Dr Ilan Davis, University of Oxford
mRNA localisation and translational regulation are common and important mechanisms for targeting protein production to specific regions of many kinds of cell types, most notably oocytes and neurons (Meignin and Davis, 2010; Weil et al., 2010a). Different transcripts contain distinct cis-acting signals, so called zip codes, that are recognized by trans-acting factors that sort them to their specific destinations. In most cases these factors specify transport by molecular motors along the cytoskeleton as well as anchoring and translational regulation. These mechanisms are essential for patterning during invertebrate and chordate oogenesis and embryogenesis as well as in the nervous system and thought to be disrupted in neurodegenerative diseases. To address the molecular details of these processes we have been using advanced imaging approaches including using 3D super-resolution microscopy on the OMX microscope (Weil et al., 2010b) as well as live cell imaging of mRNA transport (Vendra et al., 2007; Zimyanin et al., 2008) and microtubule organization (Parton et al.) in multidimensions. We have also developed new methods of image denoising, particle tracking, image analysis and statistics (Hamilton et al., 2010; Oliveira et al., 2010; Yang et al., 2010). These approaches generate huge data sets that have to stored and curated. But more importantly, the analysis of the data requires new ways of thinking about data flow and automated and systematic high throughput means of processes data. OMERO promises to be a powerful platform in which to achieve such ambitious goals. The availability of the proposed post will have a big impact of our ability to develop and implement the use of these approaches through OMERO both within my lab and across the Oxford microscopy community. The Swedlow and Davis group have a previous good track record of collaboration on OMERO and the proposed project can build on this pre-existing relationship (Beckett et al., 2009).
The post will have two synergistic roles in Oxford Biochemistry. First, they will work with Micron Oxford, an Advanced Microscopy Unit based in Biochemistry funded by a recent Wellcome Trust Award (Ref: 091911) , but including faculty and facilities in the Dunn School of Pathology, Department of Physiology, Anatomy and Genetics, the Wellcome Trust Centre for Human Genetics and the BBSRC Integrative Systems Biology Centre. They will be helping setup an OMERO server to service the data curation of the majority of the imaging activities in these advanced facilities, including OMX and a number of bespoke imaging systems as well as off the shelf instruments. The post will also work with a number of Micron staff to integrate and streamline image analysis routines within the OMERO infrastructure. Second, the post will work with the Davis lab specifically to facilitate integration of the bespoke open source image analysis routines they have written and recently published to track mRNA motility. We have already installed a number of OMERO servers at our site, which are used both within the Davis lab and within the Micron facilities. We are finding the OME’s tools essential on a number of levels, including the curation and organisation of data and its associated metadata as well as for sharing data in collaborations. The post will allow us to extend this to allow us to make better use of our image analysis algorithms and also potentially make them more widely available in a form that takes care of image formats and workflows.
Further information is available on the Micron Oxford website