Graduate Program in Molecular Medicine...The endocrine system exerts profound and significant regulatory effects upon the nervous system in humans and other species. The Brann Lab

STUDENT HANDBOOK

Graduate Program in Molecular Medicine

Ceramide (green) in motile cilia (purple)

Image from program alumnus Ji Na Kong, currently a Postdoctoral Fellow at MIT Cover of Molecular Biology of the Cell December 2015

Medical College of Georgia at Augusta University

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Welcome! The Molecular Medicine program combines the resources of basic science and clinical medicine for an interdisciplinary approach to understanding disease processes. This interdisciplinary program includes approximately 40 faculty members drawn from clinical and basic science departments. Students are encouraged to design their own program of study according to their interests and in consultation with their faculty mentor and advisory committee. Focused on discovering the molecular basis of human disease, research opportunities include neurobiology, immunology, molecular chaperones, cancer biology, regenerative medicine and reproductive medicine. This handbook is designed to guide you through the current course requirements, exam policies, and forms in concordance with The Graduate School’s PhD Guidebook: http://www.augusta.edu/gradstudies/students/current_students.php. Please know that my door is open to current, future, and past students. I look forward to assisting you in your journey towards a PhD and beyond. Sincerely,

Lynnette McCluskey, PhD Program Director

http://www.augusta.edu/gradstudies/students/current_students.php

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Program Contact Information Interim Chair, Department of Neuroscience & Regenerative Medicine Darrell Brann, PhD Regents' Professor and Interim Chair Department of Neuroscience & Regenerative Medicine Phone: (706) 721-0588 [email protected] Program Director Lynnette McCluskey, PhD Department of Neuroscience & Regenerative Medicine Office: CA-3016 Phone: 706-721-5616 Email: [email protected] Program Coordinator Deenie Cerasuolo Office: CA-4008 Phone: 706-721-0588 Email: [email protected] Molecular Medicine Graduate Education Committee (MMGEC) Lawrence Layman, MD (Clinical Representative) Department of Neuroscience & Regenerative Medicine Department of Obstetrics and Gynecology Office: CA-2006 Phone: 706-721-3832 Email: [email protected] Yukai He, MD/PhD Cancer Immunology, Inflammation and Tolerance Program Office: CN-4150 Phone: 706-721-2728 Email: [email protected] Anatolij Horuzsko, MD/PhD Chaperone Biology Program Office: CN-3154 Phone: 706-721-8736 Email: [email protected] Xingming Shi, PhD Institute of Molecular Medicine and Genetics Office: CA-2008 Phone: 706-721-1097 Email: [email protected]

mailto:[email protected]







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TABLE OF CONTENTS

Page Program Faculty……………………………………………………………5 Current Molecular Medicine Students and Alumni………………….11 Registration………………………………………………………………...12 Timeline to Graduation…………………………………………………...12 Molecular Medicine Curriculum………………………………………...13 Forms Required by the Graduate School……………………………..15 Advisory Committee and Meetings……………………………………..15 Comprehensive Exam…………………………………………………….16 Thesis Proposal……………………………………………………………17 Dissertation and Defense………………………………………………...17 Graduation…………………………………………………………………..18 Awards……………………………………………………………………....18 Leave Policy………………………………………………………………..18 Changing from a PhD to MS degree……………………………………18 Appendix: Seminar Synopsis sheet……………………………………26

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Molecular Medicine Program Faculty 2017

Darrell Brann, PhD (Department of Neuroscience & Regenerative Medicine) The endocrine system exerts profound and significant regulatory effects upon the nervous system in humans and other species. The Brann Lab focuses on understanding the actions and mechanisms of a key endocrine regulatory molecule, 17-beta-estradiol (E2), in the central nervous system. A significant difference in male and female physiology is the ability of females to secrete large amounts of E2 into the bloodstream in a cyclic pattern. Intriguingly, at menopause in females, there is a precipitous drop in E2 secretion, which coincides with an increase of neurological diseases (e.g., stroke, Alzheimer's disease and Parkinson's disease). These observations have led to the suggestion that E2 may exert neuroprotection and/or neural repair, which could delay onset and/or lessen the severity of neurological diseases. E2 also maintains a normal functioning reproductive system and has been reported to enhance working memory.

Richard Cameron, PhD (Department of Neuroscience & Regenerative Medicine) Our research is focused on understanding the cellular and molecular mechanisms that regulate the neuronal cell cycle during the development of the mammalian cerebral cortex. Specifically, we are interested in the role of the S-phase nuclear myosin, MYO16.

Esteban Celis, MD/PhD – GRA/Whitaker Eminent Scholar in Cancer (Cancer Immunology, Inflammation and Tolerance Program, AUCC) Dr. Celis’ current research pertains to recognition and destruction of tumor cells by T-lymphocytes, and his research interests focus on the development of immune-based therapies for cancer. Four areas of research are being investigated in his laboratory: 1) identification of T-cell epitopes at peptide level from known tumor-associated antigens; 2) overcoming immunological tolerance to self-non-mutated tumor-associated antigens as a way of eliciting strong and effective anti-cancer immunity; 3) regulation of T-cell responses to tumor cells by lymphokines and costimulatory signals; and 4) the role of helper T cells in the regulation for cytotoxic T cell responses to tumor antigens. Dr. Celis has been involved in several clinical trials evaluating therapeutic vaccines for cancer.

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Ahmed Chadli, PhD (Molecular Oncology Program, AUCC)

Breast cancer is the leading cause of cancer death among women worldwide and it consists of several subtypes. Hormone and targeted therapies have significantly improved the outcomes for patients with steroid receptor and HER2+ breast cancer subtypes. Most patients ultimately develop resistance to single pathway-targeted chemotherapies. Combinations of drugs have some success but they present combined side effects that decrease a patients’ quality of life. Moreover, there are no targeted therapies for triple-negative breast cancers. A critical barrier to progress in treating breast cancer is the absence of therapeutic strategies that function irrespective of subtype and that override resistance. Our goal is to improve the treatment of breast cancer by targeting tumor growth and blocking cancer cell proliferation without affecting normal cell proliferation. We aim to: 1) Identify new cancer therapeutics targeting molecular chaperones using novel highthroughput-screening strategies. 2) Dissect the Hsp90 chaperoning machine and its role in tumorigenesis using cellular and tissue-specific knockout mouse models. Our central hypotheses is that the co-chaperone UNC45A controls cancer cell proliferation through regulation of nuclear receptor transcriptional activities and that inhibition of UNC45A is a potential therapeutic strategy for all breast cancer subtypes.

Yan Cui, PhD (Cancer Immunology, Inflammation and Tolerance Program, AUCC)

Our research focuses on understanding the cellular and molecular mechanisms by which tumor-host interaction dictates the immunological landscape of the tumor microenvironment (TME). Chronic inflammation is a causative factor for cancer development. Furthermore, during tumor progression, tumor-host interaction often leads to tumor-induced immune tolerance and pro-tumor inflammation. Thus, better understanding and being able to manipulate immune landscape of the TME is of great clinical implication. Specifically, there are two research areas that we are actively pursuing: (1) illustrating the immune regulatory function of specialized fibroblastic reticular cells within the secondary lymphoid organs and the TME and their respective molecular mechanisms in mediating immune tolerance and tumor progression; (2) the immune regulatory function of p53 in tumor and the TME. The tumor suppressor p53 is the most frequently mutated/inactivated gene in tumors and sometimes in tumor stroma. Our recent study demonstrates that p53 inactivation/dysfunction in the TME skews the immunological landscape toward pro-inflammation, thereby promoting tumor progression. We are currently testing our hypothesis that targeted activation/restoration of the p53 pathway in the TME promotes antitumor immunity and can be used in combination with other active immunotherapies to maximize ultimate antitumor efficacy for tumors with wild-type p53, as well as those that incur p53 mutations.

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Quansheng Du, PhD (Department of Neuroscience & Regenerative Medicine)

One of the most critical steps during cell cycle is the correct segregation of sister chromatids into daughter cells. During mitosis, microtubules reorganize into a highly dynamic bipolar array known as mitotic spindle. Proper spindle organization and orientation are crucial for the asymmetric cell division of neuronal progenitor cells, where cell fate determinants are segregated to only one of the two daughter cells. Spindle orientation is also important during morphogenesis, for instance, in the maintenance of epithelial sheets. My lab is interested in the molecular and cellular mechanisms underlying mitotic spindle organization and spindle orientation. Our studies will help to identify therapeutic targets for cancer and birth defects.

Ali Eroglu, PhD, DVM (Department of Neuroscience & Regenerative Medicine)

My research interests include cell and tissue preservation; understanding molecular mechanisms of nuclear reprogramming; genomic imprinting and related disorders such as cancer; and gene targeting using embryonic stem cells

Yukai He, MD/PhD (Cancer Immunology, Inflammation and Tolerance Program, AUCC)

The research in my lab focuses on developing novel cancer vaccines and on effective immunological approaches for cancer therapy. We have used recombinant lentivector as the primary vaccine delivery vehicle over last decade. Our research allows us to elucidate the basic mechanism of T cell activation following recombinant viral vector immunization. Now we are focusing on the potential applications of antigen engineering and viral vectors mediated genetic immunization in tumor immunology and tumor immunotherapy. Current projects include: 1). Developing effective liver cancer vaccines; 2). Identifying and cloning TCR genes that can be used to engineer host T cells to allow adoptive T cell transfer to treat liver cancer; 3) Targeting effector phase to rescue the T cell function in immune suppressive tumor milieu; 4). Combinatorial approaches of immune therapy of vaccination and checkpoint blockade to improve cancer immune therapy.

Anatolij Horuzsko, MD/PhD ( Molecular Oncology Program, AUCC)

1) Understanding the molecular, biochemical and immunological functions of HLA-G and its potential use in organ transplantation (human and mouse models). 2) Biology of immune receptors on dendritic and T cells that promote immunological tolerance. 3) Molecular links between inflammation and cancer development, role of TREM-1 in tumorigenesis (human and mouse models).

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Carlos Isales, MD (Department of Neuroscience & Regenerative Medicine)

My main area of interest involves defining the role of nutrition in stem cell function in aging and how that impacts normal bone turnover. We have focused on dietary amino acids. We currently use both an in vitro model involving primary mouse mesenchymal stem cells and an in vivo model involving aging or calorically restricted mice. By combining these cellular and molecular approaches, we plan to define how aging decreases the stem cell regenerative potential.

Theodore Johnson, MD/PhD (Cancer Immunology, Inflammation and Tolerance Program, AUCC)

Neoplastic processes actively create immunosuppressive environments that drive systemic tolerance to cancer cells. Tumors develop exquisitely complex stromal networks that promote growth despite the presence of antigen-presenting cells (APCs) and tumor infiltrating lymphocytes. Although tumor-associated macrophages (TAMs) appear to be fully competent APCs, they process immense volumes of dead and dying tumor cells without inciting adaptive immune responses. Our laboratory uses a variety of solid tumor models to study the role of TAMs in regulating anti-tumor immune responses.

Lawrence Layman, MD (Department of Neuroscience & Regenerative Medicine)

Our laboratory is interested in genes important in human puberty, reproduction, and development. Humans with delayed puberty due to idiopathic hypogonadotropic hypogonadism (IHH)/Kallmann syndrome (KS) and women with congenital absence of the uterus and vagina are being characterized clinically and genes are being identified using innovative methods. Gene mutations are characterized and then studied in vitro to determine their functional effects; and further genotype/phenotype correlations are made. Mutations have been identified and characterized in genes including GNRHR, FSHB, CHD7, WDR11, and NELF, among others. Human, mouse, and zebrafish models are being utilized to further understand normal hypothalamic-pituitary gonadal axis development and function with regard to normal puberty and fertility.

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Santhakumar Manicassamy, MD (Cancer Immunology, Inflammation and Tolerance Program, GRUCC) Dr. Manicassamy is examining critical mechanisms that regulate adoptive immune responses at the mucosal surfaces of the gastro-intestinal track. New insights from Dr. Manicassamy’s research will shed light on interactions between commensal micro-organisms and how these interactions can become dysfunctional to cause increased risk of inflammatory bowel disease and colon cancers.

Lynnette McCluskey, PhD (Director - Graduate Program in Molecular Medicine - Department of Neuroscience & Regenerative Medicine)

My lab is interested in the role of the immune system in the normal and de/regenerating taste system. Following axotomy, taste neurons and their associated receptor cells are able to regenerate and make functional connections. This process appears to depend on a normal immune response to injury. We believe that studying the influence of leukocytes, cytokines, and adhesion molecules in the taste system will provide insight into novel ways to promote regeneration in the CNS. We are also interested in taste changes that occur during systemic and gastrointestinal inflammation.

Nahid F. Mivechi, PhD (Professor and Co-Leader, Molecular Oncology Program, AUCC ) The research interests of my laboratory are mainly focused on understanding the function of heat shock transcription factors and their downstream targets, molecular chaperones in cellular metabolism and reprograming that leads to tumorigenesis using both in vivo and in vitro model systems. Our current interest is focused on breast cancer; hepatocellular carcinoma; lung cancer and lymphoma research using both human and mouse models. For these studies, we have generated knockout mouse models to variety of molecular chaperones to determine if reduction or lack of specific molecular chaperones in specific tissues leads to altered metabolism and reduction or ablation of tumorigenesis which could serve as potential therapeutic targets.

Demetrius Moskophidis, MD (Molecular Oncology Program, AUCC )

1) Viral pathogenesis (Arenaviruses and Orthomyxoviruses). Regulatory of immune response during acute and persistent viral infections. 2) Function of stress proteins (molecular chaperones) in animal models knockout/transgenic mice) of human disease.

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David Munn, MD (Cancer Immunology, Inflammation and Tolerance Program, AUCC)

Macrophage and dendritic cell differentiation; regulation of T cell activation by antigen-presenting cells; regulation of immune function by indoleamine 2,3-dioxygenase (IDO) and tryptophan metabolism; clinical trials of IDO inhibitors in cancer and HIV.

Xingming Shi, PhD (Department of Neuroscience & Regenerative Medicine)

Osteoporosis is a major public health problem affecting 44 million Americans. The estimated direct health care costs for osteoporosis were $17 billion in 2001 and is rising. The research interest of my laboratory is to study the cellular and molecular mechanisms of glucocorticoid (GC)-induced osteoporosis and to search for new therapies for the treatment of this devastating disease.

Jianhua Xu, PhD (Department of Neuroscience & Regenerative Medicine) Synaptic transmission between neurons relies on neurotransmitter release during the precisely regulated exocytosis of synaptic vesicles. Vesicles after exocytosis are recovered via endocytosis, and mobilized to the releasable pool for future exocytosis. Such a vesicle recycling process plays an essential role in maintaining the synaptic transmission and the function of neuronal network. My lab is interested in the mechanisms of vesicle recycling in both health and disease conditions. Taking advantage of a large synapse in the brainstem - the calyx of Held, which is accessible to patch-clamp recording, optical imaging and molecular manipulation, we analyze individual steps of vesicle recycling with a temporal resolution of milliseconds.

Robert Yu, PhD, Med.Sc.D. (GRA Eminent Scholar in Molecular and Cellular Neurobiology-Department of Neuroscience & Regenerative Medicine My research concerns the chemistry, metabolism and biological function of complex glycoconjugates, particularly glycosphingolipids. These compounds play crucial roles in determining cellular properties such as intercellular interactions, recognition, and adhesion. In particular, we are developing an understanding of the role of glycoconjugates in cell proliferation and differentiation, as well as the metabolic basis and regulatory mechanisms for changes of their expression in the developing nervous system. A major trust of our more recent effort is on the glycobiology of neural stem cells. We are developing an understanding of the role of stage-specific glycoconjugates in governing events in cell differentiation and cell-fate determination via several signaling pathways. In addition, we are elucidating the basic mechanisms underlying a variety of neurodegenerative disorders, including autoimmune demyelinating neuropathies, multiple sclerosis, mucopolysaccharidoses, and sensorineural hearing loss, with a goal of developing novel strategies in disease diagnosis and therapy.

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Current Molecular Medicine Students Student Affiliation Aaron Fan Cancer Immunology, Inflammation and Tolerance Program Eun Kyung Ko Dept. Neuroscience and Regenerative Medicine Lauren Prusinski Department of OB/GYN Daniel Swafford Cancer Immunology, Inflammation and Tolerance Program Caryn Bird Cancer Immunology, Inflammation and Tolerance Program Mohamed Hussein Cancer Immunology, Inflammation and Tolerance Program Leidy Caraballo Galva Cancer Immunology, Inflammation and Tolerance Program Nada Aboellela Cancer Immunology, Inflammation and Tolerance Program

Molecular Medicine Program Graduates (Listed chronologically with most recent first)

Student Affiliation Tsadik Habtetsion, PhD Fred Hutchinson Cancer Center, Seattle, WA (Postdoctoral Fellow) Joanna Erion, PhD Augusta University (Teaching Faculty) Ji Na Kong, PhD M.I.T. (Postdoctoral Fellow) Eslam Mohamed, PhD Moffit Cancer Center (Postdoctoral Fellow) Connie Chung, PhD Associate Scientist, Vivex, Miami, FL Jill Bradley, PhD University of South Carolina Upstate (Postdoc) Devaki Kumarhia, PhD Centers for Disease Control and Prevention Rahul Shinde, PhD University of Toronto (Postdoctoral Fellow) Yan Wang, PhD Children’s Hospital of Pittsburgh (Postdoctoral Fellow) Qian He, PhD Stanford University (Postdoctoral Fellow) Haiyun Liu, PhD Johns Hopkins University (Postdoctoral Fellow) Mona El Rafaey, PhD Ohio State University (Postdoctoral Fellow) Kapil Chaudhary, PhD Washington University (Physician Scientist Fellow) Buvana Ravishankar, PhD Genentech, Inc. (Postdoctoral Fellow) Lingqian Li, PhD University of Washington (Senior Fellow) Chaitanya Patwardhan, DMD/PhD University of Pennsylvania (Clinical Fellow) ` Davies Agyekum, MD/PhD University of Pennsylvania (Resident) Samuel Quaynor, MD/PhD University of Chicago (Resident) Anthony Florschutz, MD/PhD Baycare Medical Group, Tampa, FL (Orthopedic Surgeon) Juhi Ojha, PhD University of California San Francisco (Postdoctoral Fellow) Wonkyoung Cho, PhD Augusta University Cancer Center (Research Associate) Lakiea Bailey, PhD Sickle Cell Community Consortium (Executive Director) Haixia Qin, MD/PhD Loma Linda University School of Medicine (Associate Professor) Kyungsoo Ha, PhD Augusta University (Postdoctoral Fellow) Tiffany Floyd, PhD Georgia Military College (Adjunct Faculty) Pamela Wall-Steen, PhD University of South Carolina at Aiken (Adjunct Faculty) Daniel Eisenman, PhD Medical University of South Carolina (Biosafety Officer) Durga Udayakumar, PhD UT Southwestern Medical Center (Res Asst Prof; Radiation

Oncology) Rusty Johnson, MD/PhD Johns Hopkins University (Clinical Fellow in Hematology/Oncology)

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Ceba Humphrey, MD/PhD Knoxville, TN (Surgeon) Anna Manlapat, PhD Johns Hopkins University (Staff, Office of Graduate Medical

Education) Faith Mmanywa, PhD Duke University Medical Center (Staff Scientist; Bacteriology Research Unit) Darin Keskin, MD/PhD Dana Farber Cancer Institute (Faculty) David Kahler, PhD Columbia University FACS Facility (Director) Ted Johnson, MD/PhD Augusta University (Dept. of Pediatrics and Cancer Center;

Assistant Professor) Kannan Krishnamurthy, PhD Memorial Sloan-Kettering Cancer Center, Office of Technical Development (Licensing Manager) Kris Dhandapani, PhD Augusta University (Associate Professor in Neurosurgery) Ning Xu, MD/PhD UCLA Cedars Sinai (Project Scientist) Andrew Clark, MD/PhD Carolina Ob/Gyn., Med. Health Women & Children’s Hospital (Staff Physician)

Registration Register for courses online with POUNCE when you receive an email notification from the Registrar’s Office. Please register as early as possible. If you miss the deadline, you must wait until the first day of class to register and will be assessed a $50 late fee. Also, if there is a “hold” on your account you will not be able to register until it the hold is cleared. Most holds are due to immunization issues, and may take several days to clear.

Timeline for PhD Program

A broad overview of major milestones is as follows: Program Entry Comprehensive Exam Thesis proposal and advance to candidacy Write and defend thesis. There is a 7-year limit on time to graduation. A detailed timeline can be found at the following link and in the Appendix: http://www.augusta.edu/gradstudies/students/current_students.php Note that deadlines for requirements must be completed on time. It is important that you check your progress often (i.e. at least twice a year) to make sure you are on track.


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Molecular Medicine Curriculum

Students entering the Graduate Program in Molecular Medicine will have already taken the required courses from the Fall and Spring semesters, plus 4 credit hours of selective courses of the first year. First Year Biomedical Sciences PhD Core Curriculum Semester One (Fall)

• BIOM 8012 - Scientific Communications (1 credit hour) • BIOM 8021 - Biochemistry & Gene Regulation (5 credit hours) • BIOM 8022 - Molecular Cell Biology (5 credit hours) • BIOM 8011 – Responsible Conduct of Research (1 credit hour) • BIOM 8040/BIOM 8050 – Introduction to Faculty Research (2 credit hours)

Semester Two (Spring) • BIOM 8033 - Integrated Systems Biology (6 credit hours) • BIOM 8060 - Intro to Research II (4 credit hours) AND TAKE FOUR CREDIT HOURS FROM THE FOLLOWING SELECTIVES: • BIOM 8215 - Fundamentals of Oncology I (2 credit hrs) • BIOM 8080 - Neuroscience I (4 credit hrs) • BIOM 8090 - Fundamentals of Genomic Med (2 credit hrs) • BIOM 8230 - Biology of Proteins in Disease (2 credit hrs) • BIOM 8240 - Intro to Immunology and Infectious Disease (2 credits hrs) • BIOM 8030 - Experimental Therapuetics (2 credit hrs)

Semester Three (Summer) *Students choose a lab and program at the beginning of the summer semester

• STAT 7070 Biomedical Statistics Upper-level coursework. Trainees in the Graduate Program in Molecular Medicine must complete 6 credit hours of advanced electives. Upper-level courses may be chosen from those offered by the Molecular Medicine graduate program, listed below. Students may also choose 1st year selectives previously not taken or graduate courses offered by other biomedical graduate programs. This flexibility allows students across diverse research areas to individually tailor their program of study. A course proposal is developed by the primary advisor in consultation with the thesis committee, and must be approved by Dr. McCluskey. Trainees must enroll in MOL9030 and MOL9040 each semester until graduation (not including the summer semesters). These requirements ensure attendance at research seminars and Molecular Medicine Journal Club, respectively. Research hours complete the coursework each semester.

• MOL8110 – Advanced Topics in Neurobiology (3 credit hours) This course will cover current topics in neurobiology including developmental neurobiology,

intracellular and intercellular communication, neurodegeneration and other diseases of the nervous system. The course will emphasize an understanding of the neurochemical and molecular mechanisms under normal conditions and leading to dysfunction. The course will focus on developing a critical understanding of the current scientific literature in neurobiology and preparing the students for careers in neurobiological research.

http://catalog.gru.edu/preview_program.php?catoid=16&poid=1052











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• MOL8130 - Advanced Topics in Molecular and Cellular Immunology (3 credit hours) This course will cover current topics in immunology including tolerance, thymocyte

development, lymphocyte activation, immunological memory, cell adhesion and cell cycle control. The course will emphasize an understanding of the molecular mechanisms of immune responses and will focus on gaining a critical understanding of the current scientific literature in immunology.

• MOL9010 – Advanced Seminar in Molecular Medicine (1 credit hour) Seminar-style course covers a single, current topic in Molecular Medicine on a rotating basis

each fall and spring semester. Topics include Biology of Aging, Translational Reproductive Medicine, Regenerative Medicine, Molecular Immunology, Developmental Neurobiology, and Molecular Chaperone Biology and Radiobiology.

• MOL9020/MOL9030 – Seminar in Molecular Medicine (1 credit hour) This course will provide training in critical evaluation of basic biomedical research. Students

will be expected to attend seminars given by both internal and external speakers to provide written summaries of some of the topics presented. This course is offered in the fall semester. Prerequisites: Entry into the Molecular Medicine graduate program. Required course for all Molecular Medicine students each fall (MOL9020) and spring (MOL9030) semester until completion of the dissertation defense.

Course requirements: Students may attend seminars sponsored by any academic or research

unit on campus. Please keep track of the seminar title, speaker, and date. This information must be submitted to Deenie by the end of the spring semester to receive course credit. You must attend 20 seminars and provide 5 synopses (see Appendix I) by the end of the Spring seminar. This represents seminar attendance during both the Fall and Spring semesters.

• MOL9040 – Molecular Medicine Journal Club (1 credit hour) This course will provide 1) In-depth discussion of current topics in Molecular Medicine; 2) The

opportunity to critically evaluate and present current papers; 3) Discussion of current techniques in the field; and 4) Faculty mentoring of students in career skills (e.g. searching for postdoc positions, job interviews, balancing family and science). Each week the discussion will focus on a current scientific paper, classic techniques paper, or opinion paper, depending on the goal described above. Each senior student (third year plus) will select and present a paper to the class. Presentations will be followed by a class discussion. Feedback on student performance will be provided by the faculty mentor assigned to the topic. Discussions of current techniques and career skills will be led by faculty experts. This course will enhance students’ ability to analyze and present scientific literature. Required course for all Molecular Medicine students each fall and spring semester until completion of the dissertation defense.

• The following courses offered by other departments are eligible upper-level electives. Please

see Dr. McCluskey for approval of additional courses. First year selectives that you have not already taken Spring BCMB 8201 Current Topics and Techniques in Molecular Biology (3 credits) Fall BIOM 8130 Scientific Grant Writing (1 credit) Fall GNMD 8050 Computational Methods in Genomics and Genetics (4 Credits)

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Fall GNMD 8052 Functional Genomics and Proteomics Using Animal Models (3 Credits)

Spring GNMD 8051 Translational Genomics and Proteomics (3 Credits) Research Hours • MOLM 9210 – Investigation of a Problem (variable credit hours). Investigation of a Problem

must be taken every semester until admission to candidacy requirements are complete (i.e. the research proposal is approved by the thesis committee). Adjust the number of credit hours for this course so that you are enrolled for a total full-time load of 12 credit hours/semester.

• MOLM 9300 – Research in Molecular Medicine (variable credit hours). Research must be

taken every semester after admission to candidacy (i.e. after you have submitted your approved proposal) until dissertation requirements are met. Adjust the number of credit hours for this course so that you are enrolled for a total full-time load of 12 credit hours/semester.

Forms Required by the Graduate School

It is the student’s responsibility to submit required forms to the Graduate School in a timely manner. Forms can be found on the Graduate School website and in the Appendix. Please bring completed forms to the Program Director (Dr. Lynnette McCluskey) then Program Chair (Dr. Lin Mei) for signatures as specified. Angie can also assist in getting signatures and then submitting forms to the Graduate School. **It is strongly suggested that you keep a copy of forms for your records.

Advisory Committee and Meetings

An advisory committee is formed soon after the student joins the mentor’s lab. The committee is composed of four faculty members in addition to the mentor. The purpose of the committee is to guide the student’s research and training. At least four of five committee members must hold graduate school appointments. Molecular Medicine faculty and those from other graduate programs are eligible to serve on the advisory committee, though the student’s primary mentor must have an appointment with Molecular Medicine. Students must form a committee by the end of the fifth semester. Failure to form a committee and hold a meeting by the end of the fifth semester/second Spring will result in a grade of “Unsatisfactory” in MOLM 9210 Investigation of a problem, in accordance with the policy of the Graduate School. http://www.augusta.edu/gradstudies/students/current_students.php The advisory committee must approve the student’s proposed course of study during the initial meeting (or soon after). The coursework proposal form can be found at: http://www.augusta.edu/gradstudies/students/current_students.php Students must hold a committee meeting at least every three semesters (though more frequent meetings are encouraged). For example, if you have a committee meeting in October, your next meeting must occur before the end of the fall semester in the subsequent calendar year. Failure to hold a yearly committee meeting will result in a grade of “Unsatisfactory” in MOLM 9210 / MOLM 9300. Exceptions are granted only in special circumstances and must be approved by the Dean of the Graduate School. It is important for you to document suggestions from your committee in the space provided on the form. In other words, summarize committee input, then get signatures. Submit the advisory committee meeting form found at the following link: http://www.augusta.edu/gradstudies/students/current_students.php




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Please submit the research progress report as instructed on the form above during any semesters in which committee meetings were not held.

Comprehensive Exam

• The comprehensive exam in Molecular Medicine conforms to the format required by the Graduate School. The Graduate School requires that the exam is completed by the end of the seventh semester for students. Failure to complete the exam by the end of the second year will result in a “U” (i.e. Unsatisfactory) grade in MOLM 9210 Investigation of a Problem. For students entering graduate school after Fall 2016, the entire policy can be found at the following Graduate School link: http://www.augusta.edu/gradstudies/students/current_students.php

• The purpose of the exam is to test the student’s understanding of their subdiscipline of Molecular Medicine. As part of the requirement, students should demonstrate an adequate grasp of the primary literature in the area most relevant to the student’s work. The student should also be familiar with basic concepts, paradigms, and methodology in the most relevant subdiscipline, which is expected to be broader than the student’s specific area of specialization. The Advisory Committee will evaluate whether the student exhibits these skills at a level appropriate for a student in their second year of graduate study.

• The exam will consist of the following format:

Written exam consisting of up to 5 essay questions administered over 4 hrs AND

A two-hour oral exam held within 2 weeks of the written portion

• The exam questions will be written and graded by the Advisory Committee. The Advisory Committee will appoint an Exam Chair to administer the written exam and compile grades prior to the oral exam. The student’s major Advisor is not eligible to serve as Exam Chair. The Exam Chair will also serve as a liaison to the Dean’s Office (duties formerly performed by the Dean’s Representative). Please contact Deenie Cerasuolo ([email protected]) to arrange assistance in proctoring the exam if needed. You will need to report your cumulative grades on the written and oral portions to the Graduate School (see form at the end of this section), so please ask your Exam Chair for this information if necessary.

• The Honor Code is in effect for the qualifying exam. Plagiarism and access of unauthorized

materials during the exam will result in notification of the Dean and referral to the Honor Court for possible expulsion.

• Grading will follow the following scale:

A – F (A= 5 points, B= 4points, C= 3 points, D= 2 points and F= 1 point) WRITTEN EXAM: Essay exam – No multiple choice questions. Each written exam question will be given a grade A-F. Grades will be converted to numerical value and averaged for final


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score. If multiple faculty members grade questions, the average score for each question will be used for the overall average score. A 3.5 is required for passing. ORAL EXAM: Each faculty member will provide a score of A-F either based on answers to their questions or overall (programs decide – and document for standard practice). Programs can decide if there will be a discussion among faculty prior to score submission. Faculty submit scores anonymously to the Exam Committee Chair. Chair will convert scores to numerical value and average for final score. An average score of 3.5 is required for passing. No further discussion to adjust or change scores is permitted once scores have been submitted to the Chair

• A cumulative score of 75 is required to pass the oral + written exam.

• A student failing the written or the oral part of the comprehensive exam will be granted one opportunity to retake each portion after additional study. The exam is typically retaken within 3 months, but must be completed within 6 months. Note that the student remains enrolled in research hours and is not excused from lab work. A second failure of the Comprehensive Exam will be grounds for dismissal from the Graduate School.

• Please complete and submit the following form upon completion of the comprehensive exam:


Thesis Proposal

A 5-10 page written research proposal is a separate requirement of CGS, and is independent of the comprehensive exam. This proposal should be the student’s effort developed in consultation with the Advisor and Advisory Committee. After the proposal is completed, please instruct advisory committee members to complete and submit (1) the proposal form (Appendix II) and (2) the research proposal rubric (Appendix III) to the Graduate School. Note that you must be admitted to candidacy (i.e. submit forms indicating completion of comprehensive exam and research proposal; Appendix) at least two semesters prior to the dissertation defense. Formatting requirements for the Proposal format are included in the PhD handbook: http://www.augusta.edu/gradstudies/students/current_students.php

Dissertation and Defense Please refer to the following Graduate School guide to prepare for your dissertation and defense: http://www.augusta.edu/gradstudies/students/current_students.php Reader: arrange for one faculty member to serve as a reader. Their purpose is to provide fresh input on your thesis to complement your advisory committees’ efforts. For Molecular Medicine, the reader may be from any department. Faculty outside the institution may also participate as a reader, but travel expenses are not provided by the program or MCG-AU. Consult with your mentor to determine who can best fulfill this role.




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Graduation

Students are now required to submit an application for graduation. The link to this process can be found at: http://www.augusta.edu/registrar/healthsciences.php

Awards

Molecular Medicine students are eligible for several awards associated with Graduate Research Day, including the Molecular Medicine Program Award. Awards are based on poster scores given by faculty judges. All Molecular Medicine students that present posters at Graduate Research Day are considered for this award; no additional application is necessary. Molecular Medicine students are also eligible for the Rasmussen Award, presented annually to recognize research accomplishments. This award honors the late Dr. Howard Rasmussen, founder of the Institute of Molecular Medicine and Genetics. Dr. Rasmussen was a staunch supporter of graduate student research. His own work resulted in hundreds of publications, and was recognized by numerous awards. The winner of the Rasmussen Award will receive $500. Two runners-up will receive $250 each. Mentors provide letters of nomination documenting the nominee’s research record and scientific potential. The program director will call for nominations each fall, and winners are chosen by majority vote of the Molecular Medicine Graduate Education Committee (MMGEC). Travel Award funds are available through the Graduate School for students presenting their work at national / international meetings as first author. Please complete the form found in the Appendix, have your mentor sign it, and submit to Deenie Cerasuolo. Deenie will also assist you in completing a Travel Request and the forms for travel reimbursement when you return.

Leave Policy

Students may receive permission to be off campus for up to 30 days (including weekends and holidays) while enrolled. Please get approval from your mentor and Dr. Lynnette McCluskey, and give the form to Deenie for submission to the Graduate School. The form for permission to be off-campus can be found in the Appendix. For maternity/parental leave and medical leave which may require more than the 30 days, up to 6 weeks maximum may be considered. Leave must be negotiated between the student, her/his advisor and Dr. Patricia Cameron in the Graduate School.

Changing from the PhD to a MS degree If you are considering this option it is recommended that you speak to your Advisor and Program Director for guidance.

The Doctor of Philosophy program with a major in Molecular Medicine starts as a common program for the students first year of enrollment. Students enter via a common admission process into the Biomedical Sciences PhD program not into a specific major. First year students complete a common set of core courses and at the end of their first year, choose a research mentor, join a laboratory and declare their program/major. Thus the “Biomedical Science” PhD curriculum schema from which the students will have the option to “exit” for their MS degree for the nine majors is essentially identical with the primary exception of their program/major specific electives and can be summarized as follows:

http://www.gru.edu/registrar/healthsciences.php

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“Biomedical Science” PhD Curriculum Schema - Doctor of Philosophy with a Major in Biochemistry and Cancer Biology; Cellular Biology and Anatomy; Genomic Medicine; Molecular Medicine; Neuroscience; Pharmacology; Physiology; and Vascular Biology FALL (SEMESTER 1) SPRING (SEMESTER 2) Summer (3) YEAR 1 42 credit hours

SGSS 8011(1): Responsible conduct of Research SGSS 8012(1): Scientific Communication SGSS 8021 (5): Biochemistry SGSS 8022 (5): Molecular Cell Biology SGSS 8040(2): Introduction to Faculty Research SGSS 8050 (2): Introduction to Research I

SGSS 8033: Integrative Systems Biology (6) SGSS 8060: Introduction to Research II (4)

SELECTIVE COURSES: (Choose 4 credit hours):

• SGSS 8080 (4): Neuroscience I • SGSS 8090 (2): Fundamentals of

Genomic Medicine • SGSS 8030(2): Experimental

Therapeutics • SGSS 8215 (2) Fundamentals of

Oncology • SGSS 8230 (2) Biology of

Proteins in Disease • SGSS 8240 (2) Introduction to

Immunology

STAT 7070(3): Biomedical Statistics xxxx9210(9) Investigation of A Problem

16 credit hours 14 credit hours/30 12 credit hours/42

FALL (SEMESTER 4) SPRING (SEMESTER 5) SUMMER (6) YEAR 2

36 credit

hours

XXXX 9210 (1-11): Investigation of A Problem XXXX 9010 (1) Seminar in XXXX Possible elective(s)

XXXX 9210 (1-11): Investigation of A Problem XXXX 9010 (1) Seminar in XXXX Possible elective (s)

XXXX 9210 (12): Investigation of A Problem

12 credit hours/54 12 credit hours/66 12 credit hours/78 FALL (SEMESTER 7) SPRING (SEMESTER 8) SUMMER (9) YEAR 3

36 credit hours




12 credit hours/90 + PhD COMPREHENSIVE EXAM

12 credit hours/102 12 credit hours/114 + PhD RESEARCH PROPOSAL

FALL SPRING SUMMER YEAR 4-7

XXXX 9300 (1-11): Dissertation Research XXXX 9010 (1) Seminar in XXXX

XXXX 9300 (1-11): Dissertation Research XXXX 9010 (1) Seminar in XXXX

XXXX 9300 (1-12): Dissertation Research

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XXXX

depends on the major Curriculum Revisions for the “Biomedical Science” PhD Curriculum: Change of Degree Master’s Options for Biomedical Sciences PhD Students:

I. “Fallback” to MS; post- PhD candidacy: currently BOR approved option for those who have entered into candidacy but are not able to complete the PhD program. These students are expected to have generated enough data to write and defend a Master’s thesis within one semester. These students will:

• meet with their advisor and committee to present their progress to date to assess the Masters option and determine if a plan/outline for a Master’s Thesis is sufficient or if a research proposal is first required. It is anticipated that the majority of students will have made sufficient progress and generated enough data to be able to write their MS thesis and only need an approved plan of action/outline for thesis.

• have (documented) support from their advisor and agreement/approval by PhD committee members, program director and TGS dean to change degree programs – and have determined if they will write a MS outline / plan or be required to submit a MS research proposal

• submit to TGS dean for final approval, a change of degree form (PhD MS) with all appropriate signatures, a written plan/outline with expectations (or MS research proposal), an updated coursework proposal form and a timeline (typically one semester) for completion of the MS program.

• have one full semester to complete their Master’s thesis after the final approval change to a MS degree program. Special exceptions to the one semester limit can be granted by the dean of The Graduate School.

• maintain their GRA status (stipend and insurance paid by the mentor) for at least one full semester after final approval change from PhD to a MS degree program. GRA status and funding beyond one semester is not automatic. Students may be required to pay tuition and fees after one semester in the Masters Program.

• write and defend a Master’s thesis (TGS standard or alternate format)

I.“Biomedical Science PhD”MS option: “Fallback” to MS; post- PhD candidacy FALL (SEMESTER 1) SPRING (SEMESTER 2) Summer (3) YEAR 1

SGSS 8011(1): Responsible conduct of Research SGSS 8012(1): Scientific Communication SGSS 8021 (5): Biochemistry SGSS 8022 (5): Molecular Cell Biology






12 credit hours /126-4th 12 credit hours/138-4th 12 credit hours/150 4th

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42 credit hours

SGSS 8040(2): Introduction to Faculty Research SGSS 8050 (2): Introduction to Research I


Oncology • SGSS 8230 (2) Biology of Proteins in

Disease • SGSS 8240 (2) Introduction to

Immunology 16 credit hours 14 credit hours/30 12 credit hours/42

FALL (SEMESTER 4) SPRING (SEMESTER 5) SUMMER (6) YEAR 2 36 credit hours




12 credit hours/54 12 credit hours/66 12 credit hours/78 FALL (SEMESTER 7) SPRING (SEMESTER 8) SUMMER (9) YEAR 3 XXXX 9210 (1-11): Investigation

of A Problem XXXX 9010 (1) Seminar in XXXX Possible elective (s)



12 credit hours + PhD COMPREHENSIVE EXAM

12 credit hours 12 credit hours + PhD RESEARCH PROPOSAL

Any student changing to MS degree AFTER being admitted to PhD candidacy will have completed at least 6 and typically 9 semesters in the PhD program. Changing to a MS degree at this point will be considered a FALL BACK MS option. + MS THESIS PROPOSAL or plan - approved semester before degree change

MS semester 1 (maintain GRA status) MS semester 2 – by exception with permission of mentor, program director and Dean of TGS

Upon change to MS- YEAR 3, 4, 5, 6, or 7

XXXX 7300 (11-12): Masters Research XXXX 9010 (1) Seminar in XXXX (optional)

XXXX 7300 (9-12): Masters Research

12 credit hours + MS thesis outline plan or MS THESIS PROPOSAL + MS THESIS DEFENSE unless approved for MS semester 2

9-12 credit hours + MS THESIS DEFENSE

II. “Fallback” to MS post comprehensive exam / pre- PhD candidacy: these students will

have attempted (but not passed) or completed (passed) their comprehensive exam but not entered candidacy. These students are required to have generated enough data to write a Master’s Research Proposal and write and defend a Master’s thesis typically within one semester. If they have failed their comprehensive exam, do not have enough data, and the Master’s thesis proposal is not acceptable, the student will be recommended for dismissal. These students will have the same requirements and time limitation and follow the same process as the Post-Qualifying students detailed above (I.). They will continue as GRAs in

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their mentor’s lab with stipend and insurance funding support provided by their mentor for at least one full semester. Special exceptions to extend beyond one semester limit can be granted by the dean of The Graduate School. GRA status and funding beyond one semester is not automatic. Students may be required to pay tuition and fees after one semester in the Masters Program.

II. “Biomedical Science PhD”MS option: “Fallback” to MS post comprehensive exam / pre- PhD candidacy FALL (SEMESTER 1) SPRING (SEMESTER 2) Summer (3) YEAR 1 42 credit hours

SGSS 8011(1): Responsible conduct of Research SGSS 8012(1): Scientific Communication SGSS 8021 (5): Biochemistry SGSS 8022 (5): Molecular Cell Biology SGSS 8040(2): Introduction to Faculty Research SGSS 8050 (2): Introduction to Research I






Oncology • SGSS 8230 (2) Biology of Proteins in

Disease • SGSS 8240 (2) Introduction to

Immunology



FALL (SEMESTER 4) SPRING (SEMESTER 5) SUMMER (6) YEAR 2 36 credit hours




12 credit hours/54 12 credit hours/66 12 credit hours/78 FALL (SEMESTER 7) MS semester 1

(maintain GRA status) MS semester 2 – by exception with permission of mentor, program director and Dean of TGS

YEAR 3 XXXX 9210 (1-11): Investigation of A Problem XXXX 9010 (1) Seminar in XXXX Possible elective (s)



12 credit hours /90 + PhD COMPREHENSIVE EXAM + MS THESIS PROPOSAL

12 credit hours/102 + MS THESIS PROPOSAL + MS THESIS DEFENSE or MS semester 2 if extension approved

9-12 credit hours + MS THESIS DEFENSE

Any student changing to MS degree AFTER attempting PhD COMPREHENSIVE exam will have completed at least 6– typically 7 semesters in the PhD program.

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XXXX depends on the major

III. “Step Ahead” to Master’s Degree - Change to Masters program after successful

academic completion of 1st year of biomedical science PhD core curriculum and who do not find a PhD mentor and join a permanent lab after the Spring rotations. In order to enter the Step Ahead Master’s Program, students must have at least

completed the entire first year Biomedical Sciences PhD curriculum and be in good academic standing (GPA 3.0 or higher with no unsatisfactory grades).

Most students have found a lab to complete their PhD in by the end of the Spring semester of their first year of enrollment. If no PhD mentor is identified by the end of that Spring semester, summer rotations will be arranged with the assistance of the First Year Program Director.

If no mentor is identified by the end of the registration period for the upcoming Fall semester, the student will be given the option of submitting a Change of Degree application (from PhD to Masters) to the Dean of The Graduate School.

The alternative is to follow the standard process for a student failing to progress academically.

The Graduate School dean will consult with the appropriate Program Directors and faculty before accepting the student into the Master’s Program.

If accepted into the Master’s Program, the student will not receive a GRA and will be required to pay the appropriate tuition and fees for their residency status (Georgia resident or non-resident).

If the student finds a mentor during the summer after they have submitted a Change of Degree application, they can withdraw their application and continue in the PhD program. This option would no longer be applicable after the Fall registration period closes.

Program Directors will create a list of principal investigators (PI) willing to mentor a Master’s student in their lab. Students will interview with a PI (or PIs) of their choice from this list and select a lab to join to complete their Master’s program by a mutual decision between the mentor and student.

The student will have two semesters in the Master’s mentor’s lab to complete the program

The student will be required to form a standard Master’s thesis committee by the end of the first month in the laboratory (at the latest)

A Master’s thesis proposal must be completed and approved by the end of the first semester in their Master’s lab.

A Master’s thesis must be written and successfully defended by the end of the second semester in the Program.

Special exceptions to deadlines can be granted by the dean of The Graduate School.

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III. “Biomedical Science PhD” MS option: “Step Ahead” - After successful academic completion of 1st year of biomedical science PhD core curriculum – Pre-PhD mentor selection FALL (SEMESTER 1) SPRING (SEMESTER 2) Summer (3) YEAR 1 SGSS 8011(1): Responsible

conduct of Research SGSS 8012(1): Scientific Communication SGSS 8021 (5): Biochemistry SGSS 8022 (5): Molecular Cell Biology SGSS 8040(2): Introduction to Faculty Research SGSS 8050 (2): Introduction to Research I






Oncology • SGSS 8230 (2) Biology of

Proteins in Disease • SGSS 8240 (2) Introduction to

Immunology



MS semester 1 (no GRA status)

MS semester 2 (no GRA status)

MS semester 3 – by exception with permission of mentor, program director and Dean of TGS (no GRA status)

YEAR 2 XXXX 7300 (8-12): Masters Research XXXX 9010 (1) Seminar in XXXX (optional) Possible elective(s)



9-12 credit hours/51-54 + MS THESIS PROPOSAL

9-12 credit hours/60-66 credit hours total + MS THESIS DEFENSE

9-12 credit hours/69-78 + MS THESIS DEFENSE

Any student changing to MS degree AFTER successful completion of the first year biomedical science PhD core curriculum in good academic standing will have completed 3 semesters and be required to complete an additional 2 semesters in the Master’s mentor’s lab (minimum 9 credit hours/semester). XXXX depends on the major

IV. ““Step Ahead” to Master’s Degree: Change to Master’s program post-PhD mentor selection; post-first year and Pre-comprehensive exam. The actual plan and timeline will depend on how many semesters the student has completed and how much data they have

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generated. In some cases it may be more like the “step ahead” process and in others more like the “fall back” process. The mentor, committee members and student will work together to assess progress to date and determine which process (step ahead/fall back) is most appropriate. Either way: The student will have up to 2 semesters after changing to the Master’s program to

complete the program. • The student will continue in their mentor’s lab. • GRA status and funding is not automatic. Students may be required to pay tuition

and fees after one semester in the Masters Program. If the student does not have a thesis committee and/or sufficient data to immediately write a thesis proposal then:

The student will be required to form a standard Master’s thesis committee by the end of the first month (at the latest) after approval of their change to a Masters program if they have not yet formed their PhD thesis committee

A Master’s thesis proposal must be completed and approved by the end of the first semester in their Master’s lab.

A Master’s thesis must be written and successfully defended by the end of the first or second semester in the Program.

• Special exceptions to deadlines can be granted by the dean of The Graduate School If the student does have a thesis committee and sufficient data to write a thesis proposal then they (with support and approval as outlined above (I.)) may opt for to write and defend Master’s thesis within one semester in which case they will have the same requirements and follow the process as the Post-Qualifying students detailed above in (I.). ________________________________________________________________________________ All students who fail to progress academically in the PhD or Master’s program will be subject to academic dismissal. The Dean will have the option of allowing the student to withdraw prior to any other action being taken. Curriculum revision includes the proposal of one new course to indicate enrollment in Master’s research. Course =- XXXX 7300 Masters Research; (Variable credit hour 1-12; repeatable for credit); XXXX determined by the major code (e.g. VBIO for Vascular Biology etc).

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APPENDIX Seminar synopsis sheet

Your name: _____________________ Mol Med seminar course (Fall MOLM9020/Spring 9030) requirements You must register for this course during each academic year (fall + spring semester) For Fall & Spring semesters combined you need to attend:

• 20 seminars by end of Spring semester (Provide Deenie Cerasuolo with the name of speaker, title of talk, date)

• 5 synopses by end of Spring semester

SEMINAR STUDENT SYNOPSIS SHEET

Date:

Speaker:

Topic:

What were the major questions, approaches, and conclusions?

Graduate Program in Molecular Medicine...The endocrine system exerts profound and significant regulatory effects upon the nervous system in humans and other species. The Brann Lab

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