PhD Program Curriculum
The Molecular Medicine Graduate Program in Biomedical Sciences is designed to provide our students with an initial exposure to the world of biomedical research followed by specific training and a PhD in one of our degree departments, all in preparation for careers in modern biomedical research. Our program begins with two years of didactic course work with a first year of rotation through three research laboratories. By late April of the first year, the student is expected to choose a mentor and a department. During the second year of course work, the student works with the mentor and prepares for the departmental qualifying examination. Throughout their course of study, students participate in monthly Research in Progress dinners and may also participate in Journal Clubs as required by their department or training grant.
Once students have a mentor and a degree department, they will follow the departmental schedule for advancement to candidacy. On the basis of performance in course work, research rotations, and the qualifying examination, the student is evaluated for advancement to candidacy. After passing their qualifying exams (advancement to candidacy), students concentrate on conducting independent research under the guidance of the mentor and research committee. The culmination of the research endeavor is a written dissertation that is defended orally before a faculty committee. The training experience leads to the awarding of a PhD in four to five years, granted by the department chosen by the student when the mentor was selected.
The Training Program, through the graduate mentor and department, guarantees financial support for all MolMed students in good standing throughout their course of study. This support includes payment of a stipend (or wage), remission of tuition and fees, and personal health insurance. The student's progress through the program is guided at all times by a committee of faculty advisors. Details of each aspect of the training experience are provided in this document, as are details of financial responsibilities of the Program and participating faculty. Graduate Advisory Committee:
First year students are expected to meet on a regular basis with the MolMed Graduate Advisory Committee, who will 1) be appointed upon entry into the program and 2) guide your progress throughout the training program. The chair of the Advisory Committee will require that you frequently submit an updated student profile to be kept on file.
First year students will participate in the summer Molecular Medicine Journal Club. This is an opportunity for all students in all years of the program to learn both how to critically evaluate an important paper and how to present a seminar. Papers are chosen for their relevance, quality of science, and novelty. Students are encouraged to seek out help from faculty members with which they have not yet had the opportunity to interact. Fellow students analyze presentations to provide feedback on how to improve future presentations. Additional non-directed journal clubs (Cardiovascular, Cancer, Pharmacology) are part of continuous training in later years.
Available Journal Clubs:
* Cell and Molecular Biology (CMB) journal club - BIMS 8150
Research talks by students supported on CMB training grant
* Biophysics journal club - BIOP 8050
Presentation by students of papers chosen by students
* Pathology journal club - PATH 8050
Disease focused, discussion based, with topics linked to upcoming seminar presentations
Colloquium in Human Disease Research
* Pharmacology journal club - PHAR 8110
Disease of the Month - faculty mentored with 3-4 student presentations per disease
* Immunology journal club - BIMS 8350
Current topics in immunology
* Microbiology journal club - MICR 8810
Broad based topics - faculty mentored/ student presentations
* Cell Current Topics journal club - CELL 5950
Topics selected to be complimentary to cell course - group presentations by students
The rotation consists of an approximately 8 week period wherein the student temporarily joins the research laboratory of one of the mentors in the MolMed training program. Many of our mentors have provides information on their research and possible rotation experiences in this booklet. Three rotations are normally performed before choosing a mentor. Students may petition the graduate committee to perform one of three rotations with a faculty member who is not a member of the training program faculty; however such faculty must be members of the Graduate Faculty of the University. The purpose of the rotation experience is to acquaint the student with a particular area of research, a particular laboratory setting and/or a potential mentor.
Students are required to submit a 1page description of each laboratory rotation to the Director of the graduate program for inclusion in their files. In cases where a student has extensive research experience (e.g., as a full time laboratory technician), s/he may petition the graduate committee to have this experience considered as a single laboratory rotation. Likewise, students may petition the graduate committee to perform an additional (fourth) rotation.
Student/Mentor Luncheons are a way to find out about Faculty research and techniques:
* Student/Mentor Luncheons: In the Fall of your first semester a weekly luncheon is provided, during which you will meet members of the Training Program Faculty giving you an opportunity to hear a brief description about the research and techniques performed in their laboratories.
You should contact Faculty via telephone or email to arrange for individual appointments to discuss a possible lab rotation.
During the Fall and Spring Semesters, research scientists are brought in from Academia and Industry to give seminars on their research. It is expected that you will attend our seminars whenever they are offered. Selected groups of students will meet with each seminar speaker over lunch to discuss research. This interaction is made more valuable when the attendees have familiarized themselves with the speaker's research activities prior to the luncheon.
We trust that each student will benefit from our seminar series. It is our aim to introduce students to different areas of research and to make contact with researchers from around the globe. Choosing a Mentor :
Dissertation research mentors are to be chosen from among the faculty participating in the training program. Potential mentors are listed on the web site under their primary area of research interest.
Mentor/student partnership is by mutual agreement and is subject to approval by the Program Director in consultation with the graduate committee. The student is expected to have decided on a mentor and been accepted into his/her laboratory by the end of the first year of study, or no later than April 20th. The mentor acts as chair of the student's research committee (see Research Committee) and provides the primary funding for the student's continued study. Original Research:
Students concentrate on executing an original research project under the guidance of their preceptor and research committee. The student's research is expected to advance some field of biomedical sciences. As evidence of this level of achievement, the Training Program expects that students will sign research papers, including some as first author, and these papers will appear in recognized, peer-reviewed journals. Some departments may have additional suggestions or requirements. Qualifying Examination:
After choosing a preceptor, students are required to take and pass the degree granting department's qualifying examination. The student should check with the degree granting department for more information on these requirements. Research Committee:
On successfully Advancing to Candidacy, a research committee, chaired by the mentor, and consisting of 3-4 additional graduate faculty members is formed and guides the student in executing the research project. Members of the research committee are selected in consultation with the mentor and usually have expertise in a particular area of the student's dissertation research. At least one member of each research committee will be a sitting member of the Graduate Committee. The first meeting of the student with their research committee should include a presentation by the student of his/her expected research project. Students are required to meet semi-annually (in December and June) with their committee throughout the course of their training. A committee report should be completed, signed and submitted to the Training Program Director after each meeting.
YEAR 1: Core Courses
8 weeks prior to Fall Semester:
* 1 Lab Rotation (non course activity)
* BIMS 5030 Macromolecular Structure and Function
* BIMS 8010 Gene Structure, Expression and Regulation
* BIMS 5120 Cell Structure and Function
* Pharmacology or Pathology Journal Club
* BIMS 8619 Molecular Medicine Colloquium (weekly attendance of any seminar series)
* Research in progress (RIP) Meetings (mandatory attendance)
* BIMS 8320 Graduate Physiology
* 2 Lab Rotations (non course activity)
* Pharmacology or Pathology Journal Club
* Research in progress (RIP) Meetings (mandatory attendance)
* Molecular Medicine Colloquium
Your second year courses will be directed by departmental requirements since you will have selected a mentor and degree program at this point.
YEAR 2: Elective Courses
Selection of 4 additional courses:
~ Either 2 core courses not taken previously and 2 electives or all 4 from following electives ~ ONE must be a disease-related course (***) No more than TWO of the additional FOUR can come from outside of these listings.
(NOTE: Class numbers just changed to 4-digit codes, this page will
be updated soon)
* BIMS 5030 Macromolecular Structure Determination (S)
* BIOP 803 Magnetic Resonance Spectroscopy of Macromolecules (S)
* BIMS 803 Fundamental Immunology (S)
* BIMS 824 Chromatin Structure and Function (S)
* BIMS 8131 Pt 1 Molecular Basis of Human Disease (F) ***
* BIMS 814 Pt 2 Molecular Basis of Human Disease (S) ***
* BIMS 852 Vascular Biology (S) ***
* MICR 815 Molecular Basis of Carcinogenesis (S) ***
* PHAR 9010 Human Pharmacology (S)
* PHAR 9020 Molecular Characterization of Drug Targets (S)
PATH 8620 Advanced Topics and Technologies in Cell Signaling
All courses must be completed spring of year 2 Year 3 & Beyond:
Fall and Spring Semesters:
* Non-topical research, 12 credits
* Non-topical research, 6 credits
Although, you do not formally register for Journal Club and the Department Colloquium courses, attendance is required.
BIMS COURSE DESCRIPTIONS
* BIMS 5030 (4 credits) Fall
Macromolecular Structure & Function
A survey of current knowledge and methods for understanding structure-function relationships in Biological molecules, particularly proteins. It is not a general Biochemistry course; Bioch 503 focuses on aspects of protein structure and function that are fundamental to research in Biochemistry, Molecular Biology, Physiology, and Pharmacology. The course complements similar research-focused courses in Molecular Biology and Cell Biology. Topics covered include: biochemistry of the amino acids, protein secondary structure, protein evolution, tertiary structure and protein folding, kinetics, DNA-protein interactions, protein-protein interactions, protein modification, selected catalytic mechanisms, quaternary structure, and structure and function of large macro-molecular complexes.
* BIMS 5120 (5 credits) Fall
Cell Structure & Function
A graduate course in molecular cell biology examining the functional organization of eukaryotic cells and the interactions of cells with their surroundings. The coverage of the material begins with the general and rapidly advances to the specialized with emphasis on biological membranes, cell adhesion, the cytoskeleton, mitosis, the cell cycle and cell signaling. The course utilizes a combination of textbook readings and original literature.
* BIMS 8010 (5 credits) Fall
Gene Structure & Expression
This course is an in-depth look at the "central dogma" of molecular biology: DNA goes to RNA goes to protein. The course starts with the properties of nucleotides and nucleic acids, and advances to the composition and structure of eukaryotic chromatin. Then the basic processes underlying eukaryotic gene expression are presented: DNA replication, RNA transcription, RNA splicing and metabolism, and protein translation. The course ends with a survey of gene expression from the prokaryotic point of view. The course is divided into seven sections by faculty representing the Departments of Microbiology, Biochemistry, and Pharmacology. This is an advanced graduate course with an emphasis on reading important papers from the primary literature along with presentation of basic concepts of biochemistry, genetics, and molecular biology. The course meets three days a week for 90 minutes.
* BIMS 8320 (5 credits) Spring
Studies selected topics in cellular physiology, including the physiology of the human cardiovascular, respiratory, digestive, renal, and endocrine systems. Emphasizes the cellular mechanisms involved in the functions of the various organ systems, the roles of the organ systems in homeostasis, and the control of the organ systems by neural and hormonal mechanisms. Lectures, discussions, and clinical correlations.
* BIOC 508 (3 credits) Spring
Computer Analysis of DNA and Protein Sequences
* BIOP 8020 (3 credits) Spring
Macromolecular Structure Determination
MSD treats the theory of X-ray scattering and focuses on the application of X-ray diffraction to macromolecular crystallography. Related topics (e.g., low angle scattering, electron diffraction, nuclear magnetic resonance spectroscopy, determinants of protein structure) provide a basis for interpretation of the crystallographic results. Cross-listed with PHY 810.
* BIOP 8030 (3 credits) Spring
Magnetic Resonance Spectroscopy of Macromolecules
The course focuses on the application of NMR spectroscopy to protein structure determination. Topics include classical and quantum description of NMR, density matrix theory and relaxation mechanisms, multi-dimensional homo/heteronuclear NMR, pulse sequence design, structure calculation from NMR data, molecular dynamics calculations. Two additional lectures each are devoted to solid-state NMR and EPR.
* BIMS 8
Introduces cellular and molecular immunology, emphasizing antigen-specific immune responses. Topics include structure of antigens and antigen recognition structures, development of immunologically competent cells, cell-cell interactions and signaling, development and regulation of different immune responses, and the relationship of basic immunological mechanisms to the control of disease and immunopathology.
* BIMS 824 ( credits) Spring
Chromatin Structure and Function
* BIMS 8052 (3 credits) Spring
Prerequisite: One course in mammalian physiology and one in cell biology.
A broad interdisciplinary course considering the basis for vascular function from a physiological and pathophysiological perspective. Topics include basic microcirculatory function, smooth muscle and endothelial cell function and development, capillary exchange, inflammatory processes, leukocyte endothelial cell interactions, and the pathophysiology of atherogenesis. Topics such as vascular control, angiogenesis, and inflammatory responses of the cardiovascular system will be highlighted.
* MICR 815 (4 Credits) Spring
Molecular Basis of Cancer
Advanced presentation of the mechanisms of oncogenesis, including discussions on phenotypes of tumor cells, regulation of cell cycle, oncogenes, anti-oncogenes, RNA and DNA tumor virus, tumor progression, and metastasis. Emphasizes mechanisms of proto- oncogene activation, subversion of normal growth control, and inactivation of tumor suppressors which occur in human tumors.
* PHAR 9010 (4 credits) Fall
Graduate Pharmacology course which provides a knowledge of systems-based drug intervention. Lectures emphasize the pharmacological properties of drug classes and their use in common human diseases. Discusses major issues associated with the use of these drugs and requires a familiarity with the assigned materials.
* PHAR 9020 (4 credits) Spring
Molecular Characterization of Drug Targets
Studies the biochemical and molecular aspects of the transmembrane signaling mechanisms that are known targets for important classes of clinically useful drugs. Covers potential drug targets in diseases such as cancer. Emphasizes current knowledge of important signaling mechanisms and examples of the research leading to the design of important therapeutic agents. Focuses on how an important drug target can be identified and exploited
Advanced Topics and Technologies in Cell Signaling
This course uses contemporary literature in the field of cell signal transduction
as a foundation for student driven discussion. Particular attention will be paid to an understanding of
techniques and experimental approaches applied to the study of cell signaling. Each class session will
focus on a particular signaling pathway. Pre-assigned papers will include 1 general review for
background and 2-3 research papers. Understanding of the specific signaling pathways will share
emphasis with critical examination of the work, with a focus on discussion of the chosen approach and
comparison with possible alternatives. (Offered every other year, in the Spring)