Project

Food for the gate keepers

Background

The homeostasis of small intestine, it’s mucosal immune system and the gut microbiome population are modulated by several key factors including the food consumed. In this project we propose to identify the critical mechanisms involved in intestinal homeostasis and the associated immune system using transcriptomics based analysis. Our lab has performed and is presently performing microarray gene expression experiments of human intestinal cells (Caco-2 cell lines) stimulated with various food substances.  The largest part of the study is focus on the effects of fibres.

Projects

There are two sub-projects available for interested MSc students. The first one involves developing an ‘R’ based program for analysis of large scale microarray datasets. The main challenge is in devising a good method to integrate data from different platforms, store in warehouses and use these data in large scale comparative analysis. On completion of this module, the student would have developed good programming skills in R, thorough knowledge on analysis of microarray gene expression data and deeper knowledge on application of statistical methods to biological information.

The second module involves network property analysis including detection of hubs and other important network related metrics. These networks will be metabolic, signalling and regulatory in nature and totally dedicated to biological important functions of the gut like: 1) regulation of proliferation and differentiation; 2) Tight Junctions; 3) immune responses and crosstalk with immune cells; 4) signalling, uptake and transport of nutrients and 5) energy metabolism of the epithelial. We aim to identify important network properties built from transcriptomics data and merged with data from literature and existing pathway databases. The network analysis is to be done using cytoscape and python. On successful completion of this module, the student would have developed expertise in handling cytoscape, gain deeper knowledge on network biology and related statistics and deeper knowledge on how the epithelial cells function.

The general target audiences are students of Systems Biology, Bioinformatics and Biotechnology. But anyone with relevant subject knowledge and subject interests are encouraged to apply.

Contact

For information contact

Prashannabalaji.Venkatasubramanian@wur.nl