University Bulletin 2001-02 Biology University Bulletin 2001-02
Molecular and Cell Biology


The graduate program in molecular and cell biology, leading to the degree of Doctor of Philosophy, is designed to provide each student with the theoretical foundations and research experience needed to become an independent and original investigator of basic biological phenomena. Preparation is achieved through the combination of (1) a flexible curriculum of courses tailored for each student's specific needs, (2) a set of laboratory rotations that acquaints each entering student with current research techniques and permits exploration of possible research areas, and (3) a proseminar specifically for first-year students and a series of journal clubs that keep students abreast of significant research findings and develop confidence with reading research literature and giving oral presentations. First-year students participate in all three aspects of our graduate program and are thus quickly integrated into the biological research community at Brandeis. A strength of our program is frequent interactions between students and faculty, formal and informal.

Thesis research leading to the Ph.D. degree is carried out under the personal direction of a faculty member. A complete list of faculty research interests and recent publications is available from the biology department or can be viewed on the World Wide Web at: Potential applicants are urged to obtain this information. As a general orientation, the following areas of research are among those represented in the program: molecular biology of the regulation of gene expression; chromosome structure and chromosomal rearrangements; mechanisms of recombination; developmental genetics; behavioral genetics and neural development; biophysics of single nerve cells; learning and memory; integration of neural function; immunogenetics; immune cell differentiation and development; molecular biology of the immune system; regulation of muscle contraction; molecular and cell architecture; organization of subcellular structures; structure and function of proteins.

How to Be Admitted to the Graduate Program

The general requirements for admission to the Graduate School, given in an earlier section of this Bulletin, apply to candidates for admission to this area of study. The student's undergraduate record should ordinarily include courses equivalent to those required of undergraduates concentrating in biology at this institution. Students who are deficient in some of these subjects, but whose records are otherwise superior, may make up their deficiencies while they are enrolled as graduate students. In exceptional cases, students may be excused from some of these requirements. Students with serious deficiencies must, however, expect to add additional time to their graduate program in order to satisfy the deficiencies.

Applicants must take the Graduate Record Examination.

Since the summer months provide an important opportunity for uninterrupted laboratory work, the Molecular and Cell Biology Program provides 12-month stipend support for all full-time students.


Michael Rosbash (Center for Complex Systems), Chair

RNA processing and molecular neurobiology.

Susan Birren, Senior Honors Coordinator (Center for Complex Systems)

Developmental neurobiology.

Carolyn Cohen (Rosenstiel Center)

Structural molecular biology.

David DeRosier (Rosenstiel Center)

Structural studies of actin, actin-containing cytoskeletal assemblies, and bacterial flagella.

Chandler Fulton

Cell differentiation and selective gene expression in eucaryotic cells. Morphogenesis of cell shape and assembly of cell organelles, especially flagella.

Leslie Griffith (Center for Complex Systems)

Biochemistry of synaptic plasticity.

Bruce Goode (Rosenstiel Center)

Biochemistry and genetics of yeast cytoskeleton.

James Haber (Rosenstiel Center)

Genetics and molecular biology of yeast meiotic and mitotic recombination. Mating-type switching. Repair of broken chromosomes.

Jeffrey Hall (Center for Complex Systems)

Neurogenetics and molecular neurobiology of higher behaviors in Drosophila.

Kenneth Hayes (Director, Foster Animal Lab)

Comparative nutritional pathophysiology in man and animals. Lipoprotein metabolism and atherogenesis, cholelithiasis.

Elaine Hiller

Human genetics.

Susan Lovett (Rosenstiel Center)

Genetics and molecular biology of bacteria and yeast. DNA repair. Recombination and mutogenesis.

Melissa Moore

Molecular biology of self-splicing introns and the splicesome. Mechanisms of RNA catalysis.

Gregory Petsko (Director, Rosenstiel Center)

X-ray crystallographic analysis of protein structure and enzyme mechanisms.

Joan Press (Rosenstiel Center)

Developmental immunology and immunogenetics.

Ruibao Ren (Rosenstiel Center)

Signal transduction.

Ranjan Sen (Rosenstiel Center)

Molecular immunology. Regulation of gene expression.

Piali Sengupta (Center for Complex Systems)

Developmental neurobiology in C. elegans.

Neil Simister (Rosenstiel Center)

Molecular immunology. Antibody transport.

Lawrence Wangh

Molecular controls of DNA replication in Xenopus egg.

Michael Welte (Rosenstiel Center)

Regulation of motor-driven transport.

Kalpana White (Center for Complex Systems)

Developmental neurogenetics.

Requirements for the Degree of Master of Science

Program of Study

The program is designed to guide each student toward realizing her or his potential as an independent research biologist. Students are encouraged to become experts in the theory and practice of their chosen area of research, as well as to obtain breadth in other areas strongly represented in the program. Research areas include genetics, molecular biology, developmental biology, cell biology, structural biology, immunology, and neurobiology. Graduate courses are available in all of these areas. A total of six courses are required for the degree. Each student will conduct an original investigation and submit a research thesis to the biology department graduate committee for review, or complete four, nine-week research rotations.

Residence Requirement

The minimum residence requirement is one year.

Requirements for the Degree of Doctor of Philosophy

Program of Study

Students are expected to obtain a knowledge of the principles and techniques of three of the areas represented in the program, i.e., genetics, developmental biology, molecular biology, neurobiology, immunology, cell biology, and structural biology. The background a student is expected to have in these areas will be covered in courses given by the program. Entering students also participate together in a proseminar, an introduction to the research literature of biology. Students take two courses each semester in the first year, with a total of six required for the degree. In the first year, students will complete four, nine-week rotations in at least four different laboratories. Throughout the graduate years, students remain involved in seminar courses, journal clubs, presentations of research, colloquia, and research courses.

Each student will choose his/her specific field of interest and will apply for a permanent advisor to be agreed upon by the program at the end of the first year. The advisor will assist the student in planning a well-balanced program in his/her specific field of interest. In addition, the advisor will ordinarily serve as the chair of the student's dissertation examining committee.

Teaching Requirement

At least one year of teaching experience (or equivalent) is required of all degree candidates.

Residence Requirement

The minimum residence requirement is three years.

Language Requirement

There is no foreign language requirement for the Ph.D. degree.

Qualifying Examination

The qualifying examination consists of two research propositions in which the student identifies an important and interesting research problem and then proposes the experiments to attack it. The propositions are written and the student gives an oral defense. The first proposition, which is taken at the end of the first year, must be in an area outside the student's area of thesis research. The second proposition constitutes a thesis proposal and is taken at the end of the second year.

Dissertation and Defense

Each student will conduct an original investigation. After submission of the dissertation, the candidate will be expected to present the principal results of his or her work and its significance during an examination in defense of the dissertation. The examining committee must include one faculty member from outside the University. A public seminar to the University community is also required.

Courses of Instruction

(100-199) For Both Undergraduate and Graduate Students

BIOL 102b Structural Molecular Biology

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a) and BIOL 22b; or permission of the instructor.

An introduction to the structural basis of molecular biology. It will include background material on the designs of proteins and nucleic acids and their assembly, as well as the techniques used to visualize structure. A major theme will be the physical and chemical basis for specificity in molecular recognition. Usually offered every year.

Mr. DeRosier

BIOL 103b Mechanisms of Cell Functions

[ sn ]

Prerequisite: BIOL 22b or permission of the instructor. Enrollment limited to 50.

An advanced course focusing on a mechanistic understanding of cell biological processes and the methods by which these processes are elucidated. Papers are chosen to illustrate a variety of experimental approaches including genetics, biochemistry, microscopy, and the design and use of in vitro assays. Topics include cell cycle dynamics, secretion, protein folding and degradation pathways, signal transduction, intracellular transport, nuclear architecture, and the cytoskeleton. Usually offered every second year.

Messrs. Goode and Welte

BIOL 104a Structural Approaches to Cell Biology

[ sn ]

Prerequisite: BIOL 22b.

The purpose of this course is to rigorously develop the foundations of structural cell biology. The first part of this course reviews the mathematical methods and physical principles required to understand how the structure of macromolecules and macromolecular assemblies are determined. The second part of the course deals specifically with individual methods, including light microscopy, higher resolution electron microscopy of macromolecules, and protein crystallography. Usually offered every third year. Last offered in the fall of 1996.

Mr. DeRosier

BIOL 105b Molecular Biology

(Formerly BIBC 105b)

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a) and BIOL 22b.

Examination of molecular processes in replication and expression of genetic information and techniques by which this understanding has been achieved. Topics include recombinant DNA and other molecular biological techniques, structure and organization of DNA in chromosomes, DNA replication, transcription and regulation of gene expression, RNA structure and processing, mRNA stability, and other mechanisms of post-translational control. Usually offered every year.

Messrs. Rosbash and Sen

BIOL 111a Developmental Biology

[ sn ]

Prerequisite: BIOL 22b.

How do complex organisms build themselves starting from single cells? Examines how processes such as fertilization, embryogenesis, cell differentiation, and tissue-specific gene expression occur; what is known about the key molecules and genes that orchestrate these processes; and how genetic changes affecting these processes underlie the evolution of body form. Usually offered every second year.

Ms. Birren

BIOL 112b Genes and Genomes

[ sn ]

Prerequisite: BIOL 22a (Formerly BIBC 22a).

Understanding of genes in chromosomes has been radically transformed by the complete sequencing of the genomes of several prokaryotic and eukaryotic organisms and by the continuing Human Genome Project. Explores new techniques to examine the arrangement of genes and chromosomes in the nucleus, CHIP and SAGE analysis of global gene expression, enhancer trapping and tissue-specific gene expression, and transformation and gene modification in bacteria, yeast, fruit flies, worms, mice, and humans. Usually offered every second year.

Messrs. Haber and Sen

BIOL 122a Molecular Genetics

[ sn ]

Prerequisite: BIOL 22a (Formerly BIBC 22a).

A lecture and literature-based course concerning mechanisms that control genetic change and genetic stability. Lectures cover the topics of genetic mutation, genetic recombination, repair of genetic damage, and chromosome structure and transmission. Research papers of current and historical interest will be discussed. Usually offered every second year.

Mr. Haber and Ms. Lovett

BIOL 125a Immunology

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a) and BIOL 22b.

Topics include properties, functions of cells involved in immunity; genes, structure, function of immunoglobins and T cell receptors; cell interactions; antigen recognition; lymphokines; tolerance; lymphocyte differentiation; genetic regulation; viral immunity; autoimmunity; AIDS; vaccines. Usually offered every year.

Ms. Press

BIOL 126b Protein Structure and Disease

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a) and BIOL 22b, or the equivalent, or permission of the instructor. Enrollment limited to 25.

Reviews the basic principles of protein structure, so that the functional aspects of different protein designs may be understood. Examines various protein mutations related to certain molecular diseases and the architecture of some key viruses and their infectivity. Consideration of drug design is an integral part of the course. Student presentations are essential to the course. Usually offered every third year. Last offered in the spring of 1998.

Ms. Cohen

BIOL 128a Human Genetics

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a) and BIOL 22b. Enrollment limited to 50.

Survey of classical and nonclassical patterns of inheritance; cytogenetics; applications of molecular genetics techniques in human genetics, analysis of variation, gene mapping, identification of candidate genes and genetic disease diagnoses; single gene vs. complex inheritance; computer databases for human genetic research; and human population genetics. Usually offered every year.

Ms. Hiller

BIOL 132a General Microbiology

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a) and BIOL 22b, (BCHM concentrators may substitute BCHM 100a); CHEM 25a and 25b.

A survey of the physiology of bacteria and other microorganisms. Concentrates on those aspects of cell structure and function that are important for diverse microbial lifestyles. In addition, pays special attention to the biology of disease-causing organisms and microbiological problems facing medicine today. Usually offered every second year.

Ms. Lovett

BIOL 134b Topics in Ecology

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a) and BIOL 22b. This course may be repeated for credit. Signature of the instructor required.

Annually, a different aspect of the global biosphere is selected for analysis using contemporary tools and approaches. In any year the focus may be on specific ecosystems (e.g., terrestrial, aquatic, tropical, arctic), populations, system modeling, or the contributions of physical or chemical factors defining a particular system. Please consult the Course Schedule for the particular topic. Usually offered every year.


NBIO 136b Computational Neuroscience

[ sn ]

Prerequisite: MATH 10a or PHYS 10a or approved equivalents.

An introduction to methods and results in mathematical and computer modeling of neural systems. Topics include the basic biophysics of ion conduction, single- and multi-compartment neuron models, information theory and neural codes, the representation and processing of images by the visual system, and models of synaptic plasticity, learning, and memory. Usually offered every second year.

Mr. Abbott

NBIO 140b Principles of Neuroscience

[ sn ]

Prerequisite: BIOL 22b or permission of the instructor.

Basic principles of neurobiology. Topics include ion channels and their role in generating resting and action potentials; basics of synaptic physiology and pharmacology; visual processing; learning; and brain structure. Usually offered every year.

Ms. Marder

NBIO 143b Developmental Neurobiology

[ sn ]

Prerequisite: BIOL 22b or permission of the instructor.

Discusses the mechanisms used in the development of the nervous system. Topics include determination of neuronal cell fates, neuronal differentiation and pattern formation, neuron survival and growth, and mechanisms responsible for generation of connectivity in the nervous system. Usually offered every second year.

Ms. Sengupta

NBIO 145b Systems Neuroscience

[ sn ]

Prerequisite: NBIO 140b.

Deals with the fundamental issues relating to the function of the central nervous system. Topics covered include perception, memory, consciousness and action. Emphasizes the insight that can be gained by multiple perspectives, in particular: anatomy, cellular physiology, in vivo recordings from awake-behaving animals, psychophysics (behavior), and computational modeling. Usually offered every year.

Mr. Lisman

NBIO 147a Neurogenetics

[ sn ]

Prerequisites: BIOL 18a and BIOL 22a (Formerly BIBC 22a). Signature of the instructor required.

Development and function of the nervous system and responses of excitable cells studied in neurological and behavioral mutants. Characterization and manipulation of genes, defined by these mutations and using molecular biological tools. Organisms: microbes, roundworms, fruit flies, mammals. Neurobiological areas: embryonic neural development, nerve cell differentiation and pattern formation, membrane excitability, responses to visual and chemical stimuli, biological rhythms, and reproductive behavior. Usually offered every third year. Last offered in the spring of 1999.

Mr. Hall

NBIO 148b Cellular Neuroscience

(Formerly NBCH 148b)

[ sn ]

Prerequisite: NBIO 140b or permission of the instructor. May be taken concurrently with NBIO 140b. This course may not be repeated for credit by students who have taken NBCH 148b in previous years

Focuses on the ionic and molecular basis of action and synaptic potentials. Students examine the Hodgkin-Huxley experiments on axonal action potentials and the original research literature dealing with all aspects of synaptic transmission, neuronal excitability, and their modulation. Usually offered every year.

Ms. Griffith

BIOL 149b Molecular Pharmacology

[ sn ]

Prerequisites: BIOL 22b, and CHEM 25a and b. NBIO 140b strongly recommended. Signature of the instructor required.

Covers the essentials of pharmacology and the study of the actions of chemical agents (drugs, toxins, neurotransmitters, and hormones) that interact with living systems. Emphasizes molecular mechanisms of neuropharmacology. Topics include pharmacokinetics, hormone action, autonomic pharmacology, and the psychopharmacology of drugs of abuse and mental disorders. Usually offered every third year. Last offered in the spring of 2001.

Ms. Griffith

BIOL 160b Human Reproductive Biology

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a) and BIOL 22b. Signature of the instructor required.

This course deals with hormonal, cellular, and molecular aspects of gametogenesis, fertilization, pregnancy, and birth. We will also discuss pathological and abnormal variations that occur and the available medical technologies for intervention, correction, and facilitation of these processes. Usually offered every year.

Mr. Wangh

BIOL 172b Growth Control and Cancer

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a) and BIOL 22b. Enrollment limited to 80. A library intensive course.

Covers the fundamental rules of behavior of cells in multicellular organisms. Examines cellular and molecular mechanisms that govern cell growth, differentation and survival in normal cells as well as how this regulation is disrupted in cancer. Usually offered every second year.

Ms. Birren

BIOL 173b Programmed Cell Death

[ sn ]

Prerequisites: BIOL 22a (Formerly BIBC 22a), BIOL 22b, and BCHM 100a or permission of the instructor. Enrollment limited to 24.

Apoptosis, the programmed death of vertebrate cells, is essential for normal development and health. We examine the topic through recent research papers, lectures, and student presentations, with emphasis on the mechanism of apoptosis and its role in human diseases such as cancer and neurological disorders. Usually offered every second year.

Mr. Fulton

BIOL 175b Advanced Immunology

[ sn ]

Prerequisite: BIOL 125a or permission of the instructor.

A survey of recent advances in molecular immunology. Topics include hematopoietic stem cell biology, blood lineage commitment, growth factor signal transduction, the nature and specificity of antigen receptors, the regulation and mechanism of V(D)J recombination, and B and T cell development. Usually offered every second year.

Mr. Sen


For biophysics consult biophysics offerings in this Bulletin.

(200 and above) Primarily for Graduate Students

BIOL 200a Proseminar

For first-year Ph.D. students. Emphasizes the reading, analysis, discussion, and writing of research papers. We also examine how scientists frame important questions and design appropriate experiments. Papers will be chosen for discussion, covering molecular biological, genetic, and biochemical approaches. Usually offered every year.

Messrs. Goode and Welte

BIOL 220a Clinical Genetics II

Prerequisite: Completion of BIOL 204b or permission of the instructor.

Continuation of BIOL 204 with emphasis on the genetic and developmental disorders of most major organ systems. A case-based, problem-solving approach is emphasized. Usually offered every year.


BIBC 224b The RNA World

Prerequisite: BCHM 100a, BIOL 105b (Formerly BIBC 105b), or permission of the instructor.

This course employs seminars and lectures to approach a wide range of topics in RNA research. Topics include RNA enzymes, RNA structure, protein-RNA interactions, pre-MRNA splicing, and RNA localization.

Ms. Moore

NBIO 250d Neuroscience Proseminar

Limited to first and second-year neuroscience Ph.D. students.

Required seminar for first and second year graduate students in the neuroscience Ph.D. program. Discusses relevant papers from the current literature with an emphasis on increasing oral presentation skills, experimental design, and proposal writing. Usually offered every year.

Mr. Nelson

BIOL 300a and b Biological Research

Primarily for the first-year student with the purpose of introducing him or her to biological research and to the work in progress in the laboratories of a number of faculty members. In consultation with the graduate advisor, the student plans a sequence of such tenures, each comprising nine weeks or more, and then carries out experimental investigations under the guidance of the faculty members involved. Usually offered every year.


BIOL 305d Topics in Molecular Genetics and Development

Usually offered every year.


NBIO 306d Topics in Neurobiology

Usually offered every year.

Ms. Birren

BIOL 307d Topics in Immunology

Usually offered every year.


BIOL 316d Mechanisms of Recombination

Usually offered every year.

Mr. Haber and Ms. Lovett

BIOL 320d Current Topics in Drosophila Molecular Genetics

Usually offered every year.

Ms. White

NBIO 340d Computational and Systems Neurosciences

Usually offered every year.

Mr. Abbott

BIOL 350d Graduate Student Research Seminar

Usually offered every year.


BIOL 401d Dissertation Research

Independent research for the Ph.D. degree. Specific sections for individual faculty members as requested.


CONT 300b Ethical Practice in Health-Related Sciences

Required of all first-year graduate students in health-related science programs. Not for credit.

Scientists are becoming increasingly aware of the importance of addressing ethical issues and values associated with scientific research. This course, taught by University faculty from several graduate disciplines, will cover major ethical issues germane to the broader scientific enterprise, including areas or applications from a number of fields of study. Lectures and relevant case studies will be complemented by two public lectures during the course. Usually offered every year.

Mr. Lowenstein