Pathobiology and Mechanisms of Disease

This fall semester required for all first year students course covers basic biochemical and experimental principles, such as protein and nucleic acid structure and chemistry, thermodynamics and enzyme kinetics, and bioinformatics. Also included are biochemical processes common to all cells such as genome replication and repair, regulation of gene expression, cell cycle control, and cell membrane and receptor biochemistry. Course Director: Stavros Lomvardas.

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.

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.

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.

This spring semester course provides an introduction to the basic statistics commonly used in biomedical research laboratories. Students are provided with a statistical software package for use during the course. Exercises based on relevant experimental data sets use the software to reinforce the lecture material. Topics covered include the role of statistics in biomedical research, principles of statistical analysis, and selecting and applying the appropriate statistical tests. Course Directors: Arthur Palmer.

This fall semester required for all first year students course covers aspects of molecular biology and genetics from prokaryotes to mammals; regulation of gene expression, molecular genetics of bacterial viruses, plasmids and transposable elements, as well as modern molecular genetic approaches to complex biological phenomena. Format: four to five hours of lecture and discussion per week. Course Director: Jonathan Dworkin.

This course will focus on the practical aspects of using a microscope and of applying histological procedures to recognize cell types and tissue/organ organization. The aim is to assist students in acquiring basic knowledge for analyzing tissues & organs and diseases related to these tissues & organs for application in their graduate research. Each session will consist of didactic/lecture, microscope work and/or analysis of unknown samples. Student discussion and participation is necessary and assigned reading has to be done prior to class. Course Directors: Ann-Judith Silverman and Ronald Liem.

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.

During orientation, all the first year graduate students in all the different program attend a mini-course that explains how to establish the framework for an experimental project, how to set up a system, design experiments within that system, and how to determine and use the correct set of controls. This course also covers an introduction to rigor and reproducibility in experimentation that is necessary for all the students. Students also get mandatory training in Laboratory Safety, an orientation on sexual violence and response, as well as discrimination, harassment, and gender-based misconduct policy. Students also get a lecture on Responsible Conduct of Research (RCR), where they will also receive the publication "On Being a Scientist," as well as Columbia University's institutional RCR policy.

To select a rotation, the incoming students should study the website to determine with which faculty members they may be interested in doing a laboratory rotation. The Program Director (PD) meets with each student individually to discuss his/her rotation choices and provides extensive input on the selection of the rotation. At the end of the rotation, the PD receives written evaluation from faculty mentors, and discusses the evaluation with the student to examine problems that may have arisen and how they can be addressed.

During the second year, students prepare for their qualifying examination. This examination is used as a formal evaluation of the student's potential as a candidate for the Ph.D. degree. It is designed to assess the student's ability to develop a sophisticated, in-depth understanding of their thesis project and it also serves as a tool for identifying deficiencies in the students' background that could be remedied by further coursework or additional reading.

During the fall of the third year, the students have their first meeting with their Thesis Committee. The Thesis Committee is typically the same as the qualifying examination committee, although occasionally one of the members might be replaced, especially if the student's research is going in a different direction. This Committee provides scientific expertise related to the student's projects and monitors thesis research. For the first Committee meeting that is held either in the spring or summer of the second year, the student presents a short written report that contains the Specific Aims of their proposal and any progress they have made since the qualifying examination. The Committee discusses with the student the progress to date and the priorities for the order in which the work will proceed, as well as the chosen design of experiments. It is possible that the Committee may recommend changes to the experimental design or priorities. The Committee also decides when to have the next meeting, which can be either in 3, 6 or 9 months, but no longer than one year. For these subsequent meetings, the student prepares a 1-2 page report outlining their progress on the previous aims and presents their timetable for finishing their thesis work. The Committee can and should recommend improvements to experimental strategies and fallback plans for difficult or risky experiments.

After the thesis committee gives its approval for the student to finish writing the thesis, the defense is scheduled. The final thesis committee consists of the mentor, three existing thesis committee members, and one additional examiner. If the additional examiner is outside the University, they have to be approved by the Program and the Dissertation Office as a competent examiner. The thesis should be submitted to the committee two weeks before the scheduled defense. A public presentation is given immediately before the closed defense. At the time of the closed defense, the student may be asked to make additional revisions that will then need to be approved by the mentor and one other member of the committee (assigned at the time of the defense.) On rare occasions, the student may be required to do additional experimental work, extensive thesis revisions or a second dissertation defense. Students are required to submit a first author paper before their defense.