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.
SEEK ID: https://fairdomhub.org/studies/15
The transition from growing to non-growing Bacillus subtilis cells
Projects: BaCell-SysMO
Study position:
Experimentalists: Praveen Kumar Sappa
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Created: 16th Nov 2009 at 14:52
Last updated: 22nd Nov 2011 at 19:12
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Projects: BaCell-SysMO
Institutions: University of Rostock
Expertise: Mathematical modelling, Bacillus subtilis, Deterministic modelling of gene regulation networks, stress responses, Systems Biology, sensitivity analysis, Dynamics and Control of Biological Networks, Parameter estimation
Tools: Biochemistry, Computational and theoretical biology, ODE, Matlab, linux, Stochastic models, Deterministic models, Dynamic modelling
Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.
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 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
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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
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
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 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...
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: