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Ion and solute homeostasis in enteric bacteria: an integrated view generated from the interface of modelling and biological experimentation
Programme: SysMO
SEEK ID: https://fairdomhub.org/projects/4
Public web page: http://www.sysmo.net/index.php?index=56
Organisms: Escherichia coli
FAIRDOM PALs: Maria Rodriguez-Fernandez, Stefan Gayer
Project created: 15th Jan 2009
Related items
Projects: KOSMOBAC
Institutions: University of Aberdeen
Expertise: Mathematical modelling of biosystems and bioprocesses, Mathematical modelling
Tools: Deterministic models, including:- Dynamic modelling- Parameter estimation- Optimal experimental design- Dynamic optimization, Computational Systems Biology, Stochastic models, C programming, enzymatic analyses, data modeling, linux, ODE, Computational and theoretical biology
Expertise: Mathematical modelling of biosystems and bioprocesses, Statistically and biologically inspired optimization algorithms, dynamics and control of biological networks, parameter estimation, Mathematical modelling
Tools: including: - Dynamic modelling - Parameter estimation - Optimal experimental design - Dynamic optimization, Computational Systems Biology, Mathematica, Matlab, Partial differential equations, ODE, Computational and theoretical biology
We are very interested in applying a systems approach (i.e. model-based concepts and related computational tools) to problems from the biological domain. In particular, we are doing research in computational systems biology, targetting the following topics:
- Parameter estimation (inverse problems, model calibration) in biochemical pathways
- Optimal experimental design (optimal dynamic experiments) for Systems Biology
- Dynamic optimization (optimal control) of biosystems and bioprocesses
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Projects: KOSMOBAC
Institutions: University of Aberdeen
Projects: KOSMOBAC
Institutions: University of Aberdeen
My research interests are in the physiology of bacteria subjected to stress. The focus of my recent research has been the structure and function of regulated transport systems and ion channels involved in cellular homeostasis. These transporters and channels respond to specific signals by a change in activity that either corrects the imposed stress or protects the cell during exposure to the stress. Our systems biology interests are in the interplay of different enzymes systems and transporters
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Projects: KOSMOBAC
Institutions: Max-Planck-Institute of Biochemistry Martinsried
I am a PhD student working the group of Zoya Ignatova. Cellular and extracellular changes like crowding and osmotic stress conditions play a major role in protein aggregation. A change in the cytoplasmic composition is the result of an interplay between high osmotic pressures outside the cell volume and the cellular response to it in terms of uptake of K+ and secondary organic osmolytes. My research focuses on elucidating the role of natural osmolytes (known also as chemical chaperones or compatible
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Projects: KOSMOBAC
Institutions: Ludwig-Maximilians University of Munich
Expertise: Molecular Biology, Genetics, Biochemistry, Microbiology
Tools: reporter gene analyses, spectroscopy, site-directed and random mutagenesis, plasmon resonance spectroscopy, molecular biological techniques (RNA/DNA techniques), Membrane protein biochemistry, Chromatography, Fermentation, Biochemistry and protein analysis, Genetics
I am a PhD student of the microbiology department at the Ludwig-Maximilians Universität München. I work at the chair of Prof. Kirsten Jung. The topic of our workpackage deals with "K+ homeostasis in Escherichia coli". In special I'm working on the sensor kinase KdpD that controls together with the response regulator KdpE the expression of the high-affinity K+ uptake system KdpFABC. The yet not fully understood molecular mechanism of stimulus perception and signal transduction is of particular
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Projects: KOSMOBAC
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Projects: KOSMOBAC
Institutions: Max-Planck-Institute of Biochemistry Martinsried
Expertise: sequencing, Mathematical modelling, Bioinformatics, Molecular Biology, Biochemistry, Microbiology
Tools: Transcriptomics, qPCR, molecular biological techniques (RNA/DNA techniques, rtPCR, Fermentation, Matlab, Biochemistry and protein analysis, Bioinformatics, Molecular Biology, Microbiology
Professor in Jinan University, Guangzhou, China.
My research interest is in the modeling of translation. Connecting various processes in translation, we can investigate the impact of different factors on protein biosynthesis and biogenesis in genome-wide scale. This may reveal various general mechanisms on control level of gene expression and folding efficiency regulation in different growth conditions.
Projects: KOSMOBAC
Institutions: University of Aberdeen
Projects: KOSMOBAC
Institutions: University of Aberdeen
Expertise: Programming, Physics, Mathematical modelling
Tools: PDE, C programing, Stochastic models, linux, ODE, Computational and theoretical biology
A model to describe the effect of K+ uptake by KdpFABC on the two-component system KdpD/KdpE, which enables the identification of control principles of the Kdp system
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
A kinetic model that describess the activation of a dimeric efflux system that could bind either GSH or SLG
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
A model for translation elongation, which allows the prediction of how different conditions and parameters affect the rate and throughput of translation.
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
A model to describe aggregation of homomeric protein complexes in mechanosensitive channels in E.coli.
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Measurement of the transmembrane pH gradient and thus pHi, when the external pH is known.
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
A procedure to analyse the genomic interaction of E.coli RNA polymerase (RNAP) upon methylglyoxal (MG) stress, a toxic keto-aldehyde by-product of metabolism.
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
SOP used for detecting non influential parameters and interactions in non linear dynamical models. These parameters can be estabilished which allows the prioritization of parameters that can be subsequently estimated using robust global optimizations methods.
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The model describes the series of chemical reactions in MG detoxification pathway, allowing one to predict the flux of all compounds produced during detoxification.
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Mathematical model of pH buffering, which allows the prediction of how the buffering capacity depends on the cytoplasm's composition, for any number of buffers.
Creator: Lisbeth Lyngberg
Contributor: Lisbeth Lyngberg
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: Jacek Mika, Bert Poolman, Cirac Anna D,Moiset Gemma,Koçer Armagan,Salvador Pedro,Marrink Siewert J,Sengupta Durba
Date Published: 18th May 2011
Journal: Biophys. J.
PubMed ID: 21575576
Citation:
Abstract (Expand)
Authors: Jacek Mika, Bert Poolman, Moiset Gemma,Cirac Anna D,Feliu Lidia,Bardají Eduard,Planas Marta,Sengupta Durba,Marrink Siewert J
Date Published: 19th May 2011
Journal: Not specified
PubMed ID: 21586269
Citation:
Abstract (Expand)
Authors: Bert Poolman, Spitzer Jan
Date Published: 3rd Jun 2009
Journal: Microbiol. Mol. Biol. Rev.
PubMed ID: 19487732
Citation:
Abstract (Expand)
Authors: Bert Poolman, van den Bogaart Geert,Hermans Nicolaas,Krasnikov Victor
Date Published: 28th Apr 2007
Journal: Mol. Microbiol.
PubMed ID: 17462029
Citation:
Abstract (Expand)
Authors: None
Date Published: 16th Oct 2010
Journal: Curr. Opin. Biotechnol.
PubMed ID: 20952181
Citation:
Abstract (Expand)
Authors: Jacek Mika, Bert Poolman, Van Den Bogaart Geert,Veenhoff Liesbeth,Krasnikov Victor
Date Published: 1st Jul 2010
Journal: Not specified
DOI: 10.1111/j.1365-2958.2010.07201.x
Citation:
Abstract (Expand)
Authors: None
Date Published: 7th May 2010
Journal: Not specified
PubMed ID: 20444837
Citation: