Course Descriptions

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.

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; not offered 2015-16.

CS/CNS/EE/NB 154. Artificial Intelligence. 9 units (3-3-3). For course description, see Computer Science.

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. Given in alternate years, not offered 2015-16.

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. Given in alternate years; not offered 2015-16.

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; not offered 2015–16.

Bi/CNS/NB 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. Instructor: Meister.

CNS/Bi/SS/Psy/NB 176. Cognition. 12 units (6-0-6). For course description, see Computation and Neural Systems.

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 2015–16.

Bi/CNS/NB 185. Large Scale Brain Networks. 6 units (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, offered 2015–16.

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/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; offered 2015-16.

BE/Bi/NB 203. Introduction to Programming for the Biological Sciences Bootcamp. 6 units (1-5-0); summer. For course description, see Bioengineering.

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 2015-16.

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 2015–16.

Bi/CNS/NB 220. Genetic Dissection of Neural Circuit Function. 6 units (2-0-4); third 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/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 transparancy 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 flurescent samples. Instructor: Gradinaru.

CNS/Bi/NB 247. Cerebral Cortex. 6 units (2-0-4). For course decription, see Computation and Neural Systems. Instructor: Andersen.

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 252. Responsible Conduct of Research. 4 units (2-0-2); third term. This lecture and disussion course covers relevant aspects of the responsible conduct of biomedical and biological research. Topics iclude 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. Undergraduate students require advace instuctor's permission. Graded pass/fail. Instructors: Meyerowitz, Sternberg, staff.

CNS/Bi/NB 256. Decision Making. 6 units (2-0-4).For course description, see Computation and Neural Systems.


Other Courses of Interest

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. 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. Given in alternate years; not offered 2015-16.

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, student wil construct a light sheet microscope based on the open SPIM 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 alternate years; offered 2015-16.

EE/BE/MedE 166. Optical Methods for Biomedical Imaging and Diagnosis. 

EE/CNS/CS 148 ab. Selected Topics in Computational Vision.

CNS/SS 251. Human Brain Mapping: Theory and Practice.

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.

ACM 95/100 abc. Introductory Methods of Applied Mathematics. 

Ma 112 ab. Statistics.