
of God’s overflowing gift of the Holy Spirit. In die Skriflig 41(2) 2007:295-322 318 Robin Gallaher Branch word of the Lord and see how they are doing” (Acts 15:36). In
addition, overlooking Barnabas continues in commentaries. Barclay
(1966b:15-17), commenting on Galasians 2:1-10, a passage
mentioning Barnabas twice, omits any reference to Barnabas and
instead commends Paul for his refusal to be overawed by Judaisers
advocating circumcision. Clearly, Barnabas, because there are no authenticating canonical
writings ascribed to him, declined in importance quickly over two
millennia. 30
Witherington (Shanks & Witherington, 2003:222) believes that a new millennia
encourages scholars to take a new look at the significance of early Jews like
James, and I would add, Barnabas. 12. Conclusion Yet careful study of texts in Acts (and elsewhere in Paul’s
canonical epistles) as this article begins to show, demonstrates that
at the time of the Early Church, Barnabas proved a key leader. His
influence in the early history of Christian theology and the formation
of the church structure has been bypassed by scholars who con-
centrate on Paul, Peter, and John, and because of the recent dis-
covery of the ossuary, on James (Shanks & Witherington, 2003).30 Perhaps Barnabas was martyred decades earlier than was Paul;
perhaps his life was cut off soon after he and Paul separated. The
text does not say. But what is known from Acts is that Barnabas was
a fully recognised leader in the Early Church. As one splitting his
time between Jerusalem and Antioch, he participated in Early
Church councils and saw with vision that the New Covenant
extended to the uncircumcised. Joseph Barnabas, Son of En-
couragement, receives equal status with James, John, Peter, and
Paul in the early sections of Acts and therefore not only should be
honored as a founding leader of the Early Church but also should
receive more scholarly scrutiny. List of references ACHTEMEIER, P., ed. 1985. Harper’s Bible dictionary. San Francisco: Harper &
Row. ACHTEMEIER, P., ed. 1985. Harper’s Bible dictionary. San Francisco: Harper &
Row. ARLANDSON, J.M. 2004. Lifestyles of the rich and Christian: women, wealth,
and social freedom. (In Levine, Amy-Jill, ed. A feminist companion to the
Acts of the Apostles. London: Clark International. p. 155-170.) ARLANDSON, J.M. 2004. Lifestyles of the rich and Christian: women, wealth,
and social freedom. (In Levine, Amy-Jill, ed. A feminist companion to the
Acts of the Apostles. London: Clark International. p. 155-170.) ARLANDSON, J.M. 2004. Lifestyles of the rich and Christian: women, wealth,
and social freedom. (In Levine, Amy-Jill, ed. A feminist companion to the
Acts of the Apostles. London: Clark International. p. 155-170.) p
p
)
ARNOLD, C.E., ed. 2002. Zondervan illustrated Bible backgrounds com-
mentary: Romans to Philemon. Grand Rapids: Zondervan. p
p
)
ARNOLD, C.E., ed. 2002. Zondervan illustrated Bible backgrounds com-
mentary: Romans to Philemon. Grand Rapids: Zondervan. p
p
)
ARNOLD, C.E., ed. 2002. Zondervan illustrated Bible backgrounds com
mentary: Romans to Philemon. Grand Rapids: Zondervan. y
p
AUGSBURGER, D.W. 1996. Helping people forgive. Louisville: Westminster
John Knox. y
p
AUGSBURGER, D.W. 1996. Helping people forgive. Louisville: Westminster
John Knox. AUGSBURGER, D.W. 1996. Helping people forgive. Louisville: Westminste
John Knox. BARCLAY, W. 1976a. The Acts of the Apostles. Philadelphia: Westminster. ARCLAY, W. 1976a. The Acts of the Apostles. Philadelphia: Westminster. BARCLAY, W. 1976a. The Acts of the Apostles. Philadelphia: Westminster. In die Skriflig 41(2) 2007:295-322 319 Barnabas: Early Church leader and model of encouragement BARCLAY, W. 1976b. The Letters to the Galatians and Ephesians. Phila
delphia: Westminster. BARCLAY, W. 1976b. The Letters to the Galatians and Ephesians. Phila-
delphia: Westminster. p
BARRETT, C.K. 1994. Acts. Vol. 1: 1-14. Edinburgh: Clark. BLAIKLOCK, E.M. 1961. The Acts of the Apostles: an historical commentary. London: Tyndale. y
BRANCH, R.G. 2004. The messianic dimensions of kingship in Deuteronomy
17:14-20 as fulfilled by Jesus in Matthew. Verbum et ecclesia, 25(2):378-
401. BRANCH, R.G. 2006. Understudy to Star: the courageous audacity of an
Israelite slave girl. (In Niemann, H.M. & Augustin, M., eds. Stimulation
from Leiden: collected communications of the XVIIIth Congress of the
International Organization for the study of the Old Testament, Leiden
2004. Frankfurt am Main: Peter Lang. p. 257-269.) BRUCE, F.F. 1954. Commentary on the Book of Acts: the English text with
introduction, exposition and notes. London: Eerdmans. CALVIN, J. 1965. List of references Calvin’s New Testament commentaries: Acts of the Apostles
1-13. Transl. by J.W. Fraser & W.J.G. McDonald. Grand Rapids:
Eerdmans. CALVIN, J. 1966. Calvin’s New Testament commentaries: Acts of the Apostles
14-28. Transl. by J.W. Fraser. Grand Rapids: Eerdmans. y
p
CHRYSOSTOM. 1989. Nicene and post-Nicene Fathers. Vol. 12. Edinburgh:
Clark. CROWE, J. 1979. The Acts. Wilmington: Glazier. CROWE, J. 1979. The Acts. Wilmington: Glazier. CUMMINGS, D. 1983. A study of factors relating to church growth in the North
American division of Seventh-Day Adventists. Review of religious
research, 24(4):322-333. ( )
DANIELS, J.B. 1992. Barnabas. Anchor Bible dictionary. Vol. 1. New York:
Doubleday. ELWELL, W.A. & YARBROUGH, R.W. 2005. Encountering the New Testament:
a historical and theological survey. 2nd ed. Grand Rapids: Baker
Academic. ERDMAN, C.R. 1929. The Acts. Philadelphia: Westminster. EUSEBIUS. 1986. Nicean and post-Nicean Fathers. Vol. 1. Edinburgh: Clark. GARDNER, P.D., ed. 1995. New international encyclopedia of Bible c
the complete who’s who in the Bible. Grand Rapids: Zondervan. GRISWOLD, W., KNISS, F. & NELSON, T. 1993. Straining at the tie that binds:
congregational conflict in the 1980s. Review of religious research,
34(3):193-209. ( )
HILL, A.E., & WALTON, J. 2000. A survey of the Old Testament. Grand Rapids:
Zondervan. HILL, J. 2001. Growing new members. Clergy journal, 77(8):31. HOGE, D.R. 1994. Determinants of religious giving in urban Presbyterian
congregations. Review of religious research, 36(2):197-206. HOYT-OLIVER, J. 2006. Being nice or being His. College faith, 3:21-22. Berien:
Andrews University Press. IGNATIUS. 1989. Ante-Nicean fathers: the writings of the fathers down to AD
325. Vol. 1. Edinburgh: Clark. g
JEFFRESS, R. 2003. Developing the lost art of forgiveness. Southwester
journal of theology, 35(3):6-17. j
gy,
( )
JEFFREYS, M.A. 1995. Paul’s inner circle. Christian history, 14(3):26-28. In die Skriflig 41(2) 2007:295-322 320 Robin Gallaher Branch KOLLMANN, B. 2004. Joseph Barnabas: his life and legacy. Transl. by M. Henry. Collegeville: Liturgical Press. LIGHTFOOT, J.B., ed. & transl. 1981. The Apostolic fathers: Clement, Ignatius,
and Polycarp. Vol. 2, part 1: Clement. Grand Rapids: Baker Book House. LIM, D.S. 2004. A missiological evaluation of church growth. Asian journal
pentecostal studies, 7(1):125-147. p
( )
LONG, T.G. 1997. Hebrews. Louisville: John Knox. LONGENECKER, R.N. 1981. The Acts of the Apostles. (In Gaebelein, F.E., ed. The expositor’s Bible commentary. John-Acts. Grand Rapids: Zondervan. p. 207-573.) p
)
LOSTRACCO, J. & WILKERSON, G. 1998. Analyzing short stories. Dubuque:
Kendall. LYON, K.B. 1999. List of references Paranoid-schizoid phenomena in congregational conflict:
some dilemmas of reconciliation. Pastoral psychology, 47(4):273-292. MACLAREN, A. 1944. Expositors exposition of Holy Scriptures. The Acts. chapters 1 to 12 verse 17. Grand Rapids: Eerdmans. MATTHEWS, C.R. 2000. Acts of the Apostles. (In Freedman, D.N., Myers, A.C. & Beck, A.B., eds. Eerdmans dictionary of the Bible. Grand Rapids:
Eerdmans. p. 15-18.) MORRIS, L. 1986. New Testament theology. Grand Rapids: Zondervan
NEIL, W. 1973. The Acts of the Apostles. London: Oliphants. NYBERG, R. 1999. Willow Creek’s methods gain German following. Christianity
today, 43(5):24-25. y
( )
OCHS, P. 2004. The passion and repentance. The living pulpit, 13(3):6-8. PACKER, J.W. 1966. The Acts of the Apostles. Cambridge: Cambridge
University Press. y
PAGET, J.M. 1994. The epistle of Barnabas: outlook and background. Tubingen: Mohr. PETERSEN, D.L. 2005. Shaking the world of family values. (In Yoder, C.R.,
O’Connor, K.M., Johnson, E.E. & Saunders, S.P., eds. Shaking heaven
and earth: essays in honor of Walter Brueggemann and Charles B. Cousar. Louisville: Westminster. p. 23-32.) READ-HEIMERDINGER, J. 1998. Barnabas in Acts: a study of his role in the
text of Codex Bezae. Journal for the study of the Old Testament, 72(1):23-
66. RICHARDSON, P. 2000. Barnabas. (In Freedman, D.N., Myers, A.C. & Beck,
A.B., eds. Eerdmans dictionary of the Bible. Grand Rapids: Eerdmans. p. 150-151.) p
)
RODIN, R.S. 2000. Stewards in the kingdom: a theology of life in all its fullness. Downers Grove: InterVarsity. y
ROOP, E.F. 2002. Ruth, Jonah, Esther. Scottsdale: Herald. SCHNEELMELCHER, W., ed. 1989. New Testament apocrypha. Vol. 2. Writings relating to the apostles, apocalypses and related subjects. Louisville: James Clark. SHANKS, H. & WITHERINGTON III, B. 2003. The brother of Jesus: the
dramatic story and meaning of the first archaeological link to Jesus and his
family. London: Continuum. y
SOX, D. 1994. The gospel of Barnabas. London: Allen. STAFFORD, T. 1997. Why Christians fight Christians: the Spirit unites but the
American Church divides. Christianity today, 41(11):28-34. In die Skriflig 41(2) 2007:295-322 321 Barnabas: Early Church leader and model of encouragement VAN DEUN, P., ed. 1993. Sancti Barnabae apostolie lavdatio autore Alexandro
monacho et SS. Bartholomaei et Barnabae viat pro Menogloio imperiali
conscrpta. Leuven: Leuven University Press. p
y
WAGNER, C.P. 2000. Acts of the Holy Spirit: a modern commentary on the
Book of Acts. Ventura: Regal. WALLS, A.F. 2004. Converts or proselytes? The crisis over conversion in the
Early Church. List of references International bulletin of missionary research, 28(1):2-6. WALL, R.W. 2002. The Acts of the Apostles: introduction, commentary and
reflections. (In Keck, L., ed. The new interpreter’s Bible in twelve volumes. Vol. 10: Acts, introduction to epistolary literature, Romans, 1 Corinthians. Nashville: Abingdon. p. 1-368.) g
p
)
WANGERIN, W. 2000. On the road with Paul and Barnabas. Christian century,
117(22):796-800. g
p
)
WANGERIN, W. 2000. On the road with Paul and Barnabas. Christian century,
117(22):796-800. (
)
WESTMINSTER CONFESSION OF FAITH. www.pcanet.org/general/cof_
contents.htm 3rd ed. with corrections. Presbyterian Church in America. Date of access: 17 Oct. 2007. WESTMINSTER CONFESSION OF FAITH. www.pcanet.org/general/cof_
contents.htm 3rd ed. with corrections. Presbyterian Church in America. Date of access: 17 Oct. 2007. WILLIMON, W.H. 1988. Acts. Louisville: John Knox. WILLIMON, W.H. 1988. Acts. Louisville: John Knox. WINN, A.C. 1960. The Acts of the Apostles. Richmond: John Knox. p
WUELLNER, F.S. 2001. Forgiveness, the passionate journey: nine steps to
forgiving through Jesus’ beatitudes. Nashville: Upper Room Books. p
WUELLNER, F.S. 2001. Forgiveness, the passionate journey: nine steps to
forgiving through Jesus’ beatitudes. Nashville: Upper Room Books. Key concepts:
Antioch
Barnabas
Early Church: leaders
encouragement
Jerusalem Council
Saul/Paul
Kernbegrippe:
Antiochië
Barnabas
Jerusalem Raad
Saulus/Paulus
vertroosting
Vroeë Kerk: leiers Key concepts:
Antioch
Barnabas
Early Church: leaders
encouragement
Jerusalem Council
Saul/Paul
Kernbegrippe:
Antiochië
Barnabas
Jerusalem Raad
Saulus/Paulus
vertroosting
Vroeë Kerk: leiers In die Skriflig 41(2) 2007:295-322 322
|
https://openalex.org/W3081268457
|
https://repository.escholarship.umassmed.edu/bitstream/20.500.14038/29570/2/elife_55792_v2.pdf
|
English
| null |
An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes
|
eLife
| 2,020
|
cc-by
| 20,799
|
Nathan D Lawson1*, Rui Li1, Masahiro Shin1, Ann Grosse1†, Onur Yukselen2,
Oliver A Stone3, Alper Kucukural4,5, Lihua Zhu1,4,5 Nathan D Lawson1*, Rui Li1, Masahiro Shin1, Ann Grosse1†, Onur Yukselen2,
Oliver A Stone3, Alper Kucukural4,5, Lihua Zhu1,4,5 1Department of Molecular, Cell and Cancer Biology, University of Massachusetts
Medical School, Worcester, United States; 2Bioinformatics Core, University of
Massachusetts Medical School, Worcester, United States; 3Department of
Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom;
4Program in Molecular Medicine, University of Massachusetts Medical School,
Worcester, United States; 5Program in Bioinformatics and Integrative Biology,
University of Massachusetts Medical School, Worcester, United States Abstract The zebrafish is ideal for studying embryogenesis and is increasingly applied to model
human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by
identifying transcriptome changes between experimental conditions. Application of RNA-seq relies
on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis
from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues
were due, in part, to variably annotated 3’ untranslated regions and thousands of gene models
missing from each annotation. Since these discrepancies could compromise downstream analyses
and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation
that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in
both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations,
providing an important resource for zebrafish researchers. Competing interests: The
authors declare that no
competing interests exist. An improved zebrafish transcriptome
annotation for sensitive and
comprehensive detection of cell type-
specific genes An improved zebrafish transcriptome
annotation for sensitive and
comprehensive detection of cell type-
specific genes An improved zebrafish transcriptome
annotation for sensitive and comprehensive
detection of cell type-specific genes
Item Type
Journal Article
Authors
Lawson, Nathan D.; Li, Rui; Shin, Masahiro; Grosse, Ann S.;
Yukselen, Onur; Stone, Oliver A.; Kucukural, Alper; Zhu, Lihua
Julie
Citation
<p>Lawson ND, Li R, Shin M, Grosse A, Yukselen O, Stone OA,
Kucukural A, Zhu L. An improved zebrafish transcriptome
annotation for sensitive and comprehensive detection of
cell type-specific genes. Elife. 2020 Aug 24;9:e55792. doi:
10.7554/eLife.55792. Epub ahead of print. PMID: 32831172. <a
href="https://doi.org/10.7554/eLife.55792">Link to article on
publisher's site</a></p>
DOI
10.7554/eLife.55792
Rights
Copyright Lawson et al. This article is distributed under the terms
of the Creative Commons Attribution License, which permits
unrestricted use and redistribution provided that the original
author and source are credited. Download date
24/10/2024 04:11:15
Item License
http://creativecommons.org/licenses/by/4.0/ Link to Item
http://hdl.handle.net/20.500.14038/29570 TOOLS AND RESOURCES *For correspondence:
nathan.lawson@umassmed.edu
Present address: †Scholar Rock,
Inc, Cambridge, United States
Competing interests: The
authors declare that no
competing interests exist. Introduction Funding: See page 24
Received: 06 February 2020
Accepted: 21 August 2020
Published: 24 August 2020 Funding: See page 24
Received: 06 February 2020
Accepted: 21 August 2020
Published: 24 August 2020 The zebrafish has become an ideal animal model for studying processes related to developmental
biology (e.g. Wilkinson and van Eeden, 2014). Due to its hardy nature and fecundity, it is highly
amenable to a variety of manipulations, including both forward and reverse genetic approaches
(Lawson and Wolfe, 2011). The power of these applications is enhanced by the unique characteris-
tics of the zebrafish embryo. Most notably, zebrafish embryos are transparent and develop exter-
nally, allowing direct observation and facile technical manipulation (Beis and Stainier, 2006). Moreover, the initial steps of zebrafish development are very rapid, with gastrulation completed by
24 hr post-fertilization (hpf) and a complete circulatory system online just 12 hr later. By 5 days post-
fertilization (dpf), most organ systems are fully functional. Together, these characteristics of zebrafish
life history have contributed to its establishment as a leading model to study developmental biology,
while expanding its utility to the modeling of human diseases (Lam and Peterson, 2019). Reviewing editor: Elisabeth
Busch-Nentwich, University of
Cambridge, United Kingdom
Copyright Lawson et al. This
article is distributed under the
terms of the Creative Commons
Attribution License, which
permits unrestricted use and
redistribution provided that the
original author and source are
credited. Reviewing editor: Elisabeth
Busch-Nentwich, University of
Cambridge, United Kingdom Reviewing editor: Elisabeth
Busch-Nentwich, University of
Cambridge, United Kingdom Copyright Lawson et al. This
article is distributed under the
terms of the Creative Commons
Attribution License, which
permits unrestricted use and
redistribution provided that the
original author and source are
credited. Copyright Lawson et al. This
article is distributed under the In most model systems, a common analytical approach is to profile changes in gene expression
following a particular experimental manipulation, or in comparison between wild type and mutant
siblings. With the initial advent of microarrays and, more recently, RNA-sequencing (RNA-seq), this Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 1 of 28 Tools and resources Tools and resources Developmental Biology Developmental Biology approach can be applied at a transcriptome-wide level, enabling researchers to gain crucial insights
into
molecular
defects
associated
with
a
particular
experimental
condition
(Smith,
2003;
Wang et al., 2009). Introduction Such analysis can reveal important effectors for signaling pathways, downstream
targets for transcription factors, or identify changes in cellular composition in a complex tissue. More recently, several groups have adapted RNA-seq to allow molecular profiling of transcriptomes
from single cells (Klein et al., 2015; Macosko et al., 2015). Regarding zebrafish, this powerful
method has been applied in a number of novel ways. Initial efforts integrated single-cell RNA-seq
(scRNA-seq) with a publicly available expression pattern database to provide a predictive spatial
gene map for early stage zebrafish embryos (Satija et al., 2015). Recent application of scRNA-seq
at successive developmental stages has allowed unprecedented molecular insights into lineage rela-
tionships during embryogenesis (Farrell et al., 2018; Wagner et al., 2018). More advanced applica-
tions have combined scRNA-seq with cas9-induced ‘scars’ to allow molecular lineage tracing and
define cellular hierarchies in the brain (McKenna et al., 2016; Raj et al., 2018). Together, these
studies demonstrate the power of combining the unique benefits of zebrafish embryogenesis with
scRNA-seq to gain new insights into vertebrate development. The application of RNA-seq relies on the ability to accurately and reliably process large datasets
consisting of millions of short fragment reads (Wang et al., 2009). This approach usually relies on
the availability of a genomic sequence to which reads are initially mapped. Subsequently, the posi-
tions of mapped reads matching a corresponding transcriptome annotation are used for gene
assignment and quantification across different experimental conditions. For most commonly used
model systems, gene models and transcriptome annotations are now generally robust, allowing the
universal application of RNA-seq-based analysis with a variety of standardized computational pipe-
lines. However, in this study, we have found several deficiencies in current transcriptome annotations
for the zebrafish genome that can negatively impact RNA-seq analyses. To address these issues, we
have generated a new zebrafish transcriptome annotation, and demonstrated its improved perfor-
mance over existing annotations in several contexts, including analysis of bulk and scRNA-seq data-
sets from multiple cell types. Together, our results demonstrate that this annotation will be a
valuable resource for the zebrafish community. Discrepancies in RNA-seq analysis between zebrafish Ensembl and
RefSeq annotations q
We have previously used RNA-seq to profile endothelial cell gene expression in zebrafish embryos
(Quillien et al., 2017; Whitesell et al., 2019). In unpublished observations from those studies, we
noted discrepancies between identical datasets separately quantified using Ensembl (version 95,
hereafter referred to as Ens95) and RefSeq (GCF_000002035.6_GRCz11) transcriptome annotations. For example, we performed RNA-seq on mCherry-positive (kdrlpos) and -negative (kdrlneg) cells iso-
lated by fluorescence-activated cell sorting (FACS) from Tg(kdrl:HRAS-mCherry)s896 embryos, which
express membrane-localized red fluorescence protein in endothelial cells (Chi et al., 2008;
Whitesell et al., 2019). Use of the RefSeq annotation to quantify gene expression led to the identifi-
cation of 1780 genes enriched in kdrlpos compared to kdrlneg cells, while Ens95 identified 1632 genes
(log2 fold change >1, padj <0.05, n = 3; Figure 1A,B; Figure 1—source data 1; Table 1). The inter-
section of kdrlpos-enriched genes from each dataset using NCBI ID as a common identifier yielded
132 and 222 genes that were identified only by Ens95 or RefSeq, respectively, while 1407 were com-
monly identified as such in both annotation (Figure 1C, Figure 1—source data 2). Notably, common
IDs were lacking for a sizable proportion of genes in both datasets (for example, 4215 out of 25704
in Ens95 lacked a matching NCBI ID; Table 1, Figure 1—source data 1), suggesting that each anno-
tation may be missing genes. Importantly, genes detected as enriched only by Ens95 or RefSeq
included those with previously known functional relevance. Among these were the artery-specific
gene, ephrin-B2a (efnb2a; Lawson et al., 2001), and the SRY-box transcription factor 17 (sox17;
Chung et al., 2011), which were only identified as differential by Ens95 (Figure 1A,B, Figure 1—
source data 2). By contrast, slc2a1b, one of two duplicated zebrafish genes that encodes the
GLUT1 glucose transporter, as well as other blood-brain barrier markers, such as solute carrier family
7 member 5 (slc7a5; Boado et al., 1999), were significantly enriched in kdrlpos cells using RefSeq, Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 2 of 28 Tools and resources Developmental Biology Figure 1. Comparison of Ensembl and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. (A, B) Volcano plots showing differentially
expressed genes from Tg(kdrl:HRAS-mCherry)s896-positive and negative (kdrlpos and kdrlneg) cells identified using RNA-seq reads quantified with (A)
RefSeq or (B) Ensembl, version 95 (Ens95) transcript annotations. Discrepancies in RNA-seq analysis between zebrafish Ensembl and
RefSeq annotations Genes with significant enrichment (padj <0.05) are shown as red or blue (log2 fold
change >1 or <-1, respectively) across replicate samples (n = 3). Grey dots are genes that fall below statistical cutoffs. Green dots indicate selected
genes previously found to be enriched in endothelial cells in zebrafish or other models. (C) Venn diagram illustrating the intersection of genes with a
common NCBI ID in Ens95 and RefSeq found significantly enriched in kdrlpos cells using either annotation. (D, E) Plots of commonly annotated genes
identified as kdrlpos-enriched only by Ens95 with indicated values from (D) Ens95 or (E) RefSeq. (F, G) Correlation of expression levels from indicated
annotation for kdrlpos-enriched genes identified (F) selectively as such by Ens95 (maroon) or RefSeq (grey) only, or (G) both annotations. Data are not
normally distributed, Spearman correlation, r values are indicated. The online version of this article includes the following source data and figure supplement(s) for figure 1:
Source data 1. DESeq2 output for kdrlpos and kdrlneg RNA-seq quantified with RefSeq (GCF_000002035.6_GRCz11; worksheet 1) or Ensembl, v95 (work-
p
gy efSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. (A, B) Volcano plots showing differentially
896 Figure 1. Comparison of Ensembl and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. (A, B) Volcano plots showing differentially
expressed genes from Tg(kdrl:HRAS-mCherry)s896-positive and negative (kdrlpos and kdrlneg) cells identified using RNA-seq reads quantified with (A)
RefSeq or (B) Ensembl, version 95 (Ens95) transcript annotations. Genes with significant enrichment (padj <0.05) are shown as red or blue (log2 fold
change >1 or <-1, respectively) across replicate samples (n = 3). Grey dots are genes that fall below statistical cutoffs. Green dots indicate selected
genes previously found to be enriched in endothelial cells in zebrafish or other models. (C) Venn diagram illustrating the intersection of genes with a
common NCBI ID in Ens95 and RefSeq found significantly enriched in kdrlpos cells using either annotation. (D, E) Plots of commonly annotated genes
identified as kdrlpos-enriched only by Ens95 with indicated values from (D) Ens95 or (E) RefSeq. (F, G) Correlation of expression levels from indicated
annotation for kdrlpos-enriched genes identified (F) selectively as such by Ens95 (maroon) or RefSeq (grey) only, or (G) both annotations. Data are not
normally distributed, Spearman correlation, r values are indicated. Tools and resources Developmental Biology Developmental Biology Developmental Biology Figure 1 continued
Figure supplement 1. Comparison of Ens95 and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. Figure supplement 1—source data 1. DESeq2 output for pdgfrbpos and pdgfrbneg RNA-seq quantified with RefSeq (GCF_000002035.6_GRCz11) or
Ensembl, v95. ment 1. Comparison of Ens95 and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. Figure supplement 1—source data 1. DESeq2 output for pdgfrbpos and pdgfrbneg RNA-seq quantified with RefSeq (GCF_000002035.6_GRCz11) or
Ensembl, v95. 2. Intersection of pdgfrbpos-enriched genes from RefSeq and Ens95 commonly annotated by NCBI ID. ment 1—source data 2. Intersection of pdgfrbpos-enriched genes from RefSeq and Ens95 commonly annotated Figure supplement 1—source data 2. Intersection of pdgfrbpos-enriched genes from RefSeq and Ens95 co but not Ens95 (Figure 1A,B, Figure 1—source data 2). Interestingly, slc2a1a, a second duplicate
GLUT1 ortholog (previously referred to as ‘glut1b’; Tseng et al., 2009; Umans et al., 2017) was not
identified as differential by either annotation, despite previous reports of its endothelial expression
(Figure 1A,B, Figure 1—source data 1; Umans et al., 2017). By contrast, well-known endothelial
markers, such as cadherin5 (cdh5) and kdrl itself, were robustly detected as enriched by both anno-
tations (Figure 1A,B). g
Subtle differences in Ens95 and RefSeq transcript annotations might affect data normalization
and differential analysis, slightly shifting adjusted p-values and causing genes to fall just below statis-
tical cutoffs. However, this was not the case for many of the genes identified selectively by either
annotation. For example, 58 out of 132 commonly annotated kdrlpos genes enriched only in Ens95
showed an adjusted p-value over 5-fold greater than the standard cutoff (0.05) when quantified
using RefSeq (compare Figure 1D,E, Figure 1—source data 2). Moreover, expression levels from
each annotation for genes selectively identified as kdrlpos-enriched only using Ens95 or RefSeq
showed a poor correlation, with significantly higher expression in the annotation in which the gene
was identified as differential (Figure 1F, Figure 1—figure supplement 1A, Figure 1—source data
2). By contrast, levels of kdrlpos-enriched genes for genes commonly identified as differentially
expressed displayed a high degree of correlation between Ens95 and RefSeq quantifications
(Figure 1G). To rule out that these discrepancies were unique to endothelial genes, we analyzed RNA-seq
data from TgBAC(pdgfrb:citrine)s1010 embryos. In this case, transgene-positive (pdgfrbpos) cells
include epidermis, cartilage, pericytes, and vascular smooth muscle cells (Vanhollebeke et al.,
2015). Discrepancies in RNA-seq analysis between zebrafish Ensembl and
RefSeq annotations The online version of this article includes the following source data and figure supplement(s) for figure 1:
S
d t
1 DES
2
t
t f
kd lpos
d kd lneg RNA
tifi d
ith R fS
(GCF 000002035 6 GRC 11
k h
t 1)
E
bl
95 (
k Figure 1. Comparison of Ensembl and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. (A, B) Volcano plots showing differentially
expressed genes from Tg(kdrl:HRAS-mCherry)s896-positive and negative (kdrlpos and kdrlneg) cells identified using RNA-seq reads quantified with (A)
RefSeq or (B) Ensembl, version 95 (Ens95) transcript annotations. Genes with significant enrichment (padj <0.05) are shown as red or blue (log2 fold
change >1 or <-1, respectively) across replicate samples (n = 3). Grey dots are genes that fall below statistical cutoffs. Green dots indicate selected
genes previously found to be enriched in endothelial cells in zebrafish or other models. (C) Venn diagram illustrating the intersection of genes with a
common NCBI ID in Ens95 and RefSeq found significantly enriched in kdrlpos cells using either annotation. (D, E) Plots of commonly annotated genes
identified as kdrlpos-enriched only by Ens95 with indicated values from (D) Ens95 or (E) RefSeq. (F, G) Correlation of expression levels from indicated
annotation for kdrlpos-enriched genes identified (F) selectively as such by Ens95 (maroon) or RefSeq (grey) only, or (G) both annotations. Data are not
normally distributed, Spearman correlation, r values are indicated. Th
l
f h
l
l d
h
f ll
d
d f
l
( ) f
f
1 3 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Incomplete 3’ UTRs models influence RNA-seq quantification using
existing annotations existing annotations
Since we constructed the RNA-seq libraries in the experiments noted above using oligo-dT priming
(Quillien et al., 2017; Whitesell et al., 2019), they would yield reads with a bias to the 3’ end of
transcripts. Therefore, we investigated whether discrepancies noted above were due to differences
between 3’ untranslated region (UTR) annotations in Ens95 and RefSeq. For this purpose, we sought
to assemble a reference set of transcripts with annotated 3’ UTRs from Ens95 and RefSeq. Strikingly,
in the process of assembling this reference panel, we found that nearly 20% of all coding genes in
Ens95 lacked any transcript with an annotated 3’ UTR, while a smaller proportion also lacked a stop
codon (Table 2, Figure 2—source data 1). By contrast, only about 6% of RefSeq genes lacked a 3’
UTR, and 1% lack a stop codon (Table 2, Figure 2—source data 1). Importantly, missing 3’ UTRs
appeared to contribute to the discrepancies observed in our RNA-seq analyses. For example, 64 of
the 217 kdrlpos-enriched genes identified only using RefSeq lacked an Ens95 3’ UTR, and these were
detected at significantly lower levels in Ens95 compared to RefSeq (Figure 2A, Figure 2—source
data 1). Similar results were found for pdgfrbpos-enriched genes, where 94 out of 248 genes identi-
fied only using RefSeq lacked a 3’ UTR annotation in Ens95 (Figure 2B, Figure 2—source data 1). Among the discrepant kdrlpos-enriched genes was the previously noted blood brain barrier (BBB)
marker slc7a5, where lack of a 3’ UTR in Ens95 resulted in an approximately ten-fold difference in
detected expression between the two annotations (Figure 2C; N.B.: unless otherwise indicated
UCSC browser images show a single representative transcript bearing the longest 3’ UTR for a given
gene; Figure 1—source data 2). Interestingly, the location of mapped reads from a publicly avail-
able RNA-seq dataset (referred to as GSE32900), as well the genomic position of kdrlpos reads, sug-
gested an even longer slc7a5 3’ UTR than that annotated in RefSeq (Figure 2C). A putative longer 3’
UTR would also be concordant with a ‘3P-seq’ feature on the same strand, which we annotated using
a public dataset that defines genomic locations for 3’ transcript ends based on a biochemically strin-
gent technique (Jan et al., 2011; Ulitsky et al., 2012). Tools and resources As above, most pdgfrbpos-enriched genes with a common NCBI identifier (1905) were differ-
entially expressed compared to negative (pdgfrbneg) cells using both annotations, while 172 and 248
genes were selectively identified as such by only Ens95 or RefSeq, respectively (Figure 1—figure
supplement 1B, Figure 1—figure supplement 1—source datas 1 and 2; Table 1). Among the dis-
crepant genes were well-known pericyte markers, such as potassium inwardly-rectifying channel sub-
family J member 8 (kcnj8) and chondroitin sulfate proteoglycan 4 (cspg4), which encodes the
proteoglycan epitope NG2 (Bondjers et al., 2006; Ozerdem et al., 2001). Both kcnj8 and cspg4
were pdgfrbpos-enriched using RefSeq, but not Ens95 (Figure 1—figure supplement 1C,D, Fig-
ure 1—figure supplement 1—source data 2). By contrast, angiopoietin 1 (angpt1) was identified as
pdgfrbpos-enriched only using Ens95 (Figure 1—figure supplement 1C,D, Figure 1—figure supple-
ment 1—source data 2). The pericyte marker ATP-binding cassette, sub-family C (CFTR/MRP),
member 9 (abcc9), and pdgfrb itself, are found as pdgfrbpos-enriched with both annotations (Fig-
ure 1—figure supplement 1C,D, Figure 1—figure supplement 1—source data 2). We noted Table 1. Numbers of detected and differential genes from RNA-seq datasets analyzed with Ens95
and RefSeq annotations with matched identifiers. Ens95
RefSeq
All
w/NCBI ID
All
w/Ens ID
kdrlpos – all detected
25704
21489
27516
21903
kdrlpos-enriched
1632
1538
1780
1651
pdgfrbpos – all detected
25699
21480
27598
21903
pdgfrbpos-enriched
2186
2091
2323
2188
Nr2f2pos – all detected
20516
17867
21788
18164
Nr2f2pos-enriched
568
516
580
508 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology similar discrepancies for known smooth muscle genes, including the transcription factor myocardin
(myocd), for which an annotation appears to be missing from Ens95 (data not shown), and calponin
1, basic, smooth muscle, b (cnn1b), both of which were selectively identified using RefSeq. Similar to
kdrlpos-enriched genes, 80 out of 172 of pdgfrbpos-enriched genes identified using Ens95 showed
padj values for matched RefSeq genes at least 5-fold over the statistical cutoff (Figure 1—figure
supplement 1E, Figure 1—figure supplement 1—source data 2). Likewise, expression levels for
genes selectively enriched using Ens95 or RefSeq showed poor correlation between annotations and
higher expression levels in the respective annotation in which it was detected as differentially
expressed (Figure 1—figure supplement 1F,G, Figure 1—figure supplement 1—source data 2). By contrast, the expression of pdgfrbpos-enriched genes identified by both annotations displayed a
high degree of correlation (Figure 1—figure supplement 1F). Tools and resources Taken together, these observations
suggest underlying differences in zebrafish Ensembl and RefSeq annotations that contribute to
inconsistencies in differential gene analysis from RNA-seq data. Incomplete 3’ UTRs models influence RNA-seq quantification using
existing annotations Thus, some of the discrepancies noted above
are likely due to a lack of 3’ UTR annotation for a considerable proportion of Ensembl genes. We next compared 3’ UTR lengths in cases where there existed corresponding annotations for
this feature in both Ens95 and RefSeq. For this purpose, we generated a reference set of transcripts
for 16,558 genes (see Materials and methods for details; Figure 2—source data 2). In our reference
panel, just over one-half of genes exhibited the same length 3’ UTR in both annotations (9077 out of ble 2. Number of coding genes and proportion without stop codon or 3’ UTR in indicated
t ti Table 2. Number of coding genes and proportion without stop codon or 3’ UTR in indicated
annotation. Ens95
RefSeq
All Genes
32520
30445
annotated CDS
25592
26120
CDS, missing annotated stop codon
1585
269
CDS, missing annotated 3’ UTR
4703
1580
DOI: https://doi.org/10.7554/eLife.55792
5 of 28 Table 2. Number of coding genes and proportion without stop codon or 3’ UTR in indicated
annotation. Tools and resources Figure 2. Incomplete 3’ UTRs annotations contribute to discrepancies in RNA-seq analysis. (A, B) Log10 average expression as quantified using
indicated annotation for (A) kdrlpos- or (B) pdgfrbpos-enriched genes identified as such only in RefSeq and lacking an Ens95 3’ UTR annotation. Expression levels for genes from each annotation with matched NCBI ID are shown in each case. Data are normally distributed (Shapiro-Wilks test),
paired t-test, p values are indicated; n = 3 (i.e. each point represents an average value from three separate RNA-seq replicates). (C) UCSC browser
image of slc7a5 locus on the minus strand showing 3’ UTR annotations from Ens95 and RefSeq. Mapped read depth from kdrlpos cells on the genome,
or assigned to each annotation are indicated, as is a 3P-seq feature. The GSE32900 track is consolidated RNA-seq reads from all stages indicated in
Figure 3A. The location of a putative missing 3’ UTR is indicated. (D) Pie chart showing numbers of reference genes with the same or longer 3’ UTRs in
each indicated annotation. (E) Pie charts showing the proportion of reference genes selectively identified as kdrlpos- or pdgfrbpos-enriched by Ens95
and RefSeq with indicated relative 3’ UTR length. Incomplete 3’ UTRs models influence RNA-seq quantification using
existing annotations (F, G) Correlation plots showing log10 average expression from kdrlpos RNA-seq (n = 3) quantified with
each annotation for matched reference genes with (F) longer Ens95 (maroon) or RefSeq (light blue) 3’ UTR, or (G) same 3’ UTR length. Data are not
normally distributed, Spearman correlation, r values are indicated. (H, I) UCSC browser images of (H) sox17 and (I) cspg4 loci, both on the minus strand,
showing 3’ UTR annotations from Ens95 and RefSeq. Mapped read depth of RNA-seq from (H) kdrlpos or (I) pdgfrbpos cells captured for each
annotation is indicated. Consolidated reads from GSE32900 and location of 3P-Seq features are indicated, as is putative missing 3’ UTR in cspg4. The online version of this article includes the following source data and figure supplement(s) for figure 2:
S
d t
1 Mi
i
3’ UTR
t ti
i
R fS
d E
95
Tools and resources
Developmental Biology Figure 2. Incomplete 3’ UTRs annotations contribute to discrepancies in RNA-seq analysis. (A, B) Log10 average expression as quantified using
indicated annotation for (A) kdrlpos- or (B) pdgfrbpos-enriched genes identified as such only in RefSeq and lacking an Ens95 3’ UTR annotation. Expression levels for genes from each annotation with matched NCBI ID are shown in each case. Data are normally distributed (Shapiro-Wilks test),
paired t-test, p values are indicated; n = 3 (i.e. each point represents an average value from three separate RNA-seq replicates). (C) UCSC browser
image of slc7a5 locus on the minus strand showing 3’ UTR annotations from Ens95 and RefSeq. Mapped read depth from kdrlpos cells on the genome,
or assigned to each annotation are indicated, as is a 3P-seq feature. The GSE32900 track is consolidated RNA-seq reads from all stages indicated in
Figure 3A. The location of a putative missing 3’ UTR is indicated. (D) Pie chart showing numbers of reference genes with the same or longer 3’ UTRs in
each indicated annotation. (E) Pie charts showing the proportion of reference genes selectively identified as kdrlpos- or pdgfrbpos-enriched by Ens95
and RefSeq with indicated relative 3’ UTR length. (F, G) Correlation plots showing log10 average expression from kdrlpos RNA-seq (n = 3) quantified with
each annotation for matched reference genes with (F) longer Ens95 (maroon) or RefSeq (light blue) 3’ UTR, or (G) same 3’ UTR length. Data are not
normally distributed, Spearman correlation, r values are indicated. Tools and resources Taken together, these results suggest that a large
proportion of genes in current zebrafish transcriptome annotations do not have accurate 3’ models,
which can affect the interpretation of RNA-seq analysis. Our discovery of 3’ UTR discrepancies between Ens95 and RefSeq was likely facilitated by the 3’
end-bias inherent in our RNA-Seq libraries. Therefore, we compared annotation performance using
RNA-seq data from a random-primed library. In this case, we performed RNA-Seq on endothelial
cells positive for the vein-specific transcription factor, Nr2f2 (nuclear receptor subfamily 2, group F,
member 2), versus those positive for the Tg(fli1a:egfp)y1 transgene (see Materials and methods). Accordingly, we detected several known vein-specific genes enriched in Nr2f2pos cells including fms
related receptor tyrosine kinase 4 (flt4), lymphatic vessel endothelial hyaluronic receptor 1b (lyve1b),
and nr2f2 itself (Figure 2—figure supplement 2A,B, Figure 2—source data 3). Genes identified as
Nr2f2pos-enriched with matched NCBI IDs showed a similar degree of overlap from each annotation,
as noted above for kdrlpos and pdgfrbpos analysis (Figure 2—figure supplement 2C). We also noted
a poor correlation in detection levels for Nr2f2pos-enriched genes selectively identified by either
Ens95 or RefSeq compared to commonly identified genes (Figure 2—figure supplement 2D). In
addition, we detected higher expression for discrepant genes in the annotation where the gene was
significantly enriched, although the magnitude of difference in these cases was less than that of the
3’ biased data (compare Figure 2—figure supplement 2E with Figure 1—figure supplement 1A,
G). Accordingly, many of the discrepant Nr2f2pos-enriched genes were associated with small shifts in
adjusted p-values or log2 fold change values. For example, only 10 out of 59 Nr2f2pos-enriched
genes identified by only Ens95 showed a greater than 5-fold padj compared to RefSeq values for
the same genes (Figure 2—figure supplement 2F, Figure 2—source data 3). Furthermore, a com-
parison between discrepant reference Nr2f2pos genes did not show the same trend noted with
kdrlpos and pdgfrbpos analysis regarding 3’ UTR differences (Figure 2—figure supplement 2G, com-
pare with Figure 2E). We noted a high degree of correlation between expression levels detected in
each annotation regardless of differences in 3’ UTR lengths, although we still noted a slight trend of
longer 3’UTRs displaying slightly higher expression (Figure 2—figure supplement 2H, Figure 2—
source data 3). These results suggest that differences in 3’ UTR annotations between Ensembl and
RefSeq may be somewhat mitigated when analyzing RNA-seq data from libraries constructed using
random priming. Tools and resources Developmental Biology Developmental Biology Figure 2 continued
Source data 2. Reference gene set for 3’ UTR comparisons. Source data 3. RNA-seq analysis of Nr2f2pos and NR2f2neg cells. Source data 4. Transcript based-comparison of RefSeq and Ensembl annotations. Figure supplement 1. Differences in 3’ UTR lengths between Ens95 and RefSeq for discrepant kdrlpos- and pdgfrbpos-enriched genes. Figure supplement 2. Analysis of RNA-seq reads from a random-primed library. Source data 4. Transcript based-comparison of RefSeq and Ensembl annotations. Figure supplement 1. Differences in 3’ UTR lengths between Ens95 and RefSeq for discrepant kdrlpos- and pdgfrbpos-enriched genes. Figure supplement 2. Analysis of RNA-seq reads from a random-primed library. 16558), while 4923 and 2558 genes showed longer 3’ UTRs in Ens95 or RefSeq, respectively
(Figure 2D, Figure 2—source data 2; ‘longer’ is defined as more than 50 nucleotides). Similar to
genes with missing 3’ UTRs, a large proportion of discrepant kdrlpos- and pdgfrbpos-enriched genes
identified only in Ens95 or RefSeq also had a longer 3’ UTR in the respective annotation (Figure 2E). Moreover, these 3’ UTRs were, on average, five times longer when comparing annotations (Fig-
ure 2—figure supplement 1A,B, Figure 2—source data 2). Consistent with an effect on detection,
levels of reference genes in kdrlpos and pdgfrbpos datasets quantified by Ens95 or RefSeq tended to
be higher in the respective annotation predicting a longer 3’ UTR and showed a lower correlation
between annotations than those with the same 3’ UTR length (Figure 2F,G, Figure 2—source data
2). Among these genes were several noted above as discrepant between Ens95 and RefSeq annota-
tions when quantifying kdrlpos and pdgfrbpos datasets. For example, sox17 exhibits a longer 3’ UTR
in Ens95, leading to improved detection at severalfold higher levels in kdrlpos cells (Figure 2H, Fig-
ure 1—source data 2). We also noted additional cases where an accurate 3’ UTR model is likely
missing from both annotations. For example, the pericyte marker cspg4 has a slightly longer 3’ UTR
in the RefSeq annotation (Figure 2I), where it is also detected as significantly enriched in pdgfrbpos
cells (Figure 1—figure supplement 1C,D). However, as noted above with slc7a5, the location of
mapped reads from GSE32900 and our pdgfrbpos data, as well as a 3P-Seq feature on the same
strand, suggest a much longer 3’ UTR (Figure 2I). Incomplete 3’ UTRs models influence RNA-seq quantification using
existing annotations (H, I) UCSC browser images of (H) sox17 and (I) cspg4 loci, both on the minus strand,
showing 3’ UTR annotations from Ens95 and RefSeq. Mapped read depth of RNA-seq from (H) kdrlpos or (I) pdgfrbpos cells captured for each
annotation is indicated. Consolidated reads from GSE32900 and location of 3P-Seq features are indicated, as is putative missing 3’ UTR in cspg4. The online version of this article includes the following source data and figure supplement(s) for figure 2:
S
d t
1 Mi
i
3’ UTR
t ti
i
R fS
d E
95 Source data 1. Missing 3’ UTR annotations in RefSeq and Ens95. Figure 2 continued on next page Source data 1. Missing 3’ UTR annotations in RefSeq and Ens95. Figure 2 continued on next page 6 of 28 6 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Ensembl and RefSeq annotations are missing genes During the analysis above, we noted that Ens95 and RefSeq zebrafish annotations lacked common
identifiers for a sizable proportion of genes. Moreover, relevant lineage markers, such as the smooth
muscle-specific gene myocd, were among genes missing from either annotation (see above and
Table 1). To further investigate this issue, we performed a coordinate-based transcript-level compar-
ison between Ens95 and RefSeq (see Materials and methods). This analysis revealed 3165 genes
annotated by RefSeq that were missing from Ens95 (Table 3, Figure 2—source data 4). More than
half of these missing genes encoded proteins and several hundred were curated in the Zebrafish
Information Network (ZFIN; Figure 2—source data 4). Conversely, 2116 Ens95 genes were missing
from RefSeq (Table 3, Figure 2—source data 4), including 670 protein-coding genes, 141 T-cell
receptor genes, and 546 genes curated by ZFIN (Table 3, Figure 2—source data 4). These discrep-
ancies may have been due to the older version of Ensembl that we used at the start of our studies. However, a comparison of Ens95 to a more current version (Ensembl, version 99; referred to as
Ens99), revealed identical transcript models and no new genes that have been annotated in the
intervening versions (Figure 2—source data 4), although some nomenclature has changed (data not
shown). Thus, current zebrafish transcript annotations from RefSeq and Ensembl have considerable
gaps that preclude a comprehensive assessment of gene expression and that may constrain follow-
up studies when used for RNA-seq, or analyses focused on 3’ UTR sequences (e.g. miRNA target
searches). Tools and resources Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 7 of 28 Tools and resources Tools and resources Developmental Biology As noted above, nearly 20% of Ens95 genes lack a 3’ UTR annotation (see Table 2). For these
Nr2f2pos-enriched genes, we did detect significant differences in expression levels between Ens95
and RefSeq annotations (Figure 2—figure supplement 2I). Notably, among these discrepant genes
was the essential endothelial Ets transcription factor, erg (Vijayaraj et al., 2012), which lacks any
UTR annotations in Ens95 compared to RefSeq, resulting in undersampling in Nr2f2pos cells when
using Ens95 (Figure 2—figure supplement 2J). As a result, erg is identified as differentially enriched
when using RefSeq, but not Ens95 for quantification (Figure 2—source data 3). Thus, the analysis of
RNA-seq data obtained from random-primed libraries is less dependent on 3’ UTR annotation in
existing Ensembl and RefSeq transcriptome annotations than when using 3’ biased data. However,
relevant functional genes may still be missed when using Ensembl for quantification due to the com-
plete absence of 3’ UTR annotations for many genes. Tools and resources Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Assembly of an improved zebrafish transcriptome annotation Our analyses above demonstrated two major issues with existing zebrafish transcriptome annota-
tions. First, 3’ UTR annotations are incomplete and differ between Ensembl and RefSeq. Second,
each annotation is missing a sizable number of genes. To address these issues, we sought to con-
struct a more complete zebrafish transcriptome annotation (Figure 3A). For this purpose, we used
the GSE32900 RNA-seq datasets, which comprise libraries from zebrafish embryos at dome, bud,
and shield stages, as well as 28 hr post-fertilization (hpf) and 2- and 5 days, post-fertilization (dpf). From these stages, we combined over 600 million paired-end, strand-specific reads (Figure 3—
source data 1) and mapped them to GRCz11. We generated transcript and gene models using Table 3. Coordinate-based transcriptome comparisons. Annotation
Ensembl 95
RefSeq
V4.2
V4.3
# genes
32520
30445
39988
36351
# transcripts
59876
55182
115496
111842
# exons
335075
307538
414404
411330
# RefSeq genes missing
3165
-
173
7c
# Ensembl genes missinga
-
2116
1133b
957d
a –RefSeq comparison with Ens95, V4 comparison with Ens99. b – 956/1133 classified as rRNA, snRNA, snoRNA or sRNA. c – left out from V4.2 add-back; see main text. d – 956/957 are rRNA, snRNA, snoRNA, sRNA, or miscRNA; remaining protein coding gene is a sequence duplicate. Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 8 of 28 Tools and resources Developmental Biology Figure 3. The V4.2 annotation improves detection of cell-type-specific genes from bulk RNA-seq data. (A) Schematic outline for generating a new
zebrafish transcriptome annotation. See Results and Materials and methods sections for details. (B) Pie charts showing the proportion of reference
genes with same, longer or shorter 3’ UTR in the V4.3 annotation compared to relative 3’ UTR length between Ens95 and RefSeq. (C, E) Venn diagrams
howing intersection of reference genes with commonly annotated NCBI ID that are significantly enriched in (C) kdrlpos- or (E) pdgfrbpos-cells in each
ndicated annotation. (D, F) Volcano plots of reference genes with common NCBI ID identified as (D) kdrlpos- or (F) pdgfrbpos-enriched only by Ens95 in
comparison to RefSeq. Indicated values are from the same genes quantified using V4.3. Red dots indicate log2 fold change >1 and adjp <0.05. (G) 3’
UTR lengths and (H) log10 average expression (n = 3) using RefSeq and V4.3 for reference genes in the indicated dataset. (G, H) Data are not normally
distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. Assembly of an improved zebrafish transcriptome annotation Error bars denote mean and standard deviation. (I) Log10 average Figure 3. The V4.2 annotation improves detection of cell-type-specific genes from bulk RNA-seq data. (A) Schematic outline for generating a new
zebrafish transcriptome annotation. See Results and Materials and methods sections for details. (B) Pie charts showing the proportion of reference
genes with same, longer or shorter 3’ UTR in the V4.3 annotation compared to relative 3’ UTR length between Ens95 and RefSeq. (C, E) Venn diag
showing intersection of reference genes with commonly annotated NCBI ID that are significantly enriched in (C) kdrlpos or (E) pdgfrbpos cells in ea Figure 3. The V4.2 annotation improves detection of cell-type-specific genes from bulk RNA-seq data. (A) Schematic outline for generating a new
zebrafish transcriptome annotation. See Results and Materials and methods sections for details. (B) Pie charts showing the proportion of reference
genes with same, longer or shorter 3’ UTR in the V4.3 annotation compared to relative 3’ UTR length between Ens95 and RefSeq. (C, E) Venn diagrams
showing intersection of reference genes with commonly annotated NCBI ID that are significantly enriched in (C) kdrlpos- or (E) pdgfrbpos-cells in each
indicated annotation. (D, F) Volcano plots of reference genes with common NCBI ID identified as (D) kdrlpos- or (F) pdgfrbpos-enriched only by Ens95 in
comparison to RefSeq. Indicated values are from the same genes quantified using V4.3. Red dots indicate log2 fold change >1 and adjp <0.05. (G) 3’
UTR lengths and (H) log10 average expression (n = 3) using RefSeq and V4.3 for reference genes in the indicated dataset. (G, H) Data are not normally
distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. Error bars denote mean and standard deviation. (I) Log10 average
expression (n = 3) and (J) 3’ UTR lengths across all annotations for reference genes uniquely identified as enriched in indicated transgene-positive cell
type using V4.3 (log2 fold change >1, padj <0.05). Data are not normally distributed. Friedman test to assess variance (p<0.0001 in all cases). Dunn’s
multiple comparison test was used for pairwise comparisons, p values are indicated. Error bars denote mean and standard deviation. The online version of this article includes the following source data and figure supplement(s) for figure 3:
F
3
d Figure 3 continued on next page Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources These fusion transcripts led to misassignment of gene informa-
tion in Ensembl and resulted in incorrect RNA-seq quantification, leading to shifts in detected gene
expression (for examples, see Figure 3—figure supplement 1, Figure 3—source data 2). We also
chose to remove ribosomal and small nuclear RNAs (but not miRNAs), which are present in Ensembl,
but not in RefSeq. The first working version of our annotation, referred to as version 4.2 (V4.2), comprised 115,496
transcripts from over 400,000 unique exons that give rise to nearly 40,000 genes (Table 3). A coordi-
nate-based transcript comparison with RefSeq showed good coverage by V4.2 with only 173 RefSeq
genes missing (Table 3, Figure 3—source data 3). Comparison with a more recent Ensembl tran-
scriptome annotation (Ensembl 99, released January 2020) shows nearly 1200 genes missing from
V4.2, although the majority of these (957/1133) are ribosomal or small nuclear RNAs, which we had
removed from our annotations (Table 3, Figure 3—source data 3) and which are also absent from
RefSeq. Over 6000 gene models in V4.2 did not overlap with existing annotations and are referred
to using arbitrary ‘XLOC’ numbers assigned by Cufflinks (Figure 3—source data 4). Of these,
approximately 1300 are transcripts that encode amino acid homology to zebrafish or human pro-
teins, suggesting that these are previously unidentified paralogs or orthologs, although we cannot
rule out the possibility that they may be pseudogenes. Of the XLOC genes, we also identified 45
that match previously annotated long non-coding RNAs not present in Ensembl or RefSeq (Fig-
ure 3—source data 4). We subsequently added annotations for the missing Ens99 and RefSeq genes noted above from
V4.2 (see Table 3; Figure 3—source data 3) to yield a V4.3 annotation. We also limited inclusion in
V4.3
of
XLOC
genes
to
those
that
were
supported
by
secondary
analyses
(see
Materials and methods for details; Figure 3—source data 4). For end users concerned with poten-
tial mapping or quantification issues arising from novel gene annotations (e.g. due to the presence
of pseudogenes, or repeat elements), XLOC genes can be easily removed from the annotation. Except for the cases noted above, V4.3 is missing only a single Ens99 gene (exclusive of small RNAs
noted above) and 7 RefSeq genes (Table 3). Tools and resources Developmental Biology Developmental Biology Figure 3 continued Figure 3 continued Source data 1. List of SRA accession numbers, stages, and read numbers from GSE32900 for associated RNA-seq datasets used in this study. Source data 2. List of manually-identified discrepancies in Ensembl gene annotation due to spurious fusionor overlapping transcripts. urce data 1. List of SRA accession numbers, stages, and read numbers from GSE32900 for associated RNA-seq d Source data 3. RefSeq (worksheet 1) and Ens99 (worksheet 2) genes missing from the V4.2 annotation. . RefSeq (worksheet 1) and Ens99 (worksheet 2) genes missing from the V4.2 annotation. Source data 3. RefSeq (worksheet 1) and Ens99 (worksheet 2) genes missing from the V4.2 annotation. Source data 5. V4.3 gene information table, including unique LL ID numbers, associated Ens99 gene ID, NCBI ID, and ZFIN gene ID numbers, gene
symbols, and gene names. able, including unique LL ID numbers, associated Ens99 gene ID, NCBI ID, and ZFIN gene ID numbers, gene Source data 5. V4.3 gene information table, including unique LL ID numbers, associated Ens99 gene ID, NCBI ID, and ZFIN gene ID numbers, gene
symbols, and gene names. Source data 6. Output from DESeq2 analysis comparing kdrlpos and kdrlneg RNA-seq. Source data 7. Output from DESeq2 analysis comparing pdgfrbpos and pdgfrbneg RNA-seq. Source data 8. Worksheet 1 - Output from DESeq2 analysis comparing Nr2f2pos and Nr2f2neg RNA-seq. Figure supplement 1. Ensembl naming conflicts and improved transcript diversity in V4.3. Figure supplement 2. The V4.3 annotation improves the detection of cell-type-specific genes from bulk RNA-seq data. Figure supplement 3. Analysis of Nr2f2pos and Nr2f2neg datasets using V4.3. Cufflinks (Trapnell et al., 2010) and applied Cuffmerge (Trapnell et al., 2010) to combine them
with Ens95 and RefSeq. With this approach, the naming conventions from the Ens95 annotation
were applied to all gene models and remaining known genes named with RefSeq nomenclature. Ini-
tial transcriptome versions (versions 1 through 3; V1-V3) were generated to test and identify optimal
parameters for transcript assembly (data not shown and see Materials and methods for details). Dur-
ing this process, we noted several nomenclature conflicts that arose due to spurious fusion tran-
scripts. These were identified and removed through automated and manual annotation (see
Materials and methods for details). Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 9 of 28 9 of 28 Tools and resources Tools and resources Therefore, we also include comments
in the information table regarding how Ensembl and RefSeq gene assignments were made. We rec-
ommend that users consider these when performing follow-up analyses to confirm that matching
data imported from other sources is accurate. Since our annotation comprises genes missing from
Ensembl or RefSeq, as well as potentially novel genes (e.g. those identified with ‘XLOC’ assign-
ments), and would lack a corresponding identifier from those annotations, we also assigned a unique
arbitrary gene identifier to every gene (referred to as an ‘LL’ ID number). The LL ID number is also
assigned to entries annotated in the GTF allowing easy integration of information from this table
(Figure 3—source data 5) with RNA-seq outputs following analysis. The gene information tables for
both annotations are also available for download at zf-transcriptome.umassmed.edu. Improved 3’ UTR coverage in the V4.3 transcriptome annotation
To quantify improvements in 3’ UTR coverage in V4.3, we again relied on the reference gene set
described above. For those reference genes where 3’ UTR lengths were the same between Ens95
and RefSeq, we found that 17% (1584/9077) possessed a longer 3’ UTR in the V4.3 annotation
(Figure 3B, Figure 2—source data 2). Moreover, a notable proportion of reference genes with lon-
ger 3’ UTRs in either Ens95 (688/4923) or RefSeq (865/2558), exhibited still longer 3’ UTR annota-
tions in V4.3 (Figure 3B, Figure 2—source data 2). In total, we identified 3129 genes out of the
reference gene set (16558 total genes), where V4.3 predicted a longer 3’ UTR than previously found
in Ens95 or RefSeq for matching genes. To determine how these extended annotations affect RNA-seq analysis, we quantified the 3’
biased kdrl:mcherry and pdgfrb:citrine datasets using V4.3 and compared the output to that
obtained from Ens95 and RefSeq. We observed a 20% to 30% increase in the number of kdrlpos- or
pdgfrbpos-enriched genes over that identified when using Ens95 or RefSeq (Figure 3—figure sup-
plement 2A,B; Figure 3—source datas 6 and 7; Table 4). The majority of these genes were those
commonly annotated in both existing annotations, while a smaller proportion was present in only
Ens95 or RefSeq. Only about 60 kdrlpos- or pdgfrbpos-enriched genes identified by V4.3 were those
not previously identified in Ens95 or RefSeq annotations (i.e. XLOC-annotated genes; Table 4). Tools and resources The single Ens99 gene is an exactly duplicated
sequence while missing RefSeq genes are those whose annotations are split between multiple chro-
mosomes, with most cases having just a single or partial 5’ exon as the second annotation (data not
shown; Figure 3—source data 3). In these cases, we kept the larger annotation, which had been
present in V4.2, that included the 3’ UTR. The V4.3 annotation contains 111,842 transcripts from
over 400,000 unique exons that comprise 36351 genes (Table 3). The transcript number in V4.3 is
nearly double that in Ensembl or RefSeq and is accompanied by a considerable increase in the num-
ber of transcripts per gene (Figure 3—figure supplement 1D), suggesting increased transcript Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 10 of 28 Tools and resources Tools and resources Developmental Biology Developmental Biology isoform diversity. For example, Ensembl and RefSeq each predict a single transcript for the erg
gene, each of which differs in intron-exon structure, as well as both 5’ and 3’ UTR (Figure 3—figure
supplement 1E). The V4.3 annotation predicts four transcripts for erg, including the Ensembl and
RefSeq transcripts, as well as new additional isoforms with alternative promoter or exon usage (Fig-
ure 3—figure supplement 1E). isoform diversity. For example, Ensembl and RefSeq each predict a single transcript for the erg
gene, each of which differs in intron-exon structure, as well as both 5’ and 3’ UTR (Figure 3—figure
supplement 1E). The V4.3 annotation predicts four transcripts for erg, including the Ensembl and
RefSeq transcripts, as well as new additional isoforms with alternative promoter or exon usage (Fig-
ure 3—figure supplement 1E). To facilitate the use of V4.3 by researchers, we have made Gene Transfer Format (.gtf) files with
exon, transcript, and gene-level coordinate annotations for both V4.2 and V4.3 available for down-
load at zf-transcriptome.umassmed.edu. These files can be used for standard bulk or single-cell
RNA-seq pipelines, with appropriate modification. We recommend that users apply the V4.3 annota-
tion for their studies, given that it is more complete, although we include both for those interested
in replicating studies described below. We have also compiled a gene information table containing
matching Ensembl and RefSeq gene identifiers, along with ZFIN gene IDs, and chromosomal coordi-
nates (Figure 3—source data 5). As described above, we noted some nomenclature conflicts
between Ensembl and RefSeq, and there are likely to be more. doi.org/10.7554/eLife.55792
11 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources By
contrast, the number of Nr2f2pos-enriched genes, identified using data from random-primed librar-
ies, was similar when using V4.3 (Figure 3—figure supplement 3A, Figure 3—source data 8), Table 4. Numbers of genes identified as enriched in indicated genotype with each annotation. kdrlpos-enriched
pdgfrbpos-enriched
Nr2f2pos-enriched
Ens95
1632
2186
568
RefSeq
1780
2323
580
V4.3
2141
2794
613
annotated in Ens95 and RefSeq
1938
2612
523
not annotated in Ens95
144
131
67
not annotated in RefSeq
119
113
54
only annotated in V4.3
60
62
31 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 11 of 28 11 of 28 Tools and resources Tools and resources Developmental Biology suggesting the improvements noted above were due, in part, to the expanded 3’ UTR coverage in
our annotation. To broadly compare the enriched genes from each annotation, we again utilized our reference
gene set, which also contains information on 3’ UTR lengths. As noted above, there were discrepan-
cies between differentially called reference genes between Ens95 and RefSeq for the kdrl:mcherry
and pdgfrb:citrine datasets (108 Ens95 only, 139 RefSeq only for kdrlpos-enriched; 123 Ens95 only
and 114 RefSeq only for pdgfrbpos-enriched). Importantly, the majority of these discrepancies were
eliminated by using V4.3. For example, 77 out of 108 genes identified as enriched only by Ens95 in
kdrlpos cells were now called as significant using V4.3 (Figure 3C,D). Similar results were observed
with pdgfrbpos-enriched genes, where 110 out of 139 genes detected in Ens95 only were also now
detected as significant with V4.3 (Figure 3E,F). In both cases, these genes were detected at signifi-
cantly higher levels using the V4.3 annotation compared to RefSeq and exhibited much longer 3’
UTR annotations (Figure 3G,H, Figure 2—source data 2). We also noted that approximately 10% of
all differentially called kdrlpos (153) and pdgfrbpos (189) genes found in our reference gene set were
uniquely identified using V4.3, but not Ens95 or RefSeq, despite their presence in all three annota-
tions (Figure 3C,E; Figure 3—source datas 6 and 7). As above, these genes were detected at sig-
nificantly higher levels and displayed much longer 3’ UTRs in the V4.3 annotation, compared to
Ens95 or RefSeq, (Figure 3I,J; Figure 2—source data 2). Tools and resources Although we noted similar discrepancies
between Ens95 and RefSeq annotations in the Nr2f2pos datasets (Figure 3—figure supplement 3B,
Figure 3—source data 8), many of these were not resolved using V4.3, with most discrepant genes
found just below statistical thresholds used to call Nr2f2pos-enriched genes (for example, see Fig-
ure 3—figure supplement 3C, Figure 3—source data 8). However, we did note a number of cases
where longer 3’ UTR annotations in V4.3 helped to identify genes not otherwise detected as
Nr2f2pos-enriched by one of the other annotations (Figure 3—figure supplement 3D,E, Figure 3—
source data 8). Among the genes identified as significantly enriched by V4.3 were all of the individual examples
noted above as discrepancies between Ens95 and RefSeq (Figure 3—figure supplement 2A,B). These included endothelial genes such as slc7a5, which possessed a longer 3’ UTR in RefSeq and
was initially identified as kdrlpos-enriched only in that annotation. In V4.3, slc7a5 has a 3’ UTR
approximately 5 kb longer than Ens95 or RefSeq and is detected at much higher levels (Figure 3—
figure supplement 2C). Consequently, it is detected as significantly enriched in kdrlpos cells when
using V4.3 (Figure 3—figure supplement 2A). We also identified genes expected to be in endothe-
lial cells but missed as significantly enriched by both Ens95 and RefSeq. This included slc2a1a, which
has a 3’ UTR approximately 3 kb longer in V4.3 than Ens95 and RefSeq (Figure 3—figure supple-
ment 2D). Accordingly, we detected slc2a1a at significantly higher levels in V4.3 than the other
annotations and as significantly enriched in kdrlpos cells when using V4.3 (Figure 3—figure supple-
ment 2A,D). We noted similar improvements with discrepant pdgfrbpos genes, such as cspg4, which
has a longer 3’ UTR in V4.3 when compared to Ens95 and RefSeq, concomitant with much higher
levels of expression detected by V4.3 (Figure 3—figure supplement 2B,E). Notably, in each of
these cases, the longer 3’ UTRs identified by V4.3 were supported by the presence of a 3P-seq fea-
ture (Figure 3—figure supplement 2C–E). Taken together, these results suggest that analysis of
bulk RNA-seq data using the V4.3 annotation can provide a more comprehensive and consistent out-
put than Ensembl or RefSeq annotations. V4.2 improves analysis of single-cell RNA-seq data in zebrafish
Single-cell RNA-seq (scRNA-seq) is increasingly being applied to zebrafish to address relevant devel-
opmental questions. In most cases, scRNA-seq relies on 3’ end-sequencing to identify and count
transcripts in each cell. Tools and resources Based on the increased 3’ UTR coverage in our V4 annotations, we reasoned
that they could provide improvements for analyzing scRNA-seq data. To determine if this was the
case, we used a publicly available 3’ scRNA-seq dataset obtained from zebrafish embryos at five dpf
using the 10x Genomics platform (Farnsworth et al., 2020). In this case, we separately quantified
mapped reads from this dataset to Ens95 and V4.2 annotations using the CellRanger pipeline fol-
lowed by filtering, clustering, and differential expression analysis using Seurat (Stuart et al., 2019). For cell clustering, we utilized the first 75 principal components, which contributes to a comparable
amount of the cumulative variation in both cases (see Materials and methods, Source code 1, Fig-
ure 4—figure supplement 1). 12 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Developmental Biology Developmental Biology After initial mapping with Cell Ranger, we observed an increase in the number of genes and
unique molecular identifiers (UMI) captured per cell, along with an increase in total genes detected
when using V4.2 compared to Ens95 (Figure 4—source data 1). Most other standard metrics were
comparable between the two annotations. We subsequently identified 54 cell clusters from a total of
9373 cells when using Ens95-quantified data (Figure 4A). With V4.2, both the number of cells
(11630) and the number of clusters (62) was increased (Figure 4B). This suggested that the increased
3’ UTR coverage in V4.2 allowed more reads to be captured and used for quantification, thereby
increasing the number of gene and cell calls used for clustering. Accordingly, we observed notable
increases in the number of cluster-specific genes per cluster and numbers of cells per cluster when
comparing Ens95- and V4.2-quantified data (Figure 4—figure supplement 1C,D). p
g
q
(
g
g
pp
)
The increased number of cell clusters from the V4.2 annotation versus Ens95 suggested that
some clusters may be split as a consequence of the increased numbers of genes and cells (see
below). This makes a more granular cluster-to-cluster comparison challenging. Therefore, to further
compare differences between scRNA-seq output using the two annotations, we identified cell clus-
ters that could be unambiguously identified and matched between Ens95 and V4.2. We identified
two such clusters for further analysis from browsing cluster-specific gene expression signatures from
each dataset (Figure 4—source datas 2 and 3). Tools and resources The first was a cartilage cell cluster defined by
expression of mia (MIA SH3 domain-containing) in both Ens95 and V4.2-annotated datasets
(Figure 4A–C; cluster 18 in Figure 4—source data 2, cluster 22 in Figure 4—source data 3). In
each annotation, mia-positive (miapos) cells expressed several other genes found in cartilage or cor-
responding pharyngeal arch progenitors, including matrilin 1 (matn1), collagen, type II, alpha 1a
(col2a1a), and fibroblast growth factor binding protein 2b (fgfbp2; Figure 4—figure supplement
2A, Figure 4—source datas 2 and 3; Askary et al., 2017; Xu et al., 2018). We could similarly
define an epidermis cell population in both annotations by actinodin1 (and1) expression (Figure 4A,
B,D; identified as cluster 11 in Figure 4—source data 2 and cluster 15 in Figure 4—source data 3),
along with co-expression of actinodin2 (and2), and muscle segment homeobox 2b (msx2b; Fig-
ure 4—figure supplement 2B; Figure 4—source datas 2 and 3; Akimenko et al., 1995;
Zhang et al., 2010). The cartilage cluster comprised a similar number of cells regardless of annota-
tion (197 with Ens95, 196 with V4.2), while V4.2 identified more cells in the epidermis cluster com-
pared to Ensembl (268 for V4.2, 240 for Ens95). The intersection of cluster-specific genes for
cartilage and epidermis from each annotation indicated that most genes identified by Ensembl were
likewise detected with V4.2 (Figure 5A; 139 cartilage genes, 104 epidermis genes, Figure 5—
source data 1). However, 25% more cartilage- and 15% more epidermis-specific genes were
detected when using V4.2 (Figure 5A). Reference genes from both clusters identified only using
V4.2 exhibited significantly longer 3’ UTR length in that annotation compared to Ens95 (Figure 5B). By contrast, those few cluster-specific genes identified only using Ens95 largely fell just below statis-
tical cutoffs or were cases of gene names assigned to more than one Ens95 locus that collapsed into
a single gene in V4.2. For example, carboxypeptidase N (cpn1) is assigned to two closely adjacent
genes in Ens95 and this locus is considered as a single cpn1 gene in V4.2, where it is detected as
cluster-specific by V4.2 (data not shown and Figure 5—source data 1). To further characterize the cluster-specific genes uniquely identified by V4.2, we took advantage
of the fact that the TgBAC(pdgfrb:citrine)s1010 transgene is expressed in both cartilage and epider-
mis (Vanhollebeke et al., 2015, data not shown). Tools and resources Tools and resources Therefore, corresponding cell type-specific genes
identified by scRNA-seq should be represented and will likely be enriched in the corresponding
pdgfrbpos bulk RNA-seq analysis described above. Notably, the majority of cartilage (41 out of 57)
and epidermis (20 out of 30) cluster-specific genes identified by V4.2 were also significantly enriched
in pdgfrbpos cells (Figure 5C; Figure 5—source datas 1 and 2). Thus, these are likely to be bona
fide cartilage and epidermis genes that are uniquely detected only by V4.2 in scRNA-seq data,
despite most being commonly annotated in Ens95 as well. Interestingly, many of these genes were
also detected as pdgfrbpos-enriched in bulk RNA-seq data quantified using Ens95 (Figure 5—figure
supplement 1A,B, Source datas 1 and 2), despite the failure to identify them as such by scRNA-
seq. This is likely due to the more restricted location of reads in a 3’ scRNA-seq library (i.e. at the
terminal 3’ end of the transcript) versus bulk RNA-seq, where even in the case of 3’ biased libraries
reads can still be found distributed throughout the transcript. Among the genes selectively identified by V4.2 were those encoding notable signaling molecules,
such as SRY-box transcription factor 9a (sox9a) and the Wnt signaling inhibitor frizzled class receptor Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 13 of 28 Tools and resources Developmental Biology Figure 4. The V4.2 annotation increases the number of cells and clusters detected in single cellingle-cell RNA-seq analysis. (A, B) tSNE plots of cells
from 5 day post fertilization (dpf) zebrafish embryos from the same mapped scRNA-seq reads quantified with (A) Ens95 or (B) V4.2. The total number of
clusters and cells that passed filtering are shown. Clusters of interest noted in the text are named. Cartilage and epidermis clusters are circled. (C, D). tSNE plots showing restricted expression of (C) mia in cartilate cells and (D) and1 in epidermis cells for both Ens95 and V4.2 annotations. Each cluster is
indicated by a circle. Legends indicate log-transformed and normalized expression values. The online version of this article includes the following source data and figure supplement(s) for figure 4:
Source data 1. Metrics from CellRanger output for data quantified using Ens95 and V4.2. Figure 4 continued on next page
Tools and resources
Developmental Biology Figure 4. The V4.2 annotation increases the number of cells and clusters detected in single cellingle-cell RNA-seq analysis. Tools and resources (A, B) tSNE plots of cells
from 5 day post fertilization (dpf) zebrafish embryos from the same mapped scRNA-seq reads quantified with (A) Ens95 or (B) V4.2. The total number of
clusters and cells that passed filtering are shown. Clusters of interest noted in the text are named. Cartilage and epidermis clusters are circled. (C, D). tSNE plots showing restricted expression of (C) mia in cartilate cells and (D) and1 in epidermis cells for both Ens95 and V4.2 annotations. Each cluster is
indicated by a circle. Legends indicate log-transformed and normalized expression values. The online version of this article includes the following source data and figure supplement(s) for figure 4:
Source data 1. Metrics from CellRanger output for data quantified using Ens95 and V4.2. Figure 4 continued on next page Tools and resources Developmental Biology Developmental Biology Developmental Biology Figure 4 continued
Source data 2. Cluster-specific genes from whole embryo scRNA-seq at 5 days post fertilization (dpf) identified using Seurat from data quantified with
Ens95. Source data 3. Cluster-specific genes from whole embryo scRNA-seq at five dpf identified using Seurat from data quantified with V4.2. Figure supplement 1. Standard variance and principal component comparisons for scRNA-seq analysis. Figure supplement 2. Identification of cartilage and epidermis cell clusters in scRNA-seq data. Figure 4 continued
Source data 2. Cluster-specific genes from whole embryo scRNA-seq at 5 days post fertilization (dpf) identified using Seurat from data quantified with
Ens95. Source data 3. Cluster-specific genes from whole embryo scRNA-seq at five dpf identified using Seurat from data quantified with V4.2. Figure supplement 1. Standard variance and principal component comparisons for scRNA-seq analysis. Figure supplement 2. Identification of cartilage and epidermis cell clusters in scRNA-seq data. Ens95. Source data 3. Cluster-specific genes from whole embryo scRNA-seq at five dpf identified using Seurat from data quantified with V4.2. Figure supplement 1. Standard variance and principal component comparisons for scRNA-seq analysis. Figure supplement 2. Identification of cartilage and epidermis cell clusters in scRNA-seq data. 9b (fzd9b). Both of these genes have been previously found in cartilage cells or their progenitors
(Askary et al., 2017; Xu et al., 2018) and were readily detected as significantly enriched in the carti-
lage cluster from V4.2-quantified data, but not Ens95 (Figure 5D,E, Figure 5—source data 1). 9b (fzd9b). Both of these genes have been previously found in cartilage cells or their progenitors
(Askary et al., 2017; Xu et al., 2018) and were readily detected as significantly enriched in the carti-
lage cluster from V4.2-quantified data, but not Ens95 (Figure 5D,E, Figure 5—source data 1). Figure 5. The V4.2 annotation increases the quantity of cell type-specific genes identified by scRNA-seq. (A) Venn diagrams illustrating intersection by
common LL gene ID of genes enriched in mia-positive cartilage cells and and1-positive epidermis cells by both indicated annotations. (B) 3’ UTR
lengths from Ens95 and V4.2 for reference genes identified as cartilage or epidermis-specific uniquely by V4.2. Data are not normally distributed
(Shapiro-Wilks test), comparison by Wilcoxon matched-pairs signed-rank test, p-values are shown. (C) Volcano plots showing cartilage- or epidermis-
specific genes identified selectively by V4.2 with corresponding values from bulk RNA-seq comparison of pdgfrbpos and pdgfrbneg cells. Red indicates
log2 fold change >1 (pdgfrbpos/pdgfrbneg), padj <0.05. Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 14 of 28 Tools and resources Tools and resources Tools and resources DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Tools and resources Developmental Biology Developmental Biology Developmental Biology Accordingly, both sox9a and fzd9b showed longer 3’ UTR annotations in V4.2 compared to Ens95
(Figure 5F). Similar results were noted for selected genes in the V4.2 epidermis cluster (Figure 5—
figure supplement 1C, Figure 5—source data 2). In all of these examples, the extended 3’ UTR
annotations in V4.2 were supported by 3P-seq features and would be expected to capture the
majority of reads from scRNA-seq. Notably, the 3’ UTR annotated in V4.2 for fzd9b, which is also
supported by a 3P-Seq feature, is only 350 bp longer than that in Ens95 (Figure 5F). Thus, even a
modest increase in 3’ UTR length can have a significant impact on gene detection, especially in the
case for 10x Genomics libraries where short reads are anchored at the 3’ end. We also noted cases where use of the V4.2 annotation could improve clustering resolution over
Ens95-quantified scRNA-seq data. For example, we identified several groups of blood cells, which
included cells within two clusters expressing leukocyte-specific genes (e.g. coronin, actin-binding
protein, 1A [coro1a] and Rac family small GTPase 2 [rac2]; Jones et al., 2013; Song et al., 2004;
Tell et al., 2012; Figure 6A,B) and erythroid cells expressing hemoglobin (hbae1.1; Galloway et al.,
2005; Oates et al., 1999; Figure 6A–C). The two leukocyte clusters could be further distinguished
by expression of src-like adapter 2 (sla2, Figure 6D), which is expressed in T and B cells in mammals
(Pandey et al., 2002). Interestingly, the sla2-positive (sla2pos) leukocyte cluster was split on the tSNE
plot when using Ens95-quantified reads, such that some cells were more closely associated with the
erythroid cluster (denoted by two circles connected by a line in Figure 6A,B and G). Despite their
assignment to the sla2pos leukocyte cluster, these separate cells failed to express sla2 and distinctly
expressed hbae1.1, similar to cells in the adjacent erythroid cluster (Figure 6C,D). This subset of
sla2pos cells also did not express leukocyte-specific genes, but shared expression of v-myb avian
myeloblastosis viral oncogene homolog (myb) and proliferating cell nuclear antigen (pcna), sugges-
tive of a common proliferative or progenitor-like state (Figure 6E; Liu et al., 2017; Soza-Ried et al.,
2010). Using reads quantified with the V4.2 annotation, we identified a group of cells that were simi-
larly located adjacent to, but separate from an erythroid cluster. Tools and resources However, in this case, the erythroid-
adjacent cells were also classified as separate from sla2pos-leukocytes (Figure 6F). Mapping of cell
barcodes from this V4.2 cluster onto cells clustered using Ens95-quantified reads revealed that these
are the same cells clustered with, but split from, sla2pos leukocytes (Figure 6G). This suggested that
these cells were mis-classified during clustering using Ens95-quantified data. Based on the expres-
sion of hbae1.1 in these cells (Figure 6C) and analysis presented below using V4.2, we refer to this
cluster as ‘erythroid-2’. To identify a potential source for distinct cell clustering using V4.2, we intersected cluster-specific
genes from the Ens95 and V4.2 sla2pos leukocytes, along with those from V4.2 erythroid-2 cells. Fol-
lowing intersection based on gene symbol, only a small number of genes were common to all three
clusters, including pcna and myb, which were noted above (Figure 6E,H, Figure 6—source data 1). Similarly, erythroid markers, such as hbae1.1, were shared between the erythroid-2 V4.2 and sla2pos-
leukocyte Ens95 clusters, consistent with the latter being a likely mix of the two cell populations
(Figure 6H). Importantly, the erythroid-2 cluster displayed many more unique genes than those that
were shared with the sla2pos Ens95 cluster. These included known erythroid-expressed genes such
as solute carrier family 25 member 37 (slc25a37), which encodes the Mitoferrin iron transporter,
transferrin receptor 1a (tfr1a), and integrin alpha 4 (itga4), which is expressed in hematopoietic pro-
genitor cells (Li et al., 2018; Liao et al., 2000; Shaw et al., 2006; Wingert et al., 2004). Expression
of these genes was generally low and detected in very few cells in any of these clusters when using
the Ens95 annotation, but all were readily detected with V4.2 (Figure 7A). Notably, all of these
genes appear preferentially expressed in the erythroid-2 cluster (Figure 7A). Furthermore, V4.2
shows annotated 3’ UTRs for these genes that are much longer than Ens95 and supported by the
concordance of 3P-Seq features (Figure 7B). Taken together, these observations suggest that
increased 3’UTR coverage and improved cell type-specific gene detection using the V4.2 annotation
can contribute to more accurate clustering of cells from scRNA-seq data than existing annotations. Tools and resources Tools and resources (D, E) tSNE plots of the mia-positive cartilage cluster showing expression levels of sox9a and
fzd9b using scRNA-seq data quantified using (D) Ens95 and (E) V4.2. Legends indicate log-transformed and normalized expression levels per cell. (F)
UCSC browser image of sox9a and fzd9b loci showing 3’ UTR annotations from V4.2 and Ens95. Both loci are located on the negative strand. Mapped
read depth from kdrlpos cells on the genome, or assigned to each annotation are indicated, as are 3P-seq features, all of which reside in the same
orientation as the genes themselves. The online version of this article includes the following source data and figure supplement(s) for figure 5:
S
d t
1 C
til
ifi
id
tifi d b
RNA Figure 5. The V4.2 annotation increases the quantity of cell type-specific genes identified by scRNA-seq. (A) Venn diagrams illustrating intersection by
common LL gene ID of genes enriched in mia-positive cartilage cells and and1-positive epidermis cells by both indicated annotations. (B) 3’ UTR
lengths from Ens95 and V4.2 for reference genes identified as cartilage or epidermis-specific uniquely by V4.2. Data are not normally distributed
(Shapiro-Wilks test), comparison by Wilcoxon matched-pairs signed-rank test, p-values are shown. (C) Volcano plots showing cartilage- or epidermis-
specific genes identified selectively by V4.2 with corresponding values from bulk RNA-seq comparison of pdgfrbpos and pdgfrbneg cells. Red indicates
log2 fold change >1 (pdgfrbpos/pdgfrbneg), padj <0.05. (D, E) tSNE plots of the mia-positive cartilage cluster showing expression levels of sox9a and
fzd9b using scRNA-seq data quantified using (D) Ens95 and (E) V4.2. Legends indicate log-transformed and normalized expression levels per cell. (F)
UCSC browser image of sox9a and fzd9b loci showing 3’ UTR annotations from V4.2 and Ens95. Both loci are located on the negative strand. Mapped
read depth from kdrlpos cells on the genome, or assigned to each annotation are indicated, as are 3P-seq features, all of which reside in the same
orientation as the genes themselves. Th
li
i
f thi
ti l
i
l d
th
f ll
i
d t
d fi
l
t( ) f
fi
5 Source data 1. Cartilage-specific genes identified by scRNA-seq. Source data 2. Epidermis-specific genes identified by scRNA-seq. Source data 2. Epidermis-specific genes identified by scRNA-seq. ure supplement 1. Improved detection of cartilage and epidermis genes in scRNA-seq data using V4.2. 15 of 28 Lawson et al. eLife 2020;9:e55792. Discussion In this study, we describe an improved transcriptome annotation for the zebrafish genome. We doc-
ument several discrepancies and deficiencies in the existing Ensembl and RefSeq annotations, includ-
ing incomplete 3’ UTR annotations and missing gene models. Our new transcriptome annotation
addresses many of these issues and performs better than existing annotations for the analysis of 16 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Figure 6. The V4.2 annotation improves cluster resolution in scRNA-seq data. (A) tSNE plot of all clusters from
Ensembl (Ens95)-quantified scRNA-seq of zebrafish embryos at 5 days post fertilization with one erythroid and two
leukocyte clusters indicated. (A–E, G) Circled clusters denote sla2pos leukocyte cells. Asterisk marks cells spuriously
assigned to sla2pos leukocytes, but identified as erythroid two when using the V4.2 annotation. (B–E) tSNE plots
showing only sla2pos leukocyte (circled) and erythroid clusters with expression of (B) known leukocyte markers,
coro1a, and rac2, (C) erythroid marker hbae1.1, and (D) sla2. (E) tSNE plots showing expression of pcna and myb
in sla2pos and erythrocyte clusters. (B–E) Legends indicate log-transformed and normalized expression values. (F)
Erythroid and sla2pos (leukocyte) clusters identified using the same scRNA-seq dataset as in (A) but quantified
using V4.2. A unique erythroid-like cluster (erythroid 2) is circled. (G) tSNE plot of erythroid and sla2pos leukocyte
clusters identified with Ens95 quantified data. Dark green denotes cells with identical barcodes as those in the
erythroid two cluster identified using V4.2 shown in (F). (H) Three-way Venn diagram intersecting cluster-specific
genes of indicated clusters by gene symbol. Selected genes are shown. The online version of this article includes the following source data for figure 6: Figure 6. The V4.2 annotation improves cluster resolution in scRNA-seq data. (A) tSNE plot of all clusters from
Ensembl (Ens95)-quantified scRNA-seq of zebrafish embryos at 5 days post fertilization with one erythroid and two
leukocyte clusters indicated. (A–E, G) Circled clusters denote sla2pos leukocyte cells. Asterisk marks cells spuriously
assigned to sla2pos leukocytes, but identified as erythroid two when using the V4.2 annotation. (B–E) tSNE plots
showing only sla2pos leukocyte (circled) and erythroid clusters with expression of (B) known leukocyte markers,
coro1a, and rac2, (C) erythroid marker hbae1.1, and (D) sla2. (E) tSNE plots showing expression of pcna and myb
in sla2pos and erythrocyte clusters. (B–E) Legends indicate log-transformed and normalized expression values. Discussion (F)
Erythroid and sla2pos (leukocyte) clusters identified using the same scRNA-seq dataset as in (A) but quantified
using V4.2. A unique erythroid-like cluster (erythroid 2) is circled. (G) tSNE plot of erythroid and sla2pos leukocyte
clusters identified with Ens95 quantified data. Dark green denotes cells with identical barcodes as those in the
erythroid two cluster identified using V4.2 shown in (F). (H) Three-way Venn diagram intersecting cluster-specific
genes of indicated clusters by gene symbol. Selected genes are shown. The online version of this article includes the following source data for figure 6: 17 of 28 17 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Developmental Biology Figure 7. Improved detection of erythroid markers in V4.2. (A) tSNE plots of blood cell clusters from Ens95- and V4.2-quantified data showing
expression of slc25a37, tfr1a, and itga4. Erythroid 2 cells spuriously identified as leukocyte using Ens95 quantification are circled. Legends indicate log-
transformed and normalized expression values. (B) 3’ UTR annotations from Ens95 and V4.2 for slc25a37 (on the positive strand), tfra1a (on the negative
strand), and itga4 (positive strand). The 3’ end of the cerkl gene on the negative strand overlaps the itga4 3’ UTR. Therefore, in this case we show read
densities split based on strand. Figure 7. Improved detection of erythroid markers in V4.2. (A) tSNE plots of blood cell clusters from Ens95- and V4.2-quantified data showing
expression of slc25a37, tfr1a, and itga4. Erythroid 2 cells spuriously identified as leukocyte using Ens95 quantification are circled. Legends indicate log-
transformed and normalized expression values. (B) 3’ UTR annotations from Ens95 and V4.2 for slc25a37 (on the positive strand), tfra1a (on the negative
strand), and itga4 (positive strand). The 3’ end of the cerkl gene on the negative strand overlaps the itga4 3’ UTR. Therefore, in this case we show read
densities split based on strand. both bulk and single-cell RNA-seq datasets, especially in cases where RNA-seq libraries exhibit reads
biased toward the 3’ ends of transcripts. Annotation discrepancies proved to be less noticeable
when analyzing RNA-seq libraries constructed using a random primed method. However, we noted
failure to detect important functional genes and well-known lineage markers even in this case. This
issue was especially noticeable in the Ensembl transcriptome annotation, where nearly 20% of all
coding genes lack an annotated 3’ UTR. Discussion Future studies that take advantage of long-read sequencing, along with addi-
tional 5’ and 3’ anchored sequencing, will prove helpful at further verifying and improving the tran-
script models predicted in our annotation. annotations. Therefore, we reasoned that the incorporation of existing high-quality RNA-seq data-
sets would provide an evidence-guided approach to extend 3’ UTR annotations. Indeed, our new
annotation exhibits extended 3’ UTR models for a large proportion of existing genes and improves
performance for RNA-seq analysis. Moreover, transcript diversity is drastically increased in our anno-
tation, with evidence of many more splice isoforms not evident in Ensembl or RefSeq. While we have
not comprehensively addressed the depth of isoform diversity in this study, we believe that our
improved annotation will prove useful for better characterizing splice isoform and differential 3’ UTR
usage in the zebrafish. Future studies that take advantage of long-read sequencing, along with addi-
tional 5’ and 3’ anchored sequencing, will prove helpful at further verifying and improving the tran-
script models predicted in our annotation. p
p
The increased application of scRNA-seq for molecular analysis in the zebrafish model underscores
the need for a transcriptome annotation with accurate 3’ UTR annotations. This is especially impor-
tant given the reliance on 3’ end sequencing in most scRNA-seq studies. As we show, a 3’ UTR anno-
tation missing just a few hundred nucleotides can lead to drastic differences in gene expression. With the limited sequence space captured in most scRNA-seq libraries, along with the large propor-
tion of incomplete 3’ UTRs in existing zebrafish annotations, many previous studies may be missing a
large number of cell type-specific genes. This issue subsequently has a direct impact on cell cluster-
ing. In our example, we show how improvements in 3’ UTR annotation lead to a detection of impor-
tant erythroid-specific genes that guide more accurate assignment of distinct, but related, cell types. Indeed, scRNA-seq analysis with the V4.2 annotation increased the number of clusters called by
Ens95 by fifteen percent, suggesting there are numerous examples where improved gene quantifica-
tion likely led to more refined cell clustering. Whether the V4.2 annotation might also provide similar
improvements with scRNA-seq libraries anchored at the 5’ end is not known. Anecdotally, we have
noted several genes where V4.2 shows an extended 5’ UTR annotation when compared to RefSeq
and Ensembl (e.g. fzd9b, see Figure 5F). Discussion Moreover, we also show that integration of bulk RNA-seq
and scRNA-seq from common cell types is more consistent when both datasets are mapped to the
same annotation. Thus, similar approaches to integrate bulk RNA-Seq from random-primed libraries
with scRNA-seq would still benefit from mapping both datasets on an annotation with more accurate
3’ UTR models. For these reasons, we believe that our improved annotation will be a valuable tool
for zebrafish researchers to apply in the context of their ongoing and planned RNA-seq
experiments. In the course of our previous efforts in applying RNA-seq, we had generated a custom annotation
by simply extending the existing Ensembl UTR annotations by 5 kb (previously only described as a
‘custom’ annotation in the Materials and methods section of Quillien et al., 2017). However, we
found that this could lead to several secondary issues regarding RNA-seq read and gene assign-
ment, especially in cases where an extension merged with an adjacent gene on the same strand. Indeed, as we find in this study, this is currently an issue with several loci in the recent Ensembl anno-
tations, leading to mis-quantification of RNA-seq data, aberrant assignment of gene information,
and apparent loss of genes (for examples see Figure 3—figure supplement 1A–C). We have also
found that some Ensembl genes are missing terminal exons, such that a simple 3’ extension could
lead to quantification of otherwise spurious intronic RNA-seq reads from pre-mRNA (data not
shown). In addition, several hundred genes from the reference gene set we generated here possess
3’ UTRs in the V4 annotation that are more than 5 kb longer than existing Ensembl or RefSeq Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 18 of 28 Tools and resources Tools and resources Developmental Biology Developmental Biology annotations. Therefore, we reasoned that the incorporation of existing high-quality RNA-seq data-
sets would provide an evidence-guided approach to extend 3’ UTR annotations. Indeed, our new
annotation exhibits extended 3’ UTR models for a large proportion of existing genes and improves
performance for RNA-seq analysis. Moreover, transcript diversity is drastically increased in our anno-
tation, with evidence of many more splice isoforms not evident in Ensembl or RefSeq. While we have
not comprehensively addressed the depth of isoform diversity in this study, we believe that our
improved annotation will prove useful for better characterizing splice isoform and differential 3’ UTR
usage in the zebrafish. Zebrafish lines and maintenance All studies were performed under the auspices of animal protocols approved by the University of
Massachusetts Medical School Institutional Animal Care and Use Committee. The Tg(fli1a:egfp)y1
and TgBAC(pdgfrb:citrine)s1010 trangenic lines have been described elsewhere (Lawson and Wein-
stein, 2002; Vanhollebeke et al., 2015). Discussion DOI: https://doi.org/10.7554/eLife.55792 19 of 28 Materials and methods
Tools and resources
Developmental Biology Materials and methods Materials and methods Materials and methods
Key resources table
Reagent type
(species) or resource
Designation
Source or reference
Identifiers
Additional information
Genetic reagent
(Danio rerio)
Tg(fli1a:egfp)y1
Lawson and Weinstein, 2002
RRID:ZFIN_ZDB-ALT-011017-8
Genetic reagent
(Danio rerio)
TgBAC(pdgfrb:citrine)s1010
Vanhollebeke et al., 2015
RRID:ZFIN_ZDB-ALT-150922-2
Antibody
anti-NR2F2 NR2F2
D16C4, rabbit
monoclonal
Cell Signaling Technology
Cat #6434;
RRID:AB_11220428
used at 1:100
Antibody
Goat anti-Rabbit IgG
(H+L) Cross-Adsorbed
Secondary Antibody,
Cyanine3-conjugated
Thermo Fisher Scientific
Cat #A10520;
RRID:AB_2534029
used at 1:1000
Software, algorithm
DolphinNext
Yukselen et al., 2020;
https://github.com/UMMS-
Biocore/dolphinnext
Software, algorithm
In-house bulk
RNA-seq pipeline
https://github.com/UMMS-
Biocore/rnaseq
Software, algorithm
DEBrowser
Kucukural et al., 2019;
https://github.com/UMMS-
Biocore/debrowser
Software, algorithm
Intervene
Khan and Mathelier, 2017
https://intervene.readthedocs. io/en/latest/install.html
Software, algorithm
gffcompare
Pertea and Pertea, 2020;
https://github.com/
gpertea/gffcompare
Software, algorithm
GenomicFeatures
Lawrence et al., 2013;
https://bioconductor.org/
packages/release/bioc/html/
GenomicFeatures.html
RRID:SCR_016960
Software, algorithm
bedtools
Quinlan and Hall, 2010;
https://bedtools.readthedocs. io/en/latest/content/
installation.html
RRID:SCR_006646
Software, algorithm
GSNAP
Wu and Nacu, 2010;
http://research-pub. gene.com/gmap/src/gm
ap-gsnap-2019-09-12.tar.gz
RRID:SCR_005483
Software, algorithm
Cufflinks/Cuffmerge
Trapnell et al., 2010;
http://cole-trapnell-lab. github.io/cufflinks/cuffmerge/
RRID:SCR_014597
Software, algorithm
Cell Ranger
10x Genomics;
https://support. 10xgenomics.com/single-cell-
gene-expression/software/
downloads/latest
RRID:SCR_017344
Software, algorithm
Seurat
Stuart et al., 2019;
https://satijalab.org/
seurat/install.html
RRID:SCR_007322
Zebrafish lines and maintenance
All studies were performed under the auspices of animal protocols approved by the University of
Massachusetts Medical School Institutional Animal Care and Use Committee. The Tg(fli1a:egfp)y1
and TgBAC(pdgfrb:citrine)s1010 trangenic lines have been described elsewhere (Lawson and Wein-
stein, 2002; Vanhollebeke et al., 2015). Zebrafish lines and maintenance Tools and resources Developmental Biology Discussion However, we have not quantified whether this observation
holds across most of the transcriptome. With the availability of cap analysis of gene expression
(CAGE) datasets that define the transcriptional start sites of genes in zebrafish (Haberle et al.,
2014), it would be possible in future studies to assess how complete the 5’ ends of gene models
might be across the different transcriptome annotations. The use of our annotation for read quantification can improve RNA-seq interpretation through a
more accurate estimation of gene expression. However, there remain issues to be improved
addressed in future versions. Despite improvements, our annotation is likely limited by the use of
short-read sequencing libraries. For example, in cases where genes encode multiple transcript iso-
forms with both variable 3’ UTR length and exon usage, it is not possible to accurately assign which
splice isoforms have particular 3’ UTRs. We would note that this same deficiency applies to Ensembl
and RefSeq annotations when quantifying data from RNA-seq libraries generated through short-
read deep sequencing. We also noted that some predicted XLOC loci removed from V4.2 were
located immediately adjacent and downstream of existing or extended 3’ UTR annotations, suggest-
ing that they were likely longer 3’ UTRs (data not shown). The prevalence of repetitive elements in
these 3’ UTR sequences may preclude dense enough mapping of short-read sequences to connect
these downstream annotations. As noted above, future integration of our annotation with long-read
sequencing will likely further improve both isoform assignment and 3’ UTR models. Likewise, 3’-
anchored sequencing efforts, along with more rigorous computational analysis could also better
define differential polyadenylation sites and allow improved characterization of differential 3’ UTR
usage. We would also point out that the RNA samples we used for reconstructing the V4 transcrip-
tome were limited to embryonic and early larval stages. As such, genes restricted to late larval and
adult stages may still have a preponderance of incomplete 3’ UTRs. There are also likely to be some
remaining nomenclature issues, particularly in the case of duplicated genes where official name des-
ignations have not yet been assigned, or in cases where a gene is split between remaining non-chro-
mosomal contigs. Despite these remaining issues, the current iteration of our transcriptome
annotation represents an improvement over existing annotations and will provide a valuable
resource for the zebrafish community. Lawson et al. eLife 2020;9:e55792. Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 20 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Developmental Biology Bulk RNA-seq analysis We ran mapping and quantification pipelines described below in the DolphinNext environment
(https://github.com/UMMS-Biocore/dolphinnext; Yukselen et al., 2020) using the Massachusetts
Green High Performance Computing Cluster (GHPCC). Triplicate samples of paired-end reads from
kdrl-positive and kdrl-negative cells were downloaded from GEO (GSE119718). For bulk RNA-seq
we utilized a standardized pipeline in the DolphinNext environment (https://github.com/UMMS-Bio-
core/rnaseq, Yukselen et al., 2020). Briefly, reads were mapped to GRCz11 using STAR
(Dobin et al., 2013) with default parameters to generate BAM files, which were subsequently used
for transcript quantification with RSEM (Li and Dewey, 2011) using Ensembl, version 95, RefSeq
(GCF_000002035.6_GRCz11), or V4.3 transcript annotations. We identified differentially expressed
genes using DESeq2 with gene-mapped expected count files from RSEM. DESeq2 was run using the
DEBrowser interface (Kucukural et al., 2019). We applied the Low count filtering method to remove
features with counts per million of less than 10 in at least three samples and median ratio normaliza-
tion was applied in all cases. The dispersion was estimated using a parametric fit and hypothesis
testing performed using the likelihood ratio test. p-values obtained by the Wald test were adjusted
for multiple testing using the Benjamini and Hochberg method (Benjamini and Hochberg, 1995). Differentially expressed genes were defined as those with log2 fold change less than 1 or greater
than one and adjusted p-value less than 0.05. We ran the same pipeline with identical parameters
for each annotation (RefSeq, Ens95, or V4.3). Volcano plots were generated using DESeq2 in the
DEBrowser interface. RNA-seq sample preparation For pdgfrb:citrine analysis, citrine-positive and -negative cells were obtained by fluorescent activated
cell sorting (FACS) from dissociated TgBAC(pdgfrb:citrine)s1010 embryos at five dpf and used to gen-
erate RNA-seq libraries as previously described (Quillien et al., 2017; Whitesell et al., 2019). To
isolate venous endothelial cells, we applied a modification of the MARIS protocol that we previously
adapted to zebrafish (Hrvatin et al., 2014; Quillien et al., 2017). Briefly, dechorionated and
deyolked Tg(fli1a:egfp)y1 embryos at 38 hr post-fertilization were dissociated by immersing in 1 x
TrypLE Express for 15 min at 28.5˚C. All subsequent steps took place at 4˚C. Cells were filtered
through a 70 mm cell strainer, centrifuged at 3,000 rpm for 3 min, and resuspended in 4% Parafor-
maldehyde/0.1% Saponin in phosphate buffer saline (PBS) for 30 min with rotation. Cells were
washed twice (0.25% BSA/0.1% Saponin in PBS with RNAsinPlus (280 U/mL)) to remove fixative and
then incubated with anti-NR2F2 (D16C4) Rabbit mAB (#6434, Cell Signaling) at 1:100 in blocking
buffer (1% BSA/1% Saponin in PBS with RNAsinPlus (400 U/mL)) with rotation for 15 min. Cells were
washed for 5 min twice and incubated with goat anti-rabbit IgG(H+L)-Cy3 (A10520, Invitrogen) at
1:1000 in blocking buffer for 1 hr. Cells were then washed twice and resuspended in wash buffer. Fluorescence-activated cell sorting (FACS) was performed by the UMassMed Flow Cytometry Core
to separately isolate Nr2f2/EGFP double-positive (red/green) and Nr2f2-negative/EGFP-positive
(green) cells. Total RNA was purified from double- and single-positive cells using RecoverAll Total
Nucleic Acid Isolation Kit (AM1975, Ambion), then concentrated using RNA Clean and Concentra-
tor-5 Kit (11–325, Zymo Research). After the elimination of ribosomal RNAs using mammalian Ribo-
Gone Kit (634846, Clontech), RNAseq libraries were prepared using SMARTer Stranded RNA-Seq
Kit (634836, Clontech) and deep sequencing performed on a HiSeq2000 (UMass Med Deep
Sequencing Core Facility). Libraries were constructed from Nr2f2/EGFP-positive and EGFP-positive
cells isolated from clutches of embryos generated on three different days. Comparison of 3’ UTR coverage between annotations Comparison of 3 UTR coverage between annotations
To assess the presence or absence of 3’ UTR models in coding genes in Ens95 and RefSeq, we relied
on the annotation of these features in column 3 of each respective gene transfer format file (GTF). Each feature was extracted from the respective GTF, collapsed to novel gene ID to avoid spuriously
counting alternatively spliced multi-exon 3’ UTRs, and counted. To compare 3’ UTR length, we chose
to generate a reference gene set with a single representative transcript per gene. This approach
reduces the potential for spuriously matching or assigning differentially spliced or alternative 3’ UTR
isoforms across annotations. All 3’ UTR lengths were obtained from each annotation by using
GenomicFeatures in R (Lawrence et al., 2013) with GTFs for each annotation containing only the 3’
UTR annotated entries. We next extracted all terminal exons from the Ens95 GTF annotated as a 3’
UTR. For each Ens95 gene, we then identified and chose a single transcript with the longest 3’ UTR
as representative. To accurately match a RefSeq transcript to each representative Ens95 transcript,
we first identified and extracted the longest terminal 3’ UTR exon for each RefSeq transcript. In
cases where there were identical overlapping transcript coordinates, these were collapsed into a sin-
gle entry and arbitrarily assigned one of the duplicate transcript IDs. Matching transcripts from
RefSeq were integrated using bedtools by intersecting on the last exon start coordinates on the
same strand (i.e. start coordinate on the positive stand, end coordinate on the minus strand). To
incorporate V4.3 genes, we identified the longest terminal exon for each gene, collapsed duplicates,
and assigned an arbitrary transcript ID as above for RefSeq entries. V4.3 transcripts matching the ref-
erence gene were then incorporated using bedtools to intersect on exon start coordinates on the
same strand as above. V4.3 3’ UTR lengths were then calculated based on the differences between
RefSeq or Ens95 (see Figure 2—source data 2). To visualize 3P-Seq location, we downloaded BED
files from GEO (GSE37453, Ulitsky et al., 2012) and merged these into a single file after filtering for
expression level. We then sequentially lifted these coordinates over from Zv9 to GRCz10 and then to
GRCz11 using the UCSC browser interface (http://genome.ucsc.edu/cgi-bin/hgLiftOver). For com-
parison of gene-level expression between annotations, we imported values from DESeq2 output for
indicated dataset mapped to each respective annotation using the appropriate matched ID. Annotation comparisons A GTF for RefSeq
(GCF_000002035.6_GRCz11) was downloaded from the UCSC Table browser, while Ens95 was
downloaded from the Ensembl FTP site (ftp.ensembl.org:21/pub/release-95/gtf/danio_rerio/Danio_
rerio.GRCz11.95.gtf.gz). Before running gffcompare, Ensembl-annotated GTF files were modified to
match UCSC-based chromosome annotation, while ‘alt’ chromosome variants in RefSeq were
removed. Each pairwise comparison was run with default settings using each annotation as a refer-
ence to identify relative missing and matching transcript models. To confirm that missing transcripts
represented actual missing genes, reference genomes in each case were subsequently re-searched
for matching gene IDs corresponding to each missing transcript. We subsequently surveyed between
10 to 20 missing genes manually through individual visualization of their loci on the UCSC genome
browser to confirm the results. Matched transcript outputs from gffcompare, along with missing
gene lists can be found in the associated source data files. Annotation comparisons To compare RNA-seq analyses from Ens95 and RefSeq, we downloaded matching NCBI IDs for
Ensembl-annotated genes using Biomart from the Ens95 archive (http://jan2019.archive.ensembl. org/Danio_rerio/Info/Index). Our gene-level DEbrowser output listed gene symbol with all associ-
ated transcripts. Since a number of Ens95 and RefSeq genes have identical gene symbol annota-
tions, we incorporated matching Ens95 gene and NCBI IDs using a representative transcript ID for
each gene to ensure correct matches. We then applied Intervene (Khan and Mathelier, 2017) for
intersections based on common NCBI ID and generation of Venn diagrams. Proportional Venn dia-
grams were generated using eulerr (Larsson, 2020, https://github.com/jolars/eulerr.co). A similar 21 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Developmental Biology approach was applied for comparison of RNA-seq outputs from V4.2 and V.3, except that LL gene
ID was used. All corresponding NCBI, Ensembl, and LL gene IDs for RNA-seq output are included in
the corresponding source data tables. To identify matching and missing genes between different
annotations, we applied gffcompare (Pertea and Pertea, 2020), which provides a coordinate-based
comparison of transcript intron/exon structure using GTF files as input. A GTF for RefSeq
(GCF_000002035.6_GRCz11) was downloaded from the UCSC Table browser, while Ens95 was
downloaded from the Ensembl FTP site (ftp.ensembl.org:21/pub/release-95/gtf/danio_rerio/Danio_
rerio.GRCz11.95.gtf.gz). Before running gffcompare, Ensembl-annotated GTF files were modified to
match UCSC-based chromosome annotation, while ‘alt’ chromosome variants in RefSeq were
removed. Each pairwise comparison was run with default settings using each annotation as a refer-
ence to identify relative missing and matching transcript models. To confirm that missing transcripts
represented actual missing genes, reference genomes in each case were subsequently re-searched
for matching gene IDs corresponding to each missing transcript. We subsequently surveyed between
10 to 20 missing genes manually through individual visualization of their loci on the UCSC genome
browser to confirm the results. Matched transcript outputs from gffcompare, along with missing
gene lists can be found in the associated source data files. approach was applied for comparison of RNA-seq outputs from V4.2 and V.3, except that LL gene
ID was used. All corresponding NCBI, Ensembl, and LL gene IDs for RNA-seq output are included in
the corresponding source data tables. To identify matching and missing genes between different
annotations, we applied gffcompare (Pertea and Pertea, 2020), which provides a coordinate-based
comparison of transcript intron/exon structure using GTF files as input. Comparison of 3’ UTR coverage between annotations Since our annotation comprises genes missing from
both Ensembl and RefSeq annotations, as well as novel genes (see below), we assigned a unique
identifier (prefix ‘LL’ followed by an arbitrary number) to each entry, which can be used as a common
link for the relation between the gene information file and the resulting output from the GTF follow-
ing its application in RNA-seq analysis. The GTF and gene information files for V4.2 and V4.3 are
available at http://zf-transcriptome.umassmed.edu. Comparison of 3’ UTR coverage between annotations Further
details are available upon request. Assembly of an improved zebrafish transcriptome annotation
We downloaded 75 bp Paired-end stranded RNA-seq reads from embryos staged at 28hpf, 2dpf,
5dpf, bud, dome, and shield from GEO (Accession no.: GSE32898, Pauli et al., 2012). Reads were
trimmed with Trimmomatic (adaptor removal, headcrop, and crop to retain position 10–50 bp only
along with default quality trimming) and reads shorter than 32 bp after trimming were discarded. Trimmed reads were aligned to Danio rerio genome GRCz11 with GSNAP (Wu and Nacu, 2010)
allowing 5% mismatches. Our anecdotal observations suggested a prevalence of incomplete and
spurious partial transcripts in Ensembl. Therefore, the alignment was guided by splicing sites
extracted from refseq_mRNA (GCF_000002035.6_GRCz11). We filtered alignment results so that 22 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Developmental Biology only properly paired reads with MQ 30 and more than 35 bp of mapped regions were retained. An
in-house perl script was used to add strand information and format the filtered alignment results
(Source code 2). We used mapped reads to assemble transcript and gene models using Cufflinks
and Cuffmerge (Trapnell et al., 2010). Preliminary versions of our transcriptome annotation (v1, v2)
were used to identify parameters that optimally captured isoform diversity and 3’ UTR lengths. Ver-
sion 3.1.2 (v3.1.2) used Cufflinks with the following parameters: -F 0.2 j 0.3 -a 0.0001 -A 0.4 –min-
frags-per-transfragX20 –overhang-toleranceX20 –overlap-radius 50 - 3-overhang-tol-
erance 50 to assemble transcripts for samples from each embryonic stage. Cufflinks assembly for
v3.1.2 was guided (using the -g argument in Cufflinks) by the most recently available zebrafish
RefSeq annotation (GCF_000002035.6_GRCz11). We next integrated trans-fragments assembled by
Cufflinks for each stage using Cuffmerge. We chose to use Ensembl annotations (version 95) to
guide the integration of the transcript models generated above using Cuffmerge. At this step, we
allowed low abundance transcripts to be retained in the final annotation (‘–min-isoform-frac-
tion 0.00’). Initial gene nomenclature assignments were made using v3.1.2. For this purpose, all rel-
evant matching gene information was extracted from the GTF output from Cuffmerge for v3.1.2 and
used to assign gene information to transcript ID (TCONS) generated by Cufflinks. At this point, over
1000 gene symbol conflicts were identified by comparing assigned gene names for comparing
RefSeq and Ens95 transcript IDs to those assigned by Cufflinks. Comparison of 3’ UTR coverage between annotations In many cases, these were due to
spurious fusion transcripts linking adjacent genes. Therefore, we sought to remove these using a cus-
tomized Python script (Source code 3). We also manually removed non-miRNA small RNAs. Given
the nomenclature conflicts noted above, we utilized gffcompare to accurately import matched gene
identifiers from RefSeq and a more recent Ensembl annotation (version 99, released January 2020). In cases where a perfect transcript match was not available, we subsequently compared gene coordi-
nates to further confirm overlap; we include a qualitative description for each entry in this case for
RefSeq and Ens99 matches in the V4.3 gene information file. In the course of investigating the nature
of the nomenclature conflicts noted above, we also manually corrected several incorrect gene names
assigned by Ensembl that resulted from persistent overlapping transcripts between two separate
genes that evaded filtering noted above, causing a single gene ID to be assigned to two genes (see
main text and Figure 3—source data 2). In these cases, spurious overlapping transcripts were
removed to give V4.2. To identify any remaining Ensembl or RefSeq genes missing from V4.2, we
performed pairwise comparisons with each annotation using gffcompare. The resulting missing
genes were then manually added to give V4.3. Since our annotation comprises genes missing from
both Ensembl and RefSeq annotations, as well as novel genes (see below), we assigned a unique
identifier (prefix ‘LL’ followed by an arbitrary number) to each entry, which can be used as a common
link for the relation between the gene information file and the resulting output from the GTF follow-
ing its application in RNA-seq analysis. The GTF and gene information files for V4.2 and V4.3 are
available at http://zf-transcriptome.umassmed.edu. only properly paired reads with MQ 30 and more than 35 bp of mapped regions were retained. An
in-house perl script was used to add strand information and format the filtered alignment results
(Source code 2). We used mapped reads to assemble transcript and gene models using Cufflinks
and Cuffmerge (Trapnell et al., 2010). Preliminary versions of our transcriptome annotation (v1, v2)
were used to identify parameters that optimally captured isoform diversity and 3’ UTR lengths. Ver-
sion 3.1.2 (v3.1.2) used Cufflinks with the following parameters: -F 0.2 j 0.3 -a 0.0001 -A 0.4 –min-
frags-per-transfragX20 –overhang-toleranceX20 –overlap-radius 50 - 3-overhang-tol-
erance 50 to assemble transcripts for samples from each embryonic stage. Comparison of 3’ UTR coverage between annotations Cufflinks assembly for
v3.1.2 was guided (using the -g argument in Cufflinks) by the most recently available zebrafish
RefSeq annotation (GCF_000002035.6_GRCz11). We next integrated trans-fragments assembled by
Cufflinks for each stage using Cuffmerge. We chose to use Ensembl annotations (version 95) to
guide the integration of the transcript models generated above using Cuffmerge. At this step, we
allowed low abundance transcripts to be retained in the final annotation (‘–min-isoform-frac-
tion 0.00’). Initial gene nomenclature assignments were made using v3.1.2. For this purpose, all rel-
evant matching gene information was extracted from the GTF output from Cuffmerge for v3.1.2 and
used to assign gene information to transcript ID (TCONS) generated by Cufflinks. At this point, over
1000 gene symbol conflicts were identified by comparing assigned gene names for comparing
RefSeq and Ens95 transcript IDs to those assigned by Cufflinks. In many cases, these were due to
spurious fusion transcripts linking adjacent genes. Therefore, we sought to remove these using a cus-
tomized Python script (Source code 3). We also manually removed non-miRNA small RNAs. Given
the nomenclature conflicts noted above, we utilized gffcompare to accurately import matched gene
identifiers from RefSeq and a more recent Ensembl annotation (version 99, released January 2020). In cases where a perfect transcript match was not available, we subsequently compared gene coordi-
nates to further confirm overlap; we include a qualitative description for each entry in this case for
RefSeq and Ens99 matches in the V4.3 gene information file. In the course of investigating the nature
of the nomenclature conflicts noted above, we also manually corrected several incorrect gene names
assigned by Ensembl that resulted from persistent overlapping transcripts between two separate
genes that evaded filtering noted above, causing a single gene ID to be assigned to two genes (see
main text and Figure 3—source data 2). In these cases, spurious overlapping transcripts were
removed to give V4.2. To identify any remaining Ensembl or RefSeq genes missing from V4.2, we
performed pairwise comparisons with each annotation using gffcompare. The resulting missing
genes were then manually added to give V4.3. Data access New raw datasets (pdgfrb:citrine and Nr2f2 RNA-seq), and associated processed data files, gener-
ated for this manuscript, including the V4.3 GTF, are available at the Gene Expression Omnibus
(GSE152759). All other raw datasets were otherwise obtained from GEO. Additional support files
are available at http://zf-transcriptome.umassmed.edu. Additional information Funding
Funder
Grant reference number
Author
National Heart, Lung, and
Blood Institute
R35HL140017
Nathan D Lawson
National Human Genome Re-
search Institute
U01HG007910
Onur Yukselen
Alper Kucukural
National Center for Advancing
Translational Sciences
UL1TR001453
Onur Yukselen
Alper Kucukural
National Institute of Neurolo-
gical Disorders and Stroke
R21NS105654
Nathan D Lawson
The funders had no role in study design, data collection and interpretation, or the
decision to submit the work for publication. Acknowledgements We thank members of the UMass Med GHPCC group, including Lewis Robbins and Chris Hull for
their support. We are also grateful to Yu-Huan Shih and William Frantz for their helpful comments on
the manuscript. This work was supported by NIH R35HL140017 and R21NS105654 to N D L and
U01HG007910 from NHGRI and National Center for Advancing Translational Sciences grant UL1
TR001453, which supported A K and O Y. Additional information Single-cell RNA-seq analysis Single-cell RNA-seq analysis We downloaded scRNA-seq reads from whole zebrafish embryos at five dpf from the Sequence
Read Archive (SRR10095965, Farnsworth et al., 2020). Paired-end reads were split from this file
using the SRA toolkit (https://github.com/ncbi/sra-tools; SRA Toolkit Development Team, 2020). We used Cell Ranger (10x Genomics, v3.1.0) in the DolphinNext environment (see above) for read
mapping, filtering, and counting using default parameters. We ran Cell Ranger separately with the
same set of reads and parameters for Ens95 and V4.2. Cell Ranger output files (barcodes, genes,
and matrix files) were loaded into Seurat (v3.1, Stuart et al., 2019) for clustering, identification of
differential genes, and visualization. All parameters and variables can be found in the accompanying
R file (Source code 1). Seurat was run in RStudio through a web-based portal on the GHPCC using
Open OnDemand (Hudak et al., 2018). Annotation of novel loci Our annotation yielded just over 6000 novel loci with no initial match to Ensembl or RefSeq genes. These are annotated using gene abbreviations with an ‘XLOC’ prefix assigned by cufflinks. To inves-
tigate whether these represent new genes, we took several steps. First, we used transcript sequen-
ces from each locus in blastx searches against zebrafish and human proteins. Second, we
determined whether any overlapped previously long non-coding RNAs identified in previous studies. For this purpose, we used an integrated annotation published elsewhere that includes lincRNAs not
found in Ensembl or RefSeq (Hu et al., 2018). This annotation was converted to a standard BED for-
mat, lifted from Zv9 to GRCz10, then to GRCz11 and used to generate a GTF file. We used gffcom-
pare with the lincRNA GTF file and a parallel file containing only XLOC V4.2 annotations to identify
matching or overlapping transcripts. Finally, we determined exon numbers for each XLOC entry. In
V4.2, all XLOC entries were maintained in the associated GTF and gene information files. For V4.3,
we retained XLOCs that matched one of the following criteria: 1. exhibited exact, moderate, or
high-confidence blast hits with a zebrafish or human protein, 2. exhibited matched or overlapping
intron-exon structure with the lincRNAs noted above, or 3. comprised more than one exon. We also
identified approximately 200 loci that exhibited complete overlap with existing RefSeq-annotated
transcripts already present in V4.2. These redundant XLOC loci were also removed in the update to
V4.3. Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 23 of 28 Tools and resources Developmental Biology Developmental Biology Ethics Animal experimentation: Zebrafish studies were performed in accordance with protocols #A2613
and #A2632 approved by the University of Massachusetts institutional animal care and use commit-
tee (IACUC). Decision letter and Author response Decision letter and Author response Decision letter and Author response
Decision letter https://doi.org/10.7554/eLife.55792.sa1
Author response https://doi.org/10.7554/eLife.55792.sa2 Decision letter and Author response
Decision letter https://doi.org/10.7554/eLife.55792.sa1
Author response https://doi.org/10.7554/eLife.55792.sa2 Decision letter and Author response
Decision letter https://doi.org/10.7554/eLife.55792.sa1
Author response https://doi.org/10.7554/eLife.55792.sa2 ec s o
ette
ttps //do o g/ 0 55 /e
e 55
sa
Author response https://doi.org/10.7554/eLife.55792.sa2 Additional files
Supplementary files
. Source code 1. List of R commands used to run Seurat for clustering
Ens95 and V4.2. . Source code 2. Perl script used to add strand information and filter read
GSNAP. . Source code 3. Python script to identify and remove spurious fusion trans
. Source data 1. Zebrafish transcriptome annotation V4.2. Contains geno
MB, md5sum:44c87a2bdd19ccfd9f7cd526f9e21498) and gene information
.xlsx file). . Source data 2. Zebrafish transcriptome annotation V4.3.1. Contains gen
MB, md5sum: 19759898187c47edfd9c216162851e31) and gene informat
and .xlsx file). . Transparent reporting form
Data availability
All data generated in this study are available in accompanying source data
tation files described in this study are available for download at http://zf-
edu. Raw and processed RNA-seq data generated in this study are availab
The following dataset was generated:
Author(s)
Year Dataset title
Dataset URL
Lawson ND
2020
Bulk RNA-seq data to assess an
improved zebrafish transcriptome
annotation
https://www.ncbi.nl
nih.gov/geo/query/
cgi?acc=GSE152759
The following previously published datasets were used:
Author(s)
Year Dataset title
Dataset URL
Whitesell TR,
Chrystal PW, Ryu
JR, Munsie N,
Grosse A, French
CR, Workentine
ML, Li R, Zhu LJ,
Waskiewicz A, Leh-
mann OJ, Lawson
ND, Childs SJ
2019
Morphogenesis and differentiation
of embryonic vascular smooth
muscle cells in zebrafish
https://www.ncbi.nl
nih.gov/geo/query/
cgi?acc=GSE119718
Pauli A, Valen E,
Lin MF, Garber M,
Vastenhouw NL,
Levin JZ, Sandelin
A, Rinn JL, Regev
A, Schier AF
2011
Comprehensive identification of
long non-coding RNAs expressed
during zebrafish embryogenesis
https://www.ncbi.nl
nih.gov/geo/query/
cgi?acc=GSE32900 Author contributions Nathan D Lawson, Conceptualization, Data curation, Formal analysis, Supervision, Funding acquisi-
tion, Validation, Investigation, Visualization, Methodology, Writing - original draft, Project adminis-
tration, Writing - review and editing; Rui Li, Data curation, Software, Formal analysis, Methodology,
Writing - review and editing; Masahiro Shin, Ann Grosse, Investigation, Methodology; Onur Yukse-
len, Lihua Zhu, Resources, Software, Methodology, Writing - review and editing; Oliver A Stone,
Resources; Alper Kucukural, Resources, Software, Visualization, Methodology, Writing - review and
editing Author ORCIDs
Nathan D Lawson
https://orcid.org/0000-0001-7788-9619
Alper Kucukural
http://orcid.org/0000-0001-9983-394X Author ORCIDs
Nathan D Lawson
https://orcid.org/0000-0001-7788-9619
Alper Kucukural
http://orcid.org/0000-0001-9983-394X 24 of 28 Tools and resources Tools and resources Developmental Biology Developmental Biology Additional files . Source code 1. List of R commands used to run Seurat for clustering of data quantified using
Ens95 and V4.2. . Source code 2. Perl script used to add strand information and filter reads in BAM file output from
GSNAP. . Source code 3. Python script to identify and remove spurious fusion transcripts. . Source data 1. Zebrafish transcriptome annotation V4.2. Contains genomic annotation file (153.8
MB, md5sum:44c87a2bdd19ccfd9f7cd526f9e21498) and gene information (as tab-delimited file and
.xlsx file). . Source data 2. Zebrafish transcriptome annotation V4.3.1. Contains genomic annotation file (152
MB, md5sum: 19759898187c47edfd9c216162851e31) and gene information (as tab-delimited file
and .xlsx file). Data availability Data availability
All data generated in this study are available in accompanying source data files. Transcriptome anno-
tation files described in this study are available for download at http://zf-transcriptome.umassmed. edu. Raw and processed RNA-seq data generated in this study are available at GEO (GSE152759). The following dataset was generated: The following dataset was generated:
Author(s)
Year Dataset title
Dataset URL
Database and
Identifier
Lawson ND
2020
Bulk RNA-seq data to assess an
improved zebrafish transcriptome
annotation
https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE152759
NCBI Gene
Expression Omnibus,
GSE152759
The following previously published datasets were used:
Author(s)
Year Dataset title
Dataset URL
Database and
Identifier
Whitesell TR,
Chrystal PW, Ryu
JR, Munsie N,
Grosse A, French
CR, Workentine
ML, Li R, Zhu LJ,
Waskiewicz A, Leh-
mann OJ, Lawson
ND, Childs SJ
2019
Morphogenesis and differentiation
of embryonic vascular smooth
muscle cells in zebrafish
https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE119718
NCBI Gene
Expression Omnibus,
GSE119718
Pauli A, Valen E,
Lin MF, Garber M,
Vastenhouw NL,
Levin JZ, Sandelin
A, Rinn JL, Regev
A, Schier AF
2011
Comprehensive identification of
long non-coding RNAs expressed
during zebrafish embryogenesis
https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE32900
NCBI Gene
Expression Omnibus,
GSE32900
DOI: https://doi.org/10.7554/eLife.55792
25 of 28 The following dataset was generated:
Author(s)
Year Dataset title
Dataset URL
Database and
Identifier
Lawson ND
2020
Bulk RNA-seq data to assess an
improved zebrafish transcriptome
annotation
https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE152759
NCBI Gene
Expression Omnibus,
GSE152759 Author(s)
Year Dataset title
Dataset URL
Database and
Identifier
Whitesell TR,
Chrystal PW, Ryu
JR, Munsie N,
Grosse A, French
CR, Workentine
ML, Li R, Zhu LJ,
Waskiewicz A, Leh-
mann OJ, Lawson
ND, Childs SJ
2019
Morphogenesis and differentiation
of embryonic vascular smooth
muscle cells in zebrafish
https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE119718
NCBI Gene
Expression Omnibus,
GSE119718
Pauli A, Valen E,
Lin MF, Garber M,
Vastenhouw NL,
Levin JZ, Sandelin
A, Rinn JL, Regev
A, Schier AF
2011
Comprehensive identification of
long non-coding RNAs expressed
during zebrafish embryogenesis
https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE32900
NCBI Gene
Expression Omnibus,
GSE32900 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 25 of 28 25 of 28 Tools and resources 2012
Extensive alternative
polyadenylation during zebrafish
development 2012
Extensive alternative
polyadenylation during zebrafish
development Ulitsky I, Shkuma-
tava A, Jan CH,
Subtelny AO,
Koppstein D, Bell
G, Sive H, Bartel
DP References Akimenko MA, Johnson SL, Westerfield M, Ekker M. 1995. Differential induction of four msx homeobox genes
during fin development and regeneration in zebrafish. Development 121:347–357. PMID: 7768177
Askary A, Xu P, Barske L, Bay M, Bump P, Balczerski B, Bonaguidi MA, Crump JG. 2017. Genome-wide analysis Akimenko MA, Johnson SL, Westerfield M, Ekker M. 1995. Differential induction of four msx homeobox genes
during fin development and regeneration in zebrafish. Development 121:347–357. PMID: 7768177 Akimenko MA, Johnson SL, Westerfield M, Ekker M. 1995. Differential induction of four msx homeobox genes
during fin development and regeneration in zebrafish. Development 121:347–357. PMID: 7768177
Askary A, Xu P, Barske L, Bay M, Bump P, Balczerski B, Bonaguidi MA, Crump JG. 2017. Genome-wide analysis
of facial skeletal regionalization in zebrafish. Development 144:2994–3005. DOI: https://doi.org/10.1242/dev. 151712, PMID: 28705894 Askary A, Xu P, Barske L, Bay M, Bump P, Balczerski B, Bonaguidi MA, Crump JG. 2017. Genome-wide analysis
of facial skeletal regionalization in zebrafish. Development 144:2994–3005. DOI: https://doi.org/10.1242/dev. 151712, PMID: 28705894 Beis D, Stainier DY. 2006. In vivo cell biology: following the zebrafish trend. Trends in Cell Biology 16:105–112
DOI: https://doi.org/10.1016/j.tcb.2005.12.001, PMID: 16406520 Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to
multiple testing. Journal of the Royal Statistical Society: Series B 57:289–300. DOI: https://doi.org/10.2307/
2346101 Boado RJ, Li JY, Nagaya M, Zhang C, Pardridge WM. 1999. Selective expression of the large neutral amino acid
transporter at the blood-brain barrier. PNAS 96:12079–12084. DOI: https://doi.org/10.1073/pnas.96.21.12079,
PMID: 10518579 Bondjers C, He L, Takemoto M, Norlin J, Asker N, Hellstro¨ m M, Lindahl P, Betsholtz C. 2006. Microarray analysis
of blood microvessels from PDGF-B and PDGF-Rbeta mutant mice identifies novel markers for brain pericytes. The FASEB Journal 20:1703–1705. DOI: https://doi.org/10.1096/fj.05-4944fje, PMID: 16807374 Chi NC, Shaw RM, De Val S, Kang G, Jan LY, Black BL, Stainier DY. 2008. Foxn4 directly regulates tbx2b
expression and atrioventricular canal formation. Genes & Development 22:734–739. DOI: https://doi.org/10. 1101/gad.1629408, PMID: 18347092 g
Chung MI, Ma AC, Fung TK, Leung AY. 2011. Characterization of Sry-related HMG box group F genes in
zebrafish hematopoiesis. Experimental Hematology 39:986–998. DOI: https://doi.org/10.1016/j.exphem.2011. 06.010, PMID: 21726513 Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR:
ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. DOI: https://doi.org/10.1093/bioinformatics/
bts635, PMID: 23104886 Farnsworth DR, Saunders LM, Miller AC. 2020. A single-cell transcriptome atlas for zebrafish development. Developmental Biology 459:100–108. https://www.ncbi.nlm.
nih.gov/geo/query/acc.
cgi?acc=GSE37453 https://www.ncbi.nlm.
nih.gov/geo/query/acc.
cgi?acc=GSE37453
NCBI Gene
Expression Omnibus,
GSE37453
Developmental Biology 2012
Extensive alternative
polyadenylation during zebrafish
development References Developing zebrafish disease models for in vivo small molecule screens. Current
Opinion in Chemical Biology 50:37–44. DOI: https://doi.org/10.1016/j.cbpa.2019.02.005, PMID: 30928773 p
gy
p
g
j
p
Larsson J. 2020. eulerr: Area-Proportional Euler and Venn Diagrams with Ellipses. R Package. 6.1.0.https://cran. project.org/package=Eulerr p
j
g p
g
Lawrence M, Huber W, Page` s H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ. 2013. Software
for computing and annotating genomic ranges. PLOS Computational Biology 9:e1003118. DOI: https://doi. org/10.1371/journal.pcbi.1003118, PMID: 23950696 g
j
Lawson ND, Scheer N, Pham VN, Kim CH, Chitnis AB, Campos-Ortega JA, Weinstein BM. 2001. Notch signaling
is required for arterial-venous differentiation during embryonic vascular development. Development 128:3675–
3683. Lawson ND, Weinstein BM. 2002. In vivo imaging of embryonic vascular development using transgenic zebrafi
Developmental Biology 248:307–318. DOI: https://doi.org/10.1006/dbio.2002.0711, PMID: 12167406 Lawson ND, Wolfe SA. 2011. Forward and reverse genetic approaches for the analysis of vertebrate
development in the zebrafish. Developmental Cell 21:48–64. DOI: https://doi.org/10.1016/j.devcel.2011.06. 007, PMID: 21763608 Li D, Xue W, Li M, Dong M, Wang J, Wang X, Li X, Chen K, Zhang W, Wu S, Zhang Y, Gao L, Chen Y, Chen J,
Zhou BO, Zhou Y, Yao X, Li L, Wu D, Pan W. 2018. VCAM-1+ macrophages guide the homing of HSPCs to a
vascular niche. Nature 564:119–124. DOI: https://doi.org/10.1038/s41586-018-0709-7, PMID: 30455424 p
g
Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference
genome. BMC Bioinformatics 12:323. DOI: https://doi.org/10.1186/1471-2105-12-323, PMID: 21816040 Liao EC, Paw BH, Peters LL, Zapata A, Pratt SJ, Do CP, Lieschke G, Zon LI. 2000. Hereditary spherocytosis in
zebrafish riesling illustrates evolution of erythroid beta-spectrin structure, and function in red cell
morphogenesis and membrane stability. Development 127:5123–5132. PMID: 11060238 zebrafish riesling illustrates evolution of erythroid beta-spectrin structure, and function in red cell
morphogenesis and membrane stability. Development 127:5123–5132. PMID: 11060238 Liu W, Wu M, Huang Z, Lian J, Chen J, Wang T, Leung AY, Liao Y, Zhang Z, Liu Q, Yen K, Lin S, Zon LI, Wen Z,
Zhang Y, Zhang W. 2017. c-myb hyperactivity leads to myeloid and lymphoid malignancies in zebrafish. Leukemia 31:222–233. DOI: https://doi.org/10.1038/leu.2016.170, PMID: 27457538 Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck
EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA. 2015. Highly parallel Genome-wide
expression profiling of individual cells using nanoliter droplets. References DOI: https://doi.org/10.1016/j.ydbio.2019.11.008, PMID: 31782996 Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF. 2018. Single-cell reconstruction of
developmental trajectories during zebrafish embryogenesis. Science 360:eaar3131. DOI: https://doi.org/10. 1126/science.aar3131, PMID: 29700225 Galloway JL, Wingert RA, Thisse C, Thisse B, Zon LI. 2005. Loss of gata1 but not gata2 converts erythropoiesis
to myelopoiesis in zebrafish embryos. Developmental Cell 8:109–116. DOI: https://doi.org/10.1016/j.devcel. 2004.12.001, PMID: 15621534 Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van IJcken
WFJ, Armant O, Ferg M, Stra¨hle U, Carninci P, Mu¨ ller F, Lenhard B. 2014. Two independent transcription
initiation codes overlap on vertebrate core promoters. Nature 507:381–385. DOI: https://doi.org/10.1038/
nature12974, PMID: 24531765 Hrvatin S, Deng F, O’Donnell CW, Gifford DK, Melton DA. 2014. MARIS: method for analyzing RNA following
intracellular sorting. PLOS ONE 9:e89459. DOI: https://doi.org/10.1371/journal.pone.0089459, PMID: 24594
82 Hu X, Chen W, Li J, Huang S, Xu X, Zhang X, Xiang S, Liu C. 2018. ZFLNC: a comprehensive and well-annotate
database for zebrafish lncRNA. Database 2018:bay114. DOI: https://doi.org/10.1093/database/bay114 Hudak D, Johnson D, Chalker A, Nicklas J, Franz E, Dockendorf T, L. McMichael B. 2018. Open OnDemand: a
web-based client portal for HPC centers. Journal of Open Source Software 3:622. DOI: https://doi.org/10. 21105/joss.00622 j
Jan CH, Friedman RC, Ruby JG, Bartel DP. 2011. Formation, regulation and evolution of Caenorhabditis elegans
3’UTRs. Nature 469:97–101. DOI: https://doi.org/10.1038/nature09616, PMID: 21085120 Jones RA, Feng Y, Worth AJ, Thrasher AJ, Burns SO, Martin P. 2013. Modelling of human Wiskott-Aldrich
syndrome protein mutants in zebrafish larvae using in vivo live imaging. Journal of Cell Science 126:4077–4084. DOI: https://doi.org/10.1242/jcs.128728, PMID: 23868979 p
g
j
Khan A, Mathelier A. 2017. Intervene: a tool for intersection and visualization of multiple gene or genomic region
sets. BMC Bioinformatics 18:287. DOI: https://doi.org/10.1186/s12859-017-1708-7, PMID: 28569135 Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW. 2015. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161:1187–1201. DOI: https://doi.org/10.1016/j.cell.2015.04.044, PMID: 26000487 p
g
j
,
Kucukural A, Yukselen O, Ozata DM, Moore MJ, Garber M. 2019. DEBrowser: interactive differential expression
analysis and visualization tool for count data. BMC Genomics 20:6. DOI: https://doi.org/10.1186/s12864-018-
5362-x, PMID: 30611200 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 26 of 28 Tools and resources Tools and resources Developmental Biology Lam PY, Peterson RT. 2019. References Cell 161:1202–1214. DOI: https://doi.org/10. 1016/j.cell.2015.05.002, PMID: 26000488 j
McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J. 2016. Whole-organism lineage tracing
by combinatorial and cumulative genome editing. Science 353:aaf7907. DOI: https://doi.org/10.1126/science. aaf7907, PMID: 27229144 Oates AC, Brownlie A, Pratt SJ, Irvine DV, Liao EC, Paw BH, Dorian KJ, Johnson SL, Postlethwait JH, Zon LI,
Wilks AF. 1999. Gene duplication of zebrafish JAK2 homologs is accompanied by divergent embryonic
expression patterns: only jak2a is expressed during erythropoiesis. Blood 94:2622–2636. DOI: https://doi.org/
10.1182/blood.V94.8.2622.420k39_2622_2636 Ozerdem U, Grako KA, Dahlin-Huppe K, Monosov E, Stallcup WB. 2001. NG2 proteoglycan is expressed
exclusively by mural cells during vascular morphogenesis. Developmental Dynamics 222:218–227. DOI: https://
doi.org/10.1002/dvdy.1200, PMID: 11668599 g
y
Pandey A, Ibarrola N, Kratchmarova I, Fernandez MM, Constantinescu SN, Ohara O, Sawasdikosol S, Lodish HF,
Mann M. 2002. A novel src homology 2 domain-containing molecule, Src-like adapter protein-2 (SLAP-2), which
negatively regulates T cell receptor signaling. Journal of Biological Chemistry 277:19131–19138. DOI: https://
doi.org/10.1074/jbc.M110318200, PMID: 11891219 g
j
,
Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A, Schier AF. 2012. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome
Research 22:577–591. DOI: https://doi.org/10.1101/gr.133009.111, PMID: 22110045 g
g
Pertea G, Pertea M. 2020. GFF utilities: gffread and GffCompare. F1000Research 9:304. DOI: https://doi.org/1
12688/f1000research.23297.1, PMID: 32489650 Quillien A, Abdalla M, Yu J, Ou J, Zhu LJ, Lawson ND. 2017. Robust identification of developmentally active
endothelial enhancers in zebrafish using FANS-Assisted ATAC-Seq. Cell Reports 20:709–720. DOI: https://doi. org/10.1016/j.celrep.2017.06.070 Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatic
26:841–842. DOI: https://doi.org/10.1093/bioinformatics/btq033, PMID: 20110278 Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF. 2018. Simultaneous
single-cell profiling of lineages and cell types in the vertebrate brain. Nature Biotechnology 36:442–450. DOI: https://doi.org/10.1038/nbt.4103, PMID: 29608178 p
g
Satija R, Farrell JA, Gennert D, Schier AF, Regev A. 2015. Spatial reconstruction of single-cell gene expression
data. Nature Biotechnology 33:495–502. DOI: https://doi.org/10.1038/nbt.3192, PMID: 25867923 Shaw GC, Cope JJ, Li L, Corson K, Hersey C, Ackermann GE, Gwynn B, Lambert AJ, Wingert RA, Traver D,
Trede NS, Barut BA, Zhou Y, Minet E, Donovan A, Brownlie A, Balzan R, Weiss MJ, Peters LL, Kaplan J, et al. 2006. Mitoferrin is essential for erythroid iron assimilation. Nature 440:96–100. DOI: https://doi.org/10.1038/
nature04512, PMID: 16511496 Smith L. 2003. References DNA microarrays and development. Human Molecular Genetics 12:1–8. DOI: https://doi.org/10. 1093/hmg/ddg053 27 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources T Tools and resources Developmental Biology Developmental Biology Song HD, Sun XJ, Deng M, Zhang GW, Zhou Y, Wu XY, Sheng Y, Chen Y, Ruan Z, Jiang CL, Fan HY, Zon LI,
Kanki JP, Liu TX, Look AT, Chen Z. 2004. Hematopoietic gene expression profile in zebrafish kidney marrow. PNAS 101:16240–16245. DOI: https://doi.org/10.1073/pnas.0407241101, PMID: 15520368 Soza-Ried C, Hess I, Netuschil N, Schorpp M, Boehm T. 2010. Essential role of c-myb in definitive hematopoiesis
is evolutionarily conserved. PNAS 107:17304–17308. DOI: https://doi.org/10.1073/pnas.1004640107, PMID: 20
823231 SRA Toolkit Development Team. 2020. The SRA Toolkit. GitHub. https://github.com/ncbi/sra-tools SRA Toolkit Development Team. 2020. The SRA Toolkit. GitHub. https://github.com/ncbi/sra-tools
St
t T B tl
A H ff
P H f
i t
C P
l
i E M
k WM H
Y St
ki
M S
ib
t P S tij
R SRA Toolkit Development Team. 2020. The SRA Toolkit. GitHub. https://github.com/ncbi/sra-tools
Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM, Hao Y, Stoeckius M, Smibert P, Satija R. 2019 Comprehensive integration of Single-Cell data Cell 177:1888–1902 DOI: https://doi org/10 1016/j cell p
p
g
Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM, Hao Y, Stoeckius M, Smibert P, Satija R. 2019. Comprehensive integration of Single-Cell data. Cell 177:1888–1902. DOI: https://doi.org/10.1016/j.cell. 2019.05.031, PMID: 31178118 Tell RM, Kimura K, Palic´ D. 2012. Rac2 expression and its role in neutrophil functions of zebrafish (Danio rerio). Fish & Shellfish Immunology 33:1086–1094. DOI: https://doi.org/10.1016/j.fsi.2012.07.020, PMID: 22992407 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching
during cell differentiation. Nature Biotechnology 28:511–515. DOI: https://doi.org/10.1038/nbt.1621,
PMID: 20436464 Tseng YC, Chen RD, Lee JR, Liu ST, Lee SJ, Hwang PP. 2009. Specific expression and regulation of glucose
transporters in zebrafish ionocytes. American Journal of Physiology-Regulatory, Integrative and Comparative
Physiology 297:R275–R290. DOI: https://doi.org/10.1152/ajpregu.00180.2009, PMID: 19458281 y
gy
p
g
jp
g
Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell GW, Sive H, Bartel DP. 2012. Extensive
alternative polyadenylation during zebrafish development. Genome Research 22:2054–2066. DOI: https://doi. References org/10.1101/gr.139733.112, PMID: 22722342 g
g
,
Umans RA, Henson HE, Mu F, Parupalli C, Ju B, Peters JL, Lanham KA, Plavicki JS, Taylor MR. 2017. CNS
angiogenesis and barriergenesis occur simultaneously. Developmental Biology 425:101–108. DOI: https://doi. org/10.1016/j.ydbio.2017.03.017 Vanhollebeke B, Stone OA, Bostaille N, Cho C, Zhou Y, Maquet E, Gauquier A, Cabochette P, Fukuhara S,
Mochizuki N, Nathans J, Stainier DYR. 2015. Tip cell-specific requirement for an atypical Gpr124- and Reck-
dependent wnt/b-catenin pathway during brain angiogenesis. eLife 4:e06489. DOI: https://doi.org/10.7554/
eLife.06489 Vijayaraj P, Le Bras A, Mitchell N, Kondo M, Juliao S, Wasserman M, Beeler D, Spokes K, Aird WC, Baldwin HS,
Oettgen P. 2012. Erg is a crucial regulator of endocardial-mesenchymal transformation during cardiac valve
morphogenesis. Development 139:3973–3985. DOI: https://doi.org/10.1242/dev.081596, PMID: 22932696
Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM. 2018. Single-cell mapping of gene
expression landscapes and lineage in the zebrafish embryo Science 360:981–987 DOI: https://doi org/10 Vijayaraj P, Le Bras A, Mitchell N, Kondo M, Juliao S, Wasserman M, Beeler D, Spokes K, Aird WC, Baldwin HS,
Oettgen P. 2012. Erg is a crucial regulator of endocardial-mesenchymal transformation during cardiac valve
morphogenesis. Development 139:3973–3985. DOI: https://doi.org/10.1242/dev.081596, PMID: 22932696 Oettgen P. 2012. Erg is a crucial regulator of endocardial-mesenchymal transformation during cardiac valve
morphogenesis. Development 139:3973–3985. DOI: https://doi.org/10.1242/dev.081596, PMID: 22932696
Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM. 2018. Single-cell mapping of gene
expression landscapes and lineage in the zebrafish embryo. Science 360:981–987. DOI: https://doi.org/10. 1126/science.aar4362, PMID: 29700229 Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM. 2018. Single-cell mapping of gene
expression landscapes and lineage in the zebrafish embryo. Science 360:981–987. DOI: https://doi.org/10. 1126/science.aar4362, PMID: 29700229 Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews
Genetics 10:57–63. DOI: https://doi.org/10.1038/nrg2484, PMID: 19015660 Whitesell TR, Chrystal PW, Ryu JR, Munsie N, Grosse A, French CR, Workentine ML, Li R, Zhu LJ, Waskiewicz A,
Lehmann OJ, Lawson ND, Childs SJ. 2019. foxc1 is required for embryonic head vascular smooth muscle
differentiation in zebrafish. Developmental Biology 453:34–47. DOI: https://doi.org/10.1016/j.ydbio.2019.06. 005, PMID: 31199900 Wilkinson RN, van Eeden FJ. 2014. The zebrafish as a model of vascular development and disease. Progress in
Molecular Biology and Translational Science 124:93–122. DOI: https://doi.org/10.1016/B978-0-12-386930-2. References 00005-7, PMID: 24751428 Wingert RA, Brownlie A, Galloway JL, Dooley K, Fraenkel P, Axe JL, Davidson AJ, Barut B, Noriega L, Sheng X,
Zhou Y, Zon LI. 2004. The chianti zebrafish mutant provides a model for erythroid-specific disruption of
transferrin receptor 1. Development 131:6225–6235. DOI: https://doi.org/10.1242/dev.01540, PMID: 15563524
Wu TD, Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bi i f
i
26 873 881 DOI h
//d i
/10 1093/bi i f
i
/b
057 PMID 20147302 Wingert RA, Brownlie A, Galloway JL, Dooley K, Fraenkel P, Axe JL, Davidson AJ, Barut B, Noriega L, Sheng X,
Zhou Y, Zon LI. 2004. The chianti zebrafish mutant provides a model for erythroid-specific disruption of
transferrin receptor 1. Development 131:6225–6235. DOI: https://doi.org/10.1242/dev.01540, PMID: 15563524 p
p
p
g
Wu TD, Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26:873–881. DOI: https://doi.org/10.1093/bioinformatics/btq057, PMID: 20147302 Xu P, Balczerski B, Ciozda A, Louie K, Oralova V, Huysseune A, Crump JG. 2018. Fox proteins are modular
competency factors for facial cartilage and tooth specification. Development 145:dev165498. DOI: https://doi. org/10.1242/dev.165498, PMID: 29777011 g
Yukselen O, Turkyilmaz O, Ozturk AR, Garber M, Kucukural A. 2020. DolphinNext: a distributed data processing
platform for high throughput genomics. BMC Genomics 21:310. DOI: https://doi.org/10.1186/s12864-020-
6714-x, PMID: 32306927 Zhang J, Wagh P, Guay D, Sanchez-Pulido L, Padhi BK, Korzh V, Andrade-Navarro MA, Akimenko MA. 2010. Loss of fish Actinotrichia proteins and the fin-to-limb transition. Nature 466:234–237. DOI: https://doi.org/10. 1038/nature09137, PMID: 20574421 28 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792
|
https://openalex.org/W3189715851
|
https://www.mdpi.com/2073-4360/13/16/2619/pdf?version=1628768584
|
English
| null |
In Vitro Evaluation of Biomaterials for Vocal Fold Injection: A Systematic Review
|
Polymers
| 2,021
|
cc-by
| 11,201
|
Citation: Wan-Chiew, N.; Baki, M.M.;
Fauzi, M.B.; Lokanathan, Y.; Azman,
M. In Vitro Evaluation of Biomaterials
for Vocal Fold Injection: A Systematic
Review. Polymers 2021, 13, 2619. https://doi.org/10.3390/polym13162619 Keywords: vocal fold augmentation; functional voice disorder; preliminary study; characterization;
material Academic Editors: Rossella Dorati,
Enrica Chiesa and Silvia Pisani Review
In Vitro Evaluation of Biomaterials for Vocal Fold Injection:
A Systematic Review Wan-Chiew 1
, Marina Mat Baki 1
, Mh Busra Fauzi 2
, Yogeswaran Lokanathan 2
Mawaddah A man 1,* Ng Wan-Chiew 1
, Marina Mat Baki 1
, Mh Busra Fauzi 2
, Yogeswaran Lokanathan 2
and Mawaddah Azman 1,* 1
Department of Otorhinolaryngology—Head and Neck Surgery, Faculty of Medicine,
Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; wanchiew1997@gmail.com (N.W.-C.);
marinamatbaki@ppukm.ukm.edu.my (M.M.B.) 1
Department of Otorhinolaryngology—Head and Neck Surgery, Faculty of Medicine,
Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; wanchiew1997@gmail.com (N.W.-C.);
marinamatbaki@ppukm.ukm.edu.my (M.M.B.) pp
y
2
Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine,
Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; fauzibusra@ukm
lyoges@ppukm ukm edu my (YL ) 2
Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine,
Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; fauzibusra@ukm.edu.my (M.B.F.); 2
Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine,
Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; fauzibusra@ukm.edu.my (M.B.F.);
lyoges@ppukm.ukm.edu.my (Y.L.)
*
Correspondence: mawaddah@ukm.edu.my *
Correspondence: mawaddah@ukm.edu.my Abstract: Vocal fold injection is a preferred treatment in glottic insufficiency because it is relatively
quick and cost-saving. However, researchers have yet to discover the ideal biomaterial with properties
suitable for human vocal fold application. The current systematic review employing PRISMA
guidelines summarizes and discusses the available evidence related to outcome measures used to
characterize novel biomaterials in the development phase. The literature search of related articles
published within January 2010 to March 2021 was conducted using Scopus, Web of Science (WoS),
Google Scholar and PubMed databases. The search identified 6240 potentially relevant records, which
were screened and appraised to include 15 relevant articles based on the inclusion and exclusion
criteria. The current study highlights that the characterization methods were inconsistent throughout
the different studies. While rheologic outcome measures (viscosity, elasticity and shear) were most
widely utilized, there appear to be no target or reference values. Outcome measures such as cellular
response and biodegradation should be prioritized as they could mitigate the clinical drawbacks of
currently available biomaterials. The review suggests future studies to prioritize characterization of
the viscoelasticity (to improve voice outcomes), inflammatory response (to reduce side effects) and
biodegradation (to improve longevity) profiles of newly developed biomaterials. 1. Introduction The ECM in the vocal fold consists
of collagen and elastin as the fibrous proteins proteoglycan and glycoprotein, as interstitial
proteins. These proteins play vital roles in maintaining the viscoelasticity of the human
vocal fold [17]. Elastin enables vocal fold tissue to possess elastic properties and is more
abundant in the superficial parts of the lamina propria than its deeper layers [18]. On
the other hand, collagen in the vocal fold functions as a mechanical support to withstand
high-frequency vibration and stretching [13]. The abundance of collagen was found in
the deep layer of the lamina propria. Due to its non-linear properties, it remains unclear
whether current quantification methods used by recent studies suit the viscoelasticity of
native vocal fold tissue. The vocal fold is very sensitive towards any intrusion. A previous study has ex-
plained that airborne particulate matter significantly upregulated interleukin-6 (IL-6) and
IL-1β which mounts a pro-inflammatory response. In addition, these particles could ini-
tiate mitogen-activated protein kinase (MAPK) and necrosis factor kappa beta (NF-kB)
pathways [19]. Furthermore, a recent clinical study reported that the most frequent compli-
cation after vocal fold injection was inflammation at the injection site [20]. Activation of
inflammation in the vocal fold increases fibrosis formation leading to vocal fold scarring,
subsequently causing dysphonia [21,22]. Therefore, unregulated inflammatory response is
shown to be an adverse event in the vocal fold. The molecules involved in the inflammatory
response in the vocal fold have been extensively studied for at least a decade [23,24]. The
consistency of studies in quantifying IL-1β, NF-kB, tumor necrosis factor-alpha (TNF-
α), interferon-gamma (IFN-γ), transforming growth factor-beta (TGF-β), cyclooxygenase
(COX2), HA and procollagen expression indicated that these molecules are closely related
to inflammation in the vocal fold [25]. Inflammation starts with the accumulation of IL-1β,
NF-kB and TNF-α, activating fibroblasts and promoting collagen deposition, leading to
scar formation [24]. Multiple biomaterials have been used in vocal fold injections but only CaHA and
autologous fat have a long duration without resorption [26]. However, application of CaHA
imposed the risk of migration and granuloma formation [27]. Even though HA possesses
the most favorable properties, its inconsistent resorption is the main drawback [28,29]. Well-developed biomaterials should be tolerated by the host immune system and non-
antigenic surface receptors even after degradation [30,31]. More prolonged effects of
injection and biocompatibility are the main desired outcomes in the development of future
injectable biomaterials [32,33]. 1. Introduction Population-based studies among subjects over 60 years old or more reported up
to 29% prevalence of vocal disorders, mainly from glottic insufficiency [1]. Incomplete
closure of the vocal fold, namely glottic insufficiency, results in a breathy voice and risk of
aspiration [2]. These symptoms are commonly caused by unilateral vocal fold paralysis or
paresis and are mainly subsequent to surgery. The recurrent laryngeal nerve that supplies
most intrinsic laryngeal muscles is at risk in surgeries of the thyroid gland, neck, trachea and
esophagus [3]. Other risk factors include poor regeneration due to senescence, smoking and
systemic disease [4]. Young recurrent laryngeal nerve (RLN) tissue appeared more elastic
to strain, while adolescent RLN tissue was stiffer and tended to break with strain [5]. In
treating glottic insufficiency, vocal fold injection is preferred as it is more cost-effective and
time-saving [6,7]. Currently available biomaterials for vocal fold injection include bovine
and porcine gelatin, carboxymethylcellulose, calcium hydroxylapatite (CaHA), autologous
fat, collagen-based and hyaluronic acid (HA)-based hydrogels [8]. Vocal fold injection is
also commonly performed concomitantly with nonselective laryngeal reinnervation [9]. Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article
distributed
under
the
terms
and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/). In developing a suitable biomaterial for vocal fold augmentation, the biochemical
properties of the vocal fold need to be respected. This is because the intervention has the https://www.mdpi.com/journal/polymers Polymers 2021, 13, 2619. https://doi.org/10.3390/polym13162619 2 of 21 Polymers 2021, 13, 2619 2 of 21 potential to interrupt the microenvironment of the vocal fold, which eventually affects the
quality of voice production [10]. Vocal folds are two bands of complex tissue that serve
multiple roles, including respiration, voice production and airway protection [11]. The
complex tissue consists of superficial and deep layers separated by the lamina propria [12]. Additionally, the lamina propria is further divided into three parts: (1) superficial, (2) inter-
mediate and (3) deep layers [13]. The myoelastic-aerodynamic theory explains the unique
characteristics of the vocal fold and the neuromuscular control that permits phonation [14]. The superomedial aspect of the superficial layer of the vocal fold is softer compared to its
inferomedial surface [15]. The viscoelasticity of the vocal fold is primarily determined by
the composition of the extracellular matrix (ECM) [16]. 1. Introduction Before further investigation up to in vivo and clinical
study, the optimization stage of biomaterials is performed. However, the parameters to
be assessed during preliminary study are not clear. Therefore, the myriad applications of
biomaterials in glottic insufficiency research have been chosen for discussion in this review. A literature search was performed through electronic databases to identify characterization
of biomaterials and in vitro studies performed on the application of biomaterials in acute
and chronic glottic insufficiency. The objective of this review is to describe the outcome
measures used to study the various physicomechanical characteristics of biomaterials
developed for the vocal fold. Additionally, the review will provide insight on which
aspects should be focused on in future studies. 3 of 21 Polymers 2021, 13, 2619 2.1. Search Strategy A systematic review of the literature was performed to determine relevant studies
reporting the characterization of biomaterials and in vitro studies to test their applicability
as vocal fold injections for the glottic insufficiency condition. The systematic review
was structured based on PRISMA guidelines to ensure the quality and transparency of
this review [34]. A total of four databases includes Scopus (Elsevier, Amsterdam, NH,
The Netherlands), ISI Web of Science (WoS) (Clarivate Analytics, Philadephia, PA, USA),
PubMed (National left for Biotechnology Information, NCBI, Bethesda, MD, USA) and
Google Scholar (Mountain View, CA, USA) were used to search relevant articles within
the last eleven years (from January 2010 to March 2021). The article searching process was
guided by the focus question formulated using the PICO strategy whereby population (P)
was laboratory study on biomaterials for vocal fold injection; intervention (I) was outcome
measure used to characterize the biomaterials; comparison (C) with other biomaterials was
not applicable; and outcome (O) was physicomechanical or cellular characteristics of the
biomaterials studied. The searching process was performed by two independent reviewers. g p
p
y
p
The searching method was performed by two sets of keyword combinations: (1) bio-
material* (to obtain biomaterial or biomaterials) or material* (to obtain material or materi-
als) or regenerative therap*(to obtain regenerative therapy or regenerative therapies) or
hyaluronic acid* (to obtain hyaluronic acid or hyaluronic acids) and (2) vocal fold injection*
(to obtain vocal fold injection or vocal fold injections) or glottic insufficienc* (to obtain
glottic insufficiency or glottic insufficiencies) or vocal fold medialization* (to obtain vocal
fold medialization or vocal fold medializations) or vocal fold augmentation* (to obtain
vocal fold augmentation or vocal fold augmentations). The search strategy was performed
for all databases following summary in Table 1. Table 1. Search strategy for all databases. (*: to obtain both singular and plural forms of the search
criterion). No. Terms
1
Biomaterial*
2
Material*
3
Regenerative therap*
4
Hyaluronic acid*
5
Vocal fold injection*
6
Glottic insufficienc*
7
Vocal fold medialization*
8
Vocal fold augmentation*
9
Or/1–4
10
Or/5–8
11
And/9 & 10
12
Line 11: Restrict to period: January 2010 to March 2021 Table 1. Search strategy for all databases. (*: to obtain both singular and plural forms of the search
criterion). 2.3. Exclusion Criteria 2.3. Exclusion Criteria The exclusion criteria included all secondary literature and any original articles solely
involving in vivo and clinical stage study, articles written or submitted in languages other
than English and studies focused on developing biomaterials using biological elements
such as cells, growth factors, genes and tissue components derived from animals. 2.4. Data Extraction and Management Articles were screened in three phases to fulfill part of this systematic review. The
first step included screening of titles to remove titles that did not match the inclusion
criteria. The second step included abstract screening of the remaining papers to further
remove inappropriate articles based on the inclusion criteria. The last step included
removing any papers that did not meet the inclusion criteria after full-text reading by two
independent reviewers. This review could not be published on PROSPERO because it
included in vitro studies. 2.2. Inclusion Criteria Due to limited resources for translation, only English articles were included. Original
research articles discussing the effects of biomaterials used in injection laryngoplasty
with the main priority of glottic insufficiency applications were chosen. The studies that
involved different types of biomaterials were included in this review. Studies on the cells
involved during healing in glottic insufficiency including fibroblasts, endothelial cells and
macrophages were also included. 4 of 21 Polymers 2021, 13, 2619 2.5. Quality Assessment The review was conducted in a methodological approach using the critical appraisal
instrument for systematic reviews [35]. The primary and secondary reviewers discussed
each item in the appraisal instrument for each study included in this review. All studies
included were considered acceptable to the aims of this review in terms of the specific study
characteristics. A prior discussion between the independent reviewers was performed to
determine what constitutes acceptable levels of information to allocate a positive appraisal
compared with negative, or “unclear” responses. We utilized an appraisal instrument
consisting of 11 questions where each question was answered with “yes”, “no” or “unclear”. 3.1. Searching Result 3.1. Searching Result 3.1. Searching Result Total of 6240 articles were identified as potentially relevant. The first screening
removed a total of 6089 articles which were non-original articles, not written or submitted
in English, were duplicates or had a title or abstract that did not fit the inclusion criteria. From the remaining 151 articles, reviewers read the full text and 136 articles were removed
as the articles did not fulfill the inclusion criteria. After selection, total of 15 articles were
chosen for reviewing. A flow chart of the article selection process is shown in Figure 1. Figure 1. PRISMA flow diagram. Figure 1. PRISMA flow diagram. 5 of 21 Polymers 2021, 13, 2619 3.2. Study Characteristics 3.2. Study Characteristics Among the selected articles, all articles included parameter in characterizing physi-
comechanical properties of hydrogel. Total of 5 out of 15 studies involved cellular response
study. Type of cells used for included in vitro study was listed in 3.5. Total of 7 out of
15 studies involved animal study but the data was not included as per exclusion criteria
mentioned in 2.3. With that, the data were summarized into three different aspects includ-
ing rheological properties, other characterization parameters such as pore size, particle
size, injection force, swelling ratio, drug release test, morphology and gelation time and
cellular response. All of the studies were published between January 2010 and March 2021. In general, ten studies aimed to develop new formulation of biomaterials [36–45]; three
studies focused in improving or characterizing current biomaterials [46–48]; one study
investigated the effect of the biomaterials toward inflammation [49]; three studies intended
to improve fabrication methods in order to produce better biomaterials [36,46,50]. The bio-
materials studied in the included articles were carbomer hydrogel, micronized dermal graft
tissue, crosslinked HA, HA with gelatine hydrogel, CaHA, carboxymethylcellulose (CMC),
bovine collagen, micronized alloderm (Cymetra) (Lifecell Corp, Branchburg, NJ, USA),
HA gel, carboxylic and hydroxylic multi-walled functionalized carbon, unequal particle
sized middle viscosity and low viscosity HA, Rofilan (Laborata es Filorga, Lisbonne, Paris,
France),Radiesse (Merz, Franksville, WI, USA),Restylane (Galderma Laboratories, Fort
Worth, TX, USA), dextran beads in HA microsphere (MP), polyethylene glycol-diamine
(PEG) microparticles, gelatine methacrylate MP, HA methacrylate, semi-IPN MP, glycol
chitosan hydrogel, pluronic F127 with collagen, HA with poly(ethylene glycol) diacry-
late (PEGDA) crosslinkers, silk protein based in HA suspension, resilin-like-polypeptide
hydrogel, PEG30 hydrogel and polydimethylsiloxane (PDMS) with polydopamine (PDA). 3.3. Rheological Properties The most frequent characterization of biomaterials for vocal fold injection is rheo-
logical measurement; 14 out of 15 articles quantified this measurement with different
rheometers and parameters. The outcome measures used include elastic shear modulus
(G′), loss shear modulus (G′′), loss tangent (ξ), dynamic viscosity (η′), Young modulus
(E′), strain sweep and shear storage modulus. The proportional relationship between G′
and G′′ with frequencies was investigated in most of the studies. Larger values of G′
compared to G′′ show that the biomaterials possess more elastic behavior than viscous
properties. Two studies tested viscoelasticity of the biomaterials at high frequencies, up
to 2000 Hz and 4000 Hz, whereas in other studies the tested range was 0.1 Hz to 250 Hz. Some of the studies tested in the range of 0.1 to 10 Hz because of the limitations of the
instrument settings. Results of G′ and G′′ are dependent on the range of frequency, for
instance Kazemirad et al. revealed that the outcome patterns of high and low frequency
were consistent but with a greater magnitude in lower frequency range [40]. The strain (γ)
used by the studies ranged from 0.01% to 2% but only one study applied up to 1000% to
determine the limit of the linear viscoelastic regime [42]. The phonation threshold pressure
(PTP) quantifies the minimum lung pressure needed to generate the desired voice. It is one
of the aerodynamic measurements for the vocal fold. This measurement was used by a
single study [36] in this review. The results are summarized in Table 2. Polymers 2021, 13, 2619 6 of 21 Table 2. Rheological study. Author, Year
Type of Biomaterials
Study Measure Outcome
Summary of Results
Conclusion
1. Klemuk et al., 2010 [36]
1. Carbomer hydrogel
2. Micronized dermal graft tissue
3. Crosslinked HA hydrogel
4. All biomaterials had stiffer
properties compared to earlier
studies, hence suggested for deep
injection into the vocal fold but not
into lamina propria. 3.3. Rheological Properties HA and gelatin
crosslinked hydrogel
(a) Rheology measurement by
rotational (for 0.1 to 100 Hz) and
piezoelectric rheometer (up to
2000 Hz):
shear elastic (G′) and viscous
moduli (G′′) (linear)
(b) Pressure threshold
projection (PTP)
vocal fold length and frequency:
(i) For males: 15.8 mm and 125 Hz
(ii) For females: 10.63 mm, 200 Hz
Shear elastic (G′)
Mean values: 100 to 10,000 Pa
Viscous moduli (G′′)
Mean values: 10 to 5000 Pa
Loss tangent (G′′/G′) in 100 to
1000 Hz
Hylan B, Extracel and Cbmr: 0.08 to
0.66 (widest range)
PTP value relative to nominal PTP
value (0.283 kPa)
Sample 2 had highest value (3× to
21×) and sample 4 had lowest value
(0.01× to 0.05×)
Crosslinked HA hydrogel, HA and
gelatin crosslinked hydrogel and
carbomer hydrogel are suitable for
voice production. 2. Mahboubi, Mohraz & Verma
2016 [46]
1. CaHA
2. CMC
(a) Viscosity modulus (η) by
rotational rheometer
(b) Shear elastic (G′) and loss
moduli (G′′) with frequency sweeps
at 0.01% strain and 0.1 to 200 Hz by
oscillatory rheometer (linear)
Viscosity
CaHA (43,100 Pa.s) was 10 times
more viscous than CMC (4540 Pa.s). Heating and shearing
G′′ for CaHA reduced by 52%
Heating and shearing potentially
reduces viscosity of CaHA. 3. Kimura, Mau & W Chan 2010 [47]
1. 3% bovine collagen
(atelocollagen)
2. micronized Alloderm
3. CaHA
4. 2.4% crosslinked HA gel
(a) Elastic shear modulus (G′) tested
with 0.3 to 0.5 mm gap size, 1 to 2%
strain and 1 to 250 Hz. (b) Dynamic viscosity (n′) by custom
build, controlled strain, linear
simple shear rheometer system
Elastic shear modulus (G′)
Atelocollagen performed the nearest
value (about 1000 Pa) to the vocal
fold superficial layer′s value. Dynamic viscosity (η′)
Atelocollagen performed the nearest
value (about 0.7 Pa.s) to the vocal
fold superficial layer′s value at
around 135 Hz. All biomaterials had stiffer
properties compared to earlier
studies, hence suggested for deep
injection into the vocal fold but not
into lamina propria. 4. Ravanbakhsh et al., 2019 [37]
1. Carboxylic (COOH) multi-walled
functionalized carbon
nanotube (CNTs)
2. Hydroxylic (OH) multi-walled
functionalized CNTs
Storage modulus tested at 0.1 to 10
Hz and 1000 µm gap size, <5% shear
strain by rotational
rheometer (linear)
Storage modulus*
- Increased with higher
CNT concentration
- OH-CNT had higher storage
modulus than COOH-CNT
Mechanical strength of hydrogel
was not influenced by the
concentration of CNT. Heating and shearing potentially
reduces viscosity of CaHA. 3.3. Rheological Properties Crosslinked HA hydrogel, HA and
gelatin crosslinked hydrogel and
carbomer hydrogel are suitable for
voice production. Viscosity
CaHA (43,100 Pa.s) was 10 times
more viscous than CMC (4540 Pa.s). Heating and shearing
G′′ for CaHA reduced by 52% 7 of 21 Polymers 2021, 13, 2619 Table 2. Cont. Author, Year
Type of Biomaterials
Study Measure Outcome
Summary of Results
Conclusion
5. Kim et al., 2015 [38]
1. Commercial HA
2. Unequal particle-sized middle
viscosity HA (3,000,000 cP)
3. Unequal particle-sized low
viscosity HA (30,000 cP)
Elasticity at 0.02 Hz (not specified)
Elasticity
Commercial HA: 200 to 400 Pa
Mid HA: 300 Pa
Low HA: 3 Pa
Unequal particle-size HA showed
better outcomes than commercial
HA in vivo. 6. Choi et al., 2012 [48]
1. Rofilan (non animal
stabilized biomaterial)
2. Restylane (double crosslinked
3. Dextran beads in HA (dextran
microspheres)
(a) Shear viscosity (η)
(b) Mean elastic modulus (G′)
(c) Mean viscous modulus (G′′) at
frequency of 0.1 to 10 Hz with strain
controlled rheometer (linear)
Steady state viscosity (η)
Restylane had the highest
(19.138 Pa·s) value. Mean elastic modulus (G′)
Reviderm had the highest
(464.1 Pa·s) value. Mean viscous modulus (G′′)
Reviderm had the highest
(167.8 Pa·s) value. All HA-based hydrogels had similar
shear viscosities and the values
were higher than reported human
vocal fold but in vivo study showed
that HA-based hydrogels were
compatible with viscoelasticity of
rabbit vocal fold. 7. Chan et al., 2014 [50]
1. PEG microparticles (MP)
2. Gelatin methacrylate MP
3. HA-methacrylate (HAMA) MP
4. Semi-IPN MP of HAMA
& gelatine
Shear storage modulus (G′) and
shear loss modulus (G′′) at 0.6%
strain by rotational
rheometer (linear). Viscoelasticity for PEG-DA:PEG
When the ratio of PEG-DA:PEG
increased 50 to 100%, G′ increased
from 523 Pa to 1599 a; G′′ increased
from 38 Pa to 111 Pa
Photopolymerization method was
able to synthesize soft MP with
varying stiffness which was
independent of its size. 8. Coburn et al., 2020 [49]
Glycol-chitosan hydrogel with
different crosslinker concentrations:
0.005%, 0.01% and 0.02%
Mechanical characterization at 0.1 to
100 rad/s by rotational
rheometer (linear)
Storage modulus (G′) and loss
modulus (G′′)
0.005%: around 50 and 18 Pa
0.01%: around 340 and 17 Pa
0.02%: around 740 and 15 Pa
G′ value > G′′: showing
elastic property
Hydrogel with higher stiffness
potentially caused inflammation but
delayed expression of IL-10 at 72 h
caused higher
macrophage apoptosis. 9. 3.3. Rheological Properties Fu et al., 2015 [39]
Pluronic F127 with collagen of 1%,
2% and 3%
(a) Storage modulus
(b) Loss modulus
Rheology measurement at 1.0 rad/s
and 0.5% strain by rotational
rheometer (linear)
Elastic modulus (G′) at 1.0 rad/s
Pluronic F127 with highest collagen
(3%) exhibited lowest G′ (94.0 kPa). Viscous modulus (G′′) at 10 to
100 rad/s*
Pluronic F127 with collagen did not
reduce sharply compared to
without collagen. Pluronic F127 with collagen
enhanced the drug release time and
favoured cell growth. Table 2. Cont. (a) Storage modulus
(b) Loss modulus
Rheology measurement at 1.0 rad/s
and 0.5% strain by rotational
rheometer (linear) Polymers 2021, 13, 2619 8 of 21 Table 2. Cont. Author, Year
Type of Biomaterials
Study Measure Outcome
Summary of Results
Conclusion
. Kazemirad, Heris & Mongeau
16 [40]
1. Sample 1 to 3: 0.50%HA +
crosslinker PEGDA of 0.25%,
0.5% & 1.0%
2. Sample 4 to 5: 0.45%HA + 0.05%
gelatin (Ge) of 0.1% and 0.2%
(a) Shear storage (G′)
(b) Loss moduli (G′′)
at frequency up to 4000 Hz (linear)
Shear storage (G′) & Loss moduli
(G′′)
Sample 4 (G′: 19.61 Pa; G′′: 5.00 Pa)
and 5 (G′: 12.24 Pa; G′′: 8.50 Pa)
were comparable to viscoelasticity
with human vocal fold. With optimized concentration of
HA, Ge and crosslinker, the
hydrogel showed
comparable viscoelasticity. . Brown et al., 2019 [41]
Silk protein-based in HA suspension
Mechanical properties at 0.1 to 10.0
Hz and 1% strain by dynamic
rotation shear rheometer (linear)
Mechanical properties
- Silk suspension increased stiffness
less rapid (5× lesser) than
CaHA-CMC
- Injection of silk suspension
(1.5 times) yield lesser stiffness in
vocal fold than CaHA-CMC
(4.0 times)
Silk-HA had similar viscoelasticity
properties with porcine vocal fold. . Li et al., 2018 [42]
Chemically crosslinked
resilin-like-polypeptide
(RLP) hydrogel:
1. Sample 1: 10 wt%
2. Sample 2: 15 wt%
(a) Shear storage modulus at 0.1 to
100 rad/s
(b) Storage moduli (G′) and loss
moduli (G′′) by stress
controlled rheometer
(c) strain sweep test of 0.01% to
1000% (linear)
Shear storage modulus
Sample 1 and 2 increased rapidly
until 1000 Pa and
2000 Pa respectively
Storage moduli (G′) and loss
moduli (G′′)
G′ was higher than G′′ for 100 to
200 fold. Strain sweep
Sample 1: 265%
Sample 2: 245%
High resistance to break. Rheological properties of the
hydrogels were in the range of
native vocal fold tissue. . 3.3. Rheological Properties Pruett et al., 2020 [44]
Fabrication of microporous
annealed particle (MAP) by
water-in-oil emulsion
Young’s modulus (linear), compare
with vocalis muscle
Young’s modulus
1.9 wt% MAP showed with porcine
vocal fold’s muscle comparable
(~15,000 Pa). MAP gel exhibited similar
rheological properties with porcine
vocal fold tissue. . Karajanagi et al., 2011 [45]
PEG30 hydrogel
Elastic shear properties (G′) from 1
to 10 Hz with 0.6% strain by
rotational rheometer (linear)
Viscoelasticity*
PEG30 showed softer hydrogel
compared to value reported in
literature review. PEG30 demonstrated optimal
physical properties for vocal
fold injection. Remarks: Result with * indicated no reported value. Table 2. Cont. Rheological properties of the
hydrogels were in the range of
native vocal fold tissue. Polymers 2021, 13, 2619 9 of 21 3.4. Other Characterization Parameters 3.4. Other Characterization Parameters 3.4. Other Characterization Parameters Other than the mechanical properties of the biomaterials, different features were tested
to further support the feasibility of these biomaterials for vocal fold injection. A total of
seven different tests were carried out. The most frequent tests include particle and pore size
quantification [37,38,41,43,50]. Injection force was only measured by two studies in this
review [41,50]. Swelling ratio [37,38] and drug release tests [39,50] were performed in two
studies, while morphology and gelation time were only carried out by single study [37]. The results are summarized in Table 3. Polymers 2021, 13, 2619 10 of 21 Table 3. Other characterization parameters. Author, Year
Type of Biomaterials
Study Measure Outcome
Summary of Results
Conclusion
. Ravanbakhsh et al.,
2019 [37]
1. Carboxylic (COOH) multi-walled
functionalized CNTs
2. Hydroxylic (OH) multi-walled
functionalized CNTs
(a) Morphology
(b) Pore size
(c) Swelling ratio
(d) Gelation time
Pore size
Diameter of CNTs: 45 ± 5 nm
Increased by 33% with increased concentration of
COOT-CNT but not significant in OH-CNT. Swelling ratio
Increased by 5% with increased COOT-CNT
concentration. OH-CNT had no effect on this property. Gelation time*
Increased starting 750 µg/mL of CNT
COOH-CNT hydrogel showed
larger pore size which might
enhance cell migration. 2. Kim et al., 2015 [38]
1. Commercial HA (Restylane)
2. Unequal particle-sized middle
viscosity HA
3. Unequal particle-sized low
viscosity HA
(a) Particle size
(b) Swelling ratio
Particle size
Restylane: 200 µm
Mid HA: 300 to 500 µm
Low HA: No size
Swelling ratio
Restylane: 100 to 200%
Mid HA: 130%
Low HA: 200%
Unequal particle-size HA showed
better outcomes than Restylane®
in vivo. 3. Chan et al., 2014 [50]
1. PEG MP
2. Gelatin methacrylate MP
3. HA-methacrylate (HAMA) MP
4. Semi-IPN MP of HAMA & gelatin
(a) Particle size
(b) Drug release test
Ability to inject
Can be injected through 22 gauge needle
Particle size (D90)
Range from 136 µm to 162 µm
MP produced had uniform particle distribution with
~1.5 polydispersity (PDI). Increased stirring speed up to 600 rpm or surfactant
reduced the size from 515 to 140 µm. Drug release test*
Drug encapsulation and release in PEG NS/MP was
lower than from NS alone. Higher stirring speed and surfactant
concentration reduced size of MP
and drug release time. Table 3. Other characterization parameters. COOH-CNT hydrogel showed
larger pore size which might
enhance cell migration. Remarks: result with * indicates no reported value. 3.4. Other Characterization Parameters Unequal particle-size HA showed
better outcomes than Restylane®
in vivo. Higher stirring speed and surfactant
concentration reduced size of MP
and drug release time. 11 of 21 Polymers 2021, 13, 2619 Table 3. Cont. Author, Year
Type of Biomaterials
Study Measure Outcome
Summary of Results
Conclusion
4. Fu et al., 2015 [39]
1. Pluronic F127 with collagen of 1%,
2% and 3%
(a) Morphology
(b) Drug release test
Pore size
With increased concentration of collagen incorporated
in Pluronic F127, pore size was increased (from 5–20
µm to 20–40 µm). Drug release
Collagen incorporated in Pluronic F127 reduced drug
(ofloxacin) release (43.6% to 48.1%). Pluronic F127 with collagen
enhanced the drug release time and
favoured cell growth. 5. Brown et al., 2019 [41]
Silk protein-based in HA suspension
(a) Pore size
(b) Injection force through
24 G long needle and
50 cm catheter with
1.05 mm inner diameter at
13 mm/min speed
Pore size
Diameter ranging 10 to 100 um and had ability to
return into original shape after compression. Injection force
Silk protein (34.9 N) needed less force than
CaHA-CMC (51.4 N) as control. Particle size of silk-HA allowed
macrophage passage, tissue
adherence and was biocompatible. 6. Chung et al., 2017 [43]
PDMScoated with PDA
(a) Particle size
(b) Morphology
Particle size
79.23 µm ± 2.23 with 2.81% coefficient of variation. (less than 5% showed highly uniform size distribution)
Morphology
PDMS microsphere with PDA had a rougher surface
while without PDA had a smoother surface. PDMS was injectable,
non-absorbable and showed better
cell adherence. Remarks: result with * indicates no reported value. Table 3. Cont. Pluronic F127 with collagen
enhanced the drug release time and
favoured cell growth. Particle size of silk-HA allowed
macrophage passage, tissue
adherence and was biocompatible. PDMS was injectable,
non-absorbable and showed better
cell adherence. 12 of 21 Polymers 2021, 13, 2619 12 of 21 3.5. Cellular Response To further identify suitable biomaterials, in vitro studies must include evaluations to
elucidate the cellular response when integrated with the biomaterials. In vitro outcomes
measured in this review included cell adhesion [43], cell viability/compatibility [37,39,50],
cell phenotyping [49] and production of cytokines [49]. Among the types of cell used
were human vocal fold fibroblasts (HVFF), NIH/3T3 cells, macrophages, vocal fold fi-
broblasts (VFF), Hacat cells and mouse NIH-3T3 embryonic fibroblasts. Ravanbakhsh
and co-researchers suggested a cell viability threshold of 70% [37]. However, Fu and co-
researchers compared cell viability between the sets and control to quantify the cytotoxicity
level of the biomaterials [39]. An interesting in vitro study by Coburn and co-researchers
quantified the response of macrophages when cultivated with hydrogel and vocal fold
fibroblasts [49]. The results are summarized in Table 4. 13 of 21 Polymers 2021, 13, 2619 Table 4. In vitro study. Author, Year
Type of Biomaterials
Study Measure Outcome
Summary of Results
Conclusion
nbakhsh et al.,
]
1. Carboxylic (COOH) multi-walled
functionalized CNTs
2. Hydroxylic (OH) multi-walled
functionalized CNTs
Cell viability of HVFF
Cell viability
1. COOH-CNT up to 750 ug/mL;
2. OH-CNT up to 1250 ug/mL as the
cytotoxicity level increased after
this threshold. COOH-CNT had higher cytotoxicity
than OH-CNT
et al., 2014 [50]
1. PEG MP
2. Gelatin methacrylate MP
3. HA-methacrylate (HAMA) MP
4. Semi-IPN MP of HAMA & gelatin
Cytocompatibility test on
NIH/3T3 cells
Cytocompatibility test
0.1 to 50 mg/mL PEG50 culture resulted in
cell viability of 80%. Hydrogel produced by
photopolymerization was
cytocompatible. rn et al., 2020 [49]
Glycol-chitosan hydrogel with
concentration:
1. 0.005%
2. 0.01%
3. 0.02%
(a) Production of cytokines by
macrophage
(b) Macrophage viability
(c) Macrophage phenotyping:
-CD11b (+)
CD33/CD80:proinflammatory
CD33/CD206:anti-inflammatory
Production of cytokines
TNF-α and IL-10 increased in hydrogel
culture and with increased stiffness
of hydrogel. Cell viability
Macrophage viability was reduced in
hydrogel culture. Cell phenotyping
More CD33/CD206 (anti-inflammatory)
expressing macrophage in macrophage+
VFF+hydrogel than macrophage+hydrogel. Hydrogel with higher stiffness
potentially caused inflammation but
delayed expression of IL-10 at 72 h
caused higher
macrophage apoptosis. al., 2015 [39]
Pluronic F127 with collagen of 1%,
2% and 3%
Cell viability (Hacat cells)
Cell viability
Collagen incorporated in Pluronic F127
improved cell adhesion and viability. Pluronic F127 loaded with collagen
improved cell adhesion
and viability. 4. Discussion Even with the recent advances in regenerative therapy, no treatment is able to re-
constitute a paralyzed vocal fold. Therefore, researchers have widely studied alternative
biomaterials to reconstruct the physical properties of the vocal fold [51]. Since the viscoelas-
ticity of the vocal fold is closely related to the efficiency of phonation, it is a primary concern
when developing injectable biomaterials for vocal fold augmentation. Furthermore, studies
showed that different stiffnesses of hydrogel would have different impacts on microenvi-
ronmental responses such as cell adhesion and proliferation [52,53]. Therefore, the rheology
study of injectable biomaterial is vital to understand its deformation (elasticity) and flow
of matter (viscosity) [54]. Up to date, no reference study is able to quantify the viscoelasticity of human vocal
folds precisely. This is because the viscoelasticity of the vocal fold is influenced by many
factors such as age, gender, hydration level, disease status such as laryngeal nerve paralysis,
mass lesions and fibrosis [55,56]. There are two ways to quantify the viscoelasticity of
the vocal fold: linear and non-linear measurement. Linear measurement has been used
widely and it is characterized by shear rheology which mainly is divided into two types:
(1) rotational rheometry and (2) linear skin rheometry (LSR) [57]. Studies suggested that
rotational rheometry generates more consistent results than LSR with 1% strain. Most
of the studies in this review used linear methods to quantify viscoelasticity. Across the
studies, various frequencies and strain rates were used, hence direct comparisons between
the results were hard to perform. Torsional wave experiment (TWE) was suggested
to quantify the linear behavior of viscoelasticity as it can overcome sample inertia at
higher frequencies [58]. It is recommended to include phonation frequency by humans
as conducted in the study by Kazemirad et al. [59]. The tested frequencies were in the
range of 110 Hz to 260 Hz and 220 to 440 Hz for males and females, respectively. The
current literature review did not provide a consistent range for the viscoelasticity value
of the native vocal fold. For instance, Goodyer et al. suggested a value for males of
246 Pa to 3536 Pa and for females of 286 Pa to 3332 Pa by using the simple shear model
method [55]. 3.5. Cellular Response g et al., 2017 [43]
PDMS PDA
Cell adhesion test (mouse NIH-3T3
embryonic fibroblast)
Cell adhesion test
PDMS microsphere with PDA had more cells
attached on its surface. PDMS with PDA demonstrated
better cell adherence. Table 4. In vitro study. 14 of 21 Polymers 2021, 13, 2619 14 of 21 4. Discussion However, another study has refuted this [15], suggesting the viscoelasticity
of the human vocal fold superficial layer was 5.0 kPa (ranging from 4.7 to 5.4 kPa) for the
superior medial and 7.0 kPa (ranging from 6.7 to 7.3 kPa) for the inferior medial surface. Recently, the inaccuracy of linear measurement was raised, and non-linear measurement
was proposed [60]. This study demonstrated the non-linearity properties of the human
vocal fold cover and ligament at a high strain of 0.5 (50%) with frequencies of 175 Hz and
125 Hz [60]. Tissues in this biological system, which consists of different compositions
with distinct densities and topologies, appear to be the main obstacle in developing a
suitable biomaterial for the vocal fold [61]. Therefore, this review prompts the need to
provide significant values of vocal fold viscoelasticity across reported studies by statistical
justification. Moreover, most of the studies tested the mechanical properties of biomaterials
using linear measurement, which may not reflect their similarities with the native vocal
fold. Inconsistency of testing parameters across studies highlights the insufficiency of the
benchmark and established guidelines in developing a suitable biomaterial with desirable
viscoelastic properties. p
p
Even though injectable biomaterials for vocal fold augmentation possess desired
viscoelasticity, inflammation is a main concern as foreign body reaction could lead to serious
complications such as airway edema [62]. Moreover, rare hypersensitivity cases occurred
after injection of bovine collagen which can lead to more severe onset symptoms and require
medical attention for a longer period [63]. Not to mention that a previously well-known
injectable biomaterial, Teflon (Du Pont, Wilmington, DE, USA), resulted in granuloma
formation [64]. Granuloma formation is closely associated with chronic inflammatory
response [65]. HA is widely used nowadays, but an unusual allergy response has been
observed [66]. Therefore, preliminary data on cell immune response is much needed when
evaluating a biomaterial in an in vitro study. The vocal fold consists of fibroblasts which
have been proven to be closely associated with inflammatory response [67]. Inflammation Polymers 2021, 13, 2619 15 of 21 15 of 21 in vocal fold is one of the pathological factors leading to vocal fold scarring [68]. As
biomaterials are injected into the biological system, immune cells such as leukocytes detect
them as foreign particles. The different chemistry and exterior characteristics of hosts
can trigger an immune response [69]. 4. Discussion During this immune response, pro-inflammatory
cytokines such as TNF-α, IL-6, IL-8, IL-1β and MCP-1 will be liberated whereas anti-
inflammatory cytokines such as IL-10 and IL-12 play crucial roles in quantifying the
efficiency of eliminating harmful materials while providing protection to host [67,70]. During wound repair in the vocal fold, increased pro-inflammatory cytokines IL-1β and
IL-6 by neutrophils and macrophages promote fibrosis. However, the anti-inflammatory
cytokine, IL-10 could have the potential to dampen the inflammation [71]. Nevertheless,
this review shows that only a single study has explained inflammatory responses when
developing biomaterials [49]. This test is suggested to be included for future research to
elucidate molecular mechanisms of inflammation when a novel biomaterial is developed
for tissue regeneration. Both pro- and anti-inflammatory responses should be quantified to
ensure the balanced inflammatory response after injection of biomaterial. Apart from the above-mentioned tests, biomaterials with no migration and low resorp-
tion are keys to determine practicality for injection application in the clinic [72]. Injection
of HA was observed to have low complication rates between 3 and 5%, mainly from
inflammatory reactions [66,73]. This response might be due to foreign body reaction or con-
tamination during the injection process. Biodegradation is explained when disintegration
of biomaterial occurs in the biological system [74]. Clinical measurement of biodegradation
can be achieved by resorption rate of the biomaterial [75]. Current commercial biomaterials
are divided into two categories, short term and long term injectates [76]. Bovine-based
gelatin and collagen products, human-based collagen, HA and carboxymethylcellulose
have temporary effects whereas calcium hydroxyapatite (CaHA), Teflon (Du Pont, Wilm-
ington, DE, USA), autologous fat and polydimethylsiloxane possess longer augmentation
effects. Occasionally, clinicians opt for temporary augmentation aiming for natural recov-
ery and reducing the need for medialization laryngoplasty [77]. Temporary augmentation
is also recommended during the wait of reinnervation period [78,79]. However, clinical
studies have suggested 15% to 20% over injection of short-term biomaterial to counter
resorption, especially of water-based gels [80]. Biodegradation can be quantified by using
hydrolysis by enzymes such as lysozyme and collagenase in certain natural materials
such as chitosan, gelatin and alginate [81–83]. Nevertheless, none of the reviewed articles
include biodegradation tests. Hence, this review suggests a degradation test as prolonged
degradation rates of biomaterials could positively influence local cellular activities [84]. Further investigation of the composition after degradation should be carried out to study
the cytotoxicity effect [85]. 4. Discussion Accordingly, the end-products after degradation should be
elucidated to provide evidence of background study during the initial stage of biomaterials
development, specifically during in vitro studies. This could assist in providing strong
evidence for future investigation such as in vivo and clinical studies. g
Other characterization could be carried out depending on the specific requirements of
hydrogel. The time taken for the hydrogel to polymerize should be optimized and 20 min
was recommended by Ravanbaksh et al. [37]. Short gelation time could prevent destabilized
gel washout from the desired location. On the other hand, it could result in insufficient
injection time for clinicians [85,86]. A previous study reported that swelling ratio influenced
the regulation of chondrocyte [87]. Thomas et al. conducted a swelling ratio test to
determine the stability of the biomaterial to remain its original state when immersed in
excess fluid as a simulation of the biological environment [53]. The porosity of biomaterials
influenced the effectiveness of substances’ migration and mechanical properties. Therefore,
fine-tuning between porosity and mechanical properties is needed to obtain effective
biomaterials [88]. Homogeneous distribution of pore size has been shown to reduce cell
interaction with the scaffold [89]. Among the biomaterials included in this review, some had been studied in clinical
stages including micronized alloderm (Cymetra) (Lifecell Corp, Branchburg, NJ, USA) Polymers 2021, 13, 2619 16 of 21 16 of 21 HA, CMC, collagen, Rofilan (Laborata es Filorga, Lisbonne, Paris, France), Radiesse
(Merz, Franksville, WI, USA) and Restylane (Galderma Laboratories, Fort Worth, TX,
USA) [27,29,66,90–94]. It is vita l to refer to the outcome of the clinical studies, so that
future study can address the suggested drawbacks of these biomaterials. The drawbacks
included: (1) inconvenient preparation steps and the need for over-injection for Cymetra
(Lifecell Corp, Branchburg, NJ, USA) [90]; (2) inflammatory reaction and a lack of long-
lasting effect in application of HA [29,66,94]. CMC and collagen had similar issues, making
them suitable only for short term augmentation [91,92] and lastly (3) Rofilan (Laborata es
Filorga, Lisbonne, Paris, France) was reported to show no improvement in voice acous-
tic analysis such as noise to harmonic ratio [93]. With that, this review suggests future
study ought to include parameters that can address the limitations of these current bio-
materials mainly with respect to longevity, inflammatory properties and viscoelasticity
of biomaterials. The findings from this review are limited by potential bias. 4. Discussion In this study, only in vitro
study was chosen as an inclusion criterion, leading to narrower results. Justification of
this criterion is that this study aims to illuminate the importance of the initial stage of
biomaterial development. Secondly, due to lack of facility to translate foreign languages,
non-English literatures were excluded from this study. In addition, grey literature articles
were also not evaluated in this work. We have, however, attempted to exclude duplicate ar-
ticles in this review. To enhance the outcome of this review, statistical analysis is suggested
for future evaluation. However, in vitro study should be a strong molecular support when
exploring a higher level of studies. Abbreviations CaHA
Calcium Hydroxypatite
CMC
Carboxymethylcellulose
CNTs
Carbon nanotube
COOH
Carboxylic
COX2
Cyclooxygenase
ECM
Extracellular matrix
HA
Hyaluronic acid
HAMA
HA-methacrylate MP
HVFF
Human vocal fold fibroblast
IL-1β
Interleukin-1 beta
IFN-γ
Interferon-gamma
LSR
Linear skin rheometry
MAP
Microporous annealed particle
MAPK
Mitogen-activated protein kinase
MCP-1
Monocyte chemoattractant protein-1
MP
Microparticles
NF-kB
Necrosis factor kappa beta
OH
Hydroxylic
PDA
Polydopamine
PDMS
Poly(dimethysiloxane) microspheres
PEG
Polyethylene glycol-diamine
PEGDA
Poly(ethylene glycol) diacrylate
PTP
Phonation threshold pressure
RLN
Recurrent laryngeal nerve
RLP
Resilin-like-polypeptide
TGF-β
Transforming growth factor-beta
TNF-α
Tumor necrosis factor-alpha
TWE
Torsional wave experiment 5. Conclusions In conclusion, there is a lack of benchmarks to standardize the evaluation of novel
biomaterials for vocal fold injection. After summarizing the studies included in this review
and comparing the study outcome measures used with available clinical outcomes, it is
suggested to prioritize characterization of the viscoelasticity (to improve voice outcomes),
inflammatory response (to reduce side effects) and biodegradation (to improve longevity)
profiles of biomaterials. Even though results generated by in vitro studies may not be con-
sistent with outcomes seen in in vivo and clinical studies, it should provide a fundamental
insight to consider the suitability of biomaterials for further study. If the outcomes of both
in vitro and in vivo studies support each other, it could strengthen conviction and provide
strong evidence for pre-clinical studies. Author Contributions: Conceptualization, N.W.-C., M.M.B., M.B.F., Y.L. and M.A.; methodology,
N.W.-C., M.A. and M.B.F.; validation, M.M.B., M.B.F., Y.L. and M.A.; formal analysis, N.W.-C.;
investigation, N.W.-C., M.A. and Y.L.; data curation, N.W.-C., M.A. and Y.L.; writing—original draft
preparation, N.W.-C.; writing—review and editing, M.M.B., M.B.F., Y.L. and M.A.; visualization, N.W.-
C., M.M.B., M.B.F., Y.L. and M.A; supervision, M.M.B., M.B.F., Y.L. and M.A.; project administration,
M.B.F. and M.A.; funding acquisition, Y.L. and M.A. All authors have read and agreed to the published
version of the manuscript. Funding: This research was funded by Minister of Higher Education (MOHE) Fundamental Research
Grant Scheme (FGRS), grant number FRGS/1/2020/SKK06/UKM/01/1. Institutional Review Board Statement: The study was conducted according to the ethical guidelines
underpinned by right-based theories, whereby it adheres to the principles of beneficence, non-
maleficence, justice, honesty and gratitude. The study was approved by the Institutional Review
Board (or Ethics Committee) of UNIVERSITI KEBANGSAAN MALAYSIA (protocol code FF-2020-818
on 3 February 2020). Informed Consent Statement: Informed consent was not necessary since this study included only
secondary data, with no identifiable subjects. Data Availability Statement: Data sharing is not applicable to this article as no new data were
created or analyzed in this study. 17 of 21 Polymers 2021, 13, 2619 17 of 21 Acknowledgments: We would like to thank the Otorhinolaryngology Head and Neck Surgery
department, Tissue Engineering Centre and Faculty of Medicine UKM for providing resources
to complete this review. This review was not be published on PROSPERO because it included
in vitro studies. Conflicts of Interest: The author reports no conflict of interest in this work. 9.
Mansor, W.N.W.; Azman, M.; Remli, R.; Yunus, M.R.M.; Baki, M.M. Primary Nonselective Laryngeal Reinnervation in Iatrogenic
Acute Recurrent Laryngeal Nerve Injury: Case Series and Literature Review. Ear Nose Throat J. 2021, 1–6. [CrossRef] References Function of the laryngeal muscles on the position and shape of the vocal cord
(author’s transl). Nippon. Jibiinkoka Gakkai Kaiho 1975, 78, 1249–1257. [CrossRef] [PubMed] oike, Y.; Hirano, M.; Morio, M.; Kasuya, T. Function of the laryngeal muscles on the position and shape
uthor’s transl). Nippon. Jibiinkoka Gakkai Kaiho 1975, 78, 1249–1257. [CrossRef] [PubMed] 13. Tang, S.S.; Mohad, V.; Gowda, M.; Thibeault, S.L. Insights into the Role of Collagen in Vocal Fold Health and Disease. J. Voice
2017, 31, 520–527. [CrossRef] ang, J.; Lin, E.; Hanson, D.G. Vocal fold physiology. Otolaryngol. Clin. N. Am. 2000, 33, 699–718. [CrossRef] 14. Jiang, J.; Lin, E.; Hanson, D.G. Vocal fold physiology. Otolaryngol. Clin. N. Am. 2000, 33, 699–718. [CrossRef]
15. Chhetri, D.K.; Rafizadeh, S. Young’s modulus of canine vocal fold cover layers. J. Voice 2014, 28, 406–410. [CrossRef] J
g J
p y
gy
y g
[
]
15. Chhetri, D.K.; Rafizadeh, S. Young’s modulus of canine vocal fold cover layers. J. Voice 2014, 28, 406–410. [CrossRef] 16. Miri, A.K.; Li, N.Y.K.; Avazmohammadi, R.; Thibeault, S.L.; Mongrain, R.; Mongeau, L. Study of extrace
biomechanics using a two-phase model. Biomech. Model. Mechanobiol. 2015, 14, 49–57. [CrossRef] 17. Gray, S.D.; Titze, I.R.; Alipour, F.; Hammond, T.H. Biomechanical and histologic observations of vocal fold fibrous proteins. Ann. Otol. Rhinol. Laryngol. 2000, 109, 77–85. [CrossRef] y g
18. Moore, J.; Thibeault, S. Insights into the role of elastin in vocal fold health and disease. J. Voice 2012, 26 18. Moore, J.; Thibeault, S. Insights into the role of elastin in vocal fold health and disease. J. Voice 2012, 26, 269–275. [CrossRef]
19. Won, H.-R.; Jung, S.-N.; Yeo, M.-K.; Yi, S.; Liu, L.; Lim, M.A.; Oh, C.; Kang, Y.E.; Chang, J.W.; Rha, K.S.; et al. Effect of Urban 18. Moore, J.; Thibeault, S. Insights into the role of elastin in vocal fold health and disease. J. Voice 2012, 26, 269–275. [CrossRef]
19
Won H R ; Jung S N ; Yeo M K ; Yi S ; Liu L ; Lim M A ; Oh C ; Kang YE ; Chang J W ; Rha K S ; et al Effect of Urban Particulate Matter on Vocal Fold Fibrosis through the MAPK/NF-κB Signaling Pathway. Int. J. Mol. Sci. 2020, 21, 6643. [CrossRef]
20. Enver, N.; Az˙Izl˙I, E.; Akbulut, S.; Çadalli Tatar, E.; Yelken, M.K.; ÖztÜrk, K.; Co¸skun, H.; B˙Irkent, A.H.; Büyükatalay, Z.Ç.;
ÖzgÜrsoy, O.B.; et al. References 3. Mattsson, P.; Hydman, J.; Svensson, M. Recovery of laryngeal function after intraoperative injury to the recurrent laryngeal nerve. Gland. Surg. 2015, 4, 27. [PubMed] 3. Mattsson, P.; Hydman, J.; Svensson, M. Recovery of laryngeal function after intraoperative injury to the recurrent laryngeal nerve. Gland. Surg. 2015, 4, 27. [PubMed] 4. Lynch, J.; Parameswaran, R. Management of unilateral recurrent laryngeal nerve injury after thyroid surgery: A review. Head
Neck 2017, 39, 1470–1478. [CrossRef] 4. Lynch, J.; Parameswaran, R. Management of unilateral recurrent laryngeal nerve injury after thyroid surgery: A review. Head
Neck 2017, 39, 1470–1478. [CrossRef] 5. Williams, M.J.; Utzinger, U.; Barkmeier-Kraemer, J.M.; Vande Geest, J.P. Differences in the microstructure and biomechanical
properties of the recurrent laryngeal nerve as a function of age and location. J. Biomech. Eng. 2014, 136, 810081–810089. [CrossRef]
[PubMed] 5. Williams, M.J.; Utzinger, U.; Barkmeier-Kraemer, J.M.; Vande Geest, J.P. Differences in the microstructure and biomechanical
properties of the recurrent laryngeal nerve as a function of age and location. J. Biomech. Eng. 2014, 136, 810081–810089. [CrossRef]
[PubMed] [
]
6. Schimberg, A.S.; Wellenstein, D.J.; van den Broek, E.M.; Honings, J.; van den Hoogen, F.J.A.; Marres, H.A.M.; Takes, R.P.; van
den Broek, G.B. Office-based vs. operating room-performed laryngopharyngeal surgery: A review of cost differences. Eur. Arch. Oto-Rhino-Laryngol. 2019, 276, 2963–2973. [CrossRef] y g
7. Sulica, L.; Rosen, C.A.; Postma, G.N.; Simpson, B.; Amin, M.; Courey, M.; Merati, A. Current practice in injection augmentation of
the vocal folds: Indications, treatment principles, techniques, and complications. Laryngoscope 2010, 120, 319–325. [CrossRef]
[PubMed] 8. Modi, V.K. Vocal fold injection medialization laryngoplasty. Adv. Otorhinolaryngol. 2012, 73, 90–94. [CrossRef] 9. Mansor, W.N.W.; Azman, M.; Remli, R.; Yunus, M.R.M.; Baki, M.M. Primary Nonselective Laryngeal Reinnervation in Iatrogenic
Acute Recurrent Laryngeal Nerve Injury: Case Series and Literature Review. Ear Nose Throat J. 2021, 1–6. [CrossRef] 18 of 21 18 of 21 Polymers 2021, 13, 2619 10. Mau, T.; Muhlestein, J.; Callahan, S.; Chan, R.W. Modulating phonation through alteration of vocal fold medial surface contour. Laryngoscope 2012, 122, 2005–2014. [CrossRef] 10. Mau, T.; Muhlestein, J.; Callahan, S.; Chan, R.W. Modulating phonation through alteration of vocal fold medial surface contour. Laryngoscope 2012, 122, 2005–2014. [CrossRef] y g
p
[
]
11. Lungova, V.; Thibeault, S.L. Mechanisms of larynx and vocal fold development and pathogenesis. Cell. Mol. Life Sci. 2020, 77,
3781–3795. [CrossRef] 12. Koike, Y.; Hirano, M.; Morio, M.; Kasuya, T. References A Multi-Institutional Study of Complication Rates for Vocal Fold Injection with Hyaluronic Acid: Is It Safe
to Use in Vocal Folds? Turk. J. Med. Sci. 2020, 51, 819–825. [CrossRef] 21. Benninger, M.S.; Alessi, D.; Archer, S.; Bastian, R.; Ford, C.; Koufman, J.; Sataloff, R.T.; Spiegel, J.R.; W
Current concepts and management. Otolaryngol. Head Neck Surg. 1996, 115, 474–482. [CrossRef] p
g
y g
g
22. Xu, H.; Fan, G.-K. The Role of Cytokines in Modulating Vocal Fold Fibrosis: A Contemporary Review. Laryngoscope 2021, 131,
139–145. [CrossRef] 23. Hortobagyi, D.; Grossmann, T.; Tschernitz, M.; Grill, M.; Kirsch, A.; Gerstenberger, C.; Gugatschka, M. In vitro mechanical
vibration down-regulates pro-inflammatory and pro-fibrotic signaling in human vocal fold fibroblasts. PLoS ONE 2020, 15,
e0241901. [CrossRef] [PubMed] 24. Lim, X.; Tateya, I.; Tateya, T.; Muñoz-Del-Río, A.; Bless, D.M. Immediate inflammatory response and sc
vocal folds. Ann. Otol. Rhinol. Laryngol. 2006, 115, 921–929. [CrossRef] 25. Lim, X.; Bless, D.M.; Muñoz-Del-Río, A.; Welham, N.V. Changes in cytokine signaling and extracellular matrix production
induced by inflammatory factors in cultured vocal fold fibroblasts. Ann. Otol. Rhinol. Laryngol. 2008, 117, 227–238. [CrossRef]
[PubMed] nek, M.; Walderová, R.; Formánková, D.; Komínek, P. Five-year results of vocal fold augmentation using
lcium hydroxylapatite. Eur. Arch. Oto-Rhino-Laryngol. 2021, 278, 1139–1144. [CrossRef] 26. Zeleník, K.; Formánek, M.; Walderová, R.; Formánková, D.; Komínek, P. Five-year results of vocal f
autologous fat or calcium hydroxylapatite. Eur. Arch. Oto-Rhino-Laryngol. 2021, 278, 1139–1144. [Cross 27. DeFatta, R.A.; Chowdhury, F.R.; Sataloff, R.T. Complications of injection laryngoplasty using calcium hydroxylapatite. J. Voice
2012, 26, 614–618. [CrossRef] 28. Elsaeed, A.; Afsah, O.; Moneir, W.; Elhadidy, T.; Abou-Elsaad, T. Respiratory and voice outcomes of office-based injection
laryngoplasty in patients with unilateral vocal fold paralysis. Egypt. J. Otolaryngol. 2021, 37, 1–10. [CrossRef] 29. Wang, C.-C.; Wu, S.-H.; Tu, Y.-K.; Lin, W.-J.; Liu, S.-A. Hyaluronic Acid Injection Laryngoplasty for Unilateral Vocal Fold
Paralysis-A Systematic Review and Meta-Analysis. Cells 2020, 9, 2417. [CrossRef] 30. Mariani, E.; Lisignoli, G.; Borzì, R.M.; Pulsatelli, L. Biomaterials: Foreign Bodies or Tuners for the Immune Response? Int. J. Mol. Sci. 2019, 20, 636. [CrossRef] 31. Yang, S.; Leong, K.F.; Du, Z.; Chua, C.K. The design of scaffolds for use in tissue engineering. Part I Tra
2001, 7, 679–689. [CrossRef] 31. Yang, S.; Leong, K.F.; Du, Z.; Chua, C.K. The design of scaffolds for use in tissue engineering. Part I Traditional factors. Tissue Eng. 2001, 7, 679–689. References Injectable Silk Protein Microparticle-based
terial for Potential Use in Glottic Insufficiency. J. Voice 2019, 33, 773–780. [CrossRef] 42. Li, L.; Stiadle, J.M.; Levendoski, E.E.; Lau, H.K.; Susan, L.; Kiick, K.L.; Surgery, N. Biocompatibility of Injectable Resilin-based
Hydrogels. J. Biomed. Mater. Res. Part A 2018, 106, 2229–2242. [CrossRef] 43. Chung, E.J.; Jun, D.R.; Kim, D.W.; Han, M.J.; Kwon, T.K.; Choi, S.W.; Kwon, S.K. Prevention of polydimethylsiloxane microsphere
migration using a mussel-inspired polydopamine coating for potential application in injection therapy. PLoS ONE 2017, 12,
e0186877. [CrossRef] 44. Pruett, L.; Koehn, H.; Martz, T.; Churnin, I.; Ferrante, S.; Salopek, L.; Cottler, P.; Griffin, D.R.; Daniero, J.J. Development of a
microporous annealed particle hydrogel for long-term vocal fold augmentation. Laryngoscope 2020, 130, 2432–2441. [CrossRef]
45
K
j
i S S
L
G
G
P
k H
K bl
J B
G li d
M
A
d J
M h
D D
K
i Y Gi
d
N 44. Pruett, L.; Koehn, H.; Martz, T.; Churnin, I.; Ferrante, S.; Salopek, L.; Cottler, P.; Griffin, D.R.; Daniero, J.J. Development of a
microporous annealed particle hydrogel for long-term vocal fold augmentation. Laryngoscope 2020, 130, 2432–2441. [CrossRef]
45. Karajanagi, S.S.; Lopez-Guerra, G.; Park, H.; Kobler, J.B.; Galindo, M.; Aanestad, J.; Mehta, D.D.; Kumai, Y.; Giordano, N.;
D’Almeida, A.; et al. Assessment of canine vocal fold function after injection of a new biomaterial designed to treat phonatory
mucosal scarring. Ann. Otol. Rhinol. Laryngol. 2011, 120, 175–184. [CrossRef] [PubMed] microporous annealed particle hydrogel for long-term vocal fold augmentation. Laryngoscope 2020, 130, 2432–2441. [CrossRef]
45. Karajanagi, S.S.; Lopez-Guerra, G.; Park, H.; Kobler, J.B.; Galindo, M.; Aanestad, J.; Mehta, D.D.; Kumai, Y.; Giordano, N.;
D’Almeida, A.; et al. Assessment of canine vocal fold function after injection of a new biomaterial designed to treat phonatory
mucosal scarring. Ann. Otol. Rhinol. Laryngol. 2011, 120, 175–184. [CrossRef] [PubMed] 46. Mahboubi, H.; Mohraz, A.; Verma, S.P. Evaluation of heating and shearing on the viscoelastic properties of calcium hydroxyapatite
used in injection laryngoplasty. Otolaryngol. Head Neck Surg. 2016, 154, 498–501. [CrossRef] 47. Kimura, M.; Ted, M.; Roger, W.C. Viscoelastic properties of phonosurgical biomaterials at phonatory frequencies. Laryngoscope
2010, 120, 764–768. [CrossRef] 48. Choi, J.S.; Kim, N.J.; Klemuk, S.; Jang, Y.H.; Park, I.S.; Ahn, K.H.; Lim, J.Y.; Kim, Y.M. Preservation of viscoelastic properties
of rabbit vocal folds after implantation of hyaluronic acid-based biomaterials. Otolaryngol. Head Neck Surg. 2012, 147, 515–521. [CrossRef] 49. References [CrossRef]
32
Cohen J T ; Benyamini L Voice outcome after vocal fold injection augmentation with carboxymethyl cellulose versus calcium [
]
32. Cohen, J.T.; Benyamini, L. Voice outcome after vocal fold injection augmentation with carboxymethyl cellulose versus calcium
hydroxyapatite. J. Laryngol. Otol. 2020, 134, 263–269. [CrossRef] 33. Tigges, M.; Hess, M. Glottis injection to improve voice function: Review of more than 500 operations. HNO 2015, 63, 489–496. [CrossRef] 34. Moher, D.; Liberati, A.; Tetzlaff, J.; Altman, D.G. Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The
PRISMA Statement. Ann. Intern. Med. 2009, 151, 264–269. [CrossRef] [PubMed] 35. Aromataris, E.; Fernandez, R.; Godfrey, C.M.; Holly, C.; Khalil, H.; Tungpunkom, P. Summarizing systematic reviews: Method-
ological development, conduct and reporting of an umbrella review approach. Int. J. Evid. Based Healthc. 2015, 13, 132–140. [CrossRef] 36. Klemuk, S.A.; Lu, X.; Hoffman, H.T.; Titze, I.R. Phonation threshold pressure predictions using viscoelastic properties up to 1400
Hz of injectables intended for Reinke’s space. Laryngoscope 2010, 120, 995–1001. [CrossRef] [PubMed] j
p
37. Ravanbakhsh, H.; Bao, G.; Latifi, N.; Mongeau, L.G. Carbon nanotube composite hydrogels for vocal fold tissue engineering:
Biocompatibility, rheology, and porosity. Mater. Sci. Eng. C 2019, 103, 109861. [CrossRef] p
y
gy
p
y
g
38. Kim, Y.S.; Choi, J.W.; Park, J.K.; Kim, Y.S.; Kim, H.J.; Shin, Y.S.; Kim, C.H. Efficiency and durability of hyaluronic acid of different
particle sizes as an injectable material for VF augmentation. Acta Otolaryngol. 2015, 135, 1311–1318. [CrossRef] 19 of 21 19 of 21 Polymers 2021, 13, 2619 39. Fu, C.; Ren, F.; Zhang, Q.; Lao, G.; Zhang, L.M. Effects of collagen incorporation on thermogelation and hydrogel characteristics
of aqueous Pluronic F127 copolymer system. Colloid Polym. Sci. 2015, 293, 2191–2200. [CrossRef] q
p
y
y
y
,
,
[
]
40. Kazemirad, S.; Heris, H.K.; Mongeau, L. Viscoelasticity of hyaluronic acid-gelatin hydrogels for vocal fold tissue engineering. J. Biomed. Mater. Res. 2016, 104, 283–290. [CrossRef] q
p
y
y
y
[
]
40. Kazemirad, S.; Heris, H.K.; Mongeau, L. Viscoelasticity of hyaluronic acid-gelatin hydrogels for vocal fold tissue engineering. J. Bi
d M t
R
2016 104 283 290 [C
R f] 41. Brown, J.E.; Gulka, C.P.; Giordano, J.E.M.; Montero, M.P.; Hoang, A.; Carroll, T.L. Injectable Silk Protein Microparticle-based
Fillers: A Novel Material for Potential Use in Glottic Insufficiency. J. Voice 2019, 33, 773–780. [CrossRef] C.P.; Giordano, J.E.M.; Montero, M.P.; Hoang, A.; Carroll, T.L. References Coburn, P.T.; Herbay, A.C.; Berrini, M.; Li-Jessen, N.Y.K. An in vitro assessment of the response of THP-1 macrophages to varying
stiffness of a glycol-chitosan hydrogel for vocal fold tissue engineering applications. J. Biomed. Mater. Res. Part A 2020, 109, 1–16. [CrossRef] [
]
50. Chan, K.M.C.; Li, R.H.; Chapman, J.W.; Trac, E.M.; Kobler, J.B.; Zeitels, S.M.; Langer, R.; Karajanagi, S.S. Functionalizable hydrogel
microparticles of tunable size and stiffness for soft-tissue filler applications. Acta Biomater. 2014, 10, 2563–2573. [CrossRef] 51. Fishman, J.M.; Long, J.; Gugatschka, M.; De Coppi, P.; Hirano, S.; Hertegard, S.; Thibeault, S.L.; Birchall, M.A. Stem cell approaches
for vocal fold regeneration. Laryngoscope 2016, 126, 1865–1870. [CrossRef] 52. Levental, I.; Georges, P.C.; Janmey, P.A. Soft biological materials and their impact on cell function. Soft Matter 2007, 3, 299–306. [CrossRef] 53. Thomas, L.V.; Rahul, V.G.; Prabha, D.N. Effect of stiffness of chitosan-hyaluronic acid dialdehyde hydr
growth of encapsulated chondrocytes. Int. J. Biol. Macromol. 2017, 104, 1925–1935. [CrossRef] 54. Chan, R.W.; Titze, I.R. Viscoelastic shear properties of human vocal fold mucosa: Measurement methodology and empirical
results. J. Acoust. Soc. Am. 1999, 106, 2008–2021. [CrossRef] [PubMed] J
55. Goodyer, E.; Hemmerich, S.; Müller, F.; Kobler, J.B.; Hess, M. The shear modulus of the human vocal fold, preliminary results
from 20 larynxes. Eur. Arch. Oto-Rhino-Laryngol. 2007, 264, 45–50. [CrossRef] [PubMed] 56. Yang, S.; Zhang, Y.; Mills, R.D.; Jiang, J.J. Quantitative Study of the Effects of Dehydration on the Viscoelastic Parameters in the
Vocal Fold Mucosa. J. Voice 2017, 31, 269–274. [CrossRef] 57. Miri, A.K. Mechanical characterization of vocal fold tissue: A review study. J. Voice 2014, 28, 657–667. [CrossRef]
58. Teller, S.S.; Farran, A.J.E.; Xiao, L.; Jiao, T.; Duncan, R.L.; Clifton, R.J.; Jia, X. High-frequency viscoelastic shear properties of vocal 57. Miri, A.K. Mechanical characterization of vocal fold tissue: A review study. J. Voice 2014, 28, 657 667. [CrossRef]
58. Teller, S.S.; Farran, A.J.E.; Xiao, L.; Jiao, T.; Duncan, R.L.; Clifton, R.J.; Jia, X. High-frequency viscoelastic shear properties of vocal
f ld i
I
li
i
f
l f ld i
i
i
Ti
E
P
A 2012 18 2008 2019 [C
R f] ,
y J
,
,
[
]
58. Teller, S.S.; Farran, A.J.E.; Xiao, L.; Jiao, T.; Duncan, R.L.; Clifton, R.J.; Jia, X. High-frequency viscoelastic shear properties of vocal
fold tissues: Implications for vocal fold tissue engineering. Tissue Eng. Part A 2012, 18, 2008–2019. References [CrossRef] J
J
J J
g
q
y
p
ld tissues: Implications for vocal fold tissue engineering. Tissue Eng. Part A 2012, 18, 2008–2019. [CrossRef] p
g
g
g
,
,
[
]
59. Kazemirad, S.; Bakhshaee, H.; Mongeau, L.; Kost, K. Non-invasive in vivo measurement of the shear modulus of human vocal
fold tissue. J. Biomech. 2014, 47, 1173–1179. [CrossRef] 60. Chan, R.W. Nonlinear viscoelastic characterization of human vocal fold tissues under large-amplitude oscillatory shear (LAOS). J. Rheol. 2018, 62, 695–712. [CrossRef] 61. Chen, H.; Zhao, X.; Lu, X.; Kassab, G. Non-linear micromechanics of soft tissues. Int. J. Non-Linear Mech. 2013, 58, 79–85. [CrossRef] [CrossRef]
62
G
t
J Thib
lt S L H
l
i
id h d
l f
l f ld
d h
li
Bi
tt
2013 3
23799 [C
R f] hibeault, S.L. Hyaluronic acid hydrogels for vocal fold wound healing. Biomatter 2013, 3, e23799. [CrossRef] 62. Gaston, J.; Thibeault, S.L. Hyaluronic acid hydrogels for vocal fold wound healing. Biomatter 2013, 3, e 63. Anderson, T.D.; Sataloff, R.T. Complications of collagen injection of the vocal fold: Report of several unusual cases and review of
the literature. J. Voice 2004, 18, 392–397. [CrossRef] [PubMed] 64. Nakayama, M.; Ford, C.N.; Bless, D.M. Teflon vocal fold augmentation: Failures and management in 28 cases. Otolaryngol. Head
Neck Surg. 1993, 109, 493–498. [CrossRef] el, A.H.; Smithyman, A.M. Mechanisms of Granuloma Formation BT. In Immunodermatology; Safai, B., Good
Boston, MA, USA, 1981; ISBN 978-1-4615-7228-2. 65. Hadden, J.W.; Warfel, A.H.; Smithyman, A.M. Mechanisms of Granuloma Formation BT. In Immunoder
R.A., Eds.; Springer: Boston, MA, USA, 1981; ISBN 978-1-4615-7228-2. 66. Hamdan, A.-L.; Khalifee, E. Adverse Reaction to Restylane: A Review of 63 Cases of Injection Laryngoplasty. Ear Nose Throat J. 2019, 98, 212–216. [CrossRef] 20 of 21 20 of 21 Polymers 2021, 13, 2619 67. King, S.N.; Chen, F.; Jetté, M.E.; Thibeault, S.L. Vocal fold fibroblasts immunoregulate activated macrophage phenotype. Cytokine
2013, 61, 228–236. [CrossRef] [
]
68. Kumai, Y. Pathophysiology of Fibrosis in the Vocal Fold: Current Research, Future Treatment Strategies, and Obstacles to
Restoring Vocal Fold Pliability. Int. J. Mol. Sci. 2019, 20, 2551. [CrossRef] g
y
69. Bartlett, R.S.; Thibeault, S.L.; Prestwich, G.D. Therapeutic potential of gel-based injectables for vocal fold regeneration. Biomed. Mater. 2012, 7, 24103. [CrossRef] 70. Chen, H.; Erndt-Marino, J.; Diaz-Rodriguez, P.; Kulwatno, J.; Jimenez-Vergara, A.C.; Thibeault, S.L.; Hahn, M.S. References Fundamental
C
t
f H d
l
S
th
i
P
ti
d Th i A
li
ti
Polymers 2020 12 2702 [C
R f] [P bM d] Bashir, S.; Hina, M.; Iqbal, J.; Rajpar, A.H.; Mujtaba, M.A.; Alghamdi, N.A.; Wageh, S.; Ramesh, K.; Ram
Concepts of Hydrogels: Synthesis, Properties, and Their Applications. Polymers 2020, 12, 2702. [CrossRef] q
J
jp
j
g
g
epts of Hydrogels: Synthesis, Properties, and Their Applications. Polymers 2020, 12, 2702. [CrossRef] [PubM 82. Gorgieva, S.; Kokol, V. Preparation, characterization, and in vitro enzymatic degradation of chitosan-gelatine hydrogel scaffolds
as potential biomaterials. J. Biomed. Mater. Res. A 2012, 100, 1655–1667. [CrossRef] 83. Growney Kalaf, E.A.; Pendyala, M.; Bledsoe, J.G.; Sell, S.A. Characterization and restoration of degenerated IVD function with
an injectable, in situ gelling alginate hydrogel: An in vitro and ex vivo study. J. Mech. Behav. Biomed. Mater. 2017, 72, 229–240. [CrossRef] [
]
84. Wassenaar, J.W.; Braden, R.L.; Osborn, K.G.; Christman, K.L. Modulating In Vivo Degradation Rate of Injectable Extracellular
Matrix Hydrogels. J. Mater. Chem. B 2016, 4, 2794–2802. [CrossRef] 85. Ghobril, C.; Grinstaff, M.W. The chemistry and engineering of polymeric hydrogel adhesives for wound closure: A tutorial. Chem. Soc. Rev. 2015, 44, 1820–1835. [CrossRef] 86. Latifi, N.; Asgari, M.; Vali, H.; Mongeau, L. A tissue-mimetic nano-fibrillar hybrid injectable hydroge
engineering applications. Sci. Rep. 2018, 8, 1047. [CrossRef] 87. Park, H.; Guo, X.; Temenoff, J.S.; Tabata, Y.; Caplan, A.I.; Kasper, F.K.; Mikos, A.G. Effect of Swelling Ratio of Injectable Hydrogel
Composites on Chondrogenic Differentiation of Encapsulated Rabbit Marrow Mesenchymal Stem Cells In Vitro. Biomacromolecules
2009, 10, 541–546. [CrossRef] 88. Perez, R.A.; Mestres, G. Role of pore size and morphology in musculo-skeletal tissue regeneration. Mater. Sci. Eng. C 2016, 61,
922–939. [CrossRef] [PubMed] 89. Sobral, J.M.; Caridade, S.G.; Sousa, R.A.; Mano, J.F.; Reis, R.L. Three-dimensional plotted scaffolds with controlled pore size
gradients: Effect of scaffold geometry on mechanical performance and cell seeding efficiency. Acta Biomater. 2011, 7, 1009–1018. [CrossRef] 90. Tan, M.; Woo, P. Injection laryngoplasty with micronized dermis: A 10-year experience with 381 injections in 344 patients. Laryngoscope 2010, 120, 2460–2466. [CrossRef] [PubMed] 91. Mallur, P.S.; Morrison, M.P.; Postma, G.N.; Amin, M.R.; Rosen, C.A. Safety and efficacy of carboxymethy
of glottic insufficiency. Laryngoscope 2012, 122, 322–326. [CrossRef] n, M.P.; Postma, G.N.; Amin, M.R.; Rosen, C.A. Safety and efficacy of carboxymethylcellulose in the treatment
cy. Laryngoscope 2012, 122, 322–326. References In vitro evaluation
of anti-fibrotic effects of select cytokines for vocal fold scar treatment. J. Biomed. Mater. Res. Part B Appl. Biomater. 2019, 107,
1056–1067. [CrossRef] 71. Vyas, B.; Ishikawa, K.; Duflo, S.; Chen, X.; Thibeault, S.L. Inhibitory effects of hepatocyte growth factor and interleukin-6 on
transforming growth factor-beta1 mediated vocal fold fibroblast-myofibroblast differentiation. Ann. Otol. Rhinol. Laryngol. 2010,
119, 350–357. [CrossRef] 72. Kwon, T.-K.; Buckmire, R. Injection laryngoplasty for management of unilateral vocal fold paralysis. Curr. Opin. Otolaryngol. Head Neck Surg. 2004, 12, 538–542. [CrossRef] 73. Dominguez, L.M.; Tibbetts, K.M.; Simpson, C.B. Inflammatory reaction to hyaluronic acid: A newly described complication in
vocal fold augmentation. Laryngoscope 2017, 127, 445–449. [CrossRef] 74. Tamariz, E.; Rios-Ramírez, A. Biodegradation of Medical Purpose Polymeric Materials and Their Impact on Biocompatibility. In
Biodegradation—Life of Science; Chamy, R., Rosenkranz, F., Eds.; IntechOpen: Rijeka, Croatia, 2013. 75. Long, J.L. Tissue engineering for treatment of vocal fold scar. Curr. Opin. Otolaryngol. Head Neck Surg. 2010, 18, 521–525. [CrossRef] 76. Mallur, P.S.; Rosen, C.A. Vocal fold injection: Review of indications, techniques, and materials f
Otorhinolaryngol. 2010, 3, 177–182. [CrossRef] 77. Yung, K.C.; Likhterov, I.; Courey, M.S. Effect of temporary vocal fold injection medialization on the rate of permanent medialization
laryngoplasty in unilateral vocal fold paralysis patients. Laryngoscope 2011, 121, 2191–2194. [CrossRef] 78. Ab Rani, A.; Azman, M.; Ubaidah, M.A.; Mohamad Yunus, M.R.; Sani, A.; Mat Baki, M. Nonselective Laryngeal Reinnervation
versus Type 1 Thyroplasty in Patients with Unilateral Vocal Fold Paralysis: A Single Tertiary Centre Experience. J. Voice 2021, 35,
487–492. [CrossRef] [PubMed] 79. Mat Baki, M.; Clarke, P.; Birchall, M.A. Immediate selective laryngeal reinnervation in vagal paragangl
Otol. 2018, 132, 846–851. [CrossRef] 80. Simpson, B.; Rosen, C. Principles of Vocal Fold Augmentation BT. In Operative Techniques in Laryngology; Simpson, B., Rosen, C.,
Eds.; Springer: Berlin/Heidelberg, Germany, 2008; ISBN 978-3-540-68107-6. p
g
g
y
81. Bashir, S.; Hina, M.; Iqbal, J.; Rajpar, A.H.; Mujtaba, M.A.; Alghamdi, N.A.; Wageh, S.; Ramesh, K.; Ramesh, S. Fundamental
Concepts of Hydrogels: Synthesis, Properties, and Their Applications. Polymers 2020, 12, 2702. [CrossRef] [PubMed] p
g
g
y
r, S.; Hina, M.; Iqbal, J.; Rajpar, A.H.; Mujtaba, M.A.; Alghamdi, N.A.; Wageh, S.; Ramesh, K.; Ramesh, S. 81. Bashir, S.; Hina, M.; Iqbal, J.; Rajpar, A.H.; Mujtaba, M.A.; Alghamdi, N.A.; Wageh, S.; Ramesh, K.; Ramesh, S. 93.
Woo, J.H.; Baek, M.K.; Kim, D.Y.; Park, H.-M.; An, S.; Moon, K.H.; Cha, H.E. Injection Laryngoplasty for The Treatment of Vocal
Fold Scar, and Sulcus. J. Korean Soc. Laryngol. Phoniatr. Logop. 2016, 27, 25–29. [CrossRef] y g
g p
94.
Rudolf, R.; Sibylle, B. Laryngoplasty With Hyaluronic Acid in Patients with Unilateral Vocal Fold Paralysis. J. Voice 2012, 26,
785–791. [CrossRef] 93.
Woo, J.H.; Baek, M.K.; Kim, D.Y.; Park, H.-M.; An, S.; Moon, K.H.; Cha, H.E. Injection Laryngoplasty for The Treatment of Vocal
Fold Scar, and Sulcus. J. Korean Soc. Laryngol. Phoniatr. Logop. 2016, 27, 25–29. [CrossRef]
94.
Rudolf, R.; Sibylle, B. Laryngoplasty With Hyaluronic Acid in Patients with Unilateral Vocal Fold Paralysis. J. Voice 2012, 26, 93.
Woo, J.H.; Baek, M.K.; Kim, D.Y.; Park, H. M.; An, S.; Moon, K.H.; Cha, H.E. Injection Laryngoplasty for The Treatment of Vocal
Fold Scar, and Sulcus. J. Korean Soc. Laryngol. Phoniatr. Logop. 2016, 27, 25–29. [CrossRef]
94.
Rudolf, R.; Sibylle, B. Laryngoplasty With Hyaluronic Acid in Patients with Unilateral Vocal Fold Paralysis. J. Voice 2012, 26,
785–791. [CrossRef] References [CrossRef] g
y
y g
p
92. Hertegård, S.; Hallén, L.; Laurent, C.; Lindström, E.; Olofsson, K.; Testad, P.; Dahlqvist, A. Cross-linked hyaluronan versus
collagen for injection treatment of glottal insufficiency: 2-year follow-up. Acta Otolaryngol. 2004, 124, 1208–1214. [CrossRef] 21 of 21 Polymers 2021, 13, 2619
|
https://openalex.org/W2020617938
|
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0021976&type=printable
|
English
| null |
Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on Short- and Long-Term Resting-State Functional MRI Data
|
PloS one
| 2,011
|
cc-by
| 16,756
|
Abstract 7102090) and the Scientific Research Foundation for the Returned Overseas Chinese Scholars (State Education Ministry). The funders had no role in study
design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: yong.he@bnu.edu.cn Abstract Graph-based computational network analysis has proven a powerful tool to quantitatively characterize functional
architectures of the brain. However, the test-retest (TRT) reliability of graph metrics of functional networks has not been
systematically examined. Here, we investigated TRT reliability of topological metrics of functional brain networks derived
from resting-state functional magnetic resonance imaging data. Specifically, we evaluated both short-term (,1 hour apart)
and long-term (.5 months apart) TRT reliability for 12 global and 6 local nodal network metrics. We found that reliability of
global network metrics was overall low, threshold-sensitive and dependent on several factors of scanning time interval (TI,
long-term.short-term), network membership (NM, networks excluding negative correlations.networks including negative
correlations) and network type (NT, binarized networks.weighted networks). The dependence was modulated by another
factor of node definition (ND) strategy. The local nodal reliability exhibited large variability across nodal metrics and a
spatially heterogeneous distribution. Nodal degree was the most reliable metric and varied the least across the factors
above. Hub regions in association and limbic/paralimbic cortices showed moderate TRT reliability. Importantly, nodal
reliability was robust to above-mentioned four factors. Simulation analysis revealed that global network metrics were
extremely sensitive (but varying degrees) to noise in functional connectivity and weighted networks generated numerically
more reliable results in compared with binarized networks. For nodal network metrics, they showed high resistance to noise
in functional connectivity and no NT related differences were found in the resistance. These findings provide important
implications on how to choose reliable analytical schemes and network metrics of interest. Citation: Wang J-H, Zuo X-N, Gohel S, Milham MP, Biswal BB, et al. (2011) Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on
Short- and Long-Term Resting-State Functional MRI Data. PLoS ONE 6(7): e21976. doi:10.1371/journal.pone.0021976 Editor: Marcus Kaiser, Newcastle University, United Kingdom Received February 25, 2011; Accepted June 14, 2011; Published July 19, 2011 ng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
tion, and reproduction in any medium, provided the original author and source are credited. pyright: 2011 Wang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution L
restricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the Natural Science Foundation of China (Grant Nos. 81030028 and 30870667), Beijing Natural Science Foundation (Grant
No. Graph Theoretical Analysis of Functional Brain Networks:
Test-Retest Evaluation on Short- and Long-Term Resting-
State Functional MRI Data ian Zuo2,3, Suril Gohel4, Michael P. Milham3, Bharat B. Biswal4, Yong He1* 1 State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China, 2 Laboratory for Functional Connectome and Development, Key
Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, Beijing, China, 3 Phyllis Green and Randolph Co¯wen Institute for Pediatric
Neuroscience, New York University Langone Medical Center, New York, New York, United States of America, 4 Department of Radiology, University of Medicine and
Dentistry of New Jersey, Newark, New Jersey, United States of America Citation: Wang J-H, Zuo X-N, Gohel S, Milham MP, Biswal BB, et al. (2011) Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on
Short- and Long-Term Resting-State Functional MRI Data. PLoS ONE 6(7): e21976. doi:10.1371/journal.pone.0021976 Introduction Abbreviation
Full name
Explanation
TI
Scanning time interval
Short-term: ,1 hour apart Long-term: .5 months apart
NM
Network membership
Network (+): only positive correlations
Network (+/-): both positive and negative correlations
NT
Network type
Binarized: binarized network
Weighted: weighted network
ND
Node definition
S-: Structural ROIs
F-: Functional ROIs
S-AAL
Structural Anatomical Automatic Labeling atlas
This atlas includes 90 regions
S-HOA
Structural Harvard-Oxford atlas
This atlas includes 112 regions
F-DOS
Functional ROIs from ref (40)
This set of ROIs includes 160 regions
doi:10.1371/journal.pone.0021976.t001 doi:10.1371/journal.pone.0021976.t001 fMRI data during an executive task and demonstrated excellent
reproducibility for both small-world properties and network
efficiency metrics. Despite these progresses, however, the TRT
reliability of network metrics derived from resting-state fMRI (R-
fMRI) dataset has not been well documented so far. interregional functional connectivity is dynamic in time (from
seconds to minutes) and frequency domains [18] and can be
modulated
by
the
levels
of
current
conscious
awareness
[19,20,21,22], emotional state [23] and cognitive demand prior
to resting-state scanning [24,25,26]. Using R-fMRI, Shehzad et al. [27] have demonstrated modest to good TRT reliability for some
specific functional connections. However, these states or experi-
ments related alterations in functional connectivity may further
interact with the global network topology [28]. To our best
knowledge, there are no studies to systematically examine the R–fMRI is a promising tool to non-invasively map intrinsic
functional connectivity patterns of the human brain in vivo
[2,14,15,16] and has been extensively used to investigate inherent
brain network topological organization (for a review, see [17]). Of
note, several previous R-fMRI studies suggest that the strength of Table 2. Brief descriptions of complex network metrics examined in the present study. Introduction While graph theoretical approaches provide valuable insights
into normal brain architecture and pathological mechanism for
brain disorders, the test-retest reliability has not been systemati-
cally investigated. Reliable measures are fundamental to infer
trustworthy
conclusions
and
to
serve
as
potential
clinical
biomarkers. In response to the demand, several groups examined
the TRT reliability/reproducibility of graph network metrics. In
anatomical world, Vaessen et al. [10] assessed the reproducibility
of anatomical brain networks derived from DTI data and reported
high inter-scan reproducibility of network metrics across sampling
schemes (e.g., number of gradient directions and gradient
amplitude). Bassett et al. [11] demonstrated high reproducibility
and low variability of graph metrics for both DTI and diffusion
spectrum imaging data derived networks. As for functional
imaging arena, Deuker et al. [12] investigated the TRT reliability
of functional brain networks using MEG data and reported high
reliability during a working memory task but relatively low under
resting condition for network metrics. More recently, Telesford
et al. [13] constructed functional brain networks using baseline The human brain is a highly complex system represented as a
structurally interconnected network by a dense of cortico-cortical
axonal pathways (i.e., structural connectome, [1]) and a functionally
synchronized network by external or intrinsic coherent neural
activity (i.e., functional connectome, [2]). Mapping the brain
connectome and highlighting the underlying organizational princi-
ples
are
fundamental
for
our
understanding
of
the
brain
architecture. Recent studies have manifested that human brain
connectome networks can be constructed using neuroimaging (e.g.,
functional MRI (fMRI) and diffusion tensor imaging (DTI)) or
electrophysiological (e.g., electroencephalography (EEG) and mag-
netoencephalography (MEG)) data and further investigated by
graph theoretical approaches. These brain networks have consis-
tently demonstrated many non-trivial topological properties, such as
small-worldness, modularity and highly connected hubs (for
reviews, see [3,4,5,6,7]), and exhibited distinct alterations associated
with different neurocognitive disorders (for reviews, see [8,9]). PLoS ONE | www.plosone.or PLoS ONE | www.plosone.org 1 July 2011 | Volume 6 | Issue 7 | e21976 Reliability of Brain Functional Networks Table 1. Brief descriptions of several specific acronyms used in the present study. Table 1. Brief descriptions of several specific acronyms used in the present study. Note that the formulas listed here are only for binarized networks. For details for weighted networks, see Text S1.
1First-order network metrics which are dependent on only one graph property.
2Second-order network metrics which are dependent on more than one property or are defined as rations of one property.
doi:10.1371/journal.pone.0021976.t002 Introduction Parameter
Character
Descriptions
Regional nodal parameters
1Degree
ki
The number of connections linked directly to a node
1Efficiency
ei
How efficient an index node communicates with the other nodes
2Betweenness
bi
The influences of an index node over information flow between other nodes
1Clustering coefficient
ci
The extent of interconnectivity among the neighbors of an index node
2Participant coefficient
pi
The ability of an index node in keeping the communication between its own module and the other modules
2Normalized pi
pnor
i
The normalizedpi after correcting for the effects of number of modules
Global network parameters
1Clustering coefficient
Cp
The extent of local clustering or cliquishness of a network
1Characteristic path length
Lp
The extent of overall routing efficiency of a network
2Gamma
c
The deviation of Cp of a network from those of surrogate random networks
2Lambda
l
The deviation of Lp of a network from those of surrogate random networks
2Sigma
s
The small-worldness indicating the extent of a network between randomness and order
1Local efficiency
Eloc
How efficient of information propagation over a node’s direct neighbors
1Global efficiency
Eglob
How efficient of information propagation through the whole network
2Assortativity
r
The tendency of nodes to link those nodes with similar number of edges
2Hierarchy
b
How likely it is that all nodes oscillate with the same wave pattern
1Synchronization
S
How likely that all nodes fluctuate in the same wave pattern
2Modularity
Q
The extent that nodes can be divided several subsets with dense connections within them but sparse between
them
Note that the formulas listed here are only for binarized networks. For details for weighted networks, see Text S1. 1First-order network metrics which are dependent on only one graph property. 2Second-order network metrics which are dependent on more than one property or are defined as rations of one property. doi:10.1371/journal.pone.0021976.t002 Table 2. Brief descriptions of complex network metrics examined in the present study. Note that the formulas listed here are only for binarized networks. For details for weighted networks, see Text S1. 1First-order network metrics which are dependent on only one graph property. 2Second-order network metrics which are dependent on more than one property or are defined as rations of one property. doi:10.1371/journal.pone.0021976.t002 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 2 Reliability of Brain Functional Networks TRT reliability of network topological metrics derived from R-
fMRI data. Introduction Accordingly, systematic and direct work is clearly
warranted. functional ROIs based node definition); (2) network membership
(NM, i.e., inclusion or exclusion negative correlations); and (3)
network type (NT, i.e., binarized or weighted networks). Table 1
lists those acronyms specific to the current study. In the current study, we implemented a comprehensive
estimation of TRT reliability for both global network properties
and regional nodal characteristics of intrinsic functional brain
networks constructed using a public TRT R-fMRI dataset (http://
www.nitrc.org/projects/trt). This dataset allows us to examine
both short-term (,1 hour apart) and long-term (.5 months apart)
network reliability. Moreover, given numerous discrepancies in the
analytical strategies of existing brain network studies (e.g., how to
define network nodes or how to deal with negative correlations/
connections), we further evaluated the effects of three factors on
network reliability. They are: (1) network node definition (ND, i.e,
structural regions of interest (ROIs) based node definition or Reliability of Brain Functional Networks Reliability of Brain Functional Networks Subjects We used a TRT R-fMRI dataset of 25 participants (mean age
30.7 6 8.8, 9 males) that is publicly available at NITRC (http://
www.nitrc.org/projects/trt). The
dataset
has
been
used
to
examine TRT reliability of seed-based resting-state functional
connectivity (RSFC) [27], independent component analysis and
dual regression [29], amplitude of low-frequency fluctuations [30]
and functional homotopy [31]. Figure 1. Spatial similarity and TRT reliability patterns of S-AAL-based RSFC. Mean Pearson correlation matrices (a), consistency of overall
patterns between mean matrices (b) and TRT reliability of individual connections as well as the relationship between short-term and long-term
reliability (c) are illustrated. The mean correlation matrices exhibited high similarity from both visual inspection (a) and quantitative spatial correlation
analyses (b). Further TRT reliability analyses revealed a portion of connections exhibiting fair to excellent reliability (c, also see Fig. 2). Moreover, short-
term reliability was significantly (p,0.05) correlated with long-term reliability among connections (c). Functional connections linking inter-
hemisphere homotopic regions, as highlighted by plus signs (+), showed high connectivity strength and many of them exhibited high reliability. TRT,
test-retest; RSFC, resting-state functional connectivity; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. Of note, the structural ROIs
were listed as in Table S1. doi:10.1371/journal.pone.0021976.g001 Figure 1. Spatial similarity and TRT reliability patterns of S-AAL-based RSFC. Mean Pearson correlation matrices (a), consistency of overall
patterns between mean matrices (b) and TRT reliability of individual connections as well as the relationship between short-term and long-term
reliability (c) are illustrated. The mean correlation matrices exhibited high similarity from both visual inspection (a) and quantitative spatial correlation
analyses (b). Further TRT reliability analyses revealed a portion of connections exhibiting fair to excellent reliability (c, also see Fig. 2). Moreover, short-
term reliability was significantly (p,0.05) correlated with long-term reliability among connections (c). Functional connections linking inter-
hemisphere homotopic regions, as highlighted by plus signs (+), showed high connectivity strength and many of them exhibited high reliability. TRT,
test-retest; RSFC, resting-state functional connectivity; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. Of note, the structural ROIs
were listed as in Table S1. doi:10.1371/journal.pone.0021976.g001 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 3 Data acquisition q
Three resting-state scans were obtained for each participant
using a Siemens Allegra 3.0-Tesla scanner. Each scan consisted
of 197 contiguous EPI functional volumes (time repetition
(TR) = 2000 ms; time echo (TE) = 25 ms; flip angle (FA) = 90u,
number of slices = 39, matrix = 64664; field of view (FOV) =
192 mm; acquisition voxel size = 36363 mm3). Scans 2 and 3
were conducted in a single-scan session, 45 minutes apart, and
were 5–16 months (mean 1164) after scan 1. All individuals were
asked to relax and remain still with eyes open during the scan. Additionally, a high-resolution T1-weighted magnetization pre-
pared gradient echo sequence was also obtained (MPRAGE,
TR = 2500 ms; TE = 4.35 ms; inversion time = 900 ms; FA = 8u;
number of slices = 176; FOV = 256 mm). Data preprocessing was performed using SPM5 package
(http://www.fil.ion.ucl.ac.uk/spm). First, all images were correct-
ed for intra-volume acquisition time offsets between slices using the
Sinc interpolation and inter-volume geometrical displacement due
to head movement using six-parameter (rigid body) transforma-
tion. Then all functional images were normalized into the
Montreal Neurological Institute space using an optimum 12-
parameter affine transformation and nonlinear deformations, and
then resampled to 3-mm isotropic voxels. Finally, the normalized
images were further temporally band-pass filtered (0.01–0.1 Hz) to
reduce the effects of low-frequency drift and high-frequency
physiological noise. Notably, for the extraction of mean nodal time
courses of functional defined ROIs, spatial smoothing with 6-mm Figure 2. TRT reliability distribution of RSFC. Both short-term and long-term TRT reliability exhibit approximatively normal distribution for all
ROI sets. The mean reliability was about 0.28 (short-term) and 0.24 (long-term) for both structural ROIs-based RSFC while relatively low values were
observed for functional ROIs-based RSFC. Green dots indicate the critical values used in the present study to grade reliability. RSFC, resting-state
functional connectivity; TRT, test-retest. doi:10.1371/journal.pone.0021976.g002 Figure 2. TRT reliability distribution of RSFC. Both short-term and long-term TRT reliability exhibit approximatively normal distribution for all
ROI sets. The mean reliability was about 0.28 (short-term) and 0.24 (long-term) for both structural ROIs-based RSFC while relatively low values were
observed for functional ROIs-based RSFC. Green dots indicate the critical values used in the present study to grade reliability. RSFC, resting-state
functional connectivity; TRT, test-retest. Data acquisition doi:10.1371/journal.pone.0021976.g002 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 4 Reliability of Brain Functional Networks full width at half maximum (FWHM) Gaussian kernel was
performed
before
band-pass
filtering
(see
below
for
node
definition). full width at half maximum (FWHM) Gaussian kernel was
performed
before
band-pass
filtering
(see
below
for
node
definition). across different node definitions. Specifically, to obtain structurally
defined ROIs, a prior Anatomical Automatic Labeling atlas (AAL)
[37] and Harvard-Oxford atlas (HOA) [38,39] were separately
used to divide the whole brain into different number of regions. These two structural atlases parcellated the whole brain into 45
and 56 regions in each hemisphere and were termed as S-AAL
and S-HOA, respectively. To obtain functionally defined ROIs,
160 spheres (radius = 5 mm) were generated around the peak
coordinates previously identified form meta-analytic studies of
multiple brain functions [40,41] and were termed as F-DOS. These ROIs are comprised of discrete spherical ROIs and not
completely cover the cerebral cortex and cerebellum (Fig. S1). All Functional connectivity matrix and network construction Node definition (ND). A network (i.e., graph) is comprised
of nodes and edges connecting nodes. In the current study, nodes
represent ROIs and edges represent RSFC between ROIs. Given
the accumulating evidence of effects of node definition on network
topology [32,33,34,35,36], two strategies of defining ROIs (i.e.,
anatomical and functional ROIs) were employed to provide a
comprehensive assessment of TRT reliability of brain networks Figure 3. Relationship between RSFC and TRT reliability. Scatter plots of mean connectivity strength against corresponding ICC values are
depicted to show the relationship for both S-AAL (a) and F-DOS (b) based correlation matrices. The trend lines were obtained by linear least-square
fit. Significant (p,0.05) positive correlations were found between positive RSFC and their corresponding ICC values for both ROIs sets and for both
short-term and long-term scanning. In addition, significant negative correlations were also found for negative RSFC with their corresponding ICC
values but only for F-DOS-based correlation matrices. These findings suggest higher reliability for stronger RSFC. Functional connections linking inter-
hemisphere homotopic regions are highlighted by plus signs (+) for S-AAL but not for F-DOS because of the absence of direct correspondence. RSFC,
resting-state functional connectivity; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from
Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g003 Figure 3. Relationship between RSFC and TRT reliability. Data acquisition Scatter plots of mean connectivity strength against corresponding ICC values are
depicted to show the relationship for both S-AAL (a) and F-DOS (b) based correlation matrices. The trend lines were obtained by linear least-square Figure 3. Relationship between RSFC and TRT reliability. Scatter plots of mean connectivity strength against corresponding ICC values are
depicted to show the relationship for both S-AAL (a) and F-DOS (b) based correlation matrices. The trend lines were obtained by linear least-square
fit. Significant (p,0.05) positive correlations were found between positive RSFC and their corresponding ICC values for both ROIs sets and for both
short-term and long-term scanning. In addition, significant negative correlations were also found for negative RSFC with their corresponding ICC
values but only for F-DOS-based correlation matrices. These findings suggest higher reliability for stronger RSFC. Functional connections linking inter-
hemisphere homotopic regions are highlighted by plus signs (+) for S-AAL but not for F-DOS because of the absence of direct correspondence. RSFC,
resting-state functional connectivity; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from
Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g003 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 5 Reliability of Brain Functional Networks consisting of Pearson correlation coefficients between each pair of
ROIs were therefore generated. consisting of Pearson correlation coefficients between each pair of
ROIs were therefore generated. the ROIs are associated with five different kinds of functions of
error-processing, default-mode, memory, language and sensori-
motor. There were no any overlaps between ROIs. Names of the
three sets of ROIs and their corresponding abbreviations are listed
in Table S1, S2 and S3. Network
type
(NT). Individual
correlation
matrices
Cij~ cij
derived above was converted into both a binarized
network Edge definition. To measure inter-ROI RSFC, for each of
the three sets of ROIs, a mean time series for each ROI was
calculated by averaging the time series of all voxels within that
ROI. Several
potential
nuisance
signals
associated
with
physiological processes were further removed. Specifically, we
regressed out estimated head-motion profiles and global signal
from each ROI’s mean time series [32,42]. The residuals were
then used to estimate inter-ROI RSFC that were quantified by
Pearson correlation coefficient. Reliability of Brain Functional Networks Sthr{max i,j
ð
Þ is a data-specific maximum of
Sthr for ith subject at jth scans (note that scan2 and scan3 were
used to determine the threshold range for short-term reliability
estimation and scan1 and the average of scan2 and scan3 were
used for long-term reliability estimation). Characterization of
network topology over continuous sparsity levels allows us to trace
the trajectory of TRT reliability of network properties over
varying network structures and to identify specific threshold range
of high reliability. the whole correlation matrices consisting of positive and
negative connections and positive correlation matrices con-
sisting of only positive connections (i.e., negative correlations
were set to 0). Network metrics We explored two sets of network topological attributes: 1)
regional nodal characteristics: degree ki, efficiency ei, between-
ness bi, cluster coefficient ci, participant coefficient pi, and
normalized participant coefficient pnor
i
; 2) global network metrics:
small-world parameters (clustering coefficient Cp, characteristic
path length Lp, normalized clustering coefficient c, normalized
characteristic path length l and small-worldness s), network
efficiency (local efficiency Eloc and global efficiency Eglob),
assortativity r, hierarchy b, synchronization S, modularity Q
and the number of modules NM. All the computations of network
metrics were performed using in-house custom MATLAB codes
termed as GRETNA. Text S1 and Table 2 give detailed
descriptions for above metrics. Reliability of Brain Functional Networks Reliability of Brain Functional Networks where rthr is a pre-defined correlation threshold. To determine
rthr, sparsity measure, Sthr (defined as the ratio of the number of
actual edges divided by the maximum possible number of edges in
a network) was applied to each correlation matrix. Using the
sparsity threshold, a subject-specific rthr was determined to
threshold
each
correlation
matrix
such
that
the
resulting
networks have the same sparsity level (i.e., the same number of
edges) across subjects and scans. Currently, there is no a definitive
way to accurately determine threshold and previous studies
construct brain networks either under a single threshold (e.g.,
[43,44]) or over a continuous threshold range (e.g., [45,46]) in
terms of specific constraint conditions. Here, brain networks were
constructed over the full range of sparsity, i.e., 0,Sthr,1 for the
whole
correlation
matrices
of
both
positive
and
negative
correlations and 0,Sthr,min [Sthr{max i,j
ð
Þ] for only positive
correlation matrices. Sthr{max i,j
ð
Þ is a data-specific maximum of
Sthr for ith subject at jth scans (note that scan2 and scan3 were
used to determine the threshold range for short-term reliability
estimation and scan1 and the average of scan2 and scan3 were
used for long-term reliability estimation). Characterization of
network topology over continuous sparsity levels allows us to trace
the trajectory of TRT reliability of network properties over
varying network structures and to identify specific threshold range
of high reliability. where rthr is a pre-defined correlation threshold. To determine
rthr, sparsity measure, Sthr (defined as the ratio of the number of
actual edges divided by the maximum possible number of edges in
a network) was applied to each correlation matrix. Using the
sparsity threshold, a subject-specific rthr was determined to
threshold
each
correlation
matrix
such
that
the
resulting
networks have the same sparsity level (i.e., the same number of
edges) across subjects and scans. Currently, there is no a definitive
way to accurately determine threshold and previous studies
construct brain networks either under a single threshold (e.g.,
[43,44]) or over a continuous threshold range (e.g., [45,46]) in
terms of specific constraint conditions. Here, brain networks were
constructed over the full range of sparsity, i.e., 0,Sthr,1 for the
whole
correlation
matrices
of
both
positive
and
negative
correlations and 0,Sthr,min [Sthr{max i,j
ð
Þ] for only positive
correlation matrices. Data acquisition For each subject at each scan,
three correlation matrices (corresponding to three sets of ROIs) Aij~ aij
~
1, if cij
wrthr;
0, others
(
ð1Þ ð1Þ and a weighted network Wij~ wij
~
cij
, if cij
wrthr;
0, others
(
ð2Þ ð2Þ Figure 4. Spatial similarity and TRT reliability patterns of F-DOS-based RSFC. Mean Pearson correlation matrices (a), consistency of overa
patterns between mean matrices (b) and TRT reliability of individual connections as well as the relationship between short-term and long-term
reliability (c) are illustrated. The mean correlation matrices exhibited high similarity from both visual inspection (a) and quantitative spatial correlatio
analyses (b). Further TRT reliability analyses revealed many connections exhibiting fair to excellent reliability (c, also see Fig. 2). Moreover, a significan
(p,0.05) correlation was found in the ICC matrices between short-term and long-term scans (c). No inter-hemisphere homotopic functiona
connections were highlighted because of the absence of direct inter-hemisphere correspondence for these ROIs. TRT, test-retest; RSFC, resting-stat
functional connectivity; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). Of note, the functional ROIs were listed as in Table S3. doi:10.1371/journal.pone.0021976.g004 Figure 4. Spatial similarity and TRT reliability patterns of F-DOS-based RSFC. Mean Pearson correlation matrices (a), consistency of overall
patterns between mean matrices (b) and TRT reliability of individual connections as well as the relationship between short-term and long-term
reliability (c) are illustrated. The mean correlation matrices exhibited high similarity from both visual inspection (a) and quantitative spatial correlation
analyses (b). Further TRT reliability analyses revealed many connections exhibiting fair to excellent reliability (c, also see Fig. 2). Moreover, a significant
(p,0.05) correlation was found in the ICC matrices between short-term and long-term scans (c). No inter-hemisphere homotopic functional
connections were highlighted because of the absence of direct inter-hemisphere correspondence for these ROIs. TRT, test-retest; RSFC, resting-state
functional connectivity; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). Of note, the functional ROIs were listed as in Table S3. doi:10.1371/journal.pone.0021976.g004 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 6 Test-retest reliability To investigate the TRT reliability of all graph metrics
mentioned above, we used a common index of intraclass
correlation [48]. For each global and nodal network measure
derived under each combination of the three factors mentioned
above, individual values were first merged into two 2562 matrices
(rows corresponding to subjects and column corresponding to Network membership (NM). Given the disagreements in
treating negative correlations in R-fMRI network studies (e.g.,
[46,47]), the thresholding procedure was performed on both Figure 5. TRT reliability of global network metrics as a function of sparsity threshold for S-AAL-based networks. ICC values less than
0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks
constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized,
binarized network anlysis; Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. doi:10.1371/journal.pone.0021976.g005 Figure 5. TRT reliability of global network metrics as a function of sparsity threshold for S-AAL-based networks. ICC values less than
0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks
constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized,
binarized network anlysis; Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. doi:10.1371/journal.pone.0021976.g005 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 7 7 Reliability of Brain Functional Networks Reliability of Brain Functional Networks scans), with one representing short-term intra-session across scans
2 and 3 and the other long-term inter-session between scan 1 and
the average of scans 2 and 3. Additional long-term reliability
estimation using scan 1 and scan 3 alone outputted similar results
(Table S4). Therefore, long-term reliability results were reported
based on scan 1 and the average of scan 2 and scan 3. Of note, the
average was done on individual functional connectivity matrices
rather than graph metrics between scan 2 and scan 3, followed by
graph metric calculation. Using a one-way ANOVA on each of the
two matrices, with random subject effects, we split the total sum of
the squares into between-subject (MSb) and within-subject (MSw,
i.e., residual error) sum of squares. Finally, ICC values were
calculated according to the following equation where k is the
number of repeated observations per subject [48]: ICC~
MSb{MSw
MSbz k{1
ð
ÞMSw
ð3Þ ð3Þ Of note, the ICC derived from (3) has a relationship with the F-
value derived from the one-way ANOVA as follows [49]: Of note, the ICC derived from (3) has a relationship with the F-
value derived from the one-way ANOVA as follows [49]: ICC~
F{1
Fz k{1
ð
Þ
ð4Þ ð4Þ ICC is close to 1 for reliable measures that show low within-subject
variance relative to between-subject variance and 0 (negative)
otherwise. In the current study, reliability was recorded in terms of ICC is close to 1 for reliable measures that show low within-subject
variance relative to between-subject variance and 0 (negative)
otherwise. In the current study, reliability was recorded in terms of Figure 6. TRT reliability of summarized global network metrics (a) and metric-related differences in reliability (b). Areas under curves
(AUCs) of each metrics were used to provide threshold-independent reliability estimation. Different metrics showed variable levels of reliability. Several of them were moderately reliable (e.g., lambda for S-AAL-based networks). Subsequent statistical analysis revealed significant differences in
TRT reliability among the 12 global network metrics for S-AAL- but not for F-DOS-based networks. ICC values less than 0.25 were mapped to a single
color of dark blue as well dark red color for ICC values greater than 0.75, respectively in (a). Network (+/-), networks constructed using absolute both
positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis;
Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from
Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g006 Figure 6. TRT reliability of summarized global network metrics (a) and metric-related differences in reliability (b). Areas under curves
(AUCs) of each metrics were used to provide threshold-independent reliability estimation. Different metrics showed variable levels of reliability. Several of them were moderately reliable (e.g., lambda for S-AAL-based networks). Subsequent statistical analysis revealed significant differences in
TRT reliability among the 12 global network metrics for S-AAL- but not for F-DOS-based networks. ICC values less than 0.25 were mapped to a single
color of dark blue as well dark red color for ICC values greater than 0.75, respectively in (a). Network (+/-), networks constructed using absolute both
positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis;
Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from
Dosenbach et al. (2006, 2010). doi:10 1371/journal pone 0021976 g006 Figure 6. TRT reliability of summarized global network metrics (a) and metric-related differences in reliability (b). Areas under curves
(AUCs) of each metrics were used to provide threshold-independent reliability estimation. Different metrics showed variable levels of reliability. Several of them were moderately reliable (e.g., lambda for S-AAL-based networks). Subsequent statistical analysis revealed significant differences in
TRT reliability among the 12 global network metrics for S-AAL- but not for F-DOS-based networks. ICC values less than 0.25 were mapped to a single
color of dark blue as well dark red color for ICC values greater than 0.75, respectively in (a). Network (+/-), networks constructed using absolute both
positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis;
Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from
Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g006 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 8 Reliability of Brain Functional Networks transform) for each of the three TRT scans. Initial visual
inspection suggested that mean RSFC matrices showed highly
similar spatial patterns between different time points (Fig. 1a). Further
quantitative
spatial
correlation
analysis
(Pearson
correlation) confirmed the visual inspection, as revealed by high
correlations in the mean correlation values between each pair
among the three scans (Fig. 1b, scan1 vs. scan2: r = 0.961,
p,102300; scan1 vs. scan3: r = 0.962, p,102300; scan2 vs. scan3:
r = 0.966, p,102300). the criteria of [50,51], with an ICC value from 0 to 0.25 indicating
poor; 0.25 to 0.4 indicating low; 0.4 to 0.6 indicating fair; 0.6 to
0.75 indicating good and 0.75 to 1.0 indicating excellent
reliability. Since the network construction was done over a
continuous range of sparsity threshold, ICC is a function of the
threshold. To provide a threshold-independent reliability assess-
ment, we also calculated the area under curve (AUC, i.e., the
integral) for each network metric [52] that was used to compute a
single ICC scalar for each network measure. Simulation analysis These findings indicate that reliability of functional
connectivity was partly determined by their strength, whereas
functional connectivity strength had limited predictive ability to
their reliability since the small amount of variance in the
functional connectivity reliability explained by their strength
(R2,3%). Finally, we compared
the consistency between ICC-based reliability and Pearson
correlation coefficient-based similarity analysis (across subjects)
for network metrics between scans, which was restricted to S-AAL-
based networks. Reliability of RSFC. ICC-based TRT reliability analysis on
individual functional connections demonstrated an approximate
normal distribution of the ICC values for all 4005 (i.e., 90689/2)
connections with a mean around 0.25 for both short-term and
long-term scans (Fig. 2a). In terms of the category used in the
present study, 1203 (,30.0%) functional connections exhibited
fair to excellent reliability for short-term scans (fair: 1006,
,25.1%; good: 191, ,4.8%; excellent: 6, ,0.2%) and 914
connections (,22.8%) for long-term scans (fair: 796, ,19.9%;
good: 114, ,2.9%; excellent: 4, ,0.1%). The majority of RSFC
(up to 70% for both short- and long-term scans) showed low or
poor reliability. Additionally, a significantly positive correlation
(Pearson correlation, r = 0.266, p,10264) was found in the ICC
values across connections between short-term and long-term scans
(Fig 1c) Simulation analysis To investigate the effects of numerical changes in RSFC on
network metric reliability, we performed simulation analyses as
follows: individual functional connectivity matrices based on S-
AAL were calculated using dataset of scan1 and their correspond-
ing network metrics (both global and nodal metrics) were used as
reference values. Then, for each correlation matrix, different levels
of independent Gaussian noise were added and all network metrics
were recomputed. The added Gaussian noise were zero mean and
the variances varied across six equally spaced levels corresponding
to 8.3%, 16.7%, 25.0%, 33.3%, 41.7% and 50.0% of actual
functional connectivity variances for each subject. This procedure
assures the same proportion of noise added to each correlation
matrix. Of note, the procedure of noise addition was performed 5
times. Therefore, 25 (subjects) | 6 (noise levels) | 5 (random
times) = 750 functional connectivity matrices were simulated in
total. Finally, the TRT reliability of each metric was calculated
between the reference values and those obtained from simulated
functional networks under each level of noise and then averaged
across 5 rounds of noise addition. (
g
)
Relationship between connectivity and reliability. To
explore the relationship between connectivity strength and
reliability, linearly fitted lines were obtained separately for
positive
connections
and
negative
connections
with
their
corresponding ICC values. We found significantly positive
correlations (Pearson correlation) between positive connections
and their ICC values for both short-term (r = 0.135, p,1027) and
long-term (r = 0.145, p,1028) scans (Fig. 3a). No significant
correlations were found between negative correlations and their
ICC values (p.0.3 for both short-term and long-term scans)
(Fig. 3a). These findings indicate that reliability of functional
connectivity was partly determined by their strength, whereas
functional connectivity strength had limited predictive ability to
their reliability since the small amount of variance in the
functional connectivity reliability explained by their strength
(R2,3%). Relationship between connectivity and reliability. To
explore the relationship between connectivity strength and
reliability, linearly fitted lines were obtained separately for
positive
connections
and
negative
connections
with
their
corresponding ICC values. We found significantly positive
correlations (Pearson correlation) between positive connections
and their ICC values for both short-term (r = 0.135, p,1027) and
long-term (r = 0.145, p,1028) scans (Fig. 3a). No significant
correlations were found between negative correlations and their
ICC values (p.0.3 for both short-term and long-term scans)
(Fig. 3a). TRT reliability of RSFC: S-AAL TRT reliability of RSFC: S-AAL Consistency of overall RSFC patterns. The mean RSFC
matrices across subjects were calculated (after Fisher’s r-to-z Table 3. Summary of the main findings in the present study. Factors effecting network metric reliability
Time interval
Network type
Network membership
S-AAL
Global metrics
Long.Short (Binarized)
N.S. Network (+).Network (+/-)
Nodal metrics
N.S. N.S. N.S. S-HOA
Global metrics
N.S. Binarized.Weighted
N.S. Nodal metrics
N.S. N.S. N.S. F-DOS
Global metricsa
N.S. N.S. N.S. Nodal metrics
N.S. N.S. N.S. S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; S-HOA, structural ROIs from Harvard-Oxford atlas; F-DOS, functional ROIs from ref (40); Network (+/-),
networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized
network analysis; Weighted, weighted network analysis; N.S., non-significant. aThere were no significant differences in reliability among global network metrics for F-DOS based networks while nodal network metrics for F-DOS and both global and
nodal metrics for S-ALL and S-HOA based networks were significantly different. doi:10.1371/journal.pone.0021976.t003 Table 3. Summary of the main findings in the present study. Table 3. Summary of the main findings in the present study. Factors effecting network metric reliability S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; S-HOA, structural ROIs from Harvard-Oxford atlas; F-DOS, functional ROIs from ref (40); Network (+/-),
networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized
network analysis; Weighted, weighted network analysis; N.S., non-significant. aThere were no significant differences in reliability among global network metrics for F-DOS based networks while nodal network metrics for F-DOS and both global and
nodal metrics for S-ALL and S-HOA based networks were significantly different. doi:10.1371/journal.pone.0021976.t003 S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; S-HOA, structural ROIs from Harvard-Oxford atlas; F-DOS, functional ROIs from ref (40); Network (+/-),
networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized
network analysis; Weighted, weighted network analysis; N.S., non-significant. aThere were no significant differences in reliability among global network metrics for F-DOS based networks while nodal network metrics for F-DOS and both global and
nodal metrics for S-ALL and S-HOA based networks were significantly different. TRT reliability of network metrics: S-AAL TRT reliability of network metrics: S AAL
Reliability of global network metrics. In the present
study, individual networks were constructed at the same sparsity
level
by
applying
subject-specific
correlation
thresholds
to
individual correlation matrices (see Fig. S4 for the corresponding
correlation thresholds under each sparsity level). Sparsity threshold
ensures all resultant networks to have comparable topological
structures of the same number of edges. Figure 5 shows the TRT
reliability of 12 global network metrics over the whole sparisty
range. Generally, most global network metrics exhibited poor to
low reliability, irrespective of the factors of TI, NT and NM. For
example, clustering coefficient Cp was found to uniformly exhibit
poor reliability (ICC,0.25) under all conditions. Nonetheless, we
noted that some global metrics (e.g., lambdal and assortativity r)
exhibited modest long-term reliability when the networks were
sparsely connected (sparsity,10%). Interestingly, we found that
global network reliability appeared to depend on the factors of TI
and NM but relatively insensitive to NT by qualitatively visual
inspection. Specifically, long-term scans seemed to be associated
with better reliability in compared with short-term scans and the
exclusion of negative correlations enhanced network reliability
(Fig. 5). These were reflected in both increased ICC values and the
broadened threshold range of high ICC. Finally, a threshold-
independent reliability scalar was obtained for each global network
metric by using the AUC. Again, several specific global metrics
(e.g., lambdal) demonstrated moderate long-term reliability under
certain analytical schemes (Fig. 6a, left). Of note, we found that Relationship between connectivity and reliabiflity. Con-
sistent with S-AAL, positive correlations were found between
positive RSFC and their reliability for the S-HOA-based corre-
lations (short-term: r = 0.166, p,10-17; long-term: r = 0.148,
p,10213), indicating limited determination of functional con-
fnectivity strength on their reliability (R2,3%). Additionally, a
negative correlation was demonstrated between negative corre-
lations and their reliability for long-term scans (r = 20.033,
p = 0.048) (Fig. S3). TRT reliability of RSFC: S-AAL doi:10.1371/journal.pone.0021976.t003 S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; S-HOA, structural ROIs from Harvard-Oxford atlas; F-DOS, functional ROIs from ref (40); Network (+/-),
networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized
network analysis; Weighted, weighted network analysis; N.S., non-significant. aThere were no significant differences in reliability among global network metrics for F-DOS based networks while nodal network metrics for F-DOS and both global and
nodal metrics for S-ALL and S-HOA based networks were significantly different. doi:10.1371/journal.pone.0021976.t003 PLoS ONE | www.plosone.org 9 Reliability of Brain Functional Networks Figure 7. TRT reliability of nodal metrics for S-AAL-based networks. Nodal reliability varied across nodal attributes and spatial locations. The
full names of region’s abbreviations were listed as in Table S1. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red
color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive and negative correlations; Figure 7. TRT reliability of nodal metrics for S-AAL-based networks. Nodal reliability varied across nodal attributes and spatial locations. The
full names of region’s abbreviations were listed as in Table S1. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red
color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive and negative correlations; July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 10 Reliability of Brain Functional Networks Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT,
test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. doi:10 1371/journal pone 0021976 g007 Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT,
test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. doi:10.1371/journal.pone.0021976.g007 TRT reliability of RSFC: S-HOA excellent reliability. Of note, those reliable connections were
mainly related with ROIs designated as default mode network
according to previous study [40]. In addition, short-term reliability
was found to positively correlate with long-term reliability across
all connections (Fig. 4c, Pearson correlation, r = 0.337, p,10-300). excellent reliability. Of note, those reliable connections were
mainly related with ROIs designated as default mode network
according to previous study [40]. In addition, short-term reliability
was found to positively correlate with long-term reliability across
all connections (Fig. 4c, Pearson correlation, r = 0.337, p,10-300). Consistency of overall RSFC patterns. The mean S-HOA-
based RSFC matrices across subjects also showed highly similar
spatial patterns revealed by visual inspection (Fig. S2a) and
quantitative spatial correlation analyses (Fig. S2b, r.0.95 between
any two scans). Relationship between connectivity and reliability. In the
case of functional ROIs based RSFC matrices, functional
connectivity strength explained relatively more in comparison
with structural ROIs based matrices but still low variance
(R2,8%) in connectivity reliability (positive correlations and
their reliability: r = 0.279, p,10-86 for short-term and r = 0.273,
p,10-83 for long-term scans; negative correlations and their
reliability: r = 20.098, p,10217 for short-term and r = 20.097,
p,10217 for long-term scans) (Fig. 3b). Reliability of RSFC. Similar to S-AAL, approximate normal
distributions were also found for the reliability of S-HOA-based
RSFC which had comparable mean (, 0.25) (Fig. 2b). Also
consistent
with
S-AAL,
although
there
were
quite
a
few
connections showing fair to good to excellent reliability (1874,
,30.1% for short-term and 1356, ,21.8% for long-term scans),
most connections were poorly reliable (4342, ,69.9% for short-
term and 4860, ,78.2% for long-term scans). Finally, short-term
reliability was found to positively correlate with long-term
reliability across connections (Fig. S2c, Pearson correlation,
r = 0.307, p,102135). TRT reliability of RSFC: F-DOS Furthermore, TI (F(1,11) = 8.176, p = 0.016) and NM (F(1,11) =
4.492, p = 0.058) showed significant or marginally significant
main effects on global network reliability, respectively. In addition,
a significant interaction was observed between TI and NT
(F(1,11) = 5.317 , p = 0.042). NT and other interactions were not
significant (p.0.05). Further post-hoc comparisons (paired t-tests)
revealed that long-term scans outperformed short-term scans only assortativity rshowed moderated both short-term and long-term
reliability for networks of positive correlations. Beyond the descriptive results mentioned above, we further
performed statistical analyses to test the differences in reliability
among 12 global metrics (one-way repeated-measure ANOVA)
and the effects of TI, NM and NT on the reliability of global
network metrics (three-factor repeated-measure ANOVA). Those
AUC-based ICC values were used for the statistical analyses. The
results
showed
that
TRT
reliability
differed
significantly Figure 9. Nodal TRT reliability of degree and its relationship with nodal degree centrality for S-AAL-based networks. (a) Nodal TRT
reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects
of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and
factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the
relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional
size. Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic
Labeling atlas; k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10.1371/journal.pone.0021976.g009 Figure 9. Nodal TRT reliability of degree and its relationship with nodal degree centrality for S-AAL-based networks. (a) Nodal TRT
reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects
of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and
factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the
relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional
size. TRT reliability of RSFC: F-DOS Consistency
of
overall
RSFC
patterns. Relative
to
structural ROIs-based RSFC matrices (both S-AAL and S-
HOA),
the
similarity
in
the
spatial
patterns
across
scans
decreased for the mean RSFC matrices derived on the basis of
160 functional ROIs but still remained high (Scan1 vs. Scan2:
r = 0.896, p,102300; Scan1 vs. Scan3: r = 0.915, p,102300;
Scan2 vs. Scan3: r = 0.902, p,102300) (Fig. 4a and b). Reliability of RSFC. Normal distributions were also found
for TRT reliability of functional ROIs-based RSFC, however
lower mean ICC values (,0.20) were obtained in this case in
comparison with structural ROIs-based RSFC (,0.25) (Fig. 2c). Moreover, higher percentage of connections (up to ,80.0%)
showed poor and low reliability for both short-term and long-term
scanning procedure, with ,20.0% showing fair to good to Figure 8. Boxplot of mean nodal TRT reliability for S-AAL- (a) and F-DOS- (b) based networks. Significant differences were found in the
mean nodal reliability among the six nodal metrics examined with nodal degree showing the highest ICC values and least variances for both ROIs
sets. TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g008 Figure 8. Boxplot of mean nodal TRT reliability for S-AAL- (a) and F-DOS- (b) based networks. Significant differences were found in the
mean nodal reliability among the six nodal metrics examined with nodal degree showing the highest ICC values and least variances for both ROIs
sets. TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g008 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 11 Reliability of Brain Functional Networks (F(11,77) = 3.434, p = 0.001) among 12 global network metrics
with lambda l showing the highest reliability (Fig. 6b, left). Furthermore, TI (F(1,11) = 8.176, p = 0.016) and NM (F(1,11) =
4.492, p = 0.058) showed significant or marginally significant
main effects on global network reliability, respectively. In addition,
a significant interaction was observed between TI and NT
(F(1,11) = 5.317 , p = 0.042). NT and other interactions were not
significant (p.0.05). Further post-hoc comparisons (paired t-tests)
revealed that long-term scans outperformed short-term scans only (F(11,77) = 3.434, p = 0.001) among 12 global network metrics
with lambda l showing the highest reliability (Fig. 6b, left). Reliability of Brain Functional Networks Reliability of Brain Functional Networks for binarized networks (t(23) = 5.100, p,1024) but not for
weighted networks (t(23) = 1.333, p = 0.196) and excluding nega-
tive correlations increased the reliability (t(47) = 3.228, p = 0.002)
of global network metrics. See Table 3 for the summary of all
statistical results. for binarized networks (t(23) = 5.100, p,1024) but not for
weighted networks (t(23) = 1.333, p = 0.196) and excluding nega-
tive correlations increased the reliability (t(47) = 3.228, p = 0.002)
of global network metrics. See Table 3 for the summary of all
statistical results. mapped nodal reliability of degree of all regions after averaging
over factors of TI, NM and NT (Fig. 9a). This was because nodal
degree showed higher reliability and less variance as compared to
other nodal metrics and was robust to TI and NM as well as NT. As shown in Figure 9a, some association and limbic/paralimbic
cortex regions [53] exhibited fair reliability that were predomi-
nately located in bilateral parietal and occipital lobes, such as
association cortex regions of the left angular gyrus (ANG), right
paracentral lobule (PCL), right precuneus (PCUN), bilateral
supramarginal gyrus (SMG), bilateral dorsolateral superior frontal
gyrus (SFGdor), right medial superior frontal gyrus (SFGmed) and
left superior occipital gyrus (SOG), and limbic/paralimbic regions
of the bilateral hippocampus (HIP) and the left posterior cingulate
gyrus. In addition, one primary cortex region of the left calcarine
fissure (CAL) was also found to be fairly reliable. To test whether
or not nodal reliability was related with nodal centrality, we also
mapped the mean nodal degree over TI, NM and NT (Fig. 9b)
and found visually different patterns between nodal degree and
nodal reliability. The most reliable regions located on the posterior
while the most connected regions on the anterior portions of the
brain. Further quantitative correlation analysis revealed that only
tiny variance (R2,7%) in nodal reliability could be explained by
nodal degree centrality in both cases of with (r = 0.255, p = 0.015,
Fig. 9c) and without (r = 0.263, p = 0.012, Fig. 9d) correction for
regional nodal size. To test whether there exist a relationship
between spatial location and nodal reliability, we compared nodal
degree reliability between anterior (y.0) and posterior (y,0)
regions. The results revealed that posterior regions were more Reliability of local nodal metrics. Nodal reliability was
estimated based on AUCs. TRT reliability of RSFC: F-DOS Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic
Labeling atlas; k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10.1371/journal.pone.0021976.g009 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 12 Reliability of Brain Functional Networks We found that nodal reliability showed:
(1) unconspicuous differences associated with factors of TI, NM
and NT; (2) different patterns across nodal metrics; and (3) a
spatially heterogeneous distribution over the whole brain (Fig. 7). First, nodal reliability patterns did not show remarkable
differences associated with the factors of TI, NM and NT by
visual inspection. To test whether or not there exist differences in
the TRT reliability associated with these factors, three-factor
repeated-measure ANOVA was further performed on the mean
ICC values over all nodes. Results revealed that none of these
three factors had significant main effects or interactions on the
mean nodal reliability (p.0.05) (Table 3). Second, nodal reliability exhibited variable patterns across
nodal attributes under each combination of the three factors. Further one-factor repeated-measure ANOVA on the mean nodal
reliability over regions supported this finding that there was
significant (F(5,35) = 6.578, p = 0.0002) differences among the six
nodal metrics examined, with the highest ICC values and least
variance for nodal degree (Fig. 8a). Finally, nodal reliability distributed non-uniformly over the
brain, an observation irrespective of nodal metrics and factors of
TI, NM and NT. To highlight those reliable regions, we selectively Figure 10. The similarity between inter-scan ICC-based reliability and inter-scan Pearson correlation coefficients for S-AAL-based
networks. The reliability and correlation analyses revealed highly consistent results (r.0.9 under most conditions), ruling out the possibility of linear
scaling biases of network metrics across test and retest scans that will lead to low TRT reliability. doi:10.1371/journal.pone.0021976.g010 Figure 10. The similarity between inter-scan ICC-based reliability and inter-scan Pearson correlation coefficients for S-AAL-based
networks. The reliability and correlation analyses revealed highly consistent results (r.0.9 under most conditions), ruling out the possibility of linear
scaling biases of network metrics across test and retest scans that will lead to low TRT reliability. doi:10.1371/journal.pone.0021976.g010 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 13 13 Reliability of Brain Functional Networks reliable than anterior regions even if nodal mean functional
connectivity differences were corrected (t(87) = 2.801, p = 0.006). In addition, we also found dramatically different patterns across
nodal metrics even for those most reliable regions except for the
right PCL (Fig. S5a). 0.312, p = 0.601, repeated two-way ANOVA) in the resistance to
noise between binarized and weighted network analyses (Fig. Reliability of Brain Functional Networks 12);
3) there were no differences in numerical stability against noise in
functional connectivity (p.0.05 under each noise level) between
the first-order and second-order network metrics (Table 2); 4)
nodal network metrics were more numerically reliable than global
network against noise in functional connectivity (p,1023 under
each noise level). Of note, although sensitive to functional
connectivity noise, the degree varied dramatically among global
metrics. For instance, small-world parameters and network
efficiency were extremely sensitive to even little noise in func-
tional connectivity while assortativity, hierarchy, synchronization
and modularity were relatively resistant to noise (Fig. 11). Consistency between ICC-based reliability analysis and
Pearson correlation analysis. To test the possibility of linear
scaling biases across test and retest scans which may result in low
TRT reliability, we calculated the inter-scan Pearson correlation
coefficient for each global network metric (AUC) across subjects
for both short-term and long-term scans. Further scatter plots
between ICC values and Pearson correlation coefficients revealed
highly correlated patterns (r.0.9 under most conditions) (Fig. 10),
suggesting consistent results revealed by the two measures. TRT reliability of network metrics: S-HOA Simulation results. By simulating functional connectivity
matrices with different levels of noise, we found that: 1) for global
network metrics, the TRT reliability was sensitive (F(5,55) =
23.303, p,10-11, repeated two-way ANOVA) to disturbances in
functional connectivity values and weighted network analysis
generated numerically more (F(1,11) = 5.183, p = 0.044, repeated
two-way ANOVA) reliable results than binarized network analysis
(Fig. 11); 2) for nodal network metrics, although sensitive to the
levels of noise (F(5,25) = 7.762, p,1023, repeated two-way
ANOVA), they were highly resistant to numerical changes in
functional connectivity and there were no differences (F(1,5) = Reliability of global network metrics. Analogous to results
from S-AAL-based networks, S-HOA-based networks also showed
overall low (Fig. S6a) but metric- (Fig. S6b) and threshold- (Fig. S7)
sensitive reliability. However, unlike the finding of modest long-
term reliability of multiple global metrics for S-AAL-based
networks (Fig. 5 and Fig. 6a, left), S-HOA-based networks were
mainly related with moderate short-term reliability in multiple
global metrics (except for lambda) (Fig. S6a and Fig. S7). Of note,
synchronization S was found to repeatedly show overall moderate
reliability (Fig. S6a). Subsequent statistical comparisons revealed Figure 11. TRT reliability of global network metrics as a function of noise in RSFC for S-AAL-based networks. Global network metrics
were sensitive to disturbances of RSFC and weighted network analysis generated numerically more stable results in comparison with binarized
network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle) network
analysis, respectively. Of note, the sensitivity varied dramatically among metrics. Small-world parameters and network efficiency were extremely
sensitive to even little noise in functional connectivity while assortativity, hierarchy, synchronization and modularity were relatively resistant to noise. TRT, test-retest; RSFC, resting-state functional connectivity. doi:10.1371/journal.pone.0021976.g011 Figure 11. TRT reliability of global network metrics as a function of noise in RSFC for S-AAL-based networks. Global network metrics
were sensitive to disturbances of RSFC and weighted network analysis generated numerically more stable results in comparison with binarized
network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle) network
analysis, respectively. Of note, the sensitivity varied dramatically among metrics. Small-world parameters and network efficiency were extremely
sensitive to even little noise in functional connectivity while assortativity, hierarchy, synchronization and modularity were relatively resistant to noise. TRT, test-retest; RSFC, resting-state functional connectivity. TRT reliability of network metrics: S-HOA doi:10.1371/journal.pone.0021976.g011 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 14 Reliability of Brain Functional Networks Figure 12. TRT reliability of nodal network metrics as a function of noise in RSFC for S-AAL-based networks. Nodal network metrics
were sensitive to disturbances of RSFC and no differences were observed in the resistance to noise in functional connectivity between binarized and
weighted network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle)
network analysis, respectively. Of note, although sensitive, nodal network metrics showed strong tolerance of disturbances in RSFC. TRT, test-retest;
RSFC, resting-state functional connectivity. doi:10.1371/journal.pone.0021976.g012 Figure 12. TRT reliability of nodal network metrics as a function of noise in RSFC for S-AAL-based networks. Nodal network metrics
were sensitive to disturbances of RSFC and no differences were observed in the resistance to noise in functional connectivity between binarized and
weighted network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle)
network analysis, respectively. Of note, although sensitive, nodal network metrics showed strong tolerance of disturbances in RSFC. TRT, test-retest;
RSFC, resting-state functional connectivity. doi:10.1371/journal.pone.0021976.g012 Figure 12. TRT reliability of nodal network metrics as a function of noise in RSFC for S-AAL-based networks. Nodal network metrics
were sensitive to disturbances of RSFC and no differences were observed in the resistance to noise in functional connectivity between binarized and
weighted network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle)
network analysis, respectively. Of note, although sensitive, nodal network metrics showed strong tolerance of disturbances in RSFC. TRT, test-retest;
RSFC, resting-state functional connectivity. doi:10.1371/journal.pone.0021976.g012 that TRT reliability of global network metrics were modulated by
NT factor (F(1,11) = 6.819, p = 0.024) with higher reliability
observed for binarized networks (t(47) = 2.248, p = 0.029, paired
t-test) (Table 3). characteristic path length Lp, normalized clustering coefficient c,
normalized characteristic path length l and small-worldness s)
were fairly reliable (predominantly for long-term reliability) for
positive networks. The threshold-independent reliability was
presented in the right panel of Figure 6a. Subsequent statistical
analyses revealed that, in contrast with the measure-related
differences in global network reliability observed for structural
ROIs based-networks (Fig. 6b, left and Fig. S6b), there was no
significant differences (F(11,77) = 1.298, p = 0.242) among global
metrics (Fig. TRT reliability of network metrics: S-HOA 6b, right) for functional ROIs-based networks. Furthermore, unlike the sensitivity of global network reliability
to experimental factor of TI and graph-based analytical strategies
of NM and NT for structural ROIs-based networks, reliability of
functional ROIs-based networks was robust against these factors
(p.0.05) (Table 3). Reliability of local nodal metrics. Nodal reliability of S-
HOA-based networks (Fig. S8) exhibited the same patterns as
those for S-AAL-based networks of 1) factors independent (p.0.05
for all the factors of TI, NM and NT as well as all possible
interactions)
(Table
3),
2)
metric-sensitive
(F(5,35) = 12.098,
p,1026, degree was the most reliable and least variable) (Fig. S9), and 3) spatial heterogeneous distribution over the brain (Fig. S10a). The most reliable regions were also mainly unimodal and
heteromodal association cortex regions and limbic/paralimbic
regions of temporal and parietal lobes that were not replicated by
other nodal metrics (Fig. S5b). Also, nodal centrality (Fig. S10b)
showed no significant relationship (R2,2%) with nodal reliability
(Fig. S10c and d). Reliability of local nodal metrics. Figure 14 delineated the
nodal
reliability
for
functional
ROIs-based
networks. No
significant (p.0.05) effects were observed for TI, NM and NT
on mean nodal reliability (Table 3), consistent with findings from
structural ROIs-based networks (both S-AAL and S-HOA). Also
analogous to findings of structural ROIs-based networks, nodal
degree was found to show the highest reliability and least variance
in compared with others (F(5,35) = 3.041, p = 0.022) (Fig. 8b). After averaged over factors of TI, NM and NT, mean nodal TRT reliability of network metrics: F-DOS Reliability of global network metrics. In compared with
structural ROIs-based networks, functional ROIs-based networks
showed fair reliability in more global metrics over wider threshold
range, especially for networks of positive correlations (Fig. 13). For
example,
small-world
parameters
(clustering
coefficient
Cp, PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 15 Reliability of Brain Functional Networks Figure 13. TRT reliability of global network metrics as a function of sparsity threshold for F-DOS-based networks. ICC values less than
0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Multiple network metrics showed
modest reliability in certain threshold range. Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+),
networks constructed using only positive correlations; Binarized, binarized network anlysis; Weighted, weighted network analysis; TRT: test-retest; F-
DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g013 Figure 13. TRT reliability of global network metrics as a function of sparsity threshold for F-DOS-based networks. ICC values less than
0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Multiple network metrics showed
modest reliability in certain threshold range. Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+),
networks constructed using only positive correlations; Binarized, binarized network anlysis; Weighted, weighted network analysis; TRT: test-retest; F-
DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g013 degree reliability showed that there were quite a few reliable
regions distributed in bilateral temporal, parietal and the right
frontal lobes (Fig. 15a). The nodal centrality pattern (Fig. 15b) can
only explain a small fraction (R2,6%) of nodal reliability pattern
(Fig. 15c and d). We also noted that the most reliable regions were
predominantly located in the right hemisphere (Fig. 15a) and
varied across nodal metrics (Fig. S5c). of
R-fMRI
based
brain
networks. Our
findings
suggested
continued usage of graph theoretical approaches to explore brain
networks and had potential relevance for guiding graph analytical
schemes for R-fMRI to achieve reliable results. For global network metrics, we observed overall low TRT
reliability. This observation was consistent with results reported in
a previous MEG study [12]. Indeed, compared with task
engagement, Deuker et al. (2009) found that resting state was
related with significantly lower reliability of global network
metrics. TRT reliability of network metrics: F-DOS This may be related to variable mental states of
participants across scans which induce variations in RSFC
[19,20,21,22,23,24,25]. Such discrepancies in RSFC especially
in shortcuts or inter-module/component connections [54] may
further affect the topological organization of the overall connec-
tivity network [28]. To test the possibility, we examined the
differences in RSFC strength between scans by paired t-tests. The
results revealed that no connections showed significant differences
(p,0.05, corrected) across scans, implying the temporal stability of
RSFC [27,29,31]. Despite of non-significant differences, our
simulation analysese indicated that global network metrics were
extremely sensitive to numerical changes in RSFC, especially for
small-world parameters and network efficiency. Another possible
origin of low TRT reliability is due to low between-subject
variance or low ability of global network metrics to differentiate
subjects. With that said, the low TRT reliability of global metrics
may suggest high consistency of global properties of intrinsic brain
networks across subjects. Finally, the noise resulting from MRI PLoS ONE | www.plosone.org Discussion Structural ROIs were obtained
mainly in terms of anatomical features of sulcal pattern (S-AAL)
[37] or standard anatomical boundaries (S-HOA) [38,39] whereas
functional ROIs were derived from previous meta-analyses of
fMRI activation studies which carried specific functional informa-
tion [40,41]. Furthermore, even for structural ROIs based
networks, the modulations of TI, NM and NT differed across
parcellations. Previous studies have demonstrated that network
properties were sensitive to nodal definition based on parcellation
strategies [32,36] and spatial scales [33,34,35]. Nevertheless, it’s
hard to conclude which approach or which parcellation is better
since all of them are valid and important approaches to uncover
brain
connectivity
architecture
from
different
perspectives
[40,43,61,62]. Here, our results provide references for studying
intrinsic brain networks, for example, binarized networks should
be preferred for S-HOA-based intrinsic brain networks according
to our results. data acquisition and coregistration inaccuracy may also influence
network reliability, which should be elucidated in the future work. network reliability, which should be elucidated in the future work. Despite of the overall low TRT reliability, some global metrics
showed relatively high reliability. For example, lambda showed
moderate long-term reliability for structural both S-AAL and S-
HOA-based networks. This may be due to the correction of
absolute characteristic path length to referenced random networks
which compensates for underlying differences of baseline net-
works. Further statistical analyses revealed significant differences
in TRT reliability among global metrics, suggesting an obvious
heterogeneity among different global network metrics in reliably
capturing intrinsic brain architecture. Moreover, the profiles of
global network reliability presented threshold sensitive patterns
indicating the importance of threshold selection for reliable results. These findings raise the question of how to determine threshold for
brain network studies. A compromise strategy is to investigate
brain networks over a continuum threshold range under the
circumstance that no sufficient knowledge exists for prior threshold
selection. Several factors were found to significantly affect the TRT
reliability of global network metrics. First, inclusion of negative
functional connectivity in brain networks tended to decrease TRT
reliability of global network properties. Previous evidence has
manifested that negative correlations showed greater population
and state related variance in the spatial maps [55] and lower TRT
reliability [27] relative to positive correlations. Consistent with
these findings, our results suggest that negative connectivity should
be treated with cautions for resting-state brain network studies,
which may reduce the TRT reliability. Discussion In the present study, we examined the test-retest reliability of
topological metrics of intrinsic connectivity networks derived from
human brain R-fMRI data. First, we replicated previous findings
that RSFC exhibited modest to high test-retest reliability [27]. Further reliability analyses of network metrics highlighted several
main findings: 1) that global network metrics showed overall poor
to low but threshold-sensitive reliability; 2) that local nodal metrics
were fairly reliable for association and limbic/paralimbic cortex
regions; 3) that reliability of network metrics (both global and local)
differed significantly among the measures examined; 4) that
reliability of global network metrics depended on multiple
experiment and analytical factors while nodal reliability was
robust to these factors; and 5) that weighted networks (compared
to binarized networks) and nodal (compared to global) network
metrics were numerically more reliable in the face of noise in
functional connectivity. Taken together, we provided a systemat-
ically quantitative TRT reliability evaluation of topological metrics PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 16 Reliability of Brain Functional Networks PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 17 Reliability of Brain Functional Networks Reliability of Brain Functional Networks Figure 14. TRT reliability of nodal metrics for F-DOS-based networks. Nodal reliability varied across nodal attributes and spatial locations. The full names of region’s abbreviations were listed as in Table S3. ICC values less than 0.25 were mapped to a single color of dark blue as well dark
red color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive and negative correlations;
Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT,
test-retest; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g014 indicating a robust finding. Nevertheless, further work is needed
to verify this finding and aid in our understanding of how network
topology interacts with the scanning procedure of time interval. Finally,
TRT
reliability
of
global
network
metrics
was
modulated by strategies of network node definition. Specifically,
reliability of only structural (S-AAL and S-HOA) rather than
functional (F-DOS) ROIs-based networks depended on the factors
of TI, NM and NT. The discrepancy may reflect different
approaches of generating ROIs. Discussion It should be noted that the
emergence of negative connectivity is related with the global signal
regression, a currently controversial step in preprocessing R-fMRI
data [56,57,58,59]. For local nodal metrics, nodal degree showed the highest
reliability and least variance across factors of TI, NM and NT
among the six nodal metrics. Using this metric, we found that
some association cortex and limbic/paralimbic regions exhibited
fair to good TRT reliability for S-AAL and S-HOA derived
networks, such as precuneus, angular gyrus, superior forntal
gurus, paracentral lobule, supramarginal gyrus, anterior cingulate
gyrus, hippocampus and parahippocampal gyrus. Most of these
regions have been identified to serve as structural or functional
hubs/connectors
in
human
brain
networks
[43,44,54,60,
63,64,65,66]. For F-DOS derived networks, more regions were
modestly reliable, predominately located in the right frontal lobe
and bilateral parietal and temporal lobes. Hubs are essential in
supporting the performance of high cognitive functions of the
human brain by integrating specialized brain regions into
coordinated networks. Buckner and colleagues [64] demonstrated
that the topography of human brain cortical hubs is highly similar
across populations and robust against task states, therefore
reflecting a stable property of brain functional architecture. Here, our results indicate that those reliable regions qualitatively
tend to serve as hubs in intrinsic functional brain networks. Nonetheless, our quantitative analysis found that nodal reliability
showed
low
correlations
(although
significant)
with
nodal
centrality (R2,10%), suggesting limited predictive ability of
nodal centrality on reliability. These findings imply that there
may exist other factors affecting nodal reliability, such as the
spatial locations of nodes or regions. Indeed, we found that
posterior regions were more reliable than anterior regions even
after correcting for the differences in functional connectivity
across regions. This may reflect the nature of the brain in which
the neural dynamics of spatially different brain regions are
differently constrained in the resting-state. It would be an Second, binarized networks outperformed weighted networks in
TRT reliability of global network metrics. This finding seemed
counterintuitive. Indeed, weighted networks could characterize
network topology more precisely and detect more subtle network
topological changes than binarized networks due to the consider-
ation of connectivity strength [60]. However, this is not necessary
to mean better reliability for weighted networks since the
possibility that weighted networks may introduce simultaneously
extra noise or overly model individual specific details. All these
may lead to more within-subject variance (i.e., variance across
scans) and thus lower reliability. Discussion (a) Nodal TRT
reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects
of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and
factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the
relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional
size. Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; F-DOS, functional ROIs from Dosenbach et al. (2006,
2010); k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10.1371/journal.pone.0021976.g015
Reliability of Brain Functional Networks Figure 15. Nodal TRT reliability of degree and its relationship with nodal degree centrality for F-DOS-based networks. (a) Nodal TRT
reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects
of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and
factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the
relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional
size. Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; F-DOS, functional ROIs from Dosenbach et al. (2006,
2010); k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10 1371/journal pone 0021976 g015 Figure 15. Nodal TRT reliability of degree and its relationship with nodal degree centrality for F-DOS-based networks. (a) Nodal TRT
reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects
of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and
factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the
relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional
size. Discussion Of note, our simulation results
showed that weighted networks generated numerically more stable
results against noise in functional connectivity in comparison to
binarized networks. This suggests that the observed reliability
derived from actual R-fMRI data were affected by various factors,
not a single factor of numerical changes in functional connectivity. Third, long-term scans showed higher TRT reliability of global
network metrics than short-term scans. This finding was contrast
to previous findings that RSFC exhibited higher TRT reliability
for short-term interval scans [27]. It may reflect the fact that the
average of scan2 and scan3 in the current study can potentially
improve the estimation of long-term reliability, i.e., reduce within-
session noise [29,30]. To test this interpretation, we further
calculated the long-term TRT reliability by using scan1 and scan3
and again found a long-term-larger-than-short-term pattern, Second, binarized networks outperformed weighted networks in
TRT reliability of global network metrics. This finding seemed
counterintuitive. Indeed, weighted networks could characterize
network topology more precisely and detect more subtle network
topological changes than binarized networks due to the consider-
ation of connectivity strength [60]. However, this is not necessary
to mean better reliability for weighted networks since the
possibility that weighted networks may introduce simultaneously
extra noise or overly model individual specific details. All these
may lead to more within-subject variance (i.e., variance across
scans) and thus lower reliability. Of note, our simulation results
showed that weighted networks generated numerically more stable
results against noise in functional connectivity in comparison to
binarized networks. This suggests that the observed reliability
derived from actual R-fMRI data were affected by various factors,
not a single factor of numerical changes in functional connectivity. Third, long-term scans showed higher TRT reliability of global
network metrics than short-term scans. This finding was contrast
to previous findings that RSFC exhibited higher TRT reliability
for short-term interval scans [27]. It may reflect the fact that the
average of scan2 and scan3 in the current study can potentially
improve the estimation of long-term reliability, i.e., reduce within-
session noise [29,30]. To test this interpretation, we further
calculated the long-term TRT reliability by using scan1 and scan3
and again found a long-term-larger-than-short-term pattern, July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 18 Reliability of Brain Functional Networks Figure 15. Nodal TRT reliability of degree and its relationship with nodal degree centrality for F-DOS-based networks. Reliability of Brain Functional Networks Figure S3
Relationship between RSFC and TRT reliability for
S-HOA-based
correlation
matrices. Scatter
plots
of
mean
connectivity strength against corresponding ICC values are
depicted to show the relationship. The trend lines were obtained
by linear least-square fit. Significant (p,0.05) positive correlations
were found between positive RSFC and their corresponding ICC
values for both short-term and long-term scanning. In addition,
significant negative correlations were also found for negative
RSFC with their corresponding ICC values but only for long-term
scanning. These findings suggest higher reliability for stronger
RSFC. Functional connections linking inter-hemisphere homo-
topic regions are highlighted by plus signs (+). RSFC, resting-state
functional connectivity; TRT, test-retest; S-HOA, structural ROIs
from Harvard-Oxford atlas. (DOC) Figure S3
Relationship between RSFC and TRT reliability for
S-HOA-based
correlation
matrices. Scatter
plots
of
mean
connectivity strength against corresponding ICC values are
depicted to show the relationship. The trend lines were obtained
by linear least-square fit. Significant (p,0.05) positive correlations
were found between positive RSFC and their corresponding ICC
values for both short-term and long-term scanning. In addition,
significant negative correlations were also found for negative
RSFC with their corresponding ICC values but only for long-term
scanning. These findings suggest higher reliability for stronger
RSFC. Functional connections linking inter-hemisphere homo-
topic regions are highlighted by plus signs (+). RSFC, resting-state
functional connectivity; TRT, test-retest; S-HOA, structural ROIs
from Harvard-Oxford atlas. (DOC) Figure S4
The absolute correlation thresholds under each
sparsity level for all the three sets of ROIs based networks. The
correlation thresholds decrease with the increase of sparsity and
are comparable across scans and across subjects for each set of
ROIs-based
networks. Of
note,
negative
correlations
were
included. (DOC) In conclusion, we studied the TRT reliability of graph-based
network metrics derived from resting-state fMRI data and the
effects of several factors on the reliability. Based on our findings,
we provide some methodological recommendations for resting-
state fMRI community in dealing with brain connectome studies. First, negative correlations need to be excluded or considered with
cautions
for
S-AAL-based
brain
network
studies. Second,
binarized networks should be preferred for S-HOA-based brain
network studies as compared to weighted networks. Third,
reliability of functional ROIs-based networks was robust against
the three factors of scanning time, network membership and
network type. Finally, nodal metrics (especially nodal degree) could
produce more reliable results and are more resilient to functional
connectivity disturbances, which should be popularized in future
brain network studies. (DOC) Figure S6
TRT reliability of summarized global network
metrics (a) and metric-related differences in reliability (b). The
area under curve (AUC) of each metric was used to provide
threshold-independent reliability estimation. Different metrics
showed variable levels of reliability. Several of them were
moderately reliable (e.g., lambda and synchronization). Subse-
quent statistical analysis revealed significant differences in TRT
reliability among the 12 global network metrics, with lambda
showing relatively high reliability and low variance. ICC values
less than 0.25 were mapped to a single color of dark blue as well
dark red color for ICC values greater than 0.75, respectively in (a). Network (+/-), networks constructed using absolute both positive
and negative correlations; Network (+), networks constructed using
only positive correlations; Binarized, binarized network analysis;
Weighted, weighted network analysis; TRT, test-retest; S-HOA,
structural ROIs from Harvard-Oxford atlas. (DOC) Discussion Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; F-DOS, functional ROIs from Dosenbach et al. (2006,
2010); k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10.1371/journal.pone.0021976.g015 Nodal reliability was found to be robust against the factors of
TI, NM and NT, regardless of different node definition strategies. Simulation analyses revealed that nodal metrics were highly
tolerant of fluctuations in functional connectivity values and were
numerically more stable than global network metrics in the face of
connectivity noise. The reliable and robust features of nodal interesting question for future studies. Additionally, we noted that
the most reliable regions appeared to predominately locate in the
right hemisphere for F-DOS and S-HOA based networks. Hence,
exploring brain functional asymmetry from the perspective of
reliability may provide more insights into the brain’s functional
architecture. interesting question for future studies. Additionally, we noted that
the most reliable regions appeared to predominately locate in the
right hemisphere for F-DOS and S-HOA based networks. Hence,
exploring brain functional asymmetry from the perspective of
reliability may provide more insights into the brain’s functional
architecture. PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 19 Reliability of Brain Functional Networks Reliability of Brain Functional Networks metrics propose local nodal metrics as reliable candidates to reveal
topological organization of intrinsic functional brain networks. Fig. 2). Moreover, a significant (p,0.05) correlation was found in
the ICC matrices between short-term and long-term scans (c). Functional connections linking inter-hemisphere homotopic re-
gions, as highlighted by plus signs (+), showed high connectivity
strength and many of them exhibited high reliability. TRT, test-
retest;
RSFC,
resting-state
functional
connectivity;
S-HOA,
structural ROIs from Harvard-Oxford
atlas. Of note, the
structural ROIs were listed in the order as in Table S2. (DOC) Fig. 2). Moreover, a significant (p,0.05) correlation was found in
the ICC matrices between short-term and long-term scans (c). Functional connections linking inter-hemisphere homotopic re-
gions, as highlighted by plus signs (+), showed high connectivity
strength and many of them exhibited high reliability. TRT, test-
retest;
RSFC,
resting-state
functional
connectivity;
S-HOA,
structural ROIs from Harvard-Oxford
atlas. Of note, the
structural ROIs were listed in the order as in Table S2. (DOC) There are several issues that remained to be addressed in future. First, the reliability analyses of graph-based network metrics were
conducted after several R-fMRI preprocessing steps. To date, how
different preprocessing strategies affect the TRT reliability of
network metrics is rarely investigated. Specifically, in the current
study, RSFC were obtained based on band-pass filtered data
(0.01–0.1 Hz). Previous
R-fMRI
studies
have
demonstrated
frequency specific features for RSFC [67,68,69] and network
topology [43,46,70,71]. Accordingly, exploring the impacts of
different preprocessing steps on TRT reliability, especially the
filtering frequency bands, is an important topic to determine
specific processing schemes for consistent, reliable results. Second,
we limited our examination of TRT reliability to 12 global
network properties and 6 nodal characteristics, which were widely
used to characterize brain network architectures. However, there
are still a lot of other network metrics, such as motif [72] and
vulnerability [73] (for reviews, see [74,75]) whose TRT reliability
need to be evaluated in future. Finally, using R-fMRI, we
examined the TRT reliability of intrinsic functional brain
networks. Previous studies have performed similar analyses of
structural or functional brain networks using DTI, MEG, or fMRI
data
during
resting
state
or
cognitive
task
engagement
[10,11,12,13]. Despite these advances, a systematic reliability
evaluation using multimodal data from the same cohort of
population is warranted to gain more insights into human brain’s
structural and functional architectures. Reliability of Brain Functional Networks Nonetheless, we pointed out that further
work is necessary to standardize the methodological framework on
this burgeoning field. Figure S5
Ranks of reliable regions revealed by nodal degree
over other nodal metrics. (a) S-AAL-based networks; (b), S-HOA-
based networks; (c) F-DOS-based networks. The ranks of those
most reliable regions in terms of nodal degree (regions with
ICC.0.4 in Fig. 9a, Fig. S10a and Fig. 15a) changed dramatically
over nodal metrics for all ROIs sets, indicating inconsistency for
most reliable regions. The full names of region’s abbreviations
were listed as in Table S1, S2 and S3. (DOC) References 1. Sporns O, Tononi G, Kotter R (2005) The human connectome: A structural
description of the human brain. PLoS Comput Biol 1: e42. 1. Sporns O, Tononi G, Kotter R (2005) The human connectome: A structural
description of the human brain. PLoS Comput Biol 1: e42. 15. Fox MD, Raichle ME (2007) Spontaneous fluctuations in brain activity observed
with functional magnetic resonance imaging. Nat Rev Neurosci 8: 700–711. 16. Zhang D, Raichle ME (2010) Disease and the brain’s dark energy. Nat Rev
Neurol 6: 15–28. 2. Biswal BB, Mennes M, Zuo XN, Gohel S, Kelly C, et al. (2010) Toward
discovery science of human brain function. Proc Natl Acad Sci U S A 107:
4734–4739. 17. Wang J, Zuo XN, He Y (2010) Graph-based network analysis of resting-state
functional MRI. Front Syst Neurosci 4: 16. 3. Bullmore E, Sporns O (2009) Complex brain networks: graph theoretical
analysis of structural and functional systems. Nat Rev Neurosci 10: 186–198. 18. Chang C, Glover GH (2010) Time-frequency dynamics of 18. Chang C, Glover GH (2010) Time-frequency dynamics of resting-state
connectivity measured with fMRI. Neuroimage 50: 81–98. 4. He Y, Evans A (2010) Graph theoretical modeling of brain connectivity. Curr
Opin Neurol 23: 341–350. 19. Greicius MD, Kiviniemi V, Tervonen O, Vainionpaa V, Alahuhta S, et al. (2008) Persistent default-mode network connectivity during light sedation. Hum
Brain Mapp 29: 839–847. 5. Guye M, Bettus G, Bartolomei F, Cozzone PJ (2010) Graph theoretical analysis
of structural and functional connectivity MRI in normal and pathological brain
networks. MAGMA. 20. Horovitz SG, Braun AR, Carr WS, Picchioni D, Balkin TJ, et al. (2009)
Decoupling of the brain’s default mode network during deep sleep. Proc Natl
Acad Sci U S A 106: 11376–11381. 6. Stam CJ, Reijneveld JC (2007) Graph theoretical analysis of complex networks
in the brain. Nonlinear Biomed Phys 1: 3. 7. Bullmore ET, Bassett DS (2010) Brain Graphs: Graphical Models of the Human
Brain Connectome. Annu Rev Clin Psychol. 21. Horovitz SG, Fukunaga M, de Zwart JA, van Gelderen P, Fulton SC, et al. (2008) Low frequency BOLD fluctuations during resting wakefulness and light
sleep: a simultaneous EEG-fMRI study. Hum Brain Mapp 29: 671–682. 7. Bullmore ET, Bassett DS (2010) Brain Graphs:
Brain Connectome. Annu Rev Clin Psychol. 8. He Y, Chen Z, Gong G, Evans A (2009) Neuronal networks in Alzheimer’s
disease. Neuroscientist 15: 333–350. 22. Reliability of Brain Functional Networks time interval, network type and network membership. Trend lines
were further obtained by linear least-square fit to reveal the
relationship between nodal degree centrality and their corre-
sponding reliability after with (d) and without (c) correcting for the
effects of regional size. Of note, the full names of region’s
abbreviations were listed as in Table S2. TRT, test-retest; S-HOA,
structural ROIs from Harvard-Oxford atlas; k, nodal degree; A,
anterior; P, posterior; L, left; R, right. (DOC) and negative correlations; Network (+), networks constructed using
only positive correlations; Binarized, binarized network anlysis;
Weighted, weighted network analysis; TRT: test-retest; S-HOA,
structural ROIs from Harvard-Oxford atlas. (DOC) Figure S8
TRT reliability of nodal metrics for S-HOA-based
networks. Nodal reliability varied across nodal attributes and
spatial
locations. Moreover,
removing
negative
correlations
seemed to result in more regions showing higher reliability in
more nodal attributes (predominantly for binarized networks). The
full names of region’s abbreviations were listed as in Table S2. ICC values less than 0.25 were mapped to a single color of dark
blue as well dark red color for ICC values greater than 0.75,
respectively. Network (+/-), networks constructed using absolute
both positive and negative correlations; Network (+), networks
constructed using only positive correlations; Binarized, binarized
network analysis; Weighted, weighted network analysis; TRT, test-
retest; S-HOA, structural ROIs from Harvard-Oxford atlas. (DOC) Table S1
Regions of interest from S-AAL. (DOC) Table S2
Regions of interest from S-HOA. (DOC) Table S3
Regions of interest from F-DOS. (DOC) Table S4
Correlation coefficients between long-term reliability
estimated by scan1 and the average of scan 2 and scan 3 and those
estimated by scan 1 and scan 3 alone. (DOC) Figure S9
Boxplot of mean nodal TRT reliability for S-HOA-
based networks. Significant differences were found in the mean
nodal reliability among the six nodal metrics examined with nodal
degree showing the highest ICC values and least variances. TRT,
test-retest; S-HOA, structural ROIs from Harvard-Oxford atlas. (DOC) Text S1
Mathematical definitions of network metrics. (DOC) Acknowledgments We thank Mr. Jonathan Adelstein for his assistance in language editing. We thank Mr. Jonathan Adelstein for his assistance in language editing. Figure S10
Nodal TRT reliability of degree and its relationship
with nodal degree centrality for S-HOA-based networks. (a) Nodal
TRT reliability was mapped in anatomical space after average
across scanning time interval, network type and network mem-
bership because of no effects of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical
space which was averaged across subjects and factors of scanning Author Contributions Conceived and designed the experiments: YH. Performed the experiments:
MPM. Analyzed the data: JHW XNZ. Contributed reagents/materials/
analysis tools: JHW XNZ SG MPM BBB YH. Wrote the paper: JHW
XNZ YH. Conceived and designed the experiments: YH. Performed the experiments:
MPM. Analyzed the data: JHW XNZ. Contributed reagents/materials/
analysis tools: JHW XNZ SG MPM BBB YH. Wrote the paper: JHW
XNZ YH. Supporting Information Figure S1
Spatial locations of functionally defined ROIs. These
ROIs broadly but not completely cover the cerebral cortex and
cerebellum
without
any
overlap
between
ROIs
and
were
associated with five functions of error-processing, default-mode,
memory, language and sensorimotor. A, anterior; P, posterior; L,
left; R, right. Figure S2
Spatial similarity and TRT reliability patterns of S-
HOA-based RSFC. Mean Pearson correlation matrices (a),
consistency of overall patterns between mean matrices (b) and
TRT
reliability
of
individual
connections
as
well
as
the
relationship between short-term and long-term reliability (c) are
illustrated. The
mean
correlation
matrices
exhibited
high
similarity from both visual inspection (a) and quantitative spatial
correlation analyses (b). Further TRT reliability analyses revealed
many connections exhibiting fair to excellent reliability (c, also see Figure S7
TRT reliability of global network metrics as a
function of sparsity threshold for S-HOA-based networks. ICC
values less than 0.25 were mapped to a single color of dark blue as
well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 20 Reliability of Brain Functional Networks Reliability of Brain Functional Networks Neuron 50: 799–812. 42. Fox MD, Snyder AZ, Vincent JL, Corbetta M, Van Essen DC, et al. (2005) The
human brain is intrinsically organized into dynamic, anticorrelated functional
networks. Proceedings of the National Academy of Sciences of the United States
of America 102: 9673–9678. 66. Chen ZJ, He Y, Rosa-Neto P, Germann J, Evans AC (2008) Revealing Modular
Architecture of Human Brain Structural Networks by Using Cortical Thickness
from MRI. Cereb Cortex 18: 2374–2381. 67. Salvador R, John Suckling, Schwarzbauer C, Bullmore E (2005) Undirected
graphs of frequency-dependent functional connectivity in whole brain networks. Phil Trans R Soc B 360 937–946. 43. Achard S, Salvador R, Whitcher B, Suckling J, Bullmore E (2006) A resilient,
low-frequency, small-world human brain functional network with highly
connected association cortical hubs. J Neurosci 26: 63–72. 68. Salvador R, Martinez A, Pomarol-Clotet E, Gomar J, Vila F, et al. (2008) A
simple view of the brain through a frequency-specific functional connectivity
measure. Neuroimage 39: 279–289. 44. Gong G, He Y, Concha L, Lebel C, Gross DW, et al. (2009) Mapping
Anatomical Connectivity Patterns of Human Cerebral Cortex Using In Vivo
Diffusion Tensor Imaging Tractography. Cereb Cortex 19: 524–536. 69. Salvador R, Suckling J, Schwarzbauer C, Bullmore E (2005) Undirected graphs
of frequency-dependent functional connectivity in whole brain networks. Philos
Trans R Soc Lond B Biol Sci 360: 937–946. 45. He Y, Chen Z, Evans A (2008) Structural Insights into Aberrant Topological
Patterns of Large-Scale Cortical Networks in Alzheimer’s Disease. J Neurosci 28:
4756–4766. 70. Supekar K, Musen M, Menon V (2009) Development of large-scale functional
brain networks in children. PLoS Biol 7: e1000157. 46. Achard S, Bullmore E (2007) Efficiency and cost of economical brain functional
networks. PLoS Comput Biol 3: e17. 71. Supekar K, Menon V, Rubin D, Musen M, Greicius MD (2008) Network
analysis of intrinsic functional brain connectivity in Alzheimer’s disease. PLoS
Comput Biol 4: e1000100. 47. Fair DA, Cohen AL, Power JD, Dosenbach NU, Church JA, et al. (2009)
Functional brain networks develop from a ‘‘local to distributed’’ organization. PLoS Comput Biol 5: e1000381. p
72. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network
motifs: simple building blocks of complex networks. Science 298: 824–827. p
48. Shrout PE, Fleiss JL (1979) Intraclass correlations: uses in assessing rater
reliability. Psychol Bull 86: 420–428. 73. Reliability of Brain Functional Networks 29. Zuo XN, Kelly C, Adelstein JS, Klein DF, Castellanos FX, et al. (2010) Reliable
intrinsic connectivity networks: Test-retest evaluation using ICA and dual
regression approach. NeuroImage 49: 2163–2177. 52. He Y, Dagher A, Chen Z, Charil A, Zijdenbos A, et al. (2009) Impaired small-
world efficiency in structural cortical networks in multiple sclerosis associated
with white matter lesion load. Brain 132: 3366–3379. 53. Mesulam MM (2000) Principles of behavioural and cognitive neurology. New
York: Oxford University Press. xviii540 p. g
pp
g
30. Zuo XN, Di Martino A, Kelly C, Shehzad ZE, Gee DG, et al. (2010) The
oscillating brain: complex and reliable. Neuroimage 49: 1432–1445. y
p
54. He Y, Wang J, Wang L, Chen ZJ, Yan C, et al. (2009) Uncovering intrinsic
modular organization of spontaneous brain activity in humans. PLoS One 4:
e5226. 31. Zuo XN, Kelly C, Di Martino A, Mennes M, Margulies DS, et al. (2010)
Growing together and growing apart: regional and sex differences in the lifespan
developmental trajectories of functional homotopy. J Neurosci 30: 15034–15043. 55. Tian L, Jiang T, Liang M, Li X, He Y, et al. (2007) Stabilities of negative
correlations between blood oxygen level-dependent signals associated with
sensory and motor cortices. Hum Brain Mapp 28: 681–690. p
j
py
32. Wang J, Wang L, Zang Y, Yang H, Tang H, et al. (2009) Parcellation-dependent
small-world brain functional networks: a resting-state fMRI study. Hum Brain
Mapp 30: 1511–1523. sensory and motor cortices. Hum Brain Mapp 28: 681–690. 56. Fox MD, Zhang D, Snyder AZ, Raichle ME (2009) The global signal and
observed anticorrelated resting state brain networks. J Neurophysiol 101:
3270–3283. pp
33. Hayasaka S, Laurienti PJ (2010) Comparison of characteristics between region-
and voxel-based network analyses in resting-state fMRI data. Neuroimage 50:
499–508. 57. Murphy K, Birn RM, Handwerker DA, Jones TB, Bandettini PA (2009) The
impact of global signal regression on resting state correlations: are anti-
correlated networks introduced? Neuroimage 44: 893–905. 34. Zalesky A, Fornito A, Harding IH, Cocchi L, Yucel M, et al. (2010) Whole-brain
anatomical networks: does the choice of nodes matter? Neuroimage 50:
970–983. 58. Weissenbacher A, Kasess C, Gerstl F, Lanzenberger R, Moser E, et al. (2009)
Correlations and anticorrelations in resting-state functional connectivity MRI: a
quantitative comparison of preprocessing strategies. Neuroimage 47:
1408–1416. 35. Reliability of Brain Functional Networks Fornito A, Zalesky A, Bullmore ET (2010) Network scaling effects in graph
analytic studies of human resting-state FMRI data. Front Syst Neurosci 4: 22. 36. Sanabria-Diaz G, Melie-Garcia L, Iturria-Medina Y, Aleman-Gomez Y,
Hernandez-Gonzalez G, et al. (2010) Surface area and cortical thickness
descriptors reveal different attributes of the structural human brain networks. Neuroimage 50: 1497–1510. 59. Birn RM, Diamond JB, Smith MA, Bandettini PA (2006) Separating respiratory-
variation-related fluctuations from neuronal-activity-related fluctuations in
fMRI. Neuroimage 31: 1536–1548. 37. Tzourio-Mazoyer N, Landeau B, Papathanassiou D, Crivello F, Etard O, et al. (2002) Automated anatomical labeling of activations in SPM using a
macroscopic anatomical parcellation of the MNI MRI single-subject brain. Neuroimage 15: 273–289. g
60. Cole MW, Pathak S, Schneider W (2010) Identifying the brain’s most globally
connected regions. Neuroimage 49: 3132–3148. 61. Salvador R, Suckling J, Coleman MR, Pickard JD, Menon D, et al. (2005)
Neurophysiological architecture of functional magnetic resonance images of
human brain. Cereb Cortex 15: 1332–1342. 38. Kennedy DN, Lange N, Makris N, Bates J, Meyer J, et al. (1998) Gyri of the
human neocortex: an MRI-based analysis of volume and variance. Cereb Cortex
8: 372–384. 62. Alexander-Bloch AF, Gogtay N, Meunier D, Birn R, Clasen L, et al. (2010)
Disrupted modularity and local connectivity of brain functional networks in
childhood-onset schizophrenia. Front Syst Neurosci 4: 147. 39. Makris N, Meyer JW, Bates JF, Yeterian EH, Kennedy DN, et al. (1999) MRI-
Based topographic parcellation of human cerebral white matter and nuclei II. Rationale and applications with systematics of cerebral connectivity. Neuro-
image 9: 18–45. 63. Hagmann P, Cammoun L, Gigandet X, Meuli R, Honey CJ, et al. (2008)
Mapping the Structural Core of Human Cerebral Cortex. PLoS Biol 6: e159. 64. Buckner RL, Sepulcre J, Talukdar T, Krienen FM, Liu H, et al. (2009) Cortical
hubs revealed by intrinsic functional connectivity: mapping, assessment of
stability, and relation to Alzheimer’s disease. J Neurosci 29: 1860–1873. g
40. Dosenbach NU, Nardos B, Cohen AL, Fair DA, Power JD, et al. (2010)
Prediction of individual brain maturity using fMRI. Science 329: 1358–1361. 65. Yan C, Gong G, Wang J, Wang D, Liu D, et al. (2010) Sex- and Brain Size-
Related Small-World Structural Cortical Networks in Young Adults: A DTI
Tractography Study. Cereb Cortex. 41. Dosenbach NU, Visscher KM, Palmer ED, Miezin FM, Wenger KK, et al. (2006) A core system for the implementation of task sets. References Martuzzi R, Ramani R, Qiu M, Rajeevan N, Constable RT (2010) Functional
connectivity and alterations in baseline brain state in humans. Neuroimage 49:
823–834. 9. Bassett DS, Bullmore ET (2009) Human brain networks in health and disease. Curr Opin Neurol 22: 340–347. 23. Harrison BJ, Pujol J, Ortiz H, Fornito A, Pantelis C, et al. (2008) Modulation of
brain resting-state networks by sad mood induction. PLoS ONE 3: e1794. 10. Vaessen MJ, Hofman PA, Tijssen HN, Aldenkamp AP, Jansen JF, et al. (2010)
The effect and reproducibility of different clinical DTI gradient sets on small
world brain connectivity measures. Neuroimage 51: 1106–1116. 24. Waites AB, Stanislavsky A, Abbott DF, Jackson GD (2005) Effect of prior
cognitive state on resting state networks measured with functional connectivity. Hum Brain Mapp 24: 59–68. 11. Bassett DS, Brown JA, Deshpande V, Carlson JM, Grafton ST (2011)
Conserved and variable architecture of human white matter connectivity. Neuroimage 54: 1262–1279. 25. Albert NB, Robertson EM, Miall RC (2009) The resting human brain and
motor learning. Curr Biol 19: 1023–1027. 12. Deuker L, Bullmore ET, Smith M, Christensen S, Nathan PJ, et al. (2009)
Reproducibility of graph metrics of human brain functional networks. Neuro-
image 47: 1460–1468. 26. Lewis CM, Baldassarre A, Committeri G, Romani GL, Corbetta M (2009)
Learning sculpts the spontaneous activity of the resting human brain. Proc Natl
Acad Sci U S A 106: 17558–17563. 13. Telesford QK, Morgan AR, Hayasaka S, Simpson SL, Barret W, et al. (2010)
Reproducibility of graph metrics in fMRI networks. Front Neuroinformatics 4:
12. 27. Shehzad Z, Kelly AM, Reiss PT, Gee DG, Gotimer K, et al. (2009) The resting
brain: unconstrained yet reliable. Cereb Cortex 19: 2209–2229. 28. Spoormaker VI, Schroter MS, Gleiser PM, Andrade KC, Dresler M, et al. (2010) Development of a Large-Scale Functional Brain Network during Human
Non-Rapid Eye Movement Sleep. J Neurosci 30: 11379–11387. 14. Biswal B, Yetkin FZ, Haughton VM, Hyde JS (1995) Functional connectivity in
the motor cortex of resting human brain using echo-planar MRI. Magn Reson
Med 34: 537–541. PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 21 July 2011 | Volume 6 | Issue 7 | e21976 Reliability of Brain Functional Networks Costa LdF, Rodrigues FA, Travieso G, Boas PRV (2007) Characterization of
complex networks: A survey of measurements. Advances in Physics 56: 167 -
242. y
y
49. Stratford PW (1989) Confidence limits for your ICC. Phys Ther 69: 237–238. 50. Winer BJ (1971) Statistical principles in experimental design. New York:
McGraw-Hill press. pp 283–293. 74. Rubinov M, Sporns O (2010) Complex network measures of brain connectivity:
uses and interpretations. Neuroimage 52: 1059–1069. 51. Sampat MP, Whitman GJ, Stephens TW, Broemeling LD, Heger NA, et al. (2006) The reliability of measuring physical characteristics of spiculated masses
on mammography. Br J Radiol 79 Spec No 2: S134–140. 75. Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang DU (2006) Complex
networks: Structure and dynamics. Physics Reports 424: 175–308. PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 22
|
https://openalex.org/W4238419219
|
https://figshare.com/articles/thesis/Implementation_of_SLAM_Navigation_Obstacle_Avoidance_and_Path_Planning_of_a_Robust_Mobile_Robot_Using_2D_Laser_Scanner/14643939/1/files/28122153.pdf
|
English
| null |
Implementation of SLAM, Navigation, Obstacle Avoidance, and Path Planning of a Robust Mobile Robot Using 2D Laser Scanner
| null | 2,023
|
cc-by
| 14,093
|
IMPLEMENTATION OF SLAM, NAVIGATION, OBSTACLE AVOIDANCE, AND
PATH PLANNING OF A ROBUST MOBILE ROBOT USING 2D LASER SCANNER by Omid Karimpour A project presented to Ryerson University
in partial fulfillment of the requirements for the degree of
Master of Engineering
in the program of
Electrical and Computer Engineering ©Omid Karimpour, 2019 Author's Declaration I hereby declare that I am the sole author of this project. This is a true copy of the project,
including any required final revisions, as accepted by my examiners. I authorize Ryerson University to lend this thesis to other institutions or individuals for the
purpose of scholarly research. I further authorize Ryerson University to reproduce this thesis by photocopying or by other
means, in total or in part, at the request of other institutions or individuals for the purpose of
scholarly research. I understand that my thesis may be made electronically available to the public. I understand that my thesis may be made electronically available to the public. ii 2019 Over the last decade, navigation and Simultaneous Localization and Mapping (SLAM)
have become key players in developing robust mobile robots. Several SLAM approaches
utilizing camera, laser scan, sonar and fusion of sensors were developed and improved by a
number of researchers. In this thesis, comparisons of these methods were evaluated, especially
those offering low cost benefits, and low computation and memory consumption. The aim of this
thesis was to select the most reliable and cost-efficient approach for indoor autonomous robotic
applications. Currently, there are numerous studies that have optimized these SLAM methods;
however, they still suffer from various complications such as scale drifting and excessive
computation. This study performed different experiments to observe these challenges in real-
world environments. A modified Pioneer robot was used to implement the selected SLAM
system and furthermore, perform obstacle avoidance and path planning in indoor office
environments. The results and tests show the reliable performance of Gmapping after tuning its
parameter and set right configurations. iii Acknowledgements I’m thankful to many people for their continuing support of this work. Above all, I’d like to
acknowledge my professor Dr. Alexander Ferworn, who always believed in my abilities and never
hesitated with inspirational support. His trust made me believe in myself more than ever and gave
the freedom to explore this field and pursue my passion. The collaboration and discussions
throughout my time in Network-Centric Applied Research Team (NCART) Lab, paved the way
for my future works. I’d like to acknowledge my friend Mohammadreza Mousaei, without his help
and support I would never take this path, his uninterrupted guidance is notable during this work
and my life. Last but not least, thank all lab mates. iv Dedication Dedicated to my parents who’ve supported me and trusted me, in academy and life. My mother, her infinite love and support can hardly be expressed by words. My father with spending all his life to provide us with a brighter future. My father with spending all his life to provide us with a brighter future. Table of Contents Table of Contents ABSTRACT . ................................................................................................................................................ III
LIST OF FIGURES ................................................................................................................................... VIII
GLOSSARY ................................................................................................................................................ X
SECTION 1. INTRODUCTION ...................................................................................................................... 1
1.1. OVERVIEW OF THE PROJECT ........................................................................................................... 1
SECTION 2. LITERATURE REVIEW AND PREVIOUS WORKS................................................................ 4
2.1. SIMULTANEOUS LOCALIZATION AND MAPPING .................................................................................. 4
2.1.1. Introduction to SLAM................................................................................................................... 5
2.1.2. Vision-Based SLAM Algorithms .................................................................................................. 7
2.1.2.1. Semi-direct Visual Odometry (SVO).................................................................................................... 8
2.1.2.2. Dense Piecewise Planar Tracking and Mapping SLAM ...................................................................... 8
2.1.2.3. Large Scale Direct SLAM .................................................................................................................... 8
2.1.2.4. Direct Sparse Odometry ...................................................................................................................... 9
2.1.2.5. ORB SLAM ........................................................................................................................................ 10
2.1.2.6. Stereo Parallel Tracking and Mapping .............................................................................................. 10
2.1.3. LIDAR-based SLAM Algorithms ................................................................................................ 10
2.1.3.1. KartoSLAM ........................................................................................................................................ 11
2.1.3.2. Core SLAM ........................................................................................................................................ 12
2.1.3.3. Lago SLAM........................................................................................................................................ 12
2.1.3.4. Cartographer ..................................................................................................................................... 13
2.1.3.5. HectorSLAM ...................................................................................................................................... 13
2.1.3.6. Gmapping .......................................................................................................................................... 14
2.2. PRE-MAPPING ............................................................................................................................... 14
2.3. LOOP CLOSURE ............................................................................................................................ 16
SECTION 3. IMPLEMENTATION TECHNIQUES ...................................................................................... 17 SECTION 2. LITERATURE REVIEW AND PREVIOUS WORKS................................................................ 4
2.1. SIMULTANEOUS LOCALIZATION AND MAPPING .................................................................................. 4
2.1.1. Introduction to SLAM................................................................................................................... 5
2.1.2. Vision-Based SLAM Algorithms .................................................................................................. 7
2.1.2.1. Semi-direct Visual Odometry (SVO).................................................................................................... 8
2.1.2.2. Dense Piecewise Planar Tracking and Mapping SLAM ...................................................................... 8
2.1.2.3. Large Scale Direct SLAM .................................................................................................................... 8
2.1.2.4. Direct Sparse Odometry ...................................................................................................................... 9
2.1.2.5. ORB SLAM ........................................................................................................................................ 10
2.1.2.6. Stereo Parallel Tracking and Mapping .............................................................................................. 10
2.1.3. LIDAR-based SLAM Algorithms ................................................................................................ 10
2.1.3.1. KartoSLAM ........................................................................................................................................ 11
2.1.3.2. Core SLAM ........................................................................................................................................ 12
2.1.3.3. Lago SLAM........................................................................................................................................ 12
2.1.3.4. Cartographer ..................................................................................................................................... 13
2.1.3.5. HectorSLAM ...................................................................................................................................... 13
2.1.3.6. Gmapping .......................................................................................................................................... 14
2.2. PRE-MAPPING ............................................................................................................................... 14
2.3. LOOP CLOSURE ............................................................................................................................ 16
SECTION 3. IMPLEMENTATION TECHNIQUES ...................................................................................... 17
3.1. HARDWARE SYSTEM ..................................................................................................................... 18 vi 3.2. SOFTWARE SYSTEM ...................................................................................................................... 22
3.2.1. ROS ........................................................................................................................................... 23
3.2.2. RPLIDAR Setup on ROS .......................................................................................................... 25
3.2.3. Pioneer 2DX Setup on ROS ..................................................................................................... 27
3.2.4. SLAM ......................................................................................................................................... 28
3.2.5. Localization ............................................................................................................................... 31
3.2.6. Navigation Stack ....................................................................................................................... 32
SECTION 4. CONDUCTED TESTS AND RESULTS ................................................................................. 33
4.1. CHALLENGES AND OBSERVATIONS................................................................................................. 37
4.1.1. Small and Narrow Obstacles and Different Surfaces ............................................................... 38
4.1.2. Glass Detection Challenge ....................................................................................................... 39
4.1.3. Stairs Detection and Mapping Challenge ................................................................................. 41
4.1.4. Loop Closure Challenge............................................................................................................ 44
4.1.5. Disaster Area’s Pre-mapping Practical Objection ..................................................................... 44
4.1.6. Dynamic Environments ............................................................................................................. 45
4.2. SENSOR FUSION ........................................................................................................................... 45
SECTION 5. CONCLUSION AND FUTURE WORK .................................................................................. 47
5.1. FUTURE WORK ................................................................................................................................... 47
APPENDICES ............................................................................................................................................. 49
REFERENCES ............................................................................................................................................ 59 vii List of Figures Figure 1: Table and glass manual adjustment of the map prior to the localization ...................... 15
Figure 2: Pioneer 2DX physical dimensions [24] ......................................................................... 18
Figure 3: Robot set up using pioneer 2DX, laptop and serial port [24] ........................................ 19
Figure 4: Supposed to be a RPDIDAR photo ............................................................................... 20
Figure 5: RPLIDAR dimensions [25] ........................................................................................... 21
Figure 6: Regulator DE-SWADJ .................................................................................................. 22
Figure 7: System overview ........................................................................................................... 24
Figure 8: Visualization of ROS a) Performing Gmapping in real world b) Performing Gmapping
using Gazebo simulation ............................................................................................................... 25
Figure 9: RPLIDAR placement .................................................................................................... 26
Figure 10: 2nd floor of engineering building’s map (Large loop) ................................................. 30
Figure 11: NCART lab’s map (Small loop) .................................................................................. 30
Figure 12: Initial localization process in NCART lab .................................................................. 31
Figure 13: Path being plan by this system in NCART Lab .......................................................... 32
Figure 14:: NCART map with velocity of 1 m/s ...................................................................... 35
Figure 15: NCART map with velocity of 1.5 m/s ...................................................................... 35
Figure 16: NCART map with velocity of 2 m/s ....................................................................... 35
Figure 17: NCART map with velocity of 3 m/s ....................................................................... 35
Figure 18: Loop closure test in 2nd floor Engineering building Ryerson University (The break on
top of the map shows he mismatch h) ........................................................................................... 35
Figure 19: NCART loop closure test (Small loop) ....................................................................... 36 viii Figure 20: Bumpy areas were substituted with books, metal and wood plates ............................ 39
Figure 21: Glass detection test in front of the glass ...................................................................... 40
Figure 22: The top part shows glass scans and how they fail to detect the glass ......................... 41
Figure 23: Stairs in engineering building...................................................................................... 42
Figure 24: Mapping stairs using Gmapping as the robot is going up ........................................... 43
Figure 25: Mapping stairs using Gmapping as the robot is going down ...................................... 43 ix Glossary x
Autonomous Mobile Robot
ActiveMedia Robotics Interface for Applications
Dense Piecewise Planar Tracking & Mapping
Direct Sparse Odometry
Laser Scanner
Large Scale Monocular
Network Centric Applied Research Team
Personal Computer
Particle Filter
Rao-Blackwellized particle filter
Root Mean Square Error
Robot Operating System
Real-Time Appearance-Based Mapping
Extended Kalman Filter
Simultaneous Localization & Mapping
Stereo Parallel Tracking and Mapping
Sparse Pose Adjustment
Semi-direct Visual Odometry
Unmanned Aerial Vehicle
Unmanned Ground Vehicle
Robot Model Description
Urban Search and Rescue AMR:
ARIA:
DPP-TAM:
DSO:
LIDAR:
LSM:
NCART:
PC:
PF:
RBPF:
RMSE:
ROS:
RTAB-Map:
SKF:
SLAM:
SP-TAM:
SPA:
SVO:
UAV:
UGV:
URDF:
USAR: AMR:
ARIA:
DPP-TAM:
DSO:
LIDAR:
LSM:
NCART:
PC:
PF:
RBPF:
RMSE:
ROS:
RTAB-Map:
SKF:
SLAM:
SP-TAM:
SPA:
SVO:
UAV:
UGV:
URDF:
USAR: Autonomous Mobile Robot ROS: x Section 1. Introduction Over the past decades, mobile robot applications have been a source of attention. There are
several major areas of interests such as mapping of indoor and outdoor environments, localizing
the robot in a pre-mapped environment, and performing both tasks simultaneously which is called
Simultaneous Localization and Mapping (SLAM) [1]. Nowadays, there is a dramatic increase in
mobile robotic research where new algorithms are being proposed to address SLAM and
navigation challenges. Moreover, many investigations and experience have improved these
algorithms to reduce the amount of redundant data processing resulted in more efficient
computation and the ability to utilize multi-sensors. Recent studies in the Robot Operating System (ROS), SLAM, Navigation stacks, layered
Costmap, obstacle avoidance, and other optimization techniques, make it possible to process more
data with limited processing power and memory. These findings improve the overall result by
developing other approaches such as utilizing sensor fusion. It is important however, not to assume
that these techniques will work in all cases. 1.1. Overview of the Project The objective of this project is to determine a robust and reliable SLAM system that could
perform in an indoor environment utilizing low-cost sensors and processing power. First and
foremost a survey of various SLAM systems was conducted. We avoided approaches that rely on
highly accurate sensors and high computation hardware as they come at a high cost. These methods
often utilize more than one type of sensor. We outlined the advantages and disadvantages of
popular vision and Light Imaging Detection and Ranging (LIDAR)-based algorithms and among 1 them, Gmapping provided the most reliable result. Gmapping SLAM algorithm has been
implemented on a customized Pioneer 2dx platform to perform SLAM, obstacle avoidance, and
path planning using Navigation Stack. Thereafter, we investigated several optimization methods
such as Layered Costmap. This method enhanced the map by layering different features and
landmarks especially in dynamic areas. This dynamic layer is unstable and causes a constant
change in the robot navigation. The Layered Costmap also sets other layers such as sensor fusion,
sonar and LIDAR to provide faster and reliable navigation. We dedicate part of the second section
explaining the limitations and challenges of layered Costmap in different mobile robot
applications. In general, different layers of the Costmap are configured to contain selected landmarks. These layers are being established so that the algorithm could detect different areas with their
corresponding features. This allows the navigation to plan out the fastest path by making
adjustments such as avoiding dynamic areas. These navigation decisions are being made by a path
planner; therefore, an accurate scan measurement is critical. Another navigation challenge that can
occur is detecting glass in new office buildings. Low-cost laser scanners such as RPLIDAR are
not able to fully recognize glass resulting in a misguided path. Currently, there is only a few studies
on this complication which has been reviewed in the literature review section, particularly pre-
mapping which offers a low-cost solution. Other challenges to the navigation system that are
briefly outlined are freer zone likelihood, and personal space. In the Implementation and Conducted Tests and Results sections we disclose our
experiments where a detailed step-by-step implementation of SLAM, Navigation Stack, Obstacle
avoidance, Path planning and other methodologies using RPLIDAR, and Pioneer mobile robot are 2 2 discussed. Some experiments on avoiding stairs, mapping stairs and practical glass detection. 1.1. Overview of the Project Thereafter, we proposed some possible solutions to resolve mentioned challenges such as stairs
detection. Overall in this study, we utilized the ROS, and all configurations, transforms, and
Launch files have been added to the system and discussed in detail. The implementations of this
project are performed by the ROS Kinetic and C++ Programming language. RVIZ package has
been used for visualization of the robot model, movement and other ROS visualizations. All
simulations have been performed in Gazebo (9.0.0). 3 Section 2. Literature Review and Previous Works The Robot Operating System is the most popular robotics framework used in robotic research
and development around the world. ROS provides a platform which focuses on collaborative and
rapid software development in the robotic field. The addition of libraries, packages, and tools to
the ROS have simplified roboticists endeavors to build robust robot platforms such as autonomous
mobile robot (AMR) [2]. All non-trivial mobile robots are expected to move effectively in a specified environment,
localize themselves within some form of mapped representation of the environment, and would
typically use the maps to avoid obstacles. Having a map such as this and being able to improve
this map is essential for continuous operation in the environment. To make competent decisions
about where to move, a path planner is added to the system. The path is being chosen based on the
map that has been generated. As localization and mapping are extremely important to mobile robot
applications, this section provides an overview of various SLAM systems. 2.1. Simultaneous Localization and Mapping Many AMRs localize themselves with respect to an internal map. The map is devised by
various means and is derived through the interpretation of sensor data. This map is never complete
and is constantly being augmented and corrected as new sensor data is being measured
simultaneously. This concept is a classic example of the “chicken and egg” problem, where the
robot does not know where it is, so it attempts to localize itself on a map it creates or tries to build
a map so it can determine its location within it. This apparent paradox can be explained through an example. Imagine you are on vacation
and parked your car to reach a tourist destination by walking. You know that you eventually have
to come back to where you parked. At first, you might start collecting information such as
landmarks to remind yourself later where your car is. A café, restaurant, street number and other
features or landmarks are some of the parts of a map you build inside your mind and is intended
to remind you of the path you have taken and would lead you back to your car. SLAM schemes
use a similar approach with the expectation that the location of the robot is accurate in the map
since critical mobility functions such as successful obstacle avoidance, path planning and
exploration are dependent on the accuracy of SLAM. From this point, several SLAM algorithms have been proposed, but established SLAM
algorithms have been thoroughly investigated and will be discussed here. Among all these SLAM
algorithms, Gmapping, Hector SLAM and cartographer are found to be more robust and accurate. The objective of all SLAM systems is to read the sensor measurements, send series of controls
during a period of time to compute the pose estimation of the Robot, and map the environment
simultaneously. These arguments are usually probabilistic, based on a given map, sensor
measurements, controls, and the pose. The algorithm calculates the belief which is the knowledge
of the robot from its state in the environment. The most general algorithm to calculate the robot’s
state is the Bayes filter [3]. 2.1.1. Introduction to SLAM While there is a plethora of SLAM systems that are used for indoor and outdoor mobile
robot applications, this project is focused on indoor environments. Furthermore, this section will
discuss the number of SLAM systems that exist in ROS. The state-of-the-art algorithms and ease 5 of implementation are some of ROS strengths. This section discusses the advantages and
disadvantages of several SLAM systems and how it relates to the proposed system. The proposed system is a LIDAR-based SLAM system. Further details of this selection are
presented in the next section along with the technical approach. A survey of other works that used
this approach will be explained here. In contrast, we also discussed visual SLAM systems and why
they are unsuitable for the proposed system. We also expanded some of the experiments conducted
by Maksim Filipenko and Ilya Afanasyev in some of these vision-based and LIDAR-based SLAM
methods [4]. While there are a vast variety of sensors, camera and LIDAR-based approaches, this thesis
examined monocular, stereo camera, and laser scanners because they are commonly used for this
type of system. A technique that combines these sensor data from different sources is called sensor
fusion which results in less uncertainty and more dependable data. Undoubtedly, the idea of sensor
fusion was impossible up until the last decade due to processing and memory limitations. However,
several algorithms and developments have contributed to making sensor fusion possible. One of
these developments have utilized sensor fusion to accurately map a glass office environment
without pre-mapping or adding extra adjustments. Explicit discussion in the sensor fusion utilizing
LIDAR, sonar/advanced sonar [5] and cameras; tuning SLAM parameters [6]; and their effects on
SLAM accuracy, have been conducted in the next section to search for an optimal solution for
indoor AMR applications and their challenges. These Approaches are discussed in the following two different sections: vision-based SLAM
algorithms and LIDAR-based SLAM Algorithms including the challenges of these approaches. Overall performance of vision-based SLAM systems depends on the computation resource. The focus of this project is on a limited hardware; therefore, visual SLAM approaches are not an
optimal choice. However, we will go through these vision-based methods only to analyze their
performances in different environments. A discussion on the comparison of LIDAR-based SLAM
performances shows that mapping Cartographer, and Hector SLAM provide more accurate results
compared to KartoSLAM, Core SLAM, and Lago SLAM algorithms. 2.1.1. Introduction to SLAM However, issues with these
approaches are that Cartographer suffers from the blurry effects, Hector SLAM does not provide
an accurate result when low rate laser scans are available and Gmapping increases computation
and has other challenges such as depletion problem. For the purpose of this project, Gmapping is
preferred over other LIDAR systems as an adaptive resampling technique. This technique has been
developed by [7] to optimize Gmapping performance. 2.1.2. Vision-Based SLAM Algorithms 7
Vision-based SLAM algorithms are based on either monocular or stereo cameras. Monocular-based approaches require extra modules in order to perform the scale recovery. As the
distance between features and the camera cannot be measured in real scale, recovery of these scales
is necessary to eliminate this drift of scale. In contrast, stereo cameras achieve reliable results over
monocular algorithms as they perform flawlessly without the scale recovery. However, they suffer
from the same problem when the distance between the camera and feature is high. Both of these
methods could be used as an additional source for pose estimation and mapping. Approaches such
as Semi-Direct Visual Odometry (SVO) and Dense Piecewise Planar Tracking and Mapping
(DPPTAM) suffer from losing track of robot turns when there is a lack of features in the
environment. Other monocular approaches such as Large Scale Direct (LSD) SLAM, Direct
Sparse Odometry (DSO) and ORB SLAM are accurate enough if the scale recovery is being used
as an additional module. ORB SLAM is the most stable and robust algorithm among other visual SLAMs. We will briefly discuss each of these SLAM approaches and point their advantages and
disadvantages. SLAMs. We will briefly discuss each of these SLAM approaches and point their advantages and
disadvantages. 2.1.2.2. Dense Piecewise Planar Tracking and Mapping SLAM DDPTAM method is a direct system for pose estimation and uses a similar approach as
SVO, but with more accuracy. This direct monocular SLAM algorithm was developed in [9] and
resulted in an advanced algorithm containing an uncluttered output with fewer errors in a variety
of conditions. There were several comparisons between this method and other monocular methods
and overall, higher accuracy and lower processing time was the result of DDPTAM. It is important
to mention, that this method is not robust enough and fails on tracking all robot turns. 2.1.2.1. Semi-direct Visual Odometry (SVO) SVO is a popular monocular algorithm which provides a decent accuracy and speed with
limited computation in most applications. In [8, 9], this approach has been developed by analyzing
the intensity of each pixel using a probabilistic mapping method. This method includes more
dependable points than any other monocular approach. This dependable point has been tested by
Maksim Filipenko and Ilya Afanasyev [4] in areas and environments without access to GPS. The
result is a high frame-rate motion estimation which increases the accuracy and robustness of this
method and therefore, makes a great addition for mapping and pose estimation. 2.1.2.3. Large Scale Direct SLAM LSD is another monocular SLAM algorithm which was proposed by [10] and uses a similar
approach to the last two methods. However, the advantage of this method is that it provides an
accurate pose estimation compared to other methods. The result of this featureless monocular 8 algorithm is a real-time output that filters over a large number of pixelwise stereo comparisons. LSD is a direct tracking method that contemplates the depth value and it is also less susceptible to
noise. Some of the novelties of this approach include its ability to detect scale-drift and incorporate
noise on the estimated depth using its probabilistic approach. This system also provides a loop
closure option to perform flawlessly when any drift error occurs, however, the system has
problems with identifying the robot’s initial pose shift and has a poor ROS integration [4]. 2.1.2.6. Stereo Parallel Tracking and Mapping The Stereo Parallel Tracking and Mapping (SP-TAM) SLAM is a real-time and feature-
based approach suitable for both indoor, and outdoor environments. It also includes a loop closure
with a large range of dynamic areas. This method avoids the boost mapping problem in monocular
methods by dividing the tasks into two parts. The first part is the tracking that deals with the camera
pose and the second part is mapping that updates a submap with a lower frequency [14]. Overall
this method is reliable and robust but has inaccurate localization. 2.1.2.5. ORB SLAM The ORB is a powerful SLAM algorithm, suitable for different environments. Reliable loop
closure and robust initializations are other advantages of this feature-based method. Findings from
ORB SLAM [13] show that the system produces robust and real-time results because it uses a
novel strategy of creating sparse point cloud as the map. This approach has an accurate pose
estimation and creates a 3D sparse map [4]. Automatic initialization, bundle adjustment and depth
estimation are a number of optimizations that result in a more robust approach. This method is
mostly being used in indoor robotics applications and the map is a good approximation of the real
world. The only disadvantage of this approach is that scale recovery is not solved which result in
a weak trajectory approximation [13]. 2.1.2.4. Direct Sparse Odometry DSO SLAM algorithm is a monocular visual odometry. The main features of this method
are calibration, motion bias and shutter effect. In [11], a comparison was conducted on both
feature-based and semi-supervised methods. It was found that photometric calibration results in an
improvement of direct methods. Moreover, feature-based methods have a large performance bias
on certain movements compared to direct methods, whereas direct and semi-direct methods are
more sensitive to rolling shutter effect. Therefore, feature-based methods need a higher resolution
in order to perform accurately. DSO, like many monocular SLAM systems, has a robust pose
tracking, however, it suffers from the lack of a loop closure resulting in a noisy map. The
dependency of this method to scale recovery is also a general criticism of this technique [4]. The next two methods are based on Stereo SLAM algorithms. The major advantages of
stereo compared to monocular is eliminating the scale recovery step, using the collected databases
to process them offline, and delivers an accurate state estimation [12]. 9 2.1.3. LIDAR-based SLAM Algorithms LIDAR measures the duration from sending a laser scan to receiving the reflection to detect
the distance and objects around it. LIDARs are not only robust against interference, but also are
independent from ambient lights. Some of these SLAM algorithms are more dependent to an 10 accurate LIDAR measurement than others. Among SLAM algorithms that we studied, Gmapping,
Hector SLAM, and Cartographer are more robust and reliable than Lago, Karto and CoreSLAM. These algorithms will be outlined in detailed in the sections below. Some of the general comparisons between these algorithms is that Lago SLAM has the
highest CPU usage. Another comparison is that Karto results are more accurate than Lago SLAM
and are less affected by noise in the real world. However, Karto SLAM provides a less reliable
map compared to Gmapping, Hector SLAM and Cartographer. On the other hand, Core SLAM is
a simple Particle Filter (PF) approach that requires more particles which lead to a more complex
computation. PFs are a set of Monte Carlo algorithms used to solve the filtering problem by
estimating the posterior density of the state variable based on given sensor observations [3]. Between the three most robust and reliable algorithms, Cartographer suffers from blurry effects in
some cases whereas Hector SLAM only uses scan matching and does not use the odometry data
which could be a disadvantage in some environments. Scan matching is a technique that finds the
robot’s pose by comparing its positions from two different scans. Relying on only scan matching
increases the complexity of computation, and therefore the CPU load. As the industry tries to
optimize the cost, keeping the CPU loads low is critical. Gmapping approach is less complex than
Hector SLAM and therefore, result in less computation. It also remains a robust and accurate
approach among many studies since it utilizes both scan matching and odometry to minimize the
use of particles. 2.1.3.2. Core SLAM Core SLAM is based on tiny SLAM algorithm and has been designed to have less
computation compared to other approaches [16]. Core SLAM calculates the distance with a variety
of sensor measurements and matches these scans with the map to find the optimized pose. Each
particle is being assigned a specific weight based on the final pose decision. The lowest weight
particle is the least accurate estimation and is being removed. The highest weight particle is the
most accurate pose estimation and is the robot’s pose. Finally, an optimization technique maps the
obstacles using points around each obstacle [16]. This approach has a more complex computation
and is not desirable for projects with limited resources such as this thesis. 2.1.3.1. KartoSLAM The Karto SLAM algorithm is a graph-based SLAM method that was developed by Karto
Robotics [15]. Overall, graph-based SLAMs require a loop closure improvement method to be 11 more accurate on large scales. Also, they generate higher efficiency when a higher number of
landmarks is being used which evidently requires higher computation and memory usage. Karto
SLAM is not suitable for our project not only because adding the loop closure improvement to this
method would increase the computation, but also there are other approaches such as Gmapping
that would provide a better result with the same CPU load. 2.1.3.4. Cartographer The cartographer approach focuses on the backpack mapping platform, enhancing the loop
closure in real time, as well as, other improvements such as branch and bound [18]. This system
was developed recently in 2016 and it represents the closest fitting from the 2D LIDAR map to
the real world. The tests from [19] show that the difference between trajectories of Cartographer
and Hector SLAM are less than 3cm in the root mean square error (RMSE) which means they both
demonstrate a similar result. Cartographer also uses pose estimation continuously and includes
real-time loop closure. The only downside of Cartographer is the blurry effect which was evaluated
by Anton et al. [20] based on analyzing the following metrics: number of corners in a map, enclosed
areas, and the proportion of occupied and free cells. 2.1.3.3. Lago SLAM Lago SLAM requires an initial guess of the robot’s pose [17] similar to any other graph-
based SLAM methods. Lago SLAM solves a local convex approximation in each step. Then,
updates the graph until it reaches a minimum local cost function. This method can take advantage
of any optimizer. The results of this method, even after using optimizers, are not as accurate as
Karto SLAM and it is more affected by noise than other systems [4]. 12 2.1.3.6. Gmapping Rao-Blackwellized particle filter (RBPF) base methods effectively proposed a solution to
the SLAM problem by using PF and creating a grid-based map [7]. Gmapping, a RBPT-based
SLAM approach, is an efficient indoor AMR algorithm that is also being utilized particularly in
the Search and Rescue (SAR) field. In this method, landmarks are constantly being captured in
order to estimate the robot’s pose. Low efficiency in capturing landmarks could result in poor
mapping and high efficiency landmark capturing results in lags due to low processing speed. In
the study [6], the researchers tuned Gmapping parameters to optimize the number of landmarks
with respect to the processing power. However, one of the disadvantages of this algorithm is that
a high number of particles are required to achieve an accurate result. Gmapping uses a set of
particles to approximate the probability distortion in order to solve the SLAM [7]. An improvement
approach called adaptive resampling technique [21], was created to deal with these high volumes
of particles. Considering both present and past movements of the robot, the author came up with a
distribution accuracy computation to limit the required particles. 2.1.3.5. HectorSLAM Hector SLAM is a flexible and scalable SLAM system, superior in its class, which provides
pose estimation with full 6 degrees of freedom [19]. It utilizes limited computation resources
resulting in a reduction in both the cost and weight of the robot. Hector SLAM uses an occupancy
grid map in order to represent an arbitrary environment, the LIDAR scans are being transformed
into a local frame to be stable in event of scanning across 6 degrees of freedom motion. The scans
are being converted to the point cloud of LIDAR scan endpoints. These point clouds need to be
processed to perform down-sampling. The endpoints are being sorted within the threshold of the
intended scan to limit the processing and memory [19]. Compared to Gmapping, this approach has
been successful in small case scenarios with unstructured environments such as most disaster
areas, however, it is not suitable for large loop closures as it only relies on scan matching. Therefore, Hector mapping is a desirable solution for applications that can’t rely on accurate 13 odometry. As long as high rate scans are being used, Hector SLAM is a reliable and accurate
approach. odometry. As long as high rate scans are being used, Hector SLAM is a reliable and accurate
approach. 2.2. Pre-mapping In USAR applications, having the floor map, stairs and exits of a building prior to the disaster
could help the rescue team outline the areas with more probability of possible survivors. However,
glass doors/windows and stairs pose great challenges and may require manual adjustments to
modify these areas on the map. This process of mapping is called pre-mapping [22], which serves
an important role in better understanding a disaster area. In [22], LIDAR was used to outline this 14 idea, although they faced several problems such as floor plan distortion by a catastrophic event. We will review some of these challenges in more detail in “Problem and Solution” section. It is important to note that current SLAM methods present some shortages such as failing to
detect slim objects, glasses, and obstacles that are out of the sensor’s range. A low-cost solution
to this issue is to manually adjust the map. The evidence in support of this could be found in some
of the tests that we performed on mapping the environment prior to localization shown in Figure
1. These tests result in a better understanding of certain obstacles which are not easily detectable
by most sensors and SLAM algorithms. Figure 1: Table and glass manual adjustment of the map prior to the localization Figure 1: Table and glass manual adjustment of the map prior to the localization In one particular study [22], a classroom with narrow tables has been chosen to test the
Gmapping. The first test involved an ideal classroom with wider objects and walls that were
completely covered by cardboard. This allowed them to evaluate the robot’s Gmapping 15 performance in an ideal environment. For the second test, a similar classroom with narrower spaces
and smaller objects resulted in a lack of data as expected. A third and final test was performed in
a dynamic classroom with elements from the first two tests. A major evaluation was conducted
after all experiments with respect to different SLAM methods in an effort to find the optimal
SLAM method. The results were compiled in [22] and their work has proposed pre-mapping as a
reliable solution for lack of reliable results in such environments. 2.3. Loop Closure For each SLAM algorithm test, mapping a large loop is an essential part of the process. Without a loop closure optimization, most of these approaches fail to close this loop because of
unreliable sensor measurements. In [23], an improved loop closure method was presented and
implemented by utilizing a low-cost LIDAR similar to the scanner used in this project. Gmapping
with RPLIDAR does not provide an optimal result in small indoor environments since many
landmarks need to be captured. Since RPLIDAR measurements are reliable on large scales but not
accurate enough on small scales, the loop closure improvement is still an attractive idea in both
small and large loop corrections. Loop closure consists of two areas of improvement which are
loop correction and loop detection. There are several optimizations in the loop correction,
however, loop detection still remains a major challenge. Gmapping registers several different laser
measurements including when a robot moves to a certain distance, change direction or in specific
time periods, which are all hard to control. To control these registrations, a study developed a
Kalman filter-based loop closure improvement method was developed to register the laser scans
only when the robot moves to a specific distance [23]. This method assumes that the robot detects
the loop accurately, and when the robot revisits the starting point, the loop correction procedure
starts and changes the map to result in the closure of the loop. 16 Section 3. Implementation Techniques In this section, a detailed explanation of implementation techniques and the objective behind
hardware and software used will be outlined. The types of hardware components reviewed are the
Pioneer 2DX, motor controller, RPLIDAR, batteries, host computer and connections. An overview
of software will include the ROS, ARIA client program, RPlLIDAR, Gazebo simulation, SLAM
system, costmaps, obstacle avoidance and path planning. In this project, Gmapping has been utilized and tested in variety of environments such as
offices and rough surface environments. The tests and experiments showed that Gmapping is
robust and reliable in such environments. Evidence that supports this finding can be found in the
“Conducted Test and Results” section. Since all tests are being performed in the ROS platform,
the first step is to interact with Pioneer 2DX using a host computer and Serial-USB port. A
connection is established between ARIA and ROS using ROSARIA package and then the system
is tested by publishing a velocity command through a ROS topic. Secondly, establish the
connection between Rplidar and host computer using Micro USB-USB port. In this host computer
the RPLIDAR ROS package and RVIZ simulator is being used to send the scans’ measurements
to RVIZ. Before testing the system in the real world, simulations of the EKF and Gmapping
SLAMs were run to compare the results and establish a baseline by referencing this map as an
ideal map. This system was then tested in a real-world environment by using both small and large
loop closure to compare the results. This test was conducted several times at different velocities
and scanned frequencies to find the optimal set up for our environment. After generating a map
with an optimal set up, it was saved and used in the next step so that the robot can localize itself 17 on this map and perform obstacle avoidance and path planning. In this section, hardware and
software components and their implementations are reviewed. on this map and perform obstacle avoidance and path planning. In this section, hardware and
software components and their implementations are reviewed. 3.1. Hardware System Pioneer 2DX: This mobile robot has been chosen as the base because the dimensions were
ideal compared to other available platforms. In consideration that a host computer has been used
in this project, there was no minimum requirement of computation component. Also, the weight
of this robot was decreased by applying some modifications which will be discuss in this section. The client-server architecture for this robot was originally developed by Kurt Konolige, Ph.D. Pioneer 2 DX. An ActiveMedia’s robot base has a three-wheel mobile platform including two
powered wheels and one caser wheel which allows it to freely rotate. To run this robot, it is
essential to either use the onboard microcontroller or host computer with a client server software. ARIA client server was selected because ROS packages for this client server is available and it
was suggested by the manufacturer. Physical dimensions of this robot are shown in Figure 4. 18
Figure 2: Pioneer 2DX physical dimensions [24] Figure 2: Pioneer 2DX physical dimensions [24] Figure 2: Pioneer 2DX physical dimensions [24] 18 Several expansion power and I/O ports are available for additional sensors and accessories. RS-232 serial port, digital I/O, A/D ports and other controllers are accessible for clients to
communicate with this base and made this robot an ideal choice for our project. Moreover, the
motor-power board supplies both 12 and 5 VDC for external accessories. The Pioneer 2DX
microcontroller has a 20 MHz Siemens 88C166 with 32k ROM and dynamic RAM, and other I/O
ports. A serial port is available on the consul to connect this microcontroller to the client computer
(Host) for data exchange [24]. Figure 3: Robot set up using pioneer 2DX, laptop and serial port [24] Figure 3: Robot set up using pioneer 2DX, laptop and serial port [24] The first step before using this base is performing a self-test by pressing the MOTORS button
twice after start-up. The self-test consists of two tests which are Motors Test and Sonars test. Motors test start by engaging the left and right drive wheel separately by forward and backward 19 movement. Lastly, it tests each sonar sensor range and connection separately. To confirm the data,
distance measurements were retrieved. This self-test was performed to ensure the drivers, motor-
power board and connections were working properly. 3.1. Hardware System Figure 4: Supposed to be a RPDIDAR photo Figure 4: Supposed to be a RPDIDAR photo Figure 4: Supposed to be a RPDIDAR photo 20
RPLIDAR: The RPLIDAR A1M8 was used in this project as this sensor has a reliable scan
measurement compared to other LIDARs with similar price range. Other models such as
RPLIDAR A3M1 has a more reliable scan but is susceptible to noise. However, as the industry
tries to keep the cost low. A1M8 provides a comparable result in our test environments to its costly
competitors. To process the distance and angle between object and RPLIDAR, the object is 20 sampled by reflecting a laser signal from the object. This distance is being captured more than
2000 times per second. In terms of hardware, a LIDAR typically consists of a range scanner system
and a motor system. These two systems are powered separately and that’s why a regulator has been
used to power the RPLIDAR motor system separately. This 360 scanner uses TTL serial port to
communicate with the server and power the range scanner. Figure 4 shows the regulator DE-
SWADJ that was used to power the RPLIDAR’s motor system. The dimensions of this sensor are
shown in Figure 5 [25]. Figure 5: RPLIDAR dimensions [25] Figure 5: RPLIDAR dimensions [25] 21 Regulator: As mentioned a DE-SWADJ regulator has been used to power the RPLIDAR
motor separately. This regulator plays an important role as it allows the ability to adjust the
speed of the RPLIDAR’s motor and therefore scans using this module. Figure 6: Regulator DE-SWADJ Figure 6: Regulator DE-SWADJ Power Supply: A LiPo battery replaced the old batteries of this robot to lower the weight
from 9KG to 7.5KG. This battery is a DXF Li-polymer with 32SP cells, 11.1V Voltage, Capacity
of 7000 mAh, Discharge of 35C and weight of 595g. 3.2. Software System The types of software discussed in this section are the ROS configuration full software
overview and configuring Pioneer and RPLIDAR with ROS. Detailed instructions of the SLAM,
navigation, Costmap, obstacle avoidance and other implementations will be thoroughly explained. 22 3.2.1. ROS ROS [15] is a Linux based software framework that uses packages, nodes, topics, messages
and services to operate a robot. A node receives sensor measurements and passes it to other nodes
in order to process data. The information that moves from node to node is called a message. These
messages travel through a portal called a topic. A Publisher is publishing data to this topic and
subscriber is subscribing to this topic to receive these messages. The package consists of all related
nodes and is essential for building a control system for any robot through ROS. In this thesis, ROS Kinetic was installed and the ROS environment was configured. To
create, build, and modify Catkin packages, a directory called Workspace was used. The ROS
workspace was created using the commands in A.2. The command in A.3 was added to the bashrc file so that it could automatically occur every
time the terminal is opened as only one catkin workspace was created for this thesis. 23 Figure 7: System overview Figure 7: System overview The Figure 7 shows all connections of the ROS systems including all transforms. In the
figure 8, one could find the visualization of our system computation graph in ROS which consist
of the robot, simulation, LIDAR and other components. 24 Figure 8: Visualization of ROS a) Performing Gmapping in real world b) Performing Gmapping using Gazebo simulation Figure 8: Visualization of ROS a) Performing Gmapping in real world b) Performing Gmapping using Gazebo simulation 3.2.2. RPLIDAR Setup on ROS RPLIDAR A1M8 is a 360 2D LIDAR that was used in this thesis. This LIDAR has been
placed centred on top of the robot with a height of 245 mm as shown in Figure 9. A plastic plate
was used to fix this laser scanner on top of the chassis. Maximum scanning frequency of this
LIDAR with 360 points samples is 5.5 Hz. During testing, the nominal speed of this laser scanner
was maintained at 35-40% of its max speed which is the optimal speed for this environment. A
USB connection was used to transfer the data to the LIDAR and a power supply of 5-10V was
required for the regulator to supply power for RPLIDAR motor’s system. It is important to keep
in mind that changing the value of this regulator affects our scanning speed. For any further
information, please refer to the RPLIDAR A1M8 data sheet [25]. 25 Important factors need to be considered when setting up the LIDAR on the robot. If the
LIDAR is set too low, it would affect the mapping as well as localization since it is unable to
capture enough landmarks. On the other hand, setting this laser scanner too high could result in
not detecting the obstacles that the robot is supposed to avoid. After conducting different height
tests, we placed the RPLIDAR at the centre of the robot with a height of 245 mm. This gave an
optimal navigation by easily identifying most obstacles in our test environment (2nd floor of
Ryerson Engineering Building) Figure 9: RPLIDAR placement Figure 9: RPLIDAR placement Figure 9: RPLIDAR placement Figure 9: RPLIDAR placement Powering RPLIDAR with only an USB is not sufficient for long distances and therefore,
this laser scanner needs a separate port for its power consumption. A regulator was added to not
only control the RPLIDAR motor speed, but also was a separate power source for this motor 26 system. The motor speed directly affected the map as the number of landmarks captured were
changing respectfully. system. The motor speed directly affected the map as the number of landmarks captured were
changing respectfully. 3.2.3. Pioneer 2DX Setup on ROS In order to setup the Pioneer 2DX, an interface that connects to the ActiveMedia controller
was required. This interface is called ActiveMedia Robotics Interface (ARIA) and is an open
source software based on C++. Any low-level details such as commands and serial communication
could be accessible through ARIA. The ARIA package was installed on the Linux Ubuntu 16.04,
using the commands in A.1. At this point, ARIA and ROS are installed and ROSARIA package is
required to communicate between the ARIA library and ROS. This platform automatically updates
the ARIA version and provides both control and position estimations by using ROS nodes to
connect to this library. The ROSARIA package has been retrieved to our catkin workspace and the package was
built using commands in A.5. This process had only needed to be completed once. However,
roscore must always be running so that the ROS nodes can communicate in their network. At last,
the ROS nodes are implemented as shown in Appendix A.6. The robot was connected to a host
via serial to a USB port. In such case, the command was modified in order to connect via USB0. After getting a connection to the robot using ROSARIA, the pose estimation was echoed as the
ARIA publishes the odometry data. This information is being published in RosAria/pose topic
every 100 ms. This frequency is by default and is adjustable. Two other parameters that refer to
the port and frame of the robot are base_link_frame, port. They are set to dev/ttyUSB0 and
base_link by default. 27 In the first test, different velocities were observed on the robot in order to test the velocity
commands in A.9. This velocity state is being published to the ARIA using /RosAria/cmd_vel. This command needs to be published every 100 ms in order to maintain this velocity. If the robot
does not receive the cmd_vel message for 600 ms, timeout will occur, and the robot stops for safety
reasons. In order to eliminate this, the command needs to be modified to publish a more frequent
velocity greater than 600 ms. Overall, all commands are shown in the Appendix including the laser
scanner in RVIZ, the connection of the base_link to laser_frame and launching the pioneer 2DX
robot model description (URDF). 3.2.4. SLAM SLAM algorithms are developing rapidly and high demands for smaller and lighter robots
have challenged researchers to simplify their methods and decrease the computation parts. The
rapid development in indoor 2D SLAM applications has been heavily studied, which led to several
improvements such as [7] by Grisetti et al. These approaches improved the RBPT by considering
both the recent observation of the robot and updating its motion model. The number of particles
decreased using the scan matching technique (lower computation) after reducing the resampling
step frequency. Gmapping SLAM algorithm has been used in this project which is one of the most studied
algorithms with several optimization methods. A thorough implementation and evaluation study
of Gmapping was conducted by Abdelrasoul et al. which proposed an optimization technique that
involved tuning its parameters [6]. To lower computation, they modified the number of particles
and resampled the threshold. This created a reliable map with less CPU load and memory
requirements. Our work supports these findings and will be further discussed in the “Conducted 28 Tests and Results” section where implementing this method resulted in low memory usage. This
involved conducting different speeds of the robot using Gmapping SLAM using low-cost 2D
LIDAR which resulted in different maps with different speeds. Tests and Results” section where implementing this method resulted in low memory usage. This
involved conducting different speeds of the robot using Gmapping SLAM using low-cost 2D
LIDAR which resulted in different maps with different speeds. In this test, the scan measurements from RPLIDAR and odometry of the Pioneer are used
by SLAM Gmapping to create a map using the Rao-Blackwellized particle filter base [Gmapping]
approach. Firstly, the test was conducted using Gazebo and RVIZ simulation, and thereafter, the
robot was tested in a small and large loop in a real-world environment. After the Gmapping
process, the map is saved into PGM and YAML files. These two files are respectfully an image of
the map (PGM) and a description of this map (YAML). This saved map is used later on to navigate
and localize the robot. The instructions for the simulation and practical tests are found in the
Appendix A.8, A.10 and A.11. Figure 11 and 12 also shows the final map of the NCART lab and
a loop closure of the 2nd floor, Engineering building, Ryerson University. 3.2.4. SLAM The visualization of the
system computation graph of both simulation and real tests are shown in Figure 11 and 12. 29 Figure 10: 2nd floor of engineering building’s map (Large loop) Figure 10: 2nd floor of engineering building’s map (Large loop) Figure 11: NCART lab’s map (Small loop) Figure 11: NCART lab’s map (Small loop) 30 3.2.5. Localization A localization algorithm uses odometry data, LIDAR scans, and a saved map to visualize
the map and location of the robot. To deal with different states of localization, launch files are
written and configured. Launch and configurations files are critical for the robot localization and
can be found in Appendix A.13 and A.14. During localization, the map is retrieved from the
saved map using a Map Server. Thereafter, AMCL is used to localize the robot in the map which
also requires an initial guess by the user. In Figure 13, the location of the robot is identified and
shown. As the robot moves, the algorithm captures more landmarks which increases the certainty
of localization. 31
Figure 12: Initial localization process in NCART lab Figure 12: Initial localization process in NCART lab 31 3.2.6. Navigation Stack After mapping and localizing the robot, navigation is the main objective of an AMR. A move
base package from the navigation stack [26] was used where this package provides a velocity
command and uses localization data to navigate the robot in the environment. The details of this
approach are mentioned in [26]. RVIZ tools were then configured and provided a destination for
the robot to plan a safe path, accordingly. Two launch files were set up to launch all necessary
transform connections such as roscore, ROSARIA, RPLIDAR, map server and RVIZ. The YAML
file was used and saved from the SLAM section. For further details, the commands, configurations
and launch files are found in Appendix A.13 and A.14. Figure 14 shows the planned path by this
system after manually setting a goal for the robot to reach by avoiding obstacles on its way. Figure 13: Path being plan by this system in NCART Lab Figure 13: Path being plan by this system in NCART Lab 32 Section 4. Conducted Tests and Results The tests in this section focus on providing an optimized robot set up and reveal the
challenges faced and potential solutions. The goal is to simplify some of these challenges by
creating a more reliable map and pose estimation. Some of these findings address the challenges
faced by past studies and gives future studies the foundation to further explore in this field. The
“Challenges and Observation” section offers an in-depth discussion on results of these tests. Robot speed’s modification: Mapping the environment is one of the main tasks which is
performed by capturing a sufficient number of landmarks from the environment. One factor that
could affect this process is the speed of the robot. To evaluate the effects speed has on mapping,
an experiment was conducted in the NCART lab at Ryerson University where changes in the
velocity of the robot were evaluated and SLAM was performed with each of these speeds. Additionally, this experiment involved loop closure, analyzing the SLAM accuracy and tuning
parameters. The robot speed and direction were controlled using the command line in Appendix
A.9. We started off with 1 m/s and increased this speed by 0.5m/s steps to reach 3 m/s. Figures 15-
18 shows that loop closure was completed on all scenarios. It was expected that there would be a
less reliable map when the speed was increased. However, the difference between these maps
created by various speeds were not significantly noticeable and it was concluded that the
performance of Gmapping is independent to various speeds of Pioneer 2DX. 33 Figure 14:: NCART map with velocity of 1 m/s
Figure 15: NCART map with velocity of 1.5 m/s
Figure 16: NCART map with velocity of 2 m/s
Figure 17: NCART map with velocity of 3 m/s Figure 15: NCART map with velocity of 1.5 m/s Figure 15: NCART map with velocity of 1.5 m/s Figure 14:: NCART map with velocity of 1 m/s Figure 15: NCART map with velocity of 1.5 m/s Figure 16: NCART map with velocity of 2 m/s Figure 17: NCART map with velocity of 3 m/s Figure 16: NCART map with velocity of 2 m/s Figure 17: NCART map with velocity of 3 m/s Figure 17: NCART map with velocity of 3 m/s Altering the LIDAR heights: Setting the LIDAR sensor at an appropriate height is critical
as it changes the range of obstacles and landmarks that is being captured. Section 4. Conducted Tests and Results This height could be set
differently depending on the environment and its landmarks. For the purpose of this thesis, most
of the obstacles the robot needs to avoid on the second floor of the Ryerson Engineering building
are either not dependent to height such as doors and walls, or has obstacles that are the same height
as the robot. Obstacles such as tables are not necessarily an obstacle for the robot if it can find a
better path using the space under the table. Therefore, the LIDAR was installed at the center and
top of the Pioneer with height of 245 mm which was shown in Figure 9. This setup allows the 34 robot to easily navigate the lab and office areas including passing under the table, if there is a
possible path. robot to easily navigate the lab and office areas including passing under the table, if there is a
possible path. Long and short loop closure test: Firstly, the loop closure has been tested in the NCART
lab, which is a small area compared to the Ryerson Engineering building 2nd floor. Thereafter, the
robot was tested in a larger loop on the 2nd floor. During this test, it was discovered that the
Gmapping could fail to detect this loop. In this case, the final map is not reliable as the loop
correction depends on the loop detection to happen. We hope to optimize the loop closure process
of Gmapping by manually adjusting the map in our future work. Figure 18: Loop closure test in 2nd floor Engineering building Ryerson University (The break on top of the map shows the drift) Figure 18: Loop closure test in 2nd floor Engineering building Ryerson University (The break on top of the map shows the drift) Figure 18: Loop closure test in 2nd floor Engineering building Ryerson University (The break on top of the map shows the drift) 35 Figure 19: NCART loop closure test (Small loop) Figure 19: NCART loop closure test (Small loop) Stairs mapping: A robust mobile robot should be able to autonomously navigate through a
building and move to other floors either using elevator or stairs. In case of using the stairs, the
robot should be able to detect these stairs. To evaluate stair navigation, LIDAR was used for
mapping and these results are discussed in the “Challenges and Observation” section. Section 4. Conducted Tests and Results Destroyed environment vs flat surface: During navigation, there may be some cases where
an AMR is required to navigate through different types of surfaces. These surfaces could be a
simulation of toys in a house, stack of papers on the ground of an office floor, or maybe a damaged
area after an explosion. As one can see, different applications are required for the robot to move
in various situations. We tested some of these less flat areas in our application. We extended this
section in the “challenges and observations” subsection. RPLIDAR speed’s modification: Not only does the speed and height of the robot could
influence the scans, but also RPLIDAR’s frequency directly affects the number of landmarks that 36 are being captured at a given period of time. Therefore, we dedicated a section on the overview of
RPLIDAR power and nominal speed. The implementations of this project were performed by utilizing Robot Operating System
(ROS Kinetic) and C++ Programming language. RVIZ package has been used for visualization of
the robot model, movement and other ROS visualizations. All simulations of have been performed
in Gazebo (9.0.0). 4.1. Challenges and Observations An AMR could face several challenges such as not detecting certain obstacles (tables or
glasses) due to the height of the sensors or their capabilities. There were a few optimizations that
aimed to solve these challenges. Particularly, AMR applications have been perfected in the past
decade. Being able to process the data with less computation and memory requirements is one
among many optimizations that are possible. Studies have advanced these approaches and have
paved the way to achieve more accurate results in areas such as localization, mapping, and path
planning. However, problems still remain with these approaches. In practice, mapping an indoor
environment with glass walls and stairs is one among many. The goal of this thesis is to investigate
the challenges during the mapping of glass environments and based on the findings, provide
potential solutions. One of the many solutions to this challenge had utilized the advantages of
sensor fusion and has been outlined in the introduction of sensor fusion. During the investigation
of real-world challenges, another critical challenge especially in the exploration of real buildings
is detecting and mapping stairs. This particular situation has brought us to investigate several
approaches. For instance, in uneven and unpredictable terrain, locating and mapping uneven terrain
is problematic and extremely important as seconds could change the lives of people in planning a 37 path to a trapped victim in a damaged building. The rescue team would need to be highly accurate
on their calculations beforehand. Supporting evidence on this matter can be found in situations
where the rescue team does not have access to a floorplan. Therefore, an AMR may be required
to map the uneven terrain and the rest of the environment. However, Robots utilizing 2D LIDAR
are not capable of fully mapping stairs and other similar features. Altogether, AMR applications
suffer from limitless number of challenges which requires many optimizations and developments;
however, only some significant challenges have been outlined in this section. 4.1.1. Small and Narrow Obstacles and Different Surfaces After conducting tests at the NCART lab, small and narrow obstacles were mainly
observed such as narrow tables and chairs. These types of obstacles are not detectable by the
LIDAR and result in a less accurate map. During the navigation process, the robot uses the map to
plan its path through these tables which evidently resulted in the robot crashing. In addition to
these narrow obstacles, small objects that are not detectable by the sensors create a bumpy surface. To overcome this issue, these bumpy areas were substituted with books, metal and wood plates as
shown in Figure 21. In this type of situation, the robot either has to detect these obstacles and
change its path, or pass these gravel-like surfaces which requires different robot bases. Changing
the base of the robot is not only costly, but also not effective enough as it creates other challenges
such as requiring wider paths to choose from. Subsequently, detecting these obstacles become
essential for the navigation process. It would be beneficial to use fusion sensors such as camera
and laser scanner as it is a cost-effective approach and will be discussed more in the “Future
Works” section. 38 Figure 20: Bumpy areas were substituted with books, metal and wood plates Figure 20: Bumpy areas were substituted with books, metal and wood plates 4.1.2. Glass Detection Challenge Glass detection is one of the well-known challenges that hasn’t been extensively studied
by researches until recently. However, there have been several attempts as mentioned to solve this
challenge. Despite some expensive sensors that are able to detect glass, other approaches use at
least two sensors, which require more processing power and memory. In this thesis, several tests
were conducted in glass areas to investigate this problem further. These tests involved using a
RPLIDAR that is not able to detect glass surfaces due to the reflection beam is either coming back
from the wall behind the glass or no reflection is being detected at all. Sensor fusion could be a
solution to this issue according to studies of T. Chang et al. in [27], which used both advanced
sonar and LIDAR. Despite their high computation, these methods certainly provide a solution 39 model to this current high-profile challenge. Sonar sensors are not the best choice in terms of
mapping as the sensor measurements are not reliable and accurate, however they are being used as
an additional sensor since they could detect glass surface. Using LIDAR and sonar together not
only could be more accurate, but also is able to detect these surfaces. When sonar sensor
measurements provide a significant difference from the LIDAR measurements, the surface is most
likely a glass because LIDAR is not detecting it. Figure 21 shows the LIDAR scan measurements
against glass surface. We will discuss these methods further in depth in the “Fusion Sensors”
section. Figure 21: Glass detection test in front of the glass Figure 21: Glass detection test in front of the glass 40 Figure 22: The top part shows glass scans and how they fail to detect the glass Figure 22: The top part shows glass scans and how they fail to detect the glass Figure 22: The top part shows glass scans and how they fail to detect the glass 4.1.3. Stairs Detection and Mapping Challenge One of the main challenges in robot navigation is stair detection and mapping. An advantage
to having these maps is that it could be helpful for a SAR team to use after incidents such as
bombing and certain tasks that require a immediate response in limited time manner. The number
and height of stairs could be captured and mapped by using either Unmanned Ground Vehicle
(UGV) or Unmanned Aerial Vehicle (UAV). In this section, we tried to show how this attempt
failed for 2D laser scanners going up the stairs and what are the next steps to solve this challenge
utilizing low-cost sensors. 41
Figure number 24 and 25 are demonstrating the stairs maps which has been gathered by
Gmapping and RPLIDAR A1M8. Figure 24 shows the map after the robot climbed up the stairs 41 and Figure 25 illustrates the map after the robot climbed down the stairs. Evidently, these maps
are not practicable as the scan measurements are stacked on top of each other to create a
meaningless map. Based on these tests and mentioned challenges, 3D LIDAR is preferable for
such applications. Also, separate Costmap layer could be assigned to maps of the stairs in order to
improve the behaviour of the robot. and Figure 25 illustrates the map after the robot climbed down the stairs. Evidently, these maps
are not practicable as the scan measurements are stacked on top of each other to create a
meaningless map. Based on these tests and mentioned challenges, 3D LIDAR is preferable for
such applications. Also, separate Costmap layer could be assigned to maps of the stairs in order to
improve the behaviour of the robot. To provide a more stable platform for the robot to go up and down the stairs, the robot was
centered on top of a wooden board. Certainly, an alternative platform such as a tracked robot is
more practical for future works. 4.1.4. Loop Closure Challenge Several studies have attempted to optimize the loop closure in a number of approaches such
as Gmapping. Some of these studies have led to the development of new loop closure methods and
others have added optimizations on current approaches. However, most of these studies only
focused on the loop correction and relied on an accurate loop detection. In this thesis, mismatches
on the loop detection were observed when the robot was required to close a longer loop. It was the
Gmapping loop detection that failed to detect the loop in a long loop in 2nd floor Ryerson
Engineering building. This detection is more challenging when there are similar features and
landmarks in environments such as office and dynamic areas. 4.1.3. Stairs Detection and Mapping Challenge Figure 23: Stairs in engineering building Figure 23: Stairs in engineering building 42 Figure 24: Mapping stairs using Gmapping as the robot is going up Figure 24: Mapping stairs using Gmapping as the robot is going up Figure 24: Mapping stairs using Gmapping as the robot is going up Figure 25: Mapping stairs using Gmapping as the robot is going down Figure 25: Mapping stairs using Gmapping as the robot is going down Figure 25: Mapping stairs using Gmapping as the robot is going down 43 4.1.6. Dynamic Environments AMRs face dynamic areas on a day-to-day basis as most applications require robots to
robustly navigate in such environments like in houses or offices. In the literature review section,
we discussed how indoor navigation and SLAM demand a robust navigation in dynamic areas. It
is also noteworthy to mention that the boundary of each person is their privacy and should be set
so that the robot does not get too close to a person. To address this issue, these boundaries need to
be adaptable as the environment changes. In any case, detecting a dynamic object from a static
obstacle is critical to meet these expectations. These dynamic areas could be saved in a separate
Costmap layer to simplify robot’s navigation. This argument has been supported by evidence from
Layered Costmap for Context-Sensitive Navigation in [28]. In this study, the robot could avoid
driving to close to people by navigating through paths with less dynamic areas. It was suggested
that it is more reliable to choose a path with less hazard to lower the chance of collision by
assigning a Costmap to caution zones. It is our intent to implement and improve this layer in our
future work. 4.1.5. Disaster Area’s Pre-mapping Practical Objection Pre-mapping an indoor office or public environment are necessary, in some cases. One
particular pre-mapping approach that is common among studies is mapping these environments
for emergency rescue teams to use in future natural disasters such as an earthquake. This approach
is called Disaster Areas Pre-mapping and has found to be helpful for the USAR team to
approximate the location of survivors [22]. It is critical to emphasize that currently, the number of
places which have been mapped are few which make this approach more theoretical than practical. Pre-mapping an indoor office or public environment are necessary, in some cases. One
particular pre-mapping approach that is common among studies is mapping these environments
for emergency rescue teams to use in future natural disasters such as an earthquake. This approach
is called Disaster Areas Pre-mapping and has found to be helpful for the USAR team to
approximate the location of survivors [22]. It is critical to emphasize that currently, the number of
places which have been mapped are few which make this approach more theoretical than practical. There is also the problem of the chaotic effects of forces capable of producing a disaster. For
example, a severe earthquake or bomb blast might cause of multi-story structure to collapse and
deform in ways that make any pre-mapping irrelevant. Locating the critical part of a building such
as stairs, and hallways is almost impossible in the case of a severe destruction. Disaster Area’s
Pre-mapping still remains a popular approach among current studies and we hope to provide
recommendations that addresses this issue based on improved and more complete simulations. There is also the problem of the chaotic effects of forces capable of producing a disaster. For
example, a severe earthquake or bomb blast might cause of multi-story structure to collapse and
deform in ways that make any pre-mapping irrelevant. Locating the critical part of a building such
as stairs, and hallways is almost impossible in the case of a severe destruction. Disaster Area’s
Pre-mapping still remains a popular approach among current studies and we hope to provide
recommendations that addresses this issue based on improved and more complete simulations. 44 4.2. Sensor Fusion Having considered sensor fusion, it is also reasonable to look at limitations of single-sensor-
based applications. Main sensors that are being used in indoor AMR applications are LIDAR,
camera and sonar. As we already compared vision-based and LIDAR-based advantages and
disadvantages, we will briefly go through sonar and LIDAR sensors and sensor fusion using these
two sensors. 45
Sonar Sensor: This sensor is being used in a number of indoor robotic applications and is
one of the most useful and cost-efficient sensors compared to other methods. This sensor is able to detect any transparent surface such as glass, which is commonly used in most offices and indoor
environments. However, high range of errors and the low-resolution readings of this sensor makes
it unreliable compared to other alternatives such as LIDAR and camera. LIDAR Sensor: Laser scans can provide a high resolution and highly accurate detection. This
accurate scan data is the main reason LIDAR is dramatically being used in indoor mapping,
localization and navigation. However, transparent surfaces such as glass are not fully detectable
by LIDAR. Therefore, it is not suggested to use these sensors without pre-mapping and further
map adjustment. These two sensors can complement each other where sonar results are unreliable but able to
detect transparent areas. LIDAR scans are reliable, despite not being able to detect transparent
areas. To compensate for this lack of detection, [27] developed an algorithm using both sensors. This algorithm compares both measurements of sonar and LIDAR, and if there is a significant
difference between these measurements, the algorithm assumes it detects a glass object if LIDAR
did not detect an obstacle, but sonar did. Although, significant errors in sonar sensors, especially
in edge situations, could dramatically affect the accuracy of this solution [27]. Using sensor fusion
in our future work could eliminate the number of failures that we faced in our tests and could
potentially result in a more accurate navigation in such indoor environments. 46 Section 5. Conclusion and Future Work In this thesis, the advantages and disadvantages of different LIDAR and vision-based
SLAM systems were investigated and compared. The main conclusion derived was that vision-
based SLAM approaches suffered from scale drifting, lost track of the robot and relied on a high
computation in comparison to LIDAR-based approaches. However, LIDAR-based SLAMs are
preferable as it met our requirement of limited hardware for this project. Among these LIDAR-
based approaches, Gmapping provides a reliable and cost-efficient result. This finding was based
on the modified mobile robot used to evaluate Gmapping performance in a typical office
environment. Different experiments were conducted by launching the robot in various closed-loop
trajectories. Simulation of a dynamic office environment with a bumpy area, and glass detection
areas are some of these experiments that required manual map adjustments. Sensor measurements
such as LIDAR were collected to perform Gmapping SLAM, and AMCL Navigation. This study
shows the reliability of Gmapping in indoor office environments. A.1. Installations and setups sudo dpkg -i libaria_2.9.1+ubuntu16_i368.deb A.3. bashrc modification . ~/catkin_ws/devel/setup.bash A.2. ROS workspace mkdir -p ~/catkin_ws/src cd ~/catkin_ws/src catkin_init_workspace cd ~/catkin_ws cd ~/catkin_ws catkin_make 5.1. Future Work In this thesis we explored several different techniques for exploring closed loop navigation
and traversal. We examined solutions for dealing with glass (windows) in offices and stairs. The
main challenges encountered during testing were discussed and gave us insights to the
shortcomings of dealing with static real-world environments. We assume that any AMR should be
able to navigate in any typical office environment that generally consists of stairs, glass walls,
bumpy areas and large closed loops. Based on our findings, we suggest the manual adjustment of
obstacles in the map as most low-cost sensors are not capable of accurately detecting some of these
obstacles, dynamic areas, and bumpy areas. However, the true definition of indoor autonomous 47 mobile robot requires a robot to autonomously navigate in any indoor environment without human
interaction. As this is beyond the scope of this thesis, we hope more realistic solutions will be
developed over time. Our work suggests that this will inevitably involve sensor fusion and areas
additional forms of maps used for specific purposes (unstructured area maps for example). 48 A.4. Launching RPLIDAR roslaunch rplidar_ros view_rplidar.launch Appendices A.1. Installations and setups A.7. Echo the pose using ARIA library rostopic echo /RosAria/pose A.6. Launch ARIA using ROSARIA rosrun rosaria RosAria _port:=/dev/ttyUSB1 A.8. gmapping Gazebo simulation roslaunch p3dx_gazebo gazebo.launch
roslaunch p3dx_description rviz.launch
roslaunch Rplidar_ros view Rplidar.launch
rosrun gmapping slam_gmapping scan:=/p3dx/laser/scan
rosrun tf static_transform_publisher 0 0 0.1 0 0 0 odom base_link 100
rqt_graph rqt_graph #different terminal Rosrun teleop_twist_keyboard teleop_twist_keyboard.py And add a display with a map to the RVIZ, then set it to the topic /map. A.5. ROSARIA cd ~/catkin_ws/src git clone https://github.com/amor-ros-pkg/rosaria.git make -j4 make -j4 catkin_make 49 roscore A.6. Launch ARIA using ROSARIA A.9. Publishing Velocity through ROSARIA A.9. Publishing Velocity through ROSARIA 50 The code below was used to move the robot forward The code below was used to move the robot forward rostopic pub /RosAria/cmd_vel geometry_msgs/Twist -r 3 -- '[0.1, 0.0, 0.0]' '[
0.0, 0.0, 0.0]' A.10. Gmapping using RPLIDAR A.10. Gmapping using RPLIDAR
roscore
roslaunch rplidar_ros view_rplidar.launch (rosrun rplidar_ros rplidarNode)
rostopic echo scan
dmesg | grep tty
rosrun rosaria RosAria _port:=/dev/ttyUSB1
roslaunch p3dx_description rviz.launch
rosrun tf static_transform_publisher 0 0 0.1 0 0 0 base_link laser_frame 100 rostopic echo scan dmesg | grep tty rosrun rosaria RosAria _port:=/dev/ttyUSB1 roslaunch p3dx_description rviz.launch rosrun tf static_transform_publisher 0 0 0.1 0 0 0 base_link laser_frame 100 A.11. Saving the map after SLAM Rosrun rosaria RosAria port:/dev/ttyUSB0 Transforms? Rosrun mapping slam gmapping Rosrun mapping slam gmapping Rosrun map server map saver -f mymap A.12. Localization 51 rosrun rviz rviz 52
A.13. Move Base Launch File
<launch>
<master auto="start"/>
<!-- Run the map server -->
<node name="map_server" pkg="map_server" type="map_server" args="$(fin
d my_map_package)/my_map4.pgm 4000 X 4000"/>
<!--- Run AMCL -->
<include file="$(find amcl)/examples/amcl_omni.launch" />
<node pkg="move_base" type="move_base" respawn="false" name="move_base
" output="screen">
<remap from="/odom" to="/pose" />
<remap from="cmd_vel" to="/RosAria/cmd_vel"/>
<rosparam file="$(find p3dx_2dnav)/costmap_common_params.yaml" command
="load" ns="global_costmap" />
<rosparam file="$(find p3dx_2dnav)/costmap_common_params.yaml" command
="load" ns="local_costmap" />
<rosparam file="$(find p3dx_2dnav)/local_costmap_params.yaml" command=
"load" />
<rosparam file="$(find p3dx_2dnav)/global_costmap_params.yaml" command
="load" />
<rosparam file="$(find p3dx_2dnav)/base_local_planner_params.yaml" com
mand="load" /> A.13. Move Base Launch File A.13. Move Base Launch File <rosparam file="$(find p3dx_2dnav)/base_local_planner_params.yaml" com
mand="load" /> 52 </node>
</launch>
A.14. Configuration Files
<launch>
<!-- Launch rplidar -->
<node pkg="rplidar_ros" type="rplidarNode" name="rplidarNode" output="screen"
>
<param name="serial_port" type="string" value="/dev/ttyUSB0"/>
<param name="serial_baudrate" type="int" value="115200"/><!--A1
/A2 -->
<!--param name="serial_baudrate" type="int" value="256000"--><! --A3 -->
<param name="frame_id" type="string" value="laser"/>
<param name="inverted" type="bool" value="false"/>
<param name="angle_compensate" type="bool" value="true"/>
</node>
<!-- Connect to Pioneer -->
<node pkg = "rosaria" type = "RosAria" name = "RosAria">
<param name="port" value="/dev/ttyUSB1" type="string"/>
</node>
<!-- Launch p3dx description --> </node>
</launch> A.14. Configuration Files
<launch>
<!-- Launch rplidar -->
<node pkg="rplidar_ros" type="rplidarNode" name="rplidarNode" output="screen"
>
<param name="serial_port" type="string" value="/dev/ttyUSB0"/>
<param name="serial_baudrate" type="int" value="115200"/><!--A1
/A2 -->
<!--param name="serial_baudrate" type="int" value="256000"--><! --A3 -->
<param name="frame_id" type="string" value="laser"/>
<param name="inverted" type="bool" value="false"/>
<param name="angle_compensate" type="bool" value="true"/>
</node>
<!-- Connect to Pioneer -->
<node pkg = "rosaria" type = "RosAria" name = "RosAria">
<param name="port" value="/dev/ttyUSB1" type="string"/>
</node>
<!-- Launch p3dx description --> A.14. Configuration Files <!-- Launch rplidar --> <param name="frame_id" </node> <!-- Connect to Pioneer --> <param name="port" value="/dev/ttyUSB1" type="string"/> </node> <!-- Launch p3dx description --> 53 <arg name="model" default="$(find p3dx_description)/urdf/pioneer3dx.xml"/>
<arg name="gui" default="False" /> <param name="robot_description" textfile="$(arg model)" /> <param name="use_gui" value="$(arg gui)"/> <param name="use_gui" value="$(arg gui)"/> <param name="use_gui" value="$(arg gui)"/> <node name="joint_state_publisher" pkg="joint_state_publisher" type="joint_st
ate_publisher" ></node> <node name="robot_state_publisher" pkg="robot_state_publisher" type="state_pu
blisher" /> <node name="rviz" pkg="rviz" type="rviz" args="-d $(find urdf_tutorial)/urdf. rviz" /> <!-- transfor configurations --> <node pkg="tf" type="static_transform_publisher" name="link1_broadcaster" arg
s="0 0 0.2659 0 0 0 base_link laser_frame 100"/> <node pkg="tf" type="static_transform_publisher" name="link2_broadcaster" arg
s="0 0 0.1 0 0 0 map odom 100"/> <node pkg="tf" type="static_transform_publisher" name="link3_broadcaster" arg
s="0 0 0.2659 0 0 0 base_link laser 100"/> </launch> 54 55
A.15. Navigation Launch File
<launch>
<!-- Launch rplidar -->
<node pkg="rplidar_ros" type="rplidarNode" name="rplidarNode" output="screen"
>
<param name="serial_port" type="string" value="/dev/ttyUSB0"/>
<param name="serial_baudrate" type="int" value="115200"/><!--A1
/A2 -->
<!--param name="serial_baudrate" type="int" value="256000"--><! --A3 -->
<param name="frame_id" type="string" value="laser"/>
<param name="inverted" type="bool" value="false"/>
<param name="angle_compensate" type="bool" value="true"/>
</node>
<!-- Connect to Pioneer -->
<node pkg = "rosaria" type = "RosAria" name = "RosAria">
<param name="port" value="/dev/ttyUSB1" type="string"/>
</node>
<!-- Launch p3dx description -->
<arg name="model" default="$(find p3dx_description)/urdf/pioneer3dx.xml"/> A.15. Navigation Launch File
<launch>
<!-- Launch rplidar -->
<node pkg="rplidar_ros" type="rplidarNode" name="rplidarNode" output="screen"
>
<param name="serial_port" type="string" value="/dev/ttyUSB0"/>
<param name="serial_baudrate" type="int" value="115200"/><!--A1
/A2 -->
<!--param name="serial_baudrate" type="int" value="256000"--><! --A3 -->
<param name="frame_id" type="string" value="laser"/>
<param name="inverted" type="bool" value="false"/>
<param name="angle_compensate" type="bool" value="true"/>
</node>
<!-- Connect to Pioneer -->
<node pkg = "rosaria" type = "RosAria" name = "RosAria">
<param name="port" value="/dev/ttyUSB1" type="string"/>
</node>
<!-- Launch p3dx description --> A.15. Navigation Launch File A.15. Navigation Launch File <!-- Launch rplidar --> <!-- Launch p3dx description --> 55 <param name="robot_description" textfile="$(arg model)" /> <param name="use_gui" value="$(arg gui)"/> <node name="joint_state_publisher" pkg="joint_state_publisher" type="joint_st
ate_publisher" > <node name="robot_state_publisher" pkg="robot_state_publisher" type="state_pu
blisher" /> <node name="rviz" pkg="rviz" type="rviz" args="-d $(find urdf_tutorial)/urdf. rviz" /> <!-- transfor configurations --> <node pkg="tf" type="static_transform_publisher" name="link1_broadcaster" arg
s="0 0 0.1 0 0 0 odom base_link 100"/> <!-- <node pkg="tf" type="static_transform_publisher" name="link2_broadcaster
" args="0 0 0.1 0 0 0 map odom 100"/> --> <node pkg="tf" type="static_transform_publisher" name="link3_broadcaster" arg
s="0 0 0.1 0 0 0 base_link laser 100"/> <param name="map_udpate_interval" value="1.0"/> <param name="sigma" value="0.1"/> 56 57 <param name="llsamplerange" value="0.01"/>
<param name="llsamplestep" value="0.05"/>
<param name="lasamplerange" value="0.05"/>
<param name="lasamplestep" value="0.05"/>
</node>
</launch> <param name="llsamplerange" value="0.01"/>
<param name="llsamplestep" value="0.05"/>
<param name="lasamplerange" value="0.05"/>
<param name="lasamplestep" value="0.05"/>
</node>
</launch> <param name="llsamplerange" value="0.01"/> <param name="llsamplestep" value="0.05"/> <param name="lasamplerange" value="0.05"/> </node> </node> 58 References [1] H. F. Durrant-Whyte and J. J. Leonard, "Simultaneous map building and localization for an
autonomous mobile robot,," IEEE/RSJ International Workshop on Intelligent Robots and
Systems '91, vol. 3, pp. 1442-1447, 1991. [1] H. F. Durrant-Whyte and J. J. Leonard, "Simultaneous map building and localization for an
autonomous mobile robot,," IEEE/RSJ International Workshop on Intelligent Robots and
Systems '91, vol. 3, pp. 1442-1447, 1991. [2] M. Quigley, K. Conley, B. P. Gerkey, J. Faust, T. Foote, J. Leibs, R. Wheeler and A. Y. Ng, "ROS: an open-source Robot Operating System," ICRA Workshop on Open Source
Software, 2009. [4] M. Filipenko and I. Afanasyev, "Comparison of Various SLAM Systems for Mobile Robot
in an Indoor Environment," in 9th IEEE International Conference on Intelligent Systems,
Madeira, Portugal, 2018. [5] A. Diosi, G. Taylor and L. Kleeman, "Interactive SLAM using Laser and Advanced
Sonar,," Proceedings of the 2005 IEEE International Conference on Robotics and
Automation, pp. 1103-1108, 2005. [6] Y. Abdelrasoul, A. B. S. H. Saman and P. Sebastian, "A quantitative study of tuning ROS
gmapping parameters and their effect on performing indoor 2D SLAM,," 2nd IEEE
International Symposium on Robotics and Manufacturing Automation (ROMA), pp. 1-6,
2016. [7] G. Grisetti, C. Stachniss and W. Burgard, "Improved Techniques for Grid Mapping With
Rao-Blackwellized Particle Filters," IEEE Transactions on Robotics, vol. 23, no. 1, pp. 34-
4, 2007. 59 [8] C. Forster, M. Pizzoli and D. Scaramuzza, "SVO: Fast semi-direct monocular visual
odometry,," IEEE International Con- ference on Robotics and Automation, p. 15–22, 2014. [9] J. Civera and A. Concha, "DPPTAM: Dense piecewise planar tracking and mapping from a
monocular sequence," IEEE International Confer- ence on Intelligent Robots and Systems,
p. 5686–5693, 2015. [10] J. Engel, T. Scho ̈ps and D. Cremers, "Lsd-slam: Large-scale direct monocular slam,," European Conference on Computer Vision, p. 834– 849, 2014. [11] N. Yang, R. Wang, X. Gao and D. Cremers, "Challenges in monocular visual odometry:
Photometric calibration, motion bias, and rolling shutter effect,," IEEE Robotics and
A
i
L
l 3
4
2878 2885 2018 [11] N. Yang, R. Wang, X. Gao and D. Cremers, "Challenges in monocular visual odometry:
Photometric calibration, motion bias, and rolling shutter effect,," IEEE Robotics and [11] N. Yang, R. Wang, X. Gao and D. Cremers, "Challenges in monocular visual odometry: Photometric calibration, motion bias, and rolling shutter effect,," IEEE Robotics and
Automation Letters, vol. 3, no. 4, p. 2878–2885, 2018. [15] B. Gerkey, "ROS WiKi," [Online]. Available: http://wiki.ros.org/slam_karto. [Accessed 15
12 2010]. References Photometric calibration, motion bias, and rolling shutter effect,," IEEE Robotics and
A
i
L
l 3
4
2878 2885 2018 Automation Letters, vol. 3, no. 4, p. 2878–2885, 2018. [12] M. Labbe ́ and F. Michaud, "Online global loop closure detection for large-scale multi-
session graph-based SLAM," IEEE Int. Conference on Intelligent Robots and Systems, p. 2661–2666, 2014. [13] R. Mur-Artal, J. M. M. Montiel and J. D. Tardos, "Orb-slam:aversatile and accurate
monocular slam system,," IEEE Trans. on Robotics, vol. 31, no. 5, p. 1147–1163, 2015. [14] T. Pire, T. Fischer, G. Castro, P. DeCristo ́foris, J. Civera and J. JacoboBerlles, "S-PTAM:
Stereo Parallel Tracking and Mapping,," Robotics and Autonomous Systems, vol. 93, p. 27–
42, 2017. [15] B. Gerkey, "ROS WiKi," [Online]. Available: http://wiki.ros.org/slam_karto. [Accessed 15
12 2010]. [13] R. Mur-Artal, J. M. M. Montiel and J. D. Tardos, "Orb-slam:aversatile and accurate
monocular slam system,," IEEE Trans. on Robotics, vol. 31, no. 5, p. 1147–1163, 2015. [14] T. Pire, T. Fischer, G. Castro, P. DeCristo ́foris, J. Civera and J. JacoboBerlles, "S-PTAM:
Stereo Parallel Tracking and Mapping,," Robotics and Autonomous Systems, vol. 93, p. 27–
42, 2017. [15] B. Gerkey, "ROS WiKi," [Online]. Available: http://wiki.ros.org/slam_karto. [Accessed 15
12 2010]. 60 [16] B. Steux and O. E. Hamzaoui, "tinySLAM: A SLAM algorithm in less than 200 lines C-
language program,," 11th International Conference on Control Automation Robotics &
Vision, pp. 1975-1979, 2010. [17] L. Carlone, R. Aragues, J. Castellanos and B. Bona, "A linear approximation for graph-
based simultaneous localization and mapping," In Proc. of the Int. Conf. Robotics: Science
and Systems, 2011. [18] W. Hess, D. Kohler, H. Rapp and D. Andor, "Real-time loop closure in 2d lidar slam,"
Robotics and Automation (ICRA), p. 1271–1278, 2016. [19] S. Kohlbrecher, O. Stryk, J. Meyer and U. Klingauf, "A flexible and scalable SLAM
system with full 3D motion estimation," IEEE International Symposium on Safety,
Security, and Rescue Robotics, pp. 155-160, 2011. 0] A. Filatov, A. Filatov and K. Krinkin, "2D SLAM Quality Evaluation Methods," Conference of Open Innovations Association (FRUCT), no. 21st, pp. 120 - 126, 2017. [21] J. M. Santos, D. Portugal and R. P. Rocha, "An evaluation of 2D SLAM techniques
available in Robot Operating System,," IEEE International Symposium on Safety, Security,
and Rescue Robotics (SSRR), pp. 1-6, 2013. [22] J. Esenkanova, H. Ilhan and S. References Yavuz, "Pre-Mapping System with Single Laser Sensor
Based on Gmapping Algorithm," International Journal of Electrical Energy, pp. 97-101,
2013. [23] P. Wang, Z. Chen, Q. Zhang and J. Sun, "A loop closure improvement method of
gmapping for low cost and resolution laser scanner," IFAC (International Federation of
Automatic Control), 2016. 61 [25] S. Slamtec.Co., "Slamtec," 13 03 2013. [Online]. Available: http://www.slamtec.com/en/lidar/a1. [Accessed 04 07 2016]. [26] E. Marder-Eppstein, E. Berger, T. Foote, B. Gerkey and K. Konolige, "The office
marathon: Robust navigation in an indoor office environment," IEEE international
conference on robotics and automation, pp. 300-307, 2010. [27] T. Zhang, Z. J. Chong, B. Qin, J. G. M. Fu, S. Pendleton and M. H. Ang Jr., "Sensor fusion
for localization, mapping and navigation in an indoor environment," IEEE International
Conference Humanoid, Nanotechnology, Information Technology Communication and
Control, Environment and Management (HNICEM), no. 7th, 2014. [28] D. V. Lu, D. Hershberger and W. D. Smart, "Layered costmaps for context-sensitive
navigation,," IEEE/RSJ International Conference on Intelligent Robots and Systems, pp. 709-715, 2014. [29] S. Thrun, "An online mapping algorithm for teams of mobile robots," Int. J. Robot, vol. 20,
no. 5, p. 335–36, 2001. [30] K. Konolige, G. Grisetti, R. Kümmerle, W. Burgard, B. Limketkai and B. Vincent,
"Efficient Sparse Pose Adjustment for 2D mapping,," IEEE/RSJ International Conference
on Intelligent Robots and Systems, pp. 22-29, 2010. [31] G. Dissanayake, H. Durrant-Whyte and T. Bailey, "A computation- ally efficient solution
to the simultaneous localisation and map building (SLAM) problem,," Proc. IEEE Int. Conf. Robot. Autom, p. 1009–1014, 2000. 62 63 63
|
https://openalex.org/W4382724550
|
https://www.mdpi.com/1422-0067/24/13/10750/pdf?version=1687928283
|
English
| null |
Maytenus octogona Superoxide Scavenging and Anti-Inflammatory Caspase-1 Inhibition Study Using Cyclic Voltammetry and Computational Docking Techniques
|
International journal of molecular sciences
| 2,023
|
cc-by
| 11,436
|
Citation: Caruso, F.; Rossi, M.;
Eberhardt, E.; Berinato, M.; Sakib, R.;
Surco-Laos, F.; Chavez, H. Maytenus
octogona Superoxide Scavenging and
Anti-Inflammatory Caspase-1
Inhibition Study Using Cyclic
Voltammetry and Computational
Docking Techniques. Int. J. Mol. Sci. 2023, 24, 10750. https://doi.org/
10.3390/ijms241310750 Keywords:
Maytenus;
caspase-1;
inflammation;
antioxidants;
tingenone;
pristimerin;
hydroxytingenone; docking; DFT; hydrodynamic voltammetry Academic Editor: Anna Cie´sli´nska o 1,*, Miriam Rossi 1
, Eric Eberhardt 1, Molly Berinato 1, Raiyan Sakib 1, Felipe Surco-Laos
avez 2 1
Department of Chemistry, Vassar College, Poughkeepsie, NY 12604, USA
2
Facultad de Farmacia y Bioquímica, Universidad Nacional San Luis Gonzaga, Ica 11004, Peru
*
Correspondence: caruso@vassar.edu Abstract: The relationship between oxidative stress and inflammation is well known, and exoge-
nous antioxidants, primarily phytochemical natural products, may assist the body’s endogenous
defense systems in preventing diseases due to excessive inflammation. In this study, we evaluated
the antioxidant properties of ethnomedicines from Peru that exhibit anti-inflammatory activity by
measuring the superoxide scavenging activity of ethanol extracts of Maytenus octogona aerial parts
using hydrodynamic voltammetry at a rotating ring-disk electrode (RRDE). The chemical composi-
tions of these extracts are known and the interactions of three methide-quinone compounds found in
Maytenus octogona with caspase-1 were analyzed using computational docking studies. Caspase-1 is a
critical enzyme triggered during the activation of the inflammasome and its actions are associated
with excessive release of cytokines. The most important amino acid involved in active site caspase-1
inhibition is Arg341 and, through docking calculations, we see that this amino acid is stabilized by in-
teractions with the three potential methide-quinone Maytenus octogona inhibitors, hydroxytingenone,
tingenone, and pristimerin. These findings were also confirmed after more rigorous molecular dy-
namics calculations. It is worth noting that, in these three compounds, the methide-quinone carbonyl
oxygen is the preferred hydrogen bond acceptor site, although tingenone’s other carbonyl group also
shows a similar binding energy preference. The results of these calculations and cyclovoltammetry
studies support the effectiveness and use of anti-inflammatory ethnopharmacological ethanol extract
of Maytenus octogona (L’Héritier) DC. International Journal of
Molecular Sciences International Journal of
Molecular Sciences International Journal of
Molecular Sciences International Journal of
Molecular Sciences Citation: Caruso, F.; Rossi, M.;
Eberhardt, E.; Berinato, M.; Sakib, R.;
Surco-Laos, F.; Chavez, H. Maytenus
octogona Superoxide Scavenging and
Anti-Inflammatory Caspase-1
Inhibition Study Using Cyclic
Voltammetry and Computational
Docking Techniques. Int. J. Mol. Sci.
2023, 24, 10750. https://doi.org/
10.3390/ijms241310750 1. Introduction A second signal, from various origins, involves releasing reactive oxygen
species (ROS) that stimulate inflammasome assembly, leading to the activation of caspase-1
and the subsequent processing of pro-IL-1β into IL-1β and pyroptosis [3]. In some cases,
with excessive amounts of cytokines being produced, diseases such as atherosclerosis,
cancer, and COVID-19 infection can result. Of late, several known anti-inflammatory
medicinal compounds are being reevaluated to counteract the body’s inflammatory re-
sponse to COVID-19 virus infection. Antioxidants that suppress ROS production and
caspase-1 activation may help diminish the inflammasome response and are promising for
the development of a novel therapy. Details of caspase-1 role in inflammation have been
described [6], including a recent review [10]. Recently, to analyze the inhibition of caspase-1 by anti-inflammatory drugs, our group
used computational methods and measured the antioxidant activity towards the damaging
superoxide radical using the RRDE cyclovoltammetry method that was developed in
our laboratory [11]. Previously, we associated the anti-COVID-19 biological activity of
celastrol, a natural product abundant in flowering plants of the genus Maytenus and the
family Celastraceae, with its inhibition of the COVID-19 main protease and its scavenging of
superoxide [12]. p
The roots, bark, and leaves of Maytenus plants, spread in tropical and sub-tropical
regions of the world, are a rich source of widely used triterpenoids in ethnopharmacol-
ogy and traditional medicines as anti-tumor, anti-asthmatic, analgesic, anti-inflammatory,
antimicrobial, and antiulcer agents [13,14]. These plants are common in Peru, a country
that has a rich flora that provides many useful bioactive compounds [15]. Indigenous
populations use these plants for their anti-inflammatory properties. In particular, the high
sub Andean region of the Amazonian river basin (Peru, Ecuador, Colombia) is home to a
Maytenus species named chuchuasha (or chuchuaso), whose alcoholic root bark extracts
are used in traditional medicine to reduce inflammation. Because a relationship between
oxidative stress and inflammation is known, exogenous antioxidants may provide a poten-
tial protective effect by assisting the body’s defense systems in preventing diseases due to
excessive inflammation. Phenoldienones such as tingenone and 2-hydroxytingenone are
present in the plant, and the biological activities of these compounds are in agreement with
those observed when using the plant extracts in traditional health practices [16]. Following our interest in investigating the medicinal properties of the Maytenus
genus [17–20], in this study, we analyzed the antioxidant properties of ethanol extracts from
the leaves and stems of Maytenus octogona plants. 1. Introduction Received: 13 June 2023
Revised: 24 June 2023
Accepted: 26 June 2023
Published: 28 June 2023 Received: 13 June 2023
Revised: 24 June 2023
Accepted: 26 June 2023
Published: 28 June 2023 Caspases are a highly conserved family of cysteine protease enzymes that may induce
apoptosis and inflammation [1]. Caspase-1 plays a crucial role in the inflammatory response
by cleaving proteins after triggering the release of proinflammatory cytokines such as
interleukin-1 beta (IL-1β) and interleukin-18 (IL-18). During a viral attack, the immune
system reacts strongly to this invasion, sometimes overproducing cytokines—a “cytokine
storm”. Events associated with the over-activation of the immune response have been
connected to poor outcomes in patients with COVID-19 [2,3]. For instance, high levels
of proinflammatory cytokine IL-1β were detected in the lung parenchyma of COVID-19
patients [4]. Moreover, increased levels of IL-18 are observed with increased mortality in
sepsis-induced acute respiratory distress syndrome (ARDS) [5]. Inhibition of caspase-1
and the inflammasome pathway may provide an opportunity to suppress the heightened
immune response and offer an alternative anti-COVID-19 therapy [6]. Copyright:
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article
distributed
under
the
terms
and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/). p
py
Activation of the inflammasome is a crucial function mediated by the innate immune
system [3], Figure S1. Initiation is necessary in cases of cellular or molecular damage or, on https://www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2023, 24, 10750. https://doi.org/10.3390/ijms241310750 Int. J. Mol. Sci. 2023, 24, 10750 2 of 17 infection, when interactions with foreign pathogens occur. Since inflammation is associated
with many human diseases, anomalous activation can result in uncontrolled responses
responsible for many pathogenic states besides the recent COVID-19 pandemic described
earlier. The initial step of inflammasome activation involves the binding of exogenous
ligands, such as pathogen-associated molecular patterns (PAMPs) or damage/danger-
associated molecular patterns (DAMPs), to a pattern recognition receptor (PRR). Several
families of PRRs exist, including the nucleotide-binding domain and leucine-rich repeat-
containing proteins (NLRs, also known as NOD-like receptors). PRR binding stimulates a
cascade that produces pro-IL-1β and pro-IL-18 in an NFKβ-dependent manner [7], with the
relevant NLR oligomerizing becoming a caspase-1-activating scaffold. Active caspase-1 am-
plifies the inflammasome signal by cleaving the proinflammatory IL-1 family of cytokines
into their bioactive forms, IL-1β and IL-18, and causes pyroptosis, a type of inflammatory
cell death [8,9]. 2.1. Caspase 1 Docking
2 1 1 Hydroxytingenone
2.1.1. Hydroxytingenone 2.1.1. Hydroxytingenone
Using Materials Studio Dmol3 quantum chemistry program, the molecular structure
of hydroxytingenone was obtained through modifying the related crystal structure of
celastrol [12]. Molecular geometry optimization of the structure did not include the sol-
vent effect. This was suggested by the absence of water molecules in the active site and
the resulting hydroxytingenone coordinates were input for the docking study, which was
performed using the Discovery Studio molecular mechanics program on caspase-1. From
the Protein Data Bank (PDB) [21], we retrieved the PDB 6PZP caspase-1 in complex with
a small molecule inhibitor, VX-765 [22], where caspase-1 consisted of two protein subu-
nits. After Discovery Studio application of the CHARMm forcefield [23], H atoms were
assigned, VX-765 was selected to create a sphere of radius 10 Å and was then removed. H
h d
i
i
i
l
d
k d
d 10
b
i
d
Using Materials Studio Dmol3 quantum chemistry program, the molecular structure
of hydroxytingenone was obtained through modifying the related crystal structure of
celastrol [12]. Molecular geometry optimization of the structure did not include the solvent
effect. This was suggested by the absence of water molecules in the active site and the
resulting hydroxytingenone coordinates were input for the docking study, which was
performed using the Discovery Studio molecular mechanics program on caspase-1. From
the Protein Data Bank (PDB) [21], we retrieved the PDB 6PZP caspase-1 in complex with a
small molecule inhibitor, VX-765 [22], where caspase-1 consisted of two protein subunits. After Discovery Studio application of the CHARMm forcefield [23], H atoms were assigned,
VX-765 was selected to create a sphere of radius 10 Å and was then removed. Hence,
hydroxytingenone was put in its place, docked, and 10 poses were obtained. Hence, hydroxytingenone was put in its place, docked, and 10 poses were obtained. The relevant moieties of hydroxytingenone able to interact with the active site of
caspase-1 are the two carbonyl groups, located at both ends of the structure, as discussed
previously [11]. The carbonyl at the methide-quinone end is found in pose 4. A two-di-
mensional display of the amino acid interactions of docked hydroxytingenone at the ac-
tive site is shown in Figure 2. 1. Introduction We also focused on three components
related to celastrol from these plants—tingenone, hydroxytingenone, and pristimerin—and
studied their interactions with caspase-1 by performing docking studies to analyze their
potential inhibitory effects. Figure 1 shows the studied molecules. The scavenging of
superoxide by Maytenus octogona ethanol extracts was also described in this study. The
samples used in this study were collected by biologist Alfonso Orellana García in the area
of Molletambo, district of Yauca del Rosario, Region and Department of Ica, at georeferenc-
ing points (GPS): latitude (S): 14◦11′1.73′′, longitude (W): 75◦22′47.28′′, Voucher AO-113
(UNICA). Int. J. Mol. Sci. 2023, 24, 10750 3 of 17
er AO- Tingenone C28H36O3
Hydroxytingenone C28H36O4
Pristimerin C30H40O4
Celastrol C29H38O4
Figure 1. Two-dimensional canonical structural display of compounds analyzed in this study. Syn-
onyms: hydroxytingenone = beta-hydroxytingenone; maytenin = tingenone. Figure 1. Two-dimensional canonical structural display of compounds analyzed in this study. Syn-
onyms: hydroxytingenone = beta-hydroxytingenone; maytenin = tingenone. Tingenone C28H36O3
Pristimerin C30H40O4 Hydroxytingenone C28H36O4 Tingenone C28H36O3 Hydroxytingenone C28H36O4
Celastrol C29H38O4 Celastrol C29H38O4 Pristimerin C30H40O4 Figure 1. Two-dimensional canonical structural display of compounds analyzed in this study. Syn-
onyms: hydroxytingenone = beta-hydroxytingenone; maytenin = tingenone. Figure 1. Two-dimensional canonical structural display of compounds analyzed in this study. Syn-
onyms: hydroxytingenone = beta-hydroxytingenone; maytenin = tingenone. 2.1. Caspase 1 Docking
2 1 1 Hydroxytingenone
2.1.1. Hydroxytingenone The final arrangement,
ncluding calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car-
bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl
that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone
carbonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl
that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car-
bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl
that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car-
bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl
that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone
carbonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl
that shows no interactions. igure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car-
onyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl
hat shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car-
bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl
that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone
carbonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl
that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car-
bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl
that shows no interactions. Figure 3. More detailed features of pose 4, hydroxytingenone, docking. The donor guanidino group
of Arg341 (turquoise colored C atoms) has a double H-bond interaction with O(methide-quinone)
carbonyl, 2.636 Å and 2.979 Å. The O(hydroxyl) associated with the methide-quinone inhibitor has a
double H-bond interaction, one with H(Cys285), 1.837 Å, and one with H(His237), 2.772 Å (lower left
of figure). Figure 3. More detailed features of pose 4, hydroxytingenone, docking. The donor guanidino group
of Arg341 (turquoise colored C atoms) has a double H-bond interaction with O(methide-quinone)
carbonyl, 2.636 Å and 2.979 Å. 2.1. Caspase 1 Docking
2 1 1 Hydroxytingenone
2.1.1. Hydroxytingenone Discovery Studio provides the Cdocker interaction energy,
which is the non-bonded interaction energy (composed of the van der Waals term and the
electrostatic term) between the protein and the potential inhibitor ligand related to the
force field CHARMm; this value is −22.4 kcal/mol for hydroxytingenone pose 4. A more
y
y
g
p
p
p
The relevant moieties of hydroxytingenone able to interact with the active site of
caspase-1 are the two carbonyl groups, located at both ends of the structure, as discussed
previously [11]. The carbonyl at the methide-quinone end is found in pose 4. A two-
dimensional display of the amino acid interactions of docked hydroxytingenone at the
active site is shown in Figure 2. Discovery Studio provides the Cdocker interaction energy,
which is the non-bonded interaction energy (composed of the van der Waals term and the
electrostatic term) between the protein and the potential inhibitor ligand related to the
force field CHARMm; this value is −22.4 kcal/mol for hydroxytingenone pose 4. A more
specific display of pose 4 is shown in Figure 3, where besides the H-bonds relevant to the
methide-quinone moiety (Arg341 and His237), a Cys285 interaction (upon a slight variation
in the cysteine C-C-S-H torsion angle) is seen to establish a very short H-bond distance
between H(Cys285) and the hydroxytingenone hydroxyl group, 1.837 Å. However, the
Cys285 interaction is not confirmed after a standard dynamic cascade protocol of Discovery Int. J. Mol. Sci. 2023, 24, 10750 4 of 17
varia
nd dis-
dis- Studio, while Arg341 and His237 are indeed confirmed. The final arrangement, including
calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. the Cys285 interaction is not confirmed after a standard dynamic cascade protocol of Dis
covery Studio, while Arg341 and His237 are indeed confirmed. The final arrangement,
including calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. covery Studio, while Arg341 and His237 are indeed confirmed. The final arrangement,
including calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. Studio, while Arg341 and His237 are indeed confirmed. The final arrangement, including
calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. the Cys285 interaction is not confirmed after a standard dynamic cascade protocol of Dis
covery Studio, while Arg341 and His237 are indeed confirmed. The final arrangement,
including calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. covery Studio, while Arg341 and His237 are indeed confirmed. 2.1. Caspase 1 Docking
2 1 1 Hydroxytingenone
2.1.1. Hydroxytingenone The O(hydroxyl) associated with the methide-quinone inhibitor has a
double H-bond interaction, one with H(Cys285), 1.837 Å, and one with H(His237), 2.772 Å (lower left
of figure). Figure 3. More detailed features of pose 4, hydroxytingenone, docking. The donor guanidino group
of Arg341 (turquoise colored C atoms) has a double H-bond interaction with O(methide-quinone)
carbonyl, 2.636 Å and 2.979 Å. The O(hydroxyl) associated with the methide-quinone inhibitor has a
double H-bond interaction, one with H(Cys285), 1.837 Å, and one with H(His237), 2.772 Å (lower left
of figure). 5 of 17
(lower Int. J. Mol. Sci. 2023, 24, 10750 Figure 4. After molecular dynamics pose 4, hydroxytingenone has calculated binding energy of
−13.7 kcal/mol. The H-bond interaction between the donor guanidino group of Arg341 and
O(methide-quinone) carbonyl is confirmed and strengthened, 2.109 Å, whereas an H-bond of 1.663
Å by acceptor O(Ser339) replaces the former interactions by Cys285 and His237. A comparison with
interactions shown by the inhibitor VX-765 at the crystal structure active site [22], shows involve-
ment of both amino acids, Arg341 and O(Ser339), also forming hydrogen bonds; the latter interacts
with a guanidino HN moiety. Indeed, the role of Arg341 appears very important as it has a double
hydrogen bond interaction with two different O(carbonyl) moieties of VX-765. Figure 4. After molecular dynamics pose 4, hydroxytingenone has calculated binding energy
of −13.7 kcal/mol. The H-bond interaction between the donor guanidino group of Arg341 and
O(methide-quinone) carbonyl is confirmed and strengthened, 2.109 Å, whereas an H-bond of 1.663 Å
by acceptor O(Ser339) replaces the former interactions by Cys285 and His237. A comparison with
interactions shown by the inhibitor VX-765 at the crystal structure active site [22], shows involvement
of both amino acids, Arg341 and O(Ser339), also forming hydrogen bonds; the latter interacts with a
guanidino HN moiety. Indeed, the role of Arg341 appears very important as it has a double hydrogen
bond interaction with two different O(carbonyl) moieties of VX-765. Another cluster that includes poses 5, 6, 7, 9 shows important interactions at the op-
posite end of hydroxytingenone, with Cys285 forming a H-bond to the O(carbonyl). Pose
5 was not confirmed by standard dynamics cascade as the ligand was thoroughly dis-
placed from the active site. A smaller cluster was formed by poses 1 and 2, where Cys285
and His237 show H-bonds to the carbonyl opposite the methide-quinone moiety. 2.1. Caspase 1 Docking
2 1 1 Hydroxytingenone
2.1.1. Hydroxytingenone After
applying dynamics to pose 1, the binding energy is −7.2 kcal/mol, which is markedly more
positive than that of pose 4 (−13.7 kcal/mol). Additionally, pose 3 shows an interaction
between the same carbonyl involved in pose 1, having H-bonds with Cys285 and Arg341. After dynamics, the binding energy is −8.9 kcal/mol, slightly better than that of pose 1 but
still much less favored than that of pose 4. We conclude that hydroxytingenone molecular
mechanics favor a pose 4 arrangement, shown in Figure 4. Another cluster that includes poses 5, 6, 7, 9 shows important interactions at the
opposite end of hydroxytingenone, with Cys285 forming a H-bond to the O(carbonyl). Pose 5 was not confirmed by standard dynamics cascade as the ligand was thoroughly
displaced from the active site. A smaller cluster was formed by poses 1 and 2, where Cys285
and His237 show H-bonds to the carbonyl opposite the methide-quinone moiety. After
applying dynamics to pose 1, the binding energy is −7.2 kcal/mol, which is markedly more
positive than that of pose 4 (−13.7 kcal/mol). Additionally, pose 3 shows an interaction
between the same carbonyl involved in pose 1, having H-bonds with Cys285 and Arg341. After dynamics, the binding energy is −8.9 kcal/mol, slightly better than that of pose 1 but
still much less favored than that of pose 4. We conclude that hydroxytingenone molecular
mechanics favor a pose 4 arrangement, shown in Figure 4. 2.1.2. Tingenone
2.1.2. Tingenone g
Our next docked compound was tingenone. Its atomic coordinates were derived
from hydroxytingenone and minimized with Dmol3. Poses 1 and 5 are representatives of
well-distinguished clusters in the docking as the first includes poses 2–4, 6, and 8, whereas
pose 5 cluster includes poses 7 and 9. Pose 1 has Cdocker interaction energy −27.9 kcal/mol
and shows interactions with the non-methide-quinone carbonyl, involving Arg341 and
His237, see Figures 5 and S2. After the standard dynamics cascade, pose 1 is confirmed
Our next docked compound was tingenone. Its atomic coordinates were derived
from hydroxytingenone and minimized with Dmol3. Poses 1 and 5 are representatives of
well-distinguished clusters in the docking as the first includes poses 2–4, 6, and 8, whereas
pose 5 cluster includes poses 7 and 9. Pose 1 has Cdocker interaction energy −27.9 kcal/mol
and shows interactions with the non-methide-quinone carbonyl, involving Arg341 and
His237, see Figures 5 and S2. After the standard dynamics cascade, pose 1 is confirmed and
the final arrangement obtained after binding energy calculations, −11.8 kcal/mol, is shown
in Figure 6; this does not include His237. Interestingly, a cation-π interaction from another
arginine, Arg383, is present at the other end of the molecule involving the methide-quinone
moiety (2.752 Å) and so this pose appears tightly bound at the active site. Int. J. Mol. Sci. 2023, 24, 10750 6 of 17
ng the
active
the
ctive Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide-
quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety
appears free of interactions. Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide-
quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety
appears free of interactions. Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide-
quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety
appears free of interactions. Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide-
quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety
appears free of interactions. Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide
quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety
appears free of interactions. igure 5. Pose 1. 2.1.2. Tingenone
2.1.2. Tingenone The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide-
uinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety
ppears free of interactions. Figure 6. Pose 1. The tingenone dynamics of pose 1 has a calculated binding energy of −11.8
kcal/mol. The guanidino group of Arg383 (turquoise colored) establishes a cation-π interaction with
the methide-quinone ring, 2.752 Å, whereas the originally docked Arg341 (violet colored) has a dou-
ble non-chelating H-bond from the guanidino group to the opposite carbonyl, 3.262 Å and 3.088 Å. igure 6. Pose 1. The tingenone dynamics of pose 1 has a calculated binding energy of −11.8
cal/mol. The guanidino group of Arg383 (turquoise colored) establishes a cation-π interaction with
he methide-quinone ring, 2.752 Å, whereas the originally docked Arg341 (violet colored) has a dou-
le non-chelating H-bond from the guanidino group to the opposite carbonyl, 3.262 Å and 3.088 Å. Figure 6. Pose 1. The tingenone dynamics of pose 1 has a calculated binding energy of −11.8 kcal/mol. The guanidino group of Arg383 (turquoise colored) establishes a cation-π interaction with the
methide-quinone ring, 2.752 Å, whereas the originally docked Arg341 (violet colored) has a double
non-chelating H-bond from the guanidino group to the opposite carbonyl, 3.262 Å and 3.088 Å. Interestingly, the cation-π interaction reminds us of the interaction that the same amino acid, Arg383,
establishes with an aromatic ring of original inhibitor VX-765 in the crystal structure. The
only
H-bond
shown
by
pose
5
docking
(Cdocker
interaction
ener-
gy = −25.1 kcal/mol) is with Arg341, which also involves the non-methide-quinone moiety
(Figures 7 and S3), which is confirmed by dynamics and has a calculated binding energy of Int. J. Mol. Sci. 2023, 24, 10750 7 of 17
= −25 1
25 1 −13.0 kcal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due
to the equal binding energy of poses 1 and 5. 7 and S3), which is confirmed by dynamics and has a calculated binding energy of −13.0
kcal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due to the
equal binding energy of poses 1 and 5. 7 and S3), which is confirmed by dynamics and has a calculated binding energy of −13.0
kcal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due to the
qual binding energy of poses 1 and 5. −13.0 kcal/mol, Figure 8. 2.1.3. Pristimerin
d
d The last docked compound was pristimerin. Pose 4 belongs to the most populated
cluster that includes poses 7 and 10. Its Cdocker interaction energy is −26.8 kcal/mol. There is a methide-quinone moiety involved in this cluster, interacting with Arg341 and
π-sulfur Cys285 Figure 9 and Figure S4. Dynamics confirms the arrangement and, after
calculating binding energy, −9.4 kcal/mol, Figure 10 shows three successive amino acid
residues involved, Ser339-Trp340-Arg341, forming H-bonds of 1.524 Å, 2.297 Å and 2.370 Å,
respectively. ed compound was pristimerin. Pose 4 belongs to the most populated
es poses 7 and 10. Its Cdocker interaction energy is −26.8 kcal/mol. There
ne moiety involved in this cluster, interacting with Arg341 and π-sulfur
and S4. Dynamics confirms the arrangement and, after calculating bind-
al/mol, Figure 10 shows three successive amino acid residues involved,
g341, forming H-bonds of 1.524 Å, 2.297 Å and 2.370 Å, respectively. Pristimerin docking results, two-dimensional display. Cys285 shows π-sulfur in-
methide-quinone ring and Arg341 has a H-bond to the methide-quinone O(car-
Figure 9. Pose 4. Pristimerin docking results, two-dimensional display. Cys285 shows π-sulfur inter-
action with the methide-quinone ring and Arg341 has a H-bond to the methide-quinone O(carbonyl). stimerin docking results, two-dimensional display. Cys285 shows π-sulfur in-
ethide-quinone ring and Arg341 has a H-bond to the methide-quinone O(car-
Figure 9. Pose 4. Pristimerin docking results, two-dimensional display. Cys285 shows π-sulfur inter-
action with the methide-quinone ring and Arg341 has a H-bond to the methide-quinone O(carbonyl). (non methide-quinone) located at the other end of pristimerin (pose 1)
eractions with Cys285 and Arg341, which is not confirmed by applying
merin moves out of the active site. When analyzing the cluster made by
H-bond interaction with Asp288 is seen. Upon dynamics of pose 2, this
H b
d
ith C
285
h
bi di
i
9 3 k
l/
l
i
il
The carbonyl (non methide-quinone) located at the other end of pristimerin (pose 1)
shows H-bond interactions with Cys285 and Arg341, which is not confirmed by applying
dynamics as pristimerin moves out of the active site. When analyzing the cluster made
by poses 2 and 3, an H-bond interaction with Asp288 is seen. Upon dynamics of pose 2,
this evolves towards an H-bond with Cys285, whose binding energy is −9.3 kcal/mol,
similar to that arising from pose 4. No other poses involve this carbonyl opposite the
methide-quinone. 2.1.2. Tingenone
2.1.2. Tingenone Thus, both carbonyls of tingenone show a similar preference due
to the equal binding energy of poses 1 and 5. 7 and S3), which is confirmed by dynamics and has a calculated binding energy of −13.0
kcal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due to the
equal binding energy of poses 1 and 5. and S3), which is confirmed by dynamics and has a calculated binding energy of −13.0
cal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due to the
qual binding energy of poses 1 and 5. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non-
methide-quinone moiety. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non-
methide-quinone moiety. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non-
methide-quinone moiety. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non-
methide-quinone moiety. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non-
methide-quinone moiety. gure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non-
ethide-quinone moiety. Figure 8. Pose 5. Tingenone dynamics has a calculated binding energy of −13.0 kcal/mol. It shows a
very short H-bond distance of 1.971 Å, from guanidino H(Arg341) to the O(carbonyl) opposed to the
methide-quinone carbonyl. Figure 8. Pose 5. Tingenone dynamics has a calculated binding energy of −13.0 kcal/mol. It shows a
very short H-bond distance of 1.971 Å, from guanidino H(Arg341) to the O(carbonyl) opposed to the
methide-quinone carbonyl. Figure 8. Pose 5. Tingenone dynamics has a calculated binding energy of −13.0 kcal/mol. It shows a
very short H-bond distance of 1.971 Å, from guanidino H(Arg341) to the O(carbonyl) opposed to the
methide-quinone carbonyl. Int. J. Mol. Sci. 2023, 24, 10750
very short H-bon
the methide-quin 8 of 17
o 2.1.3. Pristimerin
d
d O(methide-
quinone-carbonyl) establishes an H-bond to brown colored H(Arg341), 2.370 Å, and to turquoise
colored H(Trp340), 2.297 Å, whereas O(Ser339) is 1.524 Å from pristimerin H(hydroxy). Interest-
ingly, the above mentioned O(Ser339) interaction seen in hydroxytingenone, and found in VX-765
crystal structure through an HN moiety, is identical to that seen in pristimerin, supporting a poten-
tial role of this ligand and hydroxytingenone at the active site. In addition, the interaction between
Trp340, indicated as π-alkyl in docking (Figure 9), and directed to the ring adjacent to the methide-
quinone, transforms to hydrogen bonding with O(carbonyl) after dynamics, 2.297 Å. Figure 10. Pristimerin pose 4 dynamics after calculating the binding energy, −9.4 kcal. O(methide-
quinone-carbonyl) establishes an H-bond to brown colored H(Arg341), 2.370 Å, and to turquoise
colored H(Trp340), 2.297 Å, whereas O(Ser339) is 1.524 Å from pristimerin H(hydroxy). Interestingly,
the above mentioned O(Ser339) interaction seen in hydroxytingenone, and found in VX-765 crystal
structure through an HN moiety, is identical to that seen in pristimerin, supporting a potential role
of this ligand and hydroxytingenone at the active site. In addition, the interaction between Trp340,
indicated as π-alkyl in docking (Figure 9), and directed to the ring adjacent to the methide-quinone,
transforms to hydrogen bonding with O(carbonyl) after dynamics, 2.297 Å. Poses 5 and 8 show π-π interactions with His342 and the dynamics of pose 5 displays
no H-bonds; the binding energy of this conformation is −5.8 kcal/mol. Additionally, pose
6 was analyzed and showed only van der Waals interactions. Upon dynamics, Gly238
shows an H-bond and a binding energy of −5.8 kcal/mol. Therefore, pristimerin pose 4,
involving the methide-quinone carbonyl, and pose 2, interacting with the opposite car-
bonyl, are equally preferred: −9.4 and −9.3 kcal/mol, respectively. A summary of amino
acid interactions is displayed in Table 1. From this docking study on these three natural products, we see marked differences to
our earlier published findings on dexamethasone and other anti-inflammatory drugs [11]
that showed important interactions with Cys285. In the present study, Cys285 shows no
interaction with tingenone at docking, whereas hydroxytingenone and pristimerin do
show such an interaction, although these are not confirmed after more rigorous molecular
dynamics calculations. Here, Arg341 is the more involved amino acid at the caspase-1
active site as it is stabilized by the three potential inhibitors, hydroxytingenone, tingenone,
and pristimerin. This interaction is also present after dynamics. 2.1.3. Pristimerin
d
d n H-bond with Cys285, whose binding energy is −9.3 kcal/mol, similar
m pose 4. No other poses involve this carbonyl opposite the methide-
q
Poses 5 and 8 show π-π interactions with His342 and the dynamics of pose 5 displays
no H-bonds; the binding energy of this conformation is −5.8 kcal/mol. Additionally, pose
6 was analyzed and showed only van der Waals interactions. Upon dynamics, Gly238
shows an H-bond and a binding energy of −5.8 kcal/mol. Therefore, pristimerin pose 4,
involving the methide-quinone carbonyl, and pose 2, interacting with the opposite carbonyl,
are equally preferred: −9.4 and −9.3 kcal/mol, respectively. A summary of amino acid
interactions is displayed in Table 1. Int. J. Mol. Sci. 2023, 24, 10750
Int. J. Mol. Sci. 2023, 24, x FOR PE 9 of 17
9 of 17 9 of 17
9 of 17 PEER REVIEW
9 of 17
Figure 10. Pristimerin pose 4 dynamics after calculating the binding energy, −9.4 kcal. O(methide-
quinone-carbonyl) establishes an H-bond to brown colored H(Arg341), 2.370 Å, and to turquoise
colored H(Trp340), 2.297 Å, whereas O(Ser339) is 1.524 Å from pristimerin H(hydroxy). Interest-
ingly, the above mentioned O(Ser339) interaction seen in hydroxytingenone, and found in VX-765
crystal structure through an HN moiety, is identical to that seen in pristimerin, supporting a poten-
tial role of this ligand and hydroxytingenone at the active site. In addition, the interaction between
Trp340, indicated as π-alkyl in docking (Figure 9), and directed to the ring adjacent to the methide-
quinone, transforms to hydrogen bonding with O(carbonyl) after dynamics, 2.297 Å. Figure 10. Pristimerin pose 4 dynamics after calculating the binding energy, −9.4 kcal. O(methide-
quinone-carbonyl) establishes an H-bond to brown colored H(Arg341), 2.370 Å, and to turquoise
colored H(Trp340), 2.297 Å, whereas O(Ser339) is 1.524 Å from pristimerin H(hydroxy). Interestingly,
the above mentioned O(Ser339) interaction seen in hydroxytingenone, and found in VX-765 crystal
structure through an HN moiety, is identical to that seen in pristimerin, supporting a potential role
of this ligand and hydroxytingenone at the active site. In addition, the interaction between Trp340,
indicated as π-alkyl in docking (Figure 9), and directed to the ring adjacent to the methide-quinone,
transforms to hydrogen bonding with O(carbonyl) after dynamics, 2.297 Å. Figure 10. Pristimerin pose 4 dynamics after calculating the binding energy, −9.4 kcal. 2.1.3. Pristimerin
d
d In the three natural
products, we see the methide-quinone carbonyl group to be the preferred acceptor involved
in hydroxytingenone, tingenone, and pristimerin hydrogen bonding interactions, agreeing
with our previous findings [11]; however, the other carbonyl in tingenone shows a similar
preference. Moreover, the interactions of our three celastrol derivatives docked at the
active site of caspase-1 involve amino acids also engaged by the inhibitor VX-765 in the
crystal structure, suggesting a closely related mechanism of inhibition. This includes
hydrogen bonds for all three analyzed ligands with Arg341; cation-π interaction with
Arg383, established with an aromatic ring of tingenone, and hydrogen bond interaction
with O(Ser339) for hydroxytingenone and pristimerin. Int. J. Mol. Sci. 2023, 24, 10750 10 of 17 10 of 17 Table 1. Amino acid H-bond and other interactions (*) with three components of Maytena octogona
at the active site of Caspase-1 upon docking. “P” is for pose; “none” indicates only van der Waals
interactions; “OUT” indicates that after dynamics the potential inhibitory molecule becomes displaced
outside the active site. Numbers (kcal/mol) within each box represent binding energy after dynamics. at the active site of Caspase-1 upon docking. “P” is for pose; “none” indicates only van der Waals
interactions; “OUT” indicates that after dynamics the potential inhibitory molecule becomes displaced
outside the active site. Numbers (kcal/mol) within each box represent binding energy after dynamics. P1
P2
P3
P4
P5
P6
P7
P8
P9
P10
H-
Tingenone
Cys285
His237
−7.2
Cys285
His237
−7.2
Arg341
Cys285
−8.9
Arg341
His237
−13.7
Trp340 π
OUT
Trp340
π
OUT
Trp340
OUT
Arg341
His237
Trp340 π
OUT
Trp340
Cys285
(unfavored)
Tingenone
Arg341
His237
−11.8
His237
−11.8
His237
Cys285
−11.8
His237
−11.8
Arg341 *
−13.0
His237
−11.8
Arg341
His342
(π-π) *
−13.0
His237
Cys285
−11.8
Arg341
His342
(π-π) *
−13.0
His237
Cys285
Pristimerin
Arg341
Cys285
OUT
Asp288
−9.3
Asp288
−9.3
Arg341
Cys285
(π-S) *
−9.4
His342 (π-π) *
−5.8
none
−5.8
Arg341
Cys285
(π-S) *
−9.4
His342
(π-π) *
−5.8
none
Arg341
Cys285
(π-S) *
−9.4 2.2. RRDE 2023, 24, 10750 p
y
p
g
p
p
p
Maytenus octogona extracts, in contrast with cold-extracted extra virgin olive oil [25]. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific
color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757,
whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific
color, for instance the 70 µL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific
color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757,
whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757,
whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific
color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. 2.2. RRDE The release of ROS, a signal for inflammasome activation, may come from a variety of
pathways, including K+ efflux, lysosomal rupture or mitochondrial dysfunction [6]. Thus,
analyzing the antioxidant capability of the plant extracts may provide an explanation for
their medicinal use. In our laboratory, we developed an electrochemical method for the direct and quan-
titative analysis of scavenging superoxide [24]. Figure 11 shows a collage of the voltam-
mograms associated with such an experiment for sample MORUnica (stem extract). The
bottom part of the figure shows the amount of superoxide generated after reduction of
bubbled O2 in the electrochemical cell (reaction (1), see Section 3.3); this is detected at the
disk electrode. The top part of the figure shows superoxide detected at the ring electrode. The first experiment is a blank indicated as a 0 µL line; the last one shows the minimum
amount of detected superoxide, for aliquot 510 µL. Each added aliquot decreases the current
intensity detected at the ring electrode, and this is due to superoxide consumed by the an-
tioxidant components of the extracts. For each voltammogram, the ratio ring current/disk
current is defined as the efficiency. The physical interpretation is also associated with the
time the generated superoxide (at the disk) takes to reach the ring and be oxidized. g
p
g
In Figure 12, the efficiency of all added aliquots is included, i.e., the collection ef-
ficiency is shown at the y axis, while the x axis shows the volume of added aliquot;
ultimately, the slope of the line is associated with the antioxidant capability of scaveng-
ing. Figures 13 and 14 show equivalent graphs for MOHUnica (leaf extract). Table 2
includes slopes of other natural products studied using the same method. This shows both
Maytenus octogona extracts having weaker antioxidant activity, compared with olive oil. This is probably due to the depletion of antioxidants during ethanolic sample preparations
of Maytenus octogona extracts, in contrast with cold-extracted extra virgin olive oil [25]. Table 2. Comparison of slopes of the plant products studied in this work with other natural products
analyzed using the RRDE method. Table 2. Comparison of slopes of the plant products studied in this work with other natural products
analyzed using the RRDE method. Olive Oil [25]
Black Seed Oil [26]
Propolis [27]
MORUnica
MOHUnica
−0.0838
−0.078
−0.0864
−0.008
−0.023 11 of 17
oil. This
tions of Int. J. Mol. Sci. 2.2. RRDE Each run is associated with a specific
color, for instance the 70 µL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific
color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. Fi
11 MORU i
( t
t
t) RRDE
lt
E
h
i
i t d
ith
ifi Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific
color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific
color, for instance the 70 µL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. (stem extract) RRDE voltammograms. Each run is associated with a specific
70 μL aliquot red line can be observed in the upper part, oxidation curve,
ectrode, which is consistent with the red line detected at the disk electrode for
same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific
color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. 2.2. RRDE Each run is associated with a specific
color, for instance the 70 µL aliquot red line can be observed in the upper part, oxidation curve,
detected at the ring electrode, which is consistent with the red line detected at the disk electrode for
reduction during the same experiment and located at the bottom of the figure. a (stem extract) RRDE voltammograms. Each run is associated with a specific
e 70 μL aliquot red line can be observed in the upper part, oxidation curve,
ectrode, which is consistent with the red line detected at the disk electrode for
same experiment and located at the bottom of the figure. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757
whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757,
whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757,
whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757,
whose slope is associated with the superoxide scavenging capability of the stem extract. a collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757,
ated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757,
whose slope is associated with the superoxide scavenging capability of the stem extract. 12 of 17
12 of 17 Int. J. Mol. Sci. 2023, 24, 10750
Int. J. Mol. Sci. 2023, 24, x FOR P
23, 24, x FOR PEER REVIEW Figure 13. MOHUnica (leaf extract) RRDE voltammograms. Figure 14. MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x +10.585, R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a stronger
capability of scavenging superoxide. Table 2. Comparison of slopes of the plant products studied in this work with other natural prod-
ucts analyzed using the RRDE method. Figure 13. MOHUnica (leaf extract) RRDE voltammograms. Figure 13. MOHUnica (leaf extract) RRDE voltammograms. Figure 14. p
ucts analyzed u
using the RRDE
3.1. Reagents Olive Oil [25]
Black Seed Oil [26] Propolis [27] MORUnica
MOHUnica
−0.0838
−0.078
−0.0864
−0.008
−0.023
]
Black Seed Oil [26] Propolis [27] MORUnica
MOHUnica
−0.078
−0.0864
−0.008
−0.023
For electrochemical studies, tetrabutylammonium bromide (TBAB; TCI Chemicals,
Portland, OR, USA) and 99.9% anhydrous dimethyl sulfoxide (DMSO; Sigma-Aldrich, Inc.,
St. Louis, MO, USA). 2.2. RRDE MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x +10.585, R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a stronger
capability of scavenging superoxide. Table 2. Comparison of slopes of the plant products studied in this work with other natural prod-
ucts analyzed using the RRDE method. Figure 14. MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x + 10.585,
R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a
stronger capability of scavenging superoxide. 3. Materials and Methods
3.1. Reagents
For electrochemical studies tetrabutylammonium bromide (TBAB; TCI Chemicals Figure 13. MOHUnica (leaf extract) RRDE voltammograms. Figure 13. MOHUnica (leaf extract) RRDE voltammograms. HUnica (leaf extract) RRDE voltammograms. Figure 14. MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x +10.585, R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a stronger
capability of scavenging superoxide. HUnica collection efficiency of the ethanol leaf extract, y = −0.0232x +10.585, R2 = 0.994. h the stem extract (Figure 12), the steeper slope in this figure indicates a stronger
avenging superoxide. Figure 14. MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x + 10.585,
R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a
stronger capability of scavenging superoxide. 3.1.2. MOR UNICA (Stem Extract) One kilogram of dried and ground stems of Maytenus octagona was extracted from
ethanol 96% in a Soxhlet apparatus until exhaustion. Evaporation of the solvent at reduced
pressure provided 275 g of a reddish-brown extract. 3.1.1. MOH UNICA (Leaf Extract) Two methods were used to obtain these samples: Two methods were used to obtain these samples: Int. J. Mol. Sci. 2023, 24, 10750 13 of 17 13 of 17 Method 1. Two kilograms of dry and ground Maytenus octogona leaves were macerated
for 20 h in hot (96◦) ethanol and were filtered. After this time, additional ethanol was added
and the mixture was refluxed for 4 h. The solution was filtered hot. Method 2. One kilogram of dried and ground leaves of Maytenus octagona were
extracted from ethanol 96% in a Soxhlet apparatus until exhaustion. Evaporation of the
solvent at reduced pressure provided 260 g of a dark green extract. p
p
g
g
Both the filtrates were combined and concentrated in a Buchi rotary evaporator at
40 ◦C and 400 g of a dark green dry extract was obtained. 3.2. Electrochemistry A Pine Research WaveDriver 20 bipotentiostat with the Modulated Speed Electrode
Rotator was used to perform the hydrodynamic voltammetry at a rotating ring-disk elec-
trode (RRDE). The working electrode is the AFE6R2 gold disk and gold ring rotator tip
(Pine Research, Durham, NC, USA) combined with a coiled platinum wire counter elec-
trode and a reference electrode consisting of an AgCl coated silver wire immersed in 0.1 M
tetrabutyl ammonium bromide (TBAB) in dry DMSO in a fritted glass tube. The electrodes
were placed in a five-neck electrochemical cell together with means for either bubbling
or blanketing the solution with gas. Voltammograms were collected using Aftermath
software release 1.6.10523 provided by Pine Research. Careful cleaning of the electrodes
was performed by polishing with 0.05 µm alumina-particle suspension (Allied High Tech
Products, Inc., Rancho Dominguez, CA, USA) on a moistened polishing microcloth to
eliminate potential film formation [28]. 3.3. Hydrodynamic Voltammetry (RRDE) MOH Unica (0.924 g) and MOR Unica (0.103 g) were dissolved in 8.7 mL and 9.0 mL,
respectively, of anhydrous DMSO (99.9% purity). These were the stock solution of analyzed
samples. For the experiment, a solution of 0.1 M TBAB electrolyte in anhydrous DMSO
(99.9% purity) was bubbled for 5 min with a dry O2/N2 (35%/65%) gas mixture to establish
the dissolved oxygen level in the electrochemical cell of 50 mL. The Au/Au disc electrode
was then rotated at 1000 rpm, and potential sweep was applied to the disk from 0.2 V to
−1.2 V and then back to 0.2 V while the ring was held constant at 0.0 V; the disk voltage
sweep rate was set to 25 mV/s. The molecular oxygen reduction peak (reaction 1) was
observed around −0.6 V at the disk electrode; the oxidation current (reaction 2) occurred
at the ring electrode. An initial blank, in the absence of an antioxidant, was run on this
solution and the ratio of the ring/disk current was calculated as the “efficiency”. Next,
an antioxidant aliquot was added, the solution bubbled with the gas mixture for 5 min,
the voltammogram was rerecorded, and was efficiently obtained. In this way, the rate at
which increasing concentrations of antioxidant scavenge the generated superoxide radicals
during the electrochemical reaction was determined as each additional antioxidant aliquot
was added. Results from each run were collected on Aftermath software Release 1.6.10523
and represented as voltammograms showing current vs. potential graphs that were later
analyzed using Microsoft Excel. The used aliquots were indicated in related RRDE graphs. Ultimately, the slope of the overall decrease in efficiency with the addition of antioxidant
serves as a quantitative measure of the antioxidant activity of each sample. Any decrease
in the collection efficiency was expected to be due to the amount of superoxide removed by
the antioxidant. This method has been developed in our lab [24]. MOH Unica (0.924 g) and MOR Unica (0.103 g) were dissolved in 8.7 mL and 9.0 mL,
respectively, of anhydrous DMSO (99.9% purity). These were the stock solution of analyzed
samples. For the experiment, a solution of 0.1 M TBAB electrolyte in anhydrous DMSO
(99.9% purity) was bubbled for 5 min with a dry O2/N2 (35%/65%) gas mixture to establish
the dissolved oxygen level in the electrochemical cell of 50 mL. 3.4. Computational Study Calculations were performed using programs from Biovia (Dassault Systèmes, San
Diego, CA, USA). Density functional theory (DFT) program Dmol3 was applied to calculate
energy, geometry, and frequencies implemented in Materials Studio 7.0 [29]. We employed
the double numerical polarized (DNP) basis set that included all the occupied atomic
orbitals plus a second set of valence atomic orbitals and polarized d-valence orbitals [30];
the correlation generalized gradient approximation (GGA) was applied, including Becke
exchange [31] plus BLYP correlation. All electrons were treated explicitly and the real
space cutoff of 5 Å was imposed for numerical integration of the Hamiltonian matrix
elements. The self-consistent field convergence criterion was set to the root mean square
change in the electronic density to be less than 10−6 electron/Å3. Calculations did not
include solvent effects. The convergence criteria applied during geometry optimization
were 2.72 × 10−4 eV for energy and 0.054 eV/Å for force. Docking studies were performed
with the CDOCKER package in Discovery Studio 2020 version [23]. Standard dynamics
cascade protocol in Discovery Studio allows optimization of atomic coordinates and was
also applied to the selected poses. 3.3. Hydrodynamic Voltammetry (RRDE) The Au/Au disc electrode
was then rotated at 1000 rpm, and potential sweep was applied to the disk from 0.2 V to
−1.2 V and then back to 0.2 V while the ring was held constant at 0.0 V; the disk voltage
sweep rate was set to 25 mV/s. The molecular oxygen reduction peak (reaction 1) was
b
d
d
0 6 V t th di k l
t
d
th
id ti
t (
ti
2)
d In an RRDE voltammetry experiment, the generation of the superoxide radicals occurs
at the disk electrode while the oxidation of the residual superoxide radicals (that have not
been scavenged by the antioxidant) occurs at the ring electrode. Int. J. Mol. Sci. 2023, 24, 10750 14 of 17 14 of 17 Reaction (1): Reduction of molecular oxygen at the disk electrode: O2 + e−→O2•−
(1) (1) O2 + e−→O2•− Reverse Reaction (2): Oxidation of superoxide radicals at the ring electrode: Reverse Reaction (2): Oxidation of superoxide radicals at the ring electrode: O2•−→O2 + e−
(2) (2) O2•−→O2 + e− 4. Conclusions Since inflammation is associated with many human maladies including metabolic
and cardiovascular diseases, cancer, and COVID-19, as well as many neurodegenerative
conditions, inhibitors of the anomalous activation of the inflammasome are important to
identify [32]. Selective, potent small molecule caspase-1 inhibitors such as VX-765 (Bel-
nacasan) exist but their strong side effects limit their clinical use [33]. Recent in vivo and
in vitro studies on a small molecule caspase-1 inhibitor, NSC697923, showed its effective-
ness in an animal model of gouty arthritis. When docking studies were performed that
included NSC697923 in the binding pocket A of caspase-1, H-bonds with Arg341 were seen
and, consistent with VX-765, the caspase-1 inhibitor was present in the caspase-1 crystal
structure used in our studies [34]. In this investigation, aerial parts of Maytenus octogona (ethanol extracts), employed in
Peruvian ethnopharmacology as anti-inflammatory agents, were analyzed using a cyclo-
voltammetry method able to directly determine the scavenging of the superoxide radical. Leaf extracts were more active than those from stems. A comparison with other natural
products analyzed by our group using the same protocol (olive oil [25], propolis [26] and
black seed oil [27]) indicates slightly weaker scavenging for these extracts. Recently, a study on the potential anti-inflammatory activity of some phenolic and
methide-quinone nor-triterpenes isolated from Maytenus retusa that were evaluated for
the inhibition of the NLRP3 inflammasome in macrophages appeared [35]. One of the
most potent compounds evaluated was a semisynthetic methide-quinone Br derivative
related to the three methide-quinones described in this work. This compound showed
markedly reduced caspase-1 activity, IL-1β secretion (IC50 = 0.19 µM), and pyroptosis
(IC50 = 0.13 µM). Since caspase-1 inhibition is important in preventing excessive cytokine
production that can lead to inflammation, these findings can be associated with our results. In this investigation, three natural methide-quinones derivatives contained in
Maytenus octogona extracts were analyzed using molecular mechanics docking calcula-
tions. Results of these studies show the possible inhibition of caspase-1 by each of these
compounds, thus supporting the anti-inflammatory medicinal use by indigenous popu-
lations in the related Peruvian area. Our work shows that Arg341 is the most important Int. J. Mol. Sci. 2023, 24, 10750 15 of 17 15 of 17 amino acid involved in inhibiting the active site of caspase-1. This amino acid is stabi-
lized through strong intermolecular interactions for each of the three potential inhibitors,
hydroxytingenone, tingenone, and pristimerin. 4. Conclusions The calculated binding energies of these
three compounds are −13.7 kcal/mol for hydroxytingenone, −11.8 and 13.0 kcal/mol
for tingenone, and −9.3 and −9.4 kcal/mol for pristimerin, which indicate that all three
natural products are good inhibitors. Each of these methide-quinones is closely related to
the methide-quinone Br derivative mentioned above [35]. That these interactions remain
after the more rigorous molecular dynamics calculations underscores their significance. The methide-quinone carbonyl group in hydroxytingenone and pristimerin is preferred as a
hydrogen bond acceptor over the other possible carbonyl acceptor located in these ligands,
agreeing with results shown in a previous study [11]. This is confirmed by statistics on
the 10 poses of pristimerin, showing only poses 1–3 having H-bond interactions with the
O(carbonyl) located at the other end of the molecule, whereas for poses 4, 5, 7, 8, 10 the
methide-quinone carbonyl is engaged, also in H-bonds. Tingenone shows both carbonyls
having a similar preference due to closely related binding energy derived from poses 1
and 5. Our work supports the anti-inflammatory medicinal use of Maytenus octogona by
native populations in Peru and provides impetus for studying the chemical mechanisms
of additional established traditional remedies. Once again, we have shown that natural
products can provide the chemical scaffold that targets important receptor sites such as
caspase-1 in the inflammasome pathway for the development of a novel therapy against
human diseases. Supplementary Materials:
The following supporting information can be downloaded at:
https://www.mdpi.com/article/10.3390/ijms241310750/s1. Author Contributions: Conceptualization, F.C.; methodology, H.C.; formal analysis, E.E.; investi-
gation, F.C. and H.C.; data curation, M.B., R.S. and F.S.-L.; writing original draft preparation, F.C. and M.R.; writing-review and edit, F.C., M.R. and E.E.; visualization, M.R. All authors have read and
agreed to the published version of the manuscript. Funding: This research received no external funding. Funding: This research received no external funding. Acknowledgments: Computer center (CIS) and Karly Andreassen for computational support at
Vassar College. Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. References 1. Kesavardhana, S.; Subbarao Malireddi, R.K.; Kanneganti, T.D. Caspases in Cell Death, Inflammation, and Pyroptosis. Annu. Rev. Immunol. 2020, 38, 567. [CrossRef] 2. Meduri, G.U.; Headley, S.; Kohler, G.; Stentz, F.; Tolley, E.; Umberger, R.; Leeper, K. Persistent elevation of inflammatory cytokines
predicts a poor outcome in ARDS. Plasma IL-1 beta and IL-6 levels are consistent and efficient predictors of outcome over time. Chest 1995, 107, 1062. [CrossRef] [PubMed] 3. Mehta, P.; Mcauley, D.F.; Brown, M.; Sanchez, E.; Tattersall, R.S.; Manson, J.J. COVID-19: Consider cytokine storm syndromes and
immunosuppression. Lancet 2020, 395, 1033. [CrossRef] [PubMed] 3. Mehta, P.; Mcauley, D.F.; Brown, M.; Sanchez, E.; Tattersall, R.S.; Manson, J.J. COVID-19: Consider cytokine storm syndromes and
immunosuppression. Lancet 2020, 395, 1033. [CrossRef] [PubMed] 4. Nieto-Torres, J.L.; Dediego, M.L.; Verdia-Baguena, C.; Jimenez-Guardeno, J.M.; Regla-Nava, J.A.; Fernandez-Delgado, R.; Castaño-
Rodriguez, C.; Alcaraz, A.; Torres, J.; Aguilella, V.M.; et al. Severe acute respiratory syndrome coronavirus envelope protein ion
channel activity promotes virus fitness and pathogenesis. PloS Pathog. 2014, 10, e1004077. [CrossRef] 4. Nieto-Torres, J.L.; Dediego, M.L.; Verdia-Baguena, C.; Jimenez-Guardeno, J.M.; Regla-Nava, J.A.; Fernandez-Delgado, R.; Castaño-
Rodriguez, C.; Alcaraz, A.; Torres, J.; Aguilella, V.M.; et al. Severe acute respiratory syndrome coronavirus envelope protein ion
channel activity promotes virus fitness and pathogenesis. PloS Pathog. 2014, 10, e1004077. [CrossRef] y p
p
g
g
5. Rogers, A.J.; Guan, J.; Trtchounian, A.; Hunninghake, G.M.; Kaimal, R.; Desai, M.; Kozikowski, L.-A.; DeSouza, L.; Mogan, S.; Liu,
K.D.; et al. Association of elevated plasma interleukin-18 level with increased mortality in a clinical trial of statin treatment for
acute respiratory distress syndrome. Crit. Care Med. 2019, 47, 1089. [CrossRef] [PubMed] y p
p
g
g
5. Rogers, A.J.; Guan, J.; Trtchounian, A.; Hunninghake, G.M.; Kaimal, R.; Desai, M.; Kozikowski, L.-A.; DeSouza, L.; Mogan, S.; Liu,
K.D.; et al. Association of elevated plasma interleukin-18 level with increased mortality in a clinical trial of statin treatment for
acute respiratory distress syndrome. Crit. Care Med. 2019, 47, 1089. [CrossRef] [PubMed] p
y
y
[
] [
]
6. De Rivero Vaccari, J.C.; Dietrich, W.D.; Keane, R.W.; de Rivero Vaccari, J.P. The Inflammasome in Times of COVID-19. Front. Immunol. 2020, 11, 583373. [CrossRef] 7. Kigerl, K.A.; de Rivero Vaccari, J.P.; Dietrich, W.D.; Popovich, P.G.; Keane, R.W. Pattern recognition receptors and central nervous
system repair. Exp. Neurol. 2014, 258, 5. [CrossRef] [PubMed] 7. Kigerl, K.A.; de Rivero Vaccari, J.P.; Dietrich, W.D.; Popovich, P.G.; Keane, R.W. p
y
y
6.
De Rivero Vaccari, J.C.; Dietrich, W.D.; Keane, R.W.; de Rivero Vaccari, J.P. The Inflammasome in Ti
Immunol. 2020, 11, 583373. [CrossRef] 9.
Strowig, T.; Henao-Mejia, J.; Elinav, E.; Flavell, R. Inflammasomes in health and disease. Nature 2012, 4 y
p
8.
Lamkanfi, M.; Dixit, V.M. Inflammasomes and their roles in health and disease. Annu. Rev. Cell Dev
[CrossRef] [PubMed] References 1982, 5, 73. [CrossRef] 16. Gonzalez, J.G.; Delle Monache, G.; Delle Monache, F.; Marini Bettolò, G.B. Chuchuhuasha a drug use
Amazonian and Andean areas. A chemical study of Maytenus laevis. J. Ethnopharmacol. 1982, 5, 73. [C y
y
p
17. Oramas-Royo, S.M.; Chávez, H.; Martín-Rodríguez, P.; Fernández-Pérez, L.; Ravelo, A.G.; Estéve
penoids from Maytenus retusa. J. Nat. Prod. 2010, 73, 2029. [CrossRef] 18. Vazdekis, N.E.; Chávez, H.; Estévez-Braun, A.; Ravelo, A.G. Triterpenoids and a lignan from the aerial parts of Maytenus
apurimacensis. J. Nat. Prod. 2009, 72, 1045–1048. [CrossRef] 19. Delgado-Méndez, P.; Herrera, N.; Chávez, H.; Estévez-Braun, A.; Ravelo, A.G.; Cortes, F.; Castanys, S.; Gamarro, F. New
terpenoids from Maytenus apurimacensis as MDR reversal agents in the parasite Leishmania. Bioorg. Med. Chem. 2008, 16,
1425–1430. [CrossRef] 20. Torpocco, V.; Chávez, H.; Estévez-Braun, A.; Ravelo, A.G. New dammarane triterpenes from Maytenus macrocarpa. Chem. Pharm. Bull. 2007, 55, 812–814. [CrossRef] 21. Available online: https://www.rcsb.org/ (accessed on 25 July 2022). Available online: https://www.rcsb.org/ (accessed p
g
y
o, T.S. Crystal Structure of Caspase-1 in Complex with VX. Available online: https://www.wwpdb.org/pdb? accessed on 25 July 2022). 22. Yang, J.; Liu, Z.; Xiao, T.S. Crystal Structure of Caspase-1 in Complex with VX. Available online: https:/
id=pdb_00006pzp (accessed on 25 July 2022). y
D.H.; Brooks, C.L.; Vieth, M.J. Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A
D docking algorithm. J. Comput. Chem. 2003, 24, 1549. [CrossRef] [PubMed] 23. Wu, G.; Robertson, D.H.; Brooks, C.L.; Vieth, M.J. Detailed analysis of grid-based molecular docking: A ca
CHARMm-based MD docking algorithm. J. Comput. Chem. 2003, 24, 1549. [CrossRef] [PubMed] 24. Belli, S.; Rossi, M.; Molasky, N.; Middleton, L.; Caldwell, C.; Bartow-McKenney, C.; Duong, M.; Chiu, J.; Gibbs, E.; Caldwell, A.;
et al. Effective and novel application of superoxide radical scavenging by natural phenolic antioxidants. Antioxidants 2019, 8, 14. [CrossRef] [PubMed] 25. Rossi, M.; Caruso, F.; Kwok, L.; Lee, G.; Caruso, A.; Gionfra, F.; Candelotti, E.; Belli, S.L.; Molasky, N.; Raley-Susman, K.M.; et al. Protection by extra virgin olive oil against oxidative stress in vitro and in vivo. Chemical and biological studies on the health
benefits due to a major component of the Mediterranean diet. PLoS ONE 2017, 12, e0189341. [CrossRef] [PubMed] j
p
26. Sakib, R.; Caruso, F.; Aktar, S.; Belli, S.; Kaur, S.; Hernandez, M.; Rossi, M. References Pattern recognition receptors and central nervous
system repair. Exp. Neurol. 2014, 258, 5. [CrossRef] [PubMed] y
p
p
8. Lamkanfi, M.; Dixit, V.M. Inflammasomes and their roles in health and disease. Annu. Rev. Cell Dev. Biol. 2012, 28, 137–161. [CrossRef] [PubMed] y
p
p
8. Lamkanfi, M.; Dixit, V.M. Inflammasomes and their roles in health and disease. Annu. Rev. Cell Dev. Biol. 2012, 28, 137–161. [CrossRef] [PubMed] Int. J. Mol. Sci. 2023, 24, 10750 16 of 17 10. Tan, L.Y.; Komarasamy, T.V.; Rmt Balasubramaniam, V. Hyperinflammatory Immune Response and COVID-19: A Double Edged
Sword. Front. Immunol. 2021, 12, 742941. [CrossRef] 11. Caruso, F.; Pedersen, J.Z.; Incerpi, S.; Kaur, S.; Belli, S.; Florea, R.M.; Rossi, M. Mechanism of Caspase-1 Inhibition by Four
Anti-inflammatory Drugs Used in COVID-19 Treatment. Int. J. Mol. Sci. 2022, 23, 1849. [CrossRef] [PubMed] 12. Caruso, F.; Singh, M.; Belli, S.; Berinato, M.; Rossi, M. Interrelated mechanism by which the methide quinone celastrol, obtained
from the roots of Tripterygium wilfordii, inhibits main protease 3CLpro of COVID-19 and acts as superoxide radical scavenger. Int. J. Mol. Sci. 2020, 21, 9266. [CrossRef] J
[
]
13. Huang, Y.Y.; Chen, L.; Ma, G.X.; Xu, X.D.; Jia, X.G.; Deng, F.S.; Li, X.J.; Yuan, J.Q. A Review on Phytochemicals of the Genus
Maytenus and Their Bioactive Studies. Molecules 2021, 26, 4563. [CrossRef] [PubMed] y
14. Niero, R.; de Andrade, S.F.; Cechinel Filho, V. A review of the ethnopharmacology, phytochemistry and pharmacology of plants
of the Maytenus genus. Curr. Pharm. Des. 2011, 17, 1851. [CrossRef] [PubMed] 14. Niero, R.; de Andrade, S.F.; Cechinel Filho, V. A review of the ethnopharmacology, phytoch
of the Maytenus genus. Curr. Pharm. Des. 2011, 17, 1851. [CrossRef] [PubMed] 15. Lock, O.; Perez, E.; Villar, M.; Flores, D.; Rojas, R. Bioactive Compounds from Plants Used in Peruvian Traditional Medicine. Nat. Prod. Commun. 2016, 11, 315–337. 16. Gonzalez, J.G.; Delle Monache, G.; Delle Monache, F.; Marini-Bettolò, G.B. Chuchuhuasha–a drug use 16. Gonzalez, J.G.; Delle Monache, G.; Delle Monache, F.; Marini-Bettolò, G.B. Chuchuhuasha–a drug used in folk medicine in the
Amazonian and Andean areas. A chemical study of Maytenus laevis. J. Ethnopharmacol. 1982, 5, 73. [CrossRef]
17. Oramas-Royo, S.M.; Chávez, H.; Martín-Rodríguez, P.; Fernández-Pérez, L.; Ravelo, A.G.; Estévez-Braun, A. Cytotoxic triter- 16. Gonzalez, J.G.; Delle Monache, G.; Delle Monache, F.; Marini-Bettolò, G.B. Chuchuhuasha–a drug used in folk medicine in the
Amazonian and Andean areas. A chemical study of Maytenus laevis. J. Ethnopharmacol. 34.
Cao, D.Y.; Zhang, Z.H.; Li, R.Z.; Shi, X.K.; Xi, R.Y.; Zhang, G.L.; Li, F.; Wang, F. A small molecule inhibitor of caspase-1 inhibits
NLRP3 inflammasome activation and pyroptosis to alleviate gouty inflammation. Immunol. Lett. 2022, 244, 28–39. [CrossRef]
[PubMed]
35.
González-Cofrade, L.; Green, J.P.; Cuadrado, I.; Amesty, Á.; Oramas-Royo, S.; Brough, D.; Estévez-Braun, A.; Hortelano, S.; de Las
Heras, B. Phenolic and quinone methide nor-triterpenes as selective NLRP3 inflammasome inhibitors. Bioorg. Chem. 2023, 132,
106362. [CrossRef] [PubMed] Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual
author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to
people or property resulting from any ideas, methods, instructions or products referred to in the content. NLRP3 inflammasome activation and pyroptosis to alleviate gouty inflammation. Immunol. Lett. 2022, 244, 28–39. [CrossRef]
[PubMed]
35.
González-Cofrade, L.; Green, J.P.; Cuadrado, I.; Amesty, Á.; Oramas-Royo, S.; Brough, D.; Estévez-Braun, A.; Hortelano, S.; de Las
Heras, B. Phenolic and quinone methide nor-triterpenes as selective NLRP3 inflammasome inhibitors. Bioorg. Chem. 2023, 132,
106362. [CrossRef] [PubMed] 35.
González-Cofrade, L.; Green, J.P.; Cuadrado, I.; Amesty, Á.; Oramas-Royo, S.; Brough, D.; Estévez-Braun, A.; Hortelano, S.; de Las
Heras, B. Phenolic and quinone methide nor-triterpenes as selective NLRP3 inflammasome inhibitors. Bioorg. Chem. 2023, 132,
106362. [CrossRef] [PubMed] 34.
Cao, D.Y.; Zhang, Z.H.; Li, R.Z.; Shi, X.K.; Xi, R.Y.; Zhang, G.L.; Li, F.; Wang, F. A small molecule inhibitor of caspase-1 inhibits
NLRP3 inflammasome activation and pyroptosis to alleviate gouty inflammation. Immunol. Lett. 2022, 244, 28–39. [CrossRef]
[PubMed]
35
González-Cofrade L ; Green J P; Cuadrado I ; Amesty Á ; Oramas-Royo S ; Brough D ; Estévez-Braun A ; Hortelano S ; de Las References Antioxidant Properties of Thymoquinone, Thymohy-
droquinone and Black Cumin (Nigella sativa L.) Seed Oil: Scavenging of Superoxide Radical Studied Using Cyclic Voltammetry,
DFT and Single Crystal X-ray Diffraction. Antioxidants 2023, 12, 607. [CrossRef] 27. Caruso, F.; Berinato, M.; Hernandez, M.; Belli, S.; Smart, C.; Rossi, M. Antioxidant properties of bee propolis and an important
component, galangin, described by X-ray crystal structure, DFTD and hydrodynamic voltammetry. PLoS ONE 2022, 17, e0267624. [CrossRef] 28. Mayrhofer, K.; Strmcnik, D.; Blizanac, B.; Stamenkovic, V.; Arenz, M.; Markovic, N. Measurement of oxygen reduction activities
via the rotating disc electrode method: From Pt model surfaces to carbon-supported high surface area catalysts. Electrochim. Acta
2008, 53, 3181–3188. [CrossRef] ,
,
[
]
29. Delley, B.J. From molecules to solids with the DMol3 approach. J. Chem. Phys. 2000, 113, 7756. [CrossRef] 29. Delley, B.J. From molecules to solids with the DMol3 approach. J. Chem. Phys. 2000, 113, 7756. [CrossR 30. Perdew, J.P.; Chevary, J.A.; Vosko, S.H.; Jackson, K.A.; Pederson, M.R.; Singh, D.J.; Fiolhais, C. Atoms, molecules, solids, and
surfaces: Applications of the generalized gradient approximation for exchange and correlation. Phys. Rev. 1992, 46, 6671–6687. [CrossRef] [
]
31. Becke, A.D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 1988, 38,
3098–3100. [CrossRef] 32. Li, Y.; Huang, H.; Liu, B.; Zhang, Y.; Pan, X.; Yu, X.Y.; Shen, Z.; Song, Y.H. Inflammasomes as therapeutic targets in human
diseases. Signal Transduct. Target Ther. 2021, 6, 247. [CrossRef] 33. Wannamaker, W.; Davies, R.; Namchuk, M.; Pollard, J.; Ford, P.; Ku, G.; Decker, C.; Charifson, P.; Weber, P.; Germann,
U.A.; et al. [(S)-1-((S)-2-{[1-(4-Amino-3-chloro-phenyl)-methanoyl]-amino}-3,3-dimethyl-butanoyl)-pyrrolidine-2-carboxylic
acid ((2R,3S)-2-ethoxy-5-oxo-tetrahydro-furan-3-yl)-amide (VX-765), an Orally Available Selective Interleukin (IL)-Converting
Enzyme/Caspase-1 Inhibitor, Exhibits Potent Anti-Inflammatory Activities by Inhibiting the Release of IL-1β and IL. J. Pharmacol. Exp. Therap. 2007, 321, 509–516. [CrossRef] Int. J. Mol. Sci. 2023, 24, 10750 17 of 17 17 of 17 Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual
author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to
people or property resulting from any ideas, methods, instructions or products referred to in the content.
|
https://openalex.org/W2162456360
|
https://figshare.com/articles/journal_contribution/A_multiple-baseline_stereo/6591083/1/files/12079595.pdf
|
English
| null |
A multiple-baseline stereo
| null | 2,002
|
cc-by
| 7,713
|
NOTICE WARNING CONCERNING COPYRIGHT RESTRICTIONS:
The copyright law of the United States (title 17, U.S. Code) governs the making
of photocopies or other reproductions of copyrighted material. Any copying of this
document without permission of its author may be prohibited by law. NOTICE WARNING CONCERNING COPYRIGHT RESTRICTIONS:
The copyright law of the United States (title 17, U.S. Code) governs the making
of photocopies or other reproductions of copyrighted material. Any copying of this
document without permission of its author may be prohibited by law. A Multiple-Baseline Stereo This research was supported in part by the Defense Advanced Research Projects Agency (DOD), and monitored
by the Avionics Laboratory, Air Force Wright Aeronautical Laboratories, Aeronautical Systems Division (AFSC),
Wright-Patterson AFB, Ohio 45433-6543 under Contract F33615-87-C-1499, ARPA Order No. 4976, Amendment
20. The views and conclusions contained in this document are those of the authors and should not be interpreted as
representing the official policies, either expressed or implied, of the Defense Advanced Research Projects Agency or
of the U.S. Government. Keywords: vision, image understanding, stereo Abstract This paper presents a stereo matching method which uses multiple stereo pairs with various
baselines to obtain precise depth estimates without suffering from ambiguity. In stereo processing, a short baseline means that the estimated depth will be less precise
due to narrow triangulation. For more precise depth estimation, a longer baseline is desired. With a longer baseline, however, a larger disparity range must be searched to find a match. As
a result, matching is more difficult and there is a greater possibility of a false match. So there
is a trade-off between precision and accuracy in matching. The stereo matching method presented in this paper uses multiple stereo pairs with different
baselines generated by a lateral displacement of a camera. Matching is performed simply by
computing the sum of squared-difference (SSD) values. The SSD functions for individual
stereo pairs are represented with respect to the inverse depth (rather than the disparity, as is
usually done), and then are simply added to produce the sum of SSDs. This resulting function is
called the SSSD-in-inverse-depth. We show that the SSSD-in-inverse-depth function exhibits a
unique and clear minimum at the correct matching position even when the underlying intensity
patterns of the scene include ambiguities or repetitive patterns. An advantage of this method
is that we can eliminate false matches and increase precision without any search or sequential
filtering. This paper first defines a stereo algorithm based on the SSSD-in-inverse-depth and presents
a mathematical analysis to show how the algorithm can remove ambiguity and increase pre-
cision. Then, a few experimental results with real stereo images are presented to demonstrate
the effectiveness of the algorithm. 1
Introduction Stereo is a useful technique for obtaining 3-D information from 2-D images in computer vision. In stereo matching, we measure the disparity d, which is the distance between the corresponding
points of left and right images. The disparity d is related to the depth z by d = B F -
(1)
z d = B F - z d = B F - z (1) where B and F are baseline and focal length, respectively. where B and F are baseline and focal length, respectively. where B and F are baseline and focal length, respectively. This equation indicates that for the same depth the disparity is proportional to the baseline, or
that the baseline length B acts as a magnification factor in measuring d in order to obtain z. That is,
the estimated depth is more precise if we set the two cameras farther apart from each other, which
means a longer baseline. A longer baseline, however, poses its own problem. Because a longer
disparity range must be searched, matching is more difficult and thus there is a greater possibility
of a false match. So there is a trade-off between precision and accuracy (correctness) in matching. p
y (
)
g
One of the most common methods to deal with the problem is a coarse-to-fine control strategy
[MP79][Gri85]. Matching is done at a low resolution to reduce false matches and then the result
is used to limit the search range of matching at a high resolution, where more precise disparity
measurements are calculated. Using a coarse resolution, however, does not always remove false
matches. This is especially true when there is inherent ambiguity in matching, such as a repeated
pattern over a large part of the scene (eg., a scene of a picket fence). Another approach to remove
false matches and to increase precision is to use multiple images, especially a sequence of densely
sampled images along a camera path [BBM87, Yam88, MSK89]. A short baseline between a
pair of consecutive images makes the matching or tracking of features easy, while the structure
imposed by the camera motion allows integration of the possibly noisy individual measurements
into a precise estimate. The integration has been performed either by exploiting constraints on the
EPI [BBM87, Yam88] or by a sequential Kalman filtering technique [MSK89, Hee89]. 2
Mathematical Analysis The essence of stereo matching is, given a point in one image, to find the most similar point
in another image. The sum of squared differences (SSD) of the intensity values (or values of
preprocessed images, such as bandpass filtered images) over a window is the simplest and most
effective criterion for matching. In this section, we define the sum of SSD with respect to the
inverse depth (SSSD-in-inverse-depth) for multiple-baseline stereo, and mathematically show its
advantage in removing ambiguity and increasing precision. For this analysis, we use 1-D stereo
intensity signals, but the extension to two dimensional images is straightforward. 1
Introduction y
q
g
q
A stereo matching method presented in this paper belongs to the second approach: use of
multiple images with different baselines obtained by a lateral displacement of a camera. Matching,
however, is performed in a simple way. The sum of square-difference (SSD) values are computed
for each pair of stereo images. The SSD values are represented with respect to the inverse depth
\ (rather than the disparity d, as is usually done). Those SSD functions from all the stereo pairs
are simply added together to produce the sum of SSDs, which we call SSSD-in-inverse-depth. We
show that the SSSD-in-inverse-depth function exhibits a unique and clear minimum at the correct
matching position even when the underlying intensity patterns of the scene include ambiguities
or repetitive patterns. An advantage of this technique is that we can eliminate false matches and
increase precision without any search or sequential filtering. p
y
q
g
In the next section we present the method mathematically and show how ambiguity can be
removed and precision increased by the method. Section 3 provides a few experimental results
with real stereo images to demonstrate the effectiveness of the algorithm. PO
PI
P2
Pn
Bl
B2
Bn
Figure 1: Camera positions for stereo Pn 2.1 SSD Function Suppose that we have camera positions PO,PI,...,PH
and a resulting set of stereo pairs with
baselines
... ,BH as shown in figure 1. Let FO(X) and/,(x) be the image pair at the camera
positions PO and PI, respectively. Imagine a scene point Z whose depth is z. Its disparity dr® for
the image pair taken from PQ and P, is (2) (2) The image intensity functions FO(X) and/,-(x) near the matching positions for Z can be expressed as The image intensity functions FO(X) and/,-(x) near the matching positions for Z can be expressed as FO(X)
= F(X) + NO(X)
/.(*)
= F(X-DM)
+ RN(X),
(3) FO(X)
= F(X) + NO(X)
/.(*)
= F(X-DM)
+ RN(X),
(3) (3) assuming constant distance near Z and independent Gaussian white noise such that
NO(X)MX)~N(0,<Tl). (4) uming constant distance near Z and independent Gaussian white noise such that NO(X)MX)~N(0,<Tl). (4) NO(X)MX)~N(0,<Tl). ( (4) The SSD value
over a window W at a pixel position X for the candidate disparity
is
defined as The SSD value
over a window W at a pixel position X for the candidate disparity
is
defined as e«<(o0c,4o) =
Y,VO(X+J)-FI(X
+ D®+
J))
2
(5) (5) 2 where the Zj&r means summation over the window. The d® that gives a minimum of ed(!)(xy d®)
is determined as the estimate of the disparity at x. Since the SSD measurement e^d®)
is a
random variable, we will compute its expected value in order to analyze its behavior: where the Zj&r means summation over the window. The d® that gives a minimum of ed(!)(xy d®)
is determined as the estimate of the disparity at x. Since the SSD measurement e^d®)
is a
random variable, we will compute its expected value in order to analyze its behavior: £[e« 0(x,d( 0)] = E
= E
X)(f(*
+f> -fix + d(0 - dK0 +j) + no(x +J) - m(x +
+ j)f
£(A*+y) -fix+d®
-
dm
+ E
+ E
J2
2<f(* +J) -fix
+ d® - dr® +j)(no(x +j) - m(x + d*> + J))
X)(«o(* +j) - rnQc + d® +j))
2
-
HVix+D-fix
+ ^-drv+flf
+
W^, (6) where Nw is the number of the points within the window. For the rest of the paper, £[] denotes the
expected value of a random variable. In deriving the above equation, we have assumed that
is
constant over the window. where a £ 0 is a constant. Then, from equation (6) where a £ 0 is a constant. Then, from equation (6) Ele^ix, dr®)] = Efa©(x, d^ + a)] = 2NW<%. (8) (8) This means that ambiguity is expected in matching in terms of positions of minimum SSD values. Moreover, the false match at dr® + a appears in exactly the same way for all i"; it is separated
from the correct match by a for all the stereo pairs. Using multiple baselines does not help to
disambiguate. 2.1 SSD Function Equation (6) says that naturally the SSD function e^ix, d®) is expected
to take a minimum when d® = d^, i.e., at the right disparity. Let us examine how the SSD function ed®(x,d®) behaves when there is ambiguity in the
underlying intensity function. Suppose that the intensity signal f(x) has the same pattern around
pixel positions x and x + a, f(x+J)=f(x
+ a+f),
JEW
(7
n from equation (6) f(x+J)=f(x
+ a+f),
JEW
(7)
hen, from equation (6) f(x+J)=f(x
+ a+f),
JEW
(7)
here a £ 0 is a constant. Then, from equation (6) (7) From equation and (2), From equation and (2), q
( ),
4®
=
BIFCR
(10)
4o
=
BIFC,
(11) 4®
=
BIFCR
(10)
4o
=
BIFC,
(11) 4®
=
BIFCR
4o
=
BIFC, (10)
(11) (10) (11) where (r and C are the real and the candidate inverse depth, respectively. Substituting these into
equation (5), we have the SSD with respect to the inverse depth, where (r and C are the real and the candidate inverse depth, respectively. Substituting these into
equation (5), we have the SSD with respect to the inverse depth, ««»(*, 0 s £(f(*+y) -ffc+BIFC
+;))
2,
(12) (12) at position x for a candidate inverse depth (. Its expected value is
EBAFLCQ] - E(^Cx+i)-f(x+BIF(( - Q + ; ) )
2 + 2 A ^ . (13) at position x for a candidate inverse depth (. Its expected value is
EBAFLCQ] - E(^Cx+i)-f(x+BIF(( - Q + ; ) )
2 + 2 A ^ . (13) (13) Finally, we define a new evaluation function £(Q2..«)(x, 0» *
e
s
u
m °f SSD functions with
respect to the inverse depth (SSSD-in-inverse-depth) for multiple stereo pairs. It is obtained by
adding the SSD functions *«i)(x, Q for individual stereo pairs: t«12..«)(z, 0 = E *C©(*i 0-
(I
4) (I
4) Its expected value is £[*«i2..*)(*,C)] £[*«i2..*)(*,C)]
-
01
=
(i5) (i5) In the next three subsections, we will analyze the characteristics of these evaluation functions to
see how ambiguity is removed and precision is improved. In the next three subsections, we will analyze the characteristics of these evaluation functions to
see how ambiguity is removed and precision is improved. 2.2 SSD with respect to Inverse Depth Now, let us introduce the inverse depth C such that c-i. z
(9)
3 c-i. z
(9) (9) 3 We can prove that E[eai2)(xo, Q] > 4Nwa
2
n
= £[eC(i2)(JCb, 0)1 for C ? (18) (18) (refer to appendix A) In words, e«i2)(*o, 0 is expected to have the smallest value at the correct G-
That is, the ambiguity is likely to be eliminated by use of the new evaluation function with two
different baselines. (refer to appendix A) In words, e«i2)(*o, 0 is expected to have the smallest value at the correct G-
That is, the ambiguity is likely to be eliminated by use of the new evaluation function with two
different baselines. We can illustrate this using synthesized data. Suppose the point whose depth we want to
determine is at x = 0 and the underlying function / (x) is given by /
W
J
<
I
)
+
2
(19)
'
[ 1
if x < - 4 or 4 < x. (19) Figure 2 (a) shows a plot of / (JC). Assuming that d^\) = 5, a\ = 0.2, and the window size is 5, the
expected values of the SSD function ed(\)(xo, d(l)) are as shown in figure 2 (b). We see that there
is an ambiguity: the minima occur at the correct match d{\) = 5 and at the false match d(\) = 13. Which match will be selected will depend on the noise, search range, and search strategy. Now
suppose we have a longer baseline B2 such that §^ = 1.5. From equations (6) and (10), we obtain
E[e<i(i)] as shown in figure 2 (c). Again we encounter an ambiguity, and the separation of the tw
minima is the same. Now let us evaluate the SSD values with respect to the inverse depth ( rather than the disparity
d by using equations (12) through (15). The expected values of the SSD measurements
and £0<(2)] with baselines B\ and B2 are shown in figures 2 (d) and (e), respectively (the plot
is normalized such that B\F =1). Note that the minima at the correct inverse depth (C = 5)
does not move, while the minima for the false match changes its position as the baseline changes. When the two functions are added to produce the SSSD-in-inverse-depth, its expected values
£[£<(i2)] are as shown in figure 2 (f). We can see that the ambiguity has been reduced because the
SSSD-in-inverse-depth has a smaller value at the correct match position than at the false match. 2.3 Elimination of Ambiguity (1) As before, suppose the underlying intensity pattern/(x) has the same pattern around x and x + a
(equation (7)). Then, according to equation (13), we have As before, suppose the underlying intensity pattern/(x) has the same pattern around x and x + a
(equation (7)). Then, according to equation (13), we have We still have an ambiguity; a minimum is expected at a false inverse depth Q = C- + sg?- However,
an important point to be observed here is that this minimum for the false inverse depth Q changes 4 us position as the baseline 5, changes, while the minimum for the correct inverse depth £ does not
This is the property that the new evaluation function, the SSSD-in-inverse-depth (14), exploits to
eliminate the ambiguity. For example, suppose we use two baselines flt and B2 (5, d B2) From
equation (15) £[e«i2)C*o, C)] =
T>(f(
xo
+J)-fOco+BiF(C-0)+j))
2
+ E^
+y")-/(^+fi2F(C-C,)+;'))
2 + 4iVw<ra
2
(17) (17) 2.4 Elimination of Ambiguity (2) An extreme case of ambiguity occurs when the underlying function/ (x) is a periodic function, like
a scene of a picket fence. We can show that this ambiguity can also be eliminated. 5 (a)
(b)
(c)
(d)
(e)
(f)
•zeta
zeta
zeta
ure 2: Expected values of evaluation functions: (a) Underlying function; (b)E[ed(\)]; (c)£f
£[««i)]; («) ^I«<(2)]; (0 £[«c(i2)l
6 (a) •zeta (f)
zeta Figure 2: Expected values of evaluation functions: (a) Underlying function; (b)E[ed(\)]; (c)£fap)];
(d) £[««i)]; («) ^I«<(2)]; (0 £[«c(i2)l 6 Let/ (x) be a periodic function with period T. Then, each e<(i)(Jt, Q is expected to be a periodic
function of C with the period ^ (for the proof, refer to appendix B). This means that there will
be multiple minima of £<(o(x, 0 (i.e., ambiguity in matching) at intervals of jj? in (. When we use
two baselines and add their SSD values, the resulting e^nfa, 0 will be still a periodic function of
C, but its period T\z is increased to Tn=LCM f T
T \
\BXF'B2F)'
(20) (20) where LCMQ denotes Least Common Multiple. That is, the period of the expected value of the
new evaluation function can be made longer than that of the individual stereo pairs. Furthermore,
it can be controlled by choosing the baselines B\ and Zfe appropriately so that the expected value
of the evaluation function has only one minimum within the search range. This means that using
multiple-baseline stereo pairs simultaneously can eliminate ambiguity, although each individual
baseline stereo may suffer from ambiguity. We illustrate this by using real stereo images. Figure 3(a) shows an image of a sample scene. At the top of the scene there is a grid board whose intensity function is nearly periodic. We took ten
images of this scene by shifting the camera vertically as in figure 4. The actual distance between
consecutive camera positions is 0.05 inches. Let this distance be B. Figure 3 shows the first and
the last images of the sequence. We selected a point X within the repetitive grid board area. The
SSD values £<(,•)(*, Q over 5-by-5-pixel windows are plotted for various baseline stereo pairs in
figure 5. The horizontal axis of all the plots is the inverse depth, normalized such that SBF = 1. Figure 5 illustrates the trade-off between precision and ambiguity in terms of baselines. 2.4 Elimination of Ambiguity (2) That is,
for a shorter baseline, there are fewer minima (i.e. less ambiguity), but the SSD curve is flatter
(i.e. less precise localization). On the other hand, for a longer baseline, there are more minima (i.e. more ambiguity), but the curve near the minimum is sharper; that is. the estimated depth is more
precise if we can find the correct one. Now, let us take two stereo image pairs: one with B = 5B and the other with B = 86. In figure 6,
the dashed curve and the dotted curve show the SSD for B * 5B and B » 86, respectively. Let us
suppose the search range goes from 0 to 20 in the horizontal axis, which in this case corresponds
to 12 to 0 0 inches in depth. Though the SSD values take a minimum at the correct answer near
C = 5, there are also other minima for both cases. The solid curve shows the evaluation function
for the multiple-baseline stereo, which is the sum of the dashed curve and the dotted curve. The
solid curve shows only one clear minimum; that is, the ambiguity is resolved. 7 (a)
(b)
Figure 3: 'Town" data set: (a) ImageO; (b) Image9 (b) (a) (b) (a) Figure 3: 'Town" data set: (a) ImageO; (b) Image9 imageO
imagel
image2
image3
image4
imageS
image6
image7
image8
image9
Baseline
b 2b 3b 4b 5b 6b 7b 8b 9b
Figure 4: "Town" data set image sequence 8 8 (a)
(b)
(c)
(d)
(e)
(f)
(g)
9
7000 R
g>
60001
°>
5000
R
4000
(h)
5
10
^15
20
Figure 5: SSD values vs. inverse depth: (a) B = b; (b) B = lb; (c) B = 36; (d) 5 = 4b; (e) 5 = 5
(t)B-
6b; (g) 5 = lb; (h) 5 = Sb. The horizontal axis is normalized such that SbF = 1. Figure 5: SSD values vs. inverse depth: (a) B = b; (b) B = lb; (c) B = 36; (d) 5 = 4b; (e) 5 = 5b;
(t)B-
6b; (g) 5 = lb; (h) 5 = Sb. The horizontal axis is normalized such that SbF = 1. 9 Inverse
depth
Figure 6: Combining two stereo pairs with different baselines Figure 6: Combining two stereo pairs with different baselines So far, we have considered using only two stereo pairs. We can easily extend the idea to
multiple-baseline stereo which uses more than two stereo pairs. Corresponding to equation (20),
the period of £[*«i2 .-*t)(x, 01 becomes Tn^
= LCM
...,
(21)
\B\F B2F
BHFJ (21) where B\ ,52,. •. ,Bn are baselines for each stereo pair. We will demonstrate how the ambiguity can be further reduced by increasing the number of
stereo pairs. From the data of figure 4, we first choose image 1 and image9 as a long baseline stereo
pair, ie. (1)5 = 8ft. Then, we increase the number of stereo pairs by dividing the baseline between
imagel and imagc9, i.e. (2) B » 4b and 8ft, (3) B * 2ft, 4ft, 6ft and 8ft, (4) B = ft, 2ft, 3ft, 4ft, 5ft,
6ft, 7ft and 8ft. Figure 7 demonstrates that the SSSDs-in-inverse-depth shows the minimum at the
correct position more clearly as more stereo pairs are used. 2.5 Precision We have shown that ambiguities can be resolved by using the SSSD-in-inverse-depth computed
from multiple baseline stereo pairs. The technique also increases precision in estimating the true
inverse depth. We can show this by analyzing the statistical characteristics of the evaluation
functions near the correct match. 10 on
40000
§ 35000
1
^»
mtloi
30000
i
25000 -
20000 -
15000 -
10000 f
5000 *
0 -
B=b3,...,8b
15
20
Inverse depth
Figure 7: Combining multiple baseline stereo pairs on
40000
§ 35000
1
^»
mtloi
30000
i
25000 -
20000 -
15000 -
10000 f
5000 *
0 -
B=b3,...,8b
15
20
Inverse depth
Figure 7: Combining multiple baseline stereo pairs Figure 7: Combining multiple baseline stereo pairs p
Figure 7: Combining multiple baseline stereo pairs By using the Taylor expansion about
we obtain By using the Taylor expansion about
we obtain y
g
y
p
f(x + BiF(( - <,) +j) «/(x+7) + B,F« - 0V'(x+j). (22)
Substituting this into equation (12), we can approximate e^ix, Q near
by a quadratic form of £:
«cwU»0 « E("
5'
F(C-Cr)/
r'U+y-) + no(j:+7")-«1(x + 5JFC+;-))
2
jew
= BfF
2a(x)(C - Q
1 + WW*) - Ao(x))(C - Cr) + c,-(x),
where
(23) f(x + BiF(( - <,) +j) «/(x+7) + B,F« - 0V'(x+j). (22)
nto equation (12), we can approximate e^ix, Q near
by a quadratic form of £: f(x + BiF(( - <,) +j) «/(x+7) + B,F« - 0V'(x+j). (22)
Substituting this into equation (12), we can approximate e^ix, Q near
by a quadratic form of £:
«cwU»0 « E("
5'
F(C-Cr)/
r'U+y-) + no(j:+7")-«1(x + 5JFC+;-))
2
jew
= BfF
2a(x)(C - Q
1 + WW*) - Ao(x))(C - Cr) + c,-(x),
h
(23) f(x + BiF(( - <,) +j) «/(x+7) + B,F« - 0V'(x+j). (22)
Substituting this into equation (12), we can approximate e^ix, Q near
by a quadratic form of £: (22 (23) where yew
-
Ttf'(x+j)nk(x+j)
jew
d(x)
= £ ( , i £ t + ; ) - r t o ( ; c + ; ) )
2 . From equations (28) and (30), we see that From equations (28) and (30), we see that From equations (28) and (30), we see that 1
*
1
i
=
-
(3D
Var(l2^)(C)
tlVaruiC)' (3D The inverse of the variance represents the precision of the estimate. Therefore, equation (31) means
that by using the SSSD-in-inverse-depth with multiple baseline stereo pairs, the estimate becomes
more precise. We can confirm this characteristic in figures 6 and 7 by observing that the curve
around the correct inverse depth becomes sharper as more baselines are used. The variance of the estimated inverse depth ( r that minimizes this function is The variance of the estimated inverse depth ( r that minimizes this function is ^
•
n
w
( 3 0 ) ^
•
n
w
( 3 0 )
we see that
1
*
1
i
=
-
(3D
Var(l2^)(C)
tlVaruiC)' ( 3 0 ) 2.5 Precision (24)
(25)
(26) (24) (25) (26) The estimated inverse depth & is the value C that makes equation (23) minimum;
bi(x)-b0(x)
0 =
0 -
(27) The estimated inverse depth & is the value C that makes equation (23) minimum; The estimated inverse depth & is the value C that makes equation (23) minimum;
bi(x)-b0(x)
0 = 0 -
BiFa(x)
(27) The estimated inverse depth & is the value C that makes equation (23) minimum;
bi(x)-b0(x)
0 = 0 -
BiFa(x)
(27 bi(x)-b0(x)
0 = 0 -
BiFa(x)
(27) (27) 11 As shown in (13), the expected value of the estimate Cr is the correct value
but it varies due to
the noise. Following Appendix A in [MSK89], the variance of this estimate is given by As shown in (13), the expected value of the estimate Cr is the correct value
but it varies due to
the noise. Following Appendix A in [MSK89], the variance of this estimate is given by v " » < « - i p 4 j -
( 2 8 > ( 2 8 > Basically, for the same amount of noise o%9 the variance is smaller (the estimate is more precise)
as the baseline Bt is longer, or as the variation of intensity signal, a(x), is larger. g
y
g
g
We can follow the same analysis for £<(i2..*)0t, 0 of (14), the new evaluation function with
multiple baselines. Near C-> it is «OT2.H.)CT, 0 * f
F
2a(pc)(C - Cr)
2 +. 2 (f>iF<Mx) - b0(x))) ( C + £ cfc). (2 «OT2.H.)CT, 0 * f
F
2a(pc)(C - Cr)
2 +. 2 (f>iF<Mx) - b0(x))) ( C + £ cfc). (29 (2 3
Experimental Results This section presents experimental results of the multiple-baseline stereo based on SSSD-in-inverse-
depth with real 2D images. A complete description of the algorithm is included in Appendix C. depth with real 2D images. A complete description of the algorithm is included in Appendix C. The first result is for the "Town" data set that we showed in figure 3. Figures 8 (a) and (b) are
the depth map and its isometric plot with a short baseline, B = 3b. The result with a single long
baseline, B = 9fe, is shown in figure 9. Comparing these two results, we observe that the depth map
computed by using the long baseline is smoother on flat surfaces, i.e., more precise, but has gross
errors in matching at the top of the scene because of the repeated pattern. These results illustrate
the trade-off between ambiguity and precision. Figure 10, on the other hand, shows the depth map
and its isometric plot obtained by the new algorithm using three different baselines, 3b, 6b, and 9b. For comparison, the corresponding oblique view of the scene is shown in figure 11. We can note 12 (b) (a)
(b)
Figure 8: Result with a short baseline, B = 3b: (a) Depth map; (b) Isometric plot of the depth map
from the upper left corner. The matching is mosdy correct, but very noisy. (a) (a) (b) Figure 8: Result with a short baseline, B = 3b: (a) Depth map; (b) Isometric plot of the depth map
from the upper left corner. The matching is mosdy correct, but very noisy. correct depth
^wrong
depth
( b ) correct dept
^wron
dep
(a)
( b )
Figure 9: Result with a long baseline, B = 9b: (a) Depth map; (b) Isometric plot. The matching is
less noisy when it is correct. However, there are many gross mistakes, especially in the top of die
image where, due to a repetitive pattern, the matching is completely wrong. (a) (a) ( b ) Figure 9: Result with a long baseline, B = 9b: (a) Depth map; (b) Isometric plot. The matching is
less noisy when it is correct. However, there are many gross mistakes, especially in the top of die
image where, due to a repetitive pattern, the matching is completely wrong. 3
Experimental Results 13 (b) (a)
(b)
Figure 10: Result with multiple baseline, B = 3b, 6b, and 9b: (a) Depth map; (b) Isometric plot
Compared with figures 9(b) and 10(b), we see that the depth map is less noisy and that gross errors
have been removed. (a) (b) (a) Figure 10: Result with multiple baseline, B = 3b, 6b, and 9b: (a) Depth map; (b) Isometric plot
Compared with figures 9(b) and 10(b), we see that the depth map is less noisy and that gross errors
have been removed. Figure 11: Oblique view Figure 11: Oblique view Figure 11: Oblique view 14 14 W
(b)
Figure 12: "Coal mine" data set, long-baseline pair (b) W (b) that the computed depth map is less ambiguous and more precise than those of the single-baseline
stereo. Figure 12 shows another data set used for our experiment Figures 13 and 14 compare the
depth maps computed from the short baseline stereo and the long baseline stereo: the longer
baseline is five times longer than the short one. For comparison, the actual oblique view roughly
corresponding to the isometric plot is shown in figure 15. Though no repetitive patterns are apparent
in the images, we can still observe gross errors in the depth map obtained with the long baseline
due to false matching. In contrast, the result from the multiple-baseline stereo shown in figure 16
demonstrates both the advantage of unambiguous matching with a short baseline and that of precise
matching with a long baseline. Finally, figure 17 shows the depth map obtained by our stereo matching algorithm with a locally
adaptive window, which has been presented in [KO90], for which the depth map of figure 16 is
used as the initial estimate. The map exhibits both smoothness for flat surfaces and sharpness at
depth edges. 4
Conclusions S Z H Z ? ^
^ "
M W u
S t C r C O m
a
t
C
h
i
n
g
m
c
t
h
o
d
w
h
i
c
h
u
s « multiple baseline stereo
f^J^u
T
overcome
A
e **k-°ff between precision and accuracy (avoidance of
false matches) in stereo. The method is rather straightforward: we represent t £ SSD^Sto to
mdmdual stereo pars as a faction of the inverse depth, ami add JL
funcno's ^
S t ^ 15 (a)
(b)
Figure 13: Result with a short baseline: (a) Depth map; (b) Isometric plot of the depth map viewed
from the lower left corner (a) (b) (b) (a) (a)
(b)
Figure 13: Result with a short baseline: (a) Depth map; (b) Isometric plot of the depth map viewed
from the lower left corner (a)
0»
Figure 14: Result with a long baseline: (a) Depth map; (b) Isometric plot (a) 0» (a) ( )
Figure 14: Result with a long baseline: (a) Depth map; (b) Isometric plot 16 Figure 15: Oblique view Figure 15: Oblique view (a)
(b)
(c)
(d)
Figure 17: Isometric plots of the depth map computed by an iterative stereo algorithm with a loca
adaptive window, in which the depth map of figure 16 from the multiple-baseline stereo was u
as the initial map: (a) and (b) Isometric plot and corresponding view from the lower left corn
(c) and (d) Isometric plot and corresponding view from the upper right comer. (a)
(c)
Figure 17: Isometric plots of the depth map compu
adaptive window, in which the depth map of figur
as the initial map: (a) and (b) Isometric plot and
(c) and (d) Isometric plot and corresponding view (b) (a) (a)
(b)
(c)
(d)
Figure 17: Isometric plots of the depth map computed by an iterative stereo algorithm with a locally
adaptive window, in which the depth map of figure 16 from the multiple-baseline stereo was used
as the initial map: (a) and (b) Isometric plot and corresponding view from the lower left corner,
(c) and (d) Isometric plot and corresponding view from the upper right comer. 4
Conclusions (b) (b) (a) (c) (d) (d) (d) (c) Figure 17: Isometric plots of the depth map computed by an iterative stereo algorithm with a locally
adaptive window, in which the depth map of figure 16 from the multiple-baseline stereo was used
as the initial map: (a) and (b) Isometric plot and corresponding view from the lower left corner,
(c) and (d) Isometric plot and corresponding view from the upper right comer. Figure 17: Isometric plots of the depth map computed by an iterative stereo algorithm with a locally
adaptive window, in which the depth map of figure 16 from the multiple-baseline stereo was used
as the initial map: (a) and (b) Isometric plot and corresponding view from the lower left corner,
(c) and (d) Isometric plot and corresponding view from the upper right comer. 18 function, the SSSD-in-inverse-depth, exhibits an unambiguous and sharper minimum at the correct
matching position. As a result there is no need for search or sequential estimation procedures. function, the SSSD-in-inverse-depth, exhibits an unambiguous and sharper minimum at the correct
matching position. As a result there is no need for search or sequential estimation procedures. g p
q
p
The algorithm is easily amenable to parallel hardware implementation. Figure 4 shows a
possible scheme with multiple cameras, SSD calculators, adders and time delays. The key idea of the method is to relate SSD values to the inverse depth rather than the disparity. As an afterthought, this idea is natural. Whereas disparity is a function of the baseline, there is only
one true (inverse) depth for each pixel position for all of the stereo pairs. Therefore there must be a
single minimum for the SSD values when they are summed and plotted with respect to the inverse
depth. We have shown the advantage of the proposed method in removing ambiguity and improving
precision by analytical and experimental results. Acknowledgment Jim Rehg and Carol Novak have read the manuscript and improved its readability substantially. 19 19 Camera
Delay of
units
Figure 18: A scheme for parallel hardware implementation of the multiple baseline stereo algorithm
by SSSD-in-inverse-depth. We place n + 1 multiple cameras along an axis. All cameras are
synchronized. Pairs of camera output signals (the 0-th and the i-th) are fed into nd^ax
SSD
calculators with appropriate time delays, where d^a* is the maximum disparity for the stereo pair
with the longest baseline. Each SSD calculator computes the SSD values between a particular
image pair for a particular (quantized) inverse depth. The outputs of the SSD calculators for the
same inverse depth are connected to an adder to produce the sum of SSD's (SSSD) for that inverse
depth. These SSSD values are compared, and the inverse depth that shows the minimum is selected
as the estimate Figure 18: A scheme for parallel hardware implementation of the multiple baseline stereo algorithm
by SSSD-in-inverse-depth. We place n + 1 multiple cameras along an axis. All cameras are
synchronized. Pairs of camera output signals (the 0-th and the i-th) are fed into nd^ax
SSD
calculators with appropriate time delays, where d^a* is the maximum disparity for the stereo pair
with the longest baseline. Each SSD calculator computes the SSD values between a particular
image pair for a particular (quantized) inverse depth. The outputs of the SSD calculators for the
same inverse depth are connected to an adder to produce the sum of SSD's (SSSD) for that inverse
depth. These SSSD values are compared, and the inverse depth that shows the minimum is selected
th
ti
t o
n A
SSSD-in-inverse-depth for Ambiguous Pattern Proposition:
Suppose that there are two and only two repetitions of the same pattern around
positions x and x + A where A ^ 0 is a constant. That is, for y 6 W F(X+J)=F(Z+J),
ifandonlyif£=xor£=;c + a. (32)
^£2,forVC,C^Cr, F(X+J)=F(Z+J),
ifandonlyif£=xor£=;c + a. (32)
l ^£ forVC C^Cr F(X+J)=F(Z+J),
ifandonlyif£=xor£=;c + a. (32) F(X+J)=F(Z+J),
ifandonlyif£=xor£=;c + a. (32)
Then,iffl,^£2,forVC,C^Cr,
E[eam(x,0]
=
HVIX+Ji-FIX+BMC-Q+J))
2
jew
>
4AU* = £[<W*,C)]. (33) F(X+J)=F(Z+J),
ifandonlyif£=xor£=;c + a. (32)
Then,iffl,^£2,forVC,C^Cr,
E[eam(x,0]
=
HVIX+Ji-FIX+BMC-Q+J))
2
jew
>
4AU* = £[<W*,C)]. (33) (32) =
HVIX+Ji-FIX+BMC-Q+J))
2
jew jew
>
4AU* = £[<W*,C)]. (33) jew
>
4AU* = £[<W*,C)]. (33) (33) Proof: Tentatively suppose that for 3Q, Q ^
£ ( f ( * + y W ( * + * i F ( £ - Q + D F + EV^+FT-FB+WIQ-C)+J))
2
= 0. (34)
yew
yew (34) Then, it must be the case that F(X+J)
= /(X + fli+y)
and
F(X+F)
= F(X +
A2+J),
(35) F(X+J)
= /(X + fli+y)
and
F(X+F)
= F(X +
A2+J),
(35) F(X+J)
= /(X + fli+y)
and
F(X+F)
= F(X +
A2+J),
(35) (35) r; € W, where AX
=
BxFiQ-Q
=
B2F($-C). AX
=
BxFiQ-Q
=
B2F($-C). Since Bx ^ B2 and £ ft Q,
A\ F
A
(36) Since Bx ^ B2 and £ ft Q,
So, we have
A\ F A2. (36) A\ F A2. (36) So, we have
A\ F A2. (36) (36) So, we have FIX +J) = / (£ +y), for £ = X, X + a l f or X + a2. ( 3 7 )
S
"
(32)
(34)* °'
h ii i * ( 3 7 ) ^ssfbST"
(32)-
(34) *-
n°'
hoii ie •*
—<- 21 Then, Then,
C + *m = £[«c©C*, 0],
for VC. (41
Since this must be true for all C, let C be
From equation (13). JEW Then,
C + *m = £[«c©C*, 0],
for VC. Since this must be true for all C, let C be
From equation (13). (4 C + *m = £[«c©C*, 0],
for VC. (41
Since this must be true for all C, let C be
From equation (13). JEW Since this must be true for all C, let C be
From equation (13). JEW Proof: Let/ (x) be a periodic function with a period T. That is, for VJC, be a periodic function with a period T. That is, for VJC, /(jc)=/(x + *r),
for* = 0,±l,±2,...,
(38) /(jc)=/(x + *r),
for* = 0,±l,±2,...,
(38) (38) where T > 0 is the period, and there is no smaller value of T with this property. Using equations
(13) and (38), where T > 0 is the period, and there is no smaller value of T with this property. Using equations
(13) and (38), where T > 0 is the period, and there is no smaller value of T with this property. Using equations
(13) and (38), =
E<F(X+fi-F(X
+ BIF(C-Q+M
2
+ 2NWOL
JEW JEW
= £[*«©(*, C)]. (39) JEW
= £[*«©(*, C)]. (39) (39) That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that,
tentatively suppose V is the period such that
r
< w
m That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that,
tentatively suppose V is the period such that
r
<
m That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that,
tentatively suppose V is the period such that
r
< w
m That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that,
tentatively suppose V is the period such that That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that,
tentatively suppose V is the period such that r
< w
m m B
Period of E[E^T)(X,
Q] Proposition:
If/ (x) is a periodic function with a period T, then E[E^(X^ Q] is a periodic function
with the period Proof: Let/ (x) be a periodic function with a period T. That is, for VJC, Proof: Let/ (x) be a periodic function with a period T. That is, for VJC, Therefore, F(X)=F(X
+ KBIFT). (43) F(X)=F(X
+ KBIFT). (43) (43) F(X)=F(X
+ KBIFT). This means that/ (JC) has a period fijFT that is shorter than T because of (40). This is a contradiction
and thus V cannot be the period of £[*c(o(*i 01- Therefore, E[E^(X, 01 is a periodic function of C
with the period J^. This means that/ (JC) has a period fijFT that is shorter than T because of (40). This is a contradiction
and thus V cannot be the period of £[*c(o(*i 01- Therefore, E[E^(X, 01 is a periodic function of C
with the period J^. 22 C Multiple-Baseline Stereo Algorithm We present a complete description of the stereo algorithm using multiple-baseline stereo pairs. The
task is, given n stereo pairs, find the C that minimizes the SSSD-in-inverse-depth function, SSSD{x, 0 = £ X>o(* +J) -fi(x + BiFC +j))
2. (44) (44) We will perform this task in two steps: one at pixel resolution by minimum detection and the other
at sub-pixel resolution by iterative estimation. We will perform this task in two steps: one at pixel resolution by minimum detection and the other
at sub-pixel resolution by iterative estimation. Then, BiFC^RiBnFC^Ri^
(46) (46) where d(n) is the disparity for the stereo pair with baseline Bm. Substituting this into equation (44), where d(n) is the disparity for the stereo pair with baseline Bm. Substituting this into equation (44), isparity for the stereo pair with baseline Bm. Substituting this into equation (44), ty for the stereo pair with baseline Bm. Substituting this into equation (44), SSSD(x, din)) = £
o(* +J) -fi(x + Ri<kn) +y))
2. (47) (47) We compute the SSSD function for a range of disparity values at the pixel resolution, and identify
the disparity that gives the minimum. Note that pixel resolution for the image pair with the longest
baseline (Bn) requires calculation of SSD values at sub-pixel resolution for other shorter baseline
stereo pairs. Minimum of SSSD at Pixel Resolution For convenience, instead of using the inverse depth, we normalize the disparity values of individual
stereo pairs with different baselines to the corresponding values for the largest baseline. Suppose
B\ < B2 < • • • < Bn. We define the baseline ratio /?, such that Ri =
(45) (45) Iterative Estimation at Sub-pixel Resolution Once we obtain disparity at pixel resolution for the longest baseline stereo, we improve the disparity
estimate to sub-pixel resolution by an iterative algorithm presented in [MO89][OK90]. For this
iterative estimation, we use only the image pair fo(x) andfn(x) with the longest baseline. This is due
to a few reasons. First, since the pixel-level estimate was obtained by using the SSSD-in-inverse-
depth, the ambiguity has been eliminated and only improvement of precision is intended at this
stage. Second, using only the longest-baseline image pair reduces the computational requirement
for SSD calculation by a factor of n, and yet does not degrade precision too significantly. 23 In the experiments shown in section 3, we used the following algorithm for sub-pixel estimation:
Let db(n) be the initial disparity estimate obtained at pixel resolution. Then, a more precise estimate
is computed by calculating the following two quantities: Ad,
= ^Jew(fo(x +j) -/«(x + dbfr) +M'n{x + dm +j)
( 4 g )
Zjew<f& + d<Kn)+J))
2
- 2
_
2 < %
(
4
9
) ( 4 g (
4
9
) The value Ad{H) is the estimate of the correction of the disparity to further minimize the SSD, and
is its variance. We iterate this procedure by replacing do^ by The value Ad{H) is the estimate of the correction of the disparity to further minimize the SSD, and
is its variance. We iterate this procedure by replacing do^ by The value Ad{H) is the estimate of the correction of the disparity to further minimize the SSD, and
is its variance. We iterate this procedure by replacing do^ by dob)
<- do(ii) + ^ ( « )
(50) (50) until the estimate converges or up to a certain maximum number of iterations. until the estimate converges or up to a certain maximum number of iterations. [MSK89] Larry Matthies, Richard Szeliski, and Takeo Kanade. Kalman filter-based algorithms
for estimating depth from image sequences. International Journal of Computer Vision,
3:209-236,1989. [OK90]
Masatoshi Okutomi and Takeo Kanade. A locally adaptive window for signal matching.
In Proc. Third Infl Conference on Computer Vision, December 1990.
[Yam88] Masanobu Yamamoto. The image sequence analysis of three-dimensional dynamic
scenes. Technical Report 893, Electrotechnical Laboratory - Agency of Industrial
Science and Technology, Tsukuba, Ibaraki, Japan, May 1988. [Yam88] Masanobu Yamamoto. The image sequence analysis of three-dimensional dynamic
scenes. Technical Report 893, Electrotechnical Laboratory - Agency of Industrial
Science and Technology, Tsukuba, Ibaraki, Japan, May 1988. [OK90]
Masatoshi Okutomi and Takeo Kanade. A locally adaptive window for signal matching.
In Proc. Third Infl Conference on Computer Vision, December 1990. References [BBM87] R. C. Bolles, H. H. Baker, and D. H. Marimont. Epipolar-plane image analysis: An
approach to determining structure from motion. International Journal of Computer
Vision, l(l):7-55,1987. [BBM87] R. C. Bolles, H. H. Baker, and D. H. Marimont. Epipolar-plane image analysis: An
approach to determining structure from motion. International Journal of Computer
Vision, l(l):7-55,1987. [Gri85]
W. E. L. Grimson. Computational experiments with a feature based stereo algorithm. IEEE Transactions on Pattern Analysis and Machine Intelligence, 7(1): 17-34, January
1985. [Hee89]
Joachim Heel. Dynamic motion vision. In Proceedings of the DARPA Image Under-
standing Workshop, pages 702-713, Palo Alto, Ca, May 23-26 1989. [KO90]
Takeo Kanade and Masatoshi Okutomi. A stereo matching algorithm with an adap-
tive window: Theory and experiment Technical Report CMU-CS-90-120, School of
Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213,1990. [M089]
Larry Matthies and Masatoshi Okutomi. A bayesian foundation for active stereo vision. In SPIE, Sensor Fusion II: Human and Machine Strategies, November 1989. [MP79]
D. Marr and T. Poggio. A theory of human stereo vision. In Proc. Roy. Soc. London,
pages 301-328,1979. [MSK89] Larry Matthies, Richard Szeliski, and Takeo Kanade. Kalman filter-based algorithms
for estimating depth from image sequences. International Journal of Computer Vision,
3:209-236,1989. 24 [Yam88] Masanobu Yamamoto. The image sequence analysis of three-dimensional dynamic
scenes. Technical Report 893, Electrotechnical Laboratory - Agency of Industrial
Science and Technology, Tsukuba, Ibaraki, Japan, May 1988. 25
|
https://openalex.org/W4385609987
|
https://ejournal.iai-tabah.ac.id/index.php/madinah/article/download/1375/926
|
Indonesian
| null |
Efektifitas Sertifikasi Nadzir Dalam Sektor Pengelolaan Wakaf Di Indonesia
|
Madinah
| 2,022
|
cc-by-sa
| 4,351
|
1 Alzaina, N. (2019). Urgensi Pemberdayaan Nadzir Dalam Pengelolaan Wakaf Uang Di Indonesia.
Istismar:
Jurnal
Ekonomi
Syariah,
1,
37–42.
http://ejournal.unwaha.ac.id/index.php/istismar/article/view/303
2 Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan Muwakif Ditentukan
oleh Akuntabilitas Pengelolaan Wakaf Tunai dan Peran Nadzir ? Jurnal Akuntansi Dan Keuangan
Islam, 8(1), 71–86. https://doi.org/10.35836/jakis.v8i1.129
3Umami, N. F. dan K. (2021). Efektivitas Nazir Organisasi Di Majelis Wakil Cabang Nahdlatul
Ulama
Kecamatan
Siman
Kabupaten
Ponorogo.
Jurnal
Antologi
Hukum,
1(1),
16–33.
http://etheses.iainponorogo.ac.id/id/eprint/13759
4 Huda, N., Rini, N., Mardoni, Y., Anggraini, D., & Hudori, K. (2018). Manajemen Pengelolaan
Wakaf
Di
Indonesia
Timur.
EKUITAS
(Jurnal
Ekonomi
dan
Keuangan),
20(1),
1–17.
https://doi.org/10.24034/j25485024.y2016.v20.i1.35
5 Umami, N. F. dan K. (2021). Efektivitas Nazir Organisasi. Volume 09,
Nomor 1, Juni 2022 Volume 09,
Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Ayu Ruqayyah Yunus
Universitas Islam Negeri Alauddin Makassar, Indonesia
E-mail: Ayu.ruqayyahy@uin-alauddin.ac.id Ayu Ruqayyah Yunus
Universitas Islam Negeri Alauddin Makassar, Indonesia
E-mail: Ayu.ruqayyahy@uin-alauddin.ac.id Nurfiah Anwar
Universitas Islam Negeri Alauddin Makassar, Indonesia
E-mail: Nurfiahanwar05@gmail.com Abstrak: Topik utama dalam penelitian ini adalah bagaimana keabsahan
sertifikasi nadzir di departemen manajemen wakaf Indonesia dan validitas peran
nadzir di departemen manajemen wakaf Indonesia. pada pokok bahasan
penelitian ini? Selanjutnya, tujuan dari penelitian ini adalah untuk mengetahui
efektifitas sertifikasi nadzir pada departemen pengelolaan wakaf Indonesia dan
efektifitas peran nadzir pada departemen pengelolaan wakaf di Indonesia. Metode
pencarian yang digunakan adalah pencarian literatur. Referensi dalam artikel ini
didasarkan pada ide dan hasil penelitian sebelumnya seperti jurnal, buku, dan
artikel. Hasil penelitian ini menunjukkan bahwa Wakaf Nadzir akan
mengeluarkan sertifikat untuk berpindah dari Nadzir individu ke Nadzir
kelembagaan atau legal, memastikan keamanan manajemen dan keamanan
properti, menjaga persatuan dan masa depan umat. Ini juga menunjukkan bahwa
itu membantu untuk menghindari potensi konflik. Dengan kemampuan manusia,
manusia teknis dan hubungan yang berkualitas, Nazir yang profesional adalah
pemimpin umum di lembaga Wakaf yang mampu mencapai tujuan Wakaf. Kata kunci: Wakaf Sertiikasi Abstract: The topic of the problem in this research is how is the validity of nadzir
certification in the Indonesian waqf management department and the validity of the
nadzir's role in the Indonesian waqf management department on the subject of this
research? Furthermore, the purpose of this study is to determine the effectiveness of nadzir
certification in the Indonesian waqf management department and the effectiveness of the 111 Muslihati et al Efektifitas sertifikasi nadzir... . Efektifitas sertifikasi nadzir... . Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09,
Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah nadzir's role in the waqf management department in Indonesia. The search method used is
a literature search. The references in this article are based on the ideas and results of
previous research such as journals, books and articles. The results of this study indicate
that Wakaf Nadzir will issue certificates to move from individual Nadzir to institutional or
legal Nadzir, ensuring management security and property security, safeguarding the unity
and future of the ummah. It also shows that it helps to avoid potential conflicts. Volume 09,
Nomor 1, Juni 2022 With
human skills, technical people and quality relationships, professional Nazir is a general
leader in Waqf institutions who are able to achieve Waqf goals. Keywords: Waqf, Certification PENDAHULUAN Wakaf adalah hukum Islam, sistem kehidupan agama dan sosial. Oleh
karena itu, pengelolaan harus dilakukan dengan hati-hati karena tidak hanya
berfokus pada kepentingan spiritual masyarakat, tetapi juga pada kegiatan untuk
mencapai kemanusiaan sebagai entitas sosial1. Tergantung pada kondisi politik,
ekonomi dan budaya daerah, ada banyak perbedaan dalam perkembangan wakaf
di setiap daerah. Namun, dalam satu dekade terakhir, kesadaran kebangkitan
lembaga wakaf baru muncul di negara-negara Islam2 Islam sejak Islam masuk ke Indonesia. Praktik wakaf yang sering dilakukan
oleh masyarakat wakaf adalah harta bendanya untuk tempat ibadah. Jumlah
masjid dan musholla sangat banyak seiring dengan tradisi tempat ibadah di
Wakaf yang tumbuh dan berkembang3. Secara konseptual, Islam mengakui
lembaga wakaf sebagai sumber aset jangka panjang yang menguntungkan. Wakaf
diatur untuk memainkan peran penting dalam kesejahteraan orang4. Perkembangan
penting
dalam
Wakaf
memfasilitasi
pembentukan
manajemen Wakaf yang terperinci. Tentu saja, ini melibatkan peran yang sangat
besar dalam Nadzir. Dengan kata lain, Nadzir adalah pengelola Wakaf yang
bertanggung jawab untuk memelihara, mengelola dan mendistribusikan
keuntungan Wakaf ke tempat tujuan Wakaf yang diinginkan5. Lokasi nadzir
merupakan isu yang sangat penting dan sentral, karena pihak yang menerima Muslihati et al Efektifitas sertifikasi nadzir... . Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09,
Nomor 1, Juni 2022 harta wakaf dari wakaf perlu dikelola dan dikembangkan sesuai dengan
takdirnya6 harta wakaf dari wakaf perlu dikelola dan dikembangkan sesuai dengan
takdirnya6 Kunci pengelolaan wakaf terletak pada keberadaan pengelola wakaf,
khususnya Nadzir, dan tim kerja yang solid untuk memaksimalkan peran wakaf. Hal ini karena kemajuan wakaf sangat tergantung pada baik buruknya
pengelolaan pengelolaan wakaf. Oleh karena itu, Nadzir perlu dipromosikan
semaksimal mungkin untuk mencapai prestasi dan prestasi setinggi-tingginya 7. Nadzir adalah orang yang paling bertanggung jawab atas harta wakaf yang
dipercayakan kepadanya, baik dalam hal pemeliharaan harta wakaf maupun hasil
dan upaya pengembangannya8. Para ulama juga sepakat bahwa harta wakaf milik
Nadzir adalah amanah9. Menurut Imam Abu Honeyfa, Wakaf adalah pemindahan modal dan
keuntungan dari barang di tangan pemilik Wakaf, menggunakan arias dan
meminjamkan barang untuk tujuan saleh. saya bisa mengatakan. Dalam ketentuan
Pasal 215 Ayat 1 Hukum Islam, pengertian wakaf adalah perbuatan hukum
seseorang atau sekelompok orang atau badan hukum, memisahkan mereka dari
harta benda dan untuk kepentingan umum sesuai dengan ibadah atau ajaran
agama10. Wakaf adalah suatu perbuatan yang dilakukan dengan memegang
suatu harta dan terus menerus menyumbangkan keuntungannya untuk
kepentingan umum baik untuk keperluan ibadah maupun tujuan sosial11. y
,
(
)
,
p p
( ),
7Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan Wakaf, 1(2), 213–226
8Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf Alquran.
Ekonomi syariah, 7(2), 313 6 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 6 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118
7Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan Wakaf, 1(2), 213–226
8Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf Alquran.
Ekonomi syariah, 7(2), 313
9 Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis Wakaf Pimpinan
Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1.197
10Alzaina, N. (2019). Urgensi Pemberdayaan Nadzir Dalam Pengelolaan Wakaf Uang Di Indonesia.
Istismar:
Jurnal
Ekonomi
Syariah,
1,
37–42.
http://ejournal.unwaha.ac.id/index.php/istismar/article/view/303
11 Huda, N., Rini, N., Mardoni, Y., Anggraini, D., & Hudori, K. (2018). Manajemen Pengelolaan
Wakaf
Di
Indonesia
Timur.
EKUITAS
(Jurnal
Ekonomi
dan
Keuangan),
20(1),
1–17.
https://doi.org/10.24034/j25485024.y2016.v20.i1.35
12 Masyhar, A., Arifin, R., & Fuad, A. N. (2019). Sertifikasi Alih Nadzir Badan Hukum Wakaf
Perorangan Kepada Nadzir Badan Hukum Bagi Masjid / Musholla di Kecamatan Gunungpati
Kota Semarang. JPHI: Jurnal Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community
Engagement), 2(1), 60–67. https://journal.unnes.ac.id/sju/index.php/JPHI/article/view/34054
13 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal Diskursus Islam,
2(2), 171 14 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada
Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah
Muhammadiyah. https://journal.umy.ac.id/index.php/rab/article/view/10785 14 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada
Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah
Muhammadiyah. https://journal.umy.ac.id/index.php/rab/article/view/10785
15 Abdullah, A. (2020). Nadzir dalam Perspektif Kelembagaan Wakaf di Indonesia. Jurnal Ilmiah
Ekonomi Islam, 6(3), 403. https://doi.org/10.29040/jiei.v6i3.1216
16 Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan Muwakif Ditentukan
oleh Akuntabilitas Pengelolaan Wakaf Tunai dan Peran Nadzir ? Jurnal Akuntansi Dan Keuangan
Islam, 8(1), 71–86. https://doi.org/10.35836/jakis.v8i1.129
17 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan
Problematikanya.
Li
Falah:
Jurnal
Studi
Ekonomi
dan
Bisnis
Islam,
3(2),
62.
https://doi.org/10.31332/lifalah.v3i2.1197
18 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118
19 Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan Muwakif Ditentukan
oleh Akuntabilitas Pengelolaan Wakaf Tunai dan Peran Nadzir ? , ( ),
p //
g/
/j
16 Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan Muwakif Ditentukan
oleh Akuntabilitas Pengelolaan Wakaf Tunai dan Peran Nadzir ? Jurnal Akuntansi Dan Keuangan
Islam, 8(1), 71–86. https://doi.org/10.35836/jakis.v8i1.129
17 B h
ddi
A
Z
& I
R
Q
(2018)
N
i
W k f P
f
i
l
St
d
i
i d y
p //j
y
/
p p/
/
/
/
Abdullah, A. (2020). Nadzir dalam Perspektif Kelembagaan Wakaf di Indonesia. Jurnal Ilmia
konomi Islam, 6(3), 403. https://doi.org/10.29040/jiei.v6i3.1216 p //
g/
/
18 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 20 Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan Wakaf, 1(2), 213–
226
21 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan
Problematikanya.
Li
Falah:
Jurnal
Studi
Ekonomi
dan
Bisnis
Islam,
3(2),
62.
https://doi.org/10.31332/lifalah.v3i2.1197
22 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada
Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah
Muhammadiyah 4(2), 99–109. https://journal.umy.ac.id/index.php/rab/article/view/10785
23 Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis Wakaf Pimpinan
Daerah Muhammadiyah Ponorogo. Kodifikasia, PENDAHULUAN Menurut penyelidikan lain, wakaf menurut Syariah, memotong atau memotong
sebagian dari hartanya untuk tujuan ibadah dan / atau kesejahteraan umum,
secara permanen atau untuk jangka waktu, untuk kepentingannya. Adalah
perbuatan hukum oleh wakif untuk meninggalkan 12(Masyhar et al., 2019). p
gg
(
y
)
Harta wakaf pada dasarnya tidak dapat dipertukarkan, dan jika diperlukan
pertukaran, syarat-syaratnya disyaratkan sesuai dengan peraturan yang berlaku. Dengan kata lain, kekal berarti harta wakaf tidak boleh dikurangi, dan ada upaya
untuk
menghilangkan
keberadaan
harta
wakaf
tersebut13. 113 Muslihati et al Efektifitas sertifikasi nadzir... . Volume 09,
Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Wakaf memiliki manfaat yang besar bila digunakan dalam berbagai bidang
pendidikan, kesejahteraan sosial, kesehatan dan bisnis. Wakaf memiliki peran
yang sangat besar dalam meningkatkan taraf hidup masyarakat Indonesia,
khususnya dalam bidang sosial-ekonomi14. Nadzir secara etimologis berasal dari kata kerja Arab yang berarti melihat,
melihat. Dalam kaitannya dengan fiqh, nadzir berarti orang yang dilimpahkan
wewenang dan kewajiban untuk mengurus dan memelihara harta benda wakaf. 15. Nadzir memegang peranan terpenting dalam pengelolaan dan penghimpunan
dana wakaf dan merupakan lembaga atau individu yang paling bertanggung
jawab atas harta wakaf yang dititipkan kepadanya, baik dalam hal memelihara
harta wakaf maupun akibat dan komitmennya terhadap pembangunan16 Wakaf Nadzir, di sisi lain, berarti orang yang mengelola dan mengelola
harta dan pendapatan Wakaf dan memenuhi persyaratan yang ditetapkan oleh
Wakaf. Istilah lain yang digunakan oleh fuqaha adalah mutawalli. Secara
etimologis berarti seseorang yang mengurus dan melakukan sesuatu ketika
ditakdirkan untuknya17. Nadzir ini bertanggung jawab atas pemeliharaan,
perawatan dan pengembangan Wakaf untuk memastikan bahwa ia bekerja seperti
yang diharapkan. Ini dilakukan sesuai dengan tujuan Syariah18. Pengelolaan
Wakaf yang baik dan profesional oleh Nadzir akan meningkatkan kepercayaan
masyarakat dan terus meningkatkan jumlah muwakif19. Selain itu, Guru Besar Fakultas Syariah UIN Syarif Hidyatullah Jakarta
Fathurrahman Djamil mengatakan, Nadzir memiliki persyaratan umum lainnya. Pertama, Nazhir adalah seorang pemimpin umum dalam Wakaf. Oleh karena itu,
Nadzir harus memiliki kepribadian yang luhur, kredibilitas, pengalaman, dan
penguasaan manajemen dan keuangan. Kedua, selama masa jabatannya, Nadzir
dapat bekerja dalam hukum Wakaf sesuai dengan keputusan organisasi sosial dan
dewan. Ketiga, nadzir harus berada di bawah pengawasan Kementerian Agama
dan Dewan Direksi Wakaf Indonesia dan menyampaikan laporan keuangan dan
administrasi setidaknya triwulanan tentang Wakaf dan kegiatannya. Keempat, 114 Muslihati et al Efektifitas sertifikasi nadzir... . METODE Penelitian ini merupakan studi literatur tentang efektivitas sertifikasi
Nadzir. Bahan referensi untuk artikel ini diambil dari pemikiran dan hasil
penelitian sebelumnya tentang konsep dan gagasan tentang efektivitas sertifikasi
Nadzir di departemen manajemen Wakaf di Indonesia. Hasil dari diskusi ini
adalah ide-ide baru, kritik terhadap konsep dan ide yang dikembangkan oleh
peneliti sebelumnya, dan kesimpulan. Oleh karena itu, penelusuran literatur ini
menjadi dasar untuk penelitian selanjutnya. PENDAHULUAN Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09,
Nomor 1, Juni 2022 nadzir bertanggung jawab secara pribadi atas segala kerugian atau kewajiban
yang timbul akibat pelanggaran Undang-Undang Wakaf20 . nadzir bertanggung jawab secara pribadi atas segala kerugian atau kewajiban
yang timbul akibat pelanggaran Undang-Undang Wakaf20 . y
g
p
gg
g
g
Kewajiban nadzir adalah laporan tentang pengelolaan harta wakaf,
pengelolaan dan pengembangan harta wakaf sesuai dengan tujuan dan fungsi
penetapan, pengawasan dan perlindungan harta wakaf, dan pelaksanaan
kewajiban kepada rakyat Indonesia. Dewan Amil Wakaf. Sebagaimana
dinyatakan Tholhah Hasan, selain kewajiban dan tanggung jawab di atas, Nazir
dilarang melakukan perbuatan yang dapat menimbulkan tuduhan atau
kecurigaan, seperti: meminjam Harta Wakaf untuk diri sendiri atau keluarga
dekat21. Menurut Kamus Besar Bahasa Indonesia, efek berasal dari kata
effect. Ini memiliki beberapa arti, seperti efektif atau efektif, efektif, menghasilkan,
atau efektif. Para ahli mendefinisikan efektivitas sebagai kemampuan individu,
kelompok, lembaga, atau organisasi untuk memilih dan menentukan tujuan yang
tepat dan menggunakan alat yang tepat untuk mencapainya22. Efektivitas adalah
salah satu hasil yang harus dicapai organisasi. Untuk memperoleh teori
efektivitas, peneliti dapat menggunakan konsep-konsep dari teori manajemen dan
organisasi, terutama yang berkaitan dengan teori efektivitas23. 24 Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf Alquran.
Ekonomi syariah, 7(2), 313
25 Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan Wakaf, 1(2), 213–
226
26 Umami, N. F. dan K. (2021). Efektivitas Nazir Organisasi Di Majelis Wakil Cabang Nahdlatul
Ulama
Kecamatan
Siman
Kabupaten
Ponorogo.
Jurnal
Antologi
Hukum,
1(1),
16–33.
http://etheses.iainponorogo.ac.id/id/eprint/13759
27 Lestari, W., & Thantawi, R. (2016). Efektivitas Pengelolaan Wakaf Tunai. Syarikah, 2(1), 214–234.
28Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan
Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam.
29Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan Wakaf Produktif. Muqtasid: Jurnal
Ekonomi dan Perbankan Syariah, 3(1), 91. https://doi.org/10.18326/muqtasid.v3i1.91-109
30 Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf Alquran.
Ekonomi syariah, 7(2), 313
31 Ridwan M (2012) Nazhir Profesional Kunci Kesuksesan HASIL DAN PEMBAHASAN Menurut UIN Syarif Hidayatullah Jakarta dari Pusat Bahasa dan Budaya
(PBB), menurut survei terhadap 500 responden Nadzir di 11 negara bagian,
Nadzir tidak fokus pada manajemen, kebanyakan bekerja paruh waktu. Tidak ada
gaji yang dibayarkan (84%). Dan sangat sedikit orang yang bekerja sepenuhnya
secara intensif (16%). Selain itu, Wakaf lebih banyak dikelola oleh perorangan
(66%), juga dikenal secara tradisional, dibandingkan oleh organisasi profesi (16%)
dan badan hukum (18%) (Kasdi, 2014). Profesionalisme Nadzir dalam mengelola 115 Muslihati et al Efektifitas sertifikasi nadzir... . Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09,
Nomor 1, Juni 2022 harta wakaf tidak mungkin tercapai jika kesejahteraannya tidak terpenuhi atau
diabaikan. Mereka berhak menerima gaji dari hasil harta wakaf yang mereka
kelola sesuai dengan tugasnya dan standar gaji secara umum24. harta wakaf tidak mungkin tercapai jika kesejahteraannya tidak terpenuhi atau
diabaikan. Mereka berhak menerima gaji dari hasil harta wakaf yang mereka
kelola sesuai dengan tugasnya dan standar gaji secara umum24. g
g
y
g j
Achmad Djunaidi dan kawan-kawan menjelaskan bahwa parameter nadzir
profesional adalah amanah (dapat dipercaya), shiddiq (jujur), fathanah (cerdas),
dan tabligh (transparan). Sumber daya Nadzir yang handal adalah yang terdidik,
bermoral, berdaya saing, mampu membagi pekerjaan, memenuhi kewajiban dan
memperoleh hak yang adil, standar ketenagakerjaan yang jelas dan terarah25 . Nadzir Profesional adalah orang yang mengandalkan keterampilan dan keahlian
tinggi untuk melakukan pekerjaan penuh waktu dan bekerja pada tingkat tinggi. Komitmen pribadi ini membawa banyak tanggung jawab untuk pekerjaannya26. Nadzir harus mampu mengembangkan aset wakaf melalui program-program
yang kreatif dan inovatif27. Oleh karena itu, Anda membutuhkan seorang Nadzir
profesional dengan keterampilan manusia yang terampil, keterampilan manusia,
dan hubungan 28. Kompetensi manusia mengacu pada keahlian Nadzir di bidang tertentu
yang terkait dengan amanat pengembangan aset Wakaf. Human Technical, di sisi
lain, mengacu pada kemampuan untuk mengelola aset Wakaf. Dengan kata lain,
pengelolaan berdasarkan keterbukaan (transparency). Relasi adalah kemampuan
Nadzir membangun jaringan untuk kepentingan pengelolaan dan pengembangan
wakaf. Pengembangan jaringan sangat penting untuk mencapai tujuan produktif
wakaf. Tanpa jaringan, prinsip penawaran dan permintaan tidak dapat
diimplementasikan secara stabil29. Inovasi dalam pengembangan aset Wakaf juga sangat mengandalkan
kreativitas Nadzir. Nazir Profesional adalah seorang Nazir yang memiliki
pemahaman yang baik tentang ajaran agama dan kemampuan yang kredibel
untuk mengelola harta wakaf yang dipercayakan kepadanya30. Tugas seorang
nadzir profesional tidak hanya sebatas mengelola aset wakaf. Ia juga bertugas
mendistribusikan hasil atau manfaat Wakaf yang dikelola kepada penerima
manfaat. y
( )
31 Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan 32 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118. g g
),
35 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal Diskursus Islam, 2(2)
36 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118
37 Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan Wakaf Produktif. Muqtasid: Jurnal
Ekonomi dan Perbankan Syariah, 3(1), 91. https://doi.org/10.18326/muqtasid.v3i1.91-109
38 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 32 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118.
33 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan
Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam
34 Masyhar, A., Arifin, R., & Fuad, A. N. (2019). Sertifikasi Alih Nadzir Badan Hukum Wakaf
Perorangan Kepada Nadzir Badan Hukum Bagi Masjid / Musholla di Kecamatan Gunungpati
Kota Semarang. JPHI: Jurnal Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community
Engagement), 171
35 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal Diskursus Islam, 2(2)
36 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118
37 Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan Wakaf Produktif. Muqtasid: Jurnal
Ekonomi dan Perbankan Syariah, 3(1), 91. https://doi.org/10.18326/muqtasid.v3i1.91-109
38 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 y
J
34 Masyhar, A., Arifin, R., & Fuad, A. N. (2019). Sertifikasi Alih Nadzir Badan Hukum Wakaf
Perorangan Kepada Nadzir Badan Hukum Bagi Masjid / Musholla di Kecamatan Gunungpati
Kota Semarang. JPHI: Jurnal Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community
Engagement), 171 y
(
)
p p
( )
33 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi
Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam 32 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118.
33 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan
Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam
34 Masyhar, A., Arifin, R., & Fuad, A. N. (2019). Sertifikasi Alih Nadzir Badan Hukum Wakaf
Perorangan Kepada Nadzir Badan Hukum Bagi Masjid / Musholla di Kecamatan Gunungpati
Kota Semarang. JPHI: Jurnal Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community
Engagement), 171
35 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal Diskursus Islam, 2(2) HASIL DAN PEMBAHASAN Nadzir perlu bagi hasil Wakaf kepada Mustahik31. Muslihati et al 116 Muslihati et al Efektifitas sertifikasi nadzir... . Efektifitas sertifikasi nadzir... . Volume 09,
Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Pengelolaan wakaf yang profesional adalah suatu keharusan, dan
optimalisasi Nadzir Wakaf adalah suatu keharusan. Pengelolaan nazhir wakaf
yang optimal dapat meminimalisir permasalahan masyarakat terkait keterbatasan
ekonomi32. Untuk itu, ada beberapa istilah yang perlu diubah dalam paradigma
dalam edisi nadzir ini. Dengan kata lain, Anda perlu berubah dari kontrol
konsumen ke kontrol produktif. Dari Nadzir tradisional berdasarkan kepercayaan
murni ke Nadzir individu hingga Nadzir yang dilembagakan untuk memfasilitasi
akuntabilitas, diadopsi berdasarkan keahlian di bidangnya masing-masing33. Penerbitan akta migrasi nadzir wakaf dari nadzir individu ke nadzir
lembaga atau legal menjamin keamanan administrasi, keamanan harta benda,
menjaga persatuan umat dan menghindari potensi konflik di kemudian hari 34 . Potensi wakaf dapat memberikan dampak yang signifikan bagi kehidupan
masyarakat jika dikelola dan dikelola dengan baik berdasarkan prinsip-prinsip
profesionalisme. Untuk meningkatkan potensi wakaf produktif, diperlukan
adanya nadzir profesional pusat35 Relokasi Nazhir Wakaf dapat dilihat dari perkembangan kapasitas
kelembagaan Nazhir Wakaf. Hal ini membutuhkan pengembangan bakat
profesional di Nadzir Wakaf dan tidak terlepas dari prinsip transparansi,
akuntabilitas umum, standar operasional dan efisiensi36. Pendidikan wakaf
mencakup aspek sosial dan ekonomi, sistem manajemen yang baik, dan sumber
daya profesional yang terpercaya, sehingga lembaga Wakaf memanfaatkan dana
Wakaf
untuk
pendidikan,
dowa,
dan
bantuan
kemanusiaan. Dan
memprioritaskan kegiatan investasi37. Pengelolaan dan pengembangan nazhir merupakan bagian yang sangat
penting dari tugas pengelolaan organisasi pengelola wakaf. Seberapa baik SDM
dikelola akan menentukan kesuksesan masa depan organisasi ini. Di sisi lain, jika
sumber daya manusia tidak dikelola dengan baik, pengelolaan wakaf tidak akan
efektif38. Untuk dapat memanfaatkan harta wakaf secara produktif, lembaga
membutuhkan keahlian dalam pengelolaannya. Ini selalu mengandung gagasan
tentang efektivitas. Efektivitas pengelolaan harta wakaf dinilai penting dalam 117 Muslihati et al Efektifitas sertifikasi nadzir... . Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah
Volume 09,
Nomor 1, Juni 2022
mengukur langkah inventif dan menghindari hal-hal yang dapat merugikan
masyarakat39. Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09,
Nomor 1, Juni 2022 mengukur langkah inventif dan menghindari hal-hal yang dapat merugikan
masyarakat39. mengukur langkah inventif dan menghindari hal-hal yang dapat merugikan
masyarakat39. HASIL DAN PEMBAHASAN Optimalisasi pengelolaan harta benda wakaf ditujukan untuk memperoleh
hasil yang dapat dimanfaatkan sesuai dengan tujuan wakaf, dan ditujukan untuk
pengelolaan nilai ekonomis40. Selain itu, pengelolaan wakaf yang profesional
membutuhkan
ketelitian
dan
profesionalisme. Efektivitas
dan
efisiensi
pengelolaan aset wakaf penting untuk mengukur kemajuan dan menghindari
tabjil yang merugikan ummat. Menurut Kementerian Agama, efek ini adalah
pemanfaatan benda wakaf secara optimal untuk kepentingan umum41. Model pengelolaan yang efektif dan efisien harus dilakukan oleh penerima
harta wakaf. Keabsolutan Pengelolaan bertujuan untuk mengaktifkan kekayaan
wakaf dalam bentuk usaha yang dibutuhkannya, berupa barang dan jasa42 (Ishak,
2014). Menghubungi pengelola Wakaf yang profesional membutuhkan pembinaan
agar dapat menjalankan tugasnya secara profesional. Pembinaan dilakukan
dengan menggunakan standar manajemen saat ini, pendidikan formal dan
informal, pelatihan, atau bimbingan untuk menghasilkan pengelola dan
pengembang aset Wakaf43. BIBLIOGRAFI
Abdullah, A. (2020). Nadzir dalam Perspektif Kelembagaan Wakaf di Indonesia.
Jurnal
Ilmiah
Ekonomi
Islam,
6(3),
403.
https://doi.org/10.29040/jiei.v6i3.1216
Alzaina, N. (2019). Urgensi Pemberdayaan Nadzir Dalam Pengelolaan Wakaf (
)
g
41 Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis Wakaf Pimpinan
Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1.197
42 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf.
43 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 39 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada
Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah
Muhammadiyah 39 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada
Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah
Muhammadiyah
40 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf.
41 Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis Wakaf Pimpinan
Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1.197
42 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf.
43 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1.197
42 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf.
43 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 Efektifitas sertifikasi nadzir... . PENUTUP Keberadaan Wakaf dan pemberdayaannya sangat bergantung pada Nazhir. Nadzir berkomitmen untuk melakukan segala kemungkinan untuk melindungi
dan mengelola aset wakaf. Nazhir terdiri dari Nadzir perorangan, organisasi, atau
badan hukum. Manajemen wakaf meningkatkan kemungkinan penerapan oleh
Nadzir organisasi dan badan hukum dibandingkan dengan Nadzir individu
berdasarkan manajemen tradisional. Secara umum pengelolaan wakaf dapat
diarahkan dan didorong secara optimal jika nadzir adalah ahli yang dipercaya
(terpercaya). Kedua hal ini pada akhirnya menentukan apakah Anda dapat
mempercayai institusi tersebut. Dengan kemampuan manusia, hubungan teknis
dan manusiawi yang mumpuni, Wakaf Nadzir yang profesional adalah pemimpin
umum dalam lembaga Wakaf yang mampu mencapai tujuan Wakaf. BIBLIOGRAFI
Abdullah, A. (2020). Nadzir dalam Perspektif Kelembagaan Wakaf di Indonesia. Jurnal
Ilmiah
Ekonomi
Islam,
6(3),
403. https://doi.org/10.29040/jiei.v6i3.1216
Alzaina, N. (2019). Urgensi Pemberdayaan Nadzir Dalam Pengelolaan Wakaf 39 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada
Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah
Muhammadiyah Muslihati et al Efektifitas sertifikasi nadzir... . Efektifitas sertifikasi nadzir... . Volume 09,
Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam
ISSN : 1978-659X (Printed),: 2620-9497 (Online)
https://ejournal.iai-tabah.ac.id/index.php/madinah Uang
Di
Indonesia. Istismar:
Jurnal
Ekonomi
Syariah,
1,
37–42. http://ejournal.unwaha.ac.id/index.php/istismar/article/view Uang
Di
Indonesia. Istismar:
Jurnal
Ekonomi
Syariah,
1,
37–42. http://ejournal.unwaha.ac.id/index.php/istismar/article/view p
j
p p
Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi
dan Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam, 3(2), 62. https://doi.org/10.31332/lifalah.v3i2. g
Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis
Wakaf Pimpinan Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1. g
Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf
pada
Lembaga
Wakaf:
Studi
Kasus
pada
Majelis
Wakaf
dan
Kehartabendaan Pimpinan Daerah Muhammadiyah …. Reviu Akuntansi dan
Bisnis
Indonesia,
4(2),
99–109. https://journal.umy.ac.id/index.php/rab/article/view/10785 Hakim, A. R., Anwar, S., & Setiawan, A. I. (2016). Peran Badan Wakaf Indonesia
dalam Pengorganisasian Wakaf Produktif. Jurnal Tadbir: Jurnal Manajemen
Dakwah, 1(2) Huda, N., Rini, N., Mardoni, Y., Anggraini, D., & Hudori, K. (2018). Manajemen
Pengelolaan Wakaf Di Indonesia Timur. EKUITAS (Jurnal Ekonomi dan
Keuangan), 20(1), 1–17. https://doi.org/10.24034/j25485024.y2016.v20.i1.35 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1) Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal
Diskursus Islam, Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan
Wakaf, 1(2) Lestari, W., & Thantawi, R. (2016). Efektivitas Pengelolaan Wakaf Tunai. Syarikah,
2(1) Masyhar, A., Arifin, R., & Fuad, A. N. (2019). PENUTUP Sertifikasi Alih Nadzir Badan
Hukum Wakaf Perorangan Kepada Nadzir Badan Hukum Bagi Masjid /
Musholla di Kecamatan Gunungpati Kota Semarang. JPHI: Jurnal
Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community
Engagement),
2(1),
60–67. https://journal.unnes.ac.id/sju/index.php/JPHI/article/view/34054 Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan Wakaf Produktif. Muqtasid:
Jurnal
Ekonomi
dan
Perbankan
Syariah,
3(1),
91. https://doi.org/10.18326/muqtasid.v3i1. Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan
Muwakif Ditentukan oleh Akuntabilitas Pengelolaan Wakaf Tunai dan
Peran Nadzir ? Jurnal Akuntansi Dan Keuangan Islam, 8(1), 71–86. https://doi.org/10.35836/jakis.v8i1. Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf
Alquran. Ekonomi syariah, 7(2) Umami, N. F. dan K. (2021). Efektivitas Nazir Organisasi Di Majelis Wakil Cabang
Nahdlatul Ulama Kecamatan Siman Kabupaten Ponorogo. Jurnal Antologi
Hukum, 1(1), 16–33. http://etheses.iainponorogo.ac.id/id/eprint/13759 119 Muslihati et al Efektifitas sertifikasi nadzir... .
|
https://openalex.org/W2980186287
|
https://digibug.ugr.es/bitstream/10481/61784/1/Cockell2019_Article_SampleCollectionAndReturnFromM%20IACT.pdf
|
English
| null |
Sample Collection and Return from Mars: Optimising Sample Collection Based on the Microbial Ecology of Terrestrial Volcanic Environments
|
Space science reviews
| 2,019
|
cc-by
| 16,269
|
Space Sci Rev (2019) 215:44
https://doi.org/10.1007/s11214-019-0609-7 Space Sci Rev (2019) 215:44
https://doi.org/10.1007/s11214-019-0609-7 p
g
j
Q
y
Edited by Mahesh Anand, Sara Russell, Yangting Lin, Meenakshi Wadhwa, Kuljeet Kaur Marhas and
Shogo Tachibana Role of Sample Return in Addressing Major Questions in Planetary Sciences Role of Sample Return in Addressing Major Questions in Planetary Sciences
Edited by Mahesh Anand, Sara Russell, Yangting Lin, Meenakshi Wadhwa, Kuljeet Kaur Marhas and
Shogo Tachibana B C.S. Cockell
c.s.cockell@ed.ac.uk 1 Introduction The search for habitable conditions or life on any planetary body must necessarily be guided
by what we know about life on Earth. A very large number of ‘analog’ environments on
the Earth have been investigated to understand the factors that influence their microbial
inhabitants and determine both the biomass and diversity of life they can support. These
environments range from deserts to lakes with physico-chemical conditions, such as extreme
aridity, acidity or salinity, that correspond to extant or ancient conditions on Mars (e.g.,
Dickinson and Rosen 2003; Navarro-González et al. 2003; Cabrol et al. 2007; Preston and
Dartnell 2014; Hays et al. 2017; Lim et al. 2019). Over the last two decades our view of Mars as a homogeneous ‘red planet’ has given
way to a highly nuanced understanding of the great heterogeneity of past and present en-
vironments at kilometre scales (Cabrol and Grin 2001; Bibring et al. 2006; Ehlmann et al. 2009, 2011) down to millimetre scales, where individual mineral grains have been investi-
gated (Weitz et al. 2006). Some geochemical records indicate paleoenvironmental conditions
permissive for life (Grotzinger et al. 2013; Hurowitz et al. 2017). Despite this impressive ex-
pansion in our understanding of Mars, the fact remains that Mars is fundamentally a volcanic
planet, with a meagre rock cycle (no plate tectonics) and no extensive surface biosphere,
both of which vastly increase the range of viable habitats on the Earth. Even in the realm of
volcanic lithologies, Mars is limited in its geological diversity compared to the Earth. For
example the lack of a highly productive biosphere to generate large abundances of organic
carbon (Field et al. 1998) limits the diversity and extent of volcanic soils, called ‘andosols’,
that are a substantial habitat for microbial life on Earth. Although the Earth’s basaltic
oceanic crust offers a number of lessons about microbial distribution (Edwards et al. 2003;
Lysnes et al. 2004; Santelli et al. 2008), the specific chemical composition of Earth’s sea
water and its continuous flow through the basaltic crust over million-year time scales makes
even deep-ocean basaltic microbial habitats of potentially limited direct applicability to
Mars. On Mars, the composition of hydrothermal fluids in the subsurface is poorly con-
strained, the former presence and extent of sustained ocean(s) to generate analogous deep
ocean habitats is controversial (Head et al. Keywords Mars · Sample collection · Microbial ecology · Basaltic · Fumaroles Keywords Mars · Sample collection · Microbial ecology · Basaltic · Fumaroles Sample Collection and Return from Mars: Optimising
Sample Collection Based on the Microbial Ecology
of Terrestrial Volcanic Environments Charles S. Cockell1 · Sean McMahon1 · Darlene S.S. Lim2 · John Rummel3 ·
Adam Stevens1 · Scott S. Hughes4 · Shannon E. Kobs Nawotniak4 · Allyson L. Brady5 ·
Viggo Marteinsson6,7 · Javier Martin-Torres8,9,1 · Maria-Paz Zorzano10,8 ·
Jesse Harrison11 Received: 5 November 2018 / Accepted: 10 September 2019 / Published online: 9 October 2019
© The Author(s) 2019 Abstract With no large-scale granitic continental crust, all environments on Mars are fun-
damentally derived from basaltic sources or, in the case of environments such as ices, evap-
oritic, and sedimentary deposits, influenced by the composition of the volcanic crust. There-
fore, the selection of samples on Mars by robots and humans for investigating habitability
or testing for the presence of life should be guided by our understanding of the microbial
ecology of volcanic terrains on the Earth. In this paper, we discuss the microbial ecology
of volcanic rocks and hydrothermal systems on the Earth. We draw on microbiological in-
vestigations of volcanic environments accomplished both by microbiology-focused studies
and Mars analog studies such as the NASA BASALT project. A synthesis of these data em-
phasises a number of common patterns that include: (1) the heterogeneous distribution of B C.S. Cockell
c.s.cockell@ed.ac.uk B C.S. Cockell
c.s.cockell@ed.ac.uk 1
UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James
Clerk Maxwell Building, King’s Buildings, Edinburgh, EH9 3FD, UK 2
NASA Ames Research Center, Moffett Field, CA, USA 2
NASA Ames Research Center, Moffett Field, CA, USA 3
SETI Institute, P.O. Box 2445, Friday Harbor, WA 98250, USA 4
Dept. of Geosciences, Idaho State University, 921 S. 8th Ave, Pocatello, ID 83209, USA 5
School of Geography and Earth Sciences, McMaster University, Hamilton, Ontario, Canada 6
MATIS, Research & Innovation, Vínlandsleið 12, 113 Reykjavik, Iceland 7
Faculty of Food Science and Nutrition, University of Iceland, Reykjavik, Iceland 8
Group of Atmospheric Science, Department of Computer Science, Electrical and Space
Engineering, Luleå University of Technology, Luleå, Sweden 9
Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), Armilla, Granada, Spain 10
Centro de Astrobiología (CSIC-INTA), Torrejon de Ardoz, 28850 Madrid, Spain 11
Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland 44
Page 2 of 25 C.S. Cockell et al. Sample Collection and Return from Mars: Optimising
Sample Collection Based on the Microbial Ecology
of Terrestrial Volcanic Environments 44
Page 2 of 25 biomass and diversity in all studied materials, (2) physical, chemical, and biological factors
that can cause heterogeneous microbial biomass and diversity from sub-millimetre scales to
kilometre scales, (3) the difficulty of a priori prediction of which organisms will colonise
given materials, and (4) the potential for samples that are habitable, but contain no evidence
of a biota. From these observations, we suggest an idealised strategy for sample collection. It includes: (1) collection of multiple samples in any given material type (∼9 or more sam-
ples), (2) collection of a coherent sample of sufficient size (∼10 cm3) that takes into account
observed heterogeneities in microbial distribution in these materials on Earth, and (3) col-
lection of multiple sample suites in the same material across large spatial scales. We suggest
that a microbial ecology-driven strategy for investigating the habitability and presence of
life on Mars is likely to yield the most promising sample set of the greatest use to the largest
number of astrobiologists and planetary scientists. Keywords Mars · Sample collection · Microbial ecology · Basaltic · Fumaroles Sample Collection and Return from Mars... Page 3 of 25 44 There are, of course, environments on the Earth and Mars that are often considered to be
independent of the geology of the crust and on Earth host life or preserve biosignatures. For
example, ice-sheets and glaciers on Earth host life (Carpenter et al. 2000; Liu et al. 2015;
Anesio et al. 2017), as do evaporitic salt deposits (Maturrano et al. 2006; Oren 2008;
Robinson et al. 2015). These environments are known to exist on Mars (Head et al. 2003;
Lasue et al. 2013; Osterloo et al. 2008, 2010). However, the aqueous and particulate geo-
chemistry of these environments are influenced by the geological substratum and thus the
nutrients and energy supplies in such settings on Mars would still be linked to a vol-
canic geological context. Nevertheless, this paper will not discuss the biological poten-
tial and sampling of ices and salts. We draw lessons on sample collection by focusing
on primary volcanic rocks and derived weathering materials since they constitute the ma-
jority of materials and potentially habitable substrates that would likely be sampled by
robotic and human explorers. Although we do not review the literature here, we note
that the conclusions we will draw on the heterogeneity of microbial biomass and di-
versity in primary volcanic samples also apply to ices and salt deposits in which het-
erogeneous biomass and diversity distribution has been observed (e.g., Liu et al. 2015;
Robinson et al. 2015). The study of the microbial ecology of volcanic terrains relevant to Mars is surprisingly
underdeveloped. For example, the microbial ecology of environments with sustained inter-
actions between freshwater and volcanic rocks, including crystalline rocks and glasses, is
poorly known. Indeed, limited knowledge exists regarding the overall thickness and extent
of volcanic soils and other deposits derived by chemical weathering on Mars. However,
a sufficient number of studies have been accomplished to extract knowledge that directly
bears on what our most optimistic expectations for microbial ecology on Mars could be (as-
suming that there is or was life) and thus how one should go about collecting samples. In
this paper, we do not attempt an exhaustive review of microbiology studies in volcanic envi-
ronments. Instead, we provide examples used to draw out general principles. The selection
of studies used in this paper are shown in Table 1. In this paper, we have two objectives. Sample Collection and Return from Mars... First, we provide a review of microbial life in
volcanic rocks to inform the reader about the typical distribution of life in a diversity of ma-
terials. This review provides insight into the types of samples of interest to a biologist. One
might regard this as an introductory primer on microbial life in volcanic materials. Second,
using these examples of the microbial ecology of volcanic materials, we draw out common
patterns that allow us to suggest microbial ecology-driven sample collection approaches for
investigating habitability and testing the hypothesis of life on Mars. The conclusions we draw in this paper are applicable to the search for both extant and
extinct life. The distribution of biomarkers such as biomolecules (e.g., hopanes) and isotopic
signatures in volcanic paleohabitats will depend on the original distribution of biomass as
well as its potential to be preserved in those environments (McMahon et al. 2018). Thus, the
search for extinct life must also take into account taphonomic considerations relevant to the
microbial habitats discussed here. 1 Introduction 1999) and long-term hydrological activity ap-
pears to have been curtailed by the loss of most surface water in the late Noachian and
Hesperian (Lasue et al. 2013). Sample Collection and Return from Mars... 2 A Review of Igneous Petrology from an Astrobiological Perspective Igneous petrology is a vast area of research, but from an astrobiological perspective, sev-
eral points can be made about volcanism that are essential to the later discussion in this
paper. Volcanic rocks (i.e. igneous rocks derived from the extrusion of lava at the Earth’s
surface rather than cooling of magma in the subsurface) vary widely in composition. They 44
Page 4 of 25 C.S. Cockell et al. 44
Page 4 of 25
C.S. Cockell et al
ble 1 Studies of the microbial ecology of volcanic environments relevant to Mars used in this paper to suggest a sampling strategy
e of environment/material
Location
Comments
Reference
altic/andesitic crystalline rock
Italy
Lichen colonisation of lava flows on Mount Vesuvius
Adamo and Violante (1991), Adamo
et al. (1993)
Iceland
Studies on bacterial inhabitants of crystalline rocks (lava)
Kelly et al. (2011), Cockell et al. (2013)
Iceland
Bacterial pioneer colonists of crystalline rocks (lava)
Kelly et al. (2014)
Iceland
Inhabitants of lava flows of differing ages
Byloos et al. (2018)
USA
Inhabitants of transects from fumarolic to non-fumarolic sites
including unaltered and weathered basalts (Hawai’i)
Cockell et al. (2019)
yolitic crystalline rock
Iceland
Bacterial inhabitants of crystalline rocks (lava)
Kelly et al. (2011)
altic glass
Iceland
Bacterial inhabitants of weathered basaltic glass
Cockell et al. (2009)
Iceland
Bacterial inhabitants of weathered basaltic glass
Kelly et al. (2010)
idian (silica-rich glass)
Iceland
Bacterial inhabitants of obsidian
Herrera et al. (2008, 2009)
Iceland
Bacterial inhabitants of weathered glasses
Kelly et al. (2010)
canic fumaroles/active geothermal
strates/geothermal lakes
Italy
Endolithic inhabitants of rocks and soils in active geothermal area
Gross et al. (1998)
USA
Endolithic inhabitants of siliceous geothermal deposits
Walker et al. (2005)
New Zealand
Endolithic inhabitants of siliceous deposits in active geothermal
springs
Gaylarde et al. (2006)
Chile
Inhabitants of fumaroles and surrounding soils
Costello et al. (2009)
Antarctica
Inhabitants of fumarolic soils
Soo et al. (2009)
USA
Inhabitants of nonsulphur, sulphur and iron geothermal steam
vents
Benson et al. (2011)
USA
Inhabitants of fumaroles
Wall et al. (2015)
Iceland
Geothermal spring microbial and isotopic gradients
Cousins et al. (2018)
Costa Rica
Microbial diversity in Laguna Caliente lake
Hynek et al. (2018)
Chile
Inhabitants of fumarolic soils
Solon et al. (2018)
USA
Inhabitants of transects from fumarolic to non-fumarolic sites
(Hawai’i)
Cockell et al. 2 A Review of Igneous Petrology from an Astrobiological Perspective (2019) Table 1 Studies of the microbial ecology of volcanic environments relevant to Mars used in this paper to suggest a sampling strategy
Type of environment/material
Location
Comments
Reference
Basaltic/andesitic crystalline rock
Italy
Lichen colonisation of lava flows on Mount Vesuvius
Adamo and Violante (1991), Adamo
et al. (1993)
Iceland
Studies on bacterial inhabitants of crystalline rocks (lava)
Kelly et al. (2011), Cockell et al. (2013)
Iceland
Bacterial pioneer colonists of crystalline rocks (lava)
Kelly et al. (2014)
Iceland
Inhabitants of lava flows of differing ages
Byloos et al. (2018)
USA
Inhabitants of transects from fumarolic to non-fumarolic sites
including unaltered and weathered basalts (Hawai’i)
Cockell et al. (2019)
Rhyolitic crystalline rock
Iceland
Bacterial inhabitants of crystalline rocks (lava)
Kelly et al. (2011)
Basaltic glass
Iceland
Bacterial inhabitants of weathered basaltic glass
Cockell et al. (2009)
Iceland
Bacterial inhabitants of weathered basaltic glass
Kelly et al. (2010)
Obsidian (silica-rich glass)
Iceland
Bacterial inhabitants of obsidian
Herrera et al. (2008, 2009)
Iceland
Bacterial inhabitants of weathered glasses
Kelly et al. (2010)
Volcanic fumaroles/active geothermal
substrates/geothermal lakes
Italy
Endolithic inhabitants of rocks and soils in active geothermal area
Gross et al. (1998)
USA
Endolithic inhabitants of siliceous geothermal deposits
Walker et al. (2005)
New Zealand
Endolithic inhabitants of siliceous deposits in active geothermal
springs
Gaylarde et al. (2006)
Chile
Inhabitants of fumaroles and surrounding soils
Costello et al. (2009)
Antarctica
Inhabitants of fumarolic soils
Soo et al. (2009)
USA
Inhabitants of nonsulphur, sulphur and iron geothermal steam
vents
Benson et al. (2011)
USA
Inhabitants of fumaroles
Wall et al. (2015)
Iceland
Geothermal spring microbial and isotopic gradients
Cousins et al. (2018)
Costa Rica
Microbial diversity in Laguna Caliente lake
Hynek et al. (2018)
Chile
Inhabitants of fumarolic soils
Solon et al. (2018)
USA
Inhabitants of transects from fumarolic to non-fumarolic sites
(Hawai’i)
Cockell et al. (2019) nvironments relevant to Mars used in this paper to suggest a sampling strategy Page 5 of 25
44 Sample Collection and Return from Mars... g
Table 1 (Continued)
Type of environment/material
Location
Comments
Reference
Mud volcanoes
Romania
Microbial diversity of mud volcanoes
Dahigaonkar and Chavan (2018)
China
Microbial diversity of mud volcanoes
Huang et al. (2016)
Ash/ash soils/tephra
Iceland
Colonisation of Surtsey Island
Schwabe (1970), Schwabe and Behre
(1972); Kristinsson (1970, 1974);
Brock (1973); Henriksson and
Henriksson (1982); Stefansdottir et al. 2 A Review of Igneous Petrology from an Astrobiological Perspective Ultimately, these categories largely reflect the source composition and thermal evolu-
tion of the magma, with more mafic (iron- and magnesium-rich) minerals crystallising from
the melt at higher temperatures. Mafic and ultramafic rocks (also referred to as ‘basic’) are
formed between ∼1000–1500 ◦C and contain elevated concentrations of pyroxenes, olivines
and plagioclase (predominantly Mg, Fe and Ca-containing minerals). The precipitation of
these dense minerals within a cooling magma chamber drives the composition of the resid-
ual magma towards higher silica content; thus high-silica volcanic rocks (also referred to as
‘acidic’ or ‘felsic’ rocks) generally represent lower temperatures (typically about 700 ◦C). They also have a higher content of orthoclase feldspar (a K-containing silicate mineral) and
quartz. Although rare felsic lavas have been detected on Mars, the martian crust is dom-
inated by the mafic rock, basalt. In this paper, we will not consider samples spanning the
entire ultramafic-felsic continuum, but we will provide examples of the microbial ecology of
materials, focusing on basaltic rocks. We also provide comparisons to high-silica obsidian
where this is useful to illustrate factors that influence colonisation. A second factor of great importance for a biota is the glassiness or crystallinity of the
material. Volcanic melt that comes into contact with ice or water is rapidly quenched be-
fore crystals can form, resulting in a homogeneous glass, in contrast to other rocks that are
formed subaerially and cool slowly, forming crystalline materials. This is significant in the
Martian context because widespread glaciers and ground ice in contact with volcanically ac-
tive regions (Cousins and Crawford 2011) may imply that past episodes of volcanism have
generated substantial quantities of glass and their weathering products (Horgan and Bell
2012). Why is distinguishing crystalline rock and glass important? First, glasses present a mate-
rial with a more homogenised composition to a potential biota, whereas in crystalline mate-
rials, bioessential elements are generally localised to particular crystals, meaning that fewer
bioessential elements can be found in one location at the micron-scale. Second, basaltic
glass, in contrast to crystalline rocks, has a distinctive capacity for weathering to palag-
onite, a soft alteration product (Thorseth et al. 1991; Stroncik and Schminke 2002) that
tends to form within basaltic vesicles and fractures and may be a more bio-accessible source
of nutrients than the crystalline matrix. Third, in crystalline high-silica rocks, the silica is
primarily bound up in quartz. 2 A Review of Igneous Petrology from an Astrobiological Perspective (2014)
Iceland
Colonisation of Heimaey Island
Englund (1976)
USA
Cinder cone colonisation (Hawai’i)
Carson and Brown (1978)
USA
Soil microbial communities (Hawai’i)
Nüsslein and Tiedje (1998)
USA
Recent colonisation of ash and their lithotrophic metabolisms
(Hawai’i)
King (2003)
USA
Recent colonisation of ash and their lithotrophic metabolisms
(Hawai’i)
Nanba et al. (2004)
USA
Inhabitants of 42–300 year old Hawaiian volcanic deposits
(Hawai’i)
Dunfield and King (2005)
USA
Inhabitants of numerous soil and ash deposits of different ages
(Hawai’i)
Gomez-Alvarez et al. (2006)
Antarctica
Inhabitants of deposits on geothermally active volcano
Fermani et al. (2007)
Italy
Inhabitants of different aged soils
Hopkins et al. (2007)
USA
Inhabitants of different aged soils
Ibekwe et al. (2007)
Iceland
Biomass and microbial community in fresh volcanic tephra
Amador et al. (2015), Gentry et al. (2017) le 1 (Continued)
e of environment/material
Location
Comments
Reference
d volcanoes
Romania
Microbial diversity of mud volcanoes
Dahigaonkar and Chavan (2018)
China
Microbial diversity of mud volcanoes
Huang et al. (2016)
/ash soils/tephra
Iceland
Colonisation of Surtsey Island
Schwabe (1970), Schwabe and Behre
(1972); Kristinsson (1970, 1974);
Brock (1973); Henriksson and
Henriksson (1982); Stefansdottir et al. (2014)
Iceland
Colonisation of Heimaey Island
Englund (1976)
USA
Cinder cone colonisation (Hawai’i)
Carson and Brown (1978)
USA
Soil microbial communities (Hawai’i)
Nüsslein and Tiedje (1998)
USA
Recent colonisation of ash and their lithotrophic metabolisms
(Hawai’i)
King (2003)
USA
Recent colonisation of ash and their lithotrophic metabolisms
(Hawai’i)
Nanba et al. (2004)
USA
Inhabitants of 42–300 year old Hawaiian volcanic deposits
(Hawai’i)
Dunfield and King (2005)
USA
Inhabitants of numerous soil and ash deposits of different ages
(Hawai’i)
Gomez-Alvarez et al. (2006)
Antarctica
Inhabitants of deposits on geothermally active volcano
Fermani et al. (2007)
Italy
Inhabitants of different aged soils
Hopkins et al. (2007)
USA
Inhabitants of different aged soils
Ibekwe et al. (2007)
Iceland
Biomass and microbial community in fresh volcanic tephra
Amador et al. (2015), Gentry et al. (2017) 44
Page 6 of 25 C.S. Cockell et al. 44
Page 6 of 2 are classified into fifteen different compositional groups depending upon their silica and
alkali content (in this context alkali means the concentration of Na and K) following con-
vention established by the International Union of Geological Sciences (IUGS) (Le Bas et al. 1992). 2 A Review of Igneous Petrology from an Astrobiological Perspective However, in glass, this silica (which has no biological use)
is distributed throughout and may retard the release of more biologically useful elements
such as Fe (Wolff-Boenisch et al. 2004). A priori therefore, in parent rocks on Mars we
would expect the concentration of silica and the glassiness of the material to be important
considerations in their potential as habitable substrates and how microorganisms would be
theoretically distributed within them. These factors are explored in later sections. The weathering of these primary rock types (and of volcanic ash deposits) in aque-
ous environments leads to the formation of a variety of cation-rich aluminosilicate clays
(or palagonite in the case of basaltic glass). The types of clays formed depend on the
thermal regime and aqueous chemistry. On Mars, Fe- and Mg-rich smectites, serpen-
tine, and chlorite, resulting from the alteration of basaltic precursor minerals, are partic-
ularly widespread (e.g., Poulet et al. 2005; Milliken and Bish 2010; Ehlmann et al. 2011;
Bristow et al. 2018). Interactions with clay particles, including smectite, can profoundly
influence the fate and residence time of organic matter in the environment and inhibit or
promote the growth of different microbial groups. However, little is currently known about
the correlation of microbial diversity and biomass to different clay types formed in volcanic Sample Collection and Return from Mars... Page 7 of 25 44 environments, particularly in environments where organic input is low. Most analyses of
volcanic clays have occurred in the critical zone (soil-rock interface) in regions of the world
where the formation of economically important volcanic soils (andosols) is associated with
generally high organic/humic substance concentrations (Kimble et al. 2000). Nevertheless,
the studies that have been undertaken in volcanic terrains are sufficient to draw the conclu-
sions we make here. We recognise that present-day surface conditions on Mars are very different from the
Earth. The desiccated surface, high-ultraviolet and ionising radiation and the presence of
perchlorates (Cockell et al. 2000; Dartnell et al. 2007; Hecht et al. 2009; Wadsworth and
Cockell 2017), among other factors, make the surface inimical to life and may also impact
the preservation of ancient biosignatures (particularly organic biomarkers). 2 A Review of Igneous Petrology from an Astrobiological Perspective In this synthesis,
we are assuming that martian samples will be collected from environments that experienced
sustained contact with water in the past and have either been drilled from the subsurface or
were only exposed to martian atmosphere relatively recently, for example by wind erosion
(e.g., Farley et al. 2014; Hurowitz et al. 2017). We also note that more extreme conditions
found on Mars, particularly in later stages of its hydrological evolution, if they were to
theoretically reduce the potential biomass and diversity of life, would merely strengthen
the conclusions we draw about low biomass environments and the need for large sample
numbers required to test for life or affirm its absence. A further complication is the aeolian transport of material that becomes entrained in
rocks. Microorganisms are known to be transported in atmospheric dust on Earth (Gat et al. 2017). As well as providing a microbial inoculum to new habitats, the aerially transported
dust can potentially introduce extraneous geological material into samples, confounding ge-
ological analysis. On Mars, aeolian dust transport and mixing over the planetary scale is
ubiquitous (Lasue et al. 2018). Aerial transport of particulate matter is also widespread in
many volcanic environments on the Earth, including those in which microbial ecological
analysis described in this paper have been undertaken, such as environments in Iceland (Ar-
nalds et al. 2016). This transport does not compromise geological analysis of the origin of
samples or the conclusions about the heterogeneous distribution of biomass and diversity
within the sample that is linked to the primary sample type. This is likely to be the case for
sample selection on Mars, particularly if samples are cleaned of dust or collected from the
near-surface or interior of outcrops. 3 Limits of ‘Analogue’ Materials Not all volcanic environments and materials on Earth are useful analogues to Mars. Two
examples are andosols and marine-influenced volcanic rocks. We discuss these here to em-
phasise caution in drawing lessons about Mars from some volcanic materials on Earth. Volcanic rocks ultimately weather to soils called andosols, which form an important com-
ponent of terrestrial volcanic environments (Kimble et al. 2000). Andosols exist in a variety
of states such as extreme pH in soils surrounding geothermal pools, hot and cold desert soils,
as well as humid andosols (Oskarsson et al. 2004; Parfitt and Kimble 1989; Arnalds 2004;
Belobrov and Ovechkin 2005; Hopkins et al. 2007). However, apart from regions free of
vegetation and with low precipitation (deserts), most andosols are fertile because of many
years of microbial and floral amelioration. They are generally high in Fe and Al. These
metals, in addition to high concentrations of humic acids, make andosols highly effective at
immobilising phosphate (Lukito et al. 1998). This retention of biologically available phos-
phorus combined with the precipitation of phosphorus, impedes microbial and floral growth 44
Page 8 of 25 C.S. Cockell et al. on younger andosols (Kimble et al. 2000). It is not currently known what the initial microbial
colonists are for many andosols as it depends on the chemical composition of each individ-
ual soil. Richardson (2001) showed that microorganisms were key to the release of organic
and inorganic phosphorus. Nevertheless, even young andosols, although relatively hostile,
are capable of sustaining highly diverse microbial communities. Nüsslein and Tiedje (1998)
investigated a 200 year-old andosol in Hawai’i with high diversity. They showed that the
soil biomass was dominated by a distinct microbial diversity of Pseudomonas, Rhizobium-
Agrobacterium and Rhodospirillum species. On many andosols, plants strongly influence
microbial colonisation. Some of the first floral species to inhabit Mount St. Helens soils
following the 1980 eruption were Lupinus spp., which provide support for nitrogen-fixing
cyanobacteria (Halvorson et al. 1992). Although these data are interesting, they nevertheless
illustrate that many terrestrial andosols are likely poor analogues to past or present Martian
volcanic environments because of the extent of microbial and plant colonisation and the
relatively rich organic carbon cycle established within them. An extensive body of literature exists on the microbial ecology of the basaltic oceanic
crust. 3 Limits of ‘Analogue’ Materials Although superficially this carbon- and energy-poor environment might appear to be
a good analogue for the Martian deep subsurface, there is uncertainty as to how much the
communities associated with ocean crust, their biomass and diversity, are influenced by
ocean chemistry and factors linked with the Earth’s unusual plate tectonic regime. During
the rifting that occurs at plate boundaries in the oceans, basaltic glass is produced. The rate
of crustal production may be well over a billion tonnes a year (Bach and Edwards 2003). Insofar as basaltic glass contains many major cations that are biologically useful, including
Ca, Mg, K, Na and Fe, then it would be expected to be a source of material for microbial
growth (Staudigel et al. 1995, 1998; Thorseth et al. 2001; Santelli et al. 2008). The extent to which oceanic basaltic glass is used by a biota in-situ is unclear (Staudi-
gel et al. 1998, 2006, Torsvik et al. 1998). There is evidence for the deep-ocean biological
alteration of glass. In investigations of 0–30 Myr old basalts from the region of mid-ocean
ridge known as the Australian–Antarctic Discordance, Thorseth et al. (2003) recorded the
presence of Mn-rich encrustations which they suggested could be linked to biological Mn-
yielding reactions. Partially fossilised endolithic microorganisms were associated with rims
of altered glasses. Basaltic glass from the Knipovich Ridge, Arctic shows pervasive coloni-
sation of fractures, including stalked, coccoid, rod and filamentous forms. Organisms were
found to be associated with the alteration products in the fractures and they were often cov-
ered in Fe- and Al-rich precipitates (Thorseth et al. 2001). The organisms that might be involved in weathering glass have been the subject of several
investigations. Templeton et al. (2005) showed the presence of Mn-oxidising bacteria in
basalts from Loihi Seamount, although autotrophic Mn-oxidisers were not recovered. This
suggests Mn oxidation is a secondary process occurring in heterotrophic organisms (Tebo
et al. 2005) that might be using organic carbon compounds available in seawater. Diverse
neutrophilic Fe-oxidising bacteria have been isolated from oceanic environments (Edwards
et al. 2003), although it is not clear to what extent they might be accessing iron from basaltic
glass or from the surrounding sea water. The Fe oxide minerals found associated with deep-
ocean basalts have been shown to be similar to minerals produced by iron-oxidising bacteria
in culture (Daughney et al. 2004). 3 Limits of ‘Analogue’ Materials In a study of the microbial community of the basaltic glasses of the Knipovich Ridge,
Arctic, Thorseth et al. (2001) identified heterotrophs and some chemolithotrophs including
phylotypes closely matching with S-oxidisers. Fe-reducing organisms were cultured from
Arctic Ridge seafloor basaltic glasses by Lysnes et al. (2004) and these authors suggested
that this is evidence for an Fe-cycle within seafloor basalts. Phylogenetic analysis of seafloor Sample Collection and Return from Mars.. Page 9 of 25 44 basaltic glasses around Hawai’i show high diversity (Santelli et al. 2008; Orcutt et al. 2009)
which is hypothesised to be linked to the chemolithotrophic use of basaltic glass alteration
products (Santelli et al. 2008). In summary, there appears to be good evidence for microbial use of elements from
basaltic glass directly, particularly Fe, that may suggest that these rocks provide an ana-
logue for habitable substrates on Mars. However, the extent to which resources in seawater
are used, such as organics and other ions, and the extent to which the biomass and diver-
sity of these habitats is established by continuous water flow in the oceanic crust together
with the high production rate of fresh substrate through plate tectonics is not known. Plate
tectonics, if it existed on Mars at all, ceased early (Yin 2012). Although there is contro-
versial evidence for a northern ocean (Head et al. 1999), even if it did exist, its chemical
composition and the degree to which it might have sustained crustal hydrothermal cycling
to generate habitats analogous to the terrestrial oceanic crust is not known. For these reasons, in this paper we focus on volcanic materials in contact with freshwater,
primarily land-based crystalline and glassy volcanic rocks, including materials in land-based
volcanic hydrothermal systems. However, heterogeneous distribution of biomass and diver-
sity is observed in ocean crust materials (Santelli et al. 2008), so although we do not consider
these to be necessarily the best analogue materials to examine here, the consideration of their
microbiology would not change our conclusions. 4 Microorganisms Are Heterogeneously Distributed—the Need for
Appropriate Sample Size Cells were detected after DAPI staining under UV light (subimage C) and after
fluorescence in situ hybridisation (FISH) with bacterial Cy3-EUB338I-III primers targeting most of bacteria
(subimage D). Observations B, C and D correspond to an identical area on the thin section (data from Herrera
et al. 2008, 2009). Image 2 shown cells in basaltic glass. Subimage A shows SYBR Green I (DNA) staining
of microorganisms on a fragment of palagonite also shows in bright field (scale bar 20 µm) (subimage B). Subimage C shows a SYBR Green I stained section of a vesicle in weathered basaltic glass, arrow indicates
DNA staining at the rock–palagonite interface with staining also apparent on the surface of the palagonite
(scale bar 40 µm) (data from Cockell et al. 2009) Fig. 1 Cells are distributed heterogeneously in materials for different reasons. Examples of heterogeneity
in microbial distribution in volcanic glasses. Image 1 shows cells in obsidian. In (A), unaltered glass (G)
and altered glass (AG) at the edge of a vesicle (V) are shown. Subimage B shows the region located in
the square in image A. Cells were detected after DAPI staining under UV light (subimage C) and after
fluorescence in situ hybridisation (FISH) with bacterial Cy3-EUB338I-III primers targeting most of bacteria
(subimage D). Observations B, C and D correspond to an identical area on the thin section (data from Herrera
et al. 2008, 2009). Image 2 shown cells in basaltic glass. Subimage A shows SYBR Green I (DNA) staining
of microorganisms on a fragment of palagonite also shows in bright field (scale bar 20 µm) (subimage B). Subimage C shows a SYBR Green I stained section of a vesicle in weathered basaltic glass, arrow indicates
DNA staining at the rock–palagonite interface with staining also apparent on the surface of the palagonite
(scale bar 40 µm) (data from Cockell et al. 2009) (Fluorescence In-Situ Hybridisation), found that cells were localised to altered regions in
the obsidian glass (Fig. 1). The cells were associated with iron oxide crystals. Subsequent
cell enumeration found total bulk cell numbers less than 104 cells/gram. Because the cells
were so localised within the obsidian, whole rock cell numbers were unrepresentative. Sig-
nificantly, entire chunks to cm3 scales, contained no detectable cells. The localised biofilms
associated with alteration zones were often only found in exposed rocks or weathered re-
gions where water had penetrated into the material. 4 Microorganisms Are Heterogeneously Distributed—the Need for
Appropriate Sample Size Observations of microorganisms in contiguous cryptoendoliths biofilms (e.g., Bell 1993;
de la Torre et al. 2003) might give the impression that organisms are generally uni-
formly distributed in rocks. Although these distinctive endolithic communities can be
observed in volcanic geothermal materials (Gaylarde et al. 2006; Gross et al. 1998;
Walker et al. 2005) and cooled volcanic rocks (Herrera et al. 2009), organisms within vol-
canic materials are frequently highly heterogeneously distributed at millimetre and sub-
millimetre scales, with implications for sample collection (Fig. 1). As a case study, it is
worth considering the colonisation and distribution of microbes in basaltic glass and its felsic
counterpart, obsidian. In both materials, microbes are observed to be distributed heteroge-
neously, but apparently caused by different factors. The distribution of microbes in obsidian,
although not directly relevant to Mars as this material has not be detected, provides insights
into the factors that influence microbial distribution in surface and near-surface volcanic
materials more generally. Basaltic glass weathers to palagonite, a relatively soft weathering product, which forms
rinds on the glass (Stroncik and Schminke 2001, 2002). Although weathering of obsid-
ian occurs, it is much slower than the weathering of basaltic glass (Wolff-Boenisch et al. 2004, 2006). The higher silica concentration in obsidian impedes the degradation of the ma-
terial since the Si-O bonds result in a more extensive silica network that is thought to retard
leaching of cations, including bioessential cations, from the rock. These different weathering processes are consistent with observations of varying micro-
bial abundance. Cockell et al. (2009) observed high cell numbers in basalt glass samples
with bulk cell numbers of ∼107 cells/gram. In this material, most of the observed cells
were associated with the weathered palagonite surfaces and potentially a population be-
neath the palagonite. Very few cells were associated with the unweathered glass surface. In
obsidian, which does not so readily form weathered rinds, Herrera et al. (2008), using FISH 44
Page 10 of 25 C.S. Cockell et al. Fig. 1 Cells are distributed heterogeneously in materials for different reasons. Examples of heterogeneity
in microbial distribution in volcanic glasses. Image 1 shows cells in obsidian. In (A), unaltered glass (G)
and altered glass (AG) at the edge of a vesicle (V) are shown. Subimage B shows the region located in
the square in image A. 4 Microorganisms Are Heterogeneously Distributed—the Need for
Appropriate Sample Size Similarly heterogeneous distribution of biomass has been observed in other volcanic en-
vironments. The NASA project BASALT (Biologic Analog Science Associated with Lava
Terrains; Lim et al. 2019) carried out a study of microbial diversity and biomass in basaltic
fumaroles, weathered rocks and unweathered rocks in Hawai’i. Consistent with other stud-
ies cited here, all materials were found to host a low diversity, and biomass was highly
heterogeneous, ranging from 6.25 × 105 to 4.06 × 107 cells/gram dry weight based on DNA
concentration (means shown in Fig. 3). Lipid biomarker-based estimates of biomass also
demonstrated heterogeneous distribution within BASALT samples (Brady et al. 2017). The
heterogeneous distribution of biomass in basaltic terrains has been noted in both fresh lava
(Kelly et al. 2014) and in dispersed volcanic tephra of varying ages (Gentry et al. 2017). Factors that are likely to account for the observed heterogeneity in microbial biomass
in volcanic materials include physical influences such as variations in the availability of
fracture surfaces and pore/vesicle space for growth, differences in permeability and thus Sample Collection and Return from Mars.. Page 11 of 25 44 fluid flow through fractures, albedo and therefore tendency to absorb sunlight and heat;
chemical factors such as the proportion of glass, heterogeneity in leaching of elements from
the composite minerals or glasses available for redox couples or as nutrients, variations in the
chemical weathering reactions mediated by constituent minerals and elements, differences in
the kinetic release rates of elements from rocks (Cockell et al. 2011); and biological factors,
e.g. priority effects, whereby first colonisers influence subsequent colonists (Lee et al. 2013). Some of these factors are known to be important determinants in the colonisation of soils
(Garcia-Pichel et al. 2003; Vos et al. 2013; O’Brien et al. 2016). These observations across a variety of volcanic materials emphasise the need for appro-
priate sample size. It is not possible to state an exact size, since the optimal sample size
depends on the material. However, the presence of organisms inhabiting millimetre-scale
vesicles, crystals and fractures in many volcanic materials shows that samples with integrity
at centimetre scales are required. 4 Microorganisms Are Heterogeneously Distributed—the Need for
Appropriate Sample Size These observations of cm3 scale samples or segments of
samples devoid of life even in materials on Earth, such as obsidian, shows that typical mini-
mum sample sizes of volcanic rock collected in the field for microbiological analysis should
be of size ∼10 cm3 and this sample size applies to Mars exploration. 5 Every Sample Is a ‘Microbial Island’—the Need for Multiple Samples
from the Same Material Type Although particular volcanic materials
host distinct types of community, variations occur within those communities at small scales. Thus, multi-
ple samples are required to investigate microbial diversity. In image B, cluster analysis of glass microbial
communities was based on DGGE (30–70% denaturant) community fingerprints. The Jaccard UPGMA den-
drogram was generated from the presence-absence matrix in GelComparII. Values at nodes represent cophe-
netic correlations. Pal represents basalt glass samples from Valafell, Obs represents rhyolitic glass/obsidian
samples from Dómadalshraun. Samples ending in C are composites for the given site (data from Kelly et al. 2010, 2011). Note that obsidian and basalt glass samples tend to cluster into two separate groups, but within
each group, the microbial community of each individual sample is distinctive Fig. 2 Diversity varies across materials, but also between samples of the same material. (A) Microbial di-
versity of basaltic glass and obsidian. (B) Each sample is a ‘microbial island.’ DGGE (Denaturing Gradient
Gel Electrophoresis) shows that each rock hosts a distinct community. Although particular volcanic materials
host distinct types of community, variations occur within those communities at small scales. Thus, multi-
ple samples are required to investigate microbial diversity. In image B, cluster analysis of glass microbial
communities was based on DGGE (30–70% denaturant) community fingerprints. The Jaccard UPGMA den-
drogram was generated from the presence-absence matrix in GelComparII. Values at nodes represent cophe-
netic correlations. Pal represents basalt glass samples from Valafell, Obs represents rhyolitic glass/obsidian
samples from Dómadalshraun. Samples ending in C are composites for the given site (data from Kelly et al. 2010, 2011). Note that obsidian and basalt glass samples tend to cluster into two separate groups, but within
each group, the microbial community of each individual sample is distinctive These published findings suggest that certain factors reliably influence microbial di-
versity, but that combinations of local environmental factors, such as specific mineralogy
and age, uniquely determine the microbial community in any given environment making
the a priori prediction of which organisms will colonise a given type of environment dif-
ficult to achieve. These factors are compounded by biogeographical stochasticity caused
by the variations in local microbial populations and their dispersal (Whitaker et al. 2003;
Fierer and Jackson 2006). With respect to sample collection, a notable observation is that in all these studies indi-
vidual samples of the same material exhibit variations in microbial diversity (Fig. 2). 5 Every Sample Is a ‘Microbial Island’—the Need for Multiple Samples
from the Same Material Type Like biomass, the microbial diversity of volcanic materials varies enormously as a function
of physical, chemical and biological factors that relate to the functional requirements of
life in that environment and/or the specific organisms that first successfully colonise the
material. Microbial diversity is significant to the search for life on Mars independent of biomass. For example higher-diversity environments could include more organisms with particularly
good preservation potential compared with lower-diversity environments simply because
such environments contain a larger cross-section of microbial taxa. For an extant biota,
microbial diversity provides critical information about the range of functional capabilities
that an environment can support and so diversity can be used as a measure of the habitability
of any given environment. Studies have been undertaken on the diversity of volcanic rocks to investigate the role of
elemental composition in their colonisation. For example, statistically significant differences
were observed in the microbial diversity between basaltic and more silica-rich obsidian glass
in Iceland and between basaltic and more silica-rich rhyolitic rocks in juxtaposed locations
where environmental factors were unlikely to influence the results (Kelly et al. 2010, 2011). It is now well established that gradients in both physical parameters such as temperature
(Soo et al. 2009) and chemical parameters such as pH and sulphur content (Benson et al. 2011) cause small-scale variations in microbial diversity in volcanic environments. These
spatial variations in microbial diversity are observed in all volcanic environments investi-
gated (Table 1) ranging from geothermal fumaroles (Soo et al. 2009; Benson et al. 2011;
Wall et al. 2015) to weathered exposed crystalline and glassy volcanic rocks (Herrera et al. 2009; Kelly et al. 2010, 2011), ash and soils (Gomez-Alvarez et al. 2006; Ibekwe et al. 2007), and mud volcanoes (Huang et al. 2016; Dahigaonkar and Chavan 2018). Variations in
the microbial ecology caused by temperature and geochemical spatial gradients were exam-
ined in detail in a geothermal setting in Iceland, where differences in microbial phylogeny,
function and their associated isotope fractionation values were found in single geothermal
outflows (Cousins et al. 2018). 44
Page 12 of 25 C.S. Cockell et al. Fig. 2 Diversity varies across materials, but also between samples of the same material. (A) Microbial di-
versity of basaltic glass and obsidian. (B) Each sample is a ‘microbial island.’ DGGE (Denaturing Gradient
Gel Electrophoresis) shows that each rock hosts a distinct community. 5 Every Sample Is a ‘Microbial Island’—the Need for Multiple Samples
from the Same Material Type In that
sense, we can regard each rock or sample as a microbial island. As sample size becomes
smaller, especially in outcrops where rock heterogeneities are on a smaller scale compared
to sample size, one might expect that diversity differences could increase as smaller patches
of colonies are targeted. At large scales, biogeographical factors (such as environmental
differences) will come into play. Thus, within any given sample size, physical, chemical
and biological factors are likely to make it extremely unlikely that two samples will exhibit
exactly the same microbial diversity. Sample Collection and Return from Mars.. Page 13 of 25 44 As with biomass, much of the diversity of surface volcanic environments on Earth is ei-
ther directly influenced by the oxygenated environment on Earth (e.g., containing aerobic
microorganisms) or indirectly (e.g., the presence of electron donors such as organic matter
or electron acceptors such as sulfate or oxidised iron). Some of these factors are irrelevant
for Mars (such as widespread oxic conditions), while others are relevant; for example, al-
though Mars is generally anoxic, it does host very abundant sulfate and iron oxides (Gendrin
et al. 2005; McSween et al. 2009; Grindrod et al. 2012). Extrapolating a theoretical pattern
of colonisation of Martian volcanic materials is not possible, since Martian volcanic mate-
rials are in some sense uniquely Martian. However, the general lessons we suggest about
these environments on the Earth (such as heterogeneous microbial biomass and diversity)
would be applicable since physical, chemical and biological factors will influence microbial
colonisation of rocks at sub-millimetre to kilometre scales, even if the specific concatenation
of those factors was uniquely Martian. From the point of view of sample collection, these observations emphasise the need for
multiple samples to gain statistically meaningful insights into microbial diversity and its
variation. These conclusions also apply to the search for relict biomarkers. Indeed, the vari-
ation in microbial diversity even at single sample level suggests the conjectural possibility of
a rare organism producing a preservable biomarker that was present in one sample, but not
another. In Hawai’ian basalts, lipid biomarkers have been shown to vary between samples,
illustrating how heterogeneity in microbial diversity also translates into heterogeneity in
preservable biomarkers (Brady et al. 2017). Different molecular biomarkers have also been
shown to vary in distribution even within the same samples over centimetre scales (Gentry
et al. 2017). 6 More Hydrological Activity Does Not Imply Greater Microbial Biomass
or Diversity—Select Samples in a Non-discriminatory Way An implicit assumption in Mars sample selection is the notion that where there is more
water or more sustained water, there is likely to be more life. This paradigm has been en-
couraged by the maxim, ‘follow the water’ (Hubbard et al. 2002). Although the notion that
longer-lived hydrothermal systems or lakes are more likely to sustain long-lived habitable
conditions and therefore higher biomass and more diverse microbial communities makes in-
tuitive sense, countervailing results can be observed in many volcanic environments (Fig. 3). The results of the NASA BASALT study in Hawai’i showed several significant results
with respect to Mars sample collection. The hypothesis that active fumaroles (locations
where meteoric or magmatic water circulates through active geothermal regions) would be
sites of enhanced microbial diversity (since high water availability and the presence of di-
verse elements in solution would be conducive to life) was not supported (Cockell et al. 2019). Of all sample types, active fumaroles had the lowest diversity. One hypothesis to
explain the relatively low diversity of bacterial communities within active fumaroles is that
their high temperatures might prohibit colonisation by certain taxa. High temperatures in
geothermal settings have previously been found to restrict microbial diversity compared to
more mesophilic environments. Sharp et al. (2014) found that in geothermal environments,
peak diversity occurred at 24 ◦C. Thus, merely picking sites that appeared to have hosted
active hydrothermal systems may not a priori guarantee samples with the highest biologi-
cal potential. Similarly low diversities are observed in other volcanic Mars-analogue sites
where physical and chemical extremes, for example in volcanic lakes, limit life (Hynek et al. 44
Page 14 of 25 C.S. Cockell et al. Fig. 3 Both the abundance and diversity of microorganisms do not necessarily correlate directly with the
hydrological cycle. Investigation of different volcanic materials in Hawai’i by the NASA BASALT project. The materials are: Active fumaroles (material exposed to active venting within a fumarole), active intermedi-
ate (material from the periphery of one of the active fumaroles), intermediate fumarole (material associated
with fumaroles showing low levels of activity and/or transient activity, with temperatures between 30–70 ◦C),
relict fumarole (material associated with an inactive fumarole), unaltered (material associated with unweath-
ered basalt), syn-emplacement (material associated with basalt altered during its emplacement primarily by
magmatically associated water and gas or meteoric water associated with the heated environment around
the lava). 6 More Hydrological Activity Does Not Imply Greater Microbial Biomass
or Diversity—Select Samples in a Non-discriminatory Way The data in (A) show that microbial abundance is highly variable and not correlated with material
type and its exposure to water. Image B shows microbial diversity in the different materials at phylum level. Image C shows the microbial diversity of the materials as three different measures of diversity (Observed,
Chao 1 and Shannon diversity). Note that relict fumaroles have higher overall bacterial diversity than active
fumaroles, but this trend was not obvious for archaeal communities, with one phylum, Crenarchaeota, only
occurring in the active fumaroles (D). Data from Cockell et al. (2019) Fig. 3 Both the abundance and diversity of microorganisms do not necessarily correlate directly with the
hydrological cycle. Investigation of different volcanic materials in Hawai’i by the NASA BASALT project. The materials are: Active fumaroles (material exposed to active venting within a fumarole), active intermedi-
ate (material from the periphery of one of the active fumaroles), intermediate fumarole (material associated
with fumaroles showing low levels of activity and/or transient activity, with temperatures between 30–70 ◦C),
relict fumarole (material associated with an inactive fumarole), unaltered (material associated with unweath-
ered basalt), syn-emplacement (material associated with basalt altered during its emplacement primarily by
magmatically associated water and gas or meteoric water associated with the heated environment around
the lava). The data in (A) show that microbial abundance is highly variable and not correlated with material
type and its exposure to water. Image B shows microbial diversity in the different materials at phylum level. Image C shows the microbial diversity of the materials as three different measures of diversity (Observed,
Chao 1 and Shannon diversity). Note that relict fumaroles have higher overall bacterial diversity than active
fumaroles, but this trend was not obvious for archaeal communities, with one phylum, Crenarchaeota, only
occurring in the active fumaroles (D). Data from Cockell et al. (2019) 2018). The NASA BASALT study found that as fumaroles transition to a relict state, aver-
age alpha diversity increases. This could be explained by the development of less extreme
temperature conditions, even though the potential flux of bioavailable nutrients in fumarolic
water is reduced. 2018). The NASA BASALT study found that as fumaroles transition to a relict state, aver-
age alpha diversity increases. This could be explained by the development of less extreme
temperature conditions, even though the potential flux of bioavailable nutrients in fumarolic
water is reduced. 6 More Hydrological Activity Does Not Imply Greater Microbial Biomass
or Diversity—Select Samples in a Non-discriminatory Way Despite these findings, fumarolic environments can harbour a diversity of extremophiles
in extreme deserts where water flow is enhanced compared to persistently dry environments
that surround them (Costello et al. 2009; Soo et al. 2009; Wall et al. 2015) and although
extreme physical conditions can limit diversity, fumaroles are nevertheless high priority sites
for sample collection and for biological material that may yield insights into deep-branching
thermophilic lineages. Sample Collection and Return from Mars.. Page 15 of 25 44 The complexity of sample selection is exacerbated by the fact that the most diverse biota
may not always be the most likely to produce long-lasting biosignatures. For example, al-
though active fumaroles studied by NASA BASALT had the lowest overall bacterial diver-
sity, they contained the most diverse populations of archaea (Fig. 3; Cockell et al. 2019). Ether-bound intact polar lipids found in archaea are believed to be more stable than ester-
bound bacterial lipids and thus expected to survive longer over geological timescales (e.g. Harvey et al. 1986; Logemann et al. 2011). A preferential survival of archaeal lipids could
theoretically mean that the active fumaroles would leave a more detectable signature of past
life than other locations. The possibility for a lack of correlation between microbial biomass,
diversity and preservation potential emphasises the need for multiple samples from diverse
hydrological regimens. From the point of view of Mars sample collection, however, the lesson is clear. Ap-
parently intuitive ideas may not be borne out by microbial ecology and therefore sample
collection on Mars should be informed by terrestrial ecology. Predicting how biomass and diversity would be influenced by a series of diverse hydro-
logical regimes in any given local environment is problematic. Although the paradigm of
collecting from more hydrologically active environments is merited, the results from the
NASA BASALT project show that ideally a large number of samples from different hydro-
logical regimens should be collected to maximise the chance of finding rock materials that
could have potentially hosted the highest biomass and diversity. These observations on microbial diversity in volcanic environments on Earth suggest that
rather than ‘follow the water’ the overall strategy should be the more cumbrous, but more
accurate: ‘follow the water to large-scale environments that have been exposed to long-lived
hydrological cycles, but collect across all hydrological gradients within that area’. 7 Short-Lived or Recently Formed Habitats May Contain Low Biomass
and Diversity There are very few studies that examine the microbial communities associated with newly
formed volcanic materials that can be considered analogous to young materials on Mars
or volcanic materials that experienced transient interactions with liquid water. In gen-
eral, microbial biomass and diversity increases over time in the first years after coloni-
sation of a lava flow, but most studies have focused on lava flows many tens or even
hundreds of years old. Over these time periods, it is known that volcanic terrains on
Earth make felicitous places for microbial colonisation. It has been known for a long
time, particularly from studies before the use of molecular biology, that volcanic mate-
rials are colonised early by oxygenic photosynthesisers such as algae and cyanobacteria
(Kristinsson 1970, 1974; Schwabe 1970; Schwabe and Behre 1972; Brock 1973; Englund
1976; Henriksson and Henriksson 1982; Adamo and Violante 1991; Adamo et al. 1993;
Carson and Brown 1978; Fermani et al. 2007; Stefansdottir et al. 2014). Other studies
have also shown lithotrophs as early components of volcanic communities, such as organ-
isms that oxidise volcanically-derived CO and H2 (King 2003; Dunfield and King 2005;
Nanba et al. 2004). Dunfield and King (2005) showed that the diversity of CO-oxidisers
(based on amplification of coxL genes) was low in a recent (42 years old) lava flow in
Hawai’i, but lava between 108 and 300 years old had similar diversity. In volcanic environ-
ments where CO and sulphur gases (e.g., H2S, SO2) are actively emitted, chemoautotrophic
primary production in newly formed volcanic rocks may ultimately generate organic carbon
sufficient to sustain heterotrophs. C.S. Cockell et al. 44
Page 16 of 25 Fig. 4 Newly formed materials and those exposed to transient habitability contain highly heterogeneous,
low-diversity populations. The newly formed lava flows of the Fimmvörðuháls lava flow, Eyjafjallajökull,
Iceland in 2010 were colonised within 3 to 5 months by a low diversity biota. (A) Location of lava flows
in Iceland (arrow), (B) Map of lava flows showing sample sites 1, 5 and 9 from which diversity analy-
sis was undertaken, (C) Microbial abundance measured as direct cell counts at sample sites (error bars are
standard deviation) taken on July 5 and August 31, 2010 showing heterogeneity. (D) Microbial diversity at
phylum level shows communities dominated by Proteobacteria (specifically Betaproteobacteria). ‘J’ samples
are samples collected in July; ‘A’ samples are samples collected in August. 7 Short-Lived or Recently Formed Habitats May Contain Low Biomass
and Diversity ‘Weathered’ samples are samples
from the basaltic Hnausahraun lava flow, erupted circa 150–300 A.D. and is given for comparison. ‘Others’
phylum refers to other phyla, each represented by a maximum of two clones in any Fimmvörðuháls library
(data from Kelly et al. 2014) Fig. 4 Newly formed materials and those exposed to transient habitability contain highly heterogeneous,
low-diversity populations. The newly formed lava flows of the Fimmvörðuháls lava flow, Eyjafjallajökull,
Iceland in 2010 were colonised within 3 to 5 months by a low diversity biota. (A) Location of lava flows
in Iceland (arrow), (B) Map of lava flows showing sample sites 1, 5 and 9 from which diversity analy-
sis was undertaken, (C) Microbial abundance measured as direct cell counts at sample sites (error bars are
standard deviation) taken on July 5 and August 31, 2010 showing heterogeneity. (D) Microbial diversity at
phylum level shows communities dominated by Proteobacteria (specifically Betaproteobacteria). ‘J’ samples
are samples collected in July; ‘A’ samples are samples collected in August. ‘Weathered’ samples are samples
from the basaltic Hnausahraun lava flow, erupted circa 150–300 A.D. and is given for comparison. ‘Others’
phylum refers to other phyla, each represented by a maximum of two clones in any Fimmvörðuháls library
(data from Kelly et al. 2014) Where studies on the early (less than a year old) colonisation of volcanic terrains have
been undertaken, they have shown the extremely low diversity that is often sustained by new
volcanic materials, even on Earth, where atmospheric inoculation occurs and microbially-
accessible organic carbon is available. A study of the early colonisation of Icelandic lava
flows showed that within three months after the eruption of Eyjafjallajökull in 2010, coloni-
sation had occurred (Fig. 4) (Kelly et al. 2014). Biomass in some sites was low, but at others
exceeded 106 cells/g dry weight (Fig. 4) in samples of ∼50 cm3. Nevertheless, the diver-
sity was low and was dominated by Betaproteobacteria, in contrast to older lava flows that
typically contain an order of magnitude more biomass and have higher abundance of Aci-
dobacteria and Actinobacteria (Kelly et al. 2010, 2011; Byloos et al. 2018). 8 Is It Possible for Samples to Be Habitable, but Devoid of Life? Is there a possibility of collecting samples on Mars that fully satisfy the conditions for hab-
itability but are devoid of a biota? If Mars never hosted an origin of life or a transfer of
life to that planet then all environments that have energy sources, CHNOPS elements and
liquid water and are habitable by terrestrial standards would be devoid of life. However,
even if Mars has hosted life, transient habitats such as near-surface water melted by impacts
could be devoid of life if that habitat remained disconnected from inhabited regions (Cock-
ell 2011). If sample collection is undertaken within a confined area (for example, a single
impact crater or outflow channel), the possibility of sampling a once habitable, but never
inhabited palaeoenvironment is conceivable. As we cannot quantify this likelihood in the
absence of a knowledge of life on Mars, this theoretical possibility would suggest that col-
lecting samples from different environments, not merely within the same local environment
but across much wider areas, should be a priority to maximise the chances of collecting
samples containing life (Cockell and McMahon 2019). It is important to note that if Mars
was lifeless, this strategy will also strengthen the conclusion that the planet was lifeless by
multiplying the number of sampled habitable environments that can be shown to be devoid
of life. An important distinction is whether uncolonised regions in a sample are devoid of life
because they lack some fundamental requirement for life making them uninhabitable, or
whether they are habitable zones that can support life, but they have not yet been colonised. For example, uncolonised regions of obsidian studied by Herrera et al. (2008) are likely
uncolonised because of the lack of freely available iron. In other words, they may be unin-
habitable. On Earth, habitable samples devoid of life at the centimetre scale do seem to be rare. As organisms reproduce, fluid flow tends to carry them into new habitable spaces so that
at micron-scales, some part of that habitable space is colonised. Although not all habitable
space will be colonised, the movement of microbes does lead to the ecological reality that
when habitable samples are examined at centimetre scales, they usually contain life. 7 Short-Lived or Recently Formed Habitats May Contain Low Biomass
and Diversity Although some
of the organisms on the fresh lava may have used organic material atmospherically delivered
to the surface of the lava flows, the presence of chemoautotrophic members of the Thiobacil-
lus genus suggested that some of the population may have used iron and sulphur from the
primary volcanic materials (Kelly et al. 2014). It is a significant point that arguments about the evolutionary likelihood of particular
metabolisms on Mars (i.e. whether it is relevant to discuss searching for biomarkers of the
relatively biochemically and evolutionarily advanced oxygenic photosynthesis compared to
chemolithotrophic metabolisms) are irrelevant to the points made in this paper. All metabolic Sample Collection and Return from Mars.. Page 17 of 25 44 and taxonomic groups of microorganisms examined on early lava flows on Earth have shown
a heterogeneous distribution with a low biomass and diversity. These observations empha-
sise the points in Sects. 4–6. If volcanic materials have not been exposed to long-lived
hydrological regimens and mature microbial communities have not been established, then
the heterogeneous distribution of biomass and diversity may be exacerbated by overall low
biomass, emphasising the need for multiple samples and suitable sample size. 8 Is It Possible for Samples to Be Habitable, but Devoid of Life? Real examples on Earth of pervasive centimetre-scale habitable samples devoid of life
are recently formed lava flows in which hours to days after cooling to below the upper
temperature limit for life, microbes are so heterogeneous and sparse that at centimetre scales
some rocks remain uncolonised, particularly those beneath the surface of the flow that have
not been subject to atmospheric colonisation (Cockell 2014). These ecological considerations lead to relevant observations. In general, where life has
accessed an environment, fluid flow ensures that even though space can be habitable but
unoccupied, at macroscopic centimetre scales samples generally contain examples of life. In environments where habitable conditions were extremely transient, this assumption may
break down and habitable samples devoid of life at centimetre scales may be prevalent. In
the specific case of Mars, if the planet was lifeless or the biomass extremely localised to 44
Page 18 of 25 C.S. Cockell et al. certain regions, entire regions or environments may be habitable but devoid of life. Large
samples suites are required to test these hypotheses. certain regions, entire regions or environments may be habitable but devoid of life. Large
samples suites are required to test these hypotheses. An important question is how many samples are minimally required to determine that a
given material is devoid of life in all examples of that material. On the Earth, a high level
of biological confidence might be obtained by showing that life was not present in three
sets of three triplicates of such a material across one location with this sample set repeated
across three geographically separated regions of that material, whether on the surface or
subsurface. It may never be possible to demonstrate conclusively that Mars has always been lifeless,
since short-lived, localised pockets of life could have left scant or undetectable evidence, or
no evidence at all. However, if the sampling regimen described in the previous paragraph
was deployed across the geological records of diverse palaeohabitats with good potential
to preserve biosignatures (e.g., lake sediments, evaporitic deposits, and hydrothermal sinter
deposits) and no evidence of life was found, the balance of evidence would shift in favour of
the hypothesis that Mars has never been inhabited. In principle, a Bayesian approach could
be developed to model this shift; these statistical issues merit greater attention. 9 A Strategy for Sample Collection on Mars In this section, we summarise six recommendations for sample collection on Mars based
on observations of the microbial ecology of volcanic materials on Earth. We provide a brief
rationale for each. The strategy does not take into account cost, mass, or space restrictions
associated with specific missions such as robotic Mars sample return missions (Sherwood
et al. 2003; MEPAG 2008; iMOST 2018), but rather provides an insight into a biologically
ideal sample suite, whether it be collected by robot or human explorers. 9.1 Collect Sufficiently Large Samples Heterogeneity in microbial biomass and diversity has been observed in all volcanic materi-
als. These effects are likely to be caused by physical, chemical and biological influences that
will vary in different samples. ‘Sufficient’ size cannot be easily quantified, but observations
on volcanic rocks discussed here suggest that typical sample sizes should be a minimum
10 cm3 to retain millimetre-scale vesicles, fractures and mineral grains and their associ-
ated biological targets. Defining ideal samples based on mass is less important than volume. For example, a lower density sample can contain more pore space for potential microbial
colonisation than a higher density sample, counterintuitively making a lighter sample of
comparable volume potentially more valuable to a biologist than a more massive sample. Less is sometimes more. Less is sometimes more. 9.4 Collect Across Varied Hydrological Regimes ‘Follow the water’ is broadly a correct view with respect to the fundamental requirement that
all known life has used liquid water as a solvent. However, microbial ecology shows that lo-
cations with a high abundance of liquid water do not always harbour the most biomass and
diversity. As we have discussed here, in volcanic hydrothermal regimens, high temperatures
can limit life to lower biomass and diversity than drier locations at more mesophilic tem-
peratures. It is well known that in some locations liquid water can even be uninhabitable. For example, on the Earth, magnesium chloride brines can have water activities so low as to
be uninhabitable (Hallsworth et al. 2007) and such brines may exist on Mars. The lessons
from volcanic environments show that sampling should be carried out across hydrological
gradients and not merely in locations that appear to have hosted the most vigorous hydro-
logical regimes. Transects capture the variation in the interaction between geochemistry and
physical conditions that can influence habitability in a way independent of the quantity of
liquid water. ‘Follow the water’ is broadly a correct view with respect to the fundamental requirement that
all known life has used liquid water as a solvent. However, microbial ecology shows that lo-
cations with a high abundance of liquid water do not always harbour the most biomass and
diversity. As we have discussed here, in volcanic hydrothermal regimens, high temperatures
can limit life to lower biomass and diversity than drier locations at more mesophilic tem-
peratures. It is well known that in some locations liquid water can even be uninhabitable. F
l
h E
h
i
hl
id b i
h
i i i
l 9.5 Maintain Sample Integrity Cells are distributed heterogeneously and their locations provide information on the factors
that control life (e.g. presence of iron-bearing crystals, alteration rinds, fracture networks). It
is therefore essential to maintain sample integrity. Where possible they should be collected
with minimal damage caused by drilling, excavation etc. Sample integrity also includes the
need to collect aseptically to avoid external biological contamination. 9.3 Collect Samples of the Same Material from Different Locations Following directly from point (2) is the recognition that the heterogeneity in the biomass and
diversity of life is related to large-scale biogeographical influences. It is therefore important
to collect samples of the same material, but from different locations separated by ∼kilometre
distances. This allows for stronger statistical statements about the distribution of life over
large scales. If true replication is to be achieved, avoiding the pitfall of pseudo-replication
by sampling the same region, then the sample suite discussed in point (2) must be repeated
in three completely geographically separated regions of the same material, yielding 27 sam-
ples in total of a given sample type. If a habitable environment was transient, this strategy
maximises the chances of obtaining life-bearing rocks or being able to conclude with greater
confidence that all such materials in all geographical locations are devoid of life. 9.2 Collect Sufficiently Many Samples Heterogeneity in samples, particularly in those where habitability is short-lived, results in
high standard deviations in biomass and diversity. Statistically, to derive meaningful state-
ments on the distribution of life, multiple samples should be collected. Three samples is
a typical statistical minimum. However, microbial ecological analysis yields suggestions
on preferred numbers. For example, based on sample strategies used to investigate het-
erogeneities in low biomass volcanic rocks (Kelly et al. 2014) sample collection numbers
such as nine provide for a more comprehensive analysis, made up of three independent Sample Collection and Return from Mars.. Page 19 of 25 44 sets of three triplicates from the same material at regional scale. Additional samples add
to the robustness of the study, but might be limited by field time and cost. If environ-
ments are devoid of life, large sample sizes can increase the robustness of the conclu-
sion that they were never inhabited. These sample number recommendations do not take
into account separate samples used in other studies such as geology, atmospheric history
and investigations for future resource use that might be collected in the limited sample
sets envisaged for robotic Mars sample return (e.g., Sherwood et al. 2003; MEPAG 2008;
iMOST 2018). 10 Conclusions Mars is a planet of volcanically derived materials. The search for life on Mars and the study
of the distribution of habitable conditions is therefore greatly advanced by investigating
the microbial ecology of similar environments on Earth where biomass and diversity can
be directly quantified and related to environmental variables with a statistically high level
of confidence. Keeping in mind environmental differences between present-day Earth and
Mars, one purpose of this paper has been to provide a review of well-studied volcanic ma-
terials and their enclosed biota. We have used volcanic environments on Earth to extract
general patterns of microbial growth that are applicable across many types of volcanic ma-
terial. Using these patterns, we suggest principles of sample collection that, combined with
appropriate taphonomic considerations, will yield maximum information for astrobiologists
and planetary scientists. These principles apply to robotic exploration and to the human
exploration of the planet. Ultimately, to be able to test hypotheses with high statistical con-
fidence, sample sets with sufficient coverage and diversity, exploration across large scales,
and multiple replicates are required. Acknowledgements
This paper was made possible by support from the Science and Technology Facilities
Council (STFC). Grant: ST/R000875/1. Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps
and institutional affiliations. Open Access
This article is distributed under the terms of the Creative Commons Attribution 4.0 Inter-
national License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution,
and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source,
provide a link to the Creative Commons license, and indicate if changes were made. 9.6 Minimise Post-Collection Modifications Once collected, samples should receive minimal alteration. This includes irradiation and ex-
posure to other physical and chemical agents. Where samples are disrupted for examination, 44
Page 20 of 25 C.S. Cockell et al. information on the orientation of the sample fragments and their locations should be main-
tained so that the geological factors that control microbial distribution within the material
can be reconstructed. information on the orientation of the sample fragments and their locations should be main-
tained so that the geological factors that control microbial distribution within the material
can be reconstructed. References Byloos, P. Monsiers, M. Mysara, N. Leys, N. Boon, R. Van Houdt, Characterisation of the bacterial com-
munities on recent Icelandic volcanic deposits of different ages. BMC Microbiol. 18, 122 (2018) N.A. Cabrol, E.A. Grin, The evolution of lacustrine environments on Mars: (is Mars only hydrologica
dormant?). Icarus 149, 291–328 (2001) N.A. Cabrol, D. Wettergreen, K. Warren-Rhodes, E.A. Grin, J. Moersch, G. Chong Diaz, C.S. Cockell, P. Cop-
pin, C. Demergasso, J.M. Dohm, L. Ernst, G. Fisher, J. Glasgow, C. Hardgrove, A.N. Hock, D. Jonak,
L. Marinangeli, E. Minkley, G. Gabriele Ori, J. Piatek, E. Pudenz, T. Smith, K. Stubbs, G. Thomas, D. Thompson, A. Waggoner, M. Wagner, S. Weinstein, M. Wyatt, Life in the Atacama: Searching for life
with rovers (science overview). J. Geophys. Res. 112, G04 (2007) L. Marinangeli, E. Minkley, G. Gabriele Ori, J. Piatek, E. Pudenz, T. Smith, K. Stubbs, G. Thomas, D. Thompson, A. Waggoner, M. Wagner, S. Weinstein, M. Wyatt, Life in the Atacama: Searching for life
with rovers (science overview). J. Geophys. Res. 112, G04 (2007) E.J. Carpenter, S. Lin, D.G. Capone, Bacterial activity in South pole snow. Appl. Environ. Microbiol. 66,
4514–4517 (2000) J.L. Carson, R.M. Brown, Studies of Hawaiian freshwater and soil algae. 2. Algal colonization and succession
on a dated volcanic substrate. J. Phycol. 14, 171–178 (1978) J.L. Carson, R.M. Brown, Studies of Hawaiian freshwater and soil algae. 2. Algal
on a dated volcanic substrate. J. Phycol. 14, 171–178 (1978) C.S. Cockell, Vacant habitats in the Universe. Trends Ecol. Evol. 26, 73–80 (2011) C.S. Cockell, Types of habitat in the Universe. Int. J. Astrobiol. 13, 158–164 (2014) C.S. Cockell, S. McMahon, Lifeless Martian samples and their significance. Nat. Astron. 3, 468–470 (201 p
g
C.S. Cockell, D. Catling, W.L. Davis, R.N. Kepner, P.C. Lee, K. Snook, C.P. McKay, The ultraviolet envi-
ronment of Mars: Biological implications past, present and future. Icarus 146, 343–359 (2000) g
p
p
p
(
)
C.S. Cockell, K. Olsson-Francis, F. Knowles, L.C. Kelly, A. Herrera, T. Thorsteinsson, V. Marteinsson, Bac-
teria in weathered basaltic glass, Iceland. Geomicrobiol. J. 26, 491–507 (2009) C.S. Cockell, L.C. Kelly, S. Summers, V. Marteinsson, Following the kinetics: Iron-oxidising microbial mats
in cold Icelandic volcanic habitats and their rock-associated carbonaceous signature. Astrobiology 11,
679–694 (2011) C.S. Cockell, L.C. Kelly, V. Marteinsson, Actinobacteria: An ancient phylum active in volcanic rock weath-
ering. Geomicrobiol. J. 30, 706–720 (2013) C.S. Cockell, J.P. Harrison, A. References P. Adamo, P. Violante, Weathering of volcanic rocks from Mt. Vesuvius associated with the lichen Stereo-
caulum vesuvianum. Pedobiologia 35, 209–217 (1991) P. Adamo, A. Marchetiello, P. Violante, The weathering of mafic rocks by lichens. Lichenologist 25, 285–297
(1993) E.S. Amador, M.L. Cable, N. Chaudry, T. Cullen, D. Gentry, M.B. Jacobsen, G. Murukesan, E.W. Schwieter-
man, A.H. Stevens, A. Stockton, C. Yin, D.C. Cullen, W. Geppert, Synchronous in-field application of
life-detection techniques in planetary analog missions. Planet. Space Sci. 106, 1–10 (2015) A.M. Anesio, S. Lutz, N.A.M. Chismas, L.G. Benning, The microbiome of glaciers and ice sheets. NPJ
Biofilms Microbiomes 3, 10 (2017) O. Arnalds, Volcanic soils of Iceland. Catena 56, 3–20 (2004) O. Arnalds, P. Dagsson-Waldhauserova, H. Olafsson, The Icelandic volcanic aeolian environment: Processes
and impacts—A review. Aeolian Res. 20, 176–195 (2016) W. Bach, K.J. Edwards, Iron and sulphide oxidation within the basaltic ocean crust: Implications for
chemolithoautotrophic microbial biomass production. Geochim. Cosmochim. Acta 67, 3871–3887
(2003) R.A. Bell, Cryptoendolithic algae of hot semi-arid lands and deserts. J. Phycol. 29, 133–139 (1993) V.P. Belobrov, S.V. Ovechkin, Soils and soil cover patterns of volcanic plateaus in Indochina, Eurasian. Soil
Sci. 38, 1065–1074 (2005) Sample Collection and Return from Mars.. Page 21 of 25 44 C.A. Benson, R.W. Bizzoco, D.A. Lipson, S.T. Kelley, Microbial diversity in nonsulfur, sulfur and iron
geothermal steam vents. FEMS Microbiol. Ecol. 76, 74–88 (2011) J.-P. Bibring, Y. Langevin, J.F. Mustard, F. Poulet, R. Arvidson, A. Gendrin, B. Gondet, N. Mangold, P. Pinet, F. Forget (the OMEGA team), Global mineralogical and aqueous Mars history derived from
OMEGA/Mars Express data. Science 312, 400–404 (2006) A.L. Brady, G.F. Slater, E. Gibbons, S. Kobs Nawotniak, S.S. Hughes, S. Payler, A. Stevens, C.S. Cock-
ell, C. Haberle, A. Sehlke, R.C. Elphic, D.S.S. Lim, in Detection of Microbial Organic Biomarkers in
Terrestrial Basalts in a Mars Analogue Environment, AbSciCon, Mesa, AZ (2017) T.F. Bristow, E.B. Rampe, C.N. Achilles, D.F. Blake, S.J. Chipera, P. Craig, J.A. Crisp, D.J. Des Marais, R.T. Downs, R. Gellert, J.P. Grotzinger, S. Gupta, R.M. Hazen, B. Horgan, J.V. Hogancamp, N. Mangold,
P.R. Mhaffy, A.C. McAdam, D.W. Ming, J.M. Morookian, R.V. Morris, S.M. Morrison, A.H. Treiman,
D.T. Vaniman, A.R. Vasavada, A.S. Yen, Clay mineral diversity and abundance in sedimentary rocks of
Gale Crater, Mars. Sci. Adv. 4, eaar3330 (2018) T.D. Brock, Primary colonization of Surtsey, with special reference to the blue-green algae. Oikos 24, 239–
243 (1973) B. References Grindrod, M. West, N.H. Warner, S. Gupta, Formation of an Hesperian-aged sedimentary basin contain-
ing phyllosilicates and sulfates in Coprates Catena, Mars. Icarus 218, 178–195 (2012) W. Gross, J. Küver, G. Tischendorf, N. Bouchaala, W. Büsch, Cryptoendolithic growth of the red alga
Galdieria sulphuraria in volcanic areas. Eur. J. Phycol. 33, 25–31 (1998) J.P. Grotzinger, D.Y. Sumner, L.C. Kah, K. Stack, S. Gupta, L. Edgar, D. Rubin, K. Lewis, J. Schieber, N. Mangold, R. Milliken, P.G. Conrad, D. DesMarais, J. Farmer, K. Siebach, F. Calef, J. Hurowitz, S.M. McLennan, D. Ming, D. Vaniman, J. Crisp, A. Vasavada, K.S. Edgett, M. Malin, D. Blake, R. Geliert,
P. Mahaffy, R.C. Wiens, S. Maurice, J.A. Grant, S. Wilson, R.C. Anderson, L. Beegle, R. Arvidson, B. Hallet, R.S. Sletten, M. Rice, J. Bell, J. Griffes, B. Ehlmann, R.B. Anderson, T.F. Bristow, W.E. Dietrich,
G D
t J Ei
b
d
A F
C H d
K H k
h ff L J
d
G K
k S L J.P. Grotzinger, D.Y. Sumner, L.C. Kah, K. Stack, S. Gupta, L. Edgar, D. Rubin, K. Lewis, J. Schieber, N. Mangold, R. Milliken, P.G. Conrad, D. DesMarais, J. Farmer, K. Siebach, F. Calef, J. Hurowitz, S.M. McLennan, D. Ming, D. Vaniman, J. Crisp, A. Vasavada, K.S. Edgett, M. Malin, D. Blake, R. Geliert,
P. Mahaffy, R.C. Wiens, S. Maurice, J.A. Grant, S. Wilson, R.C. Anderson, L. Beegle, R. Arvidson, B. Hallet, R.S. Sletten, M. Rice, J. Bell, J. Griffes, B. Ehlmann, R.B. Anderson, T.F. Bristow, W.E. Dietrich,
G. Dromart, J. Eigenbrode, A. Fraeman, C. Hardgrove, K. Herkenhoff, L. Jandura, G. Kocurek, S. Lee,
L.A. Leshin, R. Leveille, D. Limonadi, J. Maki, S. McCloskey, M. Meyer, M. Minitti, H. Newsom, D. Oehler, A. Okon, M. Palucis, T. Parker, S. Rowland, M. Schmidt, S. Squyres, A. Steele, E. Stolper,
R. Summons, A. Treiman, R. Williams, A. Yingst (MSL Science Team), A habitable fluvio-lacustrine
environment at Yellowknife Bay, Gale Crater, Mars. Science 343, 1242777 (2013) G. Dromart, J. Eigenbrode, A. Fraeman, C. Hardgrove, K. Herkenhoff, L. Jandura, G. Kocurek, S. Lee,
L.A. Leshin, R. Leveille, D. Limonadi, J. Maki, S. McCloskey, M. Meyer, M. Minitti, H. Newsom, D. Oehler, A. Okon, M. Palucis, T. Parker, S. Rowland, M. Schmidt, S. Squyres, A. Steele, E. Stolper,
R. Summons, A. Treiman, R. Williams, A. Yingst (MSL Science Team), A habitable fluvio-lacustrine
environment at Yellowknife Bay, Gale Crater, Mars. References Stevens, S.J. Payler, S.S. Hughes, S.E. Kobs Nawotniak, A.L. Brady, R.C. Elphic, C.W. Haberle, A. Sehlke, K. Beaton, A. Abercromby, P. Scwendner, J. Wadsworth, H. Lan-
denmark, R. Cane, A.W. Dickinson, N. Nicholson, L. Perera, D.S.S. Lim, A low diversity microbiota
inhabits extreme terrestrial basaltic terrains and their fumaroles: Implications for the exploration of
Mars. Astrobiology 19, 284–299 (2019) E.K. Costello, S.R.P. Halloy, S.C. Reed, P. Sowell, S.K. Schmidt, Fumarole-supported islands of biodiversity
within a hyperarid, high-elevation landscape on Socompa Volcano, Puna de Atacama, Andes. Appl. Environ. Microbiol. 75, 735–747 (2009) C.R. Cousins, I.A. Crawford, Volcano-ice interaction as a microbial habitat on Earth and Mars. Astrobiology
11, 695–710 (2011) C.R. Cousins, M. Fogel, R. Bowden, I. Crawford, A. Boyce, C.S. Cockell, M. Gunn, Biogeochemical probing
of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland. Geobiology 16,
507–521 (2018) K.V. Dahigaonkar, P.N. Chavan, Diversity of microorganisms associated with pristine and extreme environ-
ment of mud volcanoes. Int. J. Sci. Res. Publ. 8, 157–164 (2018) L.R. Dartnell, L. Desorgher, J. Ward, A. Coates, Modelling the surface and subsurface Martian radiation
environment: Implications for astrobiology. Geophys. Res. Lett. 34, L02207 (2007) C.J. Daughney, J.-P. Rioux, D. Fortin, T. Pichler, Laboratory investigation of the role of bacteria in the weath-
ering of basalt near deep sea hydrothermal vents. Geomicrobiol. J. 21, 21–31 (2004) J.R. de la Torre, B.M. Goebel, E.I. Friedmann, N.R. Pace, Microbial diversity of cryptoendolithic communi-
ties from the McMurdo Dry Valleys, Antarctica. Appl. Environ. Microbiol. 69, 3858–3867 (2003) 44
Page 22 of 25 C.S. Cockell et al. W.W. Dickinson, M.R. Rosen, Antarctic permafrost: An analogue for water and diagenetic minerals on Mars. Geology 31, 199–202 (2003) K.E. Dunfield, G.M. King, Analysis of the distribution and diversity in recent Hawaiian volcanic deposits of a
putative carbon monoxide dehydrogenase large subunit gene. Environ. Microbiol. 7, 1405–1412 (2005) K.J. Edwards, D.R. Rogers, C.O. Wirsen, T.M. McCollom, Isolation and characterisation of novel psy-
chrophilic, neutrophilic, Fe-oxidising, chemolithoautotrophic α- and γ -Proteobacteria from the deep
sea. Appl. Environ. Microbiol. 69, 2906–2913 (2003) B. Ehlmann, J.F. Mustard, G.A. Swayze, R.N. Clark, J.L. Bishop, F. Poulet, D.J. Des Marais, L.H. Roach,
R.E. Milliken, J.J. Wray, O. Barnouin-Jha, S.L. Murchie, Identification of hydrated silicate minerals on
Mars using MRO-CRISM: Geologic context near Nili Fossae and implications for aqueous alteration. J. Geophys. Res. 144, E00D08 (2009) p y
(
)
B. Ehlmann, J.F. Mustard, S.L. Murchie, J.-P. References Bibring, A. Meunier, A.A. Fraeman, Y. Langevin, Subsurface
water and clay mineral formation during the early history of Mars. Nature 479, 53–60 (2011) B. Englund, Nitrogen fixation by free-living microorganisms on the lava field of Heimaey, Iceland. Oikos 27,
428–432 (1976) K.A. Farley, C. Malespin, P. Mahaffy, J.P. Grotzinger, P.M. Vasconcelos, R.E. Milliken et al., In situ radio-
metric and exposure age dating of the Martian surface. Science 343, 1247166 (2014) P. Fermani, G. Mataloni, B. Van de Vijver, Soil microalgal communities on an Antarctic active volca
(Deception Iceland, South Shetlands). Polar Biol. 30, 1381–1393 (2007) P. Fermani, G. Mataloni, B. Van de Vijver, Soil microalgal communities on an Antarctic active volcano
(Deception Iceland, South Shetlands). Polar Biol. 30, 1381–1393 (2007)
C B Field M J Behrenfeld J T Randerson P Falkowski Primary production in the biosphere: Integrating (Deception Iceland, South Shetlands). Polar Biol. 30, 1381 1393 (2007)
C.B. Field, M.J. Behrenfeld, J.T. Randerson, P. Falkowski, Primary production in the biosphere: Integrating
terrestrial and oceanic components. Science 281, 237–240 (1998) C.B. Field, M.J. Behrenfeld, J.T. Randerson, P. Falkowski, Primary production in the biosphere: Integrat
terrestrial and oceanic components. Science 281, 237–240 (1998) N. Fierer, R.B. Jackson, The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. 103, 626–631 (2006) F. Garcia-Pichel, S.L. Johnson, D. Youngkin, J. Belnap, Small-scale vertical distribution of bacterial biomass
and diversity in biological soil crusts from arid lands in the Colorado Plateau. Microb. Ecol. 46, 312–321
(2003) D. Gat, Y. Mazar, E. Cytryn, Y. Rudich, Origin-dependent variations in the atmospheric microbiome commu-
nity in Eastern Mediterranean dust storms. Environ. Sci. Technol. 51, 6709–6718 (2017) P.M. Gaylarde, A. Jungblut, C.C. Gaylarde, B.A. Neilan, Endolithic phototrophs from an active geothermal
region in New Zealand. Geomicrobiol. J. 23, 579–587 (2006) A. Gendrin, N. Mangold, J.-P. Bibring, Y. Langevin, B. Gondet, F. Poulet, G. Bonello, C. Quantin, J. Mustard,
R. Arvidson, S. LeMouélic, Sulfates in Martian layered terrains: The OMEGA/Mars Express view. Science 307, 1587–1591 (2005) D.M. Gentry, E.S. Amador, M.L. Cable, N. Chaudry, T. Cullen, M.B. Jacobsen, G. Murukesan, E.W. Schwi-
eterman, A.H. Stevens, A. Stockton, G. Tan, C. Yin, D.C. Cullen, W. Geppert, Correlations between
life-detection techniques and implications for sampling site selection in planetary analog missions. As-
trobiology 17, 1009–1021 (2017) V. Gomez-Alvarez, G.M. King, K. Nüsslein, Comparative bacterial in recent Hawaiian volcanic deposits of
different ages. FEMS Microbiol. Ecol. 60, 60–73 (2006) P.M. References Public Environ. Health
3, 244–256 (2016) G.S. Hubbard, F.M. Naderi, J.B. Garvin, Following the water, the new program for Mars exploration. Acta
Astronaut. 51, 337–350 (2002) J.A. Hurowitz, J.P. Grotzinger, W.W. Fischer, S.M. McLennan, R.E. Milliken, N. Stein, A.R. Vasavada, D.F. Blake, E. Dehouck, J.L. Eigenbrode, A.G. Fairén, J. Frydenvang, R. Gellert, J.A. Grant, S. Gupta, K.E. Herkenhoff, D.W. Ming, E.B. Rampe, M.E. Schmidt, K.L. Siebach, K. Stack-Morgan, D.Y. Sumner,
R.C. Wiens, Redox stratification of an ancient lake in Gale Crater, Mars. Science 356, 6341 (2017) B.M. Hynek, K.L. Rogers, M. Antunovich, G. Avard, G.E. Alvarado, Lack of microbial diversity in an ex
treme Mars analog setting: Poás Volcano, Costa Rica. Astrobiology 18, 923–933 (2018) A.M. Ibekwe, A.C. Kennedy, J.J. Halvorson, C.H. Yang, Characterization of developing microbial comm
nities in Mount St. Helens pyroclastic substrate. Soil Biol. Biochem. 39, 2496–2507 (2007) iMOST, The potential science and engineering value of samples delivered to Earth by Mars sample return,
(co-chairs D.W. Beaty, M.M. Grady, H.Y. McSween, E. Sefton-Nash; documentarian B.L. Carrier; plus
66 co-authors), 186 p. white paper (2018) . Kelly, C.S. Cockell, Y.M. Piceno, G. Andersen, T. Thorsteinsson, V. Marteinsson, Bacterial diversity of
weathered terrestrial Icelandic volcanic glasses. Microb. Ecol. 60, 740–752 (2010) L.C. Kelly, C.S. Cockell, A. Herrera-Belaroussi, Y. Piceno, G. Andersen, T. DeSantis, E. Brodie, T. Thorsteinsson, V. Marteinsson, F. Poly, X. LeRoux, Bacterial diversity of terrestrial crystalline volcanic
rocks, Iceland. Microb. Ecol. 62, 69–79 (2011) L.C. Kelly, C.S. Cockell, T. Thorsteinsson, V. Marteinsson, J. Stevenson, Pioneer microbial communities of
the Fimmvörðuháls Lava Flow, Eyjafjallajökull, Iceland. Microb. Ecol. 68, 504–518 (2014) J.M. Kimble, C.L. Ping, M.E. Sumner, L.P. Wilding, Andosols, in Handbook of Soil Science, ed. by M
Sumner (CRC Press, Boca Raton, 2000), pp. E209–E224 G.M. King, Contributions of atmospheric CO and hydrogen uptake to microbial dynamics on recent Hawaiian
volcanic deposits. Appl. Environ. Microbiol. 69, 4067–4075 (2003) H. Kristinsson, Report on the lichenological work on Surtsey and in Iceland. Surtsey Research Progress
Report V, 52 (1970) H. Kristinsson, Lichen colonization in Surtsey 1971–1973. Surtsey Research Progress Report VII, 9–16
(1974) J. Lasue, N. Mangold, E. Hauber, S.M. Clifford, W. Feldman, O. Gasnault, C. Grima, S. Maurice, O. Mousis,
Quantitative assessments of the Martian hydrosphere. Space Sci. Rev. 174, 155–212 (2013) y
p
p
J. Lasue, A. Cousin, P.-Y. Meslin, N. Mangold, R.C. Wiens, G. Berger, R.C. Wiens, E. Dehouck, O. Forni,
W. Goetz, O. Gasnault, W. References Science 343, 1242777 (2013) J.E. Hallsworth, M.M. Yakimov, P.N. Golyshin, J.L. Gillion, G. D’Auria, F. de Lima Alves, V. La Cono,
M. Genovese, B.A. McKew, S.L. Hayes, G. Harris, L. Giuliano, Limits of life in MgCl2-containing
environments: Chaotropicity defines the window. Environ. Microbiol. 9, 801–813 (2007) J.J. Halvorson, E.H. Franz, J.L. Smith, R.A. Black, Nitrogenase activity, nitrogen fixation, and nitrogen inputs
by lupines at Mount St. Helens. Ecology 73, 87–98 (1992) H.R. Harvey, R.D. Fallon, J.S. Patton, The effect of organic matter and oxygen on the degradation of bacterial
membrane lipids in marine sediments. Geochim. Cosmochim. Acta 50, 795–804 (1986) Sample Collection and Return from Mars.. Page 23 of 25
44 L.E. Hays, H.V. Graham, D.J. Des Marais, E.M. Hausrath, B. Horgan, T.M. McCollom, M.N. Parenteau, S.L. Potter-McIntrye, A.J. Williams, K.L.K. Lynch, Biosignature preservation and detection in Mars analog
environments. Astrobiology 17, 363–400 (2017) J.W. Head, H. Hiesinger, M.A. Ivanov, M.A. Kreslavsky, S. Pratt, B.J. Thomson, Possible ancient oceans on
Mars: Evidence from Mars Orbiter Laser Altimeter Data. Science 286, 2134–2137 (1999) J.W. Head, J.F. Mustard, M.A. Kreslavsky, R.E. Milliken, D.R. Marchant, Recent ice ages on Mars. Nat
426, 797–802 (2003) M.H. Hecht, S.P. Kounaves, R.C. Quinn, S.J. West, S.M. Young, D.W. Ming, D.C. Catling, B.C. Clark, W.V. Boynton, J. Hoffman, L.P. Deflores, K. Gospodinova, J. Kapit, P.H. Smith, Detection of perchlorate and
the soluble chemistry of martian soil at the Phoenix lander site. Science 324, 64–67 (2009) L.E. Henriksson, E. Henriksson, Concerning the biological nitrogen fixation on Surtsey. Surtsey Res. Prog. Rep. IX, 9–12 (1982) A. Herrera, C.S. Cockell, S. Self, M. Blaxter, J. Reitner, G. Arp, W. Dröse, A. Tindle, Bacterial colonizat
and weathering of terrestrial obsidian rock in Iceland. Geomicrobiol. J. 25, 25–37 (2008) g
(
)
A. Herrera, C.S. Cockell, S. Self, M. Blaxter, J. Reitner, T. Thorsteinsson, G. Arp, W. Dröse, A. Tindle,
A cryptoendolithic community in volcanic glass. Astrobiology 9, 369–381 (2009) D.W. Hopkins, L. Badalucco, L.C. English, S.M. Meli, J.A. Chudek, A. Ioppolo, Plant litter decomposition
and microbial characteristics in volcanic soils (Mt Etna, Sicily) at different stages of development. Biol. Fertil. Soils 43, 461–469 (2007) B. Horgan, J.F. Bell, Widespread weathered glass on the surface of Mars. Geology 40, 391–394 (2012) Z. Huang, S. Xu, Y. Han, Y. Gao, Y. Wang, C. Song, Comparative study of Dushanzi and Baiyanggou mud
volcano microbial communities in Junggar Basin in Xinjiang, China. Int. Res. J. References Rapin, S. Schroeder, A. Ollila, J. Johnson, S. Le Mouélic, S. Maurice, R. Anderson, D. Blaney, B. Clark, S.M. Clegg, C. d’Uston, C. Fabre, N. Lanza, M.B. Madsen, J. Martin-
Torres, N. Melikechi, H. Newsom, V. Sautter, M.P. Zorzano, Martian eolian dust probed by ChemCam. Geophys. Res. Lett. 45, 10968–10977 (2018). https://doi.org/10.1029/2018GL079210 M.J. Le Bas, R.W. Le Maitre, A.R. Woolley, The construction of the total alkali-silica chemical classification
of volcanic rocks. Mineral. Petrol. 46, 1–22 (1992) 44
Page 24 of 25 C.S. Cockell et al. J.E. Lee, H.L. Buckley, R.S. Rampal, G. Lear, Both species sorting and neutral processes drive assembly of
bacterial communities in aquatic microcosms. FEMS Microbiol. Ecol. 86, 288–302 (2013) D.S.S. Lim, A.J.F. Abercromby, S. Kobs Nawotniak, D.S. Lees, M.J. Miller, BASALT Team, The BASALT
Research Program: Designing and developing mission elements in support of human scientific explo-
ration of Mars. Astrobiology 16, 245–259 (2019) gy
(
)
Liu, Y.-G. Zhou, Y.-H. Xin, High diversity and distinctive community structure of bacteria on glaciers in
China revealed by 454 pyrosequencing. Syst. Appl. Microbiol. 38, 578–585 (2015) J. Logemann, J. Graue, K. Köster, B. Engelen, J. Rullkötter, H. Cypionka, A laboratory experiment of intact
polar lipid degradation in sandy sediments. Biogeosciences 8, 2547–2560 (2011) H.P. Lukito, K. Kouno, T. Ando, Phosphorus requirements of microbial biomass in a regosol and an andosol. Soil Biol. Biochem. 30, 865–872 (1998) K. Lysnes, I.H. Thorseth, B.O. Steinbu, L. Øvreås, T. Torsvik, R.B. Pedersen, Microbial community diversity
in seafloor basalt from the Arctic spreading ridges. FEMS Microb. Ecol. 50, 213–230 (2004) L. Maturrano, F. Santos, R. Rosselló-Mora, J. Antón, Microbial diversity in Maras Salterns, a hypersaline
environment in the Peruvian Andres. Appl. Environ. Microbiol. 72, 3887–3895 (2006) S. McMahon, T. Boask, J.P. Grotzinger, R.E. Milliken, R.E. Summons, M. Daye, S.A. Newman, A. Fraeman,
K.H. Williford, D.E.G. Briggs, A field guide to finding fossils on Mars. J. Geophys. Res. 123, 1012–
1040 (2018) (
)
H.Y. McSween, G.J. Taylor, M.B. Wyatt, Elemental composition of the Martian crust. Science 324, 736–739
(2009) MEPAG, Science priorities for Mars sample return. Astrobiology 8, 491–521 (2008) R.E. Milliken, D.L. Bish, Sources and sinks of clay minerals on Mars. Philos. Mag. 90, 2293–2308 (2010 K. Nanba, G.M. King, K. Dunfield, Analysis of facultative lithotroph distribution and diversity of volcanic
deposits by use of the large subunit of Ribulose 1,5-bisphosphate carboxylase/oxygenase. Appl. Environ. Microbiol. 70, 2245–2253 (2004) R. Navarro-González, F.A. References Rainey, P. Molina, D.R. Bagaley, B.J. Hollen, J. de la Rosa, A.M. Small, R.C. Quinn, F.J. Grunthaner, L. Cáceres, B. Gomez-Silva, C.P. McKay, Mars-like soils in the Atacama Desert,
Chile, and the dry limit of microbial life. Science 302, 1018–1021 (2003) K. Nüsslein, J.M. Tiedje, Characterization of the dominant and rare members of a young Hawaiian soil
bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis
of its guanine and cytosine composition. Appl. Environ. Microbiol. 64, 1283–1289 (1998) ,
j ,
y
g
bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis
of its guanine and cytosine composition. Appl. Environ. Microbiol. 64, 1283–1289 (1998) S.L. O’Brien, S.M. Gibbons, S.M. Owens, J. Hampton-Marcell, E.R. Johnston, J.D. Jastrow, J.A. Gilbert, F. Meyer, D.A. Antonopoulos, Spatial scale drives patterns in soil bacterial diversity. Environ. Microbiol. 18, 2039–2051 (2016) B. Orcutt, B. Bailey, H. Staudigel, B.M. Tebo, K.J. Edwards, An interlaboratory comparison of 16S-rRNA
gene-based terminal restriction fragment length polymorphism and sequencing methods for assessing
microbial diversity of seafloor basalts. Environ. Microbiol. 11, 1728–1738 (2009) A. Oren, Microbial life at high salt concentrations: Phylogenetic and metabolic diversity. Saline Syst. 4
(2008) H. Oskarsson, O. Arnalds, J. Gudmundsson, G. Gudbergsson, Organic carbon in Icelandic Andosols: Geo-
graphical variation and impact of erosion. Catena 56, 225–238 (2004) M.M. Osterloo, V.E. Hamilton, J.L. Bandfield, T.D. Glotch, A.M. Baldridge, P.R. Christensen, L.L. Torn-
abene, F.S. Anderson, Chloride-bearing materials in the southern highlands of Mars. Science 319, 1651–
1654 (2008) (
)
M.M. Osterloo, F.S. Anderson, V.E. Hamilton, B.M. Hynek, Geologic context of proposed chloride-bearing
materials on Mars. J. Geophys. Res. 115, E10012 (2010) R.L. Parfitt, J.M. Kimble, Conditions for formation of allophane in soils. Soil Sci. Soc. Am. J. 53, 971–977
(1989) F. Poulet, J.-P. Bibring, J.F. Mustard, A. Gendrin, N. Mangold, Y. Langevin, R.E. Arvidson, B. Gondet, C. Gomez, M. Berthé, S. Erard, O. Forni, N. Manaud, G. Poulleau, A. Soufflot, M. Combes, P. Drossart,
T. Encrenaz, T. Fouchet, R. Melchiorri, G. Belluci, F. Altieri, V. Formisano, S. Fonti, F. Capaccioni, P. Cerroni, A. Coradini, O. Korablev, V. Kottsoy, N. Ignatiey, D. Titov, L. Zasova, P. Pinet, V.B. Schmitt,
C. Sotin, E. Hauber, H. Hoffmann, R. Jaumann, U. Keller, F. Forget, Phyllosilicates on Mars and impli-
cations for early Martian climate. Nature 438, 623–627 (2005) L. Preston, L.R. Dartnell, Planetary habitability: Lessons learned from terrestrial analogues. Int. J. Astrobiol. References Banerjee, Y. Dilek, K. Muehlenbach, Microbes and volcanoes: A tale from the
oceans, ophiolites, and greenstone belts. GSA Today 16, 4–102 (2006) G. Stefansdottir, A.L. Aradottir, B.D. Sigurdsson, Accumulation of nitrogen and organic matter during pri-
mary succession of Leymus arenarius dunes on the volcanic island Surtsey, Iceland. Biogeosciences 11,
5763–5771 (2014) N.A. Stroncik, H.U. Schminke, Evolution of palagonite: Crystallization, chemical changes, and element bud
get. Geochem. Geophys. Geosyst. 2, 2001 (2001). https://doi.org/10.1029/2000GC000102 g
p y
y
(
)
p
g
N.A. Stroncik, H.U. Schminke, Palagonite—A review. Int. J. Earth Sci. 91, 680–697 (2002) B.M. Tebo, H.A. Johnson, J.K. McCarthy, A.S. Templeton, Geomicrobiology of manganese(II) oxidation. Trends Microbiol. 13, 421–428 (2005) A.S. Templeton, H. Staudigel, B.M. Tebo, Diverse Mn(II)-oxidising bacteria isolated from submarine basalts
at Loihi Seamount. Geomicrobiol. J. 22, 127–139 (2005) I.H. Thorseth, H. Furnes, O. Tumyr, A textural and chemical study of Icelandic palagonite of varied compo-
sition and its bearing on the mechanism of the glass-palagonite transformation. Geochim. Cosmochim. Acta 55, 731–749 (1991) ,
(
)
I.H. Thorseth, T. Torsvik, V. Torsvik, V. Torsvik, F.L. Daae, R.B. Pedersen, Diversity of life in ocean floor
basalt. Earth Planet. Sci. Lett. 194, 31–37 (2001) I.H. Thorseth, R.B. Pedersen, D.M. Christie, Microbial alteration of 0-30-Ma seafloor and sub-seafloor
basaltic glasses from the Australian Antarctic Discordance. Earth Planet. Sci. Lett. 215, 237–247 (2003) I.H. Thorseth, R.B. Pedersen, D.M. Christie, Microbial alteration of 0-30-Ma seafloor and sub-seafloor
basaltic glasses from the Australian Antarctic Discordance. Earth Planet. Sci. Lett. 215, 237–247 (2003)
T. Torsvik, H. Furnes, K. Muehlenbachs, I.H. Thorseth, O. Tumyr, Evidence for microbial activity at the T. Torsvik, H. Furnes, K. Muehlenbachs, I.H. Thorseth, O. Tumyr, Evidence for microbial activity at the
glass-alteration interface in oceanic basalts. Earth Planet. Sci. Lett. 162, 165–176 (1998) M. Vos, A.B. Wolf, S.J. Jennings, G.A. Kowalchuk, Micro-scale determinants of bacterial diversity in s
FEMS Microbiol. Rev. 37, 936–954 (2013) J. Wadsworth, C.S. Cockell, Perchlorates on Mars enhance the bacteriocidal effects of UV light. Sci. Rep. 7,
4662 (2017) (
)
J.J. Walker, J.R. Spear, N.R. Pace, Geobiology of a microbial endolithic community in the Yellowstone
geothermal environment. Nature 434, 1011–1014 (2005) K. Wall, J. Cornell, R.W. Bizzoco, S.T. Kelley, Biodiversity hot spot on a hot spot: Novel extremophile
diversity in Hawaiian fumaroles. Microbiol. Open 4, 267–281 (2015) C.M. Weitz, R.C. Anderson, J.F. Bell III., W.H. Farrand, K.E. Herkenhoff, J.R. Johnson, B.L. Jolliff, R.V. Morris, S.W. References 13, 81–98 (2014) A.E. Richardson, Prospects for using soil microorganisms to improve the acquisition of phosphorus by plants. Funct. Plant Biol. 28, 897–906 (2001)
C K R bi
J Wi
h
C Bl
k A C i
Ch i
h B M
J R
l C A
O A i d
S V l C.K. Robinson, J. Wierzchos, C. Black, A. Crits-Christoph, B. Ma, J. Ravel, C. Ascaso, O. Artieda, S. Valea,
M. Roldán, B. Gómez-Silva, J. DiRuggiero, Microbial diversity and the presence of algae in halite
endolithic communities are correlated to atmospheric moisture in the hyper-arid zone of the Atacama
Desert. Environ. Microbiol. 17, 299–315 (2015) Sample Collection and Return from Mars.. Page 25 of 25
44 44 J.C.M. Santelli, B.N. Orcutt, E. Banning, W. Bach, C.L. Moyer, M.L. Sogin, H. Staudigel, K.J. Edwards,
Abundance and diversity of microbial life in ocean crust. Nature 453, 643–657 (2008) G.H. Schwabe, On the algal settlement in craters on Surtsey during summer 1968. Surtsey Research Progress
Report V, 68–69 (1970) p
(
)
G.H. Schwabe, K. Behre, Algae on Surtsey in 1969–1970. Surtsey Research Progress Report VI, 85–89
(1972) C.E. Sharp, A.L. Brady, G.H. Sharp, S.E. Grasby, M.B. Stott, P.F. Dunfield, Humboldt’s spa: Microbial
diversity is controlled by temperature in geothermal environments. ISME J. 8, 1166–1174 (2014) B. Sherwood, D.B. Smith, R. Greeley, W. Whittaker, G.R. Woodcock, G. Barton, D.W. Pearson, W. Siegfried
Mars sample return: Architecture and mission design. Acta Astronaut. 53, 353–364 (2003) A.J. Solon, L. Vimercati, J.L. Darcy, P. Arán, D. Porazinska, C. Dorador, M.E. Farias, S.K. Schmidt, Micro-
bial communities of high-elevation fumaroles, penitentes, and dry tephra “soils” of the Puna de Atacama
volcanic zone. Microb. Ecol. 76, 340–351 (2018). https://doi.org/10.1007/s00248-017-1129-1 y
bial communities of high-elevation fumaroles, penitentes, and dry tephra “soils” of the Puna de Atacama
volcanic zone. Microb. Ecol. 76, 340–351 (2018). https://doi.org/10.1007/s00248-017-1129-1 (
)
p
g
R.M. Soo, S.A. Wood, J.J. Grzymski, I.R. McDonald, S.C. Cary, Microbial biodiversity of thermophilic
communities in hot mineral soils of Tramway Ridge, Mount Erebus, Antarctica. Environ. Microbiol. 11, 715–728 (2009) (
)
H. Staudigel, R.A. Chastain, A.Y.W. Boucier, Biologically mediated dissolution of glass. Chem. Geol. 126,
147–154 (1995) H. Staudigel, A. Yayanos, R. Chastain, G. Davies, E.A. Th Verdurmen, P. Schiffman, R. Boucier, H. de Baar,
Biologically mediated dissolution of volcanic glass in seawater. Earth Planet. Sci. Lett. 164, 233–244
(1998) (
)
H. Staudigel, H. Furnes, N.R. References Squyres, R.J. Sullivan, Soil grain analyses at Meridiani Planum, Mars. J. Geophys. Res. 111, E12S04 (2006) R.J. Whitaker, D.W. Grogan, J.W. Taylor, Geographical barriers isolate endemic populations of hyperther-
mophilic archaea. Science 301, 976–978 (2003) D. Wolff-Boenisch, S.R. Gíslason, E.H. Oelkers, C.V. Putnis, The dissolution rates of natural glasses as a
function of their composition at pH 4 and 10, and temperatures from 25 to 74◦C. Geochim. Cosmochim. Acta 68, 4843–4858 (2004) D. Wolff-Boenisch, S.R. Gíslason, E.H. Oelkers, The effect of crystallinity on dissolution rates and CO2
consumption capacity of silicates. Geochim. Cosmochim. Acta 70, 858–870 (2006) A. Yin, Structural analysis of the Valles Marineris fault zone: Possible evidence for large-scale strike-slip
faulting on Mars. Lithosphere 4, 286–330 (2012)
|
https://openalex.org/W2050681314
|
https://www.scielo.br/j/epec/a/bj5F3jdrvJLStthm4CCCjbq/?lang=pt&format=pdf
|
Portuguese
| null |
NARRATIVA, MITO, CIÊNCIA E TECNOLOGIA: O ENSINO DE CIÊNCIAS NA ESCOLA E NO MUSEU
|
Ensaio
| 2,000
|
cc-by
| 14,614
|
Volume 02 / Número 1 – Març. 2002 Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências NARRATIVA, MITO, CIÊNCIA E TECNOLOGIA: O ENSINO DE CIÊNCIAS NA ESCOLA E NO
MUSEU Maria Cristina Leal1
Guaracira Gouvêa2 Mostramos neste artigo as possibilidades e a necessidade de se trabalhar a alfabetização
científica, integrando ensino formal, não-formal e divulgação científica. Entendemos que a
perspectiva de alfabetização científica está diretamente vinculada ao ensino com base nas
relações Ciência, Tecnologia e Sociedade - CTS. Após uma breve resenha do significado de
alfabetização científica e CTS, ressaltamos a importância de se articular narrativa, mito, ciência
e tecnologia no ensino de ciências. Nos apoiamos em uma sondagem feita com 108
professores participantes de um curso, 18 participantes de um seminário e 12 observações de
turmas em visita a um museu de ciências para retratar, de um lado, as possibilidades que os
professores vislumbram de se trabalhar ciências via CTS e, de outro, as incoerências que
emergem quando certos conteúdos escolares são explorados na visita de alunos a um museu
de ciências. 1 Fac. Educação, UFF
2 Depto Educação, Mast Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 “(...) Conferimos as mais recentes tecnologias que as empresas estão
desenvolvendo... Vimos doenças erradicadas, viagens a outros planetas, deficientes
tendo uma vida melhor, plantas mais nutritivas e abundantes. Encontramos crianças
estudando a centenas de quilômetros dos professores, computadores que vêem e falam,
materiais ultra-eficientes, energias limpas e muito baratas” (França et al., 1999:37). Além do espaço reservado para essa discussão na mídia, observa-se a crescente
penetração desse debate nos livros didáticos e materiais paradidáticos. um fato a destacar é
que, nos parâmetros curriculares nacionais, elaborados pelo mec (parâmetros curriculares
nacionais, ciências naturais, 5ª a 8ª séries, brasília, mec, 1998), tanto os do ensino fundamental
como os do ensino médio, uma das diretrizes apontadas é a necessidade de se colocar, no
currículo, o debate entre ciência, tecnologia e sociedade. Tambem vale destacar “que a ciencia esta cada vez mais incorporada ao cotidiano das
pessoas, mas poucos continuam tendo acesso a sua forma de organização e ao seu corpo de
conhecimento”. assim, “as ciencias naturais, enquanto patrimonio da humanidade, parte da
cultura universal, tem justificado sua inclusão no curriculo escolar; por outro lado, não tem
garantido que os alunos passem a identificar este conhecimento como um instrumental possivel
de analise e interferencia no universo que os cerca” (pierson e hosoume, 1997: 87). A dimensão pública do impacto da C&T na sociedade nos levou a pensar na
necessidade de uma pesquisa que se debruçasse sobre a relação CTS na educação. A partir
daí, produzimos o projeto “Ciência, Tecnologia e Sociedade no contexto da alfabetização
científica”, o qual foi desenvolvido de 1997 a 1999 com o apoio da Finep, do CNPq e da Faperj. Seu objetivo foi identificar e analisar as narrativas que, em contextos de ensino-aprendizagem
formal e não-formal, discutissem a relação CTS, visando à formação do cidadão por meio da
escola e do museu. Na sua primeira etapa, a pesquisa esteve centrada, de um lado, no levantamento de
informações sobre as visões dos professores (de ciências e de outras disciplinas) a respeito da
possibilidade de se trabalhar a educação científica e tecnológica na escola através do
estabelecimento da relação CTS. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 De outro lado, foi realizado um trabalho de observação de
visitas de professores à exposição permanente do Museu de Astronomia e Ciências Afins
(Mast/MCT), além de seminários para professores, com a finalidade de se dimensionar a
relação entre educação formal e não-formal. O objeto da pesquisa - narrativas em CTS no
ensino formal e não-formal, visando à alfabetização científica - mostrou a importância de
discutirmos a relação entre narrativa, mito, ciência e tecnologia. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 INTRODUÇÃO O espaço dedicado, atualmente na mídia, à divulgação científica, por meio de filmes e
programas de TV, artigos de jornais e revistas, pode-nos dar a dimensão da importância que a
ciência e a tecnologia têm no processo de transformação do mundo de hoje. Alguns desses
veículos apresentam e discutem temas que permitem ao grande público conhecer certa
dimensão dos problemas e das transformações a serem enfrentados em face do uso
exacerbado da tecnologia. Entre eles, vale mencionar o bug do milênio, o qual faria com que o
computador confundiria os dois últimos algarismos do ano 2000 com os do ano 1900,
provocando problemas de diversos tipos e prejuízos calculados em US$600 bilhões. Exemplos
de problemas potencialmente gerados pelo bug do milênio são os satélites que sincronizam
algumas usinas elétricas e o processo de transferências internacionais de fundos. Se o
problema não fosse solucionado a tempo, as usinas deixariam de funcionar e a contagem de
tempo, para transferência de fundos, se não fosse computada em segundos (como deve ser),
seria em anos, o que acarretaria cobrança de juros que poderiam chegar à casa dos trilhões de
dólares (Zuckerman, 1999: 3). Um artigo de divulgação científica, publicado na revista Época, pode indicar como a
mídia elabora idéias sobre os tipos de transformações que a ciência e a tecnologia (C&T)
apontam para o próximo milênio: Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 5 NARRATIVA Uma das formas de se apreenderem processos interativos a respeito de resultados de
aprendizagens, que visem à ampliação do capital científico e tecnológico dos aprendizes. Consiste no levantamento de narrativas individuais e coletivas que expressem concepções de Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 6 6 Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências ciências e de seu ensino. Adotamos, para isso, o ponto de vista de Levine (1995), que defende,
como meio válido de investigação, o estudo da narrativa coletiva de determinados grupos
sociais: “(...) O exame de histórias disciplinares produzidas pelos praticantes dessas
disciplinas revela uma variedade de formas de narrativas. Em alguns casos, elas
enfatizam o valor do trabalho científico em seu campo, como quando louvam as
realizações de grandes cientistas ou glorificam a ciência como atividade humana
distintamente progressista. Em outros casos, valorizam certas direções no trabalho
científico, como quando reforçam uma determinada abordagem científica ou anunciam
uma transformação conceitual no campo. Outras ainda servem para demarcar as
fronteiras de um domínio intelectual, como quando celebram o surgimento de uma nova
disciplina ou descrevem conexões com sistemas filosóficos antecedentes” (Levine, 1995:
22). A reflexão de Levine sobre as narrativas nos inspirou em dois sentidos. O primeiro foi
buscar saber, mesmo que por meio de uma sondagem exploratória (uso de questionário), como
os professores (sujeitos partícipes de histórias disciplinares) se posicionavam diante de um
momento de transição entre uma perspectiva de ensino tradicional de ciências e a abordagem
de ensino via CTS. O segundo indicou a necessidade de se reconstituir um pouco da origem do
ensino de ciências na perspectiva de CTS. O valor da narrativa, nas pesquisas em ensino de ciências tende a crescer a partir de
argumentos como os de Bruner (1996), para quem a ela constitui instrumento importante de
compreensão do significado humano de aquisição de cultura. Para Bruner, a narrativa é um
modo de pensamento que funciona por imagens, o qual não segue uma lógica linear, mas que
é analógico e pode complementar o pensamento paradigmático (lógico-matemático ou
científico). O pensamento narrativo consiste na prática de se contarem histórias a cada um para
construir significados, dar sentido às nossas experiências. NARRATIVA Uma diferença marcante entre os
modos de pensamento narrativo e paradigmático é que, no primeiro, a capacidade abstrata
surge do interesse particular, daquilo que é inesperado, irregular, enquanto que, no segundo,
privilegia-se o abstrato isto é, os aspectos conceituais mais universais e gerais. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Volume 02 / Número 1 – Març. 2002 Como exemplo de mito na primeira acepção, trazemos à cena a narrativa tradicional
chinesa: Yi e os dez sóis. Esta relata a existência de dez sóis que, de modo revezado,
ordenado, forneciam calor e luz à Terra até que, um dia, resolvem trabalhar juntos e começam a
destruir a Terra (desordem). Somente com a intervenção do imperador da China e de um hábil
arqueiro, a ordem se restabelece pela eliminação de nove sóis e a manutenção de apenas um. A narrativa traz a marca da cultura e do poder para dar conta de fenômenos naturais que se
movimentam de forma ordenada/desordenada. Para ilustrar a segunda acepção, recorremos a um trecho da análise de Barthes (1993)
sobre o cérebro de Einstein: “... claramente o funcionamento do processo, Einstein fotografado ao lado de uma lousa
coberta de signos matemáticos de uma complexidade visível, quer dizer, como se
trabalha a imagem de Einstein sempre se referindo, tentando fazer e dar o significado da
sua genialidade; Einstein desenhando, isto é, tendo entrado portanto na lenda, uma vez
mais de giz na mão, acabando de escrever sobre uma lousa limpa, como se preparasse
a fórmula máxima do mundo. A mitologia respeita assim a natureza das tarefas, a
investigação propriamente dita mobiliza engrenagens mecânicas, tendo como sede um
órgão material monstruoso, apenas por sua complicação cibernética, a descoberta pelo
contrário da essência mágica simples como um corpo primordial.” ( Barthes, 1993: 61) Vemos, assim, a construção da representação do mito da genialidade por meio da
capacidade máxima do homem de criar fórmulas capazes de decifrar os grandes segredos da
natureza. O mito encontra-se presente no discurso científico, alimentando seus encantos e
desencantos, as suas contradições. A vontade de se superar o mito, na sua positividade, faz-se
presente na ciência quando esta recorre às perspectivas criacionistas (Big-Bang, Teoria do
Caos etc.) para explicar racionalmente as nossas origens, evolução, relações. O mito também
se apresenta na ciência quando esta passa a priorizar o poder e a alimentar a crença em sua
onipotência. Para Chrétien (1994), a hegemonia da ciência, nas sociedades modernas, coloca-a
na condição de assumir as funções cujos titulares ela expulsou, isto é, os mitos. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 Não tivemos aqui a intenção de esgotar, mas, sim, de introduzir uma discussão que
entendemos necessária para os estudiosos da ciência e para aqueles engajados na perspectiva
de educação em CTS. Consideramos necessário mencioná-la, pois ela orientou a primeira fase
de realização da pesquisa. No caso da pesquisa, os modos de pensamento narrativo e paradigmático ganham
sentido quando analisados no contexto da alfabetização científica e numa perspectiva de
ensino em CTS. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 O MITO O mito é tomado aqui em duas acepções básicas. Na primeira, identificamos o mito
como afirmação e nos reportamos às narrativas tradicionais que, por tempo bastante longo,
foram transmitidas de geração a geração para dar explicações acerca da origem do homem, do
mundo, da vida. Essas narrativas diversificadas e transpassadas pelas vozes das culturas, das
religiões, do imaginário, das relações de poder, do gênero etc. apresentam em comum o fato de
manipularem a emoção, a crença, os dogmas. Na segunda acepção de mito, encontramos a
sua negação, despolitização e esvaziamento. Tal acepção é formulada por Barthes (1993),
quando estuda as maneiras como a sociedade burguesa cria seus mitos a partir de
características como despolitização, esvaziamento de contextos, simplificação, ingenuidade e
harmonia. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 7 CIÊNCIA, TECNOLOGIA E SOCIEDADE NO ENSINO DE CIÊNCIAS O conceito de alfabetização científica pressupõe, em linhas gerais, uma discussão que
envolve a comunidade científica, a educacional e os profissionais de comunicação sobre o que
o cidadão comum sabe e deveria saber a respeito da relação CTS. Como o que o cidadão Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 8 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 comum sabe, ou deveria saber, a respeito dessa relação abrange, necessariamente, elementos
ligados à sua formação e às informações disponíveis, essa discussão está situada no ensino de
ciências praticado nas escolas e nos museus, na mídia e na Internet. Essas instâncias,
dependendo de sua maior ou menor presença na sociedade, são as principais responsáveis
pela formação da opinião pública a respeito de C&T. Ao definir o que é alfabetização científica, Shen (1975, apud Cazelli, 1992) estabelece
três dimensões capazes de identificar o conceito a partir de variações em termos de objetivos,
conteúdos, formas e público. A primeira é a dimensão prática, que habilita os indivíduos a
resolverem problemas que exigem conhecimentos básicos; a segunda é a cívica, isto é, refere-
se à consciência sobre os problemas e usos da C&T; a terceira é a cultural, que consiste na
obtenção de conhecimentos de C&T aprimorados. Para Miller (1987), a alfabetização científica
compreende a capacidade de o público entender os processos de investigação científica, as
normas e os métodos da ciência, os temas científicos básicos e a consciência do impacto da
C&T sobre a sociedade. Finalmente, para Arons (1983, apud Cazelli, 1992), o indivíduo
científica e tecnologicamente alfabetizado é aquele capaz de (1) compreender a distinção entre
observação e inferência, isto é, de realizar exames minuciosos de dedução e raciocínio,
distinguir entre papel da descoberta acidental e estratégia deliberada de formulação de
hipóteses e de entender, através de exemplos específicos, que os conceitos e as teorias
científicas são mutáveis e provisórios e precisam, portanto, de permanente aperfeiçoamento; (2)
reconhecer que os conceitos científicos são elaborados pela inteligência e imaginação humanas
e que, para serem entendidos e aplicados, devem ser operacionalizados; (3) desenvolver
conhecimentos básicos que possibilitem uma leitura inteligente e uma aprendizagem
permanente, sem necessidade de recursos exclusivos do ensino formal; finalmente, (4) ser
capaz de entender que a relação CTS envolve aspectos morais, éticos e sociais. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 CIÊNCIA, TECNOLOGIA E SOCIEDADE NO ENSINO DE CIÊNCIAS Para Barros
(1990: 86), “a sociedade moderna exige de todos os seus cidadãos uma compreensão básica
da ciência e da tecnologia, devido ao papel que estas possuem para a vida pessoal dos
indivíduos. Trata-se, pois, de pensar na alfabetização científica de todos os integrantes da
sociedade...” Morin (1996) e Angotti (1991) consideram que a sociedade deva ser alfabetizada
científica e tecnologicamente para que tenha algum controle sobre o sistema ciência e
tecnologia. A raiz deste debate é, no entanto, mais ampla e se localiza na relação CTS, questão
complexa que vem sendo discutida por filósofos, sociólogos e educadores. Os primeiros têm-se
dedicado, principalmente, a qualificar os conceitos de C&T, a estabelecer relações de
dependência entre eles, a afirmar ou negar a possibilidade de a tecnologia ter autonomia em
relação à ciência, a identificar e diferenciar os problemas metodológicos das pesquisas
científicas e tecnológicas; a refletir sobre a capacidade da tecnologia de garantir o progresso ou
de levar a humanidade à autodestruição. Já os sociólogos, a despeito de tratarem de algumas
dessas questões, estão empenhados em discutir a fundo duas teses que, no campo da ciência
social, se confrontam e antecedem qualquer outro tipo de debate sobre CTS. Trata-se do
problema determinismo da sociedade sobre a tecnologia versus autonomia da tecnologia sobre
a ordem social. Finalmente, os educadores centram-se na problemática de discutir se o ensino
em CTS representa uma crítica ou um aperfeiçoamento às formas tradicionais de ensino de Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 9 9 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 ciências, se a abordagem científica por meio de CTS deve ser ou não institucionalizada na
escola, com que objetivos e como deve ser tratada nos currículos e programas escolares. Da Filosofia da Ciência e da Tecnologia, cabe destacar que a relação CTS tem seus
primórdios na sociedade moderna, na qual se situam os conhecimentos produzidos por Galileu
e Newton. Fundamentados na Física e na Matemática, a observação e os dados ganham, por
meio desses conhecimentos científicos, representações possíveis de serem mensuradas e
logicamente aplicadas. Abre-se, a partir daí, a possibilidade de a tecnologia se firmar e se
desenvolver, uma vez que ela consiste na “aplicação de vários conhecimentos científicos
reunidos com vistas à realização de uma finalidade prática”. CIÊNCIA, TECNOLOGIA E SOCIEDADE NO ENSINO DE CIÊNCIAS (Rodrigues, 1997: 12) Na Sociologia, a discussão sobre a capacidade de a ciência e a tecnologia moldarem a
sociedade ou de serem moldadas por ela não é recente e remonta aos primórdios da
Revolução Industrial. Entre os deterministas tecnológicos atuais, encontramos Mcluhan (1967) e
Robeens e Webster (1989). Segundo esses últimos, o uso do computador deverá transformar o
mundo social em todos os níveis. Os críticos do determinismo tecnológico afirmam que os aspectos sociais e os temas
políticos contam mais do que a tecnologia em si, pois importa saber principalmente “quem usa,
quem controla, para que usa, como se amolda na estrutura de poder, como é expandida e
distribuída a tecnologia”. (Finnegan, 1988: 176) Seja ou não a tecnologia o determinante da ordem social o fato concreto é que o debate
sobre a relação entre elas se intensificou e ganhou contornos muito nítidos nos meios
intelectuais e educacionais. No contexto do ensino, a complexidade dessa relação cresce em
um mundo globalizado. Graças ao acentuado e acelerado progresso tecnológico, há uma
exigência cada vez maior de cidadãos capazes de competências cognitivas específicas para
administrar o cotidiano. Na escola, essas competências precisam ser oferecidas às novas
gerações, o que exige reformulação na cultura escolar. Vale salientar que a idéia de cultura
escolar pressupõe a transmissão de saberes, competências, formas de expressão, mitos e
símbolos socialmente reconhecidos por meio de transposições didáticas, isto é, transmissão
mediada da ciência do sábio, da obra do artista, do pensamento do filósofo nas matérias e
disciplinas, nos exercícios e textos escolares etc. A transposição didática, por sua vez, impõe o
aparecimento de configurações cognitivas específicas - saberes e modos de pensar tipicamente
escolares (Forquin, 1993). Assim, coloca-se a questão de como inserir nas práticas educativas
escolares o debate CTS. A relação educação e tecnologia é tema polêmico em voga entre educadores. Há
correntes mais ajustadas aos interesses empresariais que entendem a escola como espaço de
formação geral mínima para produção de trabalhadores flexíveis e propensos a serem
rapidamente treinados e reciclados no próprio local de trabalho. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 No Brasil, a partir da década de 90, emergem elaborações sobre o conceito de
alfabetização científica e tecnológica, apreendida por nós como o que o público deve saber
sobre ciência, tecnologia e sociedade (CTS), com base em conhecimentos adquiridos em
contextos diversos (escola, museus, revistas etc.), atitude pública sobre ciência e tecnologia,
informações obtidas em meios de divulgação científica e tecnológica. As articulações entre
ciência e tecnologia e sociedade por meio de práticas educativas, na escola e fora dela,
definirão tipos de alfabetização científica e tecnológica; assim, nas escolas, o ensino de
ciências e a divulgação científica nos meios de comunicação são elementos articuladores dessa
relação. Esse enfoque do ensino de ciências há muito é discutido em vários países. Um dos
estudiosos da questão, o pesquisador inglês Ziman é crítico do ensino tradicional fragmentado
em disciplinas, com o propósito de transmitir uma “representação esquemática idônea de um
grande repertório de observações e dados experimentais" (Ziman, 1985: 39), o qual, em geral,
consegue apenas parodiar o processo real de investigação científica. Para ele o ensino de CTS
deveria substituir o ensino tradicional, pois permitiria, de forma interdisciplinar (ciência,
tecnologia, psicologia, história, filosofia, sociologia), romper a impressão unilateral do ensino
tradicional. No seu entendimento, a principal meta do ensino de CTS deve ser a de “opor-se ao
cientificismo e tecnocracia e rechaçar qualquer fórmula estreita que pretenda conhecer todas as
perguntas e todos os problemas de nosso tempo”. (Ziman, 1985: 152) Outra estudiosa inglesa do movimento de CTS no ensino é Solomon (1993). Para ela, o
ensino de CTS deve visar, sobretudo, ao desenvolvimento de atitudes para se enfocar e
solucionar, de modo significativo, os problemas da aplicação da ciência na sociedade, além de
se ensinar a compreender o modo como a ciência atua no contexto social. Solomon aponta,
como características específicas de CTS na educação, a compreensão das ameaças
ambientais para a qualidade de vida de todo o globo, a compreensão de que a ciência tem uma
natureza falível, a discussão de opiniões e valores sociais para produção de ações
democráticas e a dimensão multicultural de visão de CTS. O movimento de CTS no ensino não ficou restrito ao contexto inglês. CIÊNCIA, TECNOLOGIA E SOCIEDADE NO ENSINO DE CIÊNCIAS As correntes contrárias a essa
visão não consideram que a escola deva fornecer o mínimo, mas algo próximo ao mínimo
múltiplo comum, ou seja, garantir
“(...) uma formação polivalente que capacite para desempenhar uma família de empregos
qualificados e, sobretudo, para compreender as bases gerais, técnico-científicas e
socioeconômicas de produção em seu conjunto, que reúna a aquisição de habilidades e
destrezas genéricas e específicas com o desenvolvimento de capacidades intelectuais e
estéticas; que unifique, em definitivo, formação teórica e prática”. (Enguita, 1988: 51) A relação educação e tecnologia é tema polêmico em voga entre educadores. Há
correntes mais ajustadas aos interesses empresariais que entendem a escola como espaço de
formação geral mínima para produção de trabalhadores flexíveis e propensos a serem
rapidamente treinados e reciclados no próprio local de trabalho. As correntes contrárias a essa
visão não consideram que a escola deva fornecer o mínimo, mas algo próximo ao mínimo
múltiplo comum, ou seja, garantir “(...) uma formação polivalente que capacite para desempenhar uma família de empregos
qualificados e, sobretudo, para compreender as bases gerais, técnico-científicas e
socioeconômicas de produção em seu conjunto, que reúna a aquisição de habilidades e
destrezas genéricas e específicas com o desenvolvimento de capacidades intelectuais e
estéticas; que unifique, em definitivo, formação teórica e prática”. (Enguita, 1988: 51) 10 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 10 ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 Revela-se, na
verdade, como a tendência dominante nos anos 90 e tem-se expandido para diversos países,
dentro dos quais destacamos os projetos: PLON (holandês), SISCON e SATIS (britânicos),
APQUA (Califórnia – EUA), e o Projeto 2001 (EUA), do qual originou-se o livro “Ciência para
todos” (Rutherford e Ahlgren, 1995). No Brasil, dentre outros, destacam-se as experiências do
Grupo de Reformulação do Ensino de Física – GREF-USP (1991) e Física – Coleção Magistério
(1991). Nos EUA, por exemplo, uma das preocupações do movimento de CTS consiste em
produzir “uma compreensão de conceitos científicos-chave que unifiquem as ciências com
outras disciplinas e que dêem conta das interações entre CTS” (Rye, 1998: 3).Outra intenção
da educação em CTS “é de fazer com que os estudantes fiquem mais motivados para aprender
ciência e conduzir melhor os experimentos científicos” (Scharmann,1998: 3). Na Austrália o
ensino de CTS é entendido de modo interdisciplinar (perspectiva de Ziman) e se preocupa em
discutir as origens, a natureza e o impacto social da C&T (Hallingen, 1998: 2). Para Menezes
(1988), Zanetic (1989) e Angotti (1991), os conhecimentos científicos, abordados nas escolas Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 11 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 brasileiras, constituem-se em fragmentos de uma ciência, descolados de qualquer outra área de
conhecimento. Ao se inserir a discussão CTS no ensino de ciências, considera-se que “o aluno é um
ser social, a apropriação do conhecimento científico como elemento importante na capacitação
do sujeito para o pleno exercício de sua cidadania. O olhar da ciência enquanto parte
importante da cultura, que, por direito, pertence ao aluno e por esta razão deve ser a ele
devolvida, decodificada, leva a uma outra organização do conhecimento” (Pierson e Hosoume,
1997: 89). Realizar esse debate “não significa defender uma ciência do como funciona. A
sociedade atual não é apenas tecnológica pelos aparatos e instrumentos que incorporou ao
nosso dia-a-dia, mas, principalmente, pela forma através da qual passamos a ver e interpretar
as coisas à nossa volta, as explicações que procuramos dar aos eventos, às profissões de fé
que fazemos a cada momento” (Pierson e Hosoume, 1997: 88). Para Auler (1997), uma forma
de se introduzirem temáticas na perspectiva CTS no currículo convencional são as intervenções
curriculares e o trabalho sistemático de acompanhamento os quais podem fazer surgir conflitos. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 “Conflitos, estes, que se estabelecem entre a satisfação de um trabalho diferenciado,
reconhecido por professores e alunos, e as práticas rotineiras. Destes conflitos emergem
espaços, aberturas, para alterações curriculares mais abrangentes”. (Auler, 1997: 191) No âmbito do ensino, é preciso mencionar as críticas dirigidas à introdução da CTS nos
currículos escolares as quais atentam para o perigo de se utilizar o conhecimento sociológico
como mais um mecanismo de controle e de reforço à valorização da C&T: “(...) Uma análise do discurso da educação CTS pode conduzir à previsão de profundas
alterações na educação científica. É, sem dúvida, uma mudança, mas não é profunda. A
educação CTS torna claras e sem ambigüidades as relações de poder entre categorias
(discursos, agentes, agências), legitimando a função reprodutora da escola. O elevado
estatuto e poder actualmente atribuídos à ciência e à tecnologia na sociedade são agora
subtilmente introduzidos na escola. E a vez dada às ciências sociais, nomeadamente à
sociologia, dentro e fora da escola, representa apenas, como foi dito, uma modalidade
de controle que permite dar mais força à força da ciência e da tecnologia .”(Moraes,
1994: 97) “(...) Uma análise do discurso da educação CTS pode conduzir à previsão de profundas
alterações na educação científica. É, sem dúvida, uma mudança, mas não é profunda. A
educação CTS torna claras e sem ambigüidades as relações de poder entre categorias
(discursos, agentes, agências), legitimando a função reprodutora da escola. O elevado
estatuto e poder actualmente atribuídos à ciência e à tecnologia na sociedade são agora
subtilmente introduzidos na escola. E a vez dada às ciências sociais, nomeadamente à
sociologia, dentro e fora da escola, representa apenas, como foi dito, uma modalidade
de controle que permite dar mais força à força da ciência e da tecnologia .”(Moraes,
1994: 97) O uso da inovação CTS para fins de reforço e de legitimação do status quo, sem dúvida,
é um dos problemas a serem considerados quando se pensa num ensino em CTS. À medida que caminhamos em direção a uma perspectiva de ensino e de alfabetização
científica e tecnológica com base na relação CTS, procede também a busca de integração entre
modos de pensamento narrativo e paradigmático que levem em consideração, inclusive, o
papel de pensamento mítico, gênese dos modos de pensamento anteriormente mencionados. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 contemporânea. Vale lembrar ainda que a tecnologia pode, em algumas circunstâncias, reforçar
a ciência como mito e ser referência importante de organização da vida social. contemporânea. Vale lembrar ainda que a tecnologia pode, em algumas circunstâncias, reforçar
a ciência como mito e ser referência importante de organização da vida social. METODOLOGIA Nossa investigação teve caráter exploratório e focalizou fragmentos de narrativas de
professores, profissionais do MAST – Museu de Astronomia e Ciências Afins e alunos que
participam de processos de alfabetização científica e tecnológica. Nas escolas e nos cursos de
atualização e aperfeiçoamento de professores, tivemos a oportunidade de aplicar um
questionário (anexo 1) para saber como eles lidam hoje com a relação CTS (mesmo que ainda
inseridos em um contexto de ensino tradicional). Foram distribuídos cerca de 500 questionários;
em geral, os professores os levavam para casa, com a promessa de devolvê-los preenchidos. Retornaram 108 (21%) deles, os quais foram digitados e tabulados no programa Sphinx. Esse
programa, além de produzir tabelas e gráficos, também quantifica termos, conceitos e
expressões
através
da
análise
de
conteúdo. Além
do
questionário,
trabalhamos
especificamente com os professores, em dois seminários, propondo-lhes atividades que
visaram a levantar as representações desses agentes sobre o tempo. A temática do tempo foi explorada em seminários de atualização realizados em duas
situações: num projeto de extensão da Universidade Federal Fluminense e no Museu de
Astronomia e Ciências Afins, ambos no Estado do Rio de Janeiro. O museu foi também o local
escolhido para acompanharmos visitas de 11 turmas à sua exposição permanente. Durante as
visitas, valemo-nos do método da observação direta para levantar dados sobre o
comportamento dos visitantes (anexo 2). Os dados e as análises a seguir dão uma idéia do que
foi investigado. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 Entendemos que a investigação de práticas educativas, por meio das narrativas, nos
ensinos formal e não-formal, pode apontar as possibilidades de articulação entre mito, ciência,
tecnologia e sociedade na medida em que o mito, além de ser considerado o ponto de partida
dos pensamentos narrativo e paradigmático, encontra-se presente no cotidiano. Além disso, o
discurso científico é considerado por alguns estudiosos como um dos mitos da sociedade Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 12 12 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 contemporânea. Vale lembrar ainda que a tecnologia pode, em algumas circunstâncias, reforçar
a ciência como mito e ser referência importante de organização da vida social. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 CTS NO ENSINO FORMAL Na pesquisa sobre alfabetização científica e tecnológica que estamos desenvolvendo
elaboramos e aplicamos, na sua fase inicial, um questionário para saber em que medida os
professores de ciências estão atentos à discussão da relação CTS. As tabelas 2 e 3 (anexo 3)
traçam um perfil dos professores pesquisados em termos de disciplina lecionada, série de
atuação, tipo de escola e tempo de magistério. Por elas, observamos que o número maior de
respondentes é da área de ciência, ecologia e biologia (40%), seguidos de professores que
lecionam no ensino de 1ª a 4ª séries - núcleo comum (18%). Os professores atuam, na sua
maioria, na rede pública (72%). Quanto ao tempo de magistério, constatamos que, em primeiro
lugar, aparecem os que lecionam pelo menos há 6 anos (22%), seguidos dos que têm entre 11
e 17 anos de magistério (11%). A despeito da variação de tempo de magistério, em geral, os
professores tendem a seguir um padrão tradicional de ensino de ciências determinado pelas
orientações contidas nos currículos oficiais e nos livros didáticos. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 13 13 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. CTS NO ENSINO FORMAL 2002 Quando perguntamos sobre a relação dos conteúdos hoje ensinados com a CTS,
obtivemos os resultados que são apresentados na tabela e nos quadros abaixo: Tabela 1 - Relação entre Conteúdos Escolares e CTS: Tabela 1 - Relação entre Conteúdos Escolares e CTS:
Respostas
1ª a 4ª séries
N = 25
5ª a 8ª séries
N = 26
Todos
11
15
Quase todos/ maioria
04
01
Ciências Biológicas
02
00
Questão ambiental
02
07
Não responde
06
03 Quadro 1 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 1ª a
4ª séries:
Relação Conteúdos Escolares e CTS
Conceitos Científicos
Identificados
Esquema corporal, tempo e relógio
Tempo, espaço
Trabalho, força, corpo e necessidades alimentares
Transformação, conservação
Recursos naturais, seres vivos, noções de higiene,
planeta
Meio ambiente, saúde
Desmatamento, alimentação, reciclagem do lixo
Transformação, conservação
Saúde, higiene, meio ambiente
Saúde, conservação
Sexo, drogas, violência, meio ambiente
Saúde, conservação Quadro 1 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 1ª a
4ª séries: Quadro 2 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 5ª a 8ª
séries:
Relação Conteúdos Escolares e CTS
Conceitos Científicos Identificados
Radiações, poluição ambiental, química dos
alimentos, fome, desperdício e reaproveitamento
de alimentos
Transformação, conservação,
preservação, saúde, acumulação
Usina nuclear, informatização
Transformação, comunicação
Formação do Universo, sistema solar, planetas
Tempo, espaço
Corpo humano, Aids, câncer, aborto, controle de
natalidade
Saúde, prevenção, demografia
Energia atômica, energia elétrica, utilidade das
máquinas no cotidiano
Transformação, conservação,
cotidiano
Sistema solar, tratamento e qualidade da água,
tecnologia ambiental, ciclos e importância das
fl
t
Tempo, espaço, transformação,
meio ambiente, ciclos Quadro 2 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 5ª a 8ª
séries: Quadro 2 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 5ª a 8ª
séries:
Relação Conteúdos Escolares e CTS
Conceitos Científicos Identificados
Radiações, poluição ambiental, química dos
alimentos, fome, desperdício e reaproveitamento
de alimentos
Transformação, conservação,
preservação, saúde, acumulação
Usina nuclear, informatização
Transformação, comunicação
Formação do Universo, sistema solar, planetas
Tempo, espaço
Corpo humano, Aids, câncer, aborto, controle de
natalidade
Saúde, prevenção, demografia
Energia atômica, energia elétrica, utilidade das
máquinas no cotidiano
Transformação, conservação,
cotidiano
Sistema solar, tratamento e qualidade da água,
tecnologia ambiental, ciclos e importância das
Tempo, espaço, transformação,
meio ambiente, ciclos 14 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 14 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 tecnologia ambiental, ciclos e importância das
florestas
meio ambiente, ciclos
Ecologia e seres vivos
Meio ambiente, ciclos
Física aplicada, energia
Conservação, cotidiano
Ecologia, corpo humano, genética
Ciclos, transformação, informação
Doenças epidemiológicas
Saúde, prevenção
Matéria, energia, poluição do ar, água, origem da
vida, nutrição e saúde
Transformação, conservação,
ciclos, evolução, saúde
Tempo, espaço, terra
Tempo, espaço, meio ambiente
Biodiversidade
Evolução, biodiversidade
Drogas, invenções e sexualidade
Prevenção, conservação, cotidiano
Genética, eletricidade, eletromagnetismo
Informação, transformação,
conservação
Clonagem, drogas, sexualidade
Informação, prevenção meio ambiente, ciclos
Meio ambiente, ciclos
Conservação, cotidiano
Ciclos, transformação, informação
Saúde, prevenção
Transformação, conservação,
ciclos, evolução, saúde
Tempo, espaço, meio ambiente
Evolução, biodiversidade
Prevenção, conservação, cotidiano
Informação, transformação,
conservação
Informação, prevenção meio ambiente, ciclos
Meio ambiente, ciclos
Conservação, cotidiano
Ciclos, transformação, informação
Saúde, prevenção
Transformação, conservação,
ciclos, evolução, saúde
Tempo, espaço, meio ambiente
Evolução, biodiversidade
Prevenção, conservação, cotidiano
Informação, transformação,
conservação
Informação, prevenção Clonagem, drogas, sexualidade A tabela 1 mostra como os professores de 1ª a 8ª séries respondem sobre os conteúdos
com os quais trabalham e as possibilidades de explorar neles a relação CTS. Para a maioria
(44% de 1ª a 4ª e 57% de 5ª a 8ª ), todos os conteúdos podem ser relacionados ao ensino de
CTS. Vale lembrar, contudo, que o significado de “todos” de 1ª a 4ª séries contempla todas as
disciplinas do núcleo comum, enquanto que o “todos” de 5ª a 8ª séries refere-se aos conteúdos
de ciências e geografia, principalmente. Um tema destacado pelos professores, em geral, e
também valorizado pelos estudiosos de CTS (Solomon, 1993) é a questão ambiental. Nos quadros 1 e 2, aparece um detalhamento dos conteúdos relacionados pelos
professores. No primeiro, séries iniciais, os aspectos vinculados à saúde do ambiente e do
corpo são priorizados nos conteúdos. No segundo (5ª a 8ª ), além de conteúdos relacionados ao
ambiente e ao corpo humano, são lembrados conteúdos decorrentes do desenvolvimento
tecnológico (clonagem, eletricidade, utilidade das máquinas no cotidiano, química dos
alimentos, tecnologia ambiental etc.). Observamos, também, que os professores de 5ª a 8ª
séries detalham mais os conceitos científicos quando se referem à relação entre conteúdos e
ensino de CTS. Ao estabelecermos relação entre essas respostas e o que é proposto pelos estudiosos
de CTS e alfabetização científica, podemos considerar que muitos dos conteúdos listados estão
próximos aos objetivos e preocupações da educação científica alinhados à CTS. No quadro 3, especificamos as respostas dos professores da área científica do ensino
médio à pergunta sobre a relação entre os conteúdos escolares e CTS (pergunta 2.2, anexo 1). Lembramos, no entanto, que, além desses 17 professores (70%), outros 6 de outras áreas
responderam ao questionário, perfazendo um total de 24. Do total de respondentes desse grau
de ensino, 73% também afirmaram que todos os conteúdos (ou a maioria) podem ser
vinculados à CTS. Dos professores da área científica, 50% eram de Biologia; 20%, de Química
e somente 5%, de Física. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 15 15 ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 O quadro apresenta uma síntese das respostas dos professores. Nelas, podemos
constatar que, em geral, o ensino de CTS diz respeito ao vivido, a problemas e soluções que
afetam o ambiente e a saúde humana, de modo positivo ou negativo. As respostas indicam
como os professores com formação específica de ciências fazem referências ao processo de
produção do conhecimento científico, relacionando-o à sociedade e à tecnologia. como os professores com formação específica de ciências fazem referências ao processo
produção do conhecimento científico, relacionando-o à sociedade e à tecnologia. Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores
ensino médio
Biologia = 12
Química = 4
Física = 2
Todos
os
conteúdos. Ciência é uma atividade
humana sujeita a influência
e
impactos
sociais;
o
aspecto
tecnológico
é
parceiro
da
ciência
no
processo de conhecimento. Todos conteúdos - Química (
necessidade que o homem
tem
de
resolver
seus
problemas
orgânicos
ou
não). Física aplicada e energia. Todos os conteúdos. A
tecnologia
como
parte
integrante da vida, e tudo
que diz respeito à vida diz
respeito à sociedade. A
maior
parte
dos
conteúdos. Porém, parece
estar fora do controle social. Conceitos
ligados
à
energia
e
sua
conservação, evolução da
física. Todos
os
conteúdos
quando abordados de uma
forma
dinâmica,
privilegiando aspectos da
natureza,
aplicação
no
cotidiano,
solução
de
problemas,
participação
ativa no meio. Conteúdos estão mais para
ciências, relacionados com a
tecnologia e a sociedade nos
pontos em que se passou
pela vivência. Todos os conteúdos. Interferência de substâncias
e
misturas
no
meio
ambiente. Quase todos. Genética
(3º
ano),
melhoramento
genético,
plantas,
animais;
importância da medicina;
questão ética. (interfere na
cultura, no pensamento, na
opinião da sociedade). Ecologia,
pesquisas
de
doenças
e
genética. Qualquer
conteúdo
de
bi l
i
( ã
tã
id
t Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do
ensino médio Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do
ensino médio Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do
ensino médio A vidente
Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 vidente
Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 16 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 doenças
e
genética. Qualquer
conteúdo
de
biologia (não tão evidente
a princípio). Conteúdos
de
ecologia,
seres vivos e química,
mais
facilmente
relacionados
com
o
cotidiano do aluno e com
fatos
que
ocorrem
no,
meio,
científico
e
tecnológico. Noções
de
Química:
criação
de
novas
substâncias
que
irão
facilitar a vida do homem. Na Química. Os aspectos
histórico
e
social
em
relação
aos
aspectos
apresentados. Instrumentos
ópticos
e
eletrônicos
sofisticados
que possibilitam entender
melhor o funcionamento de
organismos, com utilização
de fundamentos da área de
saúde. Em termos de recursos didáticos para o desenvolvimento das aulas, além do livro,
adotado assumidamente por 17 deles (15%), os professores referem-se, com mais freqüência,
ao uso de artigos de revistas e jornais (dominando as revistas). Das revistas assinaladas, vale
destacar: Globo Ciência, Superinteressante, Revista Nova Escola, Veja, Cadernos do 3º
Mundo. Há indicação de uso de vídeo (Série Cosmos), realização de experiências simples,
elaboração de modelos, pesquisa em bibliotecas, visitas a museus, postos de saúde, Jardim
Botânico, planetário, caminhadas em áreas verdes e assentamentos agrícolas. Sobre a relação desses conteúdos com a CTS, vale aqui a reflexão crítica de uma
professora de escola pública: “(...)O ensino de ciências tem-se limitado à transmissão de uma série de conceitos para
simples memorização, não se articulando com os grandes avanços obtidos pela ciência
e que são bombardeados quase que diariamente através da mídia. Apesar da precária Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000
17 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 17 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 situação do ensino público, tais recursos didáticos, quando contextualizados numa boa
prática pedagógica, podem funcionar para estabelecer o nexo entre esta ciência
proposta pelos currículos e o desenvolvimento da ciência e tecnologia que cresce a uma
velocidade extraordinária e invade a vida de todos os cidadãos. Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do
ensino médio Sendo assim, a
utilização de artigos científicos pode ser o ponto de partida para a busca de sua
fundamentação, encontrada nos conteúdos abordados em aula, ou, ao contrário, a partir
de conteúdos discutidos, caminhar no sentido de sua aplicabilidade, tendo como apoio
tais artigos científicos... A experimentação visa que o aluno vivencie o método científico
elaborando
hipóteses,
organizando
a
atividade,
estabelecendo
conclusões,
diferentemente da idéia de experimentação apresentada como receita de bolo... De
posse dos princípios fundamentais da ciência, articulando-os e aplicando-os, os alunos
poderão compreender sobre os grandes eventos realizados nesta área,... passando a
exercer o seu papel de cidadãos, posicionando-se e decidindo criticamente diante
deles.” Da ligação entre a Química e CTS, destacamos o seguinte depoimento: “(...) quando falo das substâncias químicas presentes nos alimentos, levo os alunos a
questionarem sobre a fome... levo-os à reflexão também sobre a questão do desperdício
de alimentos, e então falo sobre as alternativas para aproveitamento desses alimentos.” Além da aplicação do questionário, fizemos um trabalho voltado para identificação da
relação CTS nos ensinos formal (escola) e não-formal (museu), em duas etapas. Na primeira,
oferecemos uma palestra seguida de uma dinâmica para cerca de 70 professores da Zona
Oeste do Rio de Janeiro, sobre alfabetização científica. Na dinâmica, trabalhamos com o tema
"Tempo" de duas maneiras. Primeiro, solicitando aos professores que escrevessem e
representassem em desenho o significado da palavra tempo. Algumas das respostas estão aqui
reproduzidas: No segundo momento da dinâmica, distribuímos algumas crônicas sobre o tempo
(Lightman, 1966). Os professores, divididos em grupo, leram, discutiram e apresentaram
considerações sobre as leituras. Dos comentários finais, selecionamos um bastante
significativo: “(...) Até Newton, você tem uma idéia de tempo absoluto, de um tempo que pode ser
dito, codificado e é sempre o mesmo em qualquer lugar. Com Einstein, você tem uma
nova idéia de tempo, nesse sentido, e mais influenciado por outras pessoas, uma idéia
de que o tempo é relativo, que a massa e o espaço são relativos e que se influenciam. Isso também vai influenciar como vamos pensar a questão do tempo. Infelizmente, nas
escolas, trabalham muito pouco com as idéias da física mais moderna... Existe muito
medo da física de Einstein, e esse texto pode dar pistas também para trabalharmos essa
questão. Essa questão da velocidade, a velocidade da informação; quem não tem
acesso rápido à informação está alienado, não sabe o que está acontecendo. CTS NO ENSINO NÃO-FORMAL A pesquisa, no Museu de Ciência (Mast/MCT), foi realizada em duas fases. Na primeira,
foram feitas observações de turmas (11 no total) que visitaram o museu. Na segunda, foi
realizado um seminário dando continuação à discussão sobre o conceito de tempo,
anteriormente explorado. Foram convidados todos os professores (70) que participaram do 1º
seminário, mas somente 18 compareceram. Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do
ensino médio Existe o
computador que acessa a Internet e tem como se comunicar com o mundo inteiro. “(...) Até Newton, você tem uma idéia de tempo absoluto, de um tempo que pode ser
dito, codificado e é sempre o mesmo em qualquer lugar. Com Einstein, você tem uma
nova idéia de tempo, nesse sentido, e mais influenciado por outras pessoas, uma idéia
de que o tempo é relativo, que a massa e o espaço são relativos e que se influenciam. Isso também vai influenciar como vamos pensar a questão do tempo. Infelizmente, nas
escolas, trabalham muito pouco com as idéias da física mais moderna... Existe muito
medo da física de Einstein, e esse texto pode dar pistas também para trabalharmos essa
questão. Essa questão da velocidade, a velocidade da informação; quem não tem
acesso rápido à informação está alienado, não sabe o que está acontecendo. Existe o
computador que acessa a Internet e tem como se comunicar com o mundo inteiro. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 18 18 Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Quem não tem acesso a isso está perdendo nesse mundo da mesma forma que aqueles
que têm fome, que aqueles que não têm salário digno.” A visita O quadro 4 apresenta uma caracterização geral dos visitantes. Destacamos nele a forma
como os professores são inseridos no contexto do Mast: a maioria leva as turmas após passar
por um treinamento para compreender a proposta e poder colaborar no dia da visita. O quadro 4 apresenta uma caracterização geral dos visitantes. Destacamos nele a forma
como os professores são inseridos no contexto do Mast: a maioria leva as turmas após passar
por um treinamento para compreender a proposta e poder colaborar no dia da visita. Quadro 4 - Caracterização dos visitantes escolares ao Mast
SÉRIE
ESCOLA
FORMAÇÃO DO
PROFESSOR
ENTRADA NO
Mast
MOTIVO DA VISITA
3ª Série
Particular Administração
e
Pedagogia
Treinamento
Fixar
a
matéria
(Planetas)
Particular Matemática
e
Pedagogia
Treinamento
Por estar dando o
conteúdo
e
pela
curiosidade
das
crianças
4ª Série
Particular Sem informação
Treinamento
Matéria
dada
(astros
para
a
criança
ver
no
concreto)
Particular Pedagogia e Letras
Conta própria
Para
visualizar
o
que é dado em sala
5ª Série
Particular Biologia
Treinamento
Sem informação
Particular Supervisora em Artes
e Psicologia
Sem
informação
Sem informação
Particular História e Geografia
Sem
informação
Sem informação Quadro 4 - Caracterização dos visitantes escolares ao Mast Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 19 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 SÉRIE
ESCOLA
FORMAÇÃO DO
PROFESSOR
ENTRADA NO
Mast
MOTIVO DA VISITA
Mistas
(3ª e 4ª )
Particular Especialização
em
Literatura
Treinamento
Trabalhar conteúdos
(começa em espaço
e
termina
em
Microcosmo)
Particular Psicologia
e
Pedagogia
Treinamento
Trabalhar conteúdo
(Universo) e para
sair do abstrato. Mistas
(2ª , 3ª e
4ª )
Particular Pedagogia
Treinamento
Está
dando
o
conteúdo
Pública
Municipal
Pedagogia
Sem
informação
Sem informação. Das 11 turmas que visitaram o Mast, 10 eram de escolas particulares. Vale ainda
destacar que a maioria dos professores, além de não pertencer à área de ciências, costuma
levar os alunos para fixar conteúdos com que estão trabalhando em sala de aula. As observações ficaram restritas a uma parte da exposição permanente. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 O quadro a seguir apresenta uma síntese das reações das turmas quando visitaram a
exposição permanente. Lembramos que a coleta dessas observações foi feita por duas
bolsistas, que registravam as reações dos visitantes em um formulário próprio (anexo 3),
durante o período de duração da visita – uma hora. Foram realizadas 12 observações em um
período de quatro meses, somente na parte da exposição permanente que aborda a relação
CTS por meio da evolução do conceito de espaço e tempo. Quadro 5 - Reações das turmas em visita à exposição permanente
SÉRIE
SALA BRANCA
(Modelo Geocêntrico). SALAS INTERMEDIÁRIAS
(Modelo Heliocêntrico)
SALA ESCURA
(Visão do céu a
partir da Terra)
3ª Série
(2 e 4)
Nº 2: O monitor estimula as
crianças a falar das imagens
que
podem
retratar
as
estações do ano. Também
menciona a inclinação da
Terra, além de chamar a
atenção para a imagem do
mês de fevereiro, no qual está
nevando. As crianças dizem
que deve ser em outro país e
não no Brasil. Nº 4: A professora começou
explicando o livro das horas,
reforçou a explicação dos
STONEHENGE, falando do
pôr-do-sol, como também do
sistema
geocêntrico. A
professora pergunta para os
alunos por que, no mês de
fevereiro, seria inverno no
continente
europeu. Os
alunos
rapidamente
responderam: “Por causa da
vestimenta."
Nº 2: As crianças observam
atentamente a parte dos
descobrimentos. Percebem
o quanto é perigoso tentar
observar o Sol com luneta,
lupa etc. Averiguam que é
muito mais fácil usar um
astrolábio para medir as
estrelas. Ao chegar à parte
do sistema solar, falam dos
planetas (tudo decorado). Nº
4:
As
crianças
respondem atentamente à
rota dos descobrimentos. No diálogo, a professora
relembra uma das suas
aulas e pede que alguma
criança exponha o que já
foi visto. Explica também
como
foi
difícil
Galileu
convencer
os
outros
(mostra o diálogo). No
sistema solar, uma das
crianças menciona que a
Terra está girando muito
rápido. O monitor explica
que
é
só
uma
órbita
imaginária. Nº 2: As crianças só
fizeram ligações com
os signos. Nº 4: Ao entrarem na
sala,
as
crianças
procuram logo seus
signos. A professora
pediu que as crianças
observassem a escala
dos meses e o melhor
período para ver as
constelações de cada
signo. A visita Nessa
exposição, Quatro Cantos de Origem, o Mast se propõe a desenvolver as noções de tempo e
espaço a partir das narrativas tradicionais (mito) e das narrativas modernas (científicas).A
"musealização do acervo constitui-se como meio eficiente de enriquecimento da aprendizagem
científica, uma vez que parte do pressuposto de que o público que o visita já detém informações
preliminares sobre o que vai encontrar" (MAST, 1992). O museu pretende ser uma espécie de contexto-síntese do debate mito, ciência e
tecnologia ao confrontar os dois primeiros e ao expor provas materiais dos avanços científico e
tecnológico (relógios, lunetas, telescópios, mapas celestes etc.). Além de permitir um
aprofundamento do deslocamento do modelo geocêntrico e sua substituição pelo modelo
heliocêntrico, das noções de tempo circular e linear, de espaço e tempo limitados e infinitos, a
integração do que se aprende na escola com o que o museu possibilita ver e aprofundar
permite, inclusive, perceber de que modo fragmentos das narrativas primitivas permanecem nos
modelos e nas concepções científicas: "(...) O Zodíaco, este conjunto de estrelas distribuídas numa faixa do céu, aparece como
um elemento importante para se definir o tempo. Grupo de estrelas do Zodíaco foi
associado às figuras que transpunham, de forma simbólica, elementos terrestres para o
céu.(...) A ciência moderna teve sua base fundada na observação astronômica. Durante
o século XVII, as tabelas astronômicas servem de base para a formulação da física. O
céu simbólico serve de meio para refletir sobre o homem e seus ciclos. Homem e
Universo integram-se" .(MAST, 1992: 25). Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 20 20 ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 Partindo daí, o
monitor
aprofundou
suas
explicações sobre o motivo
que levava as pessoas a
pensarem assim. Surge uma
nova pergunta por parte de
um dos alunos, interessado
em saber se um planeta
estava dentro do outro. O
N
d
s
a
N
“d
p
N
a
d
m
C
A
q
F
p
m
c
tê
N
m
ro
N
u
o errada
no
sistema
geocêntrico. Uma
criança
afirmou que o Sol girava em
torno da Terra (todos os
outros a vaiaram). Depois
desse
acontecimento,
o
monitor explicou o sistema
geocêntrico,
conseguindo
prender a atenção de todos
os
alunos. A
partir
daí,
algumas
crianças
fizeram
perguntas
referentes
ao
assunto. Podemos citar como
exemplo: "O que significa
estas linhas azuis?” (R:
Esferas de cristais). Na parte dos planetas, eles
falam seus nomes na sua
devida seqüência. as constelações, só
depois perceberam os
signos. 5ª Série
(9, 10
e 11)
Nº 9: As crianças ouviram as
explicações
do
sistema
geocêntrico
com
muita
atenção e ainda afirmaram
que o Sol estava no centro. Nº
10:
Parece
que
a
professora já havia avisado
aos alunos sobre o que
encontrariam no museu, visto
que ela, havia participado da
visita no ano passado. Além
disso, as crianças percebem
logo a diferença no mês de
fevereiro. Nº 11: Esse grupo acertou, de
primeira, que a Terra estava
no centro. Partindo daí, o
monitor
aprofundou
suas
explicações sobre o motivo
que levava as pessoas a
pensarem assim. Surge uma
nova pergunta por parte de
um dos alunos, interessado
em
saber
se
um
planeta
Nº 9: As crianças falam dos
descobrimentos. Logo em
seguida, o monitor vai para
a parte do sistema solar. Novamente
aparece
a
“decoreba” da ordem dos
planetas. Nº 10: Um aluno perguntou
ao monitor se Cabral tinha
descoberto o Brasil na
mesma época em que
Colombo
descobriu
a
América. Outro
aluno
questionou
o
fato
de
Fernão de Magalhães ser o
primeiro a dar a volta ao
mundo,
visto
que,
se
chegou morto, não poderia
tê-lo feito. Nº
11:
As
crianças
manipulam a parte das
rotas dos descobrimentos. Na parte do sistema solar,
uma criança percebe que
Nº 9: As crianças
ficaram
fascinadas
com as figuras das
constelações e com o
fato de encontrarem
seu signo. Nº 11: As crianças
tiveram dificuldade de
encontrar seus signos,
talvez por não terem
conhecimentos
de
“latim”. Na parte dos planetas, eles
falam seus nomes na sua
devida seqüência. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 4ª Série
(7e 8)
Nº 7: As crianças observaram
que
havia
alguma
coisa
Nº
8:
Os
alunos
manuseiam o astrolábio. Nº 8: As crianças
ficaram
observando uadro 5 - Reações das turmas em visita à exposição permanente
ÉRIE
SALA BRANCA
(Modelo Geocêntrico). SALAS INTERMEDIÁRIAS
(Modelo Heliocêntrico)
SALA ESCUR
(Visão do céu
partir da Terr
Série
e 4)
Nº 2: O monitor estimula as
crianças a falar das imagens
que
podem
retratar
as
estações do ano. Também
menciona a inclinação da
Terra, além de chamar a
atenção para a imagem do
mês de fevereiro, no qual está
nevando. As crianças dizem
que deve ser em outro país e
não no Brasil. Nº 4: A professora começou
Nº 2: As crianças observam
atentamente a parte dos
descobrimentos. Percebem
o quanto é perigoso tentar
observar o Sol com luneta,
lupa etc. Averiguam que é
muito mais fácil usar um
astrolábio para medir as
estrelas. Ao chegar à parte
do sistema solar, falam dos
planetas (tudo decorado). Nº
4:
As
crianças
Nº 2: As crianç
fizeram ligações
os signos. Nº 4: Ao entrare
sala,
as
cria
procuram logo
signos. A profe
pediu que as cria
observassem a e
dos meses e o m
período para ve
constelações de Quadro 5 - Reações das turmas em visita à exposição permanente Nº 4: Ao entrarem na
sala,
as
crianças
procuram logo seus
signos. A professora
pediu que as crianças
observassem a escala
dos meses e o melhor
período para ver as
constelações de cada
signo. Nº 4: Ao entrarem na
sala,
as
crianças
procuram logo seus
signos. A professora
pediu que as crianças
observassem a escala
dos meses e o melhor
período para ver as
constelações de cada
signo. o Sol girava em
erra (todos os
devida seqüência. sig
Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 21 ENSAIO – Pesquisa em Educação em Ciências ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 errada
no
sistema
geocêntrico. Uma
criança
afirmou que o Sol girava em
torno da Terra (todos os
outros a vaiaram). Depois
desse
acontecimento,
o
monitor explicou o sistema
geocêntrico,
conseguindo
prender a atenção de todos
os
alunos. A
partir
daí,
algumas
crianças
fizeram
perguntas
referentes
ao
assunto. Podemos citar como
exemplo: "O que significa
estas linhas azuis?” (R:
Esferas de cristais). ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 Na parte dos planetas, eles
falam seus nomes na sua
devida seqüência. 5ª Série
(9, 10
e 11)
Nº 9: As crianças ouviram as
explicações
do
sistema
geocêntrico
com
muita
atenção e ainda afirmaram
que o Sol estava no centro. Nº
10:
Parece
que
a
professora já havia avisado
aos alunos sobre o que
encontrariam no museu, visto
que ela, havia participado da
visita no ano passado. Além
disso, as crianças percebem
logo a diferença no mês de
fevereiro. Nº 11: Esse grupo acertou, de
primeira, que a Terra estava
no centro. Partindo daí, o
monitor
aprofundou
suas
explicações sobre o motivo
que levava as pessoas a
pensarem assim. Surge uma
nova pergunta por parte de
um dos alunos, interessado
em saber se um planeta
estava dentro do outro. O
monitor esclareceu que as
esferas é que estavam uma
Nº 9: As crianças falam do
descobrimentos. Logo em
seguida, o monitor vai para
a parte do sistema solar
Novamente
aparece
a
“decoreba” da ordem dos
planetas. Nº 10: Um aluno pergunto
ao monitor se Cabral tinha
descoberto o Brasil na
mesma época em que
Colombo
descobriu
a
América. Outro
aluno
questionou
o
fato
de
Fernão de Magalhães ser o
primeiro a dar a volta ao
mundo,
visto
que,
se
chegou morto, não poderia
tê-lo feito. Nº
11:
As
criança
manipulam a parte das
rotas dos descobrimentos
Na parte do sistema solar
uma criança percebe que
os planetas mais próximos
do Sol giram mais rápido. errada
no
sistema
geocêntrico. Uma
criança
afirmou que o Sol girava em
torno da Terra (todos os
outros a vaiaram). Depois
desse
acontecimento,
o
monitor explicou o sistema
geocêntrico,
conseguindo
prender a atenção de todos
os
alunos. A
partir
daí,
algumas
crianças
fizeram
perguntas
referentes
ao
assunto. Podemos citar como
exemplo: "O que significa
estas linhas azuis?” (R:
Esferas de cristais). N
fa
d
5ª Série
(9, 10
e 11)
Nº 9: As crianças ouviram as
explicações
do
sistema
geocêntrico
com
muita
atenção e ainda afirmaram
que o Sol estava no centro. Nº
10:
Parece
que
a
professora já havia avisado
aos alunos sobre o que
encontrariam no museu, visto
que ela, havia participado da
visita no ano passado. Além
disso, as crianças percebem
logo a diferença no mês de
fevereiro. Nº 11: Esse grupo acertou, de
primeira, que a Terra estava
no centro. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 No
calendário,
o
monitor
menciona as estações do
ano. Nº
11:
No
sistema
geocêntrico,
uma
criança
perguntou
(em
meio
à
explicação do monitor) se
Júpiter e Plutão não eram
vistos por serem planetas
gasosos. Uma outra pergunta
que um aluno fez foi sobre o
cinturão de asteróides. O
monitor disse que naquela
Nº 5: As crianças falam
sobre os descobrimentos,
observam o astrolábio e,
na parte dos planetas, não
sabem a ordem, mas ficam
muito
interessadas
pela
luneta astronômica. Nº 11:
As
crianças
observam o quadro das
rotas,
manipulam
o
astrolábio,
ficam
encantadas olhando para o
sistema solar e percebem
que
os
planetas
mais
próximos do Sol giram
mais rápido que os mais
afastados. Nº 5: As cria
atrapalharam
procura dos
mas ao enco
tiveram
curi
em
observa
constelações. Nº 11: As
procuraram log
signo. monitor esclareceu que as
esferas é que estavam uma
dentro da outra. do Sol gir
Mistas
– 3ª e
4ª
séries
(3 e 6)
Nº 3: O monitor incentiva as
crianças a perguntarem. Elas
respondem
o
que
é
calendário;
percebem
as
diferenças entre os meses no
Brasil e na Europa. Na parte
em que é exposta a distância
entre a Terra e o Sol, a
professora pede explicação
ao monitor. Ela faz ligação da
geometria com a astronomia,
mencionando que já havia
dado a matéria de triângulos
e ângulos. Nº 6: A
estavam
interessa
sim, em
todos
o
liberdade
atenção
astrolábio
sistema s
não sabi
Arriscava
pareciam
planetas. Mistas
–
2ª ,3ª
e
4ª
séries
(5 e11)
Nº 5: Na explicação sobre o
sistema
geocêntrico,
as
crianças afirmaram que o Sol
é que estava no centro, mas,
após a explicação do monitor,
passaram a responder com
precisão às suas perguntas:
Uma criança indagou: “Por
que tem uma estrela em cada
bolinha ? O que são elas?”
Resposta: As bolinhas são os
planetas que, vistos da Terra,
parecem
estrelas. No
calendário,
o
monitor
menciona as estações do
ano. Nº
11:
No
sistema
geocêntrico,
uma
criança
perguntou
(em
meio
à
explicação do monitor) se
Júpiter e Plutão não eram
vistos por serem planetas
gasosos. Uma outra pergunta
que um aluno fez foi sobre o
cinturão de asteróides. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 Na parte dos planetas, eles
falam seus nomes na sua
devida seqüência. Nº 9: As crianças
ficaram
fascinadas
com as figuras das
constelações e com o
fato de encontrarem
seu signo. Nº 9: As crianças falam dos
descobrimentos. Logo em
seguida, o monitor vai para
a parte do sistema solar. Novamente
aparece
a
“decoreba” da ordem dos
planetas. Nº 11: As crianças
tiveram dificuldade de
encontrar seus signos,
talvez por não terem
conhecimentos
de
“latim”. Nº 10: Um aluno perguntou
ao monitor se Cabral tinha
descoberto o Brasil na
mesma época em que
Colombo
descobriu
a
América. Outro
aluno
questionou
o
fato
de
Fernão de Magalhães ser o
primeiro a dar a volta ao
mundo,
visto
que,
se
chegou morto, não poderia
tê-lo feito. ra. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 22 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 monitor esclareceu que as
esferas é que estavam uma
dentro da outra. do Sol giram mais rápido. Mistas
– 3ª e
4ª
séries
(3 e 6)
Nº 3: O monitor incentiva as
crianças a perguntarem. Elas
respondem
o
que
é
calendário;
percebem
as
diferenças entre os meses no
Brasil e na Europa. Na parte
em que é exposta a distância
entre a Terra e o Sol, a
professora pede explicação
ao monitor. Ela faz ligação da
geometria com a astronomia,
mencionando que já havia
dado a matéria de triângulos
e ângulos. Nº 6: As crianças não
estavam
muito
interessadas em ouvir e,
sim, em ver e explorar
todos
os
cantos
com
liberdade. Só deram mais
atenção à explicação do
astrolábio. Na
hora
do
sistema solar, as crianças
não sabiam a seqüência. Arriscavam
os
nomes;
pareciam não conhecer os
planetas. Nº 3: As
dizem que es
espaço flutua
somente
preocupam em
os seus signos
Nº 6: As
ficaram
entusiasmadas
pareciam esta
coisas
do
mundo. procuraram
signos, sem
atenção à expl
Mistas
–
2ª ,3ª
e
4ª
séries
(5 e11)
Nº 5: Na explicação sobre o
sistema
geocêntrico,
as
crianças afirmaram que o Sol
é que estava no centro, mas,
após a explicação do monitor,
passaram a responder com
precisão às suas perguntas:
Uma criança indagou: “Por
que tem uma estrela em cada
bolinha ? O que são elas?”
Resposta: As bolinhas são os
planetas que, vistos da Terra,
parecem
estrelas. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 O
monitor
disse
q e
naq ela
Nº 5: A
sobre os
observam
na parte
sabem a
muito
in
luneta as
Nº 11:
observam
rotas,
astrolábio
encantad
sistema s
que
os
próximos
mais ráp
afastados Nº 5: As crianças falam
sobre os descobrimentos,
observam o astrolábio e,
na parte dos planetas, não
sabem a ordem, mas ficam
muito
interessadas
pela
luneta astronômica. Nº 11:
As
crianças
observam o quadro das
rotas,
manipulam
o
astrolábio,
ficam Nº 11: As crianças
procuraram logo o seu
signo. Nº 11:
As
crianças
observam o quadro das
rotas,
manipulam
o
astrolábio,
ficam Nº 11: As crianças
procuraram logo o seu
signo. encantadas olhando para o
sistema solar e percebem
que
os
planetas
mais
próximos do Sol giram
mais rápido que os mais
afastados. conheciam. No
as, as crianças
Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 23 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002
cinturão de asteróides. O
monitor disse que naquela
época não o conheciam. No
livro das horas, as crianças
dizem que é outro país,
devido ao mês de fevereiro. Logo a seguir, o monitor
explica os hemisférios e fala
sobre as estações. cinturão de asteróides. O
monitor disse que naquela
época não o conheciam. No
livro das horas, as crianças
dizem que é outro país,
devido ao mês de fevereiro. Logo a seguir, o monitor
explica os hemisférios e fala
sobre as estações. Por esse quadro, é possível dizer que a visita ao museu expõe professores e alunos a
um conflito que resulta do fato de o museu e a escola trabalharem os mesmos temas de modo
bastante diferenciado, pois, enquanto os professores trabalham os conteúdos de modo
descontextualizado, a exposição contextualiza e ressalta a história da ciência. Pelo fato de o
museu ter uma exposição que busca articular CTS, ele se encontra mais próximo de um projeto
de alfabetização científica do que a escola. O quadro 6 confirma essa observação,
especialmente quando registra que, em geral, os alunos não sabem que o modelo geocêntrico
antecedeu o modelo heliocêntrico. Por meio dele também é possível constatar dois outros
aspectos significativos. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 O primeiro deles é a preocupação da exposição em passar certas
noções de tempo e de espaço com as quais os alunos não estão ainda familiarizados. O
segundo refere-se à identificação dos alunos com a perspectiva mítica (astrologia), quando
visitam a sala escura. Desse modo revela-se, para alunos e professores, a possibilidade,
através do ensino não-formal, de se trabalhar mais próximo da articulação CTS pela via da
narrativa, do mito, da ciência . Vale destacar que a questão tecnológica, mesmo estando
presente na exposição permanente, não é suficientemente percebida e trabalhada pelos
professores e monitores. Quadro 6 - Reações em face dos modelos geocêntrico e heliocêntrico
Série
Sala Branca
Sala Intermediária
Sala Escura
4ª Série As explicações centram-
se
no
sistema
geocêntrico. A visita às salas é corrida. Destacam-se o manuseio do
astrolábio e a ordem correta
da nomeação dos planetas. Observação
dos
signos
e
das
constelações. 5ª Série As explicações centram-
se
no
sistema
geocêntrico,
mas
os
alunos incorrem no erro
explicativo
sobre
o
modelo (vêem o Sol no
centro). Novamente
explicação
relacionando
os
descobrimentos (História) com
as novas possibilidades de
visão
e
conhecimento
do
Universo (Ciências). Destaque
para a observação de uma
criança
sobre
movimentos
mais rápidos dos planetas
As
crianças
observam,
“fascinadas”,
as
constelações e os
signos. Revelam
dificuldade
com
o
latim e, por isso,
demoram
a
identificar seu signo Quadro 6 - Reações em face dos modelos geocêntrico e heliocêntrico Quadro 6 - Reações em face dos modelos geocêntrico e heliocêntrico Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 24 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 mais rápidos dos planetas
mais próximos do Sol. identificar seu signo
respectivo. Séries
Mistas
Tanto
discutem
os
modelos
(alunos
incorrem no erro de
afirmar que o Sol está
no centro do modelo
geocêntrico) quanto as
estações do ano e a
impossibilidade de se
ver a época certa dos
planetas. Um aluno (nº
12)
busca explicação
própria para o fato de os
planetas (como Plutão)
não serem vistos (eram
gasosos). Trabalha-se a relação História
(descobrimento) e Ciências
(visão do céu). As crianças
observam
o
astrolábio,
nomeiam os planetas e notam
que
os
planetas
mais
próximos do Sol giram mais
rápido (simulação do modelo
heliocêntrico);
As crianças buscam,
principalmente,
seu
signo. ENSAIO – Pesquisa em Educação em Ciências
Volume 02 / Número 1 – Març. 2002 Por ser o tempo uma dimensão relevante para a ciência e por ela estar destacada na
exposição permanente, consideramos oportuno convidar alguns professores, que haviam
discutido o tema em um dos cursos de extensão, para visitar o museu e rediscutir a temática
por meio de um seminário. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 O seminário Os professores (18) que compareceram ao Museu de Astronomia assistiram num
primeiro momento, a uma palestra que abordou a história da construção do calendário e as
diferentes concepções de tempo ao longo da história da humanidade e de diferentes
civilizações. A idéia era caracterizar a categoria tempo como uma construção humana e abordar
questões abertas que ainda precisam ser resolvidas. Num segundo momento, visitaram a Casa
da Hora, instituição vinculada ao Observatório Nacional e responsável pela determinação da
hora local brasileira. Nessa instituição, um técnico responsável mostrou-lhes aparatos de medir
o tempo com diferentes precisões. Num terceiro momento, os professores percorreram, orientados por um técnico, os
espaços que constituem a exposição permanente do Museu de Astronomia, podendo, então,
observar como as relações espaço-tempo eram estabelecidas na Idade Média, durante o
Renascimento e na Idade Moderna. A sala dedicada aos instrumentos de medida de tempo foi
particularmente explorada. Num quarto momento, os professores foram convidados a escrever
e apresentar em desenho, o significado da palavra tempo. Algumas das respostas estão aqui
apresentadas. Os quatro desenhos e as frases escolhidas para dar significado ao conceito de tempo
entre professores (1ª a 8ª séries), comparados com os desenhos da primeira fase do trabalho,
reproduzem as mesmas concepções sobre o tempo. Observa-se que o tempo da escola, Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 25 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Volume 02 / Número 1 – Març. 2002 também, está presente, e o tempo mecânico simbolizado pelo relógio permanece com
dimensões existenciais. Em relação ao conceito de tempo ensinado, este está associado às
equações do movimento e à linha do tempo. Percebe-se, então, que os professores oscilam suas representações entre as apoiadas
em pensamento paradigmático e pensamento narrativo e, quando se expressam por meio de
pensamento paradigmático, utilizam-se de conteúdos escolares. Como a visita se dá num
tempo curto, fica difícil obter informações sobre possíveis mudanças no conceito de tempo dos
professores. Seria necessário, portanto, realizar um trabalho mais longo e contínuo junto a
esses professores para perceber possíveis mudanças. Entretanto, fica claro como o pensar
sobre a categoria tempo, expressa aqui por meio de desenhos, explicita as relações entre mito,
ciência e tecnologia. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 CONCLUSÕES A discussão teórica com que iniciamos este artigo, envolvendo o movimento de CTS no
ensino de ciências e os modos de pensamento narrativo e paradigmático, foi significativa para
procedermos a uma avaliação do estado da educação científica na escola e no museu. Ela
iluminou a construção dos instrumentos e a análise dos dados coletados, mostrando, por
exemplo, que não há sintonia entre o ensino formal (predominantemente apoiado no
pensamento paradigmático e distante do narrativo) e o ensino não-formal (mais propenso a
uma articulação entre os dois modos de pensamento). Percebemos que, no caso do ensino
não-formal apresentado pelo Mast, há uma tendência a incorporar mito e ciência na narrativa,
possibilitando, assim, um aprendizado mais próximo das concepções do cotidiano. Por outro
lado, há dificuldade por parte dos idealizadores em articular os elementos da tecnologia via
narrativas apoiadas nos objetos. Essa dificuldade está contida na fala dos estudantes e dos
professores, que discutem mais os modelos apresentados. O uso das narrativas, no ensino de ciências, apresenta condições para explorar a
relação CTS, na medida em que pode propiciar reflexões acerca dos aspectos éticos e
epistemológicos da ciência e da tecnologia, além de dar a dimensão da presença da ciência e
da tecnologia na sociedade. A análise dos dados levantados nas escolas indica que, embora os professores ainda
estejam atrelados ao ensino tradicional de ciências (em grande parte por determinação dos
currículos, programas oficiais e livros didáticos), há por parte deles um esforço no sentido de
trabalhar esses conhecimentos de modo menos fragmentado e, na medida do possível, mais
próximo das realidades social e tecnológica. Atestam essas predisposições o uso de recursos
como jornais, revistas, vídeos; o desenvolvimento de atividades como visitas a museus, postos
de saúde, assentamentos agrícolas e o empenho em promover debates e reflexões que
articulem ciência e tecnologia à nossa realidade. No desenvolvimento da relação CTS, sob a ótica do conceito de tempo, nos contextos
formal e não-formal de educação, seja nos cursos e seminários, seja nas visitas, tivemos a
oportunidade de constatar como aparatos tecnológicos (relógios) reforçam determinados
conceitos científicos, mas, por outro lado, como relações estabelecidas entre o tradicional e o
moderno, o conhecimento abstrato e a reflexão existencial possibilitam uma perspectiva Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 26 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. CONCLUSÕES 2002 interdisciplinar do debate, em que as relações mito, ciência e tecnologia podem ser abordadas. A esse respeito, vale lembrar que as representações produzidas pelos professores sobre o
conceito de tempo estão fundamentadas nos conceitos social e tecnológico, expressos nos
desenhos do relógio mecânico, e que tende a encobrir a história desse conceito, tornando-o
natural, o que é, na verdade, uma construção social do tempo. Neste trabalho, fizemos um esforço no sentido de estabelecer um paralelo entre a
educação científica formal e a não-formal disponível em escolas e no Museu de Ciências do
Estado do Rio de Janeiro, para identificar a sua proximidade com uma das tendências do
ensino de ciências: ensino de CTS. No museu, a pedagogia implementada articula as ações
envolvendo espaço, objeto e tempo, pois nos museus as narrativas construídas em torno dos
objetos que se dispõem em determinados espaços são apreendidas em tempo próprio pelos
visitantes e de forma autônoma. As narrativas presentes no museu não estão necessariamente
atreladas ao currículo escolar, permitindo ao seu elaborador escolhas diversificadas, tanto em
relação aos conteúdos científicos como aos recursos comunicacionais. Assim, constatamos que, apesar de ainda estarmos muito atrelados a um ensino
fragmentado de ciências, a oferta educacional de um museu de ciências com uma proposta
histórica e contextualizada da ciência pode contemplar uma educação em CTS. Embora no
ensino formal, verifiquemos que os currículos, programas e livros didáticos, em sua maioria,
ainda estão presos a uma visão científica fragmentada, observamos que os professores tendem
a trabalhar, na sala de aula, alguns conteúdos que se aproximam da perspectiva de CTS. Há, no entanto, necessidade de se aprofundarem as reformas de ensino de ciências,
visando à ampliação da oportunidade de se trabalhar melhor a relação CTS e levando em
conta, sobretudo, a essencial articulação entre os ensinos formal, não-formal e os meios de
divulgação científica. O aprofundamento do estudo das narrativas abordando a relação mito,
ciência e tecnologia poderia constituir um caminho interessante de integração entre o ensino
formal, o não-formal e a divulgação científica. Essa perspectiva, além de nortear cursos de
atualização de professores, poderia orientar as ações das instituições envolvidas com a
educação científica, objetivando a ampliação da alfabetização científica. As autoras agradecem à bolsista Fátima Pereira Duque (Pibic/CNPq/UFF) pela montagem dos
Quadros 4, 5 e 6. Anexo 1 - Questionário de sondagem para professores: Universidade Federal Fluminense
Centro de Estudos Sociais Aplicados
Faculdade de Educação Pesquisa CTS no contexto da alfabetização científica. Prezado(a) professor(a), Agradecimentos As autoras agradecem à bolsista Fátima Pereira Duque (Pibic/CNPq/UFF) pela montagem dos
Quadros 4, 5 e 6. 27 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Volume 02 / Número 1 – Març. 2002 Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Prezado(a) professor(a), Estamos solicitando a sua colaboração no sentido de responder às perguntas em anexo,
o que muito contribuirá para sabermos como nossas escolas têm lidado, no ensino de ciências,
com a relação CTS. Desde já agradecemos a sua valiosa colaboração. A equipe da pesquisa 1. Itens gerais de identificação: 1.1. Tipo(s) de disciplina que leciona 1.2. Série(s) em que atua 1.3. Tempo de exercício do magistério 1.4. Tipo de escola em que trabalha: pública / particular 2.1. Que tipos de conteúdo o senhor (a senhora) costuma desenvolver? 2.2. Desses conteúdos quais são, na sua opinião, aqueles em que estão presentes aspectos
ligados à relação CTS? Por quê? 3. Solicitação final: se o senhor (a senhora) dispõe de algum material produzido para transmitir
ou avaliar conteúdos relativos a CTS (textos de aula, provas ou testes de alunos, trabalhos de
aluno etc.), gostaríamos que anexasse um exemplar a este instrumento de pesquisa. Anexo 2 - Ficha de Observação MAST/CNPq
Formulário de observação: pesquisa CTS
Sala:
Data:
Hora:
Nome do bolsista:
Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000
28 Anexo 2 - Ficha de Observação MAST/CNPq
Formulário de observação: pesquisa CTS
Sala:
Data:
Hora:
Nome do bolsista: Anexo 2 - Ficha de Observação MAST/CNPq
Formulário de observação: pesquisa CTS
Sala:
Data:
Hora:
Nome do bolsista: Anexo 2 - Ficha de Observação MAST/CNPq Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000
2 28 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Explicações/ênfases Profs. Prezado(a) professor(a), e monitores
Dúvidas, questões e comentários de alunos Anexo 3 – Tabelas com informações sobre os professores
Tabela 2 - Séries em que os professores atuam e disciplina que lecionam
Nível de Ensino:
Fundamental
Médio
Superio
r
total
Disciplina:
CA a 4ª
série
5ª a 8ª série 1ª a 3ª série
Ciências e Biologia
0
11
10
0
21
Química
0
0
1
0
1
Química e Ciências
1
2
2
0
5
Ciências
2
16
0
0
18
Educação Ambiental e
Ciências
0
1
0
0
1
Física
0
0
1
0
1
Ciências, Biologia,
Programa de Saúde
0
1
1
0
2
Ciências e Programa de
Saúde
0
1
0
0
1
Química, Física e
Matemática
0
1
1
0
2
Português, Estudos
Sociais, Matemática e
Ciências
4
1
2
0
7
Ecologia e Biologia
0
1
1
0
2
Todas - Núcleo Comum
20
0
0
0
20
Biologia, Ciências e
Programa de Saúde
0
1
0
0
1
Física e Matemática
0
1
1
1
3
Outras
4
9
4
0
17
TOTAL
31
46
24
1
102
Obs: CA – Ciclo de Alfabetização, que corresponde à 1ª e 2ª séries do Ens
Fundamental REFERÊNCIAS BIBLIOGRÁFICAS: ANGOTTI, J. A. P. 1991. Fragmentos e Totalidades do Conhecimento Científico e do Ensino de
Ciências. São Paulo: Faculdade de Educação da USP. (Tese, Doutorado). ANGOTTI, J. A. P. 1991. Fragmentos e Totalidades do Conhecimento Científico e do Ensino de
Ciências. São Paulo: Faculdade de Educação da USP. (Tese, Doutorado). ARONS, A. B. 1983. Achieving Wider Scientific Literacy. Daedalus, n.112, p. 91-121. AULER, D., Stueder, D. M., CUNHA, Marcio B. O enfoque ciência-tecnologia-sociedade como
parâmetro e motivador de alterações curriculares. In: ENCONTRO NACIONAL DE
PESQUISA EM ENSINO DE CIÊNCIAS, 1, 1997, Águas de Lindóia – SP. Atas... Porto
Alegre: Instituto de Física – UFRGS, 1997. p. 187-192. BARROS, S. S. 1990. O Acidente de Goiânia - subsídio para um módulo de ensino relacionado à
ciência-tecnologia-sociedade (CTS). In: GONÇALVES, O. D. (Org.). O ensino de física e a
física da atualidade. Rio de Janeiro: Ed. UFRJ. (Trabalhos apresentados durante a 1ª
Escola de Verão para Licenciados). BARTHES, R. 1993. Mitologias. Rio de Janeiro: Bertrand Brasil. Anexo 3 – Tabelas com informações sobre os professores Tabela 2 - Séries em que os professores atuam e disciplina que lecionam Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000
29 29 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Tabela 3 - Séries em que os professores atuam e tipo de escola em que trabalham
Nível de
Ensino:
Tipo de Escola:
Fundamental
Médio
Superior
Educaçã
o
Especial
total
CA à 4ª
série
5ª à 8ª
série
1ª à 3ª
série
-
-
-
Pública
27
36
13
1
1
78
Particular
3
2
4
0
0
9
Pública/Particul
ar
2
8
7
0
0
17
Outras
1
0
0
0
0
1
total
33
46
24
1
1
105 3 - Séries em que os professores atuam e tipo de escola em que trabalham BARTHES, R. 1993. Mitologias. Rio de Janeiro: Bertrand Brasil. BRASIL. Ministério da Educação e do Desporto. Secretaria de Educação Fundamental. Parâmetros Curriculares Nacionais: terceiro e quarto ciclos do ensino fundamental: ciências
naturais. Brasília, 1998. 138p. BRUNER, J. 1996. Toward a theory of Instruction. Cambridge: Harvard University Press. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 30 30 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 CAZELLI, S. 1992. Alfabetização Científica e os Museus Interativos de Ciências. Rio de Janeiro:
Departamento de Educação da PUC-RJ. (Dissertação, Mestrado). CHRÉTIEN, C. 1994. A Ciência em ação: mitos e limites. Campinas: Papirus. (Coleção Filosofia
no Presente). ENGUITA, M. F. 1988. Tecnologia e Sociedade: a ideologia da racionalidade técnica, a origem do
trabalho e a educação. Educação e Realidade, Porto Alegre, vol. 13, n. 1, p.39-52, jan./jun. 1988. FINNEGAN, R. 1988. Literacy and Orality: Studies in the Technology of Communication. Oxford:
Basil Blackwell. FORQUIN, J.C. 1993. Escola e Cultura. Porto Alegre: Artes Médicas. FORQUIN, J.C. 1993. Escola e Cultura. Porto Alegre: Artes Médicas. FRANÇA, M. S. J. et al. O futuro é agora. Revista Época, São Paulo, n.33, p.36-103, jan. 1999. GRUPO DE REELABORAÇÃO DO ENSINO DE FÍSICA – GREF. 1991. Física. São Paulo: USP. v. 1, 2 e
3. FRANÇA, M. S. J. et al. O futuro é agora. Revista Época, São Paulo, n.33, p.36-103, jan. 1999. FRANÇA, M. S. J. et al. O futuro é agora. Revista Época, São Paulo, n.33, p.36-103, jan. 1999. GRUPO DE REELABORAÇÃO DO ENSINO DE FÍSICA – GREF. 1991. Física. São Paulo: USP. v. 1, 2 e Ç ,
S J et a O utu o é ago a
e sta
poca, São
au o,
33, p 36
03, ja
999
GRUPO DE REELABORAÇÃO DO ENSINO DE FÍSICA – GREF. 1991. Física. São Paulo: USP. v. 1, 2 e HALLINGEN, H. 1998. Science & Technology Studies. Wollongong: University of Wollongong. LEVINE, D. 1995. Visões da Tradição Sociológica. Rio de Janeiro: Zahar. LIGHTMAN, A. 1966. Sonhos de Einstein. São Paulo: Cia das Letras. MCLUHAN, M., QUENTIN, F. 1967. The Medium is the Message. New York: Bantam. MENEZES, L. 1988. Crise, Cosmos, Vida Humana: Física para uma Educação Humanista. São
Paulo: Instituto de Física da USP. (Tese, Livre Docência). MILLER, J. D. 1987. Science Literacy, in the United States. Communicating Science to the Public. In: EVERED, D., O’ CONNOR, M. (Eds.) London: Wiley. MORAES, A. BARTHES, R. 1993. Mitologias. Rio de Janeiro: Bertrand Brasil. M. 1994. A inovação ciência, tecnologia e sociedade no ensino de ciências: uma
análise sociológica. Revista de Educação, Lisboa, p.87-99. MORIN, E. 1996. Ciência com Consciência. Rio de Janeiro: Bertrand Brasil. MUSEU DE ASTRONOMIA E CIÊNCIAS AFINS - MAST. 1992. Quatro Cantos de Origem. São
Paulo. (Projeto Museológico da Exposição Permanente). Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000
31 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 31 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 PIERSON, A. H. C., HOSOUME, Y. O cotidiano, o ensino de física e a formação da cidadania. In:
ENCONTRO NACIONAL DE PESQUISA EM ENSINO DE CIÊNCIAS, 1, 1997, Águas de
Lindóia – SP. Atas... Porto Alegre: Instituto de Física – UFRGS, 1997. p.86. ROBEENS, K., WEBSTER, F. 1989. The Technical Fix: Education, Computer and Industry. London:
MacMillan. RODRIGUES, A. M. 1997. Fundamentos em Filosofia da Tecnologia. Revista Tecnologia e
Cultura, Rio de Janeiro, 1, n.1, p.11-8, jul/dez. 1997. RUTHERFORD, F. J., AHLGREEN, A. 1995. Ciência para todos. Lisboa: Publicação Lid. RYE, J. A. 1998. Teaching Beliefs and Practices of Research Scientist Faculty MemberEngaged
in Science-Technology-Society (STS). Horgantown: West University. SCHARMANN, L. C. 1998. Preservice Secundary Science Teacher’s Orientations Toward Science-
Technology-Society (STS) Education. Manhattan: Kansas State University. SHEN, B. S. P. 1975. Science Literacy. American Scientist, n. 39, p.265-68. SOLOMON, J. 1993. Teaching Science, Technology and Society. Buckingham: Open University
Press. (Coleção Developing Science and Technology Education). ZANETIC, J. 1989. Física Também é Cultura. São Paulo: Faculdade de Educação da USP. (Tese,
Doutorado). ZIMAN, J. 1985. Enseñanza y Aprendizage sobre la Ciencia y la Sociedad. México: Fondo de
Cultura Económica. ------------. 1978. Reliable Knowledge. An Exploration of the Grounds for Belief in Science. Cambridge: Cambridge University Press. ZUCKERMAN, M. J. 1999. Computadores sofrem outras ameaças. Folha de São Paulo, São
Paulo, 06 jun. 1999. Informática, 5, p.3. 32 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 32 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Abstract: The article shows that it is possible and necessary to develop scientific literacy by
integrating formal with non-formal education. It is argued that the idea of scientific literacy is
directly linked to the Science, Technology and Society approach to science education. BARTHES, R. 1993. Mitologias. Rio de Janeiro: Bertrand Brasil. The
meanings of scientific literacy and CTS are reviewed and the importance of including narrative,
myth, science and technology in science education defended. It is also reported the results of a
survey conducted with different members of the public of Museu de Astronomia e Ciências Afins
in Rio de Janeiro (108 teachers attending a course, 18 participants a seminar plus groups of
visiting students). The survey shows, on the one hand, the possibilities seen by teachers on
choosing to teach science through a CTS perspective. On the other hand, it shows the
incoherence that emerges when certain academic topics are explored when students visit a
science museum. Maria Cristina Leal; Avenida Borges de Medeiros 3371/401 –Rio de Janeiro, RJ – cep 22.470-
001. Correio eletrônico: leal4512@rionet.com.br.
Guaracira Gouvêa de Sousa; Rua Belizário Távora 431/401 – Rio de Janeiro, RJ – cep 22.245-
070. Correspondência: Maria Cristina Leal; Avenida Borges de Medeiros 3371/401 –Rio de Janeiro, RJ – cep 22.470-
001. Correio eletrônico: leal4512@rionet.com.br. Guaracira Gouvêa de Sousa; Rua Belizário Távora 431/401 – Rio de Janeiro, RJ – cep 22.245-
070. Submetido em 15/01/1998, aceito para publicação em 23/11/1999. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 33 33
|
https://openalex.org/W3012497428
|
https://ejournal.uinib.ac.id/jurnal/index.php/mashdar/article/download/612/1004
|
unk
| null |
Interpretasi Semiotika Ferdinand De Saussure dalam Hadis Liwa dan Rayah
|
Mashdar
| 2,019
|
cc-by-sa
| 3,706
|
Abstrak Artikel ini merupakan penelitian yang mengakaji interpretarsi hadis nabi dalam bedera Rayah dan Liwa
atau bendera tauhid. Di Indonesia organisasi yang menggunakan simbol bendera tauhid adalah organisasi
Hizbut Tahriri Indonesia. Bendera tersebut ada dua warana yaitu hitam dan putih. Maising-masing dari
warna tersebut bertulisan Laa illaaha illaa Allah Muhammad Rasul Allah dan keduanya mempunyai makna
yang berbeda. Dalam konteks sejarah bendera Liwa dan Rayah digunakan oleh Nabi Muhammad dan pada
konteks budaya bendera Liwa dan Rayah digunakan untuk mendirikan negara Khilafah. Dengan legitimasi
bahwa bendera Tauhid adalah bendera kemenenagan sehingga organisasi Hizbit Tahrir Indonesia
menggunakan bendera tersebut sebagai wujud akan berdirinya sistem pemerintahan yang beridiologikan
Khilafah. Hizbut Tahrir menegaskan bahwa bendera Liwa dan Rayah bukan benderanya melainkan
bendera Islam. Analisis semiotika Ferdinand De Saussure. Dengan teori semiotikanya yang terdiri dari
empat konsep, namun dalam penelitian ini peneliti hanya menggunakan dua konsep diataranya adalah yang
pertama signifiant dan signifie dan kedua kosep langue dan parole. Sebagai bentuk obyek bendera Hizbut
Tahrir dan teks hadis tentang liwa dan rayah menjadi objek fokus dalam penelitian ini. Kata kunci : Hadis Liwa dan Rayah; Hizbut Tahrir Indonesia; Semiotika Ferdinand De Saussure M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... Interpretasi Semiotika Ferdinand De Saussure dalam Hadis Liwa
dan Rayah Interpretasi Semiotika Ferdinand De Saussure dalam Hadis Liwa
dan Rayah M. Dani Habibi
UIN Sunan Kalijaga Yogyakarta
e-mail : dhany24habibi@gmail.com Keywords : Hadith Liwa and Rayah; Hizbut Tahrir Indonesia; Semiotics Ferdinand de Saussure
Ab t
k eywords : Hadith Liwa and Rayah; Hizbut Tahrir Indonesia; Semiotics Ferdinand de Saussure Abstract Abstract
This article is a study that mengakaji interpretarsi Hadith in the flag Rayah and Liwa or the flag of
monotheism. In Indonesia, an organization that uses the banner of Tawheed is the symbol of the
organization Hizbut Tahrir Indonesia. There are two warana flag that is black and white. Maising each of
the color markedLaa illaaha illaa Allah Muhammad Messenger of God and both have a different meaning. In the context of the history of Liwa and Rayah flag used by the Prophet Muhammad and the cultural
context and Rayah Liwa flag is used to establish the Khilafah state. With the legitimacy that the flag of
Tawheed is the flag of victory, so the organization Hizbut Tahrir Indonesia using the flag as a form would
be the establishment of system of government that has the ideology of Khilafah. Hizb ut-Tahrir insists that
the flag Liwa and Rayah not the flag but the flag of Islam. Semiotic analysis of Ferdinand de Saussure,
With the theory of semiotics consisting of four concepts, but in this study the researchers only used two
concepts among which the first signifiant and signifie both langue and parole. As the shape of the object
flag Hizbut Tahrir Indonesia and hadith texts about Liwa and Rayah become the object of focus in this
study. 3 Deni Junaedi, “Bendera Hizbut Tahrir
Indonesia Daerah Istimewa Yogyakarta"kajian
Konteks Sejarah, Budaya dan Estitika Semiotis,”
Jurnal Kawistara 2, no. 3 (22 Desember 2012):
265, https://doi.org/10.22146/kawistara.3938. 2 Syamsul Arifin, “Gerakan Hizbut tahrir dan
Realitas Politik Islam Kontemporer di Indonesia:
Tafsir Sosial Atas Hizbut Tahrir,” Al-Tahrir: Jurnal 1 Siti Fatkhiyatul Jannah, “Diskursus Negara
Antara Nahdlatul Ulama dan Hisbut Tahrir
Indonesia di Jawa Timur,” Paradigma 1, no. 3 (28
Agustus
2013):
hlm
2,
http://jurnalmahasiswa.unesa.ac.id/index.php/paradi
gma/article/view/4143. Pemikiran Islam 14, no. 1 (1 Mei 2014): 4,
https://doi.org/10.21154/al-tahrir.v14i1.80. Agustus
2013):
hlm
2,
http://jurnalmahasiswa.unesa.ac.id/index.php/paradi
gma/article/view/4143. 1 Siti Fatkhiyatul Jannah, “Diskursus Negara
Antara Nahdlatul Ulama dan Hisbut Tahrir
Indonesia di Jawa Timur,” Paradigma 1, no. 3 (28
Agustus
2013):
hlm
2, PENDAHULUAN mengembangkan
paham-paham
tentang
keisalaman sepeti organisasi Hizbut Tahrir
Indonesia. Hizabut
Tahrir
Indonesia
merupakan organisasi Islam yang bergerak Indonesia
dengan
negara
yang
mempunyai penduduk Muslim terbanyak
didunia menajadi sebuah media untuk 115 116 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) pergerakan perubahan dengan penawaran
baru
berupa
idiologi
dan
sistem
pemerintahan Khilafah.2 Secara harfiah HTI
atau Hizbut Tahrir mempunyai makna “
parati pembebasan”, didalam bahasa arab
kata hizb berati partai dan at-tahrir berati
pembebasan. Artinya bahwa Hizbut Tahrir
adalah sebuah gerakan partai Islam yang
bertujuan
menyatukan
umat
Muslim
diseluruh dunia dengan ideologi dan sistem
Khilafah3. dibidang dakwah. Padamulamnya organisasi
Hizbut Tahrir didikikan oleh Taqiyuddin an-
Nabhani pada tahun 1953. Organisasi Hizbut
Tahrir mempunyai sebuah tujuan yakni
mengembalikan kejayaan Islam melalui
penegakan negara Khilafah Islamiyah. Penyatuan pemerintahan berbasis sitem
Khilafah dari berbagai penjurudunia salah
satu misi besar Hizbut Tahrir. Pada tahun
1992 Hibut tahrir masuk ke Indonesia dan
menjadi organisasi Islam konserfatif dan
fundamentalis. Karena dalam mempunayi
sebuah ideologi kembali ke Al-Qur’an dan
Sunah sebagai sumber hukum Islam yang
mutkal kebenarannya. Pemahaman tekstual
ketika memahami Al-Qur’an dan Sunah
menjadikan organisasi ini radikal dan tidak
sedikit
negara-negara
yang
menolak
organisasi
Hizbut
Tahrir
termasuk
Indonesia.1 Pada saat melakukan kegiatan
terbuka maupun tertutup, Hizbut Tahrir
selalu
mengibarkan
bendera
yang
bernama Liwa dan Rayah. Bendera
tersebut masing-masing terdapat tulisan
lafaz Laa illaaha illaa Allah Muhammad
Rasul Allah. Bendera liwa adalah bendera
yang berwarna putih dan bendera rayah
mempunyai
warnah
hitam. Kedua
bendera
tersebut
masing-masing
mempunyai makna yang berbeda. Dalam
konteks budaya ketika menganalisa liwa
dan rayah terbagi menjadi tiga unsur
diantaranya sistem budaya, aktivitas, dan
artafak. Sistem budaya yang terdiri dari
kosep, gagasan, ideologi pemikiran, nilai Pasca Orde Baru, proses demokrarsi
tidak hanya ditandai dengan munculnya
partai-partai
politik. Melainkan
juga
bermunculan kelompok-kelompok gerakan
Islam termasuk HTI. Sehingga pada pasca
Orde
Baru,
kelompok
Islam
HTI
mengidentifikasikan
sebagai
kelompok M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... | 117 | 117 dan norma-norma atau jenisnya yang
bersifat abstrak. Sedangkan aktivitas
yaitu suatu tindakan dalam prilaku
budaya dan artefak adalah berupa benda
ciptaan manusia. Idelogi yang tersusun
dalam
sebuah
sistem
pemerintahan
Khilafah melalui simbol bendera HTI
disusun
untuk
menyerang
atau
mendukung suatu misi atau maksud
tertentu. 4 David Kaplan dan Albart A. Manners “ Teori
Budaya”, trj, Landang Simatupang. (Yogyakarta:
Pustaka Pelajar .2012).hlm 154 PENDAHULUAN Oleh sebab itu tidak heran
bahwa sistem pemerintahan yang di
bangun Khilafah di tolak diberbagai
negara
termasuk
Indonesia
karena
ideologi yang diperjuangkan berbeda
atau
berbenturan
dengan
ideologi
Pancasila.4
Dengan
menggunakan
bendera liwa dan rayah sebagai tanda
dimana eksistensi keberadaan kelompok
HTI bergerak dan melakukan kegiatan
dakwah-dakwahnya. rayah adalah bendera yang digunakan
oleh rasulullah. Dengan memperhatikan
kosep signifier (penanda) dan signifind
(Petanda) juga dengan memperhatikan
langue dan parole. 5Syafieh Syafieh dan Nurbaiti Nurbaiti,
“Potret Karakteristik Kepemimpinan Perempuan" (Analisis Semiotika Surat Al-Naml: 23-44),” Jurnal
At-Tibyan: Jurnal Ilmu Alquran Dan Tafsir 3, no. 1
(9
Agustus
2018):
54, (
g
)
https://doi.org/10.32505/tibyan.v3i1.477. 7
Ferdinand
de
Saussure
“Cours
de
Linguistique General” trj. Rahayu S. Hidayat.
(Yogyakarta. Gajah Mada Press.1996). hlm.374. 6 Kaelan “ Filsafat Bahasa Semiotika dan
Herrmeneutika” ( Yogyakarta : Paradigma. 2009).
hlm.181 PERSPEKTIF METODOLOGI Istilah
semiotika
modern
diperkenalkan oleh dua tokoh yaitu
Ferdinand de Saussure (1857-1913) dan
Charles Sanders Peirce (1839-1914). Dua
tokoh inilah yang sangat berpegaruh
dalam linguistik dan semiotik. Kedua
tokoh
tersebut
masing-masing
mempunyai konsep seperti Saussure
dengan konsep tanda dan penanda dan
Pierce mempunyai konsep sign, object
dan
interpretant5. Namun
dalam
penelitian ini peneliti akan berfokus pada
aplikasi teori Ferdinand De Saussure
sebagai analisis obyek dalam hal ini
adalah bendera Hizbut Tahrir Indonesia
HTI. Dengan
menggunakan
pendekatan semiotika dan meminjam
teori Ferdinand De Saussure, peneliti
mencoba untuk menganalisa problem
tanda berupa bendera liwa dan rayah
dalam konteks organisasi HTI. HTI
dengan
Benderanya
tersebut
sudah
menjadi legitimasi kebenaran mutlak
oleh mereka bahwa bendera liwa dan Ferdinand De Saussure dilahirkan di
kota Jenewa pada tanggal 26 November
pada tahun 1857. Ia dilahirkan dari keluarga
yang sangat terkenal di kotanya. Dengan
keberhasilanya dalam bidang ilmu bahasa
atau linguistik beliau mendapat sebutan 118 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) bapak linguistik. Saussure lahir sezaman
dengan Email Durkheim. Sejak kecil ia
sudah mempunyai banyak karya berupa
Essai dibidang bahasa. Dan pada tahun 1874
ia mulai memulai belajar bahsa Sansekerta. Kiprahnya dibidang linguistik semakin
terlihat ketika pada tahun 1880 ia berhasil
mempertahankan tesisnya tentang kasus
genetatif mutlak dalam bidang bahasa
Sansekerta6. berupa (tanda, suara, bentuk, gambar
maupun gerak). Kedua aspek penanda
(singnifer). Dan yang ketiga aspek petanda
(singnified)8 Sehingga hubungan antara
tanda dan penanda bersifat arbiter (bebas). Namun didalam sebuah tanda tentu memilki
nilai-nilai
tertentu
(value)
sedangkan
menurut Saussure tanda-tanda tersebut
direlasikan dengan sistem tanda-tanda yang
lain (sintagma) yang akan bisa menjadikan
perbedaan (difference)9. Namun didalam sebuah tanda tentu memilki
nilai-nilai
tertentu
(value)
sedangkan
menurut Saussure tanda-tanda tersebut
direlasikan dengan sistem tanda-tanda yang
lain (sintagma) yang akan bisa menjadikan
perbedaan (difference)9. Saussure memang terkenal dengan
sistem tanda dan penanda. Namun dalam
sejarah ia tidak pernah mencetak sebuah
buku melainkan setiap ada kuliah atau kuliah
umum catatan-catatan dari uraian diskusinya
dicatat oleh murid-muridnya lalu dijadikan
sebuah outline. Salah satu karya yang telah
terbit adalah sebuah buku yang berjudul
Course in General linguistics. Kemudian
karya tersebut menjadi sebuah karya yang
sangat berpengaruh dibidang kebahasaan
atau Linguistik. Dan karya itulah yang
dinamakan dengan istilah “strukturalisme”.7 8 Wildan Taufiq, “Ideologi di Balik Simbol-
Simbol Surga dan Kenikmatan dalam Ayat-Ayat Al-
Qur'an,”
Desember
2008,
156,
http://publikasiilmiah.ums.ac.id/handle/11617/181.
9Ferdinand
de
Saussure
“Cours
de
Linguistique General” trj. Rahayu S. Hidayat.
(Yogyakarta. Gajah Mada Press.1996). hlm.7. 8 Wildan Taufiq, “Ideologi di Balik Simbol-
Simbol Surga dan Kenikmatan dalam Ayat-Ayat Al-
Qur'an,”
Desember
2008,
156,
http://publikasiilmiah.ums.ac.id/handle/11617/181. 9Ferdinand
de
Saussure
“Cours
de
Linguistique General” trj. Rahayu S. Hidayat.
(Yogyakarta. Gajah Mada Press.1996). hlm.7. Sejarah Bendera Liwa dan Rayah Dalam sejarah bendera liwa dan
rayah terbentuk di kota madinah pada tahun
622,
dan
ketika
Nabi
Muhammad
memerintahkan penggunaan liwa (bendera)
dan rayah yang berarti panji keislaman. Liwa yang berwana putih dan rayah
berwarna hitam. Hal tersebut terdapat dalam
hadis nabi yang berbunyi : َحَدَّثَنَا مُحَمَّدُ بْنُ رَافِعٍ حَدَّثَنَا يَحْيَى بْنُ إِسْحَق
وَ هُوَ السَّالِحَانِيُّ حَدَّثَنَا يَزِ يدُ بْنُ حَيَّانَ قَال
ْسَمِعْتُ أَبَا مِجْلَزٍ َلَ حِ قَ بْنَ حُمَيْدٍ يُحَد ِثُ عَن
ابْنِ عَبَّاسٍ قَال
كَانَتْ رَايَةُ رَسُولِ َّللاَّ ِ صَلَّى Dalam kajian semiologi misalnya,
Saussure menegaskan bahwa sistem tanda
memiliki tiga aspek, yaitu itu sendiri yaitu
Pertama (sing) atau aspek material baik M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... | 119 | 119 M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... ََّللاَّ ُ عَلَيْهِ وَ سَلَّمَ سَوْ دَاءَ وَ لِوَ اؤُهُ أَبْيَض
قَالَ أَبُو
ِعِيسَى هَذَا حَدِيثٌ حَسَنٌ غَرِ يبٌ مِنْ هَذَا الْوَ جْه
ٍمِنْ حَدِيثِ ابْنِ عَبَّاس ََّللاَّ ُ عَلَيْهِ وَ سَلَّمَ سَوْ دَاءَ وَ لِوَ اؤُهُ أَبْيَض
قَالَ أَبُو
ِعِيسَى هَذَا حَدِيثٌ حَسَنٌ غَرِ يبٌ مِنْ هَذَا الْوَ جْه
ٍمِنْ حَدِيثِ ابْنِ عَبَّاس bertulisan Laa illaaha illaa Allah Muhammad
Rasul Allah. Dibawah ini adalah gambar
bendera liwa dan rayah yang digunakan oleh
ormas Hizbut Tahrir Indonesia. Garmbar 1: Liwa berwarna dasar putih dengan
kalimat sahadat berwarna hitam
(Foto: Dani Habibi, 2018) Telah
menceritakan
kepada
kami
Muhammad
bin
Rafi'
berkata,
telah
menceritakan kepada kami Yahya bin Ishaq,
yaitu
As
Salihani-
berkata,
telah
menceritakan kepada kami Yazid bin
Hayyan ia berkata; Aku mendengar Abu
Mijlaz Lahiq bin Humaid menceritakan dari
Ibnu Abbas ia berkata, "Bendera Rasulullah
shallallahu 'alaihi wasallam berwarna
hitam
dan
umbul-umbulnya
berwarna
putih." Abu Isa berkata, "Hadits ini
derajatnya hasan gharib melalui jalur ini,
dari Ibnu Abbas. Telah
menceritakan
kepada
kami
Muhammad
bin
Rafi'
berkata,
telah
menceritakan kepada kami Yahya bin Ishaq,
yaitu
As
Salihani-
berkata,
telah
menceritakan kepada kami Yazid bin
Hayyan ia berkata; Aku mendengar Abu
Mijlaz Lahiq bin Humaid menceritakan dari
Ibnu Abbas ia berkata, "Bendera Rasulullah
shallallahu 'alaihi wasallam berwarna
hitam
dan
umbul-umbulnya
berwarna
putih." Abu Isa berkata, "Hadits ini
derajatnya hasan gharib melalui jalur ini,
dari Ibnu Abbas. Liwa dan rayah memang dulu
digunakan oleh nabi Muhammad saw
sebagai tanda pemerintahan Islam waktu itu. Namun, didalam konteks saat ini tanda yang
disebut liwa dan rayah digunakan oleh
ormas HTI sebagai bendera ideologis10
Khilafah Islamiyah. Menjadi masalah jika
dalam hadis liwa dan rayah tidak tertulis
kalimat tauhid. 10 Masnun Masnun dan Zusiana Elly Triantini,
“Spiritualitas Islam, Khilafah Islamiyah dan Gerakan Politik Hukum Ingkar Nkri (Studi terhadap Gerakan
Politik Hizbut Tahrir di Indonesia),” Istinbath: Jurnal
Hukum Islam IAIN Mataram 15, no. 2 (2016): 196. Problem Interpretasi Berdera Hizbut
Tahrir Indonesia Bendera HTI diklaim bendera yang
dikabarkan oleh rasulullah dengan kata lain
siapa yang mengibarkan bendera rasulullah
maka ia termasuk kedalam golongannya12. Simbol berupa bendera identitas organisasi
Hizbut Tahrir Indonesia dinilai tidak layak Sejarah Bendera Liwa dan Rayah Berbeda dengan bendera
liwa dan rayah yang digunakan oleh HTI. Bendera tersebut berwarna hitam dan putih
yang masing-masing bertulisan kalimat Melalui bendera tersebutlah, Hizbut
Tahir menyebarkan panji-panji idiologis
politik
kepada
masyarakat
Muslim. Sehingga mereka mempunyai anggapan
bahwa bendera yang rasulullah adalah 120 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) bendera yang sama digunakan oleh Hizbut
Tahrir. Dengan
mengibarkan
bendera
tersebutlah panji-panji keislaman akan
menjadi lebih kuat dan lebih sesuai dengan
yang diajarkan oleh nabi Muhammad saw. Namun pada umumnya bendera liwa dan
rayah yang digunkana oleh nabi untuk
peperangan. Liwa yang berada dekat pada
pemimpin tertinggi dan ruyah digunakan
untuk komandan perang11. Sebagai konteks
budaya, sebuah bendera memang menjadi
sebuah
identitas
yang
menunjukan
eksistensinya didalam masyarakat. Baik
yang berfungsi sebagai tanda didaerah,
identitas
kelompok,
dan
simbol
pertempuran. Namun dalam konteks ini,
peneliti berfokus pada sebuah tanda berupa
simbol bendera rasulullah sebagai identitas
kenegaraan. dikibarkan di Negara Kesatuan Replublik
Indonesia. Sebab
sebagaian
besar
masyarakat memandang bahwa bendera HTI
adalah bedera yang menjadikan idiologi
bangsa seperti Indonesia menjadi rapuh. Namun, bagi masyarakat penganut Hizbut
Tahrir menilai bendera liwa dan rayah
adalah bendera rasulullah. Sebenarnya bendera liwa dan rayah
menjadi
kontofersi
ketika
didalamnya
terdapat idiologi tertentu yang bertujuan
merusak idiologi yang sudah ada di tiap-tiap
negara seperti Indonesia. Kebangkitan
organisasi Hizbut Tahrir di Indonesai
memang sangat di waspadai karena dapat
merusak sistem dan idiologi bangsa.13
Perbentuaran dua idiologi yang mempunyai
visi dan misi berbeda menimbulkan konflik. Sehingga setiap orang jika membawa
bendera liwa dan rayah di Indonesia maka
dinilai sebagai pengikut Hizbut Tahrir
Indonesia. 13 Rosi Selly, “Globalisasi dan Kebangkitan
Khilafah Islamiyah Dalam Perspektif Pemikiran
Hizbut
Tahrir,”
29
Agustus
2008,
28,
http://repository.uinjkt.ac.id/dspace/handle/1234567
89/7538. 11 Deni Junaedi, “Bendera Hizbut Tahrir
Indonesia
Daerah
Istimewa
Yogyakarta"kajian
Konteks Sejarah, Budaya dan Estitika Semiotis,”
Jurnal Kawistara 2, no. 3 (22 Desember 2012): 267,
https://doi.org/10.22146/kawistara.3938 12 Arifin, “Gerakan Keagamaan Baru dalam
Indonesia Kontemporer,” Komunika Jurnal dakwah
dan Komukasi hlm 6. 15
Ferdinand
de
Saussure
“Pengantar
Linguistik
Umum”
trj.
Rahayu
S.
Hidayat.
(Yogyakarta. Gajah Mada Press.1996). hlm.25. 14Ferdinand
de
Saussure
“Pengantar
Linguistik
Umum”
trj.
Rahayu
S.
Hidayat.
(Yogyakarta. Gajah Mada Press.1996). hlm 6 Analisis Interpretasi Berdera Hizbut
Tahrir Indonesia Dalam
penelitian
ini,
peneliti
menggunakan pendekatan semiotika dalam
meninterpetasikan ulang simbol bendera M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... | 12 | 121 tauhid dalam organisasi Hizbut Tahrir
Indonesia. Dengan
menggunakan
pendekatan semiotika yang digagas oleh
Ferdinand
de
Saussure
peneliti akan
mencoba untuk menafsirkan kembali simbol
bendera HTI yang bersumber sari sebuah
hadis Nabi tentang bendera. masyarakat tentunya banyak ditemukan
parole-parole
yang
mempunyai
relasi
kepada realitas. Sehingga gabungan dari
parole-parole dalam kaidah bahasa oleh
Saussure disebut dengan langue. Langue
adalah
keseluruhan
kebiasaan yang didapatkan dari masyrakat. Terjadinya komunikasi antara satu parole
dengan
parole
yang
lain
sehingga
membentuk suatu pemahaman yang klektif
di masyarakat. Kejadian seperti ini sering
dialami
oleh
masyarakat,
lebih-lebih
didalam
masyarakat
majemuk
yang
didalamnya terdapat banyak aliran dan suku. Sehingga mengerucut pada penelitian ini
yang berfokus pada interpretasi objek Liwa
dan Rayah didalam hadis nabi diatas dengan
menggunakan pendekatan semiotika dan
teori Fardinand de Saussure. ُحَدَّثَنَا مُحَمَّدُ بْنُ رَافِعٍ حَدَّثَنَا يَحْيَى بْن
َإِسْحَقَ وَ هُوَ السَّالِحَانِيُّ حَدَّثَنَا يَزِ يدُ بْنُ حَيَّان
َقَال سَمِعْتُ أَبَا مِجْل ُزٍ َلَ حِ قَ بْنَ حُمَيْدٍ ي ُحَد ِث
عَنْ ابْنِ عَبَّاسٍ قَال ِ َّكَانَتْ رَايَةُ رَسُولِ َّللا
َصَلَّى َّللاَّ ُ عَلَيْهِ وَ سَلَّمَ سَوْ دَاءَ وَ لِوَ اؤُهُ أَبْيَض
ْقَالَ أَبُو عِيسَى هَذَا حَدِيثٌ حَسَنٌ غَرِ يبٌ مِن
ٍهَذَا الْوَ جْهِ مِنْ حَدِيثِ ابْنِ عَبَّاس Saussure
mempunyai
kerangka
teoritis yang ia bangun yaitu keraka tersebut
seperti langue, parole dan langage. Didalam
buku yang berjudul Cours de Linguistique
Gernerale karya Fardinand de Saussure
yang
sudah
diterjemahkan
menjadi
Pengantar Linguistik Umum dijelaskan
bahwa yang dimaksud dengan parole adalah
keseluruhan apa yang diajarkan oleh orang,
termasuk kontruksi-kontruksi individu yang
muncul dari ucapan penutur14. Jelasnya yang
dimaksud dengan istilah parole ialah
manifestasi individu dari bahasa. Didalam Didalam buku yang Pengantar
Linguistik Umum, Saussure mendefinisiskan
beberapa istilah dalam teorinya seperti,
Parole, Langue, Sinkronik dan Diakronik. Parole adalah tuturan, tiap-tiap individu
yang menjadi sebuah satu kesatuan sistem
yang mentuk norma-norma kolektif didalam
masyarakat15. Jika merujuk pada teks hadis
diatas parole-parol yang muncul didalam
masyarakat dahulu menjadikan lagitiammsi
individu berupa liwa yang sering diucapkan 122 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (
oleh masyarkat pada zaman nabi sebagai
identitas bendera. yan
kea 122 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) yang ada dan aturan sinkronis mengatur
keadaan tiap-tiap objek. Sedangkan diakroni
kebalikan dari sinkronis. Diakroni adalah
faktor-faktor
dinamis
yang
bisa
menghasilakan
dampak,
suatu
yang
dikerjakan. 16 Kaelan “ Filsafat Bahasa Semiotika dan
Herrmeneutika” ( Yogyakarta : Paradigma.2009).hlm 191. Lihat, Ferdinand de Saussure “Pengantar
Linguistik
Umum”
trj.
Rahayu
S.
Hidayat.(Yogyakarta.Gajah Mada Press.1996).hlm 191. Lihat, Ferdinand de Saussure “Pengantar
Linguistik
Umum”
trj.
Rahayu
S.
Hidayat.(Yogyakarta.Gajah Mada Press.1996).hlm 17 Syaiful Arif, “Kontradiksi Pandangan HTI
Atas Pancasila,” Jurnal Keamanan Nasional 2, no. 1
(1 Mei 2016): 24, https://doaj.org. Analisis Interpretasi Berdera Hizbut
Tahrir Indonesia Akan
tetapi
ciri
yang
mengharuskan kurang cukup untuk bisa
menerapkan istilah aturan atau fakta yang
evolutif. Lalu parole-parole tersebut menjadi
satu kesatuan dalam sistem yang menjadi
legitimasi kolektif Langue seperti liwa
sebagai bendera pemerintahan. Langue
bersifat konveksi yang dapat diterima oleh
masyarakat yang siap untuk dipakai dan dari
pendahulu. Artinya jika Liwa dan Rayah
menajadi langue atau legitimasi kolektif
yang
sudah
ada
sejak
zaman
nabi. Kesepakatan konveksi berupa liwa sebagai
bendera dan Rayah sebagai ajaran memang
sudah ada sejak zaman nabi Muhammad
saw. Dalam kemunculanyapun tidak begitu
saja pasti mempunyai historitas sebab
musabab kemunculannya. Dalam
penerapanya
terdapat
beberapa
komponen
penting
dalam
membangun interprretasi bendera HTI
berupa liwa dan rayah dengan pendekatan
semiotika Fardinand de Saussure. Terdapat
teks yang tidak bisa berubah maknanya dan
teksnya dari dulu hingga sekarang yang
disebut parole. Liwa berati bendera “ parole”
yang didalam teks hadis tersebut mempunyai
cerita historis sebagai identitas didalam
pemerintahan nabi Muhammad saw. Lalu
liwa yang disebut oleh nabi didalam teks
hadis diatas menjadi parole-parore lain. Sehingga dari parole yang banyak diucapkan
oleh para sahabat menjadi satu kesatuan utuh
dalam interpertasi bendera liwa adalah
bendera pemerintahan. Saussure mempunyai pandangan
bahwa untuk bisa melihat lebih jauh,
bagaimana sebuah simbol terbentuk maka ia
mempunyai sebuah istilah Sinkronis dan
diakronis. Sinkronis adalah kata atau makna
yang tidak bisa dirubah dan diakronis adalah
makna yang dapat berubah dikarnakan
faktor historis.16 Sinkronis bersifat umum
yang tidak mengharuskan. Artinya didalam
langue tidak ada satu kesatuan utuh yang
dapat menjamin dan memlihara keteraturan
dalam tiap-tiap butir dalam parole. Aturan
sinkronis hanya mengungkapkan kelompok Dalam
perkembangnya
parole
menjadi satu bangunan interpretasi yang
menjadi legitimasi kebenaran mutlak oleh M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... | | 123 organisasi Hizbut Tahrir Indonesia yaitu
liwa adalah bendera Nabi Muhammad saw. bendera idiologi politik. Dengan kata lain,
simbol
bendera
tersebut
sudah
bertrensformasi menjadi bendera yang
mempunyai makna idiologis. Sassure mempunyai istilah diakrini
sebagai makna yang selalu berkembang
mengikuti zaman dan mempunyai faktir
historis. Salah satu sejarah kemunculan
bendera tersebut karena sebagai penanda
kekuasaan
atau
pemerintahan
nabi
Muhammad
saw. Namun
dalam
perkembanganya, bendera liwa dan rayah
digunakan oleh HTI sebagai identitas
idiologis. Transformasi
makna
dan
perubahan simbol liwa dan rayah pada
zaman rasul dan yang digunakan oleh HTI
disebabkan
oleh
beberapa
faktor. Diantaranya sebagai berikut : 18 Masnun dan Triantini, “Spiritualitas Islam,
Khilafah Islamiyah dan Gerakan Politik Hukum Ingkar Nkri (Studi terhadap Gerakan Politik Hizbut
Tahrir di Indonesia),” 199. SIMPULAN DAN REKOMENDASI Bendera liwa dan rayah memang
bendera yang digunakan oleh rasulullah
ketika memimpin pemerintahan kala itu. Namun, bendera yang digunakan merupakan
bendera yang tidak bertulisan kalimat tauhid
dan tidak mempunyai idiologi Khilafah. Sehingga ketika organisasi Hizbut Tahrir
Indonesia menggunakan bendera liwa dan
rayah yang bertulisakan kata tahuid tidak
sedikit masyarakat Indonesia mengklaim
bahwa itu merupakan bendera yang tidak
sesuai dengan idiologi bangsa Indonesia
yaitu pancasila. 1. Mengembalikan politik Islam yang saat
ini telah dilupakan dan diganti oleh
sistem kapitalisme dan liberalisme17. Merujuk pada pemikiran Ferddinad
de Saussure kdalam interpretasi simbol
bendera HTI, menyimpulakan bahwa setiap
parole-parole menjadi satu kesatuan sistem
utuh dan kolektif. Sehingga menjadi langue
yang membangun sistem, norma-norma
tertentu sesuai dengan yang diharapakan
oleh masyarakat. 2. Menegakakan syari’at Islam. 3. Menumbuhkan semangat juang kembali
peradaban Islam pada masa nabi. 4. Menjadikan sistem pemerintahan yang
dipimpin oleh satu Khilafah. 18 Dari beberapa faktor diatas sudah
mulai tergambarkan bahwa bendera yang
menajadi identitas oleh organisasi Hizbut
Tahrir
Indonesia
merupakan
identitas Bendera Hizbut Tahrir Indonesia
mengandung idiologi yang bertentangan 124 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) Indonesaia meniali bendera tersebut adalah
bendera kemunafikan idiologi. dengan idiologi Pancasila. Dikarnakan
ketika masyarakat Hizbut Tahrir Indonesia
mengibarkan panji-panji keislaman dan
bendera liwa dan rayah maka secara tidak
langsung visi dan misi menjadi tujuan HTI
diorasikan. Tidak heran bahwa masyarakat Sejarah,
Konteks
Budaya,
dan
Estetika
Semiotis).”
Jurnal
Kawistara 2, no. 3 (22 Desember
2012). https://doi.org/10.22146/kawistara.3
938 Sejarah,
Konteks
Budaya,
dan
Estetika
Semiotis).”
Jurnal
Kawistara 2, no. 3 (22 Desember
2012). https://doi.org/10.22146/kawistara.3
938 DAFTAR PUSTAKA Kaelan “Filsafat Bahasa Semiotika dan
Herrmeneutika”,
Yogyakarta
:
Paradigma.2009. Saussure,
Ferdinand. De. “Cours
de
Linguistique General” trj. Rahayu
S Hidayat.Yogyakarta: Gajah Mada
Press,1996. Masnun,
Masnun,
dan
Zusiana
Elly
Triantini. “Spiritualitas
Islam,
Khilafah Islamiyah dan Gerakan
Politik Hukum Ingkar NKRI" (Studi
terhadap Gerakan Politik Hizbut
Tahrir di Indonesia).” Istinbath:
Jurnal Hukum Islam IAIN Mataram
15, no. 2 (2016): 193–215. David Kaplan dan Albart A. Manners “ Teori
Budaya”, trj, Landang Simatupang. Yogyakarta: Pustaka Pelajar.2012. Arif, Syaiful. “Kontradiksi Pandangan HTI
Atas Pancasila.” Jurnal Keamanan
Nasional 2, no. 1 (1 Mei 2016). https://doaj.org. Selly, Rosi. “Globalisasi dan Kebangkitan
Khilafah
Islamiyah
Dalam
Perspektif
Pemikiran
Hizbut
Tahrir,”
29
Agustus
2008. http://repository.uinjkt.ac.id/dspace/
handle/123456789/7538. Arifin, Syamsul. “Gerakan Keagamaan
Baru dalam Indonesia Kontemporer:
Tafsir Sosial Atas Hizbut Tahrir.”
Al-Tahrir: Jurnal Pemikiran Islam
14, no. 1 (1 Mei 2014): 117–38. https://doi.org/10.21154/al-
tahrir.v14i1.80. Syafieh, Syafieh, dan Nurbaiti Nurbaiti. “Potret Karakteristik Kepemimpinan
Perempuan" (Analisis Semiotika
Surat Al-Naml: 23-44).” Jurnal At-
Tibyan: Jurnal Ilmu Alquran Dan
Tafsir 3, no. 1 (9 Agustus 2018): 52–
68. https://doi.org/10.32505/tibyan.v3i1
.477. Fatkhiyatul Jannah, Siti. “Diskursus Negara
Antara Nahdlatul Ulama dan Hizbut
Tahrir Indonesia di Jawa Timur.”
Paradigma 1, no. 3 (28 Agustus
2013). Taufiq, Wildan. “Ideologi di Balik Simbol-
Simbol Surga dan Kenikmatannya
dalam
Ayat-Ayat
al-Quran,”
Desember
2008. http://publikasiilmiah.ums.ac.id/han
dle/11617/181. http://jurnalmahasiswa.unesa.ac.id/index.ph
p/paradigma/article/view/4143. Junaedi, Deni. “Bendera di Hizbut Tahrir
Indonesia
Daerah
Istimewa
Yogyakarta
(Kajian
Konteks
|
https://openalex.org/W4318752881
|
https://zenodo.org/record/7941401/files/RLocator_Appendix.pdf
|
English
| null |
RLocator: Reinforcement Learning for Bug Localization
|
Zenodo (CERN European Organization for Nuclear Research)
| 2,023
|
cc-by
| 243
|
[2] J. Han, C. Huang, S. Sun, Z. Liu, and J. Liu, “bjXnet: an improved bug
localization model based on code property graph and attention mechanism,”
Automated Software Engineering, vol. 30, no. 1, Mar. 2023. [1] S. Cheng, X. Yan, and A. A. Khan, “A similarity integration method based
information retrieval and word embedding in bug localization,” in 2020 IEEE
20th International Conference on Software Quality, Reliability and Security
(QRS).
IEEE, Dec. 2020. A.1
Performance comparison of RLocator with
prior approaches 1 Table 1: Performance of RLocator in comparison to prior approaches Table 1: Performance of RLocator in comparison to prior approaches
Project
Model
Top 1
Top 5
Top 10
MAP
MRR
AspectJ
RLocator
0.40
0.63
0.70
0.46
0.50
Cheng et al. [1]
0.46
0.76
0.84
0.38
0.60
bjXnet [2]
-
-
-
-
-
Birt
RLocator
0.25
0.41
0.48
0.38
0.41
Cheng et al. -
-
-
-
-
bjXnet
-
-
-
-
-
Eclipse Platform UI
RLocator
0.37
0.63
0.73
0.42
0.50
Cheng et al. 0.47
0.74
0.83
0.48
0.59
bjXnet
0.60
0.83
0.90
0.70
0.61
JDT
RLocator
0.33
0.61
0.75
0.44
0.45
Cheng et al. 0.48
0.67
0.81
0.49
0.58
bjXnet
0.43
0.80
0.88
0.60
0.52
SWT
RLocator
0.30
0.51
0.58
0.42
0.44
Cheng et al. 0.60
0.82
0.89
0.62
0.70
bjXnet
0.52
0.79
0.88
0.65
Tomcat
RLocator
0.39
0.55
0.68
0.47
0.51
Cheng et al. -
-
-
-
-
bjXnet
-
-
-
-
- References 2
|
W4311440411.txt
|
https://zenodo.org/records/7328543/files/SAGW_Bulletin_3_22_Denk.pdf
|
de
|
Geldgeschichten in transepochaler Perspektive
|
Zenodo (CERN European Organization for Nuclear Research)
| 2,022
|
cc-by
| 1,731
|
Die Münze hat viele Funktionen – richtig eingesetzt wird
sie zur Glückbringerin. Das Fotomodell Margot
Nünke und der Schauspieler Ric Badaglia werfen Münzen
in den Trevi-Brunnen in Rom (Aufnahme von 1956).
Geldgeschichten
in transepochaler
Perspektive
Money in fact is the most
successful story ever invented
and told by humans, because
it is the only story everybody
believes.
Olivia Denk
Münzen haben viel zu erzählen. Den Lebenslauf einer antiken Münze genau zu verfolgen, von der Herstellung über
ihre mannigfache Verwendung bis zu ihrem Nachleben im
digitalen Sammlungskatalog, erlaubt uns, die Entwicklung
von Wirtschaftsweisen und politischen Interaktionen über
Jahrhunderte hinweg besser zu verstehen.
Yuval Noah Harari,
21 Lessons for the 21st Century, 2018
Menschen glauben schon seit langer Zeit an die «Geschichte des Geldes». Die ersten Münzen der Menschheitsgeschichte entstanden bereits im 7. Jahrhundert vor Christus in Lydien in Kleinasien – ein Prozess, der als Revolution
bezeichnet werden kann.
48
Um ein Optimum an Informationen über antike Münzen, ihren Herstellungsprozess und vor allem über ihre Verwendung zu erzielen, werden in der heutigen Numismatik
traditionelle Ansätze und moderne Methoden miteinander
verwoben. Stefan Krmnicek, Juniorprofessor für Numismatik
in Tübingen, entwickelte für Fundmünzen das Konzept der
Objektbiografie. Um die hypothetische Lebensspanne einer
Münze zu skizzieren, beginnt man in diesem Modell bei der
Herstellungsphase (A). Nach der erfolgten Prägung ist anzunehmen, dass die Münze in den Geldumlauf gerät und
somit ihre erste monetäre Funktion als Zahlungsmittel (B1)
erfüllt. Es folgt eine aktive Weiterbenutzung (B2), die möglicherweise eine monetäre Funktionserweiterung beinhaltet,
indem die Münze einen Gegenstempel bekommt und damit
als Zahlungsmittel in einem anderen Währungsraum akzeptiert wird. Die Münze läuft so durch verschiedene Hände, bis
ihr aktiver Gebrauch nach einiger Zeit endet (C), etwa indem ein Besitzer sie einbehält. Die Beweggründe für eine
solche «Thesaurierung» können vielseitig sein. Gerade in
kriegerischen Zeiten ist das Bedürfnis stets gross, gewisse
Wertgegenstände sicherzustellen; so können auch Münzen
in einen passiven Gebrauch geraten und beispielsweise als
Hort vergesellschaftet werden. Nach einiger Zeit kann die
Münze erneut in die aktive Benutzung übertreten (B3) und
wieder den Besitzer wechseln. Durch neue Eigentümer oder
die Entwertung der Münze kann das Stück einen alternativen
Gebrauch (D) erfahren: Denkbar ist eine Lochung der Münze,
um sie als Schmuckstück zu verwenden oder eine Verwendung als Talisman gegen Dämonen oder als Amulett zum
Schutz des Hauses. Andere Nutzungskontexte wie zur Kommunikation mit den Göttern sind ebenfalls vorstellbar. Bekannte Beispiele für einen alternativen Münzgebrauch sind
für die griechische Welt der Tempelschatz, der zwar unter
göttlicher Schirmherrschaft aufbewahrt wird, aber auch für
militärische Zwecke aufgewendet werden kann, sowie der
Charonspfennig, der Verstorbenen ins Grab beigegeben
wird, um den Fährmann Charon bei der Überquerung des
Flusses Styx in das Totenreich des Hades zu bezahlen.
Über Jahrhunderte hinweg war das Geld in seiner
Münzform direkt an Edelmetall gebunden. 1971 läutete USPräsident Nixon eine neue Ära in der Geschichte des Geldes
ein, indem er Geld von Edelmetall enkoppelte. Heute sprechen wir von «Fiatgeld» («Es werde Geld!»). Der Wert des
Geldes wird dabei durch die Macht einer Regierung gesichert, aber erst mit der Akzeptanz und dem Vertrauen der
Nutzer wird Geld ein Zahlungsmittel. Tag ein Tag aus zahlen
und rechnen wir mit Geld. Wir kaufen im Geschäft ein, bezahlen Rechnungen, überweisen die Miete oder kalkulieren
das Monatsbudget. Die modernen Formen des Geldes sind
dabei heute sehr divers und reichen von Münz- und Papiergeld bis zu digitalem Geld in Form von Kreditkarten oder
Kryptoassets wie Bitcoin. Kryptoassets wiederum, die ursprünglich als alternatives Währungssystem gedacht waren,
entwickelten sich in eine andere Richtung. Derzeit existieren
rund 6 000 bis 10 000 verschiedene Assets dieses «neuen
Gelds». Dieser Wandel von einem physischen Geldstück zu
elektronischen Zahlungsmitteln ist eine geldgeschichtliche
Innovation innerhalb unserer modernen Gesellschaft.
Die Vielfältigkeit der Münze
Mehr als andere Geldformen werden Münzen auch in
nicht monetärer Form verwendet. Beispielsweise wird nach
griechischer Tradition im Neujahrskuchen (Vasilopita) eine
Münze versteckt und soll dem Finder im neuen Jahr Glück
bringen. Im Zürcher Osterbrauchtum «Zwänzgerle» muss ein
Erwachsener ein 20-Rappen-Stück so auf das von einem Kind
gehaltene Ei werfen, dass die Münze darin stecken bleibt.
Ebenso übernehmen Münzen die Rolle als Sammlungsobjekt
in einer privaten Kollektion, fungieren als Glücksbringer im
Trevi-Brunnen in Rom, dienen als Schmuckstück für den persönlichen Gebrauch oder werden als modisches Accessoire
inszeniert. Das Juwelierunternehmen «Tiffany & Co.» lancierte
im April 2022 mit dem «TiffCoin» (eine 18-karätige Goldmünze) eine limitierte Neuauflage des berühmten «Tiffany-Geldes» aus den 1970er-Jahren – Gold- und Silbermünzen, die
gegen Tiffany-Schmuck eingetauscht werden konnten und
sich grosser Beliebtheit als Hochzeitsgeschenk erfreuten.
Irgendwann kommt die antike Nutzung der Münze
dann an einen Endpunkt (E). Die Münze kann verloren gehen,
wird als Opfergabe in einem Votivdepot niedergelegt oder in
Krisenzeiten mit weiteren Münzen als Münzschatz gehortet.
Die bewegten Biografien
antiker Münzen
Die Numismatik ist eine eigenständige Disziplin, die
durch das Studium von Münzen, die Vergangenheit dieser
metallischen Artefakte erschliesst und untersucht. Die Analyse von kleinen Metallstücken mit sogenannten «Typen» auf
Vorder- und Rückseite, Symbolen, Zeichen und Inschriften ermöglicht den Numismatikern, die Mechanismen des
Wirtschaftswesens sowie religiöse und politische Interaktionen zu entschlüsseln. Die Disziplin der Numismatik hat
eine lange Geschichte, die mit dem Interesse am Sammeln
von Münzen begann und ab Ende des 18. Jahrhunderts ein
erstes «goldenes Zeitalter» erlebte. Aus Schweizer Sicht ist
Friedrich Imhoof-Blumer hervorzuheben, der als Gründerfigur des Münzkabinetts Winterthur gilt.
49
Bulletin SAGW 3 | 2022
DOSSIER
Résumé
En ces temps marqués par l’inflation, le thème
de l’argent est d’une grande pertinence. Dans le pa
norama monétaire des différentes formes d’argent,
les pièces ont beaucoup à nous raconter. Suivre de
près la vie d’une pièce de monnaie antique, de sa fa
brication à ses multiples usages, jusqu’à sa postérité
dans le catalogue numérique de la collection, nous
permet de mieux comprendre l’évolution des modes
économiques et des interactions politiques au fil des
siècles. Cet article se concentre sur les différentes
utilisations des pièces de monnaie, en mettant égale
ment en lumière leurs aspects non monétaires.
Das Nachleben der
antiken Münze
Wird die Münze in moderner Zeit wiederentdeckt, sei
es in einer archäologischen Ausgrabung oder durch einen
Zufallsfund, kommen neue biografische Stationen und Benutzungsrealitäten hinzu (F1–F3). Die Münzen werden international gehandelt, landen in privaten Sammlungen oder in
staatlichen Einrichtungen wie Museen oder Münzkabinetten.
Ein interessanter Aspekt dabei: In Auktionen wird (antikes)
Geld mit (modernem) Geld bezahlt, bei besonders seltenen
Stücken mit extrem viel modernem Geld sogar.1
In Münzkabinetten oder Museen transformiert sich
die antike Münze zum Ausstellungs- und Forschungsobjekt.
Bei all diesen neuzeitlichen Anwendungsszenarien entsteht
ein transepochaler Dialog zwischen den Besitzern der Münze in der Antike und den verschiedenen Nachnutzern in der
Moderne. Obwohl die detaillierte Reise eines Münzstücks in
der Regel nicht rekonstruiert werden kann, lässt sich über
den Erhaltungszustand ein Echo der verschiedenen Zeitstufen ablesen. Durch physikalische und chemische Prozesse
treten über die Jahrhunderte hinweg bestimmte Abnutzungs- und Korrosionserscheinungen auf. Zudem wird durch
die Zirkulation der Münze das Relief im Laufe der Zeit abgerieben und einzelne Konturen können unscharf erscheinen.
1
Die Tetradrachmen Alexanders des Grossen (356–323 v. Chr.),
aus Silber hergestellt, gelten als erste Weltwährung in der
Geschichte. Vorderseite (oben): Kopf des Herakles mit Löwenfellexuvie, Rückseite: Zeus sitzt auf einem Hocker und trägt
auf der rechten Hand einen Adler und mit der linken ein Zepter.
2020 wurde für einen EID MAR Aureus des Brutus der höchste
Preis erzielt, der je für eine antike Münze bei einer Auktion bezahlt
wurde (fast 4,2 Millionen USD). Die Goldmünze wird mit der
Ermordung Caesars an den Iden des März im Jahr 44 v. Chr. assoziiert
und ist eines von insgesamt nur drei erhaltenen Exemplaren.
50
DOSSIER
Literatur
Digitale Erweiterung
• Hofmann, Kerstin P. et al. (2019): Ding-Editionen. Vom
Die geschilderte numismatische Objektbiografie lässt
sich durch die digitale Sphäre erweitern. Die Numismatik
stellt einen Idealfall für die Verwendung von digitalen Mehtoden dar, wordurch digitalisierte Münzsammlungen pionierhaften Charakter aufweisen. Das digitale Nachleben von
Münzen kann beispielsweise im interaktiven Online-Katalog
des Münzkabinetts Berlin besichtigt werden. Dort sind die
Münzen fotografisch mit Vorder- und Rückseite erfasst und
mit allen relevanten Normdaten wie Gewicht, Durchmesser,
Material sowie Beschreibung dokumentiert. Im Sinne der
Prinzipien von Linked-Open-Data werden bestimmte Informationen miteinander verknüpft und zueinander in Beziehung gesetzt,2 die Münzen werden so zu «Digital Objects»,
zu «programmierten Dingen mit neuen Handhabungsmöglichkeiten».3
archäologischen (Be-)Fund übers Corpus ins Netz
(e-Forschungsberichte des Deutschen Archäologischen
Instituts Fasz. 2), S. 1–12.
https://doi.org/10.34780/s7a5-71aj
• Jung, Matthias (2015): Das Konzept der Objektbiogra-
phie im Lichte einer Hermeneutik materieller Kultur,
in: Boschung, Dietrich, Kreuz, Patric-Alexander und Kienlin,
Tobias (Hg.), Biography of Objects: Aspekte eines kulturhistorischen Konzepts, Paderborn, S. 35–65.
• Krmnicek, Stefan (2009): Das Konzept der Objektbio
graphie in der antiken Numismatik, in: Von Kaenel,
Hans-Markus und Kemmers, Fleur (Hg.), Coins in Context
I. New perspectives for the interpretation of coin finds,
Mainz, S. 47–59.
• Schär, Fabian und Aleksander Berentsen (2020): Bitcoin,
Die Münze erhält zudem eine einmalige Objekt-ID,
wodurch stets genau dieses Stück identifiziert wird und
die Münzdokumentation als Kulturgüterschutz bezeichnet
werden kann. Der interaktive Münzkatalog von Berlin gehört
zum gemeinsamen Portal «ikmk.net» (Interaktiver Katalog
der Münzkabinette), welches seit Mai 2021 existiert und bei
dem Berlin mit seinem Dokumentationsstandard federführend ist. Insgesamt sind 29 Münzsammlungen beteiligt und
weitere wie das Münzkabinett Winterthur sowie die KIPKE
Collection des Benaki Museums in Athen folgen mit ihren
numismatischen Sammlungen. Besonders im Verlauf der
Corona-Pandemie wurde deutlich, wie relevant digitalisierte Bestände sind. Wie Matthias Jung bemerkt, können die
verschiedenen Bedeutungsebenen eines numismatischen
Objektes «nicht nur in einer diachronen Abfolge sich ablösend, sondern synchron und damit sich überlagernd sein».4
Dies gilt auch für die Münze, da sie beispielsweise aktuell
als Ausstellungsobjekt im Rahmen einer Sonderausstellung fungieren kann, aber gleichzeitig online als Digitalisat
zu Forschungszwecken für das wissenschaftliche Netzwerk
zugänglich ist. Die Funktion changiert zwischen moderner
und digitaler Welt. Als Digital Object muss die Münze in ihrer nachhaltigen und fairen Datenlandschaft digital gepflegt
werden, um sie für die Zukunft als Kulturgut zu bewahren.
Blockchain, and Cryptoassets: a Comprehensive Introduction, Cambridge.
• Wigg-Wolf, David und Frédérique Duyrat (2017): The
Links
Projekt Nomisma.org: http://nomisma.org
Interaktive Kataloge der Münzkabinette: https://ikmk.net
Inventar der Fundmünzen der Schweiz: www.fundmuenzen.ch
DOI
https://doi.org/10.5281/zenodo.7328543
Zur Autorin
Olivia Denk ist Archäologin und Numismatikerin und
schliesst derzeit ihre Promotion an der Universität Basel
ab. Sie arbeitet als wissenschaftliche Mitarbeiterin
und Spezialistin für Open Science bei den Akademien
der Wissenschaften Schweiz.
•
Numismatisches Kunstprojekt im
digitalen Raum von Olivia Denk
2
3
4
Wigg-Wolf und Duyrant 2017.
Hofmann 2019, 4.
Jung 2015, 52.
51
Bulletin SAGW 3 | 2022
Linked Open Data Revolution in Numismatics. The
examples of nomisma.org and Online Greek Coinage
(Digital Archaeology 1).
https://doi.org/10.21494/ISTE.OP.2017.0171
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.