OMPwiki - User contributions [en]

PMID:16385049

2015-06-08T20:17:29Z

Saleksander: Table edited by Saleksander via TableEdit

{{RightTOC}}



{| id="G55724df806540" class=" tableEdit PMID_info_table"

|-
!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

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|}
<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="W55724df80d125" 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"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.542.W55724df80d125&page=542&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table] || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

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

[[Category:Publication]]

PMID:16385049

2015-06-08T19:42:45Z

Saleksander: Table edited by Saleksander via TableEdit

{{RightTOC}}



{| id="G55724df806540" class=" tableEdit PMID_info_table"

|-
!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"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.542.G55724df806540&page=542&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}
<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="W55724df80d125" 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
|-
|
a mutation or genetic difference within a strain
|
*Taxon: 679895
*Strain: BW25113
*Substrain:
*NCBI Taxon ID: 679895
|
*Genotype of Reference Strain: lacIqrrnBT14 ΔlacZWJ16 hsdR514 ΔaraBADAH33 ΔrhaBADLD78
*Genotype of Experimental Strain : K-12 BW25113 ΔydgG Ω Kmr
|
*Reference Condition:
|
OMP:0007026
|
decreased biofilm formation
|
ECO:0000182
|
in vitro culture assay evidence
|
Fig 1. To confirm that the increase in biofilm formation is due to the deletion of ydgG, the mutant strain was complemented in trans and biofilm formation was measured in a 96-well biofilm assay with M9C glu and LB glu. As expected, increasing ydgG expression decreased the biofilm formation of the ydgG mutant in both M9C glu and LB glu to that of the wild-type strain. In M9C glu, at IPTG concentrations of 0.5, 0.75, 1.0, and 1.5 mM, the relative values of biofilm formation by the ydgG mutant expressing YdgG in trans were 1.9 ± 0.3, 1.8 ± 0.3, 1.1 ± 0.2, and 1.1 ± 0.2, respectively. In LB glu, at the same IPTG concentrations, the relative values of biofilm formation by the ydgG mutant expressing YdgG in trans were 1.8 ± 0.2, 1.6 ± 0.2, 1.4 ± 0.2, and 0.9 ± 0.2, respectively. Hence, YdgG represses biofilm formation.
|

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|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.542.W55724df80d125&page=542&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table] || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

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

[[Category:Publication]]

File:omplogo4.jpg

2015-04-06T21:28:18Z

Saleksander: Category:Logos Category:Logo Picture Note: any alterations to this file will not affect the site logo itself, as the logo is a different file.

[[Category:Logos]]
[[Category:Logo Picture]]

Note: any alterations to this file will not affect the site logo itself, as the logo is a different file.

File:omplogo3.png

2015-04-06T21:27:04Z

Saleksander: Courtesy of Bonnie Bassler. Image from her ASMCUE 2011 plenary talk: Tiny Conspiracies Category:Logos Category:Logo Picture Note: any alterations to this file will not affect the site logo itself, as the logo is a different file.

Courtesy of Bonnie Bassler. Image from her ASMCUE 2011 plenary talk: Tiny Conspiracies
[[Category:Logos]]
[[Category:Logo Picture]]

Note: any alterations to this file will not affect the site logo itself, as the logo is a different file.

File:omplogo2.png

2015-04-06T21:25:02Z

Saleksander:

File:omplogo2.png

2015-04-06T21:04:22Z

Saleksander: Courtesy of Bonnie Bassler. Image from her ASMCUE 2011 plenary talk: Tiny Conspiracies Category:Logos Category:Logo Picture

Courtesy of Bonnie Bassler. Image from her ASMCUE 2011 plenary talk: Tiny Conspiracies
[[Category:Logos]]
[[Category:Logo Picture]]

Help:Basic Wiki Markup

2015-03-17T17:22:10Z

Saleksander: Created page with "A brief guide to wiki markup is below. For more on editing, see the How to edit a page on Wikipedia and the metaWikipedia: Help:Editor|Wiki..."

A brief guide to wiki markup is below. For more on editing, see the [[Wikipedia:How_to_edit_a_page|How to edit a page on Wikipedia]] and the [[metaWikipedia: Help:Editor|Wikimedia Meta-wiki pages for editors]]. Go ahead and edit without worrying about having to know everything about wiki markup; one of the cool things about wikis is that more experienced users can fix your markup, and as you become more comfortable with wikis, you can fix the markup of others. The most important thing is to share your ideas...making them look pretty is secondary.
===Entering and styling text===
To enter or edit text on a PMID or other wiki page, just click on the link that says Edit. You'll get a web form, where you can modify the sections- e.g. "Materials and Methods Used". Often, you may want to post to the discussion page for a wiki page first. To do this, click on the discussion tab, and then on the edit tab for the discussion page or on any internal edit link on the page if you just want to edit a subsection.

The wiki software allows you to preview what you entered by using the "Show preview" button. For the most part, you can just type in the space and the desired text will show up. However, here are some basic ways the text can be modified using wiki markup (intentionally or unintentionally!) to change the appearance of text on the page.
{|{{Prettytable}}
|-
|Style
|Markup
|-
|''italics''
|<nowiki>''italics''</nowiki>: two single quotes on each side of the italic text
|-
|'''bold'''
|<nowiki>'''bold'''</nowiki>: three single quotes on each side of the bold text
|}

Different levels of headings can be made by flanking text with different numbers of = signs, like ==heading== or ===heading===. To show as headings, these must be at the start of a new line. Headings create new editable subsections, and also generate table of contents links.

Text on a line that starts with blank spaces will be put in a box.

: Text on a line that starts with a colon ":" will be indented.
::Different numbers of :'s give different levels of indentations

===Linking===
One important thing in this wiki is to be able to add links to other pages, or to external websites. It's also useful to be able to assign new pages to the categories that correspond to ECO nodes. Linking to another page in the wiki can be as simple as putting text between '''double square brackets'''. For example, the [[Sandbox]] is a page that users can use to play around with wiki markup. This link was generated like this:
For example, the<nowiki> [[Sandbox]]</nowiki> is a page that users can use to play around with wiki markup.
Double brackets are used to link to pages inside the wiki, or to another wiki using [[Interwiki links]]. If the linked page exists, then the link will take a reader there when it's clicked. However, you can also create a link to a page that doesn't exist yet. This will show up on the page in red, and clicking on it will take the reader to an edit page where new content can be created.

Here is an example of a link to an external website: The Evidence Ontology is at [http://evidenceontology.org/Welcome.html evidenceontology.org]
The Evidence Ontology website is at <nowiki>[http://evidenceontology.org/Welcome.html]</nowiki>
The link is surrounded by '''single square brackets'''. Inside the brackets there is the URL, a space, and then the linked text. If you leave out the linked text, it will look like this [http://evidenceontology.org/Welcome.html]. If there is no URL (no <nowiki>"http://"</nowiki>), it will look like this: [evidenceontology.org/Welcome.html]

Sometimes you want to link to a page using different linked text than the page name. For example, this links to the Sandbox page: The Sandbox is a page for [[Sandbox|trying out wiki markup]]. This is made using a vertical line (a pipe, above the backslash on US keyboards)
The Sandbox is a page for <nowiki>[[Sandbox|trying out wiki markup]]</nowiki>.
====Linking to an ECO node====
The pages for ECO nodes in this wiki are special pages called Category Pages. This means that <nowiki>[[Category:ECO:0000178_!_in_vivo_assay_evidence]]</nowiki> links to a nonexistent page. You can link to a GO node ''without'' assigning the page to that node, using <nowiki>[[:Category:ECO:0000178_!_in_vivo_assay_evidence|Category:ECO:0000178_!_in_vivo_assay_evidence]]</nowiki>, like this: [[:Category:ECO:0000178_!_in_vivo_assay_evidence|Category:ECO:0000178_!_in_vivo_assay_evidence]]. Note that here I am linking to the page for a GO term, but I don't want this Help page to be considered as an ECO code.

===Creating new pages===
As noted above, you can create a new page by linking to a new page title.

[[Category:Help|{{PAGENAME}}]]
[[Category:Editing Help|{{PAGENAME}}]]

Category:Editing Help

2015-03-16T21:56:51Z

Saleksander: Created page with "Category:Help"

[[Category:Help]]

Help:Tables-How to edit

2015-03-16T21:52:56Z

Saleksander:

Help:Tables-How to edit

2015-03-16T21:04:54Z

Saleksander:

==Basic usage==
TableEdit provides a more user-friendly way to create and edit tables in mediawiki than using the standard wiki mark-up. TableEdit tables show up in a page with their own Edit link. Registered users can then add rows and columns, add information, and/or edit information already in the table.

===Create a new table===
'''Step 1: Add a newTableEdit tag where you want the table to appear.'''

To add a new table that can be edited by TableEdit, there are two options:

*Add an empty table by putting <nowiki><newTableEdit/></nowiki> in the text where you want the table to appear.
*Add a table with defined headings by entering the following:
:<nowiki><newTableEdit></nowiki>
:Heading 1

:Heading 2

:Heading 3

:etc...

:<nowiki></newTableEdit></nowiki>

:You can edit the columns later if needed.

'''Step 2: Save the page'''.

If you used option 2, an empty table with your headings appears when you save the page.
Note that the default table has the column headings arrayed horizontally from left to right. You can change the orientation when you edit the table.

If you used option 1, there will a '''Create table here''' link. You can create the headings when you edit the table.

'''Step 3: Edit the table'''
Click on the link and use the table editor to add information.

===Example===
====Creating a New Table====
:1. Click on the "create table" quick button. This will insert the tags <nowiki><newTableEdit> and </newTableEdit></nowiki> automatically.
[[Image:Newtable_1.jpg|left|thumb|523px|Click on the quick button to create a new table]]
 
 

:2. Create the table headings by typing inside the <nowiki><newTableEdit></nowiki> tags.
::<nowiki><newTableEdit></nowiki>
::US State

::Capitol

::Governor
::<nowiki></newTableEdit></nowiki>
[[Image:Newtable_2.jpg|left|thumb|266px|Create the headings for your table]]
 
 

:3. Type a short summary of your edit and click '''save'''
[[Image:Newtable_3.jpg|left|thumb|586px|Save your work]]
 
 

:4. Click on the '''edit table''' link to go to the Table Editor.
[[Image:Newtable_4.jpg|left|511px|thumb|Click "edit table"]]
 
 

:5. Add a row.
[[Image:Newtable_5.jpg|left|542px|thumb|Click "add row"]]
 
 

:6. Add any information you know and click '''save'''.
::Lets say I don't know the governor, so I'll leave it for someone else to add.
[[Image:Newtable_6.jpg|left|432px|thumb|Add your data and save]]
 
 

====Editing the Headings====
:7. Let's add a column called "State Bird". First click '''Edit Headings'''
[[Image:Newtable_7.jpg|left|574px|thumb|Click "Edit Headings"]]

 
 

:8. Then click '''Add headings'''. You can now name your head in the box provided. Now click '''save'''..
[[Image:Newtable_8.jpg|left|629px|thumb|Click "Add Headings", type the heading name, then "save"]]
 
 

:9. Save the table back to the wiki page.
[[Image:Newtable_10.jpg|left|731px|thumb|Save the table]]
 
 

:10. Your table will look like this now:
[[Image:Newtable_11.jpg|left|707px|thumb|New Table Created]]
 
 

==Basic Table templates==
For table formats that you plan to use on more than one page, you can define a template. The template should be a Template page in the wiki that has a list of the table headings. When a table is made using a template, the headings can only be edited on the template page. Changing the template page will change the headings on all tables that use that template. Note that the changes won't be apparent until someone tries to edit the table and save it back to the page.

To add a table based on a template to a wiki page, put: <nowiki><newTableEdit>Template:TemplateName</newTableEdit></nowiki>.

To Find your specific TemplateName please see [http://ecoliwiki.net/colipedia/index.php/Category:Table_templates Table Templates].

==Advanced Table templates==
'''Using tags to specify more table properties'''

Attributes for the table can be wrapped in XML-like tags.
*Use <nowiki><type>1</type></nowiki> to create a vertical table, i.e. the headings are arrayed from top to bottom in the first column. The default is a horizontal orientation where the headings are arrayed from left to right in the first row.

*Use <nowiki><headings></headings></nowiki> for headings. Headings can have additional attributes, which can be used to customize the user interface and link content of rows to external sources (see below).

*Use <nowiki><heading_style></heading_style></nowiki> for heading style

*Use <nowiki><table_style></table_style></nowiki> for table style

'''Programming the TableEdit interface'''

Heading lists can have additional markup to modify the behavior of the Table Editor. Anything after a <nowiki>||</nowiki> in the headings list is considered part of a list of additional parameters for that heading. Individual parameters are delimited by single |s. The first parameter after the heading text is a unique column_name for the heading (this allows you to use non-unique names for the actual display). If this is not present, the heading name is assumed to be usable as the column_name. These are used for lookup and calculation fields as described below

== List of Table Templates in OMPWiki ==
See [[:Category:Table_templates]]

[[Category:Help|Tables]] [[Category:Table templates]]
[[Category:Editing Help|Tables]]

[[Category:Help]]

OMPwiki:Membership

2015-03-16T20:58:02Z

Saleksander:

You do not have to be an OMPWiki member to view the content provided on this site. However, if you wish to edit or add content, you must first become a registered user. There are many things that only registered users can do:

* Edit the content of wiki pages, or create new pages
* [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create new user accounts]
* Create your own [[Help:User Pages|custom home page]]
* Customize the [[Help:Preferences|appearance]] of OMPWiki, including using custom [[Help:Skins|"skins"]]
* Send messages to other users
It would be nice to be more open, but wikis get spammed and vandalized. We also have student accounts, which can do everything except create new users. Email us for more information.

==Becoming a registered user==
Any [[Special:ListUsers|currently registered user]] may create an account for their friends and colleagues. See [[:Category:Users who can help you get an account|Users who are willing to help you get an account]] to find someone who can not only set up an account for you, but also show you how the wiki works. Or just send [mailto:d-siegele@tamu.edu Debby Siegele] an email to tell us who you are, and we'll set up an account for you. Be sure to send us your preferred login name.

==Create a registered user==
If you are already registered and logged in, you can [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create an account] for new users.

[[Category:Help|Membership]]

User:JimHu

2015-03-16T20:52:56Z

Saleksander:

Jim hasn't added anything to his user page yet.
[[Category:Users who can help you get an account]]

User:Siegele

2015-03-16T20:52:52Z

Saleksander:

Debby Siegele

Associate Professor

Dept. of Biology

Texas A&M University

College Station, TX 77843-3258
[[Category:Users who can help you get an account]]

Category:Users who can help you get an account

2015-03-16T20:52:15Z

Saleksander:

Users listed on this page are willing to help others set up OMPWiki accounts and help them learn their way around the wiki. Finding someone at your institution means that you can get started without waiting for us to reply to an email request and you can get help in person.

The subcategories list users at different institutions or who fall into different interest groups.

To add yourself to this list add <nowiki>[[Category:Users who can help you get an account]]</nowiki> to your user page. You can also add tags for one of the subcategories. Be sure to provide enough information so that people can actually find you!

If you would like an account, but don't know anyone on this list, [mailto:d-siegele@tamu.edu email Debby Siegele].

[[Category:User Categories]]
[[Category:Help|Users who can help you get an account]]

Category:Users who can help you get an account

2015-03-16T20:48:11Z

Saleksander: Created page with "Users listed on this page are willing to help others set up OMPWiki accounts and help them learn their way around the wiki. Finding someone at your institution means that you..."

Users listed on this page are willing to help others set up OMPWiki accounts and help them learn their way around the wiki. Finding someone at your institution means that you can get started without waiting for us to reply to an email request and you can get help in person.

The subcategories list users at different institutions or who fall into different interest groups.

To add yourself to this list add <nowiki>[[Category:Users who can help you get an account]].</nowiki> to your user page. You can also add tags for one of the subcategories. Be sure to provide enough information so that people can actually find you!

If you would like an account, but don't know anyone on this list, [mailto:d-siegele@tamu.edu email Debby Siegele].

[[Category:User Categories]]
[[Category:Help|Users who can help you get an account]]

OMPwiki:Membership

2015-03-16T20:41:44Z

Saleksander:

You do not have to be an OMPWiki member to view the content provided on this site. However, if you wish to edit or add content, you must first become a registered user. There are many things that only registered users can do:

* Edit the content of wiki pages, or create new pages
* [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create new user accounts]
* Create your own [[Help:User Pages|custom home page]]
* Customize the [[Help:Preferences|appearance]] of OMPWiki, including using custom [[Help:Skins|"skins"]]
* Send messages to other users
It would be nice to be more open, but wikis get spammed and vandalized. We also have [[Student accounts|student accounts]], which can do everything except create new users.

==Becoming a registered user==
Any [[Special:ListUsers|currently registered user]] may create an account for their friends and colleagues. See [[:Category:Users who can help you get an account|Users who are willing to help you get an account]] to find someone who can not only set up an account for you, but also show you how the wiki works. Or just send [mailto:d-siegele@tamu.edu Debby Siegele] an email to tell us who you are, and we'll set up an account for you. Be sure to send us your preferred login name.

==Create a registered user==
If you are already registered and logged in, you can [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create an account] for new users.

[[Category:Help|Membership]]

Help:User Pages

2015-03-16T20:41:05Z

Saleksander:

When you join OMPwiki, it automatically creates a series of pages for you that you can access at any time from the upper right corner of the wiki '''while you are logged in'''.

==Username==
The first link, which should be your username, is to a blank page that you can customize however you want. Actually, any registered user can edit your user page, and you can edit theirs, since the user pages are just like other pages. But we view these pages as places that our users can use as their own personal home pages within the wiki.

==my talk==
This is a discussion page associated with your user page.

==my preferences==
The preference page is a series of tabs for various settings that control how the wiki behaves for you. Mostly self-explanatory; See [[Help:Preferences]] for more info.
==my watchlist==
Shows changes to pages on your watchlist. See [[Help:Watchlist]]
==my contributions==
Shows a list of all the pages you've ever edited in OMPWiki

==log out==
log out of OMPWiki.

[[Category:Help|User Pages]]

Help:Skins

2015-03-16T20:40:27Z

Saleksander:

Skins are different wrappers for the OMPWiki content that change the look and feel of the site. You can change the appearance of the wiki by choosing a different skin from your [[Special:Preferences|Preferences]].
[[Category:Help|Skins]]

Help:Skins

2015-03-16T20:38:44Z

Saleksander: Created page with "Skins are different wrappers for the OMPWiki content that change the look and feel of the site. You can change the appearance of the wiki by choosing a different skin from yo..."

Help:Preferences

2015-03-16T20:36:39Z

Saleksander: /* Watchlist */

[[Category:Help|Preferences]]
Registered users can customize OMP by changing their preferences.
==User profile==
You can edit your real name, and this section provides a link to allow the user to change their password or email. Other email options, such as the choice to receive emails when specific changes are made to wiki pages
==Appearance==
You can customize the appearance of the wiki by choosing a different skin. Monobook is the default skin. If you know of a mediawiki skin that you would like us to make available, please contact us and we'll see what we can do.
This tab also allows for image size to be specified, as well as some advanced appearance options.
==Date and time==
Change your time zone and date formatting options.
==Editing==
Alter the default editing window size, how editing is initiated, preview options and external editor capabilities. Please note, not all of these options have been extensively tested in our wiki, so please let us know if you experience any difficulties when using these settings.
==Recent changes==
This tab changes the default number of days and edits shown in the [[Special:RecentChanges |Recent Changes]] section, as well as how the changes can be displayed. You can also opt to hide minor or patrolled edits.
==Watchlist==
Vary the number of days and the changes that are displayed in the [[Special:Watchlist |Watchlist]]. Also, you can choose to hide certain edits or automatically add pages you modify to your [[Special:Watchlist |Watchlist]]. See more on the [[Help:Watchlist|Watchlist Help page]].

==Search==
Define the number of hits displayed. Importantly, you can also change which namespaces are searched by default.
==Misc.==
Options involving diffs.

Help:User Pages

2015-03-16T20:32:19Z

Saleksander:

OMPwiki:Membership

2015-03-16T20:31:20Z

Saleksander:

You do not have to be an OMPWiki member to view the content provided on this site. However, if you wish to edit or add content, you must first become a registered user. There are many things that only registered users can do:

* Edit the content of wiki pages, or create new pages
* [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create new user accounts]
* Create your own [[Help:User Pages|custom home page]]
* Customize the [[Help:Preferences|appearance]] of OMPWiki, including using custom [[Help:Skins|"skins"]]
* Send messages to other users
It would be nice to be more open, but wikis get spammed and vandalized. We also have [[Student accounts|student accounts]], which can do everything except create new users.

==Becoming a registered user==
Any [[Special:ListUsers|currently registered user]] may create an account for their friends and colleagues. See [[:Category:Users who can help you get an account|Users who are willing to help you get an account]] to find someone who can not only set up an account for you, but also show you how the wiki works. Or just send [mailto:d-siegele@tamu.edu Debby Siegele] an email to tell us who you are, and we'll set up an account for you. Be sure to send us your preferred login name.

==Create a registered user==
If you are already registered and logged in, you can [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create an account] for new users.

Help:Watchlist

2015-03-16T20:24:39Z

Saleksander: Created page with "Your watchlist is a list of the pages you are watching to keep track of changes. By clicking on "Watchlist", you can get a summary of changes made to ea..."

Your watchlist is a list of the pages you are watching to keep track of changes. By clicking on [[Special:Watchlist|"Watchlist"]], you can get a summary of changes made to each of the pages you are watching. This way you can see if anything happened on pages you're interested in, without having to click through all of them one at a time.

==Getting email notification of changes==
In your preferences, you can set OMPWiki to email you when a page on your watchlist has been edited. It only emails you once until you view the page again while logged in, so you won't be inundated with emails if someone is making a bunch of changes.

==Adding to your watchlist==
When you are logged in, a "watch" tab appears at the top of every page you are viewing. Clicking it places that page on your watchlist, sends you to a message telling you that you've added a page to your watchlist, and changes the tab to "unwatch" the next time you view that page.

==See also==
[[wikipedia:Help:Watching_pages]] for how watchlists work on Wikipedia.

[[Category:Help|Watchlist]]

OMPwiki:Membership

2015-03-16T19:55:19Z

Saleksander:

You do not have to be an OMPWiki member to view the content provided on this site. However, if you wish to edit or add content, you must first become a registered user. There are many things that only registered users can do:

* Edit the content of wiki pages, or create new pages
* [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create new user accounts]
* Create your own [[Help:User Pages|custom home page]]
* Customize the [[Help:Skins|appearance]] of OMPWiki using custom "skins"
* Send messages to other users
It would be nice to be more open, but wikis get spammed and vandalized. We also have [[Student accounts|student accounts]], which can do everything except create new users.

==Becoming a registered user==
Any [[Special:ListUsers|currently registered user]] may create an account for their friends and colleagues. See [[:Category:Users who can help you get an account|Users who are willing to help you get an account]] to find someone who can not only set up an account for you, but also show you how the wiki works. Or just send [mailto:d-siegele@tamu.edu Debby Siegele] an email to tell us who you are, and we'll set up an account for you. Be sure to send us your preferred login name.

==Create a registered user==
If you are already registered and logged in, you can [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create an account] for new users.

Help:Accounts

2015-03-16T19:17:11Z

Saleksander:

[[Category:Help|Accounts]]
==How can I get an account for OMP?==
If you would like an account to be created for you at MicrobialPhenotypes.org, simply send an email with the user name you want to use to {{Email}} and the OMP Staff will get you set up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join OMP?==
Yes, simply use the '''[[OMPwiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the '''Appearance''' tab, you may click the display ('''skin''') that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. Once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''Watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the [[Special:Preferences|my preferences link]] in the upper right hand corner of your browser. Under the '''watchlist''' tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''Contributions''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

Help:Preferences

2015-03-16T19:14:18Z

Saleksander: Created page with "Preferences Registered users can customize OMP by changing their preferences. ==User profile== You can edit your real name, and this section provides a lin..."

[[Category:Help|Preferences]]
Registered users can customize OMP by changing their preferences.
==User profile==
You can edit your real name, and this section provides a link to allow the user to change their password or email. Other email options, such as the choice to receive emails when specific changes are made to wiki pages
==Appearance==
You can customize the appearance of the wiki by choosing a different skin. Monobook is the default skin. If you know of a mediawiki skin that you would like us to make available, please contact us and we'll see what we can do.
This tab also allows for image size to be specified, as well as some advanced appearance options.
==Date and time==
Change your time zone and date formatting options.
==Editing==
Alter the default editing window size, how editing is initiated, preview options and external editor capabilities. Please note, not all of these options have been extensively tested in our wiki, so please let us know if you experience any difficulties when using these settings.
==Recent changes==
This tab changes the default number of days and edits shown in the [[Special:RecentChanges |Recent Changes]] section, as well as how the changes can be displayed. You can also opt to hide minor or patrolled edits.
==Watchlist==
Vary the number of days and the changes that are displayed in the [[Special:Watchlist |Watchlist]]. Also, you can choose to hide certain edits or automatically add pages you modify to your [[Special:Watchlist |Watchlist]].
==Search==
Define the number of hits displayed. Importantly, you can also change which namespaces are searched by default.
==Misc.==
Options involving diffs.

Help:User Pages

2015-03-16T18:52:16Z

Saleksander: Created page with "When you join OMPwiki, it automatically creates a series of pages for you that you can access at any time from the upper right corner of the wiki while you are logged in. ==U..."

When you join OMPwiki, it automatically creates a series of pages for you that you can access at any time from the upper right corner of the wiki while you are logged in.

==Username==
The first link, which should be your username, is to a blank page that you can customize however you want. Actually, any registered user can edit your user page, and you can edit theirs, since the user pages are just like other pages. But we view these pages as places that our users can use as their own personal home pages within the wiki.

==my talk==
This is a discussion page associated with your user page.

==my preferences==
The preference page is a series of tabs for various settings that control how the wiki behaves for you. Mostly self-explanatory; See [[Help:Preferences]] for more info.
==my watchlist==
Shows changes to pages on your watchlist. See [[Help:Watchlist]]
==my contributions==
Shows a list of all the pages you've ever edited in OMPWiki

==log out==
log out of OMPWiki.

OMPwiki:Membership

2015-03-16T18:48:54Z

Saleksander:

You do not have to be an OMPWiki member to view the content provided on this site. However, if you wish to edit or add content, you must first become a registered user. There are many things that only registered users can do:

* Edit the content of wiki pages, or create new pages
* [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create new user accounts]
* Create your own [[Help:User Pages|custom home page]]
* Customize the [[Help:Skins|appearance]] of OMPWiki using custom "skins"
* Send messages to other users
It would be nice to be more open, but wikis get spammed and vandalized. We also have [[Student accounts|student accounts]], which can do everything except create new users.

==Becoming a registered user==
Any [[Special:ListUsers|currently registered user]] may create an account for their friends and colleagues. See [[:Category:Users who can help you get an account|Users who are willing to help you get an account]] to find someone who can not only set up an account for you, but also show you how the wiki works. Or just send [mailto:d-siegele@tamu.edu Debby Siegele] an email to tell us who you are, and we'll set up an account for you. Be sure to send us your preferred login name.

==Create a registered user==
If you are already registered and logged in, you can [http://microbialphenotypes.org/wiki/index.php?title=Special:UserLogin&type=signup Create an account] for new users.

MediaWiki:Sidebar

2015-03-16T18:29:47Z

Saleksander:

* SEARCH

* navigation
** mainpage|mainpage-description
** Help:FAQ|FAQ
** recentchanges-url|recentchanges
** Page_Generator|Create new page
** randompage-url|randompage
** OMPwiki:Membership|Accounts
** Category:Help|help
* phenotypes (OMP)
** Category:OMP:0000000_!_microbial_phenotype|Browse OMP
** https://sourceforge.net/p/microphenotypes/code/HEAD/tree/releases/LATEST|Latest ontology versions
** http://sourceforge.net/p/microphenotypes/_list/tickets|Issue tracker
* evidence codes (ECO)
** Category:ECO:0000000_!_evidence|Browse ECO
** http://evidenceontology.org|evidenceontology.org
** http://bioportal.bioontology.org/ontologies/1012|BioPortal
** http://evidenceontology.googlecode.com/svn/trunk/|SVN
** http://code.google.com/p/evidenceontology/issues/list|Tracker
* TOOLBOX

PMID:12671177

2015-03-16T18:21:33Z

Saleksander: Table edited by Saleksander via TableEdit

{{RightTOC}}



{| id="C50575fb1b5b09" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Blanco, J , Blanco, M , Blanco, JE , Mora, A , González, EA , Bernárdez, MI , Alonso, MP , Coira, A , Rodriguez, A , Rey, J , Alonso, JM and Usera, MA ''' (2003) Verotoxin-producing Escherichia coli in Spain: prevalence, serotypes, and virulence genes of O157:H7 and non-O157 VTEC in ruminants, raw beef products, and humans. ''Exp. Biol. Med. (Maywood)'' '''228''':345-51
|-
!align=left |Abstract
||
In Spain, as in many other countries, verotoxin-producing Escherichia coli (VTEC) strains have been frequently isolated from cattle, sheep, and foods. VTEC strains have caused seven outbreaks in Spain (six caused by E. coli O157:H7 and one by E. coli O111:H- [nonmotile]) in recent years. An analysis of the serotypes indicated serological diversity. Among the strains isolated from humans, serotypes O26:H11, O111:H-, and O157:H7 were found to be more prevalent. The most frequently detected serotypes in cattle were O20:H19, O22:H8, O26:H11, O77:H41, O105:H18, O113:H21, O157:H7, O171:H2, and OUT (O untypeable):H19. Different VTEC serotypes (e.g., O5:H-, O6:H10, O91:H-, O117:H-, O128:H-, O128:H2, O146:H8, O146:H21, O156:H-, and OUT:H21) were found more frequently in sheep. These observations suggest a host serotype specificity for some VTEC. Numerous bovine and ovine VTEC serotypes detected in Spain were associated with human illnesses, confirming that ruminants are important reservoirs of pathogenic VTEC. VTEC can produce one or two toxins (VT1 and VT2) that cause human illnesses. These toxins are different proteins encoded by different genes. Another virulence factor expressed by VTEC is the protein intimin that is responsible for intimate attachment of VTEC and effacing lesions in the intestinal mucosa. This virulence factor is encoded by the chromosomal gene eae. The eae gene was found at a much less frequency in bovine (17%) and ovine (5%) than in human (45%) non-O157 VTEC strains. This may support the evidence that the eae gene contributes significantly to the virulence of human VTEC strains and that many animal non-O157 VTEC strains are less pathogenic to humans.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12671177 PubMed]

|-
!align=left |Keywords
||
Animals; Cattle; Disease Outbreaks; Escherichia coli/genetics; Escherichia coli/isolation & purification; Escherichia coli/metabolism; Escherichia coli/pathogenicity; Escherichia coli Infections/epidemiology; Escherichia coli Infections/microbiology; Foodborne Diseases/epidemiology; Foodborne Diseases/microbiology; Genes, Bacterial; Goats; Humans; Meat/microbiology; Prevalence; Sheep; Shiga Toxins/biosynthesis; Spain/epidemiology; Virulence/genetics

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3474.C50575fb1b5b09&page=3474&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==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="O50575fb1c4fc5" 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"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3474.O50575fb1c4fc5&page=3474&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table] || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

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

[[Category:Publication]]

Help talk:Accounts

2015-03-16T18:21:10Z

Saleksander: Blanked the page

Help talk:Accounts

2015-03-16T18:20:50Z

Saleksander: Created page with "test"

test

PMID:12671177

2015-03-16T18:20:07Z

Saleksander: Table edited by Saleksander via TableEdit

{{RightTOC}}



{| id="C50575fb1b5b09" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Blanco, J , Blanco, M , Blanco, JE , Mora, A , González, EA , Bernárdez, MI , Alonso, MP , Coira, A , Rodriguez, A , Rey, J , Alonso, JM and Usera, MA ''' (2003) Verotoxin-producing Escherichia coli in Spain: prevalence, serotypes, and virulence genes of O157:H7 and non-O157 VTEC in ruminants, raw beef products, and humans. ''Exp. Biol. Med. (Maywood)'' '''228''':345-51
|-
!align=left |Abstract
||
In Spain, as in many other countries, verotoxin-producing Escherichia coli (VTEC) strains have been frequently isolated from cattle, sheep, and foods. VTEC strains have caused seven outbreaks in Spain (six caused by E. coli O157:H7 and one by E. coli O111:H- [nonmotile]) in recent years. An analysis of the serotypes indicated serological diversity. Among the strains isolated from humans, serotypes O26:H11, O111:H-, and O157:H7 were found to be more prevalent. The most frequently detected serotypes in cattle were O20:H19, O22:H8, O26:H11, O77:H41, O105:H18, O113:H21, O157:H7, O171:H2, and OUT (O untypeable):H19. Different VTEC serotypes (e.g., O5:H-, O6:H10, O91:H-, O117:H-, O128:H-, O128:H2, O146:H8, O146:H21, O156:H-, and OUT:H21) were found more frequently in sheep. These observations suggest a host serotype specificity for some VTEC. Numerous bovine and ovine VTEC serotypes detected in Spain were associated with human illnesses, confirming that ruminants are important reservoirs of pathogenic VTEC. VTEC can produce one or two toxins (VT1 and VT2) that cause human illnesses. These toxins are different proteins encoded by different genes. Another virulence factor expressed by VTEC is the protein intimin that is responsible for intimate attachment of VTEC and effacing lesions in the intestinal mucosa. This virulence factor is encoded by the chromosomal gene eae. The eae gene was found at a much less frequency in bovine (17%) and ovine (5%) than in human (45%) non-O157 VTEC strains. This may support the evidence that the eae gene contributes significantly to the virulence of human VTEC strains and that many animal non-O157 VTEC strains are less pathogenic to humans.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12671177 PubMed]

|-
!align=left |Keywords
||
Animals; Cattle; Disease Outbreaks; Escherichia coli/genetics; Escherichia coli/isolation & purification; Escherichia coli/metabolism; Escherichia coli/pathogenicity; Escherichia coli Infections/epidemiology; Escherichia coli Infections/microbiology; Foodborne Diseases/epidemiology; Foodborne Diseases/microbiology; Genes, Bacterial; Goats; Humans; Meat/microbiology; Prevalence; Sheep; Shiga Toxins/biosynthesis; Spain/epidemiology; Virulence/genetics

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3474.C50575fb1b5b09&page=3474&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==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="O50575fb1c4fc5" 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
|-
|

|
*Taxon:
|
*Genotype of Reference Strain:
|
*Reference Condition:
|

|

|

|

|
test
|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.3474.O50575fb1c4fc5&page=3474&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table] || || || || || || || || ||
|}
<noinclude>

</noinclude>
</protect>

==Notes==

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

[[Category:Publication]]