Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
4
DISCUSSION
1
35
[ "ref35", "ref21", "ref23" ]
19,117,953
pmid-8662843|pmid-16682620|pmid-15314233
This is supported by our kinetic analysis demonstrating that the p35 zymogen likely has the same ability to bind substrate as the fully processed enzyme, observed as a constant Km (Table 1).
[ "35", "21", "23" ]
194
39,916
0
false
This is supported by our kinetic analysis demonstrating that the p35 zymogen likely has the same ability to bind substrate as the fully processed enzyme, observed as a constant Km (Table 1).
[]
This is supported by our kinetic analysis demonstrating that the p35 zymogen likely has the same ability to bind substrate as the fully processed enzyme, observed as a constant Km (Table 1).
true
true
true
true
true
6,896
4
DISCUSSION
1
35
[ "ref35", "ref21", "ref23" ]
19,117,953
pmid-8662843|pmid-16682620|pmid-15314233
Also, the ability of p35 to be completely labeled at the active site by benzyloxycarbonyl-VAD-fluoromethyl ketone confirmed substrate binding (supplemental Fig.
[ "35", "21", "23" ]
162
39,917
0
false
Also, the ability of p35 to be completely labeled at the active site by benzyloxycarbonyl-VAD-fluoromethyl ketone confirmed substrate binding (supplemental Fig.
[]
Also, the ability of p35 to be completely labeled at the active site by benzyloxycarbonyl-VAD-fluoromethyl ketone confirmed substrate binding (supplemental Fig.
true
true
true
true
true
6,896
4
DISCUSSION
1
35
[ "ref35", "ref21", "ref23" ]
19,117,953
pmid-8662843|pmid-16682620|pmid-15314233
These combined data show that kcat is receiving the benefit of interdomain-linker liberation and suggest that despite the unformed substrate-binding site in the crystal structure, caspase-1 can still efficiently bind substrate ligands (Table 1).
[ "35", "21", "23" ]
249
39,918
0
false
These combined data show that kcat is receiving the benefit of interdomain-linker liberation and suggest that despite the unformed substrate-binding site in the crystal structure, caspase-1 can still efficiently bind substrate ligands (Table 1).
[]
These combined data show that kcat is receiving the benefit of interdomain-linker liberation and suggest that despite the unformed substrate-binding site in the crystal structure, caspase-1 can still efficiently bind substrate ligands (Table 1).
true
true
true
true
true
6,896
4
DISCUSSION
1
35
[ "ref35", "ref21", "ref23" ]
19,117,953
pmid-8662843|pmid-16682620|pmid-15314233
Thus, the p20 C terminus and linker must affect the kcat by stabilizing the monomer and preventing the cooperative affects of the dimer.
[ "35", "21", "23" ]
138
39,919
0
false
Thus, the p20 C terminus and linker must affect the kcat by stabilizing the monomer and preventing the cooperative affects of the dimer.
[]
Thus, the p20 C terminus and linker must affect the kcat by stabilizing the monomer and preventing the cooperative affects of the dimer.
true
true
true
true
true
6,896
4
DISCUSSION
1
35
[ "ref35", "ref21", "ref23" ]
19,117,953
pmid-8662843|pmid-16682620|pmid-15314233
What is it then about the interdomain linker in procaspase-1 that imparts monomer over dimer stability?
[ "35", "21", "23" ]
105
39,920
0
false
What is it then about the interdomain linker in procaspase-1 that imparts monomer over dimer stability?
[]
What is it then about the interdomain linker in procaspase-1 that imparts monomer over dimer stability?
true
true
true
true
true
6,896
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
There is little secondary structure in most of the linker region.
[ "48" ]
65
39,921
0
false
There is little secondary structure in most of the linker region.
[]
There is little secondary structure in most of the linker region.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
After close inspection of the proteolytic events that lead to dimerization, it is clear that the first cleavage at Asp297 is not enough to increase kcat or stabilize the dimer.
[ "48" ]
179
39,922
0
false
After close inspection of the proteolytic events that lead to dimerization, it is clear that the first cleavage at Asp297 is not enough to increase kcat or stabilize the dimer.
[]
After close inspection of the proteolytic events that lead to dimerization, it is clear that the first cleavage at Asp297 is not enough to increase kcat or stabilize the dimer.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
This is certainly different from the executioner caspases, where the initial proteolytic event eliminates the constraint on the linker, which then folds back to form the active-site binding cleft, resulting in a major increase in activity.
[ "48" ]
242
39,923
0
false
This is certainly different from the executioner caspases, where the initial proteolytic event eliminates the constraint on the linker, which then folds back to form the active-site binding cleft, resulting in a major increase in activity.
[]
This is certainly different from the executioner caspases, where the initial proteolytic event eliminates the constraint on the linker, which then folds back to form the active-site binding cleft, resulting in a major increase in activity.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
Conversely, activation occurs after the second cleavage at Asp316 in procaspase-1, seen at the 4-h time point in Fig.
[ "48" ]
120
39,924
0
false
Conversely, activation occurs after the second cleavage at Asp316 in procaspase-1, seen at the 4-h time point in Fig.
[]
Conversely, activation occurs after the second cleavage at Asp316 in procaspase-1, seen at the 4-h time point in Fig.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
1B and the 45-min time point in Fig.
[ "48" ]
37
39,925
0
false
1B and the 45-min time point in Fig.
[]
1B and the 45-min time point in Fig.
false
false
true
true
false
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
1C (summarized in Table 1).
[ "48" ]
28
39,926
0
false
1C (summarized in Table 1).
[]
1C (summarized in Table 1).
false
false
true
true
false
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
Because the first cleavage could release the constraint on the linker, it is at first unclear why this is not enough to yield an active enzyme.
[ "48" ]
144
39,927
0
false
Because the first cleavage could release the constraint on the linker, it is at first unclear why this is not enough to yield an active enzyme.
[]
Because the first cleavage could release the constraint on the linker, it is at first unclear why this is not enough to yield an active enzyme.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
In the area of the second cleavage, however, is the only well defined secondary structure of the linker region, a stable α-helix (Fig.
[ "48" ]
137
39,928
0
false
In the area of the second cleavage, however, is the only well defined secondary structure of the linker region, a stable α-helix (Fig.
[]
In the area of the second cleavage, however, is the only well defined secondary structure of the linker region, a stable α-helix (Fig.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
In fact, at this site, Asp316 is situated as the penultimate residue of the α-helix.
[ "48" ]
86
39,929
0
false
In fact, at this site, Asp316 is situated as the penultimate residue of the α-helix.
[]
In fact, at this site, Asp316 is situated as the penultimate residue of the α-helix.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
Proteolysis here would eliminate the terminal residues of the helix (Fig.
[ "48" ]
74
39,930
0
false
Proteolysis here would eliminate the terminal residues of the helix (Fig.
[]
Proteolysis here would eliminate the terminal residues of the helix (Fig.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
Shortening this stretch of amino acids would destabilize the helix and in turn allow this loop to restructure with the C-terminal region of the adjacent large subunit into an extensive anti-parallel β-sheet.
[ "48" ]
209
39,931
0
false
Shortening this stretch of amino acids would destabilize the helix and in turn allow this loop to restructure with the C-terminal region of the adjacent large subunit into an extensive anti-parallel β-sheet.
[]
Shortening this stretch of amino acids would destabilize the helix and in turn allow this loop to restructure with the C-terminal region of the adjacent large subunit into an extensive anti-parallel β-sheet.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
This β-sheet occurs at both poles of the dimeric protein and has been shown to be the most important region for dimer stabilization within caspase-1 (48).
[ "48" ]
157
39,932
1
false
This β-sheet occurs at both poles of the dimeric protein and has been shown to be the most important region for dimer stabilization within caspase-1.
[ "48" ]
This β-sheet occurs at both poles of the dimeric protein and has been shown to be the most important region for dimer stabilization within caspase-1.
true
true
true
true
true
6,897
5
DISCUSSION
1
48
[ "ref48" ]
19,117,953
pmid-12873132
Again, this is in contrast to executioner caspases-3 and -7, which have strong β-sheet interaction across the central region of the dimer interface that contribute to the solution state preference for dimerization even before proteolytic activation.
[ "48" ]
253
39,933
0
false
Again, this is in contrast to executioner caspases-3 and -7, which have strong β-sheet interaction across the central region of the dimer interface that contribute to the solution state preference for dimerization even before proteolytic activation.
[]
Again, this is in contrast to executioner caspases-3 and -7, which have strong β-sheet interaction across the central region of the dimer interface that contribute to the solution state preference for dimerization even before proteolytic activation.
true
true
true
true
true
6,897
6
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
FIGURE 5.Key structural elements of caspase-1 dimer stabilization.
[ "42" ]
66
39,934
0
false
FIGURE 5.Key structural elements of caspase-1 dimer stabilization.
[]
FIGURE 5.Key structural elements of caspase-1 dimer stabilization.
true
true
true
true
true
6,898
6
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
A, schematic representation of caspase-1 zymogen (left, PDB code 3E4C) and processed ligand-free caspase-1 (right, PDB code 1SC1 (42)).
[ "42" ]
137
39,935
0
false
A, schematic representation of caspase-1 zymogen (left, PDB code 3E4C) and processed ligand-free caspase-1 ).
[ "right, PDB code 1SC1\n (42" ]
A, schematic representation of caspase-1 zymogen and processed ligand-free caspase-1 ).
true
true
true
true
true
6,898
6
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
The proenzyme shows a well defined α-helix near the putative N terminus of the p10.
[ "42" ]
84
39,936
0
false
The proenzyme shows a well defined α-helix near the putative N terminus of the p10.
[]
The proenzyme shows a well defined α-helix near the putative N terminus of the p10.
true
true
true
true
true
6,898
6
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
This element contains cleavage Site 2, which is the critical processing site for caspase-1 activation.
[ "42" ]
104
39,937
0
false
This element contains cleavage Site 2, which is the critical processing site for caspase-1 activation.
[]
This element contains cleavage Site 2, which is the critical processing site for caspase-1 activation.
true
true
true
true
true
6,898
6
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
Once proteolysis occurs at Asp316, the newly formed p20 C terminus and p10 N terminus are able to form anti-parallel β-sheets in the active enzyme.
[ "42" ]
149
39,938
0
false
Once proteolysis occurs at Asp316, the newly formed p20 C terminus and p10 N terminus are able to form anti-parallel β-sheets in the active enzyme.
[]
Once proteolysis occurs at Asp316, the newly formed p20 C terminus and p10 N terminus are able to form anti-parallel β-sheets in the active enzyme.
true
true
true
true
true
6,898
6
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
The important secondary structural elements are indicated with red circles.
[ "42" ]
76
39,939
0
false
The important secondary structural elements are indicated with red circles.
[]
The important secondary structural elements are indicated with red circles.
true
true
true
true
true
6,898
6
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
B, diagram of the backbone atoms of residues 314-321.
[ "42" ]
54
39,940
0
false
B, diagram of the backbone atoms of residues 314-321.
[]
B, diagram of the backbone atoms of residues 314-321.
true
true
true
true
true
6,898
6
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
Brackets indicate backbone interactions in the α-helix in the proenzyme structure.
[ "42" ]
83
39,941
0
false
Brackets indicate backbone interactions in the α-helix in the proenzyme structure.
[]
Brackets indicate backbone interactions in the α-helix in the proenzyme structure.
true
true
true
true
true
6,898
6
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
Two of the three hydrogen bonds in the helix are severed upon proteolysis at Asp316, indicated with an arrow.
[ "42" ]
111
39,942
0
false
Two of the three hydrogen bonds in the helix are severed upon proteolysis at Asp316, indicated with an arrow.
[]
Two of the three hydrogen bonds in the helix are severed upon proteolysis at Asp316, indicated with an arrow.
true
true
true
true
true
6,898
7
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
Key structural elements of caspase-1 dimer stabilization.
[ "42" ]
57
39,943
0
false
Key structural elements of caspase-1 dimer stabilization.
[]
Key structural elements of caspase-1 dimer stabilization.
true
true
true
true
true
6,899
7
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
A, schematic representation of caspase-1 zymogen (left, PDB code 3E4C) and processed ligand-free caspase-1 (right, PDB code 1SC1 (42)).
[ "42" ]
137
39,944
0
false
A, schematic representation of caspase-1 zymogen (left, PDB code 3E4C) and processed ligand-free caspase-1 ).
[ "right, PDB code 1SC1\n (42" ]
A, schematic representation of caspase-1 zymogen and processed ligand-free caspase-1 ).
true
true
true
true
true
6,899
7
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
The proenzyme shows a well defined α-helix near the putative N terminus of the p10.
[ "42" ]
84
39,945
0
false
The proenzyme shows a well defined α-helix near the putative N terminus of the p10.
[]
The proenzyme shows a well defined α-helix near the putative N terminus of the p10.
true
true
true
true
true
6,899
7
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
This element contains cleavage Site 2, which is the critical processing site for caspase-1 activation.
[ "42" ]
104
39,946
0
false
This element contains cleavage Site 2, which is the critical processing site for caspase-1 activation.
[]
This element contains cleavage Site 2, which is the critical processing site for caspase-1 activation.
true
true
true
true
true
6,899
7
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
Once proteolysis occurs at Asp316, the newly formed p20 C terminus and p10 N terminus are able to form anti-parallel β-sheets in the active enzyme.
[ "42" ]
149
39,947
0
false
Once proteolysis occurs at Asp316, the newly formed p20 C terminus and p10 N terminus are able to form anti-parallel β-sheets in the active enzyme.
[]
Once proteolysis occurs at Asp316, the newly formed p20 C terminus and p10 N terminus are able to form anti-parallel β-sheets in the active enzyme.
true
true
true
true
true
6,899
7
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
The important secondary structural elements are indicated with red circles.
[ "42" ]
76
39,948
0
false
The important secondary structural elements are indicated with red circles.
[]
The important secondary structural elements are indicated with red circles.
true
true
true
true
true
6,899
7
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
B, diagram of the backbone atoms of residues 314-321.
[ "42" ]
54
39,949
0
false
B, diagram of the backbone atoms of residues 314-321.
[]
B, diagram of the backbone atoms of residues 314-321.
true
true
true
true
true
6,899
7
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
Brackets indicate backbone interactions in the α-helix in the proenzyme structure.
[ "42" ]
83
39,950
0
false
Brackets indicate backbone interactions in the α-helix in the proenzyme structure.
[]
Brackets indicate backbone interactions in the α-helix in the proenzyme structure.
true
true
true
true
true
6,899
7
DISCUSSION
1
42
[ "ref42" ]
19,117,953
pmid-8035875
Two of the three hydrogen bonds in the helix are severed upon proteolysis at Asp316, indicated with an arrow.
[ "42" ]
111
39,951
0
false
Two of the three hydrogen bonds in the helix are severed upon proteolysis at Asp316, indicated with an arrow.
[]
Two of the three hydrogen bonds in the helix are severed upon proteolysis at Asp316, indicated with an arrow.
true
true
true
true
true
6,899
8
DISCUSSION
0
null
null
19,117,953
null
In response to inflammatory signaling, the initial autoactivation of procaspase-1 is triggered by inflammasome oligomerization.
null
128
39,952
0
false
null
null
In response to inflammatory signaling, the initial autoactivation of procaspase-1 is triggered by inflammasome oligomerization.
true
true
true
true
true
6,900
8
DISCUSSION
0
null
null
19,117,953
null
The crystal structure provides a view of how autoactivation by intradimer proteolysis at the first cleavage site could result from this forced oligomerization.
null
161
39,953
0
false
null
null
The crystal structure provides a view of how autoactivation by intradimer proteolysis at the first cleavage site could result from this forced oligomerization.
true
true
true
true
true
6,900
8
DISCUSSION
0
null
null
19,117,953
null
Proteolysis at the second site, Asp316, converts an α-helix in the monomer to an intradimer β-sheet resulting in a stable dimer with increased enzymatic activity.
null
164
39,954
0
false
null
null
Proteolysis at the second site, Asp316, converts an α-helix in the monomer to an intradimer β-sheet resulting in a stable dimer with increased enzymatic activity.
true
true
true
true
true
6,900
8
DISCUSSION
0
null
null
19,117,953
null
Thus, the initial instability of the caspase-1 dimer is something that must be overcome during the activation process, i.e.
null
125
39,955
0
false
null
null
Thus, the initial instability of the caspase-1 dimer is something that must be overcome during the activation process, i.e.
true
true
true
true
true
6,900
8
DISCUSSION
0
null
null
19,117,953
null
a potential target for small molecules that destabilize or prevent the formation of the dimeric form of the enzyme.
null
116
39,956
0
false
null
null
a potential target for small molecules that destabilize or prevent the formation of the dimeric form of the enzyme.
false
true
true
true
false
6,900
8
DISCUSSION
0
null
null
19,117,953
null
This type of molecule could eliminate the need for aspartic-acid-containing compounds that treat disorders involving caspase-1.
null
129
39,957
0
false
null
null
This type of molecule could eliminate the need for aspartic-acid-containing compounds that treat disorders involving caspase-1.
true
true
true
true
true
6,900
0
INTRODUCTION
1
1
[ "B1", "B2", "B1", "B3", "B4", "B5", "B6" ]
17,717,000
pmid-5222560|pmid-5936951|pmid-5222560|pmid-4237205|pmid-9508763|pmid-4128545|pmid-12511866
DNA replication is a key step of cell cycle that ensures the complete duplication of genomic DNA prior to mitosis.
[ "1", "2", "1", "3", "4", "5", "6" ]
114
39,958
0
false
DNA replication is a key step of cell cycle that ensures the complete duplication of genomic DNA prior to mitosis.
[]
DNA replication is a key step of cell cycle that ensures the complete duplication of genomic DNA prior to mitosis.
true
true
true
true
true
6,901
0
INTRODUCTION
1
1
[ "B1", "B2", "B1", "B3", "B4", "B5", "B6" ]
17,717,000
pmid-5222560|pmid-5936951|pmid-5222560|pmid-4237205|pmid-9508763|pmid-4128545|pmid-12511866
Over the past 40 years, it has been evidenced that eukaryotic genomes replicate accordingly to an invariant temporal order (1,2).
[ "1", "2", "1", "3", "4", "5", "6" ]
129
39,959
0
false
Over the past 40 years, it has been evidenced that eukaryotic genomes replicate accordingly to an invariant temporal order.
[ "1,2" ]
Over the past 40 years, it has been evidenced that eukaryotic genomes replicate accordingly to an invariant temporal order.
true
true
true
true
true
6,901
0
INTRODUCTION
1
1
[ "B1", "B2", "B1", "B3", "B4", "B5", "B6" ]
17,717,000
pmid-5222560|pmid-5936951|pmid-5222560|pmid-4237205|pmid-9508763|pmid-4128545|pmid-12511866
This has first been shown in the Myxomycete Physarum polycephalum.
[ "1", "2", "1", "3", "4", "5", "6" ]
66
39,960
0
false
This has first been shown in the Myxomycete Physarum polycephalum.
[]
This has first been shown in the Myxomycete Physarum polycephalum.
true
true
true
true
true
6,901
0
INTRODUCTION
1
1
[ "B1", "B2", "B1", "B3", "B4", "B5", "B6" ]
17,717,000
pmid-5222560|pmid-5936951|pmid-5222560|pmid-4237205|pmid-9508763|pmid-4128545|pmid-12511866
Indeed, taking advantage of the natural synchrony of several million nuclei within a single plasmodium, the authors have carried out pulse-labeling experiments and showed that sub-fractions of replicating DNA are the same through successive S phases (1,3).
[ "1", "2", "1", "3", "4", "5", "6" ]
256
39,961
0
false
Indeed, taking advantage of the natural synchrony of several million nuclei within a single plasmodium, the authors have carried out pulse-labeling experiments and showed that sub-fractions of replicating DNA are the same through successive S phases.
[ "1,3" ]
Indeed, taking advantage of the natural synchrony of several million nuclei within a single plasmodium, the authors have carried out pulse-labeling experiments and showed that sub-fractions of replicating DNA are the same through successive S phases.
true
true
true
true
true
6,901
0
INTRODUCTION
1
4
[ "B1", "B2", "B1", "B3", "B4", "B5", "B6" ]
17,717,000
pmid-5222560|pmid-5936951|pmid-5222560|pmid-4237205|pmid-9508763|pmid-4128545|pmid-12511866
More recently, the visualization of in vivo labeled replication foci within single cells strongly suggested that replicons remain associated within the same clusters throughout consecutive cell cycles (4).
[ "1", "2", "1", "3", "4", "5", "6" ]
205
39,962
1
false
More recently, the visualization of in vivo labeled replication foci within single cells strongly suggested that replicons remain associated within the same clusters throughout consecutive cell cycles.
[ "4" ]
More recently, the visualization of in vivo labeled replication foci within single cells strongly suggested that replicons remain associated within the same clusters throughout consecutive cell cycles.
true
true
true
true
true
6,901
0
INTRODUCTION
1
5
[ "B1", "B2", "B1", "B3", "B4", "B5", "B6" ]
17,717,000
pmid-5222560|pmid-5936951|pmid-5222560|pmid-4237205|pmid-9508763|pmid-4128545|pmid-12511866
Cytogenetic analyses of metaphase chromosomes also showed an invariant pattern of replication banding (5) and density shift experiments validated these results at the level of individual genes by defining their timing of replication (6).
[ "1", "2", "1", "3", "4", "5", "6" ]
237
39,963
1
false
Cytogenetic analyses of metaphase chromosomes also showed an invariant pattern of replication banding and density shift experiments validated these results at the level of individual genes by defining their timing of replication.
[ "5", "6" ]
Cytogenetic analyses of metaphase chromosomes also showed an invariant pattern of replication banding and density shift experiments validated these results at the level of individual genes by defining their timing of replication.
true
true
true
true
true
6,901
1
INTRODUCTION
1
6
[ "B6", "B7", "B8 B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
In addition, replication timing and transcriptional status of genes have been correlated in many organisms.
[ "6", "7", "8–11", "12", "13", "14", "15", "16" ]
107
39,964
0
false
In addition, replication timing and transcriptional status of genes have been correlated in many organisms.
[]
In addition, replication timing and transcriptional status of genes have been correlated in many organisms.
true
true
true
true
true
6,902
1
INTRODUCTION
1
6
[ "B6", "B7", "B8 B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
Indeed, active genes are often found to replicate early whereas inactive genes replicate later (6,7).
[ "6", "7", "8–11", "12", "13", "14", "15", "16" ]
101
39,965
0
false
Indeed, active genes are often found to replicate early whereas inactive genes replicate later.
[ "6,7" ]
Indeed, active genes are often found to replicate early whereas inactive genes replicate later.
true
true
true
true
true
6,902
1
INTRODUCTION
1
8–11
[ "B6", "B7", "B8 B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
Genome-wide analysis in human cells and in Drosophila confirmed the connection between early replication timing and transcriptional activity (8–11).
[ "6", "7", "8–11", "12", "13", "14", "15", "16" ]
148
39,966
1
false
Genome-wide analysis in human cells and in Drosophila confirmed the connection between early replication timing and transcriptional activity.
[ "8–11" ]
Genome-wide analysis in human cells and in Drosophila confirmed the connection between early replication timing and transcriptional activity.
true
true
true
true
true
6,902
1
INTRODUCTION
1
12
[ "B6", "B7", "B8 B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
However, this link is more obvious for large domains rather than at a small scale (12) and was not seen at all in budding yeast (13).
[ "6", "7", "8–11", "12", "13", "14", "15", "16" ]
133
39,967
1
false
However, this link is more obvious for large domains rather than at a small scale and was not seen at all in budding yeast.
[ "12", "13" ]
However, this link is more obvious for large domains rather than at a small scale and was not seen at all in budding yeast.
true
true
true
true
true
6,902
1
INTRODUCTION
1
14
[ "B6", "B7", "B8 B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
It was also shown that the temporal program of gene replication could change during cell differentiation or development, reinforcing therefore the concept of a co-ordination between replication and transcription (14).
[ "6", "7", "8–11", "12", "13", "14", "15", "16" ]
217
39,968
1
false
It was also shown that the temporal program of gene replication could change during cell differentiation or development, reinforcing therefore the concept of a co-ordination between replication and transcription.
[ "14" ]
It was also shown that the temporal program of gene replication could change during cell differentiation or development, reinforcing therefore the concept of a co-ordination between replication and transcription.
true
true
true
true
true
6,902
1
INTRODUCTION
1
6
[ "B6", "B7", "B8 B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
Studies of the profilin genes in Physarum and the immunoglobin heavy chain locus in mammalian cells have clearly demonstrated that, during differentiation, replication of these loci is altered by a change in the pattern of origin activation (15,16).
[ "6", "7", "8–11", "12", "13", "14", "15", "16" ]
249
39,969
0
false
Studies of the profilin genes in Physarum and the immunoglobin heavy chain locus in mammalian cells have clearly demonstrated that, during differentiation, replication of these loci is altered by a change in the pattern of origin activation.
[ "15,16" ]
Studies of the profilin genes in Physarum and the immunoglobin heavy chain locus in mammalian cells have clearly demonstrated that, during differentiation, replication of these loci is altered by a change in the pattern of origin activation.
true
true
true
true
true
6,902
2
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
Nonetheless, recent reports suggest that replication timing is not strictly defined.
[ "17", "18", "19", "20" ]
84
39,970
0
false
Nonetheless, recent reports suggest that replication timing is not strictly defined.
[]
Nonetheless, recent reports suggest that replication timing is not strictly defined.
true
true
true
true
true
6,903
2
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
Indeed, in mammalian cells, molecular combing of DNA molecules associated with FISH analyses showed that redundant origins fired randomly with no timing preference (17).
[ "17", "18", "19", "20" ]
169
39,971
1
false
Indeed, in mammalian cells, molecular combing of DNA molecules associated with FISH analyses showed that redundant origins fired randomly with no timing preference.
[ "17" ]
Indeed, in mammalian cells, molecular combing of DNA molecules associated with FISH analyses showed that redundant origins fired randomly with no timing preference.
true
true
true
true
true
6,903
2
INTRODUCTION
1
18
[ "B17", "B18", "B19", "B20" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
Stochastic firing of origins was also described in fission yeast (18), although it was not confirmed by genome-wide analyses (19).
[ "17", "18", "19", "20" ]
130
39,972
1
false
Stochastic firing of origins was also described in fission yeast, although it was not confirmed by genome-wide analyses.
[ "18", "19" ]
Stochastic firing of origins was also described in fission yeast, although it was not confirmed by genome-wide analyses.
true
true
true
true
true
6,903
2
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
In human cancer cells, studies of chromosomes 21–22 replication using micro-arrays analyses and FISH have demonstrated that a fixed timing of replication could not be assigned to large set of DNA sequences (i.e.
[ "17", "18", "19", "20" ]
211
39,973
0
false
In human cancer cells, studies of chromosomes 21–22 replication using micro-arrays analyses and FISH have demonstrated that a fixed timing of replication could not be assigned to large set of DNA sequences (i.e.
[]
In human cancer cells, studies of chromosomes 21–22 replication using micro-arrays analyses and FISH have demonstrated that a fixed timing of replication could not be assigned to large set of DNA sequences (i.e.
true
true
true
true
true
6,903
2
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
they were found to replicate early as well as late).
[ "17", "18", "19", "20" ]
52
39,974
0
false
they were found to replicate early as well as late).
[]
they were found to replicate early as well as late).
false
true
true
true
false
6,903
2
INTRODUCTION
1
20
[ "B17", "B18", "B19", "B20" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
This led the authors to propose a ‘pan-S-phase’ pattern as opposed to the classical fixed pattern of replication timing (20).
[ "17", "18", "19", "20" ]
125
39,975
1
false
This led the authors to propose a ‘pan-S-phase’ pattern as opposed to the classical fixed pattern of replication timing.
[ "20" ]
This led the authors to propose a ‘pan-S-phase’ pattern as opposed to the classical fixed pattern of replication timing.
true
true
true
true
true
6,903
3
INTRODUCTION
1
21
[ "B21", "B21", "B22", "B23" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
We have previously demonstrated by in vivo incorporation of bromodeoxyuridine that active genes are replicated early in the naturally synchronous plasmodium of P. polycephalum (21).
[ "21", "21", "22", "23" ]
181
39,976
1
false
We have previously demonstrated by in vivo incorporation of bromodeoxyuridine that active genes are replicated early in the naturally synchronous plasmodium of P. polycephalum.
[ "21" ]
We have previously demonstrated by in vivo incorporation of bromodeoxyuridine that active genes are replicated early in the naturally synchronous plasmodium of P. polycephalum.
true
true
true
true
true
6,904
3
INTRODUCTION
1
21
[ "B21", "B21", "B22", "B23" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
However, we also found that the highly expressed php gene is late replicated in plasmodia (21,22).
[ "21", "21", "22", "23" ]
98
39,977
0
false
However, we also found that the highly expressed php gene is late replicated in plasmodia.
[ "21,22" ]
However, we also found that the highly expressed php gene is late replicated in plasmodia.
true
true
true
true
true
6,904
3
INTRODUCTION
1
23
[ "B21", "B21", "B22", "B23" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
Here, we used neutral bidimensional agarose gel electrophoresis (2D-gel) method (23) to determine whether php gene late replication comes from its association to a late firing origin or from its long distance from an early firing origin.
[ "21", "21", "22", "23" ]
237
39,978
1
false
Here, we used neutral bidimensional agarose gel electrophoresis (2D-gel) method to determine whether php gene late replication comes from its association to a late firing origin or from its long distance from an early firing origin.
[ "23" ]
Here, we used neutral bidimensional agarose gel electrophoresis method to determine whether php gene late replication comes from its association to a late firing origin or from its long distance from an early firing origin.
true
true
true
true
true
6,904
3
INTRODUCTION
1
21
[ "B21", "B21", "B22", "B23" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
Surprisingly, replication forks were found on the locus at the onset of S phase and could be detected through half of S phase.
[ "21", "21", "22", "23" ]
126
39,979
0
false
Surprisingly, replication forks were found on the locus at the onset of S phase and could be detected through half of S phase.
[]
Surprisingly, replication forks were found on the locus at the onset of S phase and could be detected through half of S phase.
true
true
true
true
true
6,904
3
INTRODUCTION
1
21
[ "B21", "B21", "B22", "B23" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
We demonstrated that this observation could not be explained by random replication timing among nuclei of a plasmodium but rather by a very slow progression of the forks enhanced by fork stalling upstream the gene.
[ "21", "21", "22", "23" ]
214
39,980
0
false
We demonstrated that this observation could not be explained by random replication timing among nuclei of a plasmodium but rather by a very slow progression of the forks enhanced by fork stalling upstream the gene.
[]
We demonstrated that this observation could not be explained by random replication timing among nuclei of a plasmodium but rather by a very slow progression of the forks enhanced by fork stalling upstream the gene.
true
true
true
true
true
6,904
3
INTRODUCTION
1
21
[ "B21", "B21", "B22", "B23" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
Importantly, we also showed that the coding region of php is actually early replicated because of its proximity to a replication origin activated at the onset of S phase.
[ "21", "21", "22", "23" ]
170
39,981
0
false
Importantly, we also showed that the coding region of php is actually early replicated because of its proximity to a replication origin activated at the onset of S phase.
[]
Importantly, we also showed that the coding region of php is actually early replicated because of its proximity to a replication origin activated at the onset of S phase.
true
true
true
true
true
6,904
3
INTRODUCTION
1
21
[ "B21", "B21", "B22", "B23" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
Here again, active transcription is thus related to early replication.
[ "21", "21", "22", "23" ]
70
39,982
0
false
Here again, active transcription is thus related to early replication.
[]
Here again, active transcription is thus related to early replication.
true
true
true
true
true
6,904
3
INTRODUCTION
1
21
[ "B21", "B21", "B22", "B23" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
Furthermore, our results also demonstrated that the origin is developmentally regulated in correlation with the php gene activity and reinforced the concept of replication-transcription coupling in Physarum.
[ "21", "21", "22", "23" ]
207
39,983
0
false
Furthermore, our results also demonstrated that the origin is developmentally regulated in correlation with the php gene activity and reinforced the concept of replication-transcription coupling in Physarum.
[]
Furthermore, our results also demonstrated that the origin is developmentally regulated in correlation with the php gene activity and reinforced the concept of replication-transcription coupling in Physarum.
true
true
true
true
true
6,904
0
DISCUSSION
0
null
null
17,717,000
pmid-5222560|pmid-5936951|pmid-5222560|pmid-4237205|pmid-9508763|pmid-4128545|pmid-12511866
We found that php gene was early replicated from a bidirectional origin located in its promoter region (Figure 2).
null
114
39,984
0
false
null
null
We found that php gene was early replicated from a bidirectional origin located in its promoter region (Figure 2).
true
true
true
true
true
6,905
0
DISCUSSION
0
null
null
17,717,000
pmid-5222560|pmid-5936951|pmid-5222560|pmid-4237205|pmid-9508763|pmid-4128545|pmid-12511866
However, the 2D-gel analysis of php locus also showed a surprisingly long life span of RIs that persisted for half of the S phase (Figure 1).
null
141
39,985
0
false
null
null
However, the 2D-gel analysis of php locus also showed a surprisingly long life span of RIs that persisted for half of the S phase (Figure 1).
true
true
true
true
true
6,905
0
DISCUSSION
0
null
null
17,717,000
pmid-5222560|pmid-5936951|pmid-5222560|pmid-4237205|pmid-9508763|pmid-4128545|pmid-12511866
It should be noticed that these kinetic data were obtained with plasmodia harvested in two consecutive cell cycles, showing the invariance of this feature over S phases.
null
169
39,986
0
false
null
null
It should be noticed that these kinetic data were obtained with plasmodia harvested in two consecutive cell cycles, showing the invariance of this feature over S phases.
true
true
true
true
true
6,905
1
DISCUSSION
1
32
[ "B32", "B37", "B38", "B39", "B40", "B41", "B42", "B43", "B44" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
This unusual pattern can be explained by a slow progression of replication forks on the locus in early S phase (Figures 2 and 4) and also by a stalling of the leftward replication fork from +25 min to +60 min (Figure 1).
[ "32", "37", "38", "39", "40", "41", "42", "43", "44" ]
220
39,987
0
false
This unusual pattern can be explained by a slow progression of replication forks on the locus in early S phase (Figures 2 and 4) and also by a stalling of the leftward replication fork from +25 min to +60 min (Figure 1).
[]
This unusual pattern can be explained by a slow progression of replication forks on the locus in early S phase and also by a stalling of the leftward replication fork from +25 min to +60 min (Figure 1).
true
true
true
true
true
6,906
1
DISCUSSION
1
32
[ "B32", "B37", "B38", "B39", "B40", "B41", "B42", "B43", "B44" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
A slowing down of replication forks has been also found in Physarum upstream rRNA genes and downstream the histone H4-1 gene (32,37).
[ "32", "37", "38", "39", "40", "41", "42", "43", "44" ]
133
39,988
0
false
A slowing down of replication forks has been also found in Physarum upstream rRNA genes and downstream the histone H4-1 gene.
[ "32,37" ]
A slowing down of replication forks has been also found in Physarum upstream rRNA genes and downstream the histone H4-1 gene.
true
true
true
true
true
6,906
1
DISCUSSION
1
38
[ "B32", "B37", "B38", "B39", "B40", "B41", "B42", "B43", "B44" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
In this latter case, it has been shown that forks are stalled in DNaseI hypersensitive regions (38).
[ "32", "37", "38", "39", "40", "41", "42", "43", "44" ]
100
39,989
1
false
In this latter case, it has been shown that forks are stalled in DNaseI hypersensitive regions.
[ "38" ]
In this latter case, it has been shown that forks are stalled in DNaseI hypersensitive regions.
true
true
true
true
true
6,906
1
DISCUSSION
1
32
[ "B32", "B37", "B38", "B39", "B40", "B41", "B42", "B43", "B44" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
It is also possible that the DNA sequence of php locus might impede the replication forks.
[ "32", "37", "38", "39", "40", "41", "42", "43", "44" ]
90
39,990
0
false
It is also possible that the DNA sequence of php locus might impede the replication forks.
[]
It is also possible that the DNA sequence of php locus might impede the replication forks.
true
true
true
true
true
6,906
1
DISCUSSION
1
39
[ "B32", "B37", "B38", "B39", "B40", "B41", "B42", "B43", "B44" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
Indeed, particular sequence patterns such as trinucleotide repeats might reduce fork progression (39).
[ "32", "37", "38", "39", "40", "41", "42", "43", "44" ]
102
39,991
1
false
Indeed, particular sequence patterns such as trinucleotide repeats might reduce fork progression.
[ "39" ]
Indeed, particular sequence patterns such as trinucleotide repeats might reduce fork progression.
true
true
true
true
true
6,906
1
DISCUSSION
1
32
[ "B32", "B37", "B38", "B39", "B40", "B41", "B42", "B43", "B44" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
In fact, several examples of replication stalling have been described in eukaryotic cells.
[ "32", "37", "38", "39", "40", "41", "42", "43", "44" ]
90
39,992
0
false
In fact, several examples of replication stalling have been described in eukaryotic cells.
[]
In fact, several examples of replication stalling have been described in eukaryotic cells.
true
true
true
true
true
6,906
1
DISCUSSION
1
40
[ "B32", "B37", "B38", "B39", "B40", "B41", "B42", "B43", "B44" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
For instance, in Saccharomyces cerevisiae, almost 1500 discrete sites were found to correspond to pauses caused by DNA sequences or by local protein-DNA complexes (40).
[ "32", "37", "38", "39", "40", "41", "42", "43", "44" ]
168
39,993
1
false
For instance, in Saccharomyces cerevisiae, almost 1500 discrete sites were found to correspond to pauses caused by DNA sequences or by local protein-DNA complexes.
[ "40" ]
For instance, in Saccharomyces cerevisiae, almost 1500 discrete sites were found to correspond to pauses caused by DNA sequences or by local protein-DNA complexes.
true
true
true
true
true
6,906
1
DISCUSSION
1
41
[ "B32", "B37", "B38", "B39", "B40", "B41", "B42", "B43", "B44" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
These sites include tRNA genes (41), rDNA (42), centromeric and subtelomeric regions (43,44).
[ "32", "37", "38", "39", "40", "41", "42", "43", "44" ]
93
39,994
1
false
These sites include tRNA genes, rDNA, centromeric and subtelomeric regions.
[ "41", "42", "43,44" ]
These sites include tRNA genes, rDNA, centromeric and subtelomeric regions.
true
true
true
true
true
6,906
1
DISCUSSION
1
32
[ "B32", "B37", "B38", "B39", "B40", "B41", "B42", "B43", "B44" ]
17,717,000
pmid-12511866|pmid-3551593|pmid-15601823|pmid-12355067|pmid-15591350|pmid-14645202|pmid-15951049|pmid-11588253|pmid-12067662|pmid-12776736|pmid-16307921|pmid-10219081|pmid-7784195|pmid-9547257|pmid-15201446|pmid-14690605|pmid-1406623|pmid-3052854|NA|pmid-12050116
Clearly, variation of fork rate is not a rare event and DNA replication does not seem to be a steady process.
[ "32", "37", "38", "39", "40", "41", "42", "43", "44" ]
109
39,995
0
false
Clearly, variation of fork rate is not a rare event and DNA replication does not seem to be a steady process.
[]
Clearly, variation of fork rate is not a rare event and DNA replication does not seem to be a steady process.
true
true
true
true
true
6,906
2
DISCUSSION
1
21
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
php RIs were found in restricted DNA fragments from plasmodia harvested in early S phase.
[ "21", "22", "21", "22" ]
89
39,996
0
false
php RIs were found in restricted DNA fragments from plasmodia harvested in early S phase.
[]
php RIs were found in restricted DNA fragments from plasmodia harvested in early S phase.
false
true
true
true
false
6,907
2
DISCUSSION
1
21
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
Our previous studies showed that php gene is contained in a late replicating DNA fragment (21,22).
[ "21", "22", "21", "22" ]
98
39,997
0
false
Our previous studies showed that php gene is contained in a late replicating DNA fragment.
[ "21,22" ]
Our previous studies showed that php gene is contained in a late replicating DNA fragment.
true
true
true
true
true
6,907
2
DISCUSSION
1
21
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
This discrepancy is explained by the usage of different methods of analyses.
[ "21", "22", "21", "22" ]
76
39,998
0
false
This discrepancy is explained by the usage of different methods of analyses.
[]
This discrepancy is explained by the usage of different methods of analyses.
true
true
true
true
true
6,907
2
DISCUSSION
1
21
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
In a first study, the replication timing of php locus had been analyzed by density-shift experiment following in vivo incorporation of bromo-deoxyuridine (21).
[ "21", "22", "21", "22" ]
159
39,999
1
false
In a first study, the replication timing of php locus had been analyzed by density-shift experiment following in vivo incorporation of bromo-deoxyuridine.
[ "21" ]
In a first study, the replication timing of php locus had been analyzed by density-shift experiment following in vivo incorporation of bromo-deoxyuridine.
true
true
true
true
true
6,907
2
DISCUSSION
1
21
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
The downstream allelic 6 kb and 12 kb HindIII fragments had been studied and were found clearly enriched in the heavy-light DNA fraction only after 90 min in S phase.
[ "21", "22", "21", "22" ]
166
40,000
0
false
The downstream allelic 6 kb and 12 kb HindIII fragments had been studied and were found clearly enriched in the heavy-light DNA fraction only after 90 min in S phase.
[]
The downstream allelic 6 kb and 12 kb HindIII fragments had been studied and were found clearly enriched in the heavy-light DNA fraction only after 90 min in S phase.
true
true
true
true
true
6,907
2
DISCUSSION
1
21
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
Gene dosage analyses had confirmed these density shift experiments: the same HindIII fragments were found at 2 copies per genome only after 90 min.
[ "21", "22", "21", "22" ]
147
40,001
0
false
Gene dosage analyses had confirmed these density shift experiments: the same HindIII fragments were found at 2 copies per genome only after 90 min.
[]
Gene dosage analyses had confirmed these density shift experiments: the same HindIII fragments were found at 2 copies per genome only after 90 min.
true
true
true
true
true
6,907
2
DISCUSSION
1
22
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
This led us to conclude at a late replicating locus (22).
[ "21", "22", "21", "22" ]
57
40,002
1
false
This led us to conclude at a late replicating locus.
[ "22" ]
This led us to conclude at a late replicating locus.
true
true
true
true
true
6,907
2
DISCUSSION
1
21
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
In the present work, 2D-gel technique favored detection of low amounts of RIs and allowed analyses of fork progression in a synchronous system.
[ "21", "22", "21", "22" ]
143
40,003
0
false
In the present work, 2D-gel technique favored detection of low amounts of RIs and allowed analyses of fork progression in a synchronous system.
[]
In the present work, 2D-gel technique favored detection of low amounts of RIs and allowed analyses of fork progression in a synchronous system.
true
true
true
true
true
6,907
2
DISCUSSION
1
21
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
It revealed an ongoing and slow replication of php locus during most of the first half of S phase (Figures 1 and 2).
[ "21", "22", "21", "22" ]
116
40,004
0
false
It revealed an ongoing and slow replication of php locus during most of the first half of S phase (Figures 1 and 2).
[]
It revealed an ongoing and slow replication of php locus during most of the first half of S phase.
true
true
true
true
true
6,907
2
DISCUSSION
1
21
[ "B21", "B22", "B21", "B22" ]
17,717,000
pmid-17005913|pmid-16251353|pmid-16429127|pmid-15845769|pmid-2915922|pmid-1353456|pmid-2915922|pmid-1353456
As a result, completion of replication of php-containing HindIII fragments is achieved late in S phase.
[ "21", "22", "21", "22" ]
103
40,005
0
false
As a result, completion of replication of php-containing HindIII fragments is achieved late in S phase.
[]
As a result, completion of replication of php-containing HindIII fragments is achieved late in S phase.
true
true
true
true
true
6,907
3
DISCUSSION
1
20
[ "B20" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
In the same vein, if the php locus had been analyzed with microarrays, like DNA sequences from human chromosomes 21 and 22 (20), it is likely that it would be found to replicate both with early and late DNA and would be considered as a ‘pan S phase’ replicating locus.
[ "20" ]
268
40,006
1
false
In the same vein, if the php locus had been analyzed with microarrays, like DNA sequences from human chromosomes 21 and 22, it is likely that it would be found to replicate both with early and late DNA and would be considered as a ‘pan S phase’ replicating locus.
[ "20" ]
In the same vein, if the php locus had been analyzed with microarrays, like DNA sequences from human chromosomes 21 and 22, it is likely that it would be found to replicate both with early and late DNA and would be considered as a ‘pan S phase’ replicating locus.
true
true
true
true
true
6,908
3
DISCUSSION
1
20
[ "B20" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
The lack of strict timing of replication at php locus raises the question of homogeneity of temporal order of replication among the millions of nuclei contained within a plasmodium.
[ "20" ]
181
40,007
0
false
The lack of strict timing of replication at php locus raises the question of homogeneity of temporal order of replication among the millions of nuclei contained within a plasmodium.
[]
The lack of strict timing of replication at php locus raises the question of homogeneity of temporal order of replication among the millions of nuclei contained within a plasmodium.
true
true
true
true
true
6,908
3
DISCUSSION
1
20
[ "B20" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
We argued that a random replication of php locus would give a similar intensity of RI signal towards 1X signal at php locus and proP locus in an asynchronous population of microplasmodia.
[ "20" ]
187
40,008
0
false
We argued that a random replication of php locus would give a similar intensity of RI signal towards 1X signal at php locus and proP locus in an asynchronous population of microplasmodia.
[]
We argued that a random replication of php locus would give a similar intensity of RI signal towards 1X signal at php locus and proP locus in an asynchronous population of microplasmodia.
true
true
true
true
true
6,908
3
DISCUSSION
1
20
[ "B20" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
It is not the case, so that a long life span of php RIs is more consistent with our data (Figure 5).
[ "20" ]
100
40,009
0
false
It is not the case, so that a long life span of php RIs is more consistent with our data (Figure 5).
[]
It is not the case, so that a long life span of php RIs is more consistent with our data (Figure 5).
true
true
true
true
true
6,908
3
DISCUSSION
1
20
[ "B20" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
In addition, homogeneous replication fork progression was evidenced by the analyses of RIs obtained from DNA at specific time points of S phase (Figures 1 and 2).
[ "20" ]
162
40,010
0
false
In addition, homogeneous replication fork progression was evidenced by the analyses of RIs obtained from DNA at specific time points of S phase (Figures 1 and 2).
[]
In addition, homogeneous replication fork progression was evidenced by the analyses of RIs obtained from DNA at specific time points of S phase.
true
true
true
true
true
6,908
3
DISCUSSION
1
20
[ "B20" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
Therefore, our results rule out random replication timing among the plasmodium nuclei.
[ "20" ]
86
40,011
0
false
Therefore, our results rule out random replication timing among the plasmodium nuclei.
[]
Therefore, our results rule out random replication timing among the plasmodium nuclei.
true
true
true
true
true
6,908
3
DISCUSSION
1
20
[ "B20" ]
17,717,000
pmid-2915922|pmid-2915922|pmid-1353456|pmid-2822257|pmid-15845769
In contrast, they illustrate a local variation of replication timing within a replicon, since we demonstrated that the php gene replicated early and surrounding DNA sequences replicated later.
[ "20" ]
192
40,012
0
false
In contrast, they illustrate a local variation of replication timing within a replicon, since we demonstrated that the php gene replicated early and surrounding DNA sequences replicated later.
[]
In contrast, they illustrate a local variation of replication timing within a replicon, since we demonstrated that the php gene replicated early and surrounding DNA sequences replicated later.
true
true
true
true
true
6,908
4
DISCUSSION
1
45
[ "B45", "B46" ]
17,717,000
pmid-17139278|pmid-12539237
Replication timing of DNA sequences depends also upon how and when replication initiation occurs.
[ "45", "46" ]
97
40,013
0
false
Replication timing of DNA sequences depends also upon how and when replication initiation occurs.
[]
Replication timing of DNA sequences depends also upon how and when replication initiation occurs.
true
true
true
true
true
6,909
4
DISCUSSION
1
45
[ "B45", "B46" ]
17,717,000
pmid-17139278|pmid-12539237
The question of the nature of eukaryotic origins has been largely debated and two models seem to emerge: either specific origins fire at a fixed timing with a given efficiency, like it has been described in budding yeast, or redundant origins fire stochastically, a model that correlates with many observations made in m...
[ "45", "46" ]
339
40,014
1
false
The question of the nature of eukaryotic origins has been largely debated and two models seem to emerge: either specific origins fire at a fixed timing with a given efficiency, like it has been described in budding yeast, or redundant origins fire stochastically, a model that correlates with many observations made in m...
[ "45" ]
The question of the nature of eukaryotic origins has been largely debated and two models seem to emerge: either specific origins fire at a fixed timing with a given efficiency, like it has been described in budding yeast, or redundant origins fire stochastically, a model that correlates with many observations made in m...
true
true
true
true
true
6,909
4
DISCUSSION
1
46
[ "B45", "B46" ]
17,717,000
pmid-17139278|pmid-12539237
Thus in Xenopus egg extracts, random initiation has been described and it has been proposed that the frequency of initiation events increases during the S phase in order to ensure the completion of genome duplication (46).
[ "45", "46" ]
222
40,015
1
false
Thus in Xenopus egg extracts, random initiation has been described and it has been proposed that the frequency of initiation events increases during the S phase in order to ensure the completion of genome duplication.
[ "46" ]
Thus in Xenopus egg extracts, random initiation has been described and it has been proposed that the frequency of initiation events increases during the S phase in order to ensure the completion of genome duplication.
true
true
true
true
true
6,909