Peter Ruoff

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About Peter Ruoff:

Physical chemist with expertise in experimental kinetics, molecular biology, and mathematical modeling.

SEEK ID: https://fairdomhub.org/people/90

Location: Norway

ORCID: Not specified

Joined: 28th Sep 2009

Expertise: biophysical chemistry, Kinetics

Tools: Perl, Matlab, quantitative western blot analyses, enzyme kinetics, madonna, fortran

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SysMO

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/

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SulfoSys

Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Programme: SysMO

Public web page: http://sulfosys.com/

Organisms: Sulfolobus solfataricus

MOSES

MOSES (Micro Organism Systems biology: Energy and Saccharomyces cerevisiae) develops a new Systems Biology approach, which is called 'domino systems biology'. It uses this to unravel the role of cellular free energy ('ATP') in the control and regulation of cell function. MOSES operates though continuous iterations between partner groups through a new systems-biology driven data-management workflow. MOSES also tries to serve as a substrate for three or more other SYSMO programs.

Programme: SysMO

Public web page: http://www.moses.sys-bio.net/

Organisms: Saccharomyces cerevisiae

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University of Stavanger

Country: Norway

City: http://www.ux.uis.no/~ruoff

Web page: Not specified

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Model for ED pathway in Sulfolobus solfataricus

SulfoSys

The model describes the Entner-Doudoroff pathway in Sulfolobus solfataricus under temperature variation. The package contains source code written in FORTRAN as well as binaries for Mac OSX, Linux, and Windows. If compiling from source code, a FORTRAN compiler is required. On-line versions of the model are also available at: http://bioinfo.ux.uis.no/sulfosys http://jjj.biochem.sun.ac.za/sysmo/projects/Sulfo-Sys/index.html

Creator: Peter Ruoff

Submitter: Peter Ruoff

Model type: Ordinary differential equations (ODE)

Model format: Not specified

Environment: Not specified

Organism: Sulfolobus solfataricus

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 26th Oct 2009 at 14:48

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Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus.

SulfoSys, SulfoSys - Biotec

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Abstract (Expand)

Sulfolobus solfataricus is a thermoacidophilic Archaeon that thrives in terrestrial hot springs (solfatares) with optimal growth at 80 degrees C and pH 2-4. It catabolizes specific carbon sources, such …

Authors: A. S. Figueiredo, T. Kouril, D. Esser, P. Haferkamp, P. Wieloch, D. Schomburg, P. Ruoff, B. Siebers, J. Schaber

Date Published: 12th Jul 2017

Publication Type: Not specified

PubMed ID: 28692669

Citation: PLoS One. 2017 Jul 10;12(7):e0180331. doi: 10.1371/journal.pone.0180331. eCollection 2017.

Created: 15th Aug 2017 at 10:17, Last updated: 8th Dec 2022 at 17:26

Computer controlled automated assay for comprehensive studies of enzyme kinetic parameters

MOSES

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Abstract (Expand)

Stability and biological activity of proteins is highly dependent on their physicochemical environment. The development of realistic models of biological systems necessitates quantitative information … on the response to changes of external conditions like pH, salinity and concentrations of substrates and allosteric modulators. Changes in just a few variable parameters rapidly lead to large numbers of experimental conditions, which go beyond the experimental capacity of most research groups. We implemented a computer-aided experimenting framework ("robot lab assistant") that allows us to parameterize abstract, human-readable descriptions of micro-plate based experiments with variable parameters and execute them on a conventional 8 channel liquid handling robot fitted with a sensitive plate reader. A set of newly developed R-packages translates the instructions into machine commands, executes them, collects the data and processes it without user-interaction. By combining script-driven experimental planning, execution and data-analysis, our system can react to experimental outcomes autonomously, allowing outcome-based iterative experimental strategies. The framework was applied in a response-surface model based iterative optimization of buffer conditions and investigation of substrate, allosteric effector, pH and salt dependent activity profiles of pyruvate kinase (PYK). A diprotic model of enzyme kinetics was used to model the combined effects of changing pH and substrate concentrations. The 8 parameters of the model could be estimated from a single two-hour experiment using nonlinear least-squares regression. The model with the estimated parameters successfully predicted pH and PEP dependence of initial reaction rates, while the PEP concentration dependent shift of optimal pH could only be reproduced with a set of manually tweaked parameters. Differences between model-predictions and experimental observations at low pH suggest additional protonation-sites at the enzyme or substrates critical for enzymatic activity. The developed framework is a powerful tool to investigate enzyme reaction specifics and explore biological system behaviour in a wide range of experimental conditions.

Authors: Felix Bonowski, , , Jinda Holzwarth, Igor Kitanovic, Van Ngoc Bui, Elke Lederer,

Date Published: 23rd Dec 2009

Publication Type: Not specified

PubMed ID: 20502716

Citation:

Created: 6th Jun 2010 at 15:48, Last updated: 8th Dec 2022 at 17:25

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