CNUP: Center for Neuroscience

Graduate Course Descriptions

Core Courses:

CELLULAR AND MOLECULAR NEUROBIOLOGY I 4 cr C. 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 C. 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 D. 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 J. Yip
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.

GRADUATE STATISTICS COURSE OPTIONS

1. STATISTICAL METHODS FOR NEUROSCIENCE

MSNBIO/NROSCI 2110 (Spring Term)

 4 cr R. Kass

This course provides a brief survey of statistical methods that are of use in cognitive neuroscience. The first part of the course presents a compressed version of material often covered in a semester-long course in elementary statistics. The latter part introduces various more advanced methods. Topics include probability (laws of probability, conditional probability, bayes' theorem, random variables, binomial, poisson, and normal distributions, and poisson and other point processes), exploratory data analysis (descriptive methods for single samples and multiple samples, scatterplot smooths, histo­grams, and density esti­mators), elementary statistical inference (standard errors and confidence intervals, goodness-of-fit and significance tests, anova and regression, and maximum likelihood and bayesian inference). Additional topics may include bayesian classification, roc curves, information theory, fourier analysis and signal processing, multivariate analysis, pca and ica, the bootstrap, non­parametric regression, and integrate-and-fire models.
2. INTRO TO STATISTICAL METHODS 1

BIOST 2041 (Summer & Fall Term)

 3 cr J. Wilson

Discusses techniques for the application of statistical theory to actual data.  Topics include probability theory, estimation of parameters, and tests of hypothesis for both the discrete and continuous case.
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 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 variable crs.
MSNBIO 2690/NROSCI 2902
First-year students doing laboratory research and all other students that have declared a dissertation laboratory in the School of Medicine should register for this course.
INDEPENDENT STUDY variable crs.
NROSCI 2990
Students who have declared a dissertation laboratory and are doing research with a training faculty member in the School of Arts & Sciences should register for this course.
PhD DISSERTATION RESEARCH variable crs.
MSNBIO 3600/NROSCI 3000
Students enroll in this course to pursue original experimental laboratory research, the results of which will provide the substance of their doctoral dissertation.

Elective Courses:

Cell and Molecular Neurobiology

DEVELOPMENTAL NEUROSCIENCE  3 cr  
NROSCI 2041 (Fall Term)

This course is designed to provide an overview of principles that govern the developmental assembly of a complex nervous system. Topics covered include formation of neural tube and neural crest, birth and proliferation of neurons, cell migration, neuronal differentiation, synapse formation, synaptic plasticity, development of CNS circuits, and behavior. These topics will be discussed in the context of experimental results obtained by anatomical, biochemical and electrophysiological techniques using vertebrate and invertebrate animals.

ADVANCED DEVELOPMENTAL BIOLOGY

 2 cr

D. Chapman,

J. Hildebrand

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), BIOSCI 2010 thru 2023 (Current Topics in Molecular, Cellular, & Developmental Biology), #03-350 (CMU Developmental Biology course), or permission of the instructor.
BIOCHEMISTRY OF MACROMOLECULES 2 cr  
MSBMG 2510 (Spring Term)
Topics covered in this course include the experimental determination of macromolecular structure, protein; DNA interactions, protein; protein inter-actions, 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.
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  
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  
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.
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.
NEUROPHARMACOLOGY 3 cr (Palladino)
MSNBIO 2614 (Spring Term)

This course will examine the molecular mechanism of drug action for different classes of drugs that act on the nervous system, antidepressants, antipsychotics, drugs to relieve pain, drugs for neurological diseases, and drug abuse and addiction.
EUKARYOTIC MOLECULAR GENETICS 3 cr       
MSBMG 2520 (Spring Term)

This course covers topics on DNA replication in eukaryotes, the structure and function of human chromosomes, inheritance patterns and the phenotypic consequences of mutations in humans, the mapping and isolation of human genes, animal models of human diseases, regulation of the mammalian cell cycle, and current aspects of gene therapy.
DNA REPAIR: BIOCHEMISTRY TO HUMAN DISEASE 2 cr           
MSBMG 3530 (Spring Term)

This course will examine the molecular mechanism of drug action for different classes of drugs that act on the nervous system, antidepressants, antipsychotics, drugs to relieve pain, drugs for neurological diseases, and drug abuse and addiction.
MOLECULAR MECHANICS TISSUE GROWTH & DIFFRN 3 cr      
MSCMP 2730 (Spring Term)

The course covers the anatomy, embryology, histology, function, and growth regulation (growth factors, receptors, and signaling pathways) of various differentiated tissues (central nervous system, lung, liver, pancreas, urinary and reproductive systems, breast, endocrine system, skin, bone, skeletal muscle, bone marrow).  Multidisciplinary lectures are given by the members of the departments of pathology, cell biology and physiology, medicine, and surgery who have on going research in these areas.
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.
ADVANCED CELL BIOLOGY cr             
CMU 03-741   ( Term)

This course covers fourteen topics in which significant recent advances or controversies have been reported. For each topic there is a background lecture by the instructor, student presentations of the relevant primary research articles and a general class discussion. Example topics are: extracellular matrix control of normal and cancer cell cycles, force generating mechanisms in trans-membrane protein translocation, signal transduction control of cell motility, and a molecular mechanism for membrane fusion.

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.