CNUP: Center for Neuroscience

Graduate Course Descriptions

Core Courses:

CELLULAR AND MOLECULAR NEUROBIOLOGY I 4 cr (Lagenaur)
MSNBIO/NROSCI 2100 (Fall Term)
This course is the first component of the introductory graduate sequence designed to provide an overview of cellular and molecular aspects of neuroscience. This course covers nerve cell biology, protein chemistry, regulation of gene expression, receptor function, and second messenger signaling in a lecture format. A background in basic biology or permission of the instructor is required.
CELLULAR AND MOLECULAR NEUROBIOLOGY II 4 cr (Lagenaur)
MSNBIO/NROSCI 2101 (Fall Term)
This course is the second component of the introductory graduate sequence designed to provide an overview of cellular and molecular aspects of neuroscience. This course covers the electrical properties of neurons, synaptic transmission and neural development. . A background in basic biology or permission of the instructor is required.
SYSTEMS NEUROBIOLOGY 6 cr (Simons)
MSNBIO/NROSCI 2102 (Spring Term)
This course is a component of the introductory graduate sequence designed to provide an overview of neuroscience. This course provides an introduction to the structure of the mammalian nervous system and to the functional organization of sensory systems, motor systems, regulatory systems, and systems involved in higher brain functions. It is taught primarily in a lecture format with some laboratory work.

Required Courses:

SCIENTIFIC ETHICS 1 cr (Hastings)
MSNBIO/NROSCI 2010 (Summer Term) The course is an introduction to basic ethical issues that arise in the course of conducting scientific research. It is intended for graduate students in the Center for Neuroscience who have completed at least one year of graduate work. The course will be composed of informal lecture presentations followed by class discussion of issues.
STATISTICAL METHODS FOR NEUROSCIENCE 4 cr (Kass)
CMU 36-746 (Spring Term)
This course provides a brief survey of statistical methods that are of use in neuroscience and psychology. Examples will be drawn from these fields wherever possible. There has in the past been an emphasis on neurophysiology, and in many places examples from other fields have been used (e.g. the relationship between SAT scores and subsequent collegiate grade-point average). Much of the course will involve material often covered in most standard semester-long courses in elementary statistics; the latter part of the course will introduce a few more advanced methods.
PROSEMINAR 1 cr
MSNBIO/NROSCI 2008 (Fall & Spring Term)
Members of the Center for Neuroscience faculty presents an overview of the research on which he/she works. Critical analysis of experiments and of research is emphasized.
JOURNAL CLUB 1 cr
MSNBIO/NROSCI 2007 (Fall & Spring Term)
Papers will be selected from current periodicals in neuroscience for presentation. Emphasis is placed on a critical evaluation of experimental procedure, interpretation and presentation of data. Grade is based on the satisfactory completion of a journal or research presentation as determined by the facilitator and attendance at other presentations.
SEMINAR SERIES 1 cr
MSNBIO 2660/NROSCI 2106
This is a special series intended for graduate students. Special lectures are given by national and international investigators in the field of neuroscience. Discussions of the lectures will follow the presentation.
DIRECTED STUDY
MSNBIO 2690/NROSCI 2902
Students doing laboratory research with a training faculty member should register for this course.
INDEPENDENT STUDY

Elective Courses:

Cell and Molecular Neurobiology

ADVANCED DEVELOPMENTAL BIOLOGY 2 cr (C. Lance-Jones)
MSBNIO 2612 (Fall Term)
This course will examine selected topics in developmental biology at an advanced level. Topics may include pattern formation in insects, cell lineage analysis, cell-cell interactions and the specification of cell fates, cell adhesion molecules, genetic approaches to mammalian embryogenesis and the extracellular matrix in development. An individual subject will be introduced with a lecture by a faculty member. Within each subject, significant research papers will be assigned and discussed. Emphasis will be placed on the critical reading of papers and classroom discussion. Students may act as discussion leaders. Prerequisite: INTBP 2000 (Foundations in Biomedical Science), or BIOSCI 2010 thru 2023 (Current Topics in Molecular, Cellular, and Developmental Biology), or #03-350 (CMU Developmental Biology course), or permission of the instructor.
BIOCHEMISTRY OF MACROMOLECULES 2 cr (Cascio)
MSBMG 2510 (Spring Term)
Topics covered in this course include the experimental determination of macromolecular structure, protein; DNA interactions, protein; protein interactions, protein modification, and empirical prediction of macromolecular structure.
CELL AND MOLECULAR PHYSIOLOGY 2 cr (Frizzell)
MSCBMP 2830 (Spring Term)
This course consists of lectures, problem-solving sessions, and examination of original papers. A main focus will be on the application of modern biophysical and molecular-genetic approaches in the analysis of cellular function. Topics include: 1. membrane transport: pumps, channels and bio-electrical potentials; 2. excitable membranes; 3. regulation of ion channels; 4. absorptive and secretory functions of epithelia; 5. signal transduction; 6. molecular motors, cell motility, and muscle contraction.
MULTIPARAMETRIC MICROSCOPIC IMAGING 3 cr (Watkins)
MSCBMP 2860
A lecture/lab course which immerses students in the theory and practical aspects of modern microscopic imaging. The fields will cover the theory and implementation of all types of light and electron microscopy and computer aided imaging. Students will be expected to reach a functional capability in a selected technology.
BIOLOGY OF SIGNAL TRANSDUCTION 3 cr (Romero/Rajasekaran)
MSMPHL 3375 (Spring Term)
This course will explore different types of signaling pathways activated by receptor-ligand interactions. Topics to be covered include, but are not limited to: G-protein linked receptors, adenylate cyclases, small gtpases, kinases and phosphatases, nitric oxide, phospholipases, steroid hormone signaling, and pharmacological applications of signaling pathways.
PRINCIPLES OF PHARMACOLOGY 2 cr (Friedman)
MSMPHL 2310 (Spring Term)
This course consists of a series of lectures and tutorial sessions which focus on the general principles of pharmacology. Major topics are principles of pharmacokinetics (including drug absorption, distribution, and metabolism) and pharmacodynamics (quantitation of drug-receptor interactions).
MOLECULAR PHARMACOLOGY 3 cr (Altschuler)
MSMPHL 3360 (Fall Term)
This course examines molecular mechanisms of drug interactions with an emphasis on drugs that modulate cell signaling and cellular responses to drugs. The course will include student participation through presentation and discussion of relevant contemporary scientific literature. Topics include: cell cycle checkpoints and anti-cancer drugs, therapeutic control of ion channels, and blood glucose, nonsteroidal anti-inflammatory agents and arachidonic acid signaling, and molecular mechanisms of drug tolerance. Two sessions will be devoted to each topic.
BIOLOGICAL IMAGING AND FLUORESCENCE SPECTROSCOPY 3 cr (Lanni)
CMU 03-534
This course covers principles and applications of optical methods in the study of structure and function in biological systems. Topics to be covered include: absorption and flourescence spectroscopy; interaction of light with biological molecules, cells, and systems; design of fluorescent probes and optical biosensor molecules; genetically expressible optical probes and optical biosensor molecules; genetically expressible optical probes; photochemistry; optics and image formation; transmitted-light and fluorescence microscope systems; laser-based systems; scanning microscopes; electronic detectors and cameras: image processing; multimode imaging systems; microscopy of living cells; and the optical detection of membrane potential, molecular assembly, transcription, enzyme activity, and the action of molecular motors. This course is particularly aimed at students in science and engineering interested in gaining in depth knowledge of modern light microscopy. Prerequisites: 03-240, 03-231, 09-218, 09-144 or permission of the instructor.
STEM CELLS 3 cr (Monga)
MSCMP 3740 (Fall Term)
This course will provide a comprehensive overview of stem cell biology - an intriguing & a most-debated research area. The course will focus on the biology of stem cells & their role in health & disease with emphasis on development & carcinogenesis. Trans-differentiation of stem cells for tissue engineering applications will also be discussed. Lectures & student presentations will cover: embryonic as well as fetal & adult stem cells in blood, liver, brain, muscle, kidney, pancreas & gut. Students will also be educated on bio-ethical issues & existing laws governing stem cell research.

Clinical

BIOLOGICAL BASIS OF NEUROPSYCHIATRIC DISORDERS 3 cr (Hastings)
MSNBIO 2005/NROSCI 2078 (Spring Term, bi-annual)
This course is designed to provide a survey of some of the major neurological and psychiatric disorders for the non-clinician. Each session will focus on a particular disorder and will include a patient presentation (live or by videotape), and a discussion of the etiology, epidemiology, pathophysiology, and treatment of that disorder.
MOLECULAR PATHOBIOLOGY 3 cr (Achim/Oury)
MSCMP 2740 (Spring Term)
Some representative of major disease categories (autoimmune, inflammatory, toxic, degenerative, infectious, genetic, and Neoplastic) will be examined in terms of patient demographics (who), gross and microscopic morphology (what), and etiology/molecular mechanisms (why).

Cognitive

COGNITIVE NEUROPSYCHOLOGY 3 cr (Behrmann)
CMU 85-714 (Spring Term)
This course will review what has been learned of the neural bases of cognition through studies of brain-damaged patients as well as newer techniques such as brain stimulation mapping, regional metabolic and blood flow imaging, and attempt to relate these clinical and physiological data to theories of the mind cast in information-processing terms. The course will be organized into units corresponding to the traditionally-defined subfields of cognitive psychology such as perception, memory and language. In each area, we will ask: To what extent do the neurological phenomena make contact with the available cognitive theories? When they do, what are their implications for these theories (i.e., Can we confirm or disconfirm particular cognitive theories using neurological data?)? When they do not, what does this tell us about the parses of the mind imposed by the theories and methodologies of cognitive psychology and neuropsychology? Prerequisites: 85-211, Cognitive Psychology and either 85-310, Research Methods in Cognitive Psychology, or 85-350, Research Methods in Cognitive Neuroscience.
COGNITIVE NEUROSCIENCE 3 cr (McClelland/Olson)
NROSCI 2005 (Fall Term)
This course will cover fundamental findings and approaches in cognitive neuroscience, with the goal of providing an overview of the field at an advanced level. Topics will include high-level vision, spatial cognition, working memory, long-term memory, learning, language, executive control, and emotion. Each topic will be approached from a variety of methodological directions, for example, computational modeling, cognitive assessment in brain-damaged humans, non-invasive brain monitoring in humans, and single-neuron recording in animals. Lectures will alternate with sessions in seminar format. Prerequisite: Permission of Instructor.
PERCEPTION 3 cr (Klatzky)
CMU 85-770
Perception, broadly defined, is the construction of a representation of the external world, for purposes of thinking about it and acting in it. Although we often think of perception as the processing of inputs to the sense organs, the world conveyed by the senses is ambiguous, and cognitive and sensory systems interact to interpret it. In this course, we will examine the sensory-level mechanisms involved in perception by various sensory modalities, including vision, audition, and touch. We will learn how sensory coding interacts with top-down processing based on context and prior knowledge and how perception changes with learning and development. The goals include not only imparting basic knowledge about perception, but fostering an appreciation for the beauty of perceptual systems and providing some new insights into everyday experiences. Prerequisites: Permission of Instructor.

Computational

ARTIFICIAL NEURAL NETWORKS 4 cr (Touretzky)
CMU 15-782 (A) (Spring Term)
Artificial neural networks combine ideas from machine learning, statistics, and pattern recognition. They draw inspiration from, and provide simplified formalizations of, theories about the workings of the brain. This course offers an introduction to neural networks for computer scientists and engineers. Prerequisites are undergraduate calculus and linear algebra, and solid programming skills. An undergraduate course in artificial intelligence or machine learning would provide helpful background but is not required. The course provides hands-on experience with a variety of neural network architectures implemented in MATLAB, and an in-depth look at problems in pattern recognition and knowledge representation. Topics covered include: perceptrons; the LMS learning rule; fundamentals of pattern recognition; back propagation learning; forward and inverse models in control theory; competitive learning; self-organizing feature maps; radial basis functions, the EM algorithm; Hopfield networks, Boltzmann machines; Helmholtz machines; general recurrent networks.
INTRO TO PARALLEL DISTRIBUTED PROCESSING 3 cr (Plaut)
CMU 85-719 (Spring Term)
This course provides an overview of parallel distributed processing (PDP) models of aspects of perception, memory, language, knowledge representation, and learning. The course consists of lectures describing the mathematical and computational theory behind artificial neural network models as well as their implementation. Students also acquire substantial hands-on experience manipulating existing simulation models on computer workstations, and are expected to complete term projects involving novel simulation work. Prerequisites include course 85-211 (Cognitive Psychology), extensive experience using computers, and course 21-122 (Calculus 2) or permission of the instructor.
COMPUTATIONAL MODELS OF NEURAL SYSTEMS 4 cr (Touretzky)
CMU 15-883
This course offers an in-depth look at biological neural systems from a computational perspective. We will examine a variety of brain structures whose anatomy and physiology are sufficiently well understood that it's possible to theorize about the representations and algorithms they employ. There will be some neuroscience tutorial lectures for those with no prior background in this area. Students will also have the opportunity to experiment with some actual computational models running in Matlab. Prerequisites: Students should have prior familiarity with either artificial intelligence or neuroscience; familiarity with both is not required. Computer science students should have taken a graduate AI course. Neuroscience students should have some basic familiarity with computation, such as an undergraduate computing class.
COMPUTATIONAL NEUROSCIENCE METHODS 3 cr (Ermentrout)
MATH 3375
The course offers an introduction to modeling methods in neuroscience. It illustrates how models can extend and evaluate neuroscience concepts.
COMPUTATIONAL PERCEPTION AND SCENE ANALYSIS 4 cr (Lewicki)
CMU 15-485/785 (Spring Term)
This course teaches advanced aspects of perception, scene analysis, and recognition in both the visual and auditory modalities, concentrating on those aspects that allow us and animals to behave in natural, complex environments. The goal of this course is to teach how to reason scientifically about problems and issues in perception and scene analysis, how to extract the essential computational properties of those abstract ideas, and finally how to convert these into explicit mathematical models and computational algorithms.

Specific topics include sensory coding, perceptual invariance, spatial vision and sound localization, visual and auditory scene segmentation, many aspects of attention, and the basics of recognition in natural visual and auditory scenes. Mathematical topics covered include Bayesian inference, information theory, linear systems analysis, neural networks, independent component analysis, and various algorithms in computational vision and audition. Prerequisites: CS 15-385 (undergraduate computer vision course), Psych 85-370 (undergraduate perception course), or permission of the instructor.
COMPUTER VISION 3 cr (Lee)
CMU 15-385 (Spring Term)
An intensive introduction to the theory and practice of computer vision, i.e. the analysis of the patterns in visual images of the world with the goal of reconstructing the objects and processes in the world that are producing them. This includes the "low-level" algorithms of image processing, multi-scale analysis, segmentation of images, correspondence of multiple images and reconstruction of depth. It continues with "high-level" algorithms of pattern recognition and the analysis and recognition of shapes, objects and scenes using feature, templates and models. The discussion will be guided by comparison with human and animal vision, from psychological and biological perspectives.

Systems Neuroscience

FUNCTIONAL NEUROANATOMY 4 cr (Sesack)
NROSCI 2011 (Fall Term)
This course covers the basic structure of the central nervous system from spinal cord to cerebral cortex. The major sensory, motor and integrative neural systems of the human brain are discussed. Based on an understanding of normal neural connections and brain function, the anatomical and physiological basis of various neurological disorders of the nervous system will be explored.
HUMAN PHYSIOLOGY 4 cr (Yates)
NROSCI 2070 (Fall Term)
This course includes lectures and reading on the following: (1) functions of the cardiovascular system; (2) respiration: (3) digestion and absorption in the gut; (4) kidney function and the regulation of body fluids; (5) the regulation of metabolism; and (6) reproduction.
NEURAL PLASTICITY IN SENSORY AND MOTOR SYSTEMS 3 cr (Barth, Urban, Crowley)
NROSCI 3059 (Spring Term)
Each course meeting will center around the discussion of classic and recent papers in the area of neuronal plasticity. Topics covered in the course will include 1) Basic mechanisms of synaptic plasticity 2) Developmental specification and plasticity 3) Activity dependent regulation of connectivity and circuitry 4) Mechanisms of adult plasticity.

General:

HISTORICAL PERSPECTIVES IN NEUROSCIENCE 2 cr (Balaban)
MSNBIO 2135 (Summer Term)
This seminar course explores the origins and evolution of modern neuroscientific concepts between the 17th and mid-20th centuries. Discussions of primary and secondary source material focus on understanding the role of contemporary philosophical, scientific, social, and technological factors in the development of neuroscientific thought. A further goal is to develop an appreciation of their contributions to current neuroscientific dogma.