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Appendix E

Speaker Biographies

Yasmine Belkaid, Ph.D., obtained her Ph.D. in 1996 from the Pasteur Institute in France on innate responses to Leishmania infection. Following a postdoctoral fellowship at the National Institute of Allergy and Infectious Diseases (NIAID) on immune regulation during Leishmania infection, she joined the Children’s Hospital Research Foundation in Cincinnati as an assistant professor in 2002. In 2005, she joined the Laboratory of Parasitic Diseases as a tenure-track investigator and was appointed as a senior investigator in 2008. Since 2008, she has worked as an adjunct professor at the University of Pennsylvania. Her work focuses on immune regulation at sites colonized by commensals such as the gut and the skin. More particularly her work has demonstrated that (1) regulatory T cells play a major role during infections, (2) commensals control host defense in both the skin and the gastrointestinal (GI) tract, (3) dietary factors control the induction of effector and regulatory responses in the GI tract, and (4) in order to protect tissue integrity, the GI tract is a major site of induction of T cells and dendritic cells with regular functions.

Martin J. Blaser, M.D., has served as the Frederick King Professor of Medicine and Chair of the Department of Medicine and as Professor of Microbiology at the New York University (NYU) School of Medicine since April 2000. Dr. Blaser’s research has focused on bacterial pathogenesis and ecology. He has studied the role of Campylobacter and Helicobacter species, among other organisms, in human disease. Much work since 1985 has involved the gastric bacterium H. pylori, linking colonization to inflammation and to gastric cancer. His studies identified the two (vacA and cagA) major host-interaction genes and showed differential disease risk associated with particular alleles. He developed a conceptual



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Appendix E Speaker Biographies Yasmine Belkaid, Ph.D., obtained her Ph.D. in 1996 from the Pasteur Institute in France on innate responses to Leishmania infection. Following a postdoctoral fellowship at the National Institute of Allergy and Infectious Diseases (NIAID) on immune regulation during Leishmania infection, she joined the Children’s Hospital Research Foundation in Cincinnati as an assistant professor in 2002. In 2005, she joined the Laboratory of Parasitic Diseases as a tenure-track investi­ gator and was appointed as a senior investigator in 2008. Since 2008, she has worked as an adjunct professor at the University of Pennsylvania. Her work focuses on immune regulation at sites colonized by commensals such as the gut and the skin. More particularly her work has demonstrated that (1) regulatory T cells play a major role during infections, (2) commensals control host defense in both the skin and the gastrointestinal (GI) tract, (3) dietary factors control the induction of effector and regulatory responses in the GI tract, and (4) in order to protect tissue integrity, the GI tract is a major site of induction of T cells and dendritic cells with regular functions. Martin J. Blaser, M.D., has served as the Frederick King Professor of Medicine and Chair of the Department of Medicine and as Professor of ­ icrobiology at the M New York University (NYU) School of Medicine since April 2000. Dr. Blaser’s research has focused on bacterial pathogenesis and ecology. He has studied the role of Campylobacter and Helicobacter species, among other organisms, in ­ uman disease. Much work since 1985 has involved the gastric bacterium h H. pylori, linking colonization to inflammation and to gastric cancer. His studies identified the two (vacA and cagA) major host-interaction genes and showed dif- ferential disease risk associated with particular alleles. He developed a conceptual 513

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514 MICROBIAL ECOLOGY IN STATES OF HEALTH AND DISEASE framework involving unique dynamic equilibria between bacterial populations and colonized hosts, which has become a general model of persistence for coadapted microbes. His work identified protective roles of H. pylori against e ­sophageal adenocarcinoma, and allergic disorders, including asthma. These led to studies of the composition and function of the human microbiome, with a ­ ajor focus now on human microbiome changes due to social and medical m p ­ rogress and their downstream health consequences. He holds 24 U.S. patents and has authored more than 500 original articles. In 2011, he was elected to the Institute of Medicine and currently chairs the Advisory Board for Clinical Re- search at the National Institutes of Health (NIH). Richard S. Blumberg, M.D., trained in internal medicine (The New York Hos- pital, 1982), infectious diseases (Massachusetts General Hospital, 1986), and gastroenterology and hepatology (Brigham and Women’s Hospital, 1989). He is currently Senior Physician in Medicine and Gastroenterology at Brigham and Women’s Hospital (BWH) where he leads the Division of Gastro­nterology, e H ­ epatology and Endoscopy, is Professor of Medicine at Harvard Medical School and co-­ irector of the Harvard Digestive Diseases Center. In addition, D Dr. Blumberg serves on the Executive Advisory Committee of the Department of Medicine and is the incoming Chair of the Biomedical Research Institute at BWH. He has served as a member of the Immunology Sciences Study Section of NIAID, a member on the National Commission of Digestive Diseases of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), scientific con- sultant to the Human Microbiome Project (National Human Genome Research Institute), a member of the Vaccine Branch External Advisory Board (National Cancer Institute), and Chair of the External Scientific Consultants for the Intes- tinal Stem Cell Consortium Initiative (NIDDK) and is currently on the Board of Scientific Councilors (NIAID). He served as the Chair of the National Scientific Advisory Committee of the Crohn’s & Colitis of America (2002–2005) and President of the Society for Mucosal Immunology (2007–2009). Dr. Blumberg is an elected member of the American Association of Clinical Investigation and the Association of American Physicians and the recipient of a MERIT Award from NIH (2005), the William Beaumont Prize from the American Gastroenterological Association (2012), and the Distinguished Scientific Achievement Award from the Crohn’s and Colitis Foundation of America (2012). He is an NIH-funded investigator whose research program focuses on ­ ucosal immunology and was m Scientific Founder, Syntonix Pharmaceuticals (now Biogen-Hemophilia) that ­ developed long-acting therapeutic agents successful in the treatment of chronic diseases such as hemophilia A and B. Brendan Bohannan, Ph.D., is Professor of Environmental Studies and ­ iology, B and Director of the Institute of Ecology and Evolution at the University of ­ regon. His research is focused on understanding the causes and consequences O

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APPENDIX E 515 of microbial biodiversity. His recent work can be divided into three topical areas: the fundamental drivers of biodiversity and how these apply to microorganisms, the response of microbial biodiversity to environmental change (including global change), and microbial biodiversity in human-dominated environments. Professor ­ Bohannan is a founding member of the Microbial Ecology and Theory of ­ nimals A Center for Systems Biology (an NIH Center of Excellence focused on the appli­ cation of ecological theory to host–microbe systems) and the Biology and the Built Environment Center (a national center for the study of the microbial ecol- ogy of buildings). Professor Bohannan received a Ph.D. in microbiology from Michigan State University and postdoctoral training in Ecology at the University of Chicago, before joining the Stanford University faculty in 1999. He has been a member of the University of Oregon faculty since 2006. Hannah V. Carey, Ph.D., is a Professor in the Department of Comparative Biosciences at the University of Wisconsin School of Veterinary Medicine. She received her Ph.D. in zoology from the University of California, Davis, and completed postdoctoral training at the University of Nevada and the Ohio State University. Her research interests are in gastrointestinal and liver physiology, hibernation biology, and the translation of hibernation to biomedicine, including organ preservation, ischemia-reperfusion injury, and severe blood loss. Current projects focus on the symbiosis between hibernating mammals and their gut microbes. Dr. Carey’s research has been supported by the National Institutes of Health, the National Science Foundation, the U.S. Department of Agriculture, the U.S. Army Research Office, and the Defense Advanced Research Projects Agency. She is the North American editor of the Journal of Comparative Physiol- ogy B, is on the editorial board of the American Journal of Physiology: Gastro­ intestinal and Liver Physiology, and is a consulting editor for Physiology and the Journal of Applied Physiology. Dr. Carey is a past President of the American Physiological Society and past Chair of the Nutrition and Obesity Section of the American Gastroenterological Association, and he was a Program Director at the National Science Foundation from 2010 to 2011, working in the Division of Integrative Organismal Systems. Angela Douglas, Ph.D., is the Daljit S. and Elaine Sarkaria Professor of Insect Physiology at Cornell University. Her research expertise is animal–­ icrobial m symbioses, especially the nutritional and immunological interactions between beneficial microorganisms and their animal hosts. Her current research focus is ­nsect–bacterial symbioses: gut microbiota in Drosophila and obligate intra­ i cellular mutualists in plant-sap feeding insects. Dr. Douglas has a B.A. degree in z ­ oology (Oxford, 1978) and a Ph.D. in microbiology (Aberdeen, 1981), and she was a post­ octoral researcher at Oxford and East Anglia (1981–1986) before her d appointment to a Royal Society Research Fellowship (1996–2006), and subse- quently as a faculty member at University of York, with promotion to Personal

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516 MICROBIAL ECOLOGY IN STATES OF HEALTH AND DISEASE Chair in 2003. She moved to Cornell University in 2008. In addition to research publications and reviews, she has written three books, including The ­Symbiotic Habit (2010), Princeton University Press. Gérard Eberl, Ph.D., received his doctorate from the University of Lausanne in 1995 and completed postdoctoral training at the Ludwig Institute of Cancer Research in Lausanne and at the Skirball Institute at New York University. In 2005, he started the Lymphoid Tissue Development Unit at the Pasteur Institute in Paris and became Senior Investigator in 2010. In 2006, the Laboratory received a Marie Curie Excellence Grant to decipher the role of intestinal symbionts in the development of lymphoid tissues and cells. This work lead to the discovery of a new type of lymphoid cells, termed “innate lymphoid cells” or ILCs, which play a fundamental role in the intestinal homeostasis with microbes and the regula- tion of adaptive immunity. In 2010 and 2011, Dr. Eberl received awards from the Institut de France and the Fondation de France for his work on the constructive interaction between symbionts and the immune system. Paul L. Fidel, Jr., Ph.D., received his doctorate from the University of Oklahoma in 1988 in the discipline of microbiology/immunology. He then did postdoctoral work at Wayne State University School of Medicine in Detroit, Michigan, in the Department of Immunology and Microbiology. He was appointed Assistant Pro- fessor in the Department of Medicine, Division of Infectious Disease, in 1990. In 1995, Dr. Fidel went to the Louisiana State University (LSU) Health Sciences Center in New Orleans at the rank of Associate Professor of Microbiology, Immu­ nology, and Parasitology. He rose to the rank of Professor in 1999. In 2001 he was named recipient of the Carl Baldridge Endowed Chair in Oral and Cranio­acial f B ­ iology and appointed the Director of the Center of Excellence in Oral and Cranio­ facial Biology and Associate Dean for Research at the LSU School of Dentistry. He has authored nearly 150 publications and has served as Principal Investi­ ator g for upward of 20 investigator-initiated or center research grants totaling more than $33 million (predominantly NIH). Dr. Fidel’s research interests include immune defense mechanisms against oral and vaginal candidiasis. His scientific contribu- tions have included a number of paradigm changes and new hypotheses to explain host resistance and susceptibility to mucosal Candida infections. Michael Fischbach, Ph.D., is an Assistant Professor in the Department of Bio- engineering and Therapeutic Sciences at University of California, San Francisco (UCSF), and a member of the California Institute for Quantitative Biosciences (QB3). Dr. Fischbach is a recipient of the NIH Director’s New Innovator Award, a Fellowship for Science and Engineering from the David and Lucille Packard Foundation, a Medical Research Award from the W.M. Keck Foundation, and the Young Investigator Grant for Probiotics Research from the Global Probiotics Council. His laboratory uses a combination of genomics and chemistry to identify

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APPENDIX E 517 and characterize small molecules from microbes, with an emphasis on the human microbiome. Dr. Fischbach received his Ph.D. in chemistry from Harvard in 2007, where he studied the role of iron acquisition in bacterial pathogenesis and the biosynthesis of antibiotics. Before going to UCSF, he spent 2 years as an inde- pendent Fellow at Massachusetts General Hospital, coordinating a collaborative effort based at the Broad Institute to develop genomics-based approaches to the discovery of small molecules from microbes. Dr. Fischbach is a member of the scientific advisory boards of Schiff Nutrition, Second Genome, and Warp Drive Bio and a consultant for Achaogen, Agraquest, and Genentech. Larry Forney, Ph.D., has scientific expertise in the evolutionary ecology of ­ rokaryotes, and his research program focuses on studies of the human micro­ p biome, the adaptive evolution of prokaryotes, microbial community dynamics, and the biogeography of microorganisms. Although formally trained in microbial physiology, his interests have expanded over the years to encompass various other topics pertinent to understanding the development and distribution of microbial diversity on temporal and spatial scales. He has pioneered the development of molecular microbial ecology methods to understand the extent and distribu- tion of microbial diversity and to characterize within species genetic diversity and the evolution of novel microbial traits. His accomplishments in microbial evolution and ecology and scientific leadership have been recognized through various awards and by appointment as a Fellow of the American Academy of M ­ icrobiology. Dr. Forney is currently director of the Institute for Bioinformatics and Evolutionary Studies and director of an NIH-funded Center of Biomedical Research Excellence. In these roles he leads a vibrant community of scientists, mathematicians, and statisticians at the University of Idaho who conduct inter­ disciplinary research on a range of topics related to evolutionary and computa- tional biology with colleagues on campus and across the globe. Karen Guillemin, Ph.D., received her bachelor’s degree at Harvard and ­ adcliffe R Colleges and her Ph.D. from the Department of Biochemistry at Stanford Uni- versity Medical School, where she worked with Dr. Mark Krasnow studying ­ rosophila development. She stayed at Stanford University to pursue post­ D doctoral studies with Dr. Stanley Falkow in the Department of Microbiology and Immunology, where she worked on genomic approaches to characterizing bacterial–host interactions, focusing in the human pathogen, Helicobacter ­pylori. In 2001, she joined the faculty of the Institute of Molecular Biology at the Uni- versity of Oregon, where she is currently a Professor. As an independent principal investigator, she has developed a research program that uses zebrafish to inves- tigate the role of host-associated microbial communities in animal development. In 2012 she became the director of the Microbial Ecology and Theory of Animals Center for Systems Biology, a Center of Excellence for Systems Biology funded by NIH/National Institute of General Medical Sciences (NIGMS).

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518 MICROBIAL ECOLOGY IN STATES OF HEALTH AND DISEASE Josbert Keller, M.D., Ph.D., attended medical school at the University of A ­ msterdam/Academic Medical Center (AMC) and was a Ph.D. Fellow at the Department of Pathology at the AMC, performing research on gastrointestinal polyposis syndromes in collaboration with the Department of Gastroenterology at the Johns Hopkins University Hospital in Baltimore. During his GI fellowship at the AMC, he initiated the FECAL trial, comparing the efficacy of donor feces infusion with conventional antibiotic therapy for patients with longstanding re- current Clostridium difficile infection. The study was funded by The Netherlands Organisation for Health Research and Development, and the results were recently published. Since 2009, he works at the Haga Teaching Hospital (Hagaziekenhuis) in The Hague, the Netherlands. Dr. Keller is the Secretary of the Netherlands Society of Gastroenterology (NVGE). David Mills, Ph.D., is the Peter J. Shields Endowed Chair in the Departments of Viticulture & Enology and Food Science & Technology at the University of California, Davis. Dr. Mills studies lactic acid bacteria (LAB) and bifidobacteria used in food fermentations or active as probiotics. Dr. Mills is the founder of the LAB Genomics Consortium and is a founding member of the UC Davis Milk B ­ ioactives and Functional Glycobiology Programs. Dr. Mills is a past Chair of the Food Microbiology Division for the American Society for Microbiology, where he has also served as a Waksman Foundation Lecturer. Dr. Mills currently serves as an associate editor for the journal Microbiology. In 2010 Dr. Mills was awarded the Cargill Flavor Systems Award from the American Dairy Science Association. Forest Rohwer, Ph.D., is a Professor of Biology at San Diego State University (SDSU), California. He received his B.A. from the College of Idaho, with empha- ses in history, biology, and chemistry. His Ph.D. is from the SDSU/University of California, San Diego, Joint Doctoral program in molecular immunology, where he studied Interleukin-2 signal transduction. Dr. Rohwer then moved to Scripps Institution of Oceanography and developed metagenomic approaches to study marine viruses with Farooq Azam. In 2002, he started his lab at SDSU, where the main areas of study are viral metagenomics and coral reef microbiology. Dr. Rohwer is a Fellow of the American Academy for Advancement of Science and the Canadian Institute for Advanced Research. In 2008 he received the Young Investigators Award from the International Society of Microbial Ecology. Cur- rent major fields of research are the human virome and coral reef microbiology. Julie Segre, Ph.D., received her Ph.D. in 1996 from the Massachusetts Institute of Technology (MIT) in the laboratory of Dr. Eric Lander and the newly formed genome center. Dr. Segre then performed postdoctoral training with Elaine Fuchs, an expert in skin biology, at the University of Chicago. Dr. Segre joined the National Human Genome Research Institute of NIH in 2000 and was pro- moted to a Senior Investigator with tenure in 2007. Dr. Segre’s laboratory utilizes

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APPENDIX E 519 high-throughput sequencing and develops algorithms to study the microbial ­ ­ iversity of human skin in both health and disease states, with a focus on eczema d and primary immune deficiencies. Dr. Segre published the first topographical map of human skin bacterial diversity, followed recently by a study of fungal diversity. Dr. Segre’s laboratory also maintains an active interest in developing genomic tools to track hospital-acquired infections of multidrug-resistant organ- isms, including the NIH’s recent Klebsiella ­ neumoniae outbreak. Dr. Segre’s p research is based on active collaborations with the NIH Intramural Sequencing Center and the clinical departments of Infection Control, Microbiology, and Dermatology. Dr. Segre is a leader in the NIH Roadmap Human Microbiome Project, communicating with multiple media sources to promote the concept of humans as ecological landscapes. Dr. Segre is the 2013 recipient of the Service to America Medal. Gerald Tuskan, Ph.D., is Group Leader of the Plant Systems Biology Group in the Biosciences Division at Oak Ridge National Laboratory. Dr. Tuskan ­ eceived r a Ph.D. in 1984 from Texas A&M University in genetics. Dr. Tuskan led the Inter­ ational Populus Genome Consortium, which sequenced, assembled, anno­ n tated, and published the Populus genome. This paper has been cited more than 1,600 times and has been one of the top cited papers in Science during the past 5 years. Subsequent to that, and as Co-Lead of the Plant Genome Program at the Joint Genome Institute, Dr. Tuskan provided leadership in the sequenc- ­ ing and assembly of other plant genomes including Brachypodium, Eucalyptus, Physcomitrella, Salix, and Setaria. Dr. Tuskan has more than 154 publications in ­ the areas of genetics and genomics of perennial plants, including 45 publications, with nearly 800 citations that exclusively relate to U.S. Department of Energy (DOE) missions in the area of biomass production and bioenergy. In the past 10 years, Dr. Tuskan has led or co-led 14 proposals to DOE, the U.S. Department of Agriculture, and the National Science Foundation, which have resulted in more than $323 million in funding. During the past 5 years, Dr. Tuskan has had more than 25 invention disclosures, 6 of which have been moved forward to patent applications. David M. Underhill, Ph.D., is a Professor in the F. Widjaja Foundation Inflamma- tory Bowel and Immunobiology Research Institute at Cedars-Sinai Medical Center in Los Angeles. He is also the Director of the medical center’s Ph.D. Program in Biomedical Science and Translational Medicine and is on the faculty of the David Geffen School of Medicine at University of California, Los Angeles. He currently holds the Janis and William Wetsman Family Chair in Inflammatory Bowel Dis- ease Research. Dr. Underhill’s laboratory studies the cellular and molecular basis for microbial recognition by the innate immune system. He has made important contributions to defining Toll-like receptor ligands, characterizing Toll-like recep- tor signaling pathways, and in characterizing C-type lectin signaling pathways.

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520 MICROBIAL ECOLOGY IN STATES OF HEALTH AND DISEASE His laboratory has been particularly instrumental in developing an understanding of how the process of phagocytosis participates in directing inflammatory signal- ing in macrophages and dendritic cells. The laboratory has typically focused on understanding how bacterial and fungal pathogens are recognized, but it has more recently been exploring how commensal bacteria and fungi interact with the innate immune system and how this affects inflammatory diseases such as inflammatory bowel disease. Herbert W. “Skip” Virgin, M.D., Ph.D., received his A.B., M.D., Ph.D., internal medicine residency, and postdoctoral training at Harvard and the Brigham and Women’s Hospital and subsequently trained in infectious diseases. In 2006 he became Edward Mallinckrodt Professor and Head of the Department of Pathol- ogy and Immunology. He is the head of the Midwest Regional Center for Ex- cellence in Biodefense and Emerging Infectious Diseases Research. Dr. Virgin is the author of the definitive chapter on viral pathogenesis in Fields Virology and of reviews on the virome, AIDs, autophagy, and personalized medicine/­ metagenomics in Cell and Nature. He is on the Board of Reviewing Editors for Science magazine, is a member of the American Society for Clinical Investigation and the American Association of Physicians, and is a Fellow of the American Academy of Arts and Sciences and the American Academy for Microbiology. His laboratory is known for taking genetic, genomic, and structural approaches to defining mechanisms of immunity, chronic viral infection, viral virulence, and the pathogenesis of cancer, infection, and inflammatory diseases. Recent work has focused on pathogen discovery, mucosal immunity, the role of interferons and autophagy in immunity, and the importance of the virome and virome–gene interactions in normal immunity and disease susceptibility. Ramnik Xavier, Ph.D., is a clinical gastroenterologist and molecular biologist and is Chief of Gastroenterology at Massachusetts General Hospital. The overall goal of his laboratory is to understand the function of mediators and effectors involved in innate and adaptive immunity. A second major focus is to understand the function of genes associated with Crohn’s disease/ulcerative colitis and risk of autoimmunity using genomics, computational tools, and model systems. Recent findings in the laboratory have contributed to elucidating the role of autophagy in Crohn’s disease and the discovery of novel immune regulatory genes. In future studies, Dr. Xavier’s team hopes to gain insights into the cell–cell interactions and regulatory networks that define functional modules at the host cell–microbe inter- face in the intestinal mucosa. Dr. Xavier completed his clinical training in internal medicine, followed by subspecialty training in gastroenterology and hepatology, at Massachusetts General Hospital. His laboratory is located at the Center for Computational and Integrative Biology, of which he is a founding member, at Massachusetts General Hospital. Dr. Xavier is the Kurt Isselbacher Associate Professor of Medicine at Harvard Medical School, is a Senior Associate Member

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APPENDIX E 521 of the Broad Institute of Harvard and MIT, and sees patients at the Crohn’s and Colitis Center at Massachusetts General Hospital. Michael Zasloff, M.D., Ph.D., has centered his scientific interests on the ­nnate i immune systems of animals during the past 25 years. Dr. Zasloff received his M.D. and Ph.D. in the Medical Scientist training program at NYU School of Medicine. In the 1980s, Dr. Zasloff was Chief, Human Genetics Branch, National ­ Institutes of Child Health and Human Development, at NIH. In 1988 Dr. Zasloff founded Magainin Pharmaceuticals, Inc., a publicly traded biotechnology com- pany. In the same year he joined the faculty of the University of Pennsylvania School of Medicine as the Charles E.H. Upham Professor of Pediatrics and G ­ enetics and assumed the position of Director of the Division of Human Genetics of the Children’s Hospital of Philadelphia. In July 1992, Dr. Zasloff left Penn and ­ ­ joined Magainin on a full-time basis, and he served as Executive Vice President and President of the Magainin Research Institute, a basic research division of the company. From July 1996 through November 2000, Dr. Zasloff was Vice Chairman of the Board of Magainin Pharmaceuticals. In 2002, Dr. Zasloff was named Dean of Research and Translational Science at Georgetown University, tasked with the integration of the basic science conducted at Georgetown with the clinical environment of the Medical Center. Since 2004, Dr. Zasloff has been actively engaged in studies of innate immunity within the Transplant Institute of the Department of Surgery. His research interests remain focused on the role of antimicrobial peptides and aminosterols in health and disease, and application to the prevention and treatment of disease.

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