Department of Biological Chemistry
Department of Microbiology and Molecular Genetics
Department of Physiology and Biophysics
Building D, Room 240, Medical Sciences I; (949) 824-6051
Suzanne B. Sandmeyer, Department Chair
Faculty
Stuart M. Arfin: Gene regulation in E. coli
Pierre Baldi: Computation biology, bioinformatics, probabilistic modeling, machine learning
William Byerley: Genetics of schizophrenia
Xing Dai: Role of regulatory OVO proteins in mouse epidermal and reproductive differentiation
Deborah L. Grady: Mapping and sequence analysis of the human genome
Chris L. Greer: RNA processing and nuclear export; tRNA gene expression
Harry T. Haigler: Structure, function, and topography of annexin calcium binding proteins on membranes
Jack W. Jacobs: Cloning, expression, and characterization of leech anticoagulant proteins
Murray Korc: Molecular biology of altered signaling pathways in cancer
John Krolewski: Signal transduction and cellular growth control
Haoping Liu: Signal transduction, cell cycle regulation, hypha development in yeast
Calvin S. McLaughlin: Functional genomic analysis
Frank Meyskens: Biology of melanoma and chemoprevention of human cancer
Robert K. Moyzis: Human genome and complex genetic disease
Masayasu Nomura: RNA polymerase I; nucleolus and ribosome synthesis; nuclear structure and function
Suzanne B. Sandmeyer: Retrovirus-like elements in yeast; genomewide gene expression during stress
Moyra Smith: Development and tissue-specific changes in gene expression; human gene mapping
Robert E. Steele: Evolution of intercellular signaling in multicellular animals
Leslie M. Thompson: Molecular/biochemical analysis of skeletal dysplasias and Huntington's disease
Larry E. Vickery: Molecular chaperones and protein folding; assembly of Fels proteins
Ping H. Wang: Molecular actions of Insulin-like growth factor I (IGFI) in cardiac muscle; complications of diabetes
Kyoko Yokomori: Molecular mechanisms of chromosome dynamics and gene regulation
Faculty research interests in the Department of Biological Chemistry focus on the structure and function of chromosomes, signal transduction and its role in cell growth control, regulation of gene expression (transcription, RNA splicing, protein synthesis, and protein localization), and the molecular basis of development. Genome sequencing projects are making it possible for faculty to exploit information learned about gene function in model organisms for understanding human disease processes. Students are exposed to technical expertise in all facets of current research in molecular biochemistry from protein chemistry to genetic engineering and gene mapping. Currently, researchers in the Department are using new DNA array technology to examine changes in gene expression in response to the environment.
The Department offers graduate study under the auspices of the School of Biological Sciences and in conjunction with the program in Molecular Biology, Genetics, and Biochemistry, which is described in a previous section. Students admitted into the combined program who select a research advisor in the Department begin thesis research in the second year. Students are required to attend and participate in the departmental research seminar and are required to attend departmental seminars. In addition, students are required to complete two advanced-level graduate courses subsequent to entering the Department's Ph.D. concentration. In the third year, students take the advancement-to-candidacy examination for the Ph.D. degree by presenting and defending a proposal for specific dissertation research. Completion of the Ph.D. normally requires five years of graduate study.
200A, B, C Research in Biological Chemistry (2 to 12) F, W, S. Individual research under the supervision of a professor. Satisfactory/Unsatisfactory only. May be repeated for credit.
202A, B, C Laboratory Seminar Series (1, 1, 1) F, W, S. Study within a laboratory group including research and journal presentations. Satisfactory/ Unsatisfactory only. May be repeated for credit as topics vary.
204 Problems in Genomic Analysis (1) F, W, S. Students from the biological and computational disciplines plan and execute genomewide gene expression studies and develop algorithms to identify biological motifs involved in gene regulation. The long-term goal of these studies is to develop predictive models for cellular function. Prerequisite: consent of instructor. May be taken for credit six times.
207 Advanced Molecular Genetics (4) F, W, S. Lecture, three hours. Introduction to genetic analysis using model organisms such as yeast. Topics include meiosis, DNA repair, cell cycle, cytoskeleton, intracellular sorting (nuclear, endoplasmic, mitochondrial), signaling, prions, and genomewide gene expression analysis. Prerequisites: Molecular Biology and Biochemistry 203. May be taken for credit six times. Same as Molecular Biology and Biochemistry 207.
210A Biochemistry and Cell Biology (12) F. Lectures and seminars. Biological chemistry and cell biology for first-year medical and graduate students. Presents the metabolism and molecular biology relevant to human health and disease that form the foundation of medical science for the next century. Prerequisite: consent of instructor.
212 Signal Transduction and Growth Control (4) S. Covers various eukaryotic signaling pathways (tyrosine kinase, ras-raf-MAPK, TGFB, wnt, JAK-STAT, and FAS) with an emphasis on the experimental underpinning. The material is covered in lectures and discussions of pertinent papers. Prerequisite: consent of instructor.
218 Human Molecular Genetics (4). Topics of current interest in human molecular genetics, with emphasis on an understanding of the methods and results generated by the Human Genome Project (HGP) and associated disease gene discoveries. Prerequisite: graduate standing or consent of instructor.
285 Redox Transcriptional Factors in Health and Disease (2). Transcription factors such as NFKB and AP families are in part controlled by cellular redox status. Such signals affect viral, inflammatory, immunological, and malignant responses. Consists of a few background lectures followed by student presentations. Prerequisite: consent of instructor.
291 Topics in Gene Regulation (2) F, W, S. Seminar, two hours.
Additional courses are taught by and with faculty from the Department of Molecular Biology and Biochemistry. Topics in advanced graduate courses offered by the Department include human genetics, growth factors and oncogenes, yeast molecular genetics, and protein/nucleic acid interactions.
Building B, Room 240, Medical Sciences I; (949) 824-5261
Bert L. Semler, Department Chair
Faculty
Alan G. Barbour: Microbial pathogenesis
Vincent J. Caiozzo: Sarcomeric gene expression; contractile function; skeletal muscle plasticity
Dennis D. Cunningham: Proteases and protease nexins: regulation of neural cells
Xing Dai: Role of regulatory OVO proteins in mouse epidermal and reproductive differentiation
Mark Fisher: Mechanisms of occurence and prevention of cerebral vascular stroke
Alan L. Goldin: Molecular analysis of ion channels and their roles in human diseases
George A. Gutman: Potassium channel and immunoglobulin super-family genes
G. Wesley Hatfield: Effects of DNA topology on gene expression
Klemens J. Hertel: Regulation of gene expression by alternative splicing
W. Ian Lipkin: Molecular/cellular biology of Borna disease virus; animal models for neuropsychiatric diseases; application of subtractive cloning methods to studies in neuropathogenesis
W. Edward Robinson: Molecular pathogenesis of lentivirus infection and drug discovery against HIV
Hamid M. Said: Cellular and molecular aspects of intestinal and renal vitamin transporters
Rozanne M. Sandri-Goldin: Regulatory functions of a post-transcriptionally acting herpes virus protein
Michael E. Selsted: Innate immunity mediated by phagocytic leukocytes and mucosal epithelium
Bert L. Semler: Replication of picornavirus RNAs; RNA-protein and protein-protein interactions
Eric J. Stanbridge: Tumor suppressor genes and oncogenes in human cancer
Ming Tan: Bacterial pathogenesis; gene regulation in chlamydia
Bruce Tromberg: Optical spectroscopy in cells and tissues
Marian L. Waterman: Regulation of transcription in human T lymphocytes
The Department of Microbiology and Molecular Genetics provides advanced training to individuals interested in the regulation of gene expression and the structural and functional properties of proteins encoded by these genes. The research interests of the Department focus on the molecular biology and genetics of viruses, bacteria, and yeast; the fundamentals of the immune response; the molecular biology of cultured animal cells; the genetic basis of cancer; and the genetics and physiology of infectious agents.
The Department offers graduate study under the auspices of the School of Biological Sciences and in conjunction with the program in Molecular Biology, Genetics, and Biochemistry (MBG&B), which is described in a previous section. Students admitted into the MBG&B program who select a research advisor in the Department begin following the departmental requirements for the Ph.D. at the beginning of their second year.
Participation in the Department's seminar series and completion of at least one advanced topics course per year for three years are expected of all students. In their third year, students take the advancement-to-candidacy examination for the Ph.D. degree by presenting and defending a proposal for specific dissertation research. Completion of the Ph.D. normally requires five years of graduate study.
200A-B-C Research in Microbiology and Molecular Genetics (2 to 12 per quarter) F, W, S. Individual research supervised by a particular professor. Prerequisite: consent of instructor. May be repeated for credit.
201A-B-C Research Topics in Microbiology and Molecular Genetics (1-1-1) F, W, S. Lecture and seminar. Seminars presented by graduate students and faculty of the Department which explore research topics in specialized areas of microbiology and molecular genetics. Opportunity for students to gain experience in the organization, critical evaluation, and oral presentation of current research developments. Prerequisite: consent of instructor. May be repeated for credit. Satisfactory/Unsatisfactory only.
203A-B-C Advanced Studies in Microbiology and Molecular Genetics (1-1-1) F, W, S. Organized within each laboratory group, one to four hours. Advanced study in areas related to faculty research interests. Involves small group study based on readings, discussions, and guest speakers. May be conducted as journal clubs. Satisfactory/Unsatisfactory only. May be repeated for credit.
210A-B Medical Microbiology (4-6) W, S. Lecture, five hours; laboratory, three hours. Advanced course for medical students in the College of Medicine. Biochemical and genetic properties of infectious agents, identification and behavior of pathogens, activities of toxins, chemotherapy, biochemical genetics of drug resistance, humoral and cell-mediated immunity, introduction to diagnosis, treatment, and epidemiology of infectious diseases. Prerequisites: prior course work in microbiology and biochemistry and consent of instructor.
213 Advanced Prokaryotic Molecular Genetics (4) W. Lecture. Molecular models for biological systems draw heavily on prokaryotic organisms and their viruses. Topics: bacterial and phage genetics, regulation of transcription and translation in prokaryotes. Applies knowledge of these processes to understanding of metabolism and development at the organismic level.
215 Molecular Immunology (4) S. Lecture/seminar, three hours. Discussion and student presentation with the aim of achieving a basic understanding of the haematopoietic system, and the cellular and molecular basis of adaptive immunity. Prerequisite: consent of instructor.
216 Pathogenic Microbiology (4) S. Lecture, four hours. Biochemical and genetic properties of infectious agents; identification and behavior of pathogens; activities of toxins; the chemotherapy, biochemistry, and genetics of drug resistance; and epidemiology of infectious diseases. Prerequisite: consent of instructor.
219 Medical Virology (4) S. Lecture, four hours. Animal viruses as disease causing agents, including mechanisms of infection at both the cellular and organismic levels. Topics include comparative studies of different groups of viruses, viral transformation, and mechanisms of viral gene expression. Prerequisite: consent of instructor.
221 Immunopathogenic Mechanisms of Disease (3) S. The immune system plays a prominent role in disease. Course utilizes lectures and student presentations to teach concepts of autoimmunity and immune system interactions with bacteria, parasites, and in cancer. Prerequisite: Microbiology and Molecular Genetics 215.
222 Molecular Pathogenesis of Viral Infections (4) S. Features lectures by faculty on the molecular aspects of viral pathogensis, highlighting both viral and cellular functions. Students give oral presentations and write a research proposal on a selected topic. Prerequisite: Microbiology and Molecular Genetics 205.
240 M.D./Ph.D. Tutorial (1) F, W, S. Explores a variety of topics that impact careers of medical scientists (M.D./Ph.D students). Topics range from scientific, such as recent advances in particular research areas, to ethical problems brought on by increased technology and intervention in the disease process. May be repeated for credit.
250 Responsible Conduct of Research (2). Each session includes a formal presentation by faculty/invited speaker followed by a discussion of case studies related to the topic under consideration. Satisfactory/Unsatisfactory only. Formerly Molecular Biology and Biochemistry 219.
280A-B-C Tutorial in Microbiology and Molecular Genetics (2-2-2) F, W, S. Tutorial, two hours. Presented by various members of the faculty; relates current laboratory research to the literature.
Building D, Room 340, Medical Sciences I; (949) 824-5863
Janos K. Lanyi, Department Chair
Faculty
Nancy L. Allbritton: Signal transduction by second messengers and protein kinases
Kenneth M. Baldwin: Developmental, hormonal, and exercise factors regulating striated muscle gene expression
Michael E. Barish: Astrogial modulation of the differentiation of voltage-gated potassium currents; mechanisms of intracellular Ca2+ release
Ralph A. Bradshaw: Structure and function of polypeptide growth factors and their receptors; mechanisms of protein turnover
Michael D. Cahalan: Ion channels and Ca2+ signaling in the immune system
Vincent J. Caiozzo: Cellular and molecular mechanisms regulating the mechanical properties of skeletal muscle
K. George Chandy: Molecular biology of ion channels and their role in immune cells
J. Jay Gargus: Molecular analysis of membrane signaling proteins
Alan L. Goldin: Molecular biology of neural channels and receptors
George A. Gutman: Molecular and evolutionary studies of immunoglobulin and ion channel genes
Harry T. Haigler: Structure, function, and topography of annexin calcium binding proteins on membranes
James E. Hall: Biophysics of membrane channels, gap junctions and water channels
Frances A. Jurnak: Macromolecular crystallography; biochemical and structural studies of a model G protein; EF-Tu; structure/function of plant virulence factors
Janos K. Lanyi: Transport and energy coupling in the membrane of Halobacterium salinarium
Shin Lin: Cellular and molecular biophysics of proteins involved in membrane-associated cytoskeletal functions and signal transduction
Kenneth J. Longmuir: Intracellular metabolism, sorting, and transport of lipid in mammalian cells; membrane fusion
Hartmut Luecke: Protein crystallography; structure and function of membrane-associated proteins
Alexander McPherson: X-ray diffraction analyses of enzymes, viruses; antibodies and protein-nucleic acid complexes; crystallization methods; microgravity crystallization
Paul A. Negulescu: Physical requirements for T-cell activation; G-protein coupled receptor activation linked to ß-lactamase expression
Thomas L. Poulos: Protein crystallography; protein engineering; heme enzyme structure and function
Hamid M. Said: Cellular and molecular mechanisms and regulation of intestinal and renal vitamin transporters
Ivan Soltesz: Plasticity and modulation of inhibitory synaptic neuro-transmission
Bruce J. Tromberg: Optical spectroscopy of tissues and cells
Larry E. Vickery: Molecular chaperones and protein folding; protein engineering
Stephen H. White: Protein folding in membranes; peptide-bilayer interactions; membrane structure
The Department of Physiology and Biophysics offers research opportunities in the molecular biophysics of membranes and proteins, ion channels and signal transduction, endocrinology, molecular and cell biology, developmental neurobiology, and exercise physiology.
The Department offers graduate study under the auspices of the School of Biological Sciences and in conjunction with the program in Molecular Biology, Genetics, and Biochemistry, which is described in a previous section. Students admitted into the combined program who select a research advisor in the Department begin following the departmental requirements for the Ph.D. at the beginning of their third year.
The faculty conducts quarterly reviews of all continuing students to ensure that they are maintaining satisfactory progress within their particular academic program. Students participate in a literature review course designed to strengthen research techniques and presentation skills, and attend the weekly Department colloquium. During the third year, each student presents a seminar on a topic assigned by the formal candidacy committee. Following the seminar, the committee examines the student's qualifications for the successful conduct of doctoral dissertation research. Each student must submit a written dissertation on an original research project and successfully defend this dissertation in an oral examination. Interdisciplinary dissertation research involving more than one faculty member is encouraged. Students who have met all necessary prerequisites should be able to complete the Ph.D. in five years.
Several faculty in the Department are also members of the graduate program in Protein Engineering, which is described in a previous section.
200 Research in Physiology and Biophysics (2 to 12 per quarter) F, W, S. Individual research directed toward doctoral dissertation and supervised by a particular professor. Prerequisite: consent of instructor. May be repeated for credit.
201 Introduction to Physiology Research (1 to 4 per quarter) F, W, S. Introduction to research in physiology and related sciences. Students concentrate on techniques emphasized in the various laboratories of the Department. Prerequisite: consent of instructor. May be repeated for credit.
203 Review of the Literature of Physiology and Biophysics (2) F, W, S. Students review papers in the current literature and present ideas contained therein to other students and faculty. Prerequisite: consent of instructor. Satisfactory/Unsatisfactory only. May be repeated for credit.
204 Concepts of Biophysics (3) S. Lecture, two hours; laboratory, one hour. Principles of crystallography; introduction to time-resolved absorption and fluorescence spectroscopy; the concepts of kinetic order and kinetic rate theory. Prerequisites: graduate standing in Biological Sciences and consent of instructor. Formerly Physiology 204B. Offered only if sufficient demand exists.
205 Electronics for Biologists (4) W. Lecture, three hours; laboratory four hours. Basic principles of electricity; properties and use of discrete components and integrated circuits; circuit analysis and design. Intended for advanced students in the life sciences. Same as Neurobiology and Behavior 249.
206A-B Introduction to Medical Physiology (5-6) W, S. Lecture, six hours; discussion, two hours; other, two hours. Vertebrate physiology with emphasis on humans and on the relationship between the function of normal tissues and the processes of disease. Fundamental principles of physiology and the interrelationships which control organ function. Prerequisite: Physiology 202 and consent of Department.
209 Literature in Protein Engineering (1) F, W, S. Seminar, one hour, discussion, half-hour. Students review current papers in the field of protein engineering and present the ideas contained therein to other students and faculty. May be repeated for credit. Same as Molecular Biology 209 and Engineering CBE209.
210 Molecular Pathophysiology (3) S. Guided seminar format. Topics selected illustrate investigations into range of disease phenotypes from the organ, cell, and molecular level. Students present and guide discussion based upon assigned papers, additional research, and faculty discussions. Goal is to formulate plan of investigation. Prerequisite: consent of instructor.
211 Protein Crystallography (3) S of even years. Lecture, three hours. Introduces students to the theory and practice of macromolecular crystallography. Covers all aspects, including protein crystallization, space groups, phasing methods, electron density map interpretation, refinement and preparation of results for publication. Corequisite: calculus. Prerequisite: consent of instructor. Same as Molecular Biology and Biochemistry 254.
220 Physiology of Muscular Activity (3) W. Lecture, one hour; discussion, three hours. Lectures, tutorials, and readings on hormonal, neural, and activity-related factors regulating phenotypic expression in skeletal and cardiac muscle. Topics include organelle components regulating the contractile process; energy metabolism; protein synthesis and degradation; hormones; neural and mechanical factors. Prerequisite: consent of instructor.
232 Physiology of Ion Channels (3) F. Lecture, two hours; discussion, two hours. An introductory course on the roles ion channels play in important cellular processes such as nerve conduction, synaptic transmission, cell signaling, gene regulation, and cell-cell communication. Demonstrations include patch clamp recording, reconstitution of channels in lipid bilayers, and analysis of single channel properties. Intended for students interested in cell biology, protein structure, and neurophysiology. Prerequisite: consent of instructor. Offered only if sufficient demand exists.
242 Protein Engineering (3) W of even years. The design of novel proteins and their production by genetic manipulation. Principles of protein structure and function and techniques of molecular biology relevant to protein engineering. Applications of protein technology. Prerequisites: Molecular Biology and Biochemistry 203 and 204. Same as Biochemical Engineering CBE242.
261 Protein Stability and Structure (3) S of even years. Lecture, discussions, demonstrations; three hours. Fundamental biophysical principles of the folding and structure of proteins in aqueous and membrane environments. Analysis of key papers concerned with general structural features of proteins, protein folding, and protein structure prediction. Prerequisites: physical chemistry, graduate course in biochemistry; consent of instructor.
281 Signal Transduction (3) S. Lecture, one hour; discussion, three hours. Students read and discuss manuscripts that describe mechanisms by which extracellular signals are transduced across plasma membranes and mechanisms by which cellular response machinery (e.g., ion channels, phospholipases, protein kinases, and the mitogenic pathway) is activated. Prerequisite: consent of instructor.
290 Colloquium in Physiology (1-1-1) F, W, S. Seminar, one and one-half hours. Contemporary research problems in physiology. Research students, faculty, and other invited speakers introduce research and review topics. Prerequisite: consent of instructor. Satisfactory/Unsatisfactory only. May be repeated for credit.
299 Dissertation in Physiology and Biophysics (2 to 12 per quarter) F, W, S, Summer. Preparation and completion of the dissertation required for the Ph.D. or Master of Science degree. Prerequisite: consent of instructor. May be repeated for credit.
