Graduate Program in Cell and Molecular Biology

MGCB 30400. Protein Fundamentals. 100 Units.

The course covers the physical chemical phenomena that define protein structure and function. Topics include: three-dimensional structures of proteins; the principles of protein folding, molecular motion and molecular recognition; protein evolution, design and engineering; enzyme catalysis; regulation of protein function; proteomics and systems biology. Undergraduates are highly recommended to take BIOS 20200 (Introduction to Biochemistry) or equivalent before taking this course.

Instructor(s): E. Ozkan, J. Piccirilli, D. Arac     Terms Offered: Autumn
Equivalent Course(s): HGEN 30400, BCMB 30400

MGCB 31200. Molecular Biology I. 100 Units.

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.

Instructor(s): Bishop, D, Fei, J, Lee H.C., Rice, P, Ruthenburg, A     Terms Offered: Winter
Equivalent Course(s): DVBI 31200, BCMB 31200

MGCB 31300. Molecular Biology-II. 100 Units.

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.

Instructor(s): J. Staley, A. Ruthenburg, H.C. Lee     Terms Offered: Spring
Prerequisite(s): Molecular Biology I (MGCB 31200) or by special permission of an instructor
Equivalent Course(s): BCMB 31300, DVBI 31300

MGCB 31400. Genetic Analysis of Model Organisms. 100 Units.

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.

Instructor(s): Pincus, D, Ferguson, E, Lee, H.C, Zhang, X     Terms Offered: Autumn
Equivalent Course(s): DVBI 31400, BCMB 31400, HGEN 31400

MGCB 31600. Cell Biology I. 100 Units.

Eukaryotic protein traffic and related topics, including molecular motors and cytoskeletal dynamics, organelle architecture and biogenesis, protein translocationand sorting, compartmentalization in the secretory pathway, endocytosis and exocytosis,and mechanisms and regulation of membrane fusion.

Instructor(s): A. Turkewitz, B. Glick     Terms Offered: Autumn
Equivalent Course(s): DVBI 31600, HGEN 31600, BCMB 31600

MGCB 31700. Cell Biology II. 100 Units.

This course 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.

Instructor(s): M. Glotzer, D. Kovar     Terms Offered: Spring
Prerequisite(s): For undergraduates: Three quarters of a Biological Sciences Fundamentals Sequence.
Equivalent Course(s): BCMB 31700, BIOS 21238, DVBI 31700

MGCB 31900. Introduction to Research. 100 Units.

Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students.

Instructor(s): Staff     Terms Offered: Autumn
Equivalent Course(s): DVBI 31900, HGEN 31900, BCMB 31900, GENE 31900

MGCB 32100. Senior Graduate Student Ethics. 100 Units.

This course explores specific ethical dilemmas that may arise in laboratory settings. The format of this course will provide opportunities for all students to voice their questions and opinions. Student groups of 4-5 will act as a review board during each session. Class time will center around the case, the conclusions of the review board, and the steps that should be taken to remedy the situation, if any. Faculty will guide and stimulate discussion in each case. Faculty will also provide any relevant University bylaws and/or NIH guidelines. Following the session, review board members will submit a formal 1-2 page justified decision in writing to the instructor. Successful completion of the course requires active participation in group presentations and general class discussions as well as joint submission of review board summaries.

Instructor(s): K. Moffat     Terms Offered: Spring

MGCB 32300. Structure and Function of Membrane Proteins. 100 Units.

This course will be an in depth assessment of the structure and function of biological membranes. In addition to lectures, directed discussions of papers from the literature will be used. The main topics of the courses are: (1) Energetic and thermodynamic principles associated with membrane formation, stability and solute transport (2) membrane protein structure, (3) lipid-protein interactions, (4) bioenergetics and transmembrane transportmechanisms, and (5) specific examples of membrane protein systems and their function (channels, transporters, pumps, receptors). Emphasis will be placed on biophysical approaches in these areas. The primary literature will be the main source of reading.

Instructor(s): Perozo, E.     Terms Offered: Winter
Equivalent Course(s): BCMB 32300

MGCB 33500. Fundamentals of Biological Data Analysis. 100 Units.

The primary goals of this course are to provide first-year trainees in MCB graduate programs with a common grounding in the core tools of modern quantitative data analysis as used in molecular and cellular biology and a shared quantitative mindset and commitment to rigorous reproducible science. Our goal is not to be comprehensive, but to provide students with the conceptual foundations and practical skills they are most likely to need, regardless of research area. The expectation is that they will build upon these foundations through advanced courses, workshops and in-lab training. The course will emphasize building reproducible "data analysis workflows" that go from raw data to insights about biological process and function, and presenting those insights in rigorous and informative ways. The course will use R as the primary programming language because of its widespread use and suitability for quantitative statistical data visualization and analysis, but the majority of skills that students learn will be readily transferrable to other programming languages.

Instructor(s): Munro, Ed Rust, Michael     Terms Offered: Winter
Equivalent Course(s): DVBI 33500, BCMB 33500

MGCB 35420. Stochastic Processes in Gene Regulation. 100 Units.

This didactic course covers the fundamentals of stochastic chemical processes as they arise in the study of gene regulation. The central object of study is the Chemical Master Equation and its coarse-grainings at the Langevin/Fokker-Planck, linear noise, and deterministic levels. We will consider both mathematical and computational approaches in contexts where there are both single and multiple deterministic limits.

Instructor(s): J. Reinitz     Terms Offered: To be determined
Prerequisite(s): Consent of instructor.
Equivalent Course(s): CAAM 35420, ECEV 35420, STAT 35420

MGCB 35600. Vertebrate Development. 100 Units.

This advanced-level course combines lectures, student presentations, and discussion sessions. It covers major topics on the developmental biology of embryos (e.g. formation of the germ line, gastrulation, segmentation, nervous system development, limb pattering, organogenesis). We make extensive use of the primary literature and emphasize experimental approaches including embryology, genetics, and molecular genetics.

Instructor(s): V. Prince, P. Kratsios.     Terms Offered: Winter
Prerequisite(s): For Biological Sciences majors: Three quarters of a Biological Sciences Fundamentals Sequence including BIOS 20189 or BIOS 20235
Equivalent Course(s): ORGB 33600, DVBI 35600, BIOS 21356

MGCB 36100. Plant Development and Molecular Genetics. 100 Units.

Genetic approaches to central problems in plant development will be discussed. Emphasis will be placed on embryonic pattern formation, meristem structure and function, reproduction, and the role of hormones and environmental signals in development. Lectures will be drawn from the current literature; experimental approaches (genetic, cell biological, biochemical) used to discern developmental mechanisms will be emphasized. Graduate students will present a research proposal in oral and written form; undergraduate students will present and analyze data from the primary literature, and will be responsible for a final paper.

Instructor(s): J. Greenberg     Terms Offered: Spring
Prerequisite(s): For undergraduates only: Three quarters of a Biological Sciences Fundamentals Sequence including BIOS 20187 or BIOS 20235.
Note(s): E.
Equivalent Course(s): ECEV 32900, BIOS 23299, DVBI 36100

MGCB 36400. Developmental Mechanisms. 100 Units.

This course provides an overview of the fundamental questions of developmental biology, with particular emphasis on the genetic, molecular and cell biological experiments that have been employed to reach mechanistic answers to these questions. Topics covered will include formation of the primary body axes, the role of local signaling interactions in regulating cell fate and proliferation, the cellular basis of morphogenesis, and stem cells.

Instructor(s): E. Ferguson, R. Fehon     Terms Offered: Winter
Prerequisite(s): For undergraduates only: Three quarters of a Biological Sciences Fundamentals Sequence including BIOS 20189, or BIOS 20235. AND CONSENT OF INSTRUCTOR
Equivalent Course(s): BIOS 21237, DVBI 36400

MGCB 38500. Comparative Developmental Biology @ MBL. 100 Units.

This intensive comparative developmental biology course is designed for graduate students in their second or later year of Ph.D studies. The two-week-long course will provide exposure to a combination of well-established and emerging developmental systems. Students will develop advanced experimental embryology skills-many of which are transferable across organisms-in the handling and cellular/genetic manipulation of embryos, including microinjection, lineage tracing, microdissection, cell transplantation, in situ hybridization, CRISPR/Cas mutagenesis, and 3D in vivo imaging. Students will develop an enhanced appreciation of the advantages each species offers, will be trained to think more comparatively (in a phylogenetic context), and will gain an appreciation of how best to select the appropriate species to address a specific question. They will be exposed to classic, recent, and developing methodologies and techniques and will learn about exciting ongoing research using these approaches. Developing and completing a short independent or team-based research project will enhance skills in hypothesis generation and experimental design.

Instructor(s): Victoria Prince, Nipam Patel, Karen Echeverri, Clifton Ragsdale     Terms Offered: Autumn
Equivalent Course(s): DVBI 38500, BCMB 38500

MGCB 39200. Readings: MGCB. 100 Units.

Reading course in an area of developmental biology of special interest to the student. Must be prearranged with a faculty member and preapproved by the chair of the Curriculum Committee.

MGCB 39500. UChicago Microscopy Course. 100 Units.

The UChicago Microscopy Course is a residential research course hosted at the Marine Biological Laboratory in Woods Hole, MA. The course is designed for graduate students in year two or beyond. Travel and lodging costs will be covered in full. This intensive two-week boot camp course will teach both conceptual foundations and practical approaches to modern light microscopy, using a variety of microscopes and specimens. The central goal is to empower students to identify and master imaging strategies that are best suited to address their specific experimental problems of interest, now and in the future. Core topics will include: (a) fundamentals of microscope design, image formation, contrast, and resolution; (b) common approaches to transmitted light (e.g. phase contrast, DIC, and polarization) and fluorescence microscopy (e.g. laser scanning or spinning disk confocal, light sheet and TIRF), (c) fluorescent probes and multispectral imaging; and (d) cameras and detectors, signal: noise and strategies for optimal sampling in space and time. More advanced topics will include single-molecule approaches, super-resolution, and photokinetics (e.g.FRAP, photoactivation, and optogenetics). In the first half of the course, daily lectures will introduce basic concepts, followed by intensive hands-on experience with different specimens, microscopes, and imaging modalities. In the second half, students will explore more advanced topics of interest through a set of modular projects.

Instructor(s): Ed Munro, Rick Fehon, Abishek Kumar     Terms Offered: Autumn
Equivalent Course(s): MICR 39500, DVBI 39500, BCMB 39500

MGCB 39900. Tutorial: MGCB. 100 Units.

MGCB 47000. Thesis Research: MGCB. 300.00 Units.

Laboratory research for senior graduate students.

MGCB 47100. Non-Thesis Rsch: MGCB. 300.00 Units.

Laboratory research for first and second year graduate students.

MGCB 70000. Advanced Study: Molecular Genetics & Cell Biology. 300.00 Units.

Advanced Study: Molecular Genetics & Cell Biology