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Department of Courses of Study: Major (BA/BS) Combined BS/MS

Objectives Graduate Programs in the Biological Sciences For MS and PhD degrees in the biological sciences, see the separate listings for molecular and biology, and structural biology, Undergraduate Major , and genetic counseling programs in this Bulletin. The undergraduate program in biology, leading either to the BA or to the BS degree, is designed to give students an understanding of fundamental and current biological knowledge in a variety of fields. How to Become a Major The program offers a wide array of courses to undergraduates, ranging from introductory to advanced, specialized, graduate-level Students wishing to major in biology should enroll in general chemistry courses in many of these areas. The biology department has twenty- during their first year. Students may elect to take BIOL 15b, an five full-time faculty members with teaching and research interests introductory course in biology, in the first year. Exceptionally well- in the fields of , , development, cancer, prepared students may enroll in BIOL 22a (Genetics) in their first year. , neurobiology, motility, , structural biology, animal behavior, and . Most students begin the biology series in their sophomore year and take BIOL 22a (Genetics and Molecular Biology) and BIOL 22b (Cell Because the interests and needs of our students vary, the major is and ), plus labs. During their sophomore year, students can also designed to provide flexibility once the core courses have been enroll in CHEM 25a,b (Organic Chemistry), with associated labs. completed. Students may elect undergraduate-level courses in a Other course schedules are indeed possible, but students should note variety of areas of biology and or may choose to obtain that some biology electives have a prerequisite of completion of CHEM more-advanced, in-depth training in one particular area. Students 25a. Taking CHEM 25a,b in the sophomore year allows students to begin are also encouraged to take advantage of opportunities to become taking electives in their junior year, as well as to begin completing the integral members of research laboratories in the department and to remaining requirements for the BA or BS degree in biology. Students also attend departmental colloquia. have the option of enrolling in BIOL 99a,b (Senior Research) during the senior year. A major in biology provides excellent preparation for students To learn more about the biology major, students should attend one of intent on careers in biological research who want to go to graduate the special departmental programs held each fall or consult with the school; for those seeking careers in medicine, veterinary medicine, undergraduate advising head. and dentistry; and for those interested in the allied health professions such as public health, genetic counseling, physical therapy, or physician assistant. For those seeking courses concerned with ecology or environmental science, the biology department offers study in those areas. See “Special Note B” later in this section for additional programs in those areas.

Faculty James Haber (Rosenstiel Center) (on leave Paul Miller (Volen National Center for 2008–2009) Complex Systems) Genetics and molecular biology of yeast Computational and theoretical neuroscience. Eve Marder, Chair (Volen National Center meiotic and mitotic recombination. Mating- for Complex Systems) type switching. Repair of broken James Morris Neurotransmitter modulation of neural chromosomes. . Medicine. . History of circuits. science. Susan Birren (National Center for Behavioral Kenneth Hayes (Director, Foster Animal Lab) ; Volen National Center for Comparative nutritional pathophysiology in Sacha Nelson (National Center for Behavioral Complex Systems) man and animals. Lipoprotein Genomics; Volen National Center for Developmental neurobiology. and atherogenesis, cholelithiasis. Complex Systems) Synaptic integration in the visual cortex. Carolyn Cohen (Rosenstiel Center) Elaine Hiller Structural molecular biology. Human genetics. Daniela Nicastro (Rosenstiel Center) Electron tomography of cellular and Melissa Kosinski-Collins macromolecular . Paul Garrity (National Center for Behavioral biochemistry. Genomics; Volen National Center for Complex Systems) John Lisman (Volen National Center for Suzanne Paradis (National Center for Neural development and behavior. Complex Systems; Chair, Neuroscience) Behavioral Genomics; Volen National Center Mechanisms of phototransduction. Molecular for Complex Systems) mechanism of memory storage. Bruce Goode (Rosenstiel Center) (on leave Molecular mechanisms of synapse development. 2008–2009) Susan Lovett (Rosenstiel Center) Biochemistry and genetics of yeast Genetics and molecular biology of bacteria cytoskeleton. Dan L. Perlman (Chair, Environmental and yeast. DNA repair. Recombination and Studies) mutagenesis. Ecology, , animal Leslie Griffith (National Center for behavior. Behavioral Genomics; Volen National Center Behavioral Genomics; Volen National Center Michael Marr (Rosenstiel Center) for Complex Systems) Mechanisms controlling . Biochemistry of synaptic plasticity. Biology 87

Joan Press, Undergraduate Advising Head and Piali Sengupta (National Center for Gina Turrigiano (National Center for Senior Honors Coordinator (Rosenstiel Behavioral Genomics; Volen National Center Behavioral Genomics; Volen National Center Center) for Complex Systems) for Complex Systems) Developmental immunology and Behavioral and neuronal development in C. Activity-dependent regulation of neuronal immunogenetics. elegans. properties.

Ruibao Ren (Rosenstiel Center) (on leave Neil Simister (Rosenstiel Center) Lawrence Wangh (on leave 2008–2009) spring 2009) Molecular immunology. Antibody transport. Mammalian embryogenesis. Gene expression Signal transduction. in single cells. DNA amplification and in Judith Tsipis (Chair, Genetic Counseling) vitro DNA diagnostics. Michael Rosbash (National Center for Genetic counseling. Behavioral Genomics) RNA processing and molecular neurobiology.

Requirements for the Major Quantitative Course List CHEM 144a MATH 10a, 10b, 15a, 20a, 22a, 22b A. Required of all candidates: BIOL 22a,b; BIOL 18a,b lab; CHEM NPHY 115a 11a,b or CHEM 15a,b; CHEM 18a,b or CHEM 19a,b lab; CHEM NPSY 137b 25a,b; CHEM 29a,b lab; PHYS 10a,b or PHYS 11a,b or PHYS QBIO 110a 15a,b; PHYS 18a,b or PHYS 19a,b lab; and Option I or II below. Any one of the following statistics courses: BIOL 51a, ECON 83a, HSSP 100b, MATH 36b, or PSY 51a. Option I: The BA Degree in Biology The BA is the standard biology option that provides students with a Note: AP calculus will not satisfy the quantitative requirement. general background in biology. In addition to the courses required of all candidates (listed above), students must complete one course Category 1 Electives from the Quantitative Course List below. Students must complete a BIOL 15a (only if taken before BIOL 22a or b) total of five elective courses, three of which must come from BIOL 17b Category 1 and be taken at Brandeis. All other BIOL courses numbered higher than 22 (excluding courses numbered 90–98) Two semesters of BIOL 99 (or BCHM 99a,b or NEUR 99a,b) may BCHM 100a count as one elective in Category 1 with permission of the biology All NBIO courses (excluding courses numbered 90-98) department honors coordinator and the biology undergraduate advising head. Two semesters of BIOL 99 (or BCHM 99a,b or NEUR 99a,b) may count as one elective with permission of the biology department honors Additional courses may be taken as electives from the Quantitative coordinator and the biology undergraduate advising head. Course List, Category 1, or Category 2 (see below). Category 2 Electives Option II: The BS Degree in Biology ANTH 116a The BS is the intensive biology option that provides students with a BCHM courses numbered higher than 100 strong background in several areas of biology. In addition to the CHEM 33a, 141a, 142a, 143b, 146a, 147b courses required of all candidates (listed as in A above), students QBIO 120b must complete BCHM 100a plus two courses from the Quantitative Any one course from the quantitative course list above (a single course Course List. In addition, students must complete five elective cannot be used to fulfill both the quantitative requirement and an courses, at least three of which must come from Category 1 and be elective). taken at Brandeis. Note: Only one course may be taken from the statistics grouping (BIOL Two semesters of BIOL 99 (or BCHM 99a,b or NEUR 99a,b) may 51a, PSYC 51a, ECON 83a, MATH 36b, or HSSP 100b), either as an count as one elective for the BS in Biology in Category 1 with elective or to fulfill the quantitative requirement. permission of the biology department honors coordinator and the biology undergraduate advising head. B. Senior Research Any senior, regardless of GPA, may enroll in laboratory research (BIOL Additional courses may be taken as electives from the Quantitative 99a and b or BIOL 99e). Students petition the department during the Course List (beyond the two used to fulfill the BS quantitative beginning of their senior year for participation in Senior Research. requirement), Category 1, or Category 2 (see below). Petitions and information about Senior Research are available in the biology department office. See BIOL 99 course description for details. No course offered for major requirements in either Option I or II may be taken on a pass/fail basis. Satisfactory grades (C– or above) C. Senior Honors Program must be earned in all biology and biochemistry courses offered for Laboratory research is a major component of the senior honors program. the major and in all elective courses offered for the major in biology. Enrollment in BIOL 99 (Senior Research) is obligatory; students must No more than one D will be allowed in any other course offered fulfill the BIOL 99 requirements (see B above). At the conclusion of their toward the requirements in this department. second semester of BIOL 99 (Senior Research), candidates for senior honors will give an oral defense of their senior honors thesis to a designated faculty research committee. At the conclusion of their senior year, candidates for senior honors must either have a minimum 3.30 grade point average in all courses offered for the biology major, or have a minimum 3.00 GPA in courses offered for the biology major and have achieved an average of B+ or better in three biology electives, not including BIOL 99. Petitions and information about the senior honors program are available in the biology department office. 88 Biology

Combined BS/MS Program Semester in Environmental Science at the Marine Biological Laboratory in Woods Hole: Five courses are offered each fall as part of a residential program, including the analysis of terrestrial and aquatic , Candidates for departmental honors may be admitted to a special microbial and animal ecology, global issues, and ecological modeling. four-year BS/MS program upon recommendation of the Every student must do an independent research project during the department and approval by the Graduate School. Application to semester. Up to four semester course credits may be earned toward the the Graduate School must be made by May 1 preceding the senior Brandeis degree and two semester course credits may be counted toward year; applications should include a proposed course of study the biology BA or BS elective requirement. specifying how all degree requirements will be met, a transcript, a letter of recommendation from the research sponsor, and a brief Denmark’s International Studies Program: DIS offers a range of programs description of the proposed research project. To qualify for the in and ecology, environmental biology, medical practice BS/MS degree in biology, students must complete a total of and policy, and molecular biology and genetics. thirty-eight courses; these courses must include those needed to satisfy requirements A, option II, and B, as indicated above, plus School for Field Studies: SFS offers programs at a number of different three additional electives in biology or biochemistry or as listed sites around the world, including East Africa, Costa Rica, Baja Mexico, under requirement A, option II, above. Of the eight electives Australia, and the West Indies. required for the BS/MS degree, at least six must be at the graduate level (and completed with a grade of B– or higher) and they must include courses from at least three of the research School for International Training: SIT offers programs around the world areas of the biology department. Research areas include genetics, in ecology, conservation, and sustainable development. molecular biology, cell biology, structural biology, immunology, and neurobiology. In addition, a substantial research contribution Students should see Mr. D.L. Perlman for further information on these is required, and students must submit a research thesis to the programs, including information on the transferability of course credits biology department graduate committee for review. A thesis as biology electives. submitted for the master’s degree may also be submitted to the biology department for departmental honors. C. Biology majors who wish to enroll in PHYS 11a and b (Basic Physics), rather than PHYS 10a and b (Physics for the Life Sciences), must complete both MATH 10a and b as prerequisites. Special Notes Relating to the Undergraduate Program D. AP exam credit: Students receiving AP credit as per university guidelines may use these to satisfy the general chemistry (CHEM 11) or A. BIOL 18a and b (labs) and BIOL 22a and b will satisfy the general physics (PHYS 10, 11) requirements. However, neither AP Math AB biology entrance requirements of most medical schools. scores of 4, 5 nor AP Math BC scores of 3, 4, 5 may be used to satisfy the quantitative course requirement for the biology major. B. Biology majors wishing to study ecology, conservation, and marine studies may wish to look into the environmental studies program described in this Bulletin, as well as the following programs:

Courses of Instruction BISC 2b Genes, Culture, History: A Case BISC 3b Humans and the Environment Study [ sn ] [ sn ] Does NOT meet requirements for the major (1–99) Primarily for Undergraduate Does NOT meet requirements for the major in biology. Students in biology. Explores a range of interactions between An interdisciplinary course with and their environments. Focuses contributions from professors in three on human interactions with and impacts on BISC 2a Human , departments. Findings from the Human the natural world. Usually offered every third Explosion, Global Consequences Project are correlated with cultural year. [ sn ] and historical information about specific Mr. D.L. Perlman Does NOT meet requirements for the major human . Usually offered every in biology. third year. BISC 4a Heredity Appropriate for students interested in a Mr. Wangh [ sn ] broad range of fields, including biology, Does NOT meet requirements for the major environmental studies, and the social BISC 3a Paradigms of Biological Investigation in biology. May not be taken by students who sciences. This course progresses from a [ sn ] have completed BIOL 22a. molecular and cellular biology description Does NOT meet requirements for the major An exploration of what genes are and their of basic facts in human genetics and in biology. May not be taken by students who functions. Examines how genes are inherited, reproduction, AND an evolutionary have completed BIOL 22a or BIOL 22b. how they work, and how changes in certain description of human origins in Africa and Examines the concepts and principles of genes cause inherited diseases. Also global migration, to a demographic and scientific research with examples from its investigates recent biological developments epidemiological view of human population Greek beginnings to modern times. Topics such as the Human , growth, and a consideration of some of the from , biophysics, genomics, gene therapy, stem cells, and the very complex problems arising from the molecular biology, and physics are used to new medical and ethical challenges these presence of more than six billion people on describe the of scientific advances. developments pose in the twenty-first Earth today. Readings include scientific Concepts related to experimental design and century. Usually offered every third year. papers appropriate to students with high critical thinking are considered. Usually Ms. Sengupta school backgrounds in biology and offered every year. chemistry, essays in the social sciences, and Mr. Farber a wide variety of other texts and media. Usually offered every second year. Mr. Wangh Biology 89

BISC 4b Food, , and Health BISC 7a The Biology and Culture of Deafness BIOL 18a General Biology Laboratory [ sn ] Does NOT satisfy the school of science [ sn wi ] Does NOT meet requirements for the major requirement. Does NOT meet requirements Prerequisites: CHEM 18a or 19a, and BIOL in biology. for the major in biology. 18b, or permission of the instructor. BIOL 22a Nutrition is the science of food and its role in An exploration of the biology, sociology, and must be taken before or concurrently with health and disease. This course will introduce language of the deaf. Looks at normal this course. Yields full-course credit. the biological background to provide students mechanisms of hearing and different causes Laboratory fee: $20 per semester. This lab is with tools to better understand everything of deafness. Medical models of deafness are time-intensive and students will be expected from how we choose food to how our diet compared with social/cultural concepts of to come in to lab between regular scheduled influences our long-term health. Usually deafness. The course will also introduce lab sessions. offered every year. students to the language of the deaf Provides firsthand experience with a wide Ms. Lai , American Sign Language (ASL). array of organisms and illustrates basic Usually offered every second year. approaches to experimental design and BISC 5a Pathogens and Human Disease Mr. Morris problem solving in genetics and genomics. [ sn ] Usually offered every year. Prerequisite: High school chemistry and BISC 7b Exercise Ms. Kosinski-Collins biology. Does NOT meet requirements for [ sn ] the major in biology. May not be taken by Does NOT meet requirements for the major BIOL 18b General Biology Laboratory students who have completed BIOL 125a, in biology. Prerequisites: CHEM 18a or 19a. BIOL 22b 132a, or 175b. An introductory course in exercise must be taken before or concurrently with This course discusses the life cycle, physiology, with the focus on the muscular, this course. Yields half-course credit. pathogenesis, transmission, and neuromuscular, cardiovascular, and Laboratory fee: $20 per semester. of certain organisms (bacteria, viruses, fungi, metabolic responses and the physiological Provides firsthand experience with modern etc.) that cause important human diseases. that occur during exercise. molecular biology techniques and illustrates Other topics include emerging diseases, host Concepts related to physical fitness, body basic approaches to experimental design and defense mechanisms, vaccines, public health composition/weight control, and training problem solving in molecular and cellular concerns. Usually offered every year. principles are discussed. Usually offered every biology. Usually offered every year. Ms. Press year. Ms. Kosinski-Collins Mr. Burr BISC 5b Diseases of the Mind BIOL 22a Genetics and Molecular Biology [ sn ] BIOL 15b Biology: Human Implications [ qr1 sn ] Prerequisite: High school chemistry. Does [ sn ] Prerequisite: CHEM 10a or 11a or 15a. NOT meet requirements for the major in This course may not be taken for credit by An introduction to our current understanding biology. May not be taken by students who students who have completed BIOL 22a or of hereditary mechanisms and the cellular have completed BIOL 22b. BIOL 22b. Core course for the HSSP program. and molecular basis of gene transmission and An exploration of biology of several protein The last half-century brought an expression. Usually offered every year. folding diseases including Alzheimer’s, unprecedented expansion of our knowledge of Mr. Garrity Parkinson’s, Huntington’s, ALS, and mad cow the living world. The effects of these disease and their effect on normal brain discoveries on our lives and the effects of our BIOL 22b Cell Structure and Function function. Examines the medical and ethical lives on the rest of the living world are [ sn ] challenges of therapies, drug design, and increasing. Recent developments in biology Prerequisite: CHEM 10a or 11a or 15a. clinical trials on patients afflicted with these affect our health care choices, our consumer An introduction to the architecture and disorders. Usually offered every second year. choices, and even our choices as parents. This function of cells, , and their Ms. Kosinski-Collins course is intended as an introduction to macromolecular components. Topics include contemporary biology. It stresses the fundamental processes that are common to BISC 6b Environmental Health fundamentals of cell biology and genetics and all cells, and the functions of specialized [ sn ] explores the diversity of life, including cells. Usually offered every year. Does NOT meet requirements for the major and plants. It emphasizes Mr. Simister in biology. evolution, physiology, and ecology. The The impact on human health of course is intended to prepare students to BIOL 23a Ecology understand the biology of everyday life, and environmental contamination with toxic, [ sn ] to provide a strong foundation for those who carcinogenic, or pathogenic agents. Tools of Prerequisite: BIOL 22a or 15b, or a score of 5 continue to study the life sciences. Usually , epidemiology, and risk on the AP Biology Exam, or permission of the offered every year. assessment are applied to specific instructor. Mr. Simister environmental issues such as air and water Studies organisms and the environments in quality, petroleum, metal, and other chemical which they live. Focuses on the physical contaminations. Usually offered every second BIOL 17b Conservation Biology factors and intra- and interspecies year. [ sn wi ] interactions that explain the distribution and Staff First- and second-year students should abundance of individual species from an contact the instructor before enrolling in this evolutionary perspective. Usually offered writing-intensive course. every year. Considers the current worldwide loss of Staff biological diversity, causes of this loss, and methods for protecting and conserving . Explores biological and social aspects of the problems and their solutions. Usually offered every year. Mr. D.L. Perlman 90 Biology

BIOL 25a Molecular Motors BIOL 42a Physiology BIOL 60b Evolution [ sn ] [ sn ] [ oc qr sn ] Prerequisite: BIOL 22b. Prerequisites: BIOL 22a and BIOL 22b. CHEM Prerequisite: BIOL 22a (formerly BIBC 22a). A discussion of movement at the cellular 25a and CHEM 25b are recommended. ”Nothing in biology makes sense except in level. Analyzes how molecular motors Introduces basic physiological principles with the light of evolution,” Dobzhansky said generate motion and how their activity is an overview of neural and hormonal control famously. Evolution is a unifying theory of controlled. Topics include intracellular mechanisms. Topics include physiology of biology, because it explains almost transport, muscle contraction, rotary motion, everything about the living world—the cardiovascular and respiratory systems, moving along DNA, and cell diversity of life, similarities among electrolyte regulation, digestion and division. Usually offered every second year. organisms, and the characteristics of all living Staff absorption, and reproduction, with an things. This course examines processes and overview of immunology. Usually offered patterns of evolution, including the origin BIOL 28a Marine Biology every year. and fate of variation, natural and sexual [ sn ] Ms. Griffith selection, inbreeding and , the Prerequisites: BIOL 22a and BIOL 22b. evolution of sociality, the species concept and Survey of the basic biology, behavior, and life BIOL 43b Comparative Vertebrate the origin of species, biodiversity, and history of marine biota. Review of physical [ sn ] , as well as the history of life on , from polar to tropical waters. Prerequisite: BIOL 22b. Earth, including the fossil record and human Weekly laboratory consists of field trips to This course is designed to provide a solid evolution. Usually offered every year. different habitats and examination of basis for an understanding of vertebrate and Mr. Morris specimens from several marine phyla. Focus in particular human anatomy. The gross and is on the evolution of adaptive responses to microscopic morphology of each BIOL 93a Research Internship and Analysis the physical and biological factors in marine system is considered in depth. Correlations Supervised biological research experience in a communities. Usually offered every third between structure and function are Brandeis University laboratory. In year. emphasized. Lectures, laboratory dissections, consultation with a Brandeis faculty member, Staff and clinical cases are used to illustrate the the student will design and execute an structure and function of the human body. individual research project, culminating in an BIOL 30b Biology of Whales Usually offered every year. oral and written presentation. Students [ sn ] Mr. Morris seeking to do biology research in Brandeis Prerequisites: BIOL 22a and BIOL 22b, plus laboratories outside the biology department two upper-level biology electives. BIOL 50b Animal Behavior must obtain sponsorship of a biology Examines the biology and conservation of [ sn ] department faculty member as well as whales, dolphins, and porpoises. Topics Prerequisites: BIOL 23a or BIOL 60b. permission of the departmental curriculum include physiology, morphology, population Examines a wide range of animal behavior, committee chair (or UAH). This course is not biology, life history, molecular genetics, including mating and reproductive tactics, intended to and will not provide credit for off- distributional ecology, and social behavior. territoriality, and social behaviors. The campus internships. Offered both semesters Usually offered every third year. course employs an ecological framework to and requires permission of the instructor and Staff understand the evolution of behavior. Usually fulfillment of BIOL 93 guidelines. Students offered every second year. wishing to do a summer internship for academic credit must: obtain permission BIOL 31b Biology of Fishes Mr. D.L. Perlman [ sn ] from their biology department sponsor prior to commencing the internship; complete the Prerequisites: BIOL 22a and BIOL 22b, plus BIOL 51a summer internship (a minimum of 10 weeks two upper-level biology electives. [ sn ] full-time); and complete the appropriate Topics include evolution, , Prerequisite: MATH 10a. academic work. Credit will be awarded via anatomy, physiology, and behavior of A basic introduction to methods of statistics the student enrolling BIOL 93 in the freshwater, marine, and anadromous fishes and mathematical analysis applied to subsequent fall term. Usually offered every from temperate and tropical environments. problems in the life sciences. Topics include semester. Studies fish interactions in communities: statistical analysis of experimental data, Staff predator/prey, host/symbiont relationships, mathematical description of chemical and fish as herbivores. Also examines the reactions, and mathematical models in BIOL 98a Readings in Biology ecology of fish populations. Usually offered BIOL 98a Readings in Biology neuroscience, population biology, and Prerequisites: BIOL 22a and BIOL 22b. Does every third year. epidemiology. Usually offered every year. NOT meet requirements for the major in Staff Staff biology. May not be taken for credit by students who have satisfactorily completed BIOL 32a Field Biology BIOL 32a Field Biology BIOL 55b Diet and Health BIOL 98b. [ sn ] [ sn ] Open to exceptionally well-qualified Introduces students to the biodiversity of Prerequisite: BIOL 22b must be successfully students. This is a tutorial course with southern New England, emphasizing plants completed prior to taking BIOL 55b. readings in a specified biological field. The and insects. Course work primarily takes Reviews the current evidence concerning student will be given a reading list, including place on field trips to various terrestrial and dietary impact on the chronic diseases of current literature and reviews of the topic to aquatic habitats. Field trip scheduling will be humans. Topics include genetics and be discussed. Course requirements include discussed during the first meeting. Usually nutrition, cardiovascular disease, obesity, weekly discussions and the writing of several offered every year. diabetes, osteoporosis, and cancer. Students papers. Usually offered every year. Mr. D.L. Perlman also examine the involvement of specific Staff nutrients; for example, fat and cholesterol, vitamins, minerals, fiber, and alcohol in these BIOL 98b Readings in Biology disease processes. Usually offered every Prerequisites: BIOL 22a and BIOL 22b. Does second year. NOT meet the major requirement in biology. Mr. Hayes May not be taken for credit by students who have satisfactorily completed BIOL 98a. See BIOL 98a for course description. Usually offered every year. Staff Biology 91

BIOL 99a Senior Research BIOL 103b Mechanisms of Cell Functions BIOL 125a Immunology The first of a two-semester course involving [ sn ] [ sn ] the student in an independent research Prerequisite: BIOL 22b or permission of the Prerequisites: BIOL 22a and b. project conducted under the supervision of a instructor. Topics include properties, functions of cells staff member and serving as an intensive An advanced course focusing on a involved in innate and adaptive immunity; introduction to specific methods of biological mechanistic understanding of cell biological genes, structure, function of immunoglobins research. In cases where students are able to processes and the methods by which these and T cell receptors; cell interactions; do unusually long, intensive work in the processes are elucidated. Papers are chosen to lymphocyte differentiation; genetic laboratory, they may request a third course illustrate a variety of experimental regulation; MHC restriction; cell interactions credit during the petition process; if this approaches, including biochemistry, genetics, and signaling; tolerance and autoimmunity; request is approved by the senior honors and microscopy. Topics include cell cycle, vaccines; viral immunity; AIDS. Usually coordinator, students should register for BIOL signal transduction, cytoskeleton and cell offered every year. 99a (fall) followed by BIOL 99e (spring). The movement, membrane traffic, and Ms. Press combined enrollments for Senior Research intercellular transport. Usually offered every may not exceed three semester course credits. year. BIOL 126b and Disease To fulfill the BIOL 99 requirements, students Ms. Nicastro [ sn ] must (1) submit to their research sponsor, at Prerequisites: BIOL 22a and b, or the the conclusion of their first BIOL 99 BIOL 105b Molecular Biology equivalent, or permission of the instructor. semester, a paper that reviews the literature [ sn ] Reviews the basic principles of protein pertinent to their field of research, and (2) Prerequisites: BIOL 22a and b. structure so that the functional aspects of submit to their research sponsor, at the Examination of molecular processes in different protein designs may be understood. conclusion of their second BIOL 99 semester, replication and expression of genetic Examines various protein related a senior thesis that includes an abstract, an information and techniques by which this to certain molecular diseases and the introduction, a review of materials and understanding has been achieved. Topics architecture of some key viruses and their methods, results, discussion, and references. include recombinant DNA and other infectivity. Consideration of drug design is an Usually offered every year. molecular biological techniques, structure integral part of the course. Student Staff and organization of DNA in chromosomes, presentations are essential to the course. DNA replication, transcription and regulation Usually offered every second year. BIOL 99b Senior Research of gene expression, RNA structure and Ms. Cohen A continuation of BIOL 99a. See BIOL 99a for processing, mRNA stability, and other course description. mechanisms of post-translational control. BIOL 128a Human Genetics Staff Usually offered every year. [ sn ] Mr. Marr and Mr. Rosbash Prerequisites: BIOL 22a and b. BIOL 99e Senior Research Survey of topics, including: and See BIOL 99a for course description. Usually BIOL 111a polymorphism; molecular methodology; offered every semester. [ sn ] single-gene inheritance and complexities Staff Prerequisite: BIOL 22b. thereof; multifactorial conditions, risk How do complex organisms build themselves assessment, and Bayesian analysis; starting from single cells? Examines how ; hemoglobinopathies; population genetics; gene mapping; cancer genetics; (100–199) For Both Undergraduate processes such as fertilization, (100–199) For Both Undergraduate embryogenesis, cell differentiation, and ethical considerations in genetics; and Graduate Students -specific gene expression occur; what is immunogenetics; pharmacogenetics; genetics known about the key and genes of development; biochemistry of selected that orchestrate these processes; and how genetic diseases; gene therapy, genomics, BIOL 101a Molecular genetic changes affecting these processes , and . Usually [ sn ] underlie the evolution of body form. Usually offered every year. Prerequisite: BIOL 22a. offered every second year. Ms. Hiller A study of the molecular basis of DNA Ms. Birren replication, RNA transcription focusing on BIOL 132a General molecular biology techniques such as PCR, BIOL 122a Molecular Genetics [ sn ] DNA sequencing, genomics, cloning, [ sn ] Prerequisites: BIOL 22a and BIOL 22b. microarrays, and siRNA and their relation Prerequisite: BIOL 22a. A survey of the physiology and the properties to human disease research applications. A lecture- and literature-based course of bacteria, viruses, and other Usually offered every year. emphasizing strategies of genetic analysis in microorganisms. Topics include microbial Ms. Kosinski-Collins understanding complex processes such as the nutrition, metabolism, growth, and genetics; BIOL 102b Structural Molecular Biology control of DNA replication or the regulation immunity and other means of microbial [ sn ] of the cell cycle and cell differentiation. A control; pathogenicity, epidemiology, Prerequisites: BIOL 22a and b, or permission second emphasis is on the mechanisms that concepts in infectious disease. Selected of the instructor. preserve genetic stability and ensure accurate disease-causing organisms are discussed, Cells are filled with machines that carry transmission of genetic information from including problems they pose for medical materials about the cell, that chemically generation to generation in both somatic and control and society. Usually offered every transform molecules, that transduce , germ cells. Classical genetic methods and second year. and much more. Our understanding of how molecular genetic and genomic approaches Ms. Press these machines work depends on are examined. Research papers of current and understanding their structures. This historical interest are discussed. Usually BIOL 134b Tropical Ecology introduction to the structural basis of offered every second year. [ sn oc ] molecular biology examines the designs of Mr. Haber Prerequisite: BIOL 23a or permission of the and nucleic acids, their assembly instructor. into macromolecular complexes, and the Offers an in-depth look at tropical ecology means whereby we visualize these structures. focusing on the question: why are tropical Considers the physical and chemical basis for regions ecologically so different from specificity in molecular recognition. Usually temperate and polar regions? Usually offered offered every second year. every second year. Staff Staff 92 Biology

NBIO 136b Computational Neuroscience NBIO 145b Systems Neuroscience BIOL 149b Molecular [ sn ] [ sn ] [ sn ] Prerequisite: MATH 10a or PHYS 10a or Prerequisite: NBIO 140b. Prerequisites: BIOL 22b and CHEM 25a and b. approved equivalents. A fundamental question in neuroscience is NBIO 140b strongly recommended. An introduction to concepts and methods in how our brains extract and compute features Covers the essentials of pharmacology and computer modeling of neural systems. Topics and functions—such as direction of motion the study of the actions of chemical agents include the basic biophysics of ion from visual stimuli—and how experience (drugs, toxins, neurotransmitters, and conduction, single and multicompartment allows the microcircuits within our brains to hormones) that interact with living systems. neuron models, information representation become better tuned to such features. Emphasizes molecular mechanisms of and processing in the visual system, and Understanding these processes requires neuropharmacology. Topics include models of synaptic plasticity, working insight into the cellular and network pharmacokinetics, hormone action, memory, and decision making. Usually mechanisms that give rise to them. We will autonomic pharmacology, and the offered every second year. begin by examining the classical literature, psychopharmacology of drugs of abuse and Mr. Miller and then we will move on to recent advances mental disorders. Usually offered every third in understanding the cellular and network year. NBIO 140b Principles of Neuroscience properties of brain microcircuits. The course Ms. Marder [ sn ] emphasizes reading from original papers, and Prerequisite: BIOL 22b or permission of the extensive class discussion. Usually offered NBIO 150a Autism and Human instructor. every year. Developmental Disorders Examines the basic principles of Ms. Turrigiano [ sn ] neuroscience. Topics include resting Prerequisite: BIOL 22b. potentials, action potentials, synaptic NBIO 146a The Neurobiology of Human Autism and other developmental disorders transmission, sensory systems, motor Disease are characterized by abnormal brain systems, learning, neural circuits underlying [ sn ] development resulting in cognitive and Prerequisite: NBIO 140b. behavioral deficits. Takes an integrative behavior, neurological diseases, and mental A lecture- and literature-based overview of approach to investigate the biological, illness. Usually offered every year. the neurobiological underpinnings of behavioral, medical, and social aspects of Mr. Lisman neurological and psychiatric disorders human developmental disorders. Usually including autism, mental retardation, offered every second year. BIOL 141b Molecular Pathophysiology schizophrenia, bipolar disorder, Alzheimer’s Ms. Birren [ sn ] disease, Parkinson’s disease, and other Prerequisite: BIOL 42a, BCHM 100a, or NBIO neurodevelopmental and neurodegenerative BIOL 155a Project Laboratory in Genetics and 140b, or permission of the instructor. disorders. Usually offered every second year. Genomics An in-depth investigation of the molecular Mr. Nelson [ sn ] mechanisms by which the body’s organ Prerequisites: BIOL 18a and b and BIOL 22a systems maintain health/ and NBIO 147a Neurogenetics and b. succumb to genetic diseases (e.g., cystic [ sn ] This small, laboratory-based course provides fibrosis, Parkinson’s disease, ALS), with Prerequisites: BIOL 18a and BIOL 22a. a unique opportunity for students to pursue additional emphasis on understanding how Topics inlcude development and function of an independent research project. Each year we the body adapts to physical exertion and the nervous system and responses of excitable focus on a specific topic, such as bacterial exercise. Usually offered every second year. cells studied in neurological and behavioral genetics, epigenetic mechanisms of gene Staff mutants. Characterization and manipulation regulation, or microbial diversity, and design of genes, defined by these mutations and and carry out original experiments. Students NBIO 143b Developmental Neurobiology using molecular biological tools. Organisms: will learn basic molecular biology techniques, [ sn ] roundworms, fruit flies, fish, mammals. genetic and genomic analysis, and Prerequisite: BIOL 22b or permission of the Neurobiological areas: embryonic neural experimental design. Usually offered every instructor. development, nerve cell differentiation and year. Discusses the mechanisms used in the pattern formation, membrane excitability, Ms. Lovett and Mr. Morris development of the nervous system. Topics responses to sensory stimuli, biological include determination of neuronal cell fates, rhythms, and reproductive behavior. Usually BIOL 160b Human Reproductive and neuronal differentiation and pattern offered every third year. Developmental Biology formation, neuron survival and growth, and Ms. Paradis and Ms. Sengupta [ sn ] mechanisms responsible for generation of Prerequisites: BIOL 22a and b. connectivity in the nervous system. Usually NBIO 148b Cellular Neuroscience Course deals with hormonal, cellular, and offered every second year. [ sn ] molecular aspects of gametogenesis, Ms. Paradis and Ms. Sengupta Prerequisite: NBIO 140b or permission of the fertilization, pregnancy, and birth. instructor. May be taken concurrently with Pathological and abnormal variations that NBIO 140b. occur and the available medical technologies Focuses on cellular and molecular for intervention, correction, and facilitation mechanisms of excitability and synaptic of these processes are discussed. Usually plasticity. Students examine classic offered every year. experiments on action potentials and Ms. Jackson synaptic transmission and the original research literature dealing with the cellular BIOL 172b Growth Control and Cancer mechanisms of developmental and learning- [ sn ] related plasticity. Usually offered every year. Prerequisites: BIOL 22a and b. Mr. Nelson Covers the fundamental rules of behavior of cells in multicellular organisms. Examines cellular and molecular mechanisms that govern cell growth, and differentiation and survival in normal cells, as well as how this regulation is disrupted in cancer. Usually offered every second year. Mr. Ren Biology 93

BIOL 174b Stem Cells BIOL 175b Advanced Immunology: Topics in Cross-Listed Courses [ sn ] Infectious Disease Prerequisites: BIOL 22a and b. [ sn ] Stem cells are cells that can both undergo Prerequisites: BIOL 125a and permission of QBIO 110a self-renewal and give rise to all cells or the instructor. Numerical Modeling of Biological Systems special cell types of the body. They have the An advanced lecture- and literature-based ANTH 116a potential for the restoration of lost organ course that focuses on a select group of Human Osteology function that cannot be achieved through microorganisms (bacteria, viruses, etc.) traditional drug therapies. Covers stem cell considered important in human disease. QBIO 120b biology, cell differentiation and Topics include mechanisms/determinants of QBIO 120b Quantitative Biology Instrumentation transdifferentiation, cell lineage pathogenicity, immune evasion, host Laboratory commitment, gene expression regulation, immune responses, vaccines, public health signal transduction, cell identity memory, issues, and bioterrorism agents. Usually and cell therapies. Provides a unique way to offered every second year. COSI 230a gain insights into developmental biology, Ms. Press Topics in molecular and cell biology, cancer biology, biology of aging, and regenerative medicine, as well as bioethics and health and public policies. Usually offered every second year. Mr. Ren

A graduate program Courses of Study: Master of Science Biophysics and Structural Biology Doctor of Philosophy

Objectives Research for the PhD dissertation is carried out under the personal supervision of a faculty adviser; advisers can be from any department within the School of Science. Prospective applicants should obtain the The interdepartmental Graduate Program in Biophysics and complete list of faculty research interests and recent publications from Structural Biology, leading to the degree of Doctor of Philosophy, the program or view this information at: www.bio.brandeis.edu/ is designed to develop the student’s capacity for independent biophysics. research. The program is focused on the application of the physical sciences to important problems in molecular and cellular biology. It offers opportunities for study and research in a variety of fields, including protein crystallography and How to Be Admitted to the Graduate Program magnetic resonance spectroscopy, molecular microscopy, biophysical chemistry, neuroscience, sensory transduction, and chemo-mechanical energy transduction. Applicants are expected The general requirements for admission to the Graduate School are to have strong backgrounds in the physical sciences with given in an earlier section of this Bulletin. Applications should undergraduate majors in any related field, such as biology, include, in addition to letters of reference, a personal statement biochemistry, chemistry, engineering, mathematics, or physics. describing the reasons for the applicant’s interest in the field and The course requirements for the PhD are formulated individually previous research experience, if any. Applicants are required to take for each student to complement the student’s previous academic the Graduate Record Examination and are encouraged to visit work with the goal of providing a broad background in the Brandeis for interviews, if possible. physics and chemistry of biological processes.

Faculty Advisory Committee Jeff Gelles Jané Kondev (Biochemistry) (Physics)

Dorothee Kern, Chair Michael Hagan Christopher Miller (on leave 2008–2009) (Biochemistry) (Physics) (Biochemistry) 94 Biophysics and Structural Biology

Requirements for the Degree of Master of Science Teaching Requirement As part of their PhD training, students are required to assist with the teaching of two one-semester courses. Program of Study This graduate program does not normally admit students to pursue Residence Requirement the MS degree. In special cases, however, the MS degree may be The minimum residence requirement is three years. awarded upon completion of an approved program of study consisting of at least six graduate-level courses in biology, physics, Language Requirement biochemistry, quantitative biology, or chemistry with a grade of B– There is no language requirement. or better. Generally, the courses include BIOP 200b, BIOP 300a, and BIOP 300b. Financial Support Students may receive financial support (tuition and stipend) throughout Residence Requirement Residence Requirement their participation in the PhD program. This support is provided by a The minimum residence requirement is one year. combination of university funds, training grants, and faculty research grants. Language Requirement There is no language requirement. Qualifying Examinations To qualify for the PhD degree, each student must write and defend in Thesis oral examinations two propositions related to research in biophysics or To qualify for the MS, a student must submit a thesis reporting a structural biology. The subject of the second proposition must be outside substantial piece of original research carried out under the the immediate area of the student’s dissertation research. supervision of a research adviser or advisers. Dissertation and Defense The dissertation must report the results of an original scientific Requirements for the Degree of Doctor of Philosophy investigation into an approved subject and must demonstrate the competence of the PhD candidate in independent research. The dissertation research must be presented and defended in a final oral Program of Study examination. The PhD program in biophysics and structural biology is designed to accommodate students with previous academic majors in a wide Requirements for the Degree of Doctor of Philosophy in range of fields, including biology, biochemistry, physical chemistry, engineering, and physics. Consequently, the course requirements Biophysics and Structural Biology with Specialization in for the PhD are tailored to the needs of the particular student. In Quantitative Biology consultation with each entering student, the program chair formulates a program of study for the student based on the student’s previous academic accomplishments and scientific interests. Program of Study Successful completion of the courses listed in the program of study Students wishing to obtain this specialization must first gain fulfills the course requirements for the PhD. The required program approval of the graduate program chair or quantitative biology liaison. of study consists of seven one-semester courses, of which six are This should be done as early as possible; ideally, during the first year completed in the student’s first year. The first-year courses include of graduate studies. In order to receive the PhD in biophysics and BIOP 200b and two courses of laboratory rotations (BIOP 300a,b). In structural biology with additional specialization in quantitative addition to the seven courses, the noncredit course CONT 300b biology, candidates must complete the requirements for the PhD (Ethical Practice in Health-Related Sciences) is required of all first- described above and the course requirements for the quantitative year students. All students beyond the first year must register for biology specialization that are described in the quantitative biology BIOP 401d. Students in their third and higher years of study will section of this Bulletin. have yearly progress meetings with a faculty committee of three for the purpose of maintaining a satisfactory trajectory toward Any alteration to the quantitative biology course requirements must be completion of the thesis defense. approved by the graduate program chair and by the quantitative biology program faculty advisory committee.

Courses of Instruction Discussion focuses on understanding of the BIOP 300b Introduction to Research in scientific motivation for and experimental Biophysics design of the studies. Particular emphasis is A continuation of BIOP 300a. (200 and above) Primarily for placed on making an independent Staff Graduate Students determination of whether the author’s conclusions are well justified by the BIOP 401d Biophysical Research Problems experimental results. Usually offered every Independent research for the MS or PhD year. degrees. All graduate students beyond the BIOP 200b Reading in Macromolecular Mr. Petsko first year must register for this course. Structure-Function Analysis Usually offered every semester. Required for first-year biochemistry and BIOP 300a Introduction to Research in Staff biophysics and structural biology graduate Biophysics students. Students must consult with the program Introduces students to chemical and chair prior to enrolling in these courses. physical approaches to biological problems Students carry out four nine-week projects in through critical evaluation of the original the research laboratories of biological and literature. Students analyze scientific physical science faculty members. papers on a wide range of topics in the Staff fields of biochemistry and biophysics. Biophysics and Structural Biology 95

Required First-Year Graduate Health- BCHM 104b CHEM 129b Physical Chemistry of Special Topics in Inorganic Chemistry: Related Science Programs Course Introduction to X-ray Structure PHYS 105a Determination Biological Physics CONT 300b Ethical Practice in Health- CHEM 132b Related Sciences QBIO 110a Advanced Organic Chemistry: Spectroscopy Required of all first-year graduate students QBIO 110a Numerical Modeling of Biological Systems in health-related science programs. Not for CHEM 143b credit. CHEM 143b Kinetics, Dynamics, and Transport Ethics is an essential aspect of scientific QBIO 120b research. This course, taught by university Quantitative Biology Instrumentation faculty from several graduate disciplines, Laboratory CHEM 144a covers major ethical issues germane to the Computational Chemistry broader scientific enterprise, including CHEM 246b areas or applications from a number of Courses of Related Interest CHEM 246b fields of study. Lectures and relevant case Advanced NMR Spectroscopy studies are complemented by public lectures during the course. Usually offered BCHM 170b NBIO 140b every year. Bioinformatics Principles of Neuroscience Staff BCHM 171b NBIO 145b Protein X-ray Crystallography Systems Neuroscience Cross-Listed Courses BCHM 219b PHYS 104a Mechanisms Soft Condensed Matter BCHM 101a Advanced Biochemistry: Enzyme BCHM 220a PHYS 110a Mechanisms Proteases Mathematical Physics BCHM 102a BCHM 223a Quantitative Approaches to Biochemical BCHM 223a PHYS 163a Enzymology of Biofuels, Bioplastics, and Systems Statistical Physics and Thermodynamics Bioremediation BCHM 103b PHYS 169b BCHM 224a Advanced Biochemistry: Information Transfer BCHM 224a Advanced Laboratory Mechanisms Single- Biochemistry and Biophysics BIOL 102b Structural Molecular Biology

BIOL 103b Mechanisms of Cell Functions