MRC National Institute for Medical Research
Transcription
MRC National Institute for Medical Research
MRC National Institute for Medical Research 2009/2010 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 the internet at: http://www.nimr.mrc.ac.uk Copies obtainable from the Librarian at NIMR ISBN-13: 2 MRC National Institute for Medical Research 978-0-9546302-7-0 Contents Director’s foreword NIMR scientific highlights 2009 Science overview About the MRC National Institute for Medical Research Recent research highlights NIMR history and milestones Special topic review: Protein structure and infectious disease Student training and development Training and careers Public engagement Research groups : A to Z list Infections and Immunity Structural Biology Neurosciences Genetics and Development Emeritus scientists Scientific facilities Technology transfer In memoriam Sixty years of Immunology at NIMR Major funding sources Scientific seminars Staff honours PhD theses awarded 2009 Bibliography NIMROD social club Map, location and travel 4 6 8 10 11 12 14 16 20 24 28 30 57 73 88 101 103 120 123 124 130 131 132 134 135 146 148 MRC National Institute for Medical Research 3 Director’s foreword This 2009/10 Annual Report and Prospectus is published shortly after the end of my first year as Director of the MRC National Institute for Medical Research. The year has gone well, with some excellent new recruits, honours for our existing Programme Leaders, new equipment and infrastructure, and some welcome news about the UK Centre for Medical Research and Innovation. We also say farewell to some of our Programme Leaders and their research teams. New Programme Leader Track recruits include Pavel Tolar, who comes to us from the National Institute of Allergy and Infectious Diseases at the NIH and works on the activation of immune receptors; Andreas Wack, who did his PhD at NIMR with Dimitris Kioussis before going to the Novartis Immunobiological Research Institute in Siena to study influenza infection and vaccination against it; and John Offer from the Biochemistry Department in Oxford who is developing novel techniques to build biological macromolecules. More recently, Greg Elgar has joined us from Queen Mary University of London, and Mike Gilchrist has arrived from the Gurdon Institute in Cambridge. Both bring expertise in bioinformatics and computational biology to the study of early embryonic development, and their arrival complements our investment in high-throughput sequencing (see below). Finally, we are delighted that Troy Margrie has joined us as a Programme Leader from the Department of Neuroscience, Physiology and Pharmacology at University College London. Troy uses a multidisciplinary approach, including two-photon targeted patching, to ask how the brain integrates neuronal activities to encode a sensory stimulus. We were very pleased that he recently received the Friedrich Wilhelm Bessel Research Award as well as the Buckston Browne Prize of the Harveian Society. The research programmes of all these new colleagues are outlined in more detail later in this report. Troy was not the only Programme Leader to be recognised during the course of the year. We were all delighted that Dimitris Kioussis was elected a Fellow of the Royal Society and everyone enjoyed the party at which some of his friends and former colleagues sent videoed messages of congratulation. As well as this success, François Guillemot was elected a Fellow of the Academy of Medical Sciences and Anne O’Garra and Steve Smerdon became members of EMBO. Finally, Douglas Young was awarded the Gardner Middlebrook Award for contributions to Mycobacteriology, one of Tim Mohun’s images received a Wellcome Image Award and Gitta Stockinger’s paper on Th17 was named a citation classic in immunology. Congratulations to all. The year has also seen an expansion in our core facilities, not least with the purchase of an Illumina GAIIx highLeft to right: Dimitris Kioussis, FRS with Anne O’Garra,FRS and Jim Smith, FRS throughput sequencing machine, which is soon to be joined by a HiSeq 2000 sequencing system. The ability to carry out high-throughput sequencing will allow NIMR scientists to adopt new approaches in coming to understand the regulation of gene expression and the definition of genetic regulatory networks. Towards the end of 2009 we also took delivery of an Orbitrap mass spectrometer, and this will revolutionise our analyses of protein structure and function. This has been a busy year for everyone involved in the UK Centre for Medical Research and Innovation (UKCMRI), and especially for everyone in the workgroups dedicated to planning the new labs. The building design is taking shape and with some more hard work we should submit a planning application during the summer. We were encouraged when Prime Minister Gordon Brown, along with Lord Mandelson (Business and Skills Minister), Andy Burnham (Minister for Health) and Lord Drayson (Minister for Science) visited the UKCMRI offices to confirm £250m of government funding for the UKCMRI project. This represents a very important step towards realisation of the project. 4 MRC National Institute for Medical Research Left to right: Jim Smith, Sir David Cooksey, Sir Paul Nurse, Sir Mark Walport and Gordon Brown looking at a model of the design for the UKCMRI building And finally, departures. We were very sad that Iain Robinson took early retirement from NIMR towards the end of 2009. Iain’s contributions to NIMR have been immense, both scientifically and administratively. He worked tirelessly for the Institute in the planning of UKCMRI, and served as interim Director before my arrival at the beginning of 2009. An incoming Director could not have wished for a wiser or more generous advisor and friend, and I am enormously grateful to him. As well as Iain, Nigel Birdsall and Steve Sedgwick retired last year, Ken Raj left to join the Radiation Effects department at the Health Protection Agency’s Centre for Radiation, Chemical and Environmental Hazards and Claudia Veigel left to go to the Institute of Physiology at Ludwig Maximilians University, Munich. We wish them all well. We also said farewell to Alan Hay, who for many years was Director of the World Influenza Centre, one of the five World Health Organization (WHO) Collaborating Centres for Reference and Research on Influenza. As I describe in our scientific highlights, Alan and his team did sterling work during the 2009 swine flu pandemic, and he and new Director John McCauley dealt with the science and with the media frenzy with equal aplomb. Saddest of all, I must report the death of John Eccleston, who also retired from NIMR last year. John had worked at NIMR in the Division of Physical Biochemistry since 1984. His fluorescence stopped-flow work was world-class, and his mastery of physics, biology and chemistry was a perfect combination for a multidisciplinary institute like NIMR. John met his wife, Sally, while she was a PhD student at NIMR, and we send her our deepest sympathy. An appreciation of John by his colleagues Justin Molloy, Steve Martin and David Trentham is on page 123. MRC National Institute for Medical Research 5 Scientific highlights 2009 As home of the WHO World Influenza Centre, now directed by John McCauley, NIMR was frequently in the news during 2009. Samples of the swine-like human influenza A H1N1 were received at NIMR from around the world, and were subjected to detailed nucleic acid sequence analysis, thereby monitoring potential changes in its sensitivity to antiviral agents such as Tamiflu and Relenza. In particular, we knew from work by Steve Gamblin and colleagues (highlighted in last year’s report) that a particular mutation in the influenza surface glycoprotein would render the virus resistant to Tamiflu but still sensitive to Relenza. In the event, only a few Tamiflu-resistant samples were identified, and although the H1N1 virus spread more rapidly than expected, it was less virulent, and there were fewer deaths than feared. Nevertheless, the events of last year show clearly the importance of the work of the NIMR World Influenza Centre in monitoring influenza outbreaks and advising the Government on the best way to contain them. Of course, there have been many other scientific highlights, and like last year I will mention one or two achievements from each of the four main scientific areas of NIMR. Thus, to continue the infections theme, George Kassiotis and Dimitris Kioussis have studied how depletion of activated CD4+T cells, the targets of immunodeficiency virus replication, affects the mouse immune system. Their work suggests that the generalised immune activation caused by HIV infection may have the same origin as immune deficiency. By targeting this subset of CD4+ T cells, HIV could achieve both immune deficiency and activation without having to rely on other microbes to activate the immune response. The Nbs1 N-terminal regulatory region Cell periphery with Weibel Palade bodies Structural biologists at NIMR interact with all areas of the Institute and shed light on many aspects of biology. Using electron cryomicroscopy, Peter Rosenthal has directly imaged assemblies of the von Willebrand Factor in endothelial cells, working with Tom Carter and Matthew Hannah, while Steve Smerdon has used X-ray crystallography to reveal the structure of Nbs1, a protein that plays important roles in the DNA-damage response. 6 MRC National Institute for Medical Research In the area of developmental biology, several of the groups at NIMR, including those of Smith and Briscoe, are interested in the way in which morphogen gradients specify cell type within the developing embryo. One of the problems has long been one of precision: how can a simple gradient specify sharp boundaries between different regions of the embryo? Work in Jean-Paul Vincent’s group has shown that this occurs when cells produce secondary inhibitory signals that modulate each other’s response to the morphogen in such a way that interpretation of the gradients becomes more precise. These results, and many others, are described in more detail in the rest of this report. The response to Wg signaling is modulated by inhibitory interactions between 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 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 cryo-EM of vitrified endothelial cells. Proceedings of the National Academy of Sciences of the United States of America 106:17407-17412 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 Piddini E and Vincent J-P (2009) Interpretation of the Wingless gradient requires signaling-induced self-inhibition. Cell 136:296-307 MRC National Institute for Medical Research 7 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 auto-immunity. Auto-immunity 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 how diverse cell types and tissues 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 interactions that control developmental processes. Many of our studies focus 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 inform understanding of normal development and how defects can arise. Since many of the same processes and underlying molecular pathways are also utilised in the adult, studies of development also uncover 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. 8 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 9 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. It has three main objectives: 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, and 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, which include 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? Sixty years at Mill Hill 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? 10 MRC National Institute for Medical Research In 2010 NIMR is celebrating the 60th anniversary of opening at its present site at Mill Hill. The building was officially opened on 5th May 1950 by King George VIth and Queen Elizabeth. This year’s celebrations will begin on 5th May 2010, when NIMR hosts a meeting of the MRC Council. There will be an exhibition of NIMR science and history. Recent research highlights 2009 • • • • • 2008 • • • • • 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) 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) • • Determination of the structure and receptor binding properties of the 1918 influenza haemagglutinin (John Skehel and Steve Gamblin) Role of SOX3 in pituitary development (Iain Robinson and Robin Lovell-Badge) 2003 • Repair of spinal cord injuries by cell transplantation (Geoff Raisman) 2000 • Description of naturally occurring, post-entry, pre-integration restriction factors for retroviruses in human cells (Jonathan Stoye) 2004 MRC National Institute for Medical Research 11 NIMR history and notable milestones NIMR was the first research institute established by the MRC. Its origins go back to 1914 but it was fully established at Hampstead in 1920 under the Directorship of Sir Henry Dale. It moved to its present site in Mill Hill in 1950. 12 1920-1939 Discovery of the human influenza virus (C. Andrewes, W. Smith and P. Laidlaw) Discovery of the neuro-transmitter, acetylcholine (H. Dale) 1940-1959 Development of liquid and gas chromatography (A.J.P. Martin) World Influenza Centre established Low-temperature preservation of cells (A. Smith, C. Polge and A. Parkes) Studies of antibody structure (R.R. Porter) Steroid biosynthesis (J.W. Cornforth) Human physiology in extreme conditions, including advice to the Everest expedition (L.G.C.E. Pugh) Discovery of interferon (A. Isaacs) 1960-1979 Lymphocytes of different types co-operate in the immune system (N. Mitchison) Explanation of long-term potentiation (T. Bliss) Recombination of avian and human influenza viruses involved in pandemic influenza (H.G. Pereira) Determination of the structure of adenovirus using electron microscopy (R.C. Valentine) Discovery of interferon induced nuclease activating oligonucleotide (I. Kerr) 1980-1999 Biomedical NMR Centre established Structure of influenza haemagglutinin (J.J. Skehel) Discovery of locus control region of globin gene expression (F. Grosveld) Definition of protein nuclear location signals (A.E. Smith) Description of control sequences responsible for co-ordinated expression in yeast cell cycle of enzyme involved in DNA synthesis (L. Johnston) Discovery of interleukin 5 (C. Sanderson) Discovery that cytotoxic lymphocytes recognise antigens which are not normal surface membrane components (A. Townsend) Conservation of organisation and expression of mouse and Drosophila homeobox genes (R. Krumlauf) Discovery of mesoderm inducing factors in Xenopus embryos (J.C. Smith) Description of a novel mechanism of protein biosynthesis in mycobacteria (J. Colston, E. Davis and S. Sedgwick) Primary structure of the Herpes saimiri genome (R. Honess) Discovery of the sex determining gene (R. Lovell-Badge) Discovery of the first virus ion channel (A.J. Hay) Discovery that a locus control region is capable of preventing position effect variegation in T-cell development (R. Festenstein & D. Kioussis) Discovery of the anterior organising centre in mice (R. Beddington) Identification and mapping of plastid in apicomplexan parasites (I. Wilson and D. Williamson) Development of mammalian enteric nervous system (V. Pachnis) Role of ephrins in cell patterning and positioning in nervous system development (D. Wilkinson) Developmental diseases of pituitary gland (M. Dattani) MRC National Institute for Medical Research Five members of the Institute have gained Nobel prizes: Henry Dale discovered the important neuro-transmitter acetylcholine Archer Martin invented paper and gas chromatography Rodney Porter was a pioneer in understanding the chemistry of antibodies John Cornforth made key discoveries in understanding how steroids are made Peter Medawar discovered how transplanted organs are rejected because of attacks by white blood cells that can recognise foreign cells Henry Dale Archer Martin Rodney Porter John Cornforth Peter Medawar The Jeantet prize has been awarded to three NIMR scientists: Robin Lovell-Badge for work on sex determination John Skehel for research on influenza Frank Grosveld for work on the control of haemoglobin in blood cells Robin Lovell-Badge John Skehel Frank Grosveld MRC National Institute for Medical Research 13 Special topic review: Protein structure and infectious disease at NIMR Each NIMR Report will feature a review of an important area of research at NIMR.This year’s review focuses on protein structure and infectious disease, written by Ian Taylor and Jonathan Stoye The study of infectious diseases is fundamental to the MRC mission and has been at the heart of research carried out at NIMR since its foundation. The marriage of structural biology with research into infectious disease has been key to several notable discoveries made at the Institute. Some examples include: the application of electron microscopy to the elucidation of the structure of adenovirus; the use of NMR methods to investigate the binding specificity of antifolate drugs to bacterial dihydrofolate reductase; structural analyses of influenza A haemagglutinin proteins; and the use of analytical ultracentrifugation to analyse the oligomeric state of viral proteins. The arrival of high-field NMR and protein X-ray crystallography at the Institute in the early 1990s, and cryo-electron microscopy in 2004, have further cemented this synergy. The three research Divisions that presently constitute infectious disease research at NIMR (Virology, Mycobacterial Research and Parasitology) each include programmes that incorporate collaborations with structural biologists, and significant breakthroughs have been made in the fields covered by each Division. There are numerous examples but highlights include the elucidation of the structures of Mycobacterium tuberculosis NusB and NusA proteins, that has advanced the understanding of how this pathogen regulates rRNA synthesis. Further work with M. tuberculosis phospho-threonine binding domains employing both X-ray crystallography and high-resolution NMR spectroscopy has shed light on phosphodependent metabolic signalling in this pathogen (Fig 1). Both sets of studies have important implications for the potential design of novel therapeutic strategies for combating M. tuberculosis. In the Division of Virology, a wealth of structural data concerning the influenza virus surface proteins, haemagglutinin and neuraminidase has contributed to the understanding of influenza cross-species transmission and drug resistance. This information has important ramifications for decisions concerning the stockpiling of anti-influenza drugs. Moreover, the determination of X-ray structures of retroviral capsid proteins combined with cryo- 14 MRC National Institute for Medical Research (Fig 1) The phosphorylated FHA domain from Rv1827, the major downstream target for the M. tb signalling kinase, pknB electron microscopy (Fig 2) has been crucial to understanding the process of capsid assembly and disassembly and will be essential to understanding the interactions of the virus with natural host-cell anti-viral factors. Similar studies of retroviral structural proteins may help guide the design of effective vaccines directed against HIV-1. In the Division of Parasitology, much research is focused on the merozoite surface protein 1 (MSP1). This protein is the target of antibodies that prevent red blood cell invasion and is a leading candidate for use in the development of immunisation strategies for controlling malaria. The determination of the solution structure of MSP1 from the two major human malaria parasites, Plasmodium falciparum and P. vivax (Fig 3) and the subsequent elucidation of antibody and drug binding sites has been critical for structural biology work designed to facilitate development of such a malaria vaccine. (Fig 3) The merozoite surface protein Msp1 from Plasmodium vivax, a major target for the development of a malarial vaccine (Fig 2) Structures of retroviral capsid assemblies. Cryo-electron micrograph of in vitro assembled capsid, inset capsid monomers (i) pack into hexameric discs (ii) that associate to generate a capsid assembly (iii) These recent and current studies in general have been directed towards molecules in the pathogen that are likely to make good drug targets. However, in the near future, as a wealth of genomic, proteomic and interacteromic information becomes available, the detailed understanding of many host cell-pathogen interactions will become paramount in the fight against existing and emerging diseases. New methods from live cell imaging through visualisation of cellular ultrastructure and high-throughput molecular structure determination, single molecule manipulation and rational drug design will complement older techniques of epidemiology and physiology. It is apparent that the integration of structural biology and infectious disease research is well placed to form the vanguard of this research and what used to be proudly heralded as a science that went from genes to structures in the late eighties can confidently be rebranded as one that goes from molecules to medicines in the early 21st century. 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 Studentships There are over 80 PhD students at NIMR, approximately 80% of whom are funded through the MRC Doctoral Training Account and 20% through a variety of other studentships and progammes. All of our students have access to a wide range of state-of-the-art facilities and the extensive expertise of institute staff, and combined with a programme of internal and external workshops, courses and seminars, our students complete their PhDs with the biomedical research training and transferable skills necessary for a successful career. Donna Brown Director of Studies We recognise the importance of student support and in addition to NIMR supervisors, who do not have the teaching commitments that are often associated with universities, each student has a thesis committee comprising their head of division and two programme leaders. The purpose of the thesis committee is to ensure the student receives all of the academic support and guidance needed for the duration of the PhD. Also on hand are the Director of Studies, Student Administrator and the Student Representatives. The significance of this level of support is reflected in our improving four-year completion rates which are higher than most universities. We believe in a good work-life balance and we encourage our students to remember there is a world outside of the lab. Many of our students take the opportunity to catch up with their colleagues in the onsite licensed bar, restaurant or games room. The TV room offers a little more solitude and for those with get-up and go there are many social activities and sports teams organised through the NIMROD social club. Three on-site student cottages make the commute to work virtually non-existent. During the 2009/10 academic year, by request of the students, we are introducing a careers forum and a tools and techniques study programme, and later in the year we expect to run new internal courses on statistics, bioinformatics and microscopy. 16 MRC National Institute for Medical Research STUDENT TRAINING AND DEVELOPMENT PhD students 2009 in their own words Chris Toseland NIMR is a fantastic place to do research, learn and socialise. I was attracted to NIMR due to its excellent reputation and the diversity of its research, not to mention the countryside views and London location. My PhD has focused upon the mechanism by which DNA helicases catalyse DNA unwinding during replication and repair. Since being here, I have found that whenever I need advice there are always many postdocs and Group Leaders more than willing to help. This made my PhD more enjoyable and helped me to advance faster. It is even possible to set up new collaborations and find a job while playing sports or enjoying a drink. The excellent resources and supportive environment gives a great start to a research career. No matter where you come from, or go to, the atmosphere at NIMR will never be forgotten. Valentina Sasselli I started at NIMR almost three years ago, when I decided to pursue a PhD in developmental biology. At the time I knew what I wanted to study, no matter where and no matter how. It did not take long to realize that NIMR was the perfect place. At the Institute there is a sincere dedication to science with collaborations between laboratories and divisions. There are many facilities which make experiments technically possible and quickly feasible, and, more importantly, there are great people with great ideas which help to keep motivation high! In such an environment, my PhD life has been enjoyable and rewarding. Now, in my final year, I am planning to present my work at international conferences (thanks also to the MRC-NIMR travel prize), to finalise my thesis and, hopefully, to find my way in science, keeping in mind that, after all, the where and how do make a difference. Student Representatives There is a strong sense of community amongst the students at NIMR and this actively encourages collaboration between different departments allowing students to take up multi-disciplinary projects. Regular student seminars allow us to present our work without the pressure of supervisors or colleagues from our Division being present. With regular student socials and sporting activities, it’s easy to meet up and make new friends. With an intake of around 25 new students per year, the student body are an integral part of the Institute and as Student Reps we aim to maintain a high standard of communication between staff and the 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 2009 Student Representatives Andrea Rueker, Claire Hastings and Lasse Stach MRC National Institute for Medical Research 17 STUDENT TRAINING AND DEVELOPMENT Sandwich placements and work experience Sandwich Placements NIMR sandwich placements provide students an excellent oportunity to apply the lab skills they have learnt during the first couple of years at university. As you will see from the testimonials, sandwich students come to the Institute because of the diversity of science and to get a feel of whether research is really for them. A 12 month sandwich placement equips many of the students with the experience and expertise they need to secure a PhD studentship at NIMR or other leading research institution. We currently have 15 sandwich students and with over 350 applications received this year it is clear that the popularity of our sandwich placements is growing. 2009 Sandwich students in their own words Caroline Morris I chose to apply for a sandwich placement at NIMR after reading about the variety of projects available to students and the work conducted at the Institute. My placement was within the Division of Physical Biochemistry, working on the mechanism of interaction between single-stranded DNA binding protein from E. coli (SSB) with single-stranded DNA. Overall I was very pleased with my placement year – I thoroughly enjoyed the work I conducted, and all the people I worked with were friendly and helpful. I learned many new techniques that I have already been able to put into practice during my final year at university, which I feel demonstrates the value of a sandwich placement. After my degree I hope to study for a PhD, which I was able to decide upon after the year in the lab. I would highly recommend a sandwich placement at the Institute. Since returning to university Caroline has successfully interviewed for a PhD studentship at NIMR which will commence September 2010. Nathan Sweeny My sandwich placement at NIMR was an excellent experience and helped me to confirm my desire to start a PhD next year. I applied to NIMR because the Institute is large and well known for its excellence in biomedical research. My project was with Dr R. Buxton on transcriptional regulation in Mycobacterium tuberculosis. I enjoyed my project and the independence of my lab work. Most importantly, this year has provided me with excellent experience in molecular biology which will be useful for any research I undertake in the future. I lived in the student cottages available onsite which are excellent for meeting other students and provide a sociable atmosphere. I recommend the NIMR sandwich placement scheme to anyone considering a PhD in biological sciences. Vasja Urbancic NIMR was a great place to do a placement. Working on my project in zebrafish development, I learned and used a diverse range of techniques (molecular biology to confocal microscopy, cell culture to biochemistry), many of which I will use again in my final year or afterwards during a PhD. The multitude of talks and seminars by NIMR scientists and invited speakers provided a good opportunity to extend my knowledge into diverse areas of biomedical research, and I even got to attend an international symposium on developmental biology held in London! NIMR is a pleasant place to work: there is a friendly atmosphere, people from across different Divisions were always happy to help, and its present location is fantastic: a beautiful countryside setting, yet so close to central London. Living in the onsite cottages with other newcomers made it easy to make friends, and I thoroughly enjoyed the trips with the hill-walking club, too. If you are considering coming to NIMR, I would warmly recommend it. 18 MRC National Institute for Medical Research STUDENT TRAINING AND DEVELOPMENT 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 NIMR’s Research Summer School on page 24]. A clear indication of the success of the research summer school is the number of students who apply to the Institute for one of our sandwich placements and/or 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’s like to work in science. The 2009 intake of postgraduate research students MRC National Institute for Medical Research 19 TRAINING AND CAREERS Career development at NIMR 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 steps 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. NIMR hosts 226 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. 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. James Briscoe Developmental Neurobiology The career track system at NIMR was a great way to make the transition from postdoctoral fellow to group leader. I had funding for two researchers, a technician and my salary, together with consumable expenses and access to all the facilities at the Institute. I was able to start my research straight away without having to write grants. This, and the low administrative burden, gave me the maximum amount of time and energy to concentrate on research. The collegiate and collaborative culture of the Institute was also an enormous benefit. It offered the mentoring and encouragement necessary to launch an independent research programme and the support to keep it going. Katrin Rittinger Molecular Structure I initially came to NIMR as a postdoc and was immediately impressed by the open and highly collaborative atmosphere and the willingness of everybody to share equipment and knowledge. So when it came to taking the next step in my scientific career, I had no doubts that NIMR would be an ideal place to start my own group, not only because of this collaborative atmosphere but also because of the diversity of research carried out and the wide range of expertise available. The combination of these factors creates an ideal environment to develop an independent research programme that incorporates multiple approaches and techniques that otherwise may be too difficult to get going at this stage in one’s career. Collaborations across disciplines are actively encouraged, for example in the form of student or postdoc positions that are held jointly between different Divisions. Coming from a country where the scientific system has been much more hierarchical, I was also very attracted by the fact that at NIMR, career track positions are truly independent and that resources are available to everybody on an equal and purely scientific basis. 20 MRC National Institute for Medical Research TRAINING AND CAREERS Andreas Wack Immunoregulation I moved back to NIMR after ten years spent in an industrial research centre in Italy. Prior to that, I had done my PhD with Dimitris Kioussis here in the Institute. A common theme of NIMR is the spirit of collaboration, the fact that you can go to anyone’s office or lab (or bar table) and come up with ideas or ask for advice, and this was also for me one of the best features of this place. The chance to come back to NIMR was therefore a great opportunity. Ten years later, I found that this spirit is still wide awake, carried on by many of the old familiar faces and many new ones who have joined in. The differences between industry and academia are less than you might think. In both environments you develop scientific questions, plan a sequence of experiments and critically appraise results. The range or depth of questions asked and the hypotheses put forward tend to differ between industry and academia but can also vary a lot within both areas. The two biggest differences are the speed of change and the group size of researchers working on a specific question. In a company, decisions on the research direction are often dictated by changes in the market place, which can be fast, and your favourite research subject may be culled in a board room with little prior notice and little possibility to influence this decision, as it is driven by factors outside the researcher’s control. 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. The biggest difference for me was the team size: when companies throw many people at important projects, it can easily happen that 30 to 50 specialists tackle the same question from different angles. This makes decision-making complex and often slow, reduces the degree of identification of research staff with their project, and also means that the fun part of putting together all the pieces is reserved to only a few people. The advantage is that the technical expertise brought to the project is very high. Getting used to presenting data from colleagues, and handing over your own data to others, is an excellent exercise for big egos to be reminded of the importance of the team effort. Academia often presents the extreme opposite. One PhD student or post doc will work on one project with a very high degree of identification and personal involvement, but there is a tendency for the wheel to be frequently reinvented because of a constant loss of expertise through student and post-doc turnover. As I am mentally still in the transition phase, I currently think that doing research most efficiently requires probably a mix between the two approaches, with medium-size groups of people with different scientific backgrounds sharing in full a project. However, the fact that career and funding depend so much on authorship questions and senior responsibility certainly does not facilitate such an approach. The way it worked for me to preserve the possibility of a return to academia was simply to keep publishing and to 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 am very happy to have made the step back from one camp to the other. MRC National Institute for Medical Research 21 TRAINING AND CAREERS Research support careers Although there is no formal career structure for research support staff, there are regular opportunities for research technicians and occasional openings for research support managers. Nick Clark describes his career as Lab Manager I started at the Institute in 1972 as a Junior Technical Officer in the lab of Dr John Humphrey, Head of the Division of Immunology. For several years I worked in this and other labs in the Immunology Division, acquiring the necessary skills to provide technical expertise to the projects in hand. Equipment maintenance and laboratory upkeep were considered an essential part of the role of technical staff, and I found myself increasingly involved in the technical management of the Division, and deputising for the Head Technician, so much so that when in 1985 the post became vacant it was offered to me, and I readily accepted it. Since then I have been the Laboratory Manager for the Immunology Divisions and, for a period, the Division of Virology. The ultimate aim of my job is to enable the smooth running of the Divisions, ensuring that the work is not hampered by lack of resources. This is achieved through a good knowledge of the excellent resources and procedures within the Institute, the overseeing of maintenance, budget monitoring, coordination with service providers, both internal and external, and cooperation with my fellow Laboratory Managers, working closely as a team. It is a largely reactive role, occasionally stressful and frustrating, but hugely rewarding and enjoyable in its variety and sense of achievement. Vicky Millins describes her route to becoming a Lab Manager Most of my seven-year career at NIMR has been as a Research Technician in Parasitology, where the role morphed from a general technician to a more specialised one where I managed all the mouse lines for the lab. This gave me a high degree of autonomy, which I enjoyed. I outgrew the position and sought new challenges, and when I saw a number of Laboratory Manager posts become available, I applied. I was very happy to be appointed Laboratory Manager for the Divisions of Developmental Biology and of Molecular Neurobiology, as they are very genetic-based which is where my scientific ‘heart’ is. The job I do now is a varied one, full of challenge and I recommend it to those who like plenty of variety and a strong amount of interaction day-to-day with many people. Yan Gu explains his role as a specialist support manager Trained as a physicist, I have been involved in the biological imaging field since my first postdoc position. Becoming the manager of a microscope facility in a biomedical institute was one of the most risky decisions I have ever made. The decision to leave a welldefined physics lab wasn’t meant to be a career change, but rather a research environment change. I still believe that the most effective way to do the biological imaging is to do it with biologists. For similar reasons I joined NIMR, where the collaborative atmosphere and positive attitude towards new techniques were very attractive. Microscopy is a multi-disciplinary technique which requires comprehensive background knowledge. No routine procedures can be universally applied to all experiments. Imaging design varies with the experiment, the microscope and image processing requirements. This requires the support staff to have a high level of scientific training and research quality. The rapidly evolving imaging technology over the last decade has been stimulating the development of biology, which in return demands ever more technological innovations. Being the introducers of these fast advancing techniques, we need to constantly refresh ourselves with new knowledge through research. The Confocal Imaging and Analysis Lab will only be able to meet the ever-increasing demands from cutting edge biology if we can provide quick troubleshooting and effective microscope maintenance. Such pressure means that we work on two fronts: routine support and technological development. This allows us to provide maximum benefit to NIMR research. 22 MRC National Institute for Medical Research TRAINING AND CAREERS Alan Palmer describes the support for careers in 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 to attend workshops and seminars held on a regular basis on a variety of laboratory animal science related subjects. Visits to other scientific establishments, symposiums 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 23 SCIENCE AND SOCIETY Public engagement activities Human Biology Essay Competition 2009 Once again NIMR’s school essay competition, now in its seventh year, drew a large number of commendable essays. At a time when 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 one day at NIMR seeing visually appealing projects. The two best essays were published in the 2009 Mill Hill Essays. Research Summer School In 2009 NIMR was host to 18 students, drawn from 13 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 a poster and report of their work, to be shown at events organised by the Nuffield Foundation. These reach a very high standard and this year, as on many previous occasions, some of them were awarded prizes for their presentations at the Exscitec Science and Engineering Fair. Teachers report that Nuffield Bursary Holders are an inspiring example to the next generation at their schools. Some of our former students are starting careers in research having emerged from university with First-class degrees. The University of the Third Age (U3A) at NIMR In November 2009 NIMR hosted the seventh national meeting of the science section of the U3A. This is a self-managed organisation for retired persons with a scholarly bent who are prepared to travel quite long distances to hear presentations that interest them. This year the theme was “Making an embryo from the fertilised egg” at which the Director, Jim Smith, and David Wilkinson spoke. Once again, we had a capacity crowd of nearly 150 enthusiasts, keen to understand new approaches to biomedicine. 24 MRC National Institute for Medical Research SCIENCE AND SOCIETY Annual Schools Days (February 10th and 11th, 2010) Students in Year 12 are invited to an event designed to enrich their experience of the life sciences. We have a programme of talks based on an important theme; this year “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. Researchers in residence and Ambassadors for science Young scientists from NIMR participate in these two schemes. Workshops at NIMR have been developed by our staff on “DNA analysis in forensic science”. Others have participated in teaching of the regular curriculum in secondary schools under the guidance of a teacher on a regular basis over one term. MRC National Institute for Medical Research 25 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) Victor Newsome, Corner of a bathroom, mixed media 1975, (right) Liz Pannett, 14.1.79-8.80, mixed media 1980 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/millhillessays/archive/ 26 MRC National Institute for Medical Research This image was produced by Tim Mohun, working with Mike Bennett, in NIMR’s Division of Developmental Biology. The animation from which this still was taken received a Special Award in the Wellcome Image Awards 2009. It shows the intricate structure of a mouse head during development, and was produced using a new imaging technique called high-resolution episcopic microscopy (HREM), which enables accurate three-dimensional reconstruction at very high levels of detail. MRC National Institute for Medical Research 27 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 Sebastien Gagneux Steve Gamblin Mike Gilchrist Richard Goldstein Alex Gould François Guillemot Matthew Hannah Alan Hay 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 28 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 host-parasite interactions of severe malaria infections 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 Cell fate specification in the mammalian brain Secretory vesicle formation in human endothelial cells Influenza virus – vaccines and drugs 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 Immunology and immunopathogenesis of malaria infections Control of prolactin and growth hormone cell differentiation and function Regulation of immune responses by NF-k bB 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 behaviour Heart development in vertebrates Single molecule studies of cell motility and cell signalling MRC National Institute for Medical Research Elke Ober John Offer Anne O’Garra Vassilis Pachnis Annalisa Pastore Alexandre Potocnik Kenneth Raj Andres Ramos Katrin Rittinger Iain Robinson Peter Rosenthal Iris Salecker Benedict Seddon Steve Sedgwick Steve Smerdon Jim Smith Gitta Stockinger Jonathan Stoye Ian Taylor Willie Taylor Pavel Tolar James Turner Victor Tybulewicz Claudia Veigel Jean-Paul Vincent Andreas Wack Martin Webb David Wilkinson Robert Wilkinson Douglas Young Lyle Zimmerman Liver development in zebrafish 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 Life cycle and persistence of human papillomavirus Molecular recognition in post-transcriptional regulation Structural biology of signalling networks that regulate innate and adaptive immunity The neuroendocrine cascade of growth Cryomicroscopy of proteins, viruses and cells Axon guidance in the developing visual system of Drosophila Regulation of T cell homeostasis by antigen receptor signals and interleukin-7 Regulation of mitosis Structural biology of phosphorylation-dependent signalling pathways in the cellcycle and the response to DNA damage 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 Activation of immune receptors X chromosome inactivation, meiotic silencing and infertility Signal transduction in B and T cells Single molecule mechanics of motor proteins Cell biological basis of patterning and homeostasis in developing epithelia Immune response to influenza The molecular mechanisms of motor proteins Regulation of boundary formation and neurogenesis Steroid regulated immune responses in tuberculosis Mycobacterium tuberculosis and the host response Using frog genetics to understand vertebrate development and disease MRC National Institute for Medical Research 29 Infections and Immunity Immune Cell Biology Immunoregulation Molecular Immunology Mycobacterial Research Parasitology Virology Victor Tybulewicz (Head of Division) Steve Ley Benedict Seddon Pavel Tolar Anne O’Garra (Head of Division) George Kassiotis Andreas Wack Dimitris Kioussis (Head of Division) Alexandre Potocnik Gitta Stockinger Douglas Young (Head of Division) Elaine Davis Sebastien Gagneux Robert Wilkinson Tony Holder (Head of Division) Michael Blackman Delmiro Fernandez-Reyes Jean Langhorne Jonathan Stoye (Head of Division) Kate Bishop John Doorbar Alan Hay John McCauley Kenneth Raj WHO Collaborating Centre for Reference and Research on Influenza (WIC) see also the following groups, all in Structural Biology: Steve Gamblin Richard Goldstein Andres Ramos Katrin Rittinger Peter Rosenthal Steve Smerdon Ian Taylor 30 MRC National Institute for Medical Research 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. The latest figures report that 33 million people globally are living with HIV/AIDS. In 2006, a novel retrovirus called xenotropic murine leukaemia virus-related virus (XMRV) was isolated from patients with familial prostate cancer. Prostate cancer is the most prevalent cancer amongst men in the UK, and hereditary prostate cancer is thought to account for 9-15% of cases. More recently, XMRV has been identified in patients with chronic fatigue syndrome. At this time, it is not known whether these diseases are associated with XMRV. One area of our research is to investigate the link between XMRV and prostate cancer and chronic fatigue syndrome. We are also interested in the prevalence of the virus in the general population and the risk to human health. Our initial focus has been to set up serological assays for XMRV to test patient sera for antibodies to the virus. We can also screen for the presence of viral nucleic acid and proteins. In addition we are interested in the basic biology of the virus, including its susceptibility to restriction factors in the host. Publications 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 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 An ELISA for viral reverse transcriptase activity shows that XMRV production is reduced in the presence of mammalian restriction factors. The lighter the colour, the lower the viral titre Holmes RK, Malim MH and Bishop KN (2007) APOBEC-mediated viral restriction: not simply editing? Trends in Biochemical Sciences 32:118-128 MRC National Institute for Medical Research 31 INFECTIONS AND IMMUNITY Parasitology Michael Blackman Proteases in host cell exit and invasion by the malaria parasite Lab members: Marta Campos, Matthew Child, Christine Collins, Fiona Hackett, Natalie Silmon de Monerri, Anna Olivieri, Andrea Ruecker, Michael Shea, Robert Stallmach, Malcolm Strath, Catherine Suarez, Chrislaine Withers-Martinez, Sharon Yeoh Malaria is directly responsible for an estimated 2-3 million deaths per annum worldwide, causing terrible suffering and imposing an immense economic burden on much of the developing world. 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. The infected red cell eventually ruptures, releasing a fresh wave of parasites which rapidly invade new red cells. Invasion involves the activity of a complex set of proteins that are released onto the parasite surface to bind to the new red blood cell and penetrate it. Our work aims to improve our understanding of how these parasite proteins interact with the host red blood cell to enable invasion, and how antibodies can interfere with this process. This will help the development of new drugs and aid vaccine design. In addition, we are studying a family of parasite-derived proteases that regulate release of the parasite from red blood cells, and also modify the parasite surface to prime it for invasion. We are investigating the structure and function of these proteases, and searching for inhibitory compounds with potential to be developed as antimalarial drugs. Depiction of the role of a malarial protease called PfSUB1 in surface modification and release of malarial merozoites from the infected red blood cell Publications 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 Atomic structure of a conserved domain from a malarial red blood cell-binding protein called EBA-175 Yeoh S, O’Donnell RA, Koussis K, Dluzewski AR, Ansell KH, Osborne SA, Hackett F, Withers-Martinez C, Mitchell GH, Bannister LH, Bryans JS, Kettleborough CA and Blackman MJ (2007) Subcellular discharge of a serine protease mediates release of invasive malaria parasites from host erythrocytes. Cell 131:1072-83 See references 39, 60, 116, 120, 122 in the bibliography at the back for publications from this group in 2009. 32 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, Laura Brady, Joanna Dillury, Amanda Fivian-Hughes, Alison Gaudion, Katherine Smollett, Alan Williams Tuberculosis (TB) remains a major worldwide cause of death due to infectious disease and drug resistance is becoming an increasing problem. Furthermore, it has been estimated that one-third of the world’s population is infected with the causative agent, Mycobacterium tuberculosis, in a state termed latent infection, in which the immune system holds the bacterium in check but is unable to eliminate it. Our research is aimed at understanding how M. tuberculosis is able to adapt to and survive under the various conditions it encounters following infection. We anticipate that a clearer understanding of these processes will facilitate the development of new drugs to treat TB. During infection, M. tuberculosis becomes exposed to various stresses including conditions that damage DNA. As the repair of damaged DNA is crucial to survival, we are focusing on the bacterial response to DNA damage and the roles of particular DNA repair processes in M. tuberculosis, particularly with respect to pathogenesis. Where appropriate, we are seeking to identify inhibitors that may provide a starting point for drug development. Publications Dawson LF, Dillury J and Davis EO (2009) RecA-independent DNA damage induction of Mycobacterium tuberculosis ruvC despite an appropriately located SOS box. Journal of Bacteriology 192:599-603 Güthlein C, Wanner RM, Sander P, Davis EO, Bosshard M, Jiricny J, Böttger EC and Springer B (2009) Characterisation of the mycobacterial NER system reveals novel functions of uvrD1 helicase. Journal of Bacteriology 191:555-562 Curti E, Smerdon SJ and Davis EO (2007) Characterization of the helicase activity and substrate specificity of Mycobacterium tuberculosis UvrD. Journal of Bacteriology 189:1542-1555 During the course of infection and transmission, M. tuberculosis is exposed to a range of conditions to which it must adapt, ultimately resulting in persistence or replication See references 51, 53, 95, 198 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 33 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 See references 52, 79, 221 in the bibliography at the back for publications from this group in 2009. 34 MRC National Institute for Medical Research 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 INFECTIONS AND IMMUNITY Parasitology Delmiro Fernandez-Reyes Proteome-wide host-parasite interactions of severe malaria infections Lab members: Dimitrios Athanasakis, Francesca Battaglia, Barry Ely, Juho Rousu, Gurjinder Sandhu, Olugbemiro Sodeinde Human malaria caused by Plasmodium falciparum represents a global disease burden with an estimated 500 million clinical episodes per year. Cerebral malaria and severe malarial anaemia are major complications with significant mortality and morbidity. Our research focuses on understanding how the proteomes of host and parasite interact to establish severe disease states. Proteome-wide profiling of the infectious process provides us with disease-specific molecular fingerprints reflecting host-pathogen interactions. We study the parasite–host interactions using high-throughput proteome-wide mass spectrometry that reveals a snapshot of the state of the host during infection. We develop computational statistics and systems biology algorithms to discover complex patterns of interactions. Subsequent study of the patterns is essential for understanding the pathogenesis of different severe malaria clinical presentations and provides information for development of new diagnostic tests and therapeutic strategies. The establishment of the Childhood Malaria Research Unit with our collaborators at the Department of Paediatrics of the University College Hospital Ibadan, Nigeria allows us to sample the malaria disease process. 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 FernandezReyes D (2008) Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions. PLoS ONE 3:e1806 The Childhood Malaria Research Group (CMRG) based at University College Hospital (UCH Ibadan-Nigeria) has been established as a partnership between NIMR and the Department of Paediatrics of the College of Medicine University of Ibadan (a) Plasma proteome-wide profiles of hostparasite interactions in patients with Severe Malaria Anaemia (Red), Cerebral Malaria (Purple), Uncomplicated Malaria (Orange). (b) Principal components analysis of complex patterns within plasma proteome profiles shows discrimination between clinical classes 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 Rojas SA and Fernandez-Reyes D (2005) Adapting multiple kernel parameters for support vector machines using genetic algorithms. 2005 IEEE Congress on Evolutionary Computation, Proceedings: Edinburgh. IEEE, 2005. 1:626-631 MRC National Institute for Medical Research 35 INFECTIONS AND IMMUNITY Mycobacterial Research Sebastien Gagneux Population genomics and ecology of Mycobacterium tuberculosis Lab members: Sonia Borrell, Inaki Comas, Thembela Huna, Graham Rose We have previously shown that Mycobacterium tuberculosis, the causative agent of human tuberculosis (TB) consists of genetically distinct strain lineages that are associated with different regions of the world. Understanding the forces that shape this variation is crucial for the development of improved diagnostics, drugs, and vaccines against TB. We are using large-scale DNA sequencing of M. tuberculosis clinical strains to address this question. Recent data from 89 genes in 108 strains has shown that the genetic distance between two human strains of M. tuberculosis can be as pronounced as the distance between a human strain and M. bovis, which is a classical animal pathogen. These data also support an ‘out-of-and-back-to-Africa’ scenario for the evolutionary history of human TB. According to this scenario, M. tuberculosis originated in Africa and spread out of Africa together with ancient migrations of modern humans. More recently, the evolutionary ‘modern’ lineages of M. tuberculosis expanded as a result of the strong human population increases in Europe, India, and China, and spread globally following waves of colonization, trade, and conquest. Global phylogeny of M. tuberculosis based on 89 gene sequences in 108 strains Publications Borrell S and Gagneux S (2009) Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis. International Journal of Tuberculosis and Lung Disease 13:1456-1466 Comas I and Gagneux S (2009) The past and future of tuberculosis research. PLoS Pathogens 5:e1000600 (A) Different M. tuberculosis lineages accompanied the ‘Out-of-Africa’ migrations of modern humans ~50,000 years ago. (B) Recent gobal spread of the ‘modern’ M. tuberculosis lineages as a consequence of colonization, trade, and conquest Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW and Gagneux S (2008) High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biology 6:2658-2671 e311 See references 23, 41, 42, 55, 70, 76, 77, 145, 230 in the bibliography at the back for publications from this group in 2009. 36 MRC National Institute for Medical Research INFECTIONS AND IMMUNITY Virology Alan Hay Influenza virus – vaccines and drugs Lab members: Patrick Collins, Sergiy Tokar, Steve Wharton, Yi Pu Lin, Rod Daniels, Victoria Gregory, Xiang Zheng, Lynne Whittaker,Ting Hou, Joannes Kloess, Nicholas Cattle, Takashi Yamanaka Viruses causing influenza change in two ways: gradual small changes which reduce immunity to re-infection, and infrequent major changes which result in the emergence of novel viruses, such as the “swine-origin” H1N1 virus responsible for the 2009 influenza pandemic. Worldwide surveillance by the WHO Global Influenza Network, including the World Influenza Centre at NIMR, is therefore essential to detect and monitor such changes. This allows assessment of the pandemic risk of e.g. H5N1 Bird Flu, as well as of changes that reduce the effectiveness of vaccines and drugs. My group also researches the two target proteins of anti-influenza drugs, the virus neuraminidase (NA) and M2 proton channel. We aim to gain a better understanding of the molecular mechanisms of drug action and acquisition of resistance. Our recent X-ray crystallographic analyses of NA-drug complexes have provided a structural explanation for specific resistance to oseltamivir (Tamiflu). Such information is important in understanding the recent spread of oseltamivir resistance among seasonal A H1N1 viruses and its potential emergence among the novel pandemic H1N1 viruses. Publications Childs RA, Palma AS, Wharton S, Matrosovich T, Liu Y, Chai W, Campanero-Rhodes MA, Zhang Y, Eickmann M, Kiso M, Hay A, Matrosovich M and Feizi T (2009) Receptor-binding specificity of pandemic influenza A (H1N1) 2009 virus determined by carbohydrate microarray. Nature Biotechnology 27:797-9 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 X-ray crystallographic structures of NA-drug complexes, showing the effects of the His274 Tyr oseltamivir resistance mutation on the interactions of oseltamivir (A) and zanamivir (B) with the active sites of wild-type (green) and mutant (yellow) NAs of A H5N1 virus 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 See references 18, 19, 31, 36, 40, 61, 122, 141, 207 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 37 INFECTIONS AND IMMUNITY Parasitology Tony Holder Malaria parasites and red blood cells Lab members: 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 new red cells. This cycle is responsible for the disease. There is much interest in understanding the interaction between the parasite and the host immune system, to contribute 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 much needed new therapeutic interventions. In one project, focused on how the parasite invades host cells, we study the actomyosin-based motor that drives invasion. We have shown that an unusual calcium-dependent protein kinase phosphorylates two of the proteins in the motor complex, a process that may be important in its assembly. Together with colleagues at MRC Technology we have identified chemical compounds that inhibit this kinase and kill the parasite at very low concentrations. These compounds have the potential to be developed into drugs against malaria and are powerful reagents to dissect the exact role of this kinase in the parasite’s biology. Location of an apical rhoptry protein (RhopH2), an invasion motor protein (GAP45) and a surface protein (MSP1) in merozoites within a schizont Publications Holder AA (2009) The carboxy-terminus of merozoite surface protein 1: structure, specific antibodies and immunity to malaria. Parasitology 136:1445-1456 Within the parasite’s cycle of invasion and development we study several aspects of its cell biology and biochemistry to understand the complex interaction between parasite and host Green JL, Rees-Channer RR, Howell SA, Martin SR, Knuepfer E, Taylor HM, Grainger M and Holder AA (2008) The motor complex of Plasmodium falciparum: phosphorylation by a calcium-dependent protein kinase. Journal of Biological Chemistry 283:30980-30989 Kadekoppala M, O’Donnell RA, Grainger M, Crabb BS and Holder AA (2008) Deletion of the Plasmodium falciparum Merozoite Surface Protein 7 gene impairs parasite invasion of erythrocytes. Eukaryotic Cell 7:2123-2132 See references 20, 22, 45, 60, 98, 100, 101, 102, 120, 151, 152 in the bibliography at the back for publications from this group in 2009. 38 MRC National Institute for Medical Research INFECTIONS AND IMMUNITY Immunoregulation George Kassiotis Antiviral immunity Lab members: Urszula Eksmond, Dorothy Ng, Rebecca Pike, 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 (e.g. 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. In addition to progressive immune deficiency, HIV infection is characterised by generalized immune activation, with lymphadenopathy and accelerated turnover of lymphocytes, both infected and uninfected. The origin of immune activation in HIV infection is unknown, but it is thought to arise from increased microbial exposure due to diminishing immunity. Instead, we showed in a virus-free mouse model that conditional ablation of activated CD4+ T cells, the targets of immunodeficiency viruses, reproduces both HIV-associated immune deficiency and activation, attributable to insufficiency in memory and regulatory CD4+ T cells, respectively. This suggests activated CD4+ T cell killing as a common aetiology for both immune deficiency and activation in HIV infection. Publications 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 Pike R, Filby A, Ploquin MJ-Y, Eksmond U, Marques R, Antunes I, Hasenkrug K and Kassiotis G (2009) Race between retroviral spread and CD4+ T cell response determines the outcome of acute Friend virus infection. Journal of Virology 83 11211-11222 Lymphadenopathy (lymph node enlargement) in mice with conditional ablation of activated CD4+ T cells (DTA) in comparison with control wildtype (WT) mice Lymphocyte activation (expression of CD44) in non-targeted CD8+ T cells isolated from mice with ablation of activated CD4+ T cells (DTA) or control wild-type (WT) mice 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 See references 112, 132, 157 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 39 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 Karamitros, Trisha Norton, Keith Williams Image of mouse chromosome 6. Multi colour chromosome banding (MCB) with CD8a and CD4 gene probes 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 Kioussis D and Pachnis V (2009) Immune and nervous systems: more than just a superficial similarity? Immunity 31:705-710 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 64, 83, 115, 132, 162, 229 in the bibliography at the back for publications from this group in 2009. 40 MRC National Institute for Medical Research INFECTIONS AND IMMUNITY Parasitology Jean Langhorne Immunology and immunopathogenesis of malaria infections Lab members: Deirdre Cunningham, Peter Gardner, Ana Paula Freitas do Rosario, William Jarra, Gertrude Kiwanuka, Agathe Lang, Jennifer Lawton, Beatris Mastelic, Philip Spence, Anne-Marit Sponaas, Robin Stephens, Sophie Roetynck, Christine Tshitenge, Bettina Wagner We study the immune response to the malaria parasite, components of this response involved in protection against infection and in pathology, and parasite antigens that may stimulate these responses. For most of our work we study mouse models, but where possible also human immune reponses to Plasmodium falciparum and P. vivax. The innate immune system is an important component of the early host response to the blood stages of the malaria parasite. We have shown that a population of inflammatory monocytes is produced in the bone marrow in response to infection, and contributes to killing and removal of parasites. However, the innate response is not sufficient to eliminate an infection, and long-term protective immunity to re-infection depends on B cells and antibodies. Long-lived responses do develop after a single malaria infection to some antigens, but it is thought that protective immunity is directed towards variant antigens on the infected red blood cells, which may induce only short-lived or ineffective antibody responses. There is a large multigene family in rodent and human malaria parasites that codes for a set of variant proteins. We are investigating whether these are expressed on the surface of infected red blood cells and are the targets of a protective immune response. Publications Cunningham D, Fonager J, Jarra W, Carret C, Preiser P and Langhorne J (2009) Rapid changes in transcription profiles of the Plasmodium yoelii yir multigene family in clonal populations: lack of epigenetic memory? PLoS ONE 4:e4285 Ndungu FM, Cadman ET, Coulcher J, Nduati E, Couper E, Macdonald DW, Ng D and Langhorne J (2009) Functional memory B cells and long-lived plasma cells are generated after a single Plasmodium chabaudi infection in mice. PLoS Pathogens 5:e1000690 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 See references 22, 47, 142, 151, 183, 199, 201, 219 in the bibliography at the back for publications from this group in 2009. Immune responses to Plasmodium chabaudi malaria in mice MRC National Institute for Medical Research 41 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 specific receptors on the surface of neutrophils and macrophages. This triggers an immediate ‘innate’ immune response involving the production of 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. Coordinating the expression of genes that control innate and adaptive immune responses involves activation of the NF-κB family of transcription factors and the ERK MAP kinase signalling enzyme. We study a signalling pathway that regulates both NF-κB and ERK MAP kinase activation by inducing proteolysis of the inhibitory protein NF-κB1 p105. We have recently found that p105 regulation of NF-κB is critical for the function of CD4 T cells during an immune response. Our current studies aim to determine whether blockade of p105 proteolysis might be useful for the treatment of specific autoimmune diseases, such as rheumatoid arthritis and multiple sclerosis. TPL-2 regulates ERK MAP kinase activation in inflammatory responses Publications Kaiser F, Cook D, Papoutsopoulou S, Rajsbaum R, Wu X, Yang HT, Grant S, Ricciardi-Castagnoli P, Tsichlis PN, Ley SC and O’Garra A (2009) TPL-2 negatively regulates interferon-β production in macrophages and myeloid dendritic cells. Journal of Experimental Medicine 206:1863-1871 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 Regulation of NF-κB and ERK activation in innate immune responses Papoutsopoulou S, Symons A, Tharmalingham T, Belich MP, Kaiser F, Kioussis D, O’Garra A, Tybulewicz V and Ley SC (2006) ABIN-2 is required for optimal activation of Erk MAP kinase in innate immune responses. Nature Immunology 7:606-15 See references 108, 110, 200 in the bibliography at the back for publications from this group in 2009. 42 MRC National Institute for Medical Research 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 viruses infect a variety of species. Humans, horses and pigs are the main mammalian hosts of the virus in which infection is sustained. Avian species, particularly water fowl and gulls, harbour a very wide variety of influenza viruses. New pandemic strains of human influenza viruses arise from an animal reservoir either directly, as in the 2009 pandemic 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. In our laboratory, 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. We are also characterising the factors that influence the replication of avian influenza viruses in avian species. In collaboration with colleagues at The Institute for Animal Health, the Veterinary Laboratories Agency and the Wellcome Trust Sanger Institute we have been examining how the virus varies within the infected avian host. The techniques used have allowed us to analyse polymorphisms within the virus and the background genetic variation seen within samples amplified directly from experimentally infected birds. Publications 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 Iqbal M, Yaqub T, Reddy K and McCauley JW (2009) Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. PLoS ONE 4:e5788 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 27, 104, 105 in the bibliography at the back for publications from this group in 2009. cDNA clones were prepared directly from samples taken from an experimentally infected chickens. The numbers of nucleotide changes (black bars) and amino acid changes (grey bars) in individual clones differing from the consensus sequence clone are indicated MRC National Institute for Medical Research 43 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, Vangelis Stavropoulos, Xuemei Wu, Matthew Berry The immune system is effective in eradicating pathogens via many mechanisms, including soluble mediators called cytokines. Immune cells can produce different cytokines to control infection, but can cause host damage if uncontrolled. We are researching the molecular mechanisms underlying the development and function of discrete subsets of immune cells that produce different cytokines protective against pathogens, and the induction and function of a regulatory cytokine, IL-10. We use diverse tools to study the mechanisms of IL-10 gene regulation in macrophages, dendritic cells and T cells, and the consequences of IL-10 action in mouse models of infectious diseases, 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 signature for active TB, and longitudinal analysis revealed that this signature disappears during successful treatment. We are combining immunological research with interrogation of gene expression data to identify the immune factors involved in protection or pathogenesis important for disease control. Regulation of IL-10 production in immune cells Publications Transcriptional signatures for rapid diagnosis, disease monitoring and identification of factors involved in protection/immunopathogenesis in disease Saraiva M and O’Garra A (2010) The regulation of IL-10 production by immune cells. Nature Reviews Immunology 10:170-81 Kaiser F, Cook D, Papoutsopoulou S, Rajsbaum R, Wu X, Yang HT, Grant S, Ricciardi-Castagnoli P, Tsichlis PN, Ley SC and O’Garra A (2009) TPL-2 negatively regulates interferon-β production in macrophages and myeloid dendritic cells. Journal of Experimental Medicine 206:1863-1871 Saraiva M, Christensen JR, Veldhoen M, Murphy TL, Murphy KM and O’Garra A (2009) Interleukin-10 production by Th1 cells requires interleukin-12-induced STAT4 transcription factor and ERK MAP kinase activation by high antigen dose. Immunity 31:209-219 See references 17, 110, 112, 149, 180, 216 in the bibliography at the back for publications from this group in 2009. 44 MRC National Institute for Medical Research 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 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 Early lymphocyte development See references 199 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 45 INFECTIONS AND IMMUNITY Virology Kenneth Raj Lifecycle and persistence of human papillomavirus Lab members: Joanna Laurson, Lietta Nicolaides, Yeong-Lih Hiew, Jason Piper, Rachel Chung, Karen Cross The association between human papillomavirus (HPV) infection and cervical cancer is one of the clearest examples of how viral infection can lead to cancer. Although a single HPV infection by itself is unlikely to result in malignant transformation, the maintenance and persistence of the viral DNA in the cervical tissue considerably raises the risk of cancer development at a later stage. The main thrust of our work is to understand how HPVs infect cells, what happens to the viral DNA after infection, and how the viral DNA is replicated and maintained in the cells for prolonged periods. We are also investigating the consequences of HPVinduced inactivation of host tumour suppressor proteins and how this might be manipulated to kill cells harbouring the viral DNA. By characterising the differences between infected and non-infected cells, we hope to identify more points in the viral life cycle that might be suitable for therapeutic drug targetting. Publications Garner E and Raj K (2008) Protective mechanisms of p53-p21-pRb proteins against DNA damage-induced cell death. Cell Cycle 7:277-282 Human epithelium generated in the laboratory from cultured cells: (a) Cells harbouring HPV DNA that cannot express the viral E7 oncoprotein allow gradual differentiation of the stratified cells (diamond-shaped, granular cells), in the upper layers as is present in normal epithelia. (b) Cells harbouring wild-type HPV16 DNA form a disorganised epithelium largely consisting of proliferating cells 46 MRC National Institute for Medical Research Garner E, Martinon F, Tschopp J, Beard P and Raj K (2007) Cells with defective p53-p21-pRb pathway are susceptible to apoptosis induced by p84N5 via caspase-6. Cancer Research 67:7631-7637 Hoffmann R, Hirt B, Bechtold V, Beard P and Raj K (2006) Different modes of human papillomavirus DNA replication during maintenance. Journal of Virology 80:4431-9 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. The number and type of T cells found in the immune system is 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 within the immune system, causing them to malfunction. Abnormal responses by T cells can result in autoimmune diseases, such as diabetes, or the development of leukaemia. Furthermore, the effectiveness of vaccines can depend on the successful generation and survival of appropriate T cell types. We have developed an in vivo model in which we can specifically control expression of Zap70, a key kinase involved in transmitting T cell antigen receptor signals. Using this model, we have discovered a role for Zap70 in helping developing thymocytes make the decision to become either helper CD4 T cells or cytotoxic CD8 T cells. Publications 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 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 Dynamic regulation of Zap70 levels controls CD4+CD8+ thymocyte sensitivity to selection signals at different stages of T cell development See references 83, 97, 176, 200 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 47 INFECTIONS AND IMMUNITY Molecular Immunology Gitta Stockinger EMBO member, FMedSci Development, maintenance and regulation of peripheral T cell compartments and immune responses Lab members: Marc Veldhoen, Keiji Hirota, Joao Duarte, Ceri Wiggins, Christoph Wilhelm, Eve Hornsby, Nachima Khattoun, Ying Li Our main interest is the functional analysis of peripheral T cell responses, aiming to understand complex interactions in vivo that lead to antigen presentation, tolerance induction, activation, autoimmunity and memory formation. Our current focus is on the development and function of new CD4 effector T cells, such as Th17 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. Understanding their mode of action and regulation may ultimately lead to improved therapies for such diseases. We are currently focusing on the role of the aryl hydrocarbon receptor in Th17 cell biology, trying to unravel its impact on their physiological function in the defense against pathogens as well as their role in autoimmune diseases. Publications 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, Christensen J, O’Garra A and Stockinger B (2009) Natural agonists for aryl hydrocarbon receptor in culture medium are essential for optimal differentiation of Th17 T cells. Journal of Experimental Medicine 206:43-49 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 14, 21, 67, 133, 203, 204, 205, 216 in the bibliography at the back for publications from this group in 2009. 48 MRC National Institute for Medical Research Immune regulation by AhR ligand or inhibitor INFECTIONS AND IMMUNITY Virology Jonathan Stoye Retrovirus-host interactions Lab members: Emily Colbeck, Vicky Felton, Seti Grambas, Kate Holden-Dye, Laura Hilditch, 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 coevolution has taken place, resulting in the development of specific defence mechanisms by the host, and means to overcome such defences by the virus. Understanding such natural anti-viral genes might suggest novel means of combating retroviral infection. The primate TRIM5α genes provide an example of such a host defence gene. They can interact with the polymerised viral capsid proteins present on infecting retroviruses. One key question in their study concerns the specificity of target recognition. On the one hand, they are capable of recognising and restricting a wide range of viruses. However, each TRIM5α restricts a different panel of viruses. We are attempting to define the sequences responsible for recognition of different viruses and to describe the structures with which they interact. We anticipate that these studies will shed new light on the early stages of retrovirus replication and the control of cross-species infection. Publications 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 Ohkura S, Yap MW, Sheldon T and Stoye JP (2006) All three variable regions of the TRIM5α B30.2 domain can contribute to the specificity of retrovirus restriction. Journal of Virology 80:8554-8565 Potential restriction factor binding pocket in the N-terminal domain of the MLV CA protein. Amino acids that can affect viral tropism are highlighted See references 38, 139, 206 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 49 INFECTIONS AND IMMUNITY Immune Cell Biology Pavel Tolar Activation of immune receptors Lab members: Jason Lee, Antonio Casal Antibodies are an integral part of human immunity to infections and their induction has proven successful in many vaccines. However, some of the most dangerous pathogens of today’s world, such as HIV, influenza and 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. We focus on the B-cell antigen receptor, the primary receptor that controls the activation of B lymphocytes and the specificity of the antibody response. Our initial studies are investigating the role of membrane-proximal domains of the B-cell receptor in the mechanism of signal transduction from the pathogen binding sites to the intracellular signalling units. We combine structural techniques with molecular imaging of the B-cell receptor in living B cells that recognise a range of viral epitopes. Imaging of an individual B-cell receptor on B lymphocytes shows activation of the receptor in antigen-induced clusters Publications 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 (2008) Viewing the antigen-induced initiation of B-cell activation in living cells. Immunological Reviews 221:64-76 Schematic structure of the B-cell receptor 50 MRC National Institute for Medical Research 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 INFECTIONS AND IMMUNITY INFECTIONS AND IMMUNITY Immune Cell Biology Immune Cell Biology Victor Tybulewicz EMBO member, FMedSci Victor Tybulewicz Signal transduction in B and T cells Lab members: Alexander Saveliev, Olga Ksionda, Agnieszka Zachacz, Amy Slender, Lesley Vanes, Robert Köchl, Sheona Watson, Eva Lana Elola, Jonathan Rapley, Edina Schweighoffer, Josquin Nys, Pete Gardner 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 auto-immune 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. In a recent study 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 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. To do this, we created a novel mouse strain carrying a freely segregating copy of human chromosome 21, which displays many of the features of Down Syndrome, including learning difficulties and cardiac abnormalities. Publications Dumont C, Corsoni-Tadrzak A, Ruf S, de Boer J, Williams A, Turner M, Kioussis D and Tybulewicz VL (2009) Rac GTPases play critical roles in early T cell development. Blood 113:3990-3998 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 Rapley J, Tybulewicz VLJ and Rittinger K (2008) Crucial structural role for the PH and C1 domains of the Vav1 exchange factor. EMBO Reports 9:655-661 The Vav1 signalling protein (green) accumulates in a T cell at the interface with an antigen presenting cell (red). Nuclei are stained in blue T cells missing Rac GTPases (green) are stuck on the endothelium (purple), unable to enter the cortex of the lymph node (blue), unlike wildtype T cells (red) See references 43, 48, 64, 72, 78, 94, 170, 184, 185, 200, 212, 227 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 51 INFECTIONS AND IMMUNITY Immunoregulation Andreas Wack Immune response to influenza Lab members: Stefania Crotta, Sophia Davidson 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 contributes to lung pathology. It is not completely known which factors tip the balance between damage or death versus successful clearance of the virus with no 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 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. Complemented by in vivo studies, this approach will allow us to identify early events 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 Pesce I, Monaci E, Muzzi A, Tritto E, Tavarini S, Nuti S, De Gregorio E and Wack A (2009) Intranasal administration of CpG induces a rapid and transient cytokine response followed by dendritic and natural killer cell activation and recruitment in the mouse lung. Journal of Innate Immunity Epub ahead of print 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 52 MRC National Institute for Medical Research Mouse airway epithelial cultures stained with the tight junction protein ZO-1 (green) and the cilia constituent beta tubulin IV (magenta) INFECTIONS AND IMMUNITY Mycobacterial Research Robert Wilkinson FRCP Steroid regulated immune responses in tuberculosis Lab members: Katalin Wilkinson, Anna Coussens, Adrian Martineau Our studies are based at NIMR and at the University of Cape Town, South Africa. Our interest is the modulation of the immune response in human tuberculosis by vitamin D and corticosteroids. Both studies rely on recently completed clinical trials: first, of the efficacy of vitamin D as an adjunct to the treatment of active tuberculosis; and second of prednisone versus placebo for treatment of the HIV-TB associated immune reconstitution inflammatory syndrome (TB-IRIS). Immunopathology is a hallmark of tuberculosis, which is necessary for transmission of the disease and responsible for its sequelae, including death. TB-IRIS arises as a consequence of restoration of pathological immunity in HIV-infected persons with tuberculosis who receive antiretroviral therapy, and is an opportunity to better understand this phenomenon. It was unknown until our trial whether corticosteroids would be beneficial in reducing symptoms. Our demonstration that they are effective now focuses attention on a rich specimen bank to determine the mode of action so that more specific immune modulators of immunopathology in tuberculosis can potentially be discovered. Publications Wilkinson KA, Seldon R, Meintjes G, Rangaka MX, Hanekom WA, Maartens G and Wilkinson RJ (2009) Dissection of regenerating T cell responses against tuberculosis in HIV infected adults sensitized by Mycobacterium tuberculosis. American Journal of Respiratory and Critical Care Medicine 180:674-683 Maartens G and Wilkinson RJ (2007) Tuberculosis. Lancet 370:2030-2043 Martineau AR, Newton SM, Wilkinson KA, Kampmann B, Hall BM, Nawroly N, Packe GE, Davidson RN, Griffiths CJ and Wilkinson RJ (2007) Neutrophil-mediated innate immune resistance to mycobacteria. Journal of Clinical Investigation 117:1988-94 See references 11, 17, 49, 62, 111, 130, 134, 135, 144, 154, 155, 181, 186, 224, 225, 226, 235 in the bibliography at the back for publications from this group in 2009. Symptom score at week 2 and 4 The distribution of symptom scores in percentage at week 2 and 4 in 3 categories (deteriorated, no change, improved/resolved) is shown. There were significant differences between the 2 arms at week 2 (p=0.001) and week 4 (p=0.03) MRC National Institute for Medical Research 53 INFECTIONS AND IMMUNITY Mycobacterial Research Douglas Young FMedSci Mycobacterium tuberculosis and the host response Lab members: Kristine Arnvig, John Brennan, Stephen Coade, Damien Portevin, Vivek Rao, 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 persistence of the pathogen in an asymptomatic, latent infection. We are testing the hypothesis that the pathogen misleads the host into mounting a suboptimal response. Ultimately, we aim to develop drugs that rapidly eliminate persisting bacteria and vaccines that elicit more effective immunity. Innate immune responses to M. tuberculosis involve recognition of molecules on the surface of the bacteria by receptors expressed on phagocytic cells. Variation in surface ligands expressed by M. tuberculosis strains from different phylogenetic lineages may cause differences in immune recognition and disease. By labelling with different fluorescent colours, we can follow multiple strains in mixed infection experiments. Strains also differ in the way they respond to the host. Using next-generation sequencing to screen the entire transcriptome of M. tuberculosis, we have identified a previously unknown repertoire of regulatory RNA molecules that vary between strains. Publications Arnvig KB and Young DB (2009) Identification of small RNAs in Mycobacterium tuberculosis. Molecular Microbiology 73:397-408 Young DB, Gideon HP and Wilkinson RJ (2009) Eliminating latent tuberculosis. Trends in Microbiology 17:183-188 Labelling with red and green probes allows us to compare the behaviour of different strains of M. tuberculosis during infection of host macrophages 54 MRC National Institute for Medical Research Northern blot analysis shows differences in the expression of a small regulatory RNA molecule between different strains of M. tuberculosis Young D, Stark J and Kirschner D (2008) Systems biology of persistent infection: tuberculosis as a case study. Nature Reviews Microbiology 6:520-528 See references 7, 11, 224, 232, 234, 235 in the bibliography at the back for publications from this group in 2009. INFECTIONS AND IMMUNITY Mycobacterial Research Microarray Laboratory Molecular pathogenicity of mycobacteria Lab members: Roger Buxton, Yvonne Braun, Debbie Hunt, Kathryn Lougheed, Luisa Mori, Nathan Sweeney, Vicky Spivey Mycobacterium tuberculosis infects macrophage cells in the lungs, the very cells that have evolved to destroy most infecting pathogens. We are investigating the gene regulatory systems M. tuberculosis uses to allow it to grow in this hostile environment, particularly those controlled by cyclic AMP and protein phosphorylation. This may give clues to potential new drug targets. Reversible protein phosphorylation is a major regulatory mechanism, and in mycobacteria there is a large number of serine-threonine protein kinases (STPKs). These enzymes are attractive drug targets, as some have an essential role in virulence, they have a low sequence identity with human STPKs, and there is expertise available for the design of specific inhibitors. In collaboration with Steve Smerdon (Molecular Structure), we are investigating the mode of action of one STPK, PknF, which has an ABC transporter as a target that is essential for growth of M. tuberculosis in mice. We are also carrying out drug screening for inhibitors of another essential STPK, PknB, in collaboration with MRC Technology. High throughput screening has also been used to find anti-TB agents amongst known drugs. Mycobacterium tuberculosis is a rod-shaped bacterium with a complex cell wall containing very long and unique lipids. In this transmission electron micrograph, most bacteria have been sectioned transversely and so appear round 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 and DNA binding properties and transcription activation properties. Journal of Biological Chemistry 285, 7016-7027 Lougheed KE, Taylor DL, Osborne SA, Bryans JS and Buxton RS (2009) New anti-tuberculosis agents amongst known drugs. Tuberculosis 89:364-370 Curry JM, Whalan R, Hunt DM, Gohil K, Strom M, Rickman L, Colston MJ, Smerdon SJ and Buxton RS (2005) An ABC transporter containing a forkhead-associated domain interacts with a serinethreonine protein kinase and is required for growth of Mycobacterium tuberculosis in mice. Infection and Immunity 73:4471-7 Biolog Phenotype MicroarraysTM allow the simultaneous testing of nearly 2000 phenotypes. A redox dye is used to measure growth of bacteria in 96-well plates containing a range of sole nutrient sources and stress agents See references 127, 148, 232 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 55 INFECTIONS AND IMMUNITY Virology WHO Collaborating Centre for Reference and Research on Influenza Director: John McCauley Lab members: Rod Daniels, Yi Pu Lin, Vicky Gregory, John Xiang, Ting Hou, Lynn Whittaker, Nick Cattle, Johannes Kloess, Chandrika Halai The World Health Organisation (WHO) Influenza Centre (WIC) at NIMR has been part of the WHO Global Influenza Surveillance Network since it was established over 50 years ago. The laboratory is now one of four Collaborating Centres (the others are in Atlanta, Melbourne and Tokyo) that integrate the surveillance of influenza around the world by some 120 National Influenza Centres (NICs). With the emergence of the A/H1N1 2009 pandemic of influenza, the role of the laboratory was to assist NICs in countries around the world in their assessment of the local situation. The WIC at NIMR has collaborated with the NICs from over 60 countries in Europe, Africa, the Middle East and Asia since the onset of the spread of the new virus. We were able to confirm the first cases in many countries. Viruses have been examined for antigenic, genetic and drug resistance characteristics. In many cases, full genome sequences have been determined. To date there has been little change in the A/H1N1 2009 virus in terms of emergence of distinct genetic and antigenic groups, and only sporadic instances of resistance to anti-neuraminidase drugs have been detected as the virus continues to evolve. In addition to assessing the most appropriate virus for use as a Pandemic Vaccine, the Collaborating Centres are responsible for making twice yearly recommendations for the composition of seasonal influenza vaccines. The recommendation for the vaccine for the 2010 influenza season in the Southern Hemisphere and for the Northern Hemisphere 2010-2011 was to include the pandemic vaccine strain and change the H3N2 component to a variant that was first detected at the beginning of 2009. All the studies are carried out with the various NICs, the other WHO Collaborating Centres, the UK Health Protection Agency Centre for Infection (Colindale), members of the European Community Network of Reference Laboratories for human influenza and the Wellcome Trust Sanger Institute. See references 27, 90 in the bibliography at the back for publications from this group in 2009. 56 MRC National Institute for Medical Research The haemagglutinin based phylogenetic dendogram illustrates the relatively low divergence of the A/H1N1 2009 pandemic virus since its emergence 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 (2009) 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 Epub ahead of print Recommended composition of influenza virus vaccines for use in the 2010 southern hemisphere influenza season. http://www.who.int/csr/disease/influenza/recommendations2010south/en/index.html Recommended composition of influenza virus vaccines for use in the 2010-2011 northern hemisphere influenza season http://www.who.int/csr/disease/influenza/recommendations2010_11north/en/index.html Structural Biology Mathematical Biology Molecular Structure Physical Biochemistry Willie Taylor (Head of Division) Richard Goldstein Steve Gamblin (Joint Head of Division) Steve Smerdon (Joint Head of Division) Paul Driscoll Annalisa Pastore Andres Ramos Katrin Rittinger Ian Taylor Justin Molloy (Head of Division) Ed Hulme John Offer Peter Rosenthal Claudia Veigel 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 57 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, Simon Greenwood 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 processes include the activation of death receptor signalling cascades in apoptosis, limb regeneration in the adult newt, the regulation of phospholipases by small G proteins, and the underlying basis of antigen recognition in Hughes Syndrome. We have recently investigated the 3D solution structure and phylogeny of the protein Prod-1 which has been recognised as an important marker of the positional identity of the blastema that forms at an amputation site in the adult newt, a structure that when transplanted gives rise to regeneration of the missing limb parts. Our analysis indicates that, whilst this three-finger superfamily member is superficially similar to well known mammalian proteins, it is nevertheless restricted to salamanders. This result may have important implications for realisation of the promise of this classic example of regeneration for development of medical applications in humans. Ribbon and bundle representations of the 3D solution structure of Prod-1 Publications 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 Garza-Garcia A, Esposito D, Rieping W, Harris R, Briggs C, Brown MH and Driscoll PC (2008) Three-dimensional solution structure and conformational plasticity of the N-terminal scavenger receptor cysteine-rich domain of human CD5. Journal of Molecular Biology 378:129-144 Ferguson BJ, Esposito D, Jovanovic J, Sankar A, Driscoll PC and Mehmet H (2007) Biophysical and cell-based evidence for differential interactions between the death domains of CD95/Fas and FADD. See references 68, 82 in the bibliography at the back for publications from this group in 2009. 58 MRC National Institute for Medical Research Phylogenetic tree analysis of three-finger protein sequence: Prod-1 homologues cluster separately from the CD59 subgroup with which it had previously been associated 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, Peter Saiu, Junfeng Liu, Peter Coombs, Sebastien Vachieri, Elizabeth Underwood We study the structure and function of molecules involved in diseases such as influenza, diabetes and cancer. We use X-ray crystallography and NMR to determine the three-dimensional structures and dynamics of these molecules. In combination with other biophysical techniques, the data help us elucidate the function of relevant proteins and provide information for development of therapeutic approaches. We have a long-term interest in how covalent modifications of histones, that package DNA into chromatin, regulate gene expression through epigenetic mechanisms. Polycomb Repressive Complex 2 (PRC2) is essential for the maintenance of repressive chromatin domains in early development, and its overexpression is linked with a number of different cancers. We have uncovered how the PRC2 complex is able to trimethylate K27 on H3 in the context of existing repressive methyl marks on neighbouring chromatin, but not in the absence of these marks. We have shown that the EED subunit of PRC2 specifically recognises H3K27Me3 and that this leads to activation of the methyltransferase activity of the PRC2 complex. These collaborative studies provide the first mechanistic insight into the propagation of repressive chromatin domains, and may lead to the identification of small molecule inhibitors that could be tested for activity against certain cancers. Schematic model of the propagation of repressive chromatin domains. PRC2 (shown as its component subunits EED, Ezh2, Suz12 and RbAp48) binds to H3K27Me3 marks on pre-existing histones. Publications 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 Structure of EED bound to a trimethylated H3K27Me3 peptide (shown in stick representation) Xiao B, Heath R, Saiu P, Leiper FC, Leone P, Jing C, Walker PA, Haire L, Eccleston JF, Davis CT, Martin SR, Carling D and Gamblin SJ (2007) Structural basis for AMP binding to mammalian AMP-activated protein kinase. Nature 449:496-500 See references 40, 125, 131 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 59 STRUCTURAL BIOLOGY Mathematical Biology Richard Goldstein Modelling of evolution Lab members: Mario dos Reis Barros, Chrisantha Fernando, Kyriakos Kentzoglanakis, Seena Shah, Asif Tamuri All life 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 also are modelling the evolution of our ability to understand language, to put constraints on the way in which the brain is able to perform this task. Phylogenetic tree of influenza, showing the division into the human, ‘classical’ swine, and bird lineages. Hosts are colour-coded, red for human, blue for swine, black for avian. Notice the few cases of human influenza in the middle of the bird lineage, representing H5N1 ‘Bird-flu’. Publications 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 Goldstein RA and Soyer OS (2008) Evolution of taxis responses in virtual bacteria: non-adaptive dynamics. PLoS Computational Biology 4:e1000084 See references 61, 207 in the bibliography at the back for publications from this group in 2009. 60 MRC National Institute for Medical Research Evolution of chemotaxis in virtual bacteria inhabiting a virtual world. Bacteria quickly develop a biochemical network allowing them to explore the space and exploit the found food. Inserts show the time-averaged distribution of the bacteria. At each generation, the bacteria start at a location towards the bottom-left of the space. The food is in a Gaussian distribution at the centre of the space. STRUCTURAL BIOLOGY Physical Biochemistry Ed Hulme Structure and function of G protein-coupled receptors Lab members: Carol Curtis, Robert Kaye 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. Muscarinic acetylcholine receptors (mAChRs) regulate the activity of over 50% of the nerve cells in the brain. Recently, we have used targeted mutations of the M1 mAChR, a major mediator of cortical attention mechanisms, to show how a binding site for highly-selective activating agents may be created by a novel conformational isomerisation of a tryptophan side-chain. Such agonist ligands are targeted at the cognitive defects in Alzheimer’s and schizophrenia. We are making stable ligand complexes of M1 mAChRs, using both pharmacological and mutational methods, working towards an atomic resolution structure by X-ray crystallography. This will provide a starting point for quantitative molecular dynamics calculations of drug-receptor interactions. Conformational isomerisation of the side-chain of tryptophan 101 (purple) creates abinding pocket for 77-LH-28-1: (a) trans (b) gauche Publications 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 (a) Chemical structure of the selective M1 agonist 77-LH-28-1 (b) Interacting amino acids studied by mutation of the M1 mAChR 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 MRC National Institute for Medical Research 61 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, Martyn Stopps 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. Laserbased optical methods like optical tweezers and total internal reflection fluorescence microscopy 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, and dual-colour fluorescence imaging has allowed us to image individual G-protein coupled receptors at the cell membrane. Optical tweezers (left) and Total Internal Reflection Fluorescence Microscopy (right) enable individual molecules to be manipulated and imaged. 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 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 Epub ahead of print Actin filaments become aligned by myosin motors due to lateral mechanical interactions between neighbouring filaments. These weak mechanical forces might be responsible for the coordinated response of a cell as it migrates through tissue. 62 MRC National Institute for Medical Research Baboolal TG, Sakamoto T, Forgacs E, White HD, Jackson SM, Takagi Y, Farrow RE, Molloy JE, Knight PJ, Sellers JR and Peckham M (2009) The SAH domain extends the functional length of the myosin lever. Proceedings of the National Academy of Sciences of the United States of America 106:22193-22198 See references 9, 69 in the bibliography at the back for publications from this group in 2009. STRUCTURAL BIOLOGY Synthetic Protein Laboratory John Offer Acyl transfer for chemical biology and synthesis. Lab members: Lotta Holm, George Papageorgiou Post translationally-modified proteins can now be synthesised with a combination of ligation and optimised peptide synthesis, giving atom by atom control over the product. Chemical ligation can be combined with biological expression systems, 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 emerging ligation techniques 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. We are aso applying chemical ligation to the synthesis of chemically defined peptide-oligosaccharide glycoconjugates as HIV vaccines. Auxiliary–assisted ligation chemistry can chemoselectively join a wide range of peptides together without needing elaborate protecting group strategies. We are applying it to the synthesis of small cyclic peptides, attractive lead compounds for screening and the development of orally available therapeutics. Chemical ligation methods for the synthesis of proteins and post-translationally modified proteins Publications 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 Single amino acid incorporation using orthogonal ligation 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 MRC National Institute for Medical Research 63 STRUCTURAL BIOLOGY STRUCTURAL BIOLOGY Molecular Structure Synthetic Protein Laboratory Annalisa Pastore EMBO member Understanding the molecular bases of neurodegeneration Lab members: Laura Masino, Cesira de Chiara, Salvatore Adinolfi, John McCormick, Filippo Prischi, Miquel Adrover, Kris Pauwels, Raj Menon , Veronica Esposito, Ljiljana Sjekloca Our main line of research concerns the study of proteins involved in neurodegenerative processes of the central nervous system, with the ultimate aim of understanding the causes of pathology and developing new theurapeutic strategies. We are addressing the problem by studying the function/structure relationship of the non-pathologic forms of the proteins involved, and by investigating the mechanisms which lead to neurodegeneration, such as protein misfolding, aggregation, and misfunctioning. The families of diseases we focus on involve dominant and recessive ataxias, such as Joseph-Machado disease and Friedreich’s ataxia. We are also investigating the bases of intelligence through studying what leads to Fragile X mental retardation syndrome. To carry out our studies, we use biophysical, biochemical, and bioinformatics techniques, which range from different spectroscopies, calorimetry, molecular dymamics and comparative modelling. We use advanced Nuclear Magnetic Resonance techniques to determine the structure and dynamics of the protein we are interested in. Publications 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 de Chiara, C., Menon, R. P., Strom, M., Gibson, T. J. & Pastore, A. Phosphorylation of s776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors. PLoS ONE, 2009, 4(12): e8372. See references 2, 54, 56, 143, 153, 160, 179, 192, 237 in the bibliography at the back for publications from this group in 2009. 64 MRC National Institute for Medical Research The structure of frataxin and a model of its cellular role. Frataxin is an iron dependent inhibitor of the enzymatic activity of the desulphurase IscS, the protein responsible for formation of iron sulfur cluster formation on the transient acceptor IscU. STRUCTURAL BIOLOGY Molecular Structure Andres Ramos Molecular recognition in post-transcriptional regulation Lab members: Adela Candel, Cyprian Cukier, David Hollingworth, Silvia Kralovicova, Giuseppe Nicastro, Sunil Prasannan Post-transcriptional regulation plays a central role in cell fate and is based on the synergy existing between the different steps of mRNA metabolism (capping, polyadenylation, splicing, nuclear export, degradation and localisation) and of translation. This synergy is maintained by a network of reversible protein-protein and protein-RNA interactions. Malfunction of the post-transcriptional regulatory network is responsible for pathologies ranging from cancer to auto-immune and neurodegenerative diseases. The rules of RNA recognition by multi-domain RNA binding proteins that function at the core of post-transcriptional regulation are still largely unexplained. We use a range of techniques that enable us to relate functional and structural information in premiRNA processing, pre-mRNA processing, mRNA degradation and mRNA localisation. In this way, we are constructing a general biophysical framework for the study of inter-molecular recognition in protein-RNA regulatory complexes. 15N-1H correlation NMR spectra of KSRP KH3, KH23 and KH34 when bound to Let-7a miRNA TL. Publications 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 3D representation of a HNCACB NMR spectrum, and structure of KSRP KH2-KH3 construct. See references 58, 210 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 65 STRUCTURAL BIOLOGY Molecular Structure Katrin Rittinger Structural biology of signalling networks that regulate innate and adaptive immunity Lab memebers: Veronica Fridh, Frank Ivins, Aylin Morris-Davies, Jonathan Rapley, Kovilen Sawmynaden, Ben Stieglitz, Edmond Wong The innate immune response constitutes the first line of defence against invading micro-organisms. Pathogen recognition is mediated by specific pattern recognition receptors (PRRs) that activate diverse signalling pathways and initiate a pro-inflammatory response. These signalling events need to be tightly controlled as misregulation can lead to chronic inflammation and auto-immune disease. Innate immune responses can also trigger adaptive immunity and the two systems are linked through complex signalling networks. Our research is focused on characterisation of the structural and mechanistic properties of protein complexes that regulate signalling in innate and adaptive immunity. We are currently studying members of the NLR (NOD-like receptor) family of intracellular pattern recognition receptors. NLRs respond to the presence of bacteria and danger signals by triggering cytokine production and the activation of MAP kinases and the transcription factor NF-kB. In addition, we are examining the mechanism of activation of the IKK complex, a key regulator of NF-kB. Furthermore, we are investigating the role and regulation of Vav1, an activator of small Rho-family GTPases, in T cell development and signalling. Binding of di-ubiquitin to NEMO monitored by ITC and AUC Publications Saveliev A, Vanes L, Ksionda O, Rapley J, Smerdon SJ, Rittinger K, Tybulewicz VL Function of the nucleotide exchange activity of vav1 in T cell development and activation. Science Signaling 2:ra83 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 Rapley J, Tybulewicz VLJ and Rittinger K (2008) Crucial structural role for the PH and C1 domains of the Vav1 exchange factor. EMBO Reports 9:655-661 See references 106, 169, 173, 185, 188 in the bibliography at the back for publications from this group in 66 MRC National Institute for Medical Research Signalling through NLRs STRUCTURAL BIOLOGY Physical Biochemistry Peter Rosenthal Cryomicroscopy of proteins, viruses, and cells Lab members: Lesley Calder, Saira Hussain, Rishi Matadeen, Kasim Sader, David Wright, 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 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. Structural model for a Weibel-Palade body containing von Willebrand factor tubules. 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 Map of the pyruvate dehydrogenase E2 complex by cryomicroscopy and image analysis. 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 MRC National Institute for Medical Research 67 STRUCTURAL BIOLOGY Molecular Structure Steve Smerdon EMBO member Structural biology of phosphorylation-dependent signalling in the cell-cycle and the response to DNA damage Lab members: Julie Clapperton, Richard Li, Simon Pennell, Amy Cherry, Otto Kyrieleis, Lasse Stach, Mohamed Ismail, Jan Lloyd, Oliver De peyer The dynamic nature of signalling processes in cells requires them to be rapidly reversible, and this is generally achieved through protein phosphorylation by kinases. There are more than 500 distinct kinases encoded in the human genome and misregulation of phosphorylation is a primary cause of many cancers and other diseases. The response to DNA damage is mediated by a phosphorylation cascade that originates at the site of the lesion and is transduced to a variety of effector molecules and complexes. We are studying a group of proteins that may function as phosphorylation-dependent adaptors or scaffolding molecules in pathways that regulate the response to DNA damage. Our studies have revealed the structures of 14-3-3, Forkhead-associated, Brca1-C-terminus and Polo-box domain complexes and have found a remarkable diversity in binding modes. These observations have led to an additional interest in the regulation of several kinases that play crucial roles in the DNA damage response and its integration into the cell cycle. By understanding the molecular basis of specificity within such an extensive web of regulatory interactions, we aim to determine why these processes run amok, and how drugs might be designed to combat the devastating effects associated with cancer and other diseases. The FHA-domain protein Rv1827 regulates three enzymes of the TCA cycle in Mycobacterium tuberculosis to control glutamate flux and nitrogen assimilation. 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 doublestrand breaks. (See also erratum:Vol 124, pg 1299, 2006). Cell 123:1213-26 See references 126, 148, 185 in the bibliography at the back for publications from this group in 2009. 68 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: Christina Pancevac, David Goldstone, Joe Hedden, 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. Structures of the transcriptional 3’-end processing factor, Rna15, bound to different ribonucleotides; Left, guanosine nucleotide located in binding site. Right, uracil bound in binding site. Publications 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 Epub ahead of print Mortuza GB, Goldstone DC, Pashley C, Haire LF, Palmarini M, Taylor WR, Stoye JP and Taylor IA (2009) Structure of the capsid amino terminal domain from the Betaretrovirus, Jaagsiekte sheep retrovirus. Journal of Molecular Biology 386:1179-1192 Mapping the residues that determine MLV tropism and restriction factor susceptibility onto the viral capsid. Residues that are the major determinants of N- and B-tropism are highlighted in blue. Other residues that result in NB and other minor tropisms are highlighted in red. 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 106, 139, 192 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 69 STRUCTURAL BIOLOGY Mathematical Biology Willie Taylor Protein structure analysis and design Lab members: Viji Chelliah, James MacDonald, Katarzyna Maksimiak, Michael Sadowski, Zoe Katsimitsoulia A view of protein fold space showing the location of “dark” folds (white) between known fold families (red, green) with example structures marked by stars. Publications Sadowski MI and Taylor WR (2010) Protein structures, folds and fold spaces. Journal of Physics-Condensed Matter 22:033103 Macdonald JT, Maksimiak K, Sadowski MI and Taylor WR (2009) De novo backbone scaffolds for protein design. Proteins 78:1311-25 Taylor WR, Chelliah V, Hollup SM, MacDonald JT and Jonassen I (2009) Probing the “dark matter” of protein fold space. Structure 17:1244-52 See references 131, 139, 208 in the bibliography at the back for publications from this group in 2009. 70 MRC National Institute for Medical Research 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 three-dimensional structure. It is the aim of my group to try to understand the relationship between the protein sequence and its structure and hence to function. Such studies can help us to understand the workings of normal proteins and also how abnormal states, such as mutant proteins, can lead to disease. Computer methods that we have developed have been used to construct models for all possible protein folds and we find that only 10% of these model structures correspond to known folds. The remainder, which we call ‘dark’ folds, appear quite normal under all the computer tests we have applied. We are currently using some of these folds as frameworks for design and synthesis. STRUCTURAL BIOLOGY Physical Biochemistry Claudia Veigel Single molecule mechanics of motor proteins Lab members: Sarah Adio, Frederic Eghiaian, Iwan Schaap, Stephan Schmitz We are using single molecule techniques to study molecular mechanisms underlying cellular motility. We focus on the basic mechanisms of chemo-mechanical energy transduction and regulation of myosin motors, using mechanical and imaging techniques including optical tweezers, fluorescence and atomic force microscopy. We are also applying these techniques to study membrane fusion. Our principal aim is to study mechanisms of force generation and motility from the molecular to the cellular level. At the molecular level we aim to understand the details of conformational changes, timing and energetics of the forceproducing process. To achieve this we need to precisely identify and correlate structural, biochemical and mechanical states of these nanomachines. The mechanical interaction between motors, interactions with regulatory agents in local complexes, or in more extended networks, introduces complexity that needs to be investigated and modelled. We also study the invasion of red blood cells by malaria parasites. This process is driven by myosin class 14 molecules, interacting with a network of actin filaments and other structural and regulatory components inside the parasite. We are investigating the structural and dynamic characteristics of malarial actin and its interactions with myosin in vitro. Mechanics of cellular motors are characterised using optical tweezers. Publications Veigel C and Schmidt CF (2009) Friction in motor proteins. Science 325:826-7 Albet-Torres N, Bloemink MJ, Barman T, Candau R, Frolander K, Geeves MA, Golker K, Herrmann C, Lionne C, Piperio C, Schmitz S, Veigel C and Månsson A (2009) Drug effect unveils inter-head cooperativity and strain-dependent ADP release in fast skeletal actomyosin. Journal of Biological Chemistry 284 22926-22937 Sellers JR and Veigel C (2006) Walking with myosin V. Current Opinion in Cell Biology 18:68-73 See references 3, 91, 102, 214 in the bibliography at the back for publications from this group in 2009. Parasites and viruses are studied by atomic force microscopy (AFM). Single molecules can be localised in vitro and in vivo using fluorescence microscopy. MRC National Institute for Medical Research 71 STRUCTURAL BIOLOGY Physical Biochemistry Martin Webb The molecular mechanisms of motor proteins Lab members: Claudia Arbore, Lori Callum, Liisa Chisty, Colin Davis, Simone Kunzelmann, Gordon Reid, Lesley Southerden, Chris Toseland ParM scaffold for the ADP biosensor: structure showing position of mutations introduced and conformation change on ADP binding A major way of achieving movement within the cell is by motor proteins that move along tracks that could be filaments of proteins or nucleic acid. In particular, we are interested in the way that helicases move along double-stranded DNA, separating the two strands, which is essential for DNA replication and repair. We are developing new optical approaches to study this process. Some of our methods, such as to detect inorganic phosphate, are being used widely in research laboratories and in development of drug screening assays. In order to further understand how helicases work as part of a system, we are investigating the replication of certain plasmids that contain antibiotic resistance and 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 building up this system in vitro to study the role and mechanism of each component. We have recently developed a novel biosensor for ADP, based on a protein, ParM, that binds ADP specifically and has been labeled with either rhodamine or coumarin fluorophore. This can measure micromolar concentrations of ADP in real time, in the presence of high concentrations of ATP, so is suitable for real-time assays of kinases and ATPases. Fluorescence increase on ADP binding to the biosensor, ParM labeled with a coumarin Publications Kunzelmann S and Webb MR (2009) A biosensor for fluorescent determination of ADP with high time resolution. Journal of Biological Chemistry 284:33130-33138 Slatter AF, Thomas CD and Webb MR (2009) PcrA helicase tightly couples ATP hydrolysis to unwinding doublestranded DNA, modulated by the initiator protein for plasmid replication, RepD. Biochemistry 48:6326-6334 Sakamoto T, Webb MR, Forgacs E, White HD and Sellers JR (2008) Direct observation of the mechanochemical coupling in myosin Va during processive movement. Nature 455:128-32 See references 73, 117, 175, 196, 209, 223 in the bibliography at the back for publications from this group in 2009. 72 MRC National Institute for Medical Research Neurosciences Developmental Neurobiology David Wilkinson (Head of Division) Siew-Lan Ang James Briscoe Alex Gould Nobue Itasaki Jean-Paul Vincent Molecular Neurobiology Vassilis Pachnis (Head of Division up to Nov 2009) François Guillemot (Head of Division from Dec 2009) Iris Salecker Molecular Neuroendocrinology Iain Robinson (Head of Division up to Sept 2009) Tom Carter (Acting Head of Division from Oct 2009) Matthew Hannah Paul Le Tissier Neurophysiology Troy Margrie (Acting Head of Division) see also the following groups:: Ed Hulme (Structural Biology) Robin Lovell-Badge (Genetics and Development) Annalisa Pastore (Structural Biology) MRC National Institute for Medical Research 73 NEUROSCIENCES Developmental Neurobiology Siew-Lan Ang Neuronal subtype specification in the midbrain and hypothalamus Lab members: Neal Anthwal, Suzanne Claxton, Maria Flavia Guinazu, Melanie Kalaitzidou, Nicolaos Mathioudakis, Emmanouil Metzakopian, Wei Lin, Martin Levesque, Gautam Rishi and Simon Stott The mammalian midbrain and hypothalamus contain many types of neurons that regulate voluntary movement and energy homeostasis, respectively. How the multitude of cell types in these brain regions is generated and their identity specified 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 that regulate food intake. 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 of hypothalamic arcuate proopiomelanocortin and neuropeptide Y neurons. A combination of embryological, genetic, molecular and genomic approaches are employed, including genetic fate mapping studies, null and conditional mutant mice, brain slice culture, time lapse imaging, biochemical and transcriptome analyses. These studies will provide insights into how embryonic gene expression leads to mature neuronal phenotypes. Midbrain dopaminergic neurons generated by differentiation of mouse embryo stem cells Publications 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 Optical projection tomography of a E175 Pitx3tauLacZ/+ mouse brain 74 MRC National Institute for Medical Research Ang SL (2006) Transcriptional control of midbrain dopaminergic neuron development. Development 133:3499-3506 See references 5, 123, 233 in the bibliography at the back for publications from this group in 2009. NEUROSCIENCES Developmental Neurobiology James Briscoe EMBO member Pattern formation in the vertebrate nervous system Lab members: Nikos Balaskas, Natascha Bushati, Rachel Chung, John Jacob, Anna Kicheva, Eva Kutejova, Victoria Lawson, Steven Moore, Ana Ribeiro, Vanessa Ribes, Noriaki Sasai, Samuel Tozer A remarkable feature of embryo development is the reliable and accurate pattern in which cell types arise. This is particularly true in the nervous system where the generation of many different types of neurons in a precise organisation is the first step in the assembly of neuronal circuits. Our studies focus on the molecular and cellular mechanisms that produce and organise neuronal cell types in the spinal cord. A central interest of the lab is the secreted molecule Sonic Hedgehog (Shh), which forms a gradient that controls the pattern of cellular differentiation in the ventral neural tube. Using a range of molecular, imaging and modelling approaches in mouse, chick and zebrafish embryos we are examining how graded Shh signalling is perceived and interpreted by cells to regulate transcriptional responses and cell behaviour. This system provides insight into the mechanisms and strategies of pattern formation that are relevant to many developing tissues. In addition, understanding the process of normal neural development will shed light on conditions in which the nervous system is diseased or damaged. Publications Jacob J, Storm R, Castro DS, Milton C, Pla P, Guillemot F, Birchmeier C and Briscoe J (2009) Insm1 (IA-1) is an essential component of the regulatory network that specifies monoaminergic neuronal phenotypes in the vertebrate hindbrain. Development 136:2477-85 Kutejova E, Briscoe J and Kicheva A (2009) Temporal dynamics of patterning by morphogen gradients. Current Opinion in Genetics & Development 19:315-322 Dessaud E, Yang LL, Hill K, Cox B, Ulloa F, Ribeiro A, Mynett A, Novitch BG and Briscoe J (2007) Interpretation of the sonic hedgehog morphogen gradient by a temporal adaptation mechanism. Nature 450:717-20 A gradient of Shh (green; inset graph) controls the expression of transcription factors (red, orange, blue) in neural progenitors Serotonergic neurons in the hindbrain of an embryonic mouse See references 26, 35, 66, 80, 107, 118, 123, 166 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 75 NEUROSCIENCES Molecular Neuroendocrinology Tom Carter Secretory organelle formation, trafficking and exocytosis Lab members: Nikolai Kiskin, Nicola Hellen, Laura Knipe, Emma Cookson, Jennifer Frampton To survive and function correctly, cells must sense and respond to their environment. This is largely achieved through the cell surface expression of integral membrane proteins (e.g. hormone receptors) and the secretion of soluble proteins to the external environment (e.g. hormones, transmitters, morphogens). The correct delivery of virtually all such proteins to the cell surface or extracellular space involves a complex intracellular machine collectively called the secretory pathway. We study the secretory pathway using molecular, biochemical and live cell optical imaging techniques to analyse the formation, trafficking and exocytosis of secretory organelles, which are the containers that store and ultimately deliver proteins to the cell surface and extracellular milieu. We use endothelial cells (ECs) and the Weibel-Palade body (WPB), as our model system. In collaborative studies, high resolution cryo-EM tomographic images of individual WPBs in intact vitrified ECs have led to the elucidation of the three dimensional structure and packaging of the coagulation factor VWF, and have begun to reveal structural transformations in VWF tubules during WPB exocytosis. Human endothelial cell stained for the coagulation factor Von Willebrand factor (VWF).The rod shaped structures are Weibel Palade bodies, the storage organelle for VWF. Images courtesy of Lindsay Hewlett and Matthew Hannah Publications Babich V, Knipe L, Hewlett L, Meli A, Dempster J, Hannah MJ and Carter T (2009) Differential effect of extracellular acidosis on the release and dispersal of soluble and membrane proteins secreted from the Weibel-Palade body. Journal of Biological Chemistry 284:12459-12468 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 cryo-EM of vitrified endothelial cells. Proceedings of the National Academy of Sciences of the United States of America 106:17407-17412 Babich V, Meli A, Knipe L, Dempster JE, Skehel P, Hannah MJ and Carter T (2008) Selective release of molecules from Weibel Palade bodies during a lingering kiss. Blood 111:5282-5290 76 MRC National Institute for Medical Research Upper panel: images from time lapse movie of a fluorescently labeled WPB during hormone stimulated exocytosis. Lower panel: one section from tomogram of a marrow shaped WPB showing a thin tube like extension at one end projecting to the plasma membrane (arrow). 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, Linda Yee 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 sub-optimal nutrition during embryonic and foetal growth can lead to aberrant metabolism and insulin-resistance later on in adult life. Much of our research in this area uses the fruit fly Drosophila, a model organism that shares many genes with mammals. We recently found that restricting nutrient intake during Drosophila development reduces growth and insulin signalling in certain organs, such as the brain, to a much lesser extent than in others. We have now identified several conserved genes regulating this selective sparing process and are currently examining whether they play a similar role in mammals. A Drosophila neural stem cell (NB) divides to generate multiple neurons/glia (progeny) during development. Some of the genes expressed during this process are indicated. Data from C. Maurange et al., 2008. Publications 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 Miguel-Aliaga I, Thor S and Gould AP (2008) Postmitotic specification of Drosophila insulinergic neurons from pioneer neurons. PLoS Biology 6:e58 The head of a fruit fly in cross section, showing the brain (blue), compound eyes (red) and adipose tissue (green). Image by A. Bailey Gutierrez E, Wiggins D, Fielding B and Gould AP (2007) Specialized hepatocyte-like cells regulate Drosophila metabolism. Nature 445:275-280 lipid MRC National Institute for Medical Research 77 NEUROSCIENCES Molecular Neurobiology François Guillemot EMBO member, FMedSci Cell fate specification in the mammalian brain Lab members: Roberta Azzarelli, Diogo Castro, Daniela Drechsel, Laura Galinanes-Garcia, Matilda Haas, Barbara Hammerle, Julian Heng, Christopher Hindley, Charles Hunt Stem cells in the brain generate an amazingly diverse array of neurons and glial cells during embryonic development, and they continue to produce neurons in a few discrete brain locations during adulthood. We study the genetic programmes that control the differentiation of these neural stem cells into diverse types of neurons, focusing on the generation of neurons of the telencephalon, which are lost in neurodegenerative diseases such as Alzheimer’s disease and Huntington’s disease. We use a combination of genomic techniques, such as transcript profiling, chromatin immunoprecipitation coupled to high throughput sequencing and bioinformatics, to decipher the gene regulatory networks that control the differentiation of neural stem cells into neurons and glia. We then use functional assays and imaging techniques to identify the genetic pathways that control defined steps in neurogenesis, including the proliferation of progenitor cells and the migration of new neurons, and to determine how these pathways differ for the generation of different types of neurons. By gaining insight into mechanisms driving the differentiation of stem cells into specific types of neurons, we hope to help devise strategies to replace lost cells in diseased brains. Migrating neurons in the cerebral cortex of a mouse embryo, labelled by in utero electroporation of Green Fluorescent Protein Publications Gohlke JM, Armant O, Parham FM, Smith MV, Zimmer C, Castro DS, Nguyen L, Parker JS, Gradwohl G, Portier CJ and Guillemot F (2008) Characterization of the proneural gene regulatory network during mouse telencephalon development. BMC Biology 6:15 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 Guillemot F (2007) Spatial and temporal specification of neural fates by transcription factor codes. Development 134:3771-3780 See references 25, 85, 93, 107, 147, 150, 158, 172, 194, 220, 228, 238 in the bibliography at the back for publications from this group in 2009. 78 MRC National Institute for Medical Research Gene regulatory network for dorsal and ventral telencephalon development, based on transcript profiling datasets, evolutionary conserved transcription factor binding sites data and prior literature- based knowledge 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 stimulationdependent 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 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 cryo-EM 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 Hannah MJ, Skehel P, Erent M, Knipe L, Ogden D and Carter T (2005) Differential kinetics of cell surface loss of von Willebrand factor and its propolypeptide after secretion from Weibel-Palade bodies in living human endothelial cells. Journal of Biological Chemistry 280:22827-22830 Weibel-Palade bodies and Golgi apparatus visualised in a cultured human endothelial cell See references 8, 16, 86 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 79 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 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 Itasaki N and Hoppler S (2010) Crosstalk between Wnt and bone morphogenic protein signaling: A turbulent relationship. Developmental Dynamics 239:16-33 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 See references 4, 124 in the bibliography at the back for publications from this group in 2009. 80 MRC National Institute for Medical Research 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. NEUROSCIENCES Molecular Neuroendocrinology Paul Le Tissier Control of prolactin and growth hormone cell differentiation and function Lab members: Leonard Cheung, Arnaud Jaubert, Molly Strom, James Turton 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 interrelationship 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 different proportions of growth hormone cell ablation. The degree of ablation correlates with effects on the other pituitary hormones, with prolactin the most affected. Loss of growth hormone cells also leads to a disruption of the normal organisation of cells within the pituitary, which may have consequences for the secretory response to releasing factors. Publications 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 Real-time monitoring of inhibition of prolactin secretion from a pituitary slice in response to different concentrations of dopamine 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 Le Tissier PR, Carmignac DF, Lilley S, Sesay AK, Phelps CJ, Houston P, Mathers K, Magoulas C, Ogden D and Robinson ICAF (2005) Hypothalamic growth-hormone-releasing-hormone (GHRH) deficiency: targeted ablation of GHRH neurons in mice using a viral ion channel transgene. Molecular Endocrinology 19:1251-1262 See references 33 in the bibliography at the back for publications from this group in 2009. Growth hormone cells are normally organised in a network in the pituitary gland, shown by expression of green fluorescent protein (left panel). Ablation of growth hormone cells disrupts this organisation but cells still form clusters (middle panel), whereas transgenic mice with a loss of growth hormone cell proliferation fail to form clusters, despite a similar cell density (right panel). MRC National Institute for Medical Research 81 NEUROSCIENCES Neurophysiology Troy Margrie Sensory processing in single cells, circuits and behaviour Lab members: Alexander Arenz, Agota Biro, Ed Bracey, Ede Rancz, Bruno Pichler Our goal 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, multi-disciplinary approach towards understanding sensory representation that allows us to explore this fundamental issue from the systems to the cellular level. Specifically, we are investigating several key aspects: (1) The relationship between neuronal connectivity and function, (2) How sensory information is encoded and integrated by individual synapses and cells, (3) How sensory representation is distributed across populations of cells, and (4) The significance of distributed neuronal activity to sensory perception. One particularly useful technique, referred to as two-photon targeted patching, allows us to optically record activity over large populations of cells while simultaneously examining synaptic integration using intracellular whole-cell recordings. This technique can also be used in combination with genetic indicators that permit imaging and electrophysiological characterisation of specific populations of cells. Wherever possible we apply both optical and electrophysiological techniques in behaving animals that allow us to quantify sensory signaling through neuronal circuits. In vivo optical imaging of structure and function of the mammalian olfactory bulb. An anatomical reconstruction of the olfactory bulb (drawn by the Nobel Laureate Ramon y Cajal) highlighting the glomerular organization (red circle) of this brain structure (left). Odour-evoked patterns of glomerular activity resulting from presentation of pineapple and banana Publications 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 Pimentel DO and Margrie TW (2008) Glutamatergic transmission and plasticity between olfactory bulb mitral cells. Journal of Physiology 586:2107-2119 82 MRC National National Institute Institute for for Medical Medical Research Research MRC In vivo whole-cell recordings and two-photon imaging. Intracellular recordings carried out in anesthetized and awake mice (above). 2 photon image of calcium dye- loaded cells in the cortex of an anaesthetized mouse (below). 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: Laranjeira C and Pachnis V (2009) Enteric nervous system development: recent progress and future challenges. Autonomic Neuroscience: Basic and Clinical 151:61-69 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 Kioussis D and Pachnis V (2009) Immune and nervous systems: more than just a superficial similarity? Immunity 31:705-710 See references 12, 30, 57, 74, 75, 115, 119, 195 in the bibliography at the back for publications from this group in 2009. 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. MRC National Institute for Medical Research 83 NEUROSCIENCES Molecular Neuroendocrinology Iain Robinson FMedSci The neuroendocrine cascade of growth Lab members: Randip Bains, Danielle Carmignac, Keith Fairhall, Evelien Gevers, Zhenhe He, Catherine Peters, Molly Strom, Izbel Yusuf The brain regulates many vital functions - including growth, reproduction, metabolism and stress - by controlling the production and secretion of different hormones from the pituitary gland. Specialised neuroendocrine neurons in the hypothalamus release their products into a blood supply that carries them to the pituitary gland, containing endocrine cells that each express specific receptors for the hypothalamic neuronal products. We are particularly interested in the neuroendocrine control of growth hormone (GH), which is essential for normal growth in children and regulates metabolism in adults. We have developed transgenic approaches to identify, image, study and manipulate the activity of individual GH cells and whole populations of cells in normal and dwarf animal models. The pituitary and hypothalamus show remarkable changes in cell number and/or activity in response to changing physiological demands, pointing to the likely presence of stem cells present in the adult pituitary gland, which we have recently identified. We have identified other key genes that are important for pituitary development and normal GH secretion, shedding new light on developmental and post-natal growth and pituitary deficits in children. Fauquier T, Rizzoti K, Dattani M, Lovell-Badge R and Robinson ICAF (2008) SOX2-expressing progenitor cells generate all of the major cell types in the adult mouse pituitary gland. Proceedings of the National Academy of Sciences of the United States of America 105:2907-2912 McGuinness L, Magoulas C, Sesay AK, Mathers K, Carmignac D, Manneville JB, Christian H, Phillips JA and Robinson ICAF (2003) Autosomal dominant growth hormone deficiency disrupts secretory vesicles in vitro and in vivo in transgenic mice. Endocrinology 144:720-731 Bains RK, Wells SE, Flavell DM, Fairhall KM, Strom M, Le Tissier P, Robinson IC. (2004) Visceral obesity without insulin resistance in late-onset obesity rats. Endocrinology. 145:2666-79 See references 28, 33, 86, 96, 113, 191 in the bibliography at the back for publications from this group in 2009. 84 MRC National Institute for Medical Research Stem cells in the pituitary gland NEUROSCIENCES Molecular Neurobiology Iris Salecker Axon guidance in the developing visual system of Drosophila Lab members: Holger Apitz, Dafni Hadjieconomou, Emily Richardson, Benjamin Richier, Nana Shimosako, Katarina Timofeev A defining feature of many brain areas in vertebrates and invertebrates is the organisation of neuronal networks into columns and layers. In each of these units, afferent axons establish synaptic contacts with distinct sets of target neurons to ensure correct information processing in the mature brain. Our understanding of how such specific connections are formed during development is still limited. We use genetic and imaging approaches to study neural circuit assembly in the Drosophila visual system. Photoreceptor neurons extend axons from the retina into two areas of the optic lobe, the lamina and medulla, where they connect with target neurons in highly regular patterns. Visual circuit formation depends on intricate bidirectional interactions between photoreceptor axons, glia and target neurons. Our ongoing studies aim at identifying the molecular determinants that control the initial development of neurons and glia in the optic lobe. Furthermore, we investigate the mechanisms that mediate layer-specific targeting of photoreceptor axons and their postsynaptic partners. As the molecular mechanisms are highly conserved, our studies will provide insights into the principles underlying normal brain development and, in the long term, associated neurological dysfunctions. In the adult visual system of Drosophila, R1-R6 photoreceptor axons terminate in the lamina, connecting with sets of lamina neurons within columns, while R7 and R8 axons establish connections with target neurons in two specific layers in the medulla Publications Photoreceptor axons (red) are in close contact with glial cells and their extensive processes (green) in the late pupal visual system 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 Chotard C and Salecker I (2007) Glial cell development and function in the Drosophila visual system. Neuron Glia Biology 3:17-25 Chotard C, Leung W and Salecker I (2005) glial cells missing and gcm2 cell autonomously regulate both glial and neuronal development in the visual system of Drosophila. Neuron 48:237-51 MRC National Institute for Medical Research 85 NEUROSCIENCES Developmental Neurobiology Jean-Paul Vincent EMBO member Cell biological basis of 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 relatively small number of signaling molecules orchestrate growth and cell fate decisions during development. We are particularly interested in studying these processes in epithelia, sheets of cells that make up most tissues. We investigate the mechanisms that control the production and activity of one such signal, the secreted lipoglycoprotein encoded by wingless. This is relevant to human disease because Wingless is the fly equivalent of Wnt1, a molecule implicated in many cancers. We also investigate how this signal controls patterning, growth and cell death within developing appendages of the fly. In a distinct but related strand of work, we are exploring the homeostatic mechanisms ensuring that weak or mis-specified cells are eliminated from epithelia. How tissues recognise rogue cells and how this information is transduced to the cell death machinery remain outstanding questions in cell and developmental biology. Again, this is relevant to cancer as damaged cells that fail to be eliminated can contribute to tumours. Impaired Wingless secretion on VPS35 mutants. The Wingless gradient fails to form and Wingless accumulates in producing cells. 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 10, 99, 156, 217, 218 in the bibliography at the back for publications from this group in 2009. 86 MRC National Institute for Medical Research An apoptosis sensor. The top panel shows the design of the sensor, which is tethered to membranes in live healthy cells. Upon caspase activation, the green moiety is released and targeted to the nucleus. The bottom panel shows cultured cells either exposed to UV irradiation to trigger apoptosis (right) or mock treated (left)Note the accumulation of GFP in the nucleus of dying cells. NEUROSCIENCES Developmental Neurobiology David Wilkinson EMBO member, FMedSci Regulation of boundary formation and neurogenesis Lab members: Marie Breau, Sebastian Gerety, Rosa Gonzalez-Quevedo, Lauren Gregory, Mohamed Ismail, Rosie Morley, Alexei Poliakov, Dorothy Sobieszczuk, Javier Terriente, Hannah Williams, Qiling Xu During early stages of nervous system development in vertebrates, neural tissue is subdivided into building blocks, each with a distinct regional identity. Within these subdivisions, the proliferation and differentiation of progenitor cells is regulated in time and space to form the correct number and organisation of neuronal and glial cells. In order for these precise patterns to form and be maintained, it is essential that cells do not migrate into inappropriate locations. Disruption of the mechanisms that regulate cell proliferation, differentiation or migration can lead to diseases such as cancer. Our studies aim to elucidate molecular and cellular mechanisms that regulate formation of precise tissue subdivisions and patterns of differentiating cells in the vertebrate nervous system. We are analysing how signaling through Eph receptors and ephrins inhibits intermingling and establishes sharp boundaries between distinct cell populations. In other studies, we have identified a pathway mediated by targeted protein degradation required for the onset of neuronal differentiation, and uncovered a novel mechanism underlying spatial patterning of neurogenesis involving FGF signaling from neurons Detection of neurons (green), cell proliferation (red) and cell nuclei (blue) in the developing hindbrain 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 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 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 See references 109, 146, 190 in the bibliography at the back for publications from this group in 2009. Expression of specific genes that mark segment boundary cells (green) and alternating segments (red) in the hindbrain MRC National Institute for Medical Research 87 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 Steve Sedgwick 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 88 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, Louise Reynard 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 targeting 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 targeting 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 sperm head abnormalities and severely impaired sperm function. Publications Burgoyne PS, Mahadevaiah SK and Turner JMA (2009) The consequences of asynapsis for mammalian meiosis. Nature Reviews Genetics 10:207-16 Cocquet J, Ellis PJ, Yamauchi Y, Mahadevaiah SK, Affara NA, Ward MA and Burgoyne PS (2009) The multicopy gene Sly represses the sex chromosomes in the male mouse germline after meiosis. PLoS Biology 7:e1000244 In males, SLY protein co-localises with the X or the Y chromosome and represses sex chromosome genes in haploid post-meiotic germ cells (i.e. spermatids). Upper panel: Co-localisation of SLY protein (in green) with the X or the Y chromosome (in red) in spermatids. Bottom panel: Micro-array experiments were carried out to compare gene expression in testes from Sly-deficient mice and WT mice Reynard LN, Cocquet J and Burgoyne PS (2009) The multi-copy mouse gene Sycp3-like Y-linked (Sly) encodes an abundant spermatid protein that interacts with a histone acetyltransferase and an acrosomal protein. Biology of Reproduction 81:250-257 See references 29, 37, 50, 163, 231 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 89 GENETICS AND DEVELOPMENT Stem Cell Biology and Developmental Genetics Rita Cha Regulation of eukaryotic chromosome metabolism Lab members: Jesus Carballo, James Cauwood, Tony Johnston, Ana Penedos, and Chaim Sagal 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 Telengiectasia (AT) and Seckle syndrome. We use genetically tractable S. cerevisiae to study the molecular basis for the ATR/ATM functions. 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. Structure of human Chromosome I during mitotic or meiotic divisions. The intimate interaction between maternal (m) and paternal (p) chromosomes is observed only during meiosis Targets of ATR/ATR proteins during yeast meiosis. The targets (red circles) are activated during pairing of maternal and paternal chromosomes (red and blue lines). Targets disappear once the pairing is complete (green lines) Publications 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 Carballo JA and Cha RS (2007) Meiotic roles of Mec1, a budding yeast homolog of mammalian ATR/ATM. Chromosome Research 15:539-50 Machin F, Torres-Rosell J, De Piccoli G, Carballo JA, Cha RS, Jarmuz A and Aragon L (2006) Transcription of ribosomal genes can cause nondisjunction. Journal of Cell Biology 173:893-903 90 MRC National Institute for Medical Research 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 and Elgar G (2009) The PAX258 gene subfamily: A comparative perspective. Developmental Dynamics 238:2951-2974 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 Conservation of non-coding sequences across the Meis2/c15orf41 locus in vertebrates Transient GFP expression after the injection of a Fugu Sox21:GFP BAC into zebrafish MRC National Institute for Medical Research 91 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 plan to use these methods to study the timing and localisation of gene expression in developmental model systems such as Xenopus. In particular we will be analysing time based profiles of gene expression generated by massively parallel, deep-sequencing technology, and combining this with expression co-localisation data derived from the computational comparison of in situ expression images, in order to generate large numbers of candidate relationships between genes. These relationships will then be validated and characterised, using both bioinformatic and experimental methods, and from these we can build more extensive and informative models of the gene regulatory networks controlling early development. Publications Embryonic gene expression profiles for Xenopus tropicalis derived from existing EST data. Using cDNA library data and gene-clustered ESTs, we can reconstruct the time-based behaviour of gene expression in frog embryos from the fertilised egg (stage 1) through to late metamorphosis. Here we see a clear distinction between maternal (upper profiles) and early zygotic (lower profiles) mRNAs, with shorter and longer persistence times. Highthroughput sequencing technology will yield a hundred times better resolution and should enable clear inferences to be drawn about the progression of the embryonic transcriptional program 92 MRC National Institute for Medical Research 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 Clustering in situ image data to extract candidate gene relationships. Using computerised representation of embryonic gene expression patterns, we can cluster the images using a similarity metric, looking for pairs of genes with highly congruent expression patterns at the same stage of development. These co-localised genes are likely to have some direct or indirect functional relationship, and this can be further dissected using a combination of bioinformatic and experimental techniques 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 GENETICS AND DEVELOPMENT Developmental Biology Malcolm Logan Understanding vertebrate limb development Lab members: Anna Kucharska, Sue Miller, Natalie Butterfield, Veronique Duboc, Peleg Hasson, Satoko Nishimoto, Jutta Roth, 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 genesis 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 uniform and 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 63, 138 in the bibliography at the back for publications from this group in 2009. Confocal microscope image of the embryonic mouse forepaw, illustrating the interconnected network of muscle (red) and tendon (green) fibres. A dorsal view of the back of the hand and forearm is shown MRC National Institute for Medical Research 93 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, Maria-Victoria Gomez-Gaviro, Silvana Guioli, Susanne Jakob, Ander Matheu, Adam Nunn, 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. 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 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 Fauquier, T., Rizzoti, K., Dattani, M., Lovell-Badge, R., Robinson, ICAF. (2008). SOX2-expressing progenitor cells generate all of the major cell types in the adult mouse pituitary gland. Proc. Natl. Acad. Sci. USA. 105, 2907-12. Sekido, R. and Lovell-Badge, R (2008). SRY and SF1 act on a specific enhancer of SRY in sex determination. Nature 453, 930-4. GFP expression driven by a testis-specific enhancer of Sox9 in transgenic mice 94 MRC National Institute for Medical Research Pituispheres contain progenitors expressing SOX2 (green) and S100 protein (blue), able to differentiate into hormone-producing cells (green) See references 13, 113, 137, 189, 213, 236 in the bibliography at the back for publications from this group in 2009. GENETICS AND DEVELOPMENT Developmental Biology Tim Mohun Heart development in vertebrates Lab members: Mike Bennett, Yuval Cinnamon, Laurent Dupays, Surendra Kotecha, Catherine Shang, Stuart Smith, Norma Towers Formation of the heart is a complex process that begins very early in the vertebrate embryo. A simple pulsatile tube is progressively remodelled into a complex multichambered organ capable of supporting embryo growth. This transformation requires exquisite coordination of cell differentiation and growth, and dramatic changes in organ shape. Abnormalities affecting any step will have profound consequences on the foetal heart. Consequently, heart defects are the most common birth defect. Genetic and environmental factors are both implicated as causes, but their identities and the reasons for their effect are poorly understood. 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. Since many of the basic steps in heart formation are similar in all vertebrates, valuable information can be obtained from studying a variety of different species. We are using transgenic and genomic methods to examine how gene expression is regulated in the developing heart of frog and mouse embryos and their contribution to adult heart disease. 3D imaging and computer modelling procedures are used in parallel to monitor effects of normal and altered gene expression on heart morphology. The developing heart of a frog tadpole can be visualised by it expression of the heart muscle gene XMLC2 (A: blue staining). At high magnification, the different portions of the tadpole heart can be distinguished (B) Publications 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 3D reconstruction of a chick embryo heart reveals the complexity of its internal structure. At this stage of development, distinct heart chambers can be recognised and the inside surface of the heart wall is a complex mesh of muscle tissue Dupays L, Kotecha S and Mohun TJ (2009) Tbx2 misexpression impairs deployment of second heart field derived progenitor cells to the arterial pole of the embryonic heart. Developmental Biology 333:121-131 See references 1, 24, 65, 87 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 95 GENETICS AND DEVELOPMENT Developmental Biology Elke Ober Liver development in zebrafish Lab members: Jordi Cayuso Mas, Johanna Fischer, Katarzyna Koltowska, Despina Stamataki, Morgane Poulain During development, the liver, gall bladder and pancreas arise from neighbouring domains within the foregut, and a highly regulated network of signals is required to specify each organ. Our research aims to elucidate the molecular network and cellular mechanisms underlying liver formation in vertebrates using zebrafish as a model. Understanding the genetic programme of liver formation provides insights into embryonic development, tissue homeostasis in adults, regeneration following tissue damage and more recently, the development of novel therapies, such as hepatic stem cells. Hepatic precursors form in the ventral foregut endoderm of the embryo in response to signals from the adjacent mesoderm, ultimately differentiating into a functional liver. Previous work has uncovered that prometheus mutants, encoding the signalling factor wnt2bb, exhibit a profound but transient defect in the specification of liver fate from multipotential progenitors. Ongoing studies employ genetic approaches to uncover factors that (i) compensate for loss of wnt2bb in prometheus mutants, (ii) modulate or interact with components of the Wnt signalling pathway during liver specification, and (iii) direct the morphogenesis of the organ bud in newly specified hepatic precursor cells. Publications 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 Ober EA, Verkade H, Field HA and Stainier DY (2006) Mesodermal Wnt2b signalling positively regulates liver specification. Nature 442:688-691 96 MRC National Institute for Medical Research Newly specified liver cells (red) in the zebrafish digestive tract (green) Digestive organs at 3 days of development: liver (red), pancreas (green) and gall bladder (blue) GENETICS AND DEVELOPMENT Stem Cell Biology and Developmental Genetics Steve Sedgwick Regulation of mitosis Lab members: Marco Geymonat, Adonis Spanos Equal segregation of the newly replicated chromosomes during mitosis is one of the fundamental requirements for a successful cell cycle. For this to occur correctly, the mitotic spindle must be aligned at right angles to the plane of cell division. Complex spatial sensing systems called checkpoints exist that prevent unequal chromosome partitioning. Such mechanisms reduce the chances of progeny cells receiving no chromosomes. They also protect against cells receiving multiple complements of chromosomes, a contributory factor to malignant transformation in higher eukaryotic cells. We currently study the mechanism that coordinates the morphological development of a cell with the segregation of its replicated chromosomes in budding yeast. We have characterised how a protein called Lte1 plays a central role in both these processes. On one hand Lte1 limits the growth of the cell to a particular moment of the cell cycle while at the same time it ensures that the cell cycle is completed only when the chromosomes are correctly segregated. Publications Geymonat M, Spanos A, de Bettignies G and Sedgwick SG (2009) Lte1 contributes to Bfa1 localization rather than stimulating nucleotide exchange by Tem1. Journal of Cell Biology 187:497-511 Geymonat M, Spanos A and Sedgwick S (2009) Production of mitotic regulators using an autoselection system for protein expression in budding yeast. Methods in Molecular Biology 545:63-80 Altered budding pattern in yeast expressing a mutant Lte1 protein Colocalization of a mitotic regulator (red) with an effector of polarized growth (yellow). DNA is in blue Darieva Z, Bulmer R, Pic-Taylor A, Doris KS, Geymonat M, Sedgwick SG, Morgan BA and Sharrocks AD (2006) Polo kinase controls cell-cycle dependent transcription by targeting a coactivator protein. Nature 444:494-498 MRC National Institute for Medical Research 97 GENETICS AND DEVELOPMENT Systems Biology Jim Smith FRS, EMBO member, FMedSci The molecular basis of mesoderm formation Lab members: Liz Callery, John Cannon, Nicolette Chan, Clara Collart, Kevin Dingwell, Amand Evans, Tiago Faial, George Gentsch, Steve Harvey, Helle Jorgensen, Mary Wu The different cell types of the body are formed in the right place and at the right time in response to signals that are produced by special organiser regions of the embryo. These so-called 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 results in the formation of organs and cell types such as heart, muscle, kidney and bone. 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, as well as biochemical and mathematical approaches to ask how cells distinguish between different morphogen concentrations to activate different developmental pathways. We also use a range of molecular techniques to identify the genes that are activated by these signalling pathways and which go on to activate the genetic regulatory networks that result in the formation of specific cell types. We hope that our work will help in efforts to direct stem cells down the desired developmental pathways. Spread of labelled activin (green) through a responding tissue. The source of activin is to the left. At 2 hours (top) activin is predominantly extracellular; at 3.5 hours (bottom) much has become internalised Publications Collart C, Ramis JM, Down TA and Smith JC (2009) Smicl is required for phosphorylation of RNA polymerase II and affects 3'-end processing of RNA at the midblastula transition in Xenopus. Development 136:3451-3461 Hagemann AI, Xu X, Nentwich O, Hyvonen M and Smith JC (2009) Rab5-mediated endocytosis of activin is not required for gene activation or long-range signalling in Xenopus. Development 136:2803-2813 Harvey SA and Smith JC (2009) Visualisation and quantification of morphogen gradient formation in the zebrafish. PLoS Biology 7:e1000101 98 MRC National Institute for Medical Research Use of bimolecular fluorescence complementation reveals that signalling by nodal family members is strong near the margin of the zebrafish embryo (bottom of image) and weak near the animal pole (top) 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. Publications 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 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 Turner JMA, Mahadevaiah SK, Fernandez-Capetillo O, Nussenzweig A, Xu X, Deng CX and Burgoyne PS (2005) Silencing of unsynapsed meiotic chromosomes in the mouse. Nature Genetics 37:41-47 Localisation of BRCA1 to the X and Y chromosomes during male meiosis The inactive X chromosome, labeled with H3K27methylation, in female marsupial brain cells See references 29, 128, 129, 164 in the bibliography at the back for publications from this group in 2009. MRC National Institute for Medical Research 99 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 the tasks specific genes perform in living organisms. Our group uses genetics to describe gene roles important for initial formation and function of tissues and organs, by comparing normal embryogenesis to mutations with disruptions in individual genes. Since all vertebrates (including humans) share most gene functions, we use a frog, Xenopus tropicalis, as a genetic model because of its simple chromosomal structure and easily-studied eggs. We are developing procedures for rapidly cloning X. tropicalis mutations, taking advantage of the abundant meioses (up to 10,000) provided by a single mating and the ease of gynogenesis and haploid genetics. In the first cloning of an X. tropicalis mutation, we showed that a defect in the myh6 gene (which can lead to atrial-septal defects in human) causes the non-contractile hearts in the frog muzak phenotype. This mutation ablates both myh6 protein and heartbeat, so the roles played by myosin thick filaments and contractile activity in myofibrillogenesis and cardiogenesis can be studied, helping model human disease states in both heart and skeletal muscle. Myofibril mutation dicky ticker. Top panel, sarcomere structure in wild type skeletal muscle shown by z-discs (green, α-actinin) and actin filaments (red, phalloidin); bottom panel, disorganized sarcomeres in the dicky ticker mutation deficient in a myosin chaperone protein Cardiac development in the absence of heartbeat. 3-D models of wild type (top) and muzak mutant (bottom) X. tropicalis tadpole hearts. Endocardium is on the right; myocardium is on the left Publications Abu-Daya A, Sater AK, Wells DE, Mohun TJ and Zimmerman LB (2009) Absence of heartbeat in the Xenopus tropicalis mutation muzak is caused by a nonsense mutation in cardiac myosin myh6. Developmental Biology 336:20-29 Khokha MK, Krylov V, Reilly MJ, Gall JG, Bhattacharya D, Cheung CYJ, Kaufman S, Lam DK, Macha J, Ngo C, Prakash N, Schmidt P, Tlapakova T, Trivedi T, Tumova L, Abu-Daya A, Geach T, Vendrell E, Ironfield H, Sinzelle L, Sater AK, Wells DE, Harland RM and Zimmerman LB (2009) Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes. Developmental Dynamics 238:1398-1406 Goda T, Abu-Daya A, Carruthers S, Clark MD, Stemple DL and Zimmerman LB (2006) Genetic screens for mutations affecting development of Xenopus tropicalis. PLoS Genetics 2:e91. See references 1, 84, 113, 165 in the bibliography at the back for publications from this group in 2009. 100 MRC National Institute for Medical Research 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. Tim Bliss, FRS Tim Bliss has been a key figure in neuroscience research at NIMR, leading a productive and internationally renowned research program at Mill Hill spanning four decades. Though born in England, Tim gained his early scientific training in Canada, taking a PhD at McGill in Montreal. He was attracted back to London in 1967, to join the Division of Neurophysiology and Pharmacology at NIMR. This was the time of the ‘flower power’ generation, and whilst Tim’s experiments at the time may have concentrated on the electrophysiology of the rodent nervous system, it is clear that his own nervous system absorbed something of the zeitgeist of pyschedelia, as the colours of his socks, shirts and ties continue to remind us. Tim was keenly interested in the processes underlying learning and memory, following the conceptual and experimental studies of Hebb and Penfold, suggesting there were synaptic mechanisms of plasticity that would somehow enable neural structures to learn and encode engrams of previously experienced events. Tim’s initial hunt for this in the neocortex was fruitless, but he recognised that there were many reasons to focus on the hippocampus, not least the compelling observations from a remarkable patient (H.M.) with hippocampal damage who exhibited specific and profound deficits in new memory formation. It was Tim’s seminal studies with Terje Lømo in Per Andersen’s lab in Oslo in the late 1960’s that uncovered the phenomenon of synaptic long-term-potentiation (LTP). In LTP, certain repeated stimulus patterns are able to ‘strengthen’ hippocampal synapses, which then maintain a sustained increase in response to the same stimulus, once LTP has been induced. LTP rapidly became the dominant synaptic model of how the mammalian brain learns, and remains the benchmark paradigm for studies of neural mechanisms of memory formation. Tim’s work generated many important further questions such as: how long could LTP last; what were the molecular mechanisms of LTP; was the origin pre-synaptic (an increase in transmitter release) or post-synaptic (an increase in response to transmitter) or both; could LTP be evoked and detected at a single synapse. Over his productive career Tim and his many colleagues and collaborators have provided answers to many of these questions. Tim’s contributions to neuroscience have been widely recognised. He was elected FRS in 1994 and he has become one of the most prominent and highly cited neuroscientists in the world, with numerous prizes, honours and awards. Tim was, and is, a tireless champion of the importance of Neurosciences at NIMR and of the Institute’s great value. He became Head of the Division of Neurophysiology in 1988, and head of the Neurosciences Group in 1996 and he has nurtured a generation of neuroscientists now flourishing in labs all over the world. Although Tim formally retired in 2006 he continues as a visiting worker and, when not at home in Norwich, is to be encountered travelling to speak in response to numerous invitations from all over the world. Those that have heard Tim speak after a good dinner (or on any occasion, actually) appreciate a born raconteur and bon vivant (where did he find the time?) regaling his listeners with stories of food, wine and crewing sailing ships (perhaps not the wisest maritime combination), art and architecture. We wish him well. MRC National Institute for Medical Research 101 Emeritus scientists Guy Dodson, FRS Guy Dodson established protein crystallography at NIMR and played a leading role in integrating structural biology into the scientific life of the Institute. He came as an internationally recognised structural biologist, and quickly became intoxicated with the Institute’s biology and collegiality. Guy was educated in New Zealand, and as a PhD student solved the crystal structure of a plant alkaloid – the biggest crystal structure in the Southern hemisphere at the time! Dorothy Hodgkin’s papers had a strong influence on him and he joined her group at Oxford in 1962 to work on insulin. The symmetry of the crystals made this very technically challenging but thanks to greatly improved methods, the problem was solved in 1969 using the physics of anomalous scattering. He found Hodgkin’s laboratory a paradise: like J.D. Bernal’s laboratory, it knew no boundaries. He gained a thorough grounding in biological perspectives from Bernal and Don Steiner, and in chemical structure and mechanism from Jack Dunitz and Bob Williams. In 1971 Dorothy Hodgkin mused that perhaps Guy should move to NIMR but the idea took another twenty years to flower! After leaving Oxford in 1976, Guy established a group in the Chemistry Department at the University of York. The Professor of Chemistry, Dick Norman, was very supportive, tolerating Guy’s exclusive commitment to proteins, their crystallography, structure and mechanism. Guy focused on proteins of medical and industrial importance, especially insulin, collaborating with Eleanor Dodson. Thus the proposal by John Skehel to establish a crystallography division at NIMR fitted naturally with his interests. For Guy there were two major attractants: the Institute was screaming out for crystal structures, and the magnificent library, which was only deficient with respect to one journal – Acta Crystallographica! There was a third reason, not adequately appreciated before joining – the smooth and wholly intelligent and effective administration. Guy decided to leave his York research there and to start new interests at the Institute. The first white powder quickly appeared, thanks to Alistair Aitken, a protein egregiously called 14-3-3. At the time it was evident that the protein was important but not what it did! The division was quickly up and running, with key appointments like Kim Hendrick and Bing Xiao. Bing soon obtained good crystals of 14-3-3, and the structure was solved; it had a remarkable and lovely structure and organisation. The shape and nature of its surface suggested the molecule performed an adaptor function, and so it proved. From here on, the division developed very happily with programmes in signal transduction and cell-cycle regulation. Guy collaborated with Tony Holder on malaria, the late Jo Colston on mycobacteria and Iain Robinson on molecular endocrinology. One effect of these tough projects was that awareness grew across the Institute of the potential for crystallographic projects to inform biological interests. The division was an immediate success. Some projects were particularly close to Guy’s heart. One favourite, with Peter Bayley in Physical Biochemistry, was on the prion protein. It was ferociously difficult and had safety issues, but the combination of superb molecular biology, biochemistry, biophysics and crystallisation by Lesley Haire led to a surprising and revealing dimeric structure. Another interest was the catalytic reaction associated with particular thrombin inhibitors. This research explained the unusual binding properties of these ligands as well as revealing unexpected plasticity in the enzyme’s catalytic chemistry. Guy was a member of NIMR staff from 1993 to 2004. He appreciated particularly the Institute’s multidisciplinary approach to science.He retired, reluctantly, from research and involvement in shaping the future of NIMR. 102 MRC National Institute for Medical Research Scientific facilities Biological and Procedural Services MRC Biomedical NMR Centre Other structural biology facilities X-ray crystallography Analytical ultracentrifugation Mass spectrometry Protein sequence analysis and structure modelling Confocal imaging and analysis laboratory Histology Electron microscopy Single molecule techniques Total internal reflection fluorescence microscopy Optical tweezers Atomic force microscopy Cryo electron microscopy Bioresources Large scale laboratory Media production Freezer archive Flow cytometry facility High-throughput sequencing Affymetrix microarray facility Level 4 high-containment virus laboratory Engineering and Electronics Technology transfer Other support services Library Computing and telecommunications Web team PhotoGraphics Engineering services Safety and security MRC National Institute for Medical Research 103 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. We aim to meet all the needs of the scientific Divisions whilst ensuring the highest possible standards of health and welfare for all species. It 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 are available for advice on the health and welfare of our animals. The Division provides services for the production of antibodies and the incubation of fertile chicken eggs. Moreover, 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. 104 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Procedural Service Section The Procedural Service Section provides a range of services and facilities for the production and archiving of genetically altered rodents. More than 200 new genetically altered lines are produced each year by pronuclear and embryonic stem cell microinjection. The Section offers a comprehensive service for the cryopreservation of rodent germplasm and has extended this service to include frog and fish spermatozoa. Currently in excess of 2100 mouse strains are cryopreserved. The section also coordinates the rederivation of imported rodent lines and is skilled in a number of assisted reproduction techniques. A small DNA isolation and genotyping service is available. Every year Biological Services and Procedural Services together coordinate over 150 shipments of live animals or frozen germplasm to collaborators all over the world. Procedural Services Manager: Sarah Johnson NC3Rs/LASA Small Awards awarded to Biological and Procedural Services (2005-2008) Y. Saavedra-Torres: Ultrasound imaging of murine in utero development S. Johnson: A non-surgical method of embryo transfer. A. Palmer: CPD for Animal Technicians. M. Franchi: An assay to quantify stress in Xenopus. C. Langhorne: A reliable method for the cryopreservation of zebrafish spermatozoa. J.M. Sanchez-Morgado: Training in amphibian & zebrafish medicine. S. Wood: Training in a laser assisted method of ICSI. K. Mathers: Animal technician exchange visits and training. J M Sanchez-Morgado: Replacement of the Mouse Antibody Production test with PCR - evaluation of the quality of DNA extracted from biological samples MRC National Institute for Medical Research 105 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 1980 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 recently-funded 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 19 research groups from 16 different universities and institutes from around the UK. Within NIMR our closest links are with the Division of Structural Biology. 1 NMR study of the interaction between a signalling protein and a phosphopeptide. Left: Overlay plot of successive spectra obtained after stepwise additions of the peptide to the protein solution. The peaks that change position identify the residues involved in the binding interaction. Right: Mapping the affected residues onto the structure of the protein reveals the interaction surface. Publications 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 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 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 peptidylprolyl isomerase activity. FEBS Journal 276:4529-4544 106 MRC National Institute for Medical Research Magnet of the Centre’s 800 MHz spectrometer SCIENTIFIC FACILITIES Other structural biology facilities X-ray crystallography X-ray crystallography enables atomic resolution structures of biological molecules to be determined from protein crystals. At NIMR we have an in-house X-ray source and an automated (robotic) crystal mounting machine. We use robotic systems for protein expression and crystallisation trials and for high-throughput screening of protein expression constructs. Protein crystal X-ray diffraction atomic structure 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 107 SCIENTIFIC FACILITIES Other structural biology facilities Mass spectrometry The Institute has two mass spectrometers which are used in a range of biochemical applications. A research grade MALDITOF 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-of-flight (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. Protein sequence analysis and structure modelling The Division of Mathematical Biology contains a support service for protein sequence analysis and structure modelling. It draws on the state-of-the-art algorithms being developed by the experts in Mathematical Biology as well as the many computer programs freely available from the scientific community. There is also an inhouse, commercial computer graphics package for detailed threedimensional modelling. The service is available to all NIMR scientists and external collaborators. 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. 108 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Confocal Imaging and Analysis Laboratory Yan Gu Co-workers: Kate Sullivan, Donald Bell, Chen Qian The Confocal Imaging and Analysis Laboratory (CIAL) provides a core imaging and support facility for NIMR scientists. 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 is used by more than 160 scientists from 15 Divisions. Users operate the equipment by themselves, but the complexity of imaging makes support an extremely important part of the facility. We routinely provide users with training, troubleshooting, consultation and microscope maintenance. In 2009, we also provided special techniques such as thick tissue imaging, 2nd harmonic generation imaging, spectral unmixing of multiple labelling, quantitative imaging, deconvolution imaging, and automatic cell counting. Research in CIAL focuses on the technological development of biological microscopy and image processing methodologies that bring benefits to NIMR scientists. These include techniques of intravital imaging, super resolution imaging, correlative microscopy, high throughput imaging, automatic cell segmentation and tracking. The lab has expertise in sample preparation and labelling, live and fixed sample imaging, and in hardware and software development. In 2009, we have carried on nine projects and research collaborations, covering new imaging techniques, microscope improvements, and image enhancement and quantification. 2nd harmonic generation image (red) of the non-labelled muscle, and GFP-labelled neural network (green) in an adult mouse gut. Courtesy of Reena Lasrado. . Green, red, purple, and grey-level in the image correspond to positive labeling of transcription factors including Nkx2.2, Olig2, and Pax6, and DNA in nuclear respectively. Courtesy of Ana Ribeiro Publications D. Zhu, S. Jarmin, A. Ribeiro, F. Prin, S.Q. Xie, K. Sullivan, J. Briscoe, A.P. Gould, F.M. Marelli-Berg & Y. Gu. (2010) Applying an adaptive watershed to the tissue cell quantification during T-cell migration and embryonic development Methods in Molecular Biology 616 (in press) MRC National Institute for Medical Research 109 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 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 facility also provides training, protocols, and assistance for investigators on all aspects of histology, including tissue fixation, tissue processing, and immunohistochemical techniques. Kidney stained with Periodic acid Schiff stain (E. Grigorieva) Bone stained with Mallory’s Trichrome (E. Grigorieva) Colon stained with Hematoxylin and Eosin (E. Grigorieva) 110 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Electron microscopy Liz Hirst The Institute has both Transmission (Jeol 1200 EX conventional scattering optics) and Scanning Electron Microscope (Jeol 35CF) facilities which are currently being upgraded to CCD photography. There is also a dedicated EM processing laboratory. Staff from any department at NIMR may request TEM or SEM investigations for the purpose of providing supporting data for scientific studies ongoing within their own laboratory. TEM techniques available include ultrathin sectioning and ultrastructural analysis of experimental tissues, cell cultures or pellets. Immuno-EM techniques can be post-embedding immuno-gold labelling of antigens upon ultrathin 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 Unit. Alternatively, should staff/students wish to learn any EM techniques for themselves, technical advice, training and support can be provided. TEM M. tuberculosis infected macrophage SEM Drosophila eye mutation MRC National Institute for Medical Research 111 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 biomolecules. Some of these techniques provide high resolution images of the moelcules others give dynamic information about the interactions between proteins, DNA, lipid membranes and small ligand molecules. TIRF (right) and Optical Tweezers (left) 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 per 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 and deflections of the tip, as it rides over molecules fixed to the surface, 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 nano-wizard used at NIMR enables simultaneous imaging by optical microscopy and AFM 112 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 reveal near-atomic resolution structural information. CryoEM is well-suited to highresolution studies of both the structure and dynamics of large proteins and protein complexes (e.g. 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. 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 113 SCIENTIFIC FACILITIES Bioresources Joachim Payne Co-workers: Brian Trinnaman, Jackie Wilson, Ian Oliver, Charlotte Austin, Wioletta Berg, 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 eight research divisions at NIMR, as well as collaborating with other MRC units, the Marie Curie Research Institute, NIBSC and the Wellcome Trust Sanger Institute. Last year we grew 1200 litres of hybridoma cells and 2400 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 1200 types of product, and last year processed 2800 orders, totalling around 36000 litres of media and associated solutions including quarter of a million tubes of Drosophila food and a variety of 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 to the MRC’s Prion and Clinical Trials Units and researchers as far away as the MRC Social and Public Health Sciences Unit in Glasgow. Jackie inspects a hybridoma culture 114 MRC National Institute for Medical Research Brian sets up one of our bioreactors SCIENTIFIC FACILITIES Flow cytometry facility Aaron Rae Co-workers: Graham Preece, Nadine Biboum The Flow Cytometry Facility provides state-of-the-art technology for high speed, sterile sorting of multiple types of cell populations for cellular, molecular, signalling and in vivo studies. The facility also provides 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, the Facility trains research staff, including PhD students and postdoctoral researchers. The facility is well equipped, with four Cell Sorters that range from 4-colour to 13-colour machines (Beckman Coulter MoFlo; Becton Dickinson FACS Aria II) and eight FACS Analysers that include 4-colour and 9-colour machines (Becton Dickinson FACS Calibur, Canto and LSRII; Beckman Coulter Cyan ADP). FACS profile of T-cells dividing in different host environments. (Image courtesy of Benedict Seddon). MRC National Institute for Medical Research 115 SCIENTIFIC FACILITIES High-throughput sequencing Abdul Karim Sesay 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 facility. 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. Establishment of the sequencing service coincides with the formation of the Division of Systems Biology and the appointment of two new research Programme Leaders. High throughput sequencing data from a ChIP experiment in mouse. Major peaks show likely binding sites of the transcription factor under investigation, at different positions within a 144kb region around a known gene. Traces are derived from density of mapped sequence reads at 100 base intervals. Upper chart shows ChIP read density in blue and ‘input’ (control) read density in red; lower chart shows the difference between the ChIP and input read densities in green. Courtesy of Eva Kutejova 116 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Affymetrix microarray facility Roger Buxton Co-worker: Bob Butler This facility enables a wide range of highly parallel genomic analyses, making use of the sequence data from a diverse range of organisms. A major use is for the generation of gene expression profiles, enabling the understanding of complex biological processes and disease through approaches such as Systems Biology analysis; other applications include ChIPon-chip experiments to analyse the global interactions between DNA and regulatory proteins and single nucleotide polymorphism (SNP) analysis for use in genome wide association studies. The Institute has an Affymetrix GeneChip® system for which microarrays are available for a number of species; we have used those for Mycobacterium tuberculosis, Drosophila, Xenopus, zebrafish, chicken, dog, mouse and human. It is equipped with an Affymetrix 7G scanner and GeneChip 450 fluidics station. We have the necessary equipment for RNA and DNA QC analysis using the Nanodrop spectrophotometer and Agilent 2100 Bioanalyzer. Scientists prepare RNA or DNA which is then used to perform the necessary fluorescent labelling, hybridisation, washing and scanning. The data is then available for individuals to analyse with their preferred software; we have two licences for GeneSpring which can be used. The facility is available to NIMR scientists as well as external collaborators. Agilent Bioanalyzer trace showing minimal degradation of RNA Image of hybridised probe array MRC National Institute for Medical Research 117 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 World Influenza Centre (WIC) 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, will 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 Animal Pathogens Order. It was used for the growth and characterisation of samples of the pandemic H1N1 sent from around the world, and to generate under high containment reference post-infection ferret antisera to the emerging pandemic viruses for virus antigenic analyses. It has also been used for the isolation and characterisation of multiple human isolates of H5N1 avian influenza virus, for example from the Turkish outbreak in humans in 2006. The laboratory capacity has been extended (to 160 m2) 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 facility 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 facility • 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 facility, there are 11 level 3 laboratories scattered among the main buildings and biological research facilities of 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. 118 MRC National Institute for Medical Research SCIENTIFIC FACILITIES Engineering and Electronics Engineering workshop: Alan Ling 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 very diverse range of projects have been worked on, including: • micromanipulators • microscope set-ups • custom made parts • temperature controlled chambers • drug infusers and nebulisers • blood flow measurement devices Alternating two colour fluorescence imaging A custom-built control unit synchronises an EMCCD digital camera and two lasers together with a computer data acquisition program. Electronics: John Sawkins and Martyn Stopps An Electronics & Programming Workshop A two day practical workshop providing basic electronics and programming techniques enabling exploration of novel research beyond what commercial apparatus may provide. Electronics facilities support scientific groups requiring bespoke electronic and software-based instrumentation. Utilising up-to date technologies, employing microcontrollers and mixed signal devices we provide a complete product development lifecycle from initial specification and proof of concept to the final solution. MRC National Institute for Medical Research 119 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 120 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 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 121 SCIENTIFIC FACILITIES Other support services The NIMR library is dedicated to serving the information needs of the scientific staff and students of NIMR and MRCT. It provides access to a broad range of electronic journals and other printed and electronic information resources, harnessing the best available tools and technologies. Assistance with information searching and handling is also available. Computing and telecommunications provides a helpdesk, central computing services, network infrastructure, email, desktop computer support, wireless networks, archiving and the internal phone system. The Institute is connected to the internet via a 100Mb JANET connection. The NIMR web team is responsible for maintenance, support and development of the external website and intranet. They provide standards-compliant, cross-platform and userfriendly websites and applications and work with a range of staff throughout NIMR, collaborating in particular with Computing, the Library and PhotoGraphics. Engineering services supply internal emergency and repair services for laboratory equipment breakdown, in particular for centrifuges and incubators. Rotor inspections and pipette service/repair can also be dealt with. These services minimize downtime and costs. Safety and security provide a safe working environment at the Institute. All staff are offered 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. The Photographics section provides a professional graphic, design and imaging service offering a wide range of skills and facilities for the presentation of science through publication, digital presentation and posters. Services include illustration, graphics, audio-visual production and presentation, interactive animation, photography, publishing, binding and high quality copying. The section also provides in-house training for NIMR staff on graphic applications such as Adobe Photoshop and Microsoft Powerpoint. 122 MRC National Institute for Medical Research In memoriam John Eccleston (1943 -2009) John Eccleston was an international leader in research on small G proteins, and the mechanisms of their interactions with effector proteins. He gained a high reputation for his development and application of fluorescent probes, especially guanine nucleotide analogues. John spent 25 years as a group leader at NIMR in the Division of Physical Biochemistry and formally retired just 6 months ago, though he remained a very active scientist until he became seriously ill very recently. He died aged 66 on 30th September 2009. John began his academic career the hard way, earning his first degree over four years through the Graduate Membership education programme of the Royal Society of Chemistry at Warley Technical College and Liverpool Polytechnic. He joined David Trentham’s small research group at Bristol University in a technical post and shortly afterwards registered for a PhD. During this time he made seminal contributions towards understanding the ATPase mechanism of myosin. In 1977 John launched his independent scientific career at the University of Pennsylvania, studying the enzyme mechanisms of the GTPases EF-Tu and EF-G that were involved in protein biosynthesis. This was a very percipient choice of research topic given all that we now know about the role of small G proteins in cellular regulation. In 1984 he joined the staff of NIMR as a group leader and authored nearly 100 papers during his career at Mill Hill. He pioneered fluorescence anisotropy measurements to analyse protein association and dissociation in regulatory pathways - key events that are otherwise difficult to monitor in real time. The introduction of X-ray crystallography facilities to the Institute gave great impetus to John’s science and led to very fruitful collaborations with the new crystallographers’ research group, including three Nature papers in 1997. In the last five years he produced several papers in which seemingly intractable problems at the molecular level have been addressed, collaborating with research groups in the Virology and Parasitology Divisions. No appreciation of John would be complete without a memory of the warmth, dry humour and friendship that John extended to all around him, and his careful and committed instruction and guidance to students at all levels. MRC National Institute for Medical Research 123 Sixty years of Immunology at NIMR A history of immunology research at Mill Hill, written by Anne O’Garra and Dimitris Kioussis. Immunology at NIMR, Mill Hill, evolved from scientists in different Divisions being drawn together to address convergent questions related to how whole bodies, mouse and man, responded to threats from parasites, bacteria and viruses, and how this response impinged on the newly emerging clinical disciplines of transplantation, allergy and autoimmune disease. The Institute has served as a training ground for young fellows as well as a hub for exchange of ideas in immunology research internationally. Through the years wide collaborations and interactions between Divisions and with colleagues throughout the world have continued and remain the philosophy of NIMR research. The use of immunological techniques and/or immunological approaches has been an important driver of this process, influencing many researchers during their time at the Institute and in their later careers. We will attempt to unfold the salient points in this brief history. John Humphrey was invited in 1949 to join the Division of Biological Standards at NIMR, when it was located in Hampstead, by Sir Charles Harington, the then Director of the Institute. Humphrey’s mandate was to focus 50% of his time on Standards and for the remainder of his time to pursue his own research interests. In addition to contributing greatly to the development of Standards, Humphrey made the most of the interdisciplinary nature of the Institute. In 1950 when NIMR moved to Mill Hill, Humphrey was put in charge of development of standards for antibiotics and enzymes in clinical use and, most importantly, developed quantitative assays for biological activities and had long-lasting involvement with the WHO. His interest in immune reactivities was broad and his work on the fate of radiolabelled antigen in vivo attracted many researchers to the NIMR. In addition, in collaboration with colleagues in various Divisions at the Institute, he helped to develop immunological techniques and their application to the study of immunological problems. Projects included the application of newly available isotopes of iodine and carbon to studies of immunoglobulin metabolism, pharmacological studies of anaphylaxis and of platelet involvement in allergic reactions, and demonstration of the role of granulocytes in John Humphrey Arthus reactions. By 1957, immunology had developed so far at NIMR that Humphrey was relieved of duties in the Biological Standards Division to set up the first Immunology Division composed of researchers working on immunological problems. These included Brigitte Askonas, Walter Brocklehurst and Brigid Balfour. Askonas had been recruited earlier to the Division of Biochemistry by Tommy Work, whose Division had a strong influence on the development of immunology at NIMR. In 1958 Rodney Porter, working in the Biochemistry Division at NIMR, showed that immunoglobulin molecules could be split by enzymes into two parts; one was heterogeneous but had antigen specificity, the other was more homogeneous and could be crystallised. He later received the Nobel Prize in 1972 for his work on the structure of immunoglobulins. Among young recruits and fellows that Humphrey attracted, to name but a few, were Frank Austen, Hugh McDevitt, Gordon Ada, Charles Janeway, Abul Abbas and Gerry Klaus, the latter working on B cell responses and later demonstrating with Humphrey the role of follicular dendritic cells in B memory cell generation. Brigid Balfour was one of the first generation to appreciate the value of studying cellular morphology and ultrastructure in relation to immune function and in understanding the importance of the architecture of lymphoid tissues. She pioneered contributions to the study of dendritic cells, describing these as “veiled cells”, and realised they were derived from Langerhans cells and played an important role in promoting immune reactions. Sir Peter Medawar became director of NIMR in 1962, having been the Jodrell Professor of Zoology at University College London for the previous eleven years. His ground-breaking studies, in collaboration with Leslie Brent and Rupert Billingham, on 124 MRC National Institute for Medical Research the immunology of tissue graft rejection and the establishment of the phenomenon of acquired immunological tolerance had led to his being awarded the Nobel Prize in Medicine in 1960, together with the Australian virologist/immunologist, Frank Macfarlane Burnet. Peter Medawar’s appointment as Director in 1962 and the appointment of N.A. (Avrion) Mitchison, one of Medawar’s early PhD students in Oxford, to succeed A.S. Parkes as Head of the Division of Experimental Biology, substantially increased the overall strength in immunology at NIMR. Medawar and Brent, who accompanied him to NIMR, joined the Division of Experimental Biology. As Director, an important innovation of Medawar’s was the restructuring and modernising of the animal house, recognising the indispensable role of animals in the research of many Divisions. Medawar set up the Animal Division to provide these services, but continued to play an important role in strategic matters, arguing the case with the MRC for funding to construct the first Specific Pathogen Free (SPF) building and appointing the first veterinary pathologist. The Animal Division evolved and grew and today, under the name of Biological Services, represents one of the strongest in Europe. Another highly effective introduction by Medawar was extension of the building to Sir Peter Medawar allow the creation of a common recreational area with a bar adjacent to the cafeteria, to provide a place for scientists to exchange ideas in relaxed surroundings, an arrangement that continues to this day. Medawar loved conducting his own laboratory research, and designated two and a half days a week for working at the bench, including skin grafting mice. In addition, he set an example at the Institute by interacting with scientists in every Division, as well as bringing about infrastructural changes following negotiation of adequate funds from the Medical Research Council to support the cutting-edge research at the institute. In addition to his administrative load and his research, Medawar gave public lectures, including philosophical discourses on the scientific method, on radio and elsewhere. He became famous for these and published a number of books in this area. He represented science and the Institute widely, to lay and scientific audiences. In his area of scientific work, transplantation biology, Medawar’s research attracted surgeons, such as Gene Lance, to the Institute from the US and other countries and they contributed to the immunological work, including the use of anti-lymphocyte serum (ALS) as an immunosuppressive agent in blocking allograft rejection. Elizabeth Simpson, trained as a veterinary pathologist, joined Medawar at NIMR due to her interest in lymphocytes and used ALS in the study of tumour rejection and tolerance. Avrion Mitchison The Division of Experimental Biology, led by Avrion Mitchison, concentrated mainly on mechanisms of induced antigen-specific immunological unresponsiveness (tolerance). Interests ranged from a theoretical angle to experimental research, exploring the role of the “carrier” components of antigen in studies of anti-hapten antibody responses elicited by haptens conjugated to such “carrier” proteins. At that time an iodinecontaining synthetic immunological determinant, 4-hydroxy-3-iodo-5-nitrophenylacetic acid, NIP, was developed by Alan Brownstone, Mitchison and Rosalind Pitt-Rivers (Division of Biochemistry) and this was fundamental to the hapten-carrier work. Klaus Rajewsky joined Mitchison’s laboratory at NIMR in 1969 as an EMBO fellow with a MRC National Institute for Medical Research 125 Sixty years of Immunology at NIMR contd. desire to learn to handle experimental mice, but also intrigued by experiments in which both he and Mitchison had been involved previously which suggested a mechanism of T-B interaction. Their seminal findings demonstrated the hapten-carrier effect in T-B collaboration, describing the role of T-cells responding to the “carrier” moiety as helpers of B cells, which are responsible for hapten-specific antibody secretion. On another topic, in collaboration with David Dresser who had accompanied Mitchison from Edinburgh, they researched the mechanisms of immunological paralysis and showed that it could be achieved in adult hosts by injection of high or low doses of antigen. Thence the concept of low zone and high zone tolerance was developed by Mitchison. Mitchison not only hosted a breadth of immunological thinking and ideas, but was also broadly interested in other disciplines, and accepted to his laboratory Martin Raff, who in his own words had “been in clinical medicine and neurology and knew nothing about science”. On his arrival at Mill Hill in 1968 Mitchison suggested that Raff follow up the work of Reif and Allen and test whether the Thy-1 alloantigen, to which Mitchison had already begun to raise an antiserum, was expressed on mouse T cells but not B cells, in which case it could be used as a T-cell marker. Raff ’s subsequent work demonstrating Thy-1 as a T-cell specific marker was an important contribution to immunology. Raff collaborated with Stefanello de Petris from the Division of Biophysics, making the discovery that cross linking of surface immunoglobulin molecules, normally distributed over the entire B cell surface, leads to capped distribution at room temperature, followed by endocytosis of the surface Ig. These findings had major implications for much of cell biology and ligand receptor interactions. Through the years the Division of Biochemistry continued to contribute immensely to the development of molecular immunology and included scientists such as Alan Williamson and Michael Crumpton. Crumpton defined molecules on the surface of lymphocytes at an early stage, making reagents to study them, and leading to the isolation of major histocompatibility type (MHC) molecules. Brigitte Askonas initially focused on antibody synthesis, showing that antibody secreting cells did not just reside in lymphoid tissue, but also in bone marrow and lung. This work, in collaboration with Alan Williamson (Division of Biochemistry), enabled the characterisation of antibody forming cells, assembly of heavy and light chains and the establishment of the clonal dominance of B cells forming high affinity antibodies, studies which Andrew McMichael continued. Her second interest was macrophages and antigen processing studies, to which Emil Unanue contributed greatly. Following uptake of radio-labelled protein antigens they showed that, although most of the antigen was degraded, a small amount remained that could stimulate antibody responses in vivo. This finding set the stage for the discovery of antigen processing and peptide-MHC antigen presentation to T cells. From 1963 to 1972 the Immunology Division had remained relatively small, headed by John Humphrey and with a few staff scientists, but it was augmented by a large number of visiting scientists, so that there were often more visitors than there were NIMR scientific staff members. Collaboration was the norm and Immunology at Mill Hill grew famous internationally, becoming a hub for innovative discovery with contributions from numerous scientists, including Roger Taylor, Mel Greaves, Harvey Cantor and Henry Wortis, Stuart Schlossman, William Paul, to name but a few. When Medawar and Mitchison left the NIMR in the early 1970’s, the Divisions of Experimental Biology and Immunology were combined into one single Immunology Division and immunology continued as a strong discipline in the institute. Following work from immunologists in the USA describing IgD in humans, Abney and Parkhouse were the first to demonstrate IgD on mouse lymphocytes and went on to describe IgD in the context of the ontogeny of Ig isotype diversification. During these years Alick Isaacs, the co-discoverer of interferons and one of Britain’s leading virologists, was the Head of the Division of Bacteriology and Virus Research and then the Laboratory for Research Brigitte Askonas 126 MRC National Institute for Medical Research on Interferon at NIMR, before the strong link between innate and adaptive immunity was established. By the time Askonas took on the leadership of the Division of Immunology in 1976 it consisted of group leaders, Parkhouse, Thomas, Dresser, Klaus and herself. She had by then started her work on the immune response to infectious agents. David Sacks and Murray Selkirk worked with Askonas and Bridget Ogilvie, then in the Parasitology Division, to study immunosuppression during trypanosomiasis. Askonas also worked on the cell-mediated immune response to influenza and demonstrated that influenza virus specific cytotoxic T lymphocytes (CTL) were MHC restricted and, unexpectedly, did not distinguish influenza virus variants within a serotype. Michael Crumpton (Division of Biochemistry) and John Skehel (Division of Virology), with a joint PhD student, Sara Courtneidge, were also working on influenza/MHC interactions. Askonas and collaborators isolated and grew the first virus specific T cell clones, leading the way to understanding the nature of viral antigen presentation to T cells. Alain Townsend, a PhD student with Askonas, distinguished influenza virus subtypes; he identified its target as nucleoprotein and went on to show how viral proteins were degraded to peptides, which were presented bound to MHC proteins, a fundamental discovery in immunology. Many past PhD students and Fellows, who are now established and successful researchers in their own right, worked with Askonas through the years including Mike Bevan, Greg Bancroft, Peter Openshaw, Charles Bangham and David Wraith. A key area of research was to define the function of CTL in vitro and in vivo, where Askonas and colleagues described their role in viral clearance, and also their ability to cause lung immunopathology. Richard Flavell founded the Division of Gene Structure and Expression at NIMR in 1979. During his time at NIMR Flavell initiated his research in immunology, until then having focused his research on elucidation of molecular events in the regulation of eukaryotic genes in general and in particular the haemoglobin genes. With his highly talented Postdoctoral Fellows, Frank Grosveld and Henrik Dahl, Flavell developed the first cosmid libraries facilitating the recovery of large pieces of DNA encoding multiple genes and gene transfer experiments. He then used these technologies to isolate essentially all of the mouse MHC genes and to analyze their function and structure, and with his Postdoctoral Fellows, Andrew Mellor and Elizabeth Weiss, elucidated the molecular basis of polymorphism in MHC genes in general. This work at NIMR led to the broadening of Flavell’s interest in functional immunology, a career path that he continued to follow. Dimitris Kioussis, as a Postdoctoral Fellow with Flavell, worked with George Kollias and Frank Grosveld who introduced transgenesis to the NIMR, bearing a strong influence on Kioussis’s future work on thymic development. Richard Flavell Ita Askonas, who retired as Head of Immunology at NIMR, in 1989, has had a profound and sustained influence in the field, and in the development and advancement of major internationally acclaimed investigators in immunology (see photo below of her 80th Birthday meeting), and continues actively to advise scientists at all levels, taking a particular interest in training young researchers. Immunology continues at NIMR Kioussis, along with Rose Zamoyska, Brigitta (Gitta) Stockinger and Andrew Mellor, established a new Division of Molecular Immunology at NIMR in 1991. Kioussis has made discoveries on how chromatin regulates gene expression and therefore fate decisions during thymocyte development, including functional commitment within the T cell lineage. His work has not only had MRC National Institute for Medical Research 127 Sixty years of Immunology at NIMR contd. Ita Askonas Group Photo 80th Birthday meeting: Celebratory Immunology Meeting for Ita Askonas’s 80th Birthday, Trinity College, Oxford, 2003. From Left Standing: Alain Townsend FRCP, FRS (Prof. Molecular Immunology, Univ of Oxford), Charles Bangham (Chair of Immunology, Imperial College), Greg Bancroft (London School of Hygiene and Tropical Medicine), Peter Openshaw (Prof. Experimental Medicine, Imperial College), David Wraith (Prof. Experimental Pathology, Univ of Bristol), Alan Williamson, Helen Bodmer, (Head, MRC and Health Research Team), Tracy Hussell (Prof. Inflammatory Diseases, Imperial College), Bridget Ogilvie DBE, FRS, FAA, Emil Unanue (Prof. Pathology, Washington University Unversity School of Medicine, St. Louis), Colin Gelder, David Sacks (NIAID, NIH), Leszek Borysiewicz KBE, FRCP, FRS (Chief Executive of the MRC). From Left Sitting: Michael Parkhouse (Head of Infection and Immunity Group, Gulbenkian Institute), Andrew McMichael KBE FRS (Director Weatherall Institute of Molecular Medicine & MRC Human Immunology Unit, Oxford), Ita Askonas FRS, Hugh McDevitt (Prof. Microbiology and Immunology, Stanford University). impact on our knowledge of lymphocyte development and commitment but also on the strategies employed in transgenesis and gene therapies. Stockinger has made crucial contributions on the development, maintenance and regulation of peripheral T cell compartments and immune responses since her arrival at the NIMR in 1991. More recently she has described the mechanisms for the differentiation of a new subpopulation of CD4+ T cells, the Th17 subset, critical for eradication of fungal pathogens and yet also causal of dysregulated autoimmune processes. Gerry Klaus became Head of the Division of Cellular Immunology in 1991 after Askonas had left NIMR. He recruited Victor Tybulewicz and Steven Ley to the Division, influenced by Klaus’s original findings of signalling through the B cell receptor leading to polyphosphoinositide degradation. Tybulewicz has since taken over the Division, now renamed Immune Cell Biology, and made important contributions to two distinct areas; firstly, the field of signal transduction in the immune system, around which he has built the Division, and secondly, generation of a trans-chromosomic mouse strain to create a model of human Down Syndrome, leading to broad interactions throughout the Institute. Study of the immune response to infection has also continued at NIMR. Jean Langhorne, who joined the Division of Parasitology in 1998, has made fundamental 128 MRC National Institute for Medical Research contributions to defining the mechanisms of protection and pathogenesis in malaria. Finally, O’Garra, who completed a PhD in bacterial adhesion, followed by a Postdoctoral Fellowship on cytokines and B lymphocytes with Gerry Klaus at the NIMR. During her 15 years at the DNAX Research Institute in the USA, O’Garra collaborated with Kenneth Murphy at Washington University, St. Louis, to show how pathogens and their products induce the production of cytokines such as IL-12 in macrophages and dendritic cells and in this way induce the differentiation of TH1 T cells producing IFN-g, critical for pathogen eradication. O’Garra then demonstrated that IL-10 inhibits macrophages and dendritic cells including their production of IL-12, thus regulating TH1 responses, and demonstrating IL-10’s broad anti-inflammatory role. O’Garra returned to the UK in 2001 and set up the new Division of Immunoregulation at NIMR, whose groups focus on the immune response in tuberculosis and viral infections, bringing together the divisions of immunology and infections at the institute. Immunology at NIMR is still exciting and strong internationally and the philosophy of interaction, free exchange and collaboration still prevails. Present Immunology at NIMR Many contributed greatly to immunology at NIMR through the years. Not all of them have been acknowledged in this piece due to restrictions in space. Our apologies to all you who have not been mentioned – rest assured you have not been forgotten. We thank Brigitte Askonas, Avrion Mitchison, Elizabeth Simpson, Michael Crumpton, Richard Flavell and Martin Raff for their helpful input. MRC National Institute for Medical Research 129 Major funding sources Biotechnology and Biological Sciences Research Council (BBSRC) British Council British Heart Foundation Dana Foundation European Commission FARA Genentech GlaxoSmithKline Great Ormond Street Hospital Charity Jeantet Lady Tata Memorial Trust Leukaemia Research Fund Medical Research Council Medical Research Council Technology Novartis NC3Rs Oxford University Parkinsons Disease Society Prix Scientifique Roche Royal Society Wellcome Trust Yamanouchi 130 MRC National Institute for Medical Research Scientific seminars Selected major seminar speakers: 2009 C C Hui Chaya Kalcheim Cliff Tabin Naama Barkai Ryoichiro Kageyama Carole Goble Anne Cooke Antonio Lanzavecchia Doreen Cantrell Hergen Spits Tasuku Honjo Steve Smale Adolfo Garcia-Sastre Debbie Smith Jonathan Leis Christian Doerig Brian Kobilka Eric Rubin Jacques Banchereau John Coffin Joshua Sanes Jules Hoffmann Lew Cantley Matthew Freeman Olivier Pourquie Ottoline Leyser Peter Rigby - Harington Lecture Richard Treisman Uri AlonWeizmann Alan Jasanoff Craig M Crews Angela Gronenborn Marek Cieplak Marc Fontecave Dr Emmanuel Skordalakes Gerhard Schratt Prof Dominic M Walsh Steve Pollard Hospital for Sick Children, Toronto Hebrew University of Jerusalem, Hadassah Medical School Dept of Genetics, Harvard Medical School Weizmann Institute of Science, Israel Institute for Virus Research, Kyoto University, Japan University of Manchester Dept of Pathology, University of Cambridge IRB Institute for Research in Biomedicine, Bellinzona, Switzerland University of Dundee Genentech Kyoto University UCLA, Jonsson Comprehensive Cancer Center Mount Sinai School of Medicine Centre for Immunology and Infection, Hull, York Medical School Northwestern University, Feinberg School of Medicine, Chicago Wellcome Centre for Molecular Parasitology, Glasgow Stanford School of Medicine, California Harvard School of Public Health Director, Baylor Institute, Dallas Sackler School of Biomedical Science University of Havard, USA University of Strasbourg, France Harvard Medical School MRC Laboratory of Molecular Biology Stowers Institute for Medical Research, Kansas City University of York The Institute of Cancer Research CRUK, London Research Institute Institute of Science Department of Biological Engineering, MIT Yale University Dept of Structural Biology, University of Pittsburgh Institute of Physics, Polish Academy of Science, Warsaw, Poland Institute of Metals in Biology (CEA-UJF-CNRS), Grenoble, France The Wistar Institute, Philadelphia, USA University of Heidelberg, Interdisciplinary Center for Neurosciences (IZN) UCD School of Biomolecular and Biomedical Science, University College, Dublin Wellcome Trust Center for Stem Cell Research, Cambridge MRC National Institute for Medical Research 131 Staff honours Prizes and awards Margrie Young Alexander von Humboldt Research Award; Buckston Browne Prize (Harveian Society) Gardner Middlebrook Award (for Contributions in Mycobacteriology), May 2009 Editorial boards Ang Blackman Briscoe Buxton Doorbar Driscoll Elgar Guillemot Holder Langhorne Logan Lovell-Badge McCauley Margrie Ober O’Garra Pastore Ramos Rittinger Smith Stoye Turner Tybulewicz Wilkinson D Wilkinson R Young Zimmerman International Journal of Developmental Biology Associate Editor: PLoS Pathogens Development, Developmental Biology, Developmental Dynamics, Neural Development, Faculty of 1000 FEMS Microbiology Letters Journal of Clinical Dermatology, Journal of General Virology. Journal of Functional and Structural Genomics Genome Biology and Evolution, Managing Editor, Briefings in Functional Genomics and Proteomics BMC Developmental Biology, Neural Development. Molecular and Biochemical Parasitology, Eukaryotic Cell. Associate Editor: PLoS Pathogens, Malaria Journal, Specialist Editor: International Journal of Parasitology, Development, Developmental Biology, Developmental Dynamics Organogenesis, Sexual Development Journal of General Virology, Virus Research Frontiers in Neural Circuits Developmental Biology Journal of Experimental Medicine, Immunology Prion; The Open Biochemistry Journal; The Open Spectroscopy Journal. Open Magnetic Resonance Journal Biochemical Journal Trends in Genetics, Development (editor in chief), Biology Image Library (subject head for developmental biology) Journal of Virology Biology of Reproduction, Chromosome Research Immunology Mechanisms of Development (editor in chief ), Gene Expression Patterns (editor in chief), Developmental Biology, Biochemical Journal, Faculty of 1000, BMC Developmental Biology Tuberculosis, PLoS One, International Journal of Tuberculosis and Lung Disease. Co-Editor in Chief, Tuberculosis Genesis Scientific committees Blackman Burgoyne Briscoe Doorbar Driscoll Elgar Gould 132 Wellcome Trust Immunity and Infectious Diseases Funding Committee MRC College of Experts British Society for Developmental Biology, Company of Biologists Society for General Microbiology Translational Virology Group. Member of the External Advisory Board of the Henry Wellcome Biomolecular NMR Facility at Birmingham University BBSRC Bioinformatics and Biological Resources Panel Wellcome Trust Molecules, Genes and Cells Funding Committee. MRC National Institute for Medical Research Guillemot Hulme Kioussis Langhorne Ley Lovell-Badge McCauley Margrie Mohun Molloy O’Garra Pastore Smerdon Smith Stockinger Turner Vincent Wilkinson D Young 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 Member of the Lady Tata Memorial Trust Scientific Advisory Committee, Member of the Scientific Advisory Board of Basel University Biomedicine, Member of the Sectional Committee of the Academy of Medical Sciences, Member of EMBO long term fellowships committee ERC Advanced Investigator grant committee Scientific Advisory Board of the Research Centre for Infectious Diseases, University of Wuerzburg, MRC Infection and Immunity Board MRC Infection and Immunity Board UK Stem Cell Bank joint Clinical and User Liaison Committee, Sense about Science Advisory Council, Hinxton Group Organizing Committee, Science Media Centre Advisory Board, Scientific and Clinical Advances Advisory Committee of the Human Fertilization and Embryology Authority (co-opted member), President of the Institute of Animal Technology, Royal Society Animals in Research Committee, Academy of Medical Sciences Council, Academy of Medical Sciences Communications Group, Royal Society Sectional Committee 7, Royal Society GSK Prize Committee, Member of the jury for the BBVA Foundation Frontiers of Knowledge Biomedicine Award, Member of Academy of Medical Sciences Working Group on “Animals containing human material”,Distinguished Visiting Professor, University of Hong Kong BBSRC Animal Sciences Committee, Society for General Microbiology Virus Division Committee Human Frontier Science Programme, European Union MRC Molecular and Cellular Medicine Board; Chair LM-Section, RMS, Chair of Tools and Resources Development Fund (TDRF) Panel, BBRSC Tools and Resources Strategy Panel, Strategic Advisory Board, Dresden CBG MPI Strategic Review Panel, Dept. of Physics and LCN, UCL; Scientific Advisory Board, Baylor Institute for Immunology, Dallas, USA., Scientific Advisory Board, Institute for Biomedical Sciences, Bellinzona, Switzerland. National Grants in Italy (MURST, MIUR, PRIN), Belgium, France (Pasteur Institute, BLANC), UK (MRC, Welcolme BBSRC), Swiss National Science Foundation, Spain and Portugal, Sub-chairman for the 2009 Grant Call of the Portuguese Ministry. Advisory Boards of Structural Genomics Consortium, MRC-Technology Governing Board, ASM Scientific/ TwistDX Inc., MRC Molecular & Cellular Medicine Board, NIH Structural Genomics Study Group (PSI-1 & SGCID), BBSRC IGF & Genomics Evaluation Panel, Diamond Peer Review Panel. Member of the Scientific Advisory Board of TwistDX, Member of the Board of Directors of the Babraham Institute, Chair of the Scientific Advisory Board of the Institute for Toxicology and Genetics, Karlsruhe, Chair of the Royal Society Research Appointment Panel (Bi), Chair of the Wellcome Trust Sir Henry Wellcome Postdoctoral Fellowship Committee, Member of the Scientific Advisory Board of the Indian Institute of Science Education and Research ERC Young investigator Panel Multiple Sclerosis Society panel Hinxton GroupScientific Advisory Board; Institut de Génétique et Développement de Rennes. Interview panel: Wellcome Trust-NIH four year PhD Programme. Advisory committees: GXD Advisory Board, EMAGE Advisory Board, Grant committees: EMBO Long Term Fellowships, Academy of Finland Chair, DEFRA Vaccine Programme Advisory Group for Bovine TB, Chair, International Scientific Advisory Board, Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Board of Directors, Aeras Global TB Vaccine Foundation, Steering Committee, European Tuberculosis Vaccine Initiative (TBVI) MRC National Institute for Medical Research 133 PhD theses awarded: 2009 134 Name Division Title of thesis James Cauwood Stem Cell Biology and Developmental Genetics Identification of CIS and transfactors that regulate genetic stability in Saccharomyces Cerevisiae Timothy Nott Molecular Structure Structural and functional analysis of a Phospho Dependent Molecular Switch Rv1827 from Mycobacterium tuberculosis Ricardo Rajsbaum Immunoregulation Expression of TRIM genes in different immune cells and mechanism of regulation of their expression: implications for the immune response to pathogens Karen Houston Molecular Neuroendocrinology The role of membrane lipids in Weibel Palade Body formation Gian Felice De Nicola Molecular Structure Ines Antunes Immunoregulation Stretch Activation in Muscle: A CA 2+ Independent Mechanism 9 Role and specificity of regulatory T cells during retroviral infection Anna Garner Developmental Biology Interactions Between the Developing Limb Bud and Spinal Motor Neurons Nadia Hashash Stem Cell Biology and Developmental Genetics The molecular bases underlying chromosome fragility at Replication Slow Zones in Saccharomyces cerevisiae Alan Kennedy Virology Functional regulation of the human papillomavirus type 16 E1^E4 protein by phosphorylation Rute Marques Immunoregulation A mouse model for the pathogenesis of immunodeficiency virus infection Emily Noel Developmental Biology Early liver formation in zebrafish: a molecular and morphological approach Claire Pearson Immune Cell Biology Genetic and functional analysis of IL7 signalling in control of T cell homeostasis Andrew Slatter Physical Biochemistry Kinetic mechanism of the interaction of RepD and PcrA helicase during plasmid replication Srividya Sriskantharajah Immune Cell Biology The Role of IKK Induced NF-kB1p105 Proteolysis in T Lymphocytes MRC National Institute for Medical Research Bibliography 1. 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Zhou L, Li J, George R, Ruchaud S, Zhou H, Ladbury JE, Earnshaw WC and Yuan X (2009) Effects of full-length Borealin on the composition and protein-protein interaction activity of a binary chromosomal passenger complex. Biochemistry 48:1156-1161 MRC National Institute for Medical Research 145 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 146 MRC National Institute for Medical Research MRC National Institute for Medical Research 147 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. 148 MRC National Institute for Medical Research MRC National Institute for Medical Research 2009/20010 Annual Report and Prospectus 2009/2010 Annual Report and Prospectus MRC National Institute for Medical Research Science for health
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