Difference between revisions of "Main Page"

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<big>'''Upcoming events:'''</big>  
 
<big>'''Upcoming events:'''</big>  
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* The BACELL meeting 2015, organized by [[Leendert Hamoen]] will take place from April 14 to 15 in Amsterdam, The Netherlands. [http://www.sysbio.se/Bacell2015/ Website], [mailto:L.W.Hamoen@uva.nl Contact]
 
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* The International Conference on Metabolic Engineering, organized by [[Ivan Mijakovic]] and [[Leendert Hamoen]] will take place from April 16 to 17 in Amsterdam, The Netherlands. [http://www.sysbio.se/MEB/ Website], [mailto:L.W.Hamoen@uva.nl Contact], [[Program]]
 
 
* The [http://www.grampositiveconference.org/  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. [http://www.grampositiveconference.org/registration.html Conference website]
 
* The [http://www.grampositiveconference.org/  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. [http://www.grampositiveconference.org/registration.html Conference website]
 
* [[Past conferences]]
 
* [[Past conferences]]
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<big>'''Paper of the month: March 2015'''</big>  
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<big>'''Paper of the month: April 2015'''</big>  
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* In ''Bacillus subtilis'', [[glutamate metabolism|nitrogen acquisition]] is controlled by [[SubtInteract|protein-protein interactions]]. Regulation is brought about by [[SubtInteract|interactions]] of the [[trigger enzyme|trigger enzymes]] [[GlnA|glutamine synthetase]] with the transcription factors [[TnrA]] and [[GlnR]] to inhibit or trigger their DNA-binding activity, respectively, and by the PII protein [[NrgB]] that also interacts with [[TnrA]]. Now, [http://www.ncbi.nlm.nih.gov/pubmed/25691471 Schumacher et al.] have solved the structures of several complexes involved in nitrogen sensing. The results unravel so far unprecendented mechanisms for metabolic reprogramming of the cell in response to nitrogen availability.
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* In a [http://www.ncbi.nlm.nih.gov/pubmed/15096624 groundbreaking study from 2004], several candidate [[riboswitch]]es have been discovered in ''Bacillus subtilis''. While the [[ydaO riboswitch]] has recently been discovered to be a target of the second messenger c-di-AMP, two new studies identify manganese ions as the ligand of the [[yybP-ykoY motif]] that controls the expression of the ''[[yybP]]'' and ''[[ykoY]]'' genes. Both genes are induced in the presence of Mn<sup>2+</sup>, due to the interaction of the ion with the [[riboswitch]]. This finding implies that [[YybP]] and [[YkoY]], which have not yet been functionally studied, are implicated in the control of manganese homeostasis.
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* '''Relevant ''Subti''Wiki pages:''' [[GlnA]], [[trigger enzymes]], [[TnrA]], [[GlnR]], [[NrgB]]
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* '''Relevant ''Subti''Wiki pages:''' [[yybP-ykoY motif]], [[riboswitch]], ''[[yybP]]'', ''[[ykoY]]'', [[John Helmann]]
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<pubmed>25691471</pubmed>
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<pubmed>25794618 25794619</pubmed>
 
* [[Previous papers of the month]]
 
* [[Previous papers of the month]]
  

Revision as of 15:18, 24 April 2015

Welcome to SubtiWiki! - Bacillus subtilis annotation the "wiki" way!

Start page small.png
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Contact: General Microbiology, University of Göttingen, send mail


Upcoming events:


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

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)



Paper of the month: April 2015

Ian R Price, Ahmed Gaballa, Fang Ding, John D Helmann, Ailong Ke
Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches.
Mol Cell: 2015, 57(6);1110-1123
[PubMed:25794619] [WorldCat.org] [DOI] (I p)

Michael Dambach, Melissa Sandoval, Taylor B Updegrove, Vivek Anantharaman, L Aravind, Lauren S Waters, Gisela Storz
The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element.
Mol Cell: 2015, 57(6);1099-1109
[PubMed:25794618] [WorldCat.org] [DOI] (I p)


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)







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