OMPwiki - User contributions [en]

Main Page

2011-11-11T15:40:05Z

Azweifel:

<center>Would you like your phenotype to be included in our logo? Send your image to {{Email}}.</center>

{| style="width:100%; background:#fcfcfc; border:1px solid #ccc; border-spacing:10px;"
| style="width:55%; color:#000;" |

{| style="width:280px; border:none; background:none;"
| style="width:280px; text-align:left; white-space:nowrap; color:#000;" |
<div style="font-size:172%; border:none; margin:0; padding:.1em; color:#000;">Welcome to the [[OMPWiki:About|Microbial Phenotypes Wiki]],</div>
<div style="top:+0.2em; font-size:115%;"><span class=plainlinks>
Web-based community resource designed to display microbial phenotypes <br />
and the methods used to study them.<br /><br />
</span></div>
|}

| style="width:25%; font-size:115%;" |
* [[:Category:Gallery|Gallery of Logo Pictures]]
* [[:Category:Methods|Methods]]
* [[OmpWiki:Wishlist|Wishlist]]
* [[OmpWiki:Membership|Membership]]
* [[:Category:Help|Help]]
|}


{| style=" width:100%; font-size:115%; border-spacing:10px;"
|-
|width="60%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|

== What are microbial phenotypes & why do they need an ontology? ==

A phenotype is the expression of a genotype (i.e. the full genetic complement of an organism) in a given environment. For example, eye color, number of seeds per pod,
and coat color are phenotypic traits that can be observed in ﬂies, lupines, and ponies, respectively. Within an individual organism, both changes in genetic makeup, such as from bacterial conjugation, and variation in gene expression can result in different phenotypes under similar environmental conditions. Conversely, environmental variation can lead to different outcomes for genetically identical organisms, through variable gene expression. Myriad genetically and taxonomically diverse microbes exhibit countless variability in their morphological and physiological traits, both within and among species. Oftentimes these result in unique and exquisite manifestations, such as the symbiosis between the bioluminescent ''Vibrio ﬁscheri'' bacterium and its squid host ''Euprymna scolopes''. Characterization of phenotypes is critically important for medical microbial identiﬁcation, and many unique biotechnological applications of microbes are rooted in phenotypes. Genetic manipulation with associated phenotypic characterization remains an important tool for determining protein function in microorganisms amenable to manipulation, such as ''Escherichia coli''. To facilitate research in all of these areas, we are developing the Ontology of Microbial Phenotypes to allow for standardized capture of essential phenotypic information.

|width="40%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|
===Upcoming News===
*First OMP release is coming soon

*We are currently modifying the [[PMID Table Mock-up|phenotype annotation table]] to house OMP and ECO terms

=== Search Pages of Interest ===
*[[Categories to Search]]
*[[OMP_summary|Summary table]] of all entries in the phenotype tables.

Main Page

2011-11-11T15:39:49Z

Azweifel:

<center>Would you like your phenotype to be included in our logo? Send your image to {{Email}}.</center>

{| style="width:100%; background:#fcfcfc; border:1px solid #ccc; border-spacing:10px;"
| style="width:55%; color:#000;" |

{| style="width:280px; border:none; background:none;"
| style="width:280px; text-align:left; white-space:nowrap; color:#000;" |
<div style="font-size:172%; border:none; margin:0; padding:.1em; color:#000;">Welcome to [[OMPWiki:About|the Microbial Phenotypes Wiki]],</div>
<div style="top:+0.2em; font-size:115%;"><span class=plainlinks>
Web-based community resource designed to display microbial phenotypes <br />
and the methods used to study them.<br /><br />
</span></div>
|}

| style="width:25%; font-size:115%;" |
* [[:Category:Gallery|Gallery of Logo Pictures]]
* [[:Category:Methods|Methods]]
* [[OmpWiki:Wishlist|Wishlist]]
* [[OmpWiki:Membership|Membership]]
* [[:Category:Help|Help]]
|}


{| style=" width:100%; font-size:115%; border-spacing:10px;"
|-
|width="60%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|

== What are microbial phenotypes & why do they need an ontology? ==

A phenotype is the expression of a genotype (i.e. the full genetic complement of an organism) in a given environment. For example, eye color, number of seeds per pod,
and coat color are phenotypic traits that can be observed in ﬂies, lupines, and ponies, respectively. Within an individual organism, both changes in genetic makeup, such as from bacterial conjugation, and variation in gene expression can result in different phenotypes under similar environmental conditions. Conversely, environmental variation can lead to different outcomes for genetically identical organisms, through variable gene expression. Myriad genetically and taxonomically diverse microbes exhibit countless variability in their morphological and physiological traits, both within and among species. Oftentimes these result in unique and exquisite manifestations, such as the symbiosis between the bioluminescent ''Vibrio ﬁscheri'' bacterium and its squid host ''Euprymna scolopes''. Characterization of phenotypes is critically important for medical microbial identiﬁcation, and many unique biotechnological applications of microbes are rooted in phenotypes. Genetic manipulation with associated phenotypic characterization remains an important tool for determining protein function in microorganisms amenable to manipulation, such as ''Escherichia coli''. To facilitate research in all of these areas, we are developing the Ontology of Microbial Phenotypes to allow for standardized capture of essential phenotypic information.

|width="40%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|
===Upcoming News===
*First OMP release is coming soon

*We are currently modifying the [[PMID Table Mock-up|phenotype annotation table]] to house OMP and ECO terms

=== Search Pages of Interest ===
*[[Categories to Search]]
*[[OMP_summary|Summary table]] of all entries in the phenotype tables.

Main Page

2011-11-11T15:38:57Z

Azweifel:

<center>Would you like your phenotype to be included in our logo? Send your image to {{Email}}.</center>

{| style="width:100%; background:#fcfcfc; border:1px solid #ccc; border-spacing:10px;"
| style="width:55%; color:#000;" |

{| style="width:280px; border:none; background:none;"
| style="width:280px; text-align:left; white-space:nowrap; color:#000;" |
<div style="font-size:172%; border:none; margin:0; padding:.1em; color:#000;">Welcome to [[OMPWiki:About|OMPWiki]],</div>
<div style="top:+0.2em; font-size:115%;"><span class=plainlinks>
Web-based community resource designed to display microbial phenotypes <br />
and the methods used to study them.<br /><br />
</span></div>
|}

| style="width:25%; font-size:115%;" |
* [[:Category:Gallery|Gallery of Logo Pictures]]
* [[:Category:Methods|Methods]]
* [[OmpWiki:Wishlist|Wishlist]]
* [[OmpWiki:Membership|Membership]]
* [[:Category:Help|Help]]
|}


{| style=" width:100%; font-size:115%; border-spacing:10px;"
|-
|width="60%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|

== What are microbial phenotypes & why do they need an ontology? ==

A phenotype is the expression of a genotype (i.e. the full genetic complement of an organism) in a given environment. For example, eye color, number of seeds per pod,
and coat color are phenotypic traits that can be observed in ﬂies, lupines, and ponies, respectively. Within an individual organism, both changes in genetic makeup, such as from bacterial conjugation, and variation in gene expression can result in different phenotypes under similar environmental conditions. Conversely, environmental variation can lead to different outcomes for genetically identical organisms, through variable gene expression. Myriad genetically and taxonomically diverse microbes exhibit countless variability in their morphological and physiological traits, both within and among species. Oftentimes these result in unique and exquisite manifestations, such as the symbiosis between the bioluminescent ''Vibrio ﬁscheri'' bacterium and its squid host ''Euprymna scolopes''. Characterization of phenotypes is critically important for medical microbial identiﬁcation, and many unique biotechnological applications of microbes are rooted in phenotypes. Genetic manipulation with associated phenotypic characterization remains an important tool for determining protein function in microorganisms amenable to manipulation, such as ''Escherichia coli''. To facilitate research in all of these areas, we are developing the Ontology of Microbial Phenotypes to allow for standardized capture of essential phenotypic information.

|width="40%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|
===Upcoming News===
*First OMP release is coming soon

*We are currently modifying the [[PMID Table Mock-up|phenotype annotation table]] to house OMP and ECO terms

=== Search Pages of Interest ===
*[[Categories to Search]]
*[[OMP_summary|Summary table]] of all entries in the phenotype tables.

PMID:7748952

2011-10-21T14:30:29Z

Azweifel: Fill PMID: Page!

{{RightTOC}}



{| id="K4ea18204d17f4" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Tsui, HC and Winkler, ME''' (1994) Transcriptional patterns of the mutL-miaA superoperon of Escherichia coli K-12 suggest a model for posttranscriptional regulation.''Biochimie'' '''76''':1168-77
|-
!align=left |Abstract
||
The complex amiB-mutL-miaA-hfq-hflX-hflK-hflC superoperon of E coli contains important genes for several fundamental cellular processes, including cell-wall hydrolysis (amiB), DNA repair (mutL), tRNA modification (miaA) and proteolysis (hflX-hflK-hflC). We report here the transcriptional pattern and possible posttranscriptional regulation of mutL, miaA and hfq genes of this superoperon. RNase protection analysis of mRNA transcribed from the bacterial chromosome demonstrated that there is co-transcription of mutL and miaA. In addition, two internal promoters, PmiaA and P1hfq were identified and mapped to 201 and 837 nucleotides upstream from the respective translation start sites. PmiaA contains poor matches to the -10 and -35 regions of the sigma-70 RNA polymerase consensus sequences, but it contains multiple potential Fis-binding sites and an upstream AT-rich region with poly(A) sequences. The basic arrangement of Fis-binding sites followed by an AT rich region is shared with promoters for rRNA operons and some of the tRNA and tRNA modification genes. As part of an initial study of mutL and miaA regulation, we measured transcript amounts in isogenic rne, rnc and rne rnc double mutants which are deficient in RNase E, RNase III or both. The amounts of steady state level mutL-miaA cotranscript, PmiaA transcript and P1hfq transcript increased eight-, nine- and three-fold respectively in an rne3071 mutant when compared to the rne+ parent. In contrast, amounts of the three transcripts were the same in an rnc105 mutant and its rnc+ parent. These results indicate that mutL, miaA, and hfq expression could be regulated by multiple mechanisms, including degree of cotranscription from upstream genes, modulation of internal promoter strength, and by RNase E activity. A model is presented for RNase E-mediated posttranscriptional regulation that may coordinate mutL expression with replication and miaA with tRNA amounts under different growth conditions, especially during nutrient upshifts.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7748952 PubMed]

|-
!align=left |Keywords
||
Amino Acid Sequence; Base Sequence; Cell Division; Codon; Escherichia coli; Gene Expression Regulation, Bacterial; Genes, Bacterial; Molecular Sequence Data; Operon; Promoter Regions, Genetic; Sequence Homology, Nucleic Acid; Transcription, Genetic

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2777.K4ea18204d17f4&page=2777&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</span> ||
|}


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

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

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

{| id="G4ea18204e938d" class=" tableEdit Phenotype_Table_2"
|-
!|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"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2777.G4ea18204e938d&page=2777&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:7748952

2011-10-21T14:30:28Z

Azweifel: New PMID: Page!

PMID:7928977

2011-10-21T14:30:11Z

Azweifel: New PMID: Page!

PMID:7928977

2011-10-21T14:30:11Z

Azweifel: Fill PMID: Page!

{{RightTOC}}



{| id="J4ea181f354fa5" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Zhao, G and Winkler, ME''' (1994) An Escherichia coli K-12 tktA tktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth.''J. Bacteriol.'' '''176''':6134-8
|-
!align=left |Abstract
||
We show that a tktA tktB double mutant, which is devoid of the two known transketolase isoenzymes of Escherichia coli K-12, requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth. This pyridoxine requirement can also be satisfied by 4-hydroxy-L-threonine or glycolaldehyde. These results provide direct evidence that D-erythrose-4-phosphate is a precursor of the pyridine ring of pyridoxine. In addition, they show that the two major E. coli transketolase isoenzymes are not required for the biosynthesis of D-1-deoxyxylulose, which is thought to be another precursor of pyridoxine.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7928977 PubMed]

|-
!align=left |Keywords
||
Amino Acids; Escherichia coli; Genes, Bacterial; Isoenzymes; Mutation; Pyridoxine; Transketolase; Vitamins

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2776.J4ea181f354fa5&page=2776&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</span> ||
|}


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

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

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

{| id="J4ea181f3a9670" class=" tableEdit Phenotype_Table_2"
|-
!|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"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2776.J4ea181f3a9670&page=2776&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:7894093

2011-09-11T00:30:15Z

Azweifel: Fill PMID: Page!

{{RightTOC}}



{| id="H4e6c011730cf8" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Kawana, S and Nishiyama, S''' (1995) Pustular psoriasis and aseptic purulent arthritis: possible role of leukotrienes B4 and C4 in a flare of synovitis.''Dermatology (Basel)'' '''190''':35-8
|-
!align=left |Abstract
||
Arthritis is a frequent complication of pustular psoriasis. However, the mechanism of onset of this arthritis still remains unclear.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7894093 PubMed]

|-
!align=left |Keywords
||
Aged; Arthritis; Female; Humans; Leukotriene B4; Leukotriene C4; Leukotrienes; Male; Middle Aged; Myocardial Infarction; Neutrophils; Psoriasis; Radioimmunoassay; Synovial Fluid; Synovitis

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2765.H4e6c011730cf8&page=2765&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</span> ||
|}


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

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

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

{| id="S4e6c011755a68" class=" tableEdit Phenotype_Table_2"
|-
!|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"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2765.S4e6c011755a68&page=2765&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:7894093

2011-09-11T00:30:14Z

Azweifel: New PMID: Page!

File:Annotation mock-up.pdf

2011-09-09T04:11:54Z

Azweifel: This is the current version of the literature mockup page.

This is the current version of the literature mockup page.

PMID:19543378

2011-09-02T17:23:17Z

Azweifel: Table edited by Azweifel via TableEdit

{{RightTOC}}



{| id="G4e5ff89adba5e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Ueda, A and Wood, TK''' (2009) Connecting quorum sensing, c-di-GMP, pel polysaccharide, and biofilm formation in Pseudomonas aeruginosa through tyrosine phosphatase TpbA (PA3885).''PLoS Pathog.'' '''5''':e1000483
|-
!align=left |Abstract
||
With the opportunistic pathogen Pseudomonas aeruginosa, quorum sensing based on homoserine lactones was found to influence biofilm formation. Here we discern a mechanism by which quorum sensing controls biofilm formation by screening 5850 transposon mutants of P. aeruginosa PA14 for altered biofilm formation. This screen identified the PA3885 mutant, which had 147-fold more biofilm than the wild-type strain. Loss of PA3885 decreased swimming, abolished swarming, and increased attachment, although this did not affect production of rhamnolipids. The PA3885 mutant also had a wrinkly colony phenotype, formed pronounced pellicles, had substantially more aggregation, and had 28-fold more exopolysaccharide production. Expression of PA3885 in trans reduced biofilm formation and abolished aggregation. Whole transcriptome analysis showed that loss of PA3885 activated expression of the pel locus, an operon that encodes for the synthesis of extracellular matrix polysaccharide. Genetic screening identified that loss of PelABDEG and the PA1120 protein (which contains a GGDEF-motif) suppressed the phenotypes of the PA3885 mutant, suggesting that the function of the PA3885 protein is to regulate 3,5-cyclic diguanylic acid (c-di-GMP) concentrations as a phosphatase since c-di-GMP enhances biofilm formation by activating PelD, and c-di-GMP inhibits swarming. Loss of PA3885 protein increased cellular c-di-GMP concentrations; hence, PA3885 protein is a negative regulator of c-di-GMP production. Purified PA3885 protein has phosphatase activity against phosphotyrosine peptides and is translocated to the periplasm. Las-mediated quorum sensing positively regulates expression of the PA3885 gene. These results show that the PA3885 protein responds to AHL signals and likely dephosphorylates PA1120, which leads to reduced c-di-GMP production. This inhibits matrix exopolysaccharide formation, which leads to reduced biofilm formation; hence, we provide a mechanism for quorum sensing control of biofilm formation through the pel locus and suggest PA3885 should be named TpbA for tyrosine phosphatase related to biofilm formation and PA1120 should be TpbB.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19543378 PubMed]
Online version:[http://dx.doi.org/10.1371/journal.ppat.1000483 10.1371/journal.ppat.1000483]
|-
!align=left |Keywords
||
Adhesins, Bacterial; Bacterial Proteins; Biofilms; Cyclic GMP; Gene Expression Regulation, Bacterial; Glycolipids; Mutation; Periplasm; Phenotype; Polysaccharides, Bacterial; Protein Tyrosine Phosphatases; Pseudomonas aeruginosa; Quorum Sensing; Second Messenger Systems; Tyrosine

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2751.G4e5ff89adba5e&page=2751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</span> ||
|}


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

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

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

{| id="G4e5ff89b0ad04" class=" tableEdit Phenotype_Table_2"
|-
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status
|-
|
a mutation or genetic difference within a strain
|
*Taxon: Pseudomonas aeruginosa
*Strain: PA14
*Substrain:
*NCBI Taxon ID: 652611
|
*Genotype of Reference Strain: tpbA+
*Genotype of Experimental Strain : tpbA-
|
*Reference Condition: after 8 hours in LB at 37C
*Experimental Condition: after 8 hours in LB at 37C
|

|
increased biofilm formation
|

|
crystal violet staining
|
Figure 1A- by 147-fold
|
complete

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2751.G4e5ff89b0ad04&page=2751&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:19543378

2011-09-01T22:18:19Z

Azweifel: Table edited by Azweifel via TableEdit

{{RightTOC}}



{| id="G4e5ff89adba5e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Ueda, A and Wood, TK''' (2009) Connecting quorum sensing, c-di-GMP, pel polysaccharide, and biofilm formation in Pseudomonas aeruginosa through tyrosine phosphatase TpbA (PA3885).''PLoS Pathog.'' '''5''':e1000483
|-
!align=left |Abstract
||
With the opportunistic pathogen Pseudomonas aeruginosa, quorum sensing based on homoserine lactones was found to influence biofilm formation. Here we discern a mechanism by which quorum sensing controls biofilm formation by screening 5850 transposon mutants of P. aeruginosa PA14 for altered biofilm formation. This screen identified the PA3885 mutant, which had 147-fold more biofilm than the wild-type strain. Loss of PA3885 decreased swimming, abolished swarming, and increased attachment, although this did not affect production of rhamnolipids. The PA3885 mutant also had a wrinkly colony phenotype, formed pronounced pellicles, had substantially more aggregation, and had 28-fold more exopolysaccharide production. Expression of PA3885 in trans reduced biofilm formation and abolished aggregation. Whole transcriptome analysis showed that loss of PA3885 activated expression of the pel locus, an operon that encodes for the synthesis of extracellular matrix polysaccharide. Genetic screening identified that loss of PelABDEG and the PA1120 protein (which contains a GGDEF-motif) suppressed the phenotypes of the PA3885 mutant, suggesting that the function of the PA3885 protein is to regulate 3,5-cyclic diguanylic acid (c-di-GMP) concentrations as a phosphatase since c-di-GMP enhances biofilm formation by activating PelD, and c-di-GMP inhibits swarming. Loss of PA3885 protein increased cellular c-di-GMP concentrations; hence, PA3885 protein is a negative regulator of c-di-GMP production. Purified PA3885 protein has phosphatase activity against phosphotyrosine peptides and is translocated to the periplasm. Las-mediated quorum sensing positively regulates expression of the PA3885 gene. These results show that the PA3885 protein responds to AHL signals and likely dephosphorylates PA1120, which leads to reduced c-di-GMP production. This inhibits matrix exopolysaccharide formation, which leads to reduced biofilm formation; hence, we provide a mechanism for quorum sensing control of biofilm formation through the pel locus and suggest PA3885 should be named TpbA for tyrosine phosphatase related to biofilm formation and PA1120 should be TpbB.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19543378 PubMed]
Online version:[http://dx.doi.org/10.1371/journal.ppat.1000483 10.1371/journal.ppat.1000483]
|-
!align=left |Keywords
||
Adhesins, Bacterial; Bacterial Proteins; Biofilms; Cyclic GMP; Gene Expression Regulation, Bacterial; Glycolipids; Mutation; Periplasm; Phenotype; Polysaccharides, Bacterial; Protein Tyrosine Phosphatases; Pseudomonas aeruginosa; Quorum Sensing; Second Messenger Systems; Tyrosine

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2751.G4e5ff89adba5e&page=2751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</span> ||
|}


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

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

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

{| id="G4e5ff89b0ad04" class=" tableEdit Phenotype_Table_2"
|-
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status
|-
|
a mutation or genetic difference within a strain
|
*Taxon: Pseudomonas aeruginosa
*Strain: PA14
*Substrain:
*NCBI Taxon ID: 652611
|
*Genotype of Reference Strain: tbpA+
*Genotype of Experimental Strain : tbpA-
|
*Reference Condition: after 8 hours in LB at 37C
*Experimental Condition: after 8 hours in LB at 37C
|

|
increased biofilm formation
|

|
crystal violet staining
|
Figure 1A- by 147-fold
|
complete

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2751.G4e5ff89b0ad04&page=2751&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:19543378

2011-09-01T21:26:51Z

Azweifel: Fill PMID: Page!

{{RightTOC}}



{| id="G4e5ff89adba5e" class=" tableEdit PMID_info_table"

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!align=left |Citation
||
'''Ueda, A and Wood, TK''' (2009) Connecting quorum sensing, c-di-GMP, pel polysaccharide, and biofilm formation in Pseudomonas aeruginosa through tyrosine phosphatase TpbA (PA3885).''PLoS Pathog.'' '''5''':e1000483
|-
!align=left |Abstract
||
With the opportunistic pathogen Pseudomonas aeruginosa, quorum sensing based on homoserine lactones was found to influence biofilm formation. Here we discern a mechanism by which quorum sensing controls biofilm formation by screening 5850 transposon mutants of P. aeruginosa PA14 for altered biofilm formation. This screen identified the PA3885 mutant, which had 147-fold more biofilm than the wild-type strain. Loss of PA3885 decreased swimming, abolished swarming, and increased attachment, although this did not affect production of rhamnolipids. The PA3885 mutant also had a wrinkly colony phenotype, formed pronounced pellicles, had substantially more aggregation, and had 28-fold more exopolysaccharide production. Expression of PA3885 in trans reduced biofilm formation and abolished aggregation. Whole transcriptome analysis showed that loss of PA3885 activated expression of the pel locus, an operon that encodes for the synthesis of extracellular matrix polysaccharide. Genetic screening identified that loss of PelABDEG and the PA1120 protein (which contains a GGDEF-motif) suppressed the phenotypes of the PA3885 mutant, suggesting that the function of the PA3885 protein is to regulate 3,5-cyclic diguanylic acid (c-di-GMP) concentrations as a phosphatase since c-di-GMP enhances biofilm formation by activating PelD, and c-di-GMP inhibits swarming. Loss of PA3885 protein increased cellular c-di-GMP concentrations; hence, PA3885 protein is a negative regulator of c-di-GMP production. Purified PA3885 protein has phosphatase activity against phosphotyrosine peptides and is translocated to the periplasm. Las-mediated quorum sensing positively regulates expression of the PA3885 gene. These results show that the PA3885 protein responds to AHL signals and likely dephosphorylates PA1120, which leads to reduced c-di-GMP production. This inhibits matrix exopolysaccharide formation, which leads to reduced biofilm formation; hence, we provide a mechanism for quorum sensing control of biofilm formation through the pel locus and suggest PA3885 should be named TpbA for tyrosine phosphatase related to biofilm formation and PA1120 should be TpbB.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19543378 PubMed]
Online version:[http://dx.doi.org/10.1371/journal.ppat.1000483 10.1371/journal.ppat.1000483]
|-
!align=left |Keywords
||
Adhesins, Bacterial; Bacterial Proteins; Biofilms; Cyclic GMP; Gene Expression Regulation, Bacterial; Glycolipids; Mutation; Periplasm; Phenotype; Polysaccharides, Bacterial; Protein Tyrosine Phosphatases; Pseudomonas aeruginosa; Quorum Sensing; Second Messenger Systems; Tyrosine

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2751.G4e5ff89adba5e&page=2751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</span> ||
|}


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

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

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

{| id="G4e5ff89b0ad04" class=" tableEdit Phenotype_Table_2"
|-
!|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"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2751.G4e5ff89b0ad04&page=2751&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:19543378

2011-09-01T21:26:50Z

Azweifel: New PMID: Page!

PMID:21181144

2011-09-01T21:26:28Z

Azweifel: Table edited by Azweifel via TableEdit

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{| id="N4e5e9df10628a" class=" tableEdit PMID_info_table"

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'''Sanchez-Torres, V, Hu, H and Wood, TK''' (2011) GGDEF proteins YeaI, YedQ, and YfiN reduce early biofilm formation and swimming motility in Escherichia coli.''Appl. Microbiol. Biotechnol.'' '''90''':651-8
|-
!align=left |Abstract
||
The second messenger 3'-5'-cyclic diguanylic acid (c-di-GMP) promotes biofilm formation, and c-di-GMP is synthesized by diguanylate cyclases (characterized by a GGDEF domain) and degraded by phosphodiesterases. Here, we evaluated the effect of the 12 E. coli GGDEF-only proteins on biofilm formation and motility. Deletions of the genes encoding the GGDEF proteins YeaI, YedQ, YfiN, YeaJ, and YneF increased swimming motility as expected for strains with reduced c-di-GMP. Alanine substitution in the EGEVF motif of YeaI abolished its impact on swimming motility. In addition, extracellular DNA (eDNA) was increased as expected for the deletions of yeaI (tenfold), yedQ (1.8-fold), and yfiN (3.2-fold). As a result of the significantly enhanced motility, but contrary to current models of decreased biofilm formation with decreased diguanylate cyclase activity, early biofilm formation increased dramatically for the deletions of yeaI (30-fold), yedQ (12-fold), and yfiN (18-fold). Our results indicate that YeaI, YedQ, and YfiN are active diguanylate cyclases that reduce motility, eDNA, and early biofilm formation and contrary to the current paradigm, the results indicate that c-di-GMP levels should be reduced, not increased, for initial biofilm formation so c-di-GMP levels must be regulated in a temporal fashion in biofilms.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21181144 PubMed]
Online version:[http://dx.doi.org/10.1007/s00253-010-3074-5 10.1007/s00253-010-3074-5]
|-
!align=left |Keywords
||
Biofilms; Cyclic GMP; Escherichia coli; Escherichia coli Proteins; Gene Deletion; Gene Expression Regulation, Bacterial; Genes, Bacterial; Mutagenesis, Site-Directed; Phosphoric Diester Hydrolases; Phosphorus-Oxygen Lyases; Protein Structure, Tertiary; Second Messenger Systems

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2750.N4e5e9df10628a&page=2750&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</span> ||
|}


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

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

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

{| id="L4e5e9df128e73" class=" tableEdit Phenotype_Table_2"
|-
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status
|-
|
a mutation or genetic difference within a strain
|
*Taxon: Escherichia coli
*Strain: K-12
*Substrain: BW25113
*NCBI Taxon ID: 679895
|
*Genotype of Reference Strain: yeaI +
*Genotype of Experimental Strain : del- yeaI
|
*Reference Condition: in minimal media
*Experimental Condition: in minimal media
|

|
decreased biofilm formation
|

|
Crystal violet biofilm assay
|
Figure 1b
|
complete
|-
|
a mutation or genetic difference within a strain
|
*Taxon: Escherichia coli
*Strain: K12
*Substrain: BW25113
*NCBI Taxon ID: 679895
|
*Genotype of Reference Strain: yeaI +
*Genotype of Experimental Strain : del- yeaI
|
*Reference Condition: in LB
|

|
no significant difference in biofilm formation
|

|
Crystal violet biofilm assay
|
Figure 1
|
complete

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2750.L4e5e9df128e73&page=2750&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID:21181144

2011-08-31T20:47:45Z

Azweifel: Fill PMID: Page!

{{RightTOC}}



{| id="N4e5e9df10628a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sanchez-Torres, V, Hu, H and Wood, TK''' (2011) GGDEF proteins YeaI, YedQ, and YfiN reduce early biofilm formation and swimming motility in Escherichia coli.''Appl. Microbiol. Biotechnol.'' '''90''':651-8
|-
!align=left |Abstract
||
The second messenger 3'-5'-cyclic diguanylic acid (c-di-GMP) promotes biofilm formation, and c-di-GMP is synthesized by diguanylate cyclases (characterized by a GGDEF domain) and degraded by phosphodiesterases. Here, we evaluated the effect of the 12 E. coli GGDEF-only proteins on biofilm formation and motility. Deletions of the genes encoding the GGDEF proteins YeaI, YedQ, YfiN, YeaJ, and YneF increased swimming motility as expected for strains with reduced c-di-GMP. Alanine substitution in the EGEVF motif of YeaI abolished its impact on swimming motility. In addition, extracellular DNA (eDNA) was increased as expected for the deletions of yeaI (tenfold), yedQ (1.8-fold), and yfiN (3.2-fold). As a result of the significantly enhanced motility, but contrary to current models of decreased biofilm formation with decreased diguanylate cyclase activity, early biofilm formation increased dramatically for the deletions of yeaI (30-fold), yedQ (12-fold), and yfiN (18-fold). Our results indicate that YeaI, YedQ, and YfiN are active diguanylate cyclases that reduce motility, eDNA, and early biofilm formation and contrary to the current paradigm, the results indicate that c-di-GMP levels should be reduced, not increased, for initial biofilm formation so c-di-GMP levels must be regulated in a temporal fashion in biofilms.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21181144 PubMed]
Online version:[http://dx.doi.org/10.1007/s00253-010-3074-5 10.1007/s00253-010-3074-5]
|-
!align=left |Keywords
||
Biofilms; Cyclic GMP; Escherichia coli; Escherichia coli Proteins; Gene Deletion; Gene Expression Regulation, Bacterial; Genes, Bacterial; Mutagenesis, Site-Directed; Phosphoric Diester Hydrolases; Phosphorus-Oxygen Lyases; Protein Structure, Tertiary; Second Messenger Systems

|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2750.N4e5e9df10628a&page=2750&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</span> ||
|}


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

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

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

{| id="L4e5e9df128e73" class=" tableEdit Phenotype_Table_2"
|-
!|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"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2750.L4e5e9df128e73&page=2750&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
|}
</protect>

==Notes==

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

[[Category:Publication]]

PMID: 21181144

2011-08-31T20:47:44Z

Azweifel: New PMID: Page!

#REDIRECT [[PMID:21181144]]

2011-08-19T19:27:44Z

Azweifel:

PMID Table Mock-up

2011-08-19T19:27:01Z

Azweifel: Table edited by Azweifel via TableEdit

2011-08-19T15:56:47Z

Azweifel: /* Phenotype Annotations */

Template:Phenotype Table 2

2011-08-19T15:56:04Z

Azweifel: Created page with '<headings> Taxon Information||taxon|multifield|Taxon|Strain|Substrain|NCBI Taxon ID Genotype Information (if known)||genotype|multifield|Genotype of Parent|Object Difference OMP…'

<headings>
Taxon Information||taxon|multifield|Taxon|Strain|Substrain|NCBI Taxon ID
Genotype Information (if known)||genotype|multifield|Genotype of Parent|Object Difference
OMP ID||ontology|multifield|OMP ID (1)|OMP ID (2)
OMP Term Name||phenotype|text
Growth Details||text
ECO ID||ECO|multifield|ECO Term 1|ECO Term 2
ECO Term Name||evidence|text
Notes||notes|textbox
Status||status|text
</headings>
<type>0</type>

Main Page

2011-08-10T21:25:01Z

Azweifel: /* Upcoming News */

<center>Would you like your phenotype to be included in our logo? Send your image to {{Email}}.</center>

{| style="width:100%; background:#fcfcfc; border:1px solid #ccc; border-spacing:10px;"
| style="width:55%; color:#000;" |

{| style="width:280px; border:none; background:none;"
| style="width:280px; text-align:left; white-space:nowrap; color:#000;" |
<div style="font-size:172%; border:none; margin:0; padding:.1em; color:#000;">Welcome to [[OMPWiki:About|OMPWiki]],</div>
<div style="top:+0.2em; font-size:115%;"><span class=plainlinks>
Web-based community resource designed to display microbial phenotypes <br />
and the methods used to study them.<br /><br />
</span></div>
|}

| style="width:25%; font-size:115%;" |
* [[:Category:Gallery|Gallery of Logo Pictures]]
* [[:Category:Methods|Methods]]
* [[OmpWiki:Wishlist|Wishlist]]
* [[OmpWiki:Membership|Membership]]
* [[:Category:Help|Help]]
|}


{| style=" width:100%; font-size:115%; border-spacing:10px;"
|-
|width="60%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|

== What are microbial phenotypes & why do they need an ontology? ==

A phenotype is the expression of a genotype (i.e. the full genetic complement of an organism) in a given environment. For example, eye color, number of seeds per pod,
and coat color are phenotypic traits that can be observed in ﬂies, lupines, and ponies, respectively. Within an individual organism, both changes in genetic makeup, such as from bacterial conjugation, and variation in gene expression can result in different phenotypes under similar environmental conditions. Conversely, environmental variation can lead to different outcomes for genetically identical organisms, through variable gene expression. Myriad genetically and taxonomically diverse microbes exhibit countless variability in their morphological and physiological traits, both within and among species. Oftentimes these result in unique and exquisite manifestations, such as the symbiosis between the bioluminescent ''Vibrio ﬁscheri'' bacterium and its squid host ''Euprymna scolopes''. Characterization of phenotypes is critically important for medical microbial identiﬁcation, and many unique biotechnological applications of microbes are rooted in phenotypes. Genetic manipulation with associated phenotypic characterization remains an important tool for determining protein function in microorganisms amenable to manipulation, such as ''Escherichia coli''. To facilitate research in all of these areas, we are developing the Ontology of Microbial Phenotypes to allow for standardized capture of essential phenotypic information.

|width="40%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|
===Upcoming News===
*First OMP release is coming soon

*We are currently modifying the [[PMID Table Mock-up|phenotype annotation table]] to house OMP and ECO terms

=== Search Pages of Interest ===
*[[Categories to Search]]
*[[OMP_summary|Summary table]] of all entries in the phenotype tables.

Category:Image Analysis Tool, Center for Microbial Ecology Image Analysis System (CMEIAS)

2011-07-22T03:15:09Z

Azweifel: /* Source */

{{Pagetop}}
== Purpose ==
*Quantitative analysis of<ref name='PMID:11391457'/><ref name='PMID:20020121'/>:
**microbial abundance and phylotype diversity of single cells classified by their discriminating color within heterogeneous communities
** cell viability
**spatial relationships and intensity of bacterial gene expression involved in cellular communication between individual cells within rhizoplane biofilms
**biofilm ecophysiology based on ribotype-differentiated radioactive substrate utilization

== Source ==
*Consists of several custom plug-ins that can be used with [[:Category:Image Analysis Tool, UTHSCSA ImageTool|UTHSCSA ImageTool]]
*[http://cme.msu.edu/cmeias/ CMEIAS website]
*[http://lter.kbs.msu.edu/abstracts/414 A recent summary of CMEIAS image analysis software]

== Notes ==

== Related Ontology Terms ==

== Examples ==
<PMIDsummary />

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

[[Category:Image Analysis Tool, Microscopy]]
[[Category:Image Analysis Tool, UTHSCSA ImageTool]]
[[Category:Image Analysis Tool]]

Main Page

2011-07-12T19:58:36Z

Azweifel:

<center>Would you like your phenotype to be included in our logo? Send your image to {{Email}}.</center>

{| style="width:100%; background:#fcfcfc; border:1px solid #ccc; border-spacing:10px;"
| style="width:55%; color:#000;" |

{| style="width:280px; border:none; background:none;"
| style="width:280px; text-align:left; white-space:nowrap; color:#000;" |
<div style="font-size:172%; border:none; margin:0; padding:.1em; color:#000;">Welcome to [[OMPWiki:About|OMPWiki]],</div>
<div style="top:+0.2em; font-size:115%;"><span class=plainlinks>
Web-based community resource designed to display microbial phenotypes <br />
and the methods used to study them.<br /><br />
</span></div>
|}

| style="width:25%; font-size:115%;" |
* [[:Category:Gallery|Gallery of Logo Pictures]]
* [[:Category:Methods|Methods]]
* [[OmpWiki:Wishlist|Wishlist]]
* [[OmpWiki:Membership|Membership]]
* [[:Category:Help|Help]]
|}


{| style=" width:100%; font-size:115%; border-spacing:10px;"
|-
|width="60%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|

== What are microbial phenotypes & why do they need an ontology? ==

A phenotype is the expression of a genotype (i.e. the full genetic complement of an organism) in a given environment. For example, eye color, number of seeds per pod,
and coat color are phenotypic traits that can be observed in ﬂies, lupines, and ponies, respectively. Within an individual organism, both changes in genetic makeup, such as from bacterial conjugation, and variation in gene expression can result in different phenotypes under similar environmental conditions. Conversely, environmental variation can lead to different outcomes for genetically identical organisms, through variable gene expression. Myriad genetically and taxonomically diverse microbes exhibit countless variability in their morphological and physiological traits, both within and among species. Oftentimes these result in unique and exquisite manifestations, such as the symbiosis between the bioluminescent ''Vibrio ﬁscheri'' bacterium and its squid host ''Euprymna scolopes''. Characterization of phenotypes is critically important for medical microbial identiﬁcation, and many unique biotechnological applications of microbes are rooted in phenotypes. Genetic manipulation with associated phenotypic characterization remains an important tool for determining protein function in microorganisms amenable to manipulation, such as ''Escherichia coli''. To facilitate research in all of these areas, we are developing the Ontology of Microbial Phenotypes to allow for standardized capture of essential phenotypic information.

|width="40%" style ="background:#fcfcfc; border:1px solid #ccc; padding:10px;" align="left" valign="top"|
===Upcoming News===
*First OMP release is coming soon

*Upcoming Meetings showcasing OMP progress
**July 26-30, 2011- "International Conference on Biomedical Ontology (ICBO)" in Buffalo, NY
**August 2-7, 2011- "Molecular Genetics of Bacteria and Phage" in Madison, WI

*We are currently modifying the [[PMID Table Mock-up|phenotype annotation table]] to house OMP and ECO terms

=== Search Pages of Interest ===
*[[Categories to Search]]
*[[OMP_summary|Summary table]] of all entries in the phenotype tables.

Template:PMID Phenotype table

2011-07-12T19:46:42Z

Azweifel:

<headings>
OMP Accession||accession|text
Taxon Information||taxon|multifield|Taxon|Strain|Substrain|NCBI Taxon ID
Genotype Information (if known)||genotype|multifield|Genotype of Parent|Genetic Difference of Mutant
OMP ID||ontology|text
OMP Term Name||phenotype|text
Phenotype Details||additional|dbxref|temperature sensitive|other
Related Rows||linkages|dbxref|unique|parent|derivative of parent|complex phenotype
ECO ID||ECO|text
ECO Term Name||evidence|text
Notes||notes|textbox
Status||status|text
</headings>
<type>0</type>

PMID Table Mock-up

2011-07-08T16:09:39Z

<gallery widths=100px heights=100px perrow=8 caption="phenotype pictures">
File:bioluminescent NYC.png
File:infected C. elegans.png
File:C. violaceum.png
File:luminescence flask.png
File:bacterial community.png
File:food poisoning.png
File:toxic shock.png
File:lyme disease.png
</gallery>