MCDB Special Elective Courses

[Choose 1 for either the BA, BS or BS Intensive degree.]

MCDB 350a/MCDB 650a. Epigenetics: From Basic Mechanism to Human Health.
     Josien Van Wolfswinkel, Nadya Dimitrova
     WF 11.35-12.50
Study of epigenetic states and the various mechanisms of epigenetic regulation, including histone modification, DNA methylation, nuclear organization, and regulation by non-coding RNAs. Detailed critique of papers from primary literature and discussion of novel technologies, with specific attention to the impact of epigenetics on human health. Prerequisites: Foundational courses BIOL 101-104, and two MCDB 200-level courses (strongly recommended: MCDB 200 and MCDB 202) or with permission of instructor.

MCDB 355a. Cytoskeleton & Disease.
     Surjit Chandhoke
     W 9.25-11.15
In-depth discussion of the cytoskeleton, proteins associated with the cytoskeleton, and diseases that implicate members of these protein families. Preference given to MCDB senior majors. Prerequisite: BIOL 101-104 and at least one MCDB 200-level course.

MCDB 361bG/PHYS 562/CBB 562/MBB 562. Modeling Biological Systems II.
     Thierry Emonet, Jonathan Howard
     TTh 2.30-3.45
Advanced topics related to dynamical processes in biological systems. Processes by which cells compute, count, tell time, oscillate, and generate spatial patterns. Time-dependent dynamics in regulatory, signal-transduction, and neuronal networks; fluctuations, growth, and form. Comparisons between models and experimental data. Use of MATLAB to create models. Prerequisite: MCDB 261 or equivalent, or a 200-level biology course, or with permission of instructor.

MCDB 370bG. Biotechnology.
     Craig Crews, Nicole Clay, Kenneth Nelson, Joseph Wolenski
     MW 11.35-12.50
The principles and applications of cellular, molecular, and chemical techniques that advance biotechnology. Topics include the most recent tools and strategies used by government agencies, industrial labs, and academic research to adapt biological and chemical compounds as medical treatments, as industrial agents, or for the further study of biological systems. Prerequisites: MCDB 200 or 202 or 300.

MCDB 380aG. Advances in Plant Molecular Biology.
     Vivian Irish, Joshua Gendron, Yannick Jacob
     F 9.25-11.15
The study of basic processes in plant growth and development to provide a foundation for addressing critical agricultural needs in response to a changing climate. Topics include the latest breakthroughs in plant sciences with emphasis on molecular, cellular, and developmental biology; biotic and abiotic plant interactions; development, genomics, proteomics, epigenetics and chemical biology in the context of plant biology; and the current societal debates about agrobiotechnology.  Prerequisites: BIOL 101-104 and two MCDB 200-level courses, or permission of instructor..

MCDB 387b. The Eukaryotic Cell Cycle.
     Iain Dawson
     T or Th 7.00-8.50 p.m.
The regulation and coordination of the eukaryotic cell cycle examined by means of a detailed critique of primary literature. Particular attention to the processes of development, differentiation, and oncogenic disease. Enrollment limited, with preference to juniors and seniors. Prerequisites: BIOL 101, 102, and 103, or equivalent performance on the corresponding biological sciences placement examinations; MCDB 202, 205, or 210. Electronic permission key required. Students must contact the instructor prior to the first class meeting.

MCDB 415bG. Cellular and Molecular Physiology.
     Frederick Sigworth
     MWF 9.25-10.15
Study of the processes that transfer molecules across membranes. Topics include the different classes of molecular machines that mediate membrane transport. Emphasis on interactions among transport proteins in determining the physiologic behaviors of cells and tissues. Intended for seniors majoring in the biological sciences. Recommended preparation: MCDB 205, 310, 320, or permission of instructor.

MCDB 425aG/MB&B 425aG. Basic Concepts of Genetic Analysis.
     Lu, Jun
     MW 11.35-12.50
The universal principles of genetic analysis in eukaryotes. Reading and analysis of primary papers that illustrate the best of genetic analysis in the study of various biological issues. Focus on the concepts and logic underlying modern genetic analysis. Prerequisite: MCDB 200 or equivalent.

MCDB 430aG/IBIO 530. Biology of the Immune System.
     Eric Meffre, David Schatz, Peter Cresswell, Joao Pedro Pereira, Ruslan Medzhitov,
     Akiko Iwasaki, Craig Roy, Noah Palm, Susan Kaech, Kevan Herold, Carla Rothlin,
     Carrie Lucas
     MWF 9.25-10.15
The development of the immune system. Cellular and molecular mechanisms of immune recognition. Effector responses against pathogens; immunologic memory and vaccines. Human diseases including allergy, autoimmunity, cancer, immunodeficiency, HIV/AIDS. After MCDB 300.

MCDB 435a. Landmark Papers in Cell Biology.
     Joel Rosenbaum
     T 7.00-8.50
Discussion and critical evaluation of selected research papers that were important in determining the directions of modern cell biological research. Emphasis on the nature of the problem, evaluation of experimental approaches and results, and the authors’ interpretation of the results. The grade is highly dependent on weekly discussion by all participants. Prospective students should fill out the form sent by the MCDB Registrar, Crystal Adamchek, prior to the first week of classes. Students who have taken upper level courses in cell biology, biochemistry and genetics will be given priority. This course is only open to Seniors.

MCDB 450b. The Human Genome.
     Stephen Dellaporta, Nadya Dimitrova
     M 3.30-5.30
A focus on the primary scientific literature covering the principles of genomics and its application to the investigation of complex human traits and diseases. Topics include the technology of genome sequencing and resequencing, the characterization of sequence and structural variation in human populations, haplotype and linkage disequilibrium analysis, genome-wide association studies, the comparative genomics of humans and our closest relatives, and personalized genomics and medicine. Enrollment limited to 15. Students should contact the instructor prior to the first week of classes. Prerequisite: MCDB 202; a course in statistics is strongly recommended.

MCDB 452bG/CPSC 752b/MB&B 752b/CBB 752. Bioinformatics: Practical Application of Simulation
and Data Mining.

     Mark Gerstein
     MW 1.00-2.15
Techniques in data mining and simulation applied to bioinformatics, the computational analysis of gene sequences, macromolecular structures, and functional genomics data on a large scale. Sequence alignment, comparative genomics and phylogenetics, biological databases, geometric analysis of protein structure, molecular-dynamics simulation, biological networks, microarray normalization, and machine-learning approaches to data integration. Prerequisites: MB&B 301 and MATH 115, or permission of instructor.

MCDB 461b. Advanced Seminar in Systems Biology.
     Murat Acar
     F 3.30-5.30
A focus on the primary scientific literature covering the topics of gene network design, stochasticity in gene expression, and evolution of genes and networks, in the context of both prokaryotic and eukaryotic systems. Detailed critique of the approaches, data analysis, controls, results, and conclusions of selected current and classic papers in the field. Prerequisites: Advanced undergraduate level courses: MCDB 261 or MCDB 351 recommended.

MCDB 482a. Advanced Seminar in Cell Biology: Intracellular Signal Transduction.
     Craig Crews
     M 3.30-5.20
Discussion of intracellular signal transduction pathways. Detailed critique of experimental approaches, controls, results, and conclusions of selected current and classic papers in this field.

[These courses are bracketed for 2019-20]