The online version of the Caltech Catalog is provided as a convenience; however, the printed version is the only authoritative source of information about course offerings, option requirements, graduation requirements, and other important topics.
Bi 1. Principles of Biology. 9 units (4-0-5); third term. Advances in biotechnology have driven unprecedented integration across the hierarchy of biology, from molecules to ecosystems, as well as the integration of biology with other sciences, including geology, physics, chemistry and mathematics. The design of this biology course seeks to provide introductory students with a strong foundation built on a set of basic principles that will provide students with the intellectual tools for critical thinking in the discipline. Because the microbial world has been critical in all aspects of biology, from the environmental to human health, throughout the evolution of the biosphere, a microbiological perspective will form the nucleus around which each major topic will be developed. Specifically, we will discuss key concepts in cellular and molecular biology (e.g. cytoskeletal elements, transcription, translation), ecology, evolution, and metabolism (e.g. biosynthesis and energy generation) by providing examples from the microbial world. Instructor: Newman.
Bi 1 x. The Great Ideas of Biology: An Introduction through Experimentation. 9 units (0-6-3); third term. Introduction to concepts and laboratory methods in biology. Molecular biology techniques and advanced microscopy will be combined to explore the great ideas of biology. This course is intended for nonbiology majors and will satisfy the freshman biology course requirement. Limited enrollment. Instructor: Phillips.
Bi 2. Current Research in Biology. 3 units (1-0-2); first term. Intended for students considering the biology option; open to freshmen. Current research in biology will be discussed, on the basis of reading assigned in advance of the discussions, with members of the divisional faculty. Graded pass/fail. Instructor: Elowitz.
Bi 8. Introduction to Molecular Biology: Organization and Expression of Genetic Information. 9 units (4-0-5); second term. This course and its sequel, Bi 9, cover biology at the molecular and cellular levels. Bi 8 emphasizes genomic structure and mechanisms involved in the organization and regulated expression of genetic information. The focus is on the ways that the information content of the genome is translated into distinctive, cell type specific patterns of gene expression and protein function, with special attention to the problems of gene regulation in complex multicellular organisms. Assignments will include critical dissections of papers from current research literature and individual oral presentations by students to the class on specific topics. Instructor: Rothenberg.
Bi 9. Cell Biology. 9 units (3-0-6); third term. Continues coverage of biology at the cellular level, begun in Bi 8. Topics: cytoplasmic structure, membrane structure and function, cell motility, and cell-cell recognition. Emphasis on both the ultrastructural and biochemical approaches to these topics. Instructors: Aravin, Deshaies.
Bi 10. Cell Biology Laboratory. 6 units (1-3-2); third term. Prerequisite: Bi 8; designed to be taken concurrently with Bi 9. Introduction to basic methods in cell and molecular biological research, including polymerase chain reaction, molecular cloning, expression and purification of recombinant fusion proteins in bacteria, enzymology, and gel electrophoresis of proteins and nucleic acids. Instructor: Deshaies.
FS/Bi 13. In Search of Memory. 6 units (2-0-4). For course description, see Freshman Seminar.
Bi 22. Undergraduate Research. Units to be arranged; first, second, third terms. Special problems involving laboratory research in biology; to be arranged with instructors before registration. Graded pass/fail. Instructor: Staff.
Bi 23. Biology Tutorial. 3 or 6 units; second, third terms . Small group study and discussion in depth of special areas or problems in biology, involving regular tutorial sections with instructors. Usually given winter and/or spring terms. To be arranged with instructors before registration. Graded pass/fail. Instructor: Huang.
Bi 24. Technical Communication for Biologists. 6 units (2-0-4); first term. This course offers instruction and practice in writing and speaking relevant to professional biologists working in research, teaching, and/or medical careers. Students may write a paper for a scientific journal, based on their previous research and mentored by a faculty member. Alternatively, students may produce a variety of brief writing assignments with a range of audiences and purposes. Oral presentations will be based on writing produced in the course, with feedback from instructors and peers. Fulfills the Institute scientific writing requirement. Not offered 2013–14.
Bi 90 abc. Undergraduate Thesis. 12 or more units per term; first, second, third terms. Prerequisites: 18 units of Bi 22 (or equivalent research experience) in the research area proposed for the thesis, and instructor’s permission. Intended to extend opportunities for research provided by Bi 22 into a coherent individual research project, carried out under the supervision of a member of the biology faculty. Normally involves three or more consecutive terms of work in the junior and senior years. The student will formulate a research problem based in part on work already carried out, evaluate previously published work in the field, and present new results in a thesis format. First two terms graded pass/fail; final term graded by letter on the basis of the completed thesis. Instructor: Bjorkman.
CNS/SS/Psy/Bi 102 ab. Brains, Minds, and Society. 9 units (3-0-6). For course description, see Computation and Neural Systems.
Bi/Ge 105. Evolution. 12 units (3-4-5); second term. Maximum enrollment: 15, by application only. In 2013-2014 the course will be open to undergraduates only. Prerequisites: Completion of Core Curriculum Courses. The theory of evolution is arguably biology’s greatest idea and serves as the overarching framework for thinking about the diversity and relationships between organisms. This course will present a broad picture of evolution starting with discussions of the insights of the great naturalists, the study of the genetic basis of variation, and an introduction to the key driving forces of evolution. Following these foundations, we will then focus on a number of case studies including the following: evolution of oxygenic photosynthesis, origin of eukaryotes, multicellularity, influence of symbiosis, the emergence of life from the water (i.e. fins to limbs), the return of life to the water (i.e. limbs to fins), diversity following major extinction events, the discovery of Archaea, insights into evolution that have emerged from sequence analysis, and finally human evolution and the impact of humans on evolution (including examples such as antibiotic resistance). A specific focus for considering these issues will be the island biogeography of the Galapagos. Instructors: Phillips, Orphan. Given in alternate years; offered 2013–14.
BE/Bi/MedE 106. Introduction to Biomechanics. 9 units (3-0-6); third term. For course description, see Bioengineering.
CNS/Bi/Ph 107. Writing about Scientific Research. 9 units (3-0-6). For course description, see Computation and Neural Systems.
Bi/Ch 110. Introduction to Biochemistry. 12 units (4-0-8); first term. Prerequisite: Ch 41 abc or instructor’s permission. Lectures and recitation introducing the molecular basis of life processes, with emphasis on the structure and function of proteins. Topics will include the derivation of protein structure from the information inherent in a genome, biological catalysis, the intermediary metabolism that provides energy to an organism, and the use of DNA manipulations, cloning, and expression of proteins in foreign hosts to study protein structure and function. Instructors: Richards, Biochemistry faculty.
Bi/Ch 111. Biochemistry of Gene Expression. 12 units (4-0-8); second term. Prerequisites: Bi/Ch 110; Bi 8 and Bi 122 recommended. Lectures and recitation on the molecular basis of biological structure and function. Emphasizes the storage, transmission, and expression of genetic information in cells. Specific topics include DNA replication, recombination, repair and mutagenesis, transcription, RNA processing, and protein synthesis. Instructors: Campbell, Parker.
Bi/Ch 113. Biochemistry of the Cell. 12 units (4-0-8); third term. Prerequisites: Bi/Ch 110; Bi 9 recommended or consent of instructor. Lectures and recitation on the biochemistry of basic cellular processes in the cytosol and organelles, with emphasis on membrane and protein trafficking. Specific topics include protein secretion, virus entry, endocytosis, endoplasmic reticulum dynamics, nuclear trafficking, autophagy, apoptosis, and mitochondrial dynamics. The relationship of these processes to human disease will be discussed. Instructors: Chan, Hoelz.
Bi 114. Immunology. 9 units (3-0-6); second term. Prerequisites: Bi 8, Bi 9, Bi 122 or equivalent, and Bi/Ch 110 recommended. The course will cover the molecular and cellular mechanisms that mediate recognition and response in the mammalian immune system. Topics include cellular and humoral immunity, the structural basis of immune recognition, antigen presentation and processing, gene rearrangement of lymphocyte receptors, cytokines and the regulation of cellular responses, T and B cell development, and mechanisms of tolerance. The course will present an integrated view of how the immune system interacts with viral and bacterial pathogens and commensal bacteria. Instructors: Mazmanian, Bjorkman.
Bi 115. Attack and Repulsion: Viruses and their Hosts. 9 units (3-0-6); third term. The course will introduce the chemistry and biology of viruses, emphasizing their diverse replication strategies. It will then focus on mechanisms used by viruses to multiply in the face of host defenses. It will also discuss cancer-inducing viruses. The course will mainly consider mammalian viruses but will also discuss aspects of plant and bacterial viruses. Instructor: Baltimore. Given in alternate years; offered 2013–14.
Bi 117. Developmental Biology. 9 units (3-0-6); second term. Prerequisites: Bi 8 and Bi 9. A survey of the development of multicellular organisms. Topics will include the beginning of a new organism (fertilization), the creation of multicellularity (cellularization, cleavage), reorganization into germ layers (gastrulation), induction of the nervous system (neurulation), and creation of specific organs (organogenesis). Emphasis will be placed on the molecular mechanisms underlying morphogenetic movements, differentiation, and interactions during development, covering both classical and modern approaches to studying these processes. Instructor: Bronner.
Bi 118. Morphogenesis of Developmental Systems. 6 units (2-0-4); first term. Prerequisites: Bi 8 and Bi 9, and at least one of the following: Bi 117, Bi 122, Bi 129, Bi 145, or Bi 182 (or equivalents). Lectures on and discussion of how cells, tissues, and organs take shape: the influence of force on cell shape change; cell migration including chemotaxis and collective cell movement; adhesion/deadhesion during migration; the relationship between cell migration and metastasis; and a review/overview of general signaling principles and embryonic development of invertebrate and vertebrate animals. Instructor: Stathopoulos. Given in alternate years; not offered 2013–14.
Bi 122. Genetics. 9 units (3-0-6); first term. Prerequisite: Bi 8 or Bi 9, or instructor’s permission. Lecture and discussion course covering basic principles of genetics. Instructor: Hay.
Bi 123. Genetics Laboratory. 12 units (2-8-2); second term. Prerequisite: Bi 122. Laboratory exercises illustrating the principles of genetics, with emphasis on Mendelian inheritance in multicellular eukaryotes, including Drosophila melanogaster and Caenorhabditis elegans. Instructor: Staff Given in alternate years; not offered 2013–14.
Bi 129. Biology of Cancer. 9 units (3-0-6); second term. The first part of the course will concern the basic biology of cancer, covering oncogenes, tumor suppressors, tumor cell biology, metastasis, tumor angiogenesis, and other topics. There will also be a section on cancer genetics, which will primarily be taught from primary literature and journal reviews. The last part of the course will concern treatments, including chemotherapy, anti-angiogenic therapy, and immunotherapy. Textbook: The Biology of Cancer (2006) by Robert Weinberg. Instructor: Zinn. Given in alternate years; not offered 2013–14.
CNS/Psy/Bi 131. The Psychology of Learning and Motivation. 9 units (3-0-6). For course description, see Computation and Neural Systems.
Bi/Ch 132. Biophysics of Macromolecules. 9 units (3-0-6); first term. Recommended prerequisite: Bi/Ch 110. Structural and functional aspects of nucleic acids and proteins, including hybridization; electrophoretic behavior of nucleic acids; principles and energetics of folding of polypeptide chains in proteins; allostery and cooperativity in protein action; enzyme kinetics and mechanisms; and methods of structure determination, such as X-ray diffraction and magnetic resonance. Structure and function of metalloenzymes. Instructors: Beauchamp, Cai.
Bi 145 a. Tissue and Organ Physiology. 9 units (3-0-6); first term.Prerequisites: Bi 8, 9, 110. Bi 110 may be taken concurrently. Reviews of anatomy and histology, as well as in-depth discussion of cellular physiology. Building from cell function to tissues, the course explores human physiology in an organ-based fashion. First term topics include endocrine physiology, the skeletal system, digestive and hepatic physiology, nutrition and urinary physiology. Particular emphasis is placed on health issues and pharmaceutical therapy from both a research and a medical perspective. Instructor: Tydell.
Bi 145 b. Tissue and Organ Physiology. 9 units (3-0-6); second term. Prerequisites: Bi 145a. Building on the foundations of Bi 145a, Bi 145b will continue the exploration of human physiology incorporating anatomy and cellular physiology. Topics include muscle physiology, cardiovascular physiology, the respiratory system and reproductive physiology. Particular emphasis is placed on health issues and pharmaceutical therapy from both a research and a medical perspective. Instructor: Tydell.
Bi/CNS/NB 150. Introduction to Neuroscience. 10 units (4-0-6); first term. Prerequisites: Bi 8, 9, or instructors’ permission. General principles of the function and organization of nervous systems, providing both an overview of the subject and a foundation for advanced courses. Topics include the physical and chemical bases for action potentials, synaptic transmission, and sensory transduction; anatomy; development; sensory and motor pathways; memory and learning at the molecular, cellular, and systems level; and the neuroscience of brain diseases. Instructors: Adolphs, Lester.
BE/Bi 152. Bioengineering Principles and Practice in Cell Physiology. 9 units (3-0-6). For course description, see Bioengineering.
Bi/CNS/NB 153. Brain Circuits. 9 units (3-0-6); second term. Prerequisites: Bi/CNS/NB 150 or equivalent. What functions arise when many thousands of neurons combine in a densely connected circuit? Though the operations of neural circuits lie at the very heart of brain science, our textbooks have little to say on the topic. Through an alternation of lecture and discussion this course explores the empirical observations in this field and the analytical approaches needed to make sense of them. We begin with a foray into sensory and motor systems, consider what basic functions they need to accomplish, and examine what neural circuits are involved. Next we explore whether the circuit motifs encountered are also found in central brain areas, with an emphasis on sensory-motor integration and learning. Finally we discuss design principles for neural circuits and what constraints have shaped their structure and function in the course of evolution. Instructor: Meister. Given in alternate years; offered 2014-15.
Bi/NB 156. Molecular Basis of Behavior. 9 units (3-0-6); second term. Prerequisite: Bi/CNS/NB 150 or instructor’s permission. A lecture and discussion course on the neurobiology of behavior. Topics may include biological clocks, eating behavior, sexual behavior, addiction, mental illness, and neurodegenerative diseases. Instructor: Patterson. Given in alternate years; offered 2013–14.
Bi/CNS/NB 157. Comparative Nervous Systems. 9 units (2-3-4); third term. An introduction to the comparative study of the gross and microscopic structure of nervous systems. Emphasis on the vertebrate nervous system; also, the highly developed central nervous systems found in arthropods and cephalopods. Variation in nervous system structure with function and with behavioral and ecological specializations and the evolution of the vertebrate brain. Instructor: Allman. Given in alternate years; not offered 2013–14.
Bi/CNS 158. Vertebrate Evolution. 9 units (3-0-6); third term. An integrative approach to the study of vertebrate evolution combining comparative anatomical, behavioral, embryological, genetic, paleontological, and physiological findings. Special emphasis will be given to: (1) the modification of developmental programs in evolution; (2) homeostatic systems for temperature regulation; (3) changes in the life cycle governing longevity and death; (4) the evolution of brain and behavior. Instructor: Allman. Given in alternate years; offered 2013–14.
Bi/CNS 162. Cellular and Systems Neuroscience Laboratory. 12 units (2-7-3); third term. Prerequisite: Bi/CNS/NB 150 or instructor’s permission. A laboratory-based introduction to experimental methods used for electrophysiological studies of the central nervous system. Through the term, students investigate the physiological response properties of neurons in insect and mammalian brains, using extra- and intracellular recording techniques. Students are instructed in all aspects of experimental procedures, including proper surgical techniques, electrode fabrication, stimulus presentation, and computer-based data analysis. Graded pass/fail. Instructor: Staff. Not offered 2013–14.
Bi/CNS 164. Tools of Neurobiology. 9 units (3-0-6); second term. Prerequisites: Bi/CNS/NB 150 or equivalent. Offers a broad survey of methods and approaches to understanding in modern neurobiology. The focus is on understanding the tools of the discipline, and their use will be illustrated with current research results. Topics include: molecular genetics, disease models, transgenic and knock-in technology, virus tools, tracing methods, gene profiling, light and electron microscopy, optogenetics, optical and electrical recording, neural coding, quantitative behavior, modeling and theory. Instructors: Team of faculty. Offered 2014-15.
Bi 165. Microbiology Bootcamp. 6 units (2-3-1); first term, beginning Orientation week. The course will introduce students to the basic principles and practices of isolating, culturing, and characterizing bacteria. This course will involve a hands-on bootcamp with close interaction between students and faculty for one week prior to the start of the Fall term. During this first phase, students will be exposed to basic techniques in microbial phylogeny, physiology, cell biology and ecology through interactive discussions and lab training with relevant faculty with expertise in diverse areas of microbiology. The second phase, over the Fall term, will involve training in grant writing by drafting an NSF-type proposal, and a final oral presentation of the students’ work. Instructors: Mazmanian, Jensen.
ESE/Bi 166. Microbial Physiology. 9 units (3-1-5). For course description, see Environmental Science and Engineering.
ESE/Bi 168. Microbial Metabolic Diversity. 9 units (3-0-6). For course description, see Environmental Science and Engineering.
BMB/Bi/Ch 170 abc. Biochemistry and Biophysics of Macromolecules and Molecular Assemblies. 9 units (3-1-5). For course description, see Biochemistry and Molecular Biophysics.
CNS/Bi/SS/Psy/NB 176. Cognition. 12 units (6-0-6). For course description, see Computation and Neural Systems.
Bi/BE 177. Principles of Modern Microscopy. 9 units (3-0-6); second term. Lectures and discussions on the underlying principles behind digital, video, differential interference contrast, phase contrast, confocal, and two-photon microscopy. The course will begin with basic geometric optics, characteristics of lenses and microscopes, and principles of accurate imaging. Specific attention will be given to how different imaging elements such as filters, detectors, and objective lenses contribute to the final image. Course work will include critical evaluation of published images and design strategies for simple optical systems. Emphasis in the second half of the course will be placed on the analysis and presentation of two- and three-dimensional images. No prior knowledge of microscopy will be assumed. Instructor: Staff. Not offered 2013–14.
Bi/Ge 180. Methods in Molecular Genetics. 9 units (2-6-1); first term. Prerequisites: Bi 122, Bi 10, or instructor’s permission. An introduction to current molecular genetic techniques including basic microbiological and molecular biological procedures, phage display, bacterial two-hybrid system, protein purification, sequencing, and genomics. The first half of the course involves structured experiments designed to demonstrate the various techniques. The second half is devoted to individual research projects in which the techniques are applied to original studies on an interesting, but not well studied, organism. Graded pass/fail. Instructors: Bertani.
Bi 182. Gene Regulation Systems and the Control of Embryonic Development. 6 units (2-0-4); second term. Prerequisites: Bi 8 and at least one of the following: Bi 111, Bi 114, or Bi 122 (or equivalents). This course will cover the principles of developmental gene regulation in animals with emphasis on causal mechanism; theory, solution, and explanatory power of gene regulatory networks and how they are directly encoded in the genome; regulatory mechanisms underlying embryonic and postembryonic processes of development. Specific examples will be drawn mainly from sea urchin and Drosophila, but comparative treatment of other modes of development will be included. Instructors: Stathopoulos, Davidson. Given in alternate years; offered 2013–14.
Bi/CNS/NB 184. The Primate Visual System. 9 units (3-1-5); third term. This class focuses on the primate visual system, investigating it from an experimental, psychophysical, and computational perspective. The course will focus on two essential problems: 3-D vision and object recognition. Topics include parallel processing pathways, functional specialization, prosopagnosia, object detection and identification, invariance, stereopsis, surface perception, scene perception, navigation, visual memory, multidimensional readout, signal detection theory, oscillations, and synchrony. It will examine how a visual stimulus is represented starting in the retina, and ending in the frontal lobe, with a special emphasis placed on mechanisms for high-level vision in the parietal and temporal lobes. The course will include a lab component in which students design and analyze their own fMRI experiment. Instructor: Tsao. Given in alternate years; not offered 2013–14.
Bi/CNS/NB 185. Large Scale Brain Networks. 9 units (3-0-6); third term. This class will focus on understanding what is known about the large-scale organization of the brain, focusing on the mammalian brain. What large scale brain networks exist and what are their principles of function? How is information flexibly routed from one area to another? What is the function of thalamocortical loops? We will examine large scale networks revealed by anatomical tracing, functional connectivity studies, and mRNA expression analyses, and explore the brain circuits mediating complex behaviors such as attention, memory, sleep, multisensory integration, decision making, and object vision. While each of these topics could cover an entire course in itself, our focus will be on understanding the master plan--how the components of each of these systems are put together and function as a whole. A key question we will delve into, from both a biological and a theoretical perspective, is: how is information flexibly routed from one brain area to another? We will discuss the communication through coherence hypothesis, small world networks, and sparse coding. Instructor: Tsao. Given in alternate years, offered 2013–14.
CNS/Bi/EE/CS/NB 186. Vision: From Computational Theory to Neuronal Mechanisms. 12 units (4-4-4). For course description, see Computation and Neural Systems.
CNS/Bi/Ph/CS/NB 187. Neural Computation. 9 units (3-0-6). For course description, see Computation and Neural Systems.
Bi 188. Human Genetics and Genomics. 6 units (2-0-4); third term. Prerequisite: Bi 122; or graduate standing and instructor’s permission. Introduction to the genetics of humans. Subjects covered include human genome structure, genetic diseases and predispositions, the human genome project, forensic use of human genetic markers, human variability, and human evolution. Instructor: Wold. Given in alternate years; not offered 2013–14.
Bi 189. The Cell Cycle. 6 units (2-0-4); third term. Prerequisites: Bi 8 and Bi 9. The course covers the mechanisms by which eukaryotic cells control their duplication. Emphasis will be placed on the biochemical processes that ensure that cells undergo the key events of the cell cycle in a properly regulated manner. Instructor: Dunphy.
Bi 190. Systems Genetics. 6 units (2-0-4); third term. Prerequisites: Bi 122. Lectures covering how genetic and genomic analyses are used to understand biological systems. Emphasis is on genetic and genome-scale approaches used in model organisms such as yeast, flies, worms, and mice to elucidate the function of genes, genetic pathways and genetic networks. Instructors: Sternberg.
BE/CS/CNS/Bi 191 ab. Biomolecular Computation. 9 units. For course description, see Bioengineering.
Bi 192. Introduction to Systems Biology. 6 units (2-0-4); first term. Prerequisites: Ma 1abc, and either Bi 8, CS1, or ACM 95 or instructor’s permission. The course will explore what it means to analyze biology from a systems-level point of view. Given what biological systems must do and the constraints they face, what general properties must biological systems have? Students will explore design principles in biology, including plasticity, exploratory behavior, weak-linkage, constrains that deconstrain, robustness, optimality, and evolvability. The class will read the equivalent of 2-3 scientific papers every week. The format will be a seminar with active discussion from all students. Students from multiple backgrounds are welcome: non-biology or biology students interested in learning systems-level questions in biology. Limited enrollment. Instructors: Goentoro.
Bi/CNS/NB 195. Mathematics in Biology. 9 units (3-0-6); second term. Prerequisites: Multi-variable calculus. This course develops the mathematical methods needed for a quantitative understanding of biological phenomena, including data analysis, formulation of simple models, and the framing of quantitative questions. Topics include: probability and stochastic processes, linear algebra and transforms, dynamical systems, MATLAB programming. Instructor: Meister. Given in alternate years; offered 2013–14.
Bi 199. Introduction to MATLAB for Biologists. 6 units (3-0-3); second term. This hands-on course provides an introduction to MATLAB’s structure and syntax, writing of functions and scripts, image analysis, and data visualization. Instructor: Kennedy.
Bi/NB 202. Neurobiology of Disease. 9 units (3-0-6); first term. Prerequisite: Bi/CNS/NB 150 or instructor’s permission. This course will cover the cellular and molecular basis of diseases of the nervous system, as well as current and future therapeutic approaches. These diseases include disorders of abnormal protein structure (Alzheimer’s, Huntington’s, Parkinson’s, prion), autoimmunity (multiple sclerosis), developmental disorders of cognition and social communication (schizophrenia, autism, Fragile X, Rett syndrome), epilepsy, stroke and depression. Genetic and environmental etiologies will be explored, and animal models will be compared to the human condition. The role of the reward system in addiction will also be discussed. Instructor: Patterson. Given in alternate years; not offered 2013–14.
Bi 204. Evolution of the Animal Body Plan. 6 units (2-0-4); third term. Prerequisite: Bi 182 or equivalent. Qualified undergraduates are welcome. Evolution of animal forms will be considered mechanistically in terms of change in the genomic regulatory programs underlying the developmental ontogeny of these forms, but within the framework provided by current concepts of animal phylogeny. Evolutionary mechanisms will be considered, as well, with respect to the real-time paleontological record and the changing conditions of Earth’s environment through geological time. Principles emerging from the system biology of regulatory evolution will be emphasized. Instructor: Davidson. Given in alternate years; not offered 2013–14.
Bi 206. Biochemical and Genetic Methods in Biological Research. 6 units (2-0-4); third term. Prerequisite: graduate standing or instructor’s permission. This course will comprise in-depth discussions of selected methods in molecular biology and related fields. Given the enormous range of techniques available to a molecular biologist nowadays, the course will focus on a subset of these methods that includes recent and highly promising techniques, with an emphasis on their robustness and general applicability. Instructor: Varshavsky.
Bi 214. Hematopoiesis: A Developmental System. 6 units (2-0-4); third term. Prerequisite: Bi 114, or Bi 182, or Bi 117 plus Bi/Ch 111, or graduate standing. An advanced course with lectures and seminar presentations, based on reading from the current literature. The characteristics of blood cells offer unique insights into the molecular basis of lineage commitment and the mechanisms that control the production of diverse cell types from pluripotent precursors. The course will cover the nature of stem cells, the lineage relationships among differentiated cell types, the role of cytokines and cytokine receptors, apoptosis and lineage-specific proliferation, and how differentiation works at the level of gene regulation and regulatory networks. Roles of prominent regulatory molecules in hematopoietic development will be compared with their roles in other developmental systems. Emphasis will be on explanation of cellular and system-level phenomena in terms of molecular mechanisms. Instructor: Rothenberg. Given in alternate years; not offered 2013–14.
Bi/CNS/NB 216. Behavior of Mammals. 6 units (2-0-4); first term. A course of lectures, readings, and discussions focused on the genetic, physiological, and ecological bases of behavior in mammals. A basic knowledge of neuroanatomy and neurophysiology is desirable. Instructor: Allman. Given in alternate years; offered 2013–14.
Bi/CNS/NB 217. Central Mechanisms in Perception. 6 units (2-0-4); first term. Reading and discussions of behavioral and electrophysiological studies of the systems for the processing of sensory information in the brain. Instructor: Allman. Given in alternate years; not offered 2013–14.
Bi/CNS/NB 220. Genetic Dissection of Neural Circuit Function. 6 units (2-0-4); second term. This advanced course will discuss the emerging science of neural “circuit breaking” through the application of molecular genetic tools. These include optogenetic and pharmacogenetic manipulations of neuronal activity, genetically based tracing of neuronal connectivity, and genetically based indicators of neuronal activity. Both viral and transgenic approaches will be covered, and examples will be drawn from both the invertebrate and vertebrate literature. Interested students who have little or no familiarity with molecular biology will be supplied with the necessary background information. Lectures and student presentations from the current literature. Instructor: Anderson.
Bi/BE 227. Methods in Modern Microscopy. 12 units (2-6-4); second term. Prerequisites: Bi/BE 177 or a course in microscopy. Bi/BE 177 may be taken concurrently with this course. Discussion and laboratory-based course covering the practical use of the confocal microscope, with special attention to the dynamic analysis of living cells and embryos. Course will begin with basic optics, microscope design, Koehler illumination, and the principles of confocal microscopy. After introductory period, the course will consist of semi-independent weeklong modules organized around different imaging challenges. Early modules will focus on three-dimensional reconstruction of fixed cells and tissues, with particular attention being paid to accurately imaging very dim samples. Later modules will include time-lapse confocal analysis of living cells and embryos, including Drosophila, zebrafish, chicken, and s embryos. Dynamic analysis will emphasize the use of fluorescent proteins. No prior experience with confocal microscopy will be assumed; however, a basic working knowledge of microscopes is highly recommended. Preference is given to graduate students who will be using confocal microscopy in their research. Instructor: Staff. Not offered 2013–14.
Bi/CNS/BE/NB 230. Optogenetic Methods in Experimental Neuroscience. 9 units (3-1-5); third. Prerequisites: Graduate standing or Bi/CNS/NB 150 and instructor permission. The class covers the theoretical and practical aspects of optogenetic control and complementary readout methods in molecular, cellular, and systems neuroscience. Topics include opsin design (including natural and artificial sources), delivery (genetic targeting, viral transduction), light activation requirements (power requirements, wavelength, fiberoptics, LEDs), compatible readout modalities (electrophysiology, imaging) and applications to neuronal circuits (case studies based on recent literature). The class offers hands-on lab exposure for opsin delivery to the mammalian brain and recording of brain activity modulated by light. Instructor: Gradinaru. Not offered 2013–14
Ch/Bi 231. Advanced Topics in Biochemistry. 6 units (2-0-4). For course description, see Chemistry.
Ge/Bi 244. Paleobiology Seminar. 6 units (3-0-3). For course description, see Geological and Planetary Sciences.
Ge/Bi 246. Molecular Geobiology Seminar. 6 units (2-0-4). For course description, see Geological and Planetary Sciences.
CNS/Bi/NB 247. Cerebral Cortex. 6 units (2-0-4). For course description, see Computation and Neural Systems.
Bi 250 a. Topics in Molecular and Cellular Biology. 9 units (3-0-6); first term. Prerequisite: graduate standing. Lectures and discussion covering research methods, logic, techniques and strategies, fundamental and general principles of modern biology, and unsolved problems. Students will learn to critique papers on molecular biology, cell biology, and genetics. Instructor: Prober.
Bi 250 b. Topics in Systems Biology. 9 units (3-0-6); third term. Prerequisite: graduate standing. The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale. Instructor: Elowitz.
Bi/CNS/NB 250 c. Topics in Systems Neuroscience. 9 units (3-0-6); third term. Prerequisite: graduate standing. The class focuses on quantitative studies of problems in systems neuroscience. Students will study classical work such as Hodgkin and Huxley’s landmark papers on the ionic basis of the action potential, and will move from the study of interacting currents within neurons to the study of systems of interacting neurons. Topics will include lateral inhibition, mechanisms of motion tuning, local learning rules and their consequences for network structure and dynamics, oscillatory dynamics and synchronization across brain circuits, and formation and computational properties of topographic neural maps. The course will combine lectures and discussions, in which students and faculty will examine papers on systems neuroscience, usually combining experimental and theoretical/modeling components. Instructor: Siapas.
Bi/BMB 251 abc. Current Research in Cellular and Molecular Biology. 1 unit. Prerequisite: graduate standing. Presentations and discussion of research at Caltech in biology and chemistry. Discussions of responsible conduct of research are included. Instructors: Sternberg, Hay.
Bi 252. Responsible Conduct of Research. 4 units (2-0-2); third term. This lecture and discussion course covers relevant aspects of the responsible conduct of biomedical and biological research. Topics include guidelines and regulations, ethical and moral issues, research misconduct, data management and analysis, research with animal or human subjects, publication, conflicts of interest, mentoring, and professional advancement. This course is required of all trainees supported on the NIH training grants in cellular and molecular biology and neuroscience, and is recommended for other graduate students in labs in the Division of Biology and Biological Engineering labs. Undergraduate students require advance instructor’s permission. Graded pass/fail. Instructors: Meyerowitz, Sternberg, staff.
SS/Psy/Bi/CNS 255. Topics in Emotion and Social Cognition. 9 units (3-0-6). For course description, see Social Science.
CNS/Bi/NB 256. Decision Making. 6 units (2-0-4). For course description, see Computation and Neural Systems.
Bi 270. Special Topics in Biology. Units to be arranged; first, second, third terms. Students may register with permission of the responsible faculty member.
CNS/Bi 286 abc. Special Topics in Computation and Neural Systems. Units to be arranged. For course description, see Computation and Neural Systems.
Bi 299. Graduate Research. Units to be arranged; first, second, third terms. Students may register for research units after consultation with their adviser.