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Neurobiology (NB) Graduate Courses (2017-18)

Bi/CNS/NB 150. Introduction to Neuroscience. 10 units (4-0-6): third term. 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. 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. Given in alternate years; not offered 2017-18. Instructor: Oka.
Bi/CNS/NB 153. Brain Circuits. 9 units (3-0-6): first term. 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; not offered 2017-18. Instructor: Meister.
Bi/NB/BE 155. Neuropharmacology. 6 units (3-0-3): second term. 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 2017-18. Instructor: Lester.
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. Letter grades only. Given in alternate years; not offered 2017-18. Instructor: Allman.
Bi/CNS/NB 162. Cellular and Systems Neuroscience Laboratory. 12 units (2-7-3): third term. 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. 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. 9 units (4-0-5): 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. Instructor: Shimojo.
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. Given in alternate years; offered 2017-18. Instructor: Tsao.
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. Given in alternate years, not offered 2017-18. 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 2017-18. Instructors: Meister, Perona, Shimojo.
CNS/Bi/Ph/CS/NB 187. Neural Computation. 9 units (3-0-6): first term. 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/CNS/NB 195. Mathematics in Biology. 9 units (3-0-6): first term. 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. Given in alternate years; offered 2017-18. Instructor: Meister.
BE/Bi/NB 203. Introduction to Programming for the Biological Sciences Bootcamp. 6 units: summer. This course provides an intensive, hands-on, pragmatic introduction to computer programming aimed at biologists and bioengineers. No previous programming experience is assumed. Python is the language of instruction. Students will learn basic concepts such as data types, control structures, string processing, functions, input/output, etc., while writing code applied to biological problems. At the end of the course, students will be able to perform simple simulations, write scripts to run software packages and parse output, and analyze and plot data. This class is offered as a week long "boot camp" starting two weeks before the start of the fall term, in which students spend all day working on the course. Graded pass/fail. Instructor: Bois.
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. Given in alternate years; offered 2017-18. Instructor: Allman.
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. Given in alternate years; not offered 2017-18. Instructor: Allman.
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. 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. The class offers weekly hands-on LAB exposure for opsin viral production and delivery to neurons, recording of light-modulated activity, and tissue clearing, imaging, and 3D reconstruction of fluorescent samples. Lecture topics include: opsin design (including natural and artificial sources), delivery (genetic targeting, viral transduction), light activation requirements (power requirements, wavelength, fiberoptics), 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 of these methods to neuronal circuits (case studies based on recent literature). Instructor: Gradinaru.
CNS/Bi/NB 247. Cerebral Cortex. 6 units (2-0-4): second term. 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 2017-18. Instructor: Andersen.
Bi/CNS/NB 250 c. Topics in Systems Neuroscience. 9 units (3-0-6): third term. 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.
CNS/Bi/NB 256. Decision Making. 6 units (2-0-4): 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 2017-18. Instructor: Andersen.
NB 299. Graduate Research. Units to be arranged: first, second, third terms. Students may register for research units after consultation with their adviser.