Formal Coursework

A minimum of 9.5 didactic courses are to be selected from 7.5 required courses plus electives.  It is required that students maintain a minimum overall “B” average in their coursework.  Any Cs must be offset by As to maintain a B average and a grade of B or better must be achieved in all programmatic courses.

Students may petition the Ph.D. Curriculum Committee regarding changes in required areas of coursework. Up to two (2) required areas may be modified to provide a specific focus of study in metabolism.  Specific changes and the justification for those changes must be submitted in writing.

Accordion: 
The Programmatic Core in Metabolism (4.5 credits)
  • Molecular Nutrition 1 (MOMN 36500).  Students are exposed to a comprehensive review of nutritional physiology and requirements, including the regulated digestion, synthesis and/or metabolism of vitamins, minerals, lipids, proteins and carbohydrates.  Various lecturers specialized in specific areas of metabolic research participate throughout the quarter.  The course culminates with the students writing a comprehensive paper linking several of the topics covered throughout the quarter.  Brady and Staff.  Autumn.

    Molecular Nutrition 2 (MOMN 36600).  This course is an extension of Molecular Nutrition 1 and investigates the physiological control of systemic metabolism.  Heavy emphasis is placed on the coordinate regulation of glucose and lipid metabolism by skeletal muscle, liver, adipose tissue, pancreas and brain.  The format of the course is a combination of lectures and student presentations of primary literature.  At the end of the course, students are expected to write a grant application to investigate a current area of metabolism research and then present and defend the proposal to the lecturers and students.  Reardon and Staff.  Winter. 

  • Grant Writing (MOMN 30910).   Students will gain extensive exposure to the grant writing and review processes.  Several speakers will lecture on the various funding agencies, types of grants, and general approaches to grant writing.  Students will read funded applications from CMMN faculty to learn the proper approaches for successful grant writing, including responding to reviewers’ critiques.  Students will be expected to complete a 20-25 page R01 style grant application by the end of the quarter, which will fulfill the mock grant proposal requirement for the CMMN students.  The course culminates with a mock grant review panel in which the students read and critique each other’s applications. Brady.  (This course will be held Winter 2015).

    New Insights into Metabolic Research (MOMN 40400).  This course is conducted as a seminar series.  Students will broaden their exposure to metabolism related research through bi-weekly faculty and student presentations of research data and primary literature.  Additionally, prominent researchers from other institutions are invited to give a seminar and meet alone with the students to discuss their career paths, experiences in running successfully funded labs and use of cutting edge experimental approaches. Attendance is mandatory for first and second year students but all students are strongly to attend.  Rhodes.  Autumn, Winter, Spring, Summer. 
     

Metabolism Electives
  • Molecular Basis of Metabolic Disease (MOMN 30901).  This course covers topics in nutrition in which modern molecular and cell biology provide a greater understanding of the regulation of these metabolic pathways.  Students are required to extensively read primary literature and give oral presentations to the class and weekly discussion leader.  Wicksteed.  Autumn.
     
  • Signal Transduction and Disease (MPMM 30600).  Topics include receptor ligands, membrane receptor tyrosine kinases, G proteins, proto-oncogenes, cytoplasmic protein kinases and phosphatases, transcription factors, receptor-nucleus signaling, development and cancer, genetic dissection of signaling pathways, cell growth and proliferation, cell cycle regulators, cell cycle progression and apoptosis, and sensing of hypoxia and mechanical stimuli.  The role of signaling in disease is a theme throughout the course.  Dulin.  Winter.  
The General Basic Science Core (3 credits)

Students will be required to take 1 course in 3 of the following 4 areas.

Biochemistry

  • Proteins 1: Protein Fundamentals (BCMB 30400).  The 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.  Prereq:  BCMB 30100, which may be taken concurrently, or equivalent. Koide, Keenan.  Autumn.

 

  • Fundamentals of Structural Biology (BCMB 30500).  This course emphasizes the basic principles of protein structure determination by X-ray crystallography and NMR spectroscopy. The underlying physical concepts of these methods will be introduced and the capabilities of each will be discussed and compared in context of their uses in de novo structure determination and protein engineering studies.  Kossiakoff, Koide.  Winter.  (This course will not be offered in 2008.)

 

  • Proteins 2: Structure and Function of Membrane Proteins (BCMB 32300).  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.  Perozo, Roux.  Winter

Cell Biology

  • Cell Biology 1 (MGCB 31600). 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.  Glick, Turkewitz.  Autumn.

 

  • Cell Biology 2 (MGCB 31700). This course covers the mechanisms with which cells execute fundamental behaviors. Topics include signal transduction, cell cycle progression, mitosis, checkpoints, 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. Cell Bio I 31600 is not a prerequisite. Glotzer, Kovar.  Winter.

Genetics

  • General Principles of Genetic Analysis (GENE 31400).  Coverage of the fundamental tools of genetic analysis as used to study biological phenomena.  Topics include genetic exchanges in prokaryotes, eukaryotes, and their viruses and plasmids; principles of transformation; analysis of gene function. Bishop and Staff.  Autumn.

 

  • Genetic Mechanisms (GENE 31500).  Advanced coverage of genetic mechanisms involved in genome stability and rearrangement.  Topics include genetics of transposons, site-specific recombination, gene conversion, reciprocal crossing over, and plasmid and chromosome segregation.  Bishop.  Winter.

 

  • Human Genetics 1: Human Genetics (HGEN 47000).  This course covers classical and modern approaches to studying cytogenic, Mendelian, and complex diseases. Topics include chromosome biology, single gene and complex disease, non-Mendelian inheritance, cancer genetics, human population genetics, and genomics. The format includes lectures and student presentations.  Cox, Ober, Millen. Autumn.

Molecular Biology

  • Molecular Biology 1 (MGCB 31200).  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.  Rothman-Denes.  Winter.
  • Molecular Biology 2 (MGCB 31300).  The content of this course will cover the mechanisms and regulation of eukaryotic gene expression at the transcriptional and post-transcriptional levels. Our goal is to explore with you research frontiers and evolving methodologies. Rather than focusing on the elemental aspects of a topic, the lectures and discussions will focus on the most significant recent developments, their implications and future directions. Singh, Staley.  Spring.
Electives (2 credits)

The remaining two (or more) courses may be selected from available courses in the areas listed below.  At least one advanced metabolism course must be selected (denoted by *).  Statistics is recommended.  Students who have completed their academic requirements are encouraged to formally audit additional advanced courses.

  • Advanced Biotechniques*
  • Behavioral Aspects of Diet and Nutrition*
  • Cell and General Pathology
  • Introduction to Cancer Biology
  •  Molecular Basis of Nutrition*
  • Molecular Defense Mechanisms
  • Molecular Mechanisms of Cancer Biology*
  • Organ Physiology/Endocrinology
  • Scientific Basis of Nutrition*
  •  Specialized Topics in Nutrition*
Ethics Course

The divisional course on Scientific Integrity and the Ethical Conduct of Research and is required for all first year students in the division and held in the spring, where a variety of speakers discuss ethical issues in scientific research.  This course is graded pass/fail.

Current Topics in Nutritional Research (0.5 credit)

The Committee holds a seminar series/journal club biweekly throughout the year.   Student attendance and participation are required Autumn, Winter and Spring quarters of their first two years.  At the end of the second year, students will be graded pass/fail. Continued student participation in this series is expected until graduation.

In the Autumn, CMMN faculty members will give research talks to further expose students to research being conducted by Committee members.  In the Winter through Summer quarters, faculty presentations will either comprise research talks or presentation of a high profile, recent journal article related to Metabolism research.  Additionally, prominent outside speakers will be invited periodically to give research seminars, and students will meet with the speaker immediately after the talk.

Students are also required to present twice yearly.  In the first year, presentations will be based on the laboratory rotation performed the previous quarter.   Second year students will present a mock grant proposal in the winter (see below) and a journal article in the Spring.  In subsequent years, students are required to present on their thesis research project once a year.  The second presentation can either be discussion of a journal article, or for more advanced students, a second presentation of their own research.