Biomedical Science, Ph.D.

Transcription

1 Biomedical Science, Ph.D. Biomedical Science, Ph.D. Students interested in the Ph.D. with a major in biomedical sciences should apply to the subprogram area they choose to pursue. Biochemistry The Doctor of Philosophy in biomedical science with a biochemistry subprogram requires a minimum of 72 s.h. of graduate credit (4 s.h. of course work and 8 s.h. of research). Students must maintain a cumulative g.p.a. of at least. to earn the degree. Qualified students interested in earning the Doctor of Medicine along with the Ph.D. may apply to the Medical Scientist Training Program, which offers a combined M.D./Ph.D. program. Students have the opportunity to tailor their curriculum with courses that enhance their educational goals. They take a combination of graduate-level courses that include a first-year laboratory research rotation course, and seminar courses. The Ph.D. in biomedical science with a biochemistry subprogram requires the following course work. BMED:727 Scholarly Integrity/ BIOC:5282 Seminar -2 BIOC:526 Research Techniques (firstyear laboratory rotation) -6 Biophysical chemistry course work (typically -6 biochemistry students take 6 s.h.) Four molecular medicine courses (typically 6-8 biochemistry students take 6-8 s.h.) Additional courses offered by the Department of Biochemistry and other departments, as appropriate for student BMED:527 Principles of Molecular and BIOC:524 Biophysical Chemistry I BIOC:526 Research Techniques 4 BIOC:5282 Seminar (discussion section A) 2 BIOC:5242 Biophysical Chemistry II BIOC:5282 Seminar (discussion section 2 A) BIOC:526 Research Techniques 4 MMED:625 MMED:6226/ ACB:6226/ MPB:6226 MMED:6227/ ACB:6227/ MPB:6227 Second Year, Fall Transcription and by RNA Cell Cycle Control Cell Fate Decisions BMED:727 Scholarly Integrity/ BIOC:5282 Seminar (discussion section A2) BIOC:7292 Research Biochemistry arr. Second Year, Spring BMED:727 Scholarly Integrity/ I BIOC:7292 Research Biochemistry arr. Examples of Elective Course Work BMED:525 Practical Bioinformatics BMED:527 Principles of Molecular and BME:4/ Computational Biochemistry BIOC:4 MMED:625 Transcription and by RNA MMED:622/ ACB:622/ MPB:622 MMED:6225/ MPB:6225 MMED:624 PCOL:524 Mechanisms of Cellular Growth Factor Receptor Inflammatory Cell and Targeted Cancer Therapy Basic Biostatistics and Students rotate through at least three different laboratories during their first academic year; they enroll in BIOC:526 Research Techniques. The laboratory rotations are approximately ten weeks each. At the conclusion of each rotation, a student meets with an advisory committee of three faculty members. The student is required to present the research and training completed during that rotation. The advisory committee writes a short evaluation of the student's

2 2 Biomedical Science, Ph.D. performance and assigns a grade for the laboratory work. The evaluation and grade becomes part of the student's departmental record. Teaching Students participate in the formal teaching programs of the department for at least one semester. First-year students as well as students who are within a year of receiving their Ph.D. degree are usually not asked to teach. Teaching may take a variety of forms, including tutoring, leading discussions and laboratory groups, correcting examinations, preparing teaching materials, and lecturing. Thesis Research Proposal During the fall semester of the second year, a student in collaboration with the thesis advisor prepares a detailed thesis proposal that describes the proposed research to be conducted for the dissertation as part of BIOC:5282 Seminar. The Fifth Semester Seminar In the fall semester of the third year (the fifth semester), a student updates and revises the written Ph.D. thesis proposal prepared during the fall semester of the second year (prior to the comprehensive examination), and presents a seminar on the thesis research to the department at one of the weekly biochemistry workshops. The comprehensive examination must be taken before June of the second year. Written Examination Students receive their topic by March and their written examination is submitted to their committee by April 22. The written proposal should have a cover page followed by no more than 2 pages. For more information, a detailed guide is located in the Biochemistry Graduate Student Manual. Oral Examination Questions during the oral examination may come from the examination proposal, the Ph.D. thesis proposal, or other general areas of biochemistry. To pass the oral comprehensive examination, a student must perform satisfactorily both in defense of the examination proposal and in answering general biochemistry questions that are germane to the proposal or that are important for a full understanding of the proposed experiments and their interpretation. Final Examination The five-member Ph.D thesis committee serves as an advisory body for preparation of the thesis. This committee meets with the student to review the material that is expected to be incorporated in the thesis. Although meetings of the candidate with the committee should be yearly, the candidate, thesis advisor, or the committee can request a meeting at any time. A final draft of the thesis much be given to all members of the committee two weeks before the final examination. The final examination takes the form of a seminar presented to the department. This presentation is announced according to the Graduate College policy. Questions, comments, and discussion will follow. After the seminar, the candidate meets with the committee for the final thesis defense. The Ph.D. degree is not awarded until the thesis is signed. In some cases revisions maybe required. Cancer Biology The Doctor of Philosophy in biomedical science with a cancer biology subprogram requires a minimum of 72 s.h. of graduate credit. Students must maintain a cumulative g.p.a. of at least. to earn the degree. The subprogram provides training in many areas of research cell biology, genetics, immunology, and cell metabolism, among others that are necessary to understand the complexities of cancer etiology and treatment. The cancer biology subprogram does not offer a master's degree. Cancer biology is affiliated with the Holden Comprehensive Cancer Center, which was founded in 98 and has been designed as a National Cancer Institute NCIdesignated cancer center since 2. The curriculum is a sequence of required and elective courses that provides students with advanced knowledge in current concepts related to molecular, cellular, and genetic processes that contribute to the development and treatment of cancer. It also provides specialized training in experimental methodology used to study cancer in a laboratory setting. Cancer biology prepares students for a variety of career paths in academic, clinical, and industry environments that deal with the study and/or treatment of cancer. Students have flexibility in their research rotations and can adapt their studies to permit specialization, as well as gaining clinical exposure by shadowing oncologists. Entering students are expected to have a solid background in chemistry, mathematics, and the biological sciences. They should have completed undergraduate course work in introductory biology and chemistry, biochemistry, genetics, organic chemistry, physical chemistry, and calculus; and previous course work in cancer biology is desirable. Deficiencies in a particular area, as determined by the Graduate Studies Committee, can be remedied by completion of appropriate courses during the first year of graduate study. Selection of a Ph.D. mentor (thesis advisor) is normally finalized near the end of the spring semester of a student's first year of study. The deadline for selection is determined by the biomedical science program. Students are required to complete the core courses listed below prior to their comprehensive examination. Students who wish to take the comprehensive examination should first make arrangements in consultation with their mentor, the program director, and the Student Advisory Committee. The exam is typically completed during the second summer of study. The Ph.D. in biomedical science with a cancer biology subprogram requires the following course work. BMED:527 Principles of Molecular and BMED:727 Scholarly Integrity/ BMED:727 Scholarly Integrity/ I CBIO:5 Experimental Methodologies 6 CBIO:55 Topics in Cancer Biology CBIO:6 Seminar: Cancer Research

3 Biomedical Science, Ph.D. CBIO:65 Research in Cancer Biology arr. CBIO:7 Clinical Connections CBIO:75 Crafting a Scientific Proposal FRRB:7/ PATH:7 PCOL:524 Molecular and Cellular Biology of Cancer Basic Biostatistics and BMED:527 Principles of Molecular and CBIO:5 Experimental Methodologies 6 CBIO:55 Topics in Cancer Biology CBIO:6 Seminar: Cancer Research FRRB:7/ Molecular and Cellular PATH:7 Biology of Cancer PCOL:524 Basic Biostatistics and CBIO:55 Topics in Cancer Biology CBIO:6 Seminar: Cancer Research CBIO:65 Research in Cancer Biology arr. Elective Second Year, Fall BMED:727 Scholarly Integrity/ BMED:727 Scholarly Integrity/ I CBIO:55 Topics in Cancer Biology CBIO:6 Seminar: Cancer Research CBIO:65 Research in Cancer Biology arr. CBIO:7 Clinical Connections CBIO:75 Crafting a Scientific Proposal Elective Second Year, Spring CBIO:55 Topics in Cancer Biology CBIO:6 Seminar: Cancer Research CBIO:65 Research in Cancer Biology arr. Elective The following are possible elective choices. Students should consult the Cancer Biology Graduate Program Handbook for more elective choices, and also consult their advisor or the program director. BIOC:725 Introduction to Protein Structures BIOC:7256 Molecular Biology BIOS:42 Introduction to Biostatistics FRRB:7 Redox Biology and Medicine 4 GENE:42/ Bioinformatics 4 BIOL:42/ IGPI:42 GENE:65 Genetic Analysis of Biological Systems GENE:79 Human Molecular Genetics MMED:622/ ACB:622/ MPB:622 MMED:6227/ ACB:6227/ MPB:6227 Mechanisms of Cellular Cell Fate Decisions PATH:526 Translational Histopathology PCOL:628 G Proteins and G Protein- Coupled Receptors PCOL:629/ MPB:629/ NSCI:629 Steroid Receptor In order to gain more widespread experience in cancer biology research and to aid in selecting a laboratory home and thesis project, students perform three to seven laboratory rotations prior to selection of a thesis advisor. Laboratory rotations are normally carried out in research laboratories of the cancer biology faculty. A rotation can be completed with a faculty member outside the cancer biology program with permission of the program director. Rotations begin in the spring semester of the first year. The length of a laboratory rotation is flexible and can vary from a minimum of two to five weeks. Two laboratory rotations may be completed in the same lab with the approval of the program director. The goal of the rotations is to gain a comprehensive view of the mentor s research program, to gain exposure to experimental methods used in the mentor s lab, and to learn about the mentoring styles of faculty members. Teaching The cancer biology program does not require teaching. Students with an interest in teaching experience are encouraged to discuss their career plans with their mentor and/or the program director. Publication Requirements Students are required to have a minimum of one first-author publication in a peer-reviewed journal prior to graduation. The article must be formally accepted and be in-press status or published prior to graduation. A co-first-authored, peerreviewed publication will count toward this requirement. Students are eligible to take the comprehensive examination when they are in good academic standing as defined by the Graduate College the student has completed all program core courses with a grade of at least B or have a non-letter grade of pass.

4 4 Biomedical Science, Ph.D. Written Examination The comprehensive exam is on-topic, meaning the subject should be a student s current research being conducted in the mentor s lab. Students normally take the comprehensive exam during the second spring or summer of their enrollment in the program. They submit a written exam, if that is acceptable to the comprehensive examination committee, and then prepare for an oral examination. Oral Examination The purpose of the oral examination is to determine whether the student s written submission adequately represents the student s knowledge. A student may be queried on issues beyond the scope of the written proposal to allow the committee to determine the student s general depth of knowledge. Final Examination The thesis committee is selected by each student after the successful completion of the comprehensive examination. Students are eligible for their oral thesis defense after completing 72 s.h. of course work, publication of at least one primary author manuscript or be in-press status, and with consent of the thesis committee. The procedures are the same as for the comprehensive examination. Cell The Doctor of Philosophy in biomedical science with a cell and developmental biology subprogram requires 72 s.h. of graduate credit. Students must maintain a cumulative g.p.a. of at least. to earn the degree. They gain admission to graduate training laboratories in the Department of Anatomy and Cell Biology, Interdisciplinary Graduate Programs, or through direct admission into a specific laboratory. The Ph.D. in biomedical science with a cell and developmental biology subprogram requires the following course work. All of these: ACB:622/ MMED:622/ MPB:622 ACB:627 Mechanisms of Cellular Critical Thinking in Biochemistry and Molecular Biology ACB:628 Critical Thinking in Genetics ACB:629 Critical Thinking in Cell Biology ACB:6249 Critical Thinking in Cellular Physiology ACB:6248 Critical Thinking in Development BMED:527 Principles of Molecular and GENE:65 Genetic Analysis of Biological Systems PCOL:524 Basic Biostatistics and Three of these: MMED:625 MMED:6225/ MPB:6225 MMED:6226/ ACB:6226/ MPB:6226 MMED:6227/ ACB:6227/ MPB:6227 Transcription and by RNA Growth Factor Receptor Cell Cycle Control Cell Fate Decisions All of these: BMED:527 Principles of Molecular and BMED:727 Scholarly Integrity/ ACB:526 Graduate Research in Cell arr. ACB:5224 Graduate Seminar in Cell - GENE:65 Genetic Analysis of Biological Systems MMED:628 Critical Thinking in Molecular Medicine PCOL:524 Basic Biostatistics and Three of the following (on recommendation of the student advisory committee and the graduate program director): ACB:526 Graduate Research in Cell arr. ACB:5224 Graduate Seminar in Cell - MMED:625 Transcription and by RNA MMED:6225/ MPB:6225 MMED:6226/ ACB:6226/ MPB:6226 MMED:6227/ ACB:6227/ MPB:6227 All of these: MMED:628 Elective (optional) Growth Factor Receptor Cell Cycle Control Cell Fate Decisions Critical Thinking in Molecular Medicine (literature review)

5 Biomedical Science, Ph.D. 5 Second Year, Fall All of these: BMED:727 Scholarly Integrity/ I ACB:526 Graduate Research in Cell arr. ACB:5224 Graduate Seminar in Cell - ACB:622/ MMED:622/ MPB:622 ACB:627 Mechanisms of Cellular Critical Thinking in Biochemistry and Molecular Biology ACB:628 Critical Thinking in Genetics ACB:629 Critical Thinking in Cell Biology Elective (optional) Second Year, Spring All of these: ACB:526 Graduate Research in Cell arr. ACB:5224 Graduate Seminar in Cell - ACB:6248 Critical Thinking in Development ACB:6249 Critical Thinking in Cellular Physiology Elective (optional) The following are possible elective choices. ACB:528/ Microscopy for Biomedical arr. BIOL:528/ MICR:528 Research BIOC:524 Biophysical Chemistry I BIOC:5242 Biophysical Chemistry II BIOL:42/ GENE:42/ IGPI:42 Bioinformatics 4 NSCI:575/ BIOL:575 Developmental Neuroscience PCOL:55 Principles of Pharmacology PCOL:56 Pharmacogenetics and Pharmacogenomics PCOL:628 G Proteins and G Protein- Coupled Receptors PCOL:629/ Steroid Receptor MPB:629/ NSCI:629 PHAR:552 High Throughput Screening for Pharmaceutical and Biomedical Sciences Students rotate through at least three different laboratories during their first academic year. The rotations are approximately weeks each. At the conclusion of each rotation, students give a 2-minute presentation. Teaching Students are required to complete a s.h. teaching requirement. They may teach in a combination of or 2 s.h. courses, or one s.h. course. Teaching requirements must be met prior to the final thesis defense and graduation. Most students meet the requirement in the third year after completion of the comprehensive exam. A student must earn a satisfactory report from the course director in order to receive credit for the teaching requirement. Publication Requirements It is expected that a student will have contributed as an author to at least one research publication. The publication must demonstrate primary authorship and be at the accepted phase of the publication process. The number of publications and their quality, content, and impact is established by the thesis committee. Seminar Presentations Students present their thesis research annually in the cell and developmental biology seminar series in a -minute presentation. Evaluation critique by faculty and students is provided. The comprehensive examination must be taken before the fall semester of a student's third year. Written Examination A written proposal follows the form of a standard National Institutes of Health (NIH) R research grant and covers the area of the research proposed for the student's anticipated thesis dissertation. One aim area should be completely of the student's own design, with no input from the thesis advisor. Oral Examination The oral examination of the student's research proposal lasts approximately two to three hours. The exam begins with a brief student presentation on the proposed research project. Questions during the examination may come from the proposal, the thesis research, or other general areas of cell and developmental biology. Thesis Defense The five-member thesis committee serves as an advisory body for the preparation of the thesis. The candidate and the committee should meet yearly; however, the candidate, the thesis advisor, or the committee can request a meeting at any time. In the subultimate committee meeting, committee members review the material that is expected to be incorporated into the thesis. The final draft of the thesis is due to the committee two weeks before the final examination. The final examination takes the form of a seminar presented to the program, with questions, comments, and discussion following. After the seminar, the candidate meets with the committee for the final thesis defense.

6 6 Biomedical Science, Ph.D. Free Radical and The Doctor of Philosophy in biomedical science with a free radical and radiation biology subprogram is interdisciplinary and requires 72 s.h. of graduate credit. Students must maintain a cumulative g.p.a. of at least. to earn the degree. The possibility exists for a major emphasis in radiation biology or redox biology with a focus on cancer or degenerative diseases associated with aging. Although students with diverse academic backgrounds may enter the program, each student should have a science background which includes at least two years of chemistry, including organic chemistry; one year of physics; two years of biology; and mathematics, including at least one semester of calculus. The Ph.D. in biomedical science with a free radical and radiation biology subprogram requires the following course work. FRRB:5 4 FRRB:6 Seminar: Free Radical and FRRB:64 Research: Free Radical and arr. FRRB:66 Topics in Free Radical Biology and Medicine FRRB:68 Topics in Radiation and Cancer Biology FRRB:7 Redox Biology and Medicine 4 FRRB:7/ PATH:7 Molecular and Cellular Biology of Cancer BMED:527 Principles of Molecular and FRRB:5 (odd 4 years) FRRB:64 Research: Free Radical and arr. FRRB:64 Research: Free Radical and arr. FRRB:66 Topics in Free Radical Biology and Medicine FRRB:68 Topics in Radiation and Cancer Biology FRRB:7 Redox Biology and Medicine 4 (even years) Second Year, Fall BMED:727 Scholarly Integrity/ (both courses must be taken, but in any order) FRRB:6 Seminar: Free Radical and FRRB:64 Research: Free Radical and arr. FRRB:66 Topics in Free Radical Biology and Medicine FRRB:68 Topics in Radiation and Cancer Biology FRRB:7/ Molecular and Cellular PATH:7 Biology of Cancer Second Year, Spring BMED:727 Scholarly Integrity/ I (both courses must be taken, but in any order) FRRB:6 Seminar: Free Radical and FRRB:64 Research: Free Radical and arr. FRRB:66 Topics in Free Radical Biology and Medicine FRRB:68 Topics in Radiation and Cancer Biology Required Courses BMED:527 Principles of Molecular and BIOC:2 Biochemistry and Molecular Biology I MMED:6226/ Cell Cycle Control ACB:6226/ MPB:6226 PCOL:524 Basic Biostatistics and Recommended These electives are recommended to supplement required course work. ACB:456/ Scanning Electron arr. CBE:456/EES:456 Microscopy and X-Ray Microanalysis ACB:528/ Microscopy for Biomedical arr. BIOL:528/ MICR:528 Research BIOC: Biochemistry and Molecular Biology II

7 Biomedical Science, Ph.D. 7 BIOC:4 Experimental Biochemistry 2 BIOL:7 Molecular Genetics 4 MICR:47 Immunology and Human Disease MICR:62/ Graduate Immunology IMMU:62 MMED:625 Transcription and by RNA MMED:622/ ACB:622/ MPB:622 MMED:6225/ MPB:6225 Mechanisms of Cellular Growth Factor Receptor OEH:67 Environmental Toxicology PATH:527/ Pathogenesis of Major IGPI:527 Human Diseases PATH:8/ PTRS:8 PSQF:627/ GRAD:627 Introduction to Human 4 Pathology for Graduate Students Seminar in College Teaching - Graduate students rotate through at least three free radical and radiation biology different laboratories during their first academic year with primary and secondary faculty. Seminar and Journal Clubs Students must enroll in one seminar for credit once a year for three years as well as a thesis defense seminar. Students should not register for the seminar during their first academic year. Students enrolled for research credit are required to submit a research report to their advisor on the last day of class each semester. The report is evaluated and graded by the advisor. The report, written in a form that is appropriate for a peer-reviewed publication, should define the goals, aims, and objectives for the specific semester, and describe the progress made by the student toward completion of the research objectives. Topics in Free Radical Biology and Medicine (FRRB:66) and Topics in Radiation and Cancer Biology (FRRB:68) must be taken at least two times. Publication Requirements Students must submit at least one first-author manuscript or be ready to submit to a peer-reviewed journal prior to the thesis defense. All Ph.D. students are expected to have peer-reviewed publications prior to graduation and these publications should include first authorship. Grant Writing Opportunities National Institutes of Health (NIH) research grant proposals (i.e., F, F) and/or equivalent grant submissions are encouraged based on a student's work. The free radical and radiation biology program will provide resources and critiques of the application prior to submission. Students should review the instructions provided in the NIH publication, PHS-98, available from the National Institutes of Health website. Qualifying Exam To qualify for entry into the Ph.D. program, a student must satisfactorily complete a written qualifying examination. The student will typically take the exam after successfully completing the major required course work, but no later than the beginning of the fifth semester after entering the program. The exam is offered after the close of spring semester classes, typically Monday and Tuesday of the first week of the regular summer session. A student is allowed two attempts to satisfactorily complete the exam. Guidelines state that a score greater than 7 percent on any section constitutes a Ph.D. pass in that section, between 6 percent and 7 percent is an M.S. pass, and below 6 percent is a failing grade. A student who passes (Ph.D. pass) some sections on the first attempt are not be required to repeat an exam for that section. New questions are written for the exam sections to be repeated and students are expected to clear a 7 percent pass within eight weeks of their first attempt. An overall average of 7 percent or greater on the repeated exam sections constitutes a Ph.D. pass. An average equal to or greater than 7 percent constitutes a Ph.D. pass and progress toward completion of the Ph.D. degree requirements. Comprehensive Exam Students must successfully pass the comprehensive examination. This exam may be taken at any time after successfully completing the qualifying exam but no later than the first February after successfully completing the qualifying exam. This exam should be written in a National Institutes of Health R format and be on the topic of the student s dissertation research. Members of the exam committee should approve of the hypothesis plus a student's aims page. The members then can have no further input into the preparation of the document. If the student fails to satisfactorily complete the comprehensive exam, the student is allowed one additional attempt to satisfactorily complete the exam. The second attempt can be undertaken no sooner than June (at least four months after the first attempt) and no later than August of that same year. For the Ph.D. comprehensive examination (Secti, the student must develop a proposal, present a written copy of the proposal to each member of the examining committee, then orally defend the proposal two to four weeks later. The written proposal shall be prepared using a word processor, be no more than fifty (5) double-spaced pages, and follow the general guidelines for National Institutes of Health (NIH) R research grant proposals (minus administrative pages) (See instructions that are provided in the NIH publication PHS-98, available from the NIH web site). Final Examination The final examination is a defense of the thesis and explanation of the scientific principles involved, given in a public seminar and closed door oral exam, with committee members. The student's research must be summarized in the format required by the Graduate College. Immunology The Doctor of Philosophy in biomedical science with an immunology subprogram provides interdisciplinary training in the concepts and methodologies of basic and applied immunology. The degree requires 72 s.h. of graduate credit. Students must maintain a cumulative g.p.a. of at least. to

8 8 Biomedical Science, Ph.D. earn the degree. They complete course work in immunology and related disciplines, and are directly involved in laboratory research throughout their study. Immunology graduate courses are offered not only to teach students the current concepts and paradigms within the field, but to emphasize the scientific approaches and methods used to attain this understanding. Immunology faculty members are involved in a variety of research projects dealing with the immune system at all levels structural, functional, cellular, biochemical, and molecular. The Ph.D. in biomedical science with an immunology subprogram requires the following course work. BMED:527 Principles of Molecular and BMED:727- Scholarly Integrity/ BMED:727 -II IMMU:62/ Graduate Immunology MICR:62 IMMU:62 Immunology Seminar IMMU:6247/ MICR:6247 PCOL:524 Graduate Immunology and Human Disease Basic Biostatistics and Elective BMED:527 Principles of Molecular and IMMU:62 Immunology Seminar IMMU:6247/ Graduate Immunology and 4 MICR:6247 Human Disease PCOL:524 Basic Biostatistics and IMMU:62/ Graduate Immunology MICR:62 IMMU:62 Immunology Seminar Elective (optional) - Second Year, Fall BMED:727 Scholarly Integrity/ IMMU:62 Immunology Seminar IMMU:624 Writing a Scientific Proposal IMMU:722/ Advanced Topics in MICR:727 Immunology Elective (optional) - 4 Second Year, Spring BMED:727 Scholarly Integrity/ I IMMU:62 Immunology Seminar Elective (optional) - The following are possible elective choices. ACB:528/ Microscopy for Biomedical BIOL:528/ MICR:528 Research ACB:82 General Histology for Dental 4 Students BIOC:725 Introduction to Protein Structures BIOC:7252 Enzymes, Carbohydrates, Nucleic Acids, and Bioenergetics BIOC:725 Metabolism I BIOC:7254 Metabolism II BIOC:7255 Metabolism III and Biosignaling BIOC:7256 Molecular Biology BIOS:42 Introduction to Biostatistics MICR:6259 Graduate Bacteria and Human Disease MICR:626 Graduate Molecular Microbiology MICR:6267 Graduate Viruses and 4 Human Disease MICR:6268 Biology and Pathogenesis of 2 Viruses MICR:627 Graduate Microbial Genetics MICR:727/ IMMU:727 MMED:625 MMED:622/ ACB:622/ MPB:622 MMED:6225/ MPB:6225 MMED:6226/ ACB:6226/ MPB:6226 MMED:6227/ ACB:6227/ MPB:6227 MMED:624 Integrated Topics in Infectious Diseases Transcription and by RNA Mechanisms of Cellular Growth Factor Receptor Cell Cycle Control Cell Fate Decisions Inflammatory Cell and Targeted Cancer Therapy PATH:526 Translational Histopathology PATH:527/ Pathogenesis of Major IGPI:527 Human Diseases PCOL:627 Ion Channel Pharmacology

9 Biomedical Science, Ph.D. 9 PCOL:628 PCOL:629/ MPB:629/ NSCI:629 G Proteins and G Protein- Coupled Receptors Steroid Receptor Prior to selecting a laboratory for dissertation work, students are expected to perform three laboratory rotations, with each rotation lasting approximately 2 weeks in duration. During the first semester, students should become acquainted with the research interests of the faculty members in the immunology program. This learning process is facilitated by faculty presentations in IMMU:62 Immunology Seminar during the fall semester. Students also are encouraged to meet with specific faculty to discuss their research programs. This enables students to make an informed decision about their laboratory rotations, with the guidance and approval of their advisor and the graduate studies committee. At the latest, students should begin their first rotation within the first week of graduate study. Medical Science Training Program (MSTP) students and students with M.S. degrees that included a research-based dissertation may be excused from one rotation. Students having difficulty choosing a laboratory for dissertation work may perform a fourth rotation. The rotations are graded either satisfactory or unsatisfactory. This grade is based upon a number of criteria including attendance and work habits. When not in classes or seminars, students are expected to spend the remaining portion of the day in the laboratory. Without a strong commitment to the rotation project, it is difficult to fulfill the purpose and aims of the rotation. A satisfactory grade is required in each of the laboratory rotations. If a satisfactory grade is not received in one of the rotations, an additional rotation is assigned. Failure to receive a satisfactory grade in the extra rotation results in the student being placed on academic probation. Following each rotation, an evaluation is given to each student by the faculty member and submitted to the graduate studies committee. Teaching Students complete a teaching requirement lasting one semester. A variety of courses are available in several departments, and the program leadership place students in courses based upon interest, expertise, and scheduling. Publication Requirements It is expected that the dissertation project be of sufficient breadth, depth, and novelty to result in first-author research publications in high quality peer-reviewed journals. A minimum of one peer-reviewed paper must be published or in press prior to the completion of the Ph.D. degree. In addition, a second publication, in which the student is a coauthor on a peer-reviewed article, a review, or book chapter must be published or in press prior to the completion of the degree. Students are not permitted to schedule a dissertation defense until it has been demonstrated that both of these requirements have been met. The comprehensive examination is generally taken in the spring semester of the second year of study. MSTP students or students entering the program with a M.S. degree may choose to take the examination in the fall semester of their second year. Students taking the comprehensive examination prepare a single abstract of an original research proposal. The examination committee determines if the abstract topic is appropriate as non-overlapping, and if the abstract is scientifically sound to potentially serve as the basis for a defensible research proposal. After the abstract is accepted, students are given four weeks to complete and submit the written comprehensive examination proposal. The oral defense is scheduled -4 days after the exam is submitted, depending on availability of the committee members. The comprehensive exam is written in the form of a NIH-style pilot grant proposal based on the abstract and instructions from the comprehensive examination. A detailed Student Manual is located under "Program Information" on the Immunology Program website. Final Examination The five members of the thesis committee serve as an advisory body for preparation of the thesis. The committee meets with each student to review the material that they expect to be incorporated into the thesis. Although meetings with the committee should be yearly, the candidate, thesis advisor, or the committee can request a meeting at any time. A final draft of the thesis must be given to all members of the committee two weeks before the final examination. The final examination takes the form of a seminar presented to the program. This presentation is announced according to Graduate College policy. Questions, comments, and discussion follow. After the seminar, the candidate meets with the committee for the final thesis defense. In some cases revisions may be required. The degree is not awarded until the thesis is signed. Microbiology The Doctor of Philosophy in biomedical science with a microbiology subprogram requires a minimum of 72 s.h. of graduate credit (8 s.h. of course work and 54 s.h. of research). Students must maintain a cumulative g.p.a. of at least. to earn the degree. Qualified students interested in earning the Doctor of Medicine along with the Ph.D. may apply to the Medical Scientist Training Program, which offers a combined M.D./Ph.D. program. Students have the opportunity to tailor their curriculum with courses that enhance their educational goals. They take a combination of graduate-level courses that include seminar courses. The Ph.D. in biomedical science with a microbiology subprogram requires the following course work. BMED:727 Scholarly Integrity/ MICR:726 Graduate Student Research Seminar Additional courses offered by the Department of Microbiology and Immunology and other departments, as appropriate for each student

10 Biomedical Science, Ph.D. Typical Two-Year Curriculum First Three Semesters Students enroll for 2 s.h. in the first three semesters and select courses from the following. MICR:6247/ Graduate Immunology and 4 IMMU:6247 Human Disease MICR:6267 Graduate Viruses and 4 Human Disease MICR:627 Graduate Microbial Genetics MICR:722 Advanced Topics in Prokaryotic Biology Module -2 MICR:62/ Graduate Immunology IMMU:62 MICR:6259 Graduate Bacteria and Human Disease MICR:626 Graduate Molecular Microbiology MICR:6268 Biology and Pathogenesis of 2 Viruses MICR:7265 Topics in Virology Literature Examples of Elective Course Work BMED:527 Principles of Molecular and BIOL:42/ Bioinformatics 4 GENE:42/ IGPI:42 MMED:622/ Mechanisms of Cellular ACB:622/ MPB:622 BIOL:52/ BME:5/ ECE:522/ GENE:57/ IGPI:5 Computational Genomics Graduate students rotate through two to three different laboratories during their first academic year. The laboratory rotations are approximately ten weeks each. At the conclusion of each rotation, a student meets with the rotation mentor for an exit interview and an evaluation of the student's performance. This evaluation becomes part of the student's departmental record. The student also is required to present the research completed during the rotation in the graduate seminar course. Teaching Graduate students participate in the formal teaching activities of the department for at least two semesters. First-year students as well as students who are within a year of receiving the Ph.D. degree typically are not asked to teach. Teaching may take a variety of forms, including tutoring, leading discussions and laboratory groups, correcting examinations, preparing teaching materials, and lecturing. The comprehensive examination is designed to measure a student s ability to write and defend a research proposal. The format of this proposal follows guidelines for research proposals outlined by major external funding agencies (i.e., National Institutes of Health (NIH), National Science Foundation (NSF), and U.S. Department of Agriculture (USDA). Guidance, in the design of these proposals, is provided by the director of graduate studies and the student s comprehensive examination committee. Written Examination During the spring semester of the second year, a student prepares a detailed research proposal. The topic of the research proposal is determined in collaboration with the comprehensive examination committee. A detailed guide can be found in the Graduate Program in Microbiology Student Handbook. Oral Examination Questions during the oral examination may come from the examination proposal, course work, or other general areas of microbiology. In order to pass the comprehensive examination, a student must satisfactorily defend the written research proposal and answer questions of general microbiology that are germane to the proposal or that are important for a full understanding of the proposed experiments and their interpretation. Final Examination The five-member Ph.D. thesis committee serves as an advisory body for preparation of the thesis. This committee meets with the student to review the material that is expected to be incorporated in the thesis. Although meetings of the candidate with the committee should be yearly, the candidate, thesis advisor, or the committee can request a meeting at any time. A final draft of the thesis must be given to all members of the committee two weeks before the final examination. The final examination takes the form of a seminar presented to the department. This presentation is announced according to the Graduate College policy. Questions, comments, and discussion will follow. After the seminar, the candidate meets with the committee for the final thesis defense. The Ph.D. degree is not awarded until the thesis is signed. In some cases, revisions maybe required. Molecular Medicine The Doctor of Philosophy in biomedical science with a molecular medicine subprogram provides interdisciplinary training in the concepts and methodologies fundamental to the investigation of biological processes and molecular mechanisms that relate to human disease. The Ph.D. requires a minimum of 72 s.h. of graduate credit. Students must maintain a cumulative g.p.a. of at least. to earn the degree. The curriculum is a sequence of required and elective courses, which provides students with broad exposure to areas including molecular biology, cell biology, biochemistry, and integrative sciences. It ensures a comprehensive exposure to conceptual and experimental aspects of molecular and cellular

11 Biomedical Science, Ph.D. biology and of translational studies. Sufficient flexibility is provided so that students can adapt the program to permit specialization in their own area of interest. Faculty members are involved in a variety of research projects involving molecular and cellular biology and molecular medicine. The Ph.D. in biomedical science with a molecular medicine subprogram requires the following course work. All of these: BMED:527 Principles of Molecular and BMED:727- BMED:727 MMED:628 MMED:729 Scholarly Integrity/ -II Critical Thinking in Molecular Medicine (post-comp students must participate in a journal club of their choice) Seminars in Molecular Medicine (students must register each semester) MMED:85 Molecular Physiology PATH:527 Pathogenesis of Major Human Diseases PCOL:524 Basic Biostatistics and Medthods for molecular and translational medicine course (consult advisor) BMED:527 Principles of Molecular and MMED:628 Critical Thinking in Molecular Medicine MMED:85 Molecular Physiology PCOL:524 Basic Biostatistics and MMED:628 Critical Thinking in Molecular Medicine PATH:527 Pathogenesis of Major Human Diseases Methods for molecular and translational medicine course (consult advisor) (from second year tracks or other courses; consult advisor) Second Year Students select course work from the following three track areas: metabolic disorders, cardiovascular biology, and molecular and cellular medicine (general). BMED:727 Scholarly Integrity/ MMED:628 Critical Thinking in Molecular Medicine MMED:729 Seminars in Molecular Medicine - Metabolic Disorders BIOC:725 Metabolism I BIOC:7254 Metabolism II BIOC:7255 Metabolism III and Biosignaling MMED:628 Critical Thinking in Molecular Medicine Pathogenesis of metabolic disorders course (anatomy, physiology, pathophysiology, pharmacology; consult advisor) Translational medicine education rounds Cardiovascular Biology MMED:628 Critical Thinking in Molecular Medicine Pathogenesis of cardiovascular disorders course (anatomy, physiology, pharmacology; consult advisor) Elective Translational medicine education rounds Molecular and Cellular Medicine (General) All of these: MMED:622 Mechanisms of Cellular Related course work from list in the Molecular 2 Medicine Handbook/Guidelines Translational medicine education rounds Two of these: MMED:625 Transcription and by RNA MMED:6225 Growth Factor Receptor MMED:6226 Cell Cycle Control MMED:6227 Cell Fate Decisions To ensure that students obtain early involvement in laboratory research, they are required to register for research credits and complete three laboratory rotations during their first year of graduate study. In general, these rotations are in laboratories of three different molecular medicine faculty members. In some cases, if approved by the molecular medicine program, students may be allowed to complete two of their rotations in the same laboratory.

12 2 Biomedical Science, Ph.D. Teaching Students are required to complete a teaching requirement ( s.h.). They may teach in a combination of or 2 s.h. courses, or one s.h. course. This teaching requirement must be met prior to the final dissertation defense and graduation. It is recommended that teaching occur in the third year following completion of the comprehensive examination. Publication Requirements Students are required to have a minimum of one first-author publication in a peer-reviewed journal. The article must be formally accepted and be in-press status or be published prior to graduation. A co-first-authored, peer-reviewed publication will count toward this requirement. External Fellowship Application Requirement Students are required to submit a fellowship to an external funding agency (i.e., National Institutes of Health, American Heart Association) within one year of completing their comprehensive examination or by a date that is mutually agreed upon by the student, the dissertation advisor, and the molecular medicine program. Students are expected to complete the comprehensive examination, both written and oral components, before the beginning of their third year. The preliminary specific aims document can be submitted to the comprehensive examination committee any time after approval of the dissertation plan, but must be submitted before April. The committee evaluation of the specific aims will be returned to the student within one week. A rejected specific aims must be revised and resubmitted within three weeks. The committee then has one week to evaluate the resubmitted specific aims. The specific aims must be accepted by a majority vote of the committee before a student can proceed with development of a full proposal. Only two rounds of submission are allowed. Following acceptance of the specific aims, the student must submit the written proposal within six weeks. The committee has two weeks to review the written document. The oral presentation to defend the written proposal should be scheduled as soon after the two weeks as possible or at the convenience of the committee. It is expected that all examinations will be completed by July 5, in advance of the end of the student's second year. The detailed Molecular Medicine Student Guidelines is located under "Program Information" on the Molecular Medicine Program website. Final Examination The five-member thesis committee serves as an advisory body for preparation of the thesis. It is expected that a student meet with the committee annually, although the candidate, thesis advisor, or the committee can request a meeting at any time. The final examination takes the form of a seminar presented to the program followed by a final thesis defense with committee members. The student is required to present a complete copy of the thesis to the thesis committee members at least two weeks prior to the final defense date. Molecular Physiology and Biophysics The Doctor of Philosophy in biomedical science with a molecular physiology and biophysics subprogram offers opportunities for training and research. The degree requires a minimum of 72 s.h. of graduate credit. Students must maintain a cumulative g.p.a. of at least. to earn the degree. Students join an active group of faculty members and advanced students at a time of expanding interdisciplinary biomedical research at the University of Iowa. Faculty in the Department of Molecular Physiology and Biophysics have a strong research focus on the cellular, molecular, and physical mechanisms of physiological processes. The Ph.D. in biomedical science with a molecular physiology and biophysics subprogram requires the following course work. BMED:527 Principles of Molecular and BMED:727 Scholarly Integrity/ MPB:55 Graduate Physiology 4 MPB:62 Research Physiology and Biophysics arr. Advanced electives, approved by the director of 9 graduate studies Fall Semester BMED:527 Principles of Molecular and BMED:727 Scholarly Integrity/ MPB:55 Graduate Physiology 4 MPB:62 Research Physiology and Biophysics 6 Spring Semester BMED:727 Scholarly Integrity/ MMED:625 Transcription and by RNA (elective) MMED:6226/ Cell Cycle Control (elective) ACB:6226/ MPB:6226 MMED:6227/ Cell Fate Decisions (elective) ACB:6227/ MPB:6227 MPB:6225/ MMED:6225 Growth Factor Receptor (elective)

13 Biomedical Science, Ph.D. MPB:62 Research Physiology and Biophysics Elective Course Work Options Any elective preapproved by the director of graduate studies can be used to meet the elective requirement. A total of 9 s.h. of elective course work is required. The most common elective options are the following. BMED:525 Practical Bioinformatics GENE:65 Genetic Analysis of Biological Systems MPB:622/ ACB:622/ MMED:622 Mechanisms of Cellular NSCI:565/ Fundamental Neurobiology BIOL:565/PSY:52 IGPI:527/ PATH:527 Pathogenesis of Major Human Diseases Plan of Study In consultation with the director of graduate studies, each newly admitted student formulates a plan of study to be completed before the comprehensive examination. This plan should include projected dates for completion of the comprehensive examination as well as provision for removal of deficiencies. Before completing the comprehensive exams, the normal course load is 5 s.h. each semester. Required Courses It is the intention of the department to have a curriculum that allows course work to be mostly completed within the first year, though in some instances additional course work in subsequent years is required. The core curriculum represents a minimum of required classes; although with advice of the director of graduate studies and thesis advisor, some students may benefit from completing additional course work. Requests for waiver of required courses or change of course registration must be approved by the director of graduate studies after consultation with the faculty and the chair of the department. Evaluation of Progress Students must meet progress requirements of the Department of Molecular Physiology and Biophysics and the Graduate College. To meet departmental requirements, students must obtain a grade of B or higher in MPB:55 Graduate Physiology and BMED:527 Principles of Molecular and (B-minus or lower constitutes a non-passing grade), a grade of satisfactory (S) for BMED:727 Scholarly Integrity/, and a g.p.a.of at least. in all elective course work (a grade below B, but above D-minus, is permissible for individual electives, so long as the grade-point average of all combined electives taken during the graduate program remains higher than.). All courses receiving a letter grade must be satisfactorily completed prior to taking the comprehensive exam. According to Graduate College regulations, students cannot take a comprehensive exam in a semester in which they are on academic probation. 2 Students admitted directly to the doctoral program are required to complete the comprehensive examination by June of the second year in the program. Workshop All post-comprehensive students are required to present a workshop on the progress of their thesis research once per year. Students should consult with the workshop coordinator to arrange presentation dates. Precomprehensive students also are encouraged to present workshops, though it is not required. Students have an option to present a full or half workshop (typically 45 or 2 minutes, respectively). Teaching Experience in teaching is an important part of a student's academic training. To attain adequate teaching proficiency, students receive teaching assignments after successful completion of the comprehensive exam and in subsequent years as warranted. Individual assignments depend on the teaching needs of the department. Examples of teaching assignments include running review sessions in a graduate physiology course, formal lectures, participating in small group conferences, assisting in computer simulations, or bench mentoring of summer students. These teaching assignments are made by the director of teaching in consultation with appropriate course directors. Thesis advisors with specific suggestions concerning teaching assignments that would be particularly beneficial to the individual circumstances of a particular student are encouraged to share them with the director of teaching for consideration. However, final discretion for approval lies with the director of teaching who must pre-approve all assignments. Research Publication It is expected that thesis research will result in findings that are of sufficient quality and completeness to warrant publication in good quality peer-reviewed journals. At least one first-author peer-reviewed research paper must be accepted for publication prior to the Ph.D. thesis defense. The published paper or a letter from an editor indicating acceptance should be provided to the director of graduate studies before scheduling a final exam date. Thesis Defense and Presentation Students complete a thesis defense with their committee. Once this test is completed they must schedule a public thesis presentation. Pharmacology The Doctor of Philosophy in biomedical science with a pharmacology subprogram provides professional training for health science students and participates with other departments in educational and research activities such as the Medical Scientist Training Program, the Physician Scientist Training Pathway, the Molecular Medicine Program, the Neuroscience Program, the Holden Comprehensive Cancer Center, the Abboud Cardiovascular Research Center, and the UI Fraternal Order of Eagles Diabetes Research Center. The degree requires a minimum of 72 s.h. of graduate credit. Students must maintain a cumulative g.p.a. of at least. to earn the degree. The Ph.D. in biomedical science with a pharmacology subprogram requires the following course work.