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- Ulf Liebal

**About Ulf Liebal:**

Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.

**SEEK ID:** https://fairdomhub.org/people/280

**Location:**
Germany

**Expertise:**
sensitivity analysis, Systems Biology, stress responses, Deterministic modelling of gene regulation networks, dynamics and control of biological networks, parameter estimation, Bacillus subtilis, Mathematical modelling

**Tools:**
Dynamic modelling, Deterministic models, Stochastic models, linux, Matlab, ODE, Computational and theoretical biology, Biochemistry

**ORCID:**
Not specified

## Related items

- Projects (1)
- Institutions (1)
- Studies (3)
- Assays (6+1)
- Data files (5+1)
- Models (10)
- Publications (6)
- Presentations (8+1)
- Events (2)

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

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**Programme**: SysMO

**Public web page**: http://www.sysmo.net/index.php?index=53

**Organisms:** Bacillus subtilis

Experiments using shake flask cultures to measure dynamics associated with sigB response.

**Person responsible**: Ulf Liebal

**Snapshots: **No snapshots

**Investigation:** The transition from growing to non-growing Baci...

**Assays:** No Assays

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.

**Person responsible**: Ulf Liebal

**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.

**Person responsible**: Ulf Liebal

**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.

**Contributor**: Ulf Liebal

**Assay type**: Experimental Assay Type

**Technology type**: Technology Type

**Snapshots: **No snapshots

**Investigation:** The transition from growing to non-growing Baci...

**Study:** B. subtilis Transcription Factor Competition

**Organisms**: Bacillus subtilis

**SOPs:** No SOPs

**Data files:** No Data files

Measurement of intra- and extra-cellular metabolome.

**Contributor**: Ulf Liebal

**Assay type**: Metabolite Profiling

**Technology type**: Liquid Chromatography-tandom Mass Spectrometry

**Snapshots: **No snapshots

**Investigation:** The transition from growing to non-growing Baci...

**Study:** Batchfermentation exp-starv01_090204

**Organisms**: Bacillus subtilis

**SOPs:** No SOPs

**Data files:** No Data files

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.

**Contributor**: Ulf Liebal

**Assay type**: Proteomics

**Technology type**: Technology Type

**Snapshots: **No snapshots

**Investigation:** The transition from growing to non-growing Baci...

**Study:** Controlled sigmaB induction in shake flask

**Organisms**: Bacillus subtilis (batch)

**SOPs:** SOP for cultivation of B.Subtilis, ß-Galactosidase assay

**Data files:** 20090915_BSA115-IPTG-assay

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

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**Investigation:** The transition from growing to non-growing Baci...

**Study:** Controlled sigmaB induction in shake flask

**Organisms**: Bacillus subtilis

**Models:** Monomer Stressosome Model, Stressosome-dynamics

**SOPs:** No SOPs

**Data files:** Stressosome activation and structural represent...

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.

**Investigation:** The transition from growing to non-growing Baci...

**Study:** B. subtilis Transcription Factor Competition

**Organisms**: Bacillus subtilis : 168 (wild-type / wild-type)

**Models:** No Models

**SOPs:** No SOPs

**Data files:** B. subtilis Transcription Factor Competition - ...

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.

**Investigation:** The transition from growing to non-growing Baci...

**Study:** Controlled sigmaB induction in shake flask

**Organisms**: Bacillus subtilis : 168 (wild-type / wild-type) (batch)

**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

Data sheet generated in Greifswald to measure the response of sigB activity in response to different media composition.

**Creator: **Ulf Liebal

**Contributor**: Ulf Liebal

**Investigations:** The transition from growing to non-growing Baci... and 1 hidden item

**Studies:** Transition to starvation in shake flask and 1 hidden item

**Assays:** 2 hidden items

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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: Ulf Liebal

**Investigations:** The transition from growing to non-growing Baci...

The zip file contains two executable Matlab functions.

File named 'fnct_gen_tfcompmod.m' generates a Simbiology model based on the following interactions:

R + X RX -> R + X + Px

R + Y RY -> R + Y + Py

R + Z RZ -> R + Z + Pz

Y + Pz -> Pz

Px ->

Py ->

Pz ->

We assume much higher reaction speeds of sigma factor RNApol binding/unbinding compared to protein expression. Protein expression can therefore be represented by Michaelis-Menten like kinetic laws with three competing inhibitors

...

**Creator: **Ulf Liebal

**Contributor**: Ulf Liebal

**Model type**: Ordinary differential equations (ODE)

**Model format**: Matlab package

**Environment**: Matlab

**Organism**: Bacillus subtilis

**Investigations:** No Investigations

**Studies:** No Studies

**Modelling analyses:** No Modelling analyses

only lacZ synthesis reduced by inhibitor in BSA115

**Creator: **Ulf Liebal

**Contributor**: 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...

**Studies:** Controlled sigmaB induction in shake flask

**Modelling analyses:** IPTG induction of sigmaB in BSA115

The model file represents the expression of beta-gal from a sigB dependent promoter after sigb production was stimulated by IPTG. The model is based on an assumption that a hypothetical protein degrates the sigb factor.

**Creator: **Ulf Liebal

**Contributor**: Ulf Liebal

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

**Organism**: Bacillus subtilis

**Investigations:** No Investigations

**Studies:** No Studies

**Modelling analyses:** No Modelling analyses

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

**Contributor**: 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...

**Studies:** Controlled sigmaB induction in shake flask

**Modelling analyses:** IPTG induction of sigmaB in BSA115

The model represents a hypothetical situation in which an anti-sigmafactor reduces sigB efficacy.

**Creator: **Ulf Liebal

**Contributor**: 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...

**Studies:** Controlled sigmaB induction in shake flask

**Modelling analyses:** IPTG induction of sigmaB in BSA115

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

**Contributor**: 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

**Modelling analyses:** 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

**Contributor**: 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...

**Studies:** Controlled sigmaB induction in shake flask

**Modelling analyses:** IPTG induction of sigmaB in BSA115

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

**Contributor**: 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

**Modelling analyses:** Stressosome activation dynamics

A model of E. coli central carbon core metabolism, used as starting point for B. subtilis modelling. It is developed by Chassagnole et al. doi:10.1002/bit.10288.

**Creators: **Ulf Liebal, Fei He

**Contributor**: Ulf Liebal

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: Not specified

**Organism**: Escherichia coli

**Investigations:** No Investigations

**Studies:** No Studies

**Modelling analyses:** No Modelling analyses

The model can simulate the the dynamics of sigB dependent transcription at the transition to starvation. It is was developed along the comic in 'sigB-activation-comic_vol1'. Parameters were partly taken from Delumeau et al., 2002, J. Bact. and Igoshin et al., 2007, JMB. Parameter estimation was performed using experimental data from '0804_shake-flask'.

Use the .m-file with matlab as:

% reading initial conditions from the file:

inic = sigb_model_liebal;

% performing the simulation:

[t,y] =

...

**Creator: **Ulf Liebal

**Contributor**: Ulf Liebal

**Model type**: Ordinary differential equations (ODE)

**Model format**: Matlab package

**Environment**: Matlab

**Organism**: Bacillus subtilis

**Investigations:** No Investigations

**Studies:** No Studies

**Modelling analyses:** No Modelling analyses

**Abstract** (Expand)

**Authors: **Ulf Liebal, Thomas Millat, Jon Marles-Wright, Rick Lewis, Olaf Wolkenhauer

**Date Published**: 2013

**Journal**: BMC Syst Biol

**Citation**:

**Abstract** (Expand)

**Authors: **Ulf Liebal, Praveen Kumar Sappa, Thomas Millat, Leif Steil, Georg Homuth, Uwe Voelker, Olaf Wolkenhauer

**Date Published**: 2012

**Journal**: Mol. BioSyst.

**DOI: **10.1039/C2MB25031D

**Citation**:

**Abstract** (Expand)

**Authors: **Olaf Wolkenhauer, Jan-Hendrik S. Hofmeyr

**Date Published**: 1st May 2008

**Journal**: at - Automatisierungstechnik

**Citation**:

**Abstract** (Expand)

**Authors: **Julio Vera, Thomas Millat, Walter Kolch, Olaf Wolkenhauer

**Date Published**: 2008

**Journal**: BMC Syst Biol

**Citation**:

**Abstract** (Expand)

**Authors: **S. Nikolov, X. Lai, Ulf Liebal, Olaf Wolkenhauer, J. Vera

**Date Published**: 2010

**Journal**: Int. J. of Systems Sc.

**DOI: **10.1080/00207720903147746

**Citation**:

**Abstract** (Expand)

**Authors: **None

**Date Published**: 1st Jul 2010

**Journal**: Not specified

**DOI: **10.1111/j.1365-2958.2010.07283.x

**Citation**:

In the talk I show that an increase in the concentration of one of two channelling enzyme has no effect on the flux. In contrast a decrease in the concentration of one of two channelling enzymes has the same effect like a concentration decrease of both enzymes.

**Creator: **Ulf Liebal

**Contributor**: Ulf Liebal

Presentation given by Colin Harwood presenting results about ITC experiments to confirm interactions. Preliminary crystallisation experiments commenced on suitable candidates.

**Creator: **Colin Harwood

**Contributor**: Ulf Liebal

The talk shows that proline biosynthesis and accumulation is connected to glycine betaine availability. Glycine betaine complements proline function.

**Creator: **Tamara Hoffmann

**Contributor**: Ulf Liebal

The talk shows that position 153 in various glutamate-kinases regulates proline feed-back regulation. This difference is shown for ProB being proline sensitivie and ProJ being proline independent.

**Creator: **Adrienne Zaprasis

**Contributor**: Ulf Liebal

Michael Kohlstedt presented flux data as integrated output of cellular components. Moreover, proteomics and metabolomics data reveal significant changes in intracellular protein and metabolite level and osmoprotection (supplementing glycine betaine) creates a novel metabolic state.

**Creator: **Michael Kohlstedt

**Contributor**: Ulf Liebal

Presentation by Thomas Millat of a tool for automatized analysis of flow cytometry data. It allows characterisation of different growth modalities, statistical measures of mean and variance and estimation of population overlap all along with appropriate visualization.

**Creator: **Thomas Millat

**Contributor**: Ulf Liebal

The image file represents the activation of sigB in response to glucose starvation. It was drawn alongside the model 'sigb-response_starvation_shakeflask'.

Biomass catalyses the conversion of glucose to biomass, while a low glucose concentration will negatively affect cell viability (inverted shown in the figure, where Glc inhibits cell death).

W (RsbW) can form dimers with sigB (B) and dimers and trimers with V (RsbV)(WV, WV2) and is able to phosphorylate V to VP. A high glucose concentration

...

**Creator: **Ulf Liebal

**Contributor**: Ulf Liebal

Annual Conference of Bacillus subtilis community.

**Start Date**: 24th Apr 2012

**End Date**: 25th Apr 2012

**Event Website**: Not specified

**Country**: Ireland

**City**: Dublin

BaCell consotium in Groningen.

**Start Date**: 27th Sep 2011

**End Date**: 29th Sep 2011

**Event Website**: Not specified

**Country**: Netherlands

**City**: Groningen