BMB PhD Student Handbook - Augusta University · immune responses at the mucosal surfaces of the gastrointestinal tract. His research will shed light on interactions between commensal

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BIOCHEMISTRY &

CANCER BIOLOGY

GRADUATE PROGRAM 2017

DOCTORAL STUDENT HANDBOOK

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TABLE OF CONTENTS

General Information..................................................................................................................3 Location and Office Hours Biochemistry & Molecular Biology Phone Numbers Important Campus Phone Numbers MCG Websites Welcome to BCB at MCG Mission Statement……………………………………………………………… 4 Faculty Research………………………………………………………………… 5-7 General Expectations………………………………………………………….. 9 Overview………………………………………………………………………… ...............................9 Degree Timeline…………………………………………………………………. ..............................9 Major Advisor…………………………………………………………..... ....................................... 10 Advisory Committee……………………………………………………………… 10-11 Coursework…………………………………………………………… 11-14 Landmarks to Graduation Comprehensive Examination……………………………………………… 15-16 Research Proposal………………………………………………………… 17 Dissertation……………………………………………………………… 18 Thesis Defense……………………………………… 18-19

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General Information

Department of Biochemistry & Molecular Biology Location

1410 Laney Walker Blvd., Cancer Research Center

Department of Biochemistry & Molecular Biology Phone Numbers

Chair: Vinata Lokeshwar, PhD 706-721-3271 Program Director: Darren Browning, PhD 706-721-9526 Department Manager: Bennie Brisco 706-721-0665 Clerkship Program Specialist: Kim Lord: 706-721-7658 Administrative Office 706-721-3757

Important Campus Phone Numbers

Academic Admissions 706-721-2725

Cashier’s Office 706-721-2926

Financial Aid Office 706-721-4901

Graduate Studies Office 706-721-3278

Housing Office 706-721-3471

Registrar’s Office 706-721-2201

Student Affairs 706-721-3356

Student Health 706-721-3448

Public Safety 706-721-2911

Housekeeping 706-721-2040 Chemical Safety 706-721-2591 Radiation Safety 706-721-9826 Information Technology 706-721-4000 MCG Workshop 706-721-2040

Laboratory for Animal Services 706-721-3421 Flow Cytometry 706-721-7323 Fisher Rm. 706-721-0601 BioRad 706-721-7670 Sigma 706-721-0601

MCG on the Web

AU Home page: http://www.augusta.edu

Biochemistry & Molecular Biology: http://www. augusta.edu/mcg/bmb/

Cancer Center: http://www. augusta.edu/cancer/

College of Graduate Studies: http://www. augusta.edu/gradstudies/

CGS PhD Student Guides/Policies http://www.augusta.edu/gradstudies/current_students

http://www.augusta.edu/

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


Biochemistry and Cancer Biology

Mission Statement

The central mission of the Biochemistry and Molecular Biology Program is to apply rigorous scientific principles to understand the molecular and biochemical mechanisms underlying normal and pathological processes in humans.

The research mission of the program incorporates multidisciplinary collaboration, with both basic and clinical investigators using cutting-edge technologies to investigate normal and disease states. Research in the program will be supported by major funding agencies, and the insight gained by the work will be disseminated in reputable peer-reviewed journals.

The education mission underpins all aspects of the program, as faculty participate in the teaching of undergraduate, medical and graduate students in multidisciplinary courses where understanding at the molecular level is emphasized. The education mission is also central to the research mission as students at all levels are important contributors to laboratory research, where they are trained to be competitive for educational and research positions in diverse academic and industrial environments.

The program mission supports the institutional mission of commitment to excellence in research and teaching, and has the common goal of discovery and dissemination of knowledge that can be applied to the treatment and prevention of disease.


THE BCB FACULTY RESEARCH

Graduate Program in Biochemistry and Cancer Biology

Ande, Satyanarayana, PhD Cancer Biology, CN3150 Associate Professor of Biochemistry and Molecular Biology [email protected]

Dr. Ande’s lab investigates the regulation and function of specific transcription factors and tumor suppressors in liver tumorigenesis and liver tumor angiogenesis. His lab also studies adipose tissue metabolism and obesity and the molecular links between obesity and liver cancer by utilizing knockout and transgenic mouse models.

Arbab, Ali, PhD, MBBS

Cancer Biology, CN 3141 Professor, Biochemistry and Molecular Biology Phone: (706) 721-8909

[email protected]

Our laboratory creates different orthotropic

animal models for human glioma. We use in

vivo MRI, SPECT and optical imaging to

determine the tumor growth, tumor vascular parameters, migration and accumulation of endogenous or exogenously administered stem/progenitor cells in the tumor neovascularization, and accumul-ation of laminin avid nanoparticle based contrast agents.

Browning, Darren, PhD

Director, Graduate Program in Biochemistry and Cancer Biology Biochemistry, CN 1164 Professor, Biochemistry and Molecular Biology Phone: (706) 721-9526 DBROWNING

@augusta.edu

Our focus is cGMP signaling through protein kinases (PKG) in the gastrointestinal tract. My lab has characterized anti-tumor properties of PKG in colon cancer, including: blockade of proliferation, angiogenesis, and hypoxic adaptation. Using knockout mice, we showed that PKG2 regulates colon homeostasis and strengthens the mucosal barrier. The lab is currently testing PDE5 inhibitors for the treatment and prevention of colitis and colon cancer in preclinical models.

Celis, Esteban, MD, PhD Cancer Biology, CN 4121 Professor of Biochemistry and Molecular Biology Phone: (706) 721- 5668 [email protected]

A major challenge for developing effective cancer vaccines against is overcoming tolerance. This is where CD8 T lymphocytes that should recognize and kill tumor cells are not induced by conventional vaccines. We have designed a novel vaccination approach that uses synthetic peptides representing CD8 T cell epitopes, Toll-like receptor agonists that function as a potent immunological adjuvants and immune costimulatory monoclonal antibodies.

mailto:[email protected]









Chadli, Ahmed, MS, PhD Cancer Biology, CN 3151 Molecular Chaperone Biology Associate Professor of Medicine Phone: (706) 721-4661 [email protected]

Research in Dr. Chadli’s laboratory focuses on understanding the Hsp90 chaperoning machine and co-chaperones in the initiation and progression of breast and prostate cancers using in vitro and mouse conditional knockout models. We believe that targeting the Hsp90 machine will have a powerful impact on dysfunctional circuitries that underlie cancer, and we are developing a high-throughput technology to identify compounds to inactivate Hsp90.

Cowell, John, PhD

Interim Director, Georgia Cancer Center Cancer Biology, CN 4121 Professor of Pathology Phone: (706) 721-4381 [email protected]

Dr. John Cowell studies the molecular genetics of cancer using a variety of genomics, cell, and molecular approaches. He currently studies the role of the WASF3 gene in the promotion of cancer metastasis using in vivo models in mice and zebrafish. He also studies of the molecular etiology of Stem Cell Leukemia/Lymphoma (SCLL) syndrome which is characterized by chromosome 8p11 translocations activating the FGFR1 kinase.

Ding, Han-Fei, PhD Cancer Biology, CN 4132 Professor of Pathology Phone: (706) 721-4286 [email protected]

The research program of the Ding laboratory is to define the molecular and cellular basis of cancer development in select model systems. Ongoing projects include developmental biology of neuroblastoma and NF-kB2 signaling in the pathogenesis of lymphoma.

He, Yukai, MD, PhD Cancer Biology, CN 4150 Professor of Medicine Phone: (706) 721-2728 [email protected]

Dr. He studies the basic mechanisms of how vaccines activate the immune system and the innovative design of cancer vaccines. His research focus is on creation of cancer vaccines for melanoma and hepatocellular carcinoma in mice and on translation of animal studies into clinical applications.










Horuzsko, Anatolij, MD, PhD

Cancer Biology, CN 3154 Professor of Medicine Phone: (706) 721-8736 [email protected]

Dr. Horuzsko's studies focus on organ transplantation and the role of Human Leukocyte Antigen-G (HLA-G). His aim is to improve allograft survival in patients and address allergy, autoimmune diseases and graft-versus-host disease. His work in transplantation is relevant to cancer, but he also studies the inflammatory mechanisms of host defense and carcinogenesis.

Koni, Pandelakis, PhD

Cancer Biology, CN 4154 Associate Professor of Medicine Basic Science Faculty Phone: (706) 721-6897 [email protected]

Dr. Pandelakis Koni, runs a mouse model research lab, and focuses on which genes promote cancer and the mechanisms that allow it to happen. By turning genes off or silencing their expression in engineered mice, he compares them to normal mice and finds clues about which genes promote cancer in people. Research interests include immune regulation, inflammation, interface between antigen-presenting and T cells.

Korkaya, Hasan, DVM, PhD Cancer Biology, CN 2136 Assistant Professor of Biochemistry and Molecular Biology Phone: (706) 721-2429 [email protected]

Dr. Korkaya develops mouse xenograft models of human malignancies and uses these models to investigate the mechanisms of metastasis and therapeutic resistance. He aims to identify drivers of epithelial to mesenchymal transition and self-renewal in cancer stem cells. His lab showed that high levels of IL6 in tumors, promotes the metastatic phenotype and blocking this pathway is therapeutic in mouse preclinical models.

Li, Honglin, PhD

Biochemistry, CN 2176 Associate Professor, Biochemistry and Molecular Biology Phone: (706) 721-6143 [email protected]

Dr. Li studies the roles of the Ufm1 conjugation system (a novel ubiquitin-like system) and its associated proteins in animal development, signal transduction, stress response and tumorigenesis.










Liu, Kebin, PhD Biochemistry, CN 1173 Professor of Biochemistry and Molecular Biology Phone: (706) 721-9483 [email protected]

A graduate of the University of Oklahoma, Dr. Liu studies epigenetic and genetic regulation of tumor suppressor gene expression, molecular mechanisms of apoptosis resistance in tumor immune evasion and escape, and development of molecular target-based chemotherapy to enhance the efficacy of cancer immunotherapy.

Lokeshwar, Bal PhD Director, Graduate Program in Biochemistry and Cancer Biology Cancer Biology, CN 3130 Professor of Medicine Phone: (706) 723-0033

[email protected]

The research program is focused on two aspects of cancer: cancer prevention using natural products and understanding the mechanism of cancer progression leading to metastasis. Current projects in his laboratory investigate the role of CXC chemokines and their receptors (CXCRs) that contribute to cancer progression and metastasis. The laboratory is engaged in translational research, where the group is investigating novel compounds isolated from dietary spices that may prevent cancer development and enhance response to existing therapy for prostate and breast cancers.

Lokeshwar,Vinata, PhD Biochemistry, CN 1161 Professor and Chair Biochemistry and Molecular Biology Phone: (706) 721-7652

[email protected]

The major focus of the laboratory is to examine how extracellular matrix-driven tumor cell signaling promotes tumor growth, metastasis and angiogenesis. The emphasis is to discover and validate accurate diagnostic and prognostic biomarkers for prostate, bladder and renal cell carcinomas and to design biomarker-driven targeted treatments and chemodietary prevention strategies for metastatic cancers. The laboratory provides training in translational research and a collaborative atmosphere.

Maihle, Nita, PhD Associate Cancer Center Director of Education. Cancer Biology, CN 3114 Professor, Biochemistry and Molecular Biology [email protected]

Dr. Maihle studies fundamental aspects of receptor-extracellular matrix regulation by sEGFR/sHER’s, with an emphasis on cell survival signaling, as well as the clinical development of these newly discovered HER receptor isoforms as biotherapeutics, and also as prognostic, diagnostic, and theragnostic biomarkers (serum/tissue/tumor). More recent studies include the discovery of mechanisms underlying primary resistance to biologically-targeted HER-directed therapeutics.






Manicassamy, Kumar, PhD Cancer Biology, CN 4158A Professor, Biochemistry and Molecular Biology [email protected]

Dr. Manicassamy is examining critical mechanisms that regulate adoptive immune responses at the mucosal surfaces of the gastrointestinal tract. His research will shed light on interactions between commensal microorganisms and how these interactions can become dysfunctional to cause increased risk of inflammatory bowel disease and colon cancers.

Dr. Manicassamy is examining critical mechanisms that regulate adoptive immune responses at the mucosal surfaces of the gastrointestinal tract. His research will shed light on interactions between commensal microorganisms and how these interactions can become dysfunctional to cause increased risk of inflammatory bowel disease and colon cancers.

Martin, Pamela, PhD Biochemistry, CN 1160 Associate Professor, Biochemistry & Molecular Biology, and Ophthalmology Phone: (706) 721-4220 [email protected]

Dr. Martin's focus is on the discovery and analysis of novel biochemical transporters and receptors in retina which may be useful in the development of new therapeutic targets in the treatment and prevention of diabetic retinopathy.

Mivechi, Nahid, PhD Cancer Biology, CN 3153 Professor, Radiology/Radiation Oncology, Molecular Chaperone Biology Phone: (706) 721-8759 [email protected]

Dr. Mivechi's laboratory focuses on understanding the molecular mechanisms of stress response using genetically engineered mouse models and zebrafish. The comparison between conserved biochemical and molecular pathways in mice and zebrafish facilitates understanding of how animals and thereby humans respond and cope with their environment.

Moskofidis, Dimitrios, MD

Cancer Biology, CN 3143 Molecular Chaperone Biology Professor of Medicine Phone: (706) 721-8738 [email protected]

Dr. Moskofidis explores basic processes in the immune response against acute and persistent viral infections in well-established mouse models, with long-term goals of developing or improving vaccination strategies for the prevention and treatment of viral infections in humans. He also studies molecular chaperones in cancer and neurodegenerative diseases.

Munn, David, MD Senior Advisor to Cancer Ctr Director Cancer Biology, CN 4141 Professor of Pediatrics Phone: (706) 721-7141 [email protected]

Dr. Munn's lab studies mechanisms that suppress the immune system, making the body tolerant of a malignancy. He has identified the enzyme indoleamine 2,3-dioxygenase (IDO) as a linchpin for suppression and opened the way to novel strategies to block its activity. Research interests include macrophage and dendritic cell differentiation; regulation of T cell activation, IDO and trp metabolism; clinical trials of IDO inhibitors in cancer, HIV.










Nagendra, Singh, PhD Biochemistry, CN 1176 Associate Professor of Biochemistry and Molecular Biology Phone: (706) 721-6238 [email protected]

There are 10 times more bacteria in our gut than the total number of cells in our body. Within this “gut microbiota” are bad bacteria that can induce inflammation and cancer, but also good bacteria that are protective. Research in Dr. Singh’s laboratory focuses on how metabolites from good bacteria interact with host genes such as Gpr109a, Gpr43 to induce anti-inflammatory mechanisms such as tolerogenic dendritic cells, induction of T-regs, inhibition of inflammatory cytokines.

Pace, Betty, MD Francis J. Tedesco, MD Distinguished Chair in Pediatrics Acting Chief of Pediatrics, Section of Pediatric Hematology/Oncology, Professor of Pediatrics and Biochemistry & Molecular Biology Phone: (706) 721-6893 [email protected]

The Pace laboratory conducts research related to the developmental regulation of globin gene expression using primary erythroid progenitors. The major effort has been the role p38 MAPK cell signaling in drug-mediated fetal hemoglobin induction as a treatment for sickle cell disease. The laboratory also has conducted high throughput drug screens to identify novel gamma globin inducers. Genome-wide studies are being conducted to identify genetic modifiers of fetal hemoglobin.

Prasad, Puttur, PhD Biochemistry, CN 1163

Prof of Obstetrics and Gynecology Biochemistry & Molecular Biology Phone: (706) 721-1761 [email protected]

Dr. Prasad studies the nutrient and drug transporters in the placenta as well as post-partum depression.

Sakamuro, Daitoku, PhD Biochemistry, CN 2177 Associate Professor of Biochemistry and Molecular Biology Phone: (706) 721-1018 [email protected]

The Sakamuro laboratory is interested in the signaling mechanisms by which advanced cancer cells acquire resistance to DNA damage, p53-dependent apoptosis, and substratum dissoc-iation stress, and reverse EMT. One focus is the dual roles of the c-MYC transcription factor in genomic instability and DNA damage resistance. Another is the mechanisms of apoptosis induced by the p53 tumor suppressor in the presence of chromatin remodeling factors.






Shi, Huidong, PhD Cancer Biology, CN 2138 Professor of Biochemistry and Molecular Biology Phone: (706) 721-6000 [email protected]

Dr. Shi studies epigenomics, and development of high-throughput technologies for dissecting the complex epigenetic regulation in normal and tumor cells. Epigenetics is heritable chromatin organization and gene expression not coded by DNA sequence. While epigenetics refers to the study of single genes or sets of genes, epigenomics is the global analyses of epigenetic changes across the genome.

Thangaraju, Muthusamy, PhD Biochemistry, CN 1161 Associate Professor of Biochemistry and Molecular Biology Phone: (706) 721-0272 [email protected]

Dr. “Raju” is interested in the role of plasma membrane transporters in the uptake of histone deacetylase (HDAC) inhibitors into tumor cells; Relevance of these transporters to tumor suppression in mammary gland via HDAC inhibition; Physiologic role of these transporters in apoptosis during mammary gland involution; Epigenetic mechanisms for silencing of these transporters in breast cancer.

Thompson, Stuart, PhD Biochemistry, CB 2607 Associate Professor, Section for Infectious Diseases, and Biochemistry and Molecular Biology, Phone: (706) 721-7277

[email protected]

My lab studies Campylobacter and Helicobacter, bacteria that cause gastroenteritis and gastric cancer, respectively. We use molecular and biochemical techniques to elucidate the mechanisms by which these pathogens cause disease. Specifically, we study gene regulation events that link motility with formation of biofilms, bacterial communities that resist antibiotics and the host immune system.

Tuan-Lo, Dorothy, PhD

Biochemistry, CN 2173 Professor of Biochemistry and Molecular Biology Phone: (706) 721-6281 [email protected]

Dr. Tuan's research focuses on long-range transcriptional regulation of genes by the Locus Control Region (LCR) and the LTR retrotransposon of ERV-9 human endogenous retrovirus, in particular, roles of long, noncoding RNAs (lncRNAs) transcribed by the LCR and ERV-9 LTR in regulating red cell differentiation. An additional research interest of her lab is molecular mechanism of gamma-globin gene reactivation in sickle cell disease and thalassemia.

Van Riggelen, Jan, PhD Biochemistry, CN 2175 Assistant Professor of Biochemistry and Molecular Biology Phone: (706) 721-0856 [email protected]

Dr. Van Riggelen uses the Myc/Miz1 and Smad/TGFb signaling pathway in hematopoietic malignancies as a model system to study how dynamics in the epigenetic landscape drive proliferation vs. cellular senescence. Our main focus is on DNA methyltransferases and genome-wide DNA methylation mediated by Myc and Smad. Our goal is to understand how these pathways










control tumor maintenance, cellular senescence and tumor regression.

Yan, Chunhong, PhD Cancer Biology, CN 2134

Associate Professor [email protected]

Dr. Yan’s lab utilizes biochemical approaches and genetically-engineered mouse models to study tumor suppressor networks and understand how cancer is generated and progressed. Current interests include the p53 pathway and protein modifications (e.g., ubiquitination and acetylation) in cellular responses to DNA damage and metabolic stresses. He is also interested in developing novel therapeutic strategies targeting aberrant protein translation in cancer.

Zhou, Gang, PhD Cancer Biology, CN 4140 Associate Professor of Medicine, Section of Hematology/Oncology Phone: (706) 721-4472 [email protected]

Dr. Zhou's investigates the functions of the immune system’s CD4+ T cells in cancer using various animal models. CD4+ T cells can be primed to handle diverse assignments either as helper or suppressor (regulatory) cells. As helper cells, they can kill malignant cells directly or help to activate other immune cells to attack the tumors. Suppressor CD4+ T cells, however, act as brakes on the immune system, heading off autoimmune disorders.




THE PATHWAY TO GRADUATION The objective of the graduate program in Biochemistry & Cancer Biology at the Medical College of Georgia is to train students to be outstanding and independent scientists that effectively compete for contemporary biomedical research positions. The program is underpinned by the notion that training involves several equally important skills and focuses on academic, ethical, technical and presentation development. Training in the BCB program is designed to address each of these areas, and the key elements and expected timeline are outlined below: Year 1. Shortly after joining the BCB program, the student should immerse themselves in primary literature relevant to the systems under investigation in the laboratory and should gain first-hand expertise in a wide array of techniques. In the spring semester, students should enroll in BCMB 8201, which will complement learning of laboratory methods (see below). Students are also required to audit the BCMB 8340 course, which will strengthen their presentation skills. Within the first few months the student and mentor should establish a student advisory committee (SAC). The student should feel comfortable in reaching out to SAC members for technical or other advice at any time so that they are familiar with the student’s research efforts and progress. This is imperative to the student who must satisfy SAC member’s expectations during three important landmarks: the comprehensive exam, the research proposal and the thesis defense. It is also helpful to the mentor to have a committee that is aware of the efforts and experimental results that have directed the student’s progress over time. It is a mandatory CGS requirement that the student convenes at least one official (documented) SAC meeting within a 12 month period. The accompanying timeline indicates that this could be optimal if held in the spring to correspond with other requirements. During this first year in the program, students should be working toward the preparation of their comprehensive examination (see below). CGS guidelines make the successful completion of this important landmark mandatory by the end of the first year in the BMB program (second year in the PhD program).

Year 2. After the first year in the BCB program, students will have established a SAC, completed the mandatory BCMB 8201 course, and passed their comprehensive examination. The second year should focus on experiments that will form the basis of their research proposal. In the fall semester of the BMB student’s second year (7th semester) students should officially register for the second mandatory course BCMB 8340. CGS mandates that the research proposal must be completed by the end of the second year in the BCB program. It is recommended that the coursework proposal (see below) and the research proposal be discussed together in the spring SAC meeting.

Year 3. Effort in third year in the BCB program will mainly involve carrying out the proposed research and publishing results where possible. Students will generally also enroll in another elective course as decided upon in the previous SAC meeting. Year 4. Students in the fourth year of the BCB program (5th year at MCG) generally complete experimental work whilst preparing their thesis, which on average is defended by the end of the year. During this year it is a program requirement that the advanced students present their research in the regularly scheduled and campus-wide advertised BMB seminars. This is a great opportunity for feedback, presentation experience and for focusing thoughts on thesis defense. During this final year (on average), students should also be considering post-graduation plans, such as identification of a post-doctoral position.



THE STUDENT ADVISORY COMMITTEE

Major Advisor The major advisor chosen by the student has to be a faculty member in the BMB program. The term “major advisor” should be synonymous with “mentor” as the responsibilities reach well beyond technical direction in the laboratory. The major advisor is there to help mold the mindset of scientist; to edit/advise students with writing and presentations, to interpret reviewer’s comments and unveil some of the political and administrative realities associated with contemporary scientific practice. The major advisor should also be instrumental in helping the student to choose and interact with the SAC, and to prepare them for the thesis defense. It is not the responsibility of the major advisor to ensure that the student maintains good standing with CGS by arranging for SAC meetings or ensuring that the appropriate paperwork is submitted to the CGS in a timely manner. These latter administrative functions are the responsibility of the student in consultation with the BMB academic administrator and program director. Other Committee Members Once the student has chosen a mentor in the BCB program and has begun working in the laboratory, choosing 4 additional faculty to be members of the student advisory committee (SAC). At least four of the five members (including major advisor) must hold appointments on the faculty of the College of Graduate Studies (CGS). It is also recommended that 2 of the 4 also be BCB faculty in order to facilitate the proceedings of the comprehensive examination. While the choice of SAC members is primarily that of the major advisor, who is likely to be more familiar with colleagues having desirable expertise, it is recommended that the student also contributes to the process. Once the members of the advisory committee have agreed to serve as a member on the SAC, the student should complete the Advisory Committee Form, including obtaining each members signature and then submit to the CGS. The SAC has several functions that serve the student, the major advisor, and the CGS. The student should feel comfortable approaching SAC members regularly for technical or other or guidance and should consider them an important resource throughout their tenure in the program. The SAC members can provide valuable feedback to both student and major advisor regarding the direction and development of the project. In addition, the SAC members are essential to administer and witness several milestones throughout the program, culminating in the thesis defense. Committee Meetings

It is important that the SAC be kept informed of the major findings and setbacks associated with the student’s research in order to best serve as advisors. CGS mandates that at least one SAC meeting must occur within a 12 month period. This is important because the student must have the SAC members “on board” in order to ensure that there are no “surprises” toward the end of the program regarding whether there has been sufficient accomplishment to warrant graduation. It is expected that some SAC members will be apprised of the students research as a collaborator of the major advisor, their attendance at presentations (e.g. BCMB 8340, departmental seminars), or by less formal interactions with the student. However, other members may not be available and the SAC meeting serves to place everyone “on the same page”.


The student is responsible for scheduling the SAC meeting annually, usually by coordinating schedules of SAC member by email in advance, and when a date and time is reached, an appropriate room can be reserved by the academic administrator (usually the BMB conference room). The SAC meetings should not be viewed as intimidating or unnecessarily formal but should be anticipated in with a positive outlook as a relatively informal gathering to benefit the student. It is recommended that SAC meetings take place in the spring semester each year in accordance with required administrative milestones, including: introduction and establishing the comprehensive examination committee (year 1); finalizing the coursework proposal and presentation of the research proposal (year 2); and firming up a consensus prior to the final defense (year 4). Prior to each SAC meeting, the student should discuss the goals and structure of each meeting with their major advisor, who will chair each meeting. Generally the meetings will start with a brief welcome and overview of meeting objectives by the major advisor, followed by an oral presentation of progress by the student (15-30 min). This is usually to be followed by comments and feedback from SAC members, and then finalized by discussing any administrative issues (listed above) relevant

to the timely progression of the student. It is recommended that the student bring any forms to be signed to each meeting (e.g. approval forms for coursework and research proposals). Shortly following the SAC meeting, the student should document the central points (e.g. members of committee present/absent, a short summary of the research presented, and specific recommendations or comments by SAC members). This should be incorporated into Part B of the Report of Advisory Committee Meetings and Research Progress Report Form. After approval by the major advisor, the form should be distributed to committee members to provide the opportunity for feedback or approval, and then submitted to the BMB academic administrator who will forward to CGS. This should all take place within two weeks of the date of the SAC meeting.

COURSEWORK Entry into the BCB graduate program occurs when a student has chosen a BCB graduate faculty member as their mentor after having completed a rotation in their laboratory. Successful completion of the core coursework in the first year in the Biomedical Sciences Program ensures a well-rounded education in the fundamentals of biochemistry and molecular biology. There is therefore less coursework in the BCB program, and mandatory courses are designed to enhance the development of technical and presentation skills that are hallmarks of a good scientist. All students are required to participate in the BCMB 8340 Elements of Scientific Presentation course that is offered in the Fall Semester. This course provides a platform for continuous feedback on the students “in progress” results and on their presentation skills. Although required to participate in the course annually, BMB students will only officially enroll for a grade in their second year in the program. In the first spring semester, BMB students should enroll in BCMB 8201 Current Topics and Techniques in Biochemistry and Molecular Biology. This course will compliment technical ability in the laboratory, enhance understanding of the primary literature and will provide a working knowledge of the limitations and expectations of methods that will be drawn upon in preparation of the research proposal and the comprehensive examination.


Coursework Proposal After successful completion of the core courses within the first year of study, there are additional courses that must be completed in order to satisfy the educational requirements for each programs area of specialty. Historically at least two courses were required to be classified as “tools of research”, but the two mandatory courses in the BMB program meet these requirements. A hallmark of the BCB program is the minimal course requirements, largely due to extensive coverage during undergraduate and graduate core curricula of biochemistry and cancer biology (considered to be essential by all programs). In addition to the mandatory BCMB 8340 and BCMB 8201 courses. It is expected that the Coursework Proposal Form should be signed by SAC

members during the second year within the BCB program. Mandatory BCB Courses:

BCMB 8340 “Elements of Scientific Presentation” This course will provide graduate students in the Biochemistry and Molecular Biology program with the essential skills needed to give an effective oral presentation of academic material. Instructors will both discuss and demonstrate critical issues relevant to giving seminar or lecture (e.g. organization, slide composition, speaking style and body language). The course will provide students with multiple opportunities to practice their learned presentation skills to a large audience. By peer-review of course presentations, students will be able to develop critical analysis skills as well as receive constructive feedback on their own work. On successful completion of this course, students will be experienced orators, and will be able to present their research or teaching material in a confident and effective manner. The objective of the “Elements of Scientific Presentation” course is to provide graduate students in the Biochemistry and Molecular Biology program with instruction and opportunity to present academic material to a receptive yet critical audience. Each student will have practical presentation experience and will receive specific feedback to guide improvement for future presentations. Upon completion of the course, students are expected to have mastered the essential skill-set required to create an effective scientific lecture, journal club or seminar. Initial instruction will consist of a limited number of didactic lectures that will focus on key topics as listed above. These lectures will be complimented by instructor demonstrations that will highlight the essential “do’s and don’ts. The majority of the course will consist of presentations provided by students, which will be followed by a traditional question/answer period. Attendance by all students in the program will be mandatory, and each student will make at least one presentation, but only students in their second year in the laboratory will be officially enrolled in the course and will be graded on their performance. BCMB 8201 “Current topics and techniques in Molecular Biology” This is a 3h elective course that will benefit biomedical science graduate students in all programs. This course provides students with the technical insight into essential biochemistry and molecular biology experimental techniques. The material is delivered in a practical fashion using both didactic lecture and discussion sessions by experts that use the experimental approaches in their laboratories. This course creates a solid technical foundation for students at all stages of their doctoral work, but is recommended for new students in the design phase of their projects. Examples of the must-know topics that are covered include: -Basic DNA manipulation, PCR/RT-PCR and protein purification,


-PAC/BAC and expression cloning -Genomics, proteomics, and bioinformatics -Creation and use of viral vectors (adenovirus, retrovirus and lentivirus) -Confocal microscopy, immunohistochemistry and in situ hybridization BCMB 9010 Seminar in BMB Research presentation by MCG faculty, students and visiting research scientists. There are currently no measures of student participation or attendance at the BMB seminar series, but this is an important part of a student’s education as it provides a relatively “safe” environment to ask questions and test knowledge in the face of an external expert. As the student begins to accumulate data from his/her research, it is expected that they will present their work to the department in the regular seminar series as an essential “run through” or “practice” in anticipation of the final thesis defense. BCMB 9210 Invest. of a Problem The student works with individual faculty members on a specific investigative research problem. This provides an introduction to analytical techniques and the scientific methods in action. BMCB 9300 Research The student works closely with his faculty thesis/dissertation advisor on an in-depth study of a research problem of interest to both student and advisor. This course culminates in the preparation of a PhD dissertation or MS thesis. Prerequisites: Permanent assignment to a specific lab with a faculty advisor and a defined research project. Other Courses offered by the BCB program: BCMB 8310 Adv. Topics Micro 1 This is a highly focused course designed to provide students with in-depth Infec. Dis. I discussions of pathogenic bacteria and associated diseases. The emphasis of the course will be on the molecular mechanisms the virulence of medically important bacterial pathogens. Class time will consist of student-led lectures and discussions, facilitated by Microbiology faculty. Students will present comprehensive backgrounds of the topics of discussion by critical evaluation of scientific papers taken from recent primary literature. This course will provide students both with comprehensive knowledge of bacterial pathogenesis and increased experience with reading, presenting, and critically analyzing scientific literature. Prerequisites: CGS 8021 and CGS 8022 or approval from course director BCMB 8320 Adv. Topics Micro 2 This is a highly focused course designed to provide students with in-depth Infec. Dis. II discussions of pathogenic bacteria and associated diseases. The emphasis of the course will be on the molecular mechanisms underlying the virulence of medically important bacterial pathogens. Class time will of student-led lectures and discussions, facilitated by Microbiology faculty. Students will present comprehensive backgrounds of the topics of discussion by critical evaluation of scientific papers taken from recent primary literature. This course will provide students both with comprehensive knowledge of bacterial pathogenesis and increased experience with reading, presenting, and critically analyzing scientific literature. Prerequisites: CGS 8021 and CGS 8022 or approval from course director


Registration for courses (BEGINNING OF EACH SEMESTER) BCB students should register for BCMB 9210 every semester and BCMB 9010 every semester except summer and BCMB 8201 and BCMB 8340 in their first and second years in the program (respectively). Although this is the recommended path, it is acceptable to register for the mandatory BCB courses at a later date (e.g. alongside their elective course) so long as the minimum requirements are completed by the end of the program. Research Progress Reports (END OF EACH SEMESTER) An essential component of the research based courses (BCMB 9010 and BCMB 9300) is the preparation of a Research Progress Report Form at the end of each grading period. The student must complete Part A of the Report of Advisory Committee Meetings and Research Progress Report Form. If a SAC meeting took place during that semester then the previously submitted report (Part B of the same form) can substitute. The major advisor’s role is to review the report with the student and make additional comments if necessary. The student and Advisor signify approval of the report by signing the form and forwarding it to the academic administrator along with the student’s grade (U or S) for the grading period. Failure to file the report by the end of the grading period results in a grade of “incomplete” being sent to the Registrar’s office.


THE BIOCHEMISTRY AND CANCER BIOLOGY COMPREHENSIVE EXAMINATION Composition of the comprehensive examination committee (CEC). During the first year of laboratory study the student and mentor should establish a student advisory committee (SAC) composed of the major advisor and 4 graduate faculty members who have sufficient expertise to form a supportive team for the student. If a majority of the SAC has primary affiliation in BMB, then they can serve as the CEC, which requires a minimum of 4 members including the major advisor. If the SAC has too few BMB faculty, then the SAC and the CEC chair should identify additional BMB faculty to ensure that the majority of the CEC have primary appointments in BMB.

The Graduate Program Director is responsible for oversight of the graduate program’s Comprehensive Examinations and will serve as chair of the program’s CEC. In cases of real or perceived conflict of interest regarding the student’s performance, appointment of a faculty member other than the Program Director as Examination Committee chair is required, but must be approved by the Dean. The major advisor cannot serve as the CEC chair under any circumstances.

Responsibilities of the CEC. Before the end of the fifth semester as a student at MCG (second semester in the BMB program), the student should meet with their SAC to acquaint them with possible avenues of research and to define the specific knowledge-base that will set the stage for the Comprehensive Examination. The CEC will work with the student’s Major Advisor to create that student’s Comprehensive Exam in a manner that will test: (1) the student’s mastery of their chosen field of study, and (2) the student’s ability to thoughtfully and critically integrate this information into coherent questions that can be addressed experimentally.

The Examination Committee chair serves as liaison to the Dean’s Office and sees that all procedures of the examination are conducted within the policies and guidelines of the College of Graduate Studies. Scheduling the Comprehensive Examination should be done at least two weeks prior to the proposed date using the Comprehensive Exam Pre-Approval form, which is submitted through the CEC chair and the Department Chair to the Dean for approval. The results of the examination are submitted for approval to the Department Chair on the Comprehensive Examination Form. The Department Chair forwards the form to the Dean.

It is the responsibility of the Examination Committee, the Graduate Program Director, and the Department Chair to determine whether or not the student has passed the examination. The examination is expected to be administered by the end of the first year in the laboratory and students must have successfully completed this important landmark before the end of the sixth semester at the Medical College of Georgia. In the event of failure, a student will be afforded one opportunity to retake the exam after additional study, typically within three months. Failing the retake of the examination will result in the student being considered for dismissal from the graduate program and School of Graduate Studies.


Structure of the Comprehensive Examination. (Please NOTE: This is the OLD FORMAT BUT NEW FORM IS FORTHCOMING SOON) The comprehensive examination is composed of two sections as described below: Written Component: The student will prepare a realistic research proposal relevant to their interests and within the realm of their chosen laboratory. The proposal should not be overly focused on experimental details, but should have a robust background-introduction, and thoughtful attention to expected outcomes, and discussion of the impact of the results on the field as a whole. The proposal should conform to established post-doctoral fellowship guidelines without administrative and budgetary paperwork (see instructions from the American Cancer Society as an example). The document should contain specific hypotheses, significant background information, description of methods, and expected outcomes, and must be the student’s independent work and not excerpts from the Major Advisor’s grant proposals or manuscripts. The Major Advisor may provide minor input in the form of suggestions on content and organization, but should not directly edit or revise the document. The SAC will grade both written and oral portions of the examination using the “-1, 0, +1” scale, (unacceptable, basic understanding, outstanding respectively). The main objective of this written component of the Comprehensive Examination is to assess student aptitude as an investigator, and therefore the work proposed is not binding as a thesis plan. It is equally important to note that the dissertation Research Proposal is a separate requirement of the School of Graduate Studies that is independent of the Comprehensive Examination. Generally the Research Proposal can be compiled when the student’s research efforts have produced sufficient data to outline significant research aims that will form the framework of their thesis (not later than the end of the 9th semester). However, under rare circumstances, the CEC may recommend to the student and SAC that the written component of the Comprehensive Examination could form the basis for the official Research Proposal, and possible submission to an external funding agency. Oral Component: No more than five weeks following submission of the written component of the Comprehensive Examination, the student and CEC should convene a meeting to administer the oral component. This will consist of a brief oral presentation by the student that is based upon the written proposal (approximately 30 minutes), followed by sequential questioning by the CEC members. The question/answer period can be from 30-90 minutes, for a maximal examination time of 2 hours. When all questions have been addressed, the student will take a recess from the room while their performance during the oral component is graded in terms of their knowledge-base and their understanding of the relevant experimental design and ability to interpret results. After deliberation, the student can re-enter the room for a briefing on their performance and any recommendations for improvement. Members of the CEC will also use the “-1, 0, +1” system to grade the oral presentation component, and the final grading of the Comprehensive Examination will be based on combined scores from both written and oral components. The combined scores from both written and oral components of the exam must be equal to “+2”. A passing grade of “+1” for each of the oral and written components will therefore produce an overall passing grade of “+2”, but greater performance in either component can compensate for the other (e.g. “+2” written but “0” oral).


RESEARCH PROPOSAL The research proposal is an important milestone in the path towards graduation because it encourages the student to focus their studies on specific questions. It also forces one to look at the experimental results from a larger perspective that is key to creating the thesis later in the program. Finally, the research proposal should be considered as a structural framework that if carried out successfully, will result in a thesis of sufficient breadth and significance to warrant successful graduation. The research proposal should not be considered to be a binding contract or a promise to successfully complete the proposed experiments, but it does bind the student to a specific study area. Failure to complete experiments outlined in the research proposal should be explained to the committee in subsequent SAC meeting. The research proposal must be completed by the end of the 9th semester at GHSU (2nd year in the research laboratory). Instructions for Writing a Research Proposal Following the outline below, provide the details of the proposal.

(1) Hypothesis and Specific Aims. State the hypothesis to be tested and the specific aims of the research proposal.

(2) Background and Significance. Describe briefly the background to the proposal, including relevant studies

by other investigators. State concisely the importance of the research described in this proposal by relating the specific aims to broad, long-term research objectives in the field.

(3) Research Design and Methods. Provide a description of:

Research design and the specific procedures to be used to accomplish the specific aims;

Tentative sequence for the investigation;

Statistical procedures by which the data will be analyzed; and

Any procedures, situations, or materials that may be hazardous to personnel and the precautions to be exercised.

Potential experimental difficulties should be discussed together with alternative approaches that could achieve the desired aims.

(4) Previous Work Done in this or Related Fields. Describe briefly any work you have done that is pertinent to

this project or demonstrates your ability to carry out the study plan. (5) Personal Publications. Cite your most important published and pending scientific publications in this or

related work. Include all authors in the same order as they appear in the journals, as well as titles of articles and complete literature references.

(6) Provide Literature Citations at the end of the research proposal for any published work referenced in the

proposal. Each citation must include names of all authors, titles, book or journal, volume number, inclusive page numbers, and year of publication.

(7) Human Subjects/Vertebrate Animals. Provide the rationale for the choice of any experimental animals or

procedures involving human subjects. Also, summarize the gender and racial/ethnic composition of any human subject population.

SUBMIT RESEARCH PROPOSAL ON PLAIN 8 1/2” X 11” PAPER.


Residence and Time Limits

The minimum requirement for the Doctor of Philosophy degree is three full academic years beyond the bachelor's

degree, which cannot be satisfied through summer work alone. At least two full consecutive semesters must be spent

in residence on the campus. If the student has part-time duties (employment or an assistantship), the residence

requirements will be increased accordingly to provide the equivalent of two semesters of full-time study in residence.

All course work and other requirements for the Doctor of Philosophy degree, including the Final Oral Examination,

must be completed within seven (7) consecutive calendar years from the date of enrollment in the School of

Graduate Studies. Leaves of absence do not extend the seven-year limit. It is the student's responsibility to meet all

the requirements for the degree in the proper sequence and in the time limits specified in this document. For students

in combined MD/PhD or DMD/PhD degree programs, the seven-year limit does not include semesters of enrollment in

the professional degree program. Where circumstances warrant, a student may petition the Dean for exceptions to this

residence and time limit policy.

Admission to Candidacy for the Doctor of Philosophy Degree

A student will be admitted to candidacy for this degree by the Dean following successful completion of the research

tools requirement, acceptance of the coursework proposal and research proposal, and passing of the first and second

comprehensive exams. A completed Admission to Candidacy Form must be submitted to the Dean. The form is

included in the Appendix and available at www.mcg.edu/GradStudies/phdguide/index/html. The Dean notifies the

student in writing of his/her admission to candidacy. Until this occurs, graduate courses taken are not credited toward

the degree. A student must be eligible for candidacy for the Ph.D. degree at least two semesters before the

proposed graduation date.

Dissertation

The dissertation is required of all Ph.D. candidates. It is the culmination of an original investigation leading to new

information that gives evidence of independent thinking, scholarly ability and critical judgment, and indicates familiarity

with research methods and techniques. The dissertation should characterize in a scholarly manner the importance of

this information as it applies to the field of study. Publication of the dissertation in one or various forms is urged, but

not required. Defense (Final Oral Examination) of the dissertation is required and must be completed within two years

of admission to candidacy. Otherwise, a student must undergo re-examination. Directions for preparation of the

written aspects of the dissertation are available from the School of Graduate Studies’ office and at

www.mcg.edu/GradStudies/Thesis_Preparation_Booklet.pdf

Approval of the Dissertation

The student and Advisory Committee should follow the procedures listed for approval of the dissertation.

A good draft of the dissertation, proof-read and corrected (in pencil) by the student and approved by the Major

Advisor, is distributed by the student to members of the Advisory Committee at least five (5) weeks before the date

of the student’s final oral examination.

At least three (3) weeks before the oral examination, the dissertation should be approved by the Advisory

Committee and the Dissertation Approval Form submitted to the Dean. The signed form indicates that the members

of the committee have read the draft copy of the dissertation and find it acceptable for the purpose of examining

the student. The student will be responsible for making all changes recommended by the committee.

Final Oral Examination

Satisfactory performance on the Final Oral Examination, in which the student defends his/her dissertation before the

Advisory Committee, dissertation readers, faculty, students and the public, is required. This examination is based

primarily on the dissertation and the field of knowledge that constitutes the student's major subject. The student must

be enrolled in the semester that the examination is administered.

The Dean or his appointed representative chairs all Final Oral Examinations for the Doctor of Philosophy degree. In

addition, external examiners (readers) must be present. The readers participate in the exam and vote along with the

http://www.mcg.edu/GradStudies/phdguide/index/html

http://www.mcg.edu/GradStudies/Thesis_Preparation_Booklet.pdf


student’s Advisory Committee on the student’s performance. A majority vote of the examining committee is required

for satisfactory performance.

It is the responsibility of the student and his/her Major Advisor to select two or three readers for approval by the Dean.

After approval, the student contacts the readers to determine that they will be available to serve in this capacity. The

Graduate Studies’ office must be notified when the readers agree. The Dean and readers must receive a corrected

copy of the dissertation approved by the Advisory Committee at least two (2) weeks before the Final Oral Examination

is scheduled.

The student should contact the School of Graduate Studies office, Advisory Committee, and readers to arrange a time

that all individuals will be able to attend the oral examination. Once the time is established, notification in writing is

sent to the Dean on a completed Oral Examination Faculty Agreement Form. The examination is open to the public.

Departments will be responsible for typing the printed Program Announcement. These announcements must be mailed

to students and faculty of the area of study (i.e., graduate nursing faculty and students, biomedical sciences faculty

and students, etc.). The Graduate Studies office provides mailing labels. The student may call to request labels three

days in advance of the mailing. A sample of the Final Oral Examination announcement is included in the

"Thesis/Dissertation Preparation" document available in the School of Graduate Studies office and at

www.mcg.edu/GradStudies/Thesis_Preparation_Booklet.pdf The Final Oral Examination Form, provided by the

School of Graduate Studies office, is completed at the end of the examination by the committee, readers, and Dean.

After the Final Oral Examination, three final copies of the dissertation on Crane’s Thesis Paper bearing the signatures

of the Major Advisor and Department Chair are submitted to the Dean at least one week before graduation.

Application for Graduation

Each candidate for a graduate degree must apply for graduation. The Application for Graduation Form is available in

the Graduate Studies office. Please read the application carefully and provide ALL requested information. Return the

completed application to the Graduate Studies office. This application informs the Graduate Studies office and the

Registrar’s office whether or not you will be attending May graduation and/or the Graduate Studies Hooding Ceremony.

It also enables the MCG Bookstore to order the appropriate regalia in time for graduation. If a student believes that

s/he will complete the requirements during the spring semester, the form should be completed and returned to the

Graduate Studies office. If the form indicates that a student will graduate in time for the May commencement and the

degree requirements are not met by that time, the student will NOT be charged for ordering regalia. However, if the

requirements are completed in time for the May commencement and this form has not been returned, regalia may not

be available for participation in hooding and graduation exercises. The Registrar also uses these forms to obtain the

names for the Commencement Program for graduation and the correct names for diplomas. If an Application for

Graduation has not been completed, the student will not be listed in the program.

Satisfactory Fulfillment of All Degree Requirements

Satisfactory fulfillment of any additional requirements of the student's major department or the institution is required.

Three final, signed copies of the dissertation on Crane’s Thesis Paper must be received in the School of Graduate

Studies office at least one week prior to the date of graduation. A recommendation for graduation signed by the Chair

of the student’s department (or for nursing programs, the Associate Dean for Graduate Programs and Research), and

the Dean of the School of Graduate Studies is submitted to the Registrar verifying that the student has completed all

requirements. The recommendation for graduation memo is forwarded to the program director for the chair's signature

by the office staff of graduate studies. The completed memo is returned to the Dean’s office. It is forwarded from the

Dean’s office to the Registrar after all required program documentation has been submitted.

http://www.mcg.edu/GradStudies/Thesis_Preparation_Booklet.pdf


Checklist and PhD Timeline Biomedical Sciences http://www.augusta.edu/gradstudies/current_students/timelinetgs2016.pdf

http://www.augusta.edu/gradstudies/current_students/timelinetgs2016.pdf

BMB PhD Student Handbook - Augusta University · immune responses at the mucosal surfaces of the gastrointestinal tract. His research will shed light on interactions between commensal

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