MRC National Institute for Medical Research · PDF fileMRC National Institute for Medical Research 5 The Royal Society also recognised two of our scientific alumni: Tim Bliss has been

MRC National Institute for

Medical Research

2011/2012 Annual Report and Prospectus

© MRC National Institute for Medical Research

Enquiries about this report should be addressed to:

Assistant Director’s Office +44 (0)20 8816 2281

[email protected]

Further information is available on our website at:

http://www.nimr.mrc.ac.uk

Copies obtainable from the Librarian at NIMR

Edited by: Victor TybulewiczDesigned by: Joe Brock

Photography by: Neal Cramphorn & James BrockProduction: Christina McGuire & Frank Norman

Editorial Assistant: Eileen Clark

2 MRC National Institute for Medical Research

Contents

Director’s forewordThe Francis Crick InstituteScience overviewScientific highlightsNIMR history and milestonesCareers : PhD students Sandwich students and work experience Postdoctoral scientists Programme Leaders Research support Animal TechniciansTranslational research Support for translation Commercial translation Clinical translationPublic outreachResearch groups : Infections and Immunity Structural Biology Neurosciences Genetics and DevelopmentResearch facilitiesNobel LaureatesFive famous alumniScientific seminarsStaff honours 2011PhD theses awardedIndexes Research groups Research themesCurrent funding sourcesBibliographyNIMROD social clubMap, location and travel

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3MRC National Institute for Medical Research

This has been a very busy and successful year at NIMR. We have been doing more terrific science (see Scientific highlights, page 10), and we have completed a very successful quinquennial review. Current and former members of staff have received various honours and awards, and we have welcomed new programme leaders to the Institute. We have also made a great deal of progress towards establishing The Francis Crick Institute (see page 6).

The outcome of the Institute quinquennial review - confirmed by MRC Council in December - was very positive. The preparation of the report, and its presentation to the visiting committee, showed the Institute at its best, with everyone pulling together for a tremendous result. This is a good opportunity for me to highlight the importance to the Institute’s science of our world-class support services: they were strongly commended by the visiting committee, and I would like to thank everyone involved for their invaluable contributions to the life and work of the Institute. In particular, the work of Biological Services, under the expert direction of Kathleen Mathers, was strongly praised by the review committee, confirming my own view that we have one of the best-run facilities in the world.

My scientific proposals for the review focused on exciting new opportunities growing from recent successes. Thus the review committee endorsed the creation of a Division of Physiology and Metabolism, under Alex Gould, and a revitalised Division of Neurophysiology. Together these will allow us to drive forward some critically important emerging areas of biomedical science. Forthcoming new appointments will help realise this vision. We also took the opportunity at the quinquennial review to move James Briscoe and Jean-Paul Vincent to the Division of Developmental Biology, where, as joint heads, they are bringing new approaches to understanding the molecular and cellular mechanisms underlying embryonic development.

Institutes like NIMR thrive on turnover and the arrival of new colleagues, and we were delighted to welcome two new Programme Leaders Track this year : Eva Frickel and Luiz Pedro de Carvalho. Eva joins us from Hidde Ploegh’s lab at the Whitehead Institute, where she looked at immune surveillance of Toxoplasma gondii and the generation of parasite epitopes for recognition by CD8 T cells. Eva’s programme at NIMR builds on these studies to identify novel pathways and mechanisms of host resistance to Toxoplasma. Luiz Pedro de Carvalho worked as a postdoctoral fellow in Carl Nathan’s laboratory at the Weill Cornell Medical College, where he studied host interactions of Mycobacterium tuberculosis. In particular he contributed to LC-MS-based metabolomics methods for systems-level studies of M. tuberculosis, which forms the basis of his new lab at NIMR.

I was also delighted in the last year that my Assistant Director, John Wills, and my Director of Research, Steve Gamblin, both received external recognition. John’s outstanding contributions were recognised by the award of an MBE in the New Year Honours List for services to Science, while Steve was elected to the Fellowship of the Royal Society for his work on the structural and functional mechanisms of molecules involved in disease processes.

Director’s foreword


Alex Gould

Eva Frickel and Luiz Pedro de Carvalho


The Royal Society also recognised two of our scientific alumni: Tim Bliss has been invited to deliver the 2012 Croonian Lecture, the Society’s premier lecture in the biological sciences, and Robin Holliday has been awarded a Royal Medal. Tim’s award recognised his work on synaptic plasticity and especially long-term potentiation and long-term depression; Robin’s medal recognised his pioneering work on DNA-strand exchange that involved what is now known as the Holliday Junction.We also congratulate three of our Programme Leaders who have been awarded major external grants: Troy Margrie (Neurophysiology) has a Wellcome Trust New Investigator award, and Anne O’Garra (Immunoregulation) and Jean-Paul Vincent (Developmental Biology) have both received grants from the European Research Council.

John Wills MBE

Robin HollidayTim Bliss

Royal Society Fellows Jim Smith, Steve Gamblin, Sir John Skehel, Sir Keith Peters and Tim Bliss celebrate Steve Gamblin’s election.


The Francis Crick Institute

This year has seen the former UK Centre for Medical Research and Innovation - now named The Francis Crick Institute - really start to take shape, in terms of its people, its organisation and its building. Sir Paul Nurse, appointed as Director and Chief Executive of The Crick, will need no introduction to the readers of this report. He took up this new leadership role at The Crick after resigning in 2011 as President of the Rockefeller University and becoming President of the Royal Society. Through all of this, he has never stopped working on the cell cycle and morphogenesis in fission yeast. It was for that work that he was awarded the Nobel Prize in Physiology or Medicine in 2001.

The name, The Francis Crick Institute, celebrates one of the country’s most distinguished scientists: the co-discoverer of the structure of DNA, and someone whose work epitomised the multidisciplinary approach to be adopted by scientists at the institute that bears his name. Francis’ daughter, Gabrielle, came to a ceremony at the site of the new Institute, along with David Willetts MP, the Minister for Universities and Science, and Mayor Boris Johnson, to witness the burial of a time capsule. NIMR’s contributions included many photographs of the building, our most recent Quinquennial Review, a copy of Mill Hill Essays 2010, and a list of our collected publications, 1970–2011.

Speakers at the time capsule ceremony. The time capsule.

Computer-generated image of the interior of the new building.


King’s College London and Imperial College London have formally joined The Francis Crick Institute, bringing their clinical and scientific skills to the partnership. Representatives of the six partners (Imperial, King’s, UCL, the Wellcome Trust, CRUK’s London Research Institute and NIMR) are now involved in all aspects of planning, and we are taking every opportunity to maximise our scientific interactions to prepare for transfer into The Crick. In September 2011 we held a joint scientific retreat and we are planning a series of joint academic ventures in the coming year.

The building itself will soon be taking shape. The planning application received its final approval early in 2011, and Laing O’Rourke were selected to do the construction work, realising the design created by HOK and PLP Architecture. Building began in June 2011 and as I write, in December 2011, 100,000 tonnes of soil and concrete have been removed from the site. It is hard to convey just how big the building will be: at 83,000 m2 its internal floor area will be 10% bigger than Brent Cross shopping centre in North London and when it has been fully excavated, the waste material will be enough to fill the Albert Hall twice. Waste clay soil is being used to help restore a bird sanctuary, while heavier material, which may contain concrete, is cleaned at a washing plant and recycled. The building itself will be finished in the middle of 2013, and fitting-out is expected to take two years. There is no doubt that The Francis Crick Institute will be a fantastic place to work. As we move closer to 2015 our pace of progress will continue to accelerate: keep an eye on the NIMR and Crick websites for details.

www.crick.ac.uk

Computer-generated image of the exterior of the new building.

Science overview

Research programmes at NIMR

NIMR is one of the world’s leading medical research institutes. It is dedicated to studying important questions about the life processes that are relevant to all aspects of health. NIMR is the largest of the Medical Research Council’s institutes. NIMR’s mission is:

• to carry out innovative, high-quality, biomedical research• to be a major contributor to the MRC’s commitments in the training of scientists• technology transfer• the presentation of its science to the public

Research at NIMR covers a broad spectrum of basic biomedical science, including infectious diseases, immunology, cell and developmental biology, neuroscience and structural biology. The world-class facilities for research include biological imaging resources, the MRC Biomedical NMR Centre and the UK’s largest academic facility for small animal research. There is a major emphasis on cross-disciplinary interactions, stemming from the pervasive culture of collaboration and strategic recruitment to complement and bridge scientific areas. There are research collaborations with many other academic and clinical centres in the UK and internationally, including strong links with University College London.

Scientists at NIMR study normal biological processes and diseases at the molecular, cellular and whole organism level. Research is focused on four scientific areas: Infections and Immunity, Genetics and Development, Neurosciences and Structural Biology. Collaborations underpin progress in these areas, e.g. on the structure and function of molecules involved in infectious diseases, common mechanisms of nervous system and immune system development, and how the functioning of the brain arises during embryonic development.

Infections and Immunity

The immune system is a key part of the body’s defence against infections. Its importance is illustrated by the effects of a defective immune system, as seen in people with AIDS, which results in overwhelming infections leading to death. While an effective immune system is vital for health, an over-exuberant immune system can start to attack the body itself, a process known as autoimmunity. Autoimmunity is the cause of allergies such as hay fever and more serious conditions such as asthma, rheumatoid arthritis, and multiple sclerosis. We are analysing how the cells of the immune system are triggered to mount an immune response when faced with an infectious agent, how the process can go awry in autoimmunity, and how complex checks and balances in the system ensure activation of the immune system only when needed.

Infectious diseases result from the transmission of pathogenic micro-organisms. Examples studied at NIMR include malaria, tuberculosis, AIDS and influenza which are responsible for the deaths of millions of people every year. This death toll is exerted mainly in the poorer countries of the world, and is also a significant and increasing burden for the National Health Service. Our research seeks to understand the fundamental biology of the causative micro-organisms and their interaction with hosts. We use this understanding to promote the development of new drugs, vaccines and diagnostic reagents. The study of pathogenic agents is also a rich source of important information on basic mechanisms of cell and molecular biology.



Genetics and Development

Understanding how a fertilised egg generates a functional organism is an important area of biology that has many implications for medicine. We are studying the fundamental mechanisms that underlie embryo development, including how cells proliferate, migrate and communicate, how stem cells form and are maintained, and how diverse cell types are generated, each at the correct location in the forming organism. A major focus is on identifying the underlying genes, how they function and are regulated, and their role in networks of molecular and cellular interactions that control developmental processes. These studies include the use of powerful genome-wide techniques and systems biology approaches in order to uncover gene regulatory networks. Much of our work focuses on the development of specific tissues such as the nervous system, heart, liver, gonads and limbs. As many of the genes that control specific processes are conserved between species, our studies are carried out in a range of model organisms that have distinct strengths for uncovering mechanisms of normal development and how defects can arise. Since many of the same processes and underlying molecular pathways are utilised in the adult, studies of development also reveal the basis of disorders such as cancer in which the proliferation and migration of cells is abnormal. In addition, elucidation of the normal mechanisms that maintain stem cells and that direct them to form specific cell types is essential for potential therapeutic use of these cells.

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. Our work also examines the role of the nervous system and other tissues in energy balance and metabolism. 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.

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Scientific highlights

MRC National Institute for Medical Research

It gives me great pleasure to outline here a few of the Institute’s most exciting discoveries of the year. A major strength of NIMR is the way in which structural biology informs our understanding of infectious disease. Influenza remains an important focus of the Institute, and the significance of this work was emphasized by the news, at the end of 2011, that just five mutations in H5N1 bird flu might allow it to be transmissible between humans through the air. This observation highlights the importance of the WHO Influenza Centre at NIMR, which monitors genetic changes in circulating influenza viruses. And while it is very unlikely indeed that such a virus should appear, the work also emphasises the need to develop therapeutic agents that will block all influenza virus infections (including swine flu, bird flu and Spanish flu) and could be stockpiled for use in emergencies. One such reagent, a neutralising monoclonal antibody that confers protection to mice and ferrets, has now been characterised by John Skehel and Steve Gamblin together with colleagues from Switzerland. An understanding of the structural basis of protection will be extraordinarily valuable in helping design broad-spectrum vaccines.

Another example of structural biology informing the struggle against infectious disease comes from work by Ian Taylor, Luiz Pedro de Carvalho and Jonathan Stoye. They characterised the structure of SAMHD1, a restriction factor which inhibits the growth of HIV-1, the causative agent of AIDS. Normally expressed in dendritic and other myeloid immune cells, SAMHD1 prevents reverse transcription of the HIV-1 genome and inhibits its replication. Further study of SAMHDI will help develop new therapeutic approaches to HIV-1 and even vaccine development.

Rob Wilkinson and colleagues have found that vitamin D deficiency is extremely common in black Africans living in Cape Town, South Africa, and is associated with susceptibility to tuberculosis infection. The work suggests that vitamin D supplementation might be a cost-effective, safe and simple means to reduce the incidence of TB in South Africa and elsewhere in the world. Work on malaria at NIMR has also continued apace, with new insights into the way in which the malaria parasite invades red blood cells. Tony Holder and his colleagues have demonstrated that the malaria parasite can select from a panel of ligands to bind to receptors on the surface of host red blood cells, and this will probably confound attempts to block invasion that are based on any single ligand receptor.

Gitta Stockinger’s group, with her colleague Marc Veldhoen (now at the Babraham Institute), has discovered that nutrients found in vegetables such as broccoli and Brussels sprouts activate the aryl hydrocarbon receptor, which helps maintain intestinal epithelial cells and prevents adverse effects of pathogenic gut micro-organisms. Gitta has also studied the cytokine interleukin-9 (IL-9), which has been implicated in lung inflammation. By making a mouse in which IL-9-expressing cells carry a stable genetic mark, she has discovered that during an inflammatory response this cytokine is activated transiently by a subpopulation of innate lymphoid cells. Those cells go on to express IL-13 and IL-5, cytokines that are normally expressed in the Th2 subset of T cells and which are a major cause of allergic reactions. Blocking IL-9 reduced IL-13 and IL-5, suggesting that innate lymphoid cells represent an important link in the regulation of Th2 responses.

Cell marking techniques have also proved important in the area of neuroscience and developmental biology, where Iris Salecker has devised a genetic multi-colour cell labelling approach for Drosophila that she calls Flybow. Extending work by Josh Sanes and Jeff Lichtman at Harvard University, this technique allows workers simultaneously to visualise neurons or other cell types, in defined tissues and at defined times, through the stochastic expression of four membrane-tethered fluorescent reporters. This will prove to be a remarkably powerful technique to follow the behaviour of cells as they divide, migrate and interact with each other during development. Alex Gould’s group has investigated the mechanism by which the brain is spared in periods of nutrient deprivation during human gestation. They also found that the Drosophila brain is protected from the effects of dietary restriction and that this occurs because the receptor Anaplastic Lymphoma Kinase switches stem cells in the brain from a state where they require nutrients to grow to one where they do not. This discovery establishes a new genetic model for human intra-uterine growth restriction, and will shed light on how the mother’s diet influences health and disease in later life.

A trimer of haemagglutinin binding to three molecules of antibody.


Important insights into how progenitor cell proliferation is regulated in the developing vertebrate brain have come from François Guillemot and colleagues, who studied a proneural transcription factor, Ascl1, known to be essential for neuronal differentiation. A genome-wide analysis of transcriptional targets of Ascl1 unexpectedly found that these include genes that control cell cycle progression. Furthermore, since inactivation of Ascl1 was found to alter the proliferation of neural progenitor cells, this proneural factor contributes to the expansion of progenitor cell number as well as to their differentiation.

Jean-Paul Vincent, with Eugenia Piddini (now at the Gurdon Institute in Cambridge), has studied how Wnt signalling determines whether a cell will live or die. Previous work had indicated that cells require Wnt signalling in order to survive. Jean-Paul and Eugenia found that what really matters is the relative level of Wnt signalling. For example, if a normal cell is surrounded by cells in which the Wnt signalling pathway is hyperactive, that cell will die. This might be relevant to human cancers in which Wnt signalling is overactive, perhaps due to mutations in genes such as APC (the most common mutation in colon cancer).

In another technical advance, this time in the mouse, Troy Margrie and his colleagues have shown that the whole-cell patch clamp method can be used to transfect single cells with plasmids during neuronal recording in vivo. This allowed Troy to record the synaptic input and sensory function of a neuron and then to trace the upstream brain circuits, but the potential of the method goes beyond this to include genetic perturbation of intracellular signalling pathways, the introduction of light-activatable ion channels, and many other possibilities. This approach represents a major step forward in our attempts to understand the functional architecture of the brain.

Highlights 2007-2010

2010 • Immune signature for tuberculosis (Anne O´Garra and Robert Wilkinson) • Parasite invasion and replication (Mike Blackman) • Role of Sox9 in neural stem cell induction and maintenance (Robin Lovell-Badge and James Briscoe) • Initiation of neuronal differentiation (David Wilkinson) • Meiotic sex chromosome inactivation is essential for male fertility (Paul Burgoyne and James Turner) • Formation and dissociation of muscarinic receptor dimers (Nigel Birdsall and Justin Molloy) • Electron cryomicroscopy of influenza virus (Peter Rosenthal)2009 • Depletion of activated CD4+T cells (George Kassiotis and Dimitris Kioussis) • Structure of Nbs1 protein (Steve Smerdon) • Morphogen gradients not needed for proliferation (Jean-Paul Vincent) • Evolution of vertebrate limbs (Malcolm Logan)2008 • Neurogenin2 controls neuronal migration (François Guillemot) • A transcription factor linking environmental toxins to autoimmunity (Gitta Stockinger) • The adult pituitary gland contains stem/progenitor cells (Iain Robinson and Robin Lovell-Badge) • Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants (Steve Gamblin, Alan Hay and John Skehel) • Timer genes control brain size (Alex Gould) 2007 • A novel mechanism for reading the concentration of a signal – a clue to embryonic development (James Briscoe) • Discovery of malaria parasite escape technique leads to new drug target (Mike Blackman) • AMPK enzyme structure offers hope of effective diabetes treatment (Steve Gamblin) • Fruit fly’s fatty secrets shed light on liver disease (Alex Gould)

Activity of Flybow 1.1 in the 3rd instar larval and adult visual system.

Wnt-induced cell competition and Notum

Brain sparing in the late-stage Drosophila larva

See references 35, 42, 82, 89, 125, 135, 160, 188, 244 and 249 in the bibliography at the back for the publications mentioned.


NIMR history and milestones

1933 Discovery of flu virus Christopher Andrewes, Patrick Laidlaw and Wilson Smith first isolated the human influenza virus.

1951 Steroid biosynthesis John Cornforth completed the first total synthesis of the non-aromatic steroids and identified the chemical structure of cholesterol. He received the Nobel Prize in 1975.

1957 Interferon Alick Isaacs discovered interferon, a factor that can transfer a virus-resistant state to cells that had not been infected, and is now used to treat many infections and cancers.

1960s Cryobiology Audrey Smith discovered how to store biological material at low temperature, pioneering techniques for the freezing of sperm, blood, bone marrow, corneas and many other tissues.

1986 Globin locus control region Frank Grosveld discovered regulatory sequences that govern expression of the globin gene cluster, and that confer a copy number dependent level of transgenic gene expression. He was awarded the Louis-Jeantet Prize for Medicine in 1991.

1973 Long-term potentiation Tim Bliss and Terje Lømo discovered the phenomenon of synaptic long-term potentiation, one of the main mechanisms by which the brain learns and remembers.

1991 The sex determining gene Robin Lovell-Badge showed that the presence of the Sry gene on the Y chromosome is sufficient to cause the embryonic gonad to develop as testis rather than ovary. He received the Louis-Jeantet Prize for Medicine in 1995.

1996 Discovery of the anterior organising centre Rosa Beddington discovered a novel signalling centre in the mouse embryo required for correct formation of the head-to-tail axis during embryonic development.

2005 Mouse model of Down syndrome Victor Tybulewicz created a genetically manipulated mouse that carries almost all of human chromosome 21. The resulting strain of mice has become a valuable tool in research on Down syndrome.

1999 Eph receptors mediate cell segregation David Wilkinson uncovered a new mechanism that maintains the correct organisation of tissues, mediated by signalling through Eph receptors and ephrins.

2006 Discovery of Th17 subset Gitta Stockinger defined the developmental steps that lead to the Th17 immune response. Th17 cells are important in the pathogenesis of many autoimmune diseases.

2010 Transcriptome signature in human tuberculosis Anne O’Garra discovered a novel transcriptomic signature that provides insights into fundamental pathogenesis of tuberculosis and has application to the development of improved diagnostic tools.

2007 AMP-activated protein kinase (AMPK) structure Steve Gamblin determined the structure of the enzyme that regulates cellular energy levels, AMPK. The discovery paves the way for better treatments of Type 2 diabetes.

2007 Malaria release mechanism Mike Blackman identified an enzyme that triggers release of the malaria parasite from infected red blood cells thereby enabling it to invade new cells. The enzyme is a new target for improved anti-malarial drug design.

1989 Hox gene colinearity Robb Krumlauf showed that the linear relationship between the organisation of Hox genes along the chromosome and their expression along the head-to-tail axis is conserved in vertebrates.

1981 Structure of influenza haemagglutinin John Skehel revealed the structure of influenza virus proteins involved in the infection of cells, for which he was awarded the Louis-Jeantet Prize for Medicine in 1988. This work opened new perspectives for the design of antiviral drugs.

1993 Mesoderm-inducing factor Jim Smith discovered that activin is a mesoderm-inducing factor, opening up understanding of how signalling factors control the formation of tissues during embryo development.

1958 Immunoglobulin structure Rodney Porter was given the Nobel Prize in 1972 for the discovery of the structure of immunoglobulins. The work increased understanding of the immune system and led to novel approaches to diagnosis and therapy.

1952 Gas chromatography After receiving the Nobel Prize in 1950 for his earlier discovery of partition chromatography, Archer Martin joined NIMR and with A.T James he developed gas chromatography, a technique now widely used in laboratories and the chemical industry.

1936 The role of acetylcholine as a neurotransmitter Henry Dale established the chemical basis of neurotransmission and the role of acetylcholine as a neurotransmitter, receiving the Nobel Prize for this work in 1936.

1930 1940 1950 1960 1970 1980 1990 2000 2010


1933 Discovery of flu virus Christopher Andrewes, Patrick Laidlaw and Wilson Smith first isolated the human influenza virus.

1951 Steroid biosynthesis John Cornforth completed the first total synthesis of the non-aromatic steroids and identified the chemical structure of cholesterol. He received the Nobel Prize in 1975.

1957 Interferon Alick Isaacs discovered interferon, a factor that can transfer a virus-resistant state to cells that had not been infected, and is now used to treat many infections and cancers.

1960s Cryobiology Audrey Smith discovered how to store biological material at low temperature, pioneering techniques for the freezing of sperm, blood, bone marrow, corneas and many other tissues.

1986 Globin locus control region Frank Grosveld discovered regulatory sequences that govern expression of the globin gene cluster, and that confer a copy number dependent level of transgenic gene expression. He was awarded the Louis-Jeantet Prize for Medicine in 1991.

1973 Long-term potentiation Tim Bliss and Terje Lømo discovered the phenomenon of synaptic long-term potentiation, one of the main mechanisms by which the brain learns and remembers.

1991 The sex determining gene Robin Lovell-Badge showed that the presence of the Sry gene on the Y chromosome is sufficient to cause the embryonic gonad to develop as testis rather than ovary. He received the Louis-Jeantet Prize for Medicine in 1995.

1996 Discovery of the anterior organising centre Rosa Beddington discovered a novel signalling centre in the mouse embryo required for correct formation of the head-to-tail axis during embryonic development.

2005 Mouse model of Down syndrome Victor Tybulewicz created a genetically manipulated mouse that carries almost all of human chromosome 21. The resulting strain of mice has become a valuable tool in research on Down syndrome.

1999 Eph receptors mediate cell segregation David Wilkinson uncovered a new mechanism that maintains the correct organisation of tissues, mediated by signalling through Eph receptors and ephrins.

2006 Discovery of Th17 subset Gitta Stockinger defined the developmental steps that lead to the Th17 immune response. Th17 cells are important in the pathogenesis of many autoimmune diseases.

2010 Transcriptome signature in human tuberculosis Anne O’Garra discovered a novel transcriptomic signature that provides insights into fundamental pathogenesis of tuberculosis and has application to the development of improved diagnostic tools.

2007 AMP-activated protein kinase (AMPK) structure Steve Gamblin determined the structure of the enzyme that regulates cellular energy levels, AMPK. The discovery paves the way for better treatments of Type 2 diabetes.

2007 Malaria release mechanism Mike Blackman identified an enzyme that triggers release of the malaria parasite from infected red blood cells thereby enabling it to invade new cells. The enzyme is a new target for improved anti-malarial drug design.

1989 Hox gene colinearity Robb Krumlauf showed that the linear relationship between the organisation of Hox genes along the chromosome and their expression along the head-to-tail axis is conserved in vertebrates.

1981 Structure of influenza haemagglutinin John Skehel revealed the structure of influenza virus proteins involved in the infection of cells, for which he was awarded the Louis-Jeantet Prize for Medicine in 1988. This work opened new perspectives for the design of antiviral drugs.

1993 Mesoderm-inducing factor Jim Smith discovered that activin is a mesoderm-inducing factor, opening up understanding of how signalling factors control the formation of tissues during embryo development.

1958 Immunoglobulin structure Rodney Porter was given the Nobel Prize in 1972 for the discovery of the structure of immunoglobulins. The work increased understanding of the immune system and led to novel approaches to diagnosis and therapy.

1952 Gas chromatography After receiving the Nobel Prize in 1950 for his earlier discovery of partition chromatography, Archer Martin joined NIMR and with A.T James he developed gas chromatography, a technique now widely used in laboratories and the chemical industry.

1936 The role of acetylcholine as a neurotransmitter Henry Dale established the chemical basis of neurotransmission and the role of acetylcholine as a neurotransmitter, receiving the Nobel Prize for this work in 1936.

1930 1940 1950 1960 1970 1980 1990 2000 2010

The training of students, of all levels, is integral to NIMR and through the programmes we offer we strive to train biomedical leaders of the future.

PhD Programme

The NIMR four-year PhD programme has been designed to equip our students with the scientific and transferable skills required to make them internationally competitive. Fully integrated into the NIMR PhD programme are medical undergraduate (MB BS) students who join us in January of each year via the UCL MB PhD programme. All of our students benefit from access to the state-of-the art facilities and extensive expertise available across the Institute. We encourage innovation, interdisciplinarity and collaboration, and, indeed, many of our PhD students have projects that span multiple research themes, providing them with an excellent opportunity to broaden their general understanding of science and acquire practical expertise. As a result of this, our 80 or so students significantly contribute to the research output of NIMR.

On arrival at NIMR, students work closely with their supervisors to develop their project proposal. They also choose a thesis committee, members of which have expertise in a range of scientific areas and whose role is to advise the student for the duration of their PhD studies. Initially registered for an MPhil degree, students transfer to a PhD registration in Year 2 on the basis of an upgrade report. To support the development of our students we offer a wide range of internal training courses ranging from bioinformatics, statistics and microscopy to ethics, report preparation and presentation skills. We also run a series of careers seminars and an annual careers round table event, which reflect the broad range of careers that are available to PhDs.

We encourage a good work-life balance and onsite you’ll find a range of social activities including football, fitness classes, squash, badminton, a book club, quizzes and a licensed bar. Our student representatives (see page 15) organise a number of social events including a Christmas dinner and summer barbecue attended by PhD, Sandwich, Summer and work experience students. Social activities at NIMR contribute to the spirit of collaboration which pervades science at the Institute. For those looking for a short commute, we offer on-site accommodation for 12 students.

Exciting times lie ahead with the opening of The Francis Crick Institute in 2015. The students we recruit from 2012 will move to The Crick when it opens and plans are already in place to ensure a smooth transition. Until then NIMR students will benefit from our close relationship with our partner in The Crick, the CRUK London Research Institute.

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14

PhD students


CAREERS

Donna BrownDirector of Studies


CAREERS

Student representatives

With a varied intake of PhD, MBPhD, Summer and Sandwich year students throughout the year the student representatives aim to inspire a sense of community amongst the student body through regular social activities. Weekly student seminars and monthly journal clubs expose students to topics outside of their primary field of interest, and allow students to receive informal feedback on their presentations, to ask questions, and to establish potential collaborations with other Divisions. Additionally a Student Seminar Day is held each year in association with students based at UCL offering a further opportunity for students to present their work. The student representatives also sit on various committees within both the NIMR and UCL so that their opinions can be voiced. The 2011 student representatives:

Sam Goldsmith, Laura Robinson and Kat Collins.

The 2011 intake of PhD students

The 2011 Travel Prize

Each year NIMR awards a £1000 Travel Prize for the best Upgrade Report. This year the judges were so impressed by all of the reports they decided to introduce a runner-up prize of a £100 Amazon voucher. The prizes were presented by Steve Gamblin (Director of Research) to the winner, Jeff Cloutier (Stem Cell Biology and Developmental Genetics) and the runner up, Elizabeth Underwood (Molecular Structure).


PhD students – in their own words

Jeff Cloutier

“Over the past two years, I have been working with James Turner in the Division of Stem Cell Biology and Developmental Genetics at NIMR. Before coming here, I undertook my undergraduate education at Middlebury College, Vermont (USA), where I had my first taste of meiosis research. After attending a Gordon Conference on Meiosis, where I learned about James’ interesting research, I was inspired to pursue my PhD research in the UK. My work in the Turner lab has been focused on understanding the molecular mechanisms that lead to germ cell loss and infertility in mice.

NIMR is a unique place for research. The tightknit nature of the community encourages frequent interactions, both in the laboratory and in the canteen, corridors and onsite bar. As a PhD student, I have also had the opportunity to present my work at two big international meetings. My PhD training at NIMR has been a stimulating and exciting experience. Over the next two years, I will complete my PhD work at the National Institutes of Health (USA), as part of a collaborative training programme funded by an NIH Marshall Scholarship.”

Christine Tshitenge

“I’ve been at NIMR for almost three years as a Marie Curie PhD student. My research project focuses on characterising the differences in immunopathology in virulent and avirulent P. chabaudi infection. The ultimate aim is to identify differences in the host immune responses that correlate with disease outcome. This could hopefully provide useful information for vaccine development and also more insight into disease pathogenesis. I came to do my PhD here for various reasons. Amongst these are that NIMR has some of the top and most referenced labs in the world, national and international collaborations, a culture of learning and carrying out challenging research, the opportunity to be mentored by some of the world’s leading scientists and to interact with them on a daily basis. I could say a mouthful of adjectives to describe my experiences at NIMR, but what I will say is that NIMR has given me an edge in terms of future career aspirations.”

CAREERS


Work experience for school students

We encourage students from an early age and each year local school students work alongside our researchers, quite often PhD students, for periods of up to six weeks (also see Research Summer School on page 29). Many of these students come back as undergraduate, Summer or Sandwich students.

Sandwich students and work experience

Sandwich placementsNow, more so than ever, having practical research experience is essential for a scientific career at any level. Our Sandwich placements provide students with the opportunity to fully immerse themselves in a research lab for 12 months and to work on an independent research project. Sandwich students also have access to a wide range of lectures, seminars and training, and thus fully benefit from all that NIMR has to offer. Many of our Sandwich students go on to do a PhD at NIMR and other leading research institutions.

Rebecca Campion

“This year I spent six months doing work experience at NIMR before going to Cambridge University to study Natural Sciences (Biological). I spent three months each in two different laboratories. In all honesty, I have not the words to express how much I learnt and enjoyed my experience. Although I was exceedingly naive, lacking in both experience and knowledge, everyone I met took time to answer any and all questions that I had (and there were many of them). Not only were they incredibly patient, but also everyone I met at the Institute made me feel welcome. For anyone who is willing and eager to learn I can think of no better place for student research studies.”

The 2011 intake of sandwich students

CAREERS

Tom Flower

“I was based in Dr Ian Taylor’s lab within the Division of Molecular Structure. My project focused on a retroviral protein known as Foamy Virus Gag. During the project I obtained numerous skills including protein production, purification and crystallisation along with other analytical techniques. I am happy to say that the project was very successful and resulted in the determination of a Foamy Virus Gag crystal structure. I found the NIMR a great place to socialise outside of the lab thanks to facilities such as the onsite bar, monthly social events and weekly sporting activities. The subsidised canteen and Costa coffee shop were very reasonably priced and made living in London much more affordable. Overall this year at NIMR has strengthened my desire to work in research and as a result I aim to study for a PhD after I graduate.”


CAREERS

In addition to its role in the training of PhD students, NIMR is a major centre for further research training and career development. It attracts researchers from the UK and across the world due to the breadth and quality of the research, and the emphasis on interactions and cross-disciplinary collaborations. Researchers at all stages of their career development benefit from the very active programme of seminars and internal research meetings, and the availability of courses to acquire key scientific and complementary managerial skills.

NIMR hosts approximately 220 postdoctoral researchers, supported either by MRC core funding or externally funded fellowships. The core funding promotes careers at the postdoctoral level through three year MRC Career Development Fellowships (CDFs). In addition to the training and support offered to postdoctoral researchers by NIMR, the Postdoc Committee is very active arranging seminars, retreats and careers sessions. In 2010 The Scientist ranked NIMR third in the UK among “Best Places to Work for Postdocs”.

NIMR also has a vital role in providing research training for clinical scientists, and this is an important facilitator of translational projects and national and international collaborations. NIMR hosts many visiting postdoctoral clinical scientists from the UK and abroad carrying out research on, for example, infectious diseases and genetic disorders.

Postdoctoral scientists

The Postdoc Committee

The Postdoc Committee is composed of postdocs working at NIMR in different fields and was created to organise, inform and support the community of postdocs at NIMR. The Committee promotes communication between postdocs, runs a postdoc website, and has organised a seminar series, exclusively dedicated to and attended by postdocs of the Institute, which has featured high calibre presentations. The Committee has representation on a number of Institute committees. Finally, it organises the annual Postdoc Retreat, which, this year, took place at the Natural History Museum. This was a resounding success with interesting scientific speakers as well as career-focussed presentations and networking. In the coming year the Committee aims to continue with current activities as well as increasing the communication between postdocs at NIMR and those at institutions that will also move into The Francis Crick Institute.

The 2011 Postdoc committee:Melanie Lebel, Otto Kyrieleis, Harriet Groom, Mohamed Ismail (Soly) and TJ Ragan


CAREERS

Postdoctoral scientists – in their own words

Laurent Dupays, Division of Developmental Biology

“Working at NIMR has been a great experience over the past few years. The large size of the Institute and the wide range of expertise available allow any researcher to find what he or she needs in a matter of hours, whether it be an unusual restriction enzyme or the answer to an obscure statistical problem. One of the many assets is the incredibly well organised network of services. As a developmental biologist working on mouse heart development it’s great to have access to such a wonderful mouse facility. Our animal technicians are dedicated to taking care of our mouse colonies, which allows us as researchers to spend more time at the bench furthering our knowledge. And the mouse facility is just one part of the many dedicated services provided for scientists at the Institute.

Another benefit is the number of people working on so many different model organisms. Maybe your speciality is mouse embryology, but you would like to perform some quick functional analyses in an alternative model? Just go next door and ask about zebrafish or Xenopus embryos and you can expand your project into another organism within the week. And colleagues are always happy to help you ‘see the light’ by using their preferred model! Without doubt the great infrastructure combined with the sharing of knowledge and skills makes NIMR a wonderful place to work efficiently, and perform well.”

Otto Kyrieleis, Division of Molecular Structure

“I started at NIMR in November 2009. I am working in Steve Smerdon’s group, on the structural biology of complexes involved in ubiquitin-regulated signalling events following double-stranded DNA breaks. I have always enjoyed the friendly, collegial atmosphere at the Institute and in particular in the Division of Molecular Structure. In addition to the great working atmosphere here, the Institute offers a great variety of facilities available for everyone in the Institute. This allows you to learn many additional techniques and methods to tackle biological questions. Each facility is run by competent and friendly staff, who are willing to share their knowledge and expertise with you and to support you. This makes the life of postdocs at NIMR a lot easier compared to other institutions. And finally, I really appreciate the opportunities for social networking at NIMR including the onsite bar, various sport pitches, squash court and the seminar series such as the Mill Hill Lectures and the bi-monthly postdoc seminar series with a beer session afterwards. Taking all these things together this makes the NIMR a very inspiring and exciting place to work.”

Programme Leaders


Most Programme Leaders at NIMR are initially recruited on Programme Leader Track positions. This provides core support for a five-year period, which, following external review, can lead to promotion to an open-ended MRC Programme Leader appointment. This latter position provides 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.

Eva Frickel, Parasitology - joined NIMR in 2011

“The reason I am at NIMR is simple. I have always chosen scientific topics and projects I found most interesting, in the places that I thought did them best. I wanted to start my own small research group aiming to make a difference in my area of research with a multi-disciplinary approach. I knew that this would only work in a highly collaborative environment with research groups around me interested in similar aspects of infectious diseases, others working with similar methods, all embedded in an institute with fantastic core facilities and support staff. NIMR immediately stood out as a unique place that provides all of this.

I applied for a Wellcome Trust Career Development Award to be able to take my research to Mill Hill. I found an NIMR sponsor in Jean Langhorne, who was enthusiastic to recruit me to the Institute. NIMR welcomed me with open arms and I am convinced I made the right choice. I am looking forward to starting my independent career at this place of great history and innovation.”

Peter Thorpe, Stem Cell Biology and Developmental Genetics - joined NIMR in 2011

“I was looking to establish my own laboratory exploring how yeast can be used to understand adult stem cell function. Many institutions focus their research into narrowly-defined themes. Finding an environment that bridged basic science and clinical research was difficult. Although some larger universities achieve this balance, researchers are naturally divided into either clinical or basic research and often have limited contact or appreciation of each other’s work. I had seen how the MRC brings together scientists working at both ends of the basic–clinical science spectrum and so when I saw an opportunity to work at NIMR, I applied immediately. NIMR’s research is legendary and with so many great scientists launching their careers here, this was too good an opportunity to miss.

At NIMR the MRC support means we can spend most of our time on research. We are able to drive the research forward using new approaches to solve our scientific questions. The friendly and welcoming atmosphere helps to make interdisciplinary research a reality. I have already been working with both structural and developmental biologists to exploit our yeast system in new ways. In the coming years I hope to be able to make the most of this fantastic environment.”

CAREERS


CAREERS

Troy Margrie, Neurophysiology - joined NIMR in 2009

“As a graduate student in Australia I discovered NIMR through my reading of several key studies on synaptic transmission and plasticity that were carried out here. Later, one of my PhD advisors collaborated with Tim Bliss who visited our lab to carry out in vivo experiments. This exposure to whole animal electrophysiology seeded my long-standing interest in systems neuroscience. When I later heard of positions opening up at NIMR it immediately caught my interest as a very exciting, collegial and interdisciplinary environment.

NIMR differs from the other institutes I have worked in in two ways. Firstly, the Lab Managers make a genuine difference; they have all been outstanding in their ability and attitude. From sorting out hand towels to redesigning lab space, they work with minimal fuss and as efficiently as possible. Secondly, the open-door policy and generosity that permeates the Institute is apparent from the students and postdocs through to Programme Leaders and the Directors and their support teams. There is genuine altruism and, most importantly, a sense that the science comes first. These two main points have stood out for me and underlie the very positive psychology that exists here. I think this is also the main challenge for NIMR and its staff moving forward to The Crick. It is really not about bricks and mortar or the logistics of moving mice and microscopes but rather how one creates such a unique and positive scientific culture within a reincarnation of NIMR and its co-founding partners.”

Iris Salecker, Molecular Neurobiology - joined NIMR in 2001

“After completing my postdoctoral training in California at UCLA I came to NIMR to set up my first independent research group. Over the years, I experienced a truly supportive environment that allowed me to grow into the role of a PI and develop a long-term research programme, first as a career-track and then as a tenured Programme Leader. Within the Developmental Biology/Neurosciences community and beyond, our shared activities, such as internal seminar series, not only expose us continuously to outstanding research in a wide range of different research areas, but importantly also create a genuine spirit of collegiality. Thus, I found both real mentorship and inspiring colleagues with whom to exchange advice and expertise and to venture into new territories, such as imaging techniques, which may not have felt reachable otherwise. I also value that by running a relatively small group and because of core funding and solely voluntary teaching, I can work even as a PI, whenever possible, at the bench or in my case in the fly room or at the confocal microscope side-by-side with my students and postdocs to test ideas and share the excitement of advancing our research.”

CAREERS


Research support

NIMR offers career opportunities that can be broadly termed research support, covering many different types of jobs. Research Technicians are located within specific programmes and are directly involved in research. Laboratory Managers look after all the labs and equipment of one or more Divisions, ensuring that the science runs smoothly. Many individuals are involved in the running of NIMR’s extensive facilities, for example the biggest of which, Biological Services, provides a fully integrated laboratory animal and technical resource to the Institute. Finally, the Institute employs individuals in a range of non-scientific activities, including Divisional Administrators, Personal Assistants, Human Resources, Accounts, Procurement, Stores and Security.

Alessandra Gaiba, Laboratory Manager

“I started my scientific career with a six-month placement at Glaxo Wellcome in Stevenage straight after my degree from the University of Bologna in Italy. I decided to stay in the UK where there were more possibilities to do research outside academia than there were in Italy. I then spent 13 years working as a medicinal chemist at SmithKline Beecham (which then became GSK).

A couple of years ago, I decided to change career and came to NIMR as a Laboratory Manager. For 18 months I shadowed other Lab Managers and covered for them while they were on holiday, which gave me the opportunity to get to know all the different areas and all the key people in the Institute. From the beginning, I was struck by how different the atmosphere was at NIMR compared to industry and how much easier it was to talk to people. Since July 2011, I have taken on the role of Lab Manager for the Divisions of Immune Cell Biology and Molecular Immunology, following the retirement of Nick Clark. So far, I have really enjoyed my new role. I love interacting with other support staff and my scientists, helping them sort out problems with equipment, ordering from suppliers and coordinating lab refurbishments.”

Vangelis Christodoulou, Protein Expression Manager

“After successful stints at EMBL-Hamburg Outstation, University of Athens and the Netherlands Cancer Institute, I came to NIMR (nearly three years ago) with the rather daunting task to set-up the Protein Expression Lab within the Division of Molecular Structure. When I arrived, there was a lab packed with equipment waiting for me. And thanks to the help and support of my line manager and the members of the Division I had my lab up and running within a few weeks of my arrival. Since being at NIMR, I have benefited immensely from the freedom I was given to develop new protein expression technologies, the close working relationship with the members of my Division and the collaborative spirit amongst NIMR scientists.

So far, NIMR has been a fantastic place to work, giving me the opportunity to get involved in challenging projects while generously offering all the necessary resources and support, which makes the whole process very enjoyable.”

CAREERS


Graham Preece, Flow Cytometry Manager

“Following a decision not to pursue a teaching career I arrived at NIMR on November 14th 1977 and only really expected to stay a couple of years. However, NIMR’s invigorating and academically stimulating environment together with its unique warm and friendly atmosphere, which can only be described as mildly addictive, got in the way of moving further afield and I have thoroughly enjoyed an exciting and interesting career spanning 34 years.

I first joined Dr Mike Parkhouse’s lab in the Immunology Division and became an expert in monoclonal antibody production. Following Mike’s departure in 1990 I moved into Dr Ann Ager’s lab where I spent the next ten years working on lymphocyte trafficking. When Ann moved to Cardiff in 2000 I was recruited into the expanding Flow Cytometry labs. The research skills I had gained over the previous 23 years and in particular the experience I had working with antibodies, fluorochromes, and flow cytometric methods meant that I was easily able to slot into a very busy lab. In 2010 I successfully applied for the post of Flow Cytometry Manager. Running the Flow Cytometry labs has given me the opportunity to develop the service and we are now able to offer a cell sorting service at CL2 and have just taken delivery of a new state-of-the-art analyser.

In summary, NIMR offers a fantastic career opportunity for those who want it. Combining this with the exceptional uniqueness of the NIMR environment means that my last 34 years here have been an incredible experience. I would recommend it to anyone and I hope new staff experience the same at The Crick.”

Mike Reilly, Procurement Manager

“I began my career as a Research Technician at the Liverpool School of Tropical Medicine and moved to NIMR in 2003, continuing as a Research Technician in the Division of Developmental Biology. The position allowed me to gain experience in laboratory management and to successfully undertake research projects. Three years ago the opportunity arose to become Procurement Manager at the Institute after I expressed interest to move out of the laboratory. The transition into purchasing has been an excellent move for me professionally and personally, with my scientific background proving to be greatly beneficial. The change allowed me to remain at NIMR, as I wished, as it is an outstanding place to work, evidenced by the length of service of current staff.

One of the major benefits of working at NIMR, within the MRC, is the commitment to professional development of its staff. I have been fully supported which has allowed me to complete my first Chartered Institute of Purchasing and Supply (CIPS) qualification in 2011. This is prominently recognised in the procurement field and I continue these studies to the next qualification with sustained support. Finally, another highlight of the year was my football team winning the NIMR 8-a-side league!”

Animal Technicians

CAREERS

NIMR is 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 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, the 3Rs and a good background in biological sciences. Technicians are encouraged to spend time in NIMR research labs in order to gain hands-on experience of experimental procedures, and attend workshops and seminars held on a regular basis on subjects related to laboratory animal science. Visits to other scientific establishments, symposia and international meetings are also organised which enable technicians to gain experience in more varied aspects of laboratory animal husbandry and science, ensuring the 3Rs are embedded in all work involving animals at the Institute.

Ola Puchalska-Oosorio, Animal Technician

“I joined NIMR Biological Services two years ago as an Animal Technician. Since the beginning I was trained on how to take the best care of animals used for medical research, their welfare and how to handle different species correctly. After a few months at the Institute I had the opportunity to study the Level 3 CPD course in Animal Technology, and decided to take it because I felt it could help me to improve my knowledge in this field. This course has helped me to understand more deeply the legal and ethical aspects of using animals in medical research, their needs, welfare and environment. The course has been an important complement to my practical skills gained at the Institute. Also, I found that the flexibility of the course allows me to take more time in research and helps me to further analyse the topics studied.”

Kim Demetriou, Animal Technician

“I initially chose to complete the level 2 CPD course in Animal Technology to increase my vocational qualifications. As much as I enjoy my job as an Animal Technician, since starting the course I have begun to view my work as a career rather than just a job. I believe I have gained confidence in my abilities to control and handle animals, and I have found that learning more about animal husbandry, the scientific background and the roles of the support staff, has given me a deeper understanding of research and the importance of providing a high standard of animal welfare.”


TRANSLATIONAL RESEARCH

Laboratory-based studies at NIMR underpin the MRC’s mission to improve human health through research. Discoveries of how molecules, cells and organs are formed, regulated and function provide the knowledge that can lead to new therapies and diagnostics. This ‘intellectual property’ and its translation into products such as useful novel drugs or vaccines feeds into commercial projects that can build on this ‘know-how’, and Technology Transfer facilitates this exploitation.

Some studies are closely aligned to specific human diseases and this research benefits from close interactions with clinicians. Productive exchange between basic scientists and clinicians allows model systems to be used to their greatest advantage in scientific discovery, and provides insights into the disease process in patients as well as potential treatments and improved clinical care.

Technology Transfer

NIMR scientists are supported by a local Technology Transfer office which provides mechanisms and structure to allow basic technology transfer activities such as material transfer agreements, collaboration agreements and confidentiality agreements to be dealt with locally and speedily. The office is also responsible for raising awareness of intellectual property issues and encouraging scientists to be alert to potential exploitation opportunities.

MRC Technology (MRCT) is the exclusive technology transfer agent for the Medical Research Council and is responsible for translating cutting edge scientific discoveries into commercial products. In addition they have small molecule drug discovery and therapeutic antibody facilities, providing lead stage therapeutic assets to pharmaceutical and biotechnology companies. MRC Technology adds value to cutting-edge scientific discoveries through strategic patent protection and creative licensing of intellectual property (IP) or through partnered research with industry. Examples of licensed technology include transgenic mice and crystal structures. NIMR scientists have a variety of industrial collaborations and also act as consultants to a range of companies.

A translation club for NIMR scientists promotes collaborations/networks with MRCT, the pharmaceutical industry, clinician scientists and engineers. It aims to achieve better translational exploitation of NIMR scientists’ findings, reagents, methodologies and equipment. It meets two or three times a year and, in addition to NIMR scientists, involves representatives from key partners including MRCT and University College London Hospital to discuss new opportunities for translation and to raise the overall awareness of potential interesting opportunities. In addition, the club aims to bring in a cross-section of experts from potential partners as guest speakers on an ad hoc basis to open up new ideas and ways of thinking. Case studies of previous NIMR successes in translation have been presented to Programme Leaders at the Institute. The club aims to establish an informal network of contacts that is readily accessible to NIMR scientists, in order to help exploit their findings.

Support for translation Eileen Clark



Structure of phosphate biosensor, solved at NIMR (coumarin fluorophore in red, inorganic phosphate in blue).

The Mouse House.

Phosphate biosensor

A basic research programme on motility proteins required a rapid and sensitive way to measure inorganic phosphate, one product of ATP hydrolysis. This led to a novel approach - a fluorescent reagentless biosensor. The concept is straightforward. A protein is used as the biosensor framework to interact with the target molecule, in this case phosphate, and is modified by attachment of a fluorescent reporter. Binding of ligands often results in rapid conformational changes, and these can be read out by changes in the fluorescent reporter. A phosphate binding protein was chosen and a fluorophore was attached to this framework to provide the signal in response to phosphate binding. The resulting adduct has a millisecond response time and can measure sub-micromolar concentrations of phosphate.

Although originally designed for a particular project, the widespread study of phosphatases, ATPases and GTPases mean that this is a general tool and led to patent protection by the MRC, licensing to companies and eventually the availability of the biosensor commercially. The experience and design principles of this biosensor have also led to a number of related developments. Several biosensors using similar principles were developed at NIMR, including ones for ADP and GDP, which have now been patented.

Mouse House

NIMR Animal Technicians led the work to develop a proven enrichment device that has significantly enhanced the welfare of laboratory mice - the Mouse House - which was patented by the MRC and is now marketed by Techniplast UK. Over 200,000 Mouse Houses have been sold worldwide. The transparent red is of a specific wavelength that the mice see as dark grey. Thus when inside the Mouse House, mice feel secure while Technicians can still see in to carry out routine checks and husbandry. Studies have shown that the mouse house helps to reduce aggression and improves breeding performance, which is especially important in transgenic mouse strains. The designers of the Mouse House were awarded the 2002 ‘Animal Welfare Award’ by the Swiss Society for Laboratory Animal Science, the first non-academic recipients of this prestigious award.


Commercial translation

Waiting at the Children’s Outpatient Clinic, University College Hospital, Ibadan, Nigeria.


Clinical Research

Infectious diseases continue to blight human health worldwide. Our laboratory-based research on diseases such as influenza, malaria, and tuberculosis (TB) benefits from and informs clinical practice worldwide.

Influenza

The NIMR WHO Collaborating Centre for Reference and Research on Influenza is part of the global surveillance system and is one of six collaborating centres that assesses the antigenic and genetic characteristics of influenza viruses from around the world. These centres help to advise WHO and formulate the twice-yearly WHO recommendations for the composition of seasonal influenza vaccines (see page 54). The six collaborating centres also advise WHO on the emergence of drug-resistant viruses and on the pandemic potential of animal influenza viruses that can cause infections of humans. By harnessing the power of molecular and structural biology with virology, the antigenic properties and drug susceptibility of circulating human influenza viruses can be dissected and the pandemic potential of animal influenza viruses assessed.

Malaria

The Childhood Malaria Research Group (CMRG) has been established as a partnership between the Division of Parasitology (Fernandez-Reyes and Holder groups) and the College of Medicine, University of Ibadan, University College Hospital (COMUI-UCH) in Ibadan, Nigeria. This collaboration brings together superb clinical skills and hospital infrastructure for the management of severe malaria with the molecular expertise of NIMR in the densely populated city of Ibadan, where malaria is among the most common causes of death in children under the age of five. Nigeria has an estimated one quarter of all malaria cases worldwide. Our research on the molecular basis of cerebral malaria and severe malaria anaemia benefits from the close alignment with clinical specialists and provides a laboratory research capability close to patient point of care. Our research has already defined molecular markers that predict disease progression to severity and have the potential to be developed into clinically useful tools for disease prognosis and clinical management.

Tuberculosis and HIV-TB coinfection

Close clinical ties in South Africa (the Wilkinson group at the University of Cape Town) and London have allowed an international team of basic researchers, clinicians and bioinformaticians, led by Anne O’Garra, to identify a transcriptional signature in the blood of active TB patients that is missing in the majority of asymptomatic latent and healthy individuals. This signature of active tuberculosis correlates with the extent of lung radiographic disease and is diminished upon treatment, thus offering potential biomarkers for diagnosis and treatment monitoring. This is much needed in tuberculosis, which is difficult to diagnose and still causes 1.7 million deaths per year.


Clinical translation


Hirschsprung’s disease

The pathogenesis of Hirschsprung’s disease (the most frequent congenital abnormality of gut peristalsis) is studied by the Pachnis group in collaboration with clinicians at the UCL Institute of Child Health, Great Ormond Street Hospital. Together the groups are developing methods to isolate and characterise enteric neural stem cells from human gut tissue, and establishing experimental systems to assess their ability to colonise aganglionic gut. Having shown in a model system at NIMR that enteric glial cells function as facultative neural stem cells, the two groups are now studying how the neurogenic potential of human enteric glial cells can be activated to generate functional enteric neurons in Hirschsprung’s disease patients.

Clinical translation

The image depicts groups of enteric neurons and the network of their axonal processes. These neurons fail to develop in parts of the colon of Hirschsprung’s disease patients.


Disorders of sexual development

The Lovell-Badge group, together with clinical collaborators, has found that chromosome rearrangements around the SOX3 gene are a frequent cause of human XX male sex reversal. This finding followed work in mice where they found that ectopic expression of Sox3 in the early gonad gives XX males, with Sox3 mimicking the Y-linked testis determining gene, Sry. This work has important implications for diagnosis in the clinic.



Human Biology Essay Competition 2011

NIMR’s Essay Competition is now in its ninth year. At a time when school science students rarely write an extended essay before they go to university we provide an opportunity for enthusiasts to develop their skills. All the entrants receive a prize of the current volume of Mill Hill Essays, and the winners receive a financial prize and spend a day at NIMR seeing visually appealing projects. The best essay by Abida Gani of Mill Hill County High School on Have we anything to fear from genetic screening? can be found in the Mill Hill Essays 2011.

Research Summer School

In 2011 NIMR was host to 14 students over the summer, drawn from nine local schools. The scheme is financed by the Nuffield Foundation who award bursaries to each student. The students undertake projects devised and supervised by NIMR staff, using the core techniques of modern molecular biology and biochemistry. The course starts with a half-day induction in molecular biology, lab skills, safety and record-keeping. Students produce excellent posters and reports of their work, to be shown at events organised by the Nuffield Foundation. Teachers tell us that bursary holders are a vivid advertisement for the Summer School and they inspire the next generation of science students to follow the same route. Some of our earlier cohorts of students are now researchers having emerged from university with first-class degrees.

Annual Schools Days

Students in Year 12 are invited to an event designed to enrich their experience of the life sciences. The theme for this year’s event was Molecular biology for the future. We accommodated a capacity audience of 360 visitors over two days drawn from 23 local schools. As usual there was a lively interrogation of the speakers on their subject, careers and topical issues. We also presented a small demonstration on a developmental biology theme to provide a glimpse of real experimental material. There was a high level of participation in our quiz based on posters relating to science in the news.

PUBLIC OUTREACH

Public engagement


Professional development for teachers

In June 2011 we held a meeting for local teachers focused on recent developments in biomedical science. We had about 60 participants from 37 schools. Talks included:

• Meiosis: The crucial stage in chromosomal physiology that makes genetic re-assortment possible • Recent progress in molecular biology • How vertebrates make their limbs; new methods of studying gene function • The origins of allergy and autoimmunity • New ways of studying tuberculosis

Once again the speakers found exactly the right level with sufficient novel material to interest teachers but not too far removed from the curriculum. The lively discussion and written responses afterwards suggest the event was a great success.

Direct involvement in schools

NIMR staff participate directly in science education in the Science Ambassadors scheme providing a distinctive enrichment to complement the normal school curriculum. NIMR staff are asked to give talks about their research or other topics to Year 12 classes from time to time. A growing development is the involvement of NIMR staff in extended projects required for some A-level courses at two excellent local schools. We have set up programmes where NIMR staff answer questions and put students on the right track.

The University of the Third Age (U3A) at NIMR

In November 2011 NIMR hosted the ninth national meeting of the science section of the U3A, a self-managed organisation for retired people who enjoy learning about science. Many travel quite long distances to attend. This year the theme was Curses and benefits of parasites at which Tony Holder and Mark Wilson spoke. Once again, we had a capacity crowd of nearly 150 enthusiasts.

PUBLIC OUTREACH

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.

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.

PDF versions of all the published Mill Hill Essays can be accessed at: http://www.nimr.mrc.ac.uk/mill-hill-essays

Recent loans from the Arts Council Collection include (left) Eduardo Paolozzi, Caprese, bronze 1975, (centre) Liz Pannett, 14.1.79 - 8.80, 1980, (right) Victor Newsome, Corner of a bathroom, 1975.


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PUBLIC OUTREACH

Infections and Immunity


Immune Cell Biology

Immunoregulation

Molecular Immunology

Mycobacterial Research

Parasitology

Virology

Victor Tybulewicz (Head of Division)Steve LeyBenedict SeddonPavel Tolar

Anne O’Garra (Head of Division) George KassiotisAndreas Wack

Gitta Stockinger (Head of Division)Mark Wilson

Douglas Young (Head of Division) Luiz Pedro de CarvalhoRobert Wilkinson

Tony Holder (Head of Division)Michael BlackmanDelmiro Fernandez-ReyesEva FrickelJean Langhorne

Jonathan Stoye (Head of Division)Kate BishopJohn DoorbarJohn McCauleyWHO Collaborating Centre for Reference and Research on Influenza (WIC)

Kate Bishop

INFECTIONS AND IMMUNITY

Virology

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. There has also been much excitement and controversy recently over the association of gammaretroviruses, particularly XMRV, with prostate cancer and chronic fatigue syndrome. Innovative therapeutics for retroviral diseases will hopefully arise from a better understanding of how retroviruses reproduce in the cell, how they interact with host cell factors and how they subvert the host innate and adaptive immune systems.

We are interested in defining the specific functions of viral and cellular proteins during the early post-entry stages of the retroviral life cycle, particularly reverse transcription, viral trafficking and nuclear entry. We are using mutant viruses that cannot complete these steps to identify the cellular proteins involved in these processes and characterise the important interactions between viral components. One focus of our studies is the p12 protein from gammaretroviruses that has an unknown but essential function during the early stages of viral replication. We have identified multiple functional domains within this 84 amino acid protein.

Publications

Groom HCT, Boucherit VC, Makinson K, Randal E, Baptista S, Hagan S, Gow JW, Mattes FM, Breuer J, Kerr JR, Stoye JP and Bishop KN (2010)Absence of xenotropic murine leukaemia virus-related virus in UK patients with chronic fatigue syndrome.Retrovirology 7:10

Groom HCT, Yap MW, Galão RP, Neil SJD and Bishop KN (2010)Susceptibility of xenotropic murine leukemia virus-related virus (XMRV) to retroviral restriction factors.Proceedings of the National Academy of Sciences of the United States of America 107:5166-5171

Bishop KN, Verma M, Kim E-Y, Wolinsky SM and Malim MH (2008)APOBEC3G inhibits elongation of HIV-1 reverse transcripts.PLoS Pathogens 4:e1000231

Murine leukaemia virus infection of a D17 cell during anaphase. The viral p12 (red) and nucleocapsid (green) proteins associate with condensed cellular

chromatin (blue). Scale bars are 2 μm.

Infection and replication of retrovirusesLab members: Virginie Boucherit, Harriet Groom, Mirella Nader, Darren Wight


Proteases in host cell exit and invasion by the malaria parasiteLab members: Christine Collins, Sujaan Das, Fiona Hackett, Robert Moon, Maria Penzo, Andrea Ruecker, Robert Stallmach,Malcolm Strath, Catherine Suarez, Chrislaine Withers-Martinez, Christiaan van Ooij

Publications

Santos JM, Ferguson DJP, Blackman MJ and Soldati-Favre D (2011)Intramembrane cleavage of AMA1 triggers Toxoplasma to switch from an invasive to a replicative mode.Science 331:473-477

Child MA, Epp C, Bujard H and Blackman MJ (2010)Regulated maturation of malaria merozoite surface protein-1 is essential for parasite growth.Molecular Microbiology 78:187–202

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

Mike Blackman


Parasitology

34

Malaria causes immense suffering, killing at least one million people each year, and is a major contributor to poverty. The disease is caused by a single-celled parasite and spread by mosquitoes. There is no malaria vaccine, and resistance against mainstay antimalarial drugs is widespread. There is a need to find new ways to treat and control this devastating disease.

The malaria parasite infects and divides within red blood cells. These eventually rupture, releasing a fresh wave of parasites to invade new red cells. Our work focuses on how the parasite invades and escapes from its host red cell, in anticipation that a better understanding of this will aid the development of much-needed new antimalarial drugs and a vaccine. We have a particular interest in a family of parasite enzymes called proteases that regulate release of the parasite from the red blood cell, and also modify the parasite surface to ‘prime’ the parasite for invasion. We are investigating the structure, function and regulation of these proteases, and searching for inhibitory compounds with potential to be developed as antimalarial drugs.


Immunofluorescence images showing differences in the sub-cellular localisation of two cysteine protease-like molecules, SERA5 and SERA6,

around intracellular malaria merozoites.

Molecular model of the active site of PfSUB1, a subtilisin-like protease involved in malaria parasite release from red cells. A peptide substrate is shown docked into the active

site cleft.

See references 196 and 204 in the bibliography at the back for publications from this group in 2011.

Publications

de Carvalho LPS, Fischer SM, Marrero J, Nathan C, Ehrt S and Rhee KY (2010)Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates.Chemistry & Biology 17:1122-1131

de Carvalho LPS, Zhao H, Dickinson CE, Arango NM, Lima CD, Fischer SM, Ouerfelli O, Nathan C and Rhee KY (2010)Activity-based metabolomic profiling of enzymatic function: identification of Rv1248c as a mycobacterial 2-hydroxy-3-oxoadipate synthase.Chemistry & Biology 17:323-332

de Carvalho LPS, Lin G, Jiang X and Nathan C (2009)Nitazoxanide kills replicating and nonreplicating Mycobacterium tuberculosis and evades resistance.Journal of Medicinal Chemistry 52:5789-5792

The recent dissemination of strains of Mycobacterium tuberculosis (Mtb) resistant to multiple drugs constitutes a major health threat. Mankind might soon face the first epidemic of untreatable tuberculosis. Multidrug resistance arises and is selected for because of the complex growth pattern of Mtb, its extreme adaptation to the host, and because existing therapies are flawed. Current mycobacterial and anti-mycobacterial research programmes have clearly not been sufficiently effective at providing novel therapies that could reverse this trend in a timely fashion. New approaches and technologies are urgently needed to avoid a global health catastrophe.

Our recent work has demonstrated that biochemistry and bio-analytical chemistry can lead to better understanding of phenotypes and targets, and to the rational design and study of new small molecule therapeutics. We will continue to apply metabolomic approaches in combination with classic biochemical and microbiological methods to discover new reactions and pathways in Mtb that are essential for its survival and successful infection of human macrophages. In addition, we will continue our efforts on rational design, characterisation and testing of new antibiotic candidates that might be used in the near future as alternative treatment options for multidrug resistant tuberculosis.



Luiz Pedro de Carvalho

Mycobacterium tuberculosis systems and chemical biologyLab members: Flora Dix, Gerald Larrouy-Maumus, Gareth Prosser, Sonia Pedreno Lopez, Joao Pedro S. Pisco


Schematic representation of Activity-based Metabolomic Profiling. This method is used for functional annotation of enzymes and pathway discovery in Mycobacterium

tuberculosis.

See reference 82 in the bibliography at the back for publication from this group in 2011.

Human papillomavirus biology and diseaseLab members: Cinzia Borgogna, Clare Davy, Heather Griffin, Deborah Jackson, Pauline McIntosh, Emilio Pagliarulo, Yasmina Soneji, Christina Untersperger, Qian Wang, Zhonglin Wu.


Virology

John Doorbar

Publications

Maglennon GA, McIntosh P and Doorbar J (2011)Persistence of viral DNA in the epithelial basal layer suggests a model for papillomavirus latency following immune regression.Virology 414:153-163

Nicolaides L, Davy C, Raj K, Kranjec C, Banks L and Doorbar J (2011)Stabilization of HPV16 E6 protein by PDZ proteins, and potential implications for genome maintenance.Virology 414:137-145

Khan J, Davy CE, McIntosh PB, Jackson DJ, Hinz S, Wang Q and Doorbar J (2011)The role of calpain in the formation of HPV16 E1^E4 amyloid fibers and reorganization of the keratin network.Journal of Virology 85:9984–9997

36

Human papillomaviruses (HPV) cause a range of significant human diseases, including laryngeal papillomatosis, genital warts and cervical neoplasia. Certain HPV types, known as high-risk types, cause cervical lesions that can progress to cancer. Cervical cancer is a major female cancer worldwide, and is almost always caused by HPV. These viruses can also cause a significant proportion of head and neck tumours, and have been implicated in the development of some non-melanoma skin cancers. How the body controls infection is poorly understood, and currently there is no antiviral therapy that can reliably clear infection.

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.


During active infection the virus drives cell proliferation in the lower epithelial layers and virion assembly towards the surface. The immune system can suppress viral gene expression, but cannot

always clear viral genomes from the basal layer, allowing the potential for reactivation.

See references 23, 114, 130, 158, 184 and 203 in the bibliography at the back for publications from this group in 2011.

Pathogenesis of childhood severe malariaLab members: Samuel Abah, Dimitrios Athanasakis, Florence Burte, Ianina Conte, Barry Ely, Juho Rousu, Olugbemiro Sodeinde

Half of the world population is at risk of malaria. Human malaria caused by Plasmodium falciparum represents a global disease burden with an estimated 300 million clinical episodes per year leading to around one million deaths. Cerebral malaria and severe malarial anaemia are both major complications with significant mortality and morbidity in children under five years of age in Sub-Saharan Africa. We are focused on the study of severe malaria syndromes in children attending tertiary hospitals in densely populated holoendemic malaria areas. Malaria pathogenesis caused by the parasite’s asexual erythrocytic cycle largely occurs in the vascular compartment. We are interested in both the role of endothelial cell activation and the plasma proteome changes that occur during distinct severe malaria presentations.

We carried out a large case-control plasma proteome study of childhood severe malaria, including discovery and validation cohorts, at the main tertiary hospital of the city of Ibadan, Nigeria under the auspices of the Childhood Malaria Research Group. Our clinical proteomics study shows that plasma proteome profiles accurately discriminate severe childhood malaria from uncomplicated cases as well as from ill and healthy malaria-negative children. The defined plasma proteome patterns are composed of a combination of several differentially-expressed proteins that act as biomarkers of the severe malaria disease process.

Publications

Rojas-Galeano S, Hsieh E, Agranoff D, Krishna S and Fernandez-Reyes D (2008)Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.PLoS ONE 3:e1806

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


Parasitology

Delmiro Fernandez-Reyes


Visualisation of community control (CC, non-parasitaemic) children versus other study groups. Each sphere represents an individual

child proteome profile plotted in 3D space defined by the first three principal components. CM = Cerebral Malaria (red); SMA = Severe

Malarial Anaemia (purple); UM = Uncomplicated Malaria (yellow); DC = Disease Controls (blue); CC = Community Controls (green).

(a) CC vs. CM; (b) CC vs. SMA; (c) CC vs UM and (d) CC vs. DC.

A new perspective on anti-Toxoplasma gondii immunityLab members: Clemence Foltz, Anna Sanecka-Duin, Nadia Shabbir

The protozoan parasite Toxoplasma gondii infects a broad range of hosts, with a seroprevalence in man of about 30%. Toxoplasma maintains the intricate balance between survival and host defence. IFNγ, the main cytokine responsible for its control, activates cells to restrict intracellular parasite replication or to kill intracellular Toxoplasma. Cell-mediated immunity, driven mostly by CD8 T cells, confers resistance to the chronic phase of the parasite. The outcome of an infection with Toxoplasma is determined not only by the host’s immune status, but also by the genotype of the infecting strain. Toxoplasma pathogenesis results from parasite burden, concurrent with an over-stimulation of the immune system in the form of high levels of T helper cell type 1 cytokines.

Our long-term goal is to identify novel pathways and mechanisms of host resistance to Toxoplasma. We are studying how the parasitophorous vacuole (PV) is remodelled within host cells to limit parasite replication, as well as how antigen processing is facilitated for presentation to CD8 T cells. We are specifically interested in the functional consequences of vacuolar recognition by IFNγ-upregulated p65 GTPases (GBPs), a yet understudied class of regulatory proteins. Additionally, we are defining the requirements for recognition and functional consequences of Toxoplasma antigen-specific CD8 T cells in the chronic phase of infection in the brain.

Eva Frickel


Parasitology

(A) Optical imaging of luciferase-expressing Toxoplasma either without or in the presence of antigen-specific CD8 T cells (T57) and quantification of signal (B).

IFNγ-induced wild-type mouse embryonic fibroblasts infected with type I, II or III Toxoplasma show that mGBP1 (in green) is preferentially recruited to nonvirulent type II and III vacuoles. The right panel shows

the frequencies of mGBP1-positive vacuoles.

Publications

Winter SV, Niedelman W, Jensen KD, Rosowski EE, Julien L, Spooner E, Caradonna K, Burleigh BA, Saeij JPJ, Ploegh HL and Frickel E-M (2011)Determinants of GBP recruitment to Toxoplasma gondii vacuoles and the parasitic factors that control it.PLoS ONE 6:e24434

Kirak O, Frickel E-M, Grotenbreg GM, Suh H, Jaenisch R and Ploegh HL (2010)Transnuclear mice with predefined T cell receptor specificities against Toxoplasma gondii obtained via SCNT.Science 328:243-248

Frickel E-M, Sahoo N, Hopp J, Gubbels M-J, Craver MPJ, Knoll LJ, Ploegh HL and Grotenbreg GM (2008)Parasite stage-specific recognition of endogenous Toxoplasma gondii-derived CD8+ T cell epitopes.Journal of Infectious Diseases 198:1625-1633


Parasitology

Tony Holder

Malaria is caused by a parasitic protozoan that invades red blood cells, where it develops and multiplies before bursting out and invading fresh red cells. This cycle is responsible for the disease. Understanding the interaction between the parasite and the host immune system contributes to the development of a malaria vaccine. The identification of new targets for drugs to kill the parasite and interrupt the cycle of multiplication offers the potential of new therapeutic interventions.

In one area of research, we have focused on the post-translational modification of proteins associated with the parasite’s actomyosin-based motor that drives the invasion of erythrocytes. Some of these proteins are positioned at the right place in the cell by attaching them to membranes, for example by N-myristoylation or S-palmitoylation, which adds a C14-fatty acid to the N-terminal glycine or a C16-fatty acid to a cysteine residue, respectively. These and other proteins are also modified by phosphorylation, a process that may provide a way to regulate the motor. Together with colleagues in MRC Technology and elsewhere we are developing inhibitors of the enzymes that carry out these modifications, to investigate their role in parasite biology and their potential for therapeutic development.

Malaria parasites and red blood cellsLab members: Barbara Clough, Suraya Diaz, Muni Grainger, Judith Green, Claire Hastings, Madhu Kadekoppala, Ellen Knuepfer, Robert Moon, Sola Ogun, Kaveri Rangachari, Ridzuan Razak, Shigeharu Sato, Noor Azian Yusuf


Mapping the binding sites for protective monoclonal antibodies that bind to merozoite surface protein 1: amino acid changes shown on the structure

abolish the binding of individual antibodies.

Expression of a green fluorescent protein-tagged component of the malaria parasite motor complex within an infected red blood cell.

Publications

Ogun SA, Tewari R, Otto TD, Howell SA, Knuepfer E, Cunningham DA, Xu Z, Pain A and Holder AA (2011)Targeted disruption of py235ebp-1: Invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein.PLoS Pathogens 7:e1001288

Schmitz S, Schaap IAT, Kleinjung J, Harder S, Grainger M, Calder L, Rosenthal PB, Holder AA and Veigel C (2010)Malaria parasite actin polymerisation and filament structure.Journal of Biological Chemistry 285:36577-36585

Kadekoppala M, Ogun SA, Howell S, Gunaratne RS and Holder AA (2010)Systematic genetic analysis of the Plasmodium falciparum MSP7-like family reveals differences in protein expression, location and importance in asexual growth of the blood stage parasite.Eukaryotic Cell 9:1064-1074

See references 18, 19, 62, 83, 153, 160, 197, 202 and 232 in the bibliography at the back for publications from this group in 2011.

Antiviral immunityLab members: : Urszula Eksmond, Micol Ferro, Dorothy Ng, Mickaël Ploquin, Lara Sellés, Georgina Thorborn, George Young


Immunoregulation

George Kassiotis


Viral infections represent a major challenge to the immune system. Certain viruses cause acute infections in humans, which can be rapidly fatal within days, for example influenza A and smallpox viruses. In contrast, other viruses are able to persist chronically in infected individuals, despite induction of an immune reaction (e.g. HIV, hepatitis and herpes viruses). Almost all humans are chronically infected by one or more persistent viruses. Our understanding of the pathogenic processes of viral infection remains incomplete.

Production of antiviral antibodies relies on cognate interaction between B cells and CD4+ T helper (Th) cells. However, in addition to providing help to B cells, Th cells are assigned with a range of additional tasks, including direct antiviral activity, and may also mediate immune pathology. Using a model for retrovirus-induced leukaemia, we found that interaction with B cells dramatically inhibits the function of virus-specific Th cells. Ultimately, provision of help to B cells protects hosts from Th cell-mediated immune pathology, at the detriment of Th cell-mediated protective immunity. Our findings suggest that B cell presentation of vaccine antigens could be manipulated to direct the appropriate Th cell response.

Virus-induced leukaemia according to lymphocyte composition. Mice bearing B cells progress to leukaemia, whereas mice bearing T cells resist leukaemia. The presence of

B cells negates the protective effect of T cells.

Publications

Ploquin MJ-Y, Eksmond U and Kassiotis G (2011)B cells and TCR avidity determine distinct functions of CD4+ T cells in retroviral infection.Journal of Immunology 187:3321-3330

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

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


Immunity and immunopathogenesis in malaria infectionsLab members: Nikolai Belyaev, Thibaut Brugat, Deirdre Cunningham, Ana Paula Freitas do Rosario, William Jarra, Jennifer Lawton, Wiebke Nahrendorf, Dorothy Ng, Sophie Roetynck, Philip Spence, Anne-Marit Sponaas, Christine Tshitenge, Irene Tumwine


Parasitology

Jean Langhorne


Expression of CIR proteins in the cytoplasm and on the surface of P. chabaudi-infected RBC. (Green, CIR; Red, MSP1; Blue, parasite

nucleus)

The major focus of our group is to understand the immune response to the malaria parasite and the role it plays in the development of severe malaria disease. Part of this work is the identification of the key components of innate and adaptive immunity that control and eliminate parasites, and regulate immunopathology. Another aspect of our work is to identify parasite molecules on the surface of the infected erythrocytes that may be responsible for antigenic variation and for binding of the parasite to host endothelium, and in this way contribute to pathology.

We have identified a multigene family, cir, in the rodent malaria, Plasmodium chabaudi, that codes for antigens expressed on infected erythrocytes. These proteins are recognised by the immune system and many different CIRs can be expressed during infection suggesting a role in antigenic variation. Since variant antigens of the human pathogen Plasmodium falciparum also adhere to host endothelium, and thus contribute to pathology of severe malaria, we are investigating whether CIRs have a similar function. P. chabaudi erythrocytes do sequester in different organs, and we are now evaluating the role of CIR in cytoadherence.

Publications

Spence PJ, Cunningham D, Jarra W, Lawton J, Langhorne J and Thompson J (2011)Transformation of the rodent malaria parasite Plasmodium chabaudi.Nature Protocols 6:553-61

Stephens R and Langhorne J (2010)Effector memory Th1 CD4 T cells are maintained in a mouse model of chronic malaria.PLoS Pathogens 6:e1001208

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


The innate immune response of mammals is the first line of defence to infection by pathogenic micro-organisms, such as viruses, bacteria, fungi and parasites. This is triggered by pathogen interaction with receptors on the surface and in the cytoplasm of neutrophils and macrophages. These specialised immune cells then produce proteins called chemokines and cytokines, which attract other immune cells to the site of infection, including T lymphocytes. Together, these stimulate the adaptive immune response, which eliminates the invading pathogen by generation of antibodies and cytotoxic cells.

We study a signalling pathway that regulates the production of cytokines by macrophages in innate immune responses, which is regulated by TPL-2, a protein kinase. Our current experiments are investigating the mechanism by which TPL-2 is activated, and evaluating the potential of TPL-2 as an anti-inflammatory drug target in autoimmune diseases.

Regulation of immune responses by NF-κB and MAP kinases Lab members: Hakem Ben-Addi, Thorsten Gantke, Eva Gueckel, Emilie Jacque, Julia Janzen, Agnes Mambole, Olivia Mitchell, Matoula Papoutsopoulou, Karine Roget, Huei-Ting Yang, Rachel Zillwood


Immune Cell Biology

Steve Ley


Regulation of TPL-2 activation by NF-κB1 p105 and IκB kinase.

NF-κB1 negatively regulates interferon-β induction and STAT1 activation in macrophages.

Publications

Gantke, T., Sriskantharajah, S. and Ley, S. C. (2011) IκB kinase regulation of the TPL-2 / ERK MAP kinase pathway. Immunological Reviews (in press)

Yang H-T, Wang Y, Zhao X, Demissie E, Papoutsopoulou S, Mambole A, O’Garra A, Tomczak MF, Erdman SE, Fox JG, Ley SC and Horwitz BH (2011)NF-κB1 inhibits TLR-induced IFN-β production in macrophages through TPL-2—dependent ERK activation.Journal of Immunology 186:1989-1996

Sriskantharajah S, Belich MP, Papoutsopoulou S, Janzen J, Tybulewicz V, Seddon B and Ley SC (2009)Proteolysis of NF-κB1 p105 is essential for T cell antigen receptor-induced proliferation.Nature Immunology 10:38-47

See references 16, 75, 76, and 256 in the bibliography at the back for publications from this group in 2011.

Host specificity of influenza virusesLab members: Michael Bennett, Donald Benton, Nicole Friedrich, Saira Hussain, Ana Luisa Reis, Steve Wharton, Haixia Xiao


Virology

John McCauley


Influenza A viruses infect a variety of species, with humans, horses and pigs representing the main mammalian hosts of the virus in which infection is sustained. Avian species, particularly water-fowl and gulls, harbour a wide variety of influenza A viruses defined by their haemagglutinin (H1-16) and neuraminidase (N1-9) glycoprotein subtypes in a variety of H/N combinations. New pandemic strains of human influenza virus arise from an animal reservoir either directly, as for the 2009 pandemic A(H1N1) virus, or as a result of gene reassortment between a human and an animal influenza virus, as in the 1957 and 1968 pandemics.

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. The interaction between a virus particle and its receptor on a host cell is a key 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. Recent human H3N2 viruses show unexpected receptor-binding activities. The characteristics of this binding are being examined in collaboration with colleagues in the Divisions of Physical Biochemistry and Molecular Structure, and with Professor Ten Feizi, Imperial College London.

In culture, seasonal H3N2 influenza viruses readily mutate their neuraminidase glycoprotein to be able to bind turkey erythrocytes (left plaque). On the right is a plaque of an unchanged virus.

Publications

Lin YP, Gregory V, Collins P, Kloess J, Wharton S, Cattle N, Lackenby A, Daniels R and Hay A (2010)Neuraminidase receptor binding variants of human influenza A(H3N2) viruses due to substitution of aspartic acid 151 in the catalytic site - role in virus attachment?Journal of Virology 84:6769-6781

Iqbal M, Xiao H, Baillie G, Warry A, Essen SC, Londt B, Brookes SM, Brown IH and McCauley JW (2009)Within-host variation of avian influenza viruses.Philosophical Transactions of the Royal Society B: Biological Sciences 364:2739-2747

Kuiken T, Holmes EC, McCauley J, Rimmelzwaan GF, Williams CS and Grenfell BT (2006)Host species barriers to influenza virus infections.Science 312:394-397

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 also mediate host damage if uncontrolled. We are researching the molecular mechanisms for the development and function of discrete subsets of immune cells producing different cytokines protective against pathogens, and the induction and function of a regulatory cytokine, IL-10 produced by many cell types. We will build on our past results, using biochemical methods and genome-wide, high-throughput approaches and bioinformatics, to elucidate the molecular mechanisms for induction of IL-10 production and function in different immune cell types.

We continue to examine mechanisms of IL-10 production and function in chronic MTb infection. Leading on from our findings in human TB, where we identified a robust blood transcriptional interferon-inducible signature, we will investigate potential factors in TB pathogenesis, such as Type I IFNs and Type I IFN-inducible genes, using molecular methods and improved mouse models of TB, to identify immune mechanisms of protection or pathogenesis important for disease control in tuberculosis and other bacterial infections.

Regulation of the immune response in infectious disease Lab members: Chloe Bloom, Jillian Christensen, John Ewbank, Leona Gabrysova, Christine Graham, Ashleigh Howes, Finlay McNab, Jonathan Pitt, Paul Redford, Fotini Rozakeas, Vangelis Stavropoulos, Charlotte Whicher, Xuemei Wu


Immunoregulation

Anne O’Garra FRS, AAAS Fellow, EMBO member, FMedSci


Publications

Berry MPR, Graham CM, McNab FW, Xu Z, Bloch SAA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, Quinn C, Blankenship D, Dhawan R, Cush JJ, Mejias A, Ramilo O, Kon OM, Pascual V, Banchereau J, Chaussabel D and O’Garra A (2010)An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis.Nature 466:973-977

Redford PS, Boonstra A, Read S, Pitt J, Graham C, Stavropoulos E, Bancroft GJ and O’Garra A (2010)Enhanced protection to Mycobacterium tuberculosis infection in IL-10-deficient mice is accompanied by early and enhanced Th1 responses in the lung.European Journal of Immunology 40:2200–2210

Saraiva M and O’Garra A (2010)The regulation of IL-10 production by immune cells.Nature Reviews Immunology 10:170-81

Mechanisms of protection and pathogenesis. From experimental models to human disease: an iterative process.

See references 73, 74, 128, 147, 148, 149, 159, 189, 246 and 256 in the bibliography at the back for publications from this group in 2011.

T lymphocytes are immune cells that play a central role in regulating immune responses. There are several different T cell types, all with different functions. Having the right number and composition of T cells is therefore essential for a normal immune system. The production and maintenance of these cells is strictly controlled by mechanisms regulating cell survival and proliferation. Cellular signals transduced by the T cell antigen receptor (TCR) and from cytokines such as IL-7 play a central role in regulating homeostasis of T cells.

TCR and IL-7 signalling are both essential for regulating survival and homeostatic proliferation of T cells. Whether there is any interaction between these signals is controversial. We have recently uncovered a novel mechanism by which TCR and IL-7 signalling interact to control T cell homeostasis. We found that IL-7R expression by mature T cells critically depends on TCR signals received during their development in the thymus. This TCR signal dependent mechanism ensures that the best T cells generated during positive selection have a survival advantage that preferentially maintains them in the peripheral repertoire.

Regulation of T cell homeostasis by antigen receptor signals and cytokines Lab members: Thea Hogan, Daniel Marshall, Ina Schim van der Loeff, Ana Silva, Charles Sinclair, Sim Tung, Louise Webb


Immune Cell Biology

Benedict Seddon


Publications

Charles Sinclair, Manoj Saini, Ina Schim van der Loeff, Shimon Sakaguchi3 and Benedict Seddon (2011)Positive selection links T cell antigen receptor and IL-7 survival signaling in the homeostatic control of naive T cells. Science Signaling 4:ra77

Pearson C, Silva A, Saini M and Seddon B (2011)IL-7 determines homeostatic fitness of T cells by distinct mechanisms at different signalling thresholds in vivo.European Journal of Immunology Epub ahead of print

Sinclair CGM, Saini M and Seddon BP (2008)The role of ZAP-70 in the CD4/CD8 lineage decision.Immunology 125:28

Induction of a tetracycline-inducible Zap70 transgene restores thymocyte development in Zap70-deficient mice.

See references 175, 205, 207 and 220 in the bibliography at the back for publications from this group in 2011.

Controlling Zap70 expression in vivo reveals how TCR signalling tunes IL-7R expression during

development and maturation of newly generated CD4 T

cell in the thymus.

A single dose of inducer results in a pulse of Zap70 protein expression in thymocytes that is sufficient to

start development of CD4 T cells.

Development, maintenance and regulation of peripheral T cell compartments and immune responsesLab members: Helena Ahlfors, Judit Biro, Paola diMeglio, Joao Duarte, Keiji Hirota, Ying Li, Heike Müller, Matteo Villa, Christoph Wilhelm



Gitta Stockinger EMBO member, FMedSci

Our current focus is on the development and function of innate and adaptive IL-17 producing T cells (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.

We developed an IL-17A fate reporter model, which allows us to study development of IL-17 producing T cells and their behaviour during infection in vivo. We furthermore study the role of the aryl hydrocarbon receptor (AhR) in the immune system, trying to unravel its impact on the function of different immune cells in the defence against pathogens.

Publications

Hirota K, Duarte JH, Veldhoen M, Hornsby E, Li Y, Cua DJ, Ahlfors H, Wilhelm C, Tolaini M, Menzel U, Garefalaki A, Potocnik AJ and Stockinger B (2011)Fate mapping of IL-17-producing T cells in inflammatory responses.Nature Immunology 12:255-264

Wilhelm C, Hirota K, Stieglitz B, Van Snick J, Tolaini M, Lahl K, Sparwasser T, Helmby H and Stockinger B (2011)An IL-9 fate reporter demonstrates the induction of an innate IL-9 response in lung inflammation.Nature Immunology 12:1071-1077

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


Skin sample from a wildtype B6 mouse (left) or an AhR-deficient B6 mouse (right) stained with Oil Red indicates substantial accumulation of neutral lipids in skin in the absence of AhR.

See references 98, 99, 125, 221 and 249 in the bibliography at the back for publications from this group in 2011.

Publications

Hilditch L, Matadeen R, Goldstone DC, Rosenthal PB, Taylor IA and Stoye JP (2011)Ordered assembly of murine leukemia virus capsid protein on lipid nanotubes directs specific binding by the restriction factor, Fv1.Proceedings of the National Academy of Sciences of the United States of America 108:5771–5776

Ohkura S, Goldstone DC, Yap MW, Holden-Dye K, Taylor IA and Stoye JP (2011)Novel escape mutants suggest an extensive TRIM5α binding site spanning the entire outer surface of the murine leukemia virus capsid protein.PLoS Pathogens 7:e1002011

Goldstone DC, Yap MW, Robertson LE, Haire LF, Taylor WR, Katzourakis A, Stoye JP and Taylor IA (2010)Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface.Cell Host & Microbe 8:248-259


Virology

Jonathan Stoye

Retrovirus-host interactions Lab members: Vicky Felton, Seti Grambas, Wilson Li, Sadayuki Okura, Martha Sanz-Ramos, Melvyn Yap


Comparative genome analysis suggests that vertebrates and retroviruses have co-existed for tens of millions of years. It is thus unsurprising that a degree of co-evolution has taken place resulting in the development of specific defence mechanisms by the host and of means to overcome such defences by the virus. Understanding such natural anti-viral genes might suggest novel means of combating retroviral infection. We anticipate that these studies will shed new light on the early stages of retrovirus replication and the control of cross-species infection.

The host proteins TRIM5a and Fv1 typify such defence factors. They interact with incoming viruses, shortly after viral entry into the cell cytoplasm, binding to the viral core and inhibiting reverse transcription or nuclear transport. To help study this interaction we have isolated a number of viral mutants that escape from restriction by the different factors and used them to delineate the region of capsid recognised by Fv1 and TRIM5α. These studies implicate the whole surface of the viral core in factor binding.

Surface structure of the MLV CA protein showing positions of amino acid changes associated with escape from rhesus monkey TRIM5α.

Collaboration with Ian Taylor (Molecular Structure)See references 82, 86, 97, 148, 161,186 and 238 in the bibliography at the back for publications from this group in 2011.

Activation of immune receptors Lab members: Antonio Casal, Jason Lee, Elizabeth Natkanski


Immune Cell Biology

Pavel Tolar


Antibodies are critical for human immunity and their induction has been instrumental for the success of many vaccines. However, some of the most dangerous pathogens of today’s world, such as HIV, influenza or malaria, evade antibody responses, both natural and vaccine-induced. A better understanding of the mechanisms by which these pathogens trigger antibody responses will be necessary for the development of more effective vaccines.

We are interested in activation of B cells that detect pathogens by their B cell antigen receptors (BCRs). The BCR is a protein complex containing the membrane form of antibody and two signalling components; we are characterising the structure of this complex to gain insights into the mechanisms by which antigen binding activates the BCR. We are also developing new ways to visualise the activation and endocytosis of BCR molecules in living B cells.

Schematic structure of the BCR. The membrane proximal domains of the antibody pair with signalling components, Igα, Igβ. HSQC spectrum and NMR structure of the critical Cμ4 domain are shown.

Publications

Tolar P (2011)Inside the microcluster: antigen receptor signalling viewed with molecular imaging tools.Immunology 133:271-277

Tolar P, Hanna J, Krueger PD and Pierce SK (2009)The constant region of the membrane immunoglobulin mediates B cell-receptor clustering and signaling in response to membrane antigens.Immunity 30:44-55

Tolar P, Sohn HW and Pierce SK (2005)The initiation of antigen-induced B cell antigen receptor signaling viewed in living cells by fluorescence resonance energy transfer.Nature Immunology 6:1168-1176


B and T lymphocytes are white blood cells that are critical mediators of the immune response against a variety of pathogens. Inappropriate activation of these cells can result in autoimmune diseases such as rheumatoid arthritis. We are interested in understanding the biochemical signalling pathways within lymphocytes that control the activation, survival and migration of the cells. We have shown that proteins called Rac GTPases are critical for controlling the migration of both B and T cells into, through, and out of lymph nodes. Currently we are studying signals that control B cell homeostasis.

Mouse models of Down syndromeTrisomy of human chromosome 21 (Hsa21) occurs in around 1 in 750 live births and the resulting gene dosage imbalance gives rise to Down syndrome, the most common form of mental retardation. In collaboration with Prof E. Fisher (UCL), we are interested in identifying genes on this chromosome, which, when present in three copies, cause the many different phenotypes of Down syndrome. We have created a novel mouse strain carrying a freely segregating copy of Hsa21, which displays many of the features of Down syndrome, including learning difficulties and cardiac abnormalities. We are mapping the location of dosage-sensitive genes that cause Down syndrome phenotypes using chromosome engineering techniques.

Signal transduction in B and T cellsLab members: : Jochen Ackermann, Tiago Brazao, Natalia Dinischiotu, Harald Hartweger, Robert Köchl, Eva Lana Elola, Karen McGee, Alexander Saveliev, Edina Schweighoffer, Amy Slender, Lesley Vanes, Sheona Watson-Scales


Immune Cell Biology

Victor Tybulewicz EMBO member, FMedSci


In the absence of Rac GTPases B cell development is blocked in the red pulp of the spleen with the cells unable to enter

the white pulp.

Chromosome engineering to create duplications and deletions of megabase regions of mouse chromosomes to model Down

syndrome.

Publications

Faroudi M, Hons M, Zachacz A, Dumont C, Lyck R, Stein JV and Tybulewicz VLJ (2010)Critical roles for Rac GTPases in T cell migration to and within lymph nodes.Blood 116:5536-5547

Henderson RB, Grys K, Vehlow A, de Bettignies C, Zachacz A, Henley T, Turner M, Batista F and Tybulewicz VLJ (2010)A novel Rac-dependent checkpoint in B cell development controls entry into the splenic white pulp and cell survival.Journal of Experimental Medicine 207:837-853

Reynolds LE, Watson AR, Baker M, Jones TA, D’Amico G, Robinson SD, Joffre C, Garrido-Urbani S, Rodriguez-Manzaneque JC, Martino-Echarri E, Aurrand-Lions M, Sheer D, Dagna-Bricarelli F, Nizetic D, McCabe CJ, Turnell AS, Kermorgant S, Imhof BA, Adams R, Fisher EMC, Tybulewicz VLJ, Hart IR and Hodivala-Dilke KM (2010)Tumour angiogenesis is reduced in the Tc1 mouse model of Down’s syndrome.Nature 465:813-7

See references 37, 46, 56, 69, 120, 201, 208 and 243 in the bibliography at the back for publications from this group in 2011.

Immune response to influenza Lab members: Stefania Crotta, Sophia Davidson, Gregory Ellis, Annita Gjoka


Immunoregulation

Andreas Wack


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 that is necessary to eliminate the virus but also contributes to lung pathology. In addition to direct damage, influenza infection also increases dramatically the susceptibility to bacterial co-infections, as evidenced by epidemiological and microbiological data from seasonal and pandemic influenza waves. Both for single infections and co-infections, it is unclear which factors tip the balance between pathology and/or death, versus successful clearance of the pathogen without long term damage.

Our work aims to identify virus and host determinants of disease outcome. We focus on early events after infection, in particular on the interface between infected epithelium and the innate immune system. We use primary airway epithelial cells to determine which recognition systems are used to detect viral infection and how this information is transmitted to the immune system. The role of interferon-driven feedback systems in infection is studied in this system and in vivo, to understand the role of interferons in anti-influenza immune responses. We also investigate the roles of natural killer cells and granulocytes in influenza infection and co-infection. These studies will allow us to link early events to subsequent immune-mediated pathology or protection.

At the indicated time after air exposure, mouse AEC were fixed,

permeabilised and stained for the tight junction protein Z0-1,

for β tubulin IV to detect ciliated cells, and for CCSP and the mucin MUC5A to detect Clara cells and

Goblet cells respectively.

Schematic illustration of the primary murine

airway epithelial cell (AEC) culture system.

Publications

Wack, A., Openshaw, P., O’Garra, A. (2011)Contribution of cytokines to pathology and protection in virus infection. Current Opinion in Virology 1: 184-195

Seubert A, Calabro S, Santini L, Galli B, Genovese A, Valentini S, Aprea S, Colaprico A, D’Oro U, Giuliani MM, Pallaoro M, Pizza M, O’Hagan DT, Wack A, Rappuoli R and De Gregorio E (2011)Adjuvanticity of the oil-in-water emulsion MF59 is independent of Nlrp3 inflammasome but requires the adaptor protein MyD88.Proceedings of the National Academy of Sciences of the United States of America 108:11169-11174

Calabro S, Tortoli M, Baudner BC, Pacitto A, Cortese M, O’Hagan DT, De Gregorio E, Seubert A and Wack A (2011)Vaccine adjuvants alum and MF59 induce rapid recruitment of neutrophils and monocytes that participate in antigen transport to draining lymph nodes.Vaccine 29:1812-1823

See references 28, 200 and 246 in the bibliography at the back for publications from this group in 2011.

Understanding and intervening in HIV-associated tuberculosis Lab members: Anna Coussens, Adrian Martineau, Katalin Wilkinson



Robert Wilkinson FRCP


The programme derives its research questions from the clinical care of tuberculosis (TB) and HIV-TB co-infected persons in South Africa and London. Through clinically based studies we aim to improve knowledge of pathogenesis and thereby prevention and treatment.

We have contributed to the description of a distinct transcriptomic signature of active TB and plan further studies to validate this and extend to the study of HIV associated tuberculosis. We have determined that vitamin D deficiency is highly prevalent amongst black Africans in Cape Town, and associates with susceptibility to active tuberculosis both in the presence and absence of HIV infection. In a randomised controlled trial, administration of four doses of 2.5 mg vitamin D3 reduced time to sputum culture conversion in participants with the tt genotype of the TaqI VDR polymorphism.

Serum 25-hydroxyvitamin D (25[OH]D) concentration by HIV and TB status. Bars represent means. Dashed line represents limit of detection (10 nmol/L)

Publications

Martineau AR, Nhamoyebonde S, Oni T, Rangaka MX, Marais S, Bangani N, Tsekela R, Bashe L, de Azevedo V, Caldwell J, Venton TR, Timms PM, Wilkinson KA and Wilkinson RJ (2011)Reciprocal seasonal variation in vitamin D status and tuberculosis notifications in Cape Town, South Africa.Proceedings of the National Academy of Sciences 108:19013-7

Martineau AR, Timms PM, Bothamley GH, Hanifa Y, Islam K, Claxton AP, Packe GE, Moore-Gillon JC, Darmalingam M, Davidson RN, Milburn HJ, Baker LV, Barker RD, Woodward NJ, Venton TR, Barnes KE, Mullett CJ, Coussens AK, Rutterford CM, Mein CA, Davies GR, Wilkinson RJ, Nikolayevskyy V, Drobniewski FA, Eldridge SM and Griffiths CJ (2011)High-dose vitamin D3 during intensive-phase antimicrobial treatment of pulmonary tuberculosis: a double-blind randomised controlled trial.Lancet 377:242-50

Berry MPR, Graham CM, McNab FW, Xu Z, Bloch SAA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, Quinn C, Blankenship D, Dhawan R, Cush JJ, Mejias A, Ramilo O, Kon OM, Pascual V, Banchereau J, Chaussabel D and O’Garra A (2010)An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis.Nature 466:973-977

See references 51, 59, 109, 128, 132, 135, 136, 142, 143, 147, 163, 177 and 224 in the bibliography at the back for publications from this group in 2011.

52



Mark Wilson

Regulation of Th2 cells during allergic inflammation and anti-helminth immunity Lab members: : Stephanie Coomes, Stephanie Czieso, Nicholas Mathioudakis, Isobel Okoye, Victoria Pelly

More than a quarter of the world’s population are infected by one of four parasitic helminths (filarial worms, schistosomes, whipworms and roundworms) making them the most common infectious agents of humans in developing countries. Efficient expulsion of parasitic helminths from mammalian hosts requires a well-orchestrated immune response to activate innate immune cells and stimulate local tissue responses. CD4+ T helper 2 (Th2) lymphocytes coordinate the expulsion mechanism, placing them front and centre of anti-helminth immunity. One major aim of our work is to develop ways to promote Th2 cell responses and enhance anti-helminth immunity. An additional and complementary aim is to investigate ways to inhibit Th2 cell responses to remedy allergic disease. Allergic diseases plague hundreds of millions of people worldwide and are the result of dysregulated and hyper-active Th2 responses.

These aims are being investigated using in vivo helminth infection and allergy models. Using next-generation sequencing and gene manipulation techniques the roles of regulatory RNA species in Th2 cells and associated responses are being studied. De novo immune responses develop, often in tandem with other ongoing immune responses. Therefore, in collaboration with other NIMR programmes, we are investigating the mechanisms of Th2 cell development and function in the context of other immune responses. Together these aims will extend our knowledge of Th2 immunobiology, facilitate helminth elimination strategies, and identify novel interventions for allergic disease.


T. muris associated intestinal inflammation.

Goblet cell hyperplasia in allergic lung.


Publications

Wilson MS, Cheever AW, White SD, Thompson RW and Wynn TA (2011)IL-10 blocks the development of resistance to re-infection with Schistosoma mansoni.PLoS Pathogens 7:e1002171

Wilson MS, Ramalingam TR, Rivollier A, Shenderov K, Mentink-Kane MM, Madala SK, Cheever AW, Artis D, Kelsall BL and Wynn TA (2011)Colitis and intestinal inflammation in IL10-/- Mice Results From IL-13Rα2-mediated attenuation of IL-13 activity.Gastroenterology 140:254-264

Okoye IS and Wilson MS (2011)CD4+ T helper 2 cells - microbial triggers, differentiation requirements and effector functions.Immunology 134:368-77

One third of the global population is exposed to infection with Mycobacterium tuberculosis but only ten percent of individuals will develop tuberculosis. The outcome of infection depends on a complex series of interactions with the immune system, which can result in disease or in a persistent asymptomatic, latent infection. We are studying the way that M. tuberculosis evades host immunity by misdirecting innate immune recognition and by adapting to a form that resists killing by phagocytes. Ultimately, we aim to develop drugs that rapidly eliminate persisting bacteria and vaccines that elicit more effective immunity.

We are using high-throughput sequencing technologies to define the genetic diversity of M. tuberculosis and to study gene regulation at transcriptional and post-transcriptional levels. We have discovered an extensive repertoire of non-coding RNAs and are exploring their function, in part through participation in SysteMTb, a European consortium using a systems biology approach to characterise the fundamental biology of TB. Our work demonstrates that genetic variation amongst clinical isolates of M. tuberculosis results in phenotypic differences in their interaction with the host innate immune system. We propose that differences in innate immune recognition drive the epidemiology of this complex disease.

Understanding and intervening in HIV-associated tuberculosis Lab members: Kristine Arnvig, John Brennan, Roger Buxton, Stephen Coade, Teresa Cortes, Joanna Dillury, Deborah Hunt, Christina Kahramanoglou, Damien Portevin, Angela Rodgers, Graham Rose, Dorothee Schuessler, Min Yang


Immune Cell Biology

Victor Tybulewicz

53

Douglas Young FMedSci


sRNA mapping by RNA sequencing. The sRNA is shown in green; the red trace shows

divergent expression of an adjacent phage integrase gene (top, transcription start sites;

bottom, total transcripts).

Immunohistochemical staining provides the first demonstration of NK cells within mature TB

granulomatous lesions.




Publications

Arnvig KB, Comas I, Thomson NR, Boshoff HI, Dillury J, Croucher NJ, Rose G, Perkins TT, Parkhill J, Dougan G, Young DB. 2011. Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. PLoS Pathogens In press

Portevin D, Gagneux S, Comas I and Young D (2011)Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages.PLoS Pathogens 7:e1001307

Barry CE, 3rd, Boshoff HI, Dartois V, Dick T, Ehrt S, Flynn J, Schnappinger D, Wilkinson RJ and Young D (2009)The spectrum of latent tuberculosis: rethinking the biology and intervention strategies.Nature Reviews Microbiology 7:845-855

Director: John McCauleyLab members: Rod Daniels (Deputy Director), Yi Pu Lin (Assistant Director), Nick Cattle, Karen Cross,Vicki Gregory, Chandrika Halai, Lynn Whittaker, Zheng Xiang


Virology


WHO Collaborating Centre for Reference and Research on Influenza (WIC)

The WHO Collaborating Centre for Influenza is one of six Collaborating Centres that along with 136 WHO National Influenza Centres (NICs) form the WHO Global Influenza Surveillance and Response System (GISRS) to track influenza viruses as they circulate around the world. Viruses are characterised antigenically (genetically) in the laboratories and their resistance to antiviral drugs is determined. Results of these analyses from each collaborating centre and the national centres are used to develop recommendations for the most appropriate strains for use in seasonal influenza vaccines and provide advice to national authorities on the global and regional influenza circulation.

Research has focused on recent H3N2 viruses that show alterations in their ability to bind to sialic acid receptors. Many H3N2 virus strains agglutinate red blood cells through their neuraminidase glycoprotein, which has marked implications for the antigenic analysis of these viruses. All our studies are carried out with the NICs from around the world, with other WHO Collaborating Centres, the UK Health Protection Agency, the National Institute for Biological Standards and Control, and members of the European Community Network of Reference Laboratories for human influenza, and the Wellcome Trust Sanger Institute.

Publications

Sullivan K, Kloess J, Qian C, Bell D, Hay A, Lin YP and Gu Y (2011)High throughput virus plaque quantitation using a flatbed scanner.Journal of Virological Methods Epub ahead of print

Barr IG, McCauley J, Cox N, Daniels R, Engelhardt OG, Fukuda K, Grohmann G, Hay A, Kelso A, Klimov A, Odagiri T, Smith D, Russell C, Tashiro M, Webby R, Wood J, Ye Z and Zhang W (2010)Epidemiological, antigenic and genetic characteristics of seasonal influenza A(H1N1), A(H3N2) and B influenza viruses: basis for the WHO recommendation on the composition of influenza vaccines for use in the 2009-2010 Northern Hemisphere season.Vaccine 28:1156-67

Lin YP, Gregory V, Collins P, Kloess J, Wharton S, Cattle N, Lackenby A, Daniels R and Hay A (2010)Neuraminidase receptor binding variants of human influenza A(H3N2) viruses due to substitution of aspartic acid 151 in the catalytic site - role in virus attachment?Journal of Virology 84:6769-6781

A model of the structure of the H1 haemagglutinin glycoprotein illustrating the location of amino acid substitutions seen in three emerging genetic groups of the A(H1N1)pdm2009 influenza virus.


Structural Biology

Mathematical Biology Willie Taylor (Head of Division) Richard Goldstein Molecular Structure Steve Gamblin (Joint Head of Division) Steve Smerdon (Joint Head of Division) Paul Driscoll Annalisa Pastore Andres Ramos Katrin Rittinger Ian TaylorPhysical Biochemistry Justin Molloy (Head of Division) Tom Carter Ed Hulme John Offer Peter Rosenthal Martin Webb


One of the ways in which cells sense and respond to their environment is through the cell surface expression of integral membrane proteins (e.g. hormone receptors, ion channels, adhesion molecules, etc.) and the secretion of soluble molecules into the external environment (e.g. hormones, transmitters, morphogens). The correct delivery of such molecules to the cell surface or extracellular space involves the secretory pathway. We study the secretory pathway in order to understand the processes that underlie the formation, trafficking and exocytosis of regulated secretory organelles, the post-Golgi membrane bound containers that store and deliver proteins to the cell surface/exterior in response to external signals. We use endothelial cells (ECs) and the Weibel-Palade body (WPB) as our model system.

P-selectin is stored in WPBs and delivered to the EC surface following WPB exocytosis where it functions to facilitate leukocyte attachment and rolling. FRAP analysis of P-selectin in individual WPBs revealed that its enrichment within the organelle arises from its immobilisation within the WPB membrane through an interaction between its extracellular domain and the paracrystalline assembly of Proregion-VWF tubules within the WPB lumen. Dissolution of Proregion-VWF tubules during WPB exocytosis releases P-selectin allowing its diffusive delivery into the plasma membrane.

Tom Carter

STRUCTURAL BIOLOGY

Physical Biochemistry


Secretory organelle formation, trafficking and exocytosis Lab members: Emma Cookson, Jennifer Frampton, Nicola Hellen, Nikolai Kiskin, Laura Knipe


Single granule FRAP studies show that P-selectin is immobile within the membrane of WPBs. Immobilisation requires

the P-selectin extracellular domain and the paracrystalline arrangement of VWF tubules.

Weibel-Palade bodies are rod-shaped secretory organelles containing the haemostatic protein Von Willebrand

factor (VWF). Multimeric VWF forms flexible helical tubules that pack tightly

into a ridged paracrystalline matrix.

Publications

Kiskin NI, Hellen N, Babich V, Hewlett L, Knipe L, Hannah MJ and Carter T (2010)Protein mobilities and P-selectin storage in Weibel-Palade bodies.Journal of Cell Science 123:2964-2975

Knipe L, Meli A, Hewlett L, Bierings R, Dempster J, Skehel P, Hannah MJ and Carter T (2010)A revised model for the secretion of tPA and cytokines from cultured endothelial cells.Blood 116:2183-2191

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


Best-fit superposition of independent models for the PLCγ1 ‘specific array’ construct based upon rigid-body simulated annealing of the component domain structures to fit both experimentally derived NMR restraints and SAXS data.

Quantification by 1H NMR line shape analysis of methyl group-containing amino acids in a sample of Drosophila larva

hemolymph.

Structural and functional analysis of signalling proteins Lab members: Diego Esposito, Acely Garza-Garcia, Lily Nematollahi, Timothy Ragan, Masooma Rasheed, Christine Richter,Gemma Wildsmith

Nuclear magnetic resonance (NMR) spectroscopy provides a valuable means to probe the three-dimensional structure, dynamic characteristics and binding properties of biological molecules, large and small. Our group employs state-of-the-art methods in NMR to investigate the nature of interactions between proteins implicated in fundamental cellular and organismal processes. These include the activation of death receptor signalling cascades, limb regeneration in the adult newt model, the regulation of phospholipase C isozymes, the role of β2-glycoprotein 1 in antiphospholipid syndrome and the interaction of vascular endothelial growth factor (VEGF) with its receptors.

Recently we have applied a combination of heteronuclear NMR, microcalorimetry and small-angle X-ray scattering (SAXS) to dissect the overall 3D structure and impact of phosphotyrosine peptide ligand-binding on the multi-domain ‘specific array’ component of the second messenger enzyme phospholipase C γ1 (PLCγ1). With these data we have developed a model of the mechanism for the enzyme’s activation. In other work we have established a method to analyse small molecule metabolites in Drosophila fruitfly samples by NMR. We used this approach to contribute accurate measurements of larval hemolymph amino acid concentrations in a study of brain sparing under conditions of nutrient withdrawal.

Publications

Cheng LY, Bailey AP, Leevers SJ, Ragan TJ, Driscoll PC and Gould AP (2011)Anaplastic lymphoma kinase spares organ growth during nutrient restriction in Drosophila.Cell 146:435-47

Esposito D, Sankar A, Morgner N, Robinson CV, Rittinger K and Driscoll PC (2010)Solution NMR investigation of the CD95/FADD homotypic death domain complex suggests lack of engagement of the CD95 C terminus.Structure 18:1378-90

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

Paul Driscoll

STRUCTURAL BIOLOGY

Molecular Structure



We study the structure and function of molecules involved in disease processes such as influenza, diabetes and cancer. We use X-ray crystallography and NMR to determine the three dimensional structures and dynamics of these molecules. In combination with other biophysical, biochemical and biological techniques, the data help us elucidate the function of the proteins of interest and

provide information that may be useful for the development of therapeutic approaches.

We are interested in the structure and function of the two major surface glycoproteins of influenza virus (hemagglutinin and neuraminidase). This work has been conducted as a long-standing collaboration with John Skehel and now also involves John McCauley’s lab in Virology as well as essential contacts with NIMR’s WIC. As part of this effort, working with Antonio Lanzavecchia and his colleagues, we have found that an antibody called FI6 can combat all influenza A viruses that commonly cause disease in humans and in animals. The finding represents a potential turning point in the development of flu treatments and in time may help to pave the way for a universal flu vaccine.

Publications

Xiao B, Sanders MJ, Underwood E, Heath R, Mayer FV, Carmena D, Jing C, Walker PA, Eccleston JF, Haire LF, Saiu P, Howell SA, Aasland R, Martin SR, Carling D and Gamblin SJ (2011)Structure of mammalian AMPK and its regulation by ADP.Nature 472:230-233

Corti D, Voss J, Gamblin SJ, Codoni G, Macagno A, Jarrossay D, Vachieri SG, Pinna D, Minola A, Vanzetta F, Silacci C, Fernandez-Rodriguez BM, Agatic G, Bianchi S, Giacchetto-Sasselli I, Calder L, Sallusto F, Collins P, Haire LF, Temperton N, Langedijk JPM, Skehel JJ and Lanzavecchia A (2011)A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins.Science 333:850-856

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

Ribbons representation of two orthogonal views of active AMPK. The kinase domain is coloured in yellow with its activation loop in pink. The regulatory gamma subunit which binds AMP/ADP/ATP competitively is

coloured in red.

Ribbons representation of the crystal structure of the cross-reactive FI6 antibody binding to an HA trimer.

Steve Gamblin FRS, EMBO member, FMedSci

STRUCTURAL BIOLOGY

Molecular Structure

Structural biology of influenza, energy metabolism and cancerLab members: Patrick Collins, Peter Coombs, Valeria De Marco, Chun Jing, Neil Justin, Matthew Sanders, John Skehel, Elizabeth Underwood, Sebastien Vachieri, Bing Xiao, Alex Xiong,


Publications

Soyer OS and Goldstein RA (2011)Evolution of response dynamics underlying bacterial chemotaxis.BMC Evolutionary Biology 11:240

Goldstein RA (2011)The evolution and evolutionary consequences of marginal thermostability in proteins.Proteins 79:1396-1407

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



Richard Goldstein

STRUCTURAL BIOLOGY

Mathematical Biology

Modelling the evolution of molecular components, systems, and behavioursLab members: Martin Godany, Kyriakos Kentzoglanakis, Bhavin Khatri, Asif Tamuri, Grant Thiltgen

All biology is the result of evolution. In order to understand life, we need to investigate the evolutionary process that determines its form and function. Because living things encode this evolutionary heritage, studies of their properties can provide insights into the evolutionary process. Following the evolutionary path of specific components can provide important information about the characteristics of living organisms. Combining insights from physical chemistry, condensed matter physics, artificial intelligence, complexity theory, and mathematical biology, we are developing computational and theoretical methods to explore these areas.

We are investigating protein evolution, exploring what the evolutionary record can tell us about the effect of mutations. We also use more theoretical models to better understand how the evolution of proteins determined their observed properties. We study the evolution of viruses such as influenza in order to better understand the way they act now, how they might change in the future, and how they are able to shift from one host to another. We model the evolution of chemotaxis, the process that allows bacteria to find nutrients, providing insight into the evolution of biochemical networks. We are also studying how horizontal gene transfer affects the evolution of bacteria, especially where the interests of the genes and the organisms conflict, and where the transferred genes encode social behaviour.

Two representations of Butyrylcholinesterase (PDB 2WSL), colour-coded by evolutionary rate.

Adaptation of the haemagglutinin protein (H1) to humans (“Humanicity”) following the host shift from birds to mammals in approximately 1900. The

degree of adaptiveness in H1 isolated from other hosts is shown.


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 to underpin programs of selective drug development.

M1 muscarinic acetylcholine receptors (M1 mAChRs) regulate the activity of many output neurons in the forebrain. They are important mediators of cue detection and memory. Drugs that selectively activate M1 mAChRs are targeted at the cognitive defects in Alzheimer’s disease and schizophrenia. We can isolate stable ligand complexes of M1 mAChRs, combining pharmacological and protein engineering methods. We are focusing on a highly-selective peptide toxin, MT7, which binds to M1 with very high affinity, working towards an atomic resolution structure by X-ray crystallography. Such structures provide a firm basis for the resurgent area of rational drug design.

Publications

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

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

Kaye RG, Saldanha JW, Lu Z-L and Hulme EC (2011)Helix 8 of the M1 muscarinic acetylcholine receptor: scanning mutagenesis delineates a G protein recognition site.Molecular Pharmacology 79:701-709

Some thermostabilising mutations (yellow) in the M1 muscarinic receptor.

STRUCTURAL BIOLOGY


Ed Hulme

Structure and function of G protein-coupled receptors Lab members : Carol Curtis


Subunit counting by TIRFM. Coloured dots represent GFP tag intensity. (A) Potassium channels (4xGFP) (B) Adenosine Receptors (2xGFP).



STRUCTURAL BIOLOGY


Justin Molloy

Single molecule studies of cell motility and cell signallingLab members: Suleman Bawumia, Rachel Farrow, Andrew Howe, Stephen Martin, Gregory Mashanov, Paul Moody, Martyn Stopps

The principal goal of the group is to understand the molecular mechanism of force production by acto-myosin and how proteins and organelles move around within living cells. Laser-based optical methods like optical tweezers and total internal reflection fluorescence microscopy (TIRFM) allow us to observe, track and manipulate individual molecules either in isolated preparations or within living cells (see below). We are interested in diverse aspects of human health, including how the malarial parasite gains entry into human blood cells, how acetylcholine receptors transduce signals in the heart, and how the two strands of DNA are separated and copied.

Recently, we have used Atomic Force Microscopy (AFM) to visualise ataxin-3 fibrils, which are the causative agent of spinocerebellar ataxia. Thermal energy causes the fibrils to bend and analysis of the different shapes that they adopt gives an estimate of their mechanical rigidity. We found the fibrils are unexpectedly flexible; consistent with their structure being composed of “beads on a string”. Using a simple in vitro assay consisting of just actin, myosin and ATP, we found that actin filaments become aligned and form ordered domains. We are now using a combination of mathematical modelling and experiment to understand this simple system and test

Publications

Masino L, Nicastro G, De Simone A, Calder L, Molloy J and Pastore A (2011)The Josephin domain determines the morphological and mechanical properties of ataxin-3 fibrils.Biophysical Journal 100:2033-42

Mashanov GI, Nobles M, Harmer SC, Molloy JE and Tinker A (2010)Direct observation of individual KCNQ1 potassium channels reveals their distinctive diffusive behaviour.Journal of Biological Chemistry 285:3664-3675

Padgett, M, Molloy, JE, McGloin, D, (editors)Optical Tweezers: Methods and ApplicationsChapman & Hall, 2009

One of the most important recent developments in chemistry has been the emergence of biologically compatible ligation reactions. These reactions can be used to synthesize small proteins and introduce non-natural modifications to label proteins. Chemical ligation is usually dependent on the presence of cysteine at the ligation junction. However by simple modification of the terminus of a peptide we can modify it into a mimic of cysteine. This expands the flexibility of the synthesis so that we can cut and paste proteins and reassemble them from their component peptides.

The focus of the group is to expand the utility of ligation reactions and to look for possible existing biological roles for these elegant chemical reactions. The demand for site-specifically modified proteins for structural studies or fluorescent labelling of proteins in cells is driving the further development of these techniques. We are applying chemical ligation to the synthesis of chemically defined peptide-oligosaccharide vaccines and to activity based proteomics as well as the total synthesis of homogenous post-translationally modified proteins and self-assembling systems.

Publications

Holm L, Ackland GL, Edwards MR, Breckenridge RA, Sim RB and Offer J (2011)Chemical labelling of active serum thioester proteins for quantification.Immunobiology Epub ahead of print

Offer J (2010)Native chemical ligation with Nα acyl transfer auxiliaries.Biopolymers 94:530-541

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

Scheme 1 Peptide ligation with an N-acylsulfonamide component. Pep 1 and 2

correspond to unprotected peptides.

Procedure for labelling, pull-down and quantification of thioester containing proteins

from blood.

Synthetic protein laboratory: acyl transfer for chemical biology and synthesis Lab members: Lotta Holm, Geoffrey Knight, Caroline Morris, George Papageorgiou

STRUCTURAL BIOLOGY

Molecular Structure

62

John Offer


STRUCTURAL BIOLOGY



See references 25, 26, 60, 105, 134, 138, 140, 141, 168, 173, 174, 198, 209, 231 and 254 in the bibliography at the back for publications from this group in 2011.

Understanding the molecular bases of neurodegenerationLab members: Salvatore Adinolfi, Cesira de Chiara, Serena Faggiano, Clara Iannuzzi, John McCormick, Laura Masino, Raj Menon, Kris Pauwels, Domenico Sanfelice, Robert Yan

Annalisa Pastore


STRUCTURAL BIOLOGY

Molecular Structure

We are interested in a molecular understanding of neurodegenerative diseases. To achieve this, we study the structure, fold stability, and function of proteins involved in diseases using different but complementary biophysical, biochemical and systems biology approaches. We mainly focus on neurodegenerative processes caused by misfolding and/or mitochondrial dysfunction.

Over the last year we made substantial advances in elucidating the primary function of frataxin, the protein associated with Friedreich’s ataxia. We conclusively showed that frataxin binds to NFS1/IscS, the desulphurase central to iron-sulphur cluster formation. As a result, frataxin enhances the affinity of NFS1/IscS with the ISU/IscU scaffold protein and regulates rates of cluster formation. By identifying the regions that determine fibrillogenesis of ataxin-3, the protein responsible for Machado-Joseph disease, we have also shown that normal function and aberrant protein aggregation, as observed in several neurodegenerative diseases, are competing pathways. This result is of primary importance for understanding misfolding diseases and suggests that specific therapeutic interventions can only be achieved by studying normal function and pathology in parallel.

Publications

Adrover M, Esposito V, Martorell G, Pastore A and Temussi PA (2010)Understanding cold denaturation: the case study of Yfh1.Journal of the American Chemical Society 135:16240–16246

Prischi F, Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI and Pastore A (2010)Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly.Nature Communications 1:95

Masino L, Nicastro G, Calder L, Vendruscolo M and Pastore A (2011)Functional interactions as a survival strategy against abnormal aggregation.FASEB Journal 25:45-54

Ternary complex of CyaY/IscS/IscU obtained by combining SAXS and NMR information: in blue and cyan, the IscS protomers; in red and orange-red, IscU; and in gold and yellow, CyaY.

STRUCTURAL BIOLOGY

Molecular Structure

Post-transcriptional control plays a key role in expanding genomic diversity in complex organisms, and de-regulation of the metabolism of specific mRNAs lies at the basis of common genetic diseases, cancer, autoimmune pathologies and viral infection. Our goal is to explain how RNA-binding proteins achieve and regulate target selectivity and how they control the expression of subsets of genes. We combine information obtained from NMR experiments with that obtained by other biophysical/structural techniques and by in cell/in vivo assays.

Our recent work on the RBM38-p21 system has connected the RNA recognition properties of the RBM38 protein with its capability to counteract the miRNA binding activity on a subset of p53 targets. RBM38 is expressed under cellular stress and binds selected miRNAs in the proximity of the miRNA seed sequence, hindering miRNA activity. We show that the RRM domain of RBM38 selects U/G rich sequences and explain how this domain discriminates between two pools of p53 targets creating a further level of downstream regulation. Our data on the RBM38 system suggest a conduit to control the activity of a subset of p53 targets associated with cell replication and human cancers.

Molecular recognition in post-transcriptional regulation Lab members: Adela Candel, Katherine Collins, Belinda Faust, Christopher Gallagher, David Hollingworth, Nessim Kichik, Vijayalaxmi Manoharan, Giuseppe Nicastro

Andres Ramos


Interaction between the activator FBP and the repressor FIR in c-myc transcriptional regulation.

Role of RBM38 protein in p53 response to cellular stress.

See references 24, 45, and 124 in the bibliography at the back for publications from this group in 2011.

Publications

Léveillé N, Elkon R, Davalos V, Manoharan V, Hollingworth D, Vrielink JO, le Sage C, Melo CA, Horlings HM, Wesseling J, Ule J, Esteller M, Ramos A and Agami R (2011)Selective inhibition of microRNA accessibility by RBM38 is required for p53 activity.Nature Communications 2:513

Cukier CD, Hollingworth D, Martin SR, Kelly G, Díaz-Moreno I and Ramos A (2010)Molecular basis of FIR-mediated c-myc transcriptional control.Nature Structural & Molecular Biology 17:1058-64

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

Domain structure of LUBAC, an E3 ligase consisting of three subunits that catalyses the synthesis of linear ubiquitin chains. Indicated are

domains that mediate complex formation and recognition of ubiquitin.

In vitro synthesis of linear ubiquitin chains by the HOIL-1L and HOIP subunits of

the LUBAC complex. See reference 106 in the bibliography at the back for publication from this group in 2011.

Structural biology of signalling networks that regulate innate and adaptive immunityLab members: Nicholas Brown, Manuela Hess, Marios Koliopoulos, Aylin Morris-Davies, Rohini Rana, Kovilen Sawmynaden,Ben Stieglitz, Edmond Wong


Katrin Rittinger

STRUCTURAL BIOLOGY

Molecular Structure

Pattern recognition receptors are key components of the innate immune system that sense microbial and viral infections and initiate a pro-inflammatory response. The signalling pathways activated by these receptors need to be tightly controlled as misregulation can lead to chronic inflammation and autoimmune disease. Innate immune responses also trigger adaptive immunity and the two systems are linked through complex signalling networks.

Our research is focused on the structural characterisation of protein complexes that regulate innate immunity. In particular, we are interested in understanding how members of the NLR (NOD-like receptor) family of intracellular PRRs recognise a target and relay the signal to elicit a specific cellular response.

The post-translational modification of a protein with ubiquitin chains is often used as a regulatory signal in immunity. The type of ubiquitin chain attached to a target protein determines the physiological outcome of the modification, with K48-linked chains targeting a protein for degradation while K63 and M1-linked (“linear”) chains play an important role in signalling. We aim to elucidate, on a structural and functional level, the mechanism by which a specific type of ubiquitin chain is synthesised and attached to a target by a catalytic cascade involving the sequential action of three enzymes.

Publications

Ikeda F, Deribe YL, Skånland SS, Stieglitz B, Grabbe C, Franz-Wachtel M, van Wijk SJL, Goswami P, Nagy V, Terzic J, Tokunaga F, Androulidaki A, Nakagawa T, Pasparakis M, Iwai K, Sundberg JP, Schaefer L, Rittinger K, Macek B and Dikic I (2011)SHARPIN forms a linear ubiquitin ligase complex regulating NF-κB activity and apoptosis.Nature 471:637-41

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

Cryomicroscopy of proteins, viruses and cellsLab members: Lesley Calder, Tim Grant, Saira Hussain, Rishi Matadeen, Kasim Sader, Michael Shannon, James Streetley, Sebastian Wasilewski

Our group studies the architecture of large protein assemblies in order to understand basic molecular mechanisms that control protein and membrane traffic in the cell and in virus infection. We apply electron cryomicroscopy and image analysis to study the structure of purified protein complexes in frozen solution, and 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. We are also working to improve experimental methods for high resolution imaging of proteins and to develop new computational procedures for image analysis.

We have performed high resolution studies of influenza virus ultrastructure by cryomicroscopy that have shown us both the structure of the virus envelope and the internal architecture of the virus. We are extending these studies to directly image how viruses enter cells by membrane fusion and how new particles are assembled and released by budding through the host membrane. 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, and study their structural changes during exocytosis.

STRUCTURAL BIOLOGY


Peter Rosenthal


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

Calder LJ, Wasilewski S, Berriman JA and Rosenthal PB (2010)Structural organization of a filamentous influenza A virus.Proceedings of the National Academy of Sciences of the United States of America 107:10685-10690


Periphery of a frozen-hydrated endothelial cell.

Cryoimage of influenza virus.


Publications

Pennell S, Westcott S, Ortiz-Lombardía M, Patel D, Li J, Nott TJ, Mohammed D, Buxton RS, Yaffe MB, Verma C and Smerdon SJ (2010)Structural and functional analysis of phosphothreonine-dependent FHA domain interactions.Structure 18:1587-95

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


Steve Smerdon EMBO member

STRUCTURAL BIOLOGY

Molecular Structure

The dynamic nature of cellular signalling processes requires them to be rapidly reversible, a characteristic that is generally achieved through protein phosphorylation. The response to DNA damage is mediated by a cascade of phosphorylation that originates at the lesion and is transduced to effector molecules and complexes. Defects in the precision of phosphorylation are a primary cause of many cancers and other diseases. By understanding the molecular basis of specificity within a web of regulatory interactions, we can determine why these processes run amok, and may be able to design drugs to combat these effects. To this end, we focus on an emerging group of proteins and modules such as 14-3-3, Forkhead-associated (FHA), Brca1-C-terminus (BRCT) and Polo-box domains that function as phosphorylation-dependent adaptors or scaffolding molecules in Ser/Thr kinase pathways.

Our recent work has shown how FHA and BRCT-repeat domains of Nbs1 – a component of the MRN DNA damage complex – work in concert to orchestrate DNA break processing and signalling to the rest of the repair machinery. In a study of kinase signalling in M. tuberculosis, we have revealed a role for phospho-independent FHA interactions and a novel, intra-molecular binding mechanism in the control of core metabolic processes that likely have significance for bacterial virulence. Finally, we have resolved long-standing questions about FHA domain specificity using X-ray crystallography and molecular dynamics modelling methods.

Structural biology of phosphorylation-dependent signalling in the cell cycle and DNA Lab members: Julie Clapperton, Oliver de Peyer, Mohamed Ismail, Otto Kyrieleis, Richard Li, Jan Lloyd, Simon Pennell, Lasse Stach, Grace Yu

The origin of FHA domain specificity. A pocket on the FHA surface interacts with the extra methyl group of phosphothreonine, stabilising

a network of h-bonds (dashes) that are crucial for tight binding.


STRUCTURAL BIOLOGY

Molecular Sructure

Ian Taylor

Macromolecular assembliesLab members: Laurence Arnold, Neil Ball, Valerie Ennis-Adeniran, Joe Hedden, Dominic Pollard, Laura Robertson, David Schwefel.

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 proteins that mediate retroviral restriction in host cells. Recently, we have determined the structure of the HIV-1 restriction factor SAMHD1. This study has revealed the molecular details of the mechanism of SAMHD1 catalysis and provides an explanation for how this protein can inhibit HIV-1 infection of myeloid-derived cells.

Publications

Goldstone DC, Ennis-Adeniran V, Hedden JJ, Groom HC, Rice GI, Christodoulou E, Walker PA, Kelly G, Haire LF, Yap MW, de Carvalho LP, Stoye JP, Crow YJ, Taylor IA and Webb M (2011)HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase.Nature 480:379-82

Goldstone DC, Yap MW, Robertson LE, Haire LF, Taylor WR, Katzourakis A, Stoye JP and Taylor IA (2010)Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface.Cell Host & Microbe 8:248-259

Pancevac C, Goldstone DC, Ramos A and Taylor IA (2010)Structure of the Rna15 RRM-RNA complex reveals the molecular basis of GU specificity in transcriptional 3’-end processing factors.Nucleic Acids Research 38:3119-3132


SAMHD1 structure A ribbons representation of the SAMHD1 dimer with the major lobe (Blue), minor lobe (Grey) and C-terminal region (Red). Guanosine is shown in the nucleotide-binding site at the dimer

interface.

SAMHD1 active site. The active site contains zinc and phosphate together with histidine, aspartic acid and arginine

residues that coordinate the ions.See references 82, 97, 161 and 247 in the bibliography at the back for publications from this group in 2011.

Publications

Sadowski MI, Maksimiak K and Taylor WR (2011)Direct correlation analysis improves fold recognition.Computational Biology and Chemistry 35:323-32

Taylor WR and Sadowski MIStructural Constraints on the Covariance Matrix Derived from Multiple Aligned Protein Sequences PLoS ONE 6:e28265

Taylor WR, Jones DT and Sadowski MIProtein topology from predicted residue contacts Protein Science epub ahead of print



Willie Taylor

STRUCTURAL BIOLOGY

Mathematical Biology

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 defines 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 its function.

With the rapid increase in the volume of sequence data, we have re-examined residue contacts predicted from correlated positions in a multiple sequence alignment. In collaboration with colleagues in computer science at UCL, we have developed new methods to extract these contacts and applied them to protein structure prediction. The contacts are often sparse and uncertain but, to some extent, these limitations in the data can be overcome by grouping the contacts by secondary structure elements and enumerating the possible packing arrangements of these elements in a combinatorial manner. Strong interactions appear frequently but inconsistent interactions are down-weighted and missing interactions up-weighted. The resulting improved consistency in the predicted interactions has allowed the method to be successfully applied to proteins up to 200 residues in length, which is larger than any structure previously predicted using sequence data alone.

Protein structure analysis and design Lab members: Michael Doran, Katarzyna Maksimiak, Michael Sadowski

Residue contacts are shown in a ‘dot-plot’ with observed contacts in green and predicted contacts in red. These are sufficient to identify the

fold of the protein (PDB code: 2gj8A).

Movement of proteins along DNA is an essential feature of cells: it occurs during DNA replication and repair, for example. Helicases are enzymes responsible for separating the two strands of DNA, making them available for processing by other enzymes. We are interested in both the mechanism and control of such processes. We are developing new optical approaches, such as reagentless biosensors, to study the proteins and nucleic acids during this process of movement along DNA. In addition such reagentless biosensors provide a way to assay a wide range of enzymatic activities.

Our work on helicases is focussed on developing a complete system in which the helicase interacts with other proteins as well as moving through DNA. We are investigating the replication of certain plasmids that contain antibiotic resistance genes and that are readily transferred between bacteria. Such replicating plasmids contain a specific double-stranded origin of replication, and are bound with a replication initiation factor (RepD), a helicase and polymerase. We are currently working on building up this system in vitro to study the role and mechanism of each component in this system. The development of biosensors has included one for ADP or GDP, which has a high specificity and has properties that make it suitable for real-time assays and for high-throughput approaches.


See references 17, 68, 82, 119, 235, 258 and 259 in the bibliography at the back for publications from this group in 2011.

STRUCTURAL BIOLOGY


Martin Webb

The molecular mechanisms of motor proteinsLab members: Claudia Arbore, Lori Callum, Liisa Chisty, Colin Davis, Simone Kunzelmann, Gordon Reid, Lesley Southerden

Publications

Saikrishnan K, Powell B, Cook NJ, Webb MR and Wigley DB (2009)Mechanistic basis of 5’-3’ translocation in SF1B helicases.Cell 137:849-59

Slatter AF, Thomas CD and Webb MR (2009)PcrA helicase tightly couples ATP hydrolysis to unwinding double-stranded DNA, modulated by the initiator protein for plasmid replication, RepD.Biochemistry 48:6326-6334

Kunzelmann S and Webb MR (2010)A fluorescent, reagentless biosensor for ADP based on tetramethylrhodamine-labeled ParM.ACS Chemical Biology 5:415-25

Kinetics of nicking of supercoiled plasmid by RepD measured by quench-flow. AFM of plasmid before and after nicking and when partially unwound by the helicase, PcrA.

Nucleotide exchange on Ras at different concentrations of the exchange factor, SOS. This was measured using a GDP biosensor, rhodamine-ParM : the cartoon illustrates

changes in structure producing the fluorescence response.

Developmental Neurobiology David Wilkinson (Head of Division) Siew-Lan Ang

Molecular Neurobiology François Guillemot (Head of Division) Vassilis Pachnis Iris Salecker

Neurophysiology Troy Margrie (Acting Head of Division)

Physiology and Metabolism Alex Gould (Head of Division)


Neurosciences

NEUROSCIENCES

Developmental Neurobiology

Publications

Mavromatakis YE, Lin W, Metzakopian E, Ferri ALM, Yan CH, Sasaki H, Whisett J and Ang S-L (2011)Foxa1 and Foxa2 positively and negatively regulate Shh signalling to specify ventral midbrain progenitor identity.Mechanisms of Development 128:90-103

Pelling M, Anthwal N, McNay D, Gradwohl G, Leiter AB, Guillemot F and Ang SL (2011)Differential requirements for neurogenin 3 in the development of POMC and NPY neurons in the hypothalamus.Developmental Biology 349:406-416

Yan CH, Levesque M, Claxton S, Johnson RL and Ang S-L (2011)Lmx1a and Lmx1b function cooperatively to regulate proliferation, specification, and differentiation of midbrain dopaminergic progenitors.Journal of Neuroscience 31:12413-12425

The mammalian midbrain and hypothalamus contain many types of neurons that regulate voluntary movement and energy homeostasis, respectively. How the different types of neurons are generated and are wired into functional circuits remains a central question in developmental neurobiology. We study how neural progenitors in the brain give rise to midbrain dopaminergic (mDA) neurons and hypothalamic neurons involved in regulating feeding. Our findings have direct medical relevance, since loss of mDA neurons is the hallmark of 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, proliferation and differentiation of mDA, arcuate proopiomelanocortin and neuropeptide Y neurons. Our studies employ a combination of embryological, genetic, molecular, genomic and proteomic approaches, including genetic fate mapping studies, phenotyping null and conditional mutant mice, brain explants, time-lapse imaging, chromatin immunoprecipitation, biochemical and transcriptome analyses. These studies provide important insights into how embryonic gene expression leads to mature neuronal phenotypes. We are also interested in the role of transcription factors in maintaining neurotransmitter phenotypes and function in adult neurons.

In vitro differentiated midbrain dopaminergic progenitors. Dopaminergic progenitors expressing Lmx1a and Nestin that were generated by in vitro differentiation of mouse embryonic stem cells.

Siew-Lan Ang

Adult midbrain tyrosine hydroxylase positive neurons.Genetic fate mapping studies identify floor plate descendants in tyrosine

hydroxylase positive (TH+) midbrain nuclei including the ventral tegmental area (VTA), substantia nigra pars compacta (SN) and interfascicular nucleus (IFN).See references 144, 176 ,and 255 in the bibliography at the back for publications from this

group in 2011.

Neuronal subtype specification in the midbrain and hypothalamusLab members: Neal Anthwal, Lan Chen, Suzanne Claxton, Martin Levesque, Wei Lin, Emmanouil Metzakopian, Anna Truckenbrodt



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.

Currently, we are investigating how dietary nutrients regulate the embryonic and foetal growth of each body organ. Much of our research in this area uses the fruit fly Drosophila, a model organism that shares many genes with mammals. We recently showed that neural stem cells in the Drosophila brain need to be kick started by amino acids early on in development but, thereafter, they can grow and divide without dietary nutrients. This reflects a switch in neural stem cells from Insulin-like Receptor to Anaplastic Lymphoma Kinase signalling. Anaplastic Lymphoma Kinase lies at the heart of a molecular network ensuring that the growth of the developing brain is spared over that of the body when nutrients become limiting.

Publications


Sousa-Nunes R, Yee LL and Gould AP (2011)Fat cells reactivate quiescent neuroblasts via TOR and glial insulin relays in Drosophila.Nature 471:508-512

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

Neural stem cell clones growing in the developing Drosophila CNS. A representative clone, marked with GFP (green) and containing a single neural

stem cell (large red cell) is outlined.

The Drosophila CNS escapes growth shutdown during nutrient restriction.

NEUROSCIENCES

Physiology and Metabolism

Alex Gould EMBO member

Regulation of growth and metabolism Lab members: Andrew Bailey, Louise Cheng, Einat Cinnamon, Rami Makki, Panayotis Pachnis, Fabrice Prin, Patricia Serpente, Rita Sousa-Nunes, Irina Stefana


Neural stem cells in the developing brain produce a vast array of neurons that reach specific positions where they integrate into functional circuits. This process of neurogenesis involves the progression of neuronal precursors through a succession of cellular steps of proliferation, migration and differentiation. We study the genetic programmes that regulate and coordinate these different steps in the embryonic and adult mouse brain, using genomic approaches to identify the genetic pathways involved, and functional assays to determine the contribution of individual genes to the different steps of neurogenesis.

We recently found that the proneural transcription factor Ascl1, well known for its role of promoting neurogenesis in the embryo, also controls the division of neural stem cells during development and in the adult brain. We are now studying the molecular pathways that regulate the transcription and protein stability of Ascl1 during adult neurogenesis, as disruption of these pathways in the ageing brain might be responsible for the reduction of neurogenesis and the accompanying cognitive decline observed in old animals.

Publications

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

Pacary E, Heng J, Azzarelli R, Riou P, Castro D, Lebel-Potter M, Parras C, Bell DM, Ridley AJ, Parsons M and Guillemot F (2011)Proneural transcription factors regulate different steps of cortical neuron migration through Rnd-mediated inhibition of RhoA signaling.Neuron 69:1069-84

Castro DS, Martynoga B, Parras C, Ramesh V, Pacary E, Johnston C, Drechsel D, Lebel-Potter M, Garcia LG, Hunt C, Dolle D, Bithell A, Ettwiller L, Buckley N and Guillemot F (2011)A novel function of the proneural factor Ascl1 in progenitor proliferation identified by genome-wide characterization of its targets.Genes & Development 25:930-945

Circular representation of the neural stem cell genome showing that clusters of binding sites for transcription factors regulating neural stem cell

self-renewal associate with the expression of target genes.

FRET analysis of differentiating cortical neurons in culture showing that down-regulation of the proneural factor targets Rnd2 and Rnd3

stimulates RhoA signalling.

NEUROSCIENCES

Molecular Neurobiology

François Guillemot FMedSci, EMBO member

Genomic and functional analysis of neurogenesisLab members: Jimena Andersen, Roberta Azzarelli, Lan Chen, Daniela Dreschel, Patricia Garcez, Sebastien Gillotin, Ben Martynoga, Cristina Minieri, Emilie Pacary, Noelia Urban, Debbie Van Den Berg, Benny Yang

See references 5, 6, 31, 50, 67, 87, 90, 133, 164, 165, 176, 215, 223, 251 and 253 in the bibliography at the back for publications from this group in 2011.




Sensory processing in single cells, circuits and behaviourLab members: Ed Bracey, Alex Brown, Ninja Grewe, Bruno Pichler, Ede Rancz, Mateo Velez-Fort

Troy Margrie

The benefit of detecting and recognising information in the external world has been a key driver of the evolution of the central nervous system. The neuronal basis of sensory representation in our brains therefore underpins how we make sense of the world around us, our ability to solve problems and remember past experiences. Our lab is focused on understanding the fundamental cellular and network-based mechanisms that underlie these processes.

The goal of our lab is to understand how the brain uses the activity of individual neurons and collections of neurons to encode sensory stimuli. To achieve this we use a top-down, multidisciplinary approach that allows us to explore this key issue from the systems to the cellular level. Specifically, we are investigating several questions: (i) To what extent is sensory representation distributed across primary and secondary or multimodal brain areas? (ii) What, if any, is the relationship between local neuronal connectivity and sensory function? (iii) How is sensory information encoded and integrated by individual cells and synapses?

Classical neuronal staining approaches (such as Golgi staining, left) have revealed the brain’s complexity. The new method (right) allows scientists to record the function of a single cell (red) and identify its presynaptic

connectivity (white).

Publications

Rancz EA, Franks KM, Schwarz MK, Pichler B, Schaefer AT and Margrie TW (2011)Transfection via whole-cell recording in vivo: bridging single-cell physiology, genetics and connectomics.Nature Neuroscience 14:527-532

Angelo K, Margrie TW (2011)Population diversity and function of hyperpolarization-activated current in olfactory bulb mitral cells.Scientific Reports 1: 50

Chadderton P, Agapiou JP, McAlpine D, Margrie TW (2009)The synaptic representation of sound source location in auditory cortex.Journal of Neuroscience 29:14127-35

NEUROSCIENCES

Neurophysiology

NEUROSCIENCES

Neurophysiology


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 in 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, Sandgren K, Kessaris N, Richardson W, Potocnik A, Vanden Berghe P and Pachnis V (2011)Glial cells in the mouse enteric nervous system can undergo neurogenesis in response to injury.The Journal of Clinical Investigation 121:3412-3424

Heanue TA, Pachnis V (2011)Prospective identification and isolation of enteric nervous system progenitors using Sox2Stem Cells 29:128-40

Kioussis D, Pachnis V (2009)Immune and nervous systems: more than just a superficial similarity?Immunity 31:705-10

Development of the nervous systemLab members: Werend Boesmans, Myrto Denaxa, Tiffany Heanue, Melanie Kalaitzidou, Chryssa Konstantinidou, Catia Laranjeira, Reena Lasrado, Rita Lopes, Guillerme Neves, Valentina Sasseli

Confocal microscope image of a myenteric ganglion from the gut of adult mice. Preparations of the myenteric plexus were immunostained for neuronal and glial markers indicating the diversity of enteric ganglia.

Vassilis Pachnis EMBO member, FMedSci





Iris Salecker

Visual circuit assembly in DrosophilaLab members: Holger Apitz, Dafni Hadjieconomou, Emily Richardson, Benjamin Richier, Nana Shimosako, Katarina Timofeev

Publications

Hadjieconomou D, Rotkopf S, Alexandre C, Bell DM, Dickson BJ and Salecker I (2011)Flybow: genetic multicolor cell labeling for neural circuit analysis in Drosophila melanogaster.Nature Methods 8:260-268

Hadjieconomou D, Timofeev K and Salecker I (2010)A step-by-step guide to visual circuit assembly in Drosophila.Current Opinion in Neurobiology 21:76-84

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

In the larval optic lobe of Drosophila, progenitors (blue) in the outer and inner proliferation centres (OPC, IPC; green) generate neurons in the

medulla and lobula complex (green).

The ability of animals to perform the many tasks of their everyday lives relies on the perfect functioning of their nervous systems. These consist of a large number of neuronal and glial subtypes with strikingly diverse shapes. Our understanding of the molecular mechanisms that control the formation of these cell types and coordinate their assembly into functional neural networks during development is still limited. To address this issue, we use the visual system of the fruit fly Drosophila as a genetic model, because it enables us to study the stepwise development of a complex neural circuit with single cell resolution.

In particular, we are investigating the mechanisms that control (i) the development of specific neuronal and glial cell subtypes in higher visual information processing areas, (ii) the targeting of one colour-sensitive photoreceptor axon subtype to its temporary and final synaptic layers, and (iii) layer-specific targeting of dendritic and axonal branches of partner neurons. To facilitate the imaging of the underlying interdependent cellular interactions, we recently generated a multicolour cell-labelling approach for Drosophila, called Flybow. By studying the mechanisms underlying normal brain development, we hope in the long term to contribute to the understanding of neurological disorders that may be linked to early connectivity defects.

In the adult visual system, R1-R8 photoreceptor neurons (blue) extend axons from the retina into the lamina and medulla. Neurons

in the target area were labelled with the Flybow approach.

NEUROSCIENCES

Molecular Neurobiology


NEUROSCIENCES

Developmental Neurobiology

During the early stages of nervous system development in vertebrates, neural tissue is subdivided into regions, each with a distinct identity. Within these subdivisions, the differentiation of progenitor cells is regulated in time and space to form the correct organisation of specific neuronal and glial cell types. In order for precise patterns to form and be maintained, it is essential that sharp borders form at the interface of the distinct regions.

Our studies aim to elucidate molecular mechanisms of boundary formation and neuronal cell differentiation, and the links between these processes in the formation of the segmented pattern of the vertebrate hindbrain. We are using a combination of in vitro assays, in vivo functional studies and computer modelling to understand how signalling through Eph receptors and ephrins leads to the formation of sharp borders. In related work, we study how hindbrain boundaries, together with signalling from specific neurons, organise discrete zones of progenitor cells and neuronal differentiation. Finally, we are dissecting the mechanisms of action of an intracellular network that regulates neural stem cell maintenance and differentiation. These studies utilise the powerful genetic and transgenic tools available in the zebrafish model for analysis of gene function and in vivo imaging of cell migration and lineage.

Publications

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

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

Gonzalez-Quevedo R, Lee Y, Poss KD and Wilkinson DG (2010)Neuronal regulation of the spatial patterning of neurogenesis.Developmental Cell 18:136-147

In vitro cell segregation assay. Cell lines expressing ephrinB1 (green) or EphB2 (unlabelled) are mixed and plated in cell culture. They

segregate to form sharp borders.

Neurons (green label), segments (two labelled in blue), and segment boundaries (red) in the zebrafish hindbrain.

David Wilkinson EMBO member, FMedSci

Regulation of boundary formation and neurogenesisLab members: Marie Breau, Sean Constable, Sebastian Gerety, Andrew Georgiou, Lauren Gregory, Mohamed Ismail, Rosie Morley, Alexei Poliakov, Masanori Takahashi, Javier Terriente, Qiling Xu


Genetics and Development

Systems Biology Jim Smith (Head of Division) Greg Elgar Mike Gilchrist

Developmental Biology James Briscoe (Joint Head of Division) Jean-Paul Vincent (Joint Head of Division) Malcolm Logan Tim Mohun Elke Ober Lyle Zimmerman

Stem Cell Biology and Developmental Genetics Robin Lovell-Badge (Head of Division) Paul Burgoyne Rita Cha Peter Thorpe James Turner

We study how the central nervous system (CNS) is formed in embryos. Despite its complexity, the CNS is assembled in a remarkably reliable and accurate manner. This precision is necessary for the wiring of nerves into the functional neural circuits that give the CNS its function. Our research focuses on the spinal cord, which is the part of the CNS that contains the nerves that allow us to sense our environment and respond to it by moving muscles. Our studies contribute to understanding the development of the spinal cord as well as shed light on diseased and damaged nervous systems. We hope this will help in the development of therapies for these conditions.

Specifically, we are interested in the cellular and molecular mechanisms responsible for pattern formation in the neural tube. In ventral regions of the caudal neural tube, the secreted molecule Sonic Hedgehog (Shh) forms an extracellular gradient that governs pattern formation and tissue growth. We use a range of molecular, imaging and modelling approaches to identify and reconstruct the regulatory network that controls the growth and development of the ventral neural tube.

A gradient of Shh (green) controls the expression of genes (red, orange, blue) in neural progenitors.

A reporter of Shh signalling (top panels; green in bottom panels) provides a readout of intracellular signalling in vivo.

Publications

Cruz C, Ribes V, Kutejova E, Cayuso J, Lawson V, Norris D, Stevens J, Davey M, Blight K, Bangs F, Mynett A, Hirst E, Chung R, Balaskas N, Brody SL, Marti E and Briscoe J (2010)Foxj1 regulates floor plate cilia architecture and modifies the response of cells to sonic hedgehog signalling.Development 137:4271-4282

Dessaud E, Ribes V, Balaskas N, Yang LL, Pierani A, Kicheva A, Novitch BG, Briscoe J and Sasai N (2010)Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen Sonic hedgehog.PLoS Biology 8:e1000382

Ribes V, Balaskas N, Sasai N, Cruz C, Dessaud E, Cayuso J, Tozer S, Yang LL, Novitch B, Marti E and Briscoe J (2010)Distinct Sonic Hedgehog signaling dynamics specify floor plate and ventral neuronal progenitors in the vertebrate neural tube.Genes & Development 24:1186-1200


GENETICS AND DEVELOPMENT

Developmental Biology

James Briscoe EMBO member

Pattern formation in the vertebrate nervous systemLab members: Fahad Al Saud, Natascha Bushati, Rachel Chung, Michael Cohen, Katrina Griffin, John Jacob, Anna Kicheva, Eva Kute-jova, Steven Moore, Noriaki Sasai




Stem Cell Biology and Developmental Genetics

The Y chromosome and infertilityLab members: Fanny Decarpentrie, Shantha Mahadevaiah, Obah Ojarikre, Áine Rattigan, Nadege Vernet

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.

We have been using sex chromosomally variant mouse models in combination with the selective addition of Y genes by transgenesis to elucidate the role of specific Y genes in male and female fertility. Using this approach we, together with the Turner group, have identified important quality control functions during spermatogenesis for the Y-encoded genes Zfy1 and Zfy2. These genes encode zinc finger transcription factors that proved to be necessary for the apoptotic elimination of sex chromosomally aberrant pachytene spermatocytes in response to a failure of Y chromosome silencing, and during the first meiotic metaphase in response to the presence of an unpaired X chromosome.

Sxra encompasses18 genes from the mouse Y chromosome, including the testis determinant Sry. XO carrier males (XSxraO) are sterile because spermatocytes

are eliminated by apoptosis during the first meiotic division.

With the reduced Y gene complement of Sxrb plus Eif2s3y (spermatogonial proliferation factor), or Sry and Eif2s3y, there is no

apoptotic response; this is reinstated by the addition of Zfy2.

Publications

Vernet N, Mahadevaiah SK, Ojarikre OA, Longepied G, Prosser HM, Bradley A, Mitchell MJ and Burgoyne PS (2011)The Y-encoded gene Zfy2 acts to remove cells with unpaired chromosomes at the first meiotic metaphase in male mice.Current Biology 21:787-793

Royo H, Polikiewicz G, Mahadevaiah SK, Prosser H, Mitchell M, Bradley A, de Rooij DG, Burgoyne PS and Turner JMA (2010)Evidence that meiotic sex chromosome inactivation is essential for male fertility.Current Biology 20:2117-23

Mahadevaiah SK, Bourc’his D, de Rooij DG, Bestor TH, Turner JMA and Burgoyne PS (2008)Extensive meiotic asynapsis in mice antagonises meiotic silencing of unsynapsed chromatin and consequently disrupts meiotic sex chromosome inactivation.Journal of Cell Biology 182:263-76


Paul Burgoyne FMedSci




Rita Cha

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 kinases. These evolutionarily conserved signal transduction proteins play a key role in many fundamental DNA/chromosomal processes such as genome duplication, recombination, and checkpoint regulation. Inactivation of ATR/ATM in humans leads to cell death, genome instability, and meiotic dysfunction as well as the genetic disorders, Ataxia Telangiectasia and Seckle syndrome.

We use genetically tractable S. cerevisiae to study the molecular basis for ATR/ATM function. 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. Our research focuses on elucidating the molecular mechanism(s) by which the loss of Mec1/Tel1 function leads to these defects.

Regulation of eukaryotic chromosome metabolismLab members: Jesus Carballo and Ana Penedos

Cytological visualisation of Hop1, a Mec1/Tel1 target. Hop1 (green) is phosphorylated by Mec1/Tel1 following the initiation of meiotic recombination (red) at specific loci along the chromosome axis. Blue

(DNA).

ChIP-CHIP analysis of Rec114 reveals the impact of Mec1/Tel1 phosphorylation on its chromosome localisation. Green (WT Rec114); red (non-phosphorylatable Rec114); blue (phospho-mimetic Rec114).

Black (meiotic double strand break hotspots).

Publications

Hashash N, Johnson AL and Cha RS (2010)Regulation of fragile sites expression in budding yeast by MEC1, RRM3 and hydroxyurea.Journal of Cell Science 124:181-185

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




Regulation of early vertebrate developmentLab members: Dilrini DeSilva, Joseph Grice, Stefan Pauls, Paul Piccinelli, Hannah Stanforth

Publications

Goode DK, Callaway HA, Cerda GA, Lewis KE and Elgar G (2011)Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events.Development 138:879-884

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

Woolfe A and Elgar G (2007)Comparative genomics using Fugu reveals insights into regulatory subfunctionalization.Genome Biology 8:R53

Greg Elgar

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.

Comparative sequence analysis identifies conserved regulatory signatures in genomic DNA that drive specific patterns of hindbrain expression in developing zebrafish (a-m) and lamprey (n-q) embryos.


Systems Biology

Gene regulatory networks in early developmentLab members: Brook Cooper, Nick Owens

Embryonic 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 through complex gene regulatory networks. Our aim is to elucidate these networks using molecular and computational tools that enable a systematic and large-scale approach.

We are focusing on the period in the development of the early embryo when control passes from maternal gene products, to those derived from activation of gene transcription in the growing embryo. This maternal-zygotic transition marks a profound watershed in the growth of the embryo as it becomes reliant on the integrity of its own genetic material. Using the Xenopus model system, we have taken a high resolution time series of whole embryo mRNA samples through this transition period and analysed these

for gene expression levels using high-throughput Illumina RNA-seq technology. In order to understand our data better, we have been taking a close look at intrinsic variation in gene activity, by studying biological replicates. This has enabled us to build a robust method for detecting signatures of gene activation, and this is a first step in the process of reconstructing the gene regulatory networks involved in early development.


Systems Biology

Mike Gilchrist

Publications

Parain K, Mazurier N, Bronchain O, Borday C, Cabochette P, Chesneau A, Colozza G, El Yakoubi W, Hamdache J, Morgane L, Gilchrist MJ, Pollet N, Perron M. (2011) A large scale screen for neural stem cell markers in Xenopus retina Developmental Neurobiology (in press)

Simeoni I, Gilchrist MJ, Garrett N, Armisen J and Gurdon JB (2011)Widespread transcription in an amphibian oocyte relates to its reprogramming activity on transplanted somatic nuclei.Stem Cells and Development Epub ahead of print

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM and Rokhsar DS (2010)The genome of the Western clawed frog Xenopus tropicalis.Science 328:633-6

Visualisation methods are important for assessing reproducibility, and here we are comparing gene expression levels between two biological replicates. The quasi-volcano plot (right) gives a much better

sense of the variation in the data than the traditional scatter plot (left).

Intrinsic variation can make real effects hard to see. Compare the gene expression variation between two biological replicate controls (left) and between a control and an effective gene knock-down (right).




Understanding vertebrate limb developmentLab members: Sorrel Bickley, Natalie Bufferfield, Martin Carkett, Veronique Duboc, Anna Kucharska, Sue Miller, Satoko Nishimoto



Malcolm Logan

Limb defects are the second most common congenital abnormality present in human live births and diseases affecting the musculoskeletal system are a significant clinical problem in the older population. The goal of our work is to understand how the 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.

At early stages of embryonic development, the forelimb and hindlimb buds are a similarly shaped mass of cells. During subsequent steps of development the progenitors are transformed into a complex of interconnected bones, muscles and tendons. These limb tissues are exquisitely sculpted to become the correct size and shape and must also form the appropriate interconnections so that each muscle group attaches to the skeletal scaffold via the correct tendon. How this complex is elaborated is poorly understood.

We are using animal models to understand the mechanisms that control limb bud formation and the subsequent construction of the individual limb elements.

Section of a mouse forepaw approximately 3/4 the way through the gestation period. Forming digits (red) and muscles (green)

have been identified using antibodies that recognise tissue-specific proteins combined with fluorescent labels. Blood cells (yellow), that

autofluoresce, are also visible.


Publications

Abu-Daya A, Nishimoto S, Fairclough L, Mohun TJ, Logan MPO and Zimmerman LB (2011) The secreted integrin ligand nephronectin is necessary for forelimb formation in Xenopus tropicalis. Developmental Biology 349:204-12

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 18:148-56

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 106:21726-30



Robin Lovell-Badge FRS, EMBO member, FMedSci

Sex, stem cells and decisions of cell fateLab members: Sarah Booth, Christophe Galichet, Sam Goldsmith, Silvana Guioli, Ander Matheu, Adam Nunn, Helen O’Neill, Karine Rizzoti, Charlotte Scott, Ryohei Sekido, Clare Wise

Embryo development relies on cells making choices about which cell type to become and whether to divide, move or die. During 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); more precisely to a single gene on the Y, termed Sry. This encodes a transcription factor with an HMG box type of DNA binding domain, also present in proteins encoded by the Sox gene family.

We use many techniques to explore how SRY and other factors act to initiate and maintain testis or ovary differentiation, with mice as our main experimental model. Because male birds lack Sry, evolutionary comparisons use chick embryos, and our work informs the human situation, where disorders affecting

sex determination can have devastating physiological and social consequences. We also study pluripotent stem cells from early embryos (ES cells) or after reprogramming from adult cells (iPS cells), and multipotent stem cells from the brain and pituitary. Certain Sox genes are critical for self-renewal and stem cell potential. We therefore explore how these impact on cell fate choices, and how they might be exploited to aid treatments for clinical problems, such as stroke and cancer.

Publications

Acloque H, Ocana OH, Matheu A, Rizzoti K, Wise C, Lovell-Badge R and Nieto MA (2011)Reciprocal repression between Sox3 and Snail transcription factors defines embryonic territories at gastrulation.Developmental Cell 21:546-558

Scott CE, Wynn SL, Sesay A, Cruz C, Cheung M, Gaviro M-VG, Booth S, Gao B, Cheah KSE, Lovell-Badge R and Briscoe J (2010)SOX9 induces and maintains neural stem cells.Nature Neuroscience 13:1181–1189

Sutton E, Hughes J, White S, Sekido R, Tan J, Arboleda V, Rogers N, Knower K, Rowley L, Eyre H, Rizzoti K, McAninch D, Goncalves J, Slee J, Turbitt E, Bruno D, Bengtsson H, Harley V, Vilain E, Sinclair A, Lovell-Badge R and Thomas P (2010)Identification of SOX3 as an XX male sex reversal gene in mice and humans.Journal of Clinical Investigation 4:328-41

Reducing SoxB1 (Sox2 and Sox3) gene activity leads to increased expression of Snail and to more cells in the primitive streak of a gastrulating mouse

embryo. The two types of transcription factor mutually repress each other to control the extent and rate of epithelial to mesenchymal transition.

A sex-reversing Sox3 transgene mimics Sry and not Sox9. This explains how Sry could have

evolved from Sox3 via a regulatory mutation, and why rearrangements of the X chromosome near SOX3 are associated with human XX male sex

reversal.


See references 2, 10, 107, 116, 190, 192 and 226 in the bibliography at the back for publications from this group in 2011.


Heart development in vertebratesLab members: Mike Bennett, Laurent Dupays, Surendra Kotecha, Marianne Neary, Izabela Piotrowska, Stuart Smith, Norma Towers, Robert Wilson

Formation of the heart is a complex process that begins very early in the vertebrate embryo, remodelling a simple peristaltic tube into a complex multi-chambered organ capable of supporting embryo growth. This transformation requires exquisite coordination of cell differentiation and growth to produce the dramatic changes in organ shape. Abnormalities affecting any step will have profound consequences on the foetal heart and heart defects are the most common birth defect. By studying the roles of individual genes and cell populations in normal heart development, we will gain a better understanding of the origins of cardiac malformations and a model of how complex organs are formed in the developing embryo.

We are using transgenic techniques and genome-wide analysis to investigate how cardiac gene expression is regulated in the developing vertebrate embryo. Novel imaging and computer modelling procedures that we have developed allow us to examine the precise three-dimensional structure of the embryonic heart and identify changes in morphology resulting from altered gene expression. This approach not only helps us to understand normal gene function in the developing heart, but also to investigate possible causes of congenital heart disease and genetic conditions (such as Down syndrome) which often result in heart malformations.



Tim Mohun

Publications

Smith SJ and Mohun TJ (2011)Early cardiac morphogenesis defects caused by loss of embryonic macrophage function in Xenopus.Mechanisms of Development 128:303-315

Dunlevy L, Bennett M, Slender A, Lana-Elola E, Tybulewicz VL, Fisher EMC and Mohun T (2010)Down’s syndrome-like cardiac developmental defects in embryos of the transchromosomic Tc1 mouse.Cardiovascular Research 88:287-295

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

3D models of the mouse embryo heart (left) or the lumens of the heart chambers (right) reveal the complex mesh of muscle fibres characteristic of

the embryonic heart.

In this tadpole, muscle cells of the heart, head and body can be readily visualised through expression of a fluorescent reporter, providing a simple

way to monitor heart development.


Liver development in zebrafishLab members: Johanna Fischer, Jordi Cayuso Mas, Despina Stamataki



Elke Ober

The liver represents the largest internal organ, performing a plethora of essential functions to maintain body homeostasis. During embryogenesis, the liver, pancreas and lung originate from adjacent domains of the foregut. A well-orchestrated programme of developmental steps ensures the functional differentiation of each organ, starting with the precise allocation of multipotent foregut-endoderm to a particular organ fate. Central aims of our research are to understand how liver progenitors are specified from the foregut endoderm and how these committed precursors rearrange to shape the functional liver. We investigate these questions using the experimental advantages of zebrafish.

Using genetic approaches, we found that two Wnt ligands regulate specification and subsequent proliferation of liver progenitors. Importantly, Wnt levels need to be tightly controlled within the embryo, since excess expression of either ligand promotes liver formation at the expense of the pancreas. Our current work aims to determine the interactions of Wnt signalling with other pathways controlling liver formation to unravel the molecular network directing underlying liver specification from the pool of multipotential progenitors. The identification of organ-specific genetic programmes will provide insights into not only the mechanisms regulating embryonic development, but also tissue homeostasis and regeneration following injury in adults.

Publications

Poulain M and Ober EA (2011)Interplay between Wnt2 and Wnt2bb controls multiple steps of early foregut-derived organ development.Development 138:3557-356

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

Impaired Wnt2/Wnt2bb signalling disrupts liver (red) specification from multipotent foregut endoderm, while excess Wnt2bb promotes liver formation at the expense of the pancreas (green).




The different cell types of the body are formed in the right place and at the right time in response to signals produced by special organiser regions of the embryo. These signals, or morphogens, act in a concentration-dependent manner to induce the formation of different cell types at different positions within developing tissues. One of the earliest interactions of this kind is mesoderm induction, which causes the formation of cell types such as muscle, kidney and bone, as well as the heart and vascular system. We study the formation of the mesoderm as well as that of the neural crest.

We use frog, zebrafish and mouse embryos to study mesoderm-inducing factors and to ask how cells respond to them. In particular we use imaging approaches to understand how the signals exert long-range effects in the embryo, and biochemical and mathematical approaches to ask how cells distinguish between different morphogen concentrations. We also use sophisticated molecular techniques to elucidate the genetic regulatory networks that drive the formation of specific cell types in mesoderm (including vascular cells) and neural crest. As well as helping understand development, we hope our work will assist in efforts to direct stem cells down desired developmental pathways.

Jim Smith FRS, EMBO member, FMedSci

Top: searching for targets of the transcription factor Xbra in the Xenopus embryo by ChIP-Seq. Bottom: loss of function of Xbra and Xbra3 causes

severe posterior defects in tailbud embryos.

Publications

Collart C, Christov CP, Smith JC and Krude T. (2011). An essential Y RNA-dependent pathway for the initiation of DNA replication is activated at the mid-blastula transition in Xenopus laevis. Molecular Cell Biology 31, 3857-70.

Harvey SA, Tümpel S, Dubrulle J, Schier AF and Smith JC (2010)no tail integrates two modes of mesoderm induction.Development 137:1127-1135

Harvey SA and Smith JC (2009)Visualisation and quantification of morphogen gradient formation in the zebrafish.PLoS Biology 7:e1000101

Tmem88a was identified in an RNA-Seq screen for genes expressed in endothelial and haematopoietic cells. Loss of Tmem88a function by means

of antisense morpholino oligonucleotides causes loss of erythrocytes (brown).

Lab members: Camille Bouissou, Clara Collart, Kevin Dingwell, Alex Eve, Tiago Faial, George Gentsch, Elsie Place, Thom Spruce, Anna Strobl, Alex Watson, Mary Wu


Systems Biology

The molecular basis of mesoderm formation


Systems microscopy studies of cell fate determinationLab members: Erika Aquino, Eva Herrero, Elena Ledesma and Guðjón Ólafsson

Asymmetric cell division is the process by which one cell divides to give two cells with different fates. Repeated asymmetric divisions allow a fertilised egg to generate diverse cell types during development, and in adult stem cells such divisions maintain the population while simultaneously generating new, differentiated cells. The goal of our group is to determine how cellular asymmetry is established and maintained over multiple divisions to create cell lineages. Specifically, we focus on understanding how asymmetry of the mitotic spindle - the machinery that segregates chromosomes during division - affects how genetic information is accurately passed down to daughter cells.

Our model system is the budding yeast, Saccharomyces cerevisiae, which shows patterns of asymmetric division like those of more complex organisms. We employ high-throughput fluorescence microscopy techniques that allow us to rapidly screen the localisation, levels and dynamics of all yeast proteins and integrate them into a visual dataset. Using these tools, we aim to identify the conserved mechanisms controlling asymmetric division, lineage specification and mitotic spindle function.

Peter Thorpe



Publications

Thorpe PH, Alvaro D, Lisby M and Rothstein R (2011)Bringing Rad52 foci into focus.Journal of Cell Biology 194:665-667

Thorpe PH, Bruno J and Rothstein R (2009)Kinetochore asymmetry defines a single yeast lineage.Proceedings of the National Academy of Sciences of the United States of America 106:6673-6678

Thorpe PH, Bruno J and Rothstein R (2008)Modeling stem cell asymmetry in yeast.Cold Spring Harbor Symposia on Quantitative Biology 73:81-88

Yeast arrayed at high-density allow large-scale screening of mutants for their effect upon the kinetochore. This reverse genetics approach identifies genes that regulate kinetochore function, particularly asymmetry of cell division.

Analysis of images of fluorescently-tagged yeast kinetochore proteins allows relative quantitation of their concentration. The isosurface fluorescence image (right) corresponds to the yeast shown (left).



X chromosome inactivation, meiotic silencing and infertility Lab members: Jeff Cloutier, Jennifer Grant, Grzegorz Polikiewicz, Helene Royo, Mahesh Sangrithi

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. The role of XCI in male germ cells is unclear. 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 male germ cells is essential for fertility. This study has also allowed us to ascertain that misexpression of the gene pair, Zfy1/2, is the underlying cause of sterility in XYY males. We have found that the X chromosome is highly enriched in genes involved in sperm differentiation, with around 20% of all genes on the X chromosome being expressed only in male germ cells. Many of these genes are likely to be important for normal male fertility. In female eutherian, or ‘placental’ mammals, XCI is mediated by the non-coding RNA Xist, but how XCI is controlled in the other major class of mammals, the metatherians, is unknown. We have now discovered that the epigenetics of XCI in metatherians is similar to that of eutherians, raising the possibility that XCI in metatherians is mediated by an as yet unidentified non-coding RNA.

Publications

Royo H, Polikiewicz G, Mahadevaiah SK, Prosser H, Mitchell M, Bradley A, de Rooij DG, Burgoyne PS and Turner JMA (2010)Evidence that meiotic sex chromosome inactivation is essential for male fertility.Current Biology 20:2117-23

Mahadevaiah SK, Royo H, Van de Berg JL, McCarrey JR, Mackay S, Turner JM (2009)Key features of the X inactivation process are conserved between marsupials and eutherians.Current Biology 19:1478-84

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

In XYY males, pairing allows the two Y chromosomes to escape inactivation by gH2AX and to express Y-genes; the resulting

expression of the toxic Zfy1/2 genes leads to germ cell arrest.

Identification of Rsx, a non-coding RNA that coats the female metatherian X chromosome.



James Turner



Developmental Bioiogy

A small number of signalling molecules orchestrate growth and cell fate decisions during development. We investigate the mechanisms that control the production, spread and activity of one signal, Wingless (a member of the Wnt family). We also study the regulatory mechanisms that allow cells to compute their position within the Wingless gradient. This led us to find that cells with overactive Wnt signalling eliminate their normal neighbours, a finding that may be relevant to tumour biology. In a separate, but related strand of research, we aim to understand the mechanisms that trigger the elimination of cells following epithelial disruption.

Disruption of epithelial cell adhesion leads to widespread apoptosis, a phenomenon that likely reflects the need to eliminate cells that detach from the epithelium, thus preventing them from causing havoc. As we found recently, Jun kinase (JNK) is a key mediator of this process. However, how epithelial disruption activates JNK remains to be discovered. It will also be important to understand why in other cellular contexts, this pathway does not necessarily trigger apoptosis. We are using transcriptional profiling, confocal imaging and genetic analysis to investigate the links between epithelial disruption, JNK signalling and apoptosis.

Publications

Vincent JP, Kolahgar G, Gagliardi M and Piddini E (2011)Steep differences in wingless signaling trigger Myc-independent competitive cell interactions.Developmental Cell 21:366-74

Piddini E and Vincent J-P (2009)Interpretation of the Wingless gradient requires signaling-induced self-inhibition.Cell 136:296-307

Franch-Marro X, Wendler F, Guidato S, Griffith J, Baena-Lopez A, Itasaki N, Maurice MM and Vincent J-P (2008)Wingless secretion requires endosome-to-Golgi retrieval of Wntless/Evi/Sprinter by the retromer complex.Nature Cell Biology 10:170-7

Patterning and homeostasis in developing epitheliaLab members: Cyrille Alexandre, Luis Alberto Baena-Lopez, Karen Beckett, Maria Gagliardi, Satoshi Kakugawa, Paul Langton, Hisashi Nojima, Lucy Palmer, Alice Mitchell, Rohan Bundell

A model for Wingless transcytosis and loading onto exosomes. This working model accounts for the role of Evi (red squiggles) in Wingless (blue dots) secretion and provides a possible explanation

for the transport of Wingless from the apical to basal surface.

APC mutant cells grow at the expense of normal cells. Wild type cells (green and non-green) contribute equal amount of tissues (left). By contrast, normal cells

(green) are eliminated by APC mutant cells (non-green), which overactivate Wnt signalling.

Jean-Paul Vincent EMBO member, FMedSci


MRC National Institute for Medical Research92




Harvesting medical benefits from the human genome depends on understanding the tasks that specific genes perform in living organisms. Our group studies gene functions important for initial formation of organs and subsequent disease processes, by identifying and characterising genetic mutations that profoundly affect tissue development. Since most gene functions are shared among all vertebrates, we use the easily-studied externally-developing embryos of a frog with a simple chromosomal structure, Xenopus tropicalis.

We have used positionally mapped genes underlying a number of mutations, including several resulting in abnormalities of otoconia, inner ear crystal structures essential for vestibular/balance function. Study of these mutations may help understand a common human balance disorder, benign positional vertigo. Together with collaborators, we have also used solution-hybridisation whole-exome enrichment technology to isolate and sequence the protein-coding space of X. tropicalis genomes derived from chemically mutagenised stocks. This strategy has rapidly yielded more than 100 new mutations for further study, and includes genes that are important for a variety of processes including ciliogenesis, left-right asymmetry and erythropoiesis.

Publications

Abu-Daya A, Nishimoto S, Fairclough L, Mohun TJ, Logan MPO and Zimmerman LB (2010)The secreted integrin ligand nephronectin is necessary for forelimb formation in Xenopus tropicalis.Developmental Biology 349:204-212

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM and Rokhsar DS (2010)The genome of the Western clawed frog Xenopus tropicalis.Science 328:633-6

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, 811-825

Using frog genetics to understand vertebrate development and diseaseLab members: Anita Abu-Daya, Tosikazu Amano, Tim Geach, Holly Ironfield, Joachim Kurth

Lyle Zimmerman

Abnormal large otoconia from komimi (otoconin90) mutant tadpoles compared to wild type. (I, J) Sections showing komimi otoconia with reduced contact with inner ear sensory epithelium.



Genetically induced green fluorescent protein expression in the neural crest population of a mid gestation mouse embryo. Optical sections were captured as a confocal stack which was then colour coded according to the depth within the sample.

J Tabler (sample), Donald Bell (imaging), Chen Qian (software).

Research facilities

Biological and Procedural Services

MRC Biomedical NMR CentreX-ray crystallographyMass spectrometryOther structural biology facilities Protein sequence analysis and structure modelling Analytical ultracentrifugation

Confocal imaging and analysisHistologyElectron microscopyOPT and HREM imagingSingle molecule techniques Total internal reflection fluorescence microscopy Optical tweezers Atomic force microscopyElectron cryomicroscopy

Genomics High throughput sequencing MicroarrayBioresources Large-scale laboratory Media production Freezer archiveFlow cytometryLevel 4 high-containment virus laboratoryEngineering workshopElectronic instrument prototyping and support

PhotoGraphicsComputingLibraryWeb teamGeneral services Occupational health Safety and security Human resources Finance and purchasing

Structural biology facilities

Imaging

Other scientific facilities

Other support services


Biological and Procedural Services Kathleen Mathers

RESEARCH FACILITIES

The Division of Biological Services provides a fully integrated laboratory animal and technical resource to the Institute. The multidisciplinary research of the Institute requires a range of species and models, and to meet these needs we operate and manage a number of complex animal facilities. These include an isolation/quarantine unit, containment facilities at Levels 2, 3 and 4 for animals infected with organisms potentially harmful to man and/or the environment, specialist procedural, behavioural and surgical suites, imaging and irradiation facilities, and extensive aquatic facilities. The vast majority of animals in the facility are rodents, with large numbers of genetically altered lines of mice and rats. In addition, our facilities house ferrets, rabbits, the laboratory opossum, zebrafish and Xenopus species. The size, scope and efficiency of Biological Services provide an extraordinary service to nearly all aspects of the Institute’s science as well as to many scientists elsewhere.

Laboratory opossum with litterIndividually ventilated cages

Xenopus laevis



RESEARCH FACILITIES

We aim to meet all the needs of the scientific Divisions whilst ensuring the highest possible standards of health and welfare for all species. The Division is active in the field of laboratory animal science, conducting and promoting research and uptake of the 3Rs (replacement, reduction, refinement) and presents its work at national and international meetings. The animal care and technical staff are trained in the production, care and use of animals for research purposes to the highest standards of animal husbandry. Additionally they provide a range of centralised procedural support. A full-time veterinary surgeon and microbiologist offer advice on the health and welfare of our animals. The Division also provides services for the incubation of fertile chicken eggs and the production of antibodies. In addition, administration and licence control under the Animals (Scientific Procedures) Act 1986, and coordination of the Institute’s Local Ethical Review Process, is managed by Biological Services.

Procedural Services Manager: Sarah Johnson

Microinjection of ES cells Micromanipulation

Procedural Service Section

The Procedural Service Section provides a range of services and facilities for the production, maintenance and preservation of genetically altered rodents. The service produces approximately 200 new genetically altered rodent lines each year by both transgenic and gene-targeted technologies. A full range of techniques is employed to provide a comprehensive service for the cryopreservation of rodent germplasm, and more recently the service has expanded to include cryopreservation of frog and fish spermatozoa. In addition, the section is responsible for the rederivation of new lines imported into the Institute. Every year, together with Biological Services, the Section coordinates over 150 shipments of live animals and frozen germplasm to collaborators all over the world. The staff are also skilled in a number of assisted reproductive techniques, including in vitro fertilisation and intracytoplasmic sperm injection, which are useful for maintenance of lines with poor breeding performance or to provide age-matched cohorts for experiments. The section is also committed to investigating and implementing the 3Rs by researching and developing new refinements such as non-surgical methods of embryo transfer.

MRC Biomedical NMR Centre Tom Frenkiel

RESEARCH FACILITIES

Magnet of the 800 MHz spectrometer.

NMR spectroscopy used to monitor the reaction of the HIV restriction factor SamHD1 with dGTP. Successive 31P NMR spectra were recorded at hourly intervals, and reveal that SamHD1 possesses triphosphohydrolase activity, in this instance converting dGTP to guanosine and inorganic triphosphate. (In collaboration with Dr Ian Taylor, NIMR.)For more information see Taylor, Webb et al, Nature (2011).

The MRC Biomedical NMR Centre is a multi-user facility for biomolecular liquid-state nuclear magnetic resonance (NMR) which was set up by the MRC in 1979 to provide advanced and well-supported facilities for use by scientists from NIMR and other academic research establishments. NMR studies of the type carried out at the Centre provide a wide range of information, ranging from the atomic-level (e.g. determining the pKa of individual histidine groups in proteins), through to full determination of the structure and dynamics of proteins in solution. An important area of application is the identification of interaction surfaces between the components of macromolecular complexes.

The Centre’s facilities consist of four spectrometers, including one operating at 800 MHz, a 700 MHz instrument, and two 600 MHz instruments. Centre staff have a high level of expertise in designing, implementing, and analysing macromolecular NMR studies. The spectrometers are suitable for investigating a wide range of biological systems in solution. Three of the four are equipped with the latest cryogenically-cooled probes for enhanced sensitivity. The facilities are currently used by research groups from NIMR and 18 external groups at universities and institutes from around the UK. Within NIMR our closest links are with the Division of Molecular Structure.

Co-workers: Geoff Kelly, Alain Oregioni

Representative publications are listed on the Centre’s website, www.nmrcentre.mrc.ac.uk



RESEARCH FACILITIES

X-ray crystallography

The Protein Expression Lab was established in 2009 to provide dedicated support to members of the Division of Molecular Structure. The facility provides a comprehensive resource for the production of recombinant proteins. Currently we offer a choice of two expression systems: bacteria and insect cells. A high-throughput pipeline for cloning DNA fragments and small-scale expression tests in E. coli has been established, allowing the generation and screening of 96 expression constructs in a week. In parallel, proteins are also expressed in insect cells using the baculovirus expression vector system (BEVS). Services include the generation and amplification of high-titre baculovirus stocks, analytical scale productions for optimisation of protein expression, and preparative scale productions. In addition, the facility maintains a vector DNA repository, provides in-house vector design, troubleshooting and training.

Insect cell expression in a Wave Bioreactor™.

Protein X-ray crystallography is a technique that produces a three-dimensional model of the structure of a protein at atomic resolution. The X-ray crystallography facilities within the Division of Molecular Structure at the Institute are state-of-the art and include a high intensity X-ray source coupled with an automated robotic sample mounting system which allows the unattended screening of 80 crystals in a single experiment. Diffracting protein crystals are the culmination of an extensive series of experimental procedures which include protein purification and protein crystallisation. A range of sophisticated techniques are employed to help explore the largest number of conditions within each of the projects under investigation. These include those techniques being developed in the Protein Expression Lab together with a wide range of robotic procedures to set up multi-well dishes and to automatically screen for protein crystals.

The crystal structure of the RELIK CA-NtD-CypA complex. The Relik CA-NtD (blue) and cyclophilin (gold) molecules are displayed in cartoon representation. The solvent accessible surface of the bound cyclophilin is

shown in grey.

X-ray generator and automated sample mounting robot insert shows the loop used to hold the protein crystal.

The nano-electrospray source of the Orbitrap Velos.

The proteomics and mass spectrometry facility is housed in a purpose-built suite. It currently houses three mass spectrometers and ancillary equipment, which are used in a range of biochemical analyses. A state-of-the-art LTQ Velos Orbitrap high resolution tandem MS coupled to a nano-HPLC is utilised in proteomics studies and is capable of identifying hundreds of proteins from a single run. Protein quantification is performed using standard techniques such as SILAC or iTRAQ labelling. Identification of the sites of post-translational modifications, such as phosphorylation and ubiquitination, is also achieved on this instrument.

A quadrupole time-of-flight tandem mass spectrometer, equipped with an electrospray source, is utilised for protein and peptide characterisation. A GC-MS has recently been added to the facility and is currently used in metabolomics research, such as the quantification of fatty acids.

Phosphorylation site localisation by LC MS/MS.

RESEARCH FACILITIES

Mass spectrometry



Protein sequence analysis and structure modellingJosé Saldanha

Computational tools for prediction, analysis and visualisation can provide inspirational new ways to look at data, no matter which protein family is the main focus of research. From high-level predictions of protein topology by template-free methods (sometimes called ab initio), through three-dimensional all-atom models of protein structure, to detailed protein-ligand docking studies; theoretical methods developed both at NIMR and in the wider academic community can suggest new insights and new hypotheses leading to the design of fruitful experiments.

A support service for protein sequence analysis and structure modelling is provided. It draws on state-of-the-art algorithms being developed by experts in the Division of Mathematical Biology as well as the many computer programs freely available from the scientific community. There is also an in-house, commercial, computer graphics package for detailed three-dimensional modelling. The service is available to all NIMR scientists and external collaborators.

Ribbon visualisation of a protein model with helices in red, strands in yellow and loops in green. The ribbons are surrounded by a protein

surface mesh in blue.

Other structural biology facilities

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 panel. A fringe displacement pattern produced by a moving concentration boundary measured by the Rayleigh interference optics of the

XL-I is shown above.

RESEARCH FACILITIES

The Confocal Imaging and Analysis Laboratory (CIAL) provides an imaging core facility at NIMR. The facility has six confocal microscopes, three wide-field fluorescence microscopes, a multiphoton microscope, four offline workstations, a data storage system, and image processing software such as Volocity, Imaris, Image J, Metamorph and MatLab. Currently the facility supports 170 researchers from 16 NIMR Divisions. Users operate the system, but the complexity of imaging makes support an extremely important aspect of the facility. We routinely provide users with training, troubleshooting, consultation and microscope maintenance. We also support special techniques such as thick tissue imaging, live cell experiments, 2nd harmonic generation imaging, quantitative imaging, deconvolution imaging, and automatic cell counting.

Research activities in CIAL are focused on techniques of super resolution imaging, correlative microscopy, high-throughput imaging, automatic cell segmentation and tracking, and others relevant to NIMR research. The lab has expertise in sample preparation and labelling, live/fixed sample imaging, and hardware/software development required by NIMR researchers.

Confocal imaging and analysis Yan Gu

RESEARCH FACILITIES

Publications




Multiphoton microscopy examining the development of retinal nerve connections in Drosophilia. The left panel shows the two colour raw image whilst the right panel

represents the GFP signal with a depth-coded pseudo-colour projection.

Co-workers: Donald Bell, Chen Qian, Kate Sullivan

GFP-labelled mouse neuron showing the dendritic tree and spine formation. The image is post

processed with a depth-coded pseudo-colour projection.



Histology Radma Mahmood

RESEARCH FACILITIES

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 ten different processing programs designed to optimally maintain morphology of all tissues from mouse embryos and neonates, rats, frogs and fish, as well as human research samples. Paraffin tissue blocks are sectioned manually and the automated stainer is used for hematoxylin and eosin (HE) staining. Special stains, such as Masson’s Trichrome for collagen, are performed manually.

Shared resources available to researchers include cryostats for frozen sections and a microtome for paraffin sections. The service also provides training, protocols, and assistance for investigators on all aspects of histology, including tissue fixation, tissue processing, and immunohistochemical techniques.

HE stained mouse embryo day 16.5, sagittal section.In situ hybridisation of Xenopus embryo hearts counter-stained

with nuclear fast red.

HE and Giemsa stained bone marrow showing malaria organisms.

Periodic acid Schiff stained mouse gut with nematode.

The EM facility has both a Transmission Electron Microscope (TEM, Jeol 1200 EX set up for conventional scattering optics) and a Scanning Electron Microscope (SEM, Jeol 35CF), both of which have been recently upgraded to digital photography (Gatan Orius 1000 and SemAfore respectively). There is also a dedicated EM processing laboratory. Staff from any department at NIMR may request TEM or SEM investigations in support of their scientific studies. 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. Technical advice, training and support is also provided for staff wishing to learn EM techniques.

TEM techniques available include ultra-thin sectioning and ultra-structural analysis of experimental tissues, cell cultures or sub-cellular pellets. Immuno-EM techniques provided are post-embedding immuno-gold labelling of antigens upon ultra-thin sections or pre-embedding by 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 phase contrast EM for molecules.

Electron microscopy Liz Hirst

RESEARCH FACILITIES

Publications

Cruz C, Ribes V, Kutejova E, Cayuso J, Lawson V, Norris D, Stevens J, Davey M, Blight K, Bangs F, Mynett A, Hirst E, Chung R, Balaskas N, Brody SL, Marti E and Briscoe J (2010)Foxj1 regulates floor plate cilia architecture and modifies the response of cells to sonic hedgehog signalling.Development 137:4271-4282

Ermakov A, Stevens JL, Whitehill E, Robson JE, Pieles G, Brooker D, Goggolidou P, Powles-Glover N, Hacker T, Young SR, Dear N, Hirst E, Tymowska-Lalanne Z, Briscoe J, Bhattacharya S and Norris DP (2009)Mouse mutagenesis identifies novel roles for left-right patterning genes in pulmonary, craniofacial, ocular, and limb development.Developmental Dynamics 238:581-94

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

SEM Loss and rescue (above) of a gene function in Drosophila eye (Molecular Neurobiology).

TEM Mouse heart mitochondrial morphology changes before, during (above) and after birth.

Post-embedding Immuno EM. Gold-conjugated antibodies demonstrate that SufB and

SufC are located at the bacterial membrane of E.coli.



OPT and HREM imaging

RESEARCH FACILITIES

HREM imaging of mouse embryo tissue structure and 3D morphology.OPT imaging of the transcription factor Hnf3β (red) in the mouse embryo.

Imaging methods play an increasingly central role in enabling gene or protein activity to be linked to function and phenotype, from subcellular to whole organism levels. Within the Division of Developmental Biology, the Institute has developed dedicated facilities for imaging complex morphology and gene expression of embryonic and adult tissue in 3D using Optical Projection Tomography (OPT) and High Resolution Episcopic Microscopy (HREM). This complements existing facilities at NIMR provided by the Confocal Imaging and Analysis Lab (page 102) and Histology (page 103). Automated HREM developed at NIMR forms the basis of an ongoing project funded by the Wellcome Trust and supported by the Medical Research Council to provide comprehensive imaging of normal and mutant mouse embryos at unprecedented resolution. The freely available data (www.embryoimaging.org) complement standard anatomical texts and can form the basis for systematic analysis of mutant morphological phenotypes.

Single molecule experiments give insights into how biological molecules work and how they are structured. Several research groups at NIMR apply and develop methods to study single molecules. Some of these techniques provide high resolution images of the molecules, and others give dynamic information about the interactions between proteins, DNA, lipid membranes and small ligand molecules.

TIRF (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 (images by Gregory Mashanov and Justin Molloy).

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. As the AFM tip is scanned over the sample it rides over molecules fixed to the surface. Deflections of the tip are measured using a laser-based position sensor producing a three-dimensional topological map of the surface. 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.

Upper panel shows a single actin filament and a single microtubule (MT) (byIwan Schaap); Lower panels show different phases of bacterial Plasmid DNA

replication (by Claudia Arbore).

Single molecule techniques

RESEARCH FACILITIES

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 optically trapped particles are measured with nanometre precision so that forces and movements produced by single molecules can be measured. The resolution is around one nanometre every millisecond.



Electron cryomicroscopy

RESEARCH FACILITIES

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 forms a glass (rather than forming ice crystals) and the embedded biological material, locked in this transparent medium, can be viewed by electron microscopy. Because the electron beam has a much shorter wavelength than visible light, individual protein molecules can be visualised. Although the image contrast of each individual molecule is low, signal averaging can yield very high resolution pictures. CryoEM is well-suited to high-resolution studies of both the structure and dynamics of large proteins and protein complexes, such as cytoskeletal proteins or viral capsids. Our latest methods also enable structures within rapidly frozen mammalian cells to be visualised. By recording many digital images of a specimen held at different orientations (tomography), a three-dimensional view of the molecule or cell is obtained. Individual molecules, whole virus particles or living mammalian cells embedded in ice can be imaged in three dimensions.

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

Co-workers: Leena Bhaw-Rosun, Harsha Jani

The Genomics facility provides next-generation sequencing and microarray services to NIMR scientists. Services include sample preparation, high-throughput sequencing and microarray hybridisation. Support is also provided for data analysis. Situated within the Division of Systems Biology, the Genomics facility is equipped with state-of-the-art instrumentation for genomic sequencing, genotyping and gene expression studies, including Illumina GAIIx and HiSeq2000 sequencers, the Affymetrix Gene Chip hybridisation and Illumina iScan Systems.

High-throughput sequencing

High-throughput sequencing technologies are revolutionising molecular genetics, vastly expanding our ability to study genome structure, how genes are regulated and how cell and tissue differentiation occurs. Combined with increasingly sophisticated bioinformatics analysis, these methods of massively parallel sequencing-by-synthesis are likely to impact on all areas of basic biological research, with their ability to generate billions of bases of high-quality DNA sequence in a matter of days. In order to maintain its position at the forefront of basic research, NIMR has established a central next-generation sequencing core facility. The facility currently supports DNA/RNA sequencing using the Illumina Genome Analyzer IIx (commonly referred to as “Solexa”) for reads up to 150 bases for

both single and paired-end runs. This facility provides a cost-efficient service, producing rapid and highly accurate DNA and RNA sequence data for researchers at NIMR. By assisting at all stages from experimental design to data assembly and analysis, the service dramatically extends the ability of our scientists to make discoveries in genomics, epigenomics, gene expression analysis and protein-nucleic acid interactions. The facility now includes the Illumina HiSeq 2000 sequencer. With innovative design features, the HiSeq 2000 provides output of up to 200 Gb per run (2 x 100 bp read length), up to 25 Gb per day and two billion paired end reads/run.

DNA shearingThe Genomics facility has a Covaris system (based on Covaris Adaptive Focused Acoustics™ (AFA)) for DNA shearing for next-generation sequencing and for conventional molecular biology applications and chromatin shearing for chromatin immuno-precipitation.

Quality controlWe offer an extensive platform for quality control and quantification of DNA, RNA and proteins. The following equipment is available for QC analysis:

• Nanodrop spectrophotometer and two Agilent 2100 Bioanalyser, for quality control and quantification of DNA, RNA and proteins.

• Two Life Technology Qubit systems, for the quantification of DNA, RNA and proteins.

• Life Technology E-Gel systems for size selection of sequencing libraries. .

RESEARCH FACILITIES

Genomics Abdul Karim Sesay

The Genomics facility team.


Global analysis of the haematopoietic and endothelial transcriptome during zebrafish

Development. Data from RNASeq experiment,

courtesy of John Cannon, Systems Biology, Smith’s Lab.


RESEARCH FACILITIES

Microarray

Whilst the most common use of microarrays is examining the level of expression of many different genes or mRNA species in a sample simultaneously, there are now chips available for other protocols. These include SNP analyses, resequencing - including a human mitochondrial genome chip - exon arrays for analysis of alternative splicing, arrays for ChIP on chip experiments for investigation of gene promoters, and miRNA and snoRNA analysis with coverage of multiple organisms on a single array (human, mouse, rat, canine, and monkey). Arrays are available for many different organisms such as Mycobacterium tuberculosis, Drosophila, Xenopus, zebrafish, chicken, dog, mouse, rat and human. The microarray facility offers full technical support in the preparation and running of RNA or DNA samples prepared by the scientists. It also offers access to and training in the use of the Gene Spring software package from Agilent for preliminary analysis of microarray data.

The facility now includes the Illumina iScan System with Universal Starter Kit. Based around the iScan Reader, which incorporates high-performance lasers, optics, and detection systems, the iScan System offers sub-micron resolution, higher throughput rates and very economical BeadChips available for human, rat and mouse. Even the highest density BeadChips can be scanned in minutes, allowing processing of up to 96 multisample BeadChips per day. Applications include gene expression analysis; array-based transcriptome analysis; FFPE sample analysis; SNP genotyping and CNV analysis; whole genome, custom or focused genotyping; cytogenetic analysis; linkage analysis; copy number analysis; gene regulation and epigenetic analysis, and array-based methylation analysis.

RNA-Seq read alignment to Zv8 zebrafish genome on UCSC genome browser. Illustrative

alignments of reads from the first biological replicate of gfp+ and gfp-

libraries.

The biological functions of the 754 enriched genes using the Panther Ontology.

Tmem88a and trim2a morphants have reduced erythrocytes shown by Odianisidine staining at 48 hours post-fertilisation.


RESEARCH FACILITIES

Bioresources Joachim Payne

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 mammalian, insect, yeast and bacterial cells for ten research Divisions at NIMR, as well as collaborating with other MRC and academic units. Last year we grew around 1000 litres of hybridoma and insect cells and 3900 litres of yeast and bacterial cultures. Cells can be supplied quick-frozen or lysed using a Constant Systems cell disrupter. For concentrating supernatants we have a Sartorius crossflow filtration system and a Quixstand hollow-fibre unit.

Our in-house Media Production facility has formulae for over 1,200 products, and last year processed 3,500 orders, totalling around 36,000 litres of liquid reagents, including a quarter of a million tubes of Drosophila food and 45,000 microbiological poured plates.

The Mellanby Freezer Archive is a purpose-designed facility for the long-term, secure storage of frozen material. At the moment we are responsible for over half a million samples belonging the MRC’s Prion and Clinical Trials Units and researchers as far away as the MRC SPHSU in Glasgow.

Wioletta inspects a hybridoma culture. Brian sets up one of our bioreactors.

Co-workers: Charlotte Austin, Wioletta Berg, Viktoria Janusova, Ian Oliver, Brian Trinnaman, Jackie Wilson

Co-workers: Bhavik Patel, Wayne Turnbull


Flow cytometry Graham Preece

RESEARCH FACILITIES

The flow cytometry facility provides a state-of-the-art, high speed, sterile cell sorting service. We sort multiple types of cell populations for both in vitro and in vivo studies, single cell sorting and cloning. In addition, it offers multiparameter fluorochrome analysis of cell markers and measurement of calcium fluxes, apoptosis and cell cycle.

The facility serves a large number of NIMR researchers from the Infections and Immunity, Genetics and Development and Neurosciences groups. Training is also provided for research staff, including PhD students and postdoctoral researchers.The facility is well equipped, with four cell sorters including two 7-colour Beckman Coulter MoFlo sorters, a 13-colour Becton Dickinson FACS Aria II and a 10-colour Becton Dickinson Influx. The Influx is situated inside a containment level 2 (CL2) bio-safety cabinet for sorting samples classified at CL2. Additionally there are eight flow cytometric Analysers that include a 4-colour Becton Dickinson FACSCalibur, a 6-colour Becton Dickinson FACSVerse, an 8-colour FACSCanto, a 14-colour Becton Dickinson LSRII and a 9-colour Beckman Coulter Cyan ADP. The facility also houses an Automacs Cell separator.


Level 4 high-containment virus laboratory

RESEARCH FACILITIES

Within the complex of buildings that make up NIMR is a suite of laboratories for handling viruses with high pathogenic potential for birds, humans or other mammals. Its presence is necessitated by the work of the WHO Influenza Centre (WIC) at NIMR that involves the handling of influenza viruses from all over the world, such as the novel H1N1 virus, prior to its emergence as a full-blown pandemic virus. In addition, poorly characterised viruses are also received. Some of these viruses, notably viruses from zoonotic H5N1 infections, have considerable pathogenic potential in both birds and humans. Work with poorly characterised viruses and viruses that might, or do, have pandemic potential requires a high degree of containment to prevent the spread of influenza viruses into birds or the environment, as well as operator protection to minimise the risk of handling viruses potentially harmful to man.

The facility is built to Health and Safety Executive requirements and DEFRA regulations under the Specified Animals Pathogen Order. It was used for the growth and characterisation of samples of the pandemic H1N1 virus, sent from around the world at the early stages of its global spread, and to generate reference ferret antisera to the emerging pandemic viruses for virus antigenic analyses. It has also been used for the isolation and characterisation of human isolates of H5N1 avian influenza virus, for example from the Turkish outbreak in humans in 2006. The laboratory capacity has been extended to have two standard high containment laboratory areas and two laboratories equipped to handle infected small animals under high level containment. With the enhanced capacity, in addition to the virus surveillance and characterisation studies of the WIC, simultaneous studies of the mechanisms of disease causation by avian or other influenza viruses can be carried out.

Features of the laboratory include:

• A negative pressure air regime with HEPA filtered input and double HEPA filtered extract. • Waste treatment with heating of liquid waste and autoclave sterilisation of solid waste within the body of the laboratory. • Class III and Class I/III microbiological safety cabinets for handling samples.• Class III cabinets for handling infected small animals. • Sealable, so as to permit fumigation. • Strict codes of practice including the requirement for all workers to undergo a complete change of clothing before entering the laboratory and to shower when leaving.

In addition to the Level 4 laboratory, there are 11 Level 3 laboratories scattered among the main buildings and biological research facilities at NIMR. These laboratories allow the safe handling of a number of pathogenic organisms, permitting studies of the microbiology and immunology of Mycobacterium tuberculosis, the invasion of blood cells by the malaria parasite and the growth of the retroviruses that cause AIDS.


RESEARCH FACILITIES

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 The experienced staff can manufacture quick one-off prototypes, followed by continued development and modification to produce the desired item or apparatus. Onsite repair and maintenance of laboratory equipment is also carried out in the workshop. The varied facilities mean that a diverse range of projects can be worked on, including: • micromanipulators • microscope stage modifications • custom-made parts • temperature controlled chambers • drug infusers and nebulisers • blood flow measurement devices

Co-workers: Derek Brewer, Peter Cookson, Ray Herriott, Richard Jones

RESEARCH FACILITIES

Instruments are designed and manufactured for applications in physiology and single molecule research. Work conducted in cutting-edge science often requires new instrumentation which is not available commercially. Examples of this over the past year include:

• A multi-channel rate-controlled perfusion flow system for studying shear-dependent interactions between blood components and endothelial cells.

• A high brightness LED light source integrated with an optical trap microscope enabling automatic intensity control during the study of single myosin molecules.

• A malarial parasite counting device that enables determination of parasitemia.

Utilising current technologies, the resource in collaboration with researchers enables comprehensive system development from initial specification, through proof of concept to the final application.

Electronic instrument prototyping and support Martyn Stopps


Prototype counter assisting determination of parasitemia in blood samples.

A multi-channel perfusion flow system.


PhotoGraphics Joe Brock

RESEARCH FACILITIES

Composite image showing 3D modelling, illustration and embedded movies within a single animation describing the role of myosin in

merozoite infection of red blood cells.

Typical illustration produced by PhotoGraphics visualising scientific and biological processes.

The PhotoGraphics service provides a professional design, illustration and imaging facility to visualise the innovative research carried out at NIMR. Our fully trained team provides a wide range of specialist skills using state-of-the-art equipment, software and techniques. These include digital manipulation, illustration, Flash™ animation, film making and editing, 3D modelling, scanning and photography as well as providing a printing, copying and binding service. This facility is open to all researchers wishing to relate their science visually through publication, digital presentation and posters. Novel methods developed by us for presenting science using interactive animations provide more dynamic in-depth explanations and we regularly receive requests for copies by researchers and companies world-wide who recognise this media as a powerful informative tool. The PhotoGraphic team design and publish NIMR publications such as this report, the Mill Hill Essays and other in-house publications. We also present training courses throughout the year for researchers who wish to use applications such as Adobe Photoshop™ and Microscoft Powerpoint™ to professional level. Photographics also maintain the seminar and meeting room facilities and provide the audio-visual support to the Institute, ensuring smooth running for both in-house and visiting speakers.

Co-workers: Jamie Brock, Neal Cramphorn, Hayley Wood, Wai Han Yau


Computing and Telecommunications provides secure access to the Internet, via a firewall, over a 100Mb JANET (Joint Academic Network) connection. We provide a range of services including email with web-based access, secure remote access, web servers for intranet and public websites, IT security, including anti-virus and spam filters, data encryption, FTP server/web-based export server, database and related services, support services for both Windows and Macintosh computers and other mobile devices. We also provide and maintain the internal telephone system and are currently testing a new secure wireless networking solution for both staff and visitors.

We provide a Cisco Webex system for live collaboration and web conferencing. We are currently developing a custom file-sharing system which is secure and user-friendly, and will facilitate internal and external collaboration. We recently expanded our data storage/archival system from 100TB to 180TB, added replication and are adopting a strategy of providing backup to all desktop, laptop and scientific facilities users with a server-based system which is now in the testing phase.

Computing and Telecommunications Clive Lunny

RESEARCH FACILITIES

Co-workers: Aomar Ayad, Jose Ayala, Darsheni Fatania, John Green, Debra Harper, Ben Kesel, Kevin McInerney, Graeme Millar, Harsha Sheth, Nathan Smith


Library Frank Norman

RESEARCH FACILITIES

The Library serves the information needs of scientific staff and students at NIMR. It provides access to more than 2000 electronic journals and to literature searching tools like Scopus and Metalib. We have extensive printed journal backfiles and a printed book collection as well as easy access to a document delivery service. Library staff provide individualised help for scientists in the lab or at their desktop. Expert assistance with information searching is available, including help with systematic literature reviews, difficult-to-answer questions and search alerts for easier literature scanning. We offer assistance with citation manager software (e.g. Endnote, Reference Manager, Mendeley, Pages, Zotero) and advice on Open Access compliance. A daily news service keeps staff informed of current science policy developments.

Casual reading space and dedicated study desks for write-up are available plus some computer desks with PCs and Macs. There is a WiFi network in the Library. The Library records the Institute’s major research outputs and achievements, ensuring that these are listed on the NIMR website and in the Annual Report. It also maintains the Institute’s historical archives and repository of publications.

The students study suite. Casual seating area with new book and journal displays.

Co-workers: Patti Biggs, Lynsey Eames, Nicola Weston


The Web Team is responsible for the day-to-day management of the NIMR website, intranet and online presence, and longer-term strategic projects such as the recent redevelopment and implementation of a content management system on the external website. Our aims are to ensure that the external website reflects the excellence of science at NIMR, meets user and organisational needs, and promotes the research and outreach work at NIMR. Internally, we aim to provide easy access to information and resources through online systems which support effective and efficient working.

We produce microsites for NIMR-sponsored initiatives such as conference websites; develop innovative solutions such as our online weekly newsletter for staff; and are always willing

to provide advice and expertise. The Web Team provides not only technical infrastructure, but also training and support (including tools for easy updating). We develop cross-platform, user-friendly, visually appealing websites and applications, and ensure compliance with relevant standards and legislation. We work with staff throughout NIMR, and use one-to-one meetings, focus groups, surveys, feedback forms, instant polls, and user testing and evaluation to help inform future developments. We also have an open door policy, in common with others at NIMR.

Web Team Christina McGuire

RESEARCH FACILITIES

Online weekly newsletter for staff Customisable intranet homepage


Occupational Health Occupational Health (OH) is concerned with the effects of health on work and of work on health with consideration for the working environment. Occupational services include health protection, health promotion and lost time management. Our professional service observes Health and Safety regulations and helps to support the overall needs of NIMR. We offer impartial advice to all employees on health matters related to the working environment. The OH team also provide specific health surveillance to staff members exposed to hazards.

General services

RESEARCH FACILITIES

Safety and SecurityThe Safety section provides a safe working environment at the Institute. All staff are provided with safety training and advice. Radiation monitoring and dosimetry is undertaken as well as chemical and biological waste disposal. There are also specialised laboratories available e.g. for radioactive work, plus a cell irradiator.

Human ResourcesThe Human Resources section works in partnership across the Institute to support its objectives and a diverse group of scientific and support staff. A team of specialists work to embed shared principles and a culture that support science, and provide expert advice on employment matters such as recruitment, development, performance, reward and recognition.

Finance and PurchasingThe Finance team provides advice and support to staff in the costing of grant applications, full economic costing, expenses and sales invoices. They are also responsible for the management, reporting and forecasting of the Institute’s budgets. The Purchasing team assists staff with all aspects of procurement including tendering for capital equipment, service contracts, and consumables. They also liaise closely with the RCUK Shared Service Centre to ensure that we get best value for money in pricing.


Henry Dale, OM, FRS (1875-1968)Henry Dale worked at NIMR from its inception in 1914 and was the first Director, serving from 1928-1942. His research on the functions of nerve cells led to the discovery of acetylcholine as a neurotransmitter and to the chemical basis of neurotransmission. For this work he received the Nobel Prize for Physiology or Medicine in 1936.

Five scientists from NIMR have been awarded Nobel Prizes for their scientific research.

Nobel Laureates

Henry Dale

Archer Martin

Rodney Porter

Peter Medawar

John Cornforth

Archer Martin, CBE, FRS (1910-2002)Archer Martin worked at NIMR from 1948-1956. Before arriving at NIMR he worked on amino acid analysis and the development of partition chromatography for the purification of biological molecules. He received the Nobel Prize for Chemistry for this work in 1952. At NIMR he developed the method of gas-liquid chromatography, which has had far-reaching impact on the study of biochemistry.

Rodney Porter, FRS (1917-1985)Rodney Porter worked at NIMR from 1949-1960. His research on the many specificities of antibodies led to the separation of antigen binding (Fab) and crystalline (Fc) proteolytic fragments of antibodies, an essential step for the determination of their complete sequences of amino acids. For this work he received the 1972 Nobel Prize in Physiology or Medicine.

John Cornforth, FRS (1914-)John Cornforth worked at NIMR from 1946-1962. He completed the first total synthesis of the non-aromatic steroids and in collaboration with George Popjak he identified the chemical structure of cholesterol. He received the Nobel Prize for Chemistry in 1975.

Peter Medawar, OBE, OM, FRS (1915-1987)Peter Medawar was Director of NIMR from 1962-1971. He was one of the foremost biologists of his generation, and also a hugely gifted populariser of science. Earlier in his career he studied how the immune system rejects foreign tissue grafts and discovered the phenomenon of immune tolerance. For this work he was awarded the Nobel Prize for Physiology or Medicine in 1960.

Brigitte Askonas, FRS (1923-)Brigitte (Ita) Askonas worked at NIMR from 1952-1989. She was Head of the Division of Immunology from 1976. She made seminal contributions to our understanding of the molecular basis of lymphocyte responses to proteins, and especially to infectious agents.

Philip D’Arcy Hart, CBE (1900-2006)Philip D’Arcy Hart joined the MRC in 1937, working on dust diseases in coal miners, then moved to the MRC Tuberculosis Research Unit until he retired in 1965. In 1948 he ran the first controlled clinical trial, to show the efficacy of streptomycin against tuberculosis. A later trial led to the introduction of BCG vaccination in the UK. After he retired he moved to NIMR with an MRC research grant, working until 2002.

Robert Edwards, CBE, FRS (1925-) Robert Edwards worked at NIMR from 1958-1962. During this time his interests moved from pure science to biomedicine, and a desire to do something about human infertility. His studies on induced ovulation and superovulation in mice presaged his later work at Cambridge, with Patrick Steptoe, in which they applied such approaches to humans, thus bringing about the revolution in in vitro fertilisation. For this later work he received the Nobel Prize for Physiology or Medicine in 2010.

Charles Harington, FRS (1897-1972)Charles Harington was Director of NIMR from 1942-1962, and oversaw the Institute’s move from Hampstead to Mill Hill. He was an outstanding biochemist who contributed to our understanding of the thyroid gland and of the hormones it produces, particularly thyroxine. Another achievement was the synthesis of glutathione, and he undertook pioneering work in immunochemistry. As Director he strongly encouraged cooperation between scientists working in different departments.

James Lovelock, CBE, FRS (1919-)James Lovelock worked at NIMR from 1941-1961. His most important invention while at the Institute was the electron capture detector, which was able to detect minute amounts of chemicals. Originally designed for analytical purposes it was also able to detect industrial pollutants in the atmosphere, alerting the world to the dangers of unchecked pollution. After leaving NIMR he became an independent scientist and developed the Gaia Hypothesis.

Five famous alumni

Brigitte Askonas

Philip D’Arcy Hart

Robert Edwards

Charles Harington

James Lovelock


Charles Bangham Imperial College LondonYves-Alain Barde University of Basel, SwitzerlandDavid Barondeau Texas A&M University, USAZhijian ‘James’ Chen University of Texas Southwestern Medical Center, USAPeter Cherepanov Imperial College LondonClaude Desplan New York University, USAChen Dong University of Texas MD Anderson Cancer Center, USAWitold Filipowicz Friedrich Miescher Institute for Biomedical Research, SwitzerlandRichard Flavell Yale University, USAPaul Freemont Imperial College LondonSiamon Gordon University of OxfordJohn Gurdon Gurdon InstituteThierry Heidmann Institut Gustave Roussy, FranceBrigid Hogan Duke University Medical Center, USA Michael K Rosen University of Texas Southwestern Medical Center, USASam Li University of California San Francisco, USAMike Malim King’s College LondonPascal Meier Institute of Cancer ResearchChristien Merrifield MRC Laboratory of Molecular Biology, CambridgeKen Murphy Washington University School of Medicine, USAOnora O’Neill Cambridge University and House of LordsMassimo Palmarini MRC Centre for Virus Research, GlasgowMichele Parrinello ETH Zurich, SwitzerlandSusan Pierce National Institutes of Health, USAOrly Reiner Weizmann Institute of Science, IsraelHelen Saibil Birkbeck, University of LondonYoshiki Sasai RIKEN Center for Developmental Biology, JapanDavid Tarlinton Walter and Eliza Hall Institute, AustraliaKenneth Zaret University of Pennsylvania School of Medicine, USA

Scientific seminars

Nearly 200 seminars and lectures by visiting speakers are given at the Institute each year. Each major area of science has its own seminar series and the Mill Hill Lecture series is an annual series of about ten lectures given by eminent scientists from around the world. A selection of highlights from the past year is shown.



Prizes and awards

Tim Bliss Royal Society Croonian Lecturer 2012Steve Gamblin Feldberg Prize 2012Steve Gamblin Fellow of the Royal SocietyAlex Gould Hooke Medal 2011Robin Holliday Royal Society Royal MedalRobin Lovell-Badge Fellow of the Society of Biology

Editorial boards

Siew-Lan Ang International Journal of Developmental BiologyMike Blackman PLoS PathogensJames Briscoe Development Developmental Biology Neural DevelopmentJohn Doorbar Journal of General VirologyPaul Driscoll Journal of Structural and Functional Genomics PLoS ONEGreg Elgar Genome Biology and Evolution Briefings in Functional Genomics Richard Goldstein BMC Evolutionary Biology Journal of Chemical Biology Protein Engineering, Design and Selection Francois Guillemot Genes & Development Neural Development BMC Developmental BiologyTony Holder Eukaryotic Cell Molecular and Biochemical ParasitologyGeorge Kassiotis PLoS ONE Jean Langhorne PLoS Pathogens International Journal of ParasitologySteve Ley Cell ResearchMalcolm Logan Development Developmental Biology Developmental DynamicsRobin Lovell-Badge Biology of Sex Differences Organogenesis Sexual DevelopmentJohn McCauley Virus ResearchElke Ober Developmental BiologyAnne O’Garra Journal of Experimental MedicineAnnalisa Pastore Open Biology Prion Journal of Biological Chemistry PloS ONEAndres Ramos Open Magnetic Resonance Journal Encyclopaedia of Biophysics Katrin Rittinger Biochemical JournalBen Seddon Frontiers in Immunological Memory

Staff honours 2011

Staff honours 2011 (cont.)


Scientific Committees and Scientific Advistory Boards (SAB)

Mike Blackman Microbiology, Immunology and Infection Grant Evaluation Panel, Agence Nationale de la Recherche, FranceJames Briscoe Company of Biologists Wellcome Trust Expert Review GroupLuiz Pedro de Carvalho TB Community Annotation Project Steering Committee (NIH/NIAID)Paul Driscoll Henry Wellcome NMR Laboratories, Birmingham University SABAlex Gould Wellcome Trust Investigator Awards Selection Panel UK Metabolic Discussion GroupFrancois Guillemot ERC Advanced Investigator Grants Panel Peter and Patricia Gruber International Research Award in Neuroscience, selection committeeTony Holder Wellcome Trust Expert Review GroupEd Hulme Heptares Therapeutics SABJean Langhorne European Virtual Institute for Malaria Research Hartmut Hoffmann-Berling International Graduate School of Molecular & Cellular Biology, Heidelberg, Germany SAB Institut fuer Molekulare Infektionsbiologie, Wuerzburg, Germany SAB Scientific Subject Matter Expert attached to Laboratory of Malaria Immunology and Vaccines, NIAID/NIH, USA Wellcome Trust Expert Review GroupSteve Ley MRC Infections & Immunity Board

Jim Smith Open Biology Biology Image LibraryGitta Stockinger Frontiers in ImmunologyJonathan Stoye Journal of VirologyJames Turner Biology of Reproduction Chromosome ResearchVictor Tybulewicz Immunology Frontiers in B cell Biology Frontiers in T cell BiologyJean-Paul Vincent Developmental Biology Science SignallingRobert Wilkinson International Journal of Tuberculosis and Lung Disease Tuberculosis PLoS OneDavid Wilkinson Mechanisms of Development (Editor in Chief) Gene Expression Patterns (Editor in Chief) Developmental Biology Faculty of 1000 BMC Developmental BiologyMark Wilson Journal Clinical and Developmental Immunology Journal of Tropical DiseasesDouglas Young TuberculosisLyle Zimmerman genesis: The Journal of Genetics and Development


Robin Lovell-Badge BBVA Foundation, Frontiers of Knowledge Award, Jury Feldberg Prize Committee Human Fertility and Embryo Authority, Scientific and Clinical Advances Advisory Committee Royal Society, GSK Prize Committee Royal Society, Member of Council Understanding Animal Research, Member of CouncilJohn McCauley International Committee on Taxonomy of Viruses, Orthomyxovirus study group, Chair Royal Society & Academy of Medical Sciences, Committee on pandemic influenzaJustin Molloy Wellcome Trust Expert Review GroupJohn Offer Royal Society of Chemistry, Proteins GroupAnne O’Garra Keystone Symposia SAB Baylor Institute for Immunology, Dallas, USA, SAB Institute for Biomedical Sciences, Bellinzona, Switzerland, SAB Institute for Molecular Medicine, Lisbon, SAB World Premier International Research Center, Osaka University, Japan, SAB MRC/ABPI, UK Inflammation and Immunology Initiative - Steering GroupAnnalisa Pastore Biotechnology Institute, Helsinki, Finland, SABKatrin Rittinger Deutsche Forschungs Gemeinschaft Steve Smerdon TwistDX, SAB MRC Technology Governing Body MRC Molecular & Cellular Medicine Board Diamond Light Source Peer Review Panel Oxford Protein Production Facility UK, Management CommitteeJim Smith Wellcome Trust/Royal Society Henry Dale Fellowship Committee, Chair TwistDX, SAB Wellcome Trust Investigator Awards Selection Panel Indian Institute of Science Education and Research, SABGitta Stockinger Academy of Finland Grants Panel ERC Young Investigator Grants Panel Multiple Sclerosis SocietyVictor Tybulewicz CRUK Biological Sciences CommitteeJean-Paul Vincent Atip Grant Panel, Chair British Society for Cell Biology, Committee Member Academy of Medical Sciences, Chair Sectional Committee Wellcome Trust and NIH PhD Programme interview panelRobert Wilkinson Africa Centre for Health and Population studies, Mtubatuba, Kwa Zulu Natal, South Africa South African Centre for Epidemiological Modeling and Analysis, Cape Town, South Africa TB-PANNET European UnionDavid Wilkinson EMBO Long Term Fellowships committee Welbio Scientific Council Gene Expression Database Advisory Board EMAGE Advisory Board

PhD theses awarded in 2011

Name Division Title of thesis

Alison Gaudion Mycobacterial Research The role of the ECF sigma factor SigG in Mycobacterium tuberculosisLauren Gregory Developmental Neurobiology Eph-ephrin signalling in cell sorting and directional migrationDafni Hajieconomou Molecular Neurobiology Development of a genetic multicolor cell labeling approach for neural circuit analysis in DrosophilaSamantha Hiew Virology Examining the biological consequences of DNA damage caused by irradiated 3T3-J2 fibroblast feeder cells and HPV16Holly Ironfield Developmental Biology Genetic studies of inner ear development in Xenopus tropicalisKatarzyna Koltowska Developmental Biology Molecular and morphological analysis of organ growth and differentiation during zebrafish embryogenesisJennifer Lawton Parasitology Investigation of the cir gene family in Plasmodium chabaudiRebecca Leyland Molecular Immunology Lineage relationship analysis of lymphoid progenitor subsets in the bone marrow of naïve mice and during inflammationGareth Maglennon Virology Study of latent papillomavirus infection in an animal modelLietta Nicolaides Virology Interactions of the human papillomavirus E6 protein and their role in the persistence of viral episomesRebecca Pike Immunoregulation The role of CD4 T cells in Friend virus infectionMasooma Rasheed Molecular Structure NMR characterisation of apo- and ligand-bound states of bacterial DDAHAna Ribeiro Developmental Neurobiology Shh signaling and the dynamic pattern of the vertebrate neural tubeRobert Rowlands Molecular Neuroendocrinology The effects of statin treatment on the synthesis, processing, storage and exocytosis of von Willebrand factor in cultured human endothelial cellsValentina Sasselli Molecular Neurobiology The potential role of the Rac signalling and planar vell polarity pathway in writing of the enteric nervous systemNatalie Silmon de Monerri Parasitology Investigation into the role of PfSUB1 and two perforin-like proteins in Plasmodium falciparumCharles Sinclair Immune Cell Biology The role of Zap70 in thymocyte developmentVictoria Spivey Mycobacterial Research Functional analysis of the serine-threonine protein kinase PknF and its substrate, the ABC transporter Rv1747, in Mycobacterium tuberculosisFatima Sulaiman Developmental Biology The roles of Tbx5 and Tbx4 in the symmetrical initiation of the left and right limbSebastian Wasilewski Physical Biochemistry Computation of protein and cellular architecture from cryomicroscopy imageChristoph Wilhelm Molecular Immunology Origin and destination of Interleukin-9 producing cells



Siew-Lan Ang Kate Bishop Mike Blackman James Briscoe Paul Burgoyne Tom Carter Rita Cha Luiz Pedro de Carvalho John Doorbar Paul Driscoll Greg Elgar Delmiro Fernandez-Reyes Eva Frickel Steve Gamblin Mike Gilchrist Richard Goldstein Alex Gould Francois Guillemot Tony Holder Ed Hulme George Kassiotis Jean Langhorne Steve Ley Malcolm Logan Robin Lovell-Badge John McCauley Troy Margrie Tim Mohun Justin Molloy

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A – Z list of group leaders

Elke Ober John Offer Anne O’Garra Vassilis Pachnis Annalisa Pastore Andres Ramos Katrin Rittinger Peter Rosenthal Iris Salecker Benedict Seddon Steve Smerdon Jim Smith Gitta Stockinger Jonathan Stoye Ian Taylor Willie Taylor Peter Thorpe Pavel Tolar James Turner Victor Tybulewicz Jean-Paul Vincent Andreas Wack Martin Webb David Wilkinson Robert Wilkinson Mark Wilson Douglas Young Lyle Zimmerman

For current list visit the NIMR website: http://www.nimr.mrc.ac.uk/research/a-z

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Research themes

BiochemistryLuiz Pedro de CarvalhoEva FrickelJustin MolloyJohn OfferMartin Webb

Biophysics Tom CarterEd HulmeJustin MolloyPeter RosenthalIan TaylorMartin Webb

Cancer Rita ChaSteve GamblinAndres RamosSteve SmerdonJean-Paul VincentMartin Webb

Cell biology Kate BishopMike BlackmanTom CarterRita ChaEva FrickelTony HolderSteve LeyTim MohunJustin MolloyElke OberKatrin RittingerBenedict SeddonJim Smith

Jonathan StoyePeter ThorpePavel TolarVictor TybulewiczJean-Paul VincentDavid Wilkinson

Chromosome biology Rita ChaPeter ThorpeJames Turner

Developmental biology Siew-Lan AngJames BriscoePaul BurgoyneGreg ElgarMike GilchristAlex GouldFrançois GuillemotMalcolm LoganRobin Lovell-BadgeTim MohunElke OberVassilis PachnisAndres RamosIris SaleckerJim SmithJean-Paul VincentDavid WilkinsonLyle Zimmerman

Evolutionary biology Paul DriscollRichard GoldsteinMalcolm LoganRobin Lovell-Badge

Genetics and genomics Siew-Lan AngPaul BurgoyneRita ChaMike GilchristFrançois GuillemotMalcolm LoganRobin Lovell-BadgeTim MohunElke OberIris SaleckerJim SmithPeter ThorpeJames TurnerVictor TybulewiczJean-Paul VincentRobert WilkinsonMark WilsonLyle Zimmerman

Immunity John DoorbarEva FrickelGeorge KassiotisJean LanghorneSteve LeyAnne O’GarraAndres RamosKatrin RittingerBenedict SeddonGitta StockingerPavel TolarVictor TybulewiczAndreas WackRobert WilkinsonMark WilsonDouglas Young


Infectious disease Kate BishopMike BlackmanLuiz Pedro de CarvalhoJohn DoorbarDelmiro Fernandez-ReyesEva FrickelSteve GamblinRichard GoldsteinTony HolderGeorge KassiotisJean LanghorneJohn McCauleyAnne O’GarraPeter RosenthalSteve SmerdonGitta StockingerJonathan StoyeIan TaylorPavel TolarAndreas WackRobert WilkinsonMark WilsonDouglas Young

Mathematical biology Mike GilchristRichard GoldsteinWillie Taylor

Neurosciences Siew-Lan AngJames BriscoeAlex GouldFrançois GuillemotEd HulmeTroy Margrie

Vassilis PachnisAnnalisa PastoreIris SaleckerDavid Wilkinson

Physiology and metabolism Siew-Lan AngTom CarterLuiz Pedro de CarvalhoPaul DriscollSteve GamblinAlex GouldTroy MargrieSteve SmerdonGitta StockingerMark Wilson

Stem cell biology Alex GouldFrançois GuillemotRobin Lovell-BadgeVassilis PachnisPeter ThorpeJames TurnerDavid Wilkinson

Structural biology Mike BlackmanPaul DriscollSteve GamblinEd HulmeAnnalisa PastoreAndres RamosKatrin RittingerSteve SmerdonJonathan StoyeIan Taylor

Willie TaylorMartin Webb

Systems biology James BriscoeLuiz Pedro de CarvalhoGreg ElgarDelmiro Fernandez-ReyesMike GilchristMalcolm LoganAnnalisa PastoreDouglas Young

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Current funding sources

• A* Singapore• Academy of Medical Sciences• Alzheimer Research Trust• Arthritis Research UK• Ataxia UK • Biotechnology and Biological Sciences Research Council• British Heart Foundation• Dana Foundation Grant• Diabetes UK• Discovery Foundation (South Africa)• European Molecular Biology Organization• Engineering and Physical Sciences Research Council• European Research Council• European Union, including Marie Curie Fellowships• Federation of European Microbiological Societies• Fondation Leducq• Health Protection Agency• HIV Research Trust• International Federation of Pharmaceutical Manufacturers Association• Imperial College London• Lady TATA memorial fund• Leverhulme Trust• Marshall Foundation• Medical Research Council• Medical Research Council Technology• National Research Foundation of South Africa• National Institutes of Health, USA• Parkinsons UK• Queen Mary University of London• Royal Society• Sanofi Pasteur MSD• Swiss National Science Fund • The German National Academic Foundation • University College London• Wellcome Trust

The Medical Research Council (MRC) is the principal source of research funding. The budget - currently £42m p.a.- is set every five years following an Institute-wide review of resources. This review takes place after the five-yearly peer review (conducted by MRC Research Boards) of the programmes of the individual Divisions.

The Institute also attracts funding support from a wide range of different agencies, including medical research charities, international sources, particularly the EU, and from industrial and commercial companies:

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Adler G, Steeg C, Pfeffer K, Murphy TL, Murphy KM, Langhorne J and Jacobs T (2011)B and T lymphocyte attenuator restricts the protective immune response against experimental malaria.Journal of Immunology 187:5310-9

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Arnvig KB, Comas I, Thomson NR, Houghton J, Boshoff HI, Croucher NJ, Rose G, Perkins TT, Parkhill J, Dougan G and Young DB (2011)Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis.PLoS Pathogens 7:e1002342

Bagheri-Fam S, Sreenivasan R, Bernard P, Knower KC, Sekido R, Lovell-Badge R, Just W and Harley VR (2011)Sox9 gene regulation and the loss of the XY/XX sex-determining mechanism in the mole vole Ellobius lutescens.Chromosome Research Epub ahead of print

Bailey JL, O’Connor V, Hannah M, Hewlett L, Biggs TE, Sundstrom LE, Findlay MW and Chad JE (2011)In vitro CNS tissue analogues formed by self-organisation of reaggregated post-natal brain tissue.Journal of Neurochemistry 117:1020-32

Baillie GJ, Galiano M, Agapow P-M, et al. (2011)Evolutionary dynamics of local pandemic H1N1/2009 influenza lineages revealed by whole genome analysis.Journal of Virology 86:11-8

Bangs F, Antonio N, Thongnuek P, Welten M, Davey MG, Briscoe J and Tickle C (2011)Generation of mice with functional inactivation of talpid3, a gene first identified in chicken.Development 138:3261-72

Banks GT, Haas MA, Line S, et al. (2011)Behavioral and other phenotypes in a cytoplasmic dynein light intermediate chain 1 mutant mouse.Journal of Neuroscience 31:5483-94

Bernardo AS, Faial T, Gardner L, Niakan KK, Ortmann D, Senner CE, Callery EM, Trotter MW, Hemberger M, Smith JC, Bardwell L, Moffett A and Pedersen RA (2011)BRACHYURY and CDX2 mediate BMP-induced differentiation of human and mouse pluripotent stem cells into embryonic and extraembryonic lineages.Cell Stem Cell 9:144-55

Bi Y, Zeng N, Chanudet E, Huang Y, Hamoudi RA, Liu H, Dong G, Watkins AJ, Ley SC, Zhou L, Chen R, Zhu X and Du MQ (2011)A20 inactivation in ocular adnexal MALT lymphoma.Haematologica Epub ahead of print

Bickham DC, West TG, Webb MR, Woledge RC, Curtin NA and Ferenczi MA (2011)Millisecond-scale biochemical response to change in strain.Biophysical Journal 101:2445-54

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Mavromatakis YE, Lin W, Metzakopian E, Ferri ALM, Yan CH, Sasaki H, Whisett J and Ang S-L (2011)Foxa1 and Foxa2 positively and negatively regulate Shh signalling to specify ventral midbrain progenitor identity.Mechanisms of Development 128:90-103

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McArthur S, Robinson IC and Gillies GE (2011)Novel ontogenetic patterns of sexual differentiation in arcuate nucleus GHRH neurons revealed in GHRH-enhanced green fluorescent protein transgenic mice.Endocrinology 152:607-17

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Menzel U, Kosteas T, Tolaini M, Killeen N, Roderick K and Kioussis D (2011)Modulation of the murine CD8 gene complex following the targeted integration of human CD2-locus control region sequences.Journal of Immunology 187:3712-20

Mohun TJ and Weninger WJ (2011)Imaging heart development using high-resolution episcopic microscopy.Current Opinion in Genetics & Development 21:573-8

Moody P, Smith MEB, Ryan CP, Chudasama V, Baker JR, Molloy J and Caddick S (2011)Bromomaleimide-linked bioconjugates are cleavable in mammalian cells.Chembiochem : a European journal of chemical biology 13:39-41

Moss DK, Remarque EJ, Faber BW, Cavanagh DR, Arnot DE, Thomas AW and Holder AA (2011)Plasmodium falciparum merozoite surface protein (MSP) 119-specific antibodies that interfere with parasite growth in vitro can inhibit MSP1 processing, merozoite invasion and intracellular parasite development.Infection and Immunity Epub ahead of print

Moules V, Terrier O, Yver M, et al. (2011)Importance of viral genomic composition in modulating glycoprotein content on the surface of influenza virus particles.Virology 414:51-62

Nduati E, Gwela A, Karanja H, Mugyenyi C, Langhorne J, Marsh K and Urban BC (2011)The plasma concentration of the B cell activating factor is increased in children with acute malaria.Journal of Infectious Diseases 204:962-70

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Ohkura S, Goldstone DC, Yap MW, Holden-Dye K, Taylor IA and Stoye JP (2011)Novel escape mutants suggest an extensive TRIM5α binding site spanning the entire outer surface of the murine leukemia virus capsid protein.PLoS Pathogens 7:e1002011

Okoye IS and Wilson MS (2011)CD4+ T helper 2 cells - microbial triggers, differentiation requirements and effector functions.Immunology 134:368-77


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Oni T, Burke R, Tsekela R, Bangani N, Seldon R, Gideon HP, Wood K, Wilkinson KA, Ottenhoff THM and Wilkinson RJ (2011)High prevalence of subclinical tuberculosis in HIV-1-infected persons without advanced immunodeficiency: implications for TB screening.Thorax 66:669-73

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Schaeffer M, Hodson DJ, Meunier A-C, Lafont C, Birkenstock J, Carmignac D, Murray JF, Gavois E, Robinson IC, Le Tissier P and Mollard P (2011)Influence of estrogens on GH-cell network dynamics in females: a live in Situ imaging approach.Endocrinology 152:4789-99

Seubert A, Calabro S, Santini L, Galli B, Genovese A, Valentini S, Aprea S, Colaprico A, D’Oro U, Giuliani MM, Pallaoro M, Pizza M, O’Hagan DT, Wack A, Rappuoli R and De Gregorio E (2011)Adjuvanticity of the oil-in-water emulsion MF59 is independent of Nlrp3 inflammasome but requires the adaptor protein MyD88.Proceedings of the National Academy of Sciences of the United States of America 108:11169-74

Sheppard O, Plattner F, Rubin A, Slender A, Linehan JM, Brandner S, Tybulewicz VLJ, Fisher EMC and Wiseman FK (2011)Altered regulation of tau phosphorylation in a mouse model of down syndrome aging.Neurobiology of Aging Epub ahead of print

Shi J, McIntosh RS, Adame-Gallegos J, Dehal PK, van Egmond M, van de Winkel J, Draper SJ, Forbes EK, Corran PH, Holder AA, Woof JM and Pleass RJ (2011)The generation and evaluation of recombinant human IgA specific for Plasmodium falciparum merozoite surface protein 1-19 (PfMSP119).BMC Biotechnology 11:1-8

Shigehara K, Sasagawa T, Doorbar J, Kawaguchi S, Kobori Y, Nakashima T, Shimamura M, Maeda Y, Miyagi T, Kitagawa Y, Kadono Y, Konaka H, Mizokami A, Koh E and Namiki M (2011)Etiological role of human papillomavirus infection for inverted papilloma of the bladder.Journal of Medical Virology 83:277-85

Silmon de Monerri NC, Flynn HR, Campos MG, Hackett F, Koussis K, Withers-Martinez C, Skehel JM and Blackman MJ (2011)Global identification of multiple substrates for Plasmodium falciparum SUB1, an essential malarial processing protease.Infection and Immunity 79:1086-97

Silva A, Laranjeira ABA, Martins LR, Cardoso BA, Demengeot J, Yunes JA, Seddon B and Barata JT (2011)IL-7 contributes to the progression of human T-cell acute lymphoblastic leukemias.Cancer Research 71:4780-9

Simeoni I, Gilchrist MJ, Garrett N, Armisen J and Gurdon JB (2011)Widespread transcription in an amphibian oocyte relates to its reprogramming activity on transplanted somatic nuclei.Stem cells and development Epub ahead of print

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Singleton KL, Gosh M, Dandekar RD, Au-Yeung BB, Ksionda O, Tybulewicz VLJ, Altman A, Fowell DJ and Wülfing C (2011)Itk controls the spatiotemporal organization of T cell activation.Science Signaling 4:ra66


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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



MRC NIMR location map

MRC National Institute for Medical ResearchThe Ridgeway

Mill HillLondon NW7 1AA

Tel +44 (0)20 8959 3666Fax +44 (0)20 8816 2041

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 (A406) are within easy reach of NIMR. Onsite parking is available at NIMR.

N

Hendon

A1 North to M25, Heathrow and Stansted Airports

Mill Hill Broadway ThamesLink to Central London via King’s Cross

Northern Line to Central London

Highwood Hil l The Ridgeway The Ridgeway Bitta cy Hill

Dollis Road

H o l d er s

Hi l

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oa

d

Daws La n e

Ham

mer

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ne

A5000

A598

Hale Lane

Marsh Lane

A5109

Watford Way Barnet Bypass W

atford Way

Ba

rn

et W

ay

A5100

A1

A1

A41 to Central London

Mill Hill East

FinchleyCentral

MRC National Institute for Medical

Research

M1J2

Mill Hill Broadway

NIMR

London

A1M1

M25M25

M25


2011

/201

2 A

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l Rep

ort

and

Pros

pect

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Nat

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MRC National Institute for Medical Research Science for health

2011/2012 Annual Report and Prospectus

Documents

MRC National Institute for Medical Research · PDF fileMRC National Institute for Medical Research 5 The Royal Society also recognised two of our scientific alumni: Tim Bliss has been