Department of Molecular Biology

Chair

Lynn W. Enquist

Associate Chair

James R. Broach

Director of Graduate Studies

Bonnie L. Bassler

Professor

Bonnie L. Bassler

David Botstein, also Lewis-Sigler Institute for Integrative Genomics

James R. Broach

Edward C. Cox

Lynn W. Enquist

S. Jane Flint

Jacques R. Fresco

Ihor R. Lemischka

John J. Hopfield

Austin Newton

Mark D. Rose

Paul D. Schedl

Gertrud M. Schupbach

Jean E. Schwarzbauer

Thomas E. Shenk

Yigong Shi

Thomas J. Silhavy

Lee M. Silver, also Woodrow Wilson School

Jeffry B. Stock

David W. Tank, also Physics

Shirley M. Tilghman

Eric F. Wieschaus

Ned S. Wingreen

Virginia A. Zakian

Associate Professor

Michael J. Berry

Elizabeth Gavis

Frederick M. Hughson

Saeed Tavazoie, also Lewis-Sigler Institute for Integrative Genomics

Samuel Wang

Assistant Professor

Hilary A. Coller

Rebecca Burdine

Jonathan T. Eggenschwiler

Zemer Gitai

Yibin Kang

Manuel Linás, also Lewis-Sigler Institute for Integrative Genomics

Coleen Murphy, also Lewis-Sigler Institute for Integrative Genomics

Hays S. Rye

Lecturer with Rank of Professor

Leon Rosenberg, also Woodrow Wilson School

Senior Lecturer

Alison Gammie

Karen Malatesta

Lecturer

Philip Felton

Daniel Notterman

Heather A. Thieringer

John Douglas Welsh

Associated Faculty

William Bialek, Physics

Jannette L. Carey, Chemistry

Michael H. Hecht, Chemistry

Leonid Kruglyak, Ecology and Evolutionary Biology, Lewis-Sigler Institute for Integrative Genomics

Laura F. Landweber, Ecology and Evolutionary Biology

Joshua D. Rabinowitz, Chemistry

Clarence E. Schutt, Chemistry

Stanislav Shvartsman, Chemical Engineering

Mona Singh, Computer Science

David Stern, Ecology and Evolutionary Biology

Olga Troyanskaya, Computer Science, Lewis-Sigler Institute for Integrative Genomics

Ron Weiss, Electrical Engineering

David Wood, Chemical Engineering

 

The graduate program in the Department of Molecular Biology fosters the intellectual development of modern biologists. We welcome students from a variety of educational backgrounds, and offer an educational program that goes well beyond traditional biology. The molecular biology department at Princeton is a tightly knit, cohesive group of scientists that includes undergraduate and graduate students, postdoctoral fellows, and faculty with diverse but overlapping interests. Graduate students have a wide choice of advisers, with a broad spectrum of interdisciplinary interests and research objectives.

The graduate program offers each entering student the opportunity, with the help of faculty advisers, to design the intellectual program that best meets his or her unique scientific interests. Each student chooses a series of research rotations with faculty members in molecular biology and associated departments (chemistry, computer science, ecology and evolutionary biology, engineering, physics, and psychology). Entering students, with the aid of the graduate committee, select core and elective courses from a large number of offerings in a variety of departments and disciplines. This combination of a cohesive department, one-on-one advising, and individualized programs of course work and research, provides an ideal environment for graduate students to flourish as independent scientists.

Areas of concentration include biochemistry, biophysics, cancer, cell biology, computation and theory, development, evolution, genetics, genomics, microbiology and virology, neuroscience, policy, and structural biology.

Prior Preparation

While there are no rigid prerequisites for admission, students are expected to have taken calculus, organic chemistry, and biochemistry. Undergraduate courses in physical chemistry, molecular biology, and genetics provide important background. Students who have not taken these courses may need to take them during the first two years of their graduate study.

The Graduate Committee advises each new student on a course of study based on the student’s background and interests.

Course Work

Graduate students must complete five courses. Two of them must be core courses. Students can take more core courses if they desire and these courses count toward the five-course requirement.

Eight core courses are offered: Cellular Biochemistry (504), Molecular Biology of Prokaryotes (505), Molecular Biology of Eukaryotes (506), Developmental Biology (507), Topics in Neurobiology (508), Biological Dynamics (514), Method and Logic in Quantitative Biology (515), and Lab in Neuroscience (549).

A variety of other graduate and upper-level undergraduate courses in molecular biology and related departments are also offered to fulfill the five-course requirement. These courses normally include:

Fall

528 Developmental Genetics

545 Advanced Microbial Genetics

547 Special Topics in Molecular Biology

551 Introduction to Genomics and Computational Molecular Biology

559 Viruses: Strategy and Tactics

Spring

523 Molecular Basis of Cancer

525 Intercellular Signaling and Signal Transduction

535 Advanced Topics in Cell Biology

548 Special topics in Molecular Biology

557 Analysis and Visualization of Large-Scale Genomic Data Sets

561 Scientific Integrity in the Practice of Molecular Biology

Students with special interests may substitute the above courses with other appropriate courses from a variety of departments with the permission of the Graduate Committee. For example, many courses in chemistry, computer science, ecology and evolutionary biology, physics, and psychology are offered. The Graduate Committee encourages and helps graduate students choose broadly from among these options. Our aim is to help each graduate student successfully design an appropriate educational program to fulfill his or her unique needs and goals.

In addition to taking courses, first-year students participate in two colloquia. In the fall they attend a series of informal talks given by each faculty mentor. These discussions are designed to introduce first-year students to current research projects that might serve as rotation and thesis topics. All graduate students also attend weekly research seminars given by graduate students. This graduate colloquium provides both experience in the presentation of research results and a forum for scientific discussion with peers.

By the end of the second year, students must have completed five courses, achieving an average grade of B or better.

Research

Students complete three laboratory rotations with different advisers as part of their research training during the first year of study (MOL 540, MOL 541 Research Projects); a fourth rotation is optional.

Students who complete a full rotation (approximately 10 weeks of research) the summer before entering graduate school are assigned a rotation in September along with other entering students. Those who begin research late in the summer (after July 15) may continue in that laboratory for the September rotation.

A student may elect to work with any member or associated member of the program. Students who desire to work with members outside the program may do so with the approval of the director of graduate studies.

General Examination

The General Examination is usually administered in January of the second year of study, after students have met all formal course requirements. This three-hour oral examination is administered by three faculty members from the graduate program, none of whom may be the student’s thesis adviser. The examination consists of two parts:

The first section, the thesis proposal, probes the student’s depth of knowledge in the graduate student’s chosen research field, and examines the ability of the student to justify and defend his or her goals, experimental logic and methods, and the significance of his or her proposed research plan.

The second tests the overall skill of the graduate student in areas of molecular biology that are aligned with, but are not identical to, his or her chosen area of thesis research. Each student is given a distinct, influential paper published during the past year, covering a research topic related to the thesis proposal. This paper is assigned two weeks prior to the examination and chosen by the examining committee, with the aid of the student’s thesis adviser. In this portion of the examination, the paper serves as a starting point for a discussion of relevant findings in the field. Students who do not receive a passing grade on all parts of the examination may retake it within one year.

A Master of Arts (M.A.) degree may be awarded to students who complete the formal courses and three laboratory rotations required for Ph.D. students, and who demonstrate an appropriate level of research competency. Research experience must include at least one year of independent work in the laboratory, and competency must be demonstrated in writing. A faculty mentor and the Graduate Committee must approve the master’s paper.

Dissertation Research, Writing, and Final Public Oral Examination

Each graduate student chooses a thesis committee that consists of the thesis adviser and two other faculty members who are knowledgeable in the student’s area of research. The thesis committee meets formally with the graduate student at least once per year, and sometimes more frequently on an informal basis. The responsibility of this committee is to advise students during the course of their research. When the research is completed, the student writes the dissertation, which is then read by the adviser. Next, two second readers chosen by the student read the dissertation. Usually the second readers are the other members of the student’s thesis committee. Upon approval, the student gives a final, public oral presentation of his or her research to the department.

Teaching Experience

Students are normally required to teach in two undergraduate-level courses. Students may have the opportunity to do additional teaching if they wish to gain more experience. The first assignment is normally a laboratory course, while the second is normally a major undergraduate lecture course.

Financial Support

All students enrolled in the program receive tuition and a generous stipend. In addition, many students receive prestigious fellowships from agencies such as the National Science Foundation and the Howard Hughes Medical Institute.

Departmental Seminars

Recent research advances are presented in the weekly departmental seminars and the frequent journal clubs organized by many of the research groups. An annual retreat is held during a weekend in October, offering students an opportunity to find out about the current research activities in the department. All faculty, students, and postdoctoral fellows attend this two-day meeting, where the results of current projects are presented by each laboratory in oral and poster presentations.

Joint M.D./Ph.D. Program

The Graduate School has partnered with the Robert Wood Johnson Medical School (RWJMS) and the Rutgers University (New Brunswick) Graduate School of Biomedical Sciences to serve as a Ph.D. research training site for students enrolled in the M.D./Ph.D. program of RWJMS.

Students admitted to the M.D./Ph.D. program at RWJMS perform laboratory rotations at Princeton during the summer before and the summer after the first year of the pre-clinical portion of the program, prior to their enrollment as doctoral students, and subject to the approval of a Princeton faculty member. Following the second rotation, a student chooses a laboratory for his or her Ph.D. research by mutual agreement with a faculty adviser and with the approval of the Graduate School.

Students who are accepted to work with a faculty member in, or an affiliated faculty member of the Department of Molecular Biology enter the Ph.D. program and receive that degree from Princeton. These students fulfill Graduate School and departmental requirements, including the one-year residence requirement, and passing the general and final public oral examinations. (It is likely that pre-clinical course work at RWJMS will substitute for the department’s core curriculum.)

The Ph.D. portion of the joint program is expected to take three to four years. Extension beyond a fourth year requires the approval of the Academic Affairs Committee of the joint-degree program.

Facilities and Equipment

All areas of the department in Lewis Thomas Laboratory, Guyot Hall, Moffett Laboratory, George LaVie Schultz Laboratory, Hoyt Laboratory, and the Carl Icahn Laboratories are fully equipped for contemporary research and include tissue-culture facilities, controlled-temperature rooms, animal quarters, and instrument rooms. In addition, the department houses several specialized facilities, which are maintained and run by trained technicians and available for use by all department members. These include facilities for the production of transgenic mice and monoclonal antibodies. A flow-cytometry facility allows analysis of individual cells. The Syn/Seq facility performs nucleic acid and peptide sequencing and synthesis, as well as protein analysis by mass spectrometry. The imaging facility contains several confocal microscopes, a deconvolution microscope, and a transmission electron microscope. Microarray and computation facilities located in the Icahn building are available for the entire department. Members of the department also share the use of specialized equipment, such as X-ray crystallography facilities and electronics and machine shops. The department has extensive networked computing facilities, connecting hundreds of individual laboratory computers, a departmental computer facility with numerous personal computers, the department’s new multiprocessor LINUX cluster, and the University’s Redhat Linux cluster.

Reference books, periodicals, and texts pertinent to molecular biology are available in the biology and the chemistry libraries. Computer terminals in every laboratory, the molecular biology computer cluster, and the library provide online access to many extensive bibliographic databases and online journals. Many databases and journals are also available through the University computer network.

Courses

MOL 504 Cellular Biochemistry

Frederick M. Hughson

Cell structure and function are examined, with an emphasis on the molecules and molecular assemblies that underlie it. Topics include protein structure, biogenesis, and degradation; enzyme catalysis, membranes, and ion channels; the cytoskeleton; and intracellular trafficking. We also discuss the mechanisms cells use to integrate information derived from the extracellular matrix, growth factors, and neighboring cells. A major focus of the class is on learning to parse and discuss papers from the primary literature.

MOL 505 Molecular Biology of Prokaryotes

Thomas J. Silhavy

Advanced-level discussions of the genetics and the molecular biology of prokaryotic organisms and their associated bacteriophages. Emphasis is on original research papers, and extensive reading is required. Topics include the genetic code, mutagenesis, mechanisms of DNA replication, recombination, repair and transposition, gene structure and function and mechanisms of gene regulation, and protein synthesis and export.

MOL 506 Molecular Biology of Eukaryotes

Paul D. Schedl, Saeed Tavazoie

Discussion of gene structure and organization, chromatin and chromosome structures, mechanisms of replication and recombination, and mechanisms of gene expression and regulation in eukaryotic cells. Emphasis is on the unique features of eukaryotic systems, with examples given from higher and lower eukaryotes.

MOL 507 Developmental Biology

Rebecca Burdine

Selected topics in the cell biology and development of multicellular organisms, with an emphasis on basic principles and underlying molecular mechanisms. Topics include gradients and pattern formation during embryogenesis, receptors and intracellular signaling, cell motility and cell movements, neuronal pathfinding and patterning in the vertebrate neural tube, genetic redundancy and genomic organization. Classes center on critical reading of the primary literature.

MOL 508 Advanced Topics in Neurobiology

Michael J. Berry

Course focuses on original scientific literature and class discussion. Readings center on major problems and current research in neuroscience and cover three broad areas: information theory and neural coding; computation at the level of synapses, cells, and circuits; persistent activity and oscillations.

MOL 512 Molecular and Biomolecular Imaging (see CHM 514)

MOL 514 Biological Dynamics (also APC 514 and EEB 514)

Staff

Introduction to the mathematical description of quantitative phenomena in living systems; Hodgkin Huxley equations of nerve membranes; the generation of spatial patterns in development, single cells, and colonies of cells; chemotaxis; the population of dynamics of disease; dynamics activity of networks of neurons; intracellular chemical and gene-networks. Emphasis on formulation and experimental basis for the equations, and their relationship to significant biological issues.

MOL 515 Method and Logic in Quantitative Biology (also PHY 570)

David Botstein, Ned Wingreen

Close reading of published papers illustrating the principles, achievements, and difficulties that lie at the interface of theory and experiment in biology. Two important papers, read in advance by all students, are considered each week. Emphasis will be on student discussion; topics include cooperativity, robust adaptation, kinetic proofreading, sequence analysis, clustering, phylogenetics, analysis of fluctuations, and maximum likelihood methods.

MOL 523 Molecular Basis of Cancer

James R. Broach, Yibin Kang

Designed to explore the molecular events that contribute to the onset and progression of human cancer. We review the central elements that make up the cell cycle, followed by a survey of the signal transduction and checkpoint pathways that regulate and coordinate the cell cycle with other cellular events. We discuss oncogenes, tumor suppressor genes, and mutator genes. We then explore specific clinical case studies in light of the molecular events underlying different forms of cancer.

MOL 525 Intercellular Signaling and Signal Transduction

James Broach, Gertrud Schupbach, Jean Schwarzbauer

Explores the interactions of cells with their surroundings at a molecular and cell biological level. Begins with an introduction to a number of basic signal transduction pathways, a characterization of their respective receptors and the molecular pathways that communicate between the cell surface and the nucleus. Discusses how signaling establishes axes of cell polarity and migratory pathways by producing changes in the cytoskeleton, and how cells interact with extracellular matrix molecules. Addresses the cell’s response to nutritional cues and other extracellular signals that influence cell growth, cell division, and cell physiology.

MOL 528 Developmental Genetics

Elizabeth Gavis, Paul D. Schedl

The development of invertebrates and vertebrates, emphasizing genetic techniques used to characterize gene activity. Topics include mutagenesis, genetic mosaics and cell lineage, pattern formation during embryogenesis, cell-cell interactions, sex determination, and homeotic loci. Class discussions are held, focusing on original scientific literature and student presentations.

MOL 535 Advanced Topics in Cell Biology

Staff

Signaling in eukaryotic cells is important in diverse areas such as cancer, development, immunology, and metabolic homeostasis. Molecular mechanisms of signaling are studied through current and classic literature. Students must choose a relevant topic and present critical concepts in the area.

MOL 540, 541 Research Projects in Molecular Biology (Laboratory Rotations)

Staff

Students perform research in the laboratories of potential faculty advisers.

MOL 545 Advanced Microbial Genetics

Bonnie L. Bassler, Mark D. Rose

An in-depth discussion of the analysis of microbial systems, emphasizing examples from both prokaryotes and lower eukaryotes, including Salmonella, E. coli, and yeast. The first part of the course features journal article-based discussions of the rationale, uses and limitations of advanced methods of genetic analysis, including suppression, synthetic lethality, and unlinked non-complementation. The remainder consists of student-led seminars on topics of current interest. In addition to the scientific content, students gain considerable proficiency in the public presentation of scientific seminars.

MOL 547, 548 Special Topics in Molecular Biology

Staff

Selected topics in the areas of molecular biology, cell biology, genetics, and molecular genetics, with the subject matter changing yearly. Seminars are given by graduate students on topics related to their interests and/or thesis research areas.

MOL 549 Laboratory in Neuroscience

David W. Tank

The biophysics of neurons and synapses is explored using electrophysiological and optical recording methods. The fundamental phenomena to be studied include passive membrane properties, action potential generation, synaptic transmission and plasticity, and sensory physiology. Experiments focus on invertebrate model systems. Students record neural activity with techniques that include intracellular microelectrode, patch clamp, and optical fluorescence recording.

MOL 550 Contemporary Problems in Molecular Biophysics (see CHM 550)

MOL 551 Introduction to Computational Molecular Biology (see COS 551)

MOL 557 Analysis and Visualization of Large-Scale Genomic Data Sets (see COS 557)

MOL 559 Viruses: Strategy and Tactics

Lynn Enquist

The general strategies encoded by all known viral genomes are discussed using selected viruses as examples. The first half of the course covers the molecular biology (the tactics) inherent in these strategies. The second half introduces the biology of engagement of viruses with host defenses, what happens when viral infection leads to disease, vaccines and antiviral drugs, and the evolution of infectious agents and emergence of new viruses. Graduate students take a midterm written exam and write a final paper on a selected topic in virology. They also attend a special preceptorial session led by a postdoctoral fellow, where seminal papers in virology are analyzed and discussed. Three 50-minute lectures and one two-hour precept.

MOL 561 Scientific Integrity in the Practice of Molecular Biology

Lee Silver

Through case studies and class discussion, this course will examine the social framework for the public support of basic biomedical research, the rights and responsibilities of students and mentors in the conduct of research, and the significance of intellectual property. Course will also review regulations concerning research with human subjects and animals. The nature of, and response to, personal misconduct will be a principal focus. Course satisfies the mandate of the National Institutes of Health for training molecular biologists in the ethical practice of science.

MOL 586 Topics in STEP: Biotechnology Policy (see WWS 586a)

Pertinent Courses in Allied Departments

Chemistry

509, 510 Topics in Physical Chemistry

515, 516 Biophysical Chemistry I and II

538 Topics in Biological Chemistry

542 Principles of Macromolecular Structure

543 Advanced Topics in Structural Biology

Ecology and Evolutionary Biology

502, 504 Fundamental Concepts in Ecology, Evolution, and Behavior I and II

Physics

561, 562 Biophysics

Undergraduate Courses of Interest

Molecular Biology

408 Cellular and Systems Neuroscience

431 Advanced Topics in Developmental Neurobiology

435 Pathogenesis and Bacterial Diversity

437 Computational Neurobiology and Computing Networks

448 Chemistry, Structure, and Structure-Function Relations of Nucleic Acids