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Biology

Bi 1. Principles of Biology. 9 units (4-0-5); third term. A host of new technologies have led to an explosion of fascinating data 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. This course provides an introduction to the most exciting themes of modern biology through a series of case studies. Each of these examples, whether the examination of the critical role of keystone species in ecology or the resolution of key puzzles of modern biogeography using DNA sequencing or the advent of super resolution microscopy which provides an astonishing dynamic view of cells and the viruses that infect them, serves to demonstrate the overarching principles of modern biology. Instructor: Phillips.

Bi 1 x. The Great Ideas of Biology: Exploration 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: Bois.

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: Regulation of Gene Expression. 9 units (3-0-6); 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. Assignments will include critical dissections of papers from classical and current research literature and problem sets. Instructors: Guttman, Hong.

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. Introductory Biology Laboratory. 6 units (1-3-2); third term. Prerequisites: Bi 8; designed to be taken concurrently with Bi 9. An introduction to molecular, cellular, and biochemical techniques that are commonly used in studies of biological systems at the molecular level. Instructor: Bertani.

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 Tutorials. 3 or 6 units; second term. Small group study and discussion in depth of special areas or problems in biology or biological engineering , involving regular tutorial sections with instructors drawn from the divisional postdoctoral staff and others. Usually given winter term. To be arranged with instructors before registration. Graded pass/fail. Instructor: Huang.

Bi/BE 24. Technical Communication for Biological Scientists and Engineers. 6 units (3-0-3); first, third terms. This course offers instruction and practice in writing and speaking relevant to professional biological scientists and engineers working in research, teaching, and/or medical careers. Students will write a paper for a scientific or engineering journal, either based on their previous research or written as a review paper of current work in their field. A Caltech faculty member, a postdoctoral scholar, or technical staff member serves as a technical mentor for each student, to provide feedback on the content and style of the paper. Oral presentations will be based on writing produced in the course, with feedback from instructors and peers. Fulfills the Institute scientific writing requirement. Instructor: Anderson, B.

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.

BE/Bi 101. Order of Magnitude Biology. 6 units (3-0-3); second term. For course description, see Bioengineering.

CNS/SS/Psy/Bi 102 ab. Brains, Minds, and Society. 9 units (3-0-6); second, third terms. For course description, see Computation and Neural Systems.

BE/Bi 103. Data Analysis in the Biological Sciences. 9 units (1-3-5); first term. For course description, see Bioengineering.

Bi/Ge/ESE 105. Evolution. 12 units (3-4-5); second term. Prerequisites: Completion of Core Curriculum Courses. Maximum enrollment: 15, by application only. 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; not offered 2016–17.

BE/Bi 106. Comparative Biomechanics. 9 units (3-0-6); third term. For course description, see Bioengineering.

ChE/Ch/E/Bi 107. Social Media for Scientists. 9 units (3-0-6); third term. For course description, see Chemical Engineering.

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: Campbell, Parker.

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. Instructor: Chan.

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; not offered 2016–17.

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. 9 units (3-0-6); second term. Prerequisites: Bi 8 and Bi 9, or instructor's permission. 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. Students will choose term project involving writing a grant proposal or quantitative analysis of available datasets relating to lecture topics. Instructor: Stathopoulos. Given in alternate years; offered 2016–17.

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. Not open to freshmen. Instructor: Hay.

Bi/BE 129. The Biology and Treatment 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. The second part will concern newer information on cancer genetics and other topics, taught from the primary research literature. The last part of the course will concern treatments, including chemotherapy, anti-angiogenic therapy, and immunotherapy. Textbook: The Biology of Cancer, 2nd edition, by Robert Weinberg. Instructor: Zinn.

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. Introduction to biophysical methods in molecular and cellular biology. Biomolecule structure and dynamics, single molecule microscopy, in situ sequencing, single cell genomics, proteomics, mass spectrometry, x-ray diffraction, electron microscopy and microfluidics. Instructors: Beauchamp, Cai.

Bi 145 a. Tissue and Organ Physiology. 9 units (3-0-6); first term. Prerequisites: Bi 8, 9, Bi/Ch 110. Bi/Ch 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); third 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.

Bi/CNS/NB 152. Neural Circuits and Physiology of Appetite and Body Homeostasis. 6 units (2-0-4); third term. Prerequisites: Graduate standing or Bi/CNS/NB 150, or equivalent. An advanced course of lectures, readings, and student presentations focusing on neural basis of appetites such as hunger and thirst. This course will cover the mechanisms that control appetites both at peripheral and central level. These include genetics, neural manipulation, and viral tracing tools with particular emphasis on the logic of how the body and the brain cooperate to maintain homeostasis. Instructor: Oka. Given in alternate years; offered 2016–17.

Bi/CNS/NB 153. Brain Circuits. 9 units (3-0-6); first 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 2016–17.

Bi/NB/BE 155. Neuropharmacology. 6 units (3-0-3); second term. Prerequisites: Bi/CNS/NB 150. The neuroscience of drugs for therapy, for prevention, and for recreation. Students learn the prospects for new generations of medications in neurology, psychiatry, aging, and treatment of substance abuse. Topics: Types of drug molecules. Drug receptors. Electrophysiology. Drugs activate ion channels. Drugs block ion channels. Drugs activate and block G protein pathways. Drugs block neurotransmitter transporters. Pharmacokinetics. Recreational drugs. Nicotine Addiction. Opiate Addiction. Drugs for neurodegenerative diseases: Alzheimer's disease, Parkinson's disease. Drugs for epilepsy and migraine. Psychiatric diseases: Nosology and drugs. The course is taught at the research level. Instructor: Lester. Given in alternate years, offered 2016–17.

Bi/CNS/NB 157. Comparative Nervous Systems. 9 units (2-3-4); third term. Prerequisites: instructor's permission. 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. Letter grades only. Instructor: Allman. Given in alternate years; offered 2016–17.

Bi/CNS 158. Vertebrate Evolution. 9 units (3-0-6); third term. Prerequisites: Bi 1, Bi 8, or instructor's permission. 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. Letter grades only. Instructor: Allman. Given in alternate years; not offered 2016–17.

Bi/CNS/NB 162. Cellular and Systems Neuroscience Laboratory. 12 units (2-7-3); third term. Prerequisites: 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. Instructor: Bremner.

Bi/CNS/NB 164. Tools of Neurobiology. 9 units (3-0-6); first 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. Instructor: Meister.

Bi 165. Microbiology Research: Practice and Proposal. 6 units (2-3-1); first term. The course will serve to introduce graduate students to 1) the process of writing fellowships having a microbiology focus to train students in preparing effective funding applications ; 2) ongoing research projects on campus involving the isolation, culture, and characterization of microbes and microbial communities; and 3) presentation of research and asking questions in research presentations. The first half of the class will involve training in grant writing by drafting an NSF-GRFP proposal. The second half of the class will involve giving chalk talk research presentations. Enrollment is limited to instructor approval. Instructors: Newman and CEMI Staff.

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. Biochemistry and Biophysics of Macromolecules and Molecular Assemblies. 9 units (3- 0-6); first term. For course description, see Biochemistry and Molecular Biophysics.

BMB/Bi/Ch 173. Biophysical/Structural Methods. 9 units (3-0-6); second term. For course description, see Biochemistry and Molecular Biophysics.

BMB/Bi/Ch 174. Molecular Machines in the Cell. 9 units (3-0-6); third term. For course description, see Biochemistry and Molecular Biophysics.

CNS/Bi/SS/Psy 176. Cognition. 9 units (4-0-5); third term. 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 and characteristics of lenses and microscopes. 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 and the analysis and presentation of two- and three-dimensional images. The role of light microscopy in the history of science will be an underlying theme. No prior knowledge of microscopy will be assumed. Instructor: Collazo. Given in alternate years; offered 2016–17.

Bi/BE 182. Animal Development and Genomic Regulatory Network Design. 9 units (3-0-6); second term. Prerequisites: Bi 8 and at least one of the following: Bi/Ch 111, Bi 114, or Bi 122 (or equivalents). This course is focused on the genomic control circuitry of the encoded programs that direct developmental processes. The initial module of the course is devoted to general principles of development, with emphasis on transcriptional regulatory control and general properties of gene regulatory networks (GRNs). The second module provides mechanistic analyses of spatial control functions in multiple embryonic systems, and the third treats the explanatory and predictive power of the GRNs that control body plan development in mammalian, sea urchin, and Drosophila systems. Grades or pass/fail. Instructors: Stathopoulos, Peter. Given in alternate years; not offered 2016–17.

Bi/BE/CS 183. Introduction to Computational Biology and Bioinformatics. 9 units (3-0-6); second term. Prerequisites: Bi 8, CS 2, Ma 3; or BE/Bi 103; or instructor's permission. Biology is becoming an increasingly data-intensive science. Many of the data challenges in the biological sciences are distinct from other scientific disciplines because of the complexity involved. This course will introduce key computational, probabilistic, and statistical methods that are common in computational biology and bioinformatics. We will integrate these theoretical aspects to discuss solutions to common challenges that reoccur throughout bioinformatics including algorithms and heuristics for tackling DNA sequence alignments, phylogenetic reconstructions, evolutionary analysis, and population and human genetics. We will discuss these topics in conjunction with common applications including the analysis of high throughput DNA sequencing data sets and analysis of gene expression from RNA-Seq data sets. Instructor: Grosse.

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. We 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. An important aspect of the course is the lab component in which students design and analyze their own fMRI experiment. Instructor: Tsao. Given in alternate years; offered 2016–17.

Bi/CNS/NB 185. Large Scale Brain Networks. 6 (2-0-4); 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, not offered 2016–17.

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; offered 2016–17.

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. Instructor: 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. Instructor: Goentoro

Bi/CNS/NB 195. Mathematics in Biology. 9 units (3-0-6); first 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, scientific programming. Instructor: Meister. Given in alternate years; not offered 2016–17.

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.

BE/Bi/NB 203. Introduction to Programming for the Biological Sciences Bootcamp. 6 units; summer. For course description, see Bioengineering.

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. Stem Cells and Hematopoiesis. 9 units (3-0-6); third term. Prerequisites: Graduate standing, or at least one of Bi 114, Bi 117, Bi /Be 182, plus molecular biology. An advanced course with classes based on active discussion, lectures, and seminar presentations. Development from embryos and development from stem cells are distinct paradigms for understanding and manipulating the emergence of ordered biological complexity from simplicity. This course focuses on the distinguishing features of stem-cell based systems, ranging from the natural physiological stem cells that are responsible for life-long hematopoiesis in vertebrates (hematopoietic stem cells) to the artificial stem cells, ES and iPS cells, that have now been created for experimental manipulation. Key questions will be how the stem cells encode multipotency, how they can enter long-term self-renewal by separating themselves from the developmental clock that controls development of the rest of the organism, and how the self-renewal programs of different stem cell types can be dismantled again to allow differentiation. Does “stem-ness” have common elements in different systems? The course will also cover the lineage relationships among diverse differentiated cell types emerging from common stem cells, the role of cytokines and cytokine receptors in shaping differentiation output, apoptosis and lineage-specific proliferation, and how differentiation works at the level of gene regulation and regulatory networks. Instructor: Rothenberg. Given in alternate years; offered 2016–17.

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; not offered 2016–17.

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; offered 2016–17.

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 as well as other techniques for optical sectioning such as light sheet fluorescence microscopy (also called single plane illumination microscopy, SPIM). During the class students will construct a light sheet microscope based on the openSPIM design. Alongside the building of a light sheet microscope, the course will consist of semi-independent modules organized around different imaging challenges using confocal microscopes. Early modules will include a lab using lenses to build a cloaking device. Most of the early modules will focus on three-dimensional reconstruction of fixed cells and tissues. Later modules will include time-lapse confocal analysis of living cells and embryos. Students will also utilize the microscopes in the Beckman Institute Biological Imaging Facility to learn more advanced techniques such as spectral unmixing and fluorescence correlation spectroscopy. 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: Collazo. Given in alternate years; not offered 2016–17.

Bi/CNS/BE/NB 230. Optogenetic and CLARITY Methods in Experimental Neuroscience. 9 units (3-2-4); third term. Prerequisites: Graduate standing or Bi/CNS/NB 150 or equivalent (e.g. Bi/CNS/NB 164). The class covers the theoretical and practical aspects of using (1) optogenetic sensors and actuators to visualize and modulate the activity of neuronal ensembles; and (2) CLARITY approaches for anatomical mapping and phenotyping using tissue-hydrogel hybrids. 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); design and use of methods for tissue clearing (tissue stabilization by polymers/hydrogels and selective extractions, such as of lipids for increased tissue transparency and macromolecule access). Class will discuss applications to neuronal circuits (case studies based on recent literature). The class offers hands-on lab exposure for opsin delivery, recording of light-modulated activity, and CLARITY tissue clearing, imaging, and 3D reconstruction of fluorescent samples. Instructor: Gradinaru.

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/ESE 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. Prerequisites: graduate standing. Lectures and literature-based discussions covering research methods, scientific concepts and logic, research strategies and general principles of modern biology. Students will learn to critique papers in a wide range of fields, including molecular biology, developmental biology, genetics and neuroscience. Graded pass/fail. Instructor: Prober.

Bi 250 b. Topics in Systems Biology. 9 units (3-0-6); third term. Prerequisites: Bi 1, Bi 8, or equivalent; Ma 2 or equivalent; or Instructors' permission. 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. Instructors: Elowitz, Bois.

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 a. Special Topics in Biology — Evolutionary Biology: Principles, Debates, and Applications. 9 units (3-0-6); first term. This seminar series will discuss classical and recent studies that outline key debates and topics in evolutionary biology. In addition, we will discuss the applications of evolutionary thinking to a range of high-profile topics, including disease, antibiotic resistance and the microbiome. Instructor: Foster.

Bi 270 c. Special Topics in Biology — The World in 2050. 9 units (3-0-6); third term. This course will use computer modeling methods to explore the way in which Malthusian limits may apply to continued growth of the human population and of global economic activity. Modeling strategies will be similar to those offered in a book entitled Limits to Growth (as sponsored by the Club of Rome and published in 1972), but dozens of other, more recent perspectives will be considered. The real goal is to help students develop some facility for careful, critical thought about the long-term future, constantly asking: How much can we reasonably predict on this type of time scale? And how should this affect our current and future behavior? What can be done? Instructor: Pabo.

Bi/BE/CS 271 a. Special Topics in Computational Biology — Introduction to Sequence Analysis and Motif Discovery. 9 units (3-0-6); first term. Prerequisites: Bi 8, CS 2, or instructor's permission. Sequence analysis and motif discovery have been two cornerstones of computational biology and bioinformatics since the early days of these sciences, and their importance has been increasing with the development of next-generation sequencing techniques, the ensuing flood of large-scale genomics and epigenomics data, and the need of analyzing these valuable sequence data efficiently. This course will introduce key computational, information-theoretic, and probabilistic methods for sequence analysis and motif discovery including popular models such as Markov models, Hidden Markov models, Bayesian networks, or maximum entropy models as well as popular algorithms such as the expectation-maximization algorithm and its stochastic relatives or the Gibbs sampling algorithm and other Markov chain Monte Carlo methods. Students of this course will develop a solid understanding of these algorithms, profound skills of deriving and implementing them, and the virtuosity of applying them to diverse problems of sequence analysis and motif discovery. Undergraduates can enroll with instructor's permission. Instructor: Grosse.

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.