Experimental Biogas Research
We run lab-scale biogas reactors to study selected aspects of biogas production. Besides standard process analytics, we assess microbial community dynamics via metagenomics, metatrancriptomics, metaproteomics, flowcytometry, and microcalorimetry.
Contact:Fabian Bonk, Daniela Taraba, Denny Popp, Florian Centler
Partner:Sabine Kleinsteuber, Heike Sträuber, Thomas Maskow, Martin von Bergen, Nico Jehmlich, Susann Müller
Modeling Microbial CommunitiesWe develop mathematical models describing the dynamics of microbial communities, focussing on metabolic transformation processes. Both ordinary-differentail-equation-based and Flux-Balance-Analysis approaches, and combinations of both, are used.
Contact:Florian Centler, Denny Popp, Fabian Bonk
Partner:Steffen Klamt (MPI Magdeburg), Sabine Koch (MPI Magdeburg), Dirk Benndorf (Uni Magdeburg), Sören Weinrich (DBFZ)
Spatio-temporal ModelingSpace plays an essential role for natural microbial systems. Within the TWIN-Project, we develop experimental systems and spatio-temporal models for studying functional stability and resilience. Individual-based modeling approaches are used for analyzing bacteria-bacteria and bacteria-fungi interactions.
Kooperationspartner:Lukas Wick, Martin Thullner, Karin Frank, Thomas Banitz, Sara König, Tom Berthold, Matthias Kästner, Anja Miltner, Anja Worrich
Network analysis of microbial communitiesSpatial and temporal data on microbial community composition can provide evidence for principles of the organization of microbial life. The complex interplay at work can be visualized by co-occurrence analysis-derived networks, which can be explored by methods from network analysis and data-mining.
Kooperationspartner:Annelie Wendeberg, Annelie Steinbach, Torsten Jeske, Lukas Wick, Michael Schloter (Helmholtz-Zentrum München)
In Silico Metabolic EngineeringDetails under "M.Sc. topics" below.
Within the HIGRADE PhD program, we offer a one-day introductory Systems Biology course in cooperation with the Department Molecular Systems Biology: Introduction to Systems Biology: From OMICS data analysis to metabolic network modeling. Details available at the HIGRADE website.
The next course is on September 21, 2017.
Master students: Stefan Bauer, Paul Jähne, Lukas Hirsch
Bachelor students: Robin Goldmann, Eric Witt
Interns: Piotr Jachimowicz, Amit Nain, Ahmad Zino
We are offering research topics in the area of mathematical modeling, analysis of microbial communities and biogas reactor experiments. Please contact us if you are interested in the simulation of metabolic networks, network analysis, indiviudal-based modeling, or the development of bioinformatic tools. Besides theoretical topics, wet lab related topics are also available, find more details here.
Current we are looking for students interested in the following topics:
1. Microbial community dynamics in biogas reactors Project description
Master thesis: "Effect of propionic acid on the anaerobic digestion process" Tatjana Malycheva
Simplified lab-scale biogas reactors shall be used to study the effect of increased propionic acid concentrations on the microbial communities involved in anaerobic digestion. Therefore, reactor experiments will be combined with molecular biological approaches.
Stefan Bauer: "Comparison of methods for quantification of biomass from a biogas reactor", master thesis, University of Kassel
Robin Goldmann: "Molecular biological analysis of microbial communities in biogas reactors", bachelor thesis, Leipzig University
Paul Jähne: "Optimization of in silico metabolic engineering strategies with evolutionary algorithm using CUDA", master thesis, Leipzig University of Applied Sciences
Lukas Hirsch: "Using dynamic modeling to infer microbial interaction networks from flow cytometry data", master thesis, Leipzig University
Eric Witt: "Molecularbiological characterization of microbial communities in biogas reactors", bachelor thesis (in cooperation with the group Microbiology of Anaerobic Systems), Leipzig University