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* The cells in a biofilm experience very different conditions: While the inner cells are well protected from any harm from the environment, they have on the other hand only poor access to nutrients. For the cells on the edge of the biofilm, it is just the other way round. Now, [http://www.ncbi.nlm.nih.gov/pubmed/26200335 Liu et al.] from the lab of [[Gürol M. Süel]] have discovered oscillation in the [[biofilm formation|growth of the biofilm]]. These oscillations serve to provide the inner cells with access to nutrients. These oscillations are caused by metabolic co-dependence between cells in the biofilm periphery and interior that is driven by [[glutamate metabolism|glutamate consumption and ammonium production]], respectively. | * The cells in a biofilm experience very different conditions: While the inner cells are well protected from any harm from the environment, they have on the other hand only poor access to nutrients. For the cells on the edge of the biofilm, it is just the other way round. Now, [http://www.ncbi.nlm.nih.gov/pubmed/26200335 Liu et al.] from the lab of [[Gürol M. Süel]] have discovered oscillation in the [[biofilm formation|growth of the biofilm]]. These oscillations serve to provide the inner cells with access to nutrients. These oscillations are caused by metabolic co-dependence between cells in the biofilm periphery and interior that is driven by [[glutamate metabolism|glutamate consumption and ammonium production]], respectively. | ||
* '''Relevant ''Subti''Wiki pages:''' [[Gürol M. Süel]], [[glutamate metabolism|glutamate consumption and ammonium production]], [[biofilm formation]] | * '''Relevant ''Subti''Wiki pages:''' [[Gürol M. Süel]], [[glutamate metabolism|glutamate consumption and ammonium production]], [[biofilm formation]] | ||
Revision as of 13:16, 10 August 2015
Welcome to SubtiWiki! - Bacillus subtilis annotation the "wiki" way!
Contact: General Microbiology, University of Göttingen, send mail
Upcoming events:
- The 8th International Conference on Gram-positive Microorganisms (18th International Conference on Bacilli) in Montecatini Terme, organized by Marta Perego will take place from June 21 to 25. Conference website
- The 7th European Spores Conference, organized by Simon Cutting and Imrich Barak, will take place from April 18 to 20, 2016, at Royal Holloway, University of London. Conference website
- Past conferences
New: Subtiwiki is now on Facebook - please give it a +1!
Now online: A new description of SubtiWiki and its acompanying modules in the 2014 Database issue of Nucleic Acids Research
Paper of the month: August 2015
- The cells in a biofilm experience very different conditions: While the inner cells are well protected from any harm from the environment, they have on the other hand only poor access to nutrients. For the cells on the edge of the biofilm, it is just the other way round. Now, Liu et al. from the lab of Gürol M. Süel have discovered oscillation in the growth of the biofilm. These oscillations serve to provide the inner cells with access to nutrients. These oscillations are caused by metabolic co-dependence between cells in the biofilm periphery and interior that is driven by glutamate consumption and ammonium production, respectively.
- Relevant SubtiWiki pages: Gürol M. Süel, glutamate consumption and ammonium production, biofilm formation
- see a blog presenting this paper
New procedure for account creation:
- Due to massive spam attacks, we had to change our policy for the creation of accounts. If you want to create an account, just send me a mail. We will create the account for you as quickly as possible, then you can change your password. This does not affect existing accounts, which remain active.
- Please remember that all members of the Bacillus community are invited to create accounts and to contribute to SubtiWiki!
News in SubtiWiki:
- August 2014: The first mobile application for SubtiWiki is now available for users of Android phones: Go for SubtiWiki in Google Play! IPhone users, please be patient! You will be served next! Click here to install!
- April 2013: SubtiWiki uses a new, faster Mediawiki platform! The times for page access are significantly reduced. Enjoy!
- March 2013: updated Excel files that map all genes to categories and regulons as well as the general updated identity mapping of all genes were uploaded.
- October 2012: the essential genes have been categorized
- September 2012: 300 mutant strains available at the BGSC were added to the corresponding gene pages
- August 2012: SubtiExpress, the new compagnon of SubtiWiki devoted to gene expression is online! Try it out!
- April 2012: Links for expression data under 104 different conditions (based on Nicolas et al., 2012) have been added to the expression section of the individual gene pages
- April 2011: SubtInteract, a presentation of protein-protein interactions in B. subtilis, is online!
- December 2010: SubtiCellPublisher allows the conversion of CellDesigner diagrams to navigatable presentations in the style of SubtiPathways
| Genes (examples) | Additional pages |
| spo0A | SubtiPathways |
| glnA | SubtInteract |
| rny | SubtiExpress |
| psdA | Regulons |
| pckA | methods |
| dnaA | metabolism |
| rnpA | categories |
| sigB | genome-wide analyses |
| ptkA | list of plasmids |
| mreC | labs working on Bacillus |
| ccpA | the people behind SubtiWiki |
| sr1 | template |
Publications describing SubtiWiki and SubtiPathways:
Raphael H Michna, Fabian M Commichau, Dominik Tödter, Christopher P Zschiedrich, Jörg Stülke
SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information.
Nucleic Acids Res: 2014, 42(Database issue);D692-8
[PubMed:24178028]
[WorldCat.org]
[DOI]
(I p)
Ulrike Mäder, Arne G Schmeisky, Lope A Flórez, Jörg Stülke
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis.
Nucleic Acids Res: 2012, 40(Database issue);D1278-87
[PubMed:22096228]
[WorldCat.org]
[DOI]
(I p)
Lope A Flórez, Sebastian F Roppel, Arne G Schmeisky, Christoph R Lammers, Jörg Stülke
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki.
Database (Oxford): 2009, 2009;bap012
[PubMed:20157485]
[WorldCat.org]
[DOI]
(I p)
Christoph R Lammers, Lope A Flórez, Arne G Schmeisky, Sebastian F Roppel, Ulrike Mäder, Leendert Hamoen, Jörg Stülke
Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis.
Microbiology (Reading): 2010, 156(Pt 3);849-859
[PubMed:19959575]
[WorldCat.org]
[DOI]
(I p)
