Molecular Genetics and Microbiology


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Molecular Genetics and Microbiology

  1. 1. MOLECULAR GENETICS AND MICROBIOLOGY Molecular Genetics and Microbiology (HBM) Chair: Jorge Benach, Life Sciences Building Room 280, (631) 632-4225 Graduate Program Director: Janet Hearing, Life Sciences Building Room 250B, (631) 632-8778 Graduate Program Coordinator: Kathryn Bell, Life Sciences Building Room 130, (631) 632-8812 Degree awarded: Ph.D. in Molecular Genetics and Microbiology Graduate study in Molecular Genetics CMM, a new state-of-the-art research Bliska, James B., Ph.D., 1987, University of and Microbiology offers a diversified and teaching facility, serves as a physi- California, Berkeley: Molecular and cellular course of study leading to the Ph.D. cal and intellectual bridge between basis of bacterial-host interactions. degree. The major areas of study are the investigators in the adjacent Life Carter, Carol A., Ph.D., 1972, Yale University: basic mechanisms of viral and bacterial Sciences Building and the nearby HIV and retroviral assembly and replication. pathogenesis, cell growth, signal trans- University Health Sciences Center. The Furie, Martha,1 Ph.D., 1980, Rockefeller duction, and the molecular mechanisms Health Sciences Library and Barry S. University: Interactions among endothelial cells, of cancer. Coller Learning Center, located in the leukocytes, and pathogenic bacteria. Studies are directed toward an under- Health Sciences Center, contains collec- Futcher, Bruce, D.Phil., 1981, University of standing of cell biology, molecular genetics, tions of biological and medical books and Oxford: Control of cell division in eukaryotic cells. and microbial pathogenesis and are journals presently totaling 262,000 vol- Hayman, Michael J., Ph.D., 1973, National designed to prepare a student to become umes, including more than 3,200 journal Institute for Medical Research, England: an effective research scientist. titles. In addition, the Health Sciences Mechanism of transformation by retroviral The student prepares for a program of Library provides access to more than oncogenes; erythroid differentiation. study in consultation with an advisory 2,300 full-text electronic journals. Other Hearing, Patrick, Ph.D., 1980, Northwestern committee composed of faculty members campus libraries include the Frank University: Viral molecular genetics; eukaryotic active in several research areas. A Melville Jr. Memorial Library. transcriptional regulation; gene therapy. research advisor, selected by the student Katz, Eugene R., Ph.D., 1969, University of at the end of the first year of study, then Admission Cambridge, England: Developmental and joins the advisory committee. The individ- Predoctoral trainees in Molecular genetic studies on Dictyostelium discoideum; ualized program aims to develop breadth Genetics and Microbiology are admitted the role of membrane sterols in cell growth of understanding in the basic disciplines to the Graduate School of Stony Brook and development. through active participation in laboratory University by application to the program. Konopka, James B., Ph.D., 1985, University research, coursework, and seminars. The final decision concerning admissions is of California, Los Angeles: G-protein coupled made by the Dean of the Graduate School, receptor signal transduction; fungal pathogen- Facilities and the candidate is officially notified by let- esis (Candida albicans). The Department of Molecular Genetics ter from the Dean’s office. In addition to the Marcu, Kenneth,2 Ph.D., 1975, Stony Brook and Microbiology occupies the second minimum Graduate School requirements, University: Immunoglobulin gene expression floor of the Life Sciences Building. the following are taken into account: and recombination; regulation and mechanisms of action of the inhibitor of NF-kB kinase (IKK) Program faculty members’ laboratories A. Undergraduate performance complex. are also located on the first and second in science courses; Reich, Nancy, Ph.D., 1983, Stony Brook floors of the Centers for Molecular University: Signaling switches in gene expres- Medicine (CMM) and within other B. Percentile on the Graduate Record sion by hormones or viral infection. departments at Stony Brook University, Examination (GRE) General Test; Brookhaven National Laboratory, Cold Steigbigel, Roy,3 M.D., 1966, University of C. Three letters of recommendation Rochester School of Medicine: Treatment of Spring Harbor Laboratory, and the HIV infection. Feinstein Institute for Medical The program does not require, but prefers Research. Approximately 47,000 square to see, evidence of research activity as an Wimmer, Eckard, Ph.D., 1962, University of Gottingen, Germany: The molecular biology of feet of research space are available undergraduate. Whenever possible, prospec- poliovirus replication and the molecular basis within the Department of Molecular tive students are invited to Stony Brook for of picornaviral pathogenesis. Genetics and Microbiology. Each interviews with the program faculty. research laboratory is fully equipped All students who are accepted into the Associate Professors and, in addition, the Department pro- Molecular Genetics and Microbiology Hearing, Janet C., Ph.D., 1984, Stony Brook vides access to a variety of communal program are accepted with full support. University: Molecular analysis of Epstein-Barr central facilities and services. These The level of support for 2008-2009 is virus latent cycle DNA replication. include a cell culture and hybridoma $26,000 per calendar year plus full Leatherwood, Janet, Ph.D., 1993, Johns Hopkins facility, microinjection facility, glass- tuition scholarship. Health insurance is University: Cell cycle control of DNA replication. ware washing and sterilization facility, provided for all students. Mackow, Erich R., Ph.D., 1984, Temple analytical equipment lab, deconvolution University: Rotavirus and hantavirus microscopy facility, environmental Faculty pathogenesis. rooms, darkrooms, and fermentor facil- Professors Paul, Aniko, Ph.D., 1966, Stanford University: ity. Major items of equipment are organ- Benach, Jorge, Acting Chair, Ph.D., 1971, Biochemical and genetic studies of poliovirus ized into these central facilities, which Rutgers University: Pathogenesis of spirochetal replication. are readily available to trainees. The infections and their host responses. 262
  2. 2. MOLECULAR GENETICS AND MICROBIOLOGY Thanassi, David, Ph.D., 1995, University of Boon, Elizabeth, Assistant Professor,11 Ph.D., Number of teaching, graduate, and research California, Berkeley: Secretion of virulence fac- 2002, California Institute of Technology: Biofilms. assistants, Fall 2007: 25 tors by bacterial pathogens; pilus biogenesis Cutler, Christopher, Associate Professor,12 D.D.S., 1) Joint appointment, Department of Pathology by uropathogenic E. coli. Ph.D., 1986 and 1990, Emory University School 2) Joint appointment, Department of Biochemistry Assistant Professors of Medicine: Periodontal disease. and Cell Biology Carpino, Nicholas A., Ph.D., 1997, Stony Dean, Neta, Professor,13 Ph.D., 1988, 3) Joint appointment, Department of Medicine Brook University: Positive and negative University of California, Los Angeles: Protein trafficking in yeast. 4) Joint appointment, Department of Pediatrics regulation of T cell receptor signaling. Freimuth, Paul, Associate Biochemist, Ph.D., 7 5) Joint appointment, Department of Urology Chan, Edward,4 M.D., 1997, State University of New York, Buffalo: Growth factor receptors 1980, Stanford University: Adenovirus 6) Joint appointment, Department of Surgery and cancer. reproduction; virus-cellular receptor binding. 7) Brookhaven National Laboratory Crawford, Howard, Ph.D., 1993, University of Joshua-Torr, Leemor, Associate Professor,8 8) Cold Spring Harbor Laboratory Texas Southwestern Medical Center at Dallas: Ph.D., 1991, The Weizmann Institute, Israel: Structural biology and molecular recognition. 9) The Feinstein Institute for Medical Research Pancreatic cancer. Kew, Richard, Assistant Professor,14 Ph.D., 10) Department of Medicine Karzai, Wali,2 Ph.D., 1995, Johns Hopkins University: Structure and function of RNA- 1986, Stony Brook University: Leukocyte 11) Department of Chemistry binding proteins and biochemical studies of chemotaxis; inflammation; pulmonary 12) Deparment of Periodontics the SmpBSsrA quality control system. immunopathology. 13) Department of Biochemistry and Cell Biology Lee, Christopher,5 M.D., University of Medicine London, Erwin, Professor,13 Ph.D., 1979, Cornell University: Membrane protein folding 14) Department of Pathology and Dentistry of New Jersey-Robert Wood Johnson Medical School: Cancer vaccine and lipid interaction. 15) Department of Physiology and Biophysics development. Lowe, Scott, Professor,8 Ph.D., 1994, Patel, Kepal N.,6 M.D., 1996, University of Massachusetts Institute of Technology: Degree Requirements Medicine and Dentistry of New Jersey-Robert Apoptosis; anticancer therapy resistance. Requirements for the Ph.D. Wood Johnson Medical School: Genetic Luft, Benjamin, Professor,10 M.D., 1976, Albert Degree in Molecular Genetics profiling in the progression of thyroid cancer. Einstein Medical College: Pathobiology of and Microbiology van der Velden, Adrianus, Ph.D., 2000, Oregon Borellia and Toxoplasma. The predoctoral training program offers Health and Science University: Salmonella Miller, Todd, Professor,15 Ph.D., 1988, its students the opportunity to study pathogenesis. Rockefeller University: Signal transduction by questions in virology, bacteriology, Zong, Wei-Xing, Ph.D., 1999, University of tyrosine kinases. immunology, biochemistry, and cell Medicine and Dentistry of New Jersey-Robert Moll, Ute, Professor,14 M.D., 1985, University and developmental biology utilizing the Wood Johnson Medical School: Cell death in of Ulm: Tumor suppressor genes; role of experimental approaches of the molecular response to stress and chemotherapeutic agents. p53 in human cancer. biologist and geneticist. Instruction and Adjunct Faculty Neiman, Aaron, Assistant Professor,13 Ph.D., course planning involve faculty members 1994, University of California, San Francisco: from the Department of Molecular Anderson, Carl W., Geneticist, Ph.D., 1970, 7 Vesicle trafficking and intracellular signaling Genetics and Microbiology and selected Washington University: Cell cycle control and in yeast. members from the Departments of cellular response to DNA damage. Skowronski, Jacek, Associate Professor,8 Ph.D., Biochemistry and Cell Biology, Medicine, Dunn, John J., Senior Microbiologist,7 Ph.D., 1981, Lodz University: HIV genes and signal Pathology, Physiology and Biophysics, 1970, Rutgers University: Transcription, transduction in T cells. and Pharmacology, and from three outside processing, and translation of RNA. Spitzer, Eric, Associate Professor,10 M.D., institutions, Cold Spring Harbor Hannon, Gregory, Associate Professor,8 Ph.D., Ph.D., 1985, Johns Hopkins University: Laboratory, Brookhaven National 1992, Case Western Reserve University: Molecular biology of microbial pathogens. Laboratory, and The Feinstein Institute Cellular proliferation control; double-stranded RNA-induced gene silencing. Stenlund, Arne, Associate Professor,8 Ph.D., for Medical Research. The general phi- 1984, Uppsala University, Sweden: DNA losophy of the program is that a success- Li, Huilin, Biophysicist,7 Ph.D., 1994, replication of bovine papillomavirus. ful research career in the diverse and University of Sciences and Technology, China: Structural biology of macromolecular Studier, F. William, Professor,7 Ph.D., 1963, heterogeneous area of molecular biology assemblies and membrane proteins by Caltech: Genetics and physiology of bacterio- requires a broadly based background, cryo-electron microscopy. phage T7; structural genomics. familiarity with at least all of the above Steinberg, Bettie M., Associate Professor,9 Ph.D., Thomsen, Gerald, Associate Professor,13 Ph.D., areas, and a frame of mind that is 1976, Stony Brook University: Papilloma viruses; 1988, Rockefeller University: Embryonic receptive to new approaches. cell-virus interactions; viral transformation. induction in Xenopus. The Department of Molecular Stillman, Bruce W., Professor,8 Ph.D., 1979, Tonge, Peter J., Assistant Professor,11 Ph.D., Genetics and Microbiology has an active Australian National University: Mechanism of 1986, University of Birmingham: Enzyme seminar program of outside speakers who eukaryotic DNA replication. mechanisms and rational drug design. present topics relevant to molecular Tracey, Kevin J., Professor,9 M.D., 1983, Tonks, Nicholas, Professor,8 Ph.D., 1985, genetics and microbiology, and there is a Boston University School of Medicine: The University of Dundee: Post-translational modifi- yearly retreat in which ongoing cholinergic anti-inflammatory pathway. cation; phosphorylation and phosphatases. research in the Department and recent Wigler, Michael, Professor,8 Ph.D., 1978, progress in the field are presented and Research Faculty Columbia University: Signal transduction and discussed. This retreat is held early in Bahou, Wadie, Professor,10 M.D., 1980, growth control in eukaryotes. the fall to introduce new students to the Massachusetts Medical Center: Human genetics; gene therapy. faculty, to other students, and to the 263
  3. 3. MOLECULAR GENETICS AND MICROBIOLOGY areas of ongoing research within the HBM 690 Microbiology Seminar H. Publication Requirement Department. The Department also pres- All students must be the first author HBM 691 Readings in Microbiology ents a colloquium each fall on human dis- Literature of at least one publication of original eases, with outstanding researchers research in order to graduate. from throughout the world presenting Spring their current work on the selected topic. HBM 522 Biology of Cancer Courses Students in the program are encouraged (offered in alternate years) to attend all of these programs as part of HBM 503 Molecular Genetics HBM 599 Graduate Research Introduces the classical work and current their training. developments in lower and higher genetic In addition to the minimum require- HBM 690 Microbiology Seminar systems. Covers gene structure and regula- tion in prokaryotic and eukaryotic organisms, ments of the Graduate School, the B. Qualifying Exam mutational analysis and mapping, transpos- following are required: able elements, and biological DNA transfer After the successful completion of all mechanisms. Bacteriophage as well as lower A. Course Requirements required courses, the student must and higher eukaryotic systems are used It is the policy of the Department of pass a written qualifying examination. to illustrate aspects of molecular genetic structure and function. This course is offered Molecular Genetics and Microbiology that C. Dissertation Proposal Exam as both MCB 503 and HBM 503. a student must obtain a grade of B or Prerequisite: Matriculation in graduate pro- Within 16 months of passing the qual- higher in each course. Any course with gram or permission of instructor ifying exam, each student submits a a final grade below 3.0 must be retaken. Fall, 3 credits, ABCF grading written proposal of his or her disserta- First Year tion research (similar to an NIH grant HBM 509 Experimental Molecular Genetics proposal) and orally defends the pro- and Microbiology Fall posal before his or her dissertation An introduction to modern microbiological MCB 520 Graduate Biochemistry I research. The selection of laboratories is made committee shortly thereafter. in consultation with the student’s advisory HBM 503 Molecular Genetics committee. By taking part in ongoing projects D. Advancement to Candidacy the student will learn experimental procedures HBM 509 Experimental Microbiology After successfully completing of all and techniques and become acquainted with (laboratory rotations) required and elective courses, the writ- research opportunities in the Department. ten comprehensive exam, and the dis- Prerequisites: Matriculation in a graduate HBM 690 Microbiology Seminar program and permission of the graduate sertation proposal exam, the student studies director and the lab director MCB 517 Biomembranes will be recommended to the Graduate Fall, 1-8 credits, S/U grading BSB 515 Computational Methods in School for advancement to candidacy. Biochemistry and Structural Biology HBM 510 Experimental Molecular Genetics E. Attendance and Participation in Student and Microbiology Seminar An introduction to modern microbiological Spring Both before and after being advanced research. The selection of laboratories is made HBM 522 Biology of Cancer in consultation with the student’s advisory to candidacy, the student is expected (offered in alternate years) committee. By taking part in ongoing projects to participate actively in the program’s the student will learn experimental procedures MCB 656 Cell Biology student seminar series. and techniques and become acquainted with research opportunities in the Department. HBM 510 Experimental Microbiology F. Ph.D. Dissertation Prerequisites: Matriculation in a graduate (laboratory rotations)* The research for the Ph.D. dissertation program and permission of the graduate HBM 690 Microbiology Seminar is conducted under the supervision of the studies director and the lab director dissertation committee, which is Spring, 1-8 credits, S/U grading HBM 692 Experimental Methods in appointed by the program and HBM 511 Introduction to Biophysical Molecular Genetics and Microbiology approved by the Dean of the Graduate Chemistry GRD 500 Integrity in Science School. A formal public oral defense of Introduces the chemical principles and tech- the dissertation is scheduled, at which niques needed for the study of biological *Students rotate through three different macromolecules. Topics to be covered include the student presents his or her findings laboratories over the course of their first solution chemistry, chemical thermodynam- and is questioned by members of the year. At the end of that year, students ics, binding and dissociation equilibrium, dissertation committee and other mem- denaturation phenomena, spectroscopy, and must identify and enter the laboratory bers of the audience. A closed oral exam- hydrodynamics. This course is intended to in which they will conduct their disser- prepare non-Chemistry majors for more ination before the dissertation committee tation research. advanced work in biophysics. follows the seminar. 3 credits, ABCF grading Second Year May be repeated for credit G. Teaching Practicum Fall It is expected that each graduate HBM 522 Biology of Cancer HBM 640 Molecular Mechanisms of student completing a doctoral degree A short course with the emphasis on cancer Microbial Pathogenesis will have functioned as a teaching as a disease of man. Lectures address human assistant during at least two semesters cancer as seen by the clinician and as basic HBP 533 Immunology of his or her graduate studies. research relates to human disease. This HBM 599 Graduate Research course provides students with a link between courses in cell and molecular biology and the 264
  4. 4. MOLECULAR GENETICS AND MICROBIOLOGY application of this basic information to tumor management. Spring, even years, 1 credit, ABCF grading HBM 531 Medical Microbiology Information derived from molecular and experimental cellular biology is presented to provide a foundation for understanding the basic aspects of the growth, regulation, struc- ture, and function of viruses and prokaryotic and eukaryotic cells. The properties of the infectious agents are correlated to human diseases caused by these agents. Laboratory experiments demonstrate basic techniques to identify and quantitate microorganisms. Prerequisite: Permission of instructor; matriculation as a Stony Brook medical or dental student Fall, 1-4 credits, ABCF grading May be repeated for credit HBM 599 Graduate Research in Molecular Genetics and Microbiology Original investigations under faculty super- vision. Prerequisite: Permission of instructor Fall and spring, 1-9 credits, ABCF grading HBM 640 Molecular Mechanisms of Microbial Pathogenesis This course covers the principles and molecular mechanisms of pathogenesis of a selected group of the best understood viral and bacte- rial pathogens. A major focus of the course nal articles relating to the concepts intro- HBM 701 Dissertation Research Off relates to pathogen modification of host duced will be assigned. A separate discussion Campus–International extracellular and intracellular signalling section will be held to review and critique the Prerequisites: Must be advanced to candidacy events, as well as pathogen-host interactions articles, to be led by the students. (G5); major portion of research will take pertaining to the innate, humoral, and cellu- Prerequisite: Must be registered in the HBM place outside the U.S. and/or U.S. provinces; lar responses to infection. The material is Program domestic students have the option of presented by invited lecturers who are lead- 1 credit, ABCF grading ers in their fields. This course is directed to the health plan and may also enroll in graduate students, postdoctorate and medical MEDEX; international students who are HBM 699 Dissertation Research On Campus fellows, and advanced medical students, who in their home country are not covered by For the student who has been advanced to are are contemplating careers in infectious candidacy. Original research will be under the mandatory health plan and must contact disease research. supervision of the thesis advisor and advisory the Insurance Office for the insurance Prerequisite: HBM, BMO 503, and BMO 520 committee. charge to be removed; international students 3 credits, ABCF grading Prerequisite: Advancement to candidacy who are not in their home country are (G5); permission of thesis advisor; major charged for the mandatory health insurance HBM 690 Molecular Genetics and portion of research must take place on (if they are to be covered by another insur- Microbiology Seminar SB campus, at Cold Spring Harbor, or at ance plan, they must file a waiver by the A weekly meeting devoted to current work in second week of classes; the charge will only Brookhaven National Lab the Department. Enrolled students present Fall, spring, and summer, 1-9 credits, be removed if the other plan is deemed com- seminars each week throughout the term. S/U grading parable); all international students must Prerequisite: Permission of instructor May be repeated for credit receive clearance from an International Fall and spring, 1 credit, S/U grading Advisor; matriculation in graduate May be repeated up to ten times for credit HBM 700 Dissertation Research Off program or permission of instructor Campus–Domestic Fall, spring, and summer, 1-9 credits, HBM 691 Readings in Molecular Genetics and Microbiology Literature Prerequisites: Must be advanced to candidacy S/U grading Readings in microbiology literature covering (G5); major portion of research will take May be repeated for credit areas of molecular biology and genetics. place off campus, but in the U.S. and/or Prerequisite: Permission of instructor U.S. provinces (Brookhaven National Lab HBM 800 Full-Time Summer Research and Cold Spring Harbor Lab are considered Full-time laboratory research projects Fall, 1 credits, ABCF grading on campus); all international students supervised by staff members. May be repeated for credit must enroll in one of the graduate student Prerequisites: Permission of instructor HBM 692 Experimental Methods in insurance plans and should be advised by and full-time graduate student status Molecular Genetics and Microbiology an International Advisor; matriculation in 0 credit, S/U grading The goal of this course is to introduce stu- graduate program or permission of instructor May be repeated dents to the rationale underlying the wide Fall, spring, and summer, 1-9 credits, array of new methods in biology, as well as to S/U grading promote the critical analysis of scientific lit- erature. Lectures will be given about various May be repeated for credit scientific methods and approaches, and jour- 265