Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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6
INTRODUCTION
1
32
[ "b32", "b29", "b29", "b21", "b23" ]
17,088,290
NA|pmid-11226299|pmid-11226299|pmid-8568873|pmid-7490758
Second, each phage particle in a phage library displays up to five copies of the displayed protein (using a g3p display system), whereas only 1–10% of phage particles in a phagemid library display a single copy of the displayed protein (32).
[ "32", "29", "29", "21", "23" ]
241
7,800
1
false
Second, each phage particle in a phage library displays up to five copies of the displayed protein (using a g3p display system), whereas only 1–10% of phage particles in a phagemid library display a single copy of the displayed protein.
[ "32" ]
Second, each phage particle in a phage library displays up to five copies of the displayed protein, whereas only 1–10% of phage particles in a phagemid library display a single copy of the displayed protein.
true
true
true
true
true
1,266
6
INTRODUCTION
1
32
[ "b32", "b29", "b29", "b21", "b23" ]
17,088,290
NA|pmid-11226299|pmid-11226299|pmid-8568873|pmid-7490758
As a result, a greater number of binders in a library are recovered, and therefore antibodies tend to be more diverse.
[ "32", "29", "29", "21", "23" ]
118
7,801
0
false
As a result, a greater number of binders in a library are recovered, and therefore antibodies tend to be more diverse.
[]
As a result, a greater number of binders in a library are recovered, and therefore antibodies tend to be more diverse.
true
true
true
true
true
1,266
6
INTRODUCTION
1
29
[ "b32", "b29", "b29", "b21", "b23" ]
17,088,290
NA|pmid-11226299|pmid-11226299|pmid-8568873|pmid-7490758
However, this is counterbalanced by a lower average affinity (29): phagemid display, by virtue of the display of single proteins, results in the selection of fewer unique binders, which tend to have higher affinities (29).
[ "32", "29", "29", "21", "23" ]
222
7,802
2
true
However, this is counterbalanced by a lower average affinity : phagemid display, by virtue of the display of single proteins, results in the selection of fewer unique binders, which tend to have higher affinities.
[ "29", "29" ]
However, this is counterbalanced by a lower average affinity : phagemid display, by virtue of the display of single proteins, results in the selection of fewer unique binders, which tend to have higher affinities.
true
true
true
true
true
1,266
6
INTRODUCTION
1
32
[ "b32", "b29", "b29", "b21", "b23" ]
17,088,290
NA|pmid-11226299|pmid-11226299|pmid-8568873|pmid-7490758
For similar reasons, affinity maturation (21–23) can only be carried out using phagemid vectors.
[ "32", "29", "29", "21", "23" ]
96
7,803
0
false
For similar reasons, affinity maturation can only be carried out using phagemid vectors.
[ "21–23" ]
For similar reasons, affinity maturation can only be carried out using phagemid vectors.
true
true
true
true
true
1,266
7
INTRODUCTION
1
27
[ "b27", "b33", "b38", "b27", "b34", "b36", "b37", "b38" ]
17,088,290
pmid-9370269|pmid-7875580|pmid-11316373|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12771223|pmid-11316373|pmid-10625396|pmid-11526909
Recently, a number of groups (27,33–38) have developed alternative helper phage systems, compared in Table 1, designed to improve display in either of two ways: by increasing the display level, so that it resembles the display obtained with phage vectors (27,34–36), or by reducing the background from non-displaying pha...
[ "27", "33", "38", "27", "34", "36", "37", "38" ]
363
7,804
0
false
Recently, a number of groups have developed alternative helper phage systems, compared in Table 1, designed to improve display in either of two ways: by increasing the display level, so that it resembles the display obtained with phage vectors, or by reducing the background from non-displaying phage by rendering them n...
[ "27,33–38", "27,34–36", "37,38" ]
Recently, a number of groups have developed alternative helper phage systems, compared in Table 1, designed to improve display in either of two ways: by increasing the display level, so that it resembles the display obtained with phage vectors, or by reducing the background from non-displaying phage by rendering them n...
true
true
true
true
true
1,267
7
INTRODUCTION
1
27
[ "b27", "b33", "b38", "b27", "b34", "b36", "b37", "b38" ]
17,088,290
pmid-9370269|pmid-7875580|pmid-11316373|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12771223|pmid-11316373|pmid-10625396|pmid-11526909
However, none of these has been addressed the need for helper phage itself.
[ "27", "33", "38", "27", "34", "36", "37", "38" ]
75
7,805
0
false
However, none of these has been addressed the need for helper phage itself.
[]
However, none of these has been addressed the need for helper phage itself.
true
true
true
true
true
1,267
8
INTRODUCTION
1
35
[ "b35", "b27", "b34", "b36" ]
17,088,290
pmid-11135557|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12514927|pmid-12788548|pmid-11281835
Initial experiments to increase display involved the creation of g3p deleted helper phage, packaged in bacterial strains expressing gene 3 in trans.
[ "35", "27", "34", "36" ]
148
7,806
0
false
Initial experiments to increase display involved the creation of g3p deleted helper phage, packaged in bacterial strains expressing gene 3 in trans.
[]
Initial experiments to increase display involved the creation of g3p deleted helper phage, packaged in bacterial strains expressing gene 3 in trans.
true
true
true
true
true
1,268
8
INTRODUCTION
1
35
[ "b35", "b27", "b34", "b36" ]
17,088,290
pmid-11135557|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12514927|pmid-12788548|pmid-11281835
These allowed higher display levels, but suffered from the problem that when the g3p was derived from plasmids, although not when integrated into the Eschericia coli chromosome (35), such plasmids could also be packaged at low levels (27).
[ "35", "27", "34", "36" ]
239
7,807
1
false
These allowed higher display levels, but suffered from the problem that when the g3p was derived from plasmids, although not when integrated into the Eschericia coli chromosome, such plasmids could also be packaged at low levels.
[ "35", "27" ]
These allowed higher display levels, but suffered from the problem that when the g3p was derived from plasmids, although not when integrated into the Eschericia coli chromosome, such plasmids could also be packaged at low levels.
true
true
true
true
true
1,268
8
INTRODUCTION
1
35
[ "b35", "b27", "b34", "b36" ]
17,088,290
pmid-11135557|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12514927|pmid-12788548|pmid-11281835
Helper phage titers also tend to be very low.
[ "35", "27", "34", "36" ]
45
7,808
0
false
Helper phage titers also tend to be very low.
[]
Helper phage titers also tend to be very low.
true
true
true
true
true
1,268
8
INTRODUCTION
1
35
[ "b35", "b27", "b34", "b36" ]
17,088,290
pmid-11135557|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12514927|pmid-12788548|pmid-11281835
More recently, conditional g3p deletions have been created by the introduction of suppressible stop codons in g3 (34,36), allowing production of helper phage in suppressor strains, and the packaging of phagemids in non-suppressor strains, where the helper phage is unable to make its own g3p.
[ "35", "27", "34", "36" ]
292
7,809
0
false
More recently, conditional g3p deletions have been created by the introduction of suppressible stop codons in g3, allowing production of helper phage in suppressor strains, and the packaging of phagemids in non-suppressor strains, where the helper phage is unable to make its own g3p.
[ "34,36" ]
More recently, conditional g3p deletions have been created by the introduction of suppressible stop codons in g3, allowing production of helper phage in suppressor strains, and the packaging of phagemids in non-suppressor strains, where the helper phage is unable to make its own g3p.
true
true
true
true
true
1,268
9
INTRODUCTION
1
37
[ "b37", "b38" ]
17,088,290
pmid-12771223|pmid-11316373
Two approaches have been used to reduce background, in both of which only phagemid particles containing the recombinant g3p are infectious.
[ "37", "38" ]
139
7,810
0
false
Two approaches have been used to reduce background, in both of which only phagemid particles containing the recombinant g3p are infectious.
[]
Two approaches have been used to reduce background, in both of which only phagemid particles containing the recombinant g3p are infectious.
true
true
true
true
true
1,269
9
INTRODUCTION
1
37
[ "b37", "b38" ]
17,088,290
pmid-12771223|pmid-11316373
These involve either the deletion of the portions of g3p required for infection (37), or the incorporation of a trypsin site within the g3p of the helper phage, and using trypsin-treated phage for infection (38).
[ "37", "38" ]
212
7,811
1
false
These involve either the deletion of the portions of g3p required for infection, or the incorporation of a trypsin site within the g3p of the helper phage, and using trypsin-treated phage for infection.
[ "37", "38" ]
These involve either the deletion of the portions of g3p required for infection, or the incorporation of a trypsin site within the g3p of the helper phage, and using trypsin-treated phage for infection.
true
true
true
true
true
1,269
9
INTRODUCTION
1
37
[ "b37", "b38" ]
17,088,290
pmid-12771223|pmid-11316373
Both of these systems result in a lower background during selection by eliminating those phagemid particles which contain only helper phage derived g3p.
[ "37", "38" ]
152
7,812
0
false
Both of these systems result in a lower background during selection by eliminating those phagemid particles which contain only helper phage derived g3p.
[]
Both of these systems result in a lower background during selection by eliminating those phagemid particles which contain only helper phage derived g3p.
true
true
true
true
true
1,269
10
INTRODUCTION
0
null
null
17,088,290
null
Although these systems may overcome some of the disadvantages of helper phage, they do not avoid one of the main problems associated with the use of helper phage: the need to make helper phage and add it to growing bacterial cultures at relatively restricted phases of the growth cycle.
null
286
7,813
0
false
null
null
Although these systems may overcome some of the disadvantages of helper phage, they do not avoid one of the main problems associated with the use of helper phage: the need to make helper phage and add it to growing bacterial cultures at relatively restricted phases of the growth cycle.
true
true
true
true
true
1,270
10
INTRODUCTION
0
null
null
17,088,290
null
In this paper we describe a series of constructs which eliminate the need for helper phage altogether, creating a system in which bacterial packaging cell lines replace the use of helper phage, making the generation of pure phagemid particles as straightforward as using a phage-based system.
null
292
7,814
0
false
null
null
In this paper we describe a series of constructs which eliminate the need for helper phage altogether, creating a system in which bacterial packaging cell lines replace the use of helper phage, making the generation of pure phagemid particles as straightforward as using a phage-based system.
true
true
true
true
true
1,270
10
INTRODUCTION
0
null
null
17,088,290
null
Furthermore, by using different packaging bacteria the phagemid particles produced are either monovalent or multivalent.
null
120
7,815
0
false
null
null
Furthermore, by using different packaging bacteria the phagemid particles produced are either monovalent or multivalent.
true
true
true
true
true
1,270
10
INTRODUCTION
0
null
null
17,088,290
null
The concept is illustrated in Figure 1.
null
39
7,816
0
false
null
null
The concept is illustrated in Figure 1.
true
true
true
true
true
1,270
0
DISCUSSION
0
null
null
17,088,290
pmid-9630891|pmid-10656818|pmid-2201029|pmid-7535098|pmid-10051566|pmid-8303274|pmid-8568873|pmid-8609615|pmid-8254660
In this paper we describe a novel method to eliminate the use of helper phage from phagemid preparation, allowing the production of phagemid by simple bacterial growth.
null
168
7,817
0
false
null
null
In this paper we describe a novel method to eliminate the use of helper phage from phagemid preparation, allowing the production of phagemid by simple bacterial growth.
true
true
true
true
true
1,271
0
DISCUSSION
0
null
null
17,088,290
pmid-9630891|pmid-10656818|pmid-2201029|pmid-7535098|pmid-10051566|pmid-8303274|pmid-8568873|pmid-8609615|pmid-8254660
This has been carried out by the creation of bacterial packaging cell lines, containing helper plasmids, that are able to provide all the proteins required for phagemid packaging.
null
179
7,818
0
false
null
null
This has been carried out by the creation of bacterial packaging cell lines, containing helper plasmids, that are able to provide all the proteins required for phagemid packaging.
true
true
true
true
true
1,271
1
DISCUSSION
1
26
[ "b26", "b27", "b27", "b33", "b37", "b3", "b45", "b46", "b50", "b45", "b51", "b52" ]
17,088,290
pmid-2985470|pmid-9370269|pmid-2985470|pmid-9370269|pmid-9370269|pmid-7875580|pmid-12771223|pmid-10625396|pmid-11526909|pmid-10404162|pmid-16442560|pmid-11526909|pmid-10623552|pmid-15062775
These helper plasmids are based on M13mp19, with the phage packaging signal/origin replaced by p15a, and the addition of a chloramphenicol resistance gene.
[ "26", "27", "27", "33", "37", "3", "45", "46", "50", "45", "51", "52" ]
155
7,819
0
false
These helper plasmids are based on M13mp19, with the phage packaging signal/origin replaced by p15a, and the addition of a chloramphenicol resistance gene.
[]
These helper plasmids are based on M13mp19, with the phage packaging signal/origin replaced by p15a, and the addition of a chloramphenicol resistance gene.
true
true
true
true
true
1,272
1
DISCUSSION
1
26
[ "b26", "b27", "b27", "b33", "b37", "b3", "b45", "b46", "b50", "b45", "b51", "b52" ]
17,088,290
pmid-2985470|pmid-9370269|pmid-2985470|pmid-9370269|pmid-9370269|pmid-7875580|pmid-12771223|pmid-10625396|pmid-11526909|pmid-10404162|pmid-16442560|pmid-11526909|pmid-10623552|pmid-15062775
The absence of packaging signals in these helper plasmids prevents their DNA from being packaged.
[ "26", "27", "27", "33", "37", "3", "45", "46", "50", "45", "51", "52" ]
97
7,820
0
false
The absence of packaging signals in these helper plasmids prevents their DNA from being packaged.
[]
The absence of packaging signals in these helper plasmids prevents their DNA from being packaged.
true
true
true
true
true
1,272
1
DISCUSSION
1
26
[ "b26", "b27", "b27", "b33", "b37", "b3", "b45", "b46", "b50", "b45", "b51", "b52" ]
17,088,290
pmid-2985470|pmid-9370269|pmid-2985470|pmid-9370269|pmid-9370269|pmid-7875580|pmid-12771223|pmid-10625396|pmid-11526909|pmid-10404162|pmid-16442560|pmid-11526909|pmid-10623552|pmid-15062775
This provides a number of significant advantages over the use of both standard (26,27) and modified helper phages (27,33–37).
[ "26", "27", "27", "33", "37", "3", "45", "46", "50", "45", "51", "52" ]
125
7,821
0
false
This provides a number of significant advantages over the use of both standard and modified helper phages.
[ "26,27", "27,33–37" ]
This provides a number of significant advantages over the use of both standard and modified helper phages.
true
true
true
true
true
1,272
1
DISCUSSION
1
26
[ "b26", "b27", "b27", "b33", "b37", "b3", "b45", "b46", "b50", "b45", "b51", "b52" ]
17,088,290
pmid-2985470|pmid-9370269|pmid-2985470|pmid-9370269|pmid-9370269|pmid-7875580|pmid-12771223|pmid-10625396|pmid-11526909|pmid-10404162|pmid-16442560|pmid-11526909|pmid-10623552|pmid-15062775
Perhaps most important is the purity of the phagemids produced: we have been unable to detect contamination of phagemids prepared using these helper plasmids with any helper phage genomes whatsoever.
[ "26", "27", "27", "33", "37", "3", "45", "46", "50", "45", "51", "52" ]
199
7,822
0
false
Perhaps most important is the purity of the phagemids produced: we have been unable to detect contamination of phagemids prepared using these helper plasmids with any helper phage genomes whatsoever.
[]
Perhaps most important is the purity of the phagemids produced: we have been unable to detect contamination of phagemids prepared using these helper plasmids with any helper phage genomes whatsoever.
true
true
true
true
true
1,272
1
DISCUSSION
1
26
[ "b26", "b27", "b27", "b33", "b37", "b3", "b45", "b46", "b50", "b45", "b51", "b52" ]
17,088,290
pmid-2985470|pmid-9370269|pmid-2985470|pmid-9370269|pmid-9370269|pmid-7875580|pmid-12771223|pmid-10625396|pmid-11526909|pmid-10404162|pmid-16442560|pmid-11526909|pmid-10623552|pmid-15062775
For phage display, this avoids the occasional problem of helper phage overgrowth, which can result in failed selections.
[ "26", "27", "27", "33", "37", "3", "45", "46", "50", "45", "51", "52" ]
120
7,823
0
false
For phage display, this avoids the occasional problem of helper phage overgrowth, which can result in failed selections.
[]
For phage display, this avoids the occasional problem of helper phage overgrowth, which can result in failed selections.
true
true
true
true
true
1,272
1
DISCUSSION
1
26
[ "b26", "b27", "b27", "b33", "b37", "b3", "b45", "b46", "b50", "b45", "b51", "b52" ]
17,088,290
pmid-2985470|pmid-9370269|pmid-2985470|pmid-9370269|pmid-9370269|pmid-7875580|pmid-12771223|pmid-10625396|pmid-11526909|pmid-10404162|pmid-16442560|pmid-11526909|pmid-10623552|pmid-15062775
For other applications, the genetic purity of the phagemid particles, combined with their extremely high titers, makes this a powerful method to transfer genetic material between bacteria.
[ "26", "27", "27", "33", "37", "3", "45", "46", "50", "45", "51", "52" ]
188
7,824
0
false
For other applications, the genetic purity of the phagemid particles, combined with their extremely high titers, makes this a powerful method to transfer genetic material between bacteria.
[]
For other applications, the genetic purity of the phagemid particles, combined with their extremely high titers, makes this a powerful method to transfer genetic material between bacteria.
true
true
true
true
true
1,272
1
DISCUSSION
1
26
[ "b26", "b27", "b27", "b33", "b37", "b3", "b45", "b46", "b50", "b45", "b51", "b52" ]
17,088,290
pmid-2985470|pmid-9370269|pmid-2985470|pmid-9370269|pmid-9370269|pmid-7875580|pmid-12771223|pmid-10625396|pmid-11526909|pmid-10404162|pmid-16442560|pmid-11526909|pmid-10623552|pmid-15062775
This is likely to be particularly useful in the generation of antibody diversity by recombination (3,45), and in genetic selection protocols carried out in bacteria (46–50), in which it will be possible to replace library transfection by infection.
[ "26", "27", "27", "33", "37", "3", "45", "46", "50", "45", "51", "52" ]
248
7,825
0
false
This is likely to be particularly useful in the generation of antibody diversity by recombination, and in genetic selection protocols carried out in bacteria, in which it will be possible to replace library transfection by infection.
[ "3,45", "46–50" ]
This is likely to be particularly useful in the generation of antibody diversity by recombination, and in genetic selection protocols carried out in bacteria, in which it will be possible to replace library transfection by infection.
true
true
true
true
true
1,272
1
DISCUSSION
1
52
[ "b26", "b27", "b27", "b33", "b37", "b3", "b45", "b46", "b50", "b45", "b51", "b52" ]
17,088,290
pmid-2985470|pmid-9370269|pmid-2985470|pmid-9370269|pmid-9370269|pmid-7875580|pmid-12771223|pmid-10625396|pmid-11526909|pmid-10404162|pmid-16442560|pmid-11526909|pmid-10623552|pmid-15062775
As infection is far more efficient than transfection, this will be especially applicable to library-versus-library (45,51) selection protocols, where increased efficiency of entry by infection will result in higher sampling of library diversity (52).
[ "26", "27", "27", "33", "37", "3", "45", "46", "50", "45", "51", "52" ]
250
7,826
1
false
As infection is far more efficient than transfection, this will be especially applicable to library-versus-library selection protocols, where increased efficiency of entry by infection will result in higher sampling of library diversity.
[ "45,51", "52" ]
As infection is far more efficient than transfection, this will be especially applicable to library-versus-library selection protocols, where increased efficiency of entry by infection will result in higher sampling of library diversity.
true
true
true
true
true
1,272
2
DISCUSSION
1
27
[ "b27", "b53" ]
17,088,290
pmid-9370269|pmid-9631287
Although the helper plasmids were designed to lack the M13 packaging signal, the complete absence of packaging into phage particles is at first somewhat surprising, considering that many other plasmids, without M13 origins, do show low levels of packaging (27).
[ "27", "53" ]
261
7,827
1
false
Although the helper plasmids were designed to lack the M13 packaging signal, the complete absence of packaging into phage particles is at first somewhat surprising, considering that many other plasmids, without M13 origins, do show low levels of packaging.
[ "27" ]
Although the helper plasmids were designed to lack the M13 packaging signal, the complete absence of packaging into phage particles is at first somewhat surprising, considering that many other plasmids, without M13 origins, do show low levels of packaging.
true
true
true
true
true
1,273
2
DISCUSSION
1
27
[ "b27", "b53" ]
17,088,290
pmid-9370269|pmid-9631287
This is usually attributed to the presence of cryptic packaging signals in plasmids which can be inefficiently recognized by the M13 packaging machinery.
[ "27", "53" ]
153
7,828
0
false
This is usually attributed to the presence of cryptic packaging signals in plasmids which can be inefficiently recognized by the M13 packaging machinery.
[]
This is usually attributed to the presence of cryptic packaging signals in plasmids which can be inefficiently recognized by the M13 packaging machinery.
true
true
true
true
true
1,273
2
DISCUSSION
1
53
[ "b27", "b53" ]
17,088,290
pmid-9370269|pmid-9631287
It is likely that evolution has selected against the presence of other putative packaging sequences in the M13 genome to ensure that only the correct single site is used, so guaranteeing correct orientation within the phage particle (53).
[ "27", "53" ]
238
7,829
1
false
It is likely that evolution has selected against the presence of other putative packaging sequences in the M13 genome to ensure that only the correct single site is used, so guaranteeing correct orientation within the phage particle.
[ "53" ]
It is likely that evolution has selected against the presence of other putative packaging sequences in the M13 genome to ensure that only the correct single site is used, so guaranteeing correct orientation within the phage particle.
true
true
true
true
true
1,273
2
DISCUSSION
1
27
[ "b27", "b53" ]
17,088,290
pmid-9370269|pmid-9631287
As a result elimination provides no alternative signals in the phage, and it is clear that neither the p15a origin nor the added chloramphenicol resistance gene are able to provide alternative signals.
[ "27", "53" ]
201
7,830
0
false
As a result elimination provides no alternative signals in the phage, and it is clear that neither the p15a origin nor the added chloramphenicol resistance gene are able to provide alternative signals.
[]
As a result elimination provides no alternative signals in the phage, and it is clear that neither the p15a origin nor the added chloramphenicol resistance gene are able to provide alternative signals.
true
true
true
true
true
1,273
3
DISCUSSION
1
54
[ "b54", "b55", "b56", "b57", "b58", "b60", "b27", "b61", "b62" ]
17,088,290
pmid-3886166|pmid-3872373|pmid-2009963|pmid-2804106|pmid-9244308|NA|pmid-9370269|pmid-6955583|pmid-2319594
The helper plasmids differ in the form of g3 they contain; the g3p in M13cp is full length, that in M13cp-CT is truncated.
[ "54", "55", "56", "57", "58", "60", "27", "61", "62" ]
122
7,831
0
false
The helper plasmids differ in the form of g3 they contain; the g3p in M13cp is full length, that in M13cp-CT is truncated.
[]
The helper plasmids differ in the form of g3 they contain; the g3p in M13cp is full length, that in M13cp-CT is truncated.
true
true
true
true
true
1,274
3
DISCUSSION
1
54
[ "b54", "b55", "b56", "b57", "b58", "b60", "b27", "b61", "b62" ]
17,088,290
pmid-3886166|pmid-3872373|pmid-2009963|pmid-2804106|pmid-9244308|NA|pmid-9370269|pmid-6955583|pmid-2319594
M13cp-CT contains the portion of g3p responsible for phage assembly and release (54,55), but lacks the domains involved in bacterial toxicity (56,57), phage infection (58–60) and the inhibition of infection by bacteria carrying g3p (27,61,62).
[ "54", "55", "56", "57", "58", "60", "27", "61", "62" ]
243
7,832
0
false
M13cp-CT contains the portion of g3p responsible for phage assembly and release, but lacks the domains involved in bacterial toxicity, phage infection and the inhibition of infection by bacteria carrying g3p.
[ "54,55", "56,57", "58–60", "27,61,62" ]
M13cp-CT contains the portion of g3p responsible for phage assembly and release, but lacks the domains involved in bacterial toxicity, phage infection and the inhibition of infection by bacteria carrying g3p.
true
true
true
true
true
1,274
3
DISCUSSION
1
54
[ "b54", "b55", "b56", "b57", "b58", "b60", "b27", "b61", "b62" ]
17,088,290
pmid-3886166|pmid-3872373|pmid-2009963|pmid-2804106|pmid-9244308|NA|pmid-9370269|pmid-6955583|pmid-2319594
M13cp-dg3 contains no g3, by virtue of genetic deletion, and gave lower titers than M13cp or M13cp-CT, but ELISA and western signals intermediate between the two.
[ "54", "55", "56", "57", "58", "60", "27", "61", "62" ]
162
7,833
0
false
M13cp-dg3 contains no g3, by virtue of genetic deletion, and gave lower titers than M13cp or M13cp-CT, but ELISA and western signals intermediate between the two.
[]
M13cp-dg3 contains no g3, by virtue of genetic deletion, and gave lower titers than M13cp or M13cp-CT, but ELISA and western signals intermediate between the two.
true
true
true
true
true
1,274
4
DISCUSSION
1
58
[ "b58", "b60" ]
17,088,290
pmid-1908075|pmid-11226299|pmid-9244308|NA
When phagemid are infected into bacteria containing M13cp the plating efficiencies obtained are consistently lower than those obtained in bacteria containing the other helper plasmids, or no plasmids at all.
[ "58", "60" ]
207
7,834
0
false
When phagemid are infected into bacteria containing M13cp the plating efficiencies obtained are consistently lower than those obtained in bacteria containing the other helper plasmids, or no plasmids at all.
[]
When phagemid are infected into bacteria containing M13cp the plating efficiencies obtained are consistently lower than those obtained in bacteria containing the other helper plasmids, or no plasmids at all.
true
true
true
true
true
1,275
4
DISCUSSION
1
58
[ "b58", "b60" ]
17,088,290
pmid-1908075|pmid-11226299|pmid-9244308|NA
As this cannot be overcome by increa-sing the number of bacteria, the problem is not a reduction in infectivity (e.g.
[ "58", "60" ]
117
7,835
0
false
As this cannot be overcome by increa-sing the number of bacteria, the problem is not a reduction in infectivity (e.g.
[]
As this cannot be overcome by increa-sing the number of bacteria, the problem is not a reduction in infectivity (e.g.
true
true
true
true
true
1,275
4
DISCUSSION
1
58
[ "b58", "b60" ]
17,088,290
pmid-1908075|pmid-11226299|pmid-9244308|NA
by a reduction in the number of bacteria displaying pili), as might be expected, but a failure of these phagemids to establish themselves within the bacteria (e.g.
[ "58", "60" ]
163
7,836
0
false
by a reduction in the number of bacteria displaying pili), as might be expected, but a failure of these phagemids to establish themselves within the bacteria (e.g.
[]
by a reduction in the number of bacteria displaying pili), as might be expected, but a failure of these phagemids to establish themselves within the bacteria (e.g.
false
true
true
true
false
1,275
4
DISCUSSION
1
58
[ "b58", "b60" ]
17,088,290
pmid-1908075|pmid-11226299|pmid-9244308|NA
an inability to replicate).
[ "58", "60" ]
27
7,837
0
false
an inability to replicate).
[]
an inability to replicate).
false
true
true
true
false
1,275
4
DISCUSSION
1
58
[ "b58", "b60" ]
17,088,290
pmid-1908075|pmid-11226299|pmid-9244308|NA
This could occur at a number of different levels, including sequestration of the TolA co-receptor by the helper plasmid g3p (58,60), preventing productive phagemid particle entry into the bacteria, or a failure of phagemid DNA replication or survival after entry into the cytoplasm.
[ "58", "60" ]
282
7,838
0
false
This could occur at a number of different levels, including sequestration of the TolA co-receptor by the helper plasmid g3p, preventing productive phagemid particle entry into the bacteria, or a failure of phagemid DNA replication or survival after entry into the cytoplasm.
[ "58,60" ]
This could occur at a number of different levels, including sequestration of the TolA co-receptor by the helper plasmid g3p, preventing productive phagemid particle entry into the bacteria, or a failure of phagemid DNA replication or survival after entry into the cytoplasm.
true
true
true
true
true
1,275
5
DISCUSSION
1
63
[ "b63" ]
17,088,290
pmid-11384684|pmid-12514927|pmid-10373366
In phagemid particles packaged using M13cp most of the g3p appears to be derived from the helper plasmid, and very little from the display vector.
[ "63" ]
146
7,839
0
false
In phagemid particles packaged using M13cp most of the g3p appears to be derived from the helper plasmid, and very little from the display vector.
[]
In phagemid particles packaged using M13cp most of the g3p appears to be derived from the helper plasmid, and very little from the display vector.
true
true
true
true
true
1,276
5
DISCUSSION
1
63
[ "b63" ]
17,088,290
pmid-11384684|pmid-12514927|pmid-10373366
As a result, low levels of monovalent display occur (Figure 5).
[ "63" ]
63
7,840
0
false
As a result, low levels of monovalent display occur (Figure 5).
[]
As a result, low levels of monovalent display occur (Figure 5).
true
true
true
true
true
1,276
5
DISCUSSION
1
63
[ "b63" ]
17,088,290
pmid-11384684|pmid-12514927|pmid-10373366
However, in the case of phagemid particles made using M13cp-CT, a large proportion of the incorporated g3p in phagemid is derived from the display vector (compare the intensity of the g3p-CT fragment in Figure 5B with that of the g3p and g3p+scFv bands), and of this almost 50% is full length (compare g3p+scFv with g3p ...
[ "63" ]
400
7,841
0
false
However, in the case of phagemid particles made using M13cp-CT, a large proportion of the incorporated g3p in phagemid is derived from the display vector (compare the intensity of the g3p-CT fragment in Figure 5B with that of the g3p and g3p+scFv bands), and of this almost 50% is full length (compare g3p+scFv with g3p ...
[]
However, in the case of phagemid particles made using M13cp-CT, a large proportion of the incorporated g3p in phagemid is derived from the display vector, and of this almost 50% is full length, leading to the very high multivalent display levels seen.
true
true
true
true
true
1,276
5
DISCUSSION
1
63
[ "b63" ]
17,088,290
pmid-11384684|pmid-12514927|pmid-10373366
This is also reflected in the ELISA results shown in Figure 4B: in order to mimic the signal obtained with phagemid particles produced using M13cp-CT, 100-fold more phagmid particles produced using M13K07 or M13cp are required.
[ "63" ]
227
7,842
0
false
This is also reflected in the ELISA results shown in Figure 4B: in order to mimic the signal obtained with phagemid particles produced using M13cp-CT, 100-fold more phagmid particles produced using M13K07 or M13cp are required.
[]
This is also reflected in the ELISA results shown in Figure 4B: in order to mimic the signal obtained with phagemid particles produced using M13cp-CT, 100-fold more phagmid particles produced using M13K07 or M13cp are required.
true
true
true
true
true
1,276
5
DISCUSSION
1
63
[ "b63" ]
17,088,290
pmid-11384684|pmid-12514927|pmid-10373366
This suggests that there is a preference for the full-length g3p provided by the display vector over the truncated form provided by the helper plasmid during phage assembly.
[ "63" ]
173
7,843
0
false
This suggests that there is a preference for the full-length g3p provided by the display vector over the truncated form provided by the helper plasmid during phage assembly.
[]
This suggests that there is a preference for the full-length g3p provided by the display vector over the truncated form provided by the helper plasmid during phage assembly.
true
true
true
true
true
1,276
5
DISCUSSION
1
63
[ "b63" ]
17,088,290
pmid-11384684|pmid-12514927|pmid-10373366
Although the C-terminal domain is known to be sufficient to allow phage assembly to occur (63), this result suggests that additional portions of g3p facilitate the process, leading to increased incorporation levels when full-length g3p is used.
[ "63" ]
244
7,844
1
false
Although the C-terminal domain is known to be sufficient to allow phage assembly to occur, this result suggests that additional portions of g3p facilitate the process, leading to increased incorporation levels when full-length g3p is used.
[ "63" ]
Although the C-terminal domain is known to be sufficient to allow phage assembly to occur, this result suggests that additional portions of g3p facilitate the process, leading to increased incorporation levels when full-length g3p is used.
true
true
true
true
true
1,276
6
DISCUSSION
0
null
null
17,088,290
NA|pmid-11226299|pmid-11226299|pmid-8568873|pmid-7490758
M13cp and M13cp-CT stand out as being the most useful helper plasmids, each with potentially different applications.
null
116
7,845
0
false
null
null
M13cp and M13cp-CT stand out as being the most useful helper plasmids, each with potentially different applications.
true
true
true
true
true
1,277
6
DISCUSSION
0
null
null
17,088,290
NA|pmid-11226299|pmid-11226299|pmid-8568873|pmid-7490758
For phage display, it is likely that a selection approach combining both, in which phagemid packaged by M13cp-CT, providing multivalent display able to capture full diversity, is used in early rounds of selection, and M13cp, packaging monovalent phagemids, is used in later rounds to select higher affinity clones, will ...
null
339
7,846
0
false
null
null
For phage display, it is likely that a selection approach combining both, in which phagemid packaged by M13cp-CT, providing multivalent display able to capture full diversity, is used in early rounds of selection, and M13cp, packaging monovalent phagemids, is used in later rounds to select higher affinity clones, will ...
true
true
true
true
true
1,277
6
DISCUSSION
0
null
null
17,088,290
NA|pmid-11226299|pmid-11226299|pmid-8568873|pmid-7490758
Given the lower plating efficiency of M13cp, it should only be used once selected phagemids are well represented (e.g.
null
118
7,847
0
false
null
null
Given the lower plating efficiency of M13cp, it should only be used once selected phagemids are well represented (e.g.
true
true
true
true
true
1,277
6
DISCUSSION
0
null
null
17,088,290
NA|pmid-11226299|pmid-11226299|pmid-8568873|pmid-7490758
after the second round), in order to avoid loss of diversity.
null
61
7,848
0
false
null
null
after the second round), in order to avoid loss of diversity.
false
true
true
true
false
1,277
7
DISCUSSION
1
3
[ "b3", "b45" ]
17,088,290
pmid-9370269|pmid-7875580|pmid-11316373|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12771223|pmid-11316373|pmid-10625396|pmid-11526909
M13cp could also be very useful for transferring genetic material between bacteria when maximum diversity must be maintained (3,45), for making phagemid particles for other purposes, and also in phage display when display proteins other than p3 are used.
[ "3", "45" ]
254
7,849
0
false
M13cp could also be very useful for transferring genetic material between bacteria when maximum diversity must be maintained, for making phagemid particles for other purposes, and also in phage display when display proteins other than p3 are used.
[ "3,45" ]
M13cp could also be very useful for transferring genetic material between bacteria when maximum diversity must be maintained, for making phagemid particles for other purposes, and also in phage display when display proteins other than p3 are used.
true
true
true
true
true
1,278
7
DISCUSSION
1
3
[ "b3", "b45" ]
17,088,290
pmid-9370269|pmid-7875580|pmid-11316373|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12771223|pmid-11316373|pmid-10625396|pmid-11526909
Surprisingly, M13cp-dg3 does not appear to have any advantages over M13cp-CT, giving lower titers, and lower ELISA signals at similar titers, and at the moment it is difficult to find a use for this construct.
[ "3", "45" ]
209
7,850
0
false
Surprisingly, M13cp-dg3 does not appear to have any advantages over M13cp-CT, giving lower titers, and lower ELISA signals at similar titers, and at the moment it is difficult to find a use for this construct.
[]
Surprisingly, M13cp-dg3 does not appear to have any advantages over M13cp-CT, giving lower titers, and lower ELISA signals at similar titers, and at the moment it is difficult to find a use for this construct.
true
true
true
true
true
1,278
8
DISCUSSION
1
31
[ "b31", "b64", "b66" ]
17,088,290
pmid-11135557|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12514927|pmid-12788548|pmid-11281835
At a practical level, these helper plasmids are easier to use than helper phage-based systems.
[ "31", "64", "66" ]
94
7,851
0
false
At a practical level, these helper plasmids are easier to use than helper phage-based systems.
[]
At a practical level, these helper plasmids are easier to use than helper phage-based systems.
true
true
true
true
true
1,279
8
DISCUSSION
1
31
[ "b31", "b64", "b66" ]
17,088,290
pmid-11135557|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12514927|pmid-12788548|pmid-11281835
Bacteria containing the helper plasmid can be either infected or transformed with phagemid and then grown up in selective media without the need to further monitor bacterial OD.
[ "31", "64", "66" ]
177
7,852
0
false
Bacteria containing the helper plasmid can be either infected or transformed with phagemid and then grown up in selective media without the need to further monitor bacterial OD.
[]
Bacteria containing the helper plasmid can be either infected or transformed with phagemid and then grown up in selective media without the need to further monitor bacterial OD.
true
true
true
true
true
1,279
8
DISCUSSION
1
31
[ "b31", "b64", "b66" ]
17,088,290
pmid-11135557|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12514927|pmid-12788548|pmid-11281835
In fact, we have found that it is sufficient to add phagemid particles to a freshly diluted overnight culture of M13-cap-p15-CT bacteria and grow: bacteria become infected and phage production follows.
[ "31", "64", "66" ]
201
7,853
0
false
In fact, we have found that it is sufficient to add phagemid particles to a freshly diluted overnight culture of M13-cap-p15-CT bacteria and grow: bacteria become infected and phage production follows.
[]
In fact, we have found that it is sufficient to add phagemid particles to a freshly diluted overnight culture of M13-cap-p15-CT bacteria and grow: bacteria become infected and phage production follows.
true
true
true
true
true
1,279
8
DISCUSSION
1
31
[ "b31", "b64", "b66" ]
17,088,290
pmid-11135557|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12514927|pmid-12788548|pmid-11281835
Similarly, bacterial colonies can be scraped after overnight growth, and phagemid particles can be harvested from the supernatant after centrifugation.
[ "31", "64", "66" ]
151
7,854
0
false
Similarly, bacterial colonies can be scraped after overnight growth, and phagemid particles can be harvested from the supernatant after centrifugation.
[]
Similarly, bacterial colonies can be scraped after overnight growth, and phagemid particles can be harvested from the supernatant after centrifugation.
true
true
true
true
true
1,279
8
DISCUSSION
1
31
[ "b31", "b64", "b66" ]
17,088,290
pmid-11135557|pmid-9370269|pmid-12609549|pmid-11861923|pmid-12514927|pmid-12788548|pmid-11281835
Although these helper plasmids will simplify the use of phage display under standard selection conditions, it is in high-throughput antibody selection projects (31,64–66), where minimal oversight is desired, and it is impractical to closely monitor bacterial OD in order to add helper phage, that they will prove particu...
[ "31", "64", "66" ]
333
7,855
0
false
Although these helper plasmids will simplify the use of phage display under standard selection conditions, it is in high-throughput antibody selection projects, where minimal oversight is desired, and it is impractical to closely monitor bacterial OD in order to add helper phage, that they will prove particularly usefu...
[ "31,64–66" ]
Although these helper plasmids will simplify the use of phage display under standard selection conditions, it is in high-throughput antibody selection projects, where minimal oversight is desired, and it is impractical to closely monitor bacterial OD in order to add helper phage, that they will prove particularly usefu...
true
true
true
true
true
1,279
0
INTRODUCTION
1
1
[ "b1", "b4" ]
17,088,291
pmid-15448691|pmid-14690598|pmid-12609035
Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality control system that identifies and degrades mRNAs containing premature termination codons (PTC), thereby preventing the accumulation of truncated proteins, which might act as dominant-negative mutants.
[ "1", "4" ]
260
7,856
0
false
Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality control system that identifies and degrades mRNAs containing premature termination codons (PTC), thereby preventing the accumulation of truncated proteins, which might act as dominant-negative mutants.
[]
Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality control system that identifies and degrades mRNAs containing premature termination codons (PTC), thereby preventing the accumulation of truncated proteins, which might act as dominant-negative mutants.
true
true
true
true
true
1,280
0
INTRODUCTION
1
1
[ "b1", "b4" ]
17,088,291
pmid-15448691|pmid-14690598|pmid-12609035
In addition to eliminating aberrant mRNAs, NMD regulates the expression of wild-type genes, as ∼5–10% of the yeast, human or Drosophila transcriptome is altered in NMD deficient cells (1–4).
[ "1", "4" ]
190
7,857
0
false
In addition to eliminating aberrant mRNAs, NMD regulates the expression of wild-type genes, as ∼5–10% of the yeast, human or Drosophila transcriptome is altered in NMD deficient cells.
[ "1–4" ]
In addition to eliminating aberrant mRNAs, NMD regulates the expression of wild-type genes, as ∼5–10% of the yeast, human or Drosophila transcriptome is altered in NMD deficient cells.
true
true
true
true
true
1,280
1
INTRODUCTION
1
5
[ "b5", "b7", "b8", "b9" ]
17,088,291
pmid-15040442|pmid-16043493|pmid-15525991|pmid-16246174
To identify PTC-containing transcripts, the NMD machinery should efficiently discriminate between authentic stop codons and PTCs.
[ "5", "7", "8", "9" ]
129
7,858
0
false
To identify PTC-containing transcripts, the NMD machinery should efficiently discriminate between authentic stop codons and PTCs.
[]
To identify PTC-containing transcripts, the NMD machinery should efficiently discriminate between authentic stop codons and PTCs.
true
true
true
true
true
1,281
1
INTRODUCTION
1
5
[ "b5", "b7", "b8", "b9" ]
17,088,291
pmid-15040442|pmid-16043493|pmid-15525991|pmid-16246174
At least two (not mutually exclusive) models have been suggested to explain how NMD recognizes PTCs.
[ "5", "7", "8", "9" ]
100
7,859
0
false
At least two (not mutually exclusive) models have been suggested to explain how NMD recognizes PTCs.
[]
At least two (not mutually exclusive) models have been suggested to explain how NMD recognizes PTCs.
true
true
true
true
true
1,281
1
INTRODUCTION
1
5
[ "b5", "b7", "b8", "b9" ]
17,088,291
pmid-15040442|pmid-16043493|pmid-15525991|pmid-16246174
The first model (often referred to as the pioneer translation or nuclear marking model) suggests that cis-acting NMD elements are present in the coding region but not in the 3′-untranslated region (3′-UTR) of wild-type mRNAs.
[ "5", "7", "8", "9" ]
225
7,860
0
false
The first model (often referred to as the pioneer translation or nuclear marking model) suggests that cis-acting NMD elements are present in the coding region but not in the 3′-untranslated region (3′-UTR) of wild-type mRNAs.
[]
The first model (often referred to as the pioneer translation or nuclear marking model) suggests that cis-acting NMD elements are present in the coding region but not in the 3′-untranslated region (3′-UTR) of wild-type mRNAs.
true
true
true
true
true
1,281
1
INTRODUCTION
1
5
[ "b5", "b7", "b8", "b9" ]
17,088,291
pmid-15040442|pmid-16043493|pmid-15525991|pmid-16246174
In the nucleus, NMD trans-acting factors bind to the NMD cis elements and are transported with the mRNAs into the cytoplasm.
[ "5", "7", "8", "9" ]
124
7,861
0
false
In the nucleus, NMD trans-acting factors bind to the NMD cis elements and are transported with the mRNAs into the cytoplasm.
[]
In the nucleus, NMD trans-acting factors bind to the NMD cis elements and are transported with the mRNAs into the cytoplasm.
true
true
true
true
true
1,281
1
INTRODUCTION
1
5
[ "b5", "b7", "b8", "b9" ]
17,088,291
pmid-15040442|pmid-16043493|pmid-15525991|pmid-16246174
During the pioneer round of translation, ribosomes displace the NMD trans-acting factors from wild-type mRNAs.
[ "5", "7", "8", "9" ]
110
7,862
0
false
During the pioneer round of translation, ribosomes displace the NMD trans-acting factors from wild-type mRNAs.
[]
During the pioneer round of translation, ribosomes displace the NMD trans-acting factors from wild-type mRNAs.
true
true
true
true
true
1,281
1
INTRODUCTION
1
5
[ "b5", "b7", "b8", "b9" ]
17,088,291
pmid-15040442|pmid-16043493|pmid-15525991|pmid-16246174
However, if translation is stopped at a PTC, the NMD trans-acting factors bound downstream of the PTC are retained on the mRNA.
[ "5", "7", "8", "9" ]
127
7,863
0
false
However, if translation is stopped at a PTC, the NMD trans-acting factors bound downstream of the PTC are retained on the mRNA.
[]
However, if translation is stopped at a PTC, the NMD trans-acting factors bound downstream of the PTC are retained on the mRNA.
true
true
true
true
true
1,281
1
INTRODUCTION
1
5
[ "b5", "b7", "b8", "b9" ]
17,088,291
pmid-15040442|pmid-16043493|pmid-15525991|pmid-16246174
These mRNA-bound NMD factors recruit further NMD components including UPF1, thereby leading to formation of functional NMD complexes and rapid degradation of the PTC-containing mRNA (5–7).
[ "5", "7", "8", "9" ]
188
7,864
0
false
These mRNA-bound NMD factors recruit further NMD components including UPF1, thereby leading to formation of functional NMD complexes and rapid degradation of the PTC-containing mRNA.
[ "5–7" ]
These mRNA-bound NMD factors recruit further NMD components including UPF1, thereby leading to formation of functional NMD complexes and rapid degradation of the PTC-containing mRNA.
true
true
true
true
true
1,281
1
INTRODUCTION
1
5
[ "b5", "b7", "b8", "b9" ]
17,088,291
pmid-15040442|pmid-16043493|pmid-15525991|pmid-16246174
The second model (the faux UTR model) proposes that translation termination on PTC-containing mRNAs is aberrant because their 3′-UTR lacks the factors required for normal termination.
[ "5", "7", "8", "9" ]
183
7,865
0
false
The second model (the faux UTR model) proposes that translation termination on PTC-containing mRNAs is aberrant because their 3′-UTR lacks the factors required for normal termination.
[]
The second model (the faux UTR model) proposes that translation termination on PTC-containing mRNAs is aberrant because their 3′-UTR lacks the factors required for normal termination.
true
true
true
true
true
1,281
1
INTRODUCTION
1
5
[ "b5", "b7", "b8", "b9" ]
17,088,291
pmid-15040442|pmid-16043493|pmid-15525991|pmid-16246174
This model suggests that aberrant translation termination results in assembly of a functional NMD complex, thus leading to rapid decay of PTC-containing mRNAs (8,9).
[ "5", "7", "8", "9" ]
165
7,866
0
false
This model suggests that aberrant translation termination results in assembly of a functional NMD complex, thus leading to rapid decay of PTC-containing mRNAs.
[ "8,9" ]
This model suggests that aberrant translation termination results in assembly of a functional NMD complex, thus leading to rapid decay of PTC-containing mRNAs.
true
true
true
true
true
1,281
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
UPF3, UPF2 and UPF1 proteins are required for NMD in yeast, worm, Drosophila and mammals (10).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
94
7,867
1
false
UPF3, UPF2 and UPF1 proteins are required for NMD in yeast, worm, Drosophila and mammals.
[ "10" ]
UPF3, UPF2 and UPF1 proteins are required for NMD in yeast, worm, Drosophila and mammals.
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
Although these core trans-acting NMD factors are conserved, the cis-acting NMD elements are different in mammals and in yeast.
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
126
7,868
0
false
Although these core trans-acting NMD factors are conserved, the cis-acting NMD elements are different in mammals and in yeast.
[]
Although these core trans-acting NMD factors are conserved, the cis-acting NMD elements are different in mammals and in yeast.
true
true
true
true
true
1,282
2
INTRODUCTION
1
11
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
In mammalian cells, introns are believed to be the predominant cis-acting NMD elements (11).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
92
7,869
1
false
In mammalian cells, introns are believed to be the predominant cis-acting NMD elements.
[ "11" ]
In mammalian cells, introns are believed to be the predominant cis-acting NMD elements.
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
When either a U12 or a U2 intron is spliced, a multiprotein complex called the exon junction complex (EJC) is deposited on the mRNA 20–25 nt upstream of each exon–exon junction (12,13).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
185
7,870
0
false
When either a U12 or a U2 intron is spliced, a multiprotein complex called the exon junction complex (EJC) is deposited on the mRNA 20–25 nt upstream of each exon–exon junction.
[ "12,13" ]
When either a U12 or a U2 intron is spliced, a multiprotein complex called the exon junction complex (EJC) is deposited on the mRNA 20–25 nt upstream of each exon–exon junction.
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
As introns are rare in the 3′-UTR, the EJC marks the coding regions of mRNAs.
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
77
7,871
0
false
As introns are rare in the 3′-UTR, the EJC marks the coding regions of mRNAs.
[]
As introns are rare in the 3′-UTR, the EJC marks the coding regions of mRNAs.
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
UPF3, a component of the mammalian EJC, recruits UPF2 in the perinuclear space.
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
79
7,872
0
false
UPF3, a component of the mammalian EJC, recruits UPF2 in the perinuclear space.
[]
UPF3, a component of the mammalian EJC, recruits UPF2 in the perinuclear space.
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
If translation is stopped at a PTC, UPF3–UPF2 complexes located downstream of the PTC can recruit UPF1 and other NMD factors to form functional NMD complex.
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
156
7,873
0
false
If translation is stopped at a PTC, UPF3–UPF2 complexes located downstream of the PTC can recruit UPF1 and other NMD factors to form functional NMD complex.
[]
If translation is stopped at a PTC, UPF3–UPF2 complexes located downstream of the PTC can recruit UPF1 and other NMD factors to form functional NMD complex.
true
true
true
true
true
1,282
2
INTRODUCTION
1
14
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
As translating ribosome remove EJCs located upstream of the stop codon as well as EJCs that are located downstream but in close proximity to a stop codon, mammalian transcripts are targeted by NMD only if a stop codon resides >50–55 nt upstream of an exon–exon junction (14).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
275
7,874
1
false
As translating ribosome remove EJCs located upstream of the stop codon as well as EJCs that are located downstream but in close proximity to a stop codon, mammalian transcripts are targeted by NMD only if a stop codon resides >50–55 nt upstream of an exon–exon junction.
[ "14" ]
As translating ribosome remove EJCs located upstream of the stop codon as well as EJCs that are located downstream but in close proximity to a stop codon, mammalian transcripts are targeted by NMD only if a stop codon resides >50–55 nt upstream of an exon–exon junction.
true
true
true
true
true
1,282
2
INTRODUCTION
1
15
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
In yeast, loosely defined sequences called DSE elements can render an mRNA subject to NMD if they are located downstream of a stop codon (15).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
142
7,875
1
false
In yeast, loosely defined sequences called DSE elements can render an mRNA subject to NMD if they are located downstream of a stop codon.
[ "15" ]
In yeast, loosely defined sequences called DSE elements can render an mRNA subject to NMD if they are located downstream of a stop codon.
true
true
true
true
true
1,282
2
INTRODUCTION
1
16
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
Hrp1p specifically binds to DSE sequences and might recruit UPF proteins to the mRNAs (16).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
91
7,876
1
false
Hrp1p specifically binds to DSE sequences and might recruit UPF proteins to the mRNAs.
[ "16" ]
Hrp1p specifically binds to DSE sequences and might recruit UPF proteins to the mRNAs.
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
Both the intron (EJC) and DSE-based PTC definition systems conform to the nuclear marking model.
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
96
7,877
0
false
Both the intron (EJC) and DSE-based PTC definition systems conform to the nuclear marking model.
[]
Both the intron (EJC) and DSE-based PTC definition systems conform to the nuclear marking model.
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
However, a long 3′-UTR can also subject mRNAs to NMD in yeast, Drosophila and worm cells (8,17,18).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
99
7,878
0
false
However, a long 3′-UTR can also subject mRNAs to NMD in yeast, Drosophila and worm cells.
[ "8,17,18" ]
However, a long 3′-UTR can also subject mRNAs to NMD in yeast, Drosophila and worm cells.
true
true
true
true
true
1,282
2
INTRODUCTION
1
19
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
Moreover, mammalian mRNAs with long 3′-UTRs are also targeted by NMD, although less efficiently than mRNAs containing introns in the 3′-UTR (19).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
145
7,879
1
false
Moreover, mammalian mRNAs with long 3′-UTRs are also targeted by NMD, although less efficiently than mRNAs containing introns in the 3′-UTR.
[ "19" ]
Moreover, mammalian mRNAs with long 3′-UTRs are also targeted by NMD, although less efficiently than mRNAs containing introns in the 3′-UTR.
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
The finding that long 5′-UTRs act as NMD cis elements can be explained by the faux UTR model.
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
93
7,880
0
false
The finding that long 5′-UTRs act as NMD cis elements can be explained by the faux UTR model.
[]
The finding that long 5′-UTRs act as NMD cis elements can be explained by the faux UTR model.
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
Normal translation termination requires the interaction of terminating ribosome and poly(A)-binding protein (PABP).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
115
7,881
0
false
Normal translation termination requires the interaction of terminating ribosome and poly(A)-binding protein (PABP).
[]
Normal translation termination requires the interaction of terminating ribosome and poly(A)-binding protein (PABP).
true
true
true
true
true
1,282
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b8", "b17", "b18", "b19", "b8", "b20" ]
17,088,291
pmid-12672499|pmid-15145352|pmid-11118221|pmid-15608055|pmid-9644970|pmid-7891717|pmid-10882134|pmid-15525991|pmid-12881430|pmid-8104846|pmid-16622410|pmid-15525991|pmid-16723977|pmid-2152115|pmid-10758507|pmid-15525991|pmid-12881430|pmid-16622410|pmid-11672865|pmid-16246174|pmid-15525991
By preventing this interaction, an unusually long 3′-UTR could lead to aberrant termination and formation of functional NMD complex (8,20).
[ "10", "11", "12", "13", "14", "15", "16", "8", "17", "18", "19", "8", "20" ]
139
7,882
0
false
By preventing this interaction, an unusually long 3′-UTR could lead to aberrant termination and formation of functional NMD complex.
[ "8,20" ]
By preventing this interaction, an unusually long 3′-UTR could lead to aberrant termination and formation of functional NMD complex.
true
true
true
true
true
1,282
3
INTRODUCTION
1
21
[ "b21", "b22", "b23" ]
17,088,291
pmid-15901503|pmid-16141059|pmid-16289965|pmid-16280547|pmid-15496452
The events of NMD-mediated mRNA decay downstream of functional NMD complex formation are not well understood.
[ "21", "22", "23" ]
109
7,883
0
false
The events of NMD-mediated mRNA decay downstream of functional NMD complex formation are not well understood.
[]
The events of NMD-mediated mRNA decay downstream of functional NMD complex formation are not well understood.
true
true
true
true
true
1,283
3
INTRODUCTION
1
21
[ "b21", "b22", "b23" ]
17,088,291
pmid-15901503|pmid-16141059|pmid-16289965|pmid-16280547|pmid-15496452
In yeast and human cells, NMD complex formation results in decapping and deadenylation of PTC-containing mRNA, while in Drosophila, it leads to cleavage of aberrant mRNAs close to the PTC (21).
[ "21", "22", "23" ]
193
7,884
1
false
In yeast and human cells, NMD complex formation results in decapping and deadenylation of PTC-containing mRNA, while in Drosophila, it leads to cleavage of aberrant mRNAs close to the PTC.
[ "21" ]
In yeast and human cells, NMD complex formation results in decapping and deadenylation of PTC-containing mRNA, while in Drosophila, it leads to cleavage of aberrant mRNAs close to the PTC.
true
true
true
true
true
1,283
3
INTRODUCTION
1
22
[ "b21", "b22", "b23" ]
17,088,291
pmid-15901503|pmid-16141059|pmid-16289965|pmid-16280547|pmid-15496452
Decapped and/or deadenylated mRNAs are degraded in specific cellular compartments called P-bodies by normal mRNA decay pathways involving XRN1 and the exosome (22).
[ "21", "22", "23" ]
164
7,885
1
false
Decapped and/or deadenylated mRNAs are degraded in specific cellular compartments called P-bodies by normal mRNA decay pathways involving XRN1 and the exosome.
[ "22" ]
Decapped and/or deadenylated mRNAs are degraded in specific cellular compartments called P-bodies by normal mRNA decay pathways involving XRN1 and the exosome.
true
true
true
true
true
1,283
3
INTRODUCTION
1
21
[ "b21", "b22", "b23" ]
17,088,291
pmid-15901503|pmid-16141059|pmid-16289965|pmid-16280547|pmid-15496452
In animals, SMG-1, SMG-5, SMG-6 and SMG-7 are also required for NMD.
[ "21", "22", "23" ]
68
7,886
0
false
In animals, SMG-1, SMG-5, SMG-6 and SMG-7 are also required for NMD.
[]
In animals, SMG-1, SMG-5, SMG-6 and SMG-7 are also required for NMD.
true
true
true
true
true
1,283
3
INTRODUCTION
1
23
[ "b21", "b22", "b23" ]
17,088,291
pmid-15901503|pmid-16141059|pmid-16289965|pmid-16280547|pmid-15496452
SMG-1 phoshporylates UPF1, while SMG-5, SMG-6 and SMG-7 are involved in dephosphorylation of UPF1 (23).
[ "21", "22", "23" ]
103
7,887
1
false
SMG-1 phoshporylates UPF1, while SMG-5, SMG-6 and SMG-7 are involved in dephosphorylation of UPF1.
[ "23" ]
SMG-1 phoshporylates UPF1, while SMG-5, SMG-6 and SMG-7 are involved in dephosphorylation of UPF1.
true
true
true
true
true
1,283
4
INTRODUCTION
1
24
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
NMD also operates in higher plants, although very little is known about mechanism or function of plant NMD systems (24,25).
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
123
7,888
0
false
NMD also operates in higher plants, although very little is known about mechanism or function of plant NMD systems.
[ "24,25" ]
NMD also operates in higher plants, although very little is known about mechanism or function of plant NMD systems.
true
true
true
true
true
1,284
4
INTRODUCTION
1
10
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
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A computer search identified one putative ortholog for UPF1, UPF2 and UPF3 in Arabidopsis genome (10).
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
102
7,889
1
false
A computer search identified one putative ortholog for UPF1, UPF2 and UPF3 in Arabidopsis genome.
[ "10" ]
A computer search identified one putative ortholog for UPF1, UPF2 and UPF3 in Arabidopsis genome.
true
true
true
true
true
1,284
4
INTRODUCTION
1
26
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
Indeed, alternative splicing products containing PTCs accumulate to high levels in an Arabidopsis line carrying a UPF3 mutation (26).
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
133
7,890
1
false
Indeed, alternative splicing products containing PTCs accumulate to high levels in an Arabidopsis line carrying a UPF3 mutation.
[ "26" ]
Indeed, alternative splicing products containing PTCs accumulate to high levels in an Arabidopsis line carrying a UPF3 mutation.
true
true
true
true
true
1,284
4
INTRODUCTION
1
24
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
Moreover, it has been reported that the null mutant of putative UPF1 is lethal (27,28), while the missense mutant lba1 shows strong phenotype (27,29).
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
150
7,891
0
false
Moreover, it has been reported that the null mutant of putative UPF1 is lethal, while the missense mutant lba1 shows strong phenotype.
[ "27,28", "27,29" ]
Moreover, it has been reported that the null mutant of putative UPF1 is lethal, while the missense mutant lba1 shows strong phenotype.
true
true
true
true
true
1,284
4
INTRODUCTION
1
24
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
The cis-acting NMD elements have not yet been identified in plants.
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
67
7,892
0
false
The cis-acting NMD elements have not yet been identified in plants.
[]
The cis-acting NMD elements have not yet been identified in plants.
true
true
true
true
true
1,284
4
INTRODUCTION
1
24
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
The findings that PTC-containing mRNAs derived from intronless genes are efficiently targeted by plant NMD (30–33) suggest that long 3′-UTRs or DSE-like elements can act as cis factors in plants.
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
195
7,893
0
false
The findings that PTC-containing mRNAs derived from intronless genes are efficiently targeted by plant NMD suggest that long 3′-UTRs or DSE-like elements can act as cis factors in plants.
[ "30–33" ]
The findings that PTC-containing mRNAs derived from intronless genes are efficiently targeted by plant NMD suggest that long 3′-UTRs or DSE-like elements can act as cis factors in plants.
true
true
true
true
true
1,284
4
INTRODUCTION
1
24
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
The role of plant introns in PTC definition is still under debate.
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
66
7,894
0
false
The role of plant introns in PTC definition is still under debate.
[]
The role of plant introns in PTC definition is still under debate.
true
true
true
true
true
1,284
4
INTRODUCTION
1
24
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
In rice waxy gene, splicing of an intron upstream of the PTC affected the efficiency of NMD.
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
92
7,895
0
false
In rice waxy gene, splicing of an intron upstream of the PTC affected the efficiency of NMD.
[]
In rice waxy gene, splicing of an intron upstream of the PTC affected the efficiency of NMD.
true
true
true
true
true
1,284
4
INTRODUCTION
1
34
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
These data were interpreted to indicate that splicing and NMD were coupled in plants, as in mammals (34).
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
105
7,896
1
false
These data were interpreted to indicate that splicing and NMD were coupled in plants, as in mammals.
[ "34" ]
These data were interpreted to indicate that splicing and NMD were coupled in plants, as in mammals.
true
true
true
true
true
1,284
4
INTRODUCTION
1
24
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
However, in mammals only introns positioned downstream of the PTC could act as NMD cis elements.
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
96
7,897
0
false
However, in mammals only introns positioned downstream of the PTC could act as NMD cis elements.
[]
However, in mammals only introns positioned downstream of the PTC could act as NMD cis elements.
true
true
true
true
true
1,284
4
INTRODUCTION
1
24
[ "b24", "b25", "b10", "b26", "b27", "b28", "b27", "b29", "b30", "b33", "b34", "b35", "b36" ]
17,088,291
pmid-15951220|pmid-8980474|pmid-12672499|pmid-16098107|pmid-16540482|pmid-16813578|pmid-16540482|pmid-16740149|pmid-2152115|pmid-10758507|pmid-11244118|pmid-15331098|pmid-15546357|pmid-15331098|pmid-15331098|pmid-15546357|pmid-16116435
Moreover, other reports suggested that plant introns present in the 3′-UTR did not subject mRNAs to NMD (35,36).
[ "24", "25", "10", "26", "27", "28", "27", "29", "30", "33", "34", "35", "36" ]
112
7,898
0
false
Moreover, other reports suggested that plant introns present in the 3′-UTR did not subject mRNAs to NMD.
[ "35,36" ]
Moreover, other reports suggested that plant introns present in the 3′-UTR did not subject mRNAs to NMD.
true
true
true
true
true
1,284
5
INTRODUCTION
0
null
null
17,088,291
null
We have elaborated an agroinfiltration-based transient NMD test system to define the cis-acting elements of plant NMD and to identify plant UPF1.
null
145
7,899
0
false
null
null
We have elaborated an agroinfiltration-based transient NMD test system to define the cis-acting elements of plant NMD and to identify plant UPF1.
true
true
true
true
true
1,285