Biochemical Mechanisms in Medicine

BIOC 0003. Scientific Writing: Development and Defense of a Research Proposal. 2 Credit Hours.

The course consists of writing a progress report describing research results during the last year. The course is required of all graduate students beginning the first semester after selection of a supervising professor.

BIOC 5085. Biophysical Methods In Biology. 2 Credit Hours.

This course is required for all students enrolled in the Molecular Biophysics and Biochemistry track. The course covers modern biophysical methods for studying biological macromolecules in sufficient detail to understand the current literature. Topics to be covered include macromolecular structure determination by X-ray crystallography and NMR spectroscopy; absorbance, fluorescence, and EPR spectroscopy; circular dichroism; light scattering; mass spectrometry; and hydrodynamics, including diffusion, electrophoresis, sedimentation velocity, and sedimentation equilibrium. Open for Cross Enrollment on Space Available Basis.

BIOC 6010. Gene Expression and Omics. 2 Credit Hours.

This course presents 1) the principles of gene expression, including transcription, epigenetic regulation (histone modifications and DNA methylation), mRNA processing and degradation, translation, post-translational modifications, and protein degradation, and 2) the omics approaches for collective characterization and quantification of different aspects of gene expression, including genomics, epigenomics, proteomics, and metabolomics. Two main teaching formats are used in this course: 1) Didactic lectures in which information is delivered to the class, and 2) Paper presentations and discussions, in which students present assigned papers and lead discussions by the entire class. Although one student will present each paper, all students will be expected to read each paper and to be prepared to discuss it in the form of comments and questions. Prerequisites: Permission of the Course Director and IBMS 5000 (or equivalent).

BIOC 6033. Cell Signaling Mechanisms. 2 Credit Hours.

This course covers the molecular mechanisms of action of various extracellular mediators including hormones, neurotransmitters, growth factors, cytokines, etc., and cell signaling events. Several areas will be discussed including: (1) mechanisms of mediator synthesis; (2) interaction of mediators with specific receptors; (3) modulation by mediators of various second messenger systems including cyclic nucleotides, inositol phospholipids, calcium, protein phosphorylation, ion flux, etc.; and (4) intra- and intercellular mechanism for regulating mediator action. Open for Cross Enrollment on Space Available Basis.

BIOC 6035. Target Identification and Hit/Lead Discovery. 2 Credit Hours.

This course provides students with an understanding of the overall process of drug discovery and development. It covers the principles of target identification and validation, the basic methods of drug development, the physical biochemistry of how drugs interact with their biological targets, the role of protein structures in drug-protein interactions, the application of medicinal chemistry in lead optimization, and the development of biologicals like antibodies, vaccines, and RNAs for therapeutics. Focused lectures on specific therapeutic areas will include anti-parasite drug development and drug development for cancer. Prerequisites for the course is at the discretion of the course directors, based on adequate undergraduate courses in chemistry, biochemistry and mathematics. Open for Cross Enrollment on Space Available Basis.

BIOC 6036. Macromolecular Structure & Mechanism. 2 Credit Hours.

This course will cover the fundamentals of protein and nucleic acid structure and of enzyme catalysis. The course is required of students in the Molecular Biochemistry and Biophysics Track. Topics to be covered include: DNA and RNA structure, protein structure, protein folding, ligand binding by proteins, and enzyme catalysis. Open for Cross Enrollment on Space Available Basis.

BIOC 6037. Integration Of Metabolic Pathways. 2 Credit Hours.

The course is required of students in the Molecular Biophysics and Metabolic Pathways track. The objective is to provide an understanding of the individual reactions in intermediary metabolism and how the reactions are integrated by regulatory mechanisms. Topics include carbohydrate, lipid, and nitrogen metabolism and mechanisms of regulation of individual enzymes and metabolic pathways. Open for Cross Enrollment on Space Available Basis.

BIOC 6043. Structure & Function Of Membrane Proteins. 2 Credit Hours.

This is a course targeted at students within any of the Graduate Tracks. The objective is to provide a broad view, allowing for in depth consideration in selected areas, of the structure and diverse functions of proteins within a membrane environment. Specific topics covered will include: ion selective channels, large membrane pores, membrane transporters, membrane pumps, and membrane receptors. The format of the course will be didactic lecture followed by student presentations of relevant topics. Open for Cross Enrollment on Space Available Basis.

CSAT 5095. Experimental Design And Data Analysis. 3 Credit Hours.

The purpose of the course is to provide an introduction to experimental design and statistical analysis. The emphasis of the course will be on the selection and application of proper tests of statistical significance. Practical experience will be provided in the use of both parametric and nonparametric methods of statistical evaluation. Among the topics to be covered are: data reduction, types of distributions, hypothesis testing, scales of measurement, chi square analysis, the special case of the comparison of two groups; analysis of variance; a posteriori multiple comparisons tests, tests of the assumptions of parametric analyses, advanced forms of the analysis of variance, linear regression, and correlation analysis. This course involves the use of statistical software; therefore, access to a laptop or a computer with web access for classes and examinations is required.

CSAT 6005. Rigor & Reproducibility. 1 Credit Hour.

This course will focus on two of the cornerstones of science advancement, which are rigor in designing and performing scientific research and the ability to reproduce biomedical research findings. The course will also emphasize the application of rigor that ensures robust and unbiased experimental design, methodology, analysis, interpretation, and reporting of results. The notion that when a result can be reproduced by multiple scientists, it validates the original results and readiness to progress to the next phase of research will be covered in this course. This is especially important for preclinical studies that provide the basis for rigorous clinical trials in humans. In recent years, there has been a growing awareness of the need for rigorously designed published preclinical studies, to ensure that such studies can be reproduced. The aim of this course is to help attendees acquire the skills necessary to meet the need to enhance rigor and reproducibility in preclinical scientific research. Successful completion of CSAT 5095, or an equivalent approved by the Rigor & Reproducibility course director, is a prerequisite for this course.

IBMS 5000. Fundamentals Of Biomedical Sciences. 8 Credit Hours.

This core course covers the fundamentals of biochemistry, molecular biology, cell biology, organismal and systems biology, and microbiology and immunology. The course is designed for first-year graduate students matriculating into the Integrated Biomedical Sciences Program (IBMS).

IBMS 5008. Lab Rotations. 1-3 Credit Hours.

This course provides an opportunity for students to participate in research activities in the laboratories of faculty members in different disciplines to learn laboratory skills and to gain an introduction to the research fields of faculty members.

IBMS 6090. Seminar. 1.5 Credit Hour.

This course is required of all students in the IBMS program, except of those who have signed up for Final Hours. Students are required to attend a minimum of 16 seminars per semester and to complete a requirement to demonstrate their attendance and participation. To fulfill the minimum number of seminars, students may include seminars offered by disciplines other than their own in which they are enrolled. However, to enroll, students should obtain permission from the course Section Director affiliated with the appropriate discipline. The course numbers of the individual course sections are INTD 6090-1GEN, 6090-2BA, 6090-3CB, 6090-4CGM, 6090-5MIM, 6090-6MBB, 6090-7NS and 6090-8PP for the IBMS Disciplines: Biology of Aging (BA), Cancer Biology (CB), Cell Biology, Genetics & Molecular Medicine (CGM), Molecular Biophysics & Biochemistry (MBB), Molecular Immunology & Microbiology (MIM), Neuroscience (NS), and Physiology & Pharmacology (PP). Some students who have not declared a discipline, and have obtained the approval of their academic advisor and the Senior Associate Dean of the GSBS, may sign up for INTD 6090-1GEN. Grading will be Satisfactory or Unsatisfactory. A list of seminars from all disciplines will be posted on the Graduate School Web site. Each Section Director will determine, for the relevant IBMS-6090 section, the policy for tracking student's attendance and participation in seminars.

IBMS 6097. Research. 0.5-12 Credit Hours.

This course is required of all students in the IBMS program, except of those who have signed up for Final Hours. Students are required to attend a minimum of 16 seminars per semester and to complete a requirement to demonstrate their attendance and participation. To fulfill the minimum number of seminars, students may include seminars offered by disciplines other than their own in which they are enrolled. However, to enroll, students should obtain permission from the course Section Director affiliated with the appropriate discipline. The course numbers of the individual course sections are INTD 6090-1GEN, 6090-2BA, 6090-3CB, 6090-4CGM, 6090-5MIM, 6090-6MBB, 6090-7NS and 6090-8PP for the IBMS Disciplines: Biology of Aging (BA), Cancer Biology (CB), Cell Biology, Genetics & Molecular Medicine (CGM), Molecular Biophysics & Biochemistry (MBB), Molecular Immunology & Microbiology (MIM), Neuroscience (NS), and Physiology & Pharmacology (PP). Some students who have not declared a discipline, and have obtained the approval of their academic advisor and the Senior Associate Dean of the GSBS, may sign up for INTD 6090-1GEN. Grading will be Satisfactory or Unsatisfactory. A list of seminars from all disciplines will be posted on the Graduate School Web site. Each Section Director will determine, for the relevant IBMS-6090 section, the policy for tracking student's attendance and participation in seminars.

IBMS 7001. Qualifying Exam. 1 Credit Hour.

The objective of the Qualifying Examination (QE) is to determine if a student has met programmatic expectations with regard to: i) Acquiring a level of scientific reasoning and a knowledge base in his/her field of study appropriate for a graduate student at the current stage of training; ii) Demonstrating skills of problem-solving and development of experimental strategies designed to test hypotheses associated with a specific scientific problem; and iii) Demonstrating the ability to defend experimental strategies proposed for solving scientific problems. Successful completion of the QE is required for Advancement to Candidacy and continuation in the IBMS Ph.D. program. During the Spring semester of Year 2 (4th semester overall) of the student's program, the QE will be administered by a faculty committee approved by a student's Discipline leadership. Each IBMS discipline will administer the QE process for its students so as to achieve the goals of the discipline while satisfying the expectations of the IBMS graduate program. In general, the QE requires the solving of a relevant unsolved problem in the biomedical sciences by writing a research proposal based on an idea conceived and developed by the student, followed by an oral defense-of-proposal to explore the student's problem-solving process, and the soundness of the student's experimental design. Following the QE, a report will be submitted by the chair of the examination committee to the student's discipline leadership indicating the outcome of the exam and any recommendations that may be required to foster further academic progress by the student. IBMS 7001 is divided into 7 modules overseen by the 7 IBMS Disciplines, each that is responsible for providing its students with a detailed description of the examination process, and for ensuring that the programmatic expectations and goals of the QE are met.

IBMS 7010. Student Journal Club & Research Presentation. 1-2 Credit Hours.

This course is designed to provide graduate students with experience in critical reading of the primary literature, seminar preparation and presentation, data analysis and interpretation, and group-based learning as they relate to the graduate program in Integrated Biomedical Sciences. This course is required of all students in the IBMS program starting in their second year except of those who have signed up for Final Hours. Students are required to attend a minimum of 16 total presentations per semester (journal club or research presentations) and to complete a requirement to demonstrate their attendance and participation. Students are also required to present one journal club presentation per semester until they are Advanced to Candidacy. Once Advanced to Candidacy, the student will present one journal club presentation per academic year and one research presentation per academic year such that the student is giving at least one presentation in each semester. To enroll, students should obtain permission from the course Section Director affiliated with the appropriate discipline. The course numbers of the individual course sections are INTD 7010-1GEN, 7010-2BA, 7010-3CB, 7010-4CGM, 7010-5MIM, 7010-6MBB, 7010-7NS and 7010-8PP for the IBMS Disciplines: Biology of Aging (BA), Cancer Biology (CB), Cell Biology, Genetics & Molecular Medicine (CGM), Molecular Biophysics & Biochemistry (MBB), Molecular Immunology & Microbiology (MIM), Neuroscience (NS), and Physiology & Pharmacology (PP). Some students who have not declared a discipline, and have obtained the approval of their academic advisor and the Senior Associate Dean of the GSBS, may sign up for INTD 7010-1GEN. Grading will be by letter grade (A, B, C, etc). A list of journal clubs from all disciplines will be posted on the Graduate School Web site. Each Section Director will determine, for the relevant IBMS 7010 section, the policy for tracking student's attendance and participation and will be responsible for assigning a final grade.

IBMS 7099. Dissertation. 1-12 Credit Hours.

This course is required of all students in the IBMS program, except of those who have signed up for Final Hours. Students are required to attend a minimum of 16 seminars per semester and to complete a requirement to demonstrate their attendance and participation. To fulfill the minimum number of seminars, students may include seminars offered by disciplines other than their own in which they are enrolled. However, to enroll, students should obtain permission from the course Section Director affiliated with the appropriate discipline. The course numbers of the individual course sections are INTD 6090-1GEN, 6090-2BA, 6090-3CB, 6090-4CGM, 6090-5MIM, 6090-6MBB, 6090-7NS and 6090-8PP for the IBMS Disciplines: Biology of Aging (BA), Cancer Biology (CB), Cell Biology, Genetics & Molecular Medicine (CGM), Molecular Biophysics & Biochemistry (MBB), Molecular Immunology & Microbiology (MIM), Neuroscience (NS), and Physiology & Pharmacology (PP). Some students who have not declared a discipline, and have obtained the approval of their academic advisor and the Senior Associate Dean of the GSBS, may sign up for INTD 6090-1GEN. Grading will be Satisfactory or Unsatisfactory. A list of seminars from all disciplines will be posted on the Graduate School Web site. Each Section Director will determine, for the relevant IBMS-6090 section, the policy for tracking student's attendance and participation in seminars. Registration is only permitted following a student's admission to candidacy for the PhD degree, approval of the dissertation research proposal and approval of the membership of the candidate's Supervising Committee.

TSCI 5070. Responsible Conduct of Research. 2 Credit Hours.

This foundational course introduces students to core ethical content necessary for responsible research conduct. Through interactive seminars, students will learn about (1) scientists as responsible members of society (contemporary ethical issues in biomedical research and environmental/social impacts of research), (2) policies for research with human subjects and vertebrate animals, (3) collaborative research, (4) conflicts of interest (personal, professional, financial), (5) data acquisition and laboratory tools (management, sharing, ownership), (6) responsible authorship and publication, (7) mentor/trainee responsibilities and relationships, (8) peer review (9) research misconduct (forms of misconduct and management policies) (10) informed consent, privacy regulations, good clinical practice, and special populations in clinical investigations.