BCMB 30400 - Protein Fundamentals
This course covers the physical-chemical phenomena that define protein structure and function. Topics include: the principles of protein folding, molecular motion and molecular recognition; protein evolution, design and engineering; enzyme catalysis; regulation of protein function and molecular machines; proteomics and systems biology. Workshop of X-ray Crystallography: The workshop is an addendum to Protein Fundamentals and is required for all BCMB students. This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation.
Instructors: Keenan, Koide, Kossiakoff
BCMB 30600 - Nucleic Acid Structure and Function
This course focuses on the biochemistry of nucleic acids. Topics include nucleic acid structure, folding, and chemistry, protein-nucleic acid interactions, non-coding RNAs, and enzymology of key processes such as DNA replication, repair and recombination. A special emphasis is placed on primary literature.
Instructors: Rice, Pan
BCMB/MGCB 31400 - Genetic Analysis of Model Organisms
Fundamental principles of genetics discussed in the context of current approaches to mapping and functional characterization of genes. The relative strengths and weaknesses of leading model organisms are emphasized via problem-solving and critical reading of original literature.
Instructors: Palmer, Bishop, Ferguson, Malamy
BCMB/MGCB 31600 - Cell Biology I
Eukaryotic protein traffic and related topics, including molecular motors and cytoskeletal dynamics, organelle architecture and biogenesis, protein translocation and sorting, compartmentalization in the secretory pathway, endocytosis and exocytosis, and mechanisms and regulation of membrane fusion.
Instructors: Turkewitz, Glick
ECEV 32500 - Evolutionary Aspects of Gene Regulation
This advanced level course focuses on reading and participation. Each meeting period is dedicated to a new topic, several of which make up a module. Typical modules are: transcription factors and cis-regulatory elements, functional consequences of regulatory changes and microRNAs as a mechanism of gene regulation. Students present and discuss several papers from the primary literature during this course.
Instructors: Ruvinsky
GEOS 36650 - Environmental Microbiology
The objective of this course is to understand how microorganisms alter the geochemistry of their environment. The course will cover fundamental principles of microbial growth, metabolism, genetics, diversity, and ecology, as well as methods used to study microbial communities and activities. It will emphasize microbial roles in elemental cycling, bioremediation, climate, and ecosystem health in a variety of environments including aquatic, soil, sediment, and engineered systems.
Instructor: Coleman
IMMU 31200 - Host Pathogen Interactions
This course will explore the basic principles of host defense against pathogens and pathogens' strategies to overcome host immune mechanisms. The course will address evolutionary aspects of innate and adaptive immune responses, while also studying specific examples of viral and bacterial interactions with their hosts. The reviews of relevant immunological mechanisms necessary for appreciation of host/pathogen interactions will be incorporated in the studies of specific cases. This course explores the basic principles of host defense against pathogens, including evolutionary aspects of innate and adaptive immunity and immune evasion strategies. Specific examples of viral and bacterial interactions with their hosts are studied in depth. A review of immunological mechanisms involved in specific cases is incorporated in the course.
Instructor: Chervonsky
MICR 30600 - Fundamentals of Bacterial Physiology
This course meets one of the requirements of the microbiology specialization. This course introduces bacterial diversity, physiology, ultra-structure, envelope assembly, metabolism, and genetics. In the discussion section, students review recent original experimental work in the field of bacterial physiology.
Instructor: Missiakas
BCMB 31100 - Evolution of Biological Molecules
Evolution of Biological Molecules connects evolutionary changes imprinted in genes and genomes with the structure, function and behavior of the encoded protein an dRNA molecules. Central themes are the mechanisms and dynamics by which molecular structure and function evolve, how protein/RNA architecture shapes evolutionary trajectories, and how patterns in present-day sequence can be interpreted to reveal the interplay data of evolutionary history and molecular properties. Core concepts in macromolecule biochemistry (folding and stability of proteins and RNA, structure-function relationships, kinetics, catalysis) and pmolecular evolution (selection, mutation, drift, epistasis, effective population size, phylogenetics) will be taught, and the interplay between them explored.
Instructors: Drummond, Thornton
BCMB/MGCB 31200 - Molecular Biology I
Nucleic acid structure and DNA topology; methodology; nucleic-acid protein interactions; mechanisms and regulation of transcription in eubacteria, and of replication in eubacteria and eukaryotes; mechanisms of genome and plasmid segregation in eubacteria.
Instructors: Rothman-Denes, Bishop
BCMB 31700 - Cell Biology II
Cell Biology II covers the mechanisms with which cells execute fundamental behaviors. Topics include signal transduction, cell cycle progression, cell growth, cell death, cancer biology, cytoskeletal polymers and motors, cell motility, cytoskeletal diseases, and cell polarity. Each lecture will conclude with a dissection of primary literature with input from the students. Students will write and present a short research proposal, providing excellent preparation for preliminary exams.
Instructors: Glotzer, Kovar
ECEV 33365 - Evolutionary and Genomic Medicine: Dynamics at the Host-Microbe Interface
Evolution is regularly investigated in free-living organisms, but some of its most fascinating and important examples occur in the interface between free-living and non-free-living states. In this course, we will use evolutionary and ecological principles to study the dynamics of viruses, unicellular organisms and cells in multi-cellular organisms relevant to human medicine.
Instructors: Cobey, Wu
ECEV 35600 - Principles of Population Genetics
Examines the basic theoretical principles of population genetics, and their application to the study of variation and evolution in natural populations. Topics include selection, mutation, random genetic drift, quantitative genetics, molecular evolution and variation, the evolution of selfish genetic systems, and human evolution.
Instructors: Steinrucken, Kreitman
GEOS 33800 - Global Biogeochemical Cycles
This survey course covers the geochemistry of the surface of the Earth, focusing on biological and geological processes that shape the distributions of chemical species in the atsmosphere, oceans, and terrestrial habitats. Budgets and cycles of carbon, nitrogen, oxygen, phosphorous, and sulfur are discussed, as well as chemical fundamentals of metabolism, weathering, acid-base and dissolution equilibria, and isotopic fractionation. The course examines the central role that life plays in maintaining the chemical disequilibria that characterize Earth's surface environments. The course also explores biogeochemical cycles change (or resist change) over time, as well as the relationships between geochemistry, biological (including human) activity, and Earth's climate.
Instructor: Waldbauer
IMMU 31500- Advanced Immunology I
This course explores the basic principles of the immune system, including tolerance, the development and differentiation of lymphocyte subsets, the regulation of the class of immune responses, memory, cell homing and migration, cell-cell interactions, antigen presentation and recognition.
Instructor: Bendelac
MICR 31600 - Molecular Basis of Bacterial Disease
This course meets one of the requirements of the microbiology specialization. This lecture/discussion course involves a comprehensive analysis of bacterial pathogens, the diseases that they cause, and the molecular mechanisms involved during pathogenesis. Students discuss recent original experimental work in the field of bacterial pathogenesis.
Instructor: Chen, Missiakas
BCMB 30800 - Single Molecule Biochemistry
This course presents a series of advanced case studies designed to familiarize students with current single molecule research. Topics include: motor proteins and the cytoskeleton, nucleic acid processing enzymes, ion channels, and force spectroscopy and macromolecule folding.
Instructors: Rock, Bezanilla
BCMB/MGCB 31300 - Molecular Biology II
The content of this course covers the mechanisms and regulation of eukaryotic gene expression at the transcriptional and post-transcriptional levels. Our goal is to explore research frontiers and evolving methodologies. Rather than focusing on the elemental aspects of a topic, the lectures and discussions highlight the most significant recent developments, their implications and future directions.
Instructors: Staley, Ruthenburg
BCMB 32200 - Biophysics of Biomolecules
This course covers the properties of proteins, RNA, and DNA, as well as their interactions. We emphasize the interplay between structure, thermodynamics, folding, and function at the molecular level. Topics include cooperativity, linked equilibrium, hydrogen exchange, electrostatics, diffusion, and binding.
Instructor: Sosnick
GEOS 36600 - Geobiology
Geobiology seeks to elucidate the interactions between life and its environments that have shaped the coevolution of the Earth and the biosphere. The course will explore the ways in which biological processes affect the environment and how the evolutionary trajectories of organisms have in turn been influenced by environmental change. In order to reconstruct the history of these processes, we will examine the imprints they leave on both the rock record and on the genomic makeup of living organisms. The metabolism and evolution of microorganisms, and the biogeochemistry they drive, will be a major emphasis.
Instructors: Coleman, Waldbauer
IMMU 32000 - Advanced Immunology II
This class will explore the molecular and biochemical mechanisms by which lymphocytes develop and are activated in response to antigen. This will include the signal transduction pathways and transcriptional networks involved in these processes, as well as the molecular mechanisms underlying the generation of receptor diversity.
Instructors: Kee, Gounari
IMMU 30266 - Molecular Immunology
This course is available on alternative years (Spring of odd years) and is also considered a basic biochemistry course. Molecular Immunology examines the structural principles of immune recognition by antigen receptors of the innate and adaptive immune systems, the discrimination between self and non-self and the molecular fundamentals of cell stimulation and signaling. Primary literature is integrated with lectures on commonly used biochemical, structural and immunological techniques.
Instructor: Adams
MICR 33000 - Bacteria/Bacteriophage Genetics and Cell Biology
The graduate-level course is focused on providing students with a) an understanding of the foundational principles of bacterial genetics, and methods of genetic analysis, and b) how expression of genetic material is regulated in bacteria and phage, and c) mechanisms that govern the construction, development, and division of bacterial cells and multicellular communities.
Instructors: Crosson, Shuman, Rothman-Denes
MICR 34600 - Introduction to Virology
This class on animal viruses considers the major families of the viral kingdom with an emphasis on the molecular aspects of genome expression and virus-host interactions. Our goal is to provide students with solid appreciation of basic knowledge, as well as instruction on the frontiers of virus research.
Instructor: Golovkina