pdfMRC NIMR Annual Report - The Francis Crick Institute
Transcription
pdfMRC NIMR Annual Report - The Francis Crick Institute
2010/2011 Annual Report and Prospectus MRC National Institute for Medical Research Science for health MRC National Institute for Medical Research 2010/2011 Annual Report and Prospectus Edited by: David Wilkinson Designed by: Joe Brock Photography by: Neal Cramphorn & James Brock Production: Christina McGuire & Frank Norman Editorial Assistants: Eileen Clark & Steve Ley © MRC National Institute for Medical Research Enquiries about this report should be addressed to: Assistant Director’s Office tel +44 (0)20 8816 2281 email: [email protected] Further information is available on our website at: http://www.nimr.mrc.ac.uk Copies obtainable from the Librarian at NIMR ISBN-13: 2 MRC National Institute for Medical Research 978-0-9546302-9-4 Contents Director’s foreword Scientific highlights Science overview About the MRC National Institute for Medical Research Recent research highlights NIMR history and milestones Student training and development Careers Technology transfer Public engagement Research groups : A to Z list Infections and Immunity Structural Biology Neurosciences Genetics and Development Emeritus scientists Research facilities A history of chemistry research at NIMR In memoriam Scientific seminars Staff honours Scientific committees PhD theses awarded Current funding sources Bibliography NIMROD social club Map, location and travel 4 8 10 12 13 14 16 20 26 28 32 34 61 76 90 103 105 130 134 135 136 137 138 139 140 154 156 MRC National Institute for Medical Research 3 Director’s foreword This has been another eventful year for NIMR, with more excellent science (see Scientific Highlights, page 8), honours for current and former members of staff, a new arrival, some farewells, and the usual rounds of meetings and new initiatives. Institutions often lay tenuous claim to Nobel Prize winners, but NIMR took justified and particular pleasure in the award to Bob Edwards of the 2010 Nobel Prize in Physiology or Medicine. Bob Edwards worked at NIMR from 1958 to 1962, during which time his interests moved from pure science to biomedicine, and a desire to do something about human infertility. His studies on induced ovulation and superovulation in mice presaged his work with Patrick Steptoe in which they applied such approaches to humans, thus bringing about the revolution in in vitro fertilisation. Four million people have been born through IVF, including my eight-year-old twins. I and many others have great cause to be thankful to him. Bob Edwards Iain Robinson Some of our present and recently retired scientists have also received recognition. In particular, we were delighted that former interim Director Iain Robinson was made an MBE and that Jean-Paul Vincent was elected to the Fellowship of the Academy of Medical Sciences. In addition, Robin Lovell-Badge was awarded the Waddington Medal of the British Society for Developmental Biology and Alex Gould the Hooke Medal of the British Society for Cell Biology. It is very gratifying that NIMR scientists received this recognition from two of our national societies. And of course, NIMR joined other MRC scientists in welcoming Sir John Savill as our new Chief Executive Officer. Sir John took up his post in October, 2010. Arrivals and Departures We were joined this year by Mark Wilson, a new Programme Leader Track. Mark comes from Thomas Wynn’s lab at the National Institute of Allergy and Infectious Diseases, Bethesda, Maryland. His work, in the Division of Molecular Immunology, investigates the mechanisms by which the immune system responds to parasitic helminth infections and allergens. As we welcomed Mark, we said farewell to Dimitris Kioussis, former Head of the Division of Molecular Immunology, and to other Programme Leaders including Sebastien Gagneux (who retains close contact with the Division of Mycobacterial Research as a visiting worker), Elaine Davis, Matthew Hannah and Nobue Itasaki. Former NIMR scientists Milan Nermut, James Porterfield, Henry Rogers, Bob Rosenberger and Don Williamson all died last year or at the end of 2009, as did Jashu Mistry, Janey Antoniou, Herbert Rose and Les Rowell. We send our condolences to their families. Mark Wilson 4 MRC National Institute for Medical Research Facilities Last year I reported that we had taken order of an Illumina GAIIx sequencing machine, and this now forms the core of our new high-throughput sequencing facility. Abdul Sesay and his colleagues are already producing large amounts of valuable data, and our capacity will soon increase further, with the impending receipt of a HiSeq 2000 sequencing system. In addition, our new Orbitrap mass spectrometer has been installed and we anticipate that this will make a huge difference to our analyses of protein structure and function. Finally, a real landmark in the life of our Bioflo 5000 fermentor: its 500th run. Since its installation 13 years ago it has cultured over 30,000 litres of cells for the Institute’s scientists. Thanks to Brian Trinnaman and everyone in his team. Meetings and events May 5 2010 marked the sixtieth anniversary of the official opening of the new site at Mill Hill by King George VI and Queen Elizabeth, and the Institute celebrated by hosting an MRC Council meeting and by organising talks and a reception. Members of Council recreated a group photograph of their predecessors taken almost exactly 60 years previously. MRC Council visit 16 June 1950 MRC Council visit 5 May 2010 The same month saw the inaugural Medawar Lecture, where the PhD students chose and hosted the speaker. This first lecture was by Tom Jessell from Columbia University, who gave a beautiful talk on ‘Measured Motion: The Neurons and Networks of Spinal Motor Control’. We thank Fatima Sulaiman and all the NIMR students for organising the seminar and hosting Tom so well. The lecture was, of course, named after one of NIMR’s most distinguished Directors, Nobel Laureate Sir Peter Medawar, OM, CBE, FRS. We were delighted that Sir Peter’s daughter, Dr Caroline Garland, came to the lecture. The Institute organises many symposia and meetings, but noteworthy amongst these last year was one that celebrated the life and work of John Eccleston. Several members of the Institute spoke at the meeting, as did John’s friend and colleague Dave Jameson, from the University of Hawaii at Manoa. UKCMRI Plans for our new home at the UK Centre for Medical Research and Innovation are proceeding well at every level: 2010 has been a wonderful year for the project. I reported last year that the then Prime Minister, Gordon Brown, had visited the UKCMRI offices at the Wellcome Trust to announce his Government’s support for the project. Since then, and as part of the Spending Review, David Cameron, the Prime Minister and George Osborne, the Chancellor, have also pledged support for the project, and we MRC National Institute for Medical Research 5 are gaining in confidence that the money really will be there to fund the Institute. Certainly, the founding partners - the Medical Research Council, Cancer Research UK, the Wellcome Trust and University College London - are keen to press ahead, and a real achievement was the signing of the Joint Venture Agreement that allows the four parties (subject to agreement of the Charity Commission) to set up UKCMRI as a charitable foundation. Signing took place in the presence of David Willetts MP, Minister for Universities and Science, and Lord Howe, Health Minister. The signing of the joint venture agreement The year has seen great advances in the design of the UKCMRI building. Externally, architects PLP and HOK have produced significant changes that have responded to comments from the scientific community, from local people, from Camden Council and from bodies such as the Commission for Architecture and the Built Environment. As a result, the height of the building has been reduced, with about one-third now below ground, the roof has been changed to a curved form to reduce the effect on local views, and a north-south atrium has been introduced to give the building a more open feel. Inside the building there is an elegant state-of-the art lecture theatre, and all aspects of the design are intended to encourage interactions between UKCMRI scientists. Computer generated images of the proposed building for UKCMRI In addition to these structural changes, we have now included a community facility in the building, the public entrance has been lowered to improve access, and a new east-west route passes between UKCMRI and the British Library. These changes have resulted in a superb building that complements Sir Colin Wilson’s British Library building to the south and whose roof echoes the famous Barlow Shed of St Pancras, to the east. It was this design that was submitted to Camden Council for planning permission in September, and we were very pleased that the Camden Development Control Committee gave their 6 MRC National Institute for Medical Research consent at its meeting on 16th December. Final approval is subject to completion of a ‘Section 106’ agreement, which amongst other things provides support for local services and infrastructure, and to the agreement of the Mayor of London. While this work was under way, members of the UKCMRI team have been examining tenders for the first stage of the two-stage construction process. A decision should be made early in 2011, and construction should begin in the spring. As for the science to be carried out at UKCMRI, the fruits of the deliberations of the Scientific Planning Committee were published in abridged form in a UKCMRI Scientific Vision document that is available from the UKCMRI web site (www.ukcmri. ac.uk) Sir Paul Nurse Director and Chief Executive of UKCMRI UKCMRI Scientific Vision document And as many will know, the science will be carried out under the direction of Sir Paul Nurse, who was appointed Director and Chief Executive of UKCMRI in July 2010. Everyone knows Paul: Nobel Laureate; until recently President of Rockefeller University; President of the Royal Society; and named recently by the Times Eureka supplement as the most influential scientist in the UK. We are delighted that Paul has accepted the position of UKCMRI Director, and we look forward to working with him in the future. MRC National Institute for Medical Research 7 Scientific highlights It is always hard to select individual research highlights for a particular year, and for 2010 it was particularly difficult. One or two achievements from each of the four main scientific areas of NIMR are highlighted here. NIMR has always had great strengths in infectious disease, and one of the most important results of the year came from Anne O’Garra’s group, which has used microarray analysis to identify a unique pattern of gene activity in the blood of patients with active tuberculosis (TB). This ‘immune signature’ is not seen in the blood of people with other infections and it disappears when people are successfully treated with drugs. Intriguingly, the signature is also observed in some 10–20% of patients with latent TB, who are infected with Mycobacterium tuberculosis but are asymptomatic. This raises the exciting possibility that the immune signature will predict which patients will go on to develop the active disease. The Plasmodium species that cause malaria, and Toxoplasma gondii, the causative agent of toxoplasmosis, both replicate within the safe environment of host cells. Mike Blackman has been studying how these parasites invade the host cells, and he and his colleagues have found that the process that drives invasion simultaneously induces replication. Thus, cleavage of a protein called AMA1 by the membrane protease Rhomboid 4 releases both an extracellular domain that is required for invasion and an intracellular domain that provides a signal for the invading parasite to begin replication inside the host cell. The work provides new routes to combat this group of parasites. Expression of a dominant negative ROM4 results in arrest of parasites late in the cell cycle. Montage showing the transient formation of a muscarinic receptor dimer. In immunology it is known that CD4 helper and CD8 killer T cells both derive from common precursor cells, and that the decision to become one or the other depends on signalling through the T cell receptor (TCR). Ben Seddon has shown that Zap70, a protein essential for TCR signalling, is up-regulated during development so as to create a temporal gradient of TCR signalling activity. This, together with use of an inducible Zap70 transgenic model, has allowed him to deduce that the two lineages develop at different times and at different thresholds of TCR signalling. A similar phenomenon occurs in the development of the neural tube, where James Briscoe has shown that the duration of Sonic Hedgehog signalling specifies different cell types in the neural tube. And Sonic Hedgehog does not only specifiy different differentiated cell types. With Robin Lovell-Badge, James Briscoe has shown that it also helps induce and maintain neural stem cells. It does this by activating the expression of Sox9, which can convert early neuroepithelial cells into neural stem cells. Manipulation of the stem cell state may assist efforts to relieve degenerative diseases such as Alzheimer’s, or to treat brain tumours derived from the unregulated growth of neural stem cells. The treatment of neurodegenerative disorders will require an understanding of how to drive neural differentiation along the appropriate pathways, and work in David Wilkinson’s group has shown how the inhibitory mechanisms that maintain the progenitor cell state are relieved to allow differentiation to proceed. The process involves a positive feedback loop between several genes. Genetic 8 MRC National Institute for Medical Research regulatory networks of this sort are key to many developmental processes, and indeed these observations may also shed light on processes such as spermatogenesis. NIMR has a long history of work on sex determination and differentiation. Groups led by James Turner and Paul Burgoyne have investigated the phenomenon of meiotic sex chromosome inactivation (MSCI), in which the X and Y-chromosomes, because they do not pair during meiosis, fail to be transcribed. The two teams made use of the XYY mouse, which has two copies of the Y chromosome, rather than one, and the two copies do pair during meiosis. This pairing prevented the Y-chromosomes from undergoing MSCI. Interestingly, the resulting continual expression of Y chromosomal genes triggered a complete arrest in spermatogenesis, specifically during meiosis. The group went on to demonstrate that the cause of this germ cell arrest could be narrowed down to the expression of a specific gene on the Y chromosome called Zfy1/2. Studies of development require sophisticated imaging technologies to allow one to follow cell behaviour in the embryo in real time. Different sorts of imaging underlie work by Nigel Birdsall and Justin Molloy, who have used total internal reflection fluorescence microscopy to visualise individual molecules of the M1 muscarinic acetylcholine receptor, a G-protein-coupled receptor (GPCR). By tracking the positions of individual receptors on the membrane surface in real time, their work resolved the question of whether this GPCR exists as a monomer or a constitutive dimer. The experiments show that there is rapid conversion between monomers and dimers, such that at any given time about 20-30% of the receptors are present as dimers. And at even higher magnification, Peter Rosenthal’s group has used electron cryotomography to determine the structural organisation of filamentous influenza A virus. The remarkable new images provide an understanding of how the virus assembles itself, and may suggest new targets for drugs, and the technique offers the opportunity for new ways of looking at cells important to understanding a variety of diseases. Berry MPR, Graham CM, McNab FW, Xu Z, Bloch SAA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, Quinn C, Blankenship D, Dhawan R, Cush JJ, Mejias A, Ramilo O, Kon OM, Pascual V, Banchereau J, Chaussabel D and O’Garra A (2010) An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466:973-977 Santos JM, Ferguson DJP, Blackman MJ and Soldati-Favre D (2011) Intramembrane cleavage of AMA1 triggers Toxoplasma to switch from an invasive to a replicative mode. Science 331:473-477 Saini M, Sinclair C, Marshall D, Tolaini M, Sakaguchi S and Seddon B (2010) Regulation of Zap70 expression during thymocyte development enables temporal separation of CD4 and CD8 repertoire selection at different signaling thresholds. Science Signaling 3:ra23 Scott CE, Wynn SL, Sesay A, Cruz C, Cheung M, Gaviro M-VG, Booth S, Gao B, Cheah KSE, Lovell-Badge R and Briscoe J (2010) SOX9 induces and maintains neural stem cells. Nature Neuroscience 13:1181–1189 Sobieszczuk DF, Poliakov A, Xu Q and Wilkinson DG (2010) A feedback loop mediated by degradation of an inhibitor is required to initiate neuronal differentiation. Genes & Development 24:206-218 Royo H, Polikiewicz G, Mahadevaiah SK, Prosser H, Mitchell M, Bradley A, de Rooij DG, Burgoyne PS and Turner JMA (2010) Evidence that meiotic sex chromosome inactivation is essential for male fertility. Current Biology 20:2117-23 Cells expressing the adaptor protein Btbd6a. Hern JA, Baig AH, Mashanov GI, Birdsall B, Corrie JET, Lazareno S, Molloy JE and Birdsall NJM (2010) Formation and dissociation of M1 muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules. Proceedings of the National Academy of Sciences of the United States of America 107:2693-2698 Calder LJ, Wasilewski S, Berriman JA and Rosenthal PB (2010) Structural organization of a filamentous influenza A virus. Proceedings of the National Academy of Sciences of the United States of America 107:10685-10690 MRC National Institute for Medical Research 9 Science overview Research programmes at NIMR Research at NIMR is focused on four scientific areas: Infections and Immunity, Genetics and Development, Neurosciences and Structural Biology. There are many cross-disciplinary collaborations that underpin progress in these areas, for example on the structure and function of molecules involved in infectious diseases, common mechanisms of nervous system and immune system development, and how the functioning of the brain arises during embryonic development. Infections and Immunity The immune system is a key part of the body’s defence against infections. Its importance is illustrated by the effects of a defective immune system, as seen in people with AIDS, which results in overwhelming infections leading to death. While an effective immune system is vital for health, an over-exuberant immune system can start to attack the body itself, a process known as autoimmunity. Autoimmunity is the cause of allergies such as hay fever and more serious conditions such as asthma, rheumatoid arthritis, and multiple sclerosis. We are analysing how the cells of the immune system are triggered to mount an immune response when faced with an infectious agent, how the process can go awry in autoimmunity, and how complex checks and balances in the system ensure activation of the immune system only when needed. Infectious diseases result from the transmission of pathogenic micro-organisms. Examples studied at NIMR include malaria, tuberculosis, AIDS and influenza which are responsible for the deaths of millions of people every year. This death toll is exerted mainly in the poorer countries of the world, and is also a significant and increasing burden for the National Health Service. Our research seeks to understand the fundamental biology of the causative micro-organisms and their interaction with hosts. We use this understanding to promote the development of new drugs, vaccines and diagnostic reagents. The study of pathogenic agents is also a rich source of important information on basic mechanisms of cell and molecular biology. Genetics and Development Understanding how a fertilised egg generates a functional organism is an important area of biology that has many implications for medicine. We are studying the fundamental mechanisms that underlie embryo development, including how cells proliferate, migrate and communicate, how stem cells form and are maintained, and how diverse cell types are generated, each at the correct location in the forming organism. A major focus is on identifying the underlying genes, how they function and are regulated, and their role in networks of molecular and cellular interactions that control developmental processes. These studies include the use of powerful genome-wide techniques and systems biology approaches in order to uncover gene regulatory networks. Much of our work focuses on the development of specific tissues such as the nervous system, heart, liver, gonads and limbs. As many of the genes that control specific processes are conserved between species, our studies are carried out in a range of model organisms that have distinct strengths for uncovering mechanisms of normal development and how defects can arise. Since many of the same processes and underlying molecular pathways are utilised in the adult, studies of development also reveal the basis of disorders such as cancer in which the proliferation and migration of cells is abnormal. In addition, elucidation of the normal mechanisms that maintain stem cells and that direct them to form specific cell types is essential for potential therapeutic use of these cells. 10 MRC National Institute for Medical Research Neurosciences The nervous system carries out many crucial physiological processes, including the perception of the external environment, control of movement of the organism, formation of memories, and the hormonal regulation of tissue growth and homeostasis. Understanding how the nervous system forms and functions is an important challenge in biology with significant implications for the pathogenesis and diagnosis of neurological diseases and development of therapies. We are studying how neural stem cells are maintained and differentiate to generate the multitude of neuronal subtypes found in the central and peripheral nervous system. An important aspect of our work is understanding how neurons migrate to their appropriate destination and how they find their targets to form functional neuronal circuits during development. We are analysing how the wiring, differentiation, specification and activity patterns of neurons underlies the processing of sensory information and integrates it to achieve appropriate outputs. We are also analysing how the hypothalamic neuroendocrine system controls the function of the pituitary gland. We use high resolution methods to visualise the processes controlling secretion from neuroendocrine, endocrine and endothelial cells, leading to different patterns of protein secretion in the bloodstream. These studies take place in close collaboration with developmental biologists who are exploring the molecular and cellular basis of organogenesis and body patterning. We also have fruitful collaborations with clinical colleagues to understand the genetic and developmental processes that lead to defects in the central and the peripheral nervous system. Structural Biology Biological systems consist of large molecules such as proteins and DNA, and small molecules that act as substrates and signals to drive and control cellular processes. Understanding of the molecular basis of biological processes requires analysis at the level of the structure and interactions of individual molecules. We study the three-dimensional structures and chemical reactions that underlie the functions of a range of biologically active and medically important molecules. We use theoretical approaches that enable us to model molecular structures from gene sequences and generate predictive models about the dynamics of molecular interactions. Structural methods include X-ray crystallography, electron cryo-microscopy and NMR spectroscopy that yield high resolution information. This is complemented by a diversity of biophysical and biochemical approaches, single molecule methods and synthetic organic chemistry that enable analysis of molecular interactions both in vitro and within living cells. Our work covers a diversity of biology systems and is highly collaborative, for example with teams at NIMR who are studying infectious diseases and fundamental cellular mechanisms. MRC National Institute for Medical Research 11 About the MRC National Institute for Medical Research The MRC National Institute for Medical Research (NIMR) is one of the world’s leading medical research institutes. It is dedicated to studying important questions about the life processes that are relevant to all aspects of health. NIMR is the largest of the Medical Research Council’s institutes. NIMR’s mission is: • to carry out innovative, high-quality, biomedical research • to be a major contributor to the MRC’s commitments in the training of scientists • technology transfer • the presentation of its science to the public Research at NIMR covers a broad spectrum of basic biomedical science, including infectious diseases, immunology, cell and developmental biology, neuroscience and structural biology. The world-class facilities for research include biological imaging resources, the MRC Biomedical NMR Centre and the UK’s largest academic facility for small animal research. There is a major emphasis on cross-disciplinary interactions, stemming from the pervasive culture of collaboration and strategic recruitment to complement and bridge scientific areas. There are research collaborations with many other academic and clinical centres in the UK and internationally, including strong links with University College London. Scientists at NIMR study normal biological processes and diseases at the molecular, cellular and whole organism level. The specific research topics include: How do new influenza epidemics occur? How does the immune system fight infection? How can we cure infectious diseases such as influenza, tuberculosis and malaria? How do tissues such as the heart, liver, limbs and nervous system form? How are stem cells normally regulated? How is male-specific development controlled? How does the nervous system become wired correctly? How can we diagnose and cure genetic diseases? How do hormones control body growth? How is cell division accomplished? How do muscles generate force? How do molecules mediate cell signalling? 12 MRC National Institute for Medical Research Winners of the 2010 Travel Prize - John Ewbank, Immunoregulation (left) and Steven Moore, Developmental Neurobiology (right), pictured with with the Director, Jim Smith. Recent research highlights 2010 • • • • • • • • Immune signature for tuberculosis (Anne O´Garra and Robert Wilkinson) Parasite invasion and replication (Mike Blackman) Zap70 creates a temporal gradient in T-cell lineage development (Ben Seddon) Role of Sox9 in neural stem cell induction and maintenance (Robin Lovell-Badge and James Briscoe) Initiation of neuronal differentiation (David Wilkinson) Meiotic sex chromosome inactivation is essential for male fertility (Paul Burgoyne and James Turner) Formation and dissociation of muscarinic receptor dimers (Nigel Birdsall and Justin Molloy) Electron cryomicroscopy of influenza virus (Peter Rosenthal) 2009 • • Depletion of activated CD4+T cells (George Kassiotis and Dimitris Kioussis) Structural organisation of Weibel-Palade bodies (Tom Carter, Matthew Hannah and Peter Rosenthal) Structure of Nbs1 protein (Steve Smerdon) Morphogen gradients not needed for proliferation (Jean-Paul Vincent) Evolution of vertebrate limbs (Malcolm Logan) • • • 2008 • • • • • Neurogenin2 controls neuronal migration (François Guillemot) A transcription factor linking environmental toxins to autoimmunity (Gitta Stockinger) The adult pituitary gland contains stem/progenitor cells (Iain Robinson and Robin Lovell-Badge) Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants (Steve Gamblin, Alan Hay and John Skehel) Timer genes control brain size (Alex Gould) 2007 • • • • A novel mechanism for reading the concentration of a signal – a clue to embryonic development (James Briscoe) Discovery of malaria parasite escape technique leads to new drug target (Mike Blackman) AAMPK enzyme structure offers hope of effective diabetes treatment (Steve Gamblin) Fruit fly’s fatty secrets shed light on liver disease (Alex Gould) 2006 • • • Structural changes reveal bird flu pandemic potential (Alan Hay, Steve Gamblin and John Skehel) The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design (Alan Hay, Steve Gamblin and John Skehel) TGFß supports de novo differentiation of IL-17-producing T cells (Gita Stockinger) 2005 Development of mouse model for human Down syndrome (Victor Tybulewicz) • MRC National Institute for Medical Research 13 NIMR history and milestones 1933 Discovery of flu virus Christopher Andrewes, Patrick Laidlaw and Wilson Smith first isolated the human influenza virus. 1957 Interferon 1951 Steroid biosynthesis John Cornforth 1940 1950 1952 Gas chromatography After receiving the Nobel Prize in 1950 for his earlier discovery of partition chromatography, Archer Martin joined NIMR and with A.T James he developed gas chromatography, a technique now widely used in laboratories and the chemical industry. 1936 The role of acetylcholine as a neurotransmitter Henry Dale established the chemical basis of neurotransmission and the role of acetylcholine as a neurotransmitter, receiving the Nobel prize for this work in 1936. 14 MRC National Institute for Medical Research John Skehel revealed the structure of influenza virus proteins involved in the infection of cells, for which he was awarded the Louis-Jeantet Prize for Medicine in 1988. This work opened new perspectives for the design of antiviral drugs. 1960s Cryobiology Audrey Smith discovered how to store biological material at low temperature, pioneering techniques for the freezing of sperm, blood, bone marrow, corneas and many other tissues. completed the first total synthesis of the non-aromatic steroids and identified the chemical structure of cholesterol. He received the Nobel prize in 1975. 1930 1981 Structure of influenza haemagglutinin Alick Isaacs discovered interferon, a factor that can transfer a virus-resistant state to cells that had not been infected, and is now used to treat many infections and cancers. 1960 1970 1986 Globin locus control region Frank Grosveld discovered regulatory sequences that govern expression of the globin gene cluster, and that confer a copy number dependent level of transgenic gene expression. He was awarded the Louis-Jeantet Prize for Medicine in 1991. 1980 1973 Long-term potentiation Tim Bliss and Terje Lømo discovered the phenomenon of synaptic long-term potentiation, one of the main mechanisms by which the brain learns and remembers. 1958 Immunoglobulin structure Rodney Porter was given the Nobel Prize in 1972 for the discovery of the structure of immunoglobulins. The work increased understanding of the immune system and led to novel approaches to diagnosis and therapy. 1989 Hox gene colinearity Robb Krumlauf showed that the linear relationship between the organisation of Hox genes along the chromosome and their expression along the head-to-tail axis is conserved in vertebrates. 1993 Mesoderm-inducing factor 2005 Mouse model of Down syndrome Jim Smith discovered that activin is a mesoderm-inducing factor, opening up understanding of how signalling factors control the formation of tissues during embryo development. Victor Tybulewicz created a genetically manipulated mouse that carries almost all of human chromosome 21. The resulting strain of mice has become a valuable tool in research on Down syndrome. 2010 Transcriptome signature in human tuberculosis Anne O’Garra discovered a novel transcriptomic signature that provides insights into fundamental pathogenesis of tuberculosis and has application to the development of improved diagnostic tools. 1996 Discovery of the anterior organising centre 2007 AMP-activated protein kinase (AMPK) structure Rosa Beddington discovered a novel signalling centre in the mouse embryo required for correct formation of the head-to-tail axis during embryonic development. Steve Gamblin determined the structure of the enzyme that regulates cellular energy levels, AMPK. The discovery paves the way for better treatments of type II diabetes. 1990 2000 2010 1999 Eph receptors mediate cell segregation 2007 Malaria release mechanism David Wilkinson uncovered a new mechanism that maintains the correct organisation of tissues, mediated by signalling through Eph receptors and ephrins. Mike Blackman identified an enzyme that triggers release of the malaria parasite from infected red blood cells thereby enabling it to invade new cells. The enzyme is a new target for improved anti-malarial drug design. 1991 The sex determining gene Robin Lovell-Badge showed that the presence of the Sry gene on the Y chromosome is sufficient to cause the embryonic gonad to develop as testis rather than ovary. He received the Louis-Jeantet Prize for Medicine in 1995. 2006 Discovery of Th17 subset Gitta Stockinger defined the developmental steps that lead to the Th17 immune response. Th17 cells are important in the pathogenesis of many autoimmune diseases. MRC National Institute for Medical Research 15 STUDENT TRAINING AND DEVELOPMENT PhD studentships Student training and development The training and development of future leaders in biomedical research is one of the Institute’s key goals and we strive to achieve this by giving school students, undergraduates and graduates the opportunity to work and study at NIMR. PhD Programme Our PhD students have the opportunity to conduct their research projects in an environment where state-of-the-art facilities and an extensive range of expertise are available to all. One of the Institute’s major strengths is the interaction between scientists in all four main areas of research. Many of these interactions lead to new and exciting collaborations which our students are often a part of, thereby broadening their general understanding of science and practical expertise. There are 80 PhD students at NIMR at any one Donna Brown time, representing 14% of researchers and contributing significantly Director of Studies towards the Institute’s research output as indicated by their publication rate - 62% of students who have completed three years of research have published at least once. In addition to their supervisor, each student is allocated a thesis committee to ensure they receive all of the support and guidance they need for the duration of their PhD. Supervisors are not distracted by heavy teaching loads, as there is no undergraduate teaching at the Institute. Also on hand are the Director of Studies, Student Administrator and the Student Representatives. The significance of this level of support is reflected in the four-year submission rates which are higher than many universities, this year standing at 86%. We believe in a good work-life balance and we want our students to remember there is a world outside of the lab, so onsite you can find a licensed bar, restaurant, games room and television room. In addition there are many social activities and sports teams organised through the NIMR social club. The Institute also has three onsite student cottages which can house up to 12 students, making the commute to work virtually non-existent. One of our aims over the last academic year was to improve our training programme which we achieved through delivery of career development sessions, a methods and techniques study programme and microscopy and bioinformatics courses. Over the next year we plan to develop our training programme further still and run a four-year PhD programme which will help increase students’ skills sets, independence, publication rates and ultimately employability. The 2010 travel prize Each year NIMR awards a £1000 travel prize for the best upgrade report. This year judges split the prize between two students who wrote equally excellent upgrade reports: • Steven Moore (Developmental Neurobiology) for ‘Comparative Genomic Analysis of Pax3 and Pax7 Regulation’ • John Ewbank (Immunoregulation) for ‘An analysis of the effect of strain variation on the interactions of Mycobacteria with the immune system, and the role of type I interferon in the outcome of infection’. The prizes were awarded by Jim Smith at the student barbecue in August (see photo page 12). 16 MRC National Institute for Medical Research STUDENT TRAINING AND DEVELOPMENT Student representatives There is a strong sense of community amongst the students at NIMR. This actively encourages collaboration between different Divisions allowing students to take up multi-disciplinary projects. Regular student seminars allow them to present work without the pressure of supervisors or colleagues from their Division being present. With regular student socials and sporting activities, it is easy to meet and make new friends. With an intake of around 25 new students each year, the student body is an integral part of NIMR and student representatives aim to maintain the high standard of communication between staff and students. This is achieved by holding regular meetings with students and representing them on various committees both within NIMR and at UCL so that their opinions can be voiced. The 2010 student representatives Christina Untersperger, Sorrel Bickley and Lizzi Underwood The 2010 intake of PhD students MRC National Institute for Medical Research 17 STUDENT TRAINING AND DEVELOPMENT PhD students 2010 - in their own words John Ewbank “I started my PhD at NIMR almost three years ago, studying the innate immune response to Mycobacterium tuberculosis. NIMR is a great place to do a PhD. A key reason is the social and collaborative atmosphere of the Institute - everyone is very friendly and it is easy to wander into any lab and ask for help and advice. My own project is a collaboration between two Divisions; Immunoregulation and Mycobacterial Research. Collaborations are helped by the onsite bar, as well as sporting activities, such as a football league. I’ve also found the student study programme very enjoyable - there are various lecture series given by senior academics, as well as student seminars, where students present their work. This has enabled me to hear talks on subjects totally different to my own project - from protein structure to neurobiology. As students we are also encouraged (and funded) to attend conferences; I will be presenting my results in a Keystone meeting in Vancouver next year. It’s been a great experience and I’ll be sorry to leave NIMR.” Andrea Ruecker “I am a second year PhD student at NIMR. I was always fascinated with biology, nature and how to preserve the environment. I decided to study biology focusing on general biology but quite quickly became interested in malaria. After a three-month job in Tanzania, and suffering from malaria myself, I wanted to know more about the disease and why it is so difficult to develop drugs and vaccines against it. I completed my BSc at the University of Marburg, with a nine month undergraduate project in malaria research. I then went to the Liverpool School of Tropical Medicine to complete a Masters in Molecular Biology of Parasites and Disease Vectors where I learned about other parasitic diseases. I continued to work on malaria during my Masters project and decided to stay in malaria research. I had heard about NIMR - the Division of Parasitology is highly regarded in the field of malaria research - and I was very excited to apply for a PhD project at NIMR. Visiting the Institute for my interview I found the people that work here appeared very friendly and I was very happy when I got my PhD offer. My project in Mike Blackman’s laboratory is based around a putative malarial protease which is essential for the survival of the malarial parasite, Plasmodium falciparum. One year into my PhD I can say that NIMR is an outstanding research environment and I love to come into work in the morning. I couldn’t have had a better start in our lab and I am really looking forward to the next two years and what they will bring. It is always scary to start work at a new place but the people in the Institute and our lab make it very easy to feel comfortable to work and enjoy my time as a PhD student.” 18 MRC National Institute for Medical Research STUDENT TRAINING AND DEVELOPMENT Sandwich placements and work experience Sandwich placements There is no better way to put the lab skills learned in the first few years of your university degree into practice than to spend up to 12 months working in one of the NIMR labs. As you will see from the testimonials below, Sandwich students come to the Institute because of the diversity of science and to get a better feel of whether research is really for them. Many of our Sandwich students go on to do a PhD at NIMR and other leading research institutes. Sandwich students-in their own words The 2010 intake of sandwich students Leslie Southerden “While studying for my undergraduate degree at the University of Surrey, I applied to NIMR for my Sandwich year because of its excellent reputation for world-class research. I spent a year in the Division of Physical Biochemistry and found the collaboration between research groups particularly useful. In the Webb Lab I had my own research project for the year, investigating the interactions of fluorescently labeled single-stranded DNA binding proteins with single-stranded DNA. During the year I gained practical experience in a wide range of research techniques and also gained an insight into the demands of a research career. I found the learning experience of overcoming challenges very rewarding. Following my year at NIMR I am now keen to pursue a career as a research scientist, the next stage being a PhD. Having enjoyed my year so much, it is my hope to return to the Institute for a PhD studentship within Structural Biology.” Lih Ling Yee “At the point of applying for a Sandwich placement I was determined to look for an opportunity to work in an academic environment which would be creative and dynamic. This was indeed what I saw at NIMR. I joined Dr Alex Gould’s research team, under the supervision of Dr Rita Sousa-Nunes, on the regulation of Drosophila neural stem cells quiescence. From the start to the end, it was an amazing experience. I learnt different experimental techniques as well as scientific writing skills. It was hard work, but it definitely paid off. And the good thing is, it didn’t put me off science. I would like to keep my mind open in terms of future plans. At the moment, I am looking for a PhD position in clinical neuroscience and am also considering a job as a research assistant.” Work experience for school students At the Institute we believe in encouraging students from an early age and each year students from local schools work alongside our researchers for periods of up to four weeks (also see Research Summer School p28). Many of these students come back in subsequent years and apply to our Sandwich placements and PhD studentships. Over the course of the next year we are looking to revise our work experience programme with the aim of improving the student experience and providing the opportunity for students in the local area to discover what it is like to work in science. MRC National Institute for Medical Research 19 CAREERS Career development In addition to its role in the training of PhD students, NIMR is a major centre for further research training and career development. It attracts researchers from the UK and across the world due to the breadth and quality of the research, and the emphasis on interactions and cross-disciplinary collaborations. Researchers at all stages of their career development benefit from the very active programme of seminars and internal research meetings, and the availability of courses to learn key scientific and complementary managerial skills. Postdoctoral careers NIMR hosts approximately 220 postdoctoral researchers, supported either by MRC core funding or externally-funded fellowships. The MRC support promotes careers at the postdoctoral level through fixed-term MRC Career Development Fellowships, and for more experienced researchers by open-ended Investigator Scientist positions. NIMR also has an important role in providing research training for clinical scientists, and this is an important facilitator of translational projects and national and international collaborations. M.B. Ph.D. students are hosted at NIMR through the UCL Programme. In addition, there are many visiting postdoctoral clinical scientists from the UK and abroad carrying out research, for example on infectious diseases and genetic disorders. Martin Levesque Division of Developmental Neurobiology “For my second postdoc, I chose to come here from Canada because of NIMR’s excellent international reputation in developmental biology. Over the past two years I have enjoyed fruitful collaborations and exchange of ideas with colleagues across the Institute, and exposure to a rich and frequent programme of high calibre external and internal speakers. I also have benefited from access to extensive animal facilities and world-class scientific tools, including OPT, multiphoton microscopy, ChIP-Seq, RNA-Seq to name just a few. Furthermore the MRC offers a wide variety of useful courses, encompassing both scientific and personal development, as such I would highly recommend NIMR as a fantastic and stimulating choice for postdoctoral training.” 20 MRC National Institute for Medical Research CAREERS Harriet Groom Division of Virology “If I am honest, like most postdocs I chose to apply for a position at NIMR not because of the Institute itself but because of the group leader I would be working for, the project I would be working on and the city in which it was located. I intended to move to London after doing my PhD at Cambridge and met my current boss at a conference. When she later advertised a position at NIMR during a seminar I was very interested. Initially I had reservations about working at an Institute (my previous experiences being entirely universitybased), however when I came up for interview, the advantages of working at this particular institute became clear and I decided to accept the position when it was later offered. Since working here all of these advantages have manifest themselves along with some unforeseen ones. The high standard and availability of equipment is especially attractive, allowing you to carry out pretty much any experiment you desire. Most importantly I have found that being surrounded by enthusiastic, helpful scientists makes working here very enjoyable and the opportunity to foster collaborations is always there. It is great to always have an expert down the corridor and sometimes to be that expert!” Mohamed Ismail (Soly) Division of Molecular Structure and Division of Developmental Neurobiology “It is a privilege for any researcher at any stage of their career to experience working at NIMR. The scientific atmosphere is amazing and everyone who works here is more than willing to help. I started working at NIMR almost two years ago and I am still enjoying every moment of it. My project is a collaboration between the Divisions of Developmental Neurobiology and Molecular Structure, studying the function and structure of a ubiquitin ligase complex in the early stages of neurogenesis. NIMR strongly supports multidisciplinary projects that increase the scientific interaction between scientists from different Divisions, provides excellent training for postdocs and enhances the possibility of big discoveries. The Institute is equipped with state-of-the-art facilities that make any experiment possible. You learn something new every day at NIMR, through scientific conversations with colleagues, meetings or through the Mill Hill Lectures where world-class scientists are invited to present their work. There are plenty of opportunities to socialise through sport, social gatherings and theatre. It is not surprising that NIMR has an excellent worldwide reputation and is a place where many researchers would love to be.” MRC National Institute for Medical Research 21 CAREERS Career development Career Track appointments Many group leaders have established their laboratory through being appointed to an MRC Career Track position at NIMR. This provides core support for a five year period which, following external review, can lead to promotion to an open-ended MRC Career appointment. Career appointments provide long-term core support, subject to regular scientific review, that enables ambitious research to be carried out. A number of scientists who have established their reputation at NIMR have gone on to head institutes or university departments around the world. The following staff were appointed to Career Track positions. Greg Elgar, Systems Biology - joined NIMR in 2009 “My motivation for coming to NIMR was simple; I wanted to carry out the highest quality interdisciplinary research. This kind of research, often involving longer term projects and more than one researcher, is difficult to sustain purely through grant funding, especially in the current economic climate. It also demands more time and resources than more focused projects and is therefore well suited to a large institute. My particular area of research requires widespread collaboration and regular contact with developmental biologists. The breadth of expertise in this area at NIMR is exceptional and there is almost always someone here who is happy to discuss things over a coffee. There is great support too, which means I can spend all my time doing what I have been recruited to do. I have been here less than a year but I have already learned so much new stuff. It is what makes research so exciting.” Mark Wilson, Molecular Immunology - joined NIMR in 2010 “As with many senior postdoctoral researchers, the looming and often intimidating prospect of establishing an independent research group had to be faced. I was four years into my visiting fellowship at the National Institutes of Health (NIH) in Bethesda, USA when I was informed of the opening at NIMR, better known as Mill Hill. Although having never visited the Institute, it carried with it an immediately recognisable name and reputation for many things, including great research. This was probably influenced by the fact that my PhD supervisor and, at the time head of my division at the NIH, had both trained for several years at Mill Hill. After soliciting their, and other peoples advice I arrived for ‘the interview’. “Is that it! A fenced-in, but rather grand looking building with a strange, and frequently referenced, sea green-ish roof out on the periphery of London”, were some of my earliest thoughts. However, beyond the exterior, as I have now learned, is ‘Mill Hill’. I was welcomed with open arms and within a few weeks felt like I had been here for years. A true triumph for generosity, support and inter-dependence had me up and running within a few months of my arrival back in the UK. I, as anyone would, have benefitted immensely from the close working relationships, certainly within the immunology-related groups, and the open-door policy throughout the Institute. This, I think, is built upon the relative freedom from grant-dependent research and undergraduate teaching; in-depth financial management; extensive human resource skills; common buffer preparation and glass cleaning (all of which are expertly taken care of and for which we are extremely grateful). This is coupled with competent and supportive ‘core facilities’ which has allowed me to establish our research group and start addressing the specific aims of our projects within months of starting. NIMR, so far, has given me a fantastic start. I hope in the future I can give an equal amount back to NIMR and the NIMR community. It isn’t hard to find, but I think I can see and feel some of the ‘Mill Hill’ that I was once told about.” 22 MRC National Institute for Medical Research CAREERS Kate Bishop, Virology - returned to NIMR in 2008 “I had a fantastic time at NIMR as a PhD student. Everyone was very friendly and helpful and it was a great start to my scientific career. I particularly enjoyed the collaborative culture within the Institute and I missed the critical mass when I left to commence postdoctoral work at Kings College London. When I was offered the chance to come back and start my own group six years later, I jumped at the chance. I am enjoying catching up with old acquaintances and working with new friends.” Andreas Wack, Immunoregulation - returned to NIMR in 2008 “I moved back to NIMR after ten years spent in industrial research in Italy. Prior to that, I had done my PhD with Dimitris Kioussis here in the Institute and was glad to come back again. The spirit of collaboration, the fact that you could go to anyone’s office or lab and come up with ideas or ask for advice, was for me one of the best features of NIMR. Ten years later I find this spirit wide awake, carried on by many of the old familiar faces and many new ones. There are fewer differences between industry and academia than most people (in particular in academia) think. You develop scientific questions, plan a sequence of experiments, critically appraise results. The range or depth of questions asked and hypotheses put forward may differ between industry and academia but vary within both areas. The biggest differences are the speed of change and the research group size. In a company, decisions on research direction are often driven by factors outside your control, dictated by changes in the market place, which can be fast. Your favourite research subject may be culled in a board room with little prior notice and no chance to influence the decision. This causes pain but happens less often than one might think, as reasonable companies have a fairly stable long-term strategy and do not follow a research zigzag. When companies throw many people at important projects, there may be up to 50 specialists tackling the same question from different angles. Decision-making becomes complex and often slow, and the degree of identification of research staff with their project is relatively low. The advantage is that the technical expertise brought to the project is very high. Also getting used to presenting data from colleagues and vice versa, handing over your data to others, is an excellent exercise for big egos to be reminded of the team effort. Academia often presents the extreme opposite: one PhD student or postdoc, one project, a very high degree of identification and personal involvement, but a danger that the wheel is frequently reinvented because of a constant loss of expertise through student and postdoc turnover. I think that doing research most efficiently requires a mix between the two approaches: medium size groups of people with different scientific backgrounds sharing in full a project. However, because career and funding depend so much on authorship questions and senior responsibility such an approach can be hard to achieve. The way it worked for me to preserve the possibility of a return to academia was: keep publishing and keep the links to academia. Go to meetings, invite speakers, collaborate. Depending on the company, publishing is actually not so difficult, as intellectual property issues are less of a hurdle and cause less delay than commonly assumed. I for sure am happy to have made the step back from one camp to the other.” MRC National Institute for Medical Research 23 CAREERS Research support careers There are regular opportunities for research technicians and occasional openings for research support managers. Matt Williams - Laboratory Manager, Developmental Neurobiology / Stem Cell Biology and Developmental Genetics / Systems Biology “After some years working as a Postdoctoral Research Associate at Imperial College London I wanted a change in direction, and so I moved into research support working as a Postdoctoral Research Assistant in the Division of Developmental Biology at NIMR. This change allowed me to continue to do exciting research, but also enabled me to provide support to the other researchers in the group by maintaining the lab, keeping it up and running, and ensuring a clean, tidy and safe working environment. Then, back in spring 2008, I became a Laboratory Manager, working with the Divisions of Developmental Neurobiology, Stem Cell Biology and Developmental Genetics, and, latterly, Systems Biology. I was keen to develop my research support role, to assume a position with more responsibility, and to get involved in the organising and management of many aspects of the Institute. My experience has really helped with this position, with the significant level of knowledge and competence I have gained in the lab over the years. Being able to help a large number of researchers with their work is very satisfying, and seeing the benefits of ideas I have implemented has been extremely rewarding.” Rose Gonsalves - Laboratory Manager, Division of Virology “I joined NIMR many years ago as a technician in the WHO Influenza Centre. Ten years later I transferred to a research group, also working on influenza. Although my background was in bacteriology I gradually acquired a great deal of knowledge of virology, particularly practical issues. Then 16 years ago I became the Head Technician for the Division of Virology. I kept strong links to the lab work and even now I carry out some lab duties for one or two scientists, though this has reduced over time. My role, now called Laboratory Manager, is to ensure that the Division runs smoothly, pre-empting problems when possible and “firefighting” when necessary. I also manage the Divisional budgets. I am a problem solver, diagnosing what has gone wrong (e.g. faulty equipment) and fixing it. I enjoy talking to staff in the Division about their research and their plans, and have good interactions with those in other Divisions and with representatives from companies we deal with”. 24 MRC National Institute for Medical Research CAREERS Radma Mahmood - Specialist support manager in Histology “I never imagined myself running a research group after completing my PhD and postdoctoral training, even though I enjoyed research and was well supported and published. But then I never imagined running a core service in histology, which I have now done for ten years in New York and London. During my postdoctoral training, I decided that my future in science should not only use the knowledge I had gained and techniques I had learned, but should also use my personal strengths: my affability, my need for order (standard operating procedures) and my desire to ensure that the people who I work with are continuously learning (if they choose to be) and are thriving happily in a scientific environment. I found that both my skills and my personal strengths have been put to good use at NIMR and previously at the histology service at Albert Einstein College of Medicine in New York. NIMR has given me the freedom to develop the service through refurbishment and the introduction of new technology. The researchers and numerous support staff have been particularly welcoming and willing to give me their time and assistance with all aspects of the service’s expansion which makes the ongoing endeavor both straightforward and enjoyable.” Alan Palmer - Training and Technical Manager, Biological Services “We are committed to ensuring a high standard of training and education for animal technicians and support staff at all stages of their careers. Continuous Professional Development (CPD) for animal technicians at NIMR includes various formal and informal learning, training and experiences: competency based qualifications allow training specific to the individual and their work while Open University and Institute of Animal Technology qualifications deliver a wide knowledge of laboratory animal science and a good background in biological sciences. Technicians are also encouraged to spend time in NIMR research labs in order to gain hands-on experience of experimental procedures, and attend workshops and seminars held on a regular basis on subjects related to laboratory animal science. Visits to other scientific establishments, symposia and international meetings are also organised which enable technicians to gain experience in more varied aspects of laboratory animal husbandry and science.” MRC National Institute for Medical Research 25 SCIENTIFIC FACILITIES Technology transfer Eileen Clark Scientists are skilled in conducting research but are not expected to be experts in research protection and commercial development. NIMR’s dedicated Technology Transfer Liaison officer supports staff by providing mechanisms and structures and encouraging scientists to be alert to potential exploitation opportunities. Basic technology transfer activities such as material transfer agreements, collaboration agreements and confidentiality agreements can be dealt with locally and speedily. Research at NIMR supports the primary mission of the MRC, to encourage and support research to improve human health. Research findings can influence healthcare in many ways including bringing new drugs to the market, improving diagnostics, and assisting industry research. Scientists at NIMR actively engage in this translational process in a variety of ways. MRC Technology (MRCT), the exclusive commercialisation catalyst for the MRC, works to translate cutting-edge scientific discoveries into commercial products and it offers support to NIMR translational activities. Some NIMR research findings are patented and some patents are licensed for further development. One recent patent, that is now available for industrial exploitation, concerns the crystal structure of the influenza virus neuraminidase protein. This may help in the development of new drugs against the influenza virus. NIMR have been involved in the production of diagnostic equipment for field use in malaria and regularly supply reagents such as flu serum/viruses, hybridomas and transgenic mice for use in diagnostic and pharmaceutical research laboratories as well as other academic laboratories. Scientists are also involved in collaborations with industry or hosting/ supervising PhD students funded by industry. Many have consultancies with biotechnology and pharmaceutical companies. One major current area of collaboration is influenza research. Structure of N1 neuraminidase complexes 26 MRC National Institute for Medical Research Development of drugs against malaria Collaboration between NIMR’s Division of Parasitology and the MRC Technology Centre for Therapeutics Discovery has made substantial progress in identifying highly effective inhibitors of a malaria parasite kinase that has been implicated in parasite development and invasion of red blood cells. The kinase phosphorylates two components of an acto-myosin motor that drives the invasion process. Such inhibitors will prevent the multiplication of the parasite in the blood stream, which is the stage of the life cycle responsible for the disease. There is an urgent need for new drugs to help control and potentially eliminate malaria and the hope is that the inhibitors identified in this collaboration will be developed into such therapies. Parasites developing in a red blood cell. Each blue spot is an individual nucleus detected with a DNA-binding stain. The periphery of each parasite is marked by the red stain which identifies one of the phosphorylated proteins of the motor complex and the green stain identifies a protein essential for invasion of fresh red cells. The parasites will burst out of this red blood cell and each will bind to and invade a new cell where the cycle of development and multiplication will be repeated. Cervical cancer Studies in the Division of Virology on the life cycle of Human Papillomaviruses (HPV) have provided key information as to how these viruses cause neoplasia and cancer. A spin-off from this work is the rational selection of biomarkers which can be used to identify disease and to predict the risk of progression. We have been developing one of these markers (E4) with a commercial partner, as a disease severity marker and as an end-point marker for the current HPV vaccine trials. This approach is now attracting the attention of clinical scientists who are familiar with the problems of cytology screening for cervical cancer. E4 staining (green) identifies HPV infection in a cervical biopsy. The protein is abundant in the cells that are taken during the cervical smear test. Cell nuclei are stained in blue. Red shows cells that are driven through the cell cycle by the virus MRC National Institute for Medical Research 27 SCIENCE AND SOCIETY Public engagement activities Human Biology Essay Competition 2010 NIMR’s essay competition is now in its eighth year. At a time when school science students rarely write an extended essay before they go to university we provide an opportunity for enthusiasts to develop their skills. All the entrants receive a prize of the current volume of Mill Hill Essays, and the winners receive a financial prize and spend a day at NIMR seeing visually appealing projects. The best essay by Thomas Elliott of Queen Elizabeth’s Boys School on “What makes bone marrow such a versatile resource for curing human diseases” was published in Mill Hill Essays 2010. Research Summer School In 2010 NIMR was host to 14 students over the summer, drawn from nine local schools. The scheme is financed by the Nuffield Foundation who award bursaries to each student. The students undertake projects devised and supervised by NIMR staff, using the core techniques of modern molecular biology and biochemistry. The course starts with a half-day induction in molecular biology, lab skills, safety and record-keeping. Students produce excellent posters and reports of their work, to be shown at events organised by the Nuffield Foundation. Teachers tell us that bursary holders are a vivid advertisement for the Summer School and they inspire the next generation of science students to follow the same route. Some of our earlier cohorts of students are now researchers having emerged from university with first-class degrees. The University of the Third Age (U3A) at NIMR In December 2010 NIMR hosted the eighth national meeting of the science section of the U3A, a self-managed organisation for retired people who enjoy learning about science. Many travel quite long distances to attend. This year the theme was “Understanding the heart in health and disease” at which Tim Mohun and Ross Breckenridge spoke. Once again, we had a capacity crowd of nearly 150 enthusiasts. 28 MRC National Institute for Medical Research SCIENCE AND SOCIETY Annual Schools Days Students in Year 12 are invited to an event designed to enrich their experience of the life sciences. The theme for this years event was “Modern Cell Biology”. We accommodated a capacity audience of 360 visitors over two days drawn from 21 local schools. We encourage a lively questioning of the speakers on their subject or about careers and topical issues. We also present a small demonstration of aspects of developmental biology to provide a glimpse of real experimental material and a quiz based on posters relating to science in the news. Professional development for teachers In June 2010 we held a meeting for local teachers focused on recent developments in biomedical science. We had 75 participants from 32 schools. Talks included “New approaches to cell biology”; “Recent progress in molecular biology”; “The potential of stem cells for refurbishing the human body” and “How the brain stores memories”. The speakers found exactly the right level with sufficient novel material to interest teachers but not too far removed from the curriculum to make it irrelevant. Judging by the lively discussion the event was clearly a great success, and we look forward to welcoming teachers again to NIMR. Direct involvement in schools NIMR staff participate directly in science education in the “Science Ambassadors” scheme providing a distinctive enrichment to complement the normal school curriculum. NIMR staff are asked to give talks about their research or other topics to Year 12 classes from time to time. A growing development is the involvement of NIMR staff in “extended projects” required for some A level courses at two excellent local schools. We have set up programmes with appropriate staff members answering questions and putting students on the right track. MRC National Institute for Medical Research 29 SCIENCE AND SOCIETY Public engagement activities NIMRart NIMRart is an experimental and innovative arts programme creating opportunities for artists to make and think about art in a non-art context. A series of residencies set up in collaboration with the Arts Council and coupled with short visits, talks, exhibitions and publications has produced an ever-changing platform for ideas and creativity. By actively encouraging artists to engage with scientists and other staff at the Institute an increased consideration and comprehension of the work of both the artists and scientists involved has been achieved. NIMR also subscribes to the Arts Council Collection’s Long Loan Scheme, allowing opportunities to exhibit works by famous and established artists in our common public areas. This complements the examples obtained from the NIMRart programme and our own rolling exhibition displayed in the corridors and stairwells of images taken from current scientific projects. Recent loans from the Arts Council Collection include (left) Eduardo Paolozzi, Caprese, bronze 1975, (centre) Dick Gilbert, Approaching Wave, 1965, (right) Stassinos Paraskos, Bathing, 1968 Mill Hill Essays Since 1995, NIMR has produced an annual booklet of essays to increase public awareness of topical scientific issues. Written by members of staff, each booklet includes a range of topics, ranging from emerging infections, to stem cells and cloning. They are given to visitors and distributed to local schools and other organisations. PDF versions of all the published Mill Hill Essays can be accessed at: http://www.nimr.mrc.ac.uk/mill-hill-essays 30 MRC National Institute for Medical Research a b Using Flybow as genetic multicolor labelling tool to examine the arborization patterns of wild type (a) and N-Cadherin deficient (b) higher order neurons (green, red and yellow) in the adult visual system of Drosophila. Photoreceptor axons are labelled in blue. MRC National Institute for Medical Research 31 A – Z list of NIMR group leaders Siew-Lan Ang Kate Bishop Mike Blackman James Briscoe Paul Burgoyne Tom Carter Rita Cha Elaine Davis John Doorbar Paul Driscoll Greg Elgar Delmiro Fernandez-Reyes Sebastian Gagneux Steve Gamblin Mike Gilchrist Richard Goldstein Alex Gould Francois Guillemot Matthew Hannah Tony Holder Ed Hulme Nobue Itasaki George Kassiotis Dimitris Kioussis Jean Langhorne Paul Le Tissier Steve Ley Malcolm Logan Robin Lovell-Badge John McCauley Troy Margrie Tim Mohun Justin Molloy Elke Ober 32 Neuronal subtype specification in the midbrain and hypothalamus Infection and replication of retroviruses Proteases in host cell exit and invasion by the malaria parasite Pattern formation in the vertebrate nervous system The Y chromosome and infertility Secretory organelle formation, trafficking and exocytosis Regulation of eukaryotic chromosome metabolism Gene regulation and DNA repair in the pathogenesis of Mycobacterium tuberculosis Human papillomavirus biology and disease Structural and functional analysis of signalling proteins Regulation of early vertebrate development Proteome-wide discovery of biomarkers of childhood severe malaria Population genomics and ecology of Mycobacterium tuberculosis Structural biology of influenza, energy metabolism and cancer Gene regulatory networks in early development Modelling of evolution Regulation of growth and metabolism Genomic and functional analysis of neurogenesis Secretory vesicle formation in human endothelial cells Malaria parasites and red blood cells Structure and function of G protein-coupled receptors Wnt signalling in vertebrate embryogenesis Antiviral immunity Chromatin structure, gene expression and lymphoid development Immunity and immunopathogenesis in malaria infections Control of prolactin and growth hormone cell differentiation and function Regulation of immune responses by NF-kB and MAP kinases Understanding vertebrate limb development Sex, stem cells and decisions of cell fate Host specificity of influenza viruses Sensory processing in single cells, circuits and behavior Heart development in vertebrates Single molecule studies of cell motility and cell signalling Liver development in zebrafish MRC National Institute for Medical Research 77 35 36 78 91 79 92 37 38 62 93 39 40 63 94 64 80 81 82 41 65 83 42 43 44 84 45 95 96 46 85 97 66 98 John Offer Anne O’Garra Vassilis Pachnis Annalisa Pastore Alexandre Potocnik Andres Ramos Katrin Rittinger Peter Rosenthal Iris Salecker Benedict Seddon Steve Smerdon Jim Smith Gitta Stockinger Jonathan Stoye Ian Taylor Willie Taylor Peter Thorpe Pavel Tolar James Turner Victor Tybulewicz Jean-Paul Vincent Andreas Wack Martin Webb David Wilkinson Robert Wilkinson Mark Wilson Douglas Young Lyle Zimmerman Synthetic protein laboratory: acyl transfer for chemical biology and synthesis Regulation of the immune response in infectious disease Development of the nervous system Understanding the molecular bases of neurodegeneration Haematopoietic stem cells and lymphocyte development Molecular recognition in post-transcriptional regulation Structural biology of signalling networks that regulate innate and adaptive immunity Cryomicroscopy of proteins, viruses and cells Visual circuit assembly in Drosophila Regulation of T cell homeostasis by antigen receptor signals and interleukin-7 Structural biology of phosphorylation-dependent signalling in the cell cycle and DNA damage response The molecular basis of mesoderm formation Development, maintenance and regulation of peripheral T cell compartments and immune responses Retrovirus-host interactions Macromolecular assemblies Protein structure analysis and design Systems microscopy studies of cell fate determination Activation of immune receptors X chromosome inactivation, meiotic silencing and infertility Signal transduction in B and T cells Patterning and homeostasis in developing epithelia Immune response to influenza The molecular mechanisms of motor proteins Regulation of boundary formation and neurogenesis Understanding and intervening in HIV-associated tuberculosis Regulation of Th2 cells during allergic inflammation and anti-helminth immunity Mycobacterial pathogenesis: gene expression and innate immune response Using frog genetics to understand vertebrate development and disease 67 47 86 68 48 69 70 71 87 49 72 99 50 51 73 74 100 52 101 53 88 54 75 89 55 56 57 102 For current list visit the NIMR website: http://www.nimr.mrc.ac.uk/research/a-z MRC National Institute for Medical Research 33 Infections and Immunity Immune Cell Biology Immunoregulation Molecular Immunology Mycobacterial Research Victor Tybulewicz (Head of Division) Steve Ley Benedict Seddon Pavel Tolar Anne O’Garra (Head of Division) George Kassiotis Andreas Wack Gitta Stockinger (Head of Division) Dimitris Kioussis Alexandre Potocnik Mark Wilson Douglas Young (Head of Division) Elaine Davis Sebastien Gagneux Robert Wilkinson Microarray Laboroatory Parasitology Virology 34 MRC National Institute for Medical Research Tony Holder (Head of Division) Michael Blackman Delmiro Fernandez-Reyes Jean Langhorne Childhood Malaria Research Group Jonathan Stoye (Head of Division) Kate Bishop John Doorbar John McCauley WHO Collaborating Centre for Reference and Research on Influenza (WIC) INFECTIONS AND IMMUNITY Virology Kate Bishop Infection and replication of retroviruses Lab members: Virginie Boucherit, Harriet Groom, Mirella Nader, Darren Wight Retroviruses cause severe diseases, including immunodeficiency and cancer. The human immunodeficiency virus (HIV) is the most widely known retrovirus due to its impact on human health. In 2006, a novel retrovirus called xenotropic murine leukaemia virus-related virus (XMRV) was isolated from patients with familial prostate cancer. More recently, XMRV has been identified in chronic fatigue syndrome patients. It is not known whether the virus causes either disease. Innovative therapeutics for retroviral infections will hopefully arise from a better understanding of how retroviruses reproduce in the cell, how they interact with host cell factors, and how they subvert the host innate and adaptive immune systems. We are interested in the early post-entry stages of the retroviral life cycle, as these are potential therapeutic targets but are currently poorly defined. We are studying the p12 protein of murine leukaemia virus that is essential during these stages. By combining virological assays with biochemical/ biophysical techniques and microscopy, we hope to build up a picture of how p12 interacts with both viral and cellular factors, where p12 localises in the cell and why p12 function is important. Publications Groom HCT, Boucherit VC, Makinson K, Randal E, Baptista S, Hagan S, Gow JW, Mattes FM, Breuer J, Kerr JR, Stoye JP and Bishop KN (2010) Absence of xenotropic murine leukaemia virus-related virus in UK patients with chronic fatigue syndrome. Retrovirology 7:10 Groom HCT, Yap MW, Galão RP, Neil SJD and Bishop KN (2010) Susceptibility of xenotropic murine leukemia virus-related virus (XMRV) to retroviral restriction factors. Proceedings of the National Academy of Sciences of the United States of America 107:5166-5171 Holmes RK, Malim MH and Bishop KN (2007) APOBEC-mediated viral restriction: not simply editing? Trends in Biochemical Sciences 32:118-128 Co-localisation of the viral p12 and nucleocapsid (NC) proteins from Moloney murine leukaemia virus in a D17 cell, six hours post-infection. The cell nucleus is shown in blue. See reference 107 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 35 INFECTIONS AND IMMUNITY Parasitology Mike Blackman Proteases in host cell exit and invasion by the malaria parasite Lab members: Christine Collins, Sujaan Das, Fiona Hackett, Natalie Silmon de Monerri, Maria Penzo, Andrea Ruecker, Michael Shea, Robert Stallmach, Malcolm Strath, Catherine Suarez, Chrislaine Withers-Martinez, Sharon Yeoh Malaria causes immense suffering, killing at least one million people each year, and is a major contributor to poverty. The disease is caused by a single-celled parasite and spread by mosquitoes. There is no malaria vaccine, and resistance against mainstay antimalarial drugs is widespread. There is a need to find new ways to treat and control this devastating disease. The malaria parasite infects and divides within red blood cells. These eventually rupture, releasing a fresh wave of parasites to invade new red cells. Our work focuses on how the parasite invades and escapes from its host red cell, in anticipation that a better understanding of this will aid the development of much-needed new antimalarial drugs and a vaccine. We have a particular interest in a family of parasite enzymes called proteases that regulate release of the parasite from the red blood cell, and also modify the parasite surface to ‘prime’ the parasite for invasion. We are investigating the structure, function and regulation of these proteases, and searching for inhibitory compounds with potential to be developed as antimalarial drugs. Release of PfSUB1 from exonemes leads to parasite surface ‘priming’ and host cell rupture. Publications Child MA, Epp C, Bujard H and Blackman MJ (2010) Regulated maturation of malaria merozoite surface protein-1 is essential for parasite growth. Molecular Microbiology 78:187–202 Collins CR, Withers-Martinez C, Hackett F and Blackman MJ (2009) An inhibitory antibody blocks interactions between components of the malarial invasion machinery. PLoS Pathogens 5:e1000273 Koussis K, Withers-Martinez C, Yeoh S, Child M, Hackett F, Knuepfer E, Juliano L, Woehlbier U, Bujard H and Blackman MJ (2009) A multifunctional serine protease primes the malaria parasite for red blood cell invasion. EMBO Journal 28:725-735 Molecular structure of SERA5, a putative parasite protease involved in rupture of the parasite-infected red blood cell. See references 33, 64, 86, 272 in the bibliography at the back for publications from this group in 2010. 36 MRC National Institute for Medical Research INFECTIONS AND IMMUNITY Mycobacterial Research Elaine Davis Gene regulation and DNA repair in the pathogenesis of Mycobacterium tuberculosis Lab members: Nicola Beresford, Joanna Dillury, Amanda Fivian-Hughes, Alison Gaudion, Joe James, Dorothée Schuessler, Katherine Smollett, Alan Williams Despite the most frequent outcome of infection with Mycobacterium tuberculosis being asymptomatic latent infection, tuberculosis is a leading infectious cause of death globally, with devastating consequences in parts of the world such as South-East Asia and sub-Saharan Africa. Although a treatment regimen is available, this is a lengthy process and the development of drug resistance threatens its efficacy. Therefore, there is an urgent need for new drugs to treat TB. During infection, M. tuberculosis is exposed to adverse conditions as the host tries to defend itself. The bacteria need to adapt to and withstand these conditions in order to survive and establish an infection. One way the bacteria respond is by altering the expression of certain genes. We are investigating aspects of how M. tuberculosis does this. A key target of the host defence mechanisms is the bacterial DNA. It is vital to the bacteria that damage to its DNA is repaired. Therefore, we are also studying the processes M. tuberculosis uses for this with a view to identifying novel targets for the development of new drugs to combat TB. Publications Detection of promoter activity using a reporter construct in mycobacteria. Colonies in which the promoter is active express β-galactosidase and are identified by the blue colour. Dawson LF, Dillury J and Davis EO (2010) RecA-independent DNA damage induction of Mycobacterium tuberculosis ruvC despite an appropriately located SOS box. Journal of Bacteriology 192:599-603 Fivian-Hughes AS and Davis EO (2010) Analysing the regulatory role of the HigA antitoxin within Mycobacterium tuberculosis. Journal of Bacteriology 192:4348-4356 Assessment of the sensitivity of different strains of M. tuberculosis to a DNA damaging agent. The blue dye is reduced to produce a pink colour only by viable bacteria. Using a serial dilution of the compound across the plate, it can be seen that the strains in the middle rows are more susceptible than those in the upper and lower rows. This assay can also be used to compare the ability of potential new drugs to act on M. tuberculosis. Singh P, Patil KN, Khanduja JS, Kumar PS, Williams A, Rossi F, Rizzi M, Davis EO and Muniyappa K (2010) Mycobacterium tuberculosis UvrD1 and UvrA proteins suppress DNA strand exchange promoted by cognate and non-cognate RecA proteins. Biochemistry 49:4872-83 See references 53, 81, 230 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 37 INFECTIONS AND IMMUNITY Virology John Doorbar Human papillomavirus biology and disease Lab members: Clare Davy, Pauline McIntosh, Qian Wang, Heather Griffin. Deborah Jackson, Zhonglin Wu, Gareth Maglennon, Christina Untersperger, Emilio Pagliarulo, Rebecca Marnane Human papillomaviruses (HPV) cause a range of significant human diseases, including laryngeal papillomatosis, genital warts and cervical neoplasia. Certain HPV types, known as highrisk types, cause cervical lesions that can progress to cancer. Cervical cancer accounts for around 12% of all female cancers worldwide and is almost always caused by high-risk HPV. Central to understanding papillomavirus-associated disease are model systems, which allow us to examine in the laboratory how the virus disrupts the normal growth and differentiation of the epithelial cells that it infects. Using such approaches, we can study the initial events during lesion formation, the mechanism of disease resolution and viral persistence, and how viral latency and re-activation might be mediated. In our group, such studies are supported by strong links with clinical laboratories, and by appropriate molecular studies which look at viral protein function and the cellular pathways that they disrupt in order to support the normal or de-regulated virus life cycle. Our work is ultimately driven by the need to better understand HPV disease and how to limit its impact. The E4 protein is cleaved by the protease calpain, which removes sequences from the N-terminus (red) and exposes the C-terminal amyloid fold (purple arrows) to allow E4 multimerisation. Publications Davy C, McIntosh P, Jackson DJ, Sorathia R, Miell M, Wang Q, Khan J, Soneji Y and Doorbar J (2009) A novel interaction between the human papillomavirus type 16 E2 and E1^E4 proteins leads to stabilization of E2. Virology 394:266-275 Wang Q, Kennedy A, Das P, McIntosh PB, Howell SA, Isaacson ER, Hinz SA, Davy C and Doorbar J (2009) Phosphorylation of the human papillomavirus type 16 E1^E4 protein at T57 by ERK triggers a structural change that enhances keratin binding and protein stability. Journal of Virology 83:3668-3683 McIntosh PB, Martin SR, Jackson DJ, Khan J, Isaacson ER, Calder L, Raj K, Griffin HM, Wang Q, Laskey P, Eccleston JF and Doorbar J (2008) Structural analysis reveals an amyloid form of the HPV 16 E1^E4 protein and provides a molecular basis for its accumulation. Journal of Virology 82:8196-8203 B. E4 multimers exist as amyloid fibrils, which can be seen under the electron microscope C. HPV infection of the cervix leads to cervical neoplasia of different grades. The E4 protein (which is stained in green) assembles into amyloid structures in the upper epithelial layers. The red staining marks cells that are progressing through the cell cycle, while cell nuclei are counter-stained blue. See references 60, 146, 147, 165, 228 in the bibliography at the back for publications from this group in 2010. 38 MRC National Institute for Medical Research INFECTIONS AND IMMUNITY Parasitology Delmiro Fernandez-Reyes Proteome-wide discovery of pathogenesis biomarkers of childhood severe malaria Lab members: Ianina Conte, Dimitrios Athanasakis, Barry Ely, Juho Rousu, Olugbemiro Sodeinde Half of the world population is at risk of malaria. Human malaria caused by Plasmodium falciparum represents a global disease burden with an estimated 300 million clinical episodes per year leading to an estimated one million deaths. Cerebral malaria and severe malarial anaemia are both major complications with significant global childhood mortality and morbidity in Sub-Saharan Africa. Biomarkers that predict the commitment of the infection to a severe presentation, its specific severity factors and progression will not only be important for understanding of the pathogenesis, but could also provide clinical tools for patient care. We focus on understanding how the proteomes of host and parasite interact to establish the pathological changes observed during severe malaria in children. We use high-throughput mass spectrometry methods that enable unbiased discovery of host-parasite plasma proteomepatterns during the establishment and progression of childhood severe malarial disease. The approach employed is based on the idea that distinctive complex combinations of circulating proteins define different pathological states, reflecting hostpathogen interactions of the infectious process. We develop computational algorithms to discover disease-specific patterns of the proteome response to the infection. The establishment of a Childhood Malaria Research Unit in partnership with the College of Medicine University of Ibadan, Nigeria allows us to sample the malaria disease process in great detail. This involves recruiting severe and non-severe malaria cases, as well as associated clinical, epidemiological, demographical and geographical information. Publications Rojas-Galeano S, Hsieh E, Agranoff D, Krishna S and Fernandez-Reyes D (2008) Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions. PLoS ONE 3:e1806 Buxton, B. F., Abdallahi, H., Fernandez-Reyes, D. and Jarra, W. (2007) Development of an Extension of the Otsu Algorithm for Multidimensional Image Segmentation of Thin-Film Blood Slides International Conference on Computing: Theory and Applications, 552-562. Identification of urine hepcidin and its levels in childhood severe malaria. Hepcidin is a hormone produced by the liver involved in iron homeostasis, and its levels increase during an infection and immunological response. (Left) Hepcidin levels (red line) in control and different malaria patients by SELDIToF analysis of urine with metal affinity chemistry represented as a virtual gel. (Right) Representative spectra from one sample for each group revealing the different relative intensity of hepcidin. Agranoff D, Fernandez-Reyes D, Papadopoulos MC, Rojas SA, Herbster M, Loosemore A, Tarelli E, Sheldon J, Schwenk A, Pollak R, Rayner CFJ and Krishna S (2006) Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum. Lancet 368:1012-1021 MRC National Institute for Medical Research 39 INFECTIONS AND IMMUNITY Mycobacterial Research Sebastien Gagneux Population genomics and ecology of Mycobacterium tuberculosis Lab members: Inaki Comas, Thembela Huna, Graham Rose Many human pathogens escape host immunity by varying their antigenic genes. To test whether Mycobacterium tuberculosis uses a similar strategy to evade the human immune responses, we generated the nearly complete genome sequences of 21 M. tuberculosis’ complex (MTBC) strains representative of the organism’s global diversity (top figure). We then compared the genetic diversity and evolutionary conservation across three experimentally confirmed sets of genes, including essential genes, non-essential genes, and genes encoding known T cell epitopes. We found, as expected, that essential genes in MTBC were less diverse than non-essential genes. Essential genes were also more evolutionarily conserved than non-essential genes, as indicated by a lower ratio of non-synonymous to synonymous nucleotide changes. Surprisingly, however, we found that the known T cell epitopes were the least diverse and most evolutionarily conserved regions of the MTBC genome. This observation suggests MTBC might benefit from host immune recognition of these T cell epitopes, perhaps because the associated immunepathological processes (e.g. lung cavitation) increase disease transmission. Our findings have important implications for the development of new tuberculosis vaccines. Global phylogeny of M. tuberculosis complex based on 21 genome sequences Ratio of non-synonymous to synonymous nucleotide changes in different gene classes of M. tuberculosis complex. Publications Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, Kremer K, Ernst JD and Gagneux S (2010) Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nature Genetics 42:498-503 Coscolla M and Gagneux S (2010) Does M. tuberculosis genomic diversity explain disease diversity? Drug Discovery Today: Disease Mechanisms 7: e43-e59 de Jong BC, Antonio M and Gagneux S (2010) Mycobacterium africanum-review of an important cause of human tuberculosis in West Africa. PLoS Neglected Tropical Diseases 4:e744 See references 39, 44, 54, 180 in the bibliography at the back for publications from this group in 2010. 40 MRC National Institute for Medical Research INFECTIONS AND IMMUNITY Parasitology Tony Holder Malaria parasites and red blood cells Lab members: Eilidh Carrington, Barbara Clough, Suraya Diaz, Muni Grainger, Judith Green, Claire Hastings, Madhu Kadekoppala, Ellen Knuepfer, Robert Moon, David Moss, Sola Ogun, Kaveri Rangachari, Ridzuan Razak, Shigeharu Sato, Oniz Suleyman, Noor Azian Yusuf Malaria is caused by a parasitic protozoan that invades red blood cells, where it develops and multiplies before bursting out and invading fresh red cells. This cycle is responsible for the disease. Understanding the interaction between the parasite and the host immune system contributes to the development of a malaria vaccine. The identification of new targets for drugs to kill the parasite and interrupt the cycle of multiplication offers the potential of new therapeutic interventions. In one project, we focus on the interaction between the parasite and the surface of the host red cell that it invades. Invasion is a multistep process driven by the parasite’s actomyosin-based motor. At the parasite surface during invasion there is a complex but ordered series of events involving protein complex formation and modification, export of protein from intracellular organelles and transfer of proteins to the host cell. We are defining the role of parasite components essential for invasion using a range of genetic, molecular and cell biological techniques. Understanding the importance of specific interactions will inform the development of therapeutic strategies to block them. Publications Kadekoppala M, Ogun SA, Howell S, Gunaratne RS and Holder AA (2010) Systematic genetic analysis of the Plasmodium falciparum MSP7-like family reveals differences in protein expression, location and importance in asexual growth of the blood stage parasite. Eukaryotic Cell 9:1064-1074 Hinds L, Green JL, Knuepfer E, Grainger M and Holder AA (2009) A novel putative GPI-anchored micronemal antigen of Plasmodium falciparum that binds to erythrocytes. Eukaryotic Cell 8:1869-1879 Holder AA (2009) Malaria vaccines: where next? PLoS Pathogens 5:e1000638 Malaria can lead to severe anaemia. One mechanism may involve the destruction of uninfected red blood cells by immune mechanisms recognising antibody bound to parasite antigens coating these cells. The parasite antigens may be released as soluble proteins during invasion, which then stick to uninfected cells (A), or be transferred to the surface of cells during an aborted invasion (B). See references 41, 66, 100, 124, 125, 183, 222, 239, 244, 251, in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 41 INFECTIONS AND IMMUNITY Immunoregulation George Kassiotis Antiviral immunity Lab members: Urszula Eksmond, Dorothy Ng, Mickaël Ploquin, George Young Viral infections represent a major challenge to the immune system. Certain viruses cause acute infections in humans, which can be rapidly fatal within days, for example influenza A and smallpox viruses. In contrast, other viruses are able to persist chronically in infected individuals, despite induction of an immune reaction (e.g. HIV, hepatitis and herpes viruses) and almost all humans are chronically infected by one or more persistent viruses. Our understanding of the pathogenic processes of viral infection remains incomplete. Viral infection elicits potent innate and adaptive host immunity. However, an excessive or inappropriate immune response may also lead to host pathology, often more severe than the direct effects of viral replication. We found that, without affecting virus replication, regulatory T (Treg) cells delayed the appearance of clinical signs and prolonged survival of mice following influenza A virus infection. This correlated with reduced expression of the monocyte chemoattractant CCL8 and recruitment of monocytes into the infected lungs. The finding that part of the pathology following Influenza A virus infection is amenable to immune regulation suggests a causal involvement of the immune response. Treg cells suppress the induction of monocyte chemoattractant CCL8 by Influenza A virus infection in the lungs. Publications Antunes I and Kassiotis G (2010) Suppression of innate immune pathology by regulatory T cells during Influenza A virus infection of immunodeficient mice. Journal of Virology 84:12564-12575 Influenza A virus-induced pathology (body weight loss) is delayed by regulatory T cells (Treg cells). Marques R, Williams A, Eksmond U, Wullaert A, Killeen N, Pasparakis M, Kioussis D and Kassiotis G (2009) Generalized immune activation as a direct result of activated CD4+ T cell killing. Journal of Biology 8:93 Antunes I, Tolaini M, Kissenpfennig A, Iwashiro M, Kuribayashi K, Malissen B, Hasenkrug K and Kassiotis G (2008) Retrovirus-specificity of regulatory T cells is neither present nor required in preventing retrovirus-induced bone marrow immune pathology. Immunity 29:782-794 42 MRC National Institute for Medical Research See references 8, 181 in the bibliography at the back for publications from this group in 2010. INFECTIONS AND IMMUNITY Molecular Immunology Dimitris Kioussis FRS, EMBO member, FMedSci Chromatin structure, gene expression and lymphoid development Lab members: Mauro Tolaini, Eleni Ktistaki, Nicky Harker, Ursula Menzel, Kathleen Roderick, Amisha Patel, Anna Garefalaki, Dimitris Karamitris, Trisha Norton, Keith Williams Immune cells comprise a major component of our arsenal to fight disease. In order for the B and T lymphocytes of the immune system to function appropriately and protect the body from pathogens (viruses, bacteria) and aberrant cells (cancer) they must express specific sets of genes. This specific pattern of gene expression constitutes the signature of the cell and defines its identity and function. It is therefore important to understand what controls the decisions to establish a specific gene expression programme. We are studying how sequential gene expression patterns are controlled during the development of thymocytes to generate mature T cells. Our studies focus on two genes, CD2 and CD8, that are expressed during thymocyte differentiation. We are interested in identifying the chromatin structures established in open (expressing) or closed (non-expressing) states of these genes. In other studies, we are investigating the cellular and molecular requirements for lymphoid organ formation by in vivo and in vitro imaging of specific lymphoid cell types expressing fluorescent proteins. Imaging of the lymphoid system and associated organs. B Cell follicles: EYFP. T Cell zone: DsRed. Publications Menzel U, Ktistaki E, Tolaini M, Veiga-Fernandes H and Kioussis D (2010) Replication allows inactivation of a knocked-in locus control region in inappropriate cell lineages. Proceedings of the National Academy of Sciences of the United States of America 107:16928-16933 Image of mouse chromosome 6. Multi-colour chromosome banding (MCB) with CD8a and CD4 gene probes. Kioussis D and Georgopoulos K (2007) Epigenetic flexibility underlying lineage choices in the adaptive immune system. Science 317:620-622 Veiga-Fernandes H, Coles MC, Foster KE, Patel A, Williams A, Natarajan D, Barlow A, Pachnis V and Kioussis D (2007) Tyrosine kinase receptor RET is a key regulator of Peyer’s Patch organogenesis. Nature 446:547-551 See references 37, 38, 83, 127, 128, 137, 172, 256, 257, 274 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 43 INFECTIONS AND IMMUNITY Parasitology Jean Langhorne Immunity and immunopathogenesis in malaria infections Lab members: Deirdre Cunningham, Ana Paula Freitas do Rosario, William Jarra, Jennifer Lawton, Wiebke Nahrendorf, Dorothy Ng, Philip Spence, Anne-Marit Sponaas, Sophie Roetynck, Christine Tshitenge, Bettina Wagner CD4 T cells are crucial for development of protective immunity to blood-stage malaria, but may also contribute to the pathology of severe disease. A major focus of our laboratory is to understand how memory CD4 T cells develop, which can protect against re-infection but cause minimal pathology. Protective immunity against malaria develops only after several infections and can be lost on leaving an area in which malaria is transmitted. This suggests that the chronic infection may maintain the protective immune response. We have used a mouse model of a blood-stage malaria infection to examine the memory response of CD4 T cells during chronic infection. Understanding what constitutes a protective CD4 T cell may help us design more protective vaccines. We show that protective memory CD4 T cells persist in an activated state following a first infection, produce the inflammatory cytokines TNFα and IFNγ, and are more protective than “resting” memory CD4 T cells obtained from mice in which the infection has been eliminated. This may explain why people are better protected against malaria when they are infected frequently. Publications Stephens R and Langhorne J (2010) Effector memory Th1 CD4 T cells are maintained in a mouse model of chronic malaria. PLoS Pathogens 6:e1001208 Nduati EW, Ng DHL, Ndungu FM, Gardner P, Urban BC and Langhorne J (2010) Distinct kinetics of memory B-cell and plasma-cell responses in peripheral blood following a blood-stage Plasmodium chabaudi infection in mice. PLoS ONE 5:e15007 Belyaev NN, Brown DE, Diaz AIG, Rae A, Jarra W, Thompson J, Langhorne J and Potocnik AJ (2010) Induction of an IL7-R+c-Kithi myelolymphoid progenitor critically dependent on IFN-γ signaling during acute malaria. Nature Immunology 11:477-85 See references16, 50, 71, 85, 182, 206, 211, 237, 262 in the bibliography at the back for publications from this group in 2010. 44 MRC National Institute for Medical Research CD4 T cells remain in an activated state following a Plasmodium chabaudi infection. INFECTIONS AND IMMUNITY Immune Cell Biology Steve Ley Regulation of immune responses by NF-κB and MAP kinases Lab members: Hakem Ben-Addi, Thorsten Gantke, Emilie Jacque, Julia Janzen, Agnes Mambole, Matoula Papoutsopoulou, Srividya Sriskantharajah, Karine Roget, Huei-Ting Yang, Rachel Zillwood Following infection, pathogenic microorganisms such as viruses and bacteria are initially recognised by specialised receptors on the surface and in the cytoplasm of cells called neutrophils and macrophages. This triggers an immediate ‘innate’ immune response involving the production of specialised proteins called chemokines and cytokines. These attract other immune cells to the sites of infection and also initiate the adaptive immune response that culminates in the production of protective antibodies and killing of infected cells. We study a signalling pathway that regulates the activation of TPL-2, a protein kinase that is critical for the induction of the cytokines tumor necrosis factor and interleukin-1b in inflammatory responses. Our current experiments aim to investigate the role of TPL-2 in autoimmunity, allergy and immune responses to pathogens, and are important in the evaluation of TPL-2 as a potential anti-inflammatory drug target. TPL-2 is required for induction of TNF by macrophages. Publications Gantke, T., Sriskantharajah, S. and Ley S. C. (2011) Regulation and function of TPL-2, an IκB-regulated MAP kinase kinase kinase. Cell. Research 21:131-45 Sriskantharajah S and Ley SC (2010) Turning off inflammation signaling. Science 327:1093-4 Sriskantharajah S, Belich MP, Papoutsopoulou S, Janzen J, Tybulewicz V, Seddon B and Ley SC (2009) Proteolysis of NF-κB1 p105 is essential for T cell antigen receptor-induced proliferation. Nature Immunology 10:38-47 See references 173, 235, 261 in the bibliography at the back for publications from this group in 2010. Schematic diagram of TPL-2 / ERK signalling pathway. MRC National Institute for Medical Research 45 INFECTIONS AND IMMUNITY Virology John McCauley Host specificity of influenza viruses Lab members: Haixia Xiao, Nicole Runkler, Ana Luisa Reis, Michael Bennett, Steve Wharton, Saira Hussain Influenza A viruses infect a variety of species, with humans (also the host for influenza B viruses), horses and pigs representing the main mammalian hosts of the virus in which infection is sustained. Avian species, particularly water-fowl and gulls, harbour a wide variety of influenza A viruses defined by their haemagglutinin (H1-16) and neuraminidase (N1-9) glycoprotein subtypes in a variety of H/N combinations. New pandemic strains of human influenza virus arise from an animal reservoir either directly, as for the 2009 pandemic A(H1N1) virus, or as a result of gene reassortment, as occurred in the 1957 and 1968 pandemics. The interaction between a virus particle and its receptor on a host cell is a vital feature that limits the host range of influenza viruses, but additional factors following entry of virus into the cell also control the outcome of infection. We are investigating the determinants of host range restriction of avian and swine influenza viruses that limit their ability to infect and propagate in human cells. Our research programme is closely integrated with the surveillance activities of the WHO Collaborating Centre (WIC) in the Division. Recent human H3N2 viruses that have been examined in the WIC show unexpected receptor binding activities. For many of these viruses the neuraminidase glycoprotein rather than the haemagglutinin mediates attachment to red cells. The characteristics of this binding are being examined in collaboration with colleagues in the Divisions of Physical Biochemistry and Molecular Structure, and with Prof. Ten Feizi, Imperial College London. Publications Lin, Y.P., Gregory, V., Collins, P., Kloess, J., Wharton, S., Cattle, N., Lackenby, A., Daniels, R., and Hay, A. (2010). Neuraminidase receptor binding variants of human influenza A(H3N2) viruses due to substitution of aspartic acid 151 in the catalytic site - role in virus attachment? Journal of Virology 84:6769-6781 Iqbal M, Xiao H, Baillie G, Warry A, Essen SC, Londt B, Brookes SM, Brown IH and McCauley JW (2009) Within-host variation of avian influenza viruses. Philosophical Transactions of the Royal Society B: Biological Sciences 364:2739-2747 Kuiken T, Holmes EC, McCauley J, Rimmelzwaan GF, Williams CS and Grenfell BT (2006) Host species barriers to influenza virus infections. Science 312:394-397 See references 12, 89, 178, 218, 250 in the bibliography at the back for publications from this group in 2010. 46 MRC National Institute for Medical Research Agglutination of turkey erythrocytes by recent seasonal H3N2 viruses can be mediated by the Neuraminidase. This agglutination correlates with the presence of a glycine at position 151 of the neuraminidase and utilises the catalytic site of the enzyme. The figure shows turkey erythrocytes incubated with recombinant virus carrying the haemagglutinin and neuraminidase glycoproteins of the A/Hong Kong/4443/2005 (H3N2) virus in the absence (A) or presence (B) of a neuraminidase inhibitor which binds to the catalytic site thereby preventing agglutination. INFECTIONS AND IMMUNITY Immunoregulation Anne O’Garra FRS, AAAS Fellow, EMBO member, FMedSci Regulation of the immune response in infectious disease Lab members: Chloe Bloom, Jillian Christensen, John Ewbank, Leona Gabrysova, Christine Graham, Ashleigh Howes, Finlay McNab, Jonathan Pitt, Paul Redford, Fotini Rozakeas, Vangelis Stavropoulos, Xuemei Wu Immune cells can produce different soluble factors called cytokines to control infection, but they can mediate host damage if uncontrolled. We are researching the molecular mechanisms for the development and function of discrete subsets of immune cells producing different cytokines protective against pathogens, and the induction and function of a regulatory cytokine, IL-10. We use diverse tools to study the molecular mechanisms of IL-10 gene regulation in macrophages, dendritic cells and T cells, and the consequences of IL-10 action in mouse models of bacterial infections, with strong emphasis on tuberculosis (TB) caused by Mycobacterium tuberculosis. TB is a major global cause of morbidity and mortality. Using a systems biology approach we identified a robust blood transcriptional interferon-inducible neutrophil-driven signature in human TB, which disappears during successful treatment. Based on these findings and continued studies in human disease and in cellular and in vivo experimental models, we are continuing to identify immune mechanisms of protection or pathogenesis important for disease control in tuberculosis and other bacterial infections. Publications Berry MPR, Graham CM, McNab FW, Xu Z, Bloch SAA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, Quinn C, Blankenship D, Dhawan R, Cush JJ, Mejias A, Ramilo O, Kon OM, Pascual V, Banchereau J, Chaussabel D and O’Garra A (2010) An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466:973-977 Redford PS, Boonstra A, Read S, Pitt J, Graham C, Stavropoulos E, Bancroft GJ and O’Garra A (2010) Enhanced protection to Mycobacterium tuberculosis infection in IL-10-deficient mice is accompanied by early and enhanced Th1 responses in the lung. European Journal of Immunology 40:2200–2210 Transcriptome analysis of human TB to enhance mouse models of MTb infection for in-depth mechanistic studies. Saraiva M and O’Garra A (2010) The regulation of IL-10 production by immune cells. Nature Reviews Immunology 10:170-81 See references 18, 166, 208, 221 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 47 INFECTIONS AND IMMUNITY Molecular Immunology Alexandre Potocnik Haematopoietic stem cells and lymphocyte development Lab members: Nikolai Belyaev, Judit Biro, Douglas Brown, Rebecca Leyland, Demetrios Vassilakos, Ana Isabel, Garcia Diaz All lymphocytes derive from haematopoietic stem cells, which are located in specialised niches within the bone marrow. In the adult, these stem cells are relatively immobile. However, in the foetus, or in response to some infections in the adult, these stem cells leave the bone marrow and appear in the blood. Our main focus is on understanding the processes that govern retention of stem cells in the bone marrow or their release into the blood and migration to other organs, and their subsequent development into lymphocytes. We have shown that in the absence of β1 integrin, haematopoietic progenitors are generated normally during ontogeny in the embryo and are released into the circulation, but fail to colonise foetal liver, thymus or bone marrow. Extending this study we comprehensively analysed T cell development using a genetic approach based on the lineage restricted expression of a fluorescent reporter. Ongoing work is concentrating on the dynamic regulation of lymphoid differentiation and the role of adhesion molecules for the proper compartmentalisation in health and disease. Publications Belyaev NN, Brown DE, Diaz AIG, Rae A, Jarra W, Thompson J, Langhorne J and Potocnik AJ (2010) Induction of an IL7-R+c-Kithi myelolymphoid progenitor critically dependent on IFN-γ signaling during acute malaria. Nature Immunology 11:477-85 Sponaas A-M, Freitas do Rosario AP, Voisine C, Mastelic B, Thompson J, Koernig S, Jarra W, Renia L, Mauduit M, Potocnik AJ and Langhorne J (2009) Migrating monocytes recruited to the spleen play an important role in control of blood stage malaria. Blood 114:5522-5531 Lamikanra AA, Brown D, Potocnik A, Casals-Pascual C, Langhorne J and Roberts DJ (2007) Malarial anemia: of mice and men. Blood 110:18-28 See reference 16 in the bibliography at the back for publications from this group in 2010. Early lymphocyte development. 48 MRC National Institute for Medical Research INFECTIONS AND IMMUNITY Immune Cell Biology Benedict Seddon Regulation of T cell homeostasis by antigen receptor signals and interleukin-7 Lab members: Thea Hogan, Daniel Marshall, Ina Schim van der Loeff, Ana Silva, Charles Sinclair, Sim Tung Thymus-derived T cells play a central role in regulating immune responses. Both the numbers and types of T cells found in the immune system are carefully regulated by processes that control their production, survival and replication. Defects in any of these processes can upset the fine balance that exists between the different T cell types, causing them to malfunction. Abnormal responses by T cells can result in autoimmune diseases like diabetes or the development of leukaemia. Cellular signals transduced by the T cell antigen receptor (TCR) and from cytokines such as IL-7 play a central role in regulating homeostasis of T cells. We have developed two novel in vivo models in which we can specifically control expression of IL-7Rα, the receptor for the cytokine interleukin-7, and the Syk family kinase Zap70, which is an essential signalling component down stream of the TCR. Using these models, we are investigating the role of IL-7 and TCR signals in controlling T cell survival. T cell development and maturation depends on TCR signalling and IL-7. Mature naïve T cells cannot develop in the absence of either TCR signalling or IL-7. Our conditional expression models permit us to manipulate these signalling pathways on a temporal basis, after T cells have first developed in the thymus. Publications Saini M, Sinclair C, Marshall D, Tolaini M, Sakaguchi S and Seddon B (2010) Regulation of Zap70 expression during thymocyte development enables temporal separation of CD4 and CD8 repertoire selection at different signaling thresholds. Science Signaling 3:ra23 Saini M, Pearson C and Seddon B (2009) Regulation of T cell-dendritic cell interactions by IL7 governs T cell activation and homeostasis. Blood 113:5793-5800 Yates A, Saini M, Mathiot A and Seddon B (2008) Mathematical modeling reveals the biological program regulating lymphopenia-induced proliferation. Journal of Immunology 180:1414-22 IL-7R and Zap70 expression in TetIL-7R and TetZap70 mice are induced by administration of the inducing antibiotic, doxycycline (dox). The graphs show the death of F5 TCR transgenic T cells after loss either of IL-7R (left) or Zap70 (right) by withdrawing dox (-dox lines) from mice. See references 131, 219, 259, 268 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 49 INFECTIONS AND IMMUNITY Molecular Immunology Gitta Stockinger EMBO member, FMedSci Development, maintenance and regulation of peripheral T cell compartments and immune responses Lab members: Judit Biro, Keiji Hirota, Joao Duarte, Ceri Wiggins, Helena Ahlfors, Christoph Wilhelm, Ying Li Our current focus is on the development and function of innate and adaptive IL-17 producing T cells, and modulation of effector functions by exogenous and endogenous environmental factors. Th17 cells are important for defence against fungal pathogens and many extracellular bacteria, and are causally involved in autoimmune diseases such as rheumatoid arthritis, myocarditis, multiple sclerosis and psoriasis. We developed an IL-17A fate reporter model, which allows us to study development of IL-17 producing T cells and their behaviour during infection in vivo. We furthermore study the role of the aryl hydrocarbon receptor in the immune system, trying to unravel its impact on the function of different immune cells in the defense against pathogens. Publications Hirota K, Duarte J.H, Veldhoen M, Hornsby E, Li Y, Cua D.J, Ahlfors H, Wilhelm C, Tolaini M, Menzel U, Garefalaki A, Potocknik A.J and Stockinger B (2011) Fate mapping of interleukin-17 producing T cells in inflammatory responses. Nature Immunology 12:255–263 Martin B, Hirota K, Cua DJ, Stockinger B and Veldhoen M (2009) Interleukin-17-producing γδ T cells selectively expand in response to pathogen products and environmental signals. Immunity 31:321-330 Veldhoen M, Hirota K, Westendorf AM, Buer J, Dumoutier L, Renauld J-C and Stockinger B (2008) The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins. Nature 453:106-9 See references 24, 118, 179, 248, 258, 259, 260 in the bibliography at the back for publications from this group in 2010. Accumulation of eYFP+ cells from IL-17A fate reporter mouse in skin following infection with Candida albicans. 50 MRC National Institute for Medical Research INFECTIONS AND IMMUNITY Virology Jonathan Stoye Retrovirus-host interactions Lab members: Vicky Felton, Seti Grambas, Kate Holden-Dye,Wilson Li, Sadayuki Okura, Melvyn Yap Comparative genome analysis suggests that vertebrates and retroviruses have co-existed for tens of millions of years. It is thus unsurprising that a degree of co-evolution has taken place resulting in the development of specific defence mechanisms by the host and of means to overcome such defences by the virus. Understanding such natural anti-viral genes might suggest novel means of combating retroviral infection. We anticipate that these studies will shed new light on the early stages of retrovirus replication and the control of cross-species infection. The host proteins TRIM5α and Fv1 typify such defence factors. They interact with incoming viruses, shortly after viral entry into the cell cytoplasm, binding to the viral core and inhibiting reverse transcription or nuclear transport. Study of the binding assay has been complicated by a requirement for polymerised capsid as found in virions and difficult to isolate experimentally. We have now devised a method for polymerising retrovirus capsids on lipid nanotubes producing assemblies closely resembling those found in retroviruses. We are using these tubes for studying both retroviral assembly and mode of Fv1 binding. Publications Goldstone DC, Yap MW, Robertson LE, Haire LF, Taylor WR, Katzourakis A, Stoye JP and Taylor IA (2010) Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface. Cell Host & Microbe 8:248-259 Yap MW, Lindemann D, Stanke N, Reh J, Westphal D, Hanenberg H, Ohkura S and Stoye JP (2008) Restriction of foamy viruses by primate Trim5α. Journal of Virology 82:5429-5439 Yap MW, Mortuza GB, Taylor IA and Stoye JP (2007) The design of artificial retroviral restriction factors. Virology 365:302-314 See references 98, 106, 107, 166, 238 in the bibliography at the back for publications from this group in 2010. Electron microscope analysis of lipid nanotubes decorated with assembled retrovirus capsid protein : Left: cross-section of tube. Middle: surface of tube. Right: filtered image showing lattice. Collaboration with Peter Rosenthal (Division of Physical Biochemistry). MRC National Institute for Medical Research 51 INFECTIONS AND IMMUNITY Immune Cell Biology Pavel Tolar Activation of immune receptors Lab members: Jason Lee, Elizabeth Natkanski, Antonio Casal Antibodies are critical for human immunity and their induction has been instrumental for the success of many vaccines. However, some of the most dangerous pathogens of today’s world, such as HIV, influenza or malaria, evade antibody responses, both natural and vaccine-induced. A better understanding of the mechanisms by which these pathogens trigger antibody responses will be necessary for the development of more effective vaccines. Antibody responses are initiated by B lymphocytes that detect pathogens by surface antibodies in the form of B cell antigen receptors. Pathogen binding to the membrane antibody of the B cell receptor transduces signals to the intracellular signaling components. We are elucidating the structure of the parts of the B cell receptor that underly this process. We are also developing new ways to visualise the activation of individual B cell receptor molecules in the plasma membrane and their trafficking within B cells. Domain architecture of the B-cell antigen receptor. Publications Tolar P and Pierce SK (2010) A conformation-induced oligomerization model for B cell receptor microclustering and signaling. Current Topics in Microbiology and Immunology 340:155-69 Tolar P, Hanna J, Krueger PD and Pierce SK (2009) The constant region of the membrane immunoglobulin mediates B cell-receptor clustering and signaling in response to membrane antigens. Immunity 30:44-55 Tolar P, Sohn HW and Pierce SK (2005) The initiation of antigen-induced B cell antigen receptor signaling viewed in living cells by fluorescence resonance energy transfer. Nature Immunology 6:1168-1176 See references 149, 150 in the bibliography at the back for publications from this group in 2010. 52 MRC National Institute for Medical Research A scheme of B cell receptor clustering during formation of the immunological synapse. INFECTIONS AND IMMUNITY Immune Cell Biology Victor Tybulewicz EMBO member, FMedSci Signal transduction in B and T cells Lab members: Alexander Saveliev, Agnieszka Zachacz, Amy Slender, Lesley Vanes, Robert Köchl, Karen McGee, Sheona Watson, Eva Lana Elola, Edina Schweighoffer, Harald Hartweger B and T lymphocytes are white blood cells that are critical mediators of the immune response against a variety of pathogens. Inappropriate activation of these cells can result in autoimmune diseases such as rheumatoid arthritis. We are interested in understanding the biochemical signalling pathways within lymphocytes that control the activation, survival and migration of the cells. We have shown that proteins called Rac GTPases are critical for controlling the migration of both B and T cells into, through, and out of lymph nodes. Mouse models of Down Syndrome Trisomy of human chromosome 21 (Hsa21) occurs in around 1 in 750 live births and the resulting gene dosage imbalance gives rise to Down Syndrome, the most common form of mental retardation. In collaboration with Prof E. Fisher (UCL), we are interested in identifying genes on this chromosome, which, when present in three copies, cause the many different phenotypes of Down Syndrome. We have created a novel mouse strain carrying a freely segregating copy of Hsa21, which displays many of the features of Down Syndrome, including learning difficulties and cardiac abnormalities. In a recent study, we showed that the reduced incidence of solid tumours in Down Syndrome may be caused by decreased tumour angiogenesis. Publications Faroudi M, Hons M, Zachacz A, Dumont C, Lyck R, Stein JV and Tybulewicz VLJ (2010) Critical roles for Rac GTPases in T cell migration to and within lymph nodes. Blood 116:5536-47 Henderson RB, Grys K, Vehlow A, de Bettignies C, Zachacz A, Henley T, Turner M, Batista F and Tybulewicz VLJ (2010) A novel Rac-dependent checkpoint in B cell development controls entry into the splenic white pulp and cell survival. Journal of Experimental Medicine 207:837-853 Reynolds LE, Watson AR, Baker M, Jones TA, D’Amico G, Robinson SD, Joffre C, Garrido-Urbani S, Rodriguez-Manzaneque JC, MartinoEcharri E, Aurrand-Lions M, Sheer D, Dagna-Bricarelli F, Nizetic D, McCabe CJ, Turnell AS, Kermorgant S, Imhof BA, Adams R, Fisher EMC, Tybulewicz VLJ, Hart IR and Hodivala-Dilke KM (2010) Tumour angiogenesis is reduced in the Tc1 mouse model of Down’s syndrome. Nature 465:813-7 See references 6, 7, 52, 56, 62, 72, 116, 175, 209, 271 in the bibliography at the back for publications from this group in 2010. 3D quantitative immunohistology shows that T cells deficient in Rac GTPases (red) are mostly stuck on the endothelium of the lymph node (gold), whereas wild-type T cells (green) are able to penetrate the interstitial tissue. Sections of spleen from the Tc1 model of Down Syndrome show increased numbers of megakaryocytes compared to wild-type spleens. Megakaryocytes are visible as large red cells in the hematoxylin and eosin stained images, and brown in slides stained with antibodies to CD41. MRC National Institute for Medical Research 53 INFECTIONS AND IMMUNITY Immunoregulation Andreas Wack Immune response to influenza Lab members: Stefania Crotta, Sophia Davidson, Annita Gjoka, Gregory Ellis Seasonal influenza represents a constant burden to public health, and influenza pandemics caused by new virus strains pose a serious global threat. The influenza virus causes damage to the infected lung tissue and induces an immune response which is necessary to eliminate the virus but also contributes to lung pathology. In addition to direct damage, influenza infection also increases dramatically the susceptibility to bacterial co-infections, as evidenced by epidemiological and microbiological data from seasonal and pandemic influenza waves. Both for single and co-infections, it is unclear which factors tip the balance between pathology or death versus successful clearance of the pathogen without long term damage. Our work aims to identify which features of the virus and host determine the outcome of disease. We focus on early events after infection, and in particular on the interface between the infected epithelium and the innate immune system. We have established a culture system of mouse airway epithelium and use this in co-culture with innate immune cells to dissect cellular cross-talk after infection with a variety of influenza virus strains. These studies are complemented by in vivo studies to understand how airway epithelia contribute to the anti-influenza immune response. In addition, we are interested in the roles of natural killer cells and granulocytes in influenza infection and co-infection. These approaches will allow us the identification of early events and players that pave the way for immune-mediated pathology or protection. Publications Crotta S, Brazzoli M, Piccioli D, Valiante NM and Wack A (2010) Hepatitis C virions subvert natural killer cell activation to generate a cytokine environment permissive for infection. Journal of Hepatology 52:183-90 Gallorini S, Berti F, Mancuso G, Cozzi R, Tortoli M, Volpini G, Telford JL, Beninati C, Maione D and Wack A (2009) Toll-like receptor 2 dependent immunogenicity of glycoconjugate vaccines containing chemically derived zwitterionic polysaccharides. Proceedings of the National Academy of Sciences of the United States of America 106:17481-17486 Piccioli D, Sammicheli C, Tavarini S, Nuti S, Frigimelica E, Manetti AGO, Nuccitelli A, Aprea S, Valentini S, Borgogni E, Wack A and Valiante NM (2009) Human plasmacytoid dendritic cells are unresponsive to bacterial stimulation and require a novel type of cooperation with myeloid dendritic cells for maturation. Blood 113:4232-4239 54 MRC National Institute for Medical Research Influenza virus propagates in mouse airway epithelia. Cultures were infected with low amounts of influenza virus and stained for the tight junction protein ZO-1 (green) and influenza nucleoprotein (magenta) at the indicated time points after infection. INFECTIONS AND IMMUNITY INFECTIONS AND IMMUNITY Immune Cell Biology Robert Wilkinson FRCP Mycobacterial Research Victor Tybulewicz Understanding and intervening in HIV-associated tuberculosis Lab members: Katalin Wilkinson, Anna Coussens, Adrian Martineau, Shepherd Nhamoyebonde The programme derives its research questions from the clinical care of tuberculosis (TB) and HIV-TB co-infected persons in South Africa and London. Through clinically based studies we aim to improve knowledge of pathogenesis and thereby prevention and treatment. We have contributed to the description of a distinct transcriptomic signature of active TB and studies of interferon gamma release assays in the diagnosis of tuberculosis. We have investigated the effects and mechanisms of preventive therapies against tuberculosis. We have determined that protective antiretroviral-mediated immune recovery in HIV-TB is associated with expansion of central memory T cells rather than the commonly determined effector response. Conversely, pathological immune restoration, as exemplified by the HIV-TB immune reconstitution inflammatory syndrome, is contributed to by dysregulated Th1 expansions and by exaggerated cytokine release. We have determined that the steroid hormone, vitamin D, augments protective immunity to TB and that corticosteroids help suppress pathological immunity via downregulation of IL-6 and TNF. We have also uncovered evidence that an antigen absent from most BCG vaccine strains is a major target of the protective immune response. Publications Martineau, A.R., Timms, P.M., Bothamley, G.H., Claxton, A.P., Hanifa, Y., Islam, K., Packe, G.E., Moore-Gillon, J.C., Darmalingam, M., Davidson, R.N., Millburn, H.J., Baker, L.V., Barker, R.D., Woodward, N.J., Venton, T.R., Barnes, K.E., Mullett, C.J., Coussens, A.K., Rutterford, C.M., Mein, C.A., Davies, G.R., Wilkinson, R.J., Nikolayevskyy, V., Drobniewski, F.A., Eldridge, S.M., Griffiths, C.G. (2011) High-dose vitamin D3 during intensive phase treatment of pulmonary tuberculosis: a double-blind randomised controlled trial. Lancet 377: 242-250 Gideon, H.P., Wilkinson, K.A., Rustad, T.R., Oni, T., Guio, H., Kozak, R.A., Sherman, D.R., Meintjes, G., Behr, M.A., Vordermeier, H.M., Young, D.B., Wilkinson, R.J. (2010) Hypoxia induces an immunodominant target of tuberculosis specific T cells absent from common BCG vaccines. PLoS Pathogens 6:e1001237 Implication of TNF and IL-6 in the pathogenesis of TB-IRIS. Whilst many pro- and anti-inflammatory cytokine transcript and protein levels were elevated in TB-IRIS patients according to experimental circumstances, only IL-6 and TNF were elevated in all circumstances. Thus blockade of IL-6 or TNF may be a rational approach to immunomodulation in this condition. Berry MPR, Graham CM, McNab FW, Xu Z, Bloch SAA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, Quinn C, Blankenship D, Dhawan R, Cush JJ, Mejias A, Ramilo O, Kon OM, Pascual V, Banchereau J, Chaussabel D and O’Garra A (2010) An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466:973-977 See references 10, 13, 18, 19, 30, 34, 40, 95, 141, 144, 145, 157, 158, 160, 168, 169, 170, 190, 201, 223, 242, 249, 270, 273, in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 55 INFECTIONS AND IMMUNITY Molecular Immunology Mark Wilson Regulation of Th2 cells during allergic inflammation and anti-helminth immunity Lab members: Stephanie Czieso, Eleni Ktistaki, Nicholas Mathioudakis, Isobel Okoye, Kathleen Roderick More than a quarter of the world’s population are infected by one of four parasitic helminth’s (filarial worms, schistosomes, whipworms or roundworms) making them the most common infectious agents of humans in developing countries. Efficient expulsion of parasitic helminth’s from mammalian hosts requires a well-orchestrated immune response to activate innate immune cells and stimulate local tissue responses. CD4+ T helper 2 (Th2) lymphocytes coordinate the expulsion mechanism, placing them front and centre of anti-helminth immunity. One major aim of our work is to develop ways to promote Th2 cell responses and enhance anti-helminth immunity. An additional and complementary aim is to investigate ways to inhibit Th2 cell responses to remedy allergic disease. Allergic diseases plague hundreds of millions of people worldwide and are the result of dysregulated and hyperactive Th2 responses. These aims are being investigated using in vivo helminth infection and allergy models. Using next-generation sequencing and gene manipulation techniques the role of regulatory RNA species in Th2 cells and associated responses are being studied. De novo immune responses develop, often in tandem, with other ongoing immune responses. Therefore, in collaboration with other NIMR labs, we are investigating the mechanisms of Th2 cell development and function in the context of other immune responses. Together these aims will extend our knowledge of Th2 immunobiology, facilitate helminth elimination strategies, and identify novel allergy intervention. Hallmarks of allergic asthma using a murine model of Th2-mediated airway inflammation. Allergen-induced airway eosinophilia (A), goblet cell hyperplasia and mucus hypersecretion (B), peri-bronchial and perivascular inflammation (C). Publications Wilson MS, Pesce JT, Ramalingam TR, Thompson RW, Cheever A and Wynn TA (2008) Suppression of murine allergic airway disease by IL-2:anti-IL-2 monoclonal antibody-induced regulatory T cells. Journal of Immunology 181:6942-6954 Wilson MS, Elnekave E, Mentink-Kane MM, Hodges MG, Pesce JT, Ramalingam TR, Thompson RW, Kamanaka M, Flavell RA, Keane-Myers A, Cheever AW and Wynn TA (2007) IL-13Rα2 and IL-10 coordinately suppress airway inflammation, airway-hyperreactivity, and fibrosis in mice. Journal of Clinical Investigation 117:2941-2951 Wilson MS, Taylor MD, Balic A, Finney CAM, Lamb JR and Maizels RM (2005) Suppression of allergic airway inflammation by helminth-induced regulatory T cells. Journal of Experimental Medicine 202:1199-1212 56 MRC National Institute for Medical Research Helminth parasites of mammalian hosts. Schistosoma mansoni (A; adult male and female), Heligmosomoides polygyrus (B), Trichuris muris (C) in situ. INFECTIONS AND IMMUNITY Mycobacterial Research Douglas Young FMedSci Mycobacterial pathogenesis: gene expression and innate immune response Lab members: Kristine Arnvig, John Brennan, Stephen Coade, Teresa Cortes, Joanna Dillury, Damien Portevin, Graham Rose, Min Yang One third of the global population is exposed to infection with Mycobacterium tuberculosis but only ten percent of individuals will develop tuberculosis. The outcome of infection depends on a complex series of interactions with the immune system, which can result in disease or in a persistent asymptomatic, latent infection. We are studying the way that M. tuberculosis evades host immunity by misdirecting innate immune recognition and by adapting to a form that resists killing by phagocytes. Ultimately, we aim to develop drugs that rapidly eliminate persisting bacteria and vaccines that elicit more effective immunity. Evolutionarily diverse strains of M. tuberculosis vary widely in their induction of the host inflammatory response. Suppression of innate immune recognition by modern lineages promotes early progression to disease, while the pro-inflammatory phenotype of ancient lineages favours latent infection and reactivation. RNA sequencing has allowed us to identify an extensive network of post-transcriptional regulation that we think will be critical in adaptation of mycobacteria to survival in infected tissues. We are studying this as part of SysteMTb, a European systems biology consortium. We have identified a large number of regulatory small RNA molecules in M. tuberculosis. We are currently characterising the role of sRNAs in mycobacterial gene regulation. Publications Kirschner DE, Young D and Flynn JL (2010) Tuberculosis: global approaches to a global disease. Current Opinion in Biotechnology 21:524-531 Arnvig KB and Young DB (2009) Identification of small RNAs in Mycobacterium tuberculosis. Molecular Microbiology 73:397-408 Clinical isolates of M. tuberculosis show consistent differences in cytokine induction during infection of human monocyte-derived macrophages. We are studying the genetic basis for this variation. Barry CE, 3rd, Boshoff HI, Dartois V, Dick T, Ehrt S, Flynn J, Schnappinger D, Wilkinson RJ and Young D (2009) The spectrum of latent tuberculosis: rethinking the biology and intervention strategies. Nature Reviews Microbiology 7:845-855 See references13, 46, 133, 231, 236 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 57 INFECTIONS AND IMMUNITY Mycobacterial Research Microarray laboratory Molecular pathogenicity of mycobacteria Lab members: Roger Buxton, Debbie Hunt, Christina Kahramanoglou, Nishad Matange, Vicky Spivey To grow within a host, some pathogens manipulate their environment for their own advantage. Mycobacterium tuberculosis is a master of this ecological niche management, allowing it to grow within macrophages, cells that kill most pathogens. We are studying two signalling systems that the bacterium uses to achieve this, serine-threonine protein kinases (in collaboration with Steve Smerdon, Molecular Structure), and the global transcriptional regulator, cyclic AMP receptor protein. One of the genes that the cAMP receptor protein (CRP) controls is espA, required for secretion of the virulence factor, the protein ESAT-6. In this western blot of cell-free extracts of M. tuberculosis, the accumulation of ESAT-6 can be seen in an espA mutant (lanes 2 and 3) whereas in the wild-type virtually all of the protein is secreted (lanes 1 and 6). Complementation with the wild-type espA allele restores ESAT-6 secretion (lanes 4 and 5). The metabolic changes that the bacterium causes means, however, that gene regulation also has evolved to cope with these novel conditions. For example, mycobacteria synthesise very high levels of the small nucleotide cyclic AMP, which increase after macrophage infection. In collaboration with Jeff Green (University of Sheffield) we have examined how M. tuberculosis manages to control gene expression at these high levels of cAMP, identifying novel mechanisms of transcriptional initiation control via the cyclic AMP receptor protein. Knowing how M. tuberculosis copes with its peculiar lifestyle enables us to identify novel features that may be drug targets, and in collaboration with MRC Technology we have carried out screens for new inhibitors against these targets. Publications Stapleton M, Haq I, Hunt DM, Arnvig KB, Artymiuk PJ, Buxton RS and Green J (2010) Mycobacterium tuberculosis cAMP receptor protein (Rv3676) differs from the Escherichia coli paradigm in its cAMP-binding, DNA-binding and transcription activation properties. Journal of Biological Chemistry 285:7016-7027 Hunt DM, Saldanha JW, Brennan JF, Benjamin P, Strom M, Cole JA, Spreadbury CL and Buxton RS (2008) Single nucleotide polymorphisms causing structural changes in the CRP transcriptional regulator of the TB vaccine strain Mycobacterium bovis BCG alter global gene expression without attenuating growth. Infection and Immunity 76:2227-2234 Signalling mediated by a serine-threonine protein kinase. Autoradiogram showing phosphorylation of the ABC transporter Rv1747 in vitro by the kinase PknF on residues T150 and T208. Mutation of both these residues results in significant loss of phosphorylation. 58 MRC National Institute for Medical Research Rickman L, Scott C, Hunt DM, Hutchinson T, Menendez MC, Whalan R, Hinds J, Colston MJ, Green J and Buxton RS (2005) A member of the cAMP receptor protein family of transcription regulators in Mycobacterium tuberculosis is required for virulence in mice and controls transcription of the rpfA gene coding for a resuscitation promoting factor. Molecular Microbiology 56:1274-1286 INFECTIONS AND IMMUNITY Parasitology Childhood Malaria Research Group Childhood Malaria Research Group Tony Holder, Olugbemiro Sodeinde, Delmiro Fernandez-Reyes This clinical research unit is a partnership between the NIMR Division of Parasitology and the College of Medicine University of Ibadan, University College Hospital (COMUI-UCH), in Ibadan, Nigeria. Nigeria, the most populous African country, accounts for an estimated one-quarter of all malaria cases worldwide. Malaria in Ibadan is holoendemic with transmission occurring all year round. Ibadan is a densely populated city of at least three million people where malaria is ranked amongst the most common causes of death in children under the age of five years. The CMRG at COMUI-UCH is placed within the major clinical referral centre for severe malaria cases and provides the framework for our research on the molecular basis of the pathogenesis of cerebral malaria and severe malarial anaemia. Among its several functions the CMRG builds malaria research capability closer to the point of care, which allows more precise sampling and alignment of the clinical and molecular aspects of severe disease. The CMRG is overseen by a group of seven academics from both institutions and its infrastructure consists of a Malaria Research Laboratory situated at the Department of Paediatrics, closely coupled with the Paediatrics Emergency Ward and the Children’s Outpatient Clinics where recruitment of patients take place. For information or submitting research enquires for collaborative work please email Dr. Fernandez-Reyes at [email protected] The CMRG academic panel: • Prof. K. Osinusi. Head of Department of Paediatrics COMUI-UCH • Dr. B.J. Brown. Department of Paediatrics COMUI-UCH. • Dr. F.O. Akinbami. Department of Paediatrics, COMUI-UCH • Prof. W.A. Shokunbi. Department of Haematology, COMUI-UCH • Dr A. Holder. Head of Division of Parasitology, NIMR • Dr. D. Fernandez-Reyes. Division of Parasitology, NIMR • Prof. O. Sodeinde. Division of Parasitology, NIMR MRC National Institute for Medical Research 59 INFECTIONS AND IMMUNITY Virology WHO Collaborating Centre for Reference and Research on Influenza (WIC) Director: John McCauley Lab members: Rod Daniels (Deputy Director), Yi Pu Lin (Assistant Director), Zheng Xiang, Vicki Gregory, Lynn Whittaker, Nick Cattle, Karen Cross, Chandrika Halai, Johannes Kloess The WHO Influenza centre at NIMR is one of five WHO Collaborating Centres for Reference and Research on Influenza. These Centres, together with some 130 National Influenza Centres, comprise the WHO Global Surveillance Network which tracks influenza viruses as they circulate around the world. Viruses are characterised antigenically and genetically in the laboratories and their susceptibility to antiviral drugs is determined. Results of these analyses from Collaborating and National Influenza Centres are used to develop recommendations for the most appropriate type A and type B influenza viruses for use in seasonal influenza vaccines and provide advice to national authorities on both global and regional influenza circulation. Recent work in the WIC has highlighted the emergence of a variant of the pandemic H1N1 virus that shows distinct receptor binding characteristics and cell tropism in model systems. In addition recent H3N2 viruses show distinct alterations in their ability to bind to sialic acid receptors; these alterations in receptor binding can have marked implications on the antigenic analysis of the virus. For both the pandemic H1N1 and H3N2 viruses, recently emerged genetic groups of viruses have been detected. All studies are carried out on a collaborative basis with the various National Influenza Centres that supply specimens, the other WHO Collaborating Centres, the UK Health Protection Agency Centre for Infection (Colindale) and National Institute for Biological Standards and Control, members of the European Community Network of Reference Laboratories for human influenza and the Wellcome Trust Sanger Institute. Publications Barr IG, McCauley J, Cox N, Daniels R, Engelhardt OG, Fukuda K, Grohmann G, Hay A, Kelso A, Klimov A, Odagiri T, Smith D, Russell C, Tashiro M, Webby R, Wood J, Ye Z and Zhang W (2010) Epidemiological, antigenic and genetic characteristics of seasonal influenza A(H1N1), A(H3N2) and B influenza viruses: basis for the WHO recommendation on the composition of influenza vaccines for use in the 2009-2010 Northern Hemisphere season. Vaccine 28:1156-67 Lin YP, Gregory V, Collins P, Kloess J, Wharton S, Cattle N, Lackenby A, Daniels R and Hay A (2010) Neuraminidase receptor binding variants of human influenza A(H3N2) viruses due to substitution of aspartic acid 151 in the catalytic site - role in virus attachment? Journal of Virology 84:6769-6781 A model of the structure of the H3 haemagglutinin glycoprotein illustrating the location of amino acid substitutions seen in three emerging genetic groups of the A(H3N2) virus. Positions of substitutions are colour-coded by genetic group/subgroup as represented by A/ Hong Kong/2121/2010 (D53N, I230V, E280A/ Y94H, R208K), A/Johannesburg/310/2010 (S45N) and A/Sri Lanka/3/2010 (T48A, K92R, N312S). 60 MRC National Institute for Medical Research A model of the structure of the H1 haemagglutinin glycoprotein illustrating the location of amino acid substitutions seen in two emerging genetic groups of the pandemic A(H1N1) 2009 virus. Positions of substitutions are colour-coded by genetic group/subgroup as represented by A/ Christchurch/16/2010 (N125D/D94N,V250A) and A/Hong Kong/2213/2010 (S128P,V199A, I295V/ K163T, P271S). Liu Y, Childs RA, Matrosovich T, Wharton S, Palma AS, Chai W, Daniels R, Gregory V, Uhlendorff J, Kiso M, Klenk H-D, Hay A, Feizi T and Matrosovich M (2010) Altered receptor specificity and cell tropism of D222G haemagglutinin mutants from fatal cases of pandemic A(H1N1) 2009 influenza. Journal of Virology 84:12069-74 See references 12, 31, 148, 151, 177, 185, 277 in the bibliography at the back for publications from this group in 2010. Structural Biology Mathematical Biology Willie Taylor (Head of Division) Richard Goldstein Molecular Structure Steve Gamblin (Joint Head of Division) Steve Smerdon (Joint Head of Division) Paul Driscoll Annalisa Pastore Andres Ramos Katrin Rittinger Ian Taylor Physical Biochemistry Justin Molloy (Head of Division) Ed Hulme John Offer Peter Rosenthal Martin Webb See also the following groups: Mike Blackman (Infections and Immunity) Tom Carter (Neurosciences) Matthew Hannah (Neurosciences) Jonathan Stoye (Infections and Immunity) MRC National Institute for Medical Research 61 STRUCTURAL BIOLOGY Molecular Structure Paul Driscoll Structural and functional analysis of signalling proteins Lab members: Diego Esposito, Acely Garza-Garcia, Timothy Ragan, Andrew Sankar, Lily Nematollahi, Masooma Rasheed, Gemma Wildsmith, Lucy Murfitt Nuclear magnetic resonance (NMR) spectroscopy provides a valuable means to probe the three-dimensional structure, dynamic characteristics and binding properties of biological macromolecules. Our group employs state-of-the-art methods in NMR to probe the nature of interactions between proteins implicated in fundamental cellular and organismal processes. These include the activation of death receptor signalling cascades, limb regeneration in the adult newt, the regulation of phospholipase C isozymes, and the interaction of VEGF with its receptors. Recently we have developed a system to enable structural and biophysical investigation of the core of the so-called death-inducing signalling complex (DISC) comprised of the ‘death domains’ of the cell surface receptor CD95/Fas and its immediate adaptor protein FADD. We find that the 120 kD particle comprises ten protein chains in a 5+5 arrangement, and that the complexity of the NMR spectra derives from intrinsic asymmetry of the structure. These data are reminiscent of the asymmetric structure of the PIDDosome, an unrelated death domain complex; NMR spectra for the PIDDosome yield similar characteristics. This work provides an excellent platform for further analysis of the intact DISC. Cartoon representation of death inducing signalling complex (DISC) formation. Publications Esposito D, Sankar A, Morgner N, Robinson CV, Rittinger K and Driscoll PC (2010) Solution NMR investigation of the CD95/FADD homotypic death domain complex suggests lack of engagement of the CD95 C terminus. Structure 18:1378-90 Jarvis A, Allerston CK, Jia H, Herzog B, Garza-Garcia A, Winfield N, Ellard K, Aqil R, Lynch R, Chapman C, Hartzoulakis B, Nally J, Stewart M, Cheng L, Menon M, Tickner M, Djordjevic S, Driscoll PC, Zachary I and Selwood DL (2010) Small molecule inhibitors of the neuropilin-1 vascular endothelial growth factor A (VEGF-A) interaction. Journal of Medicinal Chemistry 53:2215-26 Garza-Garcia A, Harris R, Esposito D, Gates PB and Driscoll PC (2009) Solution structure and phylogenetics of Prod1, a member of the three-finger protein superfamily implicated in salamander limb regeneration. PLoS ONE 4:e7123 62 MRC National Institute for Medical Research Detail from ILV-methyl TROSY NMR spectra of free (black) and complexed (red) DISC death domains. See references 67, 82, 91, 122, 197 in the bibliography at the back for publications from this group in 2010. STRUCTURAL BIOLOGY Molecular Structure Steve Gamblin EMBO member, FMedSci Structural biology of influenza, energy metabolism and cancer Lab members: Neil Justin,Valeria De Marco, Bing Xiao, Chun Jing, Richard Heath, Elizabeth Underwood, Peter Coombs, Sebastien Vachieri, Rein Aasland, Steve Martin We study the structure and function of molecules involved in disease processes such as influenza, diabetes and cancer. We use X-ray crystallography and NMR to determine the threedimensional structures and dynamics of these molecules. In combination with other biophysical, biochemical and biological techniques, the data help us elucidate the function of the proteins of interest and provide information that may be useful for the development of therapeutic approaches. We have a long-term interest in how cellular energy levels are sensed and regulated by the heterotrimeric AMP activated protein kinase (AMPK). In response to increased energy utilisation AMPK activates energy producing pathways and inhibits energy consuming processes. As such it has been implicated in a number of diseases related to energy metabolism including type 2 diabetes, obesity and, most recently, cancer. In a long-term collaboration with David Carling’s laboratory we have recently shown that ADP, as well as AMP, binding to regulatory domain protects the enzyme from dephosphorylation. Our studies have shown that AMPK displays significantly tighter binding to ADP than to Mg.ATP, explaining how the enzyme is regulated under physiological conditions where the concentration of Mg.ATP is higher than that of ADP and much higher than that of AMP. We have determined the crystal structure of an active AMPK complex that shows how the binding of ADP to the regulatory subunit protects the kinase domain from dephosphorylation and have developed a model for how the energy status of a cell regulates AMPK activity. Publications Xiao B, Sanders M, Underwood E, Heath R, Mayer F, Carmena D, Jing C, Walker P, Eccleston J, Haire L, Howell S, Saiu P, Aasland R, Martin SR, Carling D & Gamblin SJ. (2011) Structure of mammalian AMPK and its regulation by ADP. Nature 472:230-3 Margueron R, Justin N, Ohno K, Sharpe ML, Son J, Drury III WJ, Voigt P, Martin SR, Taylor WR, De Marco V, Pirrotta V, Reinberg D and Gamblin SJ (2009) Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461:762-7 Collins PJ, Haire LF, Lin YP, Liu J, Russell RJ, Walker PA, Skehel JJ, Martin SR, Hay AJ and Gamblin SJ (2008) Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants. Nature 453:1258-61 Ribbons representation of two orthogonal views of active AMPK. The kinase domain is coloured in yellow with its activation loop in pink. The regulatory gamma subunit which binds AMP/ADP/ATP competitively is coloured in red. See references 88, 123, 234 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 63 STRUCTURAL BIOLOGY Mathematical Biology Richard Goldstein Modelling of evolution Lab members: Martin Godany, Kyriakos Kentzoglanakis, Asif Tamuri All biology is the result of evolution. In order to understand life, we need to investigate the evolutionary process that determines its form and function. Because living things encode this evolutionary heritage, studies of their properties can provide insights into the evolutionary process. Following the evolutionary path of specific components can provide important information about the characteristics of living organisms. Combining insights from physical chemistry, condensed matter physics, artificial intelligence, complexity theory, and mathematical biology, we are developing computational and theoretical methods to explore these areas. We are investigating the evolution of viruses such as influenza in order to better understand the way they act now and how they might change in the future. In particular, we have been investigating how influenza is able to shift from one host to another, as it did with such deadly consequences in 1918 and as it is doing now. We are modelling the evolution of chemotaxis, the process that allows bacteria to find nutrients. Insights into the evolutionary history of the chemotaxis control network can give us insight into how its form reflects the constraints of their environment. We are also studying how horizontal gene transfer affects the evolution of bacteria, espeically in cases where the interests of the genes and the organisms conflict. Publications Shah SD, Doorbar J and Goldstein RA (2010) Analysis of host-parasite incongruence in Papillomavirus evolution using importance sampling. Molecular Biology and Evolution 27:1301-14 Structure of NS1 protein from influenza, interacting with Human Cellular Factor CPSF30 (PDB 2RHK), showing in orange the locations identified as involved with the adaptation of influenza from birds to humans. Many of the locations so identified (such as locations 104 and 105 in this protein) interact with host factors, in this case, one processing celluar pre-mRNAs involved in the host imune response. See references 61, 76, 77, 78, 79, 97, 228 in the bibliography at the back for publications from this group in 2010. 64 MRC National Institute for Medical Research dos Reis M, Hay AJ and Goldstein RA (2009) Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 ‘Spanish’ influenza pandemic virus. Journal of Molecular Evolution 69:333-345 Tamuri AU, dos Reis M, Hay AJ and Goldstein RA (2009) Identifying changes in selective constraints: host shifts in influenza. PLoS Computational Biology 5:e1000564 STRUCTURAL BIOLOGY Physical Biochemistry Ed Hulme Structure and function of G protein-coupled receptors Lab members: Carol Curtis Living cells are delimited by a membrane which isolates their internal machinery from the external world. However, cells such as the neurons which form the information-transduction networks of the brain must still be able to respond to incoming chemical signals. The 7-transmembrane helix G protein-coupled receptors (GPCRs) are a superfamily of genetically-encoded nanomachines that have evolved to enable this. Since GPCRs are the targets of about 40% of clinically prescribed drugs, a detailed understanding of their structures and molecular mechanisms of action is essential for the modern program of rational drug development. M1 muscarinic acetylcholine receptors (M1 mAChRs) regulate the activity of important neurons in the forebrain. They are major mediators of cortical attention mechanisms. Drugs that selectively activate M1 mAChRs may help to alleviate the cognitive defects in Alzheimer’s and schizophrenia. We are making stable ligand complexes of M1 mAChRs, using pharmacological and mutational methods. Recently, we have focused on a high affinity peptide toxin, MT7. We are working towards an atomic resolution structure by X-ray crystallography. Such complexes will provide a starting point for structure-based drug design. Publications Hulme EC and Trevethick MA (2010) Ligand binding assays at equilibrium: validation and interpretation. British Journal of Pharmacology 161:1219-37 Lebon G, Langmead CJ, Tehan BG and Hulme EC (2009) Mutagenic mapping suggests a novel binding mode for selective agonists of M1 muscarinic acetylcholine receptors. Molecular Pharmacology 75:331-341 Goodwin JA, Hulme EC, Langmead CJ and Tehan BG (2007) Roof and floor of the muscarinic binding pocket: Variations in the binding modes of orthosteric ligands. Molecular Pharmacology 72:1484-1496 The high affinity peptide toxin MT7 may emulate the “plug” domain of the photoreceptor, rhodopsin. The tips of the three “fingers” of the disulphidestabilised β-sheet of the toxin insert themselves into the extracellular loops of the M1 mAChR to yield a stable complex . See reference 119 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 65 STRUCTURAL BIOLOGY Physical Biochemistry Justin Molloy Single molecule studies of cell motility and cell signalling Lab members : Suleman Bawumia, Rachel Farrow, Stephen Martin, Gregory Mashanov, Paul Moody The principal goal of the lab is to understand the molecular mechanism of force production by acto-myosin and how proteins and organelles move around within living cells. Laser-based optical methods like optical tweezers and total internal reflection fluorescence microscopy (TIRFM) allow us to observe, track and manipulate individual molecules either in isolated preparations or within living cells. Molecular motors convert chemical energy into mechanical work and power processes like muscle contraction, cell migration and DNA processing; they are critical to the healthy function of our cells. We are interested in diverse aspects of human health, including how the malarial parasite gains entry into human blood cells, the mechanism of human hearing, and how the two strands of DNA are separated and copied. Our laser-based tools enable us to visualise and manipulate individual molecules so that we can understand molecular mechanisms with unprecedented precision. Recent work has shown how actin filaments become aligned by myosin motors in migrating cells; dual-colour fluorescence imaging has allowed us to image individual G-protein coupled receptors at the cell membrane and a reagentless biosensor has enabled us to visualise DNA unwinding by helicases. Publications Butt T, Mufti T, Humayun A, Rosenthal PB, Khan S, Khan S and Molloy JE (2010) Myosin motors drive long-range alignment of actin filaments. Journal of Biological Chemistry 285:4964-4974 (A) Dual colour imaging to visualise the formation and dissociation of individual muscarinic acetylcholine receptors at the cell membrane of a living cell. (B) Single (upper) and dual (lower) colour imaging was used. The red (R) and green (G) dots (in the lower panel) are individual receptors. Dimers have either “RR”, “RG” or “GG” dyes. (C) By tracking individual molecules as they diffuse, we observe two-step photobleaching (upper) and see differentially-labelled dimers (RG) form and then dissociate (lower panel). Fili N, Mashanov GI, Toseland CP, Batters C, Wallace MI, Yeeles JTP, Dillingham MS, Webb MR and Molloy JE (2010) Visualizing helicases unwinding DNA at the single molecule level. Nucleic Acids Research 38:4448-4457 Hern JA, Baig AH, Mashanov GI, Birdsall B, Corrie JET, Lazareno S, Molloy JE and Birdsall NJM (2010) Formation and dissociation of M1 muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules. Proceedings of the National Academy of Sciences of the United States of America 107:2693-2698 See references 15, 25, 80, 117, 162 in the bibliography at the back for publications from this group in 2010. 66 MRC National Institute for Medical Research STRUCTURAL BIOLOGY Physical Biochemistry John Offer Synthetic protein laboratory: acyl transfer for chemical biology and synthesis Lab members: Lotta Holm, Caroline Morris, George Papageorgiou Post translationally-modified proteins can now be synthesised with a combination of ligation and optimised peptide synthesis. Emerging methods of ligation enable expressed proteins and synthetic peptides to be selectively coupled and our main goal is to increase the synthetic flexibility of these techniques, enabling the semi-synthesis of proteins containing non-natural amino acids with a broad range of applications. The focus of this laboratory is to use ligation to build biological macromolecules. However, the generality of chemical ligation is limited to a handful of favorable ligation sites, and so in our lab novel auxiliary approaches have been developed to universalise it. The demand for site-specifically modified proteins for structural studies or fluorescent labelling of proteins in cells is driving the further development of these techniques. We are also applying chemical ligation to the synthesis of chemically defined peptide-oligosaccharide glycoconjugates as HIV vaccines. Publications Offer J (2010) Native chemical ligation with Nα acyl transfer auxiliaries. Biopolymers 94:530-541 Burlina F, Dixson DD, Doyle RP, Chassaing G, Boddy CN, Dawson P and Offer J (2008) Orthogonal ligation: a three piece assembly of a PNA-peptidePNA conjugate. Chemical Communications 2785-2787 Scanlan CN, Offer J, Zitzmann N and Dwek RA (2007) Exploiting the defensive sugars of HIV-1 for drug and vaccine design. Nature 446:1038-1045 See reference 187 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 67 STRUCTURAL BIOLOGY STRUCTURAL BIOLOGY Molecular Structure Molecular Structure Annalisa Pastore EMBO member Understanding the molecular bases of neurodegeneration Lab members: Salvatore Adinolfi, Cesira de Chiara, Serena Faggiano, John McCormick, Laura Masino, Kris Pauwels, Raj Menon, Robert Yan We are interested in studying the structure and function of proteins linked to neurodegenerative diseases in order to understand the events which lead to pathology and design suitable therapeutic strategies. We focus on two distinct but converging families of diseases. We study proteins involved in diseases caused by protein aggregation and misfolding, such as Huntington’s chorea, MachadoJoseph disease and other types of spinocerebellar ataxias. We are interested in mitochondrial pathologies linked to misfunctioning of iron metabolism, such as Friedreich’s ataxia. Our approach uses different complementary biophysical, biochemical and bioinformatics techniques which range from various spectroscopies, to AFM, EM and ITC calorimetry. During the last few years, we have identified the molecular bases which explain the onset of spinocerebellar ataxia type 1and 3. In both cases, we have shown that it is essential to understand the normal functions of the proteins responsible for disease in order to understand pathology as the two aspects are intimately linked. We have also described the interactions between frataxin and the IscS/IscU complex, central to the highly conserved machinery devoted to iron sulphur cluster assembly. This knowledge will be used for drug design for the treatment of Friedreich’s ataxia. Publications Adrover M, Esposito V, Martorell G, Pastore A and Temussi PA (2010) Understanding cold denaturation: the case study of Yfh1. Journal of the American Chemical Society 135:16240–16246 Prischi F, Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI and Pastore A (2010) Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly. Nature Communications 1:95 Adinolfi S, Iannuzzi C, Prischi F, Pastore C, Iametti S, Martin SR, Bonomi F and Pastore A (2009) Bacterial frataxin CyaY is the gatekeeper of iron-sulfur cluster formation catalyzed by IscS. Nature Structural & Molecular Biology 16:390-6 See references 2, 3, 55, 58, 68, 69, 184, 196, 198, 204, 205, 214, 243, 252 in the bibliography at the back for publications from this group in 2010. Model of the ternary complex of bacterial frataxin, IscS and IscU as obtained from a combination of NMR, small angle X-ray scattering and mutagenesis data. 68 MRC National Institute for Medical Research STRUCTURAL BIOLOGY Molecular Structure Andres Ramos Molecular recognition in post-transcriptional regulation Lab members: Adela Candel, Katherine Collins, David Hollingworth, Vijayalaxmi Manoharan, Giuseppe Nicastro Post-transcriptional control plays a key role in expanding genomic diversity in complex organisms, and de-regulation of the metabolism of specific mRNAs lies at the basis of common genetic diseases, cancer, autoimmune pathologies and viral infection. Our goal is to explain how RNA-binding proteins achieve and regulate target selectivity and how they control the expression of subsets of genes. We combine information obtained from NMR experiments with that obtained by other biophysical/structural techniques and by in cell/in vivo assays. Our recent work on the FUSE element of the c-myc oncogene indicates that single stranded nucleic acid binding proteins use common strategies in transcriptional and post-transcriptional regulation. We show that an unfolded linker in the activator FUSE Binding Protein (FBP) decreases the cooperativity between DNA binding and repressor recruitment, allowing a substantial surge in c-Myc concentration. This is reminiscent of the intramolecular interdomain decoupling existing in numerous proteins regulating mRNA metabolism, such as KSRP/FBP2, which facilitates reversible interactions. Our data on the FUSE system suggest a way to control the changes in c-Myc concentration associated with cell replication and human cancers. Publications The structure and nucleobase specificity of the four KH domains of the KSRP protein indicate alternative binding modes to the AU-rich Element (ARE) and miRNA precursor target RNAs Cukier CD, Hollingworth D, Martin SR, Kelly G, Díaz-Moreno I and Ramos A (2010) Molecular basis of FIR-mediated c-myc transcriptional control. Nature Structural & Molecular Biology 17:1058-64 Díaz-Moreno I, Hollingworth D, Frenkiel TA, Kelly G, Martin S, Howell S, García-Mayoral M, Gherzi R, Briata P and Ramos A (2009) Phosphorylation-mediated unfolding of a KH domain regulates KSRP localization via 14-3-3 binding. Nature Structural & Molecular Biology 16:238-246 Trabucchi M, Briata P, Garcia-Mayoral M, Haase AD, Filipowicz W, Ramos A, Gherzi R and Rosenfeld MG (2009) The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs. Nature 459:1010-1014 See references 9, 48, 49, 59, 193 in the bibliography at the back for publications from this group in 2010. The interaction between FBP Interaction Repressor (FIR) RRM1/RRM2 (grey) and the N-box recruiting element of FIR (blue) (left) indicates that an unfolded 50-amino acid linker partially decouples activator-DNA interaction from repressor recruitment (right). MRC National Institute for Medical Research 69 STRUCTURAL BIOLOGY Molecular Structure Katrin Rittinger Structural biology of signalling networks that regulate innate and adaptive immunity Lab members: Frank Ivins, Aylin Morris-Davies, Kovilen Sawmynaden, Ben Stieglitz, Edmond Wong Pattern recognition receptors are key sensors of microbial infection and responsible for initiating a pro-inflammatory response. The signalling pathways regulating these events need to be tightly controlled as misregulation can lead to chronic inflammation and autoimmune disease. Innate immune responses can also trigger adaptive immunity and the two systems are linked through complex signalling networks. Our research is focused on the structural and mechanistic characterisation of protein complexes that regulate innate and adaptive immunity. We are particularly interested in understanding the function of the NLR (NOD-like receptor) family of intracellular pattern recognition receptors on a molecular level. Post-translational modification of proteins with ubiquitin acts as a key signal in immune signalling pathways. Unlike K48-linked polyubiquitin chains, which target a protein for proteasomal degradation, K63linked and the recently discovered M1-linked (“linear”) ubiquitin chains have emerged as key components of pathways mediating immune and inflammatory responses. We want to understand how poly-ubiquitin chains regulate the activation of NF-kB. In parallel we aim to elucidate the mechanism by which E3 ligases catalyse the formation of specific ubiquitin chains. Signalling through NLRs. Publications Ivins FJ, Montgomery MG, Smith SJ, Morris-Davies AC, Taylor IA and Rittinger K (2009) NEMO oligomerisation and its ubiquitin-binding properties. Biochemical Journal 421:243-251 Saveliev A, Vanes L, Ksionda O, Rapley J, Smerdon SJ, Rittinger K and Tybulewicz VLJ (2009) Function of the nucleotide exchange activity of Vav1 in T cell development and activation. Science Signaling 2:ra83 See references 11, 63, 67, 108 in the bibliography at the back for publications from this group in 2010. 70 MRC National Institute for Medical Research Overview of the ubiquitination cascade. The covalent attachment of ubiquitin to a protein substrate proceeds via a 3-step reaction involving an E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme and an E3 ubiquitin ligase. STRUCTURAL BIOLOGY Physical Biochemistry Peter Rosenthal Cryomicroscopy of proteins, viruses and cells Lab members: Lesley Calder, Tim Grant, Saira Hussain, Rishi Matadeen, Kasim Sader, James Streetley, Sebastian Wasilewski Our group studies the architecture of large protein assemblies in order to understand basic molecular mechanisms that control protein and membrane traffic in the cell and during virus infection. We apply electron cryomicroscopy and image analysis to study the structure of purified protein complexes in frozen solution. We use electron cryotomography to directly image cells in a frozen-hydrated state providing high resolution images of cell architecture as well as structural information on protein complexes in vivo. A major focus of the lab is the ultrastructure of viruses. We are interested in understanding how lipid-enveloped viruses such as influenza and retroviruses enter cells by membrane fusion and how new particles are assembled and released by budding through host membranes. As part of our studies of organelle formation and transformation, we build structural models for Weibel-Palade bodies, which are storage granules for the adhesive blood glycoprotein von Willebrand factor. We are working to improve experimental methods for high resolution imaging of proteins and to develop new computational procedures for image analysis. We are also interested in designing and imaging nanoscale assemblies with novel functions. Publications Calder LJ, Wasilewski S, Berriman JA and Rosenthal PB (2010) Structural organization of a filamentous influenza A virus. Proceedings of the National Academy of Sciences of the United States of America 107:10685-10690 Schmitz S, Schaap IAT, Kleinjung J, Harder S, Grainger M, Calder L, Rosenthal PB, Holder AA and Veigel C (2010) Malaria parasite actin polymerisation and filament structure. Journal of Biological Chemistry 285:36577-36585 Berriman JA, Li S, Hewlett LJ, Wasilewski S, Kiskin FN, Carter T, Hannah MJ and Rosenthal PB (2009) Structural organization of Weibel-Palade bodies revealed by cryoEM of vitrified endothelial cells. Proceedings of the National Academy of Sciences of the United States of America 106:17407-17412 See references 25, 26, 222 in the bibliography at the back for publications from this group in 2010. Map of the pyruvate dehydrogenase E2 complex by cryomicroscopy and image analysis. Structural model for a Weibel-Palade body containing von Willebrand factor tubules. MRC National Institute for Medical Research 71 STRUCTURAL BIOLOGY Molecular Structure Steve Smerdon EMBO member Structural biology of phosphorylation-dependent signalling in the cell cycle and DNA damage response Lab members: Julie Clapperton, Richard Li, Simon Pennell, Grace Yu, Otto Kyrieleis, Lasse Stach, Mohamed Ismail, Jan Lloyd, Oliver de Peyer The dynamic nature of cellular signalling processes requires them to be rapidly reversible, a characteristic that is generally achieved through protein phosphorylation. The response to DNA damage is mediated by a cascade of phosphorylation that originates at the lesion and is transduced to effector molecules and complexes. Defects in the precision of phosphorylation are a primary cause of many cancers and other diseases. By understanding the molecular basis of specificity within a web of regulatory interactions, we can determine why these processes run amok, and may be able to design drugs to combat these effects. To this end, we focus on an emerging group of proteins and modules such as 14-3-3, Forkheadassociated (FHA), Brca1-C-terminus (BRCT) and Polo-box domains that function as phosphorylation-dependent adaptors or scaffolding molecules in Ser/Thr kinase pathways. Our recent work has shown how FHA and BRCT-repeat domains of Nbs1 - a component of the MRN DNA damage complex - work in concert to orchestrate DNA break processing and signalling to the rest of the repair machinery. In a study of kinase signalling in M. tuberculosis, we have revealed a role for phospho-independent FHA interactions and a novel, intra-molecular binding mechanism in the control of core metabolic processes that likely have significance for bacterial virulence. The FHA-domain protein Rv1827 regulates three enzymes of the TCA cycle in Mycobacterium tuberculosis to control glutamate flux and nitrogen assimilation (left). It does so by phospho-independent interactions with three distinct enzyme complexes mediated through a surface on the core FHA domain.This is occluded by a novel ‘bind-back’ switch activated by threonine phosphorylation within a regulatory N-terminal region as revealed by nuclear magnetic resonance spectroscopy (right). Publications Lloyd J, Chapman JR, Clapperton JA, Haire LF, Hartsuiker E, Li J, Carr AM, Jackson SP and Smerdon SJ (2009) A supramodular FHA/BRCT-repeat architecture mediates Nbs1 adaptor function in response to DNA damage. Cell 139:100-11 Nott TJ, Kelly G, Stach L, Li J, Westcott S, Patel D, Hunt DM, Howell S, Buxton RS, O’Hare HM and Smerdon SJ (2009) An intramolecular switch regulates phosphoindependent FHA domain interactions in Mycobacterium tuberculosis. Science Signaling 2:ra12 Stucki M, Clapperton JA, Mohammad D, Yaffe MB, Smerdon SJ and Jackson SP (2005) MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. (See also erratum:Vol 124, pg 1299, 2006). Cell 123:1213-26 See references 14, 161, 200, 245, 255 in the bibliography at the back for publications from this group in 2010. 72 MRC National Institute for Medical Research The structure of Nijmegen-breakage syndrome protein 1 (Nbs1) shows how an unusual molecular architecture underpins its function through phosphorylation-dependent interactions. The green nuclear speckles show the locations of individual double-stranded DNA breaks that are under repair. STRUCTURAL BIOLOGY Molecular Structure Ian Taylor Macromolecular assemblies Lab members: David Goldstone, Joe Hedden, Tom Flower, Laura Robertson, Laurence Arnold, Valerie Ennis-Adeniran Many of the fundamental processes carried out within living cells are directed by macromolecular assemblies of protein and nucleic acid molecules, often referred to as “molecular machines”. Malfunction of a molecular machine resulting in the breakdown of a normal cellular process is the cause of many human cancers, developmental defects, neurological disorders and other congenital disease states. In order to prevent, combat or repair defects that lead to disease it is vital that we understand how the macromolecular components of molecular machines assemble, function and cooperate with one another in order to carry out complex biological processes. To understand how molecular machines function and perform their biological task we study molecular assemblies by applying structural, biophysical and biochemical methodologies. These approaches allow us to dissect a macromolecular complex, visualise the components and examine the interactions between the molecules that make up the complex. Current projects include examining complexes that mediate transcriptional elongation, 3’-end processing and polyadenylation and the investigation of the retroviral capsid, together with assemblies that mediate the retroviral restriction in host cells. In recent studies we have determined the structure of a complex of the capsid from a fossil lentivirus (RELIK) with the host cell protein cyclophilin A. This study has been critical to understanding the molecular details of this fundamental host-virus interaction. Details of the RELIK-CypA molecular interface. Residues 91-96 of RELIK CA-NtD are shown in stick representation (blue) located in the CypA binding groove, the isomeric Pro94 is indicated. CypA is shown in green cartoon, residues that make hydrogen-bonding interactions (dashed lines) are labelled and displayed as sticks. Publications Goldstone DC, Yap MW, Robertson LE, Haire LF, Taylor WR, Katzourakis A, Stoye JP and Taylor IA (2010) Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface. Cell Host & Microbe 8:248-259 Crystal structure of the RELIK-CypA complex. The structures are shown in cartoon representation, RELIK in blue, CypA in green. Secondary structure elements are labelled sequentially from the N-terminals. Pancevac C, Goldstone DC, Ramos A and Taylor IA (2010) Structure of the Rna15 RRM-RNA complex reveals the molecular basis of GU specificity in transcriptional 3’-end processing factors. Nucleic Acids Research 38:3119-3132 Mortuza GB, Dodding MP, Goldstone DC, Haire LF, Stoye JP and Taylor IA (2008) Structure of B-MLV capsid amino-terminal domain reveals key features of viral tropism, gag assembly and core formation. Journal of Molecular Biology 376:1493-1508 See references 98, 176, 193, 245 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 73 STRUCTURAL BIOLOGY Mathematical Biology Willie Taylor Protein structure analysis and design Lab members: Katarzyna Maksimiak, Michael Sadowski Proteins are the main essential active agents in biology and without them, almost none of the processes that we associate with life would take place. Proteins enact their tasks, not as the linear sequence of amino acids that defies their uniqueness, but more typically as a compact threedimensional structure. It is the aim of my group to try to understand the relationship between the protein sequence and its structure and hence its function. To test our ideas on how the protein chain can adopt different folds, we are using idealised models of small proteins, each of which has a different fold (see figure). From an abstract representation of the fold, comprising a few letters, we construct a 2D diagram of the secondary structure positions (alpha-helices and beta-strands) then make a 3D stick model which is then elaborated into amino acid (residue) positions. These are refined to make realistic all-atom models that can be used to design the best sequence to adopt the fold of each model. In collaboration with the Driscoll group, we are now making some of these proteins. Publications Grainger B, Sadowski MI and Taylor WR (2010) Re-evaluating the “rules” of protein topology. Journal of Computational Biology 17:1253-66 Hollup SM, Fuglebakk E, Taylor WR and Reuter N (2011) Exploring the factors determining the dynamics of different protein folds. Protein Science 20:197-209 Macdonald JT, Maksimiak K, Sadowski MI and Taylor WR (2010) De novo backbone scaffolds for protein design. Proteins 78:1311-25 A zoo of novel folds for a small protein, some of which will be made. 74 MRC National Institute for Medical Research See references 75, 98, 103, 129, 155, 194, 216, 217, 246, 247, in the bibliography at the back for publications from this group in 2010. STRUCTURAL BIOLOGY Physical Biochemistry Martin Webb The molecular mechanisms of motor proteins Lab members: Claudia Arbore, Lori Callum, Liisa Chisty, Colin Davis, Katy Hedgethorne, Simone Kunzelmann, Gordon Reid Movement within the cell is often driven by motor proteins that move along linear tracks. The tracks may be filaments of proteins or nucleic acid. We are interested in the way in which helicases move along double-stranded DNA, separating the two strands. Such a process is essential as part of DNA replication and repair. We are developing new optical approaches, such as reagentless biosensors, to study the proteins and nucleic acids during this process of movement along DNA. In order to develop our understanding of how helicases work as part of a complete system, we are investigating the replication of certain plasmids that contain antibiotic resistance and that are readily transferred between bacteria. The essential parts of this system are plasmids containing a specific double-stranded origin of replication, a replication initiation factor, a helicase and polymerase. We are currently working on building up this system in vitro to study the role and mechanism of each component in this system. The development of biosensors has included one for ADP or GDP, which has a high specificity and has properties that make it suitable for real-time assays and for high-throughput approaches. Scheme for asymmetric replication of a plasmid, showing the role of PcrA helicase. Rhodamine-ParM as biosensor for ADP, showing titration of ADP and ATP and schematic of its use in assaying a kinase. Publications Fili N, Mashanov GI, Toseland CP, Batters C, Wallace MI, Yeeles JTP, Dillingham MS, Webb MR and Molloy JE (2010) Visualizing helicases unwinding DNA at the single molecule level. Nucleic Acids Research 38:4448-4457 Kunzelmann S and Webb MR (2010) A fluorescent, reagentless biosensor for ADP based on tetramethylrhodamine-labeled ParM. ACS Chemical Biology 5:415-25 See references 80, 138, 139, 253, 265, 278 in the bibliography at the back for publications from this group in 2010. Toseland CP, Martinez-Senac MM, Slatter AF and Webb MR (2009) The ATPase cycle of PcrA helicase and its coupling to translocation on DNA. Journal of Molecular Biology 392:1020-1032 MRC National Institute for Medical Research 75 Neurosciences Developmental Neurobiology David Wilkinson (Head of Division) Siew-Lan Ang James Briscoe Alex Gould Nobue Itasaki Jean-Paul Vincent Molecular Neurobiology François Guillemot (Head of Division) Vassilis Pachnis Iris Salecker Molecular Neuroendocrinology Tom Carter (Acting Head of Division) Matthew Hannah Paul Le Tissier Neurophysiology Troy Margrie (Acting Head of Division) 76 MRC National Institute for Medical Research NEUROSCIENCES Developmental Neurobiology Siew-Lan Ang Neuronal subtype specification in the midbrain and hypothalamus Lab members: Neal Anthwal, Suzanne Claxton, Lan Chen, Emmanouil Metzakopian, Wei Lin, Martin Levesque, Simon Stott, Annabel Walsh The mammalian midbrain and hypothalamus contain many types of neurons that regulate voluntary movement and energy homeostasis, respectively. How the different types of neurons are generated and are wired into functional circuits remains a central question in developmental neurobiology. We study how neural progenitors in the brain give rise to midbrain dopaminergic (mDA) neurons and hypothalamic neurons involved in regulating feeding. Our findings have direct medical relevance, since loss of mDA neurons is correlated with Parkinson’s Disease, and dysfunction of feeding circuits in the brain can lead to obesity in humans. We use mouse embryos and in vitro differentiation of mouse embryonic stem cells to identify genes that regulate the specification, differentiation and migration of mDA neurons and arcuate proopiomelanocortin and neuropeptide Y. Our studies employ a combination of embryological, genetic, molecular, genomic and proteomic approaches, including genetic fate mapping studies, null and conditional mutant mice, brain slice culture, time-lapse imaging, chromatin immunoprecipitation, biochemical and transcriptome analyses. These studies provide important insights into how embryonic gene expression leads to mature neuronal phenotypes. Novel obese mouse model Publications Peling M, Anthwal N, McNay D, Gradwohl G, Leiter, AB, Guillemot F and Ang SL (2011) Differential requirements for neurogenin 3 in the development of POMC and NPY neurons in the hypothalamus. Developmental Biology 349: 406-416 Corin enhancer-lacZ transgenic mouse embryo (10.5 days)showing expression of b-galactosidase (blue) in midbrain dopaminergic progenitors and floor plate. See references 164, 199 in the bibliography at the back for publications from this group in 2010. Lin W, Metzakopian E, Mavromatakis YE, Gao N, Balaskas N, Sasaki H, Briscoe J, Whitsett JA, Goulding M, Kaestner KH and Ang SL (2009) Foxa1 and Foxa2 function both upstream of and cooperatively with Lmx1a and Lmx1b in a feedforward loop promoting mesodiencephalic dopaminergic neuron development. Developmental Biology 333:386-396 Ferri ALM, Lin W, Mavromatakis YE, Wang JC, Sasaki H, Whitsett JA and Ang S-L (2007) Foxa1 and Foxa2 regulate multiple phases of midbrain dopaminergic neuron development in a dosage-dependent manner. Development 134:2761-2769 MRC National Institute for Medical Research 77 NEUROSCIENCES Developmental Neurobiology James Briscoe EMBO member Pattern formation in the vertebrate nervous system Lab members: Nikos Balaskas, Natascha Bushati, Rachel Chung, Michael Cohen, John Jacob, Anna Kicheva, Eva Kutejova, Steven Moore, Ana Ribeiro, Vanessa Ribes, Noriaki Sasai, Samuel Tozer We study how the central nervous system (CNS) is formed in embryos. Despite its complexity, the CNS is assembled in a remarkably reliable and accurate manner. This precision is necessary for the wiring of nerves into the functional neural circuits that gives the CNS its function. Our research focuses on the spinal cord, which is the part of the CNS that contains the nerves that allow us to sense our environment and respond to it by moving muscles. The findings will contribute to understanding of the development of the spinal cord as well as shed light on diseased and damaged nervous systems. In turn, we hope this will help in the development of therapies for these conditions. Specifically, we are interested in the signalling mechanisms and transcriptional programme responsible for pattern formation in the neural tube. In ventral regions of the caudal neural tube, the secreted molecule Sonic Hedgehog (Shh) forms an extracellular gradient that governs pattern formation and tissue growth. We use a range of molecular, imaging and modelling approaches to identify Shh regulated genes that control the identity and proliferation of neural progenitors. Expression of the transcription factors Arx (blue), FoxA2 (red) and Nkx2.2 (green) is dynamic in the neural tube of mouse embryos. Publications An adaptation mechanism for Shh signalling involving Gli induced negative feedback via Ptch. Fixed concentrations of Shh are converted into temporally varying profiles of Gli activity. Dessaud E, Ribes V, Balaskas N, Yang LL, Pierani A, Kicheva A, Novitch BG, Briscoe J and Sasai N (2010) Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen Sonic hedgehog. PLoS Biology 8:e1000382 Ribes V, Balaskas N, Sasai N, Cruz C, Dessaud E, Cayuso J, Tozer S, Yang LL, Novitch B, Marti E and Briscoe J (2010) Distinct Sonic Hedgehog signaling dynamics specify floor plate and ventral neuronal progenitors in the vertebrate neural tube. Genes & Development 24:1186-1200 Kutejova E, Briscoe J and Kicheva A (2009) Temporal dynamics of patterning by morphogen gradients. Current Opinion in Genetics & Development 19:315-322 See references 23, 45, 47, 57, 132, 210, 224, 279 in the bibliography at the back for publications from this group in 2010. 78 MRC MRCNational NationalInstitute Institutefor forMedical MedicalResearch Research NEUROSCIENCES Molecular Neuroendocrinology Tom Carter Secretory organelle formation, trafficking and exocytosis Lab members: Nikolai Kiskin, Nicola Hellen, Laura Knipe, Emma Cookson, Jennifer Frampton One of the ways in which cells sense and respond to their environment is through the cell surface expression of integral membrane proteins (e.g. hormone receptors, ion channels, adhesion molecules, etc.) and the secretion of soluble proteins into the external environment (e.g. hormones, transmitters, morphogens). The correct delivery of such proteins to the cell surface or extracellular space involves a complex intracellular machine called the secretory pathway. We study the secretory pathway using molecular, biochemical and live cell optical imaging techniques in order to understand the processes that underlie the formation, trafficking and exocytosis of regulated secretory organelles, the post-Golgi membrane bound containers that store and deliver proteins to the cell surface/exterior in response to external signals. We use endothelial cells and the Weibel-Palade body as our model system. Examination of the intra-organelle properties, cargo composition and exocytosis of regulated secretory organelles responsible for the trafficking and secretion of procoagulants (e.g. von Willebrand factor), anti-coagulants (e.g. tPA) or inflammatory molecules (e.g. MCP-1, P-selectin) has led to new insights into the storage and secretion of such molecules from cultured endothelial cells. Publications Kiskin NI, Hellen N, Babich V, Hewlett L, Knipe L, Hannah MJ and Carter T (2010) Protein mobilities and P-selectin storage in Weibel-Palade bodies. Journal of Cell Science 123:2964-2975 Knipe L, Meli A, Hewlett L, Bierings R, Dempster J, Skehel P, Hannah MJ and Carter T (2010) A revised model for the secretion of tPA and cytokines from cultured endothelial cells. Blood 116:2183-2191 Weibel Palade bodies (WPBs) are rod shaped secretory organelles containing the procoagulant von Willebrand factor (VWF, green in top panel) and, under certain conditions, a cocktail of small inflammatory molecules (red and blue in top panel).VWF, the main core component of WPBs forms large polymers that condense into flexible helical tubules that pack tightly to produce a ridged paracrystal (lower panel). Berriman JA, Li S, Hewlett LJ, Wasilewski S, Kiskin FN, Carter T, Hannah MJ and Rosenthal PB (2009) Structural organization of Weibel-Palade bodies revealed by cryoEM of vitrified endothelial cells. Proceedings of the National Academy of Sciences of the United States of America 106:17407-17412 See references 134, 135 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 79 NEUROSCIENCES Developmental Neurobiology Alex Gould EMBO member Regulation of growth and metabolism Lab members: Andrew Bailey, Einat Cinnamon, Louise Cheng, Rami Makki, Panayotis Pachnis, Fabrice Prin, Patricia Serpente, Rita Sousa-Nunes, Irina Stefana All organisms regulate their growth according to internal genetic programmes and the availability of nutrients from the environment. As human and other animal embryos develop, they increase in size dramatically. We wish to identify the nutritional factors and genetic networks that promote growth during development and, equally importantly, those that shut it down in adulthood. This research also aims to shed light on the complex interactions between nutrition and the genes influencing growth, obesity and diabetes. Our current work aims to understand how dietary nutrients regulate embryonic and foetal growth. Much of our research in this area uses the fruit fly Drosophila, a model organism that shares many genes with mammals. We recently utilised Drosophila to develop a model for studying the role, during brain growth, of the mitochondrial lipid Coenzyme Q10 (sold over-the-counter as the dietary supplement Q10). We have also identified an organ-to-organ relay mechanism in Drosophila whereby aminoacid sensing by adipose tissue triggers neural stem cells to enter the cell cycle. This constitutes an important nutritional checkpoint that is active during an early phase of brain growth. Protein structural models of the catalytic domain of wild-type Qless (Qless, left panel) and an inactive mutant form of Qless (Qless109, right panel). Note that the serine at position 215 is changed to asparagine in the mutant protein (arrows). Data from J. Grant et al., 2010 A Drosophila central nervous system containing clones, marked with nuclear GFP (green), that are mutant for the Coenzyme Q10 biosynthetic gene, Qless. Neural stem cell-like progenitors are also shown (red). Data from J. Grant et al., 2010 Publications Sousa-Nunes R, Yee LL and Gould AP (2011) Fat cells reactivate quiescent neuroblasts via TOR and glial insulin relays in Drosophila. Nature 471: 508–512 Grant J, Saldanha JW and Gould AP (2010) A Drosophila model for primary Coenzyme Q deficiency and dietary rescue in the developing nervous system. Disease Models and Mechanisms 3:799-806 Maurange C, Cheng L and Gould AP (2008) Temporal transcription factors and their targets schedule the end of neural proliferation in Drosophila. Cell 133:891-902 See references 104, 233, 279 in the bibliography at the back for publications from this group in 2010. 80 MRC National Institute for Medical Research NEUROSCIENCES Molecular Neurobiology François Guillemot FMedSci, EMBO member Genomic and functional analysis of neurogenesis Lab members: Roberta Azzari, Lan Chen, Daniela Dreschel, Laura Galinanes-Garcia, Patricia Garcez, Sebastien Gillotin, Matilda Haas, Mélanie Lebel, Ben Martynoga, Cristina Minieri, Emilie Pacary, Vidya Ramesh, Noelia Urban Neural stem cells in the embryo produce a vast array of neurons that reach specific positions in the developing brain where they integrate into functional circuits. This process of neurogenesis involves the progression of neuronal precursors through a succession of cellular steps of proliferation, migration and differentiation. We study the genetic programmes that regulate and coordinate these different steps, using genomic approaches to identify the genetic pathways involved, and functional assays to determine the contribution of individual genes to the different steps of neurogenesis. We recently found that the transcription factors Neurog2 and Ascl1, which initiate the programme of neurogenesis in stem cells, also promote the migration of postmitotic neurons. Moreover, they control different steps of neuronal migration in the cerebral cortex, through induction of two distinct small GTPbinding proteins, Rnd2 and Rnd3, respectively. These proneural factors thus regulate the responsiveness of newborn neurons to multiple migratory signals, which we are currently characterising. By gaining insight into mechanisms driving the differentiation of stem cells into neurons, we are helping devise strategies to replace lost cells in diseased brains. Silencing of the small GTP-binding protein Rnd3 in a dissociated cortical neuron promotes polymerisation of actin filaments (visualised with a utrophin-GFP construct) in neuronal processes. Publications Pacary,E., Heng, J., Azzarelli,R., Riou, P., Castro, D., Lebel-Potter, M., Parras, C., Bell, D.M. Ridley, A.J., Parsons, M., Guillemot, F. (2011) Proneural transcription factors regulate different steps of cortical neuron migration through Rndmediated inhibition of RhoA signalling. Neuron 69:1069-84 Zimmer C, Lee J, Griveau A, Arber S, Pierani A, Garel S and Guillemot F (2010) Role of Fgf8 signalling in the specification of rostral Cajal-Retzius cells. Development 137:293-302 The proneural transcription factors Neurog2 and Ascl1 control two distinct steps of neuronal migration: the transition from multipolar to bipolar stages in the intermediate zone (IZ) and locomotion along radial glia fibers in the cortical plate (CP), respectively. They act by inducing the small GTP binding proteins Rnd2 and Rnd3, which, together with hypothetical extrinsic signals A and B, promote respectively the extension of the leading process and translocation of the nucleus during these two phases of migration. Heng JI-T, Nguyen L, Castro DS, Zimmer C, Wildner H, Armant O, Skowronska-Krawczyk D, Bedogni F, Matter J-M, Hevner R and Guillemot F (2008) Neurogenin 2 controls cortical neuron migration through regulation of Rnd2. Nature 455:114-8 See references 42. 96. 109, 159, 191, 199, 227, 229, 280 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 81 NEUROSCIENCES Molecular Neuroendocrinology Matthew Hannah Secretory vesicle formation in human endothelial cells Lab members: Lindsay Hewlett, Ruben Bierings, Robert Rowlands, Melanie Scarisbrick, Secretory vesicles are microscopic, membrane-bound compartments found inside cells that are essential for communication between cells and their environment. They are used to transport soluble biological signalling molecules such as enzymes, hormones or neurotransmitters out of the cell and they also deliver membrane proteins such as receptors or transporters to the cell surface. We study the formation of secretory vesicles in human endothelial cells grown in culture, focusing mostly on the Weibel-Palade body (WPB) a distinctive endothelial cell-specific secretory vesicle, responsible for the storage and stimulation-dependent release of von Willebrand factor (VWF) a protein involved in blood clotting. Analysis of this process will increase our understanding of cardiovascular biology and cellular secretory processes in general. We have recently carried out a kinetic analysis of the biosynthesis, storage and secretion of VWF in our cells using a metabolic labelling approach. Contrary to previously published work, we found that VWF was very efficiently sorted into regulated secretory vesicles, but these were not efficiently stored due to spontaneous, non-stimulated secretion. Publications Kiskin NI, Hellen N, Babich V, Hewlett L, Knipe L, Hannah MJ and Carter T (2010) Protein mobilities and P-selectin storage in Weibel-Palade bodies. Journal of Cell Science 123:2964-2975 Berriman JA, Li S, Hewlett LJ, Wasilewski S, Kiskin FN, Carter T, Hannah MJ and Rosenthal PB (2009) Structural organization of Weibel-Palade bodies revealed by cryoEM of vitrified endothelial cells. Proceedings of the National Academy of Sciences of the United States of America 106:17407-17412 Giblin JP, Hewlett LJ and Hannah MJ (2008) Basal secretion of von Willebrand factor from human endothelial cells. Blood 112:957-964 Weibel-Palade bodies (green), Golgi apparatus (white) and nucleus (blue) visualised in a cultured human endothelial cell. See references 134, 135 in the bibliography at the back for publications from this group in 2010. 82 MRC National Institute for Medical Research NEUROSCIENCES Developmental Neurobiology Nobue Itasaki Wnt signalling in vertebrate embryogenesis Lab members: Katherine Lintern, Sara Howard, Sonia Guidato, Tom Deroo During embryogenesis and in adulthood, cells undergo dynamic tissue reorganisation processes. One example is the epithelial to mesenchymal transition that occurs in gastrulation during embryogenesis and in cancer metastasis in adulthood, where cells in the epithelial layer delaminate and become migratory. While these processes are regulated by activation of specific pathways and gene expression, the cell shape changes in turn affect activities of some signal transduction pathways. Our interest is in the interplay between these. The Wnt/b-catenin pathway is involved in many aspects of biological events such as cell proliferation, differentiation, stem cell maintenance and carcinogenesis. In addition to this functional diversity, the pathway is unique in that the key regulator, b-catenin, possesses dual functions: one as a part of adherens junctions, and the other as a transcriptional coactivator of Wnt signal target genes. We currently investigate the role of b-catenin in the interplay between morphogenetic changes and pathway activation. We also study the mechanism whereby Wnt signals result in a different outcome depending on the context, and focus on extracellular factors that affect Wnt signaling. Publications Amirthalingam GS, Howard S, Alvarez S, de Lera AR and Itasaki N (2009) Regulation of Hoxb4 induction after neurulation by somite signal and neural competence. BMC Developmental Biology 9:17 Franch-Marro X, Wendler F, Guidato S, Griffith J, Baena-Lopez A, Itasaki N, Maurice MM and Vincent J-P (2008) Wingless secretion requires endosome-to-Golgi retrieval of Wntless/Evi/Sprinter by the retromer complex. Nature Cell Biology 10:170-7 Lintern KB, Guidato S, Rowe A, Saldanha JW and Itasaki N (2009) Characterization of Wise protein and its molecular mechanism to interact with both Wnt and BMP signals. Journal of Biological Chemistry 284 23159-23168 MDCK cells undergoing epithelial-to-mesenchymal transition (left to right panels), a process seen during normal embryogenesis as well as in cancer metastasis. Changes in subcellular localisation of ß-catenin (red) and E-cadherin (green), from cell borders to intracellular, are shown. See references 121, 126 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 83 NEUROSCIENCES Molecular Neuroendocrinology Paul Le Tissier Control of prolactin and growth hormone cell differentiation and function Lab members: Leonard Cheung, Molly Strom The hormones prolactin (principally involved in pregnancy and production of milk) and growth hormone (required for normal growth and metabolism) are secreted from specialised cells of the anterior pituitary gland, located just under the brain. The function, development and regulation of prolactin and growth hormone cells are closely related and we are studying the control of their function and inter-relationship using transgenic mice. These studies also reveal the effects of alterations of prolactin and growth hormone cells on other pituitary hormones regulating stress, reproduction and metabolism. Knowing how these cell populations are controlled normally is important for understanding how hormone deficiencies or pituitary tumours occur when this regulation fails. We have generated transgenic mice with cell death induced by the drug doxycycline and used these to kill prolactin cells before and after puberty - when the number of cells normally increases - and determine how quickly the pituitary gland recovers. When cells are killed before puberty, the gland rapidly recovers, whereas there is only a very slow recovery if cells are killed after puberty. This suggests that there is a limited capacity of the gland to regenerate after damage in adult animals. Induction of M2 protein expression (green) leads to loss of prolactin cells (red) in animals treated with doxycycline (right panel) compared with animals without any induction (left panel). Publications Castrique E, Fernandez-Fuente M, Le Tissier P, Herman A and Levy A (2010) Use of a prolactin-Cre/ROSA-YFP transgenic mouse provides no evidence for lactotroph transdifferentiation after weaning, or increase in lactotroph/somatotroph proportion in lactation. Journal of Endocrinology 205:49-60 Lafont C, Desarménien MG, Cassou M, Molino F, Lecoq J, Hodson D, Lacampagne A, Mennessier G, El Yandouzi T, Carmignac D, Fontanaud P, Christian H, Coutry N, Fernandez-Fuente M, Charpak S, Le Tissier P, Robinson ICAF and Mollard P (2010) Cellular in vivo imaging reveals coordinated regulation of pituitary microcirculation and GH cell network function. Proceedings of the National Academy of Sciences of the United States of America 107:4465-4470 Waite E, Lafont C, Carmignac D, Chauvet N, Coutry N, Christian H, Robinson I, Mollard P and Le Tissier P (2010) Different degrees of somatotroph ablation compromise pituitary growth hormone cell network structure and other pituitary endocrine cell types. Endocrinology 151:234-243 See references 28, 114, 140, 220, 263 in the bibliography at the back for publications from this group in 2010. 84 MRC National Institute for Medical Research Sequencing of the POU1F1 gene of a patient with short stature (subsequenty confirmed as combined pituitary hormone deficiency) shows two independent mutations (top sequencing traces) of the normal sequence (lower traces). Each mutation is inherited from one parent, who are both unaffected (lower panel shows the inheritance of the mutant alleles). NEUROSCIENCES Neurophysiology Troy Margrie Sensory processing in single cells, circuits and behaviour Lab members: Ed Bracey, Alex Brown, Ninja Grewe, Ede Rancz, Bruno Pichler, Mateo Velez-Fort The goal of our lab is to understand how the brain uses the activity of individual and collections of neurons to encode a sensory stimulus. We use a top-down, multidisciplinary approach to understanding sensory representation that allows us to explore this fundamental issue from the systems to the cellular level. Specifically, we are investigating several key questions: 1) To what extent is sensory representation distributed across primary and secondary or multimodal brain areas? 2) What is the relationship between neuronal connectivity and sensory function? 3) How is sensory information encoded and integrated by individual cells and synapses? To address this question we use a variety of in vivo techniques including behavioral experiments, fMRI, population calcium imaging and electrophysiology. By complementing this with genetic tools such as transgenic mouse lines and viral tracing and in vitro electrophysiological recordings we can explore such questions ranging from single synapses and cells to circuits and behavior. Horizontal images taken from an anaesthetised rat recorded using fMRI highlighting brain regions that respond to electrical stimulation of the vestibular nerve. Whole-cell recordings from cortical pyramidal cells in anaesthetized and awake head-restrained preparations. The histogram of membrane potential reveals a positively skewed distribution (right). In the awake case (red), the slow oscillatory activity is replaced by more high frequency fluctuations in membrane potential. Such recordings will allow us to explore the activity within individual cells while a sensory task is being performed. Publications Rancz EA, Franks KM, Schwartz M, Pichler B, Schaefer AT and Margrie TW (2011) Transfection via whole-cell recordings in vivo. Bridging single-cell physiology, genetics and connectomics. Nature Neuroscience 14(4):527-32 A three-dimensional stack of calcium dye-loaded cells in the cortex of an anaesthetised mouse imaged using a two-photon microscope. This allows us to monitor the activity of large numbers of cells during sensory stimulation. Scale bar is 50 µm. Chadderton P, Agapiou JP, McAlpine D and Margrie TW (2009) The synaptic representation of sound source location in auditory cortex. Journal of Neuroscience 29:14127-35 Arenz A, Silver RA, Schaefer AT and Margrie TW (2008) The contribution of single synapses to sensory representation in vivo. Science 321:977-980 MRC National Institute for Medical Research 85 NEUROSCIENCES Molecular Neurobiology Vassilis Pachnis EMBO member, FMedSci Development of the nervous system Lab members: Angelliki Achimastou, Myrto Denaxa, Tiffany Heanue, Chryssa Konstantinidou, Catia Laranjeira, Reena Lasrado, Rita Lopes, Ulrika Marklund, Valentina Sasseli, Nicole Verhey van Wijk The nervous system mediates the interaction of organisms with their environment, contributes to the maintenance of internal homeostasis and is the anatomical substrate of cognitive activity.Normal function of the nervous system depends on the generation, at the right time and place, of integrated cellular networks made up of a large number of diverse neurons. Understanding the mechanisms that control the generation of distinct neuronal subtypes and their migration to the appropriate location is critical for comprehending normal neuronal development and for treating neuronal deficiencies. Our studies explore the mechanisms that control the development of the enteric nervous system of the gut: how enteric neurons and their progenitors migrate during embryogenesis and how they differentiate to form complex networks that regulate gut motility and secretions. We also study the mechanisms that control neuronal differentiation in the forebrain. We have identified signals that mediate cellular interactions, molecules that underlie the functional interconnection of neurons and transcription factors underlying neuronal cell fate decisions. Our studies provide novel insight into the development and function of the nervous system in normal and disease conditions. Publications: Heanue TA and Pachnis V (2011) Prospective identification and isolation of enteric nervous system progenitors using Sox2. Stem Cells 29:128-140 Fragkouli A, van Wijk NV, Lopes R, Kessaris N and Pachnis V (2009) LIM homeodomain transcription factor-dependent specification of bipotential MGE progenitors into cholinergic and GABAergic striatal interneurons. Development 136:3841-3851 The enteric nervous system of adult mice is made up of thousands of interconnected ganglia similar to the one shown here. Each ganglion contains many different types of neurons (red nuclei) and glial cells (blue cytoplasm. 86 MRC National National Institute Institute for for Medical Medical Research Research MRC Kioussis D and Pachnis V (2009) Immune and nervous systems: more than just a superficial similarity? Immunity 31:705-710 See references 127, 128 in the bibliography at the back for publications from this group in 2010. NEUROSCIENCES Molecular Neurobiology Iris Salecker Visual circuit assembly in Drosophila Lab members: Holger Apitz, Dafni Hadjieconomou, Emily Richardson, Benjamin Richier, Nana Shimosako, Katarina Timofeev In the third instar larval optic lobe of Drosophila, progenitors in the outer and inner proliferation centers (OPC, IPC; blue) give rise to post-mitotic neurons in the medulla and lobula complex (green). The ability of animals to interpret sensory information and to produce complex behaviors relies on the perfect functioning of their nervous system, which consists of a large diversity of neurons and glia. This raises the central questions: how the generation of neurons and glia is regulated, and what enables neurons to recognise each other and to eventually form precise synaptic contacts between them during development. We use the visual system of the fruit fly Drosophila as model to investigate the mechanisms that control the formation of glia and higher-order neurons. Furthermore, we seek to determine how the axons of one color-sensitive photoreceptor neuron subtype know where to stop in a temporary layer and to correctly proceed to, as well as to recognise their final target layer and connect with their partner neurons in a series of interdependent cellular interactions. To facilitate these studies we recently have generated a multicolour cell labelling approach for Drosophila, called Flybow. We anticipate that our studies will help to advance our understanding of normal brain development, as well as related neurological disorders. Publications In the adult visual system, photoreceptor neurons (R1-R8, blue) extend axons from the retina into two areas of the optic lobe, the lamina and medulla, where they connect with target neurons in an intricate neural network characterised by a highly regular organisation of columns and layers. Using the Flybow approach, target neurons were stochastically labelled with three different fluorescent proteins (EGFP, mCitrine, mCherry). Hadjieconomou D, Rotkopf S, Alexandre C, Bell DM, Dickson BJ and Salecker I. (2011) Flybow: genetic multicolor cell labeling for neural circuit analysis in Drosophila melanogaster. Nat Methods doi:10.1038/nmeth.1567. Hadjieconomou D, Timofeev K, and Salecker I. (2010) A step-by-step guide to visual circuit assembly in Drosophila. Current Opinion in Neurobiology doi:10.1016/j.conb.2010.07.012. Bazigou E, Apitz H, Johansson J, Lorén CE, Hirst EMA, Chen PL, Palmer RH, and Salecker I. (2007) Anterograde Jelly Belly and Alk receptor tyrosine kinase signaling mediates retinal axon targeting in Drosophila. Cell 128: 961-975. See reference 110 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 87 NEUROSCIENCES Developmental Neurobiology Jean-Paul Vincent EMBO member, FMedSci Patterning and homeostasis in developing epithelia Lab members: Cyrille Alexandre, Eugenia Piddini, Maria Gagliardi, Golnar Kolahgar, Luis Alberto Baena Lopez, Karen Beckett, Paul Langton, Satoshi Kakugawa, Hisashi Nojima, Laurynas Pashakarnis A small number of signalling molecules orchestrate growth and cell fate decisions during development. We investigate the mechanisms that control the production, spread and activity of one such signal, Wingless (a member of the Wnt family of secreted proteins, which are implicated in numerous cancers). In addition, we study the regulatory mechanisms that allow cells to compute their position within the Wingless gradient. Epithelia behave like ecosystems with weak or defective cells being eliminated by a process called apoptosis (cell suicide). As Wnt signalling affects cell fitness, we have begun a research programme aimed at understanding the processes that triggers death in weak or defective cells within developing epithelia. We have uncovered a novel feedback mechanism that modulates the interpretation of the Wg gradient in responding tissue. Specifically, we showed that cells influence each other’s response to Wingless through at least two modes of lateral inhibition, one acting at short range and the other over several cell diameters. We have been able to show that medium range inhibition is mediated by Notum, a secreted GPI-specific phospholipase. High resolution distribution of Wingless. Electron micrograph of a Drosophila wing imaginal discs expressing Wingless fused to Horseradish Peroxidase. An enzyme reaction reveals the distribution of the fusion protein as a dark stain. Note the presence of Wingless on membranous structures (arrowhead). Publications Baena-Lopez LA, Franch-Marro X and Vincent J-P (2009) Wingless promotes proliferative growth in a gradient-independent manner. Science Signaling 2:ra60 Piddini E and Vincent J-P (2009) Interpretation of the Wingless gradient requires signaling-induced self-inhibition. Cell 136:296-307 Bardet P-L, Kolahgar G, Mynett A, Miguel-Aliaga I, Briscoe J, Meier P and Vincent J-P (2008) A fluorescent reporter of caspase activity for live imaging. Proceedings of the National Academy of Sciences of the United States of America 105:13901-13905 See references 23, 240, 266 in the bibliography at the back for publications from this group in 2010. 88 MRC National Institute for Medical Research Uniform Wingless signalling promotes proliferation in Drosophila wing imaginal discs. Uniform signalling (indicated by the uniform expression of the target gene vestigial) was experimentally induced in the green territory, whereas in the non-green territory (left hand side of the disc) Wingless forms its normal gradient. There is an increased density of PH3, a marker of mitosis, in the green territory. NEUROSCIENCES Developmental Neurobiology David Wilkinson EMBO member, FMedSci Regulation of boundary formation and neurogenesis Lab members: Marie Breau, Sean Constable, Sebastian Gerety, Andrew Georgiou, Lauren Gregory, Mohamed Ismail, Rosie Morley, Alexei Poliakov, Javier Terriente, Qiling Xu During early stages of nervous system development in vertebrates, neural tissue is subdivided into regions, each with a distinct identity. Within these subdivisions, the differentiation of progenitor cells is regulated in time and space to form the correct organisation of specific neuronal and glial cell types. In order for such precise patterns to form and be maintained, it is essential that cells do not move to inappropriate locations. Our studies aim to elucidate molecular mechanisms of boundary formation and cell differentiation, and the links between these processes in nervous system development. We analyse how signalling through Eph receptors and ephrins segregates distinct cell populations, leading to formation of sharp boundaries. In related work, we study how boundaries, together with signalling from specific neurons, organise discrete zones of progenitor cells and neuronal differentation in the hindbrain. Finally, we are dissecting the mechanisms of action of a transcriptional repressor and targetted protein degradation in neural stem cell maintenance and differentiation. These studies utilise the powerful genetic and transgenic tools available in the zebrafish model for analysis of gene function and imaging. Feedback loop required for the onset of primary neurogenesis. Expression of the proneural gene Neurog1 is inhibited in progenitor cells due to Notch activation and the transcriptional repressor, Plzf. Neuronal differentiation requires proneural upregulation of a ubiquitination adaptor protein, Btbd6a, that targets the degradation of Plzf. Publications Gonzalez-Quevedo R, Lee Y, Poss KD and Wilkinson DG (2010) Neuronal regulation of the spatial patterning of neurogenesis. Developmental Cell 18:136-147 Hindbrain segments and neurons in zebrafish. Immunocytochemistry was carried out to reveal segments 3 and 5 (blue signal) and neurons (red) in an embryo that has been microinjected to generate mosaic expression of green fluorescent protein. See references 83, 93, 99, 232, 275 in the bibliography at the back for publications from this group in 2010. Sobieszczuk DF, Poliakov A, Xu Q and Wilkinson DG (2010) A feedback loop mediated by degradation of an inhibitor is required to initiate neuronal differentiation. Genes and Development 24:206-218 Jørgensen C, Sherman A, Chen GI, Pasculescu A, Poliakov A, Hsiung M, Larsen B, Wilkinson DG, Linding R and Pawson T (2009) Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science 326:1502-9 MRC National Institute for Medical Research 89 Genetics and Development Systems Biology Jim Smith (Head of Division) Greg Elgar Mike Gilchrist Developmental Biology Tim Mohun (Head of Division) Malcolm Logan Elke Ober Lyle Zimmerman Stem Cell Biology and Developmental Genetics Robin Lovell-Badge (Head of Division) Paul Burgoyne Rita Cha Peter Thorpe James Turner See also the following groups, all in Neurosciences: Siew-Lan Ang James Briscoe Alex Gould Nobue Itasaki Vassilis Pachnis Iris Salecker Jean-Paul Vincent David Wilkinson 90 MRC National Institute for Medical Research GENETICS AND DEVELOPMENT Stem Cell Biology and Developmental Genetics Paul Burgoyne FMedSci The Y chromosome and infertility Lab members: Áine Rattigan, Obah Ojarikre, Shantha Mahadevaiah, Julie Cocquet, Nadege Vernet, Teruko Taketo The first evidence that the mammalian Y chromosome carried genetic information essential for male fertility was obtained in 1976 for man, and 1986 for mouse, from the study of individuals with partially deleted Y chromosomes. Evidence that the Y chromosome is incompatible with female fertility comes from studies of XY individuals that have a deletion removing the male determinant SRY. Conventional gene-targetting has so far proved unsuccessful in disrupting Y gene functions, so we have been using mouse models harbouring Y deletions in combination with the selective addition of Y genes by transgenesis to elucidate the role of specific Y genes in male and female fertility. However, very recently we have been successful in disrupting the function of a Y gene, Sly, that is present in >70 copies; this was achieved by targetting the transcripts with a transgenically delivered small interfering RNA. This gene proved to repress X and Y gene expression in developing sperm; the up-regulation of these X and Y genes in Sly-deficient mice is associated with severely impaired sperm function and associated sperm DNA damage. We have now disrupted the function of a related multi-copy X gene (Slx) which also plays an essential role in sperm development. Publications Cocquet J, Ellis PJI, Yamauchi Y, Riel JM, Karacs TPS, Rattigan Á, Ojarikre OA, Affara NA, Ward MA and Burgoyne PS (2010) Deficiency in the multicopy Sycp3-like X-linked genes Slx and Slxl1 causes major defects in spermatid differentiation. Molecular Biology of the Cell 21:3497-3505 Deficiency in the Sycp3-like X-linked genes Slx and Slxl1 leads to impaired sperm development. A) Testis tubules of a Slx/Slxl1-deficient mouse. Groups of apoptotic elongating spermatids (green) are visible in various tubular stages. Blue signal marks the nuclei and red signal the acrosomes. B-G) Electron microscopy of normal (B-C) and Slx/Slxl1-deficient (D-G) sperm show that the deficiency causes sperm abnormalities such as partial detachment of the tail, parallel alignment of the head and tail, and curved or looped tail. H) Slx/Slxl1 deficiency alters metabolic processes during sperm development. The bar graph represents the number of genes found differentially expressed in round spermatids from Slx/Slxl1deficient males compared with wild-type males. Differentially expressed genes are shown according to their likely biological function. Wijchers PJ, Yandim C, Panousopoulou E, Ahmad M, Harker N, Saveliev A, Burgoyne PS and Festenstein R (2010) Sexual dimorphism in mammalian autosomal gene regulation is determined not only by Sry but by sex chromosome complement as well. Developmental Cell 19:477-84 Yamauchi Y, Riel JM, Stoytcheva Z, Burgoyne PS and Ward MA (2010) Deficiency in mouse Y chromosome long arm gene complement is associated with sperm DNA damage. Genome Biology 11:R66 See references 36, 153, 215, 269, 276 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 91 GENETICS AND DEVELOPMENT Stem Cell Biology and Developmental Genetics Rita Cha Regulation of eukaryotic chromosome metabolism Lab members: Jesus Carballo, Tony Johnston, Ana Penedos, and Alexander Widger Genome duplication and segregation are two fundamental processes in biology. We study the ways in which signal transduction regulates these events. A key component in eukaryotic chromosome metabolism is the ATR/ATM family of proteins. These evolutionarily conserved signal transduction proteins are involved in a number of chromosomal processes including DNA replication, recombination, and checkpoint regulation. Inactivation of these genes leads to cell death, genome instability, and meiotic dysfunction as well as the genetic disorders, Ataxia Telangiectasia and Seckle syndrome. We use genetically tractable S. cerevisiae to study the molecular basis for the functions of ATR/ATM. We found that inactivation of Mec1/Tel1, the budding yeast homologues of ATR/ATM, leads to chromosome breakage during proliferation and disruption of essential meiotic chromosomal processes. Currently, our research focuses on the roles of Mec1/Tel1 in meiotic recombination and fragile site stability. The results of our studies will provide insights into how disruption of these genes leads to failure of fundamental chromosomal processes. Publications Hashash N, Johnson AL, Cha RS. (2011) Regulation of chromosome breakage at replication slow zones, a Mec1/ATR sensitive fragile site. Journal of Cell Science 124:181-185 Mec1/Tel1 (A) and ATR/ATM (B) targets during yeast and mouse meiosis. (A) Spatial and temporal distribution of phosphorylated Mec1/Tel1 targets during meiotic prophase I is visualised using a-p[S/T]Q (red), Zip1-GFP (green), and DAPI (blue). Foci are observed initially coinciding with DSBs during leptotene. a-p[S/T]Q foci number is reduced as Zip1 polymerises during zygotene. At pachytene, only few strong foci localise at the synapsed chromosomes and telomeric regions. The a-p[S/T]Q patches become more intense and thicker as chromosomes condense and Zip1 staining disappears during diplotene. (B) Immuno-signals from a-p[S/T]Q were visualised in mouse spermatocytes. Green signals from a-SCP3. (Mouse data from J. Turner) 92 MRC MRCNational NationalInstitute InstituteforforMedical MedicalResearch Research Carballo JA, Johnson AL, Sedgwick SG and Cha RS (2008) Phosphorylation of the axial element protein Hop1 by Mec1/Tel1 ensures meiotic interhomolog recombination. Cell 132:758-70 See reference 112 in the bibliography at the back for publications from this group in 2010. GENETICS AND DEVELOPMENT Systems Biology Greg Elgar Regulation of early vertebrate development Lab members: Stefan Pauls, Paul Piccinelli, Hugo Parker, Dilrini DeSilva The early development of the human embryo is an extraordinarily dynamic and exquisitely controlled process. At the molecular level, events are orchestrated by a large repertoire of transcription factors, proteins that bind to regulatory regions in genomic DNA to control gene expression. Mutations in these regulatory regions can lead to developmental anomalies and disease. Many of the patterning events that occur are common to all vertebrates, as are the transcription factors and interestingly, some of the regulatory code embedded in the genome. However, the protein-DNA interactions are poorly understood, as are the functional effects they mediate. We take a ‘systems level’ approach to decipher the language and grammar that is encoded in regulatory DNA, particularly that fraction that is common to all vertebrates, and which therefore directs some of the most fundamental aspects of vertebrate embryogenesis. We do this by combining computational approaches with functional assays in zebrafish embryos, an important and tractable model for this sort of work. Once we identify specific regulatory patterns, we can search for these throughout the genome, thereby predicting other regulatory regions. It is important that we know where these regions are in the genome, and what processes they define, as mutations in them can lead to developmental disorders and genetic disease. Publications Goode DK, Callaway HA, Cerda GA, Lewis KE and Elgar G (2011) Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events Development. Jan 19. [Epub ahead of print] McEwen GK, Goode DK, Parker HJ, Woolfe A, Callaway H and Elgar G (2009) Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genetics 5:e1000762 Elgar G and Vavouri T (2008) Tuning in to the signals: noncoding sequence conservation in vertebrate genomes. Trends in Genetics 24:344-352 Developmental enhancers containing pbx-hox bipartite binding sites drive restricted patterns of reporter expression in zebrafish and lamprey embryos. A) Graphical representation of an alignment of lamprey, Fugu and human genomic sequences adjacent to the meis2 gene. Pink peaks represent non-coding sequence conservation. B-Q) GFP reporter assays in zebrafish (B-M, Q) and lamprey (N-P) embryos demonstrating strong hindbrain expression, with some elements driving segment-restricted patterns. MRC National Institute for Medical Research 93 GENETICS AND DEVELOPMENT Systems Biology Mike Gilchrist Gene regulatory networks in early development Embryo development is a complex and tightly controlled process, with a remarkably precise outcome. The underlying control system is only partly understood. Typically, transcription factors regulate the expression of individual genes, and the many relationships between transcription factors and their target genes combine to make gene regulatory networks. Our aim is to elucidate these networks using molecular and computational tools developed in the last few years that enable a systematic and large scale approach. We will be focusing on the period in the development of the early embryo when control passes from maternal gene products, deposited in the egg before fertilisation, to those derived from activation of gene transcription in the growing embryo. This maternal-zygotic transition marks a profound watershed in the growth of the embryo as it becomes reliant on the integrity of its own genetic material, and physically marks the onset of asynchronous cell division and the development of physiologically distinct structures. Using the Xenopus model system, we have taken a high resolution time series of whole embryo mRNA samples through this transition period for transcriptome analysis using massively parallel sequencing technology, and are now inspecting the data looking for signatures of gene activation. Further experimental work will involve selective knock-down and chromatin immunoprecipitation assays of early activated genes to establish their likely downstream targets, and hence construct the regulatory networks established at this time. Publications Armisen J, Gilchrist MJ, Wilczynska A, Standart N and Miska EA (2009) Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis. Genome Research 19:1766-1775 Gilchrist MJ, Christensen MB, Bronchain O, Brunet F, Chesneau A, Fenger U, Geach TJ, Ironfield HV, Kaya F, Kricha S, Lea R, Massé K, Néant I, Paillard E, Parain K, Perron M, Sinzelle L, Souopgui J, Thuret R, Ymlahi-Ouazzani Q and Pollet N (2009) Database of queryable gene expression patterns for Xenopus. Developmental Dynamics 238:1379-1388 Gilchrist MJ, Christensen MB, Harland R, Pollet N, Smith JC, Ueno N and Papalopulu N (2008) Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data. BMC Bioinformatics 9:442 See references 115, 187 in the bibliography at the back for publications from this group in 2010. 94 MRC National Institute for Medical Research Study of gene activation at the maternal-zygotic transition in early embryogenesis. Whole genome transcript profiling will allow us to establish the validity of our model of gene activation at this developmental transition point. Families of bold and dashed coloured lines in the model represent initial activation of ‘master regulator’ transcription factors, followed by activation of their respective downstream targets. GENETICS AND DEVELOPMENT Developmental Biology Malcolm Logan Understanding vertebrate limb development Lab members: Anna Kucharska, Sue Miller, Natalie Bufferfield, Veronique Duboc, Satoko Nishimoto, Sorrel Bickley, Fatima Sulaiman Limb defects are the second most common congenital abnormality in human live births, and diseases affecting the musculoskeletal system are a significant clinical problem in older people. The goal of our work is to understand how limbs normally form during embryogenesis, the origins of limb abnormalities and disease in humans, and to provide potential therapeutic approaches to block degeneration or trigger regeneration of the musculoskeletal system. The forelimb and hindlimb buds are morphologically indistinguishable from one another at early stages of development. They are then transformed into a complex of interconnected limb elements comprised of different tissues, for example bones, muscles and tendons, that are exquisitely sculpted to the correct size and shape. Each of these individual tissue elements must form the appropriate connections so that each muscle group connects to the skeletal scaffold via the correct tendon. For each muscle to function it must connect to the central nervous system via an axon that originates from a nerve cell within the spinal cord. How this complex array of interconnected tissues is elaborated is poorly understood. We are using vertebrate animal models to understand the mechanisms that control the initiation of limb bud formation, the subsequent construction of the individual limb elements during development and the maintenance of these structures in later life. Publications Hasson P, DeLaurier A, Bennett M, Grigorieva E, Naiche LA, Papaioannou VE, Mohun TJ and Logan MPO (2010) Tbx4 and Tbx5 acting in connective tissue are required for limb muscle and tendon patterning. Developmental Cell 18:148-156 Minguillon C, Gibson-Brown JJ and Logan MP (2009) Tbx4/5 gene duplication and the origin of vertebrate paired appendages. Proceedings of the National Academy of Sciences of the United States of America 106:21726-21730 DeLaurier A, Burton N, Bennett M, Baldock R, Davidson D, Mohun TJ and Logan MPO (2008) The Mouse Limb Anatomy Atlas: An interactive 3D tool for studying embryonic limb patterning. BMC Developmental Biology 8:83 See references 1, 113 in the bibliography at the back for publications from this group in 2010. A 3D rendering of the mouse hindlimb (left) and forelimb(right) at embryonic day(E) 14.5. The images were produced by Seth Ruffins (UCLA) using datasets produced in our lab using Optical Projection Tomography and computer-assisted segmentation. MRC National Institute for Medical Research 95 GENETICS AND DEVELOPMENT Stem Cell Biology and Developmental Genetics Robin Lovell-Badge FRS, EMBO member, FMedSci Sex, stem cells and decisions of cell fate Lab members: Sarah Booth, Christophe Galichet, Sam Goldsmith, Silvana Guioli, Albie Mackintosh, Ander Matheu, Adam Nunn, Helen O’Neill, Karine Rizzoti, Charlotte Scott, Ryohei Sekido, Clare Wise Embryo development relies on cells making choices about which cell type to become and whether to divide, move or die. During the process of sex determination, cells of the early gonad have an additional choice to make: to become cells typical of testes or ovaries. In mammals this usually depends on the presence or absence of the Y chromosome (males are XY, females XX). This is due to just one gene on the Y, termed Sry, which encodes a transcription factor. SRY contains an HMG box type of DNA binding domain, also present in proteins encoded by the Sox gene family. We use a wide range of techniques to explore how SRY and other factors act to initiate and then maintain testis and ovary differentiation. Mice are our main experimental model, and we study the chick for evolutionary comparisons since the initial trigger is different, but downstream effectors are probably the same. Cells expressing GFAP (yellow), which marks neural stem cells and their astrocyte progeny in the adult brain, are no longer found in the absence of SOX9. Our work informs the human situation, which when it goes wrong leads to devastating physiological and social consequences for affected individuals. We also study stem cell types, including pluripotent stem cells from very early embryos (ES cells) or after reprogramming from adult cells (iPS cells), and multipotent stem cells from the developing and adult central nervous system and pituitary. Certain Sox genes are critical for self-renewal and to confer potential to stem cells. We therefore explore how these genes impact on cell fate choices, and how they might be exploited to aid the treatment of a range of clinical problems, such as stroke and cancer. Publications Scott CE, Wynn SL, Cruz C, Cheung M, Gomez-Gaviro MV, Gao B, Cheah, KSE, Lovell_Badge R and Briscoe J (2010) SOX9, acting downstream of Sonic hedgehog signalling, is required for the initiation and maintenance of neural stem cell properties. Nature Neuroscience 13, 1181-1189 Uhlenhaut NH, Jakob S, Anlag K, Eisenberger T, Sekido R, Kress J, Treier A-C, Klugmann C, Klasen C, Holter NI, Riethmacher D, SchG, Cooney AJ, Lovell-Badge R and Treier M (2009) Somatic sex reprogramming of adult ovaries to testes by FOXL2 ablation. Cell 139:1130-4 FOXL2 is required to maintain adult ovaries in mice (left), because, when mutant for the gene, follicle cells transdifferentiate into SOX9positive Sertoli cells, typical of testes (right). 96 MRC National Institute for Medical Research Sekido, R. and Lovell-Badge, R (2008). SRY and SF1 act on a specific enhancer of SRY in sex determination. Nature 453, 930-4. See references 29, 87, 154, 203, 212, 224, 225, 241 in the bibliography at the back for publications from this group in 2010. GENETICS AND DEVELOPMENT Developmental Biology Tim Mohun Heart development in vertebrates Lab members: Mike Bennett, Laurent Dupays, Surendra Kotecha, Marianne Neary, Stuart Smith, Norma Towers, Robert Wilson Formation of the heart is a complex process that begins very early in the vertebrate embryo, remodelling a simple peristaltic tube into a complex multi-chambered organ capable of supporting embryo growth. This transformation requires exquisite coordination of cell differentiation and growth to produce the dramatic changes in organ shape. Abnormalities affecting any step will have profound consequences on the foetal heart and heart defects are the most common birth defect. By studying the roles of individual genes and cell populations in normal heart development, we will gain a better understanding of the origins of cardiac malformations and a model of how complex organs are formed in the developing embryo. We are using transgenic and genomic methods to examine how gene expression is regulated in the developing heart of frog and mouse embryos. 3D imaging and computer modelling procedures allow us to examine the embryonic heart and identify changes in heart morphology resulting from changes in cardiac gene expression. Most recently, this approach has established that mice carrying human chromosome 21 provide an accurate model of the congenital heart defects characteristic of human Down Syndrome. The heart of a tadpole. A single muscular ventricle pumps blood to the body via a single large outflow vessel which splits symmetrically into three major vessels (pigmented) supplying each side of the body. 3D reconstruction (orange) allows the internal structure of the heart to be studied. Publications Dunlevy L, Bennett M, Slender A, Lana-Elola E, Tybulewicz VL, Fisher EMC and Mohun T (2010) Down’s syndrome-like cardiac developmental defects in embryos of the transchromosomic Tc1 mouse. Cardiovascular Research 88:287-295 Breckenridge RA, Zuberi Z, Gomes J, Orford R, Dupays L, Felkin LE, Clark JE, Magee AI, Ehler E, Birks EJ, Barton PJ, Tinker A and Mohun TJ (2009) Overexpression of the transcription factor Hand1 causes predisposition towards arrhythmia in mice. Journal of Molecular and Cellular Cardiology 47:133-141 See references 21, 22, 62, 113, 163, 167 in the bibliography at the back for publications from this group in 2010. Although very different in structure, the ventricles of the frog and mouse hearts both contain a complex, interlaced web of muscle fibres (trabeculae), modelled here from images of a mouse embryo heart. MRC National Institute for Medical Research 97 GENETICS AND DEVELOPMENT Developmental Biology Elke Ober Liver development in zebrafish Lab members: Jordi Cayuso Mas, Johanna Fischer, Katarzyna Koltowska, Despina Stamataki, Heidi Miu During development, the liver, gall bladder and pancreas arise from neighbouring domains within the foregut. Highly regulated interactions between instructive signals and tissue competence are required for the specification and differentiation of each organ. Our understanding of these signals and interactions is still limited. We combine genetic and imaging approaches in zebrafish to elucidate the molecular network and cellular mechanisms underlying vertebrate liver formation. Our studies focus on identifying the genetic programmes governing the specification of liver progenitors within the ventral foregut endoderm. Furthermore, we examine the intricate cellular and molecular mechanisms that enable these newly specified progenitors to grow into an organ bud of appropriate shape and size. We recently isolated group specific component (gc) as the only homologue of the Albumin and α-Fetoprotein family of plasma proteins. Analysis of spatiotemporal expression in wild-type and selected mutants, such as the chromatin remodelling factor histone deacetylase1, indicates that onset of gc expression is indicative of progressive hepatic differentiation and represents a specific landmark of liver development. Unravelling the genetic programme of liver formation will provide insights into embryonic development, tissue homeostasis in adults, regeneration following tissue damage, as well as the development of hepatic stem cells for therapeutic purposes. Publications Cayuso Mas J, Noël ES, and Ober EA (2010) Chromatin modification in zebrafish development Methods in Cell Biology (in press) Noël ES, dos Reis M, Arain Z and Ober EA (2010) Analysis of the albumin/α-fetoprotein/afamin/group specific component gene family in the context of zebrafish liver differentiation. Gene Expression Patterns 10:237-243 Noël ES, Casal-Sueiro A, Busch-Nentwich E, Verkade H, Dong PDS, Stemple DL and Ober EA (2008) Organ-specific requirements for Hdac1 in liver and pancreas formation. Developmental Biology 322:237-250 The newly established liver and pancreas are connected via the extrahepatopancreatic ductal system (blue) to the digestive tract in 2 day old zebrafish. 98 MRC National Institute for Medical Research Hepatocytes (green) and biliary ducts (red) in the differentiating liver. See references 51, 186 in the bibliography at the back for publications from this group in 2010. GENETICS AND DEVELOPMENT Systems Biology Jim Smith FRS, EMBO member, FMedSci The molecular basis of mesoderm formation Lab members: Camille Bouissou, John Cannon, Clara Collart, Kevin Dingwell, Tiago Faial, George Gentsch, Helle Jørgensen, Anna Strobl, Alex Watson, Mary Wu The different cell types of the body are formed in the right place and at the right time in response to signals produced by special organiser regions of the embryo. These signals, or morphogens, act in a concentration-dependent manner to induce the formation of different cell types at different positions within developing tissues. One of the earliest interactions of this kind is mesoderm induction, which causes the formation of organs and cell types such as muscle, kidney and bone, as well as the heart and vascular system. We use frog, zebrafish and mouse embryos to study mesoderm-inducing factors and to ask how cells respond to them. In particular we use imaging approaches to understand how the signals exert long-range effects in the embryo, and biochemical and mathematical approaches to ask how cells distinguish between different morphogen concentrations. We also use sophisticated molecular techniques to elucidate the genetic regulatory networks that drive the formation of specific cell types. As well as helping understand development, we hope our work will assist in efforts to direct stem cells down the desired developmental pathways. Visualising cranial blood vessels in a Fli1-GFP zebrafish embryo Chromatin immunoprecipitation followed by high-throughput sequencing identifies a new target of the Xenopus tropicalis T box protein Brachyury. Nine Brachyury binding sites are present in the 5’ region of the gene, which encodes a previously-unknown helix-loop-helix protein. Publications Callery EM, Thomsen GH and Smith JC (2010) A divergent Tbx6-related gene and Tbx6 are both required for neural crest and intermediate mesoderm development in Xenopus. Developmental Biology 340:75-87 Cannon JE, Upton PD, Smith JC and Morrell NW (2010) Intersegmental vessel formation in zebrafish: requirement for VEGF but not BMP signalling revealed by selective and non-selective BMP antagonists. British Journal of Pharmacology 161:140-149 Harvey SA, Tümpel S, Dubrulle J, Schier AF and Smith JC (2010) no tail integrates two modes of mesoderm induction. Development 137:1127-1135 Immunostaining of transgenic zebrafish embryos carrying a bacterial artificial chromosome in which the ntl protein is marked with a ‘Flag tag’. Expression of the tagged protein occurs in the margin of the embryo at 6 hours after fertilisation (A) and in the notochord at 11 hours after fertilisation (B). See references 27, 111, 207 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 99 GENETICS AND DEVELOPMENT Stem Cell Biology and Developmental Genetics Peter Thorpe Systems microscopy studies of cell fate determination Asymmetric cell division is the process by which one cell divides to give two cells with different fates. Repeated asymmetric divisions allow a fertilised egg to generate diverse cell types during development, and in adult stem cells such divisions maintain the population while simultaneously generating new, differentiated cells. The goal of our lab is to determine how cellular asymmetry is established and maintained over multiple divisions to create cell lineages. Specifically, we focus on understanding how asymmetry of the mitotic spindle - the machinery that segregates chromosomes during division - affects how genetic information is accurately passed down to daughter cells. Our model system is the budding yeast, Saccharomyces cerevisiae, which shows patterns of asymmetric division like those of more complex organisms. We employ highthroughput fluorescence microscopy techniques that allow us to rapidly screen the localisation, levels and dynamics of all yeast proteins and integrate them into a visual dataset. Using these tools, we aim to identify the conserved mechanisms controlling asymmetric division, lineage specification and mitotic spindle function. 1st division DIC m enhanced b Mtw1YFP mm 2nd mother division bm mb 2nd bud division bb Publications Thorpe, PH; Bruno, J and Rothstein, R (2009) Kinetochore asymmetry defines a single yeast lineage. Proceedings of the National Academy of Sciences of the United States of America 106, 6673-6678. Thorpe, PH; Bruno, J and Rothstein, R (2008) Modeling stem cell asymmetry in yeast. Cold Spring Harbor Symposia on Quantitative Biology 73, 81-88 Cagney, G; Alvaro, D; Reid, RJD; Thorpe, PH; Rothstein, R and Krogan, NJ (2006) Functional genomics of the yeast DNA-damage response. Genome Biology 7, 233. 100 MRC National Institute for Medical Research mmm mmb 3rd mother division mbm mbb bmm 3rd division bbm bbb bmb 3rd division 3rd division As a yeast spore undergoes successive cell divisions, the fluorescently-labelled kinetochore proteins to both daughters or protein is preferentially As a yeasteither sporesegregate undergoes equally successive cell divisions, the(symmetry) fluorescently-labelled kinetochore proteins retained in the mother (asymmetry). restricted either segregate equallycell to both daughtersAsymmetric (symmetry) kinetochore or protein issegregation preferentiallyisretained in to thea singlecell lineage of cells (left side of figure) descended from the spore. mother (asymmetry). Asymmetric kinetochore segregation is restricted to a single lineage of cells (left side of figure) descended from the spore. GENETICS AND DEVELOPMENT Stem Cell Biology and Developmental Genetics James Turner X chromosome inactivation, meiotic silencing and infertility Lab members: Jeff Cloutier, Jennifer Grant, Helene Royo, Mahesh Sangrithi, Grzegorz Polikiewicz In mammals, X chromosome inactivation (XCI) occurs in all cells in the female and in developing germ cells in the male. In females, XCI serves to equalise X-dosage with males and abnormalities in this process cause various diseases, including mental retardation. The precise role of XCI in male germ cells is unclear, but defects lead to infertility. We study the mechanisms underlying both forms of XCI and the influence of XCI on the gene content of the X chromosome. We have shown that XCI in the male occurs because the X chromosome has no pairing partner during meiosis. Furthermore this form of X-silencing requires the tumour suppressor BRCA1. We have found that male XCI drives amplification of genes involved in late spermatogenesis on the X chromosome, with 18% of X-linked genes being expressed exclusively in developing sperm. Recently, we have used a new model organism, the marsupial Monodelphis domestica, to trace the evolution of XCI in mammals. These studies showed that most of the molecular features of XCI arose very early in mammalian evolution. In XYY males, the two Y chromosomes (blue) fully pair and escape the silencing mark gH2AX (red). Publications Royo H, Polikiewicz G, Mahadevaiah SK, Prosser H, Mitchell M, Bradley A, de Rooij DG, Burgoyne PS and Turner JMA (2010) Evidence that meiotic sex chromosome inactivation is essential for male fertility. Current Biology 20:1-7 Mahadevaiah SK, Royo H, Vandeberg JL, McCarrey JR, Mackay S and Turner JMA (2009) Key features of the X inactivation process are conserved between marsupials and eutherians. Current Biology 19:1478-1484 Escape from sex chromosome silencing causes germ cell death (arrow). Mueller JL, Mahadevaiah SK, Park PJ, Warburton PE, Page DC and Turner JMA (2008) The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression. Nature Genetics 40:794-9 See references 35, 215 in the bibliography at the back for publications from this group in 2010. MRC National Institute for Medical Research 101 GENETICS AND DEVELOPMENT Developmental Biology Lyle Zimmerman Using frog genetics to understand vertebrate development and disease Lab members: Anita Abu-Daya, Tim Geach, Holly Ironfield, Tosikazu Amano, Elisenda Vendrell Harvesting medical benefits from the human genome depends on understanding tasks specific genes perform in living organisms. Our group studies gene functions important for initial formation of organs and subsequent disease processes, by identifying and characterising genetic mutations that profoundly affect tissue development. Since most gene functions are shared among all vertebrates, we use the easily-studied externally-developing embryos of a frog with a simple chromosomal structure, Xenopus tropicalis. We have identified a number of mutations that model important human disease processes including cancer. One striking mutation, xenopus de milo (xdm), results in specific failure of forelimb initiation upstream of tbx5 expression during metamorphosis, and arises from disruption of the small secreted integrin ligand nephronectin. Nephronectin has previously been associated with cancer metastasis as well as kidney function. Another mutation, white hart, is being characterised for its effects on blood formation in the embryo. White hart has been mapped to the smad4 gene, an important mediator of intercellular signalling which is frequently mutated in human pancreatic and colorectal cancers. Publications Abu-Daya A, Nishimoto S, Fairclough L, Mohun TJ, Logan MPO and Zimmerman LB (2010) The secreted integrin ligand nephronectin is necessary for forelimb formation in Xenopus tropicalis. Developmental Biology 349:204-12 smad4 mutant shows deficits in blood formation. Left: muzak mutants which have wild-type blood formation (in situ hybridisation for the blood marker globin) but defective heartbeat; Right: white hart tadpoles show deficits in ventroposterior tissues including decreased blood formation. Geach TJ and Zimmerman LB (2010) Paralysis and delayed Z-disc formation in the Xenopus tropicalis unc45b mutant dicky ticker. BMC Developmental Biology 10:75 Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM and Rokhsar DS (2010) The genome of the Western clawed frog Xenopus tropicalis. Science 328:633-6 See references 1, 92, 115 in the bibliography at the back for publications from this group in 2010. 102 MRC National Institute for Medical Research nephronectin is required for forelimb formation. Left: skeleton of a wild-type metamorphosing tadpole showing scapula (sc), humerus (hu), ulna (ul), and digits (dit). Right: forelimb skeletal elements are missing in xdm froglets, but ribs are unaffected (r1,r2,r3). Emeritus scientists Distinguished retired scientists who keep alive the connections with the place where their careers began, provide a salutary link with former times and remarkable historical milestones. David Trentham, FRS In 1983 David Trentham moved from a position in the USA to head the new Division of Physical Biochemistry at NIMR, where he remained until retiring in 2003. He developed a truly interdisciplinary Division that encompassed chemistry, physiology, physics, biochemistry and molecular biology. Early in his career David’s research moved into areas of chemistry that were relevant to biology, when he worked on nucleotide chemistry at Cambridge. After periods at the Salk Institute and the Massachussets Institute of Technology, David continued postdoctoral work with Freddie Gutfreund at the University of Bristol. He mastered techniques of rapid reaction kinetics that had been recently developed and also began his interest in myosin and muscle that continued throughout his career. He became a Reader in Biochemistry at Bristol and in 1977 moved to become Chairman of the Department of Biochemistry and Biophysics at the University of Pennsylvania. David’s research involves rigorous quantitative analysis, bringing physical methods to bear on biological problems. At Bristol he produced a series of highly cited publications using rapid-reaction techniques to delineate the reaction mechanism for ATP hydrolysis by skeletal muscle myosin. Myosin became a paradigm for understanding the wide range of motor proteins that are known today. The mechanism showed that protein conformation changes could be linked both to biochemical steps and potentially also to the motor function: a concept considered as commonplace today. In the muscle field there was considerable effort for various disciplines (biochemists, structural biologists, physiologists etc) to interact. Such an interdisciplinary focus was a crucial aspect of David’s research, and was part of the attraction of moving to NIMR. It was important to take the research methods of isolated proteins to organised systems and the cell, and David saw the potential of caged compounds for timeresolved measurements in such systems. For example, caged ATP is an inert derivative that on photolysis produces ATP. This work exemplifies David’s curiosity for new areas of research and his enthusiasm for applying chemistry to biological problems. He worked with physiologists, chemists and physicists to establish that high-power lasers enabled rapid release of ATP in muscle fibres and so initiate contraction, as well as to understand the “uncaging” itself. This led to a series of other caged compounds that could release biologically important triggers, such as IP3. As more measurements on organised systems became possible and protein crystal structures became widely available, there remained a significant gap between dynamic measurements on milliseconds scale and those static structures. David focused his more recent work on this problem. By placing fluorophores at specific locations on the cross-bridge of muscle fibres, their movement could be monitored on the millisecond time scale, so showing which parts of the cross-bridges moved and when. As well as his work on muscle in increasing organisational complexity, David maintained several long-term collaborations in which physical methods were applied to a variety of biological preparations, including chemotaxis and neural signalling. David was elected a Fellow of the Royal Society in 1977 and received the Colworth Medal of the Biochemical Society and the Feldberg Prize. Since retirement he has continued as an active scientist at NIMR and King’s College London, both with his own research programme and by encouraging and advising younger scientists. MRC National Institute for Medical Research 103 Emeritus scientists Robert G. Edwards, CBE, FRS Robert Edwards completed his PhD at the University of Edinburgh and then spent one year at the California Institute of Technology at Pasadena before coming to NIMR. Alan Parkes interviewed him at NIMR in 1957 and was much impressed, describing him as “a young man of great promise”, who had “already done some extremely good research work”. Edwards worked at NIMR from 1958-1962, in the Division of Experimental Biology headed by Alan Parkes. Other prominent members of the Division at the time were the cryobiology pioneer Audrey Smith, Chris Polge and Colin (Bunny) Austin. Polge, Smith and Parkes had earlier published a landmark paper on the freezing and revival of spermatozoa. Austin had previously discovered sperm capacitation. At NIMR Edwards was chiefly interested in the immunology of reproduction and gained an excellent reputation in this field. During his time at NIMR his interests shifted from pure science to biomedicine, and his emphasis on immunology gradually decreased. Increasingly his main ambition was to work with human gametes and embryos, and to do something about human infertility. Whenever he could, he pursued his investigations on oocyte maturation, looking at a range of species. Edwards also carried out a lot of work on induced ovulation and superovulation in mice, looking at the effects on eggs, the embryos, the mothers, parturition and offspring. Techniques to induce ovulation are relevant to IVF in humans as it is very difficult to use natural ovulation. Others had shown that egg cells from rabbits could be fertilised in test tubes when sperm was added, giving rise to offspring. Edwards decided to investigate if similar methods could be used to fertilise human egg cells, and started to obtain human samples from a nearby hospital. Edwards left NIMR in 1962 and joined John Paul’s group at the University of Glasgow. He then accepted an invitation by Alan Parkes, recently appointed as the Mary Marshall Professor of the Physiology of Reproduction at Cambridge University, to join him there. Austin also moved to the same department in Cambridge. Robert Edwards was awarded the Lasker prize in 2001 for his work on IVF, and in 2010 was awarded the Nobel Prize in physiology or medicine for his pioneering work in the development of human in vitro fertilization (IVF) therapy. 104 MRC National Institute for Medical Research Research facilities Biological and Procedural Services Structural biology facilities MRC Biomedical NMR Centre X-ray crystallography Mass spectrometry Other structural biology facilities Protein sequence analysis and structure modelling Analytical ultracentrifugation Imaging Confocal Imaging and Analysis Laboratory Histology Electron microscopy OPT and HREM imaging Single molecule techniques Total internal reflection fluorescence microscopy Optical tweezers Atomic force microscopy Cryo electron microscopy Other scientific facilities Genomics facility High throughput sequencing Microarray Bioresources Large-scale laboratory Media production Freezer archive Flow cytometry facility Level 4 high-containment virus laboratory Engineering workshop Electronic instrument prototyping and support Other support services PhotoGraphics Computing Library Web Team General services Occupational Health Safety and security Human Resources Finance and purchasing MRC National Institute for Medical Research 105 SCIENTIFIC FACILITIES Biological and Procedural Services Kathleen Mathers The Division of Biological Services provides a fully integrated laboratory animal and technical resource to the Institute. The multidisciplinary research of the Institute requires a range of species and models, and to meet these needs we operate and manage a number of complex animal facilities. These include an isolation/quarantine unit, containment facilities at Levels 2, 3 and 4 for animals infected with organisms potentially harmful to man and/or the environment, specialist procedural, behavioural and surgical suites, imaging and irradiation facilities, and extensive aquatic facilities. The vast majority of animals in the facility are rodents, with large numbers of genetically altered lines of mice and rats. In addition, our facilities house ferrets, rabbits, the laboratory opossum, zebrafish and Xenopus species. The size, scope and efficiency of Biological Services provide an extraordinary service to nearly all aspects of the Institute’s science as well as to many scientists elsewhere. Xenopus laevis Individually ventilated cages 106 MRC National Institute for Medical Research Laboratory opossum with litter SCIENTIFIC FACILITIES We aim to meet all the needs of the scientific Divisions whilst ensuring the highest possible standards of health and welfare for all species. The Division is active in the field of laboratory animal science, conducting and promoting research and uptake of the 3Rs (replacement, reduction, refinement) and presents its work at national and international meetings. The animal care and technical staff are trained in the production, care and use of animals for research purposes to the highest standards of animal husbandry. Additionally they provide a range of centralised procedural support. A full-time veterinary surgeon and microbiologist offer advice on the health and welfare of our animals. The Division also provides services for the incubation of fertile chicken eggs and the production of antibodies. In addition, administration and licence control under the Animals (Scientific Procedures) Act 1986, and coordination of the Institute’s Local Ethical Review Process, is managed by Biological Services. Procedural Service Section The Procedural Service Section provides a range of services and facilities for the production, maintenance and preservation of genetically altered rodents. The service produces approximately 200 new genetically altered rodent lines each year by both transgenic and gene-targetted technologies. A full range of techniques is employed to provide a comprehensive service for the cryopreservation of rodent germplasm, and more recently the service has expanded to include cryopreservation of frog and fish spermatozoa. In addition, the section is responsible for the rederivation of new lines imported into the Institute. Every year, together with Biological Services, the Section coordinates over 150 shipments of live animals and frozen germplasm to collaborators all over the world. The staff are also skilled in a number of assisted reproductive techniques, including in vitro fertilisation and intracytoplasmic sperm injection, which are useful for maintenance of lines with poor breeding performance or to provide age-matched cohorts for experiments. The section is also committed to investigating and implementing the 3Rs by researching and developing new refinements such as non-surgical methods of embryo transfer. Microinjection of ES cells Procedural Services Manager: Sarah Johnson Micromanipulation MRC National Institute for Medical Research 107 SCIENTIFIC FACILITIES MRC Biomedical NMR Centre Tom Frenkiel Co-workers: Geoff Kelly, Alain Oregioni The MRC Biomedical NMR Centre is a multi-user facility for biomolecular liquid-state nuclear magnetic resonance (NMR) which was set up by the MRC in 1979 to provide advanced and well-supported facilities for use by scientists from NIMR and other academic research establishments. NMR studies of the type carried out at the Centre provide a wide range of information, ranging from the atomic-level (e.g. determining the pKa of individual histidine groups in proteins), through to full determination of the structure and dynamics of proteins in solution. An important area of application is the identification of interaction surfaces between the components of macromolecular complexes. The Centre’s facilities consist of four spectrometers, including one operating at 800 MHz, a 700 MHz instrument, and two 600 MHz instruments. Centre staff have a high level of expertise in designing, implementing, and analysing macromolecular NMR studies. The spectrometers are suitable for investigating a wide range of biological systems in solution. Three of the four are equipped with the latest cryogenically-cooled probes for enhanced sensitivity. The facilities are currently used by research groups from NIMR and 16 external groups at universities and institutes from around the UK. Within NIMR our closest links are with the Division of Molecular Structure. 1 NMR structure of the two central KH domains of the KSRP protein, showing (in yellow and green) the regions of the molecule involved in recognition of AU-rich elements in mRNA. The two domains form a single structural element; each domain has an RNA binding site, but these are non-contiguous and orientated at 90 degrees to one another. These results show that the RNA molecule must be bound in a bent conformation. Publications Cukier CD, Hollingworth D, Martin SR, Kelly G, Díaz-Moreno I and Ramos A (2010) Molecular basis of FIR-mediated c-myc transcriptional control. Nature Structural & Molecular Biology 17:1058-64 Magnet of the 800 MHz spectrometer. Martino L, He Y, Hands-Taylor KLD, Valentine ER, Kelly G, Giancola C and Conte MR (2009) The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity. FEBS Journal 276:4529-4544 Nott TJ, Kelly G, Stach L, Li J, Westcott S, Patel D, Hunt DM, Howell S, Buxton RS, O’Hare HM and Smerdon SJ (2009) An intramolecular switch regulates phosphoindependent FHA domain interactions in Mycobacterium tuberculosis. Science Signaling 2:ra12 108 MRC National Institute for Medical Research SCIENTIFIC FACILITIES X-ray crystallography Protein X-ray crystallography is a technique that produces a 3-dimensional model of the structure of a protein at atomic resolution. The X-ray crystallography facilities within the Division of Molecular Structure at the Institute are state-of-theart and include a high intensity X-ray source coupled with an automated robotic sample mounting system which allows the unattended screening of 80 crystals in a single experiment. Diffracting protein crystals are the culmination of an extensive series of experimental procedures which include protein purification and protein crystallisation. A range of sophisticated techniques are employed to help explore the largest number of conditions within each of the projects under investigation. These include those techniques being developed in the Protein Expression Lab together with a wide range of robotic procedures to set up multi-well dishes and to automatically screen for protein crystals. X-ray generator and automated sample mounting robot insert shows the loop used to hold the protein crystal. The Protein Expression Lab was established in 2009 to provide dedicated support to members of the Division of Molecular Structure. The facility provides a comprehensive resource for the production of recombinant proteins. Currently we offer a choice of two expression systems: bacteria and insect cells. A high-throughput pipeline for cloning DNA fragments and small-scale expression tests in E. coli has been established, allowing the generation and screening of 96 expression constructs in a week. In parallel, protein is also expressed in insect cells using a baculovirus expression vector system. Services include the generation and amplification of high-titre baculovirus stocks, analytical scale productions for optimisation of protein expression, and preparative scale productions. In addition, the facility maintains a vector DNA repository, provides in-house vector design, troubleshooting and training. In the 20 months of operation we have produced and tested more than 1000 constructs in E. coli and have generated over 50 high-titre baculoviruses in insect cells. 3D structure of an influenza virus protein. Small scale protein test SDS-PAGE gel. Insect cell expression in a Wave Bioreactor™.. MRC National Institute for Medical Research 109 SCIENTIFIC FACILITIES Mass Spectrometry A tandem mass spectrum of an in-gel digested protein. The Institute currently has two mass spectrometers which are used in a range of biochemical applications. A research grade MALDI-TOF is primarily employed in proteomics studies, coupled with SDS-PAGE, to identify proteins from their peptide mass fingerprints by database searching. This instrument is also used to analyse peptide structure by post-source decay fragmentation. A quadrupole time-offlight (Q-TOF) tandem mass spectrometer, equipped with electrospray and nanospray sources, is utilised for protein characterisation, peptide sequence confirmation and de novo sequencing. This instrument is also used in the investigation of post-translational modifications such as phosphorylation. In the last year, the Institute has invested further in this important area and a new mass spectrometry suite is under construction. This will house the existing machines alongside a state-of-the-art LTQ Orbitrap Velos spectrometer capable of 110 MRC National Institute for Medical Research Other structural biology facilities Protein sequence analysis and structure modelling Computational tools for prediction, analysis and visualisation can provide inspirational new ways to look at data, no matter which protein family is the main focus of research. From high-level predictions of protein topology by template-free methods (sometimes called ‘ab initio’), through three-dimensional all-atom models of protein structure, to detailed protein-ligand docking studies; theoretical methods developed both at NIMR and in the wider academic community can suggest new insights and new hypotheses leading to the design of fruitful experiments. Structural model of an immunoglobulin binding site showing amino acid residues in gold, important for the shape of the binding loops (CDRs) shown in yellow. The Division of Mathematical Biology contains a support service for protein sequence analysis and structure modelling. It draws on state-of-the-art algorithms being developed by experts in the Division as well as the many computer programs freely available from the scientific community. There is also an in-house, commercial, computer graphics package for detailed three-dimensional modelling. The service is available to all NIMR scientists and external collaborators. Analytical ultracentrifugation The Institute has two analytical ultracentrifuges located in the Division of Physical Biochemistry. These instruments provide first-principle hydrodynamic and thermodynamic information concerning the size, shape and association state of macromolecules. For basic applications, the two instruments (XL-A and XL-I) are equipped with UV/Vis optics that record radial absorbance measurements and monitor evolving (sedimentation velocity) or static (sedimentation equilibrium) concentration gradients. The XL-I is additionally equipped with Rayleigh interference optics that measure concentration profiles directly from solute refractive index gradients. The interference and absorbance data are recorded simultaneously in the XL-I and are used in combination for the analysis of complex associating systems. The optical detection system of the XL-I analytical ultracentrifuge consisting of a combined UV/Vis spectrophotometer and laser interferometer is shown in the bottom image. A fringe displacement pattern produced by a moving concentration boundary measured by the Rayleigh interference optics of the XL-I is shown above. MRC National Institute for Medical Research 111 SCIENTIFIC FACILITIES Confocal Imaging and Analysis Laboratory (CIAL) Yan Gu Co-workers: Kate Sullivan, Donald Bell, Chen Qian CIAL provides an imaging core facility available to everyone at NIMR. The facility has six confocal microscopes, three wide-field fluorescence microscopes, four offline workstations, a data storage system, and image processing software such as Volocity, Imaris, Image J, Metamorph and MatLab. Currently the facility supports 170 researchers from 15 NIMR Divisions. Users operate the system, but the complexity of imaging makes support an extremely important aspect of the facility. Routinely, we provide users with training, troubleshooting, consultation and microscope maintenance. We also support special techniques such as thick tissue imaging, live experiments, 2nd harmonic generation imaging, quantitative imaging, deconvolution imaging, and automatic cell counting. Research activities in CIAL are focused on techniques of super resolution imaging, correlative microscopy, high-throughput imaging, automatic cell segmentation and tracking, and others relevant to NIMR research. The lab has expertise in sample preparation and labelling, live/ fixed sample imaging, and hardware/software development required by NIMR researchers. 2nd harmonic generation image (grey level) of the nonlabelling muscle/tendon cells, and the GFP/Alexa 488 labelled limb tissue (green) in a mouse embryo. Courtesy of Malcolm Logan High-throughput quantification of virus-infected cell population and plaque formation. Courtesy of Yipu Lin Publications Ktistaki E, Garefalaki A, Williams A, Andrews SR, Bell DM, Foster KE, Spilianakis CG, Flavell RA, Kosyakova N, Trifonov V, Liehr T and Kioussis D (2010) CD8 locus nuclear dynamics during thymocyte development. Journal of Immunology 184:5686 -5695 McIntosh PB, Laskey P, Sullivan K, Davy C, Wang Q, Jackson DJ, Griffin HM and Doorbar J (2010) E1^E4-mediated keratin phosphorylation and ubiquitylation: a mechanism for keratin depletion in HPV16-infected epithelium. Journal of Cell Science 123:2810-2822 Zhu D, Jarmin S, Ribeiro A, Prin F, Xie SQ, Sullivan K, Briscoe J, Gould AP, Marelli-Berg FM and Gu Y (2010) Applying an adaptive watershed to the tissue cell quantification during T-cell migration and embryonic development. Methods in Molecular Biology 616:207-28 112 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Histology Radma Mahmood Co-worker: Elena Grigorieva The Histology service provides a range of sectioning techniques for visualisation of tissue structure and gene expression in animal research models. By making paraffin blocks of animal tissues, we produce thin sections that when stained allow for analysis of tissues at a cellular level. Tissues are automatically processed, embedded into paraffin blocks and sectioned manually by facility histologists. Slides generated are stained for cell and nuclear structure or left unstained for the researcher’s own use. Newly acquired equipment includes the Leica automated tissue processor (ASP300) and automated slide stainer (Autostainer XL) as well as two new rotary microtomes and cryostats. The ASP300 processor utilises 10 different processing programs designed to optimally maintain morphology of all tissues from mouse embryos and neonates, rats, frogs and fish, as well as human research samples. Paraffin tissue blocks are sectioned manually and the automated stainer is used for hematoxylin and eosin staining. Special stains, such as Masson’s Trichrome for collagen, are performed manually. Shared resources available to researchers include cryostats for frozen sections and a microtome for paraffin sections. The service also provides training, protocols, and assistance for investigators on all aspects of histology, including tissue fixation, tissue processing, and immunohistochemical techniques. Bone stained with Mallory’s Trichrome (E. Grigorieva) Kidney stained with Periodic Acid Schiff stain(PAS) (E. Grigorieva) Colon stained with Hematoxylin and Eosin (E. Grigorieva) MRC National Institute for Medical Research 113 SCIENTIFIC FACILITIES Electron microscopy Liz Hirst The facility has both Transmission (Jeol 1200 EX set up for conventional scattering optics) and Scanning (Jeol 35CF) Electron Microscopes which have both been upgraded to CCD photography. There is also a dedicated EM processing laboratory. Staff from NIMR may request TEM or SEM investigations for their scientific studies. TEM techniques available include ultra-thin sectioning and ultra-structural analysis of experimental tissues, cell cultures or pellets. Immuno-EM techniques can be post-embedding immuno-gold labelling of antigens upon ultra-thin sections or pre-embedding HRP labelling. SEM techniques available include internal anatomy by dry fracture or dissection as well as external topology. Elsewhere within the Institute, a second Jeol 1200EX is set up for low dose high resolution of single molecules and viruses. Generally, samples are provided by the requester and analysed by TEM and/or SEM with reference to the questions of specific interest for their project. Results normally consist of representative micrographs and a written report of the interpretation of the ultrastructural morphology for discussion and publication. No previous experience of electron microscopy is required as expertise and advice is provided by the EM facility. Technical advice, training and support is also provided. SEM of spinal cord of 1.5 day chick embryo, electroporated to overexpress Sox9 and slug genes Publications Ermakov A, Stevens JL, Whitehill E, Robson JE, Pieles G, Brooker D, Goggolidou P, Powles-Glover N, Hacker T, Young SR, Dear N, Hirst E, Tymowska-Lalanne Z, Briscoe J, Bhattacharya S and Norris DP (2009) Mouse mutagenesis identifies novel roles for left-right patterning genes in pulmonary, craniofacial, ocular, and limb development. Developmental Dynamics 238:581-94 Polyakova O, Dear D, Stern I, Martin S, Hirst E, Bawumia S, Nash A, Dodson G, Bronstein I and Bayley PM (2009) Proteolysis of prion protein by cathepsin S generates a soluble β-structured intermediate oligomeric form, with potential implications for neurotoxic mechanisms. European Biophysics Journal 38:209-218 Bazigou E, Apitz H, Johansson J, Lorén CE, Hirst EMA, Chen P-L, Palmer RH and Salecker I (2007) Anterograde Jelly belly and Alk receptor tyrosine kinase signaling mediates retinal axon targeting in Drosophila. Cell 128:961-75 114 MRC National Institute for Medical Research Immuno-EM of Escherichia coli showing that Suf B and Suf C are localised to the bacterial membrane (10 nm gold particles). SCIENTIFIC FACILITIES OPT and HREM imaging Imaging methods play an increasingly central role in enabling gene or protein activity to be linked to function and phenotype, from subcellular to whole organism levels. Within the Division of Developmental Biology, the Institute has developed dedicated facilities for imaging complex morphology and gene expression of embryonic and adult tissue in 3D using Optical Projection Tomography (OPT) and High Resolution Episcopic Microscopy (HREM). This complements existing facilities at NIMR provided by Confocal Imaging and Histology. Automated HREM developed at NIMR forms the basis of an ongoing project funded by the Wellcome Trust and supported by the Medical Research Council to provide comprehensive imaging of normal and mutant mouse embryos at unprecedented resolution. The freely available data (www.embryoimaging.org) complement standard anatomical texts and can form the basis for systematic analysis of mutant morphological phenotypes. OPT imaging of the transcription factor Hnf3β (red) in the mouse embryo. HREM imaging of mouse embryo tissue structure and 3D MRC National Institute for Medical Research 115 SCIENTIFIC FACILITIES Single molecule techniques Single molecule experiments give insights into how biological molecules work and how they are structured. Several research groups at NIMR apply and develop methods to study single molecules. Some of these techniques provide high resolution images of the molecules, and others give dynamic information about the interactions between proteins, DNA, lipid membranes and small ligand molecules. TIRF (left) and Optical Tweezers (right) are powerful tools that assist studies of motor proteins which are the molecular machines contained in every cell of the body. We have developed methods to visualise and manipulate single molecules, with high time resolution, using two laser-based techniques; Total Internal Reflection Fluorescence (TIRF) microscopy and Optical Tweezers (OT). TIRF microscopy uses the evanescent field associated with a totally internally-reflected laser beam to excite fluorophores at the surface of a microscope coverslip. Sensitive camera systems are used to detect light emitted by the fluorophores. These measurements have a resolution of around five nanometres within 50 milliseconds. Optical Tweezers make use of radiation pressure to pick-up and manipulate individual molecules. Using fast detectors, the position of optical trapped particles are measured with nanometre precision so that forces and movements produced by single molecules can be measured. The resolution is around one nanometre every millisecond. Atomic Force Microscopy (AFM) enables us to analyse the structure of biological molecules by scanning their surface topology using a microfabricated mechanical probe or “tip”. The AFM used at NIMR (JPK NanoWizard) is ideally suited to studying biological materials in aqueous solution at room temperature. The AFM tip is scanned over the sample. As it rides over molecules fixed to the surface, deflections of the tip are measured using a laser-based position sensor. The technique is ideally suited to studies of material for which high-resolution dynamic information is required. The ultimate resolution depends on the sharpness and stiffness of the silicon tip, the mechanical properties of the specimen and also upon the mechanical stability of the laboratory and microscope system. For soft biological molecules, the resolution is around five nanometres. Atomic Force Microscopy (AFM) works by scanning an ultra-sharp, silicon probe over a surface that has been sparsely coated with biological molecules or biological cells. The JPK NanoWizard used at NIMR enables simultaneous imaging by optical microscopy and AFM. 116 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Cryo electron microscopy High resolution cryo electron microscopy (cryoEM) enables the structure of biological molecules and larger materials to be visualised in a frozen hydrated state without fixation or staining. An aqueous solution containing the specimen is frozen very rapidly to liquid nitrogen temperatures. When cooled rapidly, water turns to a glass (rather than forming ice crystals) and the embedded biological material, locked in this transparent medium, can be viewed by electron microscopy. Because the electron beam has a much shorter wavelength than visible light, individual protein molecules can be visualised. Although the image contrast of each individual molecule is low, signal averaging can yield very high resolution pictures. CryoEM is well-suited to high-resolution studies of both the structure and dynamics of large proteins and protein complexes, such as cytoskeletal proteins or viral capsids. Our latest methods also enable structures within rapidly frozen mammalian cells to be visualised. By recording many digital images of a specimen held at different orientations (tomography), a three-dimensional view of the molecule or cell is obtained. Individual molecules, whole virus particles or living mammalian cells embedded in ice can be imaged in three dimensions. Averaging of proteins can reveal near-atomic resolution structural information. Slice of a three-dimensional tomogram showing the edge of a frozen hydrated cell and a computational model for membrane organelles. Image courtesy of Sebastian Wasilewski MRC National Institute for Medical Research 117 SCIENTIFIC FACILITIES Genomics facility Abdul Karim Sesay Co-workers: Bob Butler, Harsha Jani The Genomics facility makes state-of-the-art, next-generation sequencing and microarray services available to NIMR research scientists. Services include sample preparation, highthroughput sequencing and microarray hybridisation. Support is also provided for data analysis. Situated within the Division of Systems Biology, the Genomics facility is equipped with state-of-the-art instrumentation for genomic sequencing, genotyping and gene expression studies, including Illumina GAIIx and HiSeq2000 sequencers, the Affymetrix Gene Chip hybridisation and Illumina iScan Systems. High-throughput sequencing High-throughput sequencing technologies are revolutionising molecular genetics, vastly expanding our ability to study genome structure, how genes are regulated and how cell and tissue differentiation occurs. Combined with increasingly sophisticated bioinformatic analysis, these methods of massively parallel sequencing-by-synthesis are likely to impact on all areas of basic biological research, with their ability to generate billions of bases of high-quality DNA sequence in a matter of days. In order to maintain its position at the forefront of basic research, NIMR has established a central next-generation sequencing core facility. The facility currently supports DNA/RNA sequencing using the Illumina Genome Analyzer IIx (commonly referred to as “Solexa”) for reads up to 150 bases for both single and paired-end runs. This facility provides a cost-efficient service, producing rapid and highly accurate DNA and RNA sequence data for researchers at NIMR. By assisting at all stages from experimental design to data assembly and analysis, the service dramatically extends the ability of our scientists to make discoveries in genomics, epigenomics, gene expression analysis and protein-nucleic acid interactions. The facility now includes the Illumina HiSeq 2000 sequencer. With innovative design features, the HiSeq 2000 provides output of up to 200 Gb per run (2 x 100 bp read length), up to 25 Gb per day and two billion pairedend reads/run. DNA shearing The Genomics Facility has a Covaris system (based on Covaris Adaptive Focused Acoustics™ (AFA)) for DNA shearing for next-generation sequencing and for conventional molecular biology applications and chromatin shearing for chromatin immuno-precipitation. Quality control We offer an extensive platform for quality control and quantification of DNA, RNA and proteins. The following equipment is available for QC analysis: Whole-genome chromatin IP sequencing (ChIP-Seq) to identify targets of the Brachyury transcription factor that regulates mesoderm formation, which include members of the HES gene family. The figure shows multiple binding of Xenopus • Nanodrop spectrophotometer and two Agilent 2100 Brachyury in the vicinity of hes9.1 and two novel HES genes. RNAPII (ChIP-Seq) and Bioanalyser, for quality control and quantification of DNA, RNA-Seq profiles were superimposed with Xbra ChIP-Seq. Members of the HES family are involved in the segmentation of mesodermal tissue. RNA and proteins. Courtesy of G Gentsch and J Smith. •Two Life Technology Qubit systems, for the quantification of DNA, RNA and proteins. •Life Technology E-Gel systems for size selection of sequencing libraries 118 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Microarray Whilst the most common use of microarrays is examining the level of expression of many different genes or mRNA species in a sample simultaneously, there are now chips available for other protocols. These include SNP analyses, resequencing – including a human mitochondrial genome chip - exon arrays for analysis of alternative splicing, arrays for ChIP on chip experiments for investigation of gene promoters, and miRNA and snoRNA analysis with coverage of multiple organisms on a single array (human, mouse, rat, canine, and monkey). Arrays are available for many different organisms; we have used those for Mycobacterium tuberculosis, Drosophila, Xenopus, zebrafish, chicken, dog, mouse, rat and human. The microarray facility offers full technical support in the preparation and running of RNA or DNA samples prepared by the scientists. It also offers access to and training in use of the Gene Spring software package from Agilent for preliminary analysis of microarray data. The facility now includes the Illumina iScan System with Universal Starter Kit. Based around the iScan Reader, which incorporates high-performance lasers, optics, and detection systems, the iScan System offers sub-micron resolution, higher throughput rates and very economical BeadChips available for human, rat and mouse. Even the highest density BeadChips can be scanned in minutes, allowing processing of up to 96 multisample BeadChips per day. Applications include gene expression Transcriptional profiling, using Affymetrix GeneChips, identifies Foxj1 as analysis; array-based transcriptome analysis; FFPE sample analysis; differentially regulated by Shh signalling in the neural tube. (A) Hierarchical clustering of genes up- and downregulated by Shh. Normalised expression SNP genotyping and CNV analysis; whole genome, custom or values are shown for for downregulated genes (Cluster 1; B) and upregulated focused genotyping; cytogenetic analysis; linkage analysis; copy genes (Cluster4, C). (D-K) In situ hybridisation of Foxj1 in chick (D, E) and number analysis; gene regulation and epigenetic analysis, and arraymouse (F-K) embryos. Courtesy of James Briscoe. based methylation analysis. The Genomics facility team The new HiSeq 2000 MRC National Institute for Medical Research 119 SCIENTIFIC FACILITIES Bioresources Joachim Payne Co-workers: Wioletta Berg, Brian Trinnaman, Jackie Wilson, Ian Oliver, Charlotte Austin, Viktoria Janusova The Large Scale Laboratory team has over 40 years of combined cell culture experience, and offers a full consultation service for all requests. Today we grow a wide range of animal, insect, yeast and bacterial cells for 10 research Divisions at NIMR, as well as collaborating with other MRC units, the Marie Curie Research Institute, NIBSC and the Wellcome Trust. Last year we grew 1300 litres of hybridoma cells and 3200 litres of yeast and bacterial cultures. Cells can be supplied quick-frozen or lysed using a Constant Systems cell disrupter. For concentrating supernatants we have a Sartorius crossflow filtration system and a Quixstand hollow-fibre unit. Our in-house Media Production facility has formulae for over 1,200 types of product, and last year processed 3,500 orders, totalling around 36,000 litres of media and associated solutions including a quarter of a million tubes of Drosophila food and 45,000 microbiological poured plates. The Mellanby Freezer Archive is a purpose-designed facility for the longterm, secure storage of frozen material. At the moment we are responsible for over half a million samples belonging the MRC’s Prion and Clinical Trials Units and researchers as far away as the MRC SPHSU in Glasgow. 120 MRC National Institute for Medical Research Wioletta inspects a hybridoma culture. Brian sets up one of our bioreactors. SCIENTIFIC FACILITIES Flow cytometry facility Graham Preece The flow cytometry facility provides state-of-the-art technology for high speed, sterile sorting of multiple types of cell populations for molecular, signalling and in vivo studies, single cell sorting and cloning. In addition, it offers multiparameter fluorochrome analysis of cell markers, and measurement of calcium fluxes, apoptosis and cell cycle parameters. The facility serves a large number of NIMR researchers from the Infections and Immunity, Genetics and Development and Neurosciences groups. In addition to providing NIMR scientists with an essential cell sorting service and FACS analyser facility, training is also provided for research staff, including PhD students and postdoctoral researchers. The facility is well equipped, with five cell sorters that range from 4-colour to 13-colour machines (Beckman Coulter MoFlo; Becton Dickinson FACS Aria II; Automacs Pro Bead Sorting), and eight FACS Analysers that include 4- and 9-colour machines (Becton Dickinson FACS Calibur, Canto and LSRII; Beckman Coulter Cyan ADP). MRC National Institute for Medical Research 121 SCIENTIFIC FACILITIES Level 4 high-containment virus laboratory Within the complex of buildings that make up NIMR, is a suite of laboratories for handling viruses with high pathogenic potential for birds, humans or other mammals. Its presence is necessitated by the work of the WHO Influenza Centre (WIC) at NIMR that involves the handling of influenza viruses from all over the world, such as the novel H1N1 virus, prior to its emergence as a full-blown pandemic virus. In addition, poorly characterised viruses are also received. Some of these viruses, notably viruses from zoonotic H5N1 infections, have considerable pathogenic potential in both birds and humans. Work with poorly characterised viruses and viruses that might, or do, have pandemic potential requires a high degree of containment to prevent the spread of influenza viruses into birds or the environment, as well as operator protection to minimise the risk of handling viruses potentially harmful to man. The facility is built to Health and Safety Executive requirements and DEFRA regulations under the Specified Animals Pathogen Order. It was used for the growth and characterisation of samples of the pandemic H1N1 virus, at the early stages of its global spread, sent from around the world, and to generate reference ferret antisera to the emerging pandemic viruses for virus antigenic analyses. It has also been used for the isolation and characterisation of human isolates of H5N1 avian influenza virus, for example from the Turkish outbreak in humans in 2006. The laboratory capacity has been extended to have two standard high containment laboratory areas and two laboratories equipped to handle infected small animals under high level containment. With the enhanced capacity, in addition to the virus surveillance and characterisation studies of the WIC, simultaneous studies of the mechanisms of disease causation by avian or other influenza viruses can be carried out. Features of the laboratory include: • A negative pressure air regime with HEPA filtered input and double HEPA filtered extract. • Waste treatment with heating of liquid waste and autoclave sterilisation of solid waste within the body of the laboratory. • Class III and Class I/III microbiological safety cabinets for handling samples. • Class III cabinets for handling infected small animals. • Sealable, so as to permit fumigation. • Strict codes of practice including the requirement for all workers to undergo a complete change of clothing before. entering the laboratory and to shower when leaving. In addition to the Level 4 laboratory, there are 11 Level 3 laboratories scattered among the main buildings and biological research facilities at NIMR. These laboratories allow the safe handling of a number of pathogenic organisms, permitting studies of the microbiology and immunology of Mycobacterium tuberculosis, the invasion of blood cells by the malaria parasite and the growth of the retroviruses that cause AIDS. 122 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Engineering workshop Alan Ling Co-workers: Derek Brewer, Peter Cookson, Ray Herriot, Derek Rumley The workshop provides a design, construction and commissioning facility for bespoke instruments. This can involve new developments or modifications to existing equipment. Facilities include: • 2D & 3D Design (AutoCAD) • Milling (CNC) • Turning • High precision (watch making) • Sheet metal forming • Welding • Plastic vacuum forming • Injection moulding (plastic components) The experienced staff can manufacture quick one-off prototypes, followed by continued development and modification to produce the desired item or apparatus. On-site repair and maintenance of laboratory equipment is also carried out in the workshop. The varied facilities means that a diverse range of projects can be worked on, including: • micromanipulators • microscope set-ups • custom-made parts • temperature controlled chambers • drug infusers and nebulisers • blood flow measurement devices MRC National Institute for Medical Research 123 SCIENTIFIC FACILITIES Electronic instrument prototyping and support Martyn Stopps In collaboration with Programme Leaders, instruments are designed and manufactured for applications in physiology and single molecule research. Work conducted in cutting-edge science often requires new instrumentation that is not available commercially. Examples of this over the past year include: • An optical trap with a PC interface for single molecule research. • A high speed closed-loop thermal controller for live cell imaging studies of secretary pathways. • Behavioural neuroscience apparatus enabling subtly different odours to be rapidly switched and delivered along independent odor lines. Utilising current technologies, the resource in collaboration with researchers and Mechanical Engineering, enables comprehensive system development from initial specification to proof of concept and the final solution. Alternating two-colour fluorescence imaging a custom-built control unit synchronises an EMCCD digital camera and two lasers together with a computer data acquisition programme. 124 MRC National Institute for Medical Research An Electronics and Programming Workshop a two-day practical workshop providing basic electronics and programming techniques enabling exploration of novel research beyond what commercial apparatus may provide. SCIENTIFIC FACILITIES PhotoGraphics Joe Brock Co-workers: Neal Cramphorn, Wai Han Yau, Hayley Wood, Jamie Brock The PhotoGraphics service provides a professional design, illustration and imaging facility to visualise the innovative research carried out at NIMR. Our fully trained team provides a wide range of specialist skills using state-of-the-art equipment, software and techniques. These include digital manipulation, illustration, Flash™ animation, film making and editing, 3D modelling, scanning and photography as well as providing a printing, copying and binding service. This facility is open to all researchers wishing to relate their science visually through publication, digital presentation and posters. Novel methods developed by us for presenting science using interactive animations provide more dynamic in-depth explanations and we regularly receive requests for copies by researchers and companies world-wide who recognise this media as a powerful informative tool. The PhotoGraphic team design and publish NIMR publications such as this report, the Mill Hill Essays and other in-house publications. We also present training courses throughout the year for researchers who wish to use applications such as Adobe Photoshop™ and Microscoft Powerpoint™ to professional level. Photographics also maintain the seminar and meeting room facilities and provide the audio-visual Composite image showing 3D modelling, illustration and embedded movies within a single animation describing the role of myosin in merozoite infection of red blood cells. Typical illustration produced by PhotoGraphics to visualise scientific and biological processes. MRC National Institute for Medical Research 125 SCIENTIFIC FACILITIES Computing Clive Lunny Co-workers: Aomar Ayad, Jose Ayala, Darsheni Fatania, John Green, Debra Harper, Ben Kesel, Graeme Millar, Harsha Sheth, Nathan Smith Computing and Telecommunications provides secure access to the Internet, via a firewall, over a 100Mb JANET (Joint Academic Network) connection. They provide a range of services including email with web-based access, secure remote access, web servers for intranet and public websites, IT security, including anti-virus and spam filters, data encryption, FTP server/web-based export server, database and related services, support services for both Windows and Macintosh computers and other mobile devices, secure wireless networks and an internal telephone system. Recently they have introduced Webex video collaboration services, a new 100TB data storage system and are adopting virtualisation to increase energy and space efficiency. 126 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Library Frank Norman Co-workers: Patti Biggs, Nicola Weston, Lynsey Eames The Library is dedicated to serving the information needs of scientific staff and students at NIMR. It provides access to a broad range of electronic journals (2000 plus titles) and searching tools. Extensive printed journal backfiles and a print book collection supplement these. Easy access to document delivery completes the picture. Library staff provide individualised help for scientists in the lab or at their desktop. Expert assistance with information searching is available, including help with systematic literature reviews, difficult-to-answer questions and search alerts for easier literature scanning. Support for publishing includes assistance with bibliographic management (e.g. Endnote, Reference Manager, Mendeley, Zotero) and advice on Open Access compliance. A daily news service keeps staff informed of current science policy developments. Desk space in the Library includes dedicated study desks for write-up, a cluster of computer desks with PCs and Macs, and casual reading space. There is a wifi network in the main reading room so that laptops and other mobile devices can be used. The Library records the Institute’s major research outputs and achievements, ensuring that these are listed on the NIMR website and in the Annual Report. It also maintains the Institute’s historical archives and repository of publications. The main reading room. Casual seating area with new book and journal displays. MRC National Institute for Medical Research 127 SCIENTIFIC FACILITIES Web Team Christina McGuire Co-worker: Mark Houghton The Web Team is responsible for the day-to-day management of the NIMR website, intranet and online presence, and longer-term strategic projects such as the recent redevelopment and implementation of a content management system on the external website. Our aims are to ensure that the external website reflects the excellence of science at NIMR, meets user and organisational needs, and promotes the research and outreach work at NIMR. Internally, we want to provide easy access to information and resources to enable staff to work efficiently and effectively. We produce microsites for NIMR sponsored initiatives such as conference websites; develop innovative solutions such as our online weekly newsletter for staff; and are always willing to provide advice and expertise. The Web Team provides not only technical infrastructure, but also training and support (including tools for easy updating). We develop cross-platform, user-friendly, visually appealing websites and applications, and ensure compliance with relevant standards and legislation. We work with and for staff throughout NIMR, and proactively engage at all levels through one-to-one meetings, focus groups, surveys, feedback forms, instant polls, and user testing and evaluation. We also have an open door policy, something we have in common with other support sections at NIMR. 128 MRC National Institute for Medical Research SCIENTIFIC FACILITIES General services Occupational Health Occupational Health (OH) is concerned with the effects of health on work and work on health with consideration for the working environment. Occupational services include health protection, health promotion and lost time management. The OH team assist the Institute in striving towards enhancing productivity and excellence through a fit, healthy and effective workforce. Our professional service observes Health and Safety regulations and helps to support the overall needs of NIMR. We offer impartial advice to all employees on health matters related to the working environment. We provide specific health surveillance to staff members exposed to hazards, thereby promoting their wellbeing at work. Safety and security The Safety section provides a safe working environment at the Institute. All staff are provided with safety training and advice. Radiation monitoring and dosimetry is undertaken as well as chemical and biological waste disposal. There are also specialised laboratories available e.g. for radioactive work, plus a cell irradiator. Human Resources The Human Resources section works in partnership across the Institute to support its objectives and a diverse group of science and support staff. A team of specialists work to embed shared principles and a culture that support great science, and provide expert advice on employment matters such as recruitment, development, performance, reward and recognition. Finance and Purchasing The Finance team provides advice and support to staff in the costing of grant applications, full economic costing, expenses and sales invoices. They are also responsible for the management, reporting and forecasting of the Institute’s budgets. The Purchasing team assists staff with all aspects of procurement including tendering for capital equipment, service contracts, and consumables. They also liaise closely with the RCUK Shared Service Centre to ensure that we get best value for money in pricing. MRC National Institute for Medical Research 129 A history of chemistry research at NIMR The International Year of Chemistry 2011 (IYC 2011) is a worldwide celebration of the achievements of chemistry and its contributions to the well-being of humankind. We outline here the role that research in chemistry has played at NIMR. Given the enormous importance of chemistry to our lives, and in particular to the development and production of medicines, it is not surprising that it has been a central topic of research at NIMR almost from the inception of the Institute nearly 100 years ago. It is notable that of five Nobel prizes awarded to scientists who have spent substantial parts of their careers at the Institute, two were for chemistry. During the 1920s and 1930s a plethora of important chemical discoveries were made at the Institute, some of which passed rapidly into clinical use while others were key wayposts of knowledge in particular areas. Henry Dale was head of the Department of Biochemistry and Pharmacology when the Institute was first established. He recruited several chemists with whom he had worked at the Wellcome Laboratories: George Barger and Arthur Ewins in 1914; Harold King and Harold Dudley in 1919. Working with them Dale isolated acetylcholine, one of a family of neurotransmitters that pass nerve impulses to other nerve or muscle cells. Dale and Dudley continued to work together on acetylcholine, histamine and the ergot alkaloids. Dudley isolated ergometrine from the ergot fungus that infects rye, and it is still used as a drug in obstetrics to control postdelivery haemorrhage. Harold Dudley Henry Dale After just a few years at the Institute, Ewins moved to become head of research at May & Baker while Barger took a chair in medicinal chemistry at the University of Edinburgh. Harold King, whose interests covered a wide field of organic chemistry, then became the Institute’s chief chemist. He identified and isolated tubocurarine, a muscle relaxant, from the curare toxin used in hunting by Amazonian Indians. As a direct consequence of this work, a series of synthetic compounds was developed by King and collaborators in the mid-1930s and these are still used as muscle relaxants in surgery, permitting lighter and hence safer levels of anaesthesia than would otherwise be required. One of these compounds, hexamethonium, was the first clinically-effective drug for treatment of high blood pressure. King retired in 1950, a few months after the Institute’s move to Mill Hill. King also contributed to major Institute findings in steroid chemistry. In the early 1920s he revealed the complex architecture of the cholesterol molecule and its relation to that of other sterols occurring naturally. Henry Dale noted that this change in the structural conception of a molecule, starting from purely theoretical considerations, had far-reaching effects on biochemistry, pharmacology, endocrinology and therapeutics. Separate steroid work, led by R.B. Bourdillon in Henry Dale’s Division, was on calciferol, also known as Vitamin D2. In the mid-1930s, with crucial input from Robert Callow who had joined NIMR in 1929, they prepared Vitamin D2 as the first pure, chemically-identified vitamin. In due course Robert Callow Harold King this work led to the effective elimination of rickets, previously a common and debilitating disease in the UK and elsewhere. This work and the related studies of the molecular structure of cholesterol by Rosenheim and King, carried out at about the same time, provide interesting insights into the dual competitive and collegiate nature of scientific research. On the one hand, NIMR chemists competed with the long-established chemical laboratories of German universities and industry, and on the other, like all the scientists mentioned above, they depended on close collaboration with their in-house biomedical colleagues. 130 MRC National Institute for Medical Research NIMR was the coordinating centre of the MRC Chemotherapy Committee, established in the years between the two World Wars. It aimed to foster drug development in the public sector by supporting work in various chemical and biological laboratories. Chemotherapy had effectively begun only in 1910 with the use of salvarsan as a treatment for syphilis and by the late 1920s there were still very few effective drugs. Furthermore, those that were available were largely the products of the German chemical industry and there was concern that another war would cut off supplies. It was also felt that Britain, then at the height of its imperial power, should be making efforts to combat the tropical diseases prevalent in many of the territories over which it held sway. Following the MRC-sponsored breakthrough in 1937 with sulphonamide drugs, the MRC Council proposed an intensive programme of research in chemotherapy. The Institute’s planned move to a larger building at Mill Hill helped provide room for this expansion, though it was delayed until 1950. The MRC Annual Report of 1948-1950 reported that “The greatly improved facilities in the new National Institute have made it possible to expand chemotherapeutic research in both the chemical and the equally important biological aspects.” Much work at NIMR was directed at anti-parasitic therapies, particularly malaria and sleeping sickness, but effective drugs proved hard to find. One of the more enduring legacies is the drug pentamidine, which was produced very soon after similar compounds were developed at the Institute by Harold King in a search for drugs active against trypanosomes, the parasites responsible for African Sleeping Sickness. Pentamidine was initially used to treat Sleeping Sickness but more recently has been reintroduced as a therapy for Pneumocystis carinii pneumonia (PCP - now known as Pneumocystis jirovecii) that frequently affects AIDS patients. King also discovered a series of diamidine compounds, which led to development of a drug useful in treating leishmaniasis. James Walker Archer Martin James Walker joined NIMR in 1939, later succeeding Harold King as head of Organic Chemistry during his career of 30 years at the Institute. His synthesis of the anti-malarial drug pyrimethamine, led to a method that was later adopted for commercial use. During the post-World War II period very important developments were made by A.J.P. Martin and R.L.M. Synge in separation techniques known as chromatography that allowed the analysis and purification of complex mixtures of chemical substances. Martin moved to NIMR in 1948 and further developed these techniques, notably by the invention of gas-liquid chromatography (GLC) which is still an important analytical tool. Various modern methods based on this pioneering work are in everyday use in applications such as synthetic chemistry, forensic science, industrial quality control, environmental monitoring and the detection of illicit drugs in sport. Under Martin’s guidance, I.E. Bush made related advances in another separation technique, paper chromatography. This played an important role in work from the 1950s, particularly in the isolation and characterisation of the saltregulating steroid aldosterone. The invention of the electron capture detector by J.E. Lovelock in 1957 greatly increased the sensitivity of GLC and ultimately had significant influence on the developing environmental movement in the 1960s through its ability to detect low levels of pesticide residues and chlorofluorohydrocarbons. Lovelock left NIMR in 1961 and is now more widely known for his Gaia theory of the Earth as a self-regulating system, but the ramifications of his invention of the electron capture detector remain with us today. MRC National Institute for Medical Research 131 A history of chemistry research at NIMR (contd.) Sir John Cornforth In the late 1940s Sir John Cornforth joined NIMR. He worked with Callow to show that hecogenin could be obtained from the waste-product of sisal manufacture in East Africa, so providing a starting material for the commercial manufacture of cortisone. Working with George Popjak, Cornforth began an extensive and elegant series of studies that used radioisotopes to determine how cholesterol is made in the body. This work, for which he was ultimately awarded a Nobel Prize in 1975, is directly relevant to the modern statin drugs. These reduce cholesterol levels and thereby diminish fatty deposits that otherwise restrict blood flow. Statins act on an enzyme involved in cholesterol synthesis, one of the many enzymes studied in Cornforth’s steroid work. In another area of his work past and present research at NIMR are neatly linked, since Cornforth also published a method for the synthesis of N-acetylneuraminic acid. This compound is a component of the sugars that are attached to the outer membranes of animal cells and to which the influenza virus binds as the first step in its invasion of cells that ultimately results in an attack of flu. The structural details of this binding have been a major topic of recent and current research on influenza at NIMR. Chemistry at NIMR from the 1960s was largely carried on by Roy Gigg, who was initially a student of Cornforth’s. He spent his whole career at NIMR, retiring in 1995, and did excellent work in carbohydrate synthesis, not least in glycolipids of the tuberculosis bacterium. Toward the end of his research, he developed elegant syntheses of inositol phosphates. These molecules are used by cells as internal “messengers” to control various functions in response to outside stimuli. At the time, the actions of these compounds had only just been discovered and his work greatly assisted studies of their biological function. Derek Smyth joined NIMR in 1962 and later was appointed Head of the Laboratory of Peptide Chemistry (1972 - 1992). In collaboration with Sayaki Utsumi Roy Gigg he unravelled the structure of the “hinge region” of rabbit antibody, Derek Smyth locating the bridge that links the two half molecules and revealing a new oligosaccharide chain. With Gordon Bisset he prepared a novel form of oxytocin, the N,O - dicarbamyl derivative, which proved to be a specific inhibitor of the hormone without intrinsic activity. He followed this by sequencing the C-peptide of proinsulin, modelling its contribution to the 3D structure. The enzymatic processing of prohormones to generate their active constituents was a dominant research interest. In a classic series of papers from 1975-1982 he and his collaborators showed that the C-terminal fragment of b-lipotropin, first isolated in his laboratory from pituitary, was an endogenously expressed opiate. They showed that this 31 amino acid peptide, now known as b-endorphin, is a neurohormone with potent analgesic activity and produces profound behavioural effects on the brain. Later he elucidated the mechanism of the C-terminal amidation process which is essential for activation of numerous peptide hormones. In the mid 1970s, Nigel Birdsall synthesised two “workhorse” radioligands [3H]N-methyl scopolamine and [3H]oxotremorine M, both used globally in hundreds of studies of muscarinic receptors to the present day. In 1983, David Trentham came to the Institute as head of the Division of Physical Biochemistry, bringing with him the recently developed chemistry of caged compounds. These are biological compounds made inactive by attachment of a chemical group that prevents them from displaying their normal biological activity. The attached group is designed so that, when exposed to light of the right wavelength and intensity, it splits off from the molecule in a process called photolysis, generating the active biomolecule. The term “caged compounds” is used, since the biomolecules are locked-up until released by the flash of light. 132 MRC National Institute for Medical Research The technique is used to study biological processes such as muscle contraction and cell signalling that take place in a few thousandths of a second or less. John Corrie joined the Trentham group in 1988 with interests in further development of caged compounds and of fluorescence probes. Discussions with biological colleagues, especially David Ogden and Martin Webb, revealed requirements for particular new chemical tools. One focus was the rapid release of neurotransmitter molecules that carry signals between nerve cells. By being able to release known concentrations of neurotransmitter independently of any electrical impulse, the transmission process can be analysed and manipulated John Corrie David Trentham more readily. A range of caged compounds were prepared to optimise the efficiency and speed of neurotransmitter release in a water-based environment, as required for studying live tissue. A new photochemical reaction was discovered and led to compounds that have proved optimal for neurophysiological studies. Some of these caged compounds have been licensed for commercial production and are very widely used tools for neurophysiology. John Corrie was also involved in developments using fluorescence to open up a new method for tracking the metabolism of the biological molecule adenosine 5’-triphosphate (ATP). Previous methods to do this were tedious and did not permit measurements to be made in real time. To improve existing methods, a protein produced by the common bacterium Escherichia coli was utilised. Each molecule of this protein binds one phosphate ion in a tight complex, and upon binding undergoes a large change in shape, in a manner conceptually similar to the Venus Flytrap. When the protein was tagged with a fluorescent label, designed for this purpose, the change of shape greatly increased the fluorescence intensity. This system has become widely used to monitor many biological processes and the labelled protein is now being produced commercially to make it available to other researchers. Following John Corrie’s retirement in 2006, John Offer joined the Institute to continue the tradition of chemistry. The focus of his laboratory is to use emerging ligation techniques to build biological macromolecules. Chemical ligation is a powerful enabling technology for a broad range of applications. It involves the coupling of two or more biomolecules in aqueous buffers at low concentration to give the product in its final form with no further modification. It can be considered as the next generation of bioconjugation reactions, as ligation is much more defined and selective than previous methods. John Offer’s research is focused on extending the applicability of this reaction to give greater flexibility to the synthesis of protein targets, to explore its biological relevance and to develop applications that allow modification of proteins in their native setting with minimal genetic manipulation as part of the expanding contemporary effort to apply organic chemistry to the cell. The rich history of chemical work at NIMR demonstrates how important chemistry is in medical research and this can only increase as our understanding of the mechanisms of biological activities grows. It is obvious that the continuing need for such teams will create opportunities for interesting chemistry far into the future. The importance and central position of chemistry in so many aspects of future science and industry demands the inspiration of education professionals and the chemistry community, and the interest and support of our politicians. Based on an essay written by John Corrie with contributions from several others. MRC National Institute for Medical Research 133 In memoriam Don Williamson (1930-2010) Don Williamson died on Tuesday 2nd November 2010, aged eighty. He was a programme leader at NIMR for 28 years. Don Williamson graduated from Edinburgh University in 1956 with a Ph.D. in bacteriology, and then worked in Alan Eddy’s group at the Brewing Industry Research Foundation from 1956-1962. He acquired a taste for working on yeast and developed methods for isolating protoplasts and for synchronizing cell division. After a spell at the John Innes Institute, from 1962-1965, his interest in DNA replication in the yeast cell cycle led to a sabbatical as a Research Associate Professor in Herschel Roman’s Department of Genetics in Seattle. He used that time to work on the molecular biology of Saccharomyces cerevisiae and initiated studies that eventually established patterns of yeast mitochondrial DNA replication. In 1967 he moved to NIMR’s Microbiology Division to continue his work on yeast. Although trained as a bacteriologist he saw himself primarily as a cell biologist and his recruitment was seen as a good way to build links between the Microbiology Division and other areas at NIMR. He was a gifted collaborator, forging links both within and beyond the Institute. Don was seen as a great asset to the Institute; Howard Rogers, Head of the Microbiology Division, wrote in support of a promotion for Don: “He is a leading authority on the behaviour of DNA during the cell cycle and has helped to demonstrate the great power of microorganisms as models to unravel cell cycle events. For some years Don has been concerned with the overall problem of regulation of mitochondrial DNA synthesis and the relationship between the physical nature of the mitochondrial genome and the genetic behaviour of the mitochondrial system. His major contributions were the demonstration of extensive recombination of mitochondrial DNA in growing cells and his studies on the packaging of mitochondrial DNA”. When Howard Rogers retired in 1983 Don took over as acting Head of Division for two years. The Division was disbanded in 1985 and Don became Head of the newlyformed Laboratory of Cell Propagation. Don in 1969 In the mid-1980s Don switched interests to the molecular biology of malaria parasites and, working with Iain (R.J.M.) Wilson in the Division of Parasitology, he was instrumental in analysing replication mechanisms of organelles and transfected plasmids in Plasmodium. This collaboration proved very fruitful and in 1991 Don transferred to the Division of Parasitology. He retired in 1995 though he continued as a visiting worker for several more years. Jim Smith, NIMR Director, said: “I’m so sad to hear about Don’s death. I met him in 1984, when I came to work at NIMR for the first time. He was always a terrific colleague: approachable, kind, clever, considerate and collegial. Everyone liked him.” 134 MRC National Institute for Medical Research Scientific seminars Nearly 200 seminars and lectures by visiting speakers are given at the Institute each year. Each major area of science has its own seminar series and the Mill Hill Lecture series is an annual series of about ten lectures given by eminent scientists from around the world. A selection of highlights from the past year is shown. David Barford Frédéric Barras Dennis Bray Sally Camper Anne Cooke Carole Goble Anne Cooke Christian Dahmann Hendrik Dietz Catherine Dulac Suzanne Eaton James E. Ferrell, Jr Antonio Freitas Robin Irvine Steve Jackson Tom Jessell Chaya Kalcheim Dominic Kwiatkowski Bart Lambrecht Warren Leonard Werner Muller Paul Nurse Luke O’Neil Benedita Rocha Alexander Rudensky Evan Sadler Philippe Sansonetti Jim Sellers Michael B.Yaffe Department of Pathology, University of Cambridge Trinity College, Dublin NIH/National Heart Lung and Blood Institute Pasteur Institute, Paris University of Manchester Department of Pathology, University of Cambridge IRB Institute for Research in Biomedicine, Bellinzona, Switzerland Necker Institute, Paris Pasteur Institute, Paris University of Ghent Wellcome Trust Sanger Institute Memorial Sloan-Kettering Cancer Center University of Cambridge Columbia University Medical Center Harvard University Washington University, St Louis Massachusetts Institute of Technology Gurdon Institute, Cambridge University of Cambridge Department of Medical Neurobiology, Hebrew University of Jerusalem Department of Chemical & Systems Biology, Stanford School of Medicine Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Department of Human Genetics, University of Michigan Medical School Rockefeller University, New York NIH/National Heart Lung and Blood Institute Institut Fédératif de Recherche, Biologie Structurale et Microbiologie, Centre National de la Recherche Scientifique, Marseille Institute of Cancer Research, London Center for Nanotechnology and Nanomaterials, Technische Universität München, Germany MRC National Institute for Medical Research 135 ] Staff honours Prizes and awards Alex Gould Robin Lovell-Badge 2011 Hooke Medal (awarded 2010) Waddington Medal 2010 Editorial boards Siew-Lan Ang Mike Blackman James Briscoe John Doorbar Paul Driscoll Francois Guillemot Tony Holder Jean Langhorne Paul Le Tissier Malcolm Logan Troy Margrie Anne O’Garra Annalisa Pastore Katrin Rittinger Jonathan Stoye James Turner Jean-Paul Vincent Robert Wilkinson David Wilkinson Douglas Young 136 International Journal of Developmental Biology PLoS Pathogens (associate editor) Development Developmental Biology Developmental Dynamics Neural Development Journal of General Virology Journal of Functional and Structural Genomics BMC Developmental Biology Neural Development Molecular and Biochemical Parasitology Eukaryotic Cell International Journal of Parasitology (specialist editor) PLoS Pathogens (associate editor) Cell Biochemistry & Function Journal of Neuroendocrinology Developmental Dynamics Developmental Biology Development Frontiers in Neural Circuits Journal of Experimental Medicine Prion The Open Biochemistry Journal The Open Spectroscopy Journal Journal of Biological Chemistry (scientific editor) PLoS One (scientific editor) Biochemical Journal Journal of Virology Chromosome Research Biology of Reproduction Science Signalling Tuberculosis (section editor) PLoS One, and the International Journal of Tuberculosis and Lung Disease (associate editor) Developmental Biology Faculty of 1000 BMC Developmental Biology Mechanisms of Development (editor in chief) Gene Expression Patterns (editor in chief) Tuberculosis (consulting editor) MRC National Institute for Medical Research Scientific committees Mike Blackman James Briscoe John Doorbar Alex Gould François Guillemot Ed Hulme Jean Langhorne Troy Margrie Tim Mohun Justin Molloy Anne O’Garra Steve Smerdon Jim Smith Gitta Stockinger David Wilkinson Douglas Young Wellcome Trust Immunity and Infectious Diseases Funding Committee Director, Company of Biologists British Society for Developmental Biology (Meetings Secretary) Society for General Microbiology Translational Virology Group Wellcome Trust Molecules Genes and Cells Funding Committee Patient Advisory Committee, Respiratory BRU Clinical Research Facility, Royal Brompton Hospital European Research Council Advanced Investigator Grants Neurosciences and Neural Disorders panel; Wellcome Trust Neuroscience and Mental Health Funding Committee Scientific Advisory Board of Heptares Therapeutics Wellcome Trust Expert Review Panel on the Immune system in Health and Disease Scientific Advisory Board of the Research Centre for Infectious Diseases, University of Wuerzburg Grant Committee Membership: HFSP, European Union MRC Molecular and Cellular Medicine Board BBSRC Tools and Resources Development Fund (Chair); EPSRC Peer Review College; Wellcome Trust Expert Review College Scientific Advisory Boards: Institute for Biomedical Sciences, Bellinzona, Switzerland Baylor Institute for Immunology, Dallas, USA Institute for Molecular Medicine, Lisbon World Premier International Research Center (WPI) Initiative Osaka University, Japan Keystone Symposia Scientific Advisory Board Research funding boards: MRC Developmental Pathway Funding Scheme Grant Research Board MRC/ABPI, Inflammation and Immunology Initiative - Steering Group Grant Committees: MRC Molecular & Cellular Medicine Board NIH Structural Genomics Study Group BBSRC IGF & Genomics Evaluation Panel Diamond Peer Review Panel. Advisory Boards: Structural Genomics Consortium MRC-Technology Governing Board ASM Scientific/TwistDX Inc. Wellcome Trust Investigator Awards Selection Panel Scientific Advisory Council Indian Institute of Science Education and Research Scientific Advisory Board - TwistDx (ASM Scientific) Scientific Advisory Board - Institute for Toxicology and Genetics, Karlsruhe ERC Young Investigator panel Multiple Sclerosis Society panel Academy of Finland grant panel, Atip/Avenir panel EMBO Long Term Fellowships committee, Welbio Advisory committees: GXD Advisory Board EMAGE Advisory Board Board of Directors, Aeras Global TB Vaccine Foundation Chair of International Scientific Advisory Board, Malawi-Liverpool-Wellcome Trust Clinical Research Programme Member of Governance Committee, European Tuberculosis Vaccine Initiative (TBVI) MRC National Institute for Medical Research 137 PhD theses awarded in 2010 138 Name Division Title of thesis Veronica Fridh Molecular Structure Biochemical and biophysical characterisation of a novel CARD-CARD Interaction in NOD2 Peter Gardner Parasitology Investigating the B Cell response to malaria: cloning a malariaspecific B Cell receptor and analysis of the antibody reponse Eve Hornsby Molecular Immunology The role of IL-17 in the development of autoimmunity James Turton Molecular Neuroendocrinology In vitro studies of dominant negative PIT1 mutant proteins Izbel Yusuf Molecular Neuroendocrinology Identifications of a new target tissue for growth hormone: the placenta Matthew Child Parasitology Trafficking and function of a malarial sheddase Cyprian Daniel Cukier Molecular Structure Transcription-responsive regulation of c-myc proto-oncogene - structural and biophysical studies Rachel Farrow Physical Biochemistry Single molecule characterisation of unconventional myosins Laura Galinanes-Garcia Molecular Neurobiology Molecular mechanisms underlying Mash1 function in oligodendrogenesis Katie Foster Molecular Immunology The role of neural crest cells in the development, organisation and migration of the thymus Nicolaos Balaskas Developmental Neurobiology The gene regulatory logic of Sonic hedgehog morphogen interpretation in the ventral neural tube Jameela Khan Virology Proteolytic cleavage of human papillomavirus type 16 E1^E4 Catia Laranjeira Molecular Neurobiology In vivo identification of neural stem cells in the enteric nervous systems Emmanouil Metzakopian Developmental Neurobiology Genome wide identification of transcriptional targets of Foxa2 in midbrain dopaminergic cells by ChIP-Seq Peter Saiu Molecular Structure Structural and functional studies on nucleotide binding to AMP-activated protein kinase Natalie Silmon de Monerri Parasitology Investigation into the role of PfSUB1 and two perforin-like proteins in Plasmodium falciparum Charles Sinclair Immune Cell Biology The role of Zap70 in thymocyte development Jessica Borger Molecular Immunology Visualising early signalling events in T cell activation MRC National Institute for Medical Research Current funding sources The Medical Research Council (MRC) is the principal source of research funding. A total budget of £42m p.a. is set every five years following an Institute-wide review of resources. This review takes place after the quinquennial peer review (conducted by MRC Research Boards) of the programmes of the individual Divisions. The Institute also attracts funding support from a wide range of different agencies, including medical research charities, international sources, particularly the EU, and from industrial and commercial companies: • Association for International Cancer Research (AICR) • Biotechnology and Biological Sciences Research Council (BBSRC) • European Molecular Biology Organization (EMBO) • European Research Council (ERC) • GlaxoSmithKline UK • Health Protection Agency (HPA) • Imperial College • International Federation of Pharmaceutical Manufacturers & Associations (IFPMA) • Lady Tata Memorial Trust • Leukaemia & Lymphoma Research • Leverhulme Trust • Medical Research Council • Medical Research Council Technology • National Institutes of Health (US) • Parkinson’s Disease Society • The Royal Society • University College London (UCL) • Wellcome Trust MRC National Institute for Medical Research 139 Bibliography 1. Abu-Daya A, Nishimoto S, Fairclough L, Mohun TJ, Logan MPO and Zimmerman LB (2010) The secreted integrin ligand nephronectin is necessary for forelimb formation in Xenopus tropicalis. Developmental Biology 349:204-212 2. Adrover M, Esposito V, Martorell G, Pastore A and Temussi PA (2010) Understanding cold denaturation: the case study of Yfh1. Journal of the American Chemical Society 135:16240–16246 3. Adrover M, Pauwels K, Pringent S, de Chiara C, Xu Z, Chapuis C, Pastore A and Rezaei H (2010) Prion fibrillization is mediated by a native structural element which comprises the helices H2 and H3. Journal of Biological Chemistry 285:21004-21012 4. Akbulut S, Reddi AL, Aggarwal P, Ambardekar C, Canciani B, Kim MKH, Hix L, Vilimas T, Mason J, Basson MA, Lovatt M, Powell J, Collins S, Quatela S, Phillips M and Licht JD (2010) Sprouty proteins inhibit receptor-mediated activation of phosphatidylinositol-specific phospholipase C. Molecular Biology of the Cell 21:3487-3496 5. Albesa-Jové D, Bertrand T, Carpenter EP, Swain GV, Lim J, Zhang J, Haire LF, Vasisht N, Braun V, Lange A, Von Eichel-Strelber C, Svergun DI, Fairweather NF and Brown KA (2010) Four distinct structural domains in Clostridium difficile toxin B visualized using SAXS. Journal of Molecular Biology 396:1260-1270 6. Alford K, Slender A, Vanes L, Li Z, Fisher EMC, Nizetic D, Orkin SH, Roberts I and Tybulewicz VLJ (2010) Perturbed hematopoiesis in the Tc1 mouse model of Down Syndrome. Blood 115:2928-37 7. Anderson KE, Chessa TAM, Davidson K, Henderson RB, Walker S, Tolmachova T, Grys K, Rausch O, Seabra M, Tybulewicz VLJ, Stephens LR and Hawkins PT (2010) PtdIns3P and Rac direct the assembly of the NADPH oxidase on a novel, pre-phagosomal compartment during FcR-mediated phagocytosis in primary mouse neutrophils. Blood 116:4978-4989 8. Antunes I and Kassiotis G (2010) Suppression of innate immune pathology by regulatory T cells during Influenza A virus infection of immunodeficient mice. Journal of Virology 84:12564-12575 9. Arkov AL and Ramos A (2010) Building RNA-protein granules: insight from the germline. Trends in Cell Biology 20:482-490 10. Asselman V, Thienemann F, Pepper DJ, Boulle A, Wilkinson RJ, Meintjes G and Marais S (2010) Central nervous system disorders after starting antiretroviral therapy in South Africa. AIDS 24:2871-2876 11. Autore F, Pagano B, Fornili A, Rittinger K and Fraternali F (2010) In silico phosphorylation of the autoinhibited form of p47phox: insights into the mechanism of activation. Biophysical Journal 99:3716-25 140 MRC National Institute for Medical Research 12. Barr IG, McCauley J, Cox N, Daniels R, Engelhardt OG, Fukuda K, Grohmann G, Hay A, Kelso A, Klimov A, Odagiri T, Smith D, Russell C, Tashiro M, Webby R, Wood J, Ye Z and Zhang W (2010) Epidemiological, antigenic and genetic characteristics of seasonal influenza A(H1N1), A(H3N2) and B influenza viruses: basis for the WHO recommendation on the composition of influenza vaccines for use in the 2009-2010 Northern Hemisphere season. Vaccine 28:1156-67 13. Barry CE, 3rd, Boshoff HI, Dartois V, Dick T, Ehrt S, Flynn J, Schnappinger D, Wilkinson RJ and Young D (2010) Spectrum of latent tuberculosis - existing tests cannot resolve the underlying phenotypes: authors’ reply. Nature Reviews Microbiology 8:242 14. Becherel OJ, Jakob B, Cherry AL, Gueven N, Fusser M, Kijas AW, Peng C, Katyal S, McKinnon PJ, Chen J, Epe B, Smerdon SJ, Taucher-Scholz G and Lavin MF (2010) CK2 phosphorylation-dependent interaction between aprataxin and MDC1 in the DNA damage response. Nucleic Acids Research 38:1489-1503 15. Bee C, Moshnikova A, Mellor CD, Molloy J, Koryakina Y, Stieglitz B, Khokhlatchev A and Herrmann C (2010) Growth and tumor suppressor novel ras effector 1A (NORE1A) is a regulatory node between ras signaling and microtubule nucleation. Journal of Biological Chemistry 285:16258-16266 16. Belyaev NN, Brown DE, Diaz AIG, Rae A, Jarra W, Thompson J, Langhorne J and Potocnik AJ (2010) Induction of an IL7-R+c-Kithi myelolymphoid progenitor critically dependent on IFN-γ signaling during acute malaria. Nature Immunology 11:477-85 17. Benson N, Snelder N, Ploeger B, Napier C, Sale H, Birdsall NJM, Butt RP and van der Graaf PH (2010) Estimation of binding rate constants using a simultaneous mixed-effects method: application to monoamine transporter reuptake inhibitor reboxetine. British Journal of Pharmacology 160:389-98 18. Berry MPR, Graham CM, McNab FW, Xu Z, Bloch SAA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, Quinn C, Blankenship D, Dhawan R, Cush JJ, Mejias A, Ramilo O, Kon OM, Pascual V, Banchereau J, Chaussabel D and O’Garra A (2010) An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466:973-977 19. Bhaijee F, Wainwright H, Meintjes G, Wilkinson RJ, Todd G, de Vries E and Pepper DJ (2010) Warfarin-induced skin necrosis in HIV-1-infected patients with tuberculosis and venous thrombosis. South African Medical Journal 100:372-7 20. Birdsall NJM (2010) Class A GPCR heterodimers: evidence from binding studies. Trends in Pharmacological Sciences 31:499-508 21. Breckenridge R (2010) Heart failure and mouse models. Disease Models & Mechanisms 3:138-143 Bibliography (cont.) 22. Breckenridge RA, Kelly P, Nandi M, Vallance PJ, Mohun TJ and Leiper J (2010) A role for Dimethylarginine Dimethylaminohydrolase 1 (DDAH1) in mammalian development. International Journal of Developmental Biology 54:215-220 34. Chun RF, Lauridsen AL, Suon L, Zella LA, Pike JW, Modlin RL, Martineau AR, Wilkinson RJ, Adams J and Hewison M (2010) Vitamin D-binding protein directs monocyte responses to 25-hydroxyand 1,25-dihydroxyvitamin D. Journal of Clinical Endocrinology and Metabolism 95:3368-3376 23. Briscoe J, Lawrence PA and Vincent JP (editors) Generation and Interpretation of Morphogen Gradients. New York, Cold Spring Harbor Laboratory Press, 2010 35. Cloutier JM and Turner JMA (2010) Meiotic sex chromosome inactivation. Current Biology 20:R962-3 24. Burton OT, Zaccone P, Phillips JM, De La Peña H, Fehérvári Z, Azuma M, Gibbs S, Stockinger B and Cooke A (2010) Roles for TGF-β and programmed cell death 1 ligand 1 in regulatory T cell expansion and diabetes suppression by zymosan in nonobese diabetic mice. Journal of Immunology 185:2754 -2762 36. Cocquet J, Ellis PJI, Yamauchi Y, Riel JM, Karacs TPS, Rattigan Á, Ojarikre OA, Affara NA, Ward MA and Burgoyne PS (2010) Deficiency in the multicopy Sycp3-like X-linked genes Slx and Slxl1 causes major defects in spermatid differentiation. Molecular Biology of the Cell 21:3497-3505 25. Butt T, Mufti T, Humayun A, Rosenthal PB, Khan S, Khan S and Molloy JE (2010) Myosin motors drive long-range alignment of actin filaments. Journal of Biological Chemistry 285:4964-4974 26. Calder LJ, Wasilewski S, Berriman JA and Rosenthal PB (2010) Structural organization of a filamentous influenza A virus. Proceedings of the National Academy of Sciences of the United States of America 107:10685-10690 27. Callery EM, Thomsen GH and Smith JC (2010) A divergent Tbx6-related gene and Tbx6 are both required for neural crest and intermediate mesoderm development in Xenopus. Developmental Biology 340:75-87 28. Castrique E, Fernandez-Fuente M, Le Tissier P, Herman A and Levy A (2010) Use of a prolactin-Cre/ROSA-YFP transgenic mouse provides no evidence for lactotroph transdifferentiation after weaning, or increase in lactotroph/somatotroph proportion in lactation. Journal of Endocrinology 205:49-60 37. Coles M, Kioussis D and Veiga-Fernandes H (2010) Cellular and molecular requirements in lymph node and Peyer’s patch development. Progress in Molecular Biology and Translational Science 92:177-205 38. Coles M, Kioussis D and Veiga-Fernandes H (2010) Commentary on “lymphoid tissue inducer cells and the evolution of CD4 dependent high-affinity antibody responses”. Progress in Molecular Biology and Translational Science 92:175-6 39. Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, Kremer K, Ernst JD and Gagneux S (2010) Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nature Genetics 42:498-503 40. Connell TG, Davies MA, Johannisen C, Wood K, Pienaar S, Wilkinson KA, Wilkinson RJ, Zar HJ, Beatty D, Nicol MP, Curtis N and Eley B (2010) Reversion and conversion of Mycobacterium tuberculosis IFN-γ ELISpot results during anti-tuberculous treatment in HIV-infected children. BMC Infectious Diseases 10:138 29. Caulfield T, Scott C, Hyun I, Lovell-Badge R, Kato K and Zarzeczny A (2010) Stem cell research policy and iPS cells. Nature Methods 7:28-33 41. Cook WJ, Smith CD, Senkovich O, Holder AA and Chattopadhyay D (2010) Structure of Plasmodium falciparum ADP-ribosylation factor 1. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications 66:1426-31 Chatterjee A, D’Souza D, Vira T, Bamne A, Ambe GT, Nicol MP, Wilkinson RJ and Mistry N (2010) 30. Strains of Mycobacterium tuberculosis from Western Maharashtra, India exhibit a high degree of diversity and strain-specific associations with drug resistance, cavitary disease and treatment failure. Journal of Clinical Microbiology 48:3593-3599 42. Coppola E, Rallu M, Richard J, Dufour S, Riethmacher D, Guillemot F, Goridis C and Brunet J-F (2010) Epibranchial ganglia orchestrate the development of the cranial neurogenic crest. Proceedings of the National Academy of Sciences of the United States of America 107:2066-71 Chen Z, Zheng YH, Lin Y, Collins PJ and Hay AJ (2010) [Impact of avian influenza virus H5N1 neuraminidase mutations on 31. the activity of neuraminidase and the sensibility to neuraminidase inhibitors.]. Zhonghua yi xue za zhi 90:1924-1928 43. Coscollá M, Comas I and González-Candelas F (2010) Quantifying non-vertical inheritance in the evolution of Legionella pneumophila. Molecular Biology and Evolution 28:985-1001 Chibalina MV, Poliakov A, Kendrick-Jones J and Buss F (2010) Myosin VI and optineurin are required for polarized EGFR delivery and 32. directed migration. Traffic 11:1290-1303 Child MA, Epp C, Bujard H and Blackman MJ (2010) Regulated maturation of malaria merozoite surface protein-1 is essential for parasite growth. Molecular Microbiology 78:187–202 44. Coscolla M and Gagneux S (2010) Does M. tuberculosis genomic diversity explain disease diversity? Drug Discovery Today: Disease Mechanisms 7:e43-e59 45. Cox B, Briscoe J and Ulloa F (2010) SUMOylation by Pias1 regulates the activity of the Hedgehog dependent Gli transcription factors. PLoS ONE 5:e11996 MRC National Institute for Medical Research 141 Bibliography (cont.) 46. Crack JC, Smith LJ, Stapleton MR, Peck J, Watmough NJ, Buttner MJ, Buxton RS, Green J, Oganesyan VS, Thomson AJ and Le Brun NE (2010) Mechanistic insight into the nitrosylation of the [4Fe-4S] cluster of WhiB-like proteins. Journal of the American Chemical Society 133:1112–1121 57. Dessaud E, Ribes V, Balaskas N, Yang LL, Pierani A, Kicheva A, Novitch BG, Briscoe J and Sasai N (2010) Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen Sonic hedgehog. PLoS Biology 8:e1000382 47. Cruz C, Ribes V, Kutejova E, Cayuso J, Lawson V, Norris D, Stevens J, Davey M, Blight K, Bangs F, Mynett A, Hirst E, Chung R, Balaskas N, Brody SL, Marti E and Briscoe J (2010) Foxj1 regulates floor plate cilia architecture and modifies the response of cells to sonic hedgehog signalling. Development 137:4271-4282 58. Di Bella D, Lazzaro F, Brusco A, Plumari M, Battaglia G, Pastore A, Finardi A, Cagnoli C, Tempia F, Frontali M, Veneziano L, Sacco T, Boda E, Brussino A, Bonn F, Castellotti B, Baratta S, Mariotti C, Gellera C, Fracasso V, Magri S, Langer T, Plevani P, Di Donato S, Muzi-Falconi M and Taroni F (2010) Mutations in the mitochondrial protease gene AFG3L2 cause dominant hereditary ataxia SCA28. Nature Genetics 42:313-21 48. Cukier CD, Hollingworth D, Martin SR, Kelly G, Díaz-Moreno I and Ramos A (2010) Molecular basis of FIR-mediated c-myc transcriptional control. Nature Structural & Molecular Biology 17:1058-64 49. Cukier CD and Ramos A (2010) Creating a Twin STAR. Structure 18:279-80 50. Cunningham D, Lawton J, Jarra W, Preiser P and Langhorne J (2010) The pir multigene family of Plasmodium: Antigenic variation and beyond. Molecular and Biochemical Parasitology 170:65-73 51. Curado S, Ober EA, Walsh S, Cortes-Hernandez P, Verkade H, Koehler CM and Stainier DYR (2010) The mitochondrial import gene tomm22 is specifically required for hepatocyte survival and provides a liver regeneration model. Disease Models & Mechanisms 3:486-495 52 D’Amico G, Robinson SD, Germain M, Reynolds LE, Thomas GJ, Elia G, Saunders G, Fruttiger M, Tybulewicz V, Mavria G and Hodivala-Dilke KM (2010) Endothelial-Rac1 is not required for tumor angiogenesis unless αvβ3integrin is absent. PLoS ONE 5:e9766 53. Dawson LF, Dillury J and Davis EO (2010) RecA-independent DNA damage induction of Mycobacterium tuberculosis ruvC despite an appropriately located SOS box. Journal of Bacteriology 192:599-603 54. de Jong BC, Antonio M and Gagneux S (2010) Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa. PLoS Neglected Tropical Diseases 4:e744 55. De Nicola GF, Martin S, Bullard B and Pastore A (2010) Solution structure of the apo C-terminal domain of the Lethocerus F1 troponin C isoform. Biochemistry 49:1719-26 56. De Vita S, Canzonetta C, Mulligan C, Delom F, Groet J, Baldo C, Vanes L, Dagna-Bricarelli F, Hoischen A, Veltman J, Fisher EMC, Tybulewicz VLJ and Nizetic D (2010) Trisomic dose of several chromosome 21 genes perturbs haematopoietic stem and progenitor cell differentiation in Down’s syndrome. Oncogene 29:6102–6114 142 MRC National Institute for Medical Research 59. Díaz-Moreno I, Hollingworth D, Kelly G, Martin S, García-Mayoral M, Briata P, Gherzi R and Ramos A (2010) Orientation of the central domains of KSRP and its implications for the interaction with the RNA targets. Nucleic Acids Research 38:5193-5205 60. Ding J, Doorbar J, Li B, Zhou F, Gu W, Zhao L, Saunders NA, Frazer IH and Zhao KN (2010) Expression of papillomavirus L1 proteins regulated by authentic gene codon usage is favoured in G2/M-like cells in differentiating keratinocytes. Virology 399:46-58 61. dos Reis M, Tamuri AU, Hay AJ and Goldstein RA (2010) Charting the host adaptation of influenza viruses. Molecular Biology and Evolution Epub ahead of print 62. Dunlevy L, Bennett M, Slender A, Lana-Elola E, Tybulewicz VL, Fisher EMC and Mohun T (2010) Down’s syndrome-like cardiac developmental defects in embryos of the transchromosomic Tc1 mouse. Cardiovascular Research 88:287-295 63. Dutta S and Rittinger K (2010) Regulation of NOXO1 activity through reversible interactions with p22phox and NOXA1. PLoS ONE 5:e10478 64. Dvorin JD, Martyn DC, Patel SD, Grimley JS, Collins CR, Hopp CS, Bright AT, Westenberger S, Winzeler E, Blackman MJ, Baker DA, Wandless TJ and Duraisingh MT (2010) A plant-like kinase in Plasmodium falciparum regulates parasite egress from erythrocytes. Science 328:910-912 65. Eleftheratos S, Spearpoint P, Ortore G, Kolocouris A, Martinelli A, Martin S and Hay A (2010) Interaction of aminoadamantane derivatives with the influenza A virus M2 channel-Docking using a pore blocking model. Bioorganic & Medicinal Chemistry Letters 20:4182-4187 66. Eslava I, Payares G, Pernia BM, Holder AA and Spencer LM (2010) Suppressive and additive effects in protection mediated by combinations of monoclonal antibodies specific for merozoite surface protein 1 of Plasmodium yoelii. Malaria Journal 9: 67. Esposito D, Sankar A, Morgner N, Robinson CV, Rittinger K and Driscoll PC (2010) Solution NMR investigation of the CD95/FADD homotypic death domain complex suggests lack of engagement of the CD95 C terminus. Structure 18:1378-90 Bibliography (cont.) 68. Esposito V, Guglielmi F, Martin SR, Pauwels K, Pastore A, Piccoli R and Temussi PA (2010) Aggregation mechanisms of cystatins: a comparative study of monellin and orzacystatin. Biochemistry 49:2805-2810 69. Esposito V, Musi V, Veggi D, Pastore A and Pizza M (2010) 1H, 13C and 15N assignment of the C-terminal domain of GNA2132 from Neisseria meningitidis. Biomolecular NMR Assignments 4:107-9 70. Evans P, Kayyali R, Hider RC, Eccleston J and Porter JB (2010) Mechanisms for the shuttling of plasma non-transferrin-bound iron (NTBI) onto deferoxamine by deferiprone. Translational Research 156:55-67 71. Fairlie-Clarke KJ, Lamb TJ, Langhorne J, Graham AL and Allen JE (2010) Antibody isotype analysis of malaria-nematode co-infection: problems and solutions associated with cross-reactivity. BMC immunology 11: 72. Faroudi M, Hons M, Zachacz A, Dumont C, Lyck R, Stein JV and Tybulewicz VLJ (2010) Critical roles for Rac GTPases in T cell migration to and within lymph nodes. Blood 116:5536-5547 73. Fassone E, Duncan AJ, Taanman J-W, Pagnamenta AT, Sadowski MI, Holand T, Qasim W, Rutland P, Calvo SE, Mootha VK, Bitner-Glindzicz M and Rahman S (2010) FOXRED1, encoding a FAD-dependent oxidoreductase complex-I specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy. Human Molecular Genetics 19:4837-4847 74. Feng Y and Xu Q (2010) Pivotal role of hmx2 and hmx3 in zebrafish inner ear and lateral line development. Developmental Biology 339:507-518 75. Fernandes LP, Annibale A, Kleinjung J, Coolen ACC and Fraternali F (2010) Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods. PLoS ONE 5:e12083 76. Fernando C, Goldstein R and Szathmáry E (2010) The neuronal replicator hypothesis. Neural Computation 22:2809-2857 77. Fernando C and Szathmáry E (2010) Facilitated variation. In: Evolution - the Extended Synthesis. Edited by Pigliucci M and Müller GB. MIT Press, 2010. 78. Fernando C, Valijärvi R-L and Goldstein RA (2010) A model of the mechanisms of language extinction and revitalization strategies to save endangered languages. Human Biology 82:47-75 79. Fernando CT, Goldstein RA, Husbands P and Stekel DJ (2010) In silico biology. Pacific Symposium on Biocomputing 477-80 80. Fili N, Mashanov GI, Toseland CP, Batters C, Wallace MI, Yeeles JTP, Dillingham MS, Webb MR and Molloy JE (2010) Visualizing helicases unwinding DNA at the single molecule level. Nucleic Acids Research 38:4448-4457 81. Fivian-Hughes AS and Davis EO (2010) Analysing the regulatory role of the HigA antitoxin within Mycobacterium tuberculosis. Journal of Bacteriology 192:4348-4356 82. Ford B, Rêgo AT, Ragan TJ, Pinkner J, Dodson K, Driscoll PC, Hultgren S and Waksman G (2010) Structural homology between the C-terminal domain of the PapC usher and its plug. Journal of Bacteriology 192:1824-1831 83. Foster KE, Gordon J, Cardenas K, Veiga-Fernandes H, Makinen T, Grigorieva E, Wilkinson DG, Blackburn CC, Richie E, Manley NR, Adams RH, Kioussis D and Coles MC (2010) EphB-ephrin-B2 interactions are required for thymus migration during organogenesis. Proceedings of the National Academy of Sciences of the United States of America 107:13414-9 84. Fotopoulou S, Oikonomou N, Grigorieva E, Nikitopoulou I, Paparountas T, Thanassopoulou A, Zhao Z, Xu Y, Kontoyiannis DL, Remboutsika E and Aidinis V (2010) ATX expression and LPA signalling are vital for the development of the nervous system. Developmental Biology 339:451-464 85. Freitas do Rosario AP, Langhorne J, Duffy PE and Finney OC (2010) Recent advances in malaria research: new tools to understand an old enemy. Expert Review of Anti-infective Therapy 8:863-6 86. Friedrich N, Santos JM, Liu Y, Palma AS, Leon E, Saouros S, Kiso M, Blackman MJ, Matthews S, Feizi T and Soldati-Favre D (2010) Members of a novel protein family containing microneme adhesive repeat domains act as sialic acid-binding lectins during host cell invasion by Apicomplexan parasites. Journal of Biological Chemistry 285:2064-2076 87. Galichet C, Lovell-Badge R and Rizzoti K (2010) Nestin-Cre mice are affected by hypopituitarism, which is not due to significant activity of the transgene in the pituitary gland. PLoS ONE 5:e11443 88. Gamblin SJ and Skehel JJ (2010) Influenza haemagglutinin and neuraminidase membrane glycoproteins. Journal of Biological Chemistry 285:28403-28409 89. Gamlen T, Richards K, Mankouri J, Hudson L, McCauley J, Harris M and Macdonald A (2010) Expression of the NS3 protease of cytopathogenic BVDV results in the induction of apoptosis but does not block activation of the interferon-β promoter. Journal of General Virology 91:133-144 90. Garcia MJ, Nuñez MC and Cox RA (2010) Measurement of the rates of synthesis of three components of ribosomes of Mycobacterium fortuitum: A theoretical approach to qRTPCR experimentation. PLoS ONE 5:e11575 MRC National Institute for Medical Research 143 Bibliography (cont.) 91. Garza-Garcia AA, Driscoll PC and Brockes JP (2010) Evidence for the local evolution of mechanisms underlying limb regeneration in salamanders. Integrative & Comparative Biology 50:528-535 92. Geach TJ and Zimmerman LB (2010) Paralysis and delayed Z-disc formation in the Xenopus tropicalis unc45b mutant dicky ticker. BMC Developmental Biology 10:75 103. Grainger B, Sadowski MI and Taylor WR (2010) Re-evaluating the “rules” of protein topology. Journal of Computational Biology 17:1253-66 93. Gerety SS and Wilkinson DG (2010) Morpholino artifacts provide pitfalls and reveal a novel role for proapoptotic genes in hindbrain boundary development. Developmental Biology 350:279-289 104. Grant J, Saldanha JW and Gould AP (2010) A Drosophila model for primary coenzyme Q deficiency and dietary rescue in the developing nervous system. Disease Models & Mechanisms 3:799-806 94. Geymonat M, Spanos A, Jensen S and Sedgwick SG (2010) Phosphorylation of Lte1 by Cdk prevents polarized growth during mitotic arrest in S. cerevisiae. Journal of Cell Biology 191:1097-1112 105. Grigorieva IV, Mirczuk S, Gaynor KU, Nesbit MA, Grigorieva EF, Wei Q, Ali A, Fairclough RJ, Stacey JM, Stechman MJ, Mihai R, Kurek D, Fraser WD, Hough T, Condie BG, Manley N, Grosveld F and Thakker RV (2010) Gata3-deficient mice develop parathyroid abnormalities due to dysregulation of the parathyroid-specific transcription factor Gcm2. Journal of Clinical Investigation 120:2144-2155 95. Gideon HP, Wilkinson KA, Rustad TR, Oni T, Guio H, Kozak RA, Sherman DR, Meintjes G, Behr MA, Vordermeier HM, Young DB and Wilkinson RJ (2010) Hypoxia induces an immunodominant target of tuberculosis specific T cells absent from common BCG vaccines. PLoS Pathogens 6:e1001237 96. Godin JD, Colombo K, Molina-Calavita M, Keryer G, Zala D, Charrin BC, Dietrich P, Volvert ML, Guillemot F, Dragatsis I, Bellaiche Y, Saudou F, Nguyen L and Humbert S (2010) Huntingtin is required for mitotic spindle orientation and mammalian neurogenesis. Neuron 67:392-406 97. Goldstein RA (2010) The evolution and evolutionary consequences of marginal thermostability in proteins. Proteins Epub ahead of print 98. Goldstone DC, Yap MW, Robertson LE, Haire LF, Taylor WR, Katzourakis A, Stoye JP and Taylor IA (2010) Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface. Cell Host & Microbe 8:248-259 99. Gonzalez-Quevedo R, Lee Y, Poss KD and Wilkinson DG (2010) Neuronal regulation of the spatial patterning of neurogenesis. Developmental Cell 18:136-147 100. Goodman AL, Epp C, Moss D, Holder AA, Wilson JM, Gao GP, Long CA, Remarque EJ, Thomas AW, Ammendola V, Colloca S, Dicks MDJ, Biswas S, Seibel D, van Duivenvoorde LM, Gilbert SC, Hill AVS and Draper SJ (2010) New candidate vaccines against blood-stage P. falciparum malaria: Primeboost immunization regimes incorporating human and simian adenoviral vectors and poxviral vectors expressing an optimized antigen based on merozoite surface protein 1. Infection and Immunity 78:4601-12 101. Goodworth KJ, Herve AC, Stavropoulos E, Herve G, Casades I, Hill AM, Weingarten GG, Tascon RE, Colston MJ and Hailes HC (2010) Synthesis and in vivo biological activity of large-ringed calixarenes against Mycobacterium tuberculosis. Tetrahedron 67:373-382 144 102. Gouty-Colomer L-A, Méry P-F, Storme E, Gavois E, Robinson IC, Guérineau NC, Mollard P and Desarménien MG (2010) Specific involvement of gonadal hormones in the functional maturation of growth hormone releasing hormone (GHRH) neurons. Endocrinology 151:5762-5774 MRC National Institute for Medical Research 106. Groom HCT, Boucherit VC, Makinson K, Randal E, Baptista S, Hagan S, Gow JW, Mattes FM, Breuer J, Kerr JR, Stoye JP and Bishop KN (2010) Absence of xenotropic murine leukaemia virus-related virus in UK patients with chronic fatigue syndrome. Retrovirology 7:10 107. Groom HCT, Yap MW, Galão RP, Neil SJD and Bishop KN (2010) Susceptibility of xenotropic murine leukemia virus-related virus (XMRV) to retroviral restriction factors. Proceedings of the National Academy of Sciences of the United States of America 107:5166-5171 108. Groves E, Rittinger K, Amstutz M, Berry S, Holden DW, Cornelis GR and Caron E (2010) Sequestering of Rac by the Yersinia effector YopO blocks Fcγ receptormediated phagocytosis. Journal of Biological Chemistry 285:4087-4098 109. Guillemot F and Hobert O (2010) Development. Current Opinion in Neurobiology 20:2-5 110. Hadjieconomou D, Timofeev K and Salecker I (2010) A step-by-step guide to visual circuit assembly in Drosophila. Current Opinion in Neurobiology 21:76-84 111. Harvey SA, Tümpel S, Dubrulle J, Schier AF and Smith JC (2010) no tail integrates two modes of mesoderm induction. Development 137:1127-1135 112. Hashash N, Johnson AL and Cha RS (2010) Regulation of fragile sites expression in budding yeast by MEC1, RRM3 and hydroxyurea. Journal of Cell Science 124:181-185 113. Hasson P, DeLaurier A, Bennett M, Grigorieva E, Naiche LA, Papaioannou VE, Mohun TJ and Logan MPO (2010) Tbx4 and Tbx5 acting in connective tissue are required for limb muscle and tendon patterning. Developmental Cell 18:148-156 Bibliography (cont.) 114. He Z, Fernandez-Fuente M, Strom M, Cheung L, Robinson ICAF and Le Tissier P (2010) Continuous on-line monitoring of secretion from rodent pituitary endocrine cells using fluorescent protein surrogate markers. Journal of Neuroendocrinology 23:197-207 115. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM and Rokhsar DS (2010) The genome of the Western clawed frog Xenopus tropicalis. Science 328:633-6 124. Kadekoppala M and Holder AA (2010) Merozoite surface proteins of the malaria parasite: the MSP1 complex and the MSP7 family. International Journal for Parasitology 40:1155-1161 125. Kadekoppala M, Ogun SA, Howell S, Gunaratne RS and Holder AA (2010) Systematic genetic analysis of the Plasmodium falciparum MSP7like family reveals differences in protein expression, location and importance in asexual growth of the blood stage parasite. Eukaryotic Cell 9:1064-1074 125. Kajita M, Hogan C, Harris AR, Dupre-Crochet S, Itasaki N, Kawakami K, Charras G, Tada M and Fujita Y (2010) Interaction with surrounding normal epithelial cells influences signalling pathways and behaviour of Src-transformed cells. Journal of Cell Science 153:171-80 116. Henderson RB, Grys K, Vehlow A, de Bettignies C, Zachacz A, Henley T, Turner M, Batista F and Tybulewicz VLJ (2010) A novel Rac-dependent checkpoint in B cell development controls entry into the splenic white pulp and cell survival. Journal of Experimental Medicine 207:837-853 127. Karamitros D, Kotantaki P, Lygerou Z, Veiga-Fernandes H, Pachnis V, Kioussis D and Taraviras S (2010) Differential Geminin requirement for proliferation of thymocytes and mature T cells. Journal of Immunology 184: 2432-2441 117. Hern JA, Baig AH, Mashanov GI, Birdsall B, Corrie JET, Lazareno S, Molloy JE and Birdsall NJM (2010) Formation and dissociation of M1 muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules. Proceedings of the National Academy of Sciences of the United States of America 107:2693-2698 128. Karamitros D, Kotantaki P, Lygerou Z, Veiga-Fernandes H, Pachnis V, Kioussis D and Taraviras S (2010) Life without geminin. Cell Cycle 9:3181-3185 118. Hirota K, Martin B and Veldhoen M (2010) Development, regulation and functional capacities of Th17 cells. Seminars in Immunopathology 32:3-16 129. Katsimitsoulia Z and Taylor WR (2010) A hierarchic collision detection algorithm for simple Brownian dynamics. Computational Biology and Chemistry 34:71-9 119. Hulme EC and Trevethick MA (2010) Ligand binding assays at equilibrium: validation and interpretation. British Journal of Pharmacology 161:1219-37 130. Kemp RA, Pearson CF, Cornish GH and Seddon BP (2010) Evidence of STAT5-dependent and -independent routes to CD8 memory formation and a preferential role for IL-7 over IL-15 in STAT5 activation. Immunology and Cell Biology 88:213-219 120. Ibanez-Garcia D, Requejo-Isidro J, Webb MR, West TG, French P and Ferenczi MA (2010) Fluorescence lifetime imaging reveals that the environment of the ATP binding site of myosin in muscle senses force. Biophysical Journal 99:2163-9 131. Khurshid S, Haire LF and Chayen NE (2010) Automated seeding for the optimization of crystal quality. Journal of Applied Crystallography 43:752-756 121. Itasaki N and Hoppler S (2010) Crosstalk between Wnt and bone morphogenic protein signaling: A turbulent relationship. Developmental Dynamics 239:16-33 122. Jarvis A, Allerston CK, Jia H, Herzog B, Garza-Garcia A, Winfield N, Ellard K, Aqil R, Lynch R, Chapman C, Hartzoulakis B, Nally J, Stewart M, Cheng L, Menon M, Tickner M, Djordjevic S, Driscoll PC, Zachary I and Selwood DL (2010) Small molecule inhibitors of the neuropilin-1 vascular endothelial growth factor A (VEGF-A) interaction. Journal of Medicinal Chemistry 53:2215-26 123. Justin N, De Marco V, Aasland R and Gamblin SJ (2010) Reading, writing and editing methylated lysines on histone tails: new insights from recent structural studies. Current Opinion in Structural Biology 20:730-8 132. Kicheva A and Briscoe J (2010) Limbs made to measure. PLoS Biology 8:e1000421 133. Kirschner DE, Young D and Flynn JL (2010) Tuberculosis: global approaches to a global disease. Current Opinion in Biotechnology 21:524-531 134. Kiskin NI, Hellen N, Babich V, Hewlett L, Knipe L, Hannah MJ and Carter T (2010) Protein mobilities and P-selectin storage in Weibel-Palade bodies. Journal of Cell Science 123:2964-2975 135. Knipe L, Meli A, Hewlett L, Bierings R, Dempster J, Skehel P, Hannah MJ and Carter T (2010) A revised model for the secretion of tPA and cytokines from cultured endothelial cells. Blood 116:2183-2191 MRC National Institute for Medical Research 145 136. Krashias G, Simon A-K, Wegmann F, Kok W-L, Ho L-P, Stevens D, Skehel J, Heeney JL, Moghaddam AE and Sattentau QJ (2010) Potent adaptive immune responses induced against HIV-1 gp140 and influenza virus HA by a polyanionic carbomer. Vaccine 28:2482-2489 137. Ktistaki E, Garefalaki A, Williams A, Andrews SR, Bell DM, Foster KE, Spilianakis CG, Flavell RA, Kosyakova N, Trifonov V, Liehr T and Kioussis D (2010) CD8 locus nuclear dynamics during thymocyte development. Journal of Immunology 184:5686 -5695 148. Liu W, Sohn HW, Tolar P and Pierce SK (2010) It’s all about change: the antigen-driven initiation of B-cell receptor signaling. Cold Spring Harbor Perspectives in Biology 2:a002295 138. Kunzelmann S, Morris C, Chavda AP, Eccleston JF and Webb MR (2010) Mechanism of interaction between single-stranded DNA binding protein and DNA. Biochemistry 49:843-852 149. Liu W, Won Sohn H, Tolar P, Meckel T and Pierce SK (2010) Antigen-induced oligomerization of the B cell receptor is an early target of FcγRIIB inhibition. Journal of Immunology 184:1977-1989 139. Kunzelmann S and Webb MR (2010) A fluorescent, reagentless biosensor for ADP based on tetramethylrhodamine-labeled ParM. ACS Chemical Biology 5:415-25 150. Liu Y, Childs RA, Matrosovich T, Wharton S, Palma AS, Chai W, Daniels R, Gregory V, Uhlendorff J, Kiso M, Klenk H-D, Hay A, Feizi T and Matrosovich M (2010) Altered receptor specificity and cell tropism of D222G haemagglutinin mutants from fatal cases of pandemic A(H1N1) 2009 influenza. Journal of Virology 84:12069-74 140. Lafont C, Desarménien MG, Cassou M, Molino F, Lecoq J, Hodson D, Lacampagne A, Mennessier G, El Yandouzi T, Carmignac D, Fontanaud P, Christian H, Coutry N, Fernandez-Fuente M, Charpak S, Le Tissier P, Robinson ICAF and Mollard P (2010) Cellular in vivo imaging reveals coordinated regulation of pituitary microcirculation and GH cell network function. Proceedings of the National Academy of Sciences of the United States of America 107:4465-4470 141. Lange C and Wilkinson RJ (2010) Vitamin D and active tuberculosis: a futile quest? American Journal of Respiratory and Critical Care Medicine 181:95 142. Laskey MA, de Bono S, Zhu D, Shaw CN, Laskey PJ, Ward KA and Prentice A (2010) Evidence for enhanced characterization of cortical bone using novel pQCT shape software. Journal of Clinical Densitometry 13:247-255 143. Laurson J, Khan S, Chung R, Cross K and Raj K (2010) Epigenetic repression of E-cadherin by Human papillomavirus 16 E7 protein. Carcinogenesis 31:918-926 144. Lawn SD and Wilkinson RJ (2010) Primate model to study reactivation of TB associated with retroviral infection. Future Virology 5:391-395 145. Lawn SD, Wood R and Wilkinson RJ (2010) Changing concepts of “latent tuberculosis infection” in patients living with HIV infection. Clinical & Developmental Immunology 2011:980594 146. Leong CM, Doorbar J, Nindl I, Yoon HS and Hibma MH (2010) Deregulation of E-cadherin by human papillomavirus is not confined to high-risk, cancer-causing types. British Journal of Dermatology 163:1253–1263 Leong CM, Doorbar J, Nindl I, Yoon H-S and Hibma MH (2010) Loss of epidermal Langerhans cells occurs in human papillomavirus α, γ, and μ but not β genus infections. Journal of Investigative Dermatology 130:472-480 146 147. Lin YP, Gregory V, Collins P, Kloess J, Wharton S, Cattle N, Lackenby A, Daniels R and Hay A (2010) Neuraminidase receptor binding variants of human influenza A(H3N2) viruses due to substitution of aspartic acid 151 in the catalytic site role in virus attachment? Journal of Virology 84:6769-6781 MRC National Institute for Medical Research 151. Lochmatter D, Strom M, Eblé A, Petkovic V, Flück CE, Bidlingmaier M, Robinson IC and Mullis PE (2010) Isolated GH deficiency type II: knockdown of the harmful Δ3GH recovers wt-GH secretion in rat tumor pituitary cells. Endocrinology 151:4400-4409 152. Lopes AM, Burgoyne PS, Ojarikre A, Bauer J, Sargent CA, Amorim A and Affara NA (2010) Transcriptional changes in response to X chromosome dosage in the mouse: implications for X inactivation and the molecular basis of Turner Syndrome. BMC Genomics 11:82 153. Lovell-Badge R (2010) The early history of the Sox genes. International Journal of Biochemistry & Cell Biology 42:378-80 154. Macdonald JT, Maksimiak K, Sadowski MI and Taylor WR (2010) De novo backbone scaffolds for protein design. Proteins 78:1311-25 155. Mantsyzov AB, Ivanova EV, Birdsall B, Alkalaeva EZ, Kryuchkova PN, Kelly G, Frolova LY and Polshakov VI (2010) NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor. FEBS Journal 277:2611-2627 156. Marais S, Scholtz P, Pepper DJ, Meintjes G, Wilkinson RJ and Candy S (2010) Neuroradiological features of the tuberculosis-associated immune reconstitution inflammatory syndrome. International Journal of Tuberculosis and Lung Disease 14:188-196 157. Marais S, Thwaites G, Schoeman JF, Török ME, Misra UK, Prasad K, Donald PR, Wilkinson RJ and Marais BJ (2010) Tuberculous meningitis: a uniform case definition for use in clinical research. Lancet Infectious Diseases 10:803-812 Bibliography (cont.) 158. Marteau L, Pacary E, Valable S, Bernaudin M, Guillemot F and Petit E (2010) Angiopoietin-2 regulates cortical neurogenesis in the developing telencephalon. Cerebral Cortex Epub ahead of print 159. Martineau AR, Leandro ACCS, Anderson ST, Newton SM, Wilkinson KA, Nicol MP, Pienaar SM, Skolimowska KH, Rocha MA, Rolla VC, Levin M, Davidson RN, Bremner SA, Griffiths CJ, Eley BS, Bonecini-Almeida MG and Wilkinson RJ (2010) Association between Gc genotype and susceptibility to TB is dependent on vitamin D status. European Respiratory Journal 35:1106-12 160. Masania J, Li J, Smerdon SJ and Macmillan D (2010) Access to phosphoproteins and glycoproteins through semi-synthesis, Native Chemical Ligation and N→S acyl transfer. Organic & Biomolecular Chemistry 8:5113-5119 161. Mashanov GI, Nobles M, Harmer SC, Molloy JE and Tinker A (2010) Direct observation of individual KCNQ1 potassium channels reveals their distinctive diffusive behaviour. Journal of Biological Chemistry 285:3664-3675 162. Matsui H, Mohun T and Gardiner HM (2010) Three-dimensional reconstruction imaging of the human foetal heart in the first trimester. European Heart Journal 31:415 163. Mavromatakis YE, Lin W, Metzakopian E, Ferri ALM, Yan CH, Sasaki H, Whisett J and Ang S-L (2010) Foxa1 and Foxa2 positively and negatively regulate Shh signalling to specify ventral midbrain progenitor identity. Mechanisms of Development 128:90-103 164. McIntosh PB, Laskey P, Sullivan K, Davy C, Wang Q, Jackson DJ, Griffin HM and Doorbar J (2010) E1^E4-mediated keratin phosphorylation and ubiquitylation: a mechanism for keratin depletion in HPV16-infected epithelium. Journal of Cell Science 123:2810-2822 165. McNab FW, Rajsbaum R, Stoye JP and O’Garra A (2010) Tripartite-motif proteins and innate immune regulation. Current Opinion in Immunology 23:46-56 166. Medioni C, Bertrand N, Mesbah K, Hudry B, Dupays L, Wolstein O, Washkowitz AJ, Papaioannou VE, Mohun TJ, Harvey RP and Zaffran S (2010) Expression of Slit and Robo genes in the developing mouse heart. Developmental Dynamics 239:3303–3311 167. Meintjes G and Wilkinson RJ (2010) Optimum timing of antiretroviral therapy for HIV-infected patients with concurrent serious opportunistic infections. Clinical Infectious Diseases 50:1539-41 168. Meintjes G and Wilkinson RJ (2010) Undiagnosed active tuberculosis in HIV-infected patients commencing antiretroviral therapy. Clinical Infectious Diseases 51:830-2 169. Meintjes G, Wilkinson RJ, Morroni C, Pepper DJ, Rebe K, Rangaka MX, Oni T and Maartens G (2010) Randomized placebo-controlled trial of prednisone for paradoxical tuberculosis-associated immune reconstitution inflammatory syndrome. AIDS 24:2381–2390 170. Menke LA, Sas TC, de Muinck Keizer-Schrama SM, Zandwijken GR, de Ridder MA, Odink RJ, Jansen M, Delemarre-van de Waal HA, StokvisBrantsma WH, Waelkens JJ, Westerlaken C, Reeser HM, van Trotsenburg ASP, Gevers EF, van Buuren S, Dejonckere PH, Hokken-Koelega ACS, Otten BJ and Wit JM (2010) Efficacy and safety of oxandrolone in growth hormone-treated girls with Turner syndrome. Journal of Clinical Endocrinology and Metabolism 95:1151-1160 171. Menzel U, Ktistaki E, Tolaini M, Veiga-Fernandes H and Kioussis D (2010) Replication allows inactivation of a knocked-in locus control region in inappropriate cell lineages. Proceedings of the National Academy of Sciences of the United States of America 107:16928-16933 172. Mieulet V, Yan L, Choisy C, Sully K, Procter J, Kouroumalis A, Krywawych S, Pende M, Ley SC, Moinard C and Lamb RF (2010) TPL-2-mediated activation of MAPK downstream of TLR4 signaling is coupled to arginine availability. Science Signaling 3:ra61 173. Miquerol L, Moreno-Rascon N, Beyer S, Dupays L, Meilhac SM, Buckingham ME, Franco D and Kelly RG (2010) Biphasic development of the mammalian ventricular conduction system. Circulation Research 107:153-161 174. Mócsai A, Ruland J and Tybulewicz VLJ (2010) The SYK tyrosine kinase: a crucial player in diverse biological functions. Nature Reviews Immunology 10:387-402 175. Montgomery MG, Coker AR, Taylor IA and Wood SP (2010) Assembly of a 20nm protein cage by Escherichia coli 2-hydroxypentadienoic acid hydratase (MhpD). Journal of Molecular Biology 396:1379-91 176. Moules V, Ferraris O, Terrier O, Giudice E, Yver M, Rolland JP, BouscambertDuchamp M, Bergeron C, Ottmann M, Fournier E, Traversier A, Boule C, Rivoire A, Lin Y, Hay A, Valette M, Marquet R, Rosa-Calatrava M, Naffakh N, Schoehn G, Thomas D and Lina B (2010) In vitro characterization of naturally occurring influenza H3NA- viruses lacking the NA gene segment: Toward a new mechanism of viral resistance? Virology 404:215-224 177. Murcia PR, Baillie GJ, Daly J, Elton D, Jervis C, Mumford JA, Newton R, Parrish CR, Hoelzer K, Dougan G, Parkhill J, Lennard N, Ormond D, Moule S, Whitwham A, McCauley JW, McKinley TJ, Holmes EC, Grenfell BT and Wood JLN (2010) The intra- and inter-host evolutionary dynamics of equine influenza virus. Journal of Virology 84:6943-6954 178. Murphy KM and Stockinger B (2010) Effector T cell plasticity: flexibility in the face of changing circumstances. Nature Immunology 11:674-80 179. Nahid P, Bliven EE, Kim EY, Mac Kenzie WR, Stout JE, Diem L, Johnson JL, Gagneux S, Hopewell PC, Kato-Maeda M and The Tuberculosis Trials Consortium (2010) Influence of M. tuberculosis lineage variability within a clinical trial for pulmonary tuberculosis. PLoS ONE 5:e10753 MRC National Institute for Medical Research 147 Bibliography (cont.) 180. Nair SR, Zelinskyy G, Schimmer S, Gerlach N, Kassiotis G and Dittmer U (2010) Mechanisms of control of acute Friend virus infection by CD4+ helper T cells and their functional impairment by regulatory T cells. Journal of General Virology 91:440-451 181. Nduati EW, Ng DHL, Ndungu FM, Gardner P, Urban BC and Langhorne J (2010) Distinct kinetics of memory B-cell and plasma-cell responses in peripheral blood following a blood-stage Plasmodium chabaudi infection in mice. PLoS ONE 5:e15007 182. Ngoundou-Landji J, Nwuba RI, Anumudu CI, Odaibo AB, Matondo Maya WD, Awobode HO, Okafor CM, Morenikeji OA, Asinobi A, Nwagwu M, Holder AA and Ntoumi F (2010) Fine specificity of anti-MSP119 antibodies and multiplicity of Plasmodium falciparum Merozoite Surface Protein 1 types in individuals in Nigeria with sub-microscopic infection. Malaria Journal 9:287 183. Nicastro G, Todi SV, Karaca E, Bonvin AMJJ, Paulson HL and Pastore A (2010) Understanding the role of the Josephin domain in the polyUb binding and cleavage properties of ataxin-3. PLoS ONE 5:e12430 184. Njouom R, Mba SAS, Noah DN, Gregory V, Collins P, Cappy P, Hay A and Rousset D (2010) Circulation of human influenza viruses and emergence of Oseltamivirresistant A(H1N1) viruses in Cameroon, Central Africa. BMC Infectious Diseases 10:56 185. Noël ES, dos Reis M, Arain Z and Ober EA (2010) Analysis of the albumin/α-fetoprotein/afamin/group specific component gene family in the context of zebrafish liver differentiation. Gene Expression Patterns 10:237-243 186. Nygard A-B, Cirera S, Gilchrist M, Gorodkin J, Jørgensen C and Fredholm M (2010) A study of alternative splicing in the pig. BMC Research Notes 3:123 187. Offer J (2010) Native chemical ligation with Nα acyl transfer auxiliaries. Biopolymers 94:530-541 188. Omosun YO, Adoro S, Anumudu CI, Odaibo A, Holder AA, Nwagwu M and Nwuba RI (2010) Total immunoglobulin G and IgG1 subclass levels specific for the MSP119 of Plasmodium falciparum are different in individuals with either processing-inhibitory, blocking or neutral antibodies. African Health Sciences 10:106-110 189. Oni T, Patel J, Gideon HP, Seldon R, Wood K, Hlombe Y, Wilkinson KA, Rangaka MX, Mendelson M and Wilkinson RJ (2010) Enhanced diagnosis of HIV-1 associated tuberculosis by relating T-SPOT. TB and CD4 counts. European Respiratory Journal 36:594-600 190.. Onorati M, Binetti M, Conti L, Camnasio S, Calabrese G, Albieri I, Di Febo F, Toselli M, Biella G, Martynoga B, Guillemot F, Consalez GG and Cattaneo E (2010) Preservation of positional identity in fetus-derived neural stem (NS) cells from different mouse central nervous system compartments. Cellular and Molecular Life Sciences Epub ahead of print 148 MRC National Institute for Medical Research 191. Osterstock G, Escobar P, Mitutsova V, Gouty-Colomer L-A, Fontanaud P, Molino F, Fehrentz J-A, Carmignac D, Martinez J, Guerineau NC, Robinson ICAF, Mollard P and Méry P-F (2010) Ghrelin stimulation of growth hormone-releasing hormone neurons is direct in the arcuate nucleus. PLoS ONE 5:e9159 192. Pancevac C, Goldstone DC, Ramos A and Taylor IA (2010) Structure of the Rna15 RRM-RNA complex reveals the molecular basis of GU specificity in transcriptional 3’-end processing factors. Nucleic Acids Research 38:3119-3132 193. Pandini A, Fornili A and Kleinjung J (2010) Structural alphabets derived from attractors in conformational space. BMC Bioinformatics 11:97 194. Papadopoulou K, Chen J-S, Mead E, Feoktistova A, Petit C, Agarwal M, Jamal M, Malik A, Spanos A, Sedgwick SG, Karagiannis J, Balasubramanian MK, Gould KL and McInerny CJ (2010) Regulation of cell cycle-specific gene expression in fission yeast by the Cdc14p-like phosphatase Clp1p. Journal of Cell Science 123:4374-4381 195. Pastore A (2010) Further insights into the ubiquitin pathway: understanding the scarlet letter code. Structure 18:891-892 196. Patel S, Hussain S, Harris R, Sardiwal S, Kelly JM, Wilkinson SR, Driscoll PC and Djordjevic S (2010) Structural insights into the catalytic mechanism of Trypanosoma cruzi GPXI - glutathione peroxidase-like enzyme I. Biochemical Journal 425:513-22 197. Pecci A, Panza E, De Rocco D, Pujol-Moix N, Girotto G, Podda L, Paparo C, Bozzi V, Pastore A, Balduini CL, Seri M and Savoia A (2010) MYH9 related disease: four novel mutations of the tail domain of myosin-9 correlating with a mild clinical phenotype. European Journal of Haematology 84:291-297 198. Pelling M, Anthwal N, McNay D, Gradwohl G, Leiter AB, Guillemot F and Ang SL (2010) Differential requirements for neurogenin 3 in the development of POMC and NPY neurons in the hypothalamus. Developmental Biology 349:406-416 199. Pennell S, Westcott S, Ortiz-Lombardía M, Patel D, Li J, Nott TJ, Mohammed D, Buxton RS, Yaffe MB, Verma C and Smerdon SJ (2010) Structural and functional analysis of phosphothreonine-dependent FHA domain interactions. Structure 18:1587-95 200. Pepper DJ, Marais S, Wilkinson RJ, Bhaijee F, Maartens G, McIlleron H, De Azevedo V, Cox H, McDermid C, Sokhela S, Patel J and Meintjes G (2010) Clinical deterioration during anti-tuberculosis treatment in Africa: Incidence, causes and risk factors. BMC Infectious Diseases 10:83 201. Petkovic V, Godi M, Lochmatter D, Eblé A, Flück CE, Robinson IC and Mullis PE (2010) Growth hormone (GH)-releasing hormone increases the expression of the dominant-negative GH isoform in cases of isolated GH deficiency due to GH splice-site mutations. Endocrinology 151:2650-2658 Bibliography (cont.) 202. Poulou M, Bell D, Bozonelos K, Alexiou M, Gavalas A, Lovell-Badge R and Remboutsika E (2010) Development of a chromosomally integrated metabolite-inducible Leu3p-α-IPM “Off-_n” gene switch. PLoS ONE 5:e12488 212. Robinson ICAF (2010) GH & IGF1: Aspects of global and local release and actions. In: IGFS: Local Repair and Survival Factors Throughout Life Span. Edited by Clemmons D, Robinson ICAF and Christen Y. Berlin, Springer, 2010. 1-10 (Research and Perspectives in Endocrine Interactions) 203. Prischi F, Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI and Pastore A (2010) Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly. Nature Communications 1:95 213. Rossetti G, Magistrato A, Pastore A and Carloni P (2010) Hydrogen bonding cooperativity in polyQ β-sheets from first principle calculations. Journal of Chemical Theory and Computation 6:1777-1782 204. Prischi F, Pastore C, Carroni M, Iannuzzi C, Adinolfi S, Temussi P and Pastore A (2010) Of the vulnerability of orphan complex proteins: The case study of the E. coli IscU and IscS proteins. Protein Expression and Purification 73:161-6 214. Royo H, Polikiewicz G, Mahadevaiah SK, Prosser H, Mitchell M, Bradley A, de Rooij DG, Burgoyne PS and Turner JMA (2010) Evidence that meiotic sex chromosome inactivation is essential for male fertility. Current Biology 20:2117-23 205. Raiber EA, Tulone C, Zhang Y, Martinez-Pomares L, Steed E, Sponaas A, Langhorne J, Noursadeghi M, Chain B and Tabor AB (2010) Targeted delivery of antigen processing inhibitors to antigen presenting cells via mannose receptors. ACS Chemical Biology 5:461-76 215. Sadowski MI and Taylor WR (2010) On the evolutionary origins of “Fold Space Continuity”: A study of topological convergence and divergence in mixed alpha-beta domains. Journal of Structural Biology 172:244-252 206. Rana AA, Roper SJ, Palmer EA and Smith JC (2010) Loss of Xenopus tropicalis EMSY causes impairment of gastrulation and upregulation of p53. New Biotechnology Epub ahead of print 207. Redford PS, Boonstra A, Read S, Pitt J, Graham C, Stavropoulos E, Bancroft GJ and O’Garra A (2010) Enhanced protection to Mycobacterium tuberculosis infection in IL-10deficient mice is accompanied by early and enhanced Th1 responses in the lung. European Journal of Immunology 40:2200–2210 208. Reynolds LE, Watson AR, Baker M, Jones TA, D’Amico G, Robinson SD, Joffre C, Garrido-Urbani S, Rodriguez-Manzaneque JC, Martino-Echarri E, Aurrand-Lions M, Sheer D, Dagna-Bricarelli F, Nizetic D, McCabe CJ, Turnell AS, Kermorgant S, Imhof BA, Adams R, Fisher EMC, Tybulewicz VLJ, Hart IR and Hodivala-Dilke KM (2010) Tumour angiogenesis is reduced in the Tc1 mouse model of Down’s syndrome. Nature 465:813-7 209. Ribes V, Balaskas N, Sasai N, Cruz C, Dessaud E, Cayuso J, Tozer S, Yang LL, Novitch B, Marti E and Briscoe J (2010) Distinct Sonic Hedgehog signaling dynamics specify floor plate and ventral neuronal progenitors in the vertebrate neural tube. Genes & Development 24:1186-1200 216. Sadowski MI and Taylor WR (2010) Protein structures, folds and fold spaces. Journal of Physics-Condensed Matter 22:033103 217. Saenz RA, Quinlivan M, Elton D, MacRae S, Blunden AS, Mumford JA, Daly JM, Digard P, Cullinane A, Grenfell BT, McCauley JW, Wood JLN and Gog JR (2010) Dynamics of infection and pathology in influenza. Journal of Virology 84:3974-3983 218. Saini M, Sinclair C, Marshall D, Tolaini M, Sakaguchi S and Seddon B (2010) Regulation of Zap70 expression during thymocyte development enables temporal separation of CD4 and CD8 repertoire selection at different signaling thresholds. Science Signaling 3:ra23 219. Sanchez-Cardenas C, Fontanaud P, He Z, Lafont C, Meunier A-C, Schaeffer M, Carmignac D, Molino F, Coutry N, Bonnefont X, Gouty-Colomer L-A, Gavois E, Hodson DJ, Le Tissier P, Robinson ICAF and Mollard P (2010) Pituitary growth hormone network responses are sexually dimorphic and regulated by gonadal steroids in adulthood. Proceedings of the National Academy of Sciences of the United States of America 107:21878-21883 220. Saraiva M and O’Garra A (2010) The regulation of IL-10 production by immune cells. Nature Reviews Immunology 10:170-81 210. Riley EM, Couper KN, Helmby H, Hafalla JCR, de Souza JB, Langhorne J, Jarra W and Zavala F (2010) Neuropathogenesis of human and murine malaria. Trends in Parasitology 26:277-8 221. Schmitz S, Schaap IAT, Kleinjung J, Harder S, Grainger M, Calder L, Rosenthal PB, Holder AA and Veigel C (2010) Malaria parasite actin polymerisation and filament structure. Journal of Biological Chemistry 285:36577-36585 211. Rizzoti K (2010) Adult pituitary progenitors/stem cells: from in vitro characterization to in vivo function. European Journal of Neuroscience 32:2053-62 222. Schutz C, Meintjes G, Almajid F, Wilkinson RJ and Pozniak A (2010) Clinical management of tuberculosis and HIV-1 co-infection. European Respiratory Journal 36:1460-1481 223. Scott CE, Wynn SL, Sesay A, Cruz C, Cheung M, Gaviro M-VG, Booth S, Gao B, Cheah KSE, Lovell-Badge R and Briscoe J (2010) SOX9 induces and maintains neural stem cells. Nature Neuroscience 13:1181–1189 MRC National Institute for Medical Research 149 Bibliography (cont.) 224. Sekido R (2010) SRY: A transcriptional activator of mammalian testis determination. International Journal of Biochemistry & Cell Biology 42:417-420 225. Sellers JR and Veigel C (2010) Direct observation of the myosin-Va power stroke and its reversal. Nature Structural & Molecular Biology 17:590-5 226. Sergaki MC, Guillemot F and Matsas R (2010) Impaired cerebellar development and deficits in motor coordination in mice lacking the neuronal protein BM88/Cend1. Molecular and Cellular Neurosciences 44:15-29 227. Shah SD, Doorbar J and Goldstein RA (2010) Analysis of host-parasite incongruence in papillomavirus evolution using importance sampling. Molecular Biology and Evolution 27:1301-14 228. 229. Sheng N, Xie Z, Wang C, Bai G, Zhang K, Zhu Q, Song J, Guillemot F, Chen YG, Lin A and Jing N (2010) Retinoic acid regulates bone morphogenic protein signal duration by promoting the degradation of phosphorylated Smad1. Proceedings of the National Academy of Sciences of the United States of America 107:18886-91 235. Stephens R and Langhorne J (2010) Effector memory Th1 CD4 T cells are maintained in a mouse model of chronic malaria. PLoS Pathogens 6:e1001208 236. Stoye JP, Silverman RH, Boucher CA and Le Grice SFJ (2010) The xenotropic murine leukemia virus-related retrovirus debate continues at first international workshop. Retrovirology 7: 237. Straschil U, Talman AM, Ferguson DJP, Bunting KA, Xu Z, Bailes E, Sinden RE, Holder AA, Smith EF, Coates JC and Tewari R (2010) The Armadillo repeat protein PF16 is essential for flagellar structure and function in Plasmodium male gametes. PLoS ONE 5:e12901 238. Strutt D and Vincent J-P (2010) Frizzled signaling: Gαo and Rab5 at the crossroads of the canonical and PCP pathways? Science Signaling 3:pe43 Singh P, Patil KN, Khanduja JS, Kumar PS, Williams A, Rossi F, Rizzi M, Davis EO and Muniyappa K (2010) Mycobacterium tuberculosis UvrD1 and UvrA proteins suppress DNA strand exchange promoted by cognate and non-cognate RecA proteins. Biochemistry 49:4872-83 239. Sutton E, Hughes J, White S, Sekido R, Tan J, Arboleda V, Rogers N, Knower K, Rowley L, Eyre H, Rizzoti K, McAninch D, Goncalves J, Slee J, Turbitt E, Bruno D, Bengtsson H, Harley V, Vilain E, Sinclair A, Lovell-Badge R and Thomas P (2010) Identification of SOX3 as an XX male sex reversal gene in mice and humans. Journal of Clinical Investigation 4:328-41 230. Smith LJ, Stapleton MR, Fullstone GJM, Crack JC, Thomson AJ, Le Brun NE, Hunt DM, Harvey E, Adinolfi S, Buxton RS and Green J (2010) Mycobacterium tuberculosis WhiB1 is an essential DNA-binding protein with a nitric oxide sensitive iron-sulphur cluster. Biochemical Journal 432:417-427 240. Tadokera R, Meintjes G, Skolimowska KH, Wilkinson KA, Matthews K, Seldon R, Chegou NN, Maartens G, Rangaka MX, Rebe K, Walzl G and Wilkinson RJ (2010) Hypercytokinaemia accompanies HIV-tuberculosis immune reconstitution inflammatory syndrome. European Respiratory Journal Epub ahead of print 231. Sobieszczuk DF, Poliakov A, Xu Q and Wilkinson DG (2010) A feedback loop mediated by degradation of an inhibitor is required to initiate neuronal differentiation. Genes & Development 24:206-218 241. Tapia VE, Nicolaescu E, McDonald CB, Musi V, Oka T, Inayoshi Y, Satteson AC, Mazack V, Humbert J, Gaffney CJ, Beullens M, Schwartz CE, Landgraf C, Volkmer R, Pastore A, Farooq A, Bollen M and Sudol M (2010) Y65C missense mutation in the WW domain of the Golabi-Ito-Hall syndrome protein PQBP1 affects its binding activity and deregulates premRNA splicing. Journal of Biological Chemistry 285:19391-19401 Sousa-Nunes R, Cheng LY and Gould AP (2010) Regulating neural proliferation in the Drosophila CNS. Current Opinion in Neurobiology 20:50-7 232. 233. 150 234. Stapleton M, Haq I, Hunt DM, Arnvig KB, Artymiuk PJ, Buxton RS and Green J (2010) Mycobacterium tuberculosis cAMP receptor protein (Rv3676) differs from the Escherichia coli paradigm in its cAMP-binding, DNA-binding and transcription activation properties. Journal of Biological Chemistry 285:7016-7027 Spencer J, Murphy LM, Conners R, Sessions RB and Gamblin SJ (2010) Crystal structure of the LasA virulence factor from Pseudomonas aeruginosa: Substrate specificity and mechanism of M23 metallopeptidases. Journal of Molecular Biology 396:908-23 Sriskantharajah S and Ley SC (2010) Turning off inflammation signaling. Science 327:1093-4 MRC National Institute for Medical Research 242. Taylor HM, McRobert L, Grainger M, Sicard A, Dluzewski AR, Hopp CS, Holder AA and Baker DA (2010) The malaria parasite cyclic GMP-dependent protein kinase plays a central role in blood stage schizogony. Eukaryotic Cell 9:37-45 243. Taylor IA, Goldstone DC, Pala P, Haire LF and Smerdon SJ (2010) Structure of the amino-terminal domain from the cell-cycle regulator Swi6. Proteins 78:2861–2865 244. Taylor WR and Katsimitsoulia Z (2010) A coarse-grained molecular model for actin-myosin simulation. Journal of Molecular Graphics & Modelling 29:266-279 Taylor WR and Katsimitsoulia Z (2010) A soft collision detection algorithm for simple Brownian dynamics. Computational Biology and Chemistry 34:1-10 Bibliography (cont.) 245. Teixeira-Coelho M, Cruz A, Carmona J, Sousa C, Ramos-Pereira D, Saraiva AL, Veldhoen M, Pedrosa J, Castro AG and Saraiva M (2010) TLR2 deficiency by compromising p19 (IL-23) expression limits Th 17 cell responses to Mycobacterium tuberculosis. International Immunology 23:89-96 257. Verstrepen L, Verhelst K, van Loo G, Carpentier I, Ley SC and Beyaert R (2010) Expression, biological activities and mechanisms of action of A20 (TNFAIP3). Biochemical Pharmacology 80:2009-20 246. Tena-Coki NG, Scriba TJ, Peteni N, Eley B, Wilkinson RJ, Andersen P, Hanekom WA and Kampmann B (2010) CD4 and CD8 T cell responses to mycobacterial antigens in African children. American Journal of Respiratory and Critical Care Medicine 182:120-9 258. Voisine C, Mastelic B, Sponaas A-M and Langhorne J (2010) Classical CD11c+ dendritic cells, not plasmacytoid dendritic cells, induce T cell responses to Plasmodium chabaudi malaria. International Journal for Parasitology 40:711-9 247. Thébaud G, Chadœuf J, Morelli MJ, McCauley JW and Haydon DT (2010) The relationship between mutation frequency and replication strategy in positive-sense single-stranded RNA viruses. Proceedings of the Royal Society B: Biological Sciences 277:809-817 248. Thomas JC, Green JL, Howson RI, Simpson P, Moss DK, Martin SR, Holder AA, Cota E and Tate EW (2010) Interaction and dynamics of the Plasmodium falciparum MTIP-MyoA complex, a key component of the invasion motor in the malaria parasite. Molecular BioSystems 6:494-8 249. Todi SV, Scaglione KM, Blount JR, Basrur V, Conlon KP, Pastore A, Elenitoba-Johnson K and Paulson HL (2010) Activity and cellular functions of the deubiquitinating enzyme and polyglutamine disease protein ataxin-3 are regulated by ubiquitination at lysine 117. Journal of Biological Chemistry 285:39303-39313 250. Toseland CP and Webb MR (2010) Fluorescence tools to measure helicase activity in real time. Methods 51:259-68 251. Trigo FF, Bouhours B, Rostaing P, Papageorgiou G, Corrie JET, Triller A, Ogden D and Marty A (2010) Presynaptic miniature gabaergic currents in developing interneurons. Neuron 66:235-47 252. van Vugt MATM, Gardino AK, Linding R, Ostheimer GJ, Reinhardt HC, Ong S-E, Tan CS, Miao H, Keezer SM, Li J, Pawson T, Lewis TA, Carr SA, Smerdon SJ, Brummelkamp TR and Yaffe MB (2010) A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G2/M DNA damage checkpoint. PLoS Biology 8:e1000287 253. Veiga-Fernandes H, Foster K, Patel A, Coles M and Kioussis D (2010) Visualisation of lymphoid organ development. Methods in Molecular Biology 616:161-79 259. Waite E, Lafont C, Carmignac D, Chauvet N, Coutry N, Christian H, Robinson I, Mollard P and Le Tissier P (2010) Different degrees of somatotroph ablation compromise pituitary growth hormone cell network structure and other pituitary endocrine cell types. Endocrinology 151:234-243 260. Webb EA, Pringle PJ, Robinson ICAF and Hindmarsh PC (2010) Repetitive stimulation of the pituitary with growth-hormone-releasing hormone alters the proportion of 22 and 20 kilodalton human-growth hormone released. International Journal of Pediatric Endocrinology 2010:781317 261. Webb MR (2010) Fluorescent biosensors to investigate helicase activity. Methods in Molecular Biology 587:13-27 262. Wendler F, Gillingham AK, Sinka R, Rosa-Ferreira C, Gordon DE, FranchMarro X, Peden AA, Vincent J-P and Munro S (2010) A genome-wide RNA interference screen identifies two novel components of the metazoan secretory pathway. EMBO Journal 29:304-314 263. Westwood M, Maqsood AR, Solomon M, Whatmore AJ, Davis JRE, Baxter RC, Gevers EF, Robinson ICAF and Clayton PE (2010) The effect of different patterns of growth hormone administration on the IGF axis, somatic and skeletal growth of the dwarf rat. American Journal of Physiology. Endocrinology and Metabolism 298:E467-E476 264. White AJ, Nakamura K, Jenkinson WE, Saini M, Sinclair C, Seddon B, Narendran P, Pfeffer K, Nitta T, Takahama Y, Caamano JH, Lane PJL, Jenkinson EJ and Anderson G (2010) Lymphotoxin signals from positively selected thymocytes regulate the terminal differentiation of medullary thymic epithelial cells. Journal of Immunology 185:4769-4776 254. Veiga-Fernandes H, Kioussis D and Coles M (2010) Natural killer receptors: the burden of a name. Journal of Experimental Medicine 207:269-272 265. Wijchers PJ, Yandim C, Panousopoulou E, Ahmad M, Harker N, Saveliev A, Burgoyne PS and Festenstein R (2010) Sexual dimorphism in mammalian autosomal gene regulation is determined not only by Sry but by sex chromosome complement as well. Developmental Cell 19:477-84 255. Veldhoen M and Duarte JH (2010) The aryl hydrocarbon receptor: fine-tuning the immune-response. Current Opinion in Immunology 22:747-752 266. Wilkinson KA and Wilkinson RJ (2010) Polyfunctional T cells in human tuberculosis. European Journal of Immunology 40:2139-2142 256. Veldhoen M and Seddon B (2010) Empowering T helper 17 cells in autoimmunity. Nature Medicine 16:166-8 Veldhoen M and Stockinger B (2010) Response: Characteristics of IL-17-producing γδ T cells. Immunity 32:2 266. Wiseman FK, Sheppard O, Linehan JM, Brandner S, Tybulewicz VLJ and Fisher EMC (2010) Generation of a panel of antibodies against proteins encoded on human chromosome 21. Journal of Negative Results in Biomedicine 9:7 MRC National Institute for Medical Research 151 Bibliography (cont.) 267. Woehlbier U, Epp C, Hackett F, Blackman MJ and Bujard H (2010) Antibodies against multiple merozoite surface antigens of the human malaria parasite Plasmodium falciparum inhibit parasite maturation and red blood cell invasion. Malaria Journal 9:77 268. Wood R, Liang H, Wu H, Middelkoop K, Oni T, Rangaka MX, Wilkinson RJ, Bekker L-G and Lawn SD (2010) Changing prevalence of tuberculosis infection with increasing age in high-burden townships in South Africa. International Journal of Tuberculosis and Lung Disease 14:406-12 269. Woodward MJ, de Boer J, Heidorn S, Hubank M, Kioussis D, Williams O and Brady HJM (2010) Tnfaip8 is an essential gene for the regulation of glucocorticoidmediated apoptosis of thymocytes. Cell Death and Differentiation 17:316-323 270. Xu Q and Wilkinson D (2010) New molecular connections in angiogenesis. Cell Research 20:980-1 271. Yamauchi Y, Riel JM, Stoytcheva Z, Burgoyne PS and Ward MA (2010) Deficiency in mouse Y chromosome long arm gene complement is associated with sperm DNA damage. Genome Biology 11:R66 272. Yavarian J, Azad TM, Zheng X, Gregory V, Lin YP and Hay A (2010) Amantadine resistance in relation to the evolution of influenza A(H3N2) viruses in Iran. Antiviral Research 88:193-196 273. Yeeles JTP, Gwynn EJ, Webb MR and Dillingham MS (2010) The AddAB helicase-nuclease catalyses rapid and processive DNA unwinding using a single Superfamily 1A motor domain. Nucleic Acids Research Epub ahead of print 274. Zhu D, Jarmin S, Ribeiro A, Prin F, Xie SQ, Sullivan K, Briscoe J, Gould AP, Marelli-Berg FM and Gu Y (2010) Applying an adaptive watershed to the tissue cell quantification during T-cell migration and embryonic development. Methods in Molecular Biology 616:207-28 275. Zimmer C, Lee J, Griveau A, Arber S, Pierani A, Garel S and Guillemot F (2010) Role of Fgf8 signalling in the specification of rostral Cajal-Retzius cells. Development 137:293-302 276. Ziosi M, Baena-López LA, Grifoni D, Froldi F, Pession A, Garoia F, Trotta V, Bellosta P, Cavicchi S and Pession A (2010) dMyc functions downstream of Yorkie to promote the supercompetitive behavior of Hippo pathway mutant cells. PLoS Genetics 6:e1001140 152 MRC National Institute for Medical Research 5 Peter Medawar, OM, CBE, FRS Peter Medawar was the Director of NIMR from 1962-1971. He was the foremost biologist of his generation. Largely through his work a new branch of science was created – the immunology of transplantation. He was also a philosopher, a humanist and humanitarian – in short, a rounded scholar – and a gifted science communicator. The inaugural Medawar Lecture was held on 26 May 2010. NIMR’s PhD students chose and hosted the speaker, Tom Jessell. MRC National Institute for Medical Research 153 NIMROD NIMROD is the NIMR social club. Membership is open to all staff for a very small annual subscription. A number of functions are organised throughout the year, including quiz nights, live music, barbecues, ceilidhs and discos. The NIMROD bar is open Monday to Friday evenings and provides a relaxed atmosphere in which to meet colleagues. The club also organises a wide range of sporting activities and tournaments. These include football, volleyball, tennis, netball, running, snooker, pool, table football, table tennis and darts. In addition, a number of smaller clubs exist within NIMROD, including: • Hillwalking - regular excursions in the UK and abroad • Magazine club - allows sharing of club purchased magazines • Drama - NIMDram regularly stages performances • Gardening - exchanging knowledge and hosting an annual summer sale • Book club – roughly monthly meetings 154 MRC National Institute for Medical Research MRC National Institute for Medical Research 155 MRC National Institute for Medical Research The Ridgeway Mill Hill London NW7 1AA Tel +44 (0)20 8959 3666 Fax +44 (0)20 8816 2041 MRC NIMR location map A1 North to M25, Heathrow and Stansted Airports od Hi London La ay ew ers MRC National Institute for Medical Research dg Ri rd W ay The Ri dgew M25 A1 Bit t a cy ll Hi Mill Hill East Dollis R M1 J2 d Lan W atfo Hendon rd W ay ll R oa H ale N La n ass B a r ne t B y p Mill Hill Broadway ThamesLink to Central London via King’s Cross Daws e Mill Hill Broadway ay A5100 e M25 NIMR ll e Th W at fo A41 to Central London e ne A5109 an Marsh L A1 M25 H a mm B a r n e t Way Hi gh wo M1 A598 Finchley Central A5000 Northern Line to Central London e rs Hi A1 oad H ol d Bus number 240 connects NIMR to both Mill Hill East and Mill Hill Broadway stations. Trains run from Mill Hill East station on the Northern Line into central London. Main line trains run from Mill Hill Broadway station to Luton Airport, Gatwick Airport and St Pancras station in central London.The M1, M25 and North Circular Road are within easy reach of NIMR. On-site parking is available at NIMR. 156 MRC National Institute for Medical Research
Similar documents
MRC National Institute for Medical Research
http://www.nimr.mrc.ac.uk Copies obtainable from the Librarian at NIMR ISBN-13:
More information