1999-2000 Biology

1999-2000 Bulletin Entry for:

Molecular and Cell Biology

(file last updated: [7/6/1999 - 13:19:29])


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: www.bio.brandeis.edu. 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, especially during development; chromosome structure and chromosomal rearrangements; mechanisms of recombination; developmental genetics; behavior 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.


James Haber (Rosenstiel Center), Chair

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

Kalpana White (Center for Complex Systems), Cochair

Developmental neurogenetics.

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

Developmental neurobiology.

Carolyn Cohen (Rosenstiel Center)

Structural molecular biology.

Laura Davis (Rosenstiel Center)

Cell biology and genetics of yeast. Structure and function of nuclear pores.

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.

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.

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 catlysis.

Marvin Natowicz

Clinical genetics.

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.

Michael Rosbash (Center for Complex Systems)

RNA processing and molecular neurobiology.

Ranjan Sen (Rosenstiel Center)

Molecular immunology. Transcription factors.

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.

Pieter Wensink (Rosenstiel Center)

Structure and function of proteins that regulate transcription.

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.

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 in the middle of the second year, must be in an area outside the student's area of thesis research. The second proposition constitutes a thesis proposal and is taken in the third 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

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Prerequisites: 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

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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 other year.

Ms. Davis

BIOL 104a Structural Approaches to Cell Biology

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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

BIBC 105b Molecular Biology

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Prerequisites: 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

(Formerly BIOL 61a)

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Prerequisites: BIOL 18a,b; BIBC 22a, BIOL 22b. This course may not be repeated for credit by students who have taken BIOL 61a in previous years.

How do complex organisms build themselves starting from single cells? We will examine 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 in even years.

Ms. White

BIOL 112b Genes and Genomes

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Prerequisites: BIBC 22a and BIOL 22b.

Our 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. We explore 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 in even years.

Messrs. Haber and Sen

BIOL 122a Molecular Genetics

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

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 in even years.

Mr. Haber and Ms. Lovett

BIOL 125a Immunology

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Prerequisites: 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

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Prerequisites: 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. We examine 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

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Prerequisites: 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

(Formerly BIOL 32a)

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Prerequisites: 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. We will concentrate on those aspects of cell structure and function that are important for diverse microbial lifestyles. In addition, we will pay special attention to the biology of disease-causing organisms and microbiological problems facing medicine today. Usually offered in odd years.

Ms. Lovett

BIOL 133b Marine Microbial Ecology

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Prerequisites: BIBC 22a and BIOL 22b.

Diversity and evolution of microbial life in the ocean. The fundamental importance of aquatic microbial assemblages in the biosphere. Aerobic, anaerobic, and extreme environments, global biogeochemical cycles, trophic structure of natural communities, energy flow in ecosystems, global warming, bioremediation.

Mr. Epstein

BIOL 134b Topics in Ecology

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Prerequisites: BIBC 22a and BIOL 22b. This course may be repeated for credit. Signature of the instructor required. A library intensive course.

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

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Prerequisites: MATH 10a and b, and either PHYS 10a and 10b, CHEM 11a and 11b, BIBC 22a and BIOL 22b, 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 in odd years.

Mr. Abbott

NBIO 140b Principles of Neuroscience

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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; locomotion, visual processing; learning, among others. Usually offered every year.

Ms. Marder

NBIO 143b Developmental Neurobiology

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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, and mechanisms responsible for generation of connectivity in the nervous system. Usually offered in even years.

Ms. Sengupta

NBIO 144b The Neurobiology of Memory

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Prerequisite: NBIO 140b. Signature of the instructor required.

Topics include definition of the types of memory, genetic and pharmacological perturbations of memory, and neural network approaches to memory. Principal focus on the cellular and molecular basis of memory. Anatomical, biochemical, and physiological work on long-term potentiation in the hippocampus will be extensively discussed. Usually offered in odd years.

Mr. Lisman

NBIO 145b Systems Neuroscience

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Prerequisite: NBIO 140b.

Analysis of how the nervous system processes information and generates behavior, with emphasis on understanding how circuit dynamics result from the interaction of cellular and synaptic processes. Topics include generation of rhythmic behaviors, structure and function of the auditory, visual, and sematosensory systems, representation of sensory information, learning, and memory. Usually offered every year.

Mr. Lisman

NBIO 147a Neurogenetics

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Prerequisites: BIOL 18a, b, BIBC 22a and BIOL 22b. 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

NBCH 148b Cellular Neuroscience

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Prerequisite: NBIO 140b or permission of the instructor. May be taken concurrently with NBIO 140b.

Focuses on the ionic and molecular basis of action and synaptic potentials. Students examine the Hodgkin-Huxley experiments on axonal action potentials and the propagation of action potentials in the dendrites of CNS neurons. Students also examine ionotropic glutamate receptors; including their electrical and molecular properties, interaction with other proteins, and their involvement in synaptic plasticity. Usually offered every year.

Ms. Turrigiano

BIOL 149b Molecular Pharmacology

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Prerequisites: BIBC 22a, 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 pharmaco-kinetics, 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 1996.

Ms. Griffith

BIOL 160b Human Reproductive Biology

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Prerequisites: 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. Hayes

BIOL 172b Cancer

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Prerequisite: BIBC 22a and BIOL 22b. Enrollment limited to 80.

Cancers are a collection of diseases that disturb the most fundamental rules of behavior of the cells in a multicellular organism. This course will cover the nature and cause of cancer, the molecular mechanism of oncogenesis, and the molecular biology of tumor viruses. Usually offered in even years.

Mr. Ren

BIOL 173b Programmed Cell Death

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Prerequisites: 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 in even years.

Mr. Fulton

BIOL 175b Advanced Immunology

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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 in odd years.

Messrs. Ren and Sen


For biophysics consult biophysics offerings in this Bulletin.

(200 and above) Primarily for Graduate Students

BIOL 200a Proseminar

For first year graduate 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.

Mr. Simister

BIOL 220a Clinical Genetics II

Prerequisites: 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.

Mr. Natowicz

BIOL 221b Advanced Topics in Structural Biology

Prerequisites: BIBC 22a and BIOL 22b, or the equivalent.

Analysis of current literature on cell structure. Usually offered every year.

Mr. DeRosier

BIBC 224b The RNA World

Prerequisite: BCHM 100a, 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. Usually offered every year.

Ms. Moore

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 302b Readings in Plant Development

Offered on demand.

Mr. Klein

BIOL 305d Topics in Molecular Genetics and Development

Usually offered every year.

Mr. Rosbash

NBIO 306d Topics in Neurobiology

Usually offered every year.

Ms. Turrigiano

BIOL 307d Topics in Immunology

Usually offered every year.


BIOL 310d Structural Biology Journal Club

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. Fulton