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,
SEEK ID: https://fairdomhub.org/investigations/2
Projects: BaCell-SysMO
Investigation position:
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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
Organisms: Bacillus subtilis
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.
Submitter: Praveen kumar Sappa
Investigation: The transition from growing to non-growing Baci...
Assays: No Assays
Snapshots: No snapshots
Experiments using shake flask cultures to measure dynamics associated with sigB response.
Submitter: Ulf Liebal
Investigation: The transition from growing to non-growing Baci...
Assays: No Assays
Snapshots: No snapshots
In this kind of studies sigmaB stress response is induced by the addition of artificial inducers of sigmaB. For example simgaB is downstream of a Pspac promoter and induced by the addition of IPTG. A ctc::lacZ reporter gene is used to monitor sigmaB activity.
Submitter: Ulf Liebal
Investigation: The transition from growing to non-growing Baci...
Assays: IPTG induction of sigmaB in BSA115, IPTG induction of sigmaB in BSA115, Stressosome activation dynamics
Snapshots: No snapshots
The aim of the study is to test the interplay of the effects of different transcriptional regulators on gene expression during different environmental responses in B. subtilis. For a selected set of transcriptional regulators native proteins are fusion-labelled. The intensity of expression of each reporter protein is measured in the absence of several transcriptional regulators that compete for the RNA polymerase.
Submitter: Ulf Liebal
Investigation: The transition from growing to non-growing Baci...
Assays: B. subtilis Transcription Factor Competition - theoretical interpretation, B. subtilis Transcription Factor Competition - theoretical interpretation
Snapshots: No snapshots
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.
Submitter: Praveen kumar Sappa
Investigation: The transition from growing to non-growing Baci...
Assays: 2D-gelbased analysis of intracellular proteins, Absolute quantification of proteins by the AQUA-technology, Fermentation-BM5_SysMo, Gene expression(Transcriptome), Relative quantification of proteins by metabolic labeling, metabolome-LCMS
Snapshots: No snapshots
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Custom Array
Investigation: The transition from growing to non-growing Baci...
Organisms: Bacillus subtilis
SOPs: RNA isolation and quality check by Agilent bioa..., SOP for cDNA labelling and Microarray hybridizaton
Data files: batchfermentation exp-starv01 transcriptome_Mic..., batchfermentation exp-starv01 transcriptome_Mic...
Snapshots: No snapshots
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...
Organisms: Bacillus subtilis, Bacillus subtilis
SOPs: 1 hidden item
Data files: Batchfermentation_exp-starv01_2D-proteomics
Snapshots: No snapshots
Submitter: Sandra Maass
Assay type: Protein Expression Profiling
Technology type: Mass Spectrometry
Investigation: The transition from growing to non-growing Baci...
Organisms: Bacillus subtilis, Bacillus subtilis
SOPs: 1 hidden item
Data files: batchfermentation exp-starv01 quant-proteomics
Snapshots: No snapshots
Submitter: Sandra Maass
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: The transition from growing to non-growing Baci...
We use BSA115 strain which lacks RsbU and RsbW proteins. Therefore, there is limited post-transcriptional regulation of sigmaB activity. SigmaB itself is placed downstream of Pspac, inducible by IPTG. The lacZ reporter gene is downstream of Pctc promoter. IPTG concentrations of 0.1, 0.2 and 1 mM are added in mid-exponential phase at an OD of appr. 0.3. The whole experiment runs for about eight hours.
Submitter: Ulf Liebal
Assay type: Proteomics
Technology type: Technology Type
Investigation: The transition from growing to non-growing Baci...
Organisms: Bacillus subtilis
SOPs: SOP for cultivation of B.Subtilis, ß-Galactosidase assay
Data files: 20090915_BSA115-IPTG-assay
Snapshots: No snapshots
Theoretical analysis of hypothetical sigma factor competition. Based on the model 'transcription factor competition' possible dynamics of sigma factor competition are simulated and analysed using Lineweaver-Burk representations.
Submitter: Ulf Liebal
Assay type: Experimental Assay Type
Technology type: Technology Type
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...
Organisms: Bacillus subtilis
SOPs: 1 hidden item
Data files: Batchfermentation_Exp-Starv01_Fermentationdetai..., batchfermentation exp-starv01 transcriptome_Mic..., batchfermentation exp-starv01 transcriptome_Mic...
Snapshots: No snapshots
Theoretical analysis of hypothetical sigma factor competition. Based on the model 'transcription factor competition' possible dynamics of sigma factor competition are simulated and analysed using Lineweaver-Burk representations.
Submitter: Ulf Liebal
Biological problem addressed: Gene Expression
Investigation: The transition from growing to non-growing Baci...
Organisms: Bacillus subtilis : 168 (wild-type / wild-type)
Models: No Models
SOPs: No SOPs
Data files: B. subtilis Transcription Factor Competition - ...
Snapshots: No snapshots
We use BSA115 strain which lacks RsbU and RsbW proteins. Therefore, there is limited post-transcriptional regulation of sigmaB activity.
There occurs an unexpected drop in the beta-Gal activity after sigB induction. This modelling effort aims to clarify the reasons.
Submitter: Ulf Liebal
Biological problem addressed: Gene Expression
Investigation: The transition from growing to non-growing Baci...
Organisms: Bacillus subtilis : 168 (wild-type / wild-type)
Models: BSA115 Post-transcriptional instability, BSA115-lacz-synth, BSA115-sigB-adaptation, BSA115-transcription inhibition model
SOPs: No SOPs
Data files: 20090915_BSA115-IPTG-assay, Model-representations-BSA115-Experiments and 1 hidden item
Snapshots: No snapshots
The stressosome is an important sensor of environmental stresses in B. subtilis. It is formed by three protein types that form an icosahedral geometric protein complex. There are uncertanties how protein interactions take place, what the effects on the response behaviour of activation and inhibition of phosphorylation among proteins is, and what kind of proximal signal activates the stressosome in the first place. To answer these questions a computational modelling approach was developed. This ...
Submitter: Ulf Liebal
Biological problem addressed: Signal Induction
Investigation: The transition from growing to non-growing Baci...
Organisms: Bacillus subtilis
Models: Monomer Stressosome Model, Stressosome-dynamics
SOPs: No SOPs
Data files: Stressosome activation and structural represent...
Snapshots: No snapshots
batch fermatation - The transition from growing to non-growing Bacillus subtilis cells
Creator: Sandra Maass
Submitter: The JERM Harvester
Investigations: The transition from growing to non-growing Baci...
Studies: Batchfermentation exp-starv01_090204
batch fermatation - The transition from growing to non-growing Bacillus subtilis cells
Creator: Sandra Maass
Submitter: Sandra Maass
Investigations: The transition from growing to non-growing Baci...
Studies: Batchfermentation exp-starv01_090204
Creator: Praveen kumar Sappa
Submitter: The JERM Harvester
Investigations: The transition from growing to non-growing Baci...
Studies: Batchfermentation exp-starv01_090204
Assays: Fermentation-BM5_SysMo, Gene expression(Transcriptome)
Array hybridisation was done at Roche Nimblegen Inc. It cannot be displayed over here.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Investigations: The transition from growing to non-growing Baci...
Studies: Batchfermentation exp-starv01_090204
Assays: Fermentation-BM5_SysMo, Gene expression(Transcriptome)
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Investigations: The transition from growing to non-growing Baci...
Studies: Batchfermentation exp-starv01_090204
Assays: Fermentation-BM5_SysMo
Data sheet generated in Greifswald to measure the response of sigB activity in response to different media composition.
Creator: Ulf Liebal
Submitter: Ulf Liebal
Investigations: The transition from growing to non-growing Baci..., Using SEEK and I-S-A structure to integrate ex...
Studies: Experimental study for hands on session, Transition to starvation in shake flask
Assays: How to use templates to structure experimental ... and 1 hidden item
Strain BSA115 is grown until appr. OD 0.25 then expression of sigB is induced by the addition of IPTG. The extend of stress response is measured by the expression of lacZ via beta-Gal assay. The experiment lasts for appr. 400 min.
Creator: Ulf Liebal
Submitter: Ulf Liebal
The stressosome is composed of three proteins that assemble in the form of an icosahedron. Icosahedra can be modelled in different ways with different abstraction levels regarding the original stressosome structure. The pdf-figure introduces geometric modelling of the stressosome using origami and particle dynamics simulations.
Creator: Ulf Liebal
Submitter: Ulf Liebal
Investigations: The transition from growing to non-growing Baci...
Studies: Controlled sigmaB induction in shake flask
Assays: Stressosome activation dynamics
The pdf-file shows simulations of a hypothetical model of sigma factor competition. It simulates the dynamics that we can expect from the experiments and prepares for the analysis of the experimental data. Analysis of sigma factor competition is based on a Lineweaver-Burk representation of RNApolymerase and competing sigma factors.
Creator: Ulf Liebal
Submitter: Ulf Liebal
The figure contains information necessary to understand the mathematical model of experiments in BSA115. In these experiments sigB response is artificially initiated by the addition of IPTG while sigB is downstream of a Pspac promoter. The figure shows a flow-chart diagram that combines three hypotheses to explain experiments. It contains the ODEs and the fit of the respective models to the data.
Creator: Ulf Liebal
Submitter: Ulf Liebal
Investigations: The transition from growing to non-growing Baci...
only lacZ synthesis reduced by inhibitor in BSA115
Creator: Ulf Liebal
Submitter: Ulf Liebal
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Bacillus subtilis
Investigations: The transition from growing to non-growing Baci...
This is a JWS model of the successful model for data representation. It realises regulation by a hypothetical sigB dependent protein that degrades beta-Gal.
Creator: Ulf Liebal
Submitter: Ulf Liebal
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Bacillus subtilis
Investigations: The transition from growing to non-growing Baci...
The model represents a hypothetical situation in which an anti-sigmafactor reduces sigB efficacy.
Creator: Ulf Liebal
Submitter: Ulf Liebal
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Bacillus subtilis
Investigations: The transition from growing to non-growing Baci...
The zip folder contains files that allow simulation of stressosome dynamics. The models are based on a cellular automaton approach. Each protein of RsbR and RsbS is located in the crystal structure of the stressosome. The proteins can be phosphorylated or not and these states determine the future of neighbouring proteins. To simulate the model open the file 'liebal_stressosome-model_12_workflow-matlab.m' in Matlab. It is written in the cell-model, put the cursor into a cell that you wish to ...
Creator: Ulf Liebal
Submitter: Ulf Liebal
Model type: Agent based modelling
Model format: Matlab package
Environment: Matlab
Organism: Bacillus subtilis
Investigations: The transition from growing to non-growing Baci...
Studies: Controlled sigmaB induction in shake flask
Assays: Stressosome activation dynamics
The zip file contains model files and an experiment file. Unpack it in a directory and navigate with matlab to there. Use the 'matlab_execution_guide.m' for simulation and visualisation of the model. This file is written in matlab cell mode, so it is not a stand alone function.
Three models have been developed to test their capacity to reproduce the experimental data from Study: 'Controlled sigmaB induction in shake flask' with Assay: 'IPTG induction of sigmaB in BSA115'. One model assumes a ...
Creator: Ulf Liebal
Submitter: Ulf Liebal
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Matlab
Organism: Bacillus subtilis
Investigations: The transition from growing to non-growing Baci...
The zip-folder contains files for execution in matlab that allow for the simulation of stressosome dynamics and reproduction of published data on the stressosome. The important file for execution is 'liebal_stressosome-model_12_workflow-matlab.m'.
Creator: Ulf Liebal
Submitter: Ulf Liebal
Model type: Agent based modelling
Model format: Matlab package
Environment: Matlab
Organism: Bacillus subtilis
Investigations: The transition from growing to non-growing Baci...
Studies: Controlled sigmaB induction in shake flask
Assays: Stressosome activation dynamics
SOP for ß-Galactosidase assay.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Investigations: The transition from growing to non-growing Baci...
SOP for shake flask cultivation of B.Subtilis in Bacell-Sysmo
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Investigations: Redefining the Complete Transcriptome of Bacill..., The transition from growing to non-growing Baci...
Studies: Controlled sigmaB induction in shake flask, Transcriptome analysis of glucose starvation in...
Assays: IPTG induction of sigmaB in BSA115, Tiling Array analysis of glucose strarved B. su...
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
Investigations: Identification of targets of the essential RNas..., Multiomics study of Bacillus subtilis under osm..., The transition from growing to non-growing Baci...
Studies: B. subtilis_SysMo2_Chemostat_growthrate-salt, Batchfermentation exp-starv01_090204, Identification of targets of the essential RNas...
Assays: Gene expression(Transcriptome), Transcriptome data for chemostat cultivated sam..., Transcritome data_Identification of targets of ...
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
Investigations: Identification of targets of the essential RNas..., Multiomics study of Bacillus subtilis under osm..., The transition from growing to non-growing Baci...
Studies: B. subtilis_SysMo2_Chemostat_growthrate-salt, Batchfermentation exp-starv01_090204, Identification of targets of the essential RNas...
Assays: Gene expression(Transcriptome), Transcriptome data for chemostat cultivated sam..., Transcritome data_Identification of targets of ...
Abstract (Expand)
Authors: , , Jon Marles-Wright, ,
Date Published: 2013
Publication Type: Not specified
Citation:
Abstract (Expand)
Authors: , , , , Georg Homuth, ,
Date Published: 2012
Publication Type: Not specified
DOI: 10.1039/C2MB25031D
Citation: