SEEK ID: https://fairdomhub.org/studies/27
Experimentalists: Praveen Kumar Sappa
Created: 18th May 2010 at 15:45
Last updated: 22nd Nov 2011 at 20:12
I am PhD student at Prof.Uwe Voelker lab in Department of Functional Genomics. My area of research is microbial functional genomics in particular analysing the whole transcriptome(by microarray and other molecular biolology methods) of B.subtilis under various stress conditions.
I use QconCAT strategy for absolute quantification of carbon metabolic enzymes via MRM(multiple reaction monitoring) by LC-MS/MS.
I also perofrm experiments for understanding of dynamics of SigmaB network for modelling.
Modelling carbon core metabolism in Bacillus subtilis – Exploring the contribution of protein complexes in core carbon and nitrogen metabolism.
Bacillus subtilis is a prime model organism for systems biology approaches because it is one of the most advanced models for functional genomics. Furthermore, comprehensive information on cell and molecular biology, physiology and genetics is available and the European Bacillus community (BACELL) has a well-established reputation for applying
Bacillus subtilis was subjected to various stress conditions like high temperature(57°C), low temperature(16°C), high osmalarity(1.2M NaCl). The above mentioned stress conditions are again split into two different types as 'continuous stress condition' and 'sudden shock'. All the conditions were then done in biological triplicates.
Transcriptome for these samples was then analysed with Nimblegen Tiling array.
Snapshots: No snapshots
B. subtilis was grown in M9 media with glucose as carbon source and the samples were harvested during exponential phase (OD600nm- 0.4), early stationary phase(OD600nm- 1.3), late stationary phase(OD600nm- 1.0).
All the samples were analysed for transcriptome as biological triplicates.
Contributor: Praveen Kumar Sappa
Assay type: Transcriptomics
Technology type: Microarray
Snapshots: No snapshots
Investigation: Redefining the Complete Transcriptome of Bacill...
Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an
Contributor: Leif Steil
Investigations: Redefining the Complete Transcriptome of Bacill...
Isolation of total RNA from Bacillus Subtilis using phenol-chloroform extraction method by maintaining cryogenec conditions initailly to prevent RNA degradation. Quality of the obtained RNA is then tested with Agilent Bioanalyser before proceeding for gene expression analysis.
SOP for shake flask cultivation of B.Subtilis in Bacell-Sysmo
Authors: Ulrike Mäder, Colin Harwood, Rick Lewis, Ruben Mars, Priyanka Nannapaneni, Praveen Kumar Sappa, Leif Steil, Joerg Stuelke, Jan Maarten Van Dijl, Michael Hecker, Uwe Voelker, Nicolas Pierre,Dervyn Etienne,Rochat Tatiana,Leduc Aurélie,Pigeonneau Nathalie,Bidnenko Elena,Marchadier Elodie,Hoebeke Mark,Aymerich Stéphane,Becher Dörte,Bisicchia Paola,Botella Eric,Delumeau Olivier,Doherty Geoff,Denham Emma L,Fogg Mark J,Fromion Vincent,Goelzer Anne,Hansen Annette,Härtig Elisabeth,Homuth Georg,Jarmer Hanne,Jules Matthieu,Klipp Edda,Le Chat Ludovic,Lecointe François,Liebermeister Wolfram,March Anika,Noone David,Pohl Susanne,Rinn Bernd,Rügheimer Frank,Samson Franck,Schaffer Marc,Schwikowski Benno,Wiegert Thomas,Devine Kevin M,Wilkinson Anthony J,Bessières Philippe,Noirot Philippe
Date Published: 3rd Mar 2012
PubMed ID: 22383849