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University College London (UCL) is offering a fully funded Ph.D. studentship in collaboration with Microsoft Research Cambridge (MSRC) for the project "Dynamic modelling of HIV recognition by the immune system". This position will be based in the Department of Chemistry at UCL, supervised by Professor Peter Coveney from the Centre for Computational Science. There will be an internship opportunity at MSRC associated with the studentship; the student will additionally be co-supervised by Dr Neil Dalchau, a researcher in the Biological Computation group at MSRC.
The immune system is one of the most complex biological sub-systems within a single individual, capable of protecting us from pathogens by distinguishing their components from our own. Cytotoxic T lymphocytes (CTLs; white blood cells) recognise and then destroy virus-infected or cancerous cells, thus preventing disease progression. CTLs express unique receptors that recognize Major Histocompatibility Complex (MHC) class I molecules displayed on the surface of infected cells. MHC class I molecules present protein fragments (peptides) arising from intracellular protein degradation and thus provide a snapshot of the internal contents of the cell. Consequently, the abundance of intracellular virus-derived peptides that are capable of binding to MHC class I molecules is of central importance to eliciting immune responses. Our ability to understand and predict the immune response to viral infection is, in part, limited by a lack of a quantitative description of the abundance of viral proteins, their degradation products, and the ability of MHC class I molecules to deliver these peptides to the surface of the cell.
The collaboration between the Coveney and Dalchau research groups has been set up to combine quantitative knowledge of protein degradation and peptide processing with MHC class I presentation to investigate, through quantitative modelling, infections by Human Immunodeficiency Virus (HIV). Our recent work has resulted in predictive computational models of heteropolymer degradation by the HIV protease (Sadiq et al., J Phys Chem B 2011), and MHC class I binding and transit to the cell surface, specifically applied to cells infected by HIV (Dalchau et al., PLoS Comput Biol 2011). This project seeks to understand how peptide processing by HIV influences MHC class I presentation, and to use this as a vehicle to more generally understand how our immune system responds to viral infections, and gain insight into reasons for its failure. Underpinning this will be the development of computational models that integrate the viral response pathway and virus life-cycles.
This is a very exciting project offering an opportunity for a student with a strong mathematical or computer science background to tackle the complexity arising in this fascinating area of biology. Prior experience of experimental biology is not necessary.
Application deadline is 5 p.m. on Monday 16 July 2012. However, please note that applications will be assessed and interviews arranged as they are received, so the studentships may all be filled before the deadline.
Funding Notes:
To apply, please complete the online UCL graduate application form. Please ensure you apply for the 'Research Degree:CoMPLEX', then make it clear in the personal statement section of the application form, which post you are applying for. Once submitted, it is essential that you email CoMPLEX, complex.admin@ucl.ac.uk, stating your name, UCL application number, the post you are applying for and the date you submitted your application. Informal enquiries including CVs should be sent to Prof PV Coveney, p.v.coveney@ucl.ac.uk.
Studentships for Home/EU students will be available covering tuition fees and paying a tax-free stipend (2012/13 rate is £15,090 - £17,090).