Batchfermentation exp-starv01_090204
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The main aim of this experiment is to actively grow B.subtilis in presense of glucose until high optical density in an aerobic fermentor and then, at a definite point of the growth, the glucose supply is shut down which leads to complete glucose exhaustion in the media. Simultaneusly samples for transcriptomics, intra and extracellular metabolomics, intra and extracellular proteomics are harvested through out the experiment.
SEEK ID: https://fairdomhub.org/studies/24
The transition from growing to non-growing Bacillus subtilis cells
Projects: BaCell-SysMO
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Created: 12th May 2010 at 14:30
Last updated: 22nd Nov 2011 at 19:12
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Projects: BaCell-SysMO
Institutions: University of Greifswald
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.
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
BaCell-SysMO 2 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 ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=53
The objective of this project is an integrated understanding the metabolic, proteomic and genetic network that controls the transition from growth to glucose starvation. This transition is a fundamental ecophysiological response that serves as a scientific model for environmental signal integration and is pivotal for industrial fermentations of Bacillus that occur predominantly under nutrient starvation.
Keywords: Glucose starvation, Transcriptomics, Proteomics, Metabolomics,Bacillus subtilis,
Submitter: Praveen kumar Sappa
Studies: B. subtilis Transcription Factor Competition, Batchfermentation exp-starv01_090204, Biphase Batch Fermentation(2009/02/04), Controlled sigmaB induction in shake flask, Transition to starvation in shake flask
Assays: 2D-gelbased analysis of intracellular proteins, Absolute quantification of proteins by the AQUA-technology, B. subtilis Transcription Factor Competition - theoretical interpretation, B. subtilis Transcription Factor Competition - theoretical interpretation, Fermentation-BM5_SysMo, Gene expression(Transcriptome), IPTG induction of sigmaB in BSA115, IPTG induction of sigmaB in BSA115, Relative quantification of proteins by metabolic labeling, Stressosome activation dynamics, metabolome-LCMS
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Custom Array
Investigation: The transition from growing to non-growing Baci...
Measurement of intra- and extra-cellular metabolome.
Submitter: Ulf Liebal
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: The transition from growing to non-growing Baci...
Submitter: Sandra Maass
Assay type: Proteomics
Technology type: 2D Gel Electrophoresis
Investigation: The transition from growing to non-growing Baci...
Submitter: Sandra Maass
Assay type: Protein Expression Profiling
Technology type: Mass Spectrometry
Investigation: The transition from growing to non-growing Baci...
Submitter: Sandra Maass
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: The transition from growing to non-growing Baci...
Submitter: Praveen kumar Sappa
Assay type: Glucose Pulse
Technology type: Technology Type
Investigation: The transition from growing to non-growing Baci...
batch fermatation - The transition from growing to non-growing Bacillus subtilis cells
Creator: Sandra Maass
Submitter: The JERM Harvester
batch fermatation - The transition from growing to non-growing Bacillus subtilis cells
Creator: Sandra Maass
Submitter: Sandra Maass
Creator: Praveen kumar Sappa
Submitter: The JERM Harvester
Array hybridisation was done at Roche Nimblegen Inc. It cannot be displayed over here.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
The reverse transcriptase synthesizes DNA, which complements the mRNA template (complementary DNA, cDNA). Cy3/Cy5-dCTP are incorporated into cDNA during Reverse transcription. The obtained Cy3/Cy5 cDNA are then competitively hybridised onto Agilent microarray slide and subsequently scanned.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Cells were harvested from culture keeping the cells cold to quench the physiological condition of RNA and the cells were mechanically disrupted. RNA was isolated from the cells by conventional acid-phenol method and the quality was checked by Agilent bioanalyser.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
