OMPwiki - User contributions [en]

PMID:791131

2019-03-06T04:56:07Z

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{| id="E5c7f52e7d48df" class=" tableEdit PMID_info_table"

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!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.E5c7f52e7d48df&page=3363&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="O5c7f52e7e2fc2" 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.O5c7f52e7e2fc2&page=3363&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:7287890

2019-03-06T04:55:52Z

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{| id="K5c7f52d7c43d6" class=" tableEdit PMID_info_table"

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!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Wallis, C, Melnick, JL and Longoria, CJ''' (1981) Colorimetric method for rapid determination of bacteriuria. ''J. Clin. Microbiol.'' '''14''':342-6
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
An inexpensive, rapid, and simple colorimetric test for detection of bacteriuria is described. This test does not require bacterial growth and has the marked advantage of being able to quantify bacteria, even when the organisms are present in the urine of bacteriuric patients who are being treated with antibiotics. The test is carried out with 1 ml of urine, which is processed through a 10-mm-diameter filter than entraps the bacteria on its surface. Safranine dye is passed through the filter to stain the bacteria and the filter fibers. A decolorizer, which removes the dye from the filter fibers but not from the bacteria, is then passed through the filter. If there are greater than or equal to 10(5) colony-forming units of bacteria per ml in the sample, the 10-mm filter disk manifests a pink to red color. If there are less than 10(5)colony-forming units of bacteria per ml, the filter disk remains white or becomes slightly yellow. The entire procedure has been adapted to a semiautomated instrument and the time required per test is less than 1 min. The results obtained on the test card are a permanent record to be filled with the patient's chart. The bacteria can be quickly classified as gram positive or gram negative by selective staining of a second milliliter of urine on the filter. Of 441 urine specimens tested, 430 (98%) were correctly classified as containing more or less than 10(5) colony-forming units per ml. A total of 62 urine specimens were positive by bacterial plating (greater than or equal to 10(5) colony-forming units per ml), and 59 were positive by the colorimetric test. Eight false-positives (colorimetric test positive, plate counts less than 10(5)) were encountered in patients (bacteriuric) being prescribed antibiotics. Removal of the antibiotics from these urine specimens, with subsequent replating of the samples, indicated the presence of greater than or equal to 10(5) colony-forming units of bacteria per ml in three representative cases tested, indicating that the results of the colorimetric tests were not false-positives but that the plate counts were low because of the inhibition of bacterial growth by the residual antibiotics present in the urine.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7287890 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC271966 PMC271966]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Bacteria/isolation & purification; Bacteriuria/diagnosis; Colorimetry/methods; Coloring Agents; Gentian Violet/diagnostic use; Humans; Indicators and Reagents; Phenazines/diagnostic use; Species Specificity; Urine/microbiology

|- class="tableEdit_footer"
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|}


==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="Z5c7f52d801b4d" 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.3513.Z5c7f52d801b4d&page=3513&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:16385049

2019-03-06T04:55:39Z

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{| id="H5c7f52cb6d113" class=" tableEdit PMID_info_table"

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!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Herzberg, M, Kaye, IK, Peti, W and Wood, TK''' (2006) YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. ''J. Bacteriol.'' '''188''':587-98
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
YdgG is an uncharacterized protein that is induced in Escherichia coli biofilms. Here it is shown that deletion of ydgG decreased extracellular and increased intracellular concentrations of autoinducer 2 (AI-2); hence, YdgG enhances transport of AI-2. Consistent with this hypothesis, deletion of ydgG resulted in a 7,000-fold increase in biofilm thickness and 574-fold increase in biomass in flow cells. Also consistent with the hypothesis, deletion of ydgG increased cell motility by increasing transcription of flagellar genes (genes induced by AI-2). By expressing ydgG in trans, the wild-type phenotypes for extracellular AI-2 activity, motility, and biofilm formation were restored. YdgG is also predicted to be a membrane-spanning protein that is conserved in many bacteria, and it influences resistance to several antimicrobials, including crystal violet and streptomycin (this phenotype could also be complemented). Deletion of ydgG also caused 31% of the bacterial chromosome to be differentially expressed in biofilms, as expected, since AI-2 controls hundreds of genes. YdgG was found to negatively modulate expression of flagellum- and motility-related genes, as well as other known products essential for biofilm formation, including operons for type 1 fimbriae, autotransporter protein Ag43, curli production, colanic acid production, and production of polysaccharide adhesin. Eighty genes not previously related to biofilm formation were also identified, including those that encode transport proteins (yihN and yihP), polysialic acid production (gutM and gutQ), CP4-57 prophage functions (yfjR and alpA), methionine biosynthesis (metR), biotin and thiamine biosynthesis (bioF and thiDFH), anaerobic metabolism (focB, hyfACDR, ttdA, and fumB), and proteins with unknown function (ybfG, yceO, yjhQ, and yjbE); 10 of these genes were verified through mutation to decrease biofilm formation by 40% or more (yfjR, bioF, yccW, yjbE, yceO, ttdA, fumB, yjiP, gutQ, and yihR). Hence, it appears YdgG controls the transport of the quorum-sensing signal AI-2, and so we suggest the gene name tqsA.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16385049 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347309 PMC1347309]
Online version:[http://dx.doi.org/10.1128/JB.188.2.587-598.2006 10.1128/JB.188.2.587-598.2006]
|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Biofilms/growth & development; Biological Transport/genetics; Escherichia coli K12/physiology; Escherichia coli Proteins/genetics; Escherichia coli Proteins/physiology; Gene Deletion; Genes, Bacterial/genetics; Homoserine/analogs & derivatives; Homoserine/metabolism; Lactones/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.542.H5c7f52cb6d113&page=542&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="K5c7f52cbc6e19" 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.542.K5c7f52cbc6e19&page=542&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:334074

2019-03-06T04:55:27Z

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{| id="W5c7f52bf2e7b6" class=" tableEdit PMID_info_table"

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!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.W5c7f52bf2e7b6&page=3399&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="P5c7f52bf71d0a" 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.P5c7f52bf71d0a&page=3399&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:11929534

2019-03-06T04:55:05Z

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{| id="M5c7f52a92daad" class=" tableEdit PMID_info_table"

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!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.M5c7f52a92daad&page=3338&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="F5c7f52a930ca2" 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.F5c7f52a930ca2&page=3338&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:20474363

2019-03-06T04:54:49Z

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{| id="Z5c7f529942cb5" class=" tableEdit PMID_info_table"

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!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.Z5c7f529942cb5&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="N5c7f529952cff" 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.N5c7f529952cff&page=3411&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:20474244

2019-03-06T04:54:26Z

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{| id="S5c7f5282445e8" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Macconkey, A''' (1906) On the Liquefaction of Gelatin by the Bacillus cloacae. ''J Hyg (Lond)'' '''6''':23-32
|-
!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=20474244 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2236042 PMC2236042]

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

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3412.S5c7f5282445e8&page=3412&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="S5c7f5282541aa" 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.3412.S5c7f5282541aa&page=3412&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:20474229

2019-03-06T04:53:47Z

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{| id="K5c7f525b25bb5" 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.K5c7f525b25bb5&page=3413&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="O5c7f525b48fb9" 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.O5c7f525b48fb9&page=3413&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:1100857

2019-03-05T23:47:19Z

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{| id="E5c7f0a86e9158" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Aswad, D and Koshland, DE Jr''' (1975) Isolation, characterization and complementation of Salmonella typhimurium chemotaxis mutants. ''J. Mol. Biol.'' '''97''':225-35
|-
!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=1100857 PubMed]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Chemotaxis; Genes, Dominant; Genes, Recessive; Genetic Complementation Test; Genotype; Mutation; Recombination, Genetic; Salmonella typhimurium/isolation & purification; Salmonella typhimurium/physiology; Species Specificity

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.120.E5c7f0a86e9158&page=120&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="N5c7f0a8717b64" 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.120.N5c7f0a8717b64&page=120&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:16738554

2019-03-05T23:46:40Z

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{| id="X5c7f0a5f88764" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
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'''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.X5c7f0a5f88764&page=3345&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="Y5c7f0a6005343" 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.Y5c7f0a6005343&page=3345&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:3278319

2019-03-05T12:37:51Z

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{| id="A5c7e6d9f058a8" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Strauch, KL and Beckwith, J''' (1988) An Escherichia coli mutation preventing degradation of abnormal periplasmic proteins. ''Proc. Natl. Acad. Sci. U.S.A.'' '''85''':1576-80
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
A fusion between tsr (encoding the inner membrane protein Tsr) and phoA (encoding the periplasmic protein alkaline phosphatase, AP) generates a membrane-bound hybrid protein (Tsr-AP 2) with AP enzymatic activity. The hybrid protein is proteolytically unstable and is broken down to yield a smaller, soluble species with AP activity. We devised a genetic screen to distinguish between cells containing only membrane-bound AP and those containing soluble AP. The screen depends on diffusion of soluble AP away from cells with a leaky outer membrane to produce a halo of AP activity around colonies on solid growth medium. Several mutants lacking this halo show reduced degradation of Tsr-AP 2. One mutant is also defective in breakdown of five other abnormal periplasmic proteins but not of two cytoplasmic proteins. The mutation in this strain, degP4::Tn5, defines a locus distinct from previously identified loci that affect protein stability or protease activities. This strain may be useful for preventing the breakdown of unstable foreign proteins in Escherichia coli.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3278319 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC279816 PMC279816]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Alkaline Phosphatase/metabolism; Bacterial Proteins/metabolism; Escherichia coli/enzymology; Escherichia coli/genetics; Membrane Proteins/metabolism; Molecular Weight; Mutation; Peptide Hydrolases/genetics; Peptide Hydrolases/metabolism; Recombinant Fusion Proteins/metabolism; Recombinant Proteins/metabolism

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.32383.A5c7e6d9f058a8&page=32383&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="V5c7e6d9f2c55c" 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.32383.V5c7e6d9f2c55c&page=32383&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:3278319

2019-03-05T12:37:50Z

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PMID:9045630

2019-03-05T12:31:33Z

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{| id="T5c7e6c24d0118" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Sone, M, Kishigami, S, Yoshihisa, T and Ito, K''' (1997) Roles of disulfide bonds in bacterial alkaline phosphatase. ''J. Biol. Chem.'' '''272''':6174-8
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
Alkaline phosphatase of Escherichia coli (a homodimeric protein found in the periplasmic space) contains two intramolecular disulfide bonds (Cys-168-Cys-178 and Cys-286-Cys-336) that are formed after export to the periplasmic space. The location-specific folding character of this enzyme allowed its wide usage as a reporter of protein localization in prokaryotic cells. To study the roles of disulfide bonds in alkaline phosphatase, we eliminated each of them by Cys to Ser mutations. Intracellular stability of alkaline phosphatase decreased in the absence of either one or both of the disulfide bonds. The mutant proteins were stabilized in a DegP protease-deficient strain, allowing accumulation at significant levels and subsequent characterization. A mutant protein that lacked the N-terminally located disulfide bond (Cys-168-Cys-178) was found to have Cys-286 and Cys-336 residues disulfide-bonded, to have a dimeric structure, and to have almost full enzymatic activity. Nevertheless, the mutant protein lost the trypsin-resistant conformation that is characteristically observed for the wild-type enzyme. In contrast, mutants lacking Cys-286 and Cys-336 were monomeric and inactive. These results indicate that the Cys-286-Cys-336 disulfide bond is required and is sufficient for correctly positioning the active site region of this enzyme, but such an active conformation is still insufficient for the conformational stability of the enzyme. Thus, a fully active state of this enzyme can be formed without full protein stability, and the two disulfide bonds differentially contribute to these properties.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9045630 PubMed]

|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Alkaline Phosphatase/chemistry; Bacterial Proteins/chemistry; Binding Sites; Cysteine/chemistry; Disulfides/chemistry; Mutagenesis, Site-Directed; Protein Conformation; Protein Denaturation; Protein Folding; Serine/chemistry; Structure-Activity Relationship; Trypsin/pharmacology

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.32382.T5c7e6c24d0118&page=32382&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="I5c7e6c2536c02" 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.32382.I5c7e6c2536c02&page=32382&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:9045630

2019-03-05T12:31:32Z

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PMID on Demand placeholder

PMID:18067575

2019-03-05T11:35:36Z

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PMID:18067575

2019-03-05T11:35:36Z

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{| id="S5c7e5f08423e4" class=" tableEdit PMID_info_table"

|-
!align=left align='left' bgcolor='#CCCCFF' |Citation
||
'''Lee, Y, Kim, Y, Yeom, S, Kim, S, Park, S, Jeon, CO and Park, W''' (2008) The role of disulfide bond isomerase A (DsbA) of Escherichia coli O157:H7 in biofilm formation and virulence. ''FEMS Microbiol. Lett.'' '''278''':213-22
|-
!align=left align='left' bgcolor='#CCCCFF' |Abstract
||
The role of periplasmic disulfide oxidoreductase DsbA in Shiga toxin-producing Escherichia coli O157:H7 (STEC) was investigated. Deletion of dsbA (DeltadsbA) significantly decreased cell motility and alkaline phosphatase activity in STEC. STEC DeltadsbA also showed greater sensitivity to menadione and under low pH conditions. Significant reductions in surface attachment to both biotic (HT-29 epithelial cells) and abiotic (polystyrene and polyvinyl chloride) surfaces were observed in STEC DeltadsbA. In addition, no biofilm formation was detected in STEC DeltadsbA compared to wild-type cells in glass capillary tubes under continuous flow-culture system conditions. In the nematode model Caenorhabditis elegans-killing assay, the deletion of dsbA in STEC resulted in attenuated virulence compared to wild-type cells. STEC DeltadsbA was also found to have a reduced ability to colonize the nematode gut. These results suggest that DsbA plays important roles in biofilm formation and virulence in STEC cells.
|-
!align=left align='left' bgcolor='#CCCCFF' |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18067575 PubMed]
Online version:[http://dx.doi.org/10.1111/j.1574-6968.2007.00993.x 10.1111/j.1574-6968.2007.00993.x]
|-
!align=left align='left' bgcolor='#CCCCFF' |Keywords
||
Alkaline Phosphatase/metabolism; Animals; Bacterial Adhesion/genetics; Bacterial Adhesion/physiology; Biofilms/growth & development; Blotting, Northern; Caenorhabditis elegans/microbiology; Cell Line, Tumor; Escherichia coli O157/drug effects; Escherichia coli O157/genetics; Escherichia coli O157/pathogenicity; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Escherichia coli Proteins/physiology; Gene Expression Regulation, Bacterial; Green Fluorescent Proteins/genetics; Green Fluorescent Proteins/metabolism; Humans; Hydrogen-Ion Concentration; Luminescent Proteins/genetics; Luminescent Proteins/metabolism; Models, Genetic; Mutation; Protein Disulfide-Isomerases/genetics; Protein Disulfide-Isomerases/metabolism; Protein Disulfide-Isomerases/physiology; Virulence/genetics; Vitamin K 3/pharmacology

|- class="tableEdit_footer"
|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.32381.S5c7e5f08423e4&page=32381&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="D5c7e5f08b65c4" 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.32381.D5c7e5f08b65c4&page=32381&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</div> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]