Graduate Courses

Advanced Biochemistry 03-740
This is a special topics course in which selected topics in biochemistry will be analyzed in depth with emphasis on class discussion of papers from the recent research literature. Topics change yearly. Recent topics have included single molecule analysis of catalysis and conformational changes; intrinsically disordered proteins; cooperative interactions of aspartate transcarbamoylase; and the mechanism of ribosomal protein synthesis.

Advanced Cell Biology 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.

Advanced Developmental Biology 03-751
The course will emphasize recent, important experimental studies in the areas of early patterning and axis specification (sea urchins, Drosophila, amphibians and mammals), organogenesis of eyes and appendages (Drosophila and vertebrates), morphogenesis (cell guidance), and late-breaking "hot topics". The course is intended to be primarily a literature- and discussion-based course, with introductory lectures at the beginning of each major section. Student grades will be based on participation in discussion and the preparation of written material. Undergraduates must have previously taken Developmental Biology or Developmental Genetics, AND have permission from one of the instructors.

Advanced Genetics 03-730
This course considers selected current topics in genetics at an advanced level. The emphasis is on classroom discussion of research papers, supplemented with individual and group exercises. Topics change yearly. Recent topics have included genome imprinting in mammals, chromatin boundaries and long distance gene regulation, learning and memory in Drosophila,and the kinetochore complex in yeast.

Biological Imaging and Fluorescence Spectroscopy 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 fluorescence spectroscopy; interaction of light with biological molecules, cells, and systems; design of fluorescent 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; multi-mode 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.

Computational Biology 03-510/03-710
This course covers a range of applications of computers to solve problems in biology and medicine. Specific topics covered are computational molecular biology (analysis of protein and nucleic acid sequences), biological modeling and simulation (including computer models of single and multiple neuron behavior, biochemical kinetics, and simulation of mutation), graphics and statistics, and biological imaging. Course work will include use of software packages for these applications, reading of scientific papers, programming assignments, and writing of a research paper. This is a core course for the M.S. in Computational Biology program.

Computational Biology Internship 03-601

Computational Methods for Biological Modeling and Simulation 03-512/03-712
This course covers a variety of computational methods important for modeling and simulation of biological systems. It is intended for graduates and advanced undergraduates with either biological or computational backgrounds who are interested in developing computer models and simulations of biological systems. The course will emphasize practical algorithms and algorithm design methods drawn from various disciplines of computer science and applied mathematics that are useful in biological applications. The general topics covered will be models for optimization problems, simulation and sampling, and parameter tuning. Course work will include problems sets with significant programming components and independent or group final projects. This is a core course for the M.S. in Computational Biology program.

Computational Molecular Biology and Genomics 03-511/03-711
An advanced introduction to computational molecular biology, using an applied algorithms approach. The first part of the course will cover established algorithmic methods, including pairwise sequence alignment and dynamic programming, multiple sequence alignment, fast database search heuristics, hidden Markov models for molecular motifs and phylogeny reconstruction. The second part of the course will explore emerging computational problems driven by the newest genomic research. Course work includes four to six problem sets, one midterm and final exam. A project based on recent results from the genomics literature will be required of students taking 03-711. This is a core course for the M.S. in Computational Biology program.

Computational Structural Biology 03-714

Core Course in Biochemistry and Cell Biology 03-743
This course is designed to provide first year doctoral students in the Department of Biological Sciences with a broad foundation in biochemistry and cell biology. The textbook for both the biochemistry and cell biology sections of the course is Molecular Biology of the Cell, 4th edition, by Alberts et al. Drs. Hackney and Minden will cover topics in biochemistry including, but not be limited to, protein structure, enzymology, and methods to characterize protein structure and function.  Drs. Linstedt, McCartney, Minden and Ettensohn will cover topics in cell biology including, but not limited to, intracellular trafficking, signal transduction, the cytoskeleton, the cell cycle, and cell-cell interactions.  This is a lecture-based course and will include some discussion of the primary literature.  Students will be evaluated weekly, and with mid-term and final exams.  Students who are interested in the course who are not incoming first year doctoral students in the Department of Biological Sciences should contact Dr. McCartney for permission (bmccartney@cmu.edu). 

Molecular Biology 03-742
The structure and expression of eukaryotic genes are discussed, focusing on model systems from a variety of organisms. Current topics discussed include (1) isolation of specific DNA sequences using recombinant DNA technology, (2) the control of gene expression at the level of transcription, splicing and translation, (3) chromosome structure, including origins of replication, centromeres, telomeres, and transposons, and (4) molecular biology of humans. This is a core course for the Ph.D. in Biological Sciences program.

Introduction to Magnetic Resonance Imaging in Neuroscience 03-315
The course is designed to introduce students to the fundamental principles of magnetic resonance imaging (MRI) and its application in neuroscience. MRI is emerging as the preeminent method to obtain structural and functional information about the living human brain. This methodology has helped to revolutionize neuroscience and the study of human cognition. The specific topics covered in this course will include: introduction to spin gymnastics, survey of imaging methods, structural brain mapping, functional MRI (fMRI), and MR spectroscopy (MRS). Approximately, one third of the course will be devoted to introductory concepts of magnetic resonance, another third to the discussion of MRI methods, and the remaining third will cover a broad range of neuroscience applications. Guest lectures will be incorporated into the course from neuroscientists and psychologists who use MRI in their own research.

Membrane Trafficking 03-744
While the focus of this course is to analyze membrane/protein traffic along both the biosynthetic and endocyctic pathways, our general goal is to teach students how to read and interpret the literature. In particular, we emphasize the conclusions and discuss their validity. The course is updated each year to include topics in which new and interesting developments have occurred. Emphasis is placed on how membrane traffic is regulated and where applicable how it is disrupted or subverted during disease processes. The course is of general interest to students, fellows, and faculty interested in cell biology, immunology, neurobiology, pharmacology, and virology.

Neural Plasticity in Sensory and Motor Systems 03-761
Neural plasticity underlies the capacity of the central nervous system to encode new information, develop new abilities and adapt to the environment. Plasticity is required for learning and is modulated during development and by disorders of the brain. Recent advances in experimental methodology have led to new insights on the biological mechanisms underlying neural plasticity. The topics if the papers chosen for review will center on recent experimental and theoretical studies of topics such as synaptic plasticity, developmental and activity dependent changes in sensory and motor maps.

NMR in Biomedical Sciences 03-533
The aim of this course is to introduce the students to new advances in the field of NMR in biomedical sciences. This one semester course covers the following topics: (1) fundamentals of NMR; (2) new techniques such as NMR imaging and in vivo spectroscopy as well as pulse techniques and NMR microscopy; and (3) applications of NMR to investigate macromolecular structures, interactions, and dynamics. This course is open to graduate and advanced undergraduate students. Graduate students are expected to carry out an independent project in addition to fulfilling the usual requirements of the course.

Structural Biophysics 03-871 (course page)
A graduate level introduction to the use of biophysical methods in studying the structure of biological macromolecules such as DNA and proteins and assemblies of these molecules including DNA-protein complexes, viruses and membranes. Lecture material will cover the study of macromolecules, both in vitro, and if appropriate, in vivo. Topics covered include X-ray crystallography, NMR, microscopy, molecular dynamics and spectroscopic methods.

Techniques in Electron Microscopy 03-620
This course is designed to teach basic methods in transmission electron microscopy to graduate and undergraduate students. Sophomores with an interest in electron microscopy are encouraged to enroll, and will have the option and opportunity to utilize their skills in various laboratories during their junior or senior year. The course will be offered once each year, during the spring semester. Course enrollment will be limited to 4-6 students. Preferen-tial enrollment will be given to graduate students and undergraduate students who have demonstrated a need for this technique in their research. The class will include one hour of lecture and 4 hours of laboratory each week (some additional laboratory time outside of the scheduled laboratory time is required). Students will learn basic methods in specimen preparation for both transmission and scanning electron microscopy (fixation, embedding and ultramicrotomy, drying and metal coating) and will be trained in the operation of both the Hitachi 7100 and 2460N electron microscopes. Lectures and laboratories during the last few weeks of the semester will introduce the students to special techniques (e.g. immunoelectron microscopy , cryoultramicrotomy, freeze substitution, variable pressure SEM, etc.) and will allow them to work with samples from their own research. Experimentation using living organisms and/or their tissues, cells or molecules is an essential component of this course.

Principles of Biotechnology 38-710
This course is intended to provide an introduction to a set of core areas currently highlighted in the biotechnology industries. The objective is to provide the appropriate background for management level personnel to optimize their decision-making based on knowledgeable background in today s technologies. The focus will be on weekly modules of similar technologies with an introduction to technology/science behind the topic area and the applications of the technology in today s industries and markets.