Department of Biochemistry and Molecular Biology

Section Contents
Requirements for Admission | Course Requirements for the M.S. Degree | Course Requirements for the Ph.D. Degree | Conversion from M.S. to Ph.D. Degree | Major Areas of Training | Course Descriptions | Faculty Research Interests

Requirements for Admission
The Department of Biochemistry and Molecular Biology offers programs leading to the M.S. and Ph.D. degrees. The Department is primarily located on the 5^th and 7^th floors of the Basic Science Building, which is immediately adjacent to the Library Administration Building. To us, mentoring graduate students with the incentive to innovate, discover, and challenge tradition is considered the very best application of the resources of the Department of Biochemistry and Molecular Biology. Students in our Department present a seminar once a year, and they are encouraged to attend and present their data in national and/or international meetings. Applicants to the biochemistry program must fulfill all requirements outlined by the College of Graduate Studies. They must have completed all requirements for a major in either a physical or biological science at the bachelor’s level prior to entering a degree program. General information about admission to the Graduate School at MUSC can be obtained at: http://www.musc.edu/grad/admissions. Applicants apply online at http://academicdepartments.musc.edu/em/admissions/apply.htm. Please make sure you select “Biochemistry” if you are interested in our Program of Study. Students who select the Department of Biochemistry and Molecular Biology for the graduate studies should have a strong background in biological sciences. Undergraduate training in organic chemistry and biology are advantageous. For more information regarding the program, students are encouraged to contact Dr. Maurizio Del Poeta, Director of the Graduate Training Program in the Department of Biochemistry and Molecular Biology at delpoeta@musc.edu, (843) 792-8381.

Course Requirements for the M.S. Degree
The course requirements for the M.S. degree are the same as listed below for the first year of the Ph.D., except that only one of the following courses is required:  Comprehensive Biochemistry (BMB-601), Molecular Basis of Medicine (BMB-610), or Bio-Organic Chemistry (BMB-753).  One additional course, a minimum of four credit hours, is required in subsequent years.

Course Requirements for the Ph.D. Degree
A typical course of study for the Ph.D. in Biochemistry is outlined below.  A student enrolled the Biochemistry and Molecular Biology Program must take a total of 12 credit hours between the first day of their second year and their dissertation day.  Given the multi-disciplinary areas of research available in the Department of Biochemistry and Molecular Biology, it is the responsibility of the student and his/her mentor to choose which courses are most appropriate for the student.

First Year
Basic Biomedical Science - Core curriculum. There are two main elements in the first year of graduate study at MUSC: a core curriculum and laboratory rotations. The core curriculum is offered by the College of Graduate Studies and provides molecular and cellular foundations in biomedical sciences. During the first year, students participate in a program of laboratory rotations. These laboratory rotations serve to expose the students both to new experimental methods and techniques. At the end of the first year, students choose the laboratory they wish to affiliate with for the rest of their program at MUSC.

Second Year
The principal events occurring during this year for a graduate student in Biochemistry is the selection of the Thesis Committee, the initial committee meeting, and the Written Qualifying Exam. The thesis committee is chosen at the beginning of the Spring semester, after consultation among the student, the student’s advisor, and the Chair of the Department or the Graduate Coordinator. The thesis committee consists of the advisor plus four (4) additional faculty, one of whom should be outside the department. The first committee meeting takes place before May 1st of the second year. The overall purpose is to acquaint the faculty members with the student and the student’s proposed research project. After the completion of the second year and before starting the third year, students take the Written Qualifying Exam. The Written Qualifying Exam is administered by the Graduate Training Committee of the Department of Biochemistry during the first or second week of June. The objective of the examination is to determine whether the student understands the principles of biochemistry and molecular biology, can read and comprehend relevant literature related to the question, and then synthesize a coherent response convincing the committee that the student has a solid background in biochemistry and molecular biology. Among four/five questions formulated by the graduate training committee members, the students will need to answer two of them, in a period of one week. In case of failure passing the written qualifying, the student may be permitted to retake the exam in not less than one month and not more that one year from the time the decision was made. Failure of the second examination will result in the termination of the student’s Ph.D. program.

Third Year
During the third year, students take the Oral Qualifying Exam, administered by the thesis committee. The Oral Qualifying exam must be taken within one year from the Written Qualifying Exam. The student will submit a research proposal in a NIH grant format on his/her research topic. The research proposal must be submitted to each member of the thesis committee at least one week before the oral defense. The examination will include a public presentation of the research project followed by general questions from the audience. Subsequently, a closed session with the student, the thesis committee members and other program faculty who further wants to question the student on the research proposal or/and on general knowledge will follow. The students in the second year are strongly encouraged to attend the oral defenses of their fellow students in order to get an idea of what it is expected. Guidelines for the written proposal following NIH format are available in the Director’s office.

After passing both written and oral qualifying exams and approval of the research proposal, the student will be certified as a candidate for the Ph.D. degree. Such admission to the candidacy must occur at least one year prior the completing requirements for the degree.

Fourth/Fifth Year
During the fourth and subsequent years of graduate study in biochemistry, students are primarily responsible for conducting their research. A dissertation based on original investigation is required, which gives evidence of mature scholarship and critical judgement, indicates knowledge of research methods and techniques, and demonstrates the ability to carry out independent investigation. Publication of doctoral dissertation is required of all students. After your mentor has approved your written dissertation, it should be submitted to each of your Thesis Committee members. The Thesis Committee requires 7-14 days to review your dissertation before they sign the Dissertation Defense Notice certifying that it is ready to defend. The Dissertation Defense Notice needs to be turned into the Graduate Office at least two weeks before the scheduled public defense. In other words, students must give the written dissertation to the thesis committee at least one month before the dissertation date. On the dissertation day, the candidate is required to present his work in a public seminar. Following this presentation of 30-40 minutes, general questions are taken from the audience which includes students and faculty members of the Biochemistry graduate program as well as general graduate faculty. After general questions, a closed session is conducted by the student’s thesis committee and graduate faculty. The thesis committee will have the primary responsibility for evaluating the student’s research including the written dissertation, the formal oral presentation,  handling of questions, and for administrating the final oral examination. Approval of the thesis committee with no more than one dissenting vote is necessary for awarding the Ph.D. degree. In the event of disapproval, the candidate may be permitted to retake the examination in not less than six months and not more than two years from the time this decision was made. Only one opportunity for re-examination is given.

Conversion From M.S. to Ph.D. Degree
With the agreement of their Advisory Committee, the Graduate Training Committee, and the Graduate Council, M.S. students may convert to the Ph.D. program. M.S. students wishing to take required courses for the Ph.D. degree may do so, if desired, before formally converting. Failure of the Ph.D. qualifying examination by a M.S. student will not prejudice the awarding of a M.S. degree. However, the same rules will apply with respect to the Ph.D. degree as apply to a Ph.D. student who fails a qualifying examination.

Major Areas of Training
The Department of Biochemistry offers an interdisciplinary research program with a variety of disciplines (cardiovascular diseases, cancer biology, genetics, pharmacology, endocrinology, inflammatory and infectious diseases, and immunology).  Particular topics under study in Biochemistry Faculty’s labs include: pathogenesis of hypertension, gene therapy in cardiovascular diseases, mechanisms of initiation and termination of DNA replication, biochemistry of the eye and pathological vision processes, folate metabolism and carcinogenesis, cancer immunotherapy, molecular mechanisms of apoptosis, sphingolipid-mediated apoptosis, anti-cancer role of ceramide, sphingolipids’ turnover and cellular regulation, sphingolipid-mediated fungal pathogenesis, sphingolipids as new targets for antifungal development, sphingolipid hydroxilation, biochemistry of anticancer agents, lipid-protein interactions, protein-RNA interactions, protein chemistry, biochemical evolution, serpin regulation of gene expression, lipid chemistry, lipid metabolism, connective tissue, collagen metabolism, marine genomics, shrimp antimicrobial peptides, mechanism of drug-induced gene amplification, and X-ray crystallography to determine the structures of medically important macromolecules.

Faculty Research Interests
Faculty research interests can be found on the web at http://biochemistry.musc.edu/faculty.htm.

Biochemistry Course Descriptions
Fall Semester
BMB-753. Bio-organic Chemistry. A systematic study of the electronic and structural properties of biomolecules and their function as a result of these properties. The material represents a natural extension of the principles of both organic chemistry and biochemistry. Protein chemistry, enzyme mechanisms and cofactor functionality are among the topics covered. Prerequisite: basic organic chemistry. 4 s.h. Fall.

BMB-610. Molecular Basis of Medicine. 10 s.h. Fall.

BMB-601. Comprehensive Biochemistry. An in-depth course emphasizing the basic metabolic reactions of living systems. 3 s.h.

Spring Semester

BMB 702. Contemporary topics in Biochemistry: Molecular Basis of Apoptosis. This course introduces students to one of the fastest growing fields of modern molecular/cellular biology. The primary focus of this course is to provide a current overview of the apoptotic pathways and the involvement of apoptosis in the maintenance of cellular homeostasis and in pathological states such as cancer, ischemia, and degenerative diseases.  Students will also be introduced to the current techniques involved in apoptosis detection and in the characterization of the different components of the apoptotic pathways. Students will be given opportunities to discuss with their peers the latest findings in the apoptosis research in the form of a journal review. Note: Depending on the number of students enrolled, this course will be offered either annually or bi-annually. 3 s.h.

BMB-605. Molecular Foundations of Medicine. BMB-605 consists of BMB-605A, BMB-605B, BMB-605C, BMB-605D, and BMB-605E.  Only one of these courses will be offered each year. Please see below for each course description. 3 s.h.

BMB-605A. Mechanism of Aging and Life Span. Many pathological processes have become amenable to study using the various tools and approaches of biochemistry, molecular biology, genetics, chemistry, and bioinformatics.  This is perhaps best illustrated in the study of aging. After decades of little progress, it is now apparent that fundamental processes regulate lifespan of organisms ranging from yeast to Caenorhabditis elegans, to Drosophila, to mice, and, by extension, to humans. These common mechanisms involve transcription factors, insulin-like signaling, lipid signaling pathways, and telomerase. Disorders in these pathways result in disturbances in lifespan, and in some cases in human diseases.

This course will provide the students with the necessary foundation in understanding the various models employed for the study of aging and lifespan. The course will rely primarily on original literature and in-depth discussion of key foundation papers. The discussion will be led by expert faculty who will introduce each topic and provide the students with the necessary foundations.

BMB-605B. Mechanisms of Cancer Pathogenesis. The abnormal behavior of neoplastic cells can often be traced to alterations in cell death and apoptosis. Lipids, in particular sphingolipids such as ceramide, represent the major regulatory mechanism of the apoptotic process.

This course will provide the study of lipid metabolism and lipid cell signaling mechanisms involved in the transformation process, the study of altered levels of specific growth factors, intracellular processes for conveying lipid membrane signals to the nucleus, portions of the transcription apparatus, and genes involved in the cell cycle and the regulation of DNA replication

BMB-605C. Mechanisms of Inflammation. One of the emerging areas of research is the understanding of the mechanism involved in the inflammation process. In particular, bioactive molecules produced by immune system cells are involved in inflammatory diseases such as rheumatoid arthritis, sepsis, asthma, inflammatory bowel disease, and atherosclerosis.

This course will provide a study of mechanisms leading to and maintaining the inflammation process, such as dyslipidemia, the leading cause of the inflammation process that leads to the atherothrombotic disease, and the oxidative stress, the pathological factor responsible for this damage. In addition, the course will focus on a variety of stimuli, such as mechanical, anoxic, chemical (e.g. oxidized LDL), immunological or infectious ones, that are responsible for activation of the endothelium. Finally, the course will also examine how many infectious agents regulate the inflammation process, leading either to the control of the infection or the development of infectious disease, depending on the cross talk between the host and the pathogen.

BMB-605D. Pathogenesis of Diabetes. Diabetes is the most common disease in developed countries. Understating its pathogenesis will potentially improve new therapeutic interventions. The role of a particular life style as well as inflammation and autoimmunity have been implicated as crucial factors for the development of diabetes.

This course will discuss the molecular mechanisms by which obesity, dyslipidemia, hyperglycemia, inflammation and autoimmunity can lead to the development of diabetes. 
 
BMB-605E.  Autophagy and Human Disease. Autophagy is a cellular process in which the cell self-digests its own components to recycle nutrients and to eliminate unnecessary or damaged proteins and organelles. Recent studies have demonstrated the fundamental importance of autophagy in health and disease.  Participants will be introduced to the historical overview of the field, the current knowledge on the molecular and cellular mechanisms of autophagy, and how autophagy plays a role in various aspects of human pathophysiology. The discussion topics include autophagy in stress response, infectious diseases, cancer, and neurodegenerative diseases.

7-week course meeting 9:00-11:00 BSB 553 - March-April, 45 contact hours.

Grade based on class participation (25%) and outside assignments (75%). Outside assignments include written review of scientific manuscripts (40%) and presentation of paper in class (30%); Merit-based. No minimum number of students; Open to M.S. and Ph.D. students. Spring

Other Courses

BMB 607-02. Biochemistry Journal Club. Students provide relevant background papers before class and then present his/her own data during the session. This will be a chance for Biochemistry students to get together to discuss their own research projects, while getting to know each other and learn about the projects going on in the department.

BMB-705-01. Principles of Computing and Algorithms for Bioinformatics.  This course introduces students to the principle of scientific computing and common algorithms in bioinformatics. It covers the following topics: algorithms and computational complexity, design principles computing algorithms, exhaustive search, greedy algorithms, dynamic programming, combinatorial patter matching and graph algorithms.  In addition to the textbook, relevant scientific journal papers will be distributed and discussed. Homework will be assigned for each chapter, including paper and pencil writing and programming.  The course requires a final course project requiring implementing an algorithm to solve a bioinformatics problem of interest to the student.

BMB 706-01. Specialized Studies in Lipidomics and Pathobiology. For each meeting, one student in consultation with one of the above faculty, chooses 1 of 2 recent and cutting edge research studies for presentation and discussion. Each student will prepare a short presentation on relevant background information (methods, prior key studies). this will be followed by an in depth and critical presentation of the manuscript under discussion. The faculty member will be responsible for streamlining and organizing the discussion during each meeting. Dr. Hannun will supervise the overall planning and conduct of the course. In addition, Dr. Hannun will give 2 formal lectures at the beginning of each academic year on "reading the scientific literature".

The Molecular Biology Journal Club encourages graduate students, postdoctoral fellows and faculty members to thoroughly discuss a current selected topic on molecular biology, molecular basis of development, molecular neurobiology, etc. The Journal Club meets every week at noon in the 502 BSB lecture hall. After each presentation, the students, postdoctoral fellows and faculty are encouraged to participate in a discussion. We have had three sessions already and these have all been very productive. The topics covered so far are:(i)trans activation of genes and selection of active olfactory receptors in a neuron; gene silencing mechanisms, checkpoint pathway and the one scheduled for this week is on heterochromatic formation. Significant new work from the top journals such as Cell, Nature, Science, Genes and Development, PNSA, etc. are selected for discussions. A week before, the papers in the pdf format are sent to each participating individual for preparatory reading.

BMB-744. Introduction to Bioinformatics.  The course gives a comprehensive entry-level intro to bioinformatics. It covers a wide variety of topics in bioinformatics, including sequence analysis, protein structure, genome analysis, proteomics data analysis, database, transcription profiling, etc. Two major goals are 1) to help students to understand the scope, the basic concepts and the theory of bioinformatics and 2) to get familiar with tools for bioinformatics related data analysis. Programming skills are not necessary. Prerequisite: Basic molecular biology concepts

BMB-761. Molecular Aspects of DNA/RNA Transactions. The Molecular Biology Journal Club encourages graduate students, postdoctoral fellows and faculty members to thoroughly discuss a current selected topic on molecular biology, molecular basis of development, molecular neurobiology, etc. The Journal Club meets every week at noon in the 502 BSB lecture hall. After each presentation, the students, postdoctoral fellows and faculty are encouraged to participate in a discussion. We have had three sessions already and these have all been very productive. The topics covered so far are:(i)trans activation of genes and selection of active olfactory receptors in a neuron; gene silencing mechanisms, checkpoint pathway and the one scheduled for this week is on heterochromatic formation. Significant new work from the top journals such as Cell, Nature, Science, Genes and Development, PNSA, etc. are selected for discussions. A week before, the papers in the pdf format are sent to each participating individual for preparatory reading.

BMB-762. Models in Biology and Medicine. The course introduces the student to a representative set of models that elucidate the nature of biological and medical phenomena. Upon completion of the course, the student will understand the rationale behind the models, explore their potential and limits, and execute standard analyses and simulations. Examples that are discussed include classical models, such as biochemical system models and parasite-host models, as well as modern models taken from the current literature.

BMB-775. Biochemical Systems Analysis.The course introduces students interested in bioinformatics to the computational analysis of biochemical systems. It briefly reviews traditional concepts of enzyme catalyzed reactions, but places its main emphasis on modern methods of biochemical systems analysis with algebraic and computational means. The course discusses alternative modeling approaches, the design of pathway models, parameter estimation, steady states and stability, sensitivity and gain analysis, numerical evaluation of transients, phase-plane analysis, and the simulation of biomedically relevant scenarios.  The theoretical concepts are applied in comprehensive case studies.

BMB-790. Machine Learning and Data Mining. This course introduces students to the concepts of statistical learning. Machine learning and data mining are concerned with developing computing agents that are capable of learning from past experiences, e.g., a collection of data, in order to make future prediction and propose actions that maximize utility returns. This course covers the following major topics. 1) Various classification approaches including linear discriminative analysis, logistic regression, and support vector machines. 2) Feature construction and selection in classifications; 3) information theory and its application in machine learning; 4) probabilistic graphical models, e.g., Bayesian network and Markov random fields; 5) temporal modeling; and 6) latent variable models and unsupervised learning. Homework usually includes mathematical derivation and programming in R. The course requires a final project applying methods learned in the class to a real world problem, which usually involves in programming in R.

BMB 730. Seminar in Biochemistry. In this series, students give a seminar based on their own research to their fellow students, graduate training committee, thesis committee, faculty and post-doctoral fellows in the Department of Biochemistry. This is a great opportunity for the students to present their work in an informal setting and to receive feedback on his/her studies from a large audience with different scientific backgrounds. Students are required to give at least two seminars during their training. Every Fall & Spring.

BMB-706. Special Topics. Special topics in biochemistry and molecular biology.

BMB 703. Seminar in Lipidomics. In this series, the role and mechanisms by which lipids regulate important cellular functions involved in the development of medically important diseases is discussed. Lectures are given by local as well as invited speakers, scientists whose research focuses on lipid metabolism, signaling, genetics, as well as their relationship to pathobiological disorders, such as cardiovascular and neurological diseases, cancer, inflammation and infection. Every Fall & Spring.

BMB 711. Statistics for Biochemistry. This course provides a survey of descriptive statistics commonly used in biomedical basis research. This course is intended for graduate students studying in the Biochemistry Department who seek a working knowledge of biostatistical methods and their applications. Fall. 2 s.h.

BMB-970.  Research.  Variable s.h., All.

BMB-980.  Thesis.  Variable s.h.  All.

BMB-990.  Dissertation.  Variable s.h.  All.

For more information about the program and courses, please contact the corresponding course director, Dr. Maurizio Del Poeta, Director Graduate Program in Biochemistry and Molecular Biology at (843) 792-8381/4321, delpoeta@musc.edu or Ms. Belinole Anderson, Administrative Coordinator at (843) 843-792-2476, anderseb@musc.edu.  Please visit our website at http://biochemistry.musc.edu.edu/graduate/index.htm.