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A bioinformatics and systems biology approach for the functional analysis of a growth-regulating MAP kinase pathway in Arabidopsis (ARA-MKK-D)
Start date: 01 Aug 2007, End date: 31 Jul 2009 PROJECT  FINISHED 

This proposal contains fundamental science, but within one of the central aspects that make plants of vital importance for humanity: their growth and development. It is increasingly clear that biomass is one of the few sustainable energy alternatives. The mitogen-activated protein kinase (MAPK) phosphorylation cascades are conserved signalling modules in all eukaryotes and have pivotal roles to regulate cell division and cell growth in animals but such roles in plants are just emerging. Specifically, in my work I recently discovered that group D MAPK kinases potentially regulate plant growth and development. Within this project I propose to focus on MKK9, because it is also stress induced, and bioinformatics analysis shows co-regulation with genes important in growth and environmental adaptation. A close collaboration between the School of Biological Sciences, and the Computer Sciences at Royal Holloway, University of London, will enable me to build a novel system's biology approach to reach my goals.My work program is designed around six modules;1. molecular genetics studies of MKK9 by analysing insertional mutants, RNAi and over-expression lines,2. detailed phenotypic analysis of these lines3. genome-wide transcriptomics with inducible gain of function mutant forms to find downstream targets,4. bioinformatics analysis of the transcriptome data that we obtain, and the public databases to find candidate target genes, and coregulated genes,5. high-throughput functional analysis of the MKK9 signalling pathway by a cell transfection system and promoter reporter gene readout and finally6. model building that utilise gene antology (GO) terms and computer language, which will allow to make predictions and plan further experiments on the whole plant level towards the goal of attaining plants with better yield and stress tolerance.This multidisciplinary program should enable me to reach professional maturity and to establish a research career upon return to Hungary.
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