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ANNUAL REVIEW 1 October 2005–30 September
WELLCOME TRUST ANNUAL REVIEW 1 October 2005–30 September 2006 ANNUAL REVIEW 2006 The Wellcome Trust is the largest charity in the UK and the second largest medical research charity in the world. It funds innovative biomedical research, in the UK and internationally, spending around £500 million each year to support the brightest scientists with the best ideas. The Wellcome Trust supports public debate about biomedical research and its impact on health and wellbeing. www.wellcome.ac.uk THE WELLCOME TRUST The Wellcome Trust is the largest charity in the UK and the second largest medical research charity in the world. 123 CONTENTS BOARD OF GOVERNORS 2 Director’s statement William Castell 4 Advancing knowledge Chairman 16 Using knowledge Martin Bobrow Deputy Chairman 24 Engaging society Adrian Bird 30 Developing people Leszek Borysiewicz 36 Facilitating research Patricia Hodgson 40 Developing our organisation Richard Hynes 41 Wellcome Trust 2005/06 Ronald Plasterk 42 Financial summary 2005/06 Alastair Ross Goobey 44 Funding developments 2005/06 Peter Smith 46 Streams funding 2005/06 Jean Thomas 48 Technology Transfer Edward Walker-Arnott 49 Wellcome Trust Genome Campus As at January 2007 50 Public Engagement 51 Library and information resources 52 Advisory committees Images 1 Surface of the gut. 3 Zebrafish. 5 Cells in a developing This Annual Review covers the 2 Young children in 4 A scene from Y fruit fly. Wellcome Trust’s financial year, from Kenya. Touring’s Every Breath. 6 Data management at the Sanger Institute. 1 October 2005 to 30 September 2006. CONTENTS 1 45 6 EXECUTIVE BOARD MAKING A DIFFERENCE Developing people: To foster a Mark Walport The Wellcome Trust’s mission is research community and individual Director to foster and promote research with researchers who can contribute to the advancement and use of knowledge Ted Bianco the aim of improving human and Director of Technology Transfer animal health. -
Predicting and Characterising Protein-Protein Complexes
Predicting and Characterising Protein-Protein Complexes Iain Hervé Moal June 2011 Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute and Department of Biochemistry and Molecular Biology, University College London A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Biochemistry at the University College London. 2 I, Iain Hervé Moal, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Abstract Macromolecular interactions play a key role in all life processes. The con- struction and annotation of protein interaction networks is pivotal for the understanding of these processes, and how their perturbation leads to dis- ease. However the extent of the human interactome and the limitations of the experimental techniques which can be brought to bear upon it necessit- ate theoretical approaches. Presented here are computational investigations into the interactions between biological macromolecules, focusing on the structural prediction of interactions, docking, and their kinetic and thermo- dynamic characterisation via empirical functions. Firstly, the use of normal modes in docking is investigated. Vibrational analysis of proteins are shown to indicate the motions which proteins are intrinsically disposed to under- take, and the use of this information to model flexible deformations upon protein-protein binding is evaluated. Subsequently SwarmDock, a docking algorithm which models flexibility as a linear combination of normal modes, is presented and benchmarked on a wide variety of test cases. This algorithm utilises state of the art energy functions and metaheuristics to navigate the free energy landscape. -
Functional Effects Detailed Research Plan
GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data. -
Features China Introduction
Features China Introduction Tom Blundell (President, the Biochemical Society) This issue of The Biochemist is focused on biochemistry in China. It is timely because it reflects the history of biochemical research collaboration between Chinese and UK scientists, not only by looking back over the last century, but also by reviewing some of the strengths of biochemical research in China in 2011. Downloaded from http://portlandpress.com/biochemist/article-pdf/33/5/4/3914/bio033050004.pdf by guest on 27 September 2021 It has been a busy year for the Biochemical Society, which both in the UK and China. But there were interactions is celebrating its first century. It will do so at the Centenary before Needham became involved. In this issue, Randy Celebration event at the Royal Society in London in Poon draws our attention to one of these, the first paper December, but it has already done so very impressively in from China published in a journal of the Biochemical Shanghai in May with a Joint Sino–UK Protein Symposium. Society. In 1926 Ernest Tso of the Peking Union Medical There we heard about truly momentous contributions College described vitamins in preserved duck eggs, arising from interactions of influential scientists from maintaining they are “as much used on the table as is both China and UK during the last century. Just before cheese in Western countries”. the Symposium, also in May 2011, the Biochemical Journal We should also celebrate Wang Ying-Lai, who did his opened its China office in Beijing with a mini-symposium. PhD in Cambridge between 1938 and 1941. -
Cambridge University Reporter Special Number 3
2 OFFICERS NUMBER–MICHAELMAS TERM 2000 SPECIAL NO.3 PA RT I Chancellor: H.R.H. The Prince PHILIP, Duke of Edinburgh, T Vice-Chancellor: Prof. Sir Alec BROERS, CHU Deputy Vice-Chancellors: for –,A.M.LONSDALE, NH,O.S.O’NEILL, N,Q.R.D.SKINNER, CHR, D. E. NEWLAND, SE, Prof. D. H. MELLOR, DAR Pro-Vice-Chancellors: ,A.M.LONSDALE, NH, June , D. H. MELLOR, DAR, Dec. High Steward: Vacant Deputy High Steward: , The Rt Hon. Lord RICHARDSON, CAI Commissary: , The Rt Hon. Lord OLIVER, TH Proctors for ‒: F. H. KING, M Deputy: C. A. T. MALONE, NH R. J. STIBBS, DOW Deputy: S. A. T. REDFERN, JE Orator: ,A.J.BOWEN, JE Registrary: ,T.J.MEAD, W Deputy Registrary: ,N.J.B.A.BRANSON, DAR Secretary General of the Faculties: ,D.A.LIVESEY, EM Deputy Secretary General of the Faculties: ,G.P.ALLEN, W Librarian: ,P.K.FOX, SE Deputy Librarians: ,D.J.HALL, W , A. MURRAY, W Treasurer: ,J.M.WOMACK, TH Director of the Fitzwilliam Museum and Marlay Curator: ,D.D.ROBINSON, CL Development Director: Vacant Esquire Bedells: ,J.P.EMMINES, PET ,J.H.WILLIAMS, HH University Advocate: ,N.M.PADFIELD, F, Deputy University Advocate: ,P.J.ROGERSON, CAI, OFFICERS IN INSTITUTIONS PLACED UNDER THE SUPERVISION OF THE GENERAL BOARD PROFESSORS Aeronautical Engineering, Francis Mond W. N. D AWES, CHU Aerothermal Technology Vacant African History J. I LIFFE, JN American History, Paul Mellon A. J. BADGER, SID American History and Institutions, Pitt Vacant Anatomy W.A. HARRIS, CL Anaesthesia D. K. MENON Ancient History M. -
Development of Novel Strategies for Template-Based Protein Structure Prediction
Imperial College London Department of Life Sciences PhD Thesis Development of novel strategies for template-based protein structure prediction Stefans Mezulis supervised by Prof. Michael Sternberg Prof. William Knottenbelt September 2016 Abstract The most successful methods for predicting the structure of a protein from its sequence rely on identifying homologous sequences with a known struc- ture and building a model from these structures. A key component of these homology modelling pipelines is a model combination method, responsible for combining homologous structures into a coherent whole. Presented in this thesis is poing2, a model combination method using physics-, knowledge- and template-based constraints to assemble proteins us- ing information from known structures. By combining intrinsic bond length, angle and torsional constraints with long- and short-range information ex- tracted from template structures, poing2 assembles simplified protein models using molecular dynamics algorithms. Compared to the widely-used model combination tool MODELLER, poing2 is able to assemble models of ap- proximately equal quality. When supplied only with poor quality templates or templates that do not cover the majority of the query sequence, poing2 significantly outperforms MODELLER. Additionally presented in this work is PhyreStorm, a tool for quickly and accurately aligning the three-dimensional structure of a query protein with the Protein Data Bank (PDB). The PhyreStorm web server provides comprehensive, current and rapid structural comparisons to the protein data bank, providing researchers with another tool from which a range of biological insights may be drawn. By partitioning the PDB into clusters of similar structures and performing an initial alignment to the representatives of each cluster, PhyreStorm is able to quickly determine which structures should be excluded from the alignment. -
Crystal Structures of Native and Inhibitedforms of Human Cathepsin
Proc. Natl. Acad. Sci. USA Vol. 90, pp. 6796-6800, July 1993 Biochemustry Crystal structures of native and inhibited forms of human cathepsin D: Implications for lysosomal targeting and drug design (aspartic protcase/N-linked oligosaccharide/pepstatin A) ERic T. BALDWIN*, T. NARAYANA BHAT*, SERGEI GULNIK*, MADHUSOODAN V. HOSUR*t, RAYMOND C. SOWDER Il, RAUL E. CACHAU*, JACK COLLINS*, ABELARDO M. SILVA*, AND JOHN W. ERICKSON*§ *Structural Biochemistry Program, Frederick Biomedical Supercomputing Center and tAIDS Vaccine Program, Program Resources Inc./DynCorp, National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, MD 21702 Communicated by David R. Davies, March 24, 1993 (receivedfor review February 4, 1993) ABSTRACT Cathepsin D (EC 3.4.23.5) is a lysosomal duced in the vicinity of the growing tumor, may degrade the protease suspected to play important roles in protein catabo- extracellular matrix and thereby promote the escape of lism, antigen processing, degenerative diseases, and breast cancer cells to the lymphatic and circulatory systems and cancer progresson. Determination of the crystal structures of enhance the invasion of new tissues (17, 18). The design of cathepsin D and a complex with pepstatin at 2.5 A resolution potent and specific inhibitors of cathepsin D will aid the provides insights into inhibitor binding and lysosomal targeting further elucidation of the roles of this enzyme in human for this two-chain, N-glycosylated aspartic protease. Compar- disease. We previously described the purification and crys- ison with the structures of a complex of pepstatin bound to tallization ofhuman cathepsin D from liver (3); similar studies rhizopuspepsin and with a human renin-bihbitor complex have been reported recently for cathepsin D isolated from revealed differences in subsite structures and inhibitor-enzyme bovine liver (19) and human spleen (20). -
Part I Officers in Institutions Placed Under the Supervision of the General Board
2 OFFICERS NUMBER–MICHAELMAS TERM 2009 [SPECIAL NO.7 PART I Chancellor: H.R.H. The Prince PHILIP, Duke of Edinburgh, T Vice-Chancellor: 2003, Prof. ALISON FETTES RICHARD, N, 2010 Deputy Vice-Chancellors for 2009–2010: Dame SANDRA DAWSON, SID,ATHENE DONALD, R,GORDON JOHNSON, W,STUART LAING, CC,DAVID DUNCAN ROBINSON, M,JEREMY KEITH MORRIS SANDERS, SE, SARAH LAETITIA SQUIRE, HH, the Pro-Vice-Chancellors Pro-Vice-Chancellors: 2004, ANDREW DAVID CLIFF, CHR, 31 Dec. 2009 2004, IAN MALCOLM LESLIE, CHR, 31 Dec. 2009 2008, JOHN MARTIN RALLISON, T, 30 Sept. 2011 2004, KATHARINE BRIDGET PRETTY, HO, 31 Dec. 2009 2009, STEPHEN JOHN YOUNG, EM, 31 July 2012 High Steward: 2001, Dame BRIDGET OGILVIE, G Deputy High Steward: 2009, ANNE MARY LONSDALE, NH Commissary: 2002, The Rt Hon. Lord MACKAY OF CLASHFERN, T Proctors for 2009–2010: JEREMY LLOYD CADDICK, EM LINDSAY ANNE YATES, JN Deputy Proctors for MARGARET ANN GUITE, G 2009–2010: PAUL DUNCAN BEATTIE, CC Orator: 2008, RUPERT THOMPSON, SE Registrary: 2007, JONATHAN WILLIAM NICHOLLS, EM Librarian: 2009, ANNE JARVIS, W Acting Deputy Librarian: 2009, SUSANNE MEHRER Director of the Fitzwilliam Museum and Marlay Curator: 2008, TIMOTHY FAULKNER POTTS, CL Director of Development and Alumni Relations: 2002, PETER LAWSON AGAR, SE Esquire Bedells: 2003, NICOLA HARDY, JE 2009, ROGER DERRICK GREEVES, CL University Advocate: 2004, PHILIPPA JANE ROGERSON, CAI, 2010 Deputy University Advocates: 2007, ROSAMUND ELLEN THORNTON, EM, 2010 2006, CHRISTOPHER FORBES FORSYTH, R, 2010 OFFICERS IN INSTITUTIONS PLACED UNDER THE SUPERVISION OF THE GENERAL BOARD PROFESSORS Accounting 2003 GEOFFREY MEEKS, DAR Active Tectonics 2002 JAMES ANTHONY JACKSON, Q Aeronautical Engineering, Francis Mond 1996 WILLIAM NICHOLAS DAWES, CHU Aerothermal Technology 2000 HOWARD PETER HODSON, G Algebra 2003 JAN SAXL, CAI Algebraic Geometry (2000) 2000 NICHOLAS IAN SHEPHERD-BARRON, T Algebraic Geometry (2001) 2001 PELHAM MARK HEDLEY WILSON, T American History, Paul Mellon 1992 ANTHONY JOHN BADGER, CL American History and Institutions, Pitt 2009 NANCY A. -
Iisc-Alumni Association- M.Vijayan Lecture. Cross Fertilisation: How
IISc-Alumni Association- M.Vijayan Lecture. Cross Fertilisation: How Crystallography has built on Mathematics. Eleanor Dodson 17th August 2017 Nostalgia time: I cannot resist revisiting old photographs! Oxford 1968? Wedding Day – July 1969 DCH building first insulin model Vijayan lost in shadows? Oxford lab - 1969 Britishx5, Indian, NZ, Aust. David Phillips, Dorothy, Tony North, Thomas, Vijaya, Tom Blundell, Ted Baker, EJD Bangalore – 1970? Bangalore 1970s Kalyani, Vijayan, Tom Blundell -1975? Bangalore – 1979-80. Vijanan Davi Kalyani Bangalore 2007: Guy's 70th Birthday Cake Workshop 2008 DCH & Siv Ramasechan – 1965 our Anomalous Dispersion Guru First anomalous data measurements done in Oxford ~ 1960 on B12 derivative by K. Venkatesan Validation: More Thought Experiments: G.N. Ramachandran Mathematics in the Service of Science? Michael Mosley -BBC 2010 “Knowledge leaps forward when brilliant experiments are analysed by independent minds.” He was referring to the discovery that Mars moves in an elliptical orbit around the sun – established by Johannes Kepler -1599 using the observations of Tycho Brahe. Mathematics in the Service of Crystallography? Structure Solution exploits: Fundamental Mathematical concepts (Some elegant, but restricted to 3D for structure, and 2D for diffraction) Technical Mathematics and Computation (messy and very easy to get wrong!) Statistics (Much needed but messy too) Why crystallography? Quote: DCH: I also first learnt at the same time about biochemistry which provided me with the molecules it seemed most desirable to 'see'. …[The] great advantage of X-ray analysis as a method of chemical structure analysis is its power to show some totally unexpected and surprising structure and to do so with absolute certainty…. -
Centre for Bioinformatics Imperial College London
Centre for Bioinformatics Imperial College London Inaugural Report January 2003 Centre Director: Prof Michael Sternberg www.imperial.ac.uk/bioinformatics [email protected] Support Service Head: Dr Sarah Butcher www.codon.bioinformatics.ic.ac.uk [email protected] Centre for Bioinformatics - Imperial College London - Inaugural Report - January 2003 1 Contents Summary..................................................................................................................... 3 1. Background and Objectives .................................................................................... 4 1.1 Background ....................................................................................................... 4 1.2 Objectives of the Centre for Bioinformatics ....................................................... 4 1.3 Objectives of the Bioinformatics Support Service.............................................. 5 1.4 Historical Notes ................................................................................................. 5 2. Management ........................................................................................................... 6 3. Biographies of the Team......................................................................................... 7 4. Bioinformatics Research at Imperial ....................................................................... 8 4.1 Affiliates of the Centre ....................................................................................... 8 4.2 Research Grants -
Centre for Bioinformatics Imperial College London Second Report 31
Centre for Bioinformatics Imperial College London Second Report 31 May 2004 Centre Director: Prof Michael Sternberg www.imperial.ac.uk/bioinformatics [email protected] Support Service Head: Dr Sarah Butcher www.codon.bioinformatics.ic.ac.uk [email protected] Centre for Bioinformatics - Imperial College London - Second Report - May 2004 1 Contents Summary..................................................................................................................... 3 1. Background and Objectives .................................................................................. 4 1.1 Objectives of the Report........................................................................................ 4 1.2 Background........................................................................................................... 4 1.3 Objectives of the Centre for Bioinformatics........................................................... 5 1.4 Objectives of the Bioinformatics Support Service ................................................. 5 2. Management ......................................................................................................... 6 3. Biographies of the Team....................................................................................... 7 4. Bioinformatics Research at Imperial ..................................................................... 8 4.1 Affiliates of the Centre........................................................................................... 8 4.2 Research.............................................................................................................. -
Physiologynews
PHYSIOLOGYNEWS winter 2005 | number 61 Meetings UCL Images of Oxford Bristol revisited Also featuring: Physiology in space Richard Naftalin’s ‘desert island’ selection Cutting through the melatonin hype Reflections of a ex-Chair Letter from Russia What turned us on to physiology Winter books special A publication of The Physiological Society OXFORD FOCUSED MEETING Ion channels, genes and regulation in smooth muscle 5-7 September 2005 More photos and a report from the Oxford Focused Meeting appear on p. 5 (photos by Prem Kumar and Roger Thomas) PHYSIOLOGYNEWS Editorial 3 Movement neuroscience at UCL Philip Harrison 4 Ion channels, genes and regulation in smooth The Society’s dog. ‘Rudolf Magnus gave muscle David Beech, Anant Parekh, Phil Aaronson 5 me to Charles Sherrington, who gave me ‘Stan-power’ 7 to Henry Dale, who gave me to the Judy Harris Physiological Society in October 1942’ Bristol revisited Austin Elliott 8 My 10 key papers 10 My top 10 papers on biological salt, water and sugar transport Published quarterly by the Physiological Society Richard Naftalin Contributions and Queries Executive Editor A week in the life of... 14 Linda Rimmer A short month in the life of the Vice Chair Ian McGrath The Physiological Society Publications Office P.O. Box 502 What turned me on to physiology? Thelma Lovick, 15 Cambridge CB1 0AL UK Bill Winlow, Austin Elliott Tel: +44 (0)1223 400180 Letter from...Russia Evgeny Nikolsky, Ellya Bukharaeva 17 Fax: +44 (0)1223 246858 Email: [email protected] The Society web server: http://www.physoc.org Physiology