Penn BGS book


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16 page brochure for Biomedical Graduate Studies program at the University of Pennsylvania

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Penn BGS book

  1. 1. Biomedicalg r a d uat e s t u dies
  2. 2. graduate group. Consequently, students may enroll in any relevant graduate level course and may conduct research with virtually any faculty member within a given field. Training consists of a multi-faceted program of formal coursework, informal journal clubs and seminars, interactions with outside senior scientists, and a formal research experience. During the first year of study, students take fundamental courses in the areas of biochemistry, molecular biology, and cell biology and specialized courses in their chosen field of interest. They also begin structured laboratory rotations that expose them to hands-on research. The second year is devoted to focused laboratory work and a limited number of advanced elective courses and seminars. Beginning in year three, students conduct dissertation research in the laboratory of their choice; this research typically takes three to four years. CONTENTS 1 Program Overview B iomedical Graduate Studies (BGS) serves as the academic home within the University of Pennsylvania for over 700 graduate students pursing a PhD in the basic biomedical sciences. The program is Students may also participate in several certificate programs that provide additional training. These include the Graduate Training in Medical Sciences Certificate Program, which integrates focused organized into seven interdisciplinary graduate groups: Biochemistry medical education into the doctoral curriculum, affording PhD students 3 Certificate Programs and Molecular Biophysics, Cell and Molecular Biology, an appreciation of medicine and human biology, and the Public Health Epidemiology and Biostatistics, Genomics and Computational Certificate Program, which provides training in population-based 5 Biochemistry and Molecular Biophysics Biology, Immunology, Neuroscience, and Pharmacological approaches and applications for those with expertise in molecular, Sciences. The seven BGS graduate groups consist of over 600 scientists cellular, and biochemical sciences. 6 Cell and Molecular Biology and educators representing more than 30 academic departments The BGS program also provides supplemental training in bioethics and and seven schools – Medicine, Dental Medicine, Veterinary Medicine, career development to students at all stages. Most program graduates 7 Epidemiology and Biostatistics Engineering and Applied Science, Wharton, Nursing, and Arts and accept a prestigious academic postdoctoral fellowship, while other Sciences – as well as several associated research institutions. BGS faculty alumni find highly suitable positions in the biomedical industry, in 8 Genomics and Computational Biology cooperate in admitting, funding, advising, teaching, training, and government agencies, or in professions such as patent law, science providing career development advice to BGS students. Two affiliated journalism, or science education. 9 Immunology graduate groups, Biology and Bioengineering, are not administered by BGS but overlap with BGS groups in faculty membership, course 10 Neuroscience offerings, and other program attributes. BGS students have ample time and opportunity to explore modern 11 Pharmacological Sciences biomedical science and develop their true academic interests. The Graduate groups provide flexible, broad-based, interdisciplinary training; many courses are cross-listed by two or more graduate programs, and most faculty members belong to more than oneOn the cover: A neurosphere: Primary rat neuroglialcultures triple stained for MAP-2 (Red), DAPI (blue), andphospho-pRb (green). (Cagla Akay from lab of KellyJordan-Sciutto) BIOMEDICAL GRADUATE STUDIES 1
  3. 3. a component of the Fox Chase Cancer Center, is another institution Certificate Programs closely associated with BGS; its strengths are in the areas of molecular Students enrolling in BGS doctoral programs have the option of oncology, virology, and immunology. In addition, researchers at the applying to certificate programs in medicine and public health. National Institutes of Health have joined the BGS faculty to participate The programs offer intensive supplemental training provided by in training students in the Immunology Graduate Group. expert practitioners and researchers in these fields. Participants are expected to complete the certificate program and doctoral program requirements concurrently. Combined Degree Opportunities In recognition of the close relationship between the biomedical Graduate Training in Medical Sciences disciplines and clinical medicine, Penn offers combined doctoral and The Graduate Training in Medical Sciences (GTMS) program professional degree programs with the School of Medicine, the School integrates focused medical education into the doctoral curriculumResearch Training Environment of Veterinary Medicine, and the School of Dental Medicine. Students and experience, affording Ph.D. students an appreciation ofPenn is a leader in biomedical research and research training in its in these programs are generally able to earn both degrees in seven medicine and human biology not formerly available. The programlevels of sponsored research and its commitment to interdisciplinary or eight years. Entrance into a combined degree program requires aims to promote clinically relevant research by producing basicresearch and training. The university ranks second in the nation in separate application to, and acceptance by, the Combined Degree scientists who not only have a clearer understanding of humanfunding from the National Institutes of Health, and the School of Program and professional school. Further information about these biology and pathology, but who can effectively interact withMedicine is ranked first in NIH training grant funding. programs can be found at clinical scientists to tackle medically relevant research problems. Students take fundamental courses in pathophysiology andPenn’s commitment to interdisciplinary training, embodied in the medicine, “bench to bedside” electives, and clinical clerkships instructure of graduate groups, is matched by its commitment to addition to their graduate group’s requirements.interdisciplinary research through campus centers and institutes.The Genomics Institute and the Penn Center for Bioinformatics foster Public Health Certificate Programresearch projects integrating biology, medicine, engineering and The Public Health Certificate Program (PHCP) provides supplementalcomputer science. Similarly, the Institute for Medicine and Engineering training to doctoral candidates who are interested in public health.promotes basic and clinical research at the interface of biomedicine and This program prepares students for careers in academic, industrial,bioengineering. Other important biomedical centers and institutes and government institutions by providing training in populationon campus include the Institute for Neurological Sciences, the Cancer based approaches and applications for those with expertise inCenter, the Institute for Translational Medicine and Therapeutics, the molecular, cellular, and biochemical sciences. Students take four Application and Financial AidLeonard Davis Institute for Health Economics, and the Center for courses in public health in addition to their regular doctoral Students accepted to Biomedical Graduate Studies receive a fullyBioethics. The integrative nature of research and training at Penn is coursework and participate in either a short-term (six week) public funded fellowship – including tuition, fees, health insurance, and amade possible by the physical layout of the campus. All of Penn’s health research project or independent study with a member of competitive stipend – regardless of financial need. Application shouldschools are located on a single campus, and most classrooms, offices, the MPH faculty for elective credit. It is anticipated that students be initiated in the fall of the academic year preceding the one in whichand laboratories are located within just a few blocks of one another. will explore aspects of public health related to the PhD research the individual proposes to matriculate. Applications are accepted project during the independent study. online via the BGS website. Applicants considered for admissionFaculty investigators at independent institutions associated with Penn are invited to campus for interviews during the months of Januaryalso play a significant role in graduate student training. Members through March; offers of admissions are made on a rolling basis duringof the Wistar Institute, a research institution in the heart of campus this period.with outstanding programs in genetics, oncology, immunology, andvirology, are active participants in BGS. The Institute for Cancer Research,2 w w n .e du/bgs BIOMEDICAL GRADUATE STUDIES 3
  4. 4. Biochemistry and Molecular BiophysicsThe p53 tumor suppressor protein binds to DNA as adimer of dimers to regulate transcription of genes thatmediate responses to cellular stress. Shown is thestructure of a p53 core domain dimer bound to DNAwith the DNA in red, protein subunits in blue andaqua and bound zinc ions in yellow. (J. Biol. Chem.281:20494-20502, 2006, Ronen Marmorstein)Control of gene expression and cellular Chemical and structural biology The central focus of the Graduate Groupprogramming In the area of chemical and structural in Biochemistry and Molecular BiophysicsResearch focuses on RNA splicing and biology, topics of research include thedisease, transcriptional regulation, histone structural basis of molecular recognition, is the relationship between structure andacetylation, cell cycle control/cancer, protein design and engineering, function of molecules involved in biologicalchromosome structure and segregation, pathways of protein folding, enzymeand programming and function of reaction mechanisms, and computational processes. The goal of the program is tospecialized cell types. approaches to molecular biophysics. provide students with a foundation in theCell signaling and intracellular Bioenergetics, metabolism, and physical, chemical and quantitative methodstrafficking membranesResearch in this area examines mechanisms This area involves radical mechanisms in necessary to explore the molecular basis ofof transmembrane signaling, nuclear metalloenzymes, insulin action/diabetes, biological events.import/export of RNA, membranes and electron transfer/redox proteins, integrationion channels, and intracellular signaling of metabolism, and membrane proteinpathways, apoptosis versus cell survival. structure. Biomedical imaging and supramolecular assemblies Research topics include optical imaging in tissues/cancer, in vivo Magnetic Resonance Imaging, spectroscopy, structure and function of macromolecular motors, and electron microscopy. BIOMEDICAL GRADUATE STUDIES 5
  5. 5. Cell and Molecular Biology Epidemiology and BiostatisticsThe Cell and Molecular Biology Graduate Cell Biology and Physiology Developmental Biology The Program in Cell Biology and Physiology The Program in Developmental BiologyGroup offers programs in six related areas focuses on basic functions of the cell and offers interdisciplinary training in theof study: Cell Biology and Physiology, Cancer its links to metabolism and disease, with embryology of animals and plants. The concentrations in signal transduction, program encompasses research in gameto-Biology, Developmental Biology, Gene subcellular protein trafficking, cytoskeleton genesis, fertilization, pattern formation,Therapy and Vaccines, Genetics and Gene and cell motility, cross-membrane transport, signal transduction, gene regulation, cell cell cycle regulation and cellular metabolism. cycle control, cell death, cytoskeletal dynam-Regulation, and Microbiology, Virology and Much of the research in this program is ics, cell motility, neural connectivity, andParasitology, each composed of faculty with directed toward dissecting disease models, adult and embryonic stem cells. Utilizing a such as diabetes, muscular dystrophy, and diversity of experimental systems, research ininterests focused on similar areas of research. cancer, in systems ranging from yeast to developmental biology contributes to the humans. identification of genes and regulatory path- ways implicated in congenital malformations Cancer Biology and human disease. The Program in Cancer Biology provides the opportunity to study the basic biological Genetics and Gene Regulation DNA damage associated with processes that underlie the initiation and The Genetics and Gene Regulation Program pesticide exposure shown using the progression of cancer. The program stresses provides comprehensive training in the COMET assay. (Linda A. McCauley) the importance of fundamental genetic fundamentals of modern genetics (including and molecular pathways regulating cell both model organism and human genetics proliferation, differentiation, movement, and and genomics) and in the regulation of Epidemiology Biostatistics The Graduate Group in Epidemiology and survival. Current research programs include eukaryotic gene expression. Research oncogenesis, cell migration/metatasis, and areas include developmental, behavioral The Epidemiology program trains students The Biostatistics program is concerned Biostatistics offers graduate training in two cancer immunology. and cancer genetics, the genetics of human in the study of the distribution and with the development and application of programs: Epidemiology and Biostatistics. disease, and transcriptional and post- determinants of health and disease in statistical theory and methods to the health transcriptional gene regulation. populations, and the basic science underly- sciences. Biostatisticians play a crucial role in Graduate Group faculty are engaged in ing much of public health and preventive the research process, from inception of the Gene Therapy and Vaccines multiple active clinical and basic research medicine. Training in clinical epidemiology research plan through the analysis and pub- The Gene Therapy and Vaccines Program extends the principles of epidemiology lication of study results. Every biomedical projects, many of which focus on content- focuses on using gene transfer for therapeu- to the critical evaluation of diagnosis and field of study employs biostatistical methods tic purposes or for vaccination. Although specific areas of interest and include relevant therapeutic modalities in clinical practice. to some extent. For example, biostatistical the goals of the research are disease-based Clinical epidemiologists investigate the tools are used to assess the magnitude, methodologic work. with an ultimate objective directed to frequency, outcome, prognosis, etiology, reliability, validity, and precision of associa- prophylactic and therapeutic applications, treatment, prevention, diagnosis, costs, and tions (e.g., between exposures and disease) the research training focuses on basic policy implications of disease. Specific areas to make inferences about target populations investigations relevant to understanding the of interest include: adherence, aging, cancer using sample data, and to derive conclusions pathobiology of diseases and to developing epidemiology, cardiovascular epidemiology, about treatment effects from clinical trials. approaches for achieving efficient and clinical pharmacogenomic epidemiology, Methodologic interests include: Bayesian effective gene transfer in humans. complementary and alternative medicine, modeling, categorical data, causal inference, Microbiology, Virology, and Parasitology dermatoepidemiology, gastrointestinal clinical trials, clustered data, complex sample Infectious diseases resulting from viruses, epidemiology, genetic epidemiology, surveys, diagnostic testing, epidemiologic parasites, prions, and bacteria are a major infectious diseases epidemiology, injury methods, health services research, longitu- cause of human morbidity and mortality. epidemiology, international health, medical dinal methods, measurement errors, missing By studying pathogens, it is possible to informatics, molecular epidemiology, data, multivariate analysis, nonparametric learn much about normal cell biology, nutrition, pharmacoepidemiology, models, patient-oriented research, repeated molecular biology, and immunology. Major prevention, public health, pulmonary measures, statistical genetics and genomics, research interests include virology, bacterial epidemiology, renal epidemiology, repro- survival analysis, and time series. pathogenesis, parasitology, pathogen ductive epidemiology, social epidemiology, immunology, tumor virology, microbial and women’s health. Image of the crystal structure glycoprotein B of herpes simplex virus. genomics and evolution, and emerging (Science 213:217-220, 2006, Roselyn Eisenberg) infectious diseases.6 w w n .e du/bgs BIOMEDICAL GRADUATE STUDIES 7
  6. 6. Genomics and Computational Biology Immunology Cell, Molecular, and Developmental PENN – NIH Partnership The Immunology Graduate Group provides Biology of the Immune System A distinguished group of investigators from each trainee with an understanding of the Studies in this area include molecular the Bethesda, MD campus of the NIH have immunology, such as signal transduction joined Penn’s faculty in Immunology, conceptual and experimental foundation and transcriptional control, cell biology of bringing to the Immunology Graduate of modern immunology and imparts lymphocyte activation, and developmental Group the extraordinary resources and biology of lymphoid and myeloid subsets. scientific expertise present at the NIH, one of comprehensive knowledge of the immune the largest and most renowned biomedical system and its regulation while teaching Immunity to Infections research centers in the world. Particular foci of research include elucidating the skills necessary for a career in biomedical A graph of yeast gene interactions estimated the role of innate immune responses, the Educational opportunities on the NIH cam- from whole-genome gene expression data. Each pus are offered to all Immunology students. science. dot represents a gene and each edge represents CD4+ T cell subsets that secrete inflamma- tory cytokines and CD8+ cytolytic T cells in The NIH faculty participates fully in all a significant interaction. The high-lighted and aspects of our teaching programs at Penn’s colored ellipses represent groups of genes with the defense against microbes and viruses, both at the site of infection, such as the Philadelphia campus, including service on known gene function showing that genes with mucosal surfaces of the gut and lung, and in thesis committees. The partnership also similar biological function tends to have high degree of mutual interaction. (Junhyong Kim) peripheral lymphoid organ. allows students to pursue laboratory rota- tions and a limited number to pursue thesis Cancer Immunology research in the NIH laboratories. Cancer immunology research at Penn encompasses the entire spectrum from basicGenomics and Computational Biology Evolutionary Genomics methods for genetic association studies research to clinical trials. Specific research work includes the and gene-gene interactions, methods forlies at the center of a rapid convergence of evolution of the transcriptome in natural systems biology, comparative sequence Autoimmunity and Tolerancebiomedical research fields. Research in this species and cell lines of different genetic analysis, evolutionary modeling, machine Using a variety of different approaches and composition, the evolution of large gene learning in genomics, statistical models forgraduate group focuses on the entire models, several groups of investigators at families, gene duplication and loss in the analysis of microarray data, and statistical Penn are focusing their efforts in this area,genome (as DNA) and the entire material evolution, the evolutionary frequency and methods for mapping genes associated with with the ultimate goal of developing strate- significance of horizontal gene transfer, diseases.determined by genes (as RNA or protein), gies to block deleterious immune responses. methods for detecting functional non- cod-and asks about the origins, function, and ing sequences, and the role of retroviral Microbiology elements in the evolution of new genomic Research programs focus on the investiga-interactions of the system as a whole. Such function. tion of the growth and inhibition ofquestions and other developments in this medically significant pathogens, replication Human Genomics of human transposons and consequencesfield stimulate experimental laboratory work In the area of human genomics research for human biology, and retroviral-hostin genomics, as well as computational activi- topics include the analysis of structurally interactions. variant chromosome regions, the genomicties in bioinformatics. analysis of predisposition to diseases, Computing genome-wide analysis of gene expression, Studies in this area include computational the genetics of complex diseases, devel- analysis and modeling of real-time, systems- opmental genomics, and chromosome level genomics, nanotechnology, com- organization. putational simulations of the evolutionary processes of cancer, ,machine learning and Statistics datamining, and bioinformatics including Statistics research includes the develop- management, analysis, and visualization of A dividing, microbe-specific T lymphocyte displaying unequal inheritance ment of statistical methods for discovery information generated in molecular biology. of signaling proteins to its daughter cells. Asymmetric cell division may be and clustering of conserved patterns in a mechanism to generate the spectrum of cell fates required for immunity. DNA sequences, evolution of viral genomes, (Steve Reiner)8 w w n .e du/bgs BIOMEDICAL GRADUATE STUDIES 9
  7. 7. Neuroscience Pharmacological SciencesThe Neuroscience Graduate Group Cell and Molecular Neuroscience Neurological Disease and Dysfunction Research focuses on the molecular Research programs focus on the cellularoffers training in virtually all areas of mechanisms of intra- and intercellular signal- and molecular bases of a variety of Progressive microglialneuroscience research including cellular ing that underlies plasticity in both the neurological and psychiatric diseases, includ- activation in the central developing and adult nervous system, as ing Alzheimer’s disease, traumatic brain nervous systemand molecular aspects of the brain; well as changes in signaling underlying injury, autoimmune diseases of the nervous of transgenic tau mice.development, regeneration, and plasticity; diseases of the nervous system and involves system, diseases of the motor system, and Microglia are progressive- cutting edge molecular biological, genetic, the neuronal basis of addiction. ly activated with age insystems neuroscience; behavior and the brains of transgenic immunological, electrophysiological, and mice (PS19, 3 monthscognition; the pathology of brain disease; behavioral approaches. Systems Neuroscience to 9 months) compared The study of how information is encoded,and computational neuroscience. Neuronal Development, Regeneration, to normal mice (nTg). processed in the brain and used to generate and Plasticity (Virginia Lee) coordinated movement depends in part on Current research uses multidisciplinary the organization of neurons into networks approaches to address the molecular and and systems. Approaches here include cel- cellular processes that lead to the formation lular-level analyses of small model systems in Cancer Pharmacology cardiovascular disease). Graduates of the Pharmacological Sciences Research employs of a functioning brain, including how nerve vitro and larger scale systems studied in vivo. Specific research work includes site-directed program will be prepared for careers in toxi- cells migrate to their final destination, how a variety of experimental approaches to All of these studies include realistic neural mutagenesis, structural and functional cology, risk-assessment, environmental and axons are guided to appropriate targets, and network. characteristics of GTP-binding regulatory occupational health sciences. identify natural and design synthetic agents how neurons make and maintain synaptic connections. proteins, mass spectrometry detection of Behavioral Neuroscience for both treatment of diseases and experi- molecular markers of tumor growth and Neuropharmacology Animal behavior represents the external design of molecular interventions in cancer. The overall focus of neuropharmacology mental interventions in animal and cellular expression of complex patterned activity in research and training is to provide students the brain and is continually modulated by in- models. Understanding the action of these Cardiovascular Pharmacology with an integrated understanding of ternal and external sensory information and Research programs explore the cellular the interactions of neurotransmitters with agents, both desirable and toxic, is the key by internal drives and states. Penn has an and molecular basis of atherosclerosis, receptors and the biochemical and active interdisciplinary program that studies mission of the graduate training program. thrombosis, hypertension and inflamma- functional effects of these interactions. the complex relationship between cellular tion using a variety of approaches including The program’s resources allow students to and molecular events and external patterns knockout and transgenic technologies, gene Pharmacogenetics of behavior. concentrate on basic science research and to therapy techniques, recombinant fusion This program focuses on the genetic basis proteins and modern approaches in chemis- of inter-individual variation in response to participate in translational research where Cognitive Neuroscience try, biochemistry, molecular biology, and various classes of drugs and therapeutic Cognitive Neuroscience has a distinctive fundamental discoveries in the laboratory cell biology. protocols and makes use of this information goal: the mechanistic understanding of to develop rational “personalized” therapeu- are taken through stages of discovery and human thought. How do people learn, Cell Signaling tic regimens and to identify genetic understand language, and plan complex development and culminate in the clinical Signals of special interest include hormones, susceptibility factors for diseases. It encom- action? Research programs include those neurotransmitters, sensory stimuli, and passes the study of genetic factors that domain. focused on understanding visual perception, cell-cell or cell-substratum contacts. Specific influence drug delivery, bio-availability, learning and memory, and cognition- research works include studies of cellular metabolism and clearance, and toxicity. emotion interactions. receptors and membrane channels, signal transduction pathways and nuclear respons- Pharmacological Chemistry Computational Neuroscience es in diverse models of (patho)physiological Understanding the chemistry of molecular The objective of Computational processes. recognition between drugs and their targetsA picture of a zebrafish brain. Green is rhombere, Mauthner neuron, and muscle staining. Blue is a pre-synaptic marker. Neuroscience is to uncover basic neuronal (receptors, ion-channels, enzymes, andRed is a post-synaptic marker. (Yuanquan Song, Paul Scherer, and Rita Balice-Gordon) mechanisms through simulation and Environmental Health Sciences nucleic acids) is a primary focus of research prediction based on experimental findings. This program explores the mechanisms, and training in Pharmacological Chemistry. To carry out these studies, collaborations pathogenesis, prevention and treatment Research work includes synthesizing recep- between experimentalists and of diseases of environmental etiology tor subtype specific ligands and isoform computational neuroscientists have led to a (e.g., lung and airway disease, cancer, specific enzyme inhibitors and X-ray crystal- PhD Thesis with co-Advisors. neurodegenerative disease, reproductive lography of membrane bound drug targets. and developmental disorders, obesity and10 w w pen n .edu/bgs BIOMEDICAL GRADUATE STUDIES 11
  8. 8. Biomedical Graduate StudiesUniversity of Pennsylvania160 BRB II/III421 Curie BoulevardPhiladelphia, PA