Dandekar T. Z- Project
Host adapted metabolism of bacterial infections: Data integration and refined metabolic modelling
We developed a joined software platform for modelling metabolism in extracellular and intracellular infections. We established collaborations, software compatibility and exchange throughout the SPP1316, service, data integration and a web platform. The progress achieved is also testified by a number of publications. For the next period we want to join the numerous collaborations and individual results achieved by the bioinformatics platform of SPP1316 in the context of an integrated view on metabolism during infection: Metabolism in host – pathogen interactions is a tight and complicated interaction which can and has to be studied by several and very diverse methods and data sets. We will combine a number of different approaches to achieve here optimal data integration and integrated models. Furthermore, the metabolic modelling achieved in the last period delineates also required new steps: This includes data-driven modelling for the extra- and intracellular pathogen examples studied as well as tackling the data generation itself with respect to isotopolog modelling, automatic development of metabolic models based on an extended genome annotation, modelling of metabolic fluxes and fit to experimental data. We want to establish new approaches allowing an integrated view and mathematical description of metabolism and its changes during bacterial infections.
Mitarbeiter
Prof. Thomas Dandekar
Dr. Muhammed Naseem, Dr. Ahmed Zeeshan (Z-Projekt)
Astrid Fieselmann (Salmonella Projekt)
Dr. Tobias Müller
Dr. Beate Krüger
Stefan Obermeyer
Bioinformatik, Biozentrum,
Universitaet Wuerzburg
Am Hubland, D-97074
Tel.: +49 (0)931 31-84551,
Fax: +49 (0)931 31-84552
Email: dandekar@biozentrum.uni-wuerzburg.de
Infection-related publications
Dandekar,T. and Xiao,K. (2010) New bioinformaic strategies against apicomplexan parasites pp. 21-33. In: Katja Becker (Ed.), Apicomplexan Parasites: Molecular Approaches toward Targeted Drug Development. Wiley-VCH, Weinheim.
Eisenreich, W., Dandekar, T., Heesemann,J., and Goebel,W. (2010). Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nature Reviews Microbiology 8, 401-412.
Vainshtein, Y.*, Sanchez,M., Brazma,A., Hentze,M.W., Dandekar T* and Martina U. Muckenthaler* (2010) The IronChip Evaluation Package: A package of Perl modules for robust analysis of custom microarrays. BMC Bioinformatics 11:112.
Beisser D, Klau GW, Dandekar T, Mueller T, Dittrich M. BioNet: an R-Package for the Functional Analysis of Biological Networks. Bioinformatics 2010 Apr 15;26(8):1129-30.
Friedrich T, Rahmann S, Weigel W, Rabsch W, Fruth A, Ron E, Gunzer F, Dandekar T, Hacker J, Müller T, Dobrindt U. High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis. BMC Genomics. 2010 Oct 21;11:591. PubMed PMID: 20964857;
Schauer K, Geginat G, Liang C, Goebel W, Dandekar T, Fuchs TM. Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling. BMC Genomics. 2010 Oct 18;11:573. PubMed PMID: 20955543; PubMed Central PMCID: PMC3091722.
Fuchs S, Mehlan H, Kusch H, Teumer A, Zühlke D, Berth M, Wolf C, Dandekar T, Hecker M, Engelmann S, Bernhardt J. Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL. Proteomics. 2010 Aug;10(16):2982-3000. PubMed PMID: 20662099.
Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J. 2011 Jan;5(1):61-70. Epub 2010 Jul 8. PubMed PMID: 20613790.
Ratzka C, Liang C, Dandekar T, Gross R, Feldhaar H. Immune response of the ant Camponotus floridanus against pathogens and its obligate mutualistic endosymbiont. Insect Biochem Mol Biol. 2011 Aug;41(8):529-36. doi: 10.1016/j.ibmb.2011.03.002.
Cecil A, Rikanovic C, Ohlsen K, Liang C, Bernhardt J, Oelschlaeger TA, Gulder T, Bringmann G, Holzgrabe U, Unger M, Dandekar T. Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells. Genome Biol. 2011 Mar 21;12(3):R24. [Epub ahead of print] PubMed PMID: 21418624.
Liebeke M, Dörries K, Zühlke D, Bernhardt J, Fuchs S, Pané-Farré J, Engelmann S, Völker U, Bode R, Dandekar T, Lindequist U, Hecker M, Lalk M. A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. Mol Biosyst. 2011 Apr 1;7(4):1241-53. Epub 2011 Feb 16. PubMed PMID: 21327190.
Agarwal S, Kern S, Halbert J, Przyborski JM, Baumeister S, Dandekar T, Doerig C, Pradel G. Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor. J Cell Biochem. 2011 Feb 10. doi: 10.1002/jcb.23034. [Epub ahead of print] PubMed PMID: 21312235.
Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. Staphylococcus aureus physiological growth limitations: Insights from flux calculations built on proteomics and external metabolite data. Proteomics. 2011 May;11(10):1915-35.
Zeeshan A, Dandekar T, Majeed S (2012) Semantic Web; Ontology Specific Languages for Web Application Development. International Journal of Web applications 4 (1), pp. 42-50.
Naseem M, Philippi N, Hussain A, Wangorsch G, Ahmed N, and Dandekar T (2012) Integrated Systems View on Networking by Hormones in Arabidopsis Immunity Reveals Multiple Crosstalk for Cytokinin. Plant Cell 24, 1793-814.
Krueger B, Friedrich T, Förster F, Bernhardt J, Gross R, Dandekar T. (2012) Different evolutionary modifications as a guide to rewire two-component systems. Bioinform Biol Insights. 6, 97-128.
Beisser D, Brunkhorst S, Dandekar T, Klau GW, Dittrich MT, Müller T. Robustness and accuracy of functional modules in integrated network analysis. Bioinformatics. 2012 May 11. [Epub ahead of print] PubMed PMID: 22581175.
Dandekar T, Astrid F, Jasmin P, Hensel M. Salmonella enterica: a surprisingly well-adapted intracellular lifestyle. Front Microbiol. 2012;3:164. Epub 2012 May 3. PubMed PMID: 22563326; PubMed Central PMCID: PMC3342586.
Fuchs TM, Eisenreich W, Kern T, Dandekar T. Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection. Front Microbiol. 2012;3:23. Epub 2012 Feb 3. PubMed PMID: 22347216; PubMed Central PMCID: PMC3271275.
Ratzka C, Förster F, Liang C, Kupper M, Dandekar T, Feldhaar H, Gross R. (2012) Molecular characterization of antimicrobial peptide genes of the carpenter ant Camponotus floridanus. PLoS One 7(8):e43036.
Beisser D, Grohme MA, Kopka J, Frohme M, Schill RO, Hengherr S, Dandekar T, Klau GW, Dittrich M, Müller T. (2012) Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Syst Biol. 6(1):72.
Zirkel J, Cecil A, Schäfer F, Rahlfs S, Ouedraogo A, Xiao K, Sawadogo S, Coulibaly B, Becker K, Dandekar T. Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling. Bioinform Biol Insights. 2012;6:287-302. doi: 10.4137/BBI.S10193.
Zeeshan A., Saman M., Dandekar T. (2012) Unified Modeling and HCI Mockup Designing towards MIDA. International Journal of Emerging Sciences, Vol. 2, No. 3, Pages: 361-382.
Zeeshan A., Saman M., Dandekar T. (2012) Formal UML Modelling of Isotopo, Bioinformatical Software for Mass Isotopomers Distribution Analysis. Software Engineering Journal, SAP Publishing, 2(4): 147-159.
Dandekar T, Fieselmann A, Majeed S, Ahmed Z. Software applications toward quantitative metabolic flux analysis and modeling. Brief Bioinform. 2012 Nov 9. [Epub ahead of print] PMID: 23142828.
Naseem M and Dandekar T. The role of auxin-cytokinin antagonism in plant-pathogen interactions. PLoS Pathog. 2012 Nov;8(11):e1003026.
Krüger B, Liang C, Prell F, Fieselmann A, Moya A, Schuster S, Voelker U, Dandekar T (2012) Metabolic Adaptation and Protein Complexes in Prokaryotes Metabolites 2(4), 940-958; doi:10.3390/metabo2040940
