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All application materials are due 5:00 PM, Wednesday, February 1, 2017
Grant information and application instructions are available in December by request.
The adult Infectious Disease and Basic Microbiological Mechanisms Training Program is a Harvard-wide training program dedicated to the education of those infectious disease fellows and PhD postdoctoral fellows interested in pursuing careers as physician-scientists or scientists with a focus on investigation into important questions in non-HIV microbiology and infectious diseases.
Since 1976, the program has been supported by an National Institutes of Health-funded post-doctoral training grant (T32). The training of infectious disease physician-scientist fellows consists of an initial year in clinical infectious diseases (funded by the hospitals), followed by two or more years of mentored research.
The training grant provides support directly to selected infectious disease fellows during their years of mentored research and, by providing support to selected PhD trainees in Harvard Medical School infectious disease and microbiology laboratories focused on areas that have significant clinical relevance, supports the rich research-training environment for scientists within these laboratories.
Laurie E. Comstock, PhD: Symbiotic relationships among intestinal bacteriaAssociate Professor of Medicine (Microbiology and Immunobiology), Harvard Medical School
Joseph El-Khoury, MD: Macrophages and microglia in infection, host defense, and neurodegenerationAssociate Professor of Medicine, Harvard Medical School
Sarah Fortune, MD: Interactions of M. tuberculosis with the hostProfessor of Immunology and Infectious Diseases, Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health
Wendy S. Garrett, MD, PhD: Interactions of intestinal microbiota and the immune system in inflammatory bowel diseaseProfessor of Immunology and Infectious Diseases (Genetics and Complex Diseases), Harvard TH Chan School of Public Health
Michael S. Gilmore, PhD: Molecular biology of multi-drug resistant bacterial pathogensSir William Osler Professor of Ophthalmology (Microbiology and Immunobiology), Harvard Medical School
Marcia B. Goldberg, MD: Bacterial host-pathogen interactions and rapid diagnostics of infectionProfessor of Medicine (Microbiology and Immunobiology), Harvard Medical School; Professor of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health; Associate Member, The Broad Institute
Jason B. Harris, MD, MPH: Human immune response to cholera and cholera vaccinesAssociate Professor of Pediatrics, Harvard Medical School
Darren E. Higgins, PhD: Molecular determinants of intracellular bacterial pathogenesisProfessor of Microbiology and Immunobiology, Harvard Medical School
David C. Hooper, MD: Molecular mechanisms and epidemiology of antibiotic resistanceProfessor of Medicine, Harvard Medical School
Deborah T. Hung, MD, PhD: Chemical genetics approach to bacterial pathogenesis:Associate Professor of Microbiology and Immunobiology and of Molecular Biology, Harvard Medical School; Co-Director, Infectious Disease and Microbiome Program, Broad Institute
Dennis L. Kasper, MD: Bacterial-host interactions in symbiosis and pathogenesisWilliam Ellery Channing Professor of Medicine and Professor of Microbiology and Immunobiology, Harvard Medical School
Kenneth M. Kaye, MD: Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8) pathogenesis:Associate Professor of Medicine, Harvard Medical School
Elliott Kieff, MD, PhD: Molecular pathogenesis of Epstein Barr herpesvirus infectionAlbee Professor of Medicine and of Microbiology and Immunobiology, Harvard Medical School
Igor Koralnik, MD: Immunopathogenesis of neurotropic virusesProfessor of Neurology, Harvard Medical School
Jean C. Lee, PhD: Biosynthesis and function of S. aureus extracellular bacterial polysaccharidesAssociate Professor of Medicine, Harvard Medical School
Cammie F. Lesser, MD, PhD: Modeling mechanisms of bacterial pathogenesisAssociate Professor of Medicine (Microbiology and Immunobiology), Harvard Medical School
Marc Lipsitch, DPhil: Effects of host immunity on pathogen populationsProfessor of Epidemiology (Immunology and Infectious Diseases), Harvard School of Public Health
Stephen Lory, PhD: Pathogenesis of opportunistic gram-negative bacterial pathogens of humansProfessor of Microbiology and Immunobiology, Harvard Medical School
Megan B. Murray, MD, MPH, ScD: Epidemiology and genomics of tuberculosisProfessor of Global Health and Social Medicine, Harvard Medical SchoolProfessor of Epidemiology, Harvard School of Public Health.
Edward A. Nardell, MD: Control of multidrug resistant tuberculosisProfessor of Medicine, Harvard Medical School
Gerald B. Pier, PhD: Bacterial pathogenesis and vaccine developmentProfessor of Medicine (Microbiology and Molecular Genetics)
Richard Platt, MD, MS: Epidemiology of infectionProfessor and Chair, Population Medicine, Harvard Medical School; Director of Research, Harvard Pilgrim Health Care
Eric. J. Rubin, MD, PhD: Bacterial genetics of tuberculosisIrene Heinz Given Professor of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health; Assistant Professor of Medicine (Microbiology and Immunobiology), Harvard Medical School
Edward T. Ryan, MD: Immune responses and vaccines for enteric bacteriaProfessor of Medicine, Harvard Medical SchoolAssociate Professor of Immunology and Infectious Diseases, Harvard School of Public Health
Jatin M. Vyas, MD, PhD: Dendritic cells in fungal infectionAssociate Professor of Medicine, Harvard Medical School
Matthew K. Waldor, MD, PhD: Biology and virulence of enteric pathogensEdward H. Kass Professor of Medicine (Microbiology and Immunobiology), Harvard Medical School; Investigator, Howard Hughes Medical Institute; Associate Member, Broad Institute
Rochelle Walensky, MD, MPH: Outcomes research, cost-effectiveness analysis, and infection controlProfessor of Medicine, Harvard Medical School
Suzanne Walker, PhD: Chemical biology, enzymology, antibiotics, glycosyltransferases, and inhibitorsProfessor of Microbiology and Immunobiology, Harvard Medical School; Affiliate Faculty Member, Chemistry and Chemical Biology, Harvard University; Associate Member, Broad Institute
Frederick C. S. Wang, MD: Molecular pathogenesis of Epstein-Barr virusProfessor of Medicine, Harvard Medical School
H. Shaw Warren, MD: Pathogenesis and treatment of sepsis and induced secondary inflammationAssociate Professor of Pediatrics, Harvard Medical School
Sean Whelan, PhD: Transcriptional regulation of viral and mammalian genesProfessor of Microbiology and Immunobiology, Harvard Medical School
Dyann F. Wirth, PhD: Molecular biology of parasitesRichard Pearson Strong Professor and Chair, Immunology and Infectious Diseases, Harvard TH Chan School of Public Health; Senior Associate Member, Broad Institute; Director, Harvard Malaria Initiative, Harvard TH Chan School of Public Health
Priscilla Yang, PhD: Chemistry and biology of host-virus interactionsAssociate Professor of Microbiology and Immunobiology, Harvard Medical School
Antimicrobial resistance mechanisms, discovery of new antimicrobial targets or drugsFortune, Gilmore, Hooper, Hung, Lory, Wirth, Walker
Vaccine and immunotherapy developmentCalderwood, Koralnik, Lee, Pier, Ryan
Emerging and re-emerging infectious diseasesCalderwood, Fortune, Gilmore, Goldberg, Higgins, Hooper, Hung, Kasper, Kaye, Lesser, Lipsitch, Mekalanos, Murray, Rubin, Ryan, Waldor, Walker, Whelan, Yang
Nosocomial infectionsHooper, Lory, Pier, Platt, Walensky
Virulence mechanisms of pathogensCalderwood, Fortune, Goldberg, Harris, Higgins, Hung, Lesser, Lory, Mekalanos, Rubin, Waldor
Host-pathogen interactionsFortune, Garrett, Goldberg, Harris, Hung, Kaye, Kieff, Koralnik, Lesser, Mekalanos, Pier, Waldor, Wang, Whelan
Cell biology of pathogenesisGoldberg, Higgins, Kaye, Kieff, Lesser, Waldor
Host susceptibility to infectionCalderwood, Harris, Ryan
Innate immunity in infectionEl Khoury, Vyas, Warren, Weller
Systemic immune responses to pathogensCalderwood, Higgins, Koralnik, Poznansky, Ryan, Vyas
Mucosal immune responses to pathogensCalderwood, Garrett, Ryan
Oncogenic mechanisms of microorganisms Kaye, Kieff, Wang
Transmission and epidemiology of infectionFortune, Lipsitch, Murray, Platt, Walensky, Wirth
Tyler Bold, MD, PhD Under the mentorship Eric Rubin, MD, PhD at the Harvard T. Chan School of Public Health, Dr. Bold is developing systems to test the hypothesis that T cell exhaustion contributes to the inability of endogenous adaptive immunity to eradicate Mycobacterium tuberculosis and prevent future infection. A hallmark of M. tuberculosis infection is bacterial persistence, which may cause chronic T cell antigenic stimulation that results in the development of exhaustion phenotypes, limiting the efficacy of effector and memory responses.
Thea Brennan-Krohn, MD Under the mentorship of James Kirby, MD, at Beth Israel-Deaconess Medical Center, Dr. Brennan-Krohn is studying antimicrobial synergy for carbapenem resistant Enterobacteriacae (CRE), which are among the most drug-resistant bacteria known. Treatment options for these pathogens are limited, but there is evidence that patients have better outcomes when treated with more than one antibiotic in combination. However, testing for such antimicrobial synergy in the lab is challenging and is not available in the clinical setting. Dr. Brennan-Krohn's project involves the development of new methods to test for synergy and investigation of the impact of drug combinations in a mouse model of CRE infection.
Heather Eshleman, PhD Under the mentorship of Marcia Goldberg, MD, at Massachusetts General Hospital, Dr. Eshleman is investigating the mechanism of action of the Shigella flexneri effector protein OspB. Shigella spp. deliver into host cells effector proteins that alter the function of host cell pathways in ways that promote infection. OspB induces cell proliferation of host cells. Dr. Eshleman is defining the pathway that is impacted by OspB and the mechanism by which OspB manipulates it.
Patricia Grace, PhD Patty is mentored by Galit Alter, PhD, at the Ragon Institute of MGH, MIT, and Harvard, and Sarah Fortune, MD, at the Harvard T. Chan School of Public Health, to combine human and mouse immunological approaches to understand the role of antibodies in the control of M. tuberculosis infection. Using a mouse model of M. tuberculosis infection, she is testing whether human antibodies from different tuberculosis disease states can confer control of M. tuberculosis growth and/or protection against disease pathology.
Jacob Lazarus, MD, PhD Enterobacteriaceae are a large group of Gram-negative bacteria than can colonize the human gut peacefully as commensals or cause life-threatening infections as invasive pathogens. Under the mentorship of Matthew Waldor, MD, PhD, Dr. Lazarus is working to identify host and pathogen factors that influence induction of antibiotic resistance, the switch from commensal to pathogen, and promote bloodstream translocation by these organisms.
Alaina Ritter, MD Working with Jason Harris, MD, and Ana Weil, MD, Dr. Ritter is investigating the impact of gut microbiota on the innate immune response during Vibrio cholerae infection. Preliminary data from the Harris lab identified several anaerobic bacteria associated with protection from V. cholerae. Dr. Ritter is assessing the impact of these bacteria on the immune response to V. cholerae.
Fabian Rivera-Chavez, PhD Under the mentorship of Dr. John Mekalanos, Dr. Rivera-Chavez is investigating the role of complement resistance by Vibrio cholera and other intestinal pathogens during colonization of the intestine.
Adult Infectious Disease and Basic Microbiologic Mechanisms Training Program
Massachusetts General Hospital
American Association of Immunologists Advanced Course in ImmunologySponsor/Location: American Association of Immunologists, Seaport World Trade Center, Boston, MAWhen: Annually, in July-AugustThis intensive course is directed toward advanced trainees and scientists who wish to expand or update their understanding of the field of Immunology. Leading experts present recent advances in the biology of the immune system and address its role in health and disease. Each day consists of a series of lectures on various topics in the field of Immunology. The overall quality of the course was excellent and assumes each participant has a firm understanding of the principles of immunology.
Harvard University CFAR Workshop on Metagenomics and TranscriptomicsSponsor/Location: Harvard University Center for AIDS Research, Joseph B. Martin Conference Center Harvard Medical School Boston, MAWhen: Annually, in SeptemberThe focus of this five-day intensive workshop was to provide an introduction to fundamental computational skills, genomics study design, and data interpretation. Specific topics covered included an introduction to Unix and R, an overview of metagenomics study design and data analysis tools with a focus on QIIME, and transcriptomics study design and data analysis pipelines. Each day consisted of lectures in the morning and laboratory sessions in the afternoon with access to teacher assistants.
High-Throughput Biology: From Sequence to Networks Sponsors/ Location: Cold Spring Harbor Laboratory, Canadian Bioinformatics Workshops, New York Genome CenterWhen: In the SpringThis week-long intensive course covered the bioinformatics concepts and tools required to analyze DNA and RNA-sequence reads using a reference genome. Two days were focused on DNA sequencing data analysis with topics including reference genome alignment, data visualization, De Novo assembly, small variant calling and annotation, and structural variation calling. The next two days were devoted the RNA-seq analysis with topics including alignment and visualization, expression and differential expression analysis, and isoform discovery and alternative expression. While the course included an introduction to the Galaxy environment, it predominantly focused on the use of command-line tools in the Unix and R environment for carrying out analyses. Data visualization tools were also reviewed. Following the DNA and RNA-seq analysis course segments, two and half days were devoted to pathway and network analysis along with gene function prediction and gene regulation network analysis. Each day consisted of didactic lectures followed by hands-on tutorials using example data sets provided by the course. In the evenings, there were optional hands-on tutorials with additional data sets. Overall, this was an excellent course with outstanding instructors. Basic working knowledge of Unix and R is a prerequisite.
MassBioSciences Career Development WorkshopSponsor/Location: Postdoctoral Associations at Boston Children’s Hospital, Harvard School or Public Health, Tufts University, Dana-Farber Cancer Institute and The Broad Institute hosted at The Broad Institute When: In the SpringThis workshop was organized to bring together area scientists, mostly targeted at postdocs and graduate students. This was a two-day training event to learn about transferable skills, leadership and management styles, non-academic alternative career paths and networking skills. They also provided tools and information to further career development after the workshop.
Strategies and techniques for analyzing microbial population structureSponsor/Location: Marine Biological Laboratories, Wood's Hole, MA. Room/board is provided in class fees. When: Annually in August, 10 days from 8:00 am to 9:00 pm, with one day off.The course is focused on concrete skills for analyzing genomic data of biological populations generated by next-generation sequencing technology ("big data"). The theory, technical aspects, and best practices of data generation and analysis are discussed by experts in the field. Most valuable are the daily programming computer labs with excellent TAs to help with questions. Although prior experience in programming is not required, participants with some familiarity with Unix or R will be able to complete more of the class material.
Note that participants are often accepted after the deadline listed on the website.Contact person for the course if anyone has questions: Ana Weil.
Jonathan Abraham, MD, PhD, 2016 Trainee: Dr. Abraham transitioned to a DP5 award from NIH and a Burroughs-Wellcome Career Award for Medical Scientists. He is currently a faculty member in the Department of Microbiology and Immunobiology at Harvard Medical School. His work focuses on profiling the human antibody response in survivors of viral hemorrhagic fevers and on development of antibody therapies for human viral hemorrhagic fevers and the prevention of late neurological complications of these infections.
Kelly Bachta, MD, PhD, 2014-2016 Trainee: Dr. Bachta has recently begun additional mentored postdoctoral training at Northwestern Memorial Hospital. Under the mentorship of Dr. John Mekalanos, Dr. Bachta’s project focused on the mechanisms of multi-drug resistance in Pseudomonas aeruginosa. Pseudomonas aeruginosa is an opportunistic pathogen that commonly affects immunocompromised hosts including those with cystic fibrosis and neutropenia. These patients tend to receive multiple courses of antibiotics and, as a result, P. aeruginosa is serially exposed to selective pressure to develop and maintain mechanisms of antibiotic resistance. One such mechanism involves the coordination of drug-efflux pumps. P. aeruginosa has several known multi-drug efflux pumps which efflux a variety of antibiotics including beta-lactams, fluoroquinolones and aminoglycosides. Dr. Bachta’s project characterized these efflux pumps with the hope of developing novel inhibitors to expand the array of clinically useful anti-pseudomonal therapies.
Roby Bhattacharyya, MD, PhD, 2012-2013 Trainee: Dr. Bhattacharyya transitioned to a Foundation for Medical Discovery individual fellowship from the Mass General Executive Committee on Research and a K08 award from NIH. He is currently a junior faculty member in the Mass General Division of Infectious Diseases. Dr. Bhattacharyya is working with Dr. Deborah Hung to develop rapid, non-culture based diagnostics for a variety of pathogens and from a range of samples. Dr. Hung has shown that RNA expression signatures can be used to identify a variety of common pathogens rapidly and specifically; the RNA probes used target sequences highly conserved within but not shared between pathogenic species. Moreover, targeting RNA expression signatures of stress response pathways that respond early to antibiotic therapy enables discrimination of susceptible strains from resistant ones. Dr. Bhattacharyya is (1) optimizing assays for molecular signatures in frequently encountered human pathogens that allow discrimination in patient samples, using nanostring technology, and (2) characterizing the transcriptional response of a panel of frequently encountered human pathogens to an array of antimicrobial compounds. The development of rapid diagnostic methods for important human pathogens has the potential to revolutionize early diagnosis and treatment, particularly in resource-poor settings, with enormous impact on the control and prevention of transmission of infectious diseases.
Daniel Bourque, MD, 2014-2016 Trainee: Under the mentorship of Dr. Jason Harris, Dr. Bourque investigated the innate immune response to Vibrio cholerae infection to define the mechanisms that promote long-term immunity from natural infection. The aims of his research were to identify mucosal innate immune pathways and early B cell responses, which lead to the development of long lasting B cell memory after natural infection as compared to oral vaccination. Achieving further insight into the mechanisms of the innate immune response to infection with V. cholerae will provide key insights that may lead to an improved cholera vaccine.
Allison Carey, MD, 2015-2017 Trainee: Under the mentorship of Sarah Fortune, MD, Dr. Carey investigated the modulating features and genetic determinants of tuberculosis infection. Tuberculosis, the disease caused by the pathogen Mycobacterium tuberculosis, is a global health crisis, with over 9 million new cases of active disease and more than a million deaths annually. Tuberculosis was long thought to be a genetically monomorphic pathogen, but recent work has uncovered substantial genetic diversity among circulating clinical strains. She used genome-wide genetic screening and quantitative molecular tools to explore the impact of genetic diversity among clinical strains in the settings of reinfection and vaccination.
Sanjat Kanjilal, MD, MPH, 2015-2017 Trainee: Under the mentorship of Marc Lipsitch, PhD, and Yonatan Grad, MD PhD, Dr. Kanjilal worked to define population dynamics and genotypic correlates of invasion and antibiotic resistance of methicillin-resistant Staphylococcus aureus (MRSA). With the goal of defining S. aureus genes and regulatory networks that underlie clinically important phenotypes and defining patterns of transmission through human populations, Dr. Kanjilal investigated the population structure, antibiotic resistance, and virulence factors of MRSA, using phylogenetic and statistical tools to analyze a data set of over 1400 genomes from well-characterized isolates.
Philip Lederer, MD, 2015-2016 Trainee Under the mentorship of Dr. Edward Nardell, Dr. Lederer worked to evaluate the impact of “FAST” (Find cases Actively, Separate temporarily, and promptly Treat effectively) on tuberculosis treatment delays and health care worker infections in Peru.
Kelly Miller, PhD, 2014-2016 Trainee: Under the mentorship of Marcia Goldberg, MD, Dr. Miller characterized interactions of Shigella flexneri and host cells at the molecular level to better understand Shigella pathogenesis. S. flexneri is an intracellular bacterial pathogen that is the most common cause of diarrheal disease worldwide. To establish successful infection bacteria must induce uptake into human colonic epithelial cells, evade host innate immune responses, and spread into neighboring cells within the epithelium. Many steps in this process require the activity of bacterial “effector” proteins that are translocated into host cells using a conserved syringe-like secretion apparatus called a type three secretion system. Dr. Miller investigated how interaction of bacterial effector proteins and host proteins interfere with the host cell innate immune response during Shigella infection.
Anne Piantadosi, MD, PhD, 2016 Trainee: Dr. Piantadosi has transitioned to a KL2 MeRIT fellowship. Under the mentorship of Dr. Pardis Sabeti, she is using next-generation sequencing to identify known and unknown viral pathogens in infectious encephalitis and is then characterizing a selected subset of these pathogens.
Jennifer Reedy, MD, PhD, 2012-2014 Trainee: Dr. Reedy transitioned to a KL2 MeRIT fellowship. Under the mentorship of Jay Vyas, MD, PhD, Dr. Reedy investigated how the innate immune system recognizes and responds to fungal pathogens. Her research focused on the dematiaceous mold Exserohilum rostratum and elucidating the mechanisms by which the innate immune system recognizes and responds to this fungi. Specifically, she analyzed the carbohydrate composition of spores and hyphae of E. rostratum and evaluated the cytokine response elicited by macrophages in response to E. rostratum.
Chanu Rhee, MD, MPH, 2014-2015 Trainee: Dr. Rhee is a faculty member in the Department of Population Medicine, Brigham and Women’s Hospital. Under the mentorship of Richard Platt, MD, MSc, Dr. Rhee focused on the epidemiology, surveillance, and prevention of healthcare-associated infections, particularly in critically ill patients. His research project, a multicenter observational study being conducted with the CDC Prevention Epicenters, aimed at using objective clinical data captured by electronic health records to improve the public health system’s capacity to accurately track the incidence and burden of severe sepsis and septic shock.
Jonathan Robbins, MD, PhD, 2014-2017 Trainee: Now a Medical Director at Merck & Co., Dr. Robbins studied malaria, a parasitic disease responsible for hundreds of thousands of deaths each year, under the mentorship of Jeffrey Drovin, MD PhD. Dr. Robbins used a combination of forward and reverse genetic approaches to better understand the cell division cycle of P. falciparum.
William Robins, PhD, 2012-2013 Trainee: Dr. Robins is working with John Mekalanos, PhD, to characterize the transcriptional regulation of V. cholerae, the agent of cholera, during its exit from the host into the environment. Where cholera is present, a substantial number of environmental V. cholerae organisms exist as clumps of metabolically-inhibited cells that persist for weeks or months. These conditionally viable environmental cells resist growth under standard conditions, but revert to an infectious and virulent form when introduced into animals. Dr. Robins’ goals are to understand the transcriptional patterns occurring in conditionally viable environmental cholera as they form and persist in environmental water and then as they are resuscitated by exposure to autoinducers.
Brian Russo, PhD, 2014-2016 Trainee: Under the mentorship of Marcia Goldberg, MD, Dr. Russo works to define molecular mechanisms required for the virulence of the bacterium Shigella, the most common cause of diarrhea worldwide. To establish disease Shigella infects epithelial cells lining the intestine and spreads to adjacent cells. Bacterial effector proteins, delivered into the epithelial cells by Shigella, usurp host signaling in ways that promote infection. These bacterial effector proteins are delivered using the highly conserved type 3 secretion system. The Goldberg laboratory performed a genome-scale selection in which they identified that host intermediate filaments factors activate the type 3 secretion system. Dr. Russo is investigating the mechanisms by which intermediate filaments contribute to type 3 secretion function.
Ana Weil, MD, 2014-2015 Trainee: Dr. Weil is currently supported on a K08 and is a junior faculty member in the Division of Infectious Diseases at Massachusetts General Hospital. Under the mentorship of Edward Ryan, MD, and Regina LaRocque, MD, Dr. Weil investigates factors that modulate the spread of cholera among humans, focusing on the human gut microbiome. Analyzing the microbial population structure of samples taken from household contacts of cholera patients, she determined specific bacterial groups associated with a higher likelihood of becoming infected with V. cholerae.
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