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Biological SciencesBIOSCI 104/200. Advanced Molecular Biology—Molecular mechanisms that govern the replication, recombination, and expression of eukaryotic genomes. Topics: DNA replication, DNA recombination, gene transcription, RNA splicing, regulation of gene expression, protein synthesis, and protein folding. Prerequisite: Biological Sciences core. GER:DB-NatSci BIOSCI 109A/209A. The Human Genome and Disease—(Same as HUMBIO 158.) The variability of the human genome and the role of genomic information in research, drug discovery, and human health. Concepts and interpretations of genomic markers in medical research and real life applications. Human genomes in diverse populations. Original contributions from thought leaders in academia and industry and interaction between students and guest lecturers. GER:DB-NatSci BIOSCI 109B/209B. The Human Genome and Disease: Genetic Diversity and Personalized Medicine—Continuation of 109A/209A. Genetic drift: the path of human predecessors out of Africa to Europe and then either through Asia to Australia or through northern Russia to Alaska down to the W. Coast of the Americas. Support for this idea through the histocompatibility genes and genetic sequences that predispose people to diseases. Guest lectures from academia and pharmaceutical companies. Prerequisite: Biological Sciences or Human Biology core. GER:DBNatSci BIOSCI 112/212. Human Physiology—(Same as HUMBIO 133.) The functioning of organ systems emphasizing mechanisms of control and regulation. Topics: structure and function of endocrine and central nervous systems, cardiovascular physiology, respiration, salt and water balance, exercise, and gastrointestinal physiology. Prerequisite: Biological Sciences or Human Biology core. GER:DB-NatSci BIOSCI 113/244. Fundamentals of Molecular Evolution—The inference of key molecular evolutionary processes from DNA and protein sequences. Topics include random genetic drift, coalescent models, effects and tests of natural selection, combined effects of linkage and natural selection, codon bias and genome evolution. Prerequisites: Biological Sciences core or graduate standing in any department, and consent of instructor. GER:DB-NatSci BIOSCI 118/218. Genetic Analysis of Biological Processes—Genetic principles and their experimental applications. Emphasis is on the identification and use of mutations to study cellular function. Prerequisite: Biological Sciences core. GER:DB-NatSci BIOSCI 132/232. Advanced Imaging Lab in Biophysics—(Same as BIOPHYS 232, MCP 232.) Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, and optical trapping. Limited enrollment. Recommended: basic physics, Biological Sciences core or equivalent, and consent of instructor. GER:DB-NatSci BIOSCI 137/237. Plant Genetics—Gene analysis, mutagenesis, transposable elements; developmental genetics of flowering and embryo development; biochemical genetics of plant metabolism; scientific and societal lessons from transgenic plants. Prerequisite: Biological Sciences core or consent of instructor. GER:DB-NatSci BIOSCI 142/242. Topics in Theoretical Ecology—Issues include foraging theory, demography and life history theory, population dynamics and species interactions including ecosystem stability, ecological economics and marine reserve design, evolutionary theory, evolutionary ecology, and evolution of gender sexuality and family structure. Prerequisites: 43 or 101, calculus, and computer programming. Recommended: linear algebra and differential equations. GER:DB-NatSci BIOSCI 143/243. Evolution—The basic facts and principles of the evolution of all life. The logic of and evidence for the correctness of Darwin’s argument for evolution by natural selection. How Mendelian genetics was integrated into evolutionary thinking. The integration of physiological and ecological perspectives into the study of evolutionary adaptation within species. Species formation and evolutionary divergence among species. Patterns of evolution over long time scales. GER:DB-NatSci BIOSCI 145/245. Behavioral Ecology—Animal behavior from an evolutionary and ecological perspective. Topics: foraging, territoriality, reproductive behavior, social groups. Lecture/seminar format; seminars include discussion of journal articles. Independent research projects. Prerequisites: Biological Sciences or Human Biology core, or consent of instructor. Recommended: statistics. GER:DB-NatSci, WIM BIOSCI 147/247. Controlling Climate Change in the 21st Century—(Same as EARTHSYS 147/247, HUMBIO 116.) The science, economics, and environmental diplomacy of global climate change. Topics: the science of climate change, climate change and global environmental law; global economic approaches to carbon abatement, taxes, and tradable permits; joint implementation, consensus, and division in the EU; gaining the support of China, other developing countries, and U.S. corporations; alternative energy and energy efficiencies for less carbon-intensive electric power and transport. GER:DB-NatSci BIOSCI 149/249. The Neurobiology of Sleep—(Same as HUMBIO 161.) Preference to seniors and graduate students. The neurochemistry and neurophysiology of changes in brain activity and conscious awareness associated with changes in the sleep/wake state. Behavioral and neurobiological phenomena including sleep regulation, sleep homeostasis, circadian rhythms, sleep disorders, sleep function, and the molecular biology of sleep. Enrollment limited to 16. GER:DB-NatSci BIOSCI 150/250. Human Behavioral Biology—(Same as HUMBIO 160.) Multidisciplinary. How to approach complex normal and abnormal behaviors through biology. How to integrate disciplines including sociobiology, ethology, neuroscience, and endocrinology to examine behaviors such as aggression, sexual behavior, language use, and mental illness. GER:DB-NatSci BIOSCI 154/254. Molecular and Cellular Neurobiology—(Same as NBIO 254.) For advanced undergraduates and graduate students. Cellular and molecular mechanisms in the organization and functions of the nervous system. Topics: wiring of the neuronal circuit, synapse structure and synaptic transmission, signal transduction in the nervous system, sensory systems, molecular basis of behavior including learning and memory, molecular pathogenesis of neurological diseases. Prerequisite for undergraduates: Biological Sciences core or equivalent, or consent of instructors. GER:DB-NatSci BIOSCI 157/257. Plant Biochemistry—The biochemistry of plants relevant to their physiology and cell biology. Topics include: the biosynthesis, assembly, function, and regulation of cell walls; lipids; pigments; photoreceptors; transporters; and the response of plants to pathogens and stresses. Prerequisite: Biological Sciences core or equivalent, or consent of instructors. GER:DB-NatSci BIOSCI 159/259. Chromatin Biology in Health and Disease— Molecular principles of chromatin dynamics, such as modification and remodeling, in the regulation of nuclear functions, and the relationship of these activities to human diseases. Topics include the role of chromatin biology in gene expression, gene silencing, DNA damage responses and repair, DNA recombination, and epigenetics. The molecular mechanisms behind chromatin signaling networks, and their perturbations in disease processes. Students identify open questions in the field and design experimental strategies to address these issues. Prerequisite: Biological Sciences core. GER:DB-NatSci BIOSCI 163/263. Neural Systems and Behavior—(Same as HUMBIO 163.) The field of neuroethology and its vertebrate and invertebrate model systems. Research-oriented. Readings include reviews and original papers. How animal brains compare; how neural circuits are adapted to species typical behavior; and how the sensory worlds of different species represent the world. Prerequisites: BIOSCI 42, HUMBIO 4A, or equivalents. GER:DB-NatSci BIOSCI 164/264. Biosphere-Atmosphere Interactions—Physiological, ecological, and physical aspects of ecosystem function, emphasizing how ecosystems influence and are influenced by the atmosphere. Prerequisites: 42, 43; or consent of instructor. GER:DB-NatSci BIOSCI 165/265. Cellular and Molecular Therapeutic Approaches to Neurological Disorders—Current therapeutic research for neurological conditions, including stroke, epilepsy, neurodegenerative disorders, depression, anxiety, and aging. Sources include primary literature. Guest lecturers. BIOSCI 180/280. Fundamentals of Sustainable Agriculture—(Same as EARTHSYS 180/280.) Ecological, economic, and social dimensions of sustainable agriculture in the context of a growing world population. Focus is on management and technological approaches, and historical content of agricultural growth and change, organic agriculture, soil and water resource management, nutrient and pest management, biotechnology, ecosystem services, and climate change. GER:DB-NatSci BIOSCI 183/283. Theoretical Population Genetics—Models in population genetics and evolution. Selection, random drift, gene linkage, migration, and inbreeding, and their influence on the evolution of gene frequencies and chromosome structure. Models are related to DNA sequence evolution. Prerequisites: calculus and linear algebra, or consent of instructor. BIOSCI 188/288. Biochemistry I—(Same as CHEMENG 181/281, CHEM 181; CHEMENG and CHEM offerings formerly listed as 188/288.) Chemistry of major families of biomolecules including proteins, nucleic acids, carbohydrates, lipids, and cofactors. Structural and mechanistic analysis of properties of proteins including molecular recognition, catalysis, signal transduction, membrane transport, and harvesting of energy from light. Molecular evolution. Pre- or corequisites: CHEM 131; and CHEM 135 or 171. GER:DB-NatSci BIOSCI 189/289. Biochemistry II—(Same as CHEMENG 183/283, CHEM 183; CHEMENG and CHEM offerings formerly listed as 189/289.) Metabolism. Glycolysis, gluconeogenesis, citric acid cycle, oxidative phosphorylation, pentose phosphate pathway, glycogen metabolism, fatty acid metabolism, protein degradation and amino acid catabolism, protein translation and amino acid biosynthesis, nucleotide biosynthesis, DNA replication, recombination and repair, lipid and steroid biosynthesis. Medical consequences of impaired metabolism. Therapeutic intervention of metabolism. Prerequisite: BIOSCI 188/288 or CHEM 181 or CHEMENG 181/281 (formerly 188/288). GER:DB-NatSci BIOSCI 203. Advanced Genetics—(Same as DBIO 203, GENE 203.) For graduate students in Bioscience programs; may be appropriate for other graduate students. The genetic toolbox. Examples of analytic methods, genetic manipulation, genome analysis, and human genetics. Emphasis is on use of genetic tools in dissecting complex biological pathways, developmental processes, and regulatory systems. Faculty-led discussion sections with evaluation of papers. Students with minimal experience in genetics should prepare by working out problems in college level textbooks. BIOSCI 205. DNA Repair and Genomic Stability—Interactions of endogenous and environmental mutagens with cellular DNA. Cellular responses to damaged DNA including molecular mechanisms for DNA repair, translesion DNA synthesis, and genetic recombination. Inducible repair responses and error-prone mechanisms. Human hereditary diseases that predispose to cancer. Relationships of DNA repair to mutagenesis, carcinogenesis, aging, and human genetic disease. Current research literature. Prerequisites: 41 and 118, or consent of instructor. BIOSCI 206. Field Studies in Earth Systems—(Same as EARTHSYS 189.) For advanced upper-division undergraduates and graduate students. Field-based, focusing on the components and processes by which terrestrial ecosystems function. Topics from biology, chemistry, ecology, geology, and soil science. Lecture, field, and lab studies emphasize standard field techniques, experimental design, analysis of data, and written and oral presentation. Small team projects test the original questions in the functioning of natural ecosystems. Admission by application; see Time Schedule. Prerequisites: BIOSCI 141 or GES 160, or equivalent. BIOSCI 213. Biology of Viruses—Principles of virus growth, genetics, architecture, and assembly. The relation of temperate viruses and other episomes to the host cell. Prerequisite: Biological Sciences core. Recommended: 118. BIOSCI 214. Cell Biology of Physiological Processes—(Same as BIOC 224.) For Ph.D. students. Current research on cell structure, function, and dynamics. Topics include complex cell phenomena such as cell division, apoptosis, compartmentalization, transport and trafficking, motility and adhesion, differentiation, and multicellularity. Current papers from the primary literature. Prerequisite for advanced undergraduates: BIOSCI 129A,B, and consent of instructor. BIOSCI 215. Biochemical Evolution—Biochemical viewpoints on the evolutionary process. Topics: prebiotic biochemistry and the origins of life; adaptive organization of metabolism; enzyme polymorphisms and other biochemical aspects of population genetics; macromolecular phylogeny and protein clocks. Prerequisites: Biological Sciences core or substantial equivalent. BIOSCI 216. Terrestrial Biogeochemistry—Nutrient cycling and the regulation of primary and secondary production in terrestrial, freshwater, and marine ecosystems; land-water and biosphere-atmosphere interactions; global element cycles and their regulation; human effects on biogeochemical cycles. Prerequisite: graduate standing in science or engineering; consent of instructor for undergraduates or coterminal students. BIOSCI 217. Neuronal Biophysics—Biophysical descriptions and mechanisms of passive and excitable membranes, ion channels and pumps, action potential propagation, and synaptic transmission. Introduction to dynamics of single neurons and neuronal networks. Emphasis is on the experimental basis for modern research applications. Interdisciplinary aspects of biology and physics. Literature, problem sets, and student presentations. Prerequisites: undergraduate physics, calculus, and biology. BIOSCI 221. Methods of Theoretical Population Biology—Formulation and analysis of problems in population biology using theoretical and computational numerical methods. Topics include deterministic and stochastic models, structured populations, stability and bifurcations, and data-driven models with applications in ecology and genetics. Prerequisites: recent courses in advanced calculus and linear algebra. BIOSCI 222. Exploring Neural Circuits—Seminar. The logic of how neural circuits control behavior; how neural circuits are assembled during development and modified by experience. Emphasis is on primary literature. Topics include: neurons as information processing units; simple and complex circuits underlying sensory information processing and motor control; and development and plasticity of neural circuits. Advanced undergraduates with background in physical science, engineering, and biological science may apply to enroll. Recommended: background in neuroscience. BIOSCI 223. Stochastic and Nonlinear Dynamics—(Same as APPPHYS 223.) Theoretical analysis of dynamical processes: dynamical systems, stochastic processes, and spatiotemporal dynamics. Motivations and applications from biology and physics. Emphasis is on methods including qualitative approaches, asymptotics, and multiple scale analysis. Prerequisites: ordinary and partial differential equations, complex analysis, and probability or statistical physics. BIOSCI 230. Molecular and Cellular Immunology—For graduate students and advanced undergraduates. Components of the immune system: structure and functions of antibody molecules; cellular basis of immunity and its regulation; molecular biology and biochemistry of antigen receptors and signaling pathways; genetic control of immunity and disease susceptibility. Emphasis is on key experimental approaches. Prerequisite for undergraduates: Biological Sciences or Human Biology core, or consent of instructor. BIOSCI 230A. Molecular and Cellular Immunology Literature Review—Supplement to 230. Corequisite: 230. BIOSCI 258. Neural Development—For Ph.D. students. Seminar; students also attend BIOSCI 158 lectures. Topics: neural induction and patterning, cell lineage, neurogenesis, neuronal migration, axonal path-finding, synapse elimination, the role of activity, critical periods, and the development of behavior. BIOSCI 261A. Advanced Topics in Behavioral Biology—Seminar. The biological roots of aggression, competition, cooperation, and altruism. Prerequisite: 150/250, and consent of instructor. BIOSCI 261B. Advanced Topics in Behavioral Biology—Seminar. The biological roots of aggression, competition, cooperation, and altruism. Prerequisite: 150/250, and consent of instructor. BIOSCI 267. Molecular Mechanisms of Neurodegenerative Disease— (Same as NENS 267.) The epidemic of neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease occasioned by an aging human population. Genetic, molecular, and cellular mechanisms. Clinical aspects through case presentations. BIOSCI 290. Teaching of Biological Sciences—Open to upper-division undergraduates and graduate students. Practical experience in teaching lab biology or serving as an assistant in a lecture course. May be repeated for credit. Prerequisite: consent of instructor. BIOSCI 290X. Out-of-Department Teaching of Biological Science— May be repeated for credit. Prerequisite: consent of instructor. BIOSCI 291. Development and Teaching of Core Experimental Laboratories—Preparation for teaching the core experimental courses (44X and 44Y). Emphasis is on lab, speaking, and writing skills. Focus is on updating the lab to meet the changing technical needs of the students. Must be taken prior to teaching either of the above courses. May be repeated for credit. Prerequisite: selection by instructor. BIOSCI 294. Cellular Biophysics—(Same as APPPHYS 294.) Physical biology of dynamical and mechanical processes in cells. Emphasis is on qualitative understanding of biological functions through quantitative analysis and simple mathematical models. Sensory transduction, signaling, adaptation, switches, molecular motors, actin and microtubules, motility, and circadian clocks. Prerequisites: differential equations and introductory statistical mechanics. BIOSCI 300. Graduate Research—For graduate students only. Individual research by arrangement with in-department instructors. BIOSCI 300X. Out-of-Department Graduate Research—Individual research by arrangement with out-of-department instructors. Master’s students: credit for work arranged with out-of-department instructors is restricted to Biological Sciences students and requires approved department petition. See http://biohonors.stanford.edu for information on research sponsors, units, petitions, deadlines, credit for summer research, and out-of-Stanford research, or email gastrula@stanford.edu. May be repeated for credit. BIOSCI 301. Frontiers in Biology—Limited to and required of first-year Ph.D. students in molecular, cellular, and developmental biology. Current research in molecular, cellular, and developmental biology emphasizing primary research literature. Held in conjunction with the department’s Monday seminar series. Students and faculty meet weekly before the seminar for a student presentation and discussion of upcoming papers. BIOSCI 302. Current Topics and Concepts in Population Biology, Ecology, and Evolution—Required of first-year graduate students in population biology, and ecology and evolution; open to all graduate students. Major conceptual issues and developing topics. BIOSCI 303. Current Topics and Concepts in Population Biology, Ecology, and Evolution—Required of first-year graduate students in population biology, and ecology and evolution; open to all graduate students. Major conceptual issues and developing topics. BIOSCI 304. Current Topics and Concepts in Population Biology, Ecology, and Evolution—Required of first-year graduate students in population biology, and ecology and evolution; open to all graduate students. Major conceptual issues and developing topics. BIOSCI 306. Current Topics in Integrative Organismal Biology— Limited to and required of graduate students doing research in this field. At Hopkins Marine Station. BIOSCI 312. Ethical Issues in Ecology and Evolutionary Biology—Focus is on ethical issues addressed in Donald Kennedy’s Academic Duty and others of importance to academics and scientists in the fields of ecology, behavior, and evolutionary biology. Discussions led by faculty and outside guests. Satisfies ethics course requirement for ecology and evolutionary biology. Prerequisite: graduate standing in the ecology and evolutionary biology or marine program, or consent of instructor. BIOSCI 315. Seminar in Biochemical Evolution—Literature review and discussion of current topics in biochemical evolution and molecular evolutionary genetics. Prerequisite: consent of instructor. BIOSCI 325. The Evolution of Body Size—(Same as GES 325.) The influence of organism size on evolutionary and ecological patterns and processes. Focus is on integration of theoretical principles, observations of living organisms, and data from the fossil record. What are the physiological and ecological correlates of body size? Is there an optimum size? Do organisms tend to evolve to larger size? Does productivity control the size distribution of consumers? Does size affect the likelihood of extinction or speciation? How does size scale from the genome to the phenotype? How is metabolic rate involved in evolution of body size? What is the influence of geographic area on maximum body size? BIOSCI 342. Plant Biology Seminar—Topics announced at the beginning of each quarter. Current literature. May be repeated for credit. See http://carnegiedpb.stanford.edu/seminars/seminars.php. BIOSCI 344. Advanced Seminar in Cellular Biology—Enrollment limited to graduate students directly associated with departmental research groups working in cell biology. BIOSCI 346. Advanced Seminar on Prokaryotic Molecular Biology—Enrollment limited to graduate students associated with departmental research groups in genetics or molecular biology. BIOSCI 358. Advanced Topics in Biological Sciences—Restricted to doctoral and medical students in neurobiology labs. May be repeated for credit. BIOSCI 383. Seminar in Population Genetics—Literature review, research, and current problems in the theory and practice of population genetics and molecular evolution. Prerequisite: consent of instructor. BIOSCI 384. Theoretical Ecology—Recent and classical research papers in ecology, and presentation of work in progress by participants. Prerequisite: consent of instructor. BIOSCI 385. Speaking About Science—Communication about science occurs in settings such as presenting scientific work to an audience of peers, communicating difficult concepts in a classroom, or describing a new finding to a reporter. Focus is on practice in speaking about science, emphasizing strategies for making difficult ideas easy to understand and integrating visual aids into oral presentations. Limited to Ph.D. students. BIOSCI 459. Frontiers in Interdisciplinary Biosciences—(Same as BIOC 459, BIOE 459, CHEMENG 459, CHEM 459, PSYCH 459.) (Crosslisted in departments in the schools of H&S, Engineering, and Medicine; students register through their affiliated department; otherwise register for CHEMENG 459.) For specialists and non-specialists. Sponsored by the Stanford BioX Program. Three seminars per quarter address scientific and technical themes related to interdisciplinary approaches in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and the world present breakthroughs and endeavors that cut across core disciplines. Pre-seminars introduce basic concepts and background for non-experts. Registered students attend all pre-seminars; others welcome. See http://www.stanford.edu/group/biox/courses/459.html. Recommended: basic mathematics, biology, chemistry, and physics. See respective department listings for course descriptions and General Education Requirements (GER) information. See degree requirements above or the department’s student services office for applicability of these courses to a major or minor program. CEE 274A. Environmental Microbiology I—(Same as CHEMENG 174/274.) CEE 274B. Metabolic Biochemistry of Microorganisms—(Same as CHEMENG 456.) DBIO 210. Developmental Biology SBIO 241. Biological Macromolecules—(Same as BIOC 241, BIOPHYS 241.) |
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