OMPwiki - User contributions [en]

PMID:20474363

2017-03-16T17:08:04Z

46.229.168.65: Fill PMID: Page!

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{| id="V58cac6744b7c7" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Macconkey, AT''' (1908) Bile Salt Media and their advantages in some Bacteriological Examinations. ''J Hyg (Lond)'' '''8''':322-34
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
No abstract in PubMed
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20474363 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2167122 PMC2167122]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3411.V58cac6744b7c7&page=3411&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="M58cac6748c5a0" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3411.M58cac6748c5a0&page=3411&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:334074

2017-03-03T21:32:11Z

46.229.168.65: Fill PMID: Page!

{{RightTOC}}



{| id="T58b9e0db801c5" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Powers, EM and Latt, TG''' (1977) Simplified 48-hour IMVic test: an agar plate method. ''Appl. Environ. Microbiol.'' '''34''':274-9
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
An agar plate method was developed for the performance of the IMVic (indole, methyl red, Voges-Proskauer, and citrate) tests in lieu of the conventional tubed liquid media. By modifying the composition of the media and adding agar, a single "X"-compartmented petri dish was prepared containing all four IMVic test media. Ease of performance and simplification of the test were achieved by inoculating all four media simultaneously from a single colony (single inoculum) on eosin-methylene blue agar. Tests with 87 cultures, representing 7 genera in the family Enterobacteriaceae, were completed with typical (correct) IMVic patterns for all cultures within 48 h. Parallel tests with conventional media showed that the agar plate method was superior, more sensitive, faster, and simpler to perform, and less time was required to identify Escherichia coli by 72 h.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=334074 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC242642 PMC242642]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Bacteriological Techniques; Citrates/metabolism; Enterobacteriaceae/classification; Enterobacteriaceae/metabolism; Escherichia coli/classification; Escherichia coli/metabolism; Indoles/metabolism

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3399.T58b9e0db801c5&page=3399&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="S58b9e0dbb6e8c" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3399.S58b9e0dbb6e8c&page=3399&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:791131

2017-03-01T15:44:46Z

46.229.168.65: Fill PMID: Page!

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{| id="F58b6ec6e41756" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Palleroni, NJ''' (1976) Chamber for bacterial chemotaxis experiments. ''Appl. Environ. Microbiol.'' '''32''':729-30
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
A design for a chemotaxis chamber and its use in bacterial chemotaxis experiments are described. Some of the advantages of the new design are discussed.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=791131 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC170392 PMC170392]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Actinomycetales/physiology; Bacterial Physiological Phenomena; Bacteriological Techniques/instrumentation; Chemotaxis

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3363.F58b6ec6e41756&page=3363&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="P58b6ec6e848f9" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3363.P58b6ec6e848f9&page=3363&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:16738554

2017-02-28T23:02:33Z

46.229.168.65: Fill PMID: Page!

{{RightTOC}}



{| id="J58b60189696ba" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Baba, T, Ara, T, Hasegawa, M, Takai, Y, Okumura, Y, Baba, M, Datsenko, KA, Tomita, M, Wanner, BL and Mori, H''' (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. ''Mol. Syst. Biol.'' '''2''':2006.0008
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16738554 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681482 PMC1681482]
Online version:[http://dx.doi.org/10.1038/msb4100050 10.1038/msb4100050]
|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Escherichia coli/genetics; Gene Deletion; Internet; Mutation; Organisms, Genetically Modified

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3345.J58b60189696ba&page=3345&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="K58b60189bd979" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3345.K58b60189bd979&page=3345&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:11929534

2017-02-26T02:36:54Z

46.229.168.65: Fill PMID: Page!

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{| id="G58b23f46467b7" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Sperandio, V, Torres, AG and Kaper, JB''' (2002) Quorum sensing Escherichia coli regulators B and C (QseBC): a novel two-component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli. ''Mol. Microbiol.'' '''43''':809-21
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
Quorum sensing is a cell-to-cell signalling mechanism in which bacteria secrete hormone-like compounds called autoinducers. When these auto-inducers reach a certain threshold concentration, they interact with bacterial transcriptional regulators, thereby regulating gene expression. Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 as well as E. coli K-12 produces the autoinducer-2 (AI-2), which is synthesized by the product of the luxS gene, and previous work from our laboratory has shown that genes encoding the EHEC type III secretion system were activated by quorum sensing. Recently, by hybridizing an E. coli K-12 gene array with cDNA synthesized from RNA extracted from EHEC strain 86-24 and its isogenic luxS mutant, we observed that other potential virulence-associated factors, such as genes encoding the expression and assembly of flagella, motility and chemotaxis, were also activated by quorum sensing. The array data also indicated that several genes encoding putative E. coli regulators were controlled by quorum sensing. In this report, we describe a two-component system regulated by quorum sensing that shares homology with Salmonella typhimurium PmrAB, which we have named quorum sensing E. coli regulator B and C (QseBC). The qseBC genes, previously identified only as open reading frames b3025 and b3026, are organized in an operon in the E. coli chromosome, with qseB encoding the response regulator and qseC the sensor kinase. We confirmed the regulation of qseBC by quorum sensing using qseB::lacZ transcriptional fusions and characterized the phenotypes of an isogenic qseC mutation in EHEC. This mutant expressed less flagellin and had reduced motility compared with the wild-type and complemented strains. Transcription of flhD, fliA, motA and fliC::lacZ fusions was decreased in the qseC mutant, suggesting that qseBC is a transcriptional regulator of flagella genes. A qseC mutant was also generated in E. coli K-12 strain MC1000 that showed the same phenotypes as the EHEC mutant, indicating that qseBC regulates flagella and motility by quorum sensing in both EHEC and K-12. QseBC activates transcription of flhDC, which is the master regulator for the flagella and motility genes and, in the absence of flhD, QseBC failed to activate the transcription of fliA. Motility of a luxS, but not of a qseC, mutant can be restored by providing AI-2 exogenously as preconditioned media, suggesting that the qseC mutant is unable to respond to AI-2. However, QseC has no effect on the expression of other quorum sensing-controlled genes such as those encoding for the type III secretion system. These data indicate that QseBC is one component of the quorum-sensing regulatory cascade in both EHEC and K-12 that is involved in the regulation of flagella and motility genes, but that additional regulators in this cascade remain to be characterized.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11929534 PubMed]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
DNA-Binding Proteins/genetics; DNA-Binding Proteins/metabolism; Escherichia coli/physiology; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Flagella/physiology; Gene Expression Regulation, Bacterial; Molecular Sequence Data; Mutation; Promoter Regions, Genetic; Regulon; Trans-Activators/genetics; Trans-Activators/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3338.G58b23f46467b7&page=3338&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="H58b23f4657b44" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3338.H58b23f4657b44&page=3338&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:20474363

2017-02-15T03:41:00Z

46.229.168.65: Fill PMID: Page!

{{RightTOC}}



{| id="P58a3cdcc947a5" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Macconkey, AT''' (1908) Bile Salt Media and their advantages in some Bacteriological Examinations. ''J Hyg (Lond)'' '''8''':322-34
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
No abstract in PubMed
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20474363 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2167122 PMC2167122]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3411.P58a3cdcc947a5&page=3411&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="F58a3cdccd3a2e" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3411.F58a3cdccd3a2e&page=3411&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:334074

2017-02-10T07:43:15Z

46.229.168.65: Fill PMID: Page!

{{RightTOC}}



{| id="L589d6f1323372" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Powers, EM and Latt, TG''' (1977) Simplified 48-hour IMVic test: an agar plate method. ''Appl. Environ. Microbiol.'' '''34''':274-9
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
An agar plate method was developed for the performance of the IMVic (indole, methyl red, Voges-Proskauer, and citrate) tests in lieu of the conventional tubed liquid media. By modifying the composition of the media and adding agar, a single "X"-compartmented petri dish was prepared containing all four IMVic test media. Ease of performance and simplification of the test were achieved by inoculating all four media simultaneously from a single colony (single inoculum) on eosin-methylene blue agar. Tests with 87 cultures, representing 7 genera in the family Enterobacteriaceae, were completed with typical (correct) IMVic patterns for all cultures within 48 h. Parallel tests with conventional media showed that the agar plate method was superior, more sensitive, faster, and simpler to perform, and less time was required to identify Escherichia coli by 72 h.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=334074 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC242642 PMC242642]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Bacteriological Techniques; Citrates/metabolism; Enterobacteriaceae/classification; Enterobacteriaceae/metabolism; Escherichia coli/classification; Escherichia coli/metabolism; Indoles/metabolism

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3399.L589d6f1323372&page=3399&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="I589d6f1358ad6" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3399.I589d6f1358ad6&page=3399&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:16738554

2017-02-07T02:50:33Z

46.229.168.65: Fill PMID: Page!

{{RightTOC}}



{| id="U589935f8b1293" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Baba, T, Ara, T, Hasegawa, M, Takai, Y, Okumura, Y, Baba, M, Datsenko, KA, Tomita, M, Wanner, BL and Mori, H''' (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. ''Mol. Syst. Biol.'' '''2''':2006.0008
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16738554 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681482 PMC1681482]
Online version:[http://dx.doi.org/10.1038/msb4100050 10.1038/msb4100050]
|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Escherichia coli/genetics; Gene Deletion; Internet; Mutation; Organisms, Genetically Modified

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3345.U589935f8b1293&page=3345&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="F589935f8dadd7" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3345.F589935f8dadd7&page=3345&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:11929534

2017-02-05T08:04:11Z

46.229.168.65: Fill PMID: Page!

{{RightTOC}}



{| id="H5896dc7b54f8e" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Sperandio, V, Torres, AG and Kaper, JB''' (2002) Quorum sensing Escherichia coli regulators B and C (QseBC): a novel two-component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli. ''Mol. Microbiol.'' '''43''':809-21
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
Quorum sensing is a cell-to-cell signalling mechanism in which bacteria secrete hormone-like compounds called autoinducers. When these auto-inducers reach a certain threshold concentration, they interact with bacterial transcriptional regulators, thereby regulating gene expression. Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 as well as E. coli K-12 produces the autoinducer-2 (AI-2), which is synthesized by the product of the luxS gene, and previous work from our laboratory has shown that genes encoding the EHEC type III secretion system were activated by quorum sensing. Recently, by hybridizing an E. coli K-12 gene array with cDNA synthesized from RNA extracted from EHEC strain 86-24 and its isogenic luxS mutant, we observed that other potential virulence-associated factors, such as genes encoding the expression and assembly of flagella, motility and chemotaxis, were also activated by quorum sensing. The array data also indicated that several genes encoding putative E. coli regulators were controlled by quorum sensing. In this report, we describe a two-component system regulated by quorum sensing that shares homology with Salmonella typhimurium PmrAB, which we have named quorum sensing E. coli regulator B and C (QseBC). The qseBC genes, previously identified only as open reading frames b3025 and b3026, are organized in an operon in the E. coli chromosome, with qseB encoding the response regulator and qseC the sensor kinase. We confirmed the regulation of qseBC by quorum sensing using qseB::lacZ transcriptional fusions and characterized the phenotypes of an isogenic qseC mutation in EHEC. This mutant expressed less flagellin and had reduced motility compared with the wild-type and complemented strains. Transcription of flhD, fliA, motA and fliC::lacZ fusions was decreased in the qseC mutant, suggesting that qseBC is a transcriptional regulator of flagella genes. A qseC mutant was also generated in E. coli K-12 strain MC1000 that showed the same phenotypes as the EHEC mutant, indicating that qseBC regulates flagella and motility by quorum sensing in both EHEC and K-12. QseBC activates transcription of flhDC, which is the master regulator for the flagella and motility genes and, in the absence of flhD, QseBC failed to activate the transcription of fliA. Motility of a luxS, but not of a qseC, mutant can be restored by providing AI-2 exogenously as preconditioned media, suggesting that the qseC mutant is unable to respond to AI-2. However, QseC has no effect on the expression of other quorum sensing-controlled genes such as those encoding for the type III secretion system. These data indicate that QseBC is one component of the quorum-sensing regulatory cascade in both EHEC and K-12 that is involved in the regulation of flagella and motility genes, but that additional regulators in this cascade remain to be characterized.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11929534 PubMed]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
DNA-Binding Proteins/genetics; DNA-Binding Proteins/metabolism; Escherichia coli/physiology; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Flagella/physiology; Gene Expression Regulation, Bacterial; Molecular Sequence Data; Mutation; Promoter Regions, Genetic; Regulon; Trans-Activators/genetics; Trans-Activators/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3338.H5896dc7b54f8e&page=3338&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="V5896dc7ba2a2a" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3338.V5896dc7ba2a2a&page=3338&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:11929534

2017-02-03T02:02:39Z

46.229.168.65: Fill PMID: Page!

{{RightTOC}}



{| id="R5893e4bf7a540" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Sperandio, V, Torres, AG and Kaper, JB''' (2002) Quorum sensing Escherichia coli regulators B and C (QseBC): a novel two-component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli. ''Mol. Microbiol.'' '''43''':809-21
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
Quorum sensing is a cell-to-cell signalling mechanism in which bacteria secrete hormone-like compounds called autoinducers. When these auto-inducers reach a certain threshold concentration, they interact with bacterial transcriptional regulators, thereby regulating gene expression. Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 as well as E. coli K-12 produces the autoinducer-2 (AI-2), which is synthesized by the product of the luxS gene, and previous work from our laboratory has shown that genes encoding the EHEC type III secretion system were activated by quorum sensing. Recently, by hybridizing an E. coli K-12 gene array with cDNA synthesized from RNA extracted from EHEC strain 86-24 and its isogenic luxS mutant, we observed that other potential virulence-associated factors, such as genes encoding the expression and assembly of flagella, motility and chemotaxis, were also activated by quorum sensing. The array data also indicated that several genes encoding putative E. coli regulators were controlled by quorum sensing. In this report, we describe a two-component system regulated by quorum sensing that shares homology with Salmonella typhimurium PmrAB, which we have named quorum sensing E. coli regulator B and C (QseBC). The qseBC genes, previously identified only as open reading frames b3025 and b3026, are organized in an operon in the E. coli chromosome, with qseB encoding the response regulator and qseC the sensor kinase. We confirmed the regulation of qseBC by quorum sensing using qseB::lacZ transcriptional fusions and characterized the phenotypes of an isogenic qseC mutation in EHEC. This mutant expressed less flagellin and had reduced motility compared with the wild-type and complemented strains. Transcription of flhD, fliA, motA and fliC::lacZ fusions was decreased in the qseC mutant, suggesting that qseBC is a transcriptional regulator of flagella genes. A qseC mutant was also generated in E. coli K-12 strain MC1000 that showed the same phenotypes as the EHEC mutant, indicating that qseBC regulates flagella and motility by quorum sensing in both EHEC and K-12. QseBC activates transcription of flhDC, which is the master regulator for the flagella and motility genes and, in the absence of flhD, QseBC failed to activate the transcription of fliA. Motility of a luxS, but not of a qseC, mutant can be restored by providing AI-2 exogenously as preconditioned media, suggesting that the qseC mutant is unable to respond to AI-2. However, QseC has no effect on the expression of other quorum sensing-controlled genes such as those encoding for the type III secretion system. These data indicate that QseBC is one component of the quorum-sensing regulatory cascade in both EHEC and K-12 that is involved in the regulation of flagella and motility genes, but that additional regulators in this cascade remain to be characterized.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11929534 PubMed]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
DNA-Binding Proteins/genetics; DNA-Binding Proteins/metabolism; Escherichia coli/physiology; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Flagella/physiology; Gene Expression Regulation, Bacterial; Molecular Sequence Data; Mutation; Promoter Regions, Genetic; Regulon; Trans-Activators/genetics; Trans-Activators/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3338.R5893e4bf7a540&page=3338&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="V5893e4bfa5ad2" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3338.V5893e4bfa5ad2&page=3338&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:20474363

2016-12-28T03:07:17Z

46.229.168.65: Fill PMID: Page!

{{RightTOC}}



{| id="X58632c65c4543" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Macconkey, AT''' (1908) Bile Salt Media and their advantages in some Bacteriological Examinations. ''J Hyg (Lond)'' '''8''':322-34
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
No abstract in PubMed
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20474363 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2167122 PMC2167122]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3411.X58632c65c4543&page=3411&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Q58632c65cddea" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3411.Q58632c65cddea&page=3411&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:20474229

2016-11-29T20:14:52Z

46.229.168.65: Fill PMID: Page!

{{RightTOC}}



{| id="Z583de1bbce85c" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Macconkey, A''' (1905) Lactose-Fermenting Bacteria in Faeces. ''J Hyg (Lond)'' '''5''':333-79
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
No abstract in PubMed
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20474229 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2236133 PMC2236133]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3413.Z583de1bbce85c&page=3413&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</div> ||
|}
<noinclude>

</noinclude>


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X583de1bbdce73" class=" tableEdit Phenotype_Table_2"
|- align='left' bgcolor='#CCCCFF'
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3413.X583de1bbdce73&page=3413&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]