Nutritional and Metabolic Biology

This course provides an in-depth analysis of several organ systems and diseases associated with each organ system. The course has four modules; each module describes the basic physiology, nutritional status and anatomy of the organ system, the genetics, cell and biochemical mechanisms and pathologies associated with the disease, as well as basic pharmacology and therapeutics to treat the disease. Course Directors: Ronald Liem and Steven Spitalnik.

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Gross and microscopic study of lesions of the nervous system, with attention to functional derangement associated with them. Lectures, laboratory, conferences, and assigned readings. Course Director: Ronald Liem.

Required for all first year students in spring semester, this course is an Introduction to eukaryotic cell biology and covers such topics as membrane trafficking, the mitochondria, the nucleus, viral biology, apoptosis as well as the cytoskeleton and its role in various cellular processes, including mitosis, cell migration, cell polarity and cell adhesion. Course Directors: Gregg Gundersen and Ai Yamamoto.

Explores molecular and cellular mechanisms of nutrient action. Six major foci of modern nutritional science. These include the actions of nutrients in transcriptional regulation, in signaling pathways, on intra- and extracellular trafficking, in assuring normal development, in the maintenance of antioxidant defense and nutrient/gene interactions. Course Director: Lori Zeltser.

This spring semester course explores a variety of ethical and policy issues that arise during the conduct of basic and clinical scientific research. Course sessions include lectures, discussion periods, and analyses of case studies. Columbia requires that all graduate students share in the discussions of this course. You will hear from your faculty speaking honestly about problems that you may face. You will find the discussions interesting. Course Directors: Arthur Palmer and Jaime Rubin.

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An integrated and critical review of cancer biology, emphasizing recent research. Topics discussed include: natural history and epidemiology of cancer; morphology and behavior of cancer cells; DNA and RNA tumor viruses; oncogenes; tumor suppressor genes; signal transduction; the genetics of cancer; cancer and cellular differentiation; cancer causation: physical and chemical agents; multistage carcinogenesis; hormones, nutrients, and growth factors in cancer. Readings are largely original research papers and review articles. One 2-hour seminar per week. Course director: Richard Baer.

The Course will comprise general lectures, analyses and discussions of primary literature on stem cell and cell lineage specification biology as well as student presentations. The themes to be presented include basic cell and molecular biological characterization of stem cells, regulation of self-replication versus lineage restriction and differentiation of cells, model systems used in studies of stem cells, and the relevance of tissue formation, regeneration and disease states. Course Directors: Stephen Tsang and Dietrich Egli.

Basic Unix, web-site usage, sequence comparison, database searching, multiple sequence alignment, profile methods, secondary structure prediction, mapping, primer design, genomic analysis, and functional genomics including microarray analysis. Course Director: Richard Friedman.

The course emphasizes the molecular control of vertebrate embryogenesis. Divided into three main areas: early embryogenesis, developmental neurobiology, and the development and differentiation of specialized organs or lineages. Course Director: Andrew Tomlinson.

This course focuses on fundamental principles in systems pharmacology and their application. Topics include: the effect of body biochemical processes on the disposition of drugs, including quantitative expression of drug absorption, distribution, metabolism, and excretion (ADME); specific aspects of systems pharmacology, including autonomic and cardiovascular pharmacology, neuropharmacology and toxicology. These lectures deal with both basic principles and current topics within these disciplines. Course Director: David Goldberg.

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The goal of the laboratory rotations is to familiarize students with the research being carried out by the training faculty and to identify a research mentor. Students should note that the research mentor must be a member of the Graduate School of Arts and Sciences (GSAS) faculty and is usually selected from among the NMB training faculty. The approximate schedule for the three rotations is: October through December for the first rotation, January through March for the second rotation, and April through June for the third rotation. Although not encouraged, students may undertake a fourth rotation in July and August. Students are permitted one out-of-program rotation without notifying the NMB Training Committee. Students who wish to undertake a second out-of-program rotation must obtain approval from the NMB Training Committee prior to finalizing the rotation with the proposed mentor.

The level of activity in a rotation is decided upon by mutual agreement between the laboratory director and the student. Typically, a student carries out a well-defined independent research project in the laboratory. It is very important that a clear understanding of obligations on the part of the student and expectations from the mentor be established at the outset of each rotation and that there is constant dialogue between the student and mentor throughout the rotation.

Students complete their Qualifying Examination by June 30th of the second year. Students must select three faculty members to serve on their Qualifying Exam Committee. All three faculty should be members of the Training Faculty of the Nutritional and Metabolic Biology PhD program. At least one member must also be a part of the NMB Training Committee and this member is the de facto Chair. The faculty should have expertise related to the proposed research topic. Students are allowed to request the inclusion of one non-NMB faculty member if their expertise is highly appropriate.

Your Qual cannot be on your thesis research topic, but rather must be “off topic.” Simply put, the core hypotheses and research questions of your Qual must be distinct from those of your thesis research. However, your Qual topic may be tangentially related to your thesis research. For example, if your thesis focuses on the role of a transcription factor in the vascular biology of atherosclerosis, your Qual can be on transcription, vascular biology, and/or atherosclerosis. However, you cannot simply replace your transcription factor of interest with a different one. Approval of a Qual topic is at the discretion of the Qual Committee. Students must write a one-page document describing both their thesis research, their proposed Qual topic, and how the two are distinct from each other.

Students must write a research proposal in the format of an NIH pre-doctoral F31 fellowship application, including Specific Aims (1 page), Research Strategy (6 pages), and Literature Cited. Because this proposal is “off topic,” the preliminary data section of the proposal is de-emphasized. The use of published data to support the premise of the proposal is allowed, if it is appropriately cited. The written proposal should be distributed to Committee Members no less than 2 weeks prior to the Oral Defense.

Students must take the lead in scheduling their Oral Defense with their committee and share the date with PhD Program Coordinator once scheduled. The Oral Defense will consist of a 20–30-minute presentation from the student covering relevant background, the scientific premise of the proposed research, the research aims, the experimental plan, expected results and alternative outcomes. The remainder of the exam will be comprised of questions from the Committee relating to both the written proposal and the oral presentation. The Thesis Mentor will be present, but will not participate in examining the student’s performance, or in voting for a pass or fail in the examination.

Within 6 months of successful completion of the Qualifying Examination, students select faculty to serve on their Dissertation Research Advisory Committee (DRAC) and have the first meeting with the committee. This committee is normally composed of three members of the NMB training faculty, including the student’s mentor, who are knowledgeable in the student’s field of research. The role of the DRAC is to provide direction and guidance for the student’s thesis research. In addition, the committee provides a formal mechanism for evaluating a student’s research progress and professional growth.

Following each DRAC meeting, the student, mentor, and DRAC chair jointly complete a written report on the meeting, which is signed by the student and the committee members. This report, which should contain detailed comments on the research progress of the student and specific recommendations for research to be carried out in the time until the next meeting. The DRAC meets at a minimum every 6-9 months (preferably twice a year).

A carefully selected DRAC that meets regularly with the student assures regular supervision of the research progress and identifies any problems that need to be corrected and stumbling blocks that have been encountered and is a great asset to the student. The members of the DRAC frequently end up constituting part and sometimes all of the final thesis defense committee. Thus, the DRAC truly serves a mentoring and monitoring capacity to guide the student’s research progress. Students should plan to have a ‘final’ DRAC meeting 3-6 months prior to defending.

The doctoral defense will be conducted by a defense committee that is composed of five members. At least three of the members of the final defense committee are from the NMB Training Faculty and at least one of the five must be from outside the NMB program faculty.

Ideally, at the end of the fifth or sixth year the research is completed and the dissertation is defended and deposited with the University.

Although not strictly required, it is strongly recommended that one member of the defense committee serve as the Reader of the thesis. The Reader works with the student and the mentor during the writing of the thesis, before it is distributed to the full committee.

The defense is divided into two parts. The first is an hour long oral presentation of the research findings which is open to the public and is announced in advance. The second part, which follows immediately after the public presentation, is a closed session conducted by the Thesis Defense Committee, and chaired by an NMB faculty member who is not the student’s mentor. When questioning is completed to the satisfaction of the Defense Committee, the student steps outside, while the final decision is discussed. The Defense Committee may rule to award an evaluation of Approved as Submitted, Approved Pending Revisions, Referred, or Fail.

After the defense of the thesis, revisions to the written dissertation are made as needed. Copies of the final version are deposited with the Dissertation Secretary of GSAS, as well as to the Director of the Institute and the theses preceptor.