Diatoms contribute about 25% of total primary production on Earth. But even more than that, they are nature's nanotechonology masters, able to lay down complex structures of silica in high order at the sub-nanometer range exceeding any current capabilities of human nano-technology (e.g. Drum & Gordon 2003). These unique structures are the reason why diatoms became model organisms for bio-nanotechnology. However, our knowledge about genes and proteins responsible for synthesis of silica shells is still very limited although major proteins for uptake of silicate and deposition of silica have been indentified over the last decade (e.g. Kroeger et al. 1999). The availability of the first diatom genome sequences has revealed many novel genes putatively involved in a genetic network responsible for the synthesis of complex silica nano-patterns (e.g. Mock et al. 2008). One of the most interesting discoveries was a novel Myb-like transcription factor fused with a domain from a silicon transporter identified in the genome of Fragilariopsis cylindrus. We assume the protein encoded by this gene might coordinate the expression of genes involved in either the uptake of silicate, silicification or even still unknown processes necessary to make the silica shell of F. cylindrus. Thus, we expect to identify the first genetic network involved in diatom silicon metabolism including parts of its regulatory machinery. Workpackage 1 of this studentship aims to characterize the novel transcription factor by i) expression analysis over the cell cycle and under Si-limitation, ii) heterologous expression in Phaeodactylum tricornutum and Thalassiosira pseudonana including phenotyping of transgenic cell lines, and iii) an electrophoretic mobility shift assay to confirm DNA binding. Workpackage 2 will identify the DNA binding sites of the Myb-like transcription factor by using chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-Seq). Next generation sequencing will be conducted at The Genome Analysis Centre (TGAC) in Norwich. A pilot project to establish ChIP-Seq for several different diatoms is currently being conducted in partnership with TGAC. Thus, the PhD candidate will have access to the latest sequencing and bioinformatics tools and should therefore not only have a strong interest in molecular biology but also bioinformatics. Acceptable first degree subject areas include biology, molecular environmental science, molecular biology, genetics and bioinformatics. 

Drum RW, Gordon R (2003) Star Trek replicators and diatom nanotechnology. Trends in Biotechnology, 21:325-328

 Mock et al. (2008) Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. PNAS, 105:1579-1584

Kroeger et al. (1999) Polycationic peptides from diatom biosilica that direct silica nanosphere formation. Science, 286:1129-1132