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Cell Analysis and Modeling Graduate Program

Program Description

The Cell Analysis and Modeling graduate program at the University of Connecticut Health Center offers training leading to a Ph.D. in biomedical sciences. The curriculum for the first year includes a choice of core courses in the basic biomedical sciences that have been specially formulated to acquaint the student with the principles and practice of modern biomedical research. These core courses include Immunology, Genetics, Biochemistry, Cell Biology and Developmental Biology. In addition to these core courses students also participate in the Computational Analysis and Modeling Journal Club and Laboratory Rotations during the first year. During the second year students can choose from advanced courses in a number of topics. In consultation with their advisory committee, students work out a supplementary program of advanced courses, laboratory and computer experiences and independent study based on their previous experiences and interests that is designed to prepare them for general examinations near the end of their second year. All courses are described in the Course Offerings Catalogue found on the Registration page. Thesis research begins in the second or third year, and research and thesis writing normally occupy the third and fourth years.


Guide for Graduate Students


Course Work

Course work requirements are consistent with the current Graduate Program in Biomedical Sciences requirements. The PhD degree requires at least 44 credits beyond the baccalaureate or its equivalent. These credits will be composed of a set of core courses and a number of electives, as outlined below.


Core Courses

At least 15 credits of GRAD 6950 (Dissertation Research) must be included in the Plan of Study, representing the research effort the student devotes to the dissertation.

The Ph.D. course work will be consistent with the standard Graduate School credit requirement for students. The credits required for the Ph.D. may be earned through regular courses which include BMS required and elective courses, journal clubs and lab rotations/independent studies. This includes all courses numbered in the 5300 or 6400 series. Special topics courses may account for 9 credit hours and at least 8 credit hours will typically be from the Cell Analysis and Modeling journal clubs. Additional credit hours should be taken as lab rotations/independent study.

Strongly recommended courses:

MEDS 5380. Cell Biology
Faculty: Cowan
4 credits. Lecture. Prerequisite: MEDS 350.
Basic eucaryotic cell biology. Major topics include: Methods in Cell Biology; Cell Growth and Proliferation; Cytoskeleton; Transport: Hormone Response; Cytoplasmic Organelles and Membrane Structure, Function, Biogenesis, Transport and Sorting; Cell Motility; Chromatin Structure and Organization; and Extracellular Matrix and Cell Adhesion.

MEDS 5382. From Microscope to Model: Quantitative Approaches in Cell Biology
Faculty Rodionov
2 credits. Lecture (Currently listed as Molecular Mechanisms of Signal Transduction).
Modern cell biology builds upon a combination of sophisticated methods of high resolution microscopy and computational approaches to modeling of cell physiological processes in the context of the actual three dimensional structure of individual cells. The objective of this course is to develop a general view on the basic cell biology problems from a multidisciplinary perspective. The participating faculty members will give lectures, advise students on modeling exercises and supervise the microscopy laboratory in the key areas of cell biology and modeling. The following topics will be covered: Dynamics of cytoskeleton; growth control; organelle biogenesis; intracellular trafficking; nuclear transport; regulation of ion channels; cell locomotion; signal transduction. Labs will include hands-on experience in the following microscopy techniques: Fluorescence microscopy of living cells; microinjection; fluorescence recovery after photobleaching (FRAP); fluorescence correlation spectroscopy (FCS); 4D imaging; time-lapse microscopy. Co- or prerequisite: This course is designed to be a companion course with Cell Biology I.

MEDS 6450. Optical Microscopy and Bioimaging
Faculty Yu
3 credits. Lecture/Laboratory.
The course presents the current state of the art of optical imaging techniques and their applications in biomedical research. The course materials cover both traditional microscopies (DIC, fluorescence etc.) that have been an integrated part of biologists’ tool-box, as well as more advance topics, such as single-molecule imaging and laser tweezers. Four lab sessions are incorporated in the classes to help students to gain some hand-on experiences. Strong emphasis will be given on current research and experimental design.

MEDS 6460. Advanced Optical Microscopy and Bio-imaging
Faculty Yu
3 credits. Lecture/Laboratory y. Prerequisite: BME 341.
This course will cover several aspects of state of the art biological and biophysical imaging. We will focus on advanced techniques including nonlinear optical processes (multi-photon excitation, second harmonic generation, and stimulated Raman processes), as well as optical coherence tomography. Three lab projects will supplement the lectures, providing hands-on experience with nonlinear optical methods. Special emphasis will be given to current imaging literature and experimental design.


BME 6150. Computational Cell Biology for Biomedical Engineers
Faculty Wolgemuth
3 credits. Lecture.
In the last decade, interdisciplinary science has established itself as a leading area of scientific investigation. The use of physics and mathematics to help understand biological systems hints at being one of the major scientific frontiers of this coming century. This course looks at biology at three separate length scales: molecular, cellular, and organismal/population. We will find that the math/physics of elasticity, hydrodynamics, statistical mechanics and reaction/diffusion can explain a broad range of phenomena throughout these size ranges. This course stresses the physical intuition of how to apply quantitative methods to the study of biology through the use of dimensional analysis, analytic calculation and computer modeling


MEDS 5351. Biochemistry II
3 credits. Lecture.
This course covers fundamentals of biomolecular interactions and protein structure. Additionally, the course covers the structure/function of select proteins and enzymes essential to the following: metabolic pathways, DNA/RNA transactions, gene expression, cell cycle and signal transduction, and the cytoskeleton.

In addition to the 15 credit hours of Doctoral Dissertation research, students are required to take the Cell Analysis and Modeling journal club associated with CCAM.

MEDS 6497 Journal Club in Cell Analysis and Modeling.
2 credits.
Reading and discussion of research at the interface of physical and cell biological research with emphasis on molecular aspects. Students and postdoctoral fellows present and discuss with faculty a recent paper from the literature.

Trainees in the Cell Analysis and Modeling AoC will also participate in CCAM Group meeting. The weekly CCAM Group Meeting features research updates from all CCAM-associated laboratories. Because this meeting is attended by all scientific personnel associated with the Center, it provides not only scientific continuity but also the social continuity that helps to maintain the unique interdisciplinary focus of the AoC as a whole. Talks at this meeting encompass all research areas, including cell and molecular biology, mathematical modeling, optical engineering, organic chemistry and computational techniques. The diversity of topics makes this a unique learning environment for both trainees and faculty.


Seminar Program, Group Meetings and Journal Club

Students will have access to a diverse set of seminar programs and research meetings. The Center for Cell Analysis and Modeling (CCAM) Seminar Series features invited speakers of international renown. In addition to the main seminar program there is also a “Physics in Biology Seminars” series, and often a single invited speaker will present a seminar in each of these series, the former designed for a cell biology audience and the latter for a more theoretical audience.

 

Elective Courses

Courses available to trainees during the first and second years include all courses in the Biomedical Sciences and Graduate School curricula. As well, the independent study mechanism will be used to alleviate specific deficiencies in a cross-disciplinary area primarily through short, modular study rotations with an identified set of CCAM faculty members. These may be pursued in the first year, for example for students who lack sufficient biology background to successfully complete traditional first year courses, or may be pursued in the second year, for example for students lacking sufficient training in mathematics, physics, or optical engineering.

The electives related to the degree contain computational and/or biophysical methods developed by faculty associated with CCAM and may be also listed in other programs, specifically Biomedical Engineering (BME). These courses are:

MEDS 5327 The Biochemical and Genetic Language of Modern Biology
4 credits. Lecture
This course covers the fundamental biochemical and genetic principles that underlie all areas of modern biology. The biochemistry and genetics of both prokaryotes and eukaryotes and addressed. Reading and discussion of papers in the literature is an important element of the course. Instructor consent required.

BME 5100 Physiological Modeling
3 credits. Lecture. Recommended preparation: BME 3100 and BM 3400 (or equivalent).
Unified study of engineering techniques and basic principles in modeling physiological systems. Focuses on membrane biophysics, biological modeling, and systems control theory. Significant engineering and software design is incorporated in homework assignments using MATLAB and SIMULINK.

MEDS 5378 Computational Neuroscience
3 – 4 credits
Students study the function of single neurons and neural systems by the use of simulations on a computer. The course will combine lectures and classroom discussions with conducting computer simulations. The simulations will include exercises and a term project. Each student will complete a term project of neural simulation to be developed during the second half of the semester. The topic of the term project should be approved by the instructor by the middle of the semester. The grade will be based on the exercise and the term project.

BME 5800. Bioinformatics
3 credits. Lecture. Recommended preparation: BME 4800 (or equivalent).
Advanced mathematical models and computational techniques in bioinformatics. Topics covered include genome mapping and sequencing, sequence alignment, database search, gene prediction, genome rearrangements, phylogenetic trees, and computational proteomics.

BME 6140. Cellular Systems Modeling
3 credits. Lecture. Prerequisite: BME 5600.
Cellular response to drugs and toxins, as well as normal cell processes such as proliferation, growth and motility often involve receptor-ligand binding and subsequent intracellular processes. Focuses on mathematical formulation of equations for key cellular events including binding of ligands with receptors on the cell surface, trafficking of the receptor-ligand complex within the cell and cell signaling by second messengers. Background material in molecular biology, cell physiology, estimation of parameters needed for the model equations from published literature and solution of the equations using available computer programs are included. Examples from the current literature of cell processes such as response to drugs and proliferation will be simulated with the model equations.

MEDS 5325. Practical Applications of Sequence Analysis
2 credits. Lecture.
Provides an understanding of how to analyze genetic sequence information by computer. Includes basic analyses such as restriction mapping and detection of coding sequences, to more advanced analyses such as sequence similarity searching, sequence comparisons and multi-sequence alignment, prediction of functional motifs from primary sequence information, and current tools for mapping, assembly, and analysis of genomic sequence information. The course emphasizes NCBI and other Web-based tools currently available for use. Students will be exposed to the Genetic Computer Group (GCG) series of sequence analysis programs, but these are not emphasized. Students are required to complete a series of computer-based exercises to demonstrate proficiency in the application and use of the various computer programs presented in class

BME 6110. Computational Neuroscience
3 credits. Lecture.
Explores the function of single neurons and neural systems by the use of simulations on a computer.
Combines lectures and classroom discussions with conducting computer simulations. The simulations
include exercises and a term project.

The following faculty will be responsible for the subsequent list of courses: Blinov, Carson, Cowan, Huber, Loew, Mayer, Mohler, Moraru, Rodionov, Schaff, Schiller, Slepchenko, Wolgemuth, and Yu.

MEDS 5395. Independent Study
1-6 credits. Independent Study.

MEDS 6495. Independent Study
1-6 credits. Independent study.
A reading course for those wishing to pursue special topics in the biomedical sciences under faculty supervision.

MEDS 6496. Laboratory Rotation
1-6 credits. Laboratory.

MEDS 6497. Graduate Seminar
1-6 credits. Seminar. May be repeated for credit with a change of content. Reading and discussion of recent research developments in various areas of biomedical science.

GRAD 6950. Doctoral Dissertation Research,
Variable credit. Hours by arrangement

GRAD 6998. Special Readings (Doctoral).
Noncredit. Continuing registration for doctoral students prior to reaching candidacy.

GRAD 6999. Dissertation Preparation.
Noncredit. Continuing registration for doctoral candidates.


Advisory Committee

First year students generally enter the biomedical sciences program uncommitted to a specific AoC and are each assigned a first year advisory committee by the Associate Dean of the Graduate School at the Health Center. Once a thesis research laboratory has been chosen (typically at the start of the second year), a thesis advisory committee is formed after consultation between the student and the major advisor. It includes at least two associate advisors. The major advisor and at least one associate advisor are members of the graduate faculty appointed to advise Ph.D. students in the student’s field of study and AoC. One associate advisor may be chosen from outside the University in accordance with Graduate School procedures.


Plan of Study

The student must prepare a Plan of Study that must be approved by the advisory committee and the Executive Committee of the Graduate School. The plan will specify all formal courses which are to be completed, the scheduling of the General Examination, and the general area of the thesis research. The Plan of Study must gain the approval of the student’s advisory committee before the General Examination can be taken.


General Examination

The general examination is taken near the end of the student's sequence of formal courses, as contained on the Plan of Study. There will be both a written and oral examination. No fewer than five faculty members, including all members of the student’s advisory committee, participate in the examination. No fewer than five faculty shall be invited to submit questions and to evaluate the student's answers.

For the Cell Analysis and Modeling AoC, the examination will be set by the executive committee of the AoC with approval by the Graduate Programs Committee at UCHC. Initially the examination will consist of the preparation and defense of a research proposal, following the format of the NIH National Research Service Award (NRSA).


Dissertation Proposal

 

As the student reaches the point of undertaking the major part of the dissertation research, he or she prepares a proposal (10 pages in length) that is composed of several parts. These include the background and context of the proposed topic, a description of the work to be done, and the methodology through which it will be accomplished. The thesis committee typically reviews the proposal, followed by the Graduate Programs Committee. It is finally approved by the GFC Executive Committee.


Candidacy

Upon approval of the Plan of Study, passing the General Examination, and having had the Dissertation Proposal fully approved by the Executive Committee of the Graduate Faculty Council, the student becomes a candidate for the degree of Doctor of Philosophy. Students are notified of their advancement to Candidacy.


Dissertation

A dissertation representing a significant contribution to ongoing research in the candidate’s field is required. The advisory committee gives final approval of the dissertation following the final examination.


Final Examination

The final examination is oral and under the jurisdiction of the advisory committee. It deals mainly with the subject matter of the dissertation. Invitation to participate in the examination will be issued by the advisory committee, although members of the faculty may attend. No fewer than five members of the faculty, including all members of the candidate’s advisory committee, participate in the final examination.


  
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