PhD Position (as part of the Wageningen Center for System Biology)
Systems Biology of Fatty Acid Sensing
Job description
The peroxisome proliferator-activated receptor alpha (PPARα) is a transcription factor that functions as an important nutrient sensor for fatty acids and their metabolites. It is well expressed in liver, heart, kidney, skeletal muscle, small intestine, and several inflammatory/immune cell types. Although much is known about the function of PPARα in hepatic lipid metabolism or in regulation of inflammatory responses, in most other organs many PPARα-dependent pathways and genes have yet to be discovered.
To obtain an comprehensive overview of PPARα-regulated genes relevant to nutrient metabolism, we have identified and investigated in several studies novel candidate PPARα target genes. In those studies animal models in which PPARα was activated and/or disabled were used in combination with gene expression profiling on Affymetrix whole genome GeneChip arrays.
In this current project we aim to better understand the system (organism)-wide impact of PPARα activation by integrating individual organ responses. To this end we are looking for a PhD-student who will develop new mathematical and statistical models and novel algorithms for the analysis of large microarray data sets from functional genomics experiments, and apply those on existing and new data sets. This project is closely associated to other more ‘biology-driven’ PhD projects as well as to other "Systems Biology" PhD projects of the WCSB. Our group have extensive expertise in microarray analysis using a state-of-the-art analysis pipeline based on Bioconductor scripts, ErmineJ, GSEA, Ingenuity Pathway analysis, Metacore or Genomarix packages..
Some objectives we want to address in this project:
Identification of PPARa core function target genes that are expressed in most organs and that are relevant for nutrition
Identification of early and late PPARa response genes from time course experiments
Comparative organ analysis of the PPARa-transcriptomes of mouse liver and intestine
Development of Systems Biology model(s) for PPARa responses in vitro (with mouse hepatocytes);
Application of this SB model to data sets derived from PPARa activation experiments with hepatocytes from mice, rats and humans;
Development of SB model(s) for PPARa responses in vivo (e.g. intestine, liver, heart).
Requirements
University Graduate
A completed academic curriculum in biological/molecular sciences (e.g. Biochemistry, Bioinformatics, Molecular Life Sciences, Biotechnology) or equivalent curricula with a proven interest and experience in systems biology modeling or mathematical/biostatistical procedures to describe molecular processes. Knowledge on microarray analysis, pathway statistics or some of the analysis tools mentioned above is a pro.
Additional information about the job:
For more information about the project please contact prof.dr. Michael Müller e-mail michael.muller@wur.nl
Organization
Agrotechnology & Food Sciences Group (AFSG) Human Nutrition
Agrotechnology & Food Sciences Group (AFSG) is the organisation for development and transfer of knowledge in the field of sustainable applications of agro-components for safe and healthy food and non-food products.
Conditions of employment
Estimated maximum salary per month: 2000 - 2500 Euro
Salary scale 10.
Maximum salary amount in Euro's a month 2558
Employment basis: Temporary for specified period
Duration of the contract: 1,5 year + 2,5 years
Maximum hours per week: 38
Additional information about the vacancy can be obtained from: prof.dr. Michael Müller
Telephone number: 31-(0)317-482590/482589 (secretary) michael.muller@wur.nl
Application
You can apply for this job before end of July 2008 by sending your application to: michael.muller@wur.nl
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