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
Prerequisites: 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/Ph/Bi 13
Freshman Seminar: In Search of Memory
6 units (2-0-4)
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first term
An exploration of brain function based on weekly readings in an autobiographical account by a Nobel Prize willing neurobiologist. No lectures. Each week there will be reading from chapters of the book plus relevant research papers, discussing trail-blazing neuroscience experiments.
Instructor:
Pine
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)
|
second, third terms
Prerequisites: Bi/CNS/NB 150 and CNS/Bi/Ph/CS/NB 187, or instructor's permission.
Introduction to the computations made by the brain during economic and social decision making and their neural substrates. First quarter: Signal detection theory. Unconscious and conscious processing. Emotion and the somatic marker hypothesis. Perceptual decision making. Reinforcement learning. Goal and habit learning. Facial processing in social neuroscience. Second quarter: Optimal Bayesian decision making and prospect theory. Standard and behavioral game theory. Evolution and group decision making. Collective decision making by animals. Exploration. Risk learning. Probabilistic sophistication. Part b offered 2013-14; part a not offered 2013-14.
Instructors:
Adolphs, Bossaerts, Camerer, O'Doherty
Bi/Ge 105
Evolution
12 units (3-4-5); second term
|
Maximum enrollment: 15, by application 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
BE/Bi/MedE 106
Introduction to Biomechanics
9 units (3-0-6)
|
third term
Introduction to the basic concepts of applying engineering principles of solid and fluid mechanics to the study of biological systems. The course emphasizes the organismal, rather than the molecular, level of complexity. It draws on a wide array of biological phenomena from plants and animals, and is not intended as a technical introduction to medically related biomechanics. Topics may include fundamental properties of solids and fluids, viscoelasticity, drag, biological pumps, locomotion, and muscle mechanics. Not offered 2013-14.
Instructor:
Staff
CNS/Bi/Ph 107
Writing about Scientific Research
9 units (3-0-6)
|
second term
This will be a hands-on course in which students learn how to write a long essay or a book explaining complex scientific research. The course will focus on learning to write clearly and compellingly, to rewrite and edit, and, especially, to find one's own writing voice. In the first part of the course, students will read, analyze, and critique published works, including some early drafts of well-known books. Together, we will study different writing styles; how chapters, articles, and books are structured; and basic narrative techniques and their execution. In the second part of the course students will select a cutting-edge scientific research topic to write about and produce a book chapter on that topic. Students' works-in-progress will be analyzed each week in class. The finished chapters will be included in a manuscript for a book one might call The Caltech Student's Guide to the Most Awesome Cutting Edge Science. Limited enrollment. Not offered 2013-14.
Instructor:
Mlodinow
Bi/Ch 110
Introduction to Biochemistry
12 units (4-0-8)
|
first term
Prerequisites: 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. Given in alternate years; offered 2013-14.
Instructor:
Baltimore
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. Given in alternate years; not offered 2013-14.
Instructor:
Stathopoulos
Bi 122
Genetics
9 units (3-0-6)
|
first term
Prerequisites: 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
Prerequisites: Bi 122.
Laboratory exercises illustrating the principles of genetics, with emphasis on Mendelian inheritance in multicellular eukaryotes, including Drosophila melanogaster and Caenorhabditis elegans. Given in alternate years; not offered 2013-14.
Instructor:
Staff
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. Given in alternate years; not offered 2013-14.
Instructor:
Zinn
CNS/Psy/Bi 131
The Psychology of Learning and Motivation
9 units (3-0-6)
|
second term
This course will serve as an introduction to basic concepts, findings, and theory from the field of behavioral psychology, covering areas such as principles of classical conditioning, blocking and conditioned inhibition, models of classical conditioning, instrumental conditioning, reinforcement schedules, punishment and avoidance learning. The course will track the development of ideas from the beginnings of behavioral psychology in the early 20th century to contemporary learning theory. Not offered 2013-14.
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)
|
second term
Prerequisites: None.
This course will explore our current knowledge based on the fundamental properties of nerves and synapses, and present the bioengineering principles and developments that drive new avenues of research in cell physiology. We will present the tools used for making current research measurements, dissect the protocols, equipment, and physics that enable the approaches, and discuss the current limitations that limit performance. Students will be expected to engage in one of the technologies and develop a greater understanding in both written and oral presentations to the class. Areas to be investigated will be drawn from electrophysiology, single channel recording, imaging with indicator dyes, and screening technologies. Not offered 2013-14.
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. Given in alternate years; offered 2014-15.
Instructor:
Meister
Bi/NB 156
Molecular Basis of Behavior
9 units (3-0-6)
|
second term
Prerequisites: 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. Given in alternate years; offered 2013-14.
Instructor:
Patterson
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. Given in alternate years; not offered 2013-14.
Instructor:
Allman
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. Given in alternate years; offered 2013-14.
Instructor:
Allman
Bi/CNS 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. Graded pass/fail. Not offered 2013-14.
Instructor:
Staff
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. Offered 2014-15.
Instructor:
Team of faculty
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); first term
|
Recommended prerequisite: one year of general biology
A course on growth and functions in the prokaryotic cell. Topics covered: growth, transport of small molecules, protein excretion, membrane bioenergetics, energy metabolism, motility, chemotaxis, global regulators, and metabolic integration.
Instructor:
Leadbetter
ESE/Bi 168
Microbial Metabolic Diversity
9 units (3-0-6)
|
second term
Prerequisites: ESE 142, ESE/Bi 166.
A course on the metabolic diversity of microorganisms. Basic thermodynamic principles governing energy conservation will be discussed, with emphasis placed on photosynthesis and respiration. Students will be exposed to genetic, genomic, and biochemical techniques that can be used to elucidate the mechanisms of cellular electron transfer underlying these metabolisms. Given in alternate years; not offered 2013-14.
BMB/Bi/Ch 170 abc
Biochemistry and Biophysics of Macromolecules and Molecular Assemblies
9 units (3-1-5)
|
first, second, third terms
Prerequisites: Bi/Ch 110.
First term: detailed analysis of the structures of the four classes of biological molecules and the forces that shape them. Introduction to molecular biological and visualization techniques. Second term: basic principles of modern biophysical and structural methods to interrogate macromolecules from the atomic to cellular levels, including X-ray crystallography, NMR spectroscopy, molecular dynamics, electron and light microscopy, AFM, single molecule techniques, and systems biological simulations. Third term: detailed analysis of specific macromolecular machines and systems that illustrate the principles and biophysical methods taught in the first two terms.
Instructors:
Clemons, Jensen, Shan, Hoelz,staff
CNS/Bi/SS/Psy/NB 176
Cognition
12 units (6-0-6)
|
third term
The cornerstone of current progress in understanding the mind, the brain, and the relationship between the two is the study of human and animal cognition. This course will provide an in-depth survey and analysis of behavioral observations, theoretical accounts, computational models, patient data, electrophysiological studies, and brain-imaging results on mental capacities such as attention, memory, emotion, object representation, language, and cognitive development. Not offered 2013-14.
Instructor:
Shimojo
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. Not offered 2013-14.
Instructor:
Staff
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.
Instructor:
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. Given in alternate years; offered 2013-14.
Instructors:
Stathopoulos, Davidson
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. Given in alternate years; not offered 2013-14.
Instructor:
Tsao
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. Given in alternate years, offered 2013-14.
Instructor:
Tsao
CNS/Bi/EE/CS/NB 186
Vision: From Computational Theory to Neuronal Mechanisms
12 units (4-4-4)
|
second term
Lecture, laboratory, and project course aimed at understanding visual information processing, in both machines and the mammalian visual system. The course will emphasize an interdisciplinary approach aimed at understanding vision at several levels: computational theory, algorithms, psychophysics, and hardware (i.e., neuroanatomy and neurophysiology of the mammalian visual system). The course will focus on early vision processes, in particular motion analysis, binocular stereo, brightness, color and texture analysis, visual attention and boundary detection. Students will be required to hand in approximately three homework assignments as well as complete one project integrating aspects of mathematical analysis, modeling, physiology, psychophysics, and engineering. Given in alternate years; offered 2013-14.
CNS/Bi/Ph/CS/NB 187
Neural Computation
9 units (3-0-6)
|
first term
Prerequisites: familiarity with digital circuits, probability theory, linear algebra, and differential equations. Programming will be required.
This course investigates computation by neurons. Of primary concern are models of neural computation and their neurological substrate, as well as the physics of collective computation. Thus, neurobiology is used as a motivating factor to introduce the relevant algorithms. Topics include rate-code neural networks, their differential equations, and equivalent circuits; stochastic models and their energy functions; associative memory; supervised and unsupervised learning; development; spike-based computing; single-cell computation; error and noise tolerance.
Instructor:
Perona
Bi 188
Human Genetics and Genomics
6 units (2-0-4)
|
third term
Prerequisites: 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. Given in alternate years; not offered 2013-14.
Instructor:
Wold
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 (3-0-6) second term
|
(2-4-3) third term
Prerequisites: none. Recommended: ChE/BE 163, CS 21, CS 129 ab, or equivalent.
This course investigates computation by molecular systems, emphasizing models of computation based on the underlying physics, chemistry, and organization of biological cells. We will explore programmability, complexity, simulation of and reasoning about abstract models of chemical reaction networks, molecular folding, molecular self-assembly, and molecular motors, with an emphasis on universal architectures for computation, control, and construction within molecular systems. If time permits, we will also discuss biological example systems such as signal transduction, genetic regulatory networks, and the cytoskeleton; physical limits of computation, reversibility, reliability, and the role of noise, DNA-based computers and DNA nanotechnology. Part a develops fundamental results; part b is a reading and research course: classic and current papers will be discussed, and students will do projects on current research topics.
Instructor:
Winfree
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)
|
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. Given in alternate years; offered 2013-14.
Instructor:
Meister
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
Prerequisites: 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. Given in alternate years; not offered 2013-14.
Instructor:
Patterson
Bi 204
Evolution of the Animal Body Plan
6 units (2-0-4)
|
third term
Prerequisites: 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. Given in alternate years; not offered 2013-14.
Instructor:
Davidson
Bi 206
Biochemical and Genetic Methods in Biological Research
6 units (2-0-4)
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third term
Prerequisites: 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
Prerequisites: 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. Given in alternate years; not offered 2013-14.
Instructor:
Rothenberg
Bi/CNS/NB 216
Behavior of Mammals
6 units (2-0-4)
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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. Given in alternate years; offered 2013-14.
Instructor:
Allman
Bi/CNS/NB 217
Central Mechanisms in Perception
6 units (2-0-4)
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first term
Reading and discussions of behavioral and electrophysiological studies of the systems for the processing of sensory information in the brain. Given in alternate years; not offered 2013-14.
Instructor:
Allman
Bi/CNS/NB 220
Genetic Dissection of Neural Circuit Function
6 units (2-0-4)
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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)
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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, zebra fish, 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. Not offered 2013-14.
Instructor:
Staff
Bi/CNS/BE/NB 230
Optogenetic Methods in Experimental Neuroscience
9 units (3-1-5)
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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. Not offered 2013-14.
Instructor:
Gradinaru
Ch/Bi 231
Advanced Topics in Biochemistry
6 units (2-0-4)
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third term
Transcriptional regulation in eukaryotes. Topics: the subunit structure of eukaryotic RNA polymerases and their role in transcriptional reactions; the composition of eukaryotic promoters, including regulatory units; general and specific transcription factors; developmental regulatory circuits and factors; structural motifs involved in DNA binding and transcriptional initiation and control.
Instructors:
Campbell, Parker
Ge/Bi 244
Paleobiology Seminar
6 units (3-0-3)
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third term
Critical reviews and discussion of classic investigations and current research in paleoecology, evolution, and biogeochemistry.
Instructor:
Kirschvink
Ge/Bi 246
Molecular Geobiology Seminar
6 units (2-0-4); second term
|
Recommended preparation: ESE/Bi 166
Critical reviews and discussion of classic papers and current research in microbiology and geomicrobiology. As the topics will vary from year to year, it may be taken multiple times. Not offered 2013-14.
CNS/Bi/NB 247
Cerebral Cortex
6 units (2-0-4)
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second term
Prerequisites: Bi/CNS/NB 150 or equivalent.
A general survey of the structure and function of the cerebral cortex. Topics include cortical anatomy, functional localization, and newer computational approaches to understanding cortical processing operations. Motor cortex, sensory cortex (visual, auditory, and somatosensory cortex), association cortex, and limbic cortex. Emphasis is on using animal models to understand human cortical function and includes correlations between animal studies and human neuropsychological and functional imaging literature. Given in alternate years; not offered 2013-14.
Instructor:
Andersen
Bi 250 a
Topics in Molecular and Cellular Biology
9 units (3-0-6)
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first term
Prerequisites: 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
Prerequisites: 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
Prerequisites: 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
Prerequisites: 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)
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third term
Prerequisites: Bi/CNS/NB 150 or instructor's permission.
This course will cover recent findings in the psychology and neurobiology of emotion and social behavior. What role does emotion play in other cognitive processes, such as memory, attention, and decision making? What are the component processes that guide social behavior? To what extent is the processing of social information domain-specific? Readings from the current literature will emphasize functional imaging, psychophysical, and lesion studies in humans. Not offered 2013-14.
CNS/Bi/NB 256
Decision Making
6 units (2-0-4)
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third term
This special topics course will examine the neural mechanisms of reward, decision making, and reward-based learning. The course covers the anatomy and physiology of reward and action systems. Special emphasis will be placed on the representation of reward expectation; the interplay between reward, motivation, and attention; and the selection of actions. Links between concepts in economics and the neural mechanisms of decision making will be explored. Data from animal and human studies collected using behavioral, neurophysiological, and functional magnetic resonance techniques will be reviewed. Given in alternate years; offered 2013-14.
Bi 270
Special Topics in Biology
Units to be arranged
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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
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First, second, third terms
Students may register with permission of the responsible faculty member.
Bi 299
Graduate Research
Units to be arranged
|
first, second, third terms
Students may register for research units after consultation with their adviser.
Published Date:
July 28, 2022