Cell and Molecular Neurobiology

Advanced Cell Biology
CMU 03-741

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.

Biological Imaging and Fluorescence Spectroscopy3crLanni
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.

Molecular Mechanics Tissue Growth & Diffrn3cr
MSCMP 2730Spring

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.

DNA Repair: Biochemistry to Human Disease3cr
MSCMP 3530Spring

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 Genetics3cr
MSBMG 2520Spring

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.

MSNBIO 2614Spring

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.

Stem Cells3crMonga
MSCMP 3740Fall

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.

Molecular Pharmacology3cr
MSMPHL 3360Fall

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.

Principles of Pharmacology2cr
MSMPHL 2310Spring

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).

Biology of Signal Transduction3crRomero / Rajasekaran
MSMPHL 3375Spring

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.

Cell and Molecular Physiology2crFrizzell
MSCBMP 2830Spring

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.

Biochemistry of Macromolecules2cr
MSBMG 2510Spring

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.

Developmental Neuroscience3cr
NROSCI 2041Fall

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 Biology2crD. Chapman / J. Hildebrand
MSBNIO 2612Fall

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.


Molecular Pathobiology3crAchim / Oury
MSCMP 2740 Spring

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).

Biological Basis of Neuropsychiatric3crHastings
MSNBIO 2005/NROSCI 2078Spring

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.


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.

Cognitive Neuroscience3crMcClelland / Olson
NROSCI 2005Fall

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.

Cognitive Neuropsychology3crBehrmann
CMU 85-714Spring

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.


Computer Vision3crLee
CMU 15-385Spring

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.

Computational Neuroscience Methods3crErmentrout
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 Analysis4crLewicki
CMU 15-485/785 Spring

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.

Computational Models of Neural Systems4crTouretzky
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.

Intro to Parallel Distributed Processing3crPlaut
CMU 85-719Spring

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.

Artificial Neural Networks4crTouretzky
CMU 15-782 (A) Spring

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.

Systems Neuroscience

Neural Plasticity in Sensory and Motor Systems3crBarth, Urban, Crowley
NROSCI 3059Spring

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.
Human Physiology4crYates
NROSCI 2070Fall

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.
Functional Neuroanatomy4crSesack
NROSCI 2011Fall

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.


Historical Perspectives in Neuroscience2crBalaban
MSNBIO 2135Summer

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.