Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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4
DISCUSSION
1
33
[ "B25", "B28", "B41", "B33", "B34", "B58", "B61", "B33", "B61", "B53", "B62" ]
17,488,845
pmid-7908060|pmid-8139028|pmid-8313914|pmid-9651582|pmid-10205180|pmid-10074205|pmid-17267598|pmid-9651582|pmid-17267598|pmid-17132145|pmid-12791298
These results suggest that, in addition to the block of cellular, spliced mRNA export, mediated by the inhibition of cellular mRNA 3′-end processing (33) or by targetting the TAP/p15 mRNA export pathway (61), NS1 knocks down the export of its own virus mRNA, a non-spliced mRNA, by RNA-binding.
[ "25", "28", "41", "33", "34", "58", "61", "33", "61", "53", "62" ]
294
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1
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These results suggest that, in addition to the block of cellular, spliced mRNA export, mediated by the inhibition of cellular mRNA 3′-end processing or by targetting the TAP/p15 mRNA export pathway, NS1 knocks down the export of its own virus mRNA, a non-spliced mRNA, by RNA-binding.
[ "33", "61" ]
These results suggest that, in addition to the block of cellular, spliced mRNA export, mediated by the inhibition of cellular mRNA 3′-end processing or by targetting the TAP/p15 mRNA export pathway, NS1 knocks down the export of its own virus mRNA, a non-spliced mRNA, by RNA-binding.
true
true
true
true
true
1,126
4
DISCUSSION
1
53
[ "B25", "B28", "B41", "B33", "B34", "B58", "B61", "B33", "B61", "B53", "B62" ]
17,488,845
pmid-7908060|pmid-8139028|pmid-8313914|pmid-9651582|pmid-10205180|pmid-10074205|pmid-17267598|pmid-9651582|pmid-17267598|pmid-17132145|pmid-12791298
The mechanism for this nuclear retention is not clear at this point in time but a recent publication showing that nuclear export of some virus mRNAs, including NS1 mRNA, requires their association to the cellular transcription machinery might shed some light (53).
[ "25", "28", "41", "33", "34", "58", "61", "33", "61", "53", "62" ]
264
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The mechanism for this nuclear retention is not clear at this point in time but a recent publication showing that nuclear export of some virus mRNAs, including NS1 mRNA, requires their association to the cellular transcription machinery might shed some light.
[ "53" ]
The mechanism for this nuclear retention is not clear at this point in time but a recent publication showing that nuclear export of some virus mRNAs, including NS1 mRNA, requires their association to the cellular transcription machinery might shed some light.
true
true
true
true
true
1,126
4
DISCUSSION
1
25
[ "B25", "B28", "B41", "B33", "B34", "B58", "B61", "B33", "B61", "B53", "B62" ]
17,488,845
pmid-7908060|pmid-8139028|pmid-8313914|pmid-9651582|pmid-10205180|pmid-10074205|pmid-17267598|pmid-9651582|pmid-17267598|pmid-17132145|pmid-12791298
Thus, NS1 might act by avoiding the coupling of the viral transcription events to the RNA polymerase II complex after virus RNP-mediated cap-snatching and hence interfering with the association of shuttling hnRNP proteins to the virus transcripts.
[ "25", "28", "41", "33", "34", "58", "61", "33", "61", "53", "62" ]
247
6,902
0
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Thus, NS1 might act by avoiding the coupling of the viral transcription events to the RNA polymerase II complex after virus RNP-mediated cap-snatching and hence interfering with the association of shuttling hnRNP proteins to the virus transcripts.
[]
Thus, NS1 might act by avoiding the coupling of the viral transcription events to the RNA polymerase II complex after virus RNP-mediated cap-snatching and hence interfering with the association of shuttling hnRNP proteins to the virus transcripts.
true
true
true
true
true
1,126
4
DISCUSSION
1
62
[ "B25", "B28", "B41", "B33", "B34", "B58", "B61", "B33", "B61", "B53", "B62" ]
17,488,845
pmid-7908060|pmid-8139028|pmid-8313914|pmid-9651582|pmid-10205180|pmid-10074205|pmid-17267598|pmid-9651582|pmid-17267598|pmid-17132145|pmid-12791298
This interference would not take place on the spliced NEP(NS2) mRNA because it would associate to the standard EJC/TAP-p15-dependent mRNA export pathway (62).
[ "25", "28", "41", "33", "34", "58", "61", "33", "61", "53", "62" ]
158
6,903
1
false
This interference would not take place on the spliced NEP(NS2) mRNA because it would associate to the standard EJC/TAP-p15-dependent mRNA export pathway.
[ "62" ]
This interference would not take place on the spliced NEP mRNA because it would associate to the standard EJC/TAP-p15-dependent mRNA export pathway.
true
true
true
true
true
1,126
5
DISCUSSION
0
null
null
17,488,845
null
The nuclear retention of NS1 mRNA could be a way to improve the possibilities for this collinear transcript to form a spliceosomal complex in the context of general splicing inhibition described above.
null
201
6,904
0
false
null
null
The nuclear retention of NS1 mRNA could be a way to improve the possibilities for this collinear transcript to form a spliceosomal complex in the context of general splicing inhibition described above.
true
true
true
true
true
1,127
5
DISCUSSION
0
null
null
17,488,845
null
Thus, complete inhibition of the splicing of the NS collinear transcript would be deletereous for virus infection, as no NEP(NS2) protein would be formed, and the virus might have evolved an escape mechanism to avoid a complete block of viral mRNA splicing.
null
257
6,905
0
false
null
null
Thus, complete inhibition of the splicing of the NS collinear transcript would be deletereous for virus infection, as no NEP(NS2) protein would be formed, and the virus might have evolved an escape mechanism to avoid a complete block of viral mRNA splicing.
true
true
true
true
true
1,127
5
DISCUSSION
0
null
null
17,488,845
null
Such scenario is compatible with the phenotypes observed in the genetic analysis presented here.
null
96
6,906
0
false
null
null
Such scenario is compatible with the phenotypes observed in the genetic analysis presented here.
true
true
true
true
true
1,127
5
DISCUSSION
0
null
null
17,488,845
null
When NS1 protein is not expressed (ΔNS1), no inhibition of splicing and export is produced, the collinear NS1 transcript is almost fully spliced and NEP(NS2) mRNA is efficiently exported.
null
187
6,907
0
false
null
null
When NS1 protein is not expressed (ΔNS1), no inhibition of splicing and export is produced, the collinear NS1 transcript is almost fully spliced and NEP(NS2) mRNA is efficiently exported.
true
true
true
true
true
1,127
5
DISCUSSION
0
null
null
17,488,845
null
If a RNA-binding mutant of NS1 is expressed, splicing inhibition persists but the export block is eliminated because no RNA recognition can take place, leading to an efficient export of collinear NS transcript.
null
210
6,908
0
false
null
null
If a RNA-binding mutant of NS1 is expressed, splicing inhibition persists but the export block is eliminated because no RNA recognition can take place, leading to an efficient export of collinear NS transcript.
true
true
true
true
true
1,127
6
DISCUSSION
0
null
null
17,488,845
null
In summary, the results presented in this report demonstrate that NS1 regulates the splicing and nucleo-cytoplasmic export of its own collinear mRNA, in addition to the previously reported inhibitions of cellular mRNA processing and export.
null
240
6,909
0
false
null
null
In summary, the results presented in this report demonstrate that NS1 regulates the splicing and nucleo-cytoplasmic export of its own collinear mRNA, in addition to the previously reported inhibitions of cellular mRNA processing and export.
true
true
true
true
true
1,128
6
DISCUSSION
0
null
null
17,488,845
null
The simplest interpretation of these results implies that the mechanisms for splicing and export inhibition are distinct and at least in part different from the way NS1 appears to alter cellular mRNA metabolism.
null
211
6,910
0
false
null
null
The simplest interpretation of these results implies that the mechanisms for splicing and export inhibition are distinct and at least in part different from the way NS1 appears to alter cellular mRNA metabolism.
true
true
true
true
true
1,128
0
INTRODUCTION
0
null
null
17,145,713
null
The National Microbial Pathogen Data Resource (NMPDR) is one of eight Bioinformatics Resource Centers funded by the National Institute of Allergy and Infectious Disease (NIAID) to provide the comprehensive bioinformatics environment needed to support research in biodefense, emerging infectious diseases, and re-emerging...
null
331
6,911
0
false
null
null
The National Microbial Pathogen Data Resource (NMPDR) is one of eight Bioinformatics Resource Centers funded by the National Institute of Allergy and Infectious Disease (NIAID) to provide the comprehensive bioinformatics environment needed to support research in biodefense, emerging infectious diseases, and re-emerging...
true
true
true
true
true
1,129
0
INTRODUCTION
0
null
null
17,145,713
null
The NMPDR focus organisms are NIAID Category B priority pathogens, including the food and water-borne diarrheagenic bacteria Campylobacter jejuni, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, and Listeria monocytogenes.
null
235
6,912
0
false
null
null
The NMPDR focus organisms are NIAID Category B priority pathogens, including the food and water-borne diarrheagenic bacteria Campylobacter jejuni, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, and Listeria monocytogenes.
true
true
true
true
true
1,129
0
INTRODUCTION
0
null
null
17,145,713
null
Also included are the nosocomial pathogens Staphylococcus aureus, Streptococcus pneumoniae and Streptococcus pyogenes (Group A Strep).
null
134
6,913
0
false
null
null
Also included are the nosocomial pathogens Staphylococcus aureus, Streptococcus pneumoniae and Streptococcus pyogenes (Group A Strep).
true
true
true
true
true
1,129
0
INTRODUCTION
0
null
null
17,145,713
null
NMPDR is both a central repository for a wide variety of scientific data on these pathogenic microorganisms and a platform for software tools that support investigator-driven data analysis.
null
189
6,914
0
false
null
null
NMPDR is both a central repository for a wide variety of scientific data on these pathogenic microorganisms and a platform for software tools that support investigator-driven data analysis.
true
true
true
true
true
1,129
0
INTRODUCTION
0
null
null
17,145,713
null
Its goal is to provide the most accurate functional annotations for its focus organisms in the context of comprehensive comparative analysis.
null
141
6,915
0
false
null
null
Its goal is to provide the most accurate functional annotations for its focus organisms in the context of comprehensive comparative analysis.
true
true
true
true
true
1,129
0
INTRODUCTION
0
null
null
17,145,713
null
To this end, NMPDR integrates genomic and functional data for hundreds of complete or nearly complete other bacterial, eukaryotic and archaeal genomes, the ‘supporting genomes’, that provide a rich phylogenetic context for data analysis.
null
237
6,916
0
false
null
null
To this end, NMPDR integrates genomic and functional data for hundreds of complete or nearly complete other bacterial, eukaryotic and archaeal genomes, the ‘supporting genomes’, that provide a rich phylogenetic context for data analysis.
true
true
true
true
true
1,129
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
Key to the correct interpretation of genomic data is the accuracy and consistency of functional annotations.
[ "1", "2", "3", "4" ]
108
6,917
0
false
Key to the correct interpretation of genomic data is the accuracy and consistency of functional annotations.
[]
Key to the correct interpretation of genomic data is the accuracy and consistency of functional annotations.
true
true
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1,130
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
The annotation environment underlying NMPDR is the SEED ().
[ "1", "2", "3", "4" ]
59
6,918
0
false
The annotation environment underlying NMPDR is the SEED ().
[]
The annotation environment underlying NMPDR is the SEED ().
true
true
true
true
true
1,130
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
Developed as an international collaboration, the SEED is a distributed system that organizes genomic data in the form of populated subsystems, rather than on an organism-by-organism basis (1).
[ "1", "2", "3", "4" ]
192
6,919
1
false
Developed as an international collaboration, the SEED is a distributed system that organizes genomic data in the form of populated subsystems, rather than on an organism-by-organism basis.
[ "1" ]
Developed as an international collaboration, the SEED is a distributed system that organizes genomic data in the form of populated subsystems, rather than on an organism-by-organism basis.
true
true
true
true
true
1,130
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
Subsystems are two-dimensional (2-D) integrations of biological functions with genome sequences, which are represented in spreadsheets as columns of functional roles, rows of genomes, and cells populated by the genes responsible for each function.
[ "1", "2", "3", "4" ]
247
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0
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Subsystems are two-dimensional integrations of biological functions with genome sequences, which are represented in spreadsheets as columns of functional roles, rows of genomes, and cells populated by the genes responsible for each function.
[ "2-D" ]
Subsystems are two-dimensional integrations of biological functions with genome sequences, which are represented in spreadsheets as columns of functional roles, rows of genomes, and cells populated by the genes responsible for each function.
true
true
true
true
true
1,130
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
Subsystems for the NMPDR focus organisms are created in a private instance of the SEED.
[ "1", "2", "3", "4" ]
87
6,921
0
false
Subsystems for the NMPDR focus organisms are created in a private instance of the SEED.
[]
Subsystems for the NMPDR focus organisms are created in a private instance of the SEED.
true
true
true
true
true
1,130
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
Functional roles are first manually assigned to a group of proteins in a limited number of microbial genomes, creating a populated subsystem.
[ "1", "2", "3", "4" ]
141
6,922
0
false
Functional roles are first manually assigned to a group of proteins in a limited number of microbial genomes, creating a populated subsystem.
[]
Functional roles are first manually assigned to a group of proteins in a limited number of microbial genomes, creating a populated subsystem.
true
true
true
true
true
1,130
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
Tools for comparative analysis, including precomputed sequence similarity and gene co-localization (functional coupling) (2,3), are used to extend the subsystem to additional genomes, resulting in consistent annotation of proteins that play the same functional role in a variety of organisms.
[ "1", "2", "3", "4" ]
292
6,923
0
false
Tools for comparative analysis, including precomputed sequence similarity and gene co-localization (functional coupling), are used to extend the subsystem to additional genomes, resulting in consistent annotation of proteins that play the same functional role in a variety of organisms.
[ "2,3" ]
Tools for comparative analysis, including precomputed sequence similarity and gene co-localization (functional coupling), are used to extend the subsystem to additional genomes, resulting in consistent annotation of proteins that play the same functional role in a variety of organisms.
true
true
true
true
true
1,130
1
INTRODUCTION
1
4
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
Clustering analysis, combined with functional subsystems, is used to identify genes that encode functions known to be present in an organism, but that are performed by divergent proteins not automatically recognized by sequence similarity (4).
[ "1", "2", "3", "4" ]
243
6,924
1
false
Clustering analysis, combined with functional subsystems, is used to identify genes that encode functions known to be present in an organism, but that are performed by divergent proteins not automatically recognized by sequence similarity.
[ "4" ]
Clustering analysis, combined with functional subsystems, is used to identify genes that encode functions known to be present in an organism, but that are performed by divergent proteins not automatically recognized by sequence similarity.
true
true
true
true
true
1,130
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
These tools allow NMPDR to offer the most accurate and consistent annotations to date.
[ "1", "2", "3", "4" ]
86
6,925
0
false
These tools allow NMPDR to offer the most accurate and consistent annotations to date.
[]
These tools allow NMPDR to offer the most accurate and consistent annotations to date.
true
true
true
true
true
1,130
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
To ensure the integrity of the annotations, NMPDR is read-only.
[ "1", "2", "3", "4" ]
63
6,926
0
false
To ensure the integrity of the annotations, NMPDR is read-only.
[]
To ensure the integrity of the annotations, NMPDR is read-only.
true
true
true
true
true
1,130
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,145,713
pmid-16214803|pmid-11471247|pmid-10077608|pmid-12714058
Links are provided to the public SEED for community annotation of genes and for the construction of new subsystems by independent investigators.
[ "1", "2", "3", "4" ]
144
6,927
0
false
Links are provided to the public SEED for community annotation of genes and for the construction of new subsystems by independent investigators.
[]
Links are provided to the public SEED for community annotation of genes and for the construction of new subsystems by independent investigators.
true
true
true
true
true
1,130
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
Restriction endonucleases have been the workhorse of molecular biology for the past 30 years (1).
[ "1", "2", "3", "4" ]
97
6,928
1
false
Restriction endonucleases have been the workhorse of molecular biology for the past 30 years.
[ "1" ]
Restriction endonucleases have been the workhorse of molecular biology for the past 30 years.
true
true
true
true
true
1,131
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
They catalyze the breakage of phosphodiester bonds on DNA backbones at specific sites and, together with their companion methyltransferases, are part of bacterial defense systems against the invasion of bacteriophages.
[ "1", "2", "3", "4" ]
218
6,929
0
false
They catalyze the breakage of phosphodiester bonds on DNA backbones at specific sites and, together with their companion methyltransferases, are part of bacterial defense systems against the invasion of bacteriophages.
[]
They catalyze the breakage of phosphodiester bonds on DNA backbones at specific sites and, together with their companion methyltransferases, are part of bacterial defense systems against the invasion of bacteriophages.
true
true
true
true
true
1,131
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
Expression of restriction endonucleases in Escherichia coli without the proper protection of the companion methyltransferases usually results in cell death.
[ "1", "2", "3", "4" ]
156
6,930
0
false
Expression of restriction endonucleases in Escherichia coli without the proper protection of the companion methyltransferases usually results in cell death.
[]
Expression of restriction endonucleases in Escherichia coli without the proper protection of the companion methyltransferases usually results in cell death.
true
true
true
true
true
1,131
0
INTRODUCTION
1
2
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
For this reason, restriction endonucleases have proven to be difficult candidates for direct cloning or for engineering efforts to change their properties using living hosts (2).
[ "1", "2", "3", "4" ]
178
6,931
1
false
For this reason, restriction endonucleases have proven to be difficult candidates for direct cloning or for engineering efforts to change their properties using living hosts.
[ "2" ]
For this reason, restriction endonucleases have proven to be difficult candidates for direct cloning or for engineering efforts to change their properties using living hosts.
true
true
true
true
true
1,131
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
For example, the traditional cloning approach (3) relies on the fact that the restriction endonuclease gene (RE gene hereafter) and its companion DNA methyltransferase gene often sit close on the chromosome allowing selection for the methyltransferase gene and its flanks to carry along the RE gene.
[ "1", "2", "3", "4" ]
299
6,932
1
false
For example, the traditional cloning approach relies on the fact that the restriction endonuclease gene (RE gene hereafter) and its companion DNA methyltransferase gene often sit close on the chromosome allowing selection for the methyltransferase gene and its flanks to carry along the RE gene.
[ "3" ]
For example, the traditional cloning approach relies on the fact that the restriction endonuclease gene (RE gene hereafter) and its companion DNA methyltransferase gene often sit close on the chromosome allowing selection for the methyltransferase gene and its flanks to carry along the RE gene.
true
true
true
true
true
1,131
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
A complete in vitro approach would diminish the effect of cell toxicity and may be better suited for many purposes.
[ "1", "2", "3", "4" ]
115
6,933
0
false
A complete in vitro approach would diminish the effect of cell toxicity and may be better suited for many purposes.
[]
A complete in vitro approach would diminish the effect of cell toxicity and may be better suited for many purposes.
true
true
true
true
true
1,131
0
INTRODUCTION
1
4
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
One such scheme has previously been applied to the selection of restriction enzyme genes (4), in which the selection is based on using a DNA polymerase to incorporate dUTP-biotin to the sticky ends generated by the restriction endonuclease in water-in-oil emulsion.
[ "1", "2", "3", "4" ]
265
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1
false
One such scheme has previously been applied to the selection of restriction enzyme genes, in which the selection is based on using a DNA polymerase to incorporate dUTP-biotin to the sticky ends generated by the restriction endonuclease in water-in-oil emulsion.
[ "4" ]
One such scheme has previously been applied to the selection of restriction enzyme genes, in which the selection is based on using a DNA polymerase to incorporate dUTP-biotin to the sticky ends generated by the restriction endonuclease in water-in-oil emulsion.
true
true
true
true
true
1,131
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
DNA templates with dUTP-biotin extensions are then captured on streptavidin-coated beads and amplified.
[ "1", "2", "3", "4" ]
103
6,935
0
false
DNA templates with dUTP-biotin extensions are then captured on streptavidin-coated beads and amplified.
[]
DNA templates with dUTP-biotin extensions are then captured on streptavidin-coated beads and amplified.
true
true
true
true
true
1,131
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
Using this method, a selection efficiency of ∼10-fold enrichment was obtained in a single round.
[ "1", "2", "3", "4" ]
96
6,936
0
false
Using this method, a selection efficiency of ∼10-fold enrichment was obtained in a single round.
[]
Using this method, a selection efficiency of ∼10-fold enrichment was obtained in a single round.
true
true
true
true
true
1,131
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
This relatively low efficiency limits the use of this method to certain specific applications.
[ "1", "2", "3", "4" ]
94
6,937
0
false
This relatively low efficiency limits the use of this method to certain specific applications.
[]
This relatively low efficiency limits the use of this method to certain specific applications.
true
true
true
true
true
1,131
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
For instance, six rounds of selections were needed to select an active FokI gene from a randomized FokI library at three codon positions.
[ "1", "2", "3", "4" ]
137
6,938
0
false
For instance, six rounds of selections were needed to select an active FokI gene from a randomized FokI library at three codon positions.
[]
For instance, six rounds of selections were needed to select an active FokI gene from a randomized FokI library at three codon positions.
true
true
true
true
true
1,131
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B5", "B8" ]
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
An ideal selection system is a simplified Darwinian process, in which only genes surviving the imposed selection criteria are allowed to propagate.
[ "5", "6", "7", "5", "8" ]
147
6,939
0
false
An ideal selection system is a simplified Darwinian process, in which only genes surviving the imposed selection criteria are allowed to propagate.
[]
An ideal selection system is a simplified Darwinian process, in which only genes surviving the imposed selection criteria are allowed to propagate.
true
true
true
true
true
1,132
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B5", "B8" ]
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
Among many crucial requirements of this process are the separation of distinct genotypes and the linkage between genotype and phenotype.
[ "5", "6", "7", "5", "8" ]
136
6,940
0
false
Among many crucial requirements of this process are the separation of distinct genotypes and the linkage between genotype and phenotype.
[]
Among many crucial requirements of this process are the separation of distinct genotypes and the linkage between genotype and phenotype.
true
true
true
true
true
1,132
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B5", "B8" ]
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
Living hosts such as E. coli cells fulfill these requirements by cell membrane encapsulations and by the viability of the selected clones.
[ "5", "6", "7", "5", "8" ]
138
6,941
0
false
Living hosts such as E. coli cells fulfill these requirements by cell membrane encapsulations and by the viability of the selected clones.
[]
Living hosts such as E. coli cells fulfill these requirements by cell membrane encapsulations and by the viability of the selected clones.
true
true
true
true
true
1,132
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B5", "B8" ]
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
In vitro methods that have been developed based on these considerations include in vitro compartmentalization (IVC) (5), mRNA display (6) and ribosomal display (7) etc.
[ "5", "6", "7", "5", "8" ]
168
6,942
1
false
In vitro methods that have been developed based on these considerations include in vitro compartmentalization (IVC), mRNA display and ribosomal display etc.
[ "5", "6", "7" ]
In vitro methods that have been developed based on these considerations include in vitro compartmentalization (IVC), mRNA display and ribosomal display etc.
true
true
true
true
true
1,132
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B5", "B8" ]
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
While the various display methods are useful choices for the selection of binding, in vitro compartmentalization provides the necessary ingredients for carrying out activity-based selections in a cell-like environment.
[ "5", "6", "7", "5", "8" ]
218
6,943
0
false
While the various display methods are useful choices for the selection of binding, in vitro compartmentalization provides the necessary ingredients for carrying out activity-based selections in a cell-like environment.
[]
While the various display methods are useful choices for the selection of binding, in vitro compartmentalization provides the necessary ingredients for carrying out activity-based selections in a cell-like environment.
true
true
true
true
true
1,132
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B5", "B8" ]
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
Since its introduction in 1998 (5), IVC has been applied to a wide range of biomolecular engineering applications (8).
[ "5", "6", "7", "5", "8" ]
118
6,944
1
false
Since its introduction in 1998, IVC has been applied to a wide range of biomolecular engineering applications.
[ "5", "8" ]
Since its introduction in 1998, IVC has been applied to a wide range of biomolecular engineering applications.
true
true
true
true
true
1,132
2
INTRODUCTION
1
5
[ "B5", "B9" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
The in vitro compartmentalization (IVC) (5) technique generates as many as 109–1010 individual aqueous droplets in oil.
[ "5", "9" ]
119
6,945
1
false
The in vitro compartmentalization (IVC) technique generates as many as 109–1010 individual aqueous droplets in oil.
[ "5" ]
The in vitro compartmentalization (IVC) technique generates as many as 109–1010 individual aqueous droplets in oil.
true
true
true
true
true
1,133
2
INTRODUCTION
1
9
[ "B5", "B9" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
In our selection procedure, the aqueous phase in each droplet contains the reconstituted transcription/translation system (9) and is capable of protein translation from the linear DNA templates dispersed inside.
[ "5", "9" ]
211
6,946
1
false
In our selection procedure, the aqueous phase in each droplet contains the reconstituted transcription/translation system and is capable of protein translation from the linear DNA templates dispersed inside.
[ "9" ]
In our selection procedure, the aqueous phase in each droplet contains the reconstituted transcription/translation system and is capable of protein translation from the linear DNA templates dispersed inside.
true
true
true
true
true
1,133
2
INTRODUCTION
1
5
[ "B5", "B9" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
Being stable over the process of selection, these droplets provide a simplified means to mimic E. coli cells as ‘artificial cells’.
[ "5", "9" ]
131
6,947
0
false
Being stable over the process of selection, these droplets provide a simplified means to mimic E. coli cells as ‘artificial cells’.
[]
Being stable over the process of selection, these droplets provide a simplified means to mimic E. coli cells as ‘artificial cells’.
true
true
true
true
true
1,133
2
INTRODUCTION
1
5
[ "B5", "B9" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
The selection scheme utilizes the restriction endonuclease's ability to generate defined sticky ends on DNA templates, which, in cellular compartments, ensures the linkage between genotype and phenotype for selection.
[ "5", "9" ]
217
6,948
0
false
The selection scheme utilizes the restriction endonuclease's ability to generate defined sticky ends on DNA templates, which, in cellular compartments, ensures the linkage between genotype and phenotype for selection.
[]
The selection scheme utilizes the restriction endonuclease's ability to generate defined sticky ends on DNA templates, which, in cellular compartments, ensures the linkage between genotype and phenotype for selection.
true
true
true
true
true
1,133
2
INTRODUCTION
1
5
[ "B5", "B9" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
Briefly, active endonuclease is expressed in vitro and cleaves its encoding DNA templates in the same droplet, leaving a defined sticky end at the tail.
[ "5", "9" ]
152
6,949
0
false
Briefly, active endonuclease is expressed in vitro and cleaves its encoding DNA templates in the same droplet, leaving a defined sticky end at the tail.
[]
Briefly, active endonuclease is expressed in vitro and cleaves its encoding DNA templates in the same droplet, leaving a defined sticky end at the tail.
true
true
true
true
true
1,133
2
INTRODUCTION
1
5
[ "B5", "B9" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
The recovered DNA templates and an excess of double-stranded adaptors with compatible sticky ends are then ligated.
[ "5", "9" ]
115
6,950
0
false
The recovered DNA templates and an excess of double-stranded adaptors with compatible sticky ends are then ligated.
[]
The recovered DNA templates and an excess of double-stranded adaptors with compatible sticky ends are then ligated.
true
true
true
true
true
1,133
2
INTRODUCTION
1
5
[ "B5", "B9" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
Only those templates that have been cleaved by the encoded endonuclease and carry intact sticky ends can be ligated efficiently.
[ "5", "9" ]
128
6,951
0
false
Only those templates that have been cleaved by the encoded endonuclease and carry intact sticky ends can be ligated efficiently.
[]
Only those templates that have been cleaved by the encoded endonuclease and carry intact sticky ends can be ligated efficiently.
true
true
true
true
true
1,133
2
INTRODUCTION
1
5
[ "B5", "B9" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
They are then amplified using adaptor-specific PCR to enrich the RE genes.
[ "5", "9" ]
74
6,952
0
false
They are then amplified using adaptor-specific PCR to enrich the RE genes.
[]
They are then amplified using adaptor-specific PCR to enrich the RE genes.
true
true
true
true
true
1,133
3
INTRODUCTION
1
10
[ "B10" ]
17,567,609
pmid-16847605
Model selections were carried out using libraries containing an excess of a Green Fluorescent Protein (GFP) gene spiked with various amounts of the gene encoding the PstI restriction endonuclease (recognition sequence CTGCA↓G), which would generate a four-base 3′-overhang.
[ "10" ]
273
6,953
0
false
Model selections were carried out using libraries containing an excess of a Green Fluorescent Protein (GFP) gene spiked with various amounts of the gene encoding the PstI restriction endonuclease (recognition sequence CTGCA↓G), which would generate a four-base 3′-overhang.
[]
Model selections were carried out using libraries containing an excess of a Green Fluorescent Protein (GFP) gene spiked with various amounts of the gene encoding the PstI restriction endonuclease (recognition sequence CTGCA↓G), which would generate a four-base 3′-overhang.
true
true
true
true
true
1,134
3
INTRODUCTION
1
10
[ "B10" ]
17,567,609
pmid-16847605
We show that at least 100-fold enrichment is reached in a single round of selection.
[ "10" ]
84
6,954
0
false
We show that at least 100-fold enrichment is reached in a single round of selection.
[]
We show that at least 100-fold enrichment is reached in a single round of selection.
true
true
true
true
true
1,134
3
INTRODUCTION
1
10
[ "B10" ]
17,567,609
pmid-16847605
Multiple rounds of selection are carried out to achieve successive enrichment.
[ "10" ]
78
6,955
0
false
Multiple rounds of selection are carried out to achieve successive enrichment.
[]
Multiple rounds of selection are carried out to achieve successive enrichment.
true
true
true
true
true
1,134
3
INTRODUCTION
1
10
[ "B10" ]
17,567,609
pmid-16847605
Finally, as a ‘real’ test of the system's selection power, we challenge it by using libraries constructed from the genomic DNA of a single bacterial species.
[ "10" ]
157
6,956
0
false
Finally, as a ‘real’ test of the system's selection power, we challenge it by using libraries constructed from the genomic DNA of a single bacterial species.
[]
Finally, as a ‘real’ test of the system's selection power, we challenge it by using libraries constructed from the genomic DNA of a single bacterial species.
true
true
true
true
true
1,134
3
INTRODUCTION
1
10
[ "B10" ]
17,567,609
pmid-16847605
We show that by three rounds of iterative in vitro selections, the RE gene becomes the single dominating DNA species in the resulting library.
[ "10" ]
142
6,957
0
false
We show that by three rounds of iterative in vitro selections, the RE gene becomes the single dominating DNA species in the resulting library.
[]
We show that by three rounds of iterative in vitro selections, the RE gene becomes the single dominating DNA species in the resulting library.
true
true
true
true
true
1,134
3
INTRODUCTION
1
10
[ "B10" ]
17,567,609
pmid-16847605
Using this method, we have cloned the PstI gene from Providencia stuartii and the TspMI gene (10) from Thermus sp.
[ "10" ]
114
6,958
1
false
Using this method, we have cloned the PstI gene from Providencia stuartii and the TspMI gene from Thermus sp.
[ "10" ]
Using this method, we have cloned the PstI gene from Providencia stuartii and the TspMI gene from Thermus sp.
true
true
true
true
true
1,134
4
INTRODUCTION
0
null
null
17,567,609
pmid-15247348|pmid-17202163
We believe that the in vitro approach offers a unique route for endonuclease selection and engineering.
null
103
6,959
0
false
null
null
We believe that the in vitro approach offers a unique route for endonuclease selection and engineering.
true
true
true
true
true
1,135
4
INTRODUCTION
0
null
null
17,567,609
pmid-15247348|pmid-17202163
The general principle demonstrated here may be applicable to a broad range of other genes encoding selectable enzymatic activities.
null
131
6,960
0
false
null
null
The general principle demonstrated here may be applicable to a broad range of other genes encoding selectable enzymatic activities.
true
true
true
true
true
1,135
0
DISCUSSION
1
16
[ "B16", "B2" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
Reconstructing biological systems in vitro is one of the many interesting challenges in synthetic biology (16).
[ "16", "2" ]
111
6,961
1
false
Reconstructing biological systems in vitro is one of the many interesting challenges in synthetic biology.
[ "16" ]
Reconstructing biological systems in vitro is one of the many interesting challenges in synthetic biology.
true
true
true
true
true
1,136
0
DISCUSSION
1
2
[ "B16", "B2" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
When compared with the in vivo host, an in vitro system sometimes offers unique advantages, for instance, it is ideal for toxic genes such as restriction endonucleases for which approaches using living hosts have proven to be difficult (2).
[ "16", "2" ]
240
6,962
1
false
When compared with the in vivo host, an in vitro system sometimes offers unique advantages, for instance, it is ideal for toxic genes such as restriction endonucleases for which approaches using living hosts have proven to be difficult.
[ "2" ]
When compared with the in vivo host, an in vitro system sometimes offers unique advantages, for instance, it is ideal for toxic genes such as restriction endonucleases for which approaches using living hosts have proven to be difficult.
true
true
true
true
true
1,136
0
DISCUSSION
1
16
[ "B16", "B2" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
Minimal in vitro systems are in general more configurable and reaction intermediates are more accessible, making them more amenable to engineering.
[ "16", "2" ]
147
6,963
0
false
Minimal in vitro systems are in general more configurable and reaction intermediates are more accessible, making them more amenable to engineering.
[]
Minimal in vitro systems are in general more configurable and reaction intermediates are more accessible, making them more amenable to engineering.
true
true
true
true
true
1,136
0
DISCUSSION
1
16
[ "B16", "B2" ]
17,567,609
pmid-15840723|NA|pmid-6254840|pmid-15247328|pmid-17151344|NA
For the genetic selection of DNA or RNA, without the barrier of a cell membrane and the limitations of transformation, an in vitro system is capable of exploring even larger libraries and functionalities.
[ "16", "2" ]
204
6,964
0
false
For the genetic selection of DNA or RNA, without the barrier of a cell membrane and the limitations of transformation, an in vitro system is capable of exploring even larger libraries and functionalities.
[]
For the genetic selection of DNA or RNA, without the barrier of a cell membrane and the limitations of transformation, an in vitro system is capable of exploring even larger libraries and functionalities.
true
true
true
true
true
1,136
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
In this article, by using in vitro compartmentalization to generate myriad aqueous droplets in oil as artificial cells, we are able to selectively amplify RE genes from bacterial genomes.
null
187
6,965
0
false
null
null
In this article, by using in vitro compartmentalization to generate myriad aqueous droplets in oil as artificial cells, we are able to selectively amplify RE genes from bacterial genomes.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
The so-called ‘artificial cells’ themselves do not undergo Darwinian selection, but simply provide a means to link genotype and phenotype.
null
138
6,966
0
false
null
null
The so-called ‘artificial cells’ themselves do not undergo Darwinian selection, but simply provide a means to link genotype and phenotype.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
The selection itself requires a method to distinguish those genotypes that have been changed from those that have not.
null
118
6,967
0
false
null
null
The selection itself requires a method to distinguish those genotypes that have been changed from those that have not.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
With over 100-fold enrichment in each round of selection, typically three rounds are needed to enrich a specific gene to ‘homogeneity’ from a bacterial genome.
null
159
6,968
0
false
null
null
With over 100-fold enrichment in each round of selection, typically three rounds are needed to enrich a specific gene to ‘homogeneity’ from a bacterial genome.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
From the genomic selection of PstI, we observe that actually most of the contaminating genes have been removed from the library after the second round of selection.
null
164
6,969
0
false
null
null
From the genomic selection of PstI, we observe that actually most of the contaminating genes have been removed from the library after the second round of selection.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
We used inverse PCR and DNA sequencing to determine the ends of the selected genomic fragments containing the PstI gene after the second round selection, and found that there is only one variant present in the library at that point, which was later amplified in the third round (data not shown).
null
295
6,970
0
false
null
null
We used inverse PCR and DNA sequencing to determine the ends of the selected genomic fragments containing the PstI gene after the second round selection, and found that there is only one variant present in the library at that point, which was later amplified in the third round (data not shown).
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
This contradicted our intuition that many different templates encompassing the PstI gene would be selected and the final result would be a DNA smear on the gel.
null
160
6,971
0
false
null
null
This contradicted our intuition that many different templates encompassing the PstI gene would be selected and the final result would be a DNA smear on the gel.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
It can be explained from several perspectives.
null
46
6,972
0
false
null
null
It can be explained from several perspectives.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
First, it seems that there is a strong selection pressure on the translation efficiency of the DNA templates, which gives a selective advantage to those templates with ribosome-binding sites very close to the start codon of the target gene for efficient translation.
null
266
6,973
0
false
null
null
First, it seems that there is a strong selection pressure on the translation efficiency of the DNA templates, which gives a selective advantage to those templates with ribosome-binding sites very close to the start codon of the target gene for efficient translation.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
In the genomic selection of the PstI gene, one end of the selected DNA fragment is just 3 nt upstream of the start codon.
null
121
6,974
0
false
null
null
In the genomic selection of the PstI gene, one end of the selected DNA fragment is just 3 nt upstream of the start codon.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
On the other hand, the ‘substrate’ ends of the templates provide little influence on the translation efficiency and is presumably less strictly selected.
null
153
6,975
0
false
null
null
On the other hand, the ‘substrate’ ends of the templates provide little influence on the translation efficiency and is presumably less strictly selected.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
This is supported by the TspMI selection, in which the selected genomic fragments end at variable points after the stop codon as far as ∼300 nt apart.
null
150
6,976
0
false
null
null
This is supported by the TspMI selection, in which the selected genomic fragments end at variable points after the stop codon as far as ∼300 nt apart.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
However, we have no explanation for the lack of variability observed in the PstI genomic selection.
null
99
6,977
0
false
null
null
However, we have no explanation for the lack of variability observed in the PstI genomic selection.
true
true
true
true
true
1,137
1
DISCUSSION
0
null
null
17,567,609
pmid-9661199|pmid-9356443|pmid-7522328|pmid-9661199|pmid-16843558
Second, it may result from the non-randomness of the shearing process using the nebulizer, in which strand breakage is heavily influenced by the local AT content of the genomic DNA (YZ and Chudi Guan, to be published).
null
218
6,978
0
false
null
null
Second, it may result from the non-randomness of the shearing process using the nebulizer, in which strand breakage is heavily influenced by the local AT content of the genomic DNA (YZ and Chudi Guan, to be published).
true
true
true
true
true
1,137
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
Doi, N. et al.
[ "4" ]
14
6,979
0
false
Doi, N. et al.
[]
Doi, N. et al.
true
true
true
true
true
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
have previously applied IVC in selecting RE genes (4).
[ "4" ]
54
6,980
1
false
have previously applied IVC in selecting RE genes.
[ "4" ]
have previously applied IVC in selecting RE genes.
false
true
true
true
false
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
Their method uses a DNA polymerase to incorporate dUTP-biotin to the sticky ends generated by the restriction endonuclease, permitting affinity-based purification of the genes.
[ "4" ]
176
6,981
0
false
Their method uses a DNA polymerase to incorporate dUTP-biotin to the sticky ends generated by the restriction endonuclease, permitting affinity-based purification of the genes.
[]
Their method uses a DNA polymerase to incorporate dUTP-biotin to the sticky ends generated by the restriction endonuclease, permitting affinity-based purification of the genes.
true
true
true
true
true
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
Using this method, they were only able to obtain a selection efficiency of ∼10-fold in a single round.
[ "4" ]
102
6,982
0
false
Using this method, they were only able to obtain a selection efficiency of ∼10-fold in a single round.
[]
Using this method, they were only able to obtain a selection efficiency of ∼10-fold in a single round.
true
true
true
true
true
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
This is likely due to the fact that any DNA fragments that might have resulted from non-specific cleavage in the compartments could have become labeled and hence, selected.
[ "4" ]
172
6,983
0
false
This is likely due to the fact that any DNA fragments that might have resulted from non-specific cleavage in the compartments could have become labeled and hence, selected.
[]
This is likely due to the fact that any DNA fragments that might have resulted from non-specific cleavage in the compartments could have become labeled and hence, selected.
true
true
true
true
true
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
Due to this relatively low efficiency, more iterations are required to recover the desired genotype, which severely limits the potential applications.
[ "4" ]
150
6,984
0
false
Due to this relatively low efficiency, more iterations are required to recover the desired genotype, which severely limits the potential applications.
[]
Due to this relatively low efficiency, more iterations are required to recover the desired genotype, which severely limits the potential applications.
true
true
true
true
true
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
For instance, six rounds of selections are needed to select active FokI gene from a randomized FokI library at three codon positions (expected library complexity of ∼8000).
[ "4" ]
172
6,985
0
false
For instance, six rounds of selections are needed to select active FokI gene from a randomized FokI library at three codon positions (expected library complexity of ∼8000).
[]
For instance, six rounds of selections are needed to select active FokI gene from a randomized FokI library at three codon positions (expected library complexity of ∼8000).
true
true
true
true
true
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
In contrast, our method exploits the full potential of the sequence specificity available at the sticky end by requiring ligation of the adaptor.
[ "4" ]
145
6,986
0
false
In contrast, our method exploits the full potential of the sequence specificity available at the sticky end by requiring ligation of the adaptor.
[]
In contrast, our method exploits the full potential of the sequence specificity available at the sticky end by requiring ligation of the adaptor.
true
true
true
true
true
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
Non-specific cleavage products or damaged ends would not result in amplification.
[ "4" ]
81
6,987
0
false
Non-specific cleavage products or damaged ends would not result in amplification.
[]
Non-specific cleavage products or damaged ends would not result in amplification.
true
true
true
true
true
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
This results in much higher enrichment during each round of selection and experimentally we find that greater than 100-fold enrichment can be obtained.
[ "4" ]
151
6,988
0
false
This results in much higher enrichment during each round of selection and experimentally we find that greater than 100-fold enrichment can be obtained.
[]
This results in much higher enrichment during each round of selection and experimentally we find that greater than 100-fold enrichment can be obtained.
true
true
true
true
true
1,138
2
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-9661199|pmid-11479568|pmid-15247328
This has allowed us to select genes from genomic libraries and would also permit a much greater sampling of sequence space during the selection of mutants.
[ "4" ]
155
6,989
0
false
This has allowed us to select genes from genomic libraries and would also permit a much greater sampling of sequence space during the selection of mutants.
[]
This has allowed us to select genes from genomic libraries and would also permit a much greater sampling of sequence space during the selection of mutants.
true
true
true
true
true
1,138
3
DISCUSSION
0
null
null
17,567,609
pmid-16847605
When compared with the conventional methylase selection, which often requires a purified endonuclease and the selection process targets the DNA methylase, the in vitro method directly targets the RE genes in the library and merely requires a specified recognition site and a set of DNA adaptors.
null
295
6,990
0
false
null
null
When compared with the conventional methylase selection, which often requires a purified endonuclease and the selection process targets the DNA methylase, the in vitro method directly targets the RE genes in the library and merely requires a specified recognition site and a set of DNA adaptors.
true
true
true
true
true
1,139
3
DISCUSSION
0
null
null
17,567,609
pmid-16847605
Thus, it should provide a possible route for searching environmental DNA samples for RE genes with desired specificities, which in principle contains a much greater genetic diversity from many co-existing microbial species.
null
223
6,991
0
false
null
null
Thus, it should provide a possible route for searching environmental DNA samples for RE genes with desired specificities, which in principle contains a much greater genetic diversity from many co-existing microbial species.
true
true
true
true
true
1,139
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
There are possible limitations with the current approach.
[ "17", "14" ]
57
6,992
0
false
There are possible limitations with the current approach.
[]
There are possible limitations with the current approach.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
Because the ligation is the key step in selection, it may be less effective to select endonucleases which generate shorter overhangs or blunt cuts.
[ "17", "14" ]
147
6,993
0
false
Because the ligation is the key step in selection, it may be less effective to select endonucleases which generate shorter overhangs or blunt cuts.
[]
Because the ligation is the key step in selection, it may be less effective to select endonucleases which generate shorter overhangs or blunt cuts.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
This may be alleviated by placing the recognition site of a nicking enzyme close to the blunt cut site and use the nicking enzyme to convert the blunt end to a suitable sticky end (17).
[ "17", "14" ]
185
6,994
1
false
This may be alleviated by placing the recognition site of a nicking enzyme close to the blunt cut site and use the nicking enzyme to convert the blunt end to a suitable sticky end.
[ "17" ]
This may be alleviated by placing the recognition site of a nicking enzyme close to the blunt cut site and use the nicking enzyme to convert the blunt end to a suitable sticky end.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
Frequent cutters, such as those recognizing 4-base sites, sometimes fall outside of the application range since they tend to destroy their own genes.
[ "17", "14" ]
149
6,995
0
false
Frequent cutters, such as those recognizing 4-base sites, sometimes fall outside of the application range since they tend to destroy their own genes.
[]
Frequent cutters, such as those recognizing 4-base sites, sometimes fall outside of the application range since they tend to destroy their own genes.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
These enzymes are completely fine in living bacteria since there is always a companion DNA methyltransferase to protect the host.
[ "17", "14" ]
129
6,996
0
false
These enzymes are completely fine in living bacteria since there is always a companion DNA methyltransferase to protect the host.
[]
These enzymes are completely fine in living bacteria since there is always a companion DNA methyltransferase to protect the host.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
Nevertheless, it appears that the selective disadvantage of having self-destructing sites has driven a significant proportion of frequent cutters to lose the recognition sites within their genes.
[ "17", "14" ]
195
6,997
0
false
Nevertheless, it appears that the selective disadvantage of having self-destructing sites has driven a significant proportion of frequent cutters to lose the recognition sites within their genes.
[]
Nevertheless, it appears that the selective disadvantage of having self-destructing sites has driven a significant proportion of frequent cutters to lose the recognition sites within their genes.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
Table 2 lists the statistics of those RE genes having their own recognition sites within their genes.
[ "17", "14" ]
101
6,998
0
false
Table 2 lists the statistics of those RE genes having their own recognition sites within their genes.
[]
Table 2 lists the statistics of those RE genes having their own recognition sites within their genes.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
For example, for a gene of 1kb in size, the probability that it does not have a particular 4-base site is ∼0.0004 [i.e.
[ "17", "14" ]
119
6,999
0
false
For example, for a gene of 1kb in size, the probability that it does not have a particular 4-base site is ∼0.0004 [i.e.
[]
For example, for a gene of 1kb in size, the probability that it does not have a particular 4-base site is ∼0.0004 [i.e.
true
true
true
true
true
1,140